From gitlab at salsa.debian.org  Wed Jul  1 02:42:32 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Wed, 01 Jul 2026 01:42:32 +0000
Subject: [med-svn] [Git][med-team/community/helper-scripts][master]
 automatic update
Message-ID: <6a447088527a3_55b14a5328c351582a@godard.mail>



Andreas Tille pushed to branch master at Debian Med / community / helper-scripts


Commits:
deaa4eb8 by Andreas Tille at 2026-07-01T01:42:27+00:00
automatic update

- - - - -


4 changed files:

- debian-med-tests.txt
- debian-science-tests.txt
- outdated_med-packages.txt
- python-team-tests.txt


Changes:

=====================================
debian-med-tests.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Tue, 30 Jun 2026 13:42:03 +0000
+Last-Update: Wed, 01 Jul 2026 01:42:04 +0000
 
  Source                        | Vote   | Tasks                                      |                                 Tags                                 
 -------------------------------+--------+--------------------------------------------+----------------------------------------------------------------------


=====================================
debian-science-tests.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Tue, 30 Jun 2026 13:42:05 +0000
+Last-Update: Wed, 01 Jul 2026 01:42:04 +0000
 
        Source                              | Vote   |             Tasks                                                   |                          Tags                          
 -------------------------------------------+--------+---------------------------------------------------------------------+--------------------------------------------------------


=====================================
outdated_med-packages.txt
=====================================
The diff for this file was not included because it is too large.

=====================================
python-team-tests.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Tue, 30 Jun 2026 13:42:05 +0000
+Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
 
      Source                             | Vote   |                          Tags                          
 ----------------------------------------+--------+--------------------------------------------------------



View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/deaa4eb8cc3b6acfa9c162afecb195e5ee128652

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From gitlab at salsa.debian.org  Wed Jul  1 06:04:54 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Wed, 01 Jul 2026 05:04:54 +0000
Subject: [med-svn] [Git][med-team/mcaller][master] 5 commits: Changes made
 by cme
Message-ID: <6a449ff69dcfd_55b54a8a1c3530935@godard.mail>



Andreas Tille pushed to branch master at Debian Med / mcaller


Commits:
c16c55f7 by Andreas Tille at 2026-07-01T06:24:49+02:00
Changes made by cme

- - - - -
f570467c by Andreas Tille at 2026-07-01T06:24:53+02:00
Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)

- - - - -
afe1445d by Andreas Tille at 2026-07-01T06:24:53+02:00
Drop 'Rules-Requires-Root: no' from d/control (routine-update)

- - - - -
9ddf5988 by Andreas Tille at 2026-07-01T06:28:24+02:00
routine-update: Ready to upload to unstable

- - - - -
0fea4772 by Andreas Tille at 2026-07-01T07:04:40+02:00
DEP3

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/python2to3.patch
- debian/patches/shebang.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-mcaller (1.0.3+git20210624.b415090-4) UNRELEASED; urgency=medium
+mcaller (1.0.3+git20210624.b415090-4) unstable; urgency=medium
 
   * Team upload.
   * d/watch: version=5
@@ -6,8 +6,11 @@ mcaller (1.0.3+git20210624.b415090-4) UNRELEASED; urgency=medium
   * Update standards version to 4.7.4, no changes needed.
   * Fix multiprocessing with Python3.14
     Closes: #1140947
+  * Reflow Uploaders field (cme)
+  * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+  * Drop 'Rules-Requires-Root: no' from d/control (routine-update)
 
- -- Andreas Tille <tille at debian.org>  Tue, 30 Jun 2026 21:52:47 +0200
+ -- Andreas Tille <tille at debian.org>  Wed, 01 Jul 2026 06:24:58 +0200
 
 mcaller (1.0.3+git20210624.b415090-3) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -1,41 +1,43 @@
 Source: mcaller
-Section: science
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper-compat (= 13),
-               dh-python,
-               python3-all,
-               python3-setuptools,
-               python3-seaborn,
-               python3-biopython,
-               python3-numpy,
-               python3-sklearn
 Standards-Version: 4.7.4
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders:
+ Steffen Moeller <moeller at debian.org>,
+Section: science
+Testsuite: autopkgtest-pkg-python
+Build-Depends:
+ debhelper-compat (= 14),
+ dh-sequence-python3,
+ python3-all,
+ python3-setuptools,
+ python3-seaborn,
+ python3-biopython,
+ python3-numpy,
+ python3-sklearn,
 Vcs-Browser: https://salsa.debian.org/med-team/mcaller
 Vcs-Git: https://salsa.debian.org/med-team/mcaller.git
 Homepage: https://github.com/al-mcintyre/mCaller
-Testsuite: autopkgtest-pkg-python
-Rules-Requires-Root: no
 
 Package: mcaller
 Architecture: all
-Depends: python3,
-         ${python3:Depends},
-         ${misc:Depends},
-         python3-sklearn,
-         python3-h5py,
-         python3-biopython,
-         python3-matplotlib,
-         python3-seaborn,
-         python3-numpy,
-         python3-pysam,
-         python3-scipy,
-         python3-pandas
+Depends:
+ python3,
+ ${python3:Depends},
+ ${misc:Depends},
+ python3-sklearn,
+ python3-h5py,
+ python3-biopython,
+ python3-matplotlib,
+ python3-seaborn,
+ python3-numpy,
+ python3-pysam,
+ python3-scipy,
+ python3-pandas,
 Recommends:
-         nanopolish|poretools
+ nanopolish|poretools,
 Suggests:
-         graphmap,
-         bwa
+ graphmap,
+ bwa,
 Description: find methylation in nanopore reads
     H
     |


=====================================
debian/patches/python2to3.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen M?ller
+Last-Update: 2020-09-04
+Description: Result from 2to3
+
 Index: mcaller/make_bed.py
 ===================================================================
 --- mcaller.orig/make_bed.py


=====================================
debian/patches/shebang.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen M?ller
+Last-Update: 2020-09-04
+Description: Make sure the shebang line calls python3
+
 Index: mcaller-0.0/compare_genomes.py
 ===================================================================
 --- mcaller-0.0.orig/compare_genomes.py


=====================================
debian/rules
=====================================
@@ -7,7 +7,7 @@ UVERSION=`head -n1 debian/changelog |cut -f1 -d- | cut -f2 -d'(' `
 include /usr/share/dpkg/default.mk
 
 %:
-	dh $@ --with python3
+	dh $@
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))



View it on GitLab: https://salsa.debian.org/med-team/mcaller/-/compare/cdd58c2c6247e6bcf35ce700c0cb4d862d0a22bb...0fea47722870d8c774ba9e7c8aab83871b6d010f

-- 
View it on GitLab: https://salsa.debian.org/med-team/mcaller/-/compare/cdd58c2c6247e6bcf35ce700c0cb4d862d0a22bb...0fea47722870d8c774ba9e7c8aab83871b6d010f
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From gitlab at salsa.debian.org  Wed Jul  1 06:04:56 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Wed, 01 Jul 2026 05:04:56 +0000
Subject: [med-svn] [Git][med-team/mcaller] Pushed new tag
 debian/1.0.3+git20210624.b415090-4
Message-ID: <6a449ff866b5d_55bc8df4583531238@godard.mail>



Andreas Tille pushed new tag debian/1.0.3+git20210624.b415090-4 at Debian Med / mcaller

-- 
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From gitlab at salsa.debian.org  Wed Jul  1 07:14:13 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Wed, 01 Jul 2026 06:14:13 +0000
Subject: [med-svn] [Git][med-team/scikit-bio-binaries][master] 2 commits:
 Upload to unstable
Message-ID: <6a44b03518bbd_55b82c2ed43537354@godard.mail>



Andreas Tille pushed to branch master at Debian Med / scikit-bio-binaries


Commits:
e997f1e8 by Andreas Tille at 2026-06-19T16:49:31+02:00
Upload to unstable

- - - - -
2664f640 by Andreas Tille at 2026-07-01T08:13:58+02:00
Build reproducibly

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/reproducible.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,5 +1,11 @@
-scikit-bio-binaries (1.0.3-1) UNRELEASED; urgency=medium
+scikit-bio-binaries (1.0.3-2) UNRELEASED; urgency=medium
+
+  * Build reproducibly
+
+ -- Andreas Tille <tille at debian.org>  Wed, 01 Jul 2026 08:13:47 +0200
+
+scikit-bio-binaries (1.0.3-1) unstable; urgency=medium
 
   * Initial release (Closes: #1140298)
 
- -- Andreas Tille <tille at debian.org>  Fri, 19 Jun 2026 09:41:00 +0200
+ -- Andreas Tille <tille at debian.org>  Fri, 19 Jun 2026 16:48:49 +0200


=====================================
debian/patches/reproducible.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-07-01
+Description: Build reprocucibly
+
+--- a/src/tools/skbb_generate_helper.py
++++ b/src/tools/skbb_generate_helper.py
+@@ -234,7 +234,7 @@ def print_body(method,lines,nmspace):
+             line = lines[i]
+             i+=1
+         
+-        for ft in ftypes:
++        for ft in sorted(ftypes):
+             print_func_args(method,ftype,nmspace,fname,ft,fargs)
+             print('');
+ 


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ openblas.patch
 no_install.patch
 shared-lib.patch
 hardening.patch
+reproducible.patch



View it on GitLab: https://salsa.debian.org/med-team/scikit-bio-binaries/-/compare/d75a724cb5af491f1ac0154934d4418f29db577f...2664f64088383e2220550f4e9b9b7c670da982bd

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From gitlab at salsa.debian.org  Wed Jul  1 08:04:05 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Wed, 01 Jul 2026 07:04:05 +0000
Subject: [med-svn] [Git][med-team/scikit-bio-binaries][master] Upload to
 unstable
Message-ID: <6a44bbe54f41b_55b947fec4354821a@godard.mail>



Andreas Tille pushed to branch master at Debian Med / scikit-bio-binaries


Commits:
6c549512 by Andreas Tille at 2026-07-01T09:03:40+02:00
Upload to unstable

- - - - -


1 changed file:

- debian/changelog


Changes:

=====================================
debian/changelog
=====================================
@@ -1,8 +1,8 @@
-scikit-bio-binaries (1.0.3-2) UNRELEASED; urgency=medium
+scikit-bio-binaries (1.0.3-2) unstable; urgency=medium
 
   * Build reproducibly
 
- -- Andreas Tille <tille at debian.org>  Wed, 01 Jul 2026 08:13:47 +0200
+ -- Andreas Tille <tille at debian.org>  Wed, 01 Jul 2026 09:02:29 +0200
 
 scikit-bio-binaries (1.0.3-1) unstable; urgency=medium
 



View it on GitLab: https://salsa.debian.org/med-team/scikit-bio-binaries/-/commit/6c5495127572027a29e240fe7ba278a3c8078c95

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From gitlab at salsa.debian.org  Wed Jul  1 08:04:09 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Wed, 01 Jul 2026 07:04:09 +0000
Subject: [med-svn] [Git][med-team/scikit-bio-binaries] Pushed new tag
 debian/1.0.3-1
Message-ID: <6a44bbe9774ee_55bfcdb43548557@godard.mail>



Andreas Tille pushed new tag debian/1.0.3-1 at Debian Med / scikit-bio-binaries

-- 
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From gitlab at salsa.debian.org  Wed Jul  1 08:04:09 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Wed, 01 Jul 2026 07:04:09 +0000
Subject: [med-svn] [Git][med-team/scikit-bio-binaries] Pushed new tag
 debian/1.0.3-2
Message-ID: <6a44bbe9b5263_55b94643403548871@godard.mail>



Andreas Tille pushed new tag debian/1.0.3-2 at Debian Med / scikit-bio-binaries

-- 
View it on GitLab: https://salsa.debian.org/med-team/scikit-bio-binaries/-/tree/debian/1.0.3-2
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From gitlab at salsa.debian.org  Wed Jul  1 08:12:52 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Wed, 01 Jul 2026 07:12:52 +0000
Subject: [med-svn] [Git][med-team/unifrac-tools][master] 2 commits: Merge
 changelog paragraphs
Message-ID: <6a44bdf499a8c_55b947fec43549378@godard.mail>



Andreas Tille pushed to branch master at Debian Med / unifrac-tools


Commits:
a8700f8f by Andreas Tille at 2026-07-01T07:08:04+02:00
Merge changelog paragraphs

- - - - -
6295f42c by Andreas Tille at 2026-07-01T09:12:37+02:00
Do not explicitly specify -noshlib

- - - - -


3 changed files:

- debian/changelog
- debian/control
- debian/patches/enable_linking_to_shared_hdf5_lib.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -7,15 +7,13 @@ unifrac-tools (1.6.1-1) UNRELEASED; urgency=medium
   * Reflow Uploaders field (cme)
   * Remove Priority field (cme)
   * Drop 'Rules-Requires-Root: no' from d/control (routine-update)
-  TODO: https://github.com/scikit-bio/scikit-bio-binaries
+  * Build-Depends: libskbb-dev
+  * Reformat the Last-Update date as ISO YYYY-MM-DD.
 
   [ Gilles Filippini ]
   * Fix FTBFS against HDF5 2.1.0
     Closes: #1139615
 
-  [ Andreas Tille ]
-  * Reformat the Last-Update date as ISO YYYY-MM-DD.
-
  -- Andreas Tille <tille at debian.org>  Tue, 16 Jun 2026 22:24:42 +0200
 
 unifrac-tools (1.4-3) unstable; urgency=medium


=====================================
debian/control
=====================================
@@ -14,6 +14,7 @@ Build-Depends:
  liblz4-dev,
  libblas-dev,
  liblapacke-dev,
+ libskbb-dev,
  chrpath,
  gfortran,
  python3 <!nocheck>,


=====================================
debian/patches/enable_linking_to_shared_hdf5_lib.patch
=====================================
@@ -2,7 +2,7 @@ From: ucko at debian.org (Aaron M. Ucko)
       Andreas Tille <tille at debian.org>
 Date: 2026-06-17
 Origin: https://lists.debian.org/debian-med/2022/07/msg00078.html
-Description: Enable linking ro shared hdf5 library
+Description: Enable linking to shared hdf5 library
 Forwarded: not-needed
 FIXME: Aaron, please review the changes
 
@@ -21,7 +21,7 @@ FIXME: Aaron, please review the changes
  lib$(SSU).so: tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)
  #	h5c++ $(LDDFLAGS) -o lib$(SSU).so tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 $(SKBBLIB) -L$(PREFIX)/lib -noshlib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
 -	h5c++ $(LDDFLAGS) -o lib$(SSU).so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,lib$(SSU).so.0 $(SKBBLIB) -L$(PREFIX)/lib -noshlib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
-+	h5c++ $(LDDFLAGS) -o lib$(SSU).so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -Wl,-soname,lib$(SSU).so.0 $(SKBBLIB) -L$(PREFIX)/lib -noshlib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
++	h5c++ $(LDDFLAGS) -o lib$(SSU).so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -Wl,-soname,lib$(SSU).so.0 $(SKBBLIB) -L$(PREFIX)/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
  	ln -sf lib$(SSU).so.0 lib$(SSU).so
  	# FIXME: Should build static lib as well
  	# $(CXX) $(LDDFLAGS) -o libssu.a tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 $(BLASLIB) -L$(PREFIX)/lib



View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/65ac418aae895faafe1ec1a7d25af50caa58caf4...6295f42c390df38d1598576dc91ef4c4b12c5c5b

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From gitlab at salsa.debian.org  Wed Jul  1 08:16:00 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Wed, 01 Jul 2026 07:16:00 +0000
Subject: [med-svn] [Git][med-team/scikit-bio-binaries][master] Forwarded
 patch
Message-ID: <6a44beb04923e_55b1213b674355062e@godard.mail>



Andreas Tille pushed to branch master at Debian Med / scikit-bio-binaries


Commits:
1cf5d9b6 by Andreas Tille at 2026-07-01T09:15:48+02:00
Forwarded patch

- - - - -


1 changed file:

- debian/patches/reproducible.patch


Changes:

=====================================
debian/patches/reproducible.patch
=====================================
@@ -1,6 +1,7 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Update: 2026-07-01
 Description: Build reprocucibly
+Forwarded: https://github.com/scikit-bio/scikit-bio-binaries/issues/14
 
 --- a/src/tools/skbb_generate_helper.py
 +++ b/src/tools/skbb_generate_helper.py



View it on GitLab: https://salsa.debian.org/med-team/scikit-bio-binaries/-/commit/1cf5d9b69db57dd5eb8b87dd1319e708344db2fb

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From gitlab at salsa.debian.org  Wed Jul  1 09:33:34 2026
From: gitlab at salsa.debian.org (Gioele Barabucci (@gioele))
Date: Wed, 01 Jul 2026 08:33:34 +0000
Subject: [med-svn] [Git][med-team/parallel][master] d/changelog: Release
 Debian version 20240222+ds-4
Message-ID: <6a44d0de7d2e2_55b1213010c35749d1@godard.mail>



Gioele Barabucci pushed to branch master at Debian Med / parallel


Commits:
fb7fb2f7 by Gioele Barabucci at 2026-07-01T10:27:45+02:00
d/changelog: Release Debian version 20240222+ds-4

- - - - -


1 changed file:

- debian/changelog


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+parallel (20240222+ds-4) unstable; urgency=medium
+
+  * Team upload.
+  * d/rules: Remove code needed for debhelper compat level <= 12
+  * d/control: Build-Depend on libreoffice-core-nogui instead of full version
+    (Closes: #1141151)
+  * Add support for <nodoc> build profile (Closes: #1141153)
+
+ -- Gioele Barabucci <gioele at debian.org>  Wed, 01 Jul 2026 10:15:32 +0200
+
 parallel (20240222+ds-3) unstable; urgency=medium
 
   * Team upload.



View it on GitLab: https://salsa.debian.org/med-team/parallel/-/commit/fb7fb2f7395e725ee6ebc7abdda3eb1e1c3e57d1

-- 
View it on GitLab: https://salsa.debian.org/med-team/parallel/-/commit/fb7fb2f7395e725ee6ebc7abdda3eb1e1c3e57d1
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From gitlab at salsa.debian.org  Wed Jul  1 09:36:48 2026
From: gitlab at salsa.debian.org (Gioele Barabucci (@gioele))
Date: Wed, 01 Jul 2026 08:36:48 +0000
Subject: [med-svn] [Git][med-team/parallel] Pushed new tag
 debian/20240222+ds-4
Message-ID: <6a44d1a06366_55b15084034357559b@godard.mail>



Gioele Barabucci pushed new tag debian/20240222+ds-4 at Debian Med / parallel

-- 
View it on GitLab: https://salsa.debian.org/med-team/parallel/-/tree/debian/20240222+ds-4
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From gitlab at salsa.debian.org  Wed Jul  1 09:53:24 2026
From: gitlab at salsa.debian.org (=?UTF-8?B?S2Fyc3RlbiBTY2jDtmtlIChAa2Fyc28p?=)
Date: Wed, 01 Jul 2026 08:53:24 +0000
Subject: [med-svn] [Git][med-team/python-biopython][master] 3 commits:
 extending Fix-Endian-issue-with-binary-CIF.patch
Message-ID: <6a44d58452a1a_55b54a99bc35808e6@godard.mail>



Karsten Sch?ke pushed to branch master at Debian Med / python-biopython


Commits:
c2ac4ae3 by Karsten Sch?ke at 2026-07-01T07:58:53+02:00
extending Fix-Endian-issue-with-binary-CIF.patch

- - - - -
a6704887 by Karsten Sch?ke at 2026-07-01T08:00:22+02:00
Update changelog for 1.87+dfsg-3 release

- - - - -
f8a63189 by Karsten Sch?ke at 2026-07-01T08:19:28+02:00
commend Fix-Endian-issue-with-binary-CIF.patch

- - - - -


2 changed files:

- debian/changelog
- debian/patches/Fix-Endian-issue-with-binary-CIF.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-biopython (1.87+dfsg-3) unstable; urgency=medium
+
+  * Team upload.
+  * extending Fix-Endian-issue-with-binary-CIF.patch
+
+ -- Karsten Sch?ke <karsten.schoeke at geobasis-bb.de>  Wed, 01 Jul 2026 08:00:11 +0200
+
 python-biopython (1.87+dfsg-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/Fix-Endian-issue-with-binary-CIF.patch
=====================================
@@ -1,11 +1,16 @@
 From: =?utf-8?q?Karsten_Sch=C3=B6ke?= <karsten.schoeke at geobasis-bb.de>
-Date: Mon, 29 Jun 2026 08:14:31 +0200
+Date: Wed, 1 Jul 2026 07:56:58 +0200
 Subject: Fix Endian issue with binary CIF
+Fix _bcif_helper.integer_unpack() to accept PEP 3118 buffer format strings
+with optional endianness prefixes. 
+This fixes test failures on ppc64 where the buffer format
+is reported as "<H" instead of "H".
 
 Forwarded: https://github.com/biopython/biopython/pull/5252
 ---
  Bio/PDB/bcifhelpermodule.c | 4 +++-
- 1 file changed, 3 insertions(+), 1 deletion(-)
+ Bio/PDB/binary_cif.py      | 3 +++
+ 2 files changed, 6 insertions(+), 1 deletion(-)
 
 diff --git a/Bio/PDB/bcifhelpermodule.c b/Bio/PDB/bcifhelpermodule.c
 index 31aa652..60680cb 100644
@@ -29,3 +34,17 @@ index 31aa652..60680cb 100644
  
      if (format == 'B') {
          integer_unpack_u8(&in_view, &out_view);
+diff --git a/Bio/PDB/binary_cif.py b/Bio/PDB/binary_cif.py
+index 4fa7e83..2c1e94a 100644
+--- a/Bio/PDB/binary_cif.py
++++ b/Bio/PDB/binary_cif.py
+@@ -125,6 +125,9 @@ def _integer_packing_decoder(column):
+         dtype = np.dtype("<i4")
+ 
+     data = column["data"]["data"]
++    # Convert to native endianness
++    data = data.astype(data.dtype.newbyteorder("="))
++
+     assert byte_count == data.dtype.itemsize
+     assert np.issubdtype(data.dtype, np.unsignedinteger) == is_unsigned
+     decoded_data = np.empty((src_size,), dtype)



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/586745a4b3a7b176b4ce2a3caf4bbbcee9993411...f8a6318925b469010cbec7130bf017bdd29c935a

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/586745a4b3a7b176b4ce2a3caf4bbbcee9993411...f8a6318925b469010cbec7130bf017bdd29c935a
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From gitlab at salsa.debian.org  Wed Jul  1 11:54:50 2026
From: gitlab at salsa.debian.org (=?UTF-8?B?S2Fyc3RlbiBTY2jDtmtlIChAa2Fyc28p?=)
Date: Wed, 01 Jul 2026 10:54:50 +0000
Subject: [med-svn] [Git][med-team/python-biopython] Pushed new tag
 debian/1.87+dfsg-3
Message-ID: <6a44f1fa1c104_55b14c7e7783622570@godard.mail>



Karsten Sch?ke pushed new tag debian/1.87+dfsg-3 at Debian Med / python-biopython

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/tree/debian/1.87+dfsg-3
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From gitlab at salsa.debian.org  Wed Jul  1 14:42:25 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Wed, 01 Jul 2026 13:42:25 +0000
Subject: [med-svn] [Git][med-team/community/helper-scripts][master]
 automatic update
Message-ID: <6a451941398c4_55b94cc2603674228@godard.mail>



Andreas Tille pushed to branch master at Debian Med / community / helper-scripts


Commits:
052f400f by Andreas Tille at 2026-07-01T13:42:18+00:00
automatic update

- - - - -


4 changed files:

- debian-med-tests.txt
- debian-science-tests.txt
- outdated_med-packages.txt
- python-team-tests.txt


Changes:

=====================================
debian-med-tests.txt
=====================================
@@ -1,23 +1,25 @@
-Last-Update: Wed, 01 Jul 2026 01:42:04 +0000
+Last-Update: Wed, 01 Jul 2026 13:42:03 +0000
 
  Source                        | Vote   | Tasks                                      |                                 Tags                                 
 -------------------------------+--------+--------------------------------------------+----------------------------------------------------------------------
- dicomscope                    |     23 | {imaging}                                  | 
+ dicomscope                    |     24 | {imaging}                                  | 
  jebl2                         |     13 | {bio-dev}                                  | 
  adun.app                      |     12 | {bio}                                      | 
  biojava-live                  |     12 | {bio-dev}                                  | 
  icb-utils                     |     12 | {bio-dev}                                  | 
+ mrtrix3                       |     12 | {imaging}                                  | 
  oscar                         |     12 | {tools,practice,data}                      | 
- mrtrix3                       |     11 | {imaging}                                  | 
  orthanc-gdcm                  |     11 | {imaging}                                  | 
+ sight                         |     11 | {imaging}                                  | 
  gnumed-server                 |     10 | {covid-19,practice}                        | 
- sight                         |     10 | {imaging}                                  | 
  embassy-domsearch             |      9 | {cloud,bio}                                | 
- pixelmed                      |      8 | {imaging}                                  | 
+ pixelmed                      |      9 | {imaging}                                  | 
+ ants                          |      7 | {imaging}                                  | 
  embassy-domainatrix           |      7 | {cloud,bio}                                | 
  embassy-domalign              |      7 | {cloud,bio}                                | 
  saint                         |      7 | {bio}                                      | 
- ants                          |      6 | {imaging}                                  | 
+ sight                         |      7 | {imaging}                                  | 
+ bart-view                     |      6 | {imaging}                                  | 
  beast-mcmc                    |      6 | {bio,bio-phylogeny}                        | 
  dextractor                    |      6 | {bio,covid-19}                             | 
  ipig                          |      6 | {bio}                                      | 
@@ -29,9 +31,7 @@ Last-Update: Wed, 01 Jul 2026 01:42:04 +0000
  orthanc-postgresql            |      6 | {imaging}                                  | 
  proalign                      |      6 | {bio,bio-phylogeny}                        | 
  sga                           |      6 | {bio}                                      | 
- sight                         |      6 | {imaging}                                  | 
  sprai                         |      6 | {bio}                                      | 
- bart-view                     |      5 | {imaging}                                  | 
  biojava6-live                 |      5 | {bio-dev}                                  | 
  bio-tradis                    |      5 | {bio,bio-dev}                              | 
  fastml                        |      5 | {bio}                                      | 
@@ -128,8 +128,8 @@ Last-Update: Wed, 01 Jul 2026 01:42:04 +0000
  papyrus                       |      0 | {imaging-dev}                              | 
  pbcopper                      |      0 | {bio-dev}                                  | 
  pbseqlib                      |      0 | {bio-dev}                                  | 
- python-seqcluster             |      0 | {covid-19,bio-dev}                         | 
  python-seqcluster             |      0 | {bio}                                      | 
+ python-seqcluster             |      0 | {covid-19,bio-dev}                         | 
  resfinder-db                  |      0 | {bio}                                      | 
  savvy                         |      0 | {bio-dev}                                  | 
  sbmltoolbox                   |      0 | {bio-dev}                                  | 


=====================================
debian-science-tests.txt
=====================================
@@ -1,35 +1,35 @@
-Last-Update: Wed, 01 Jul 2026 01:42:04 +0000
+Last-Update: Wed, 01 Jul 2026 13:42:05 +0000
 
        Source                              | Vote   |             Tasks                                                   |                          Tags                          
 -------------------------------------------+--------+---------------------------------------------------------------------+--------------------------------------------------------
- gts                                       |   5475 | {viewing}                                                           | 
- nltk                                      |   3186 | {linguistics}                                                       | 
- libaec                                    |    382 | {meteorology-dev}                                                   | 
- spacenavd                                 |    283 | {tools}                                                             | 
- opencascade                               |    239 | {simulations}                                                       | 
- armadillo                                 |    187 | {mathematics-dev}                                                   | 
+ gts                                       |   5491 | {viewing}                                                           | 
+ nltk                                      |   3182 | {linguistics}                                                       | 
+ libaec                                    |    396 | {meteorology-dev}                                                   | 
+ spacenavd                                 |    279 | {tools}                                                             | 
+ opencascade                               |    232 | {simulations}                                                       | 
+ armadillo                                 |    195 | {mathematics-dev}                                                   | 
  open-coarrays                             |    159 | {meteorology-dev}                                                   | 
- arpack                                    |    102 | {mathematics-dev}                                                   | 
- refmac-dictionary                         |     73 | {highenergy-physics-dev,chemistry}                                  | 
- mbpoll                                    |     66 | {simulations}                                                       | 
- giac                                      |     53 | {mathematics}                                                       | 
- muparser                                  |     45 | {mathematics-dev}                                                   | 
- imview                                    |     44 | {viewing}                                                           | 
- guiqwt                                    |     38 | {numericalcomputation,viewing}                                      | 
+ arpack                                    |    106 | {mathematics-dev}                                                   | 
+ refmac-dictionary                         |     75 | {highenergy-physics-dev,chemistry}                                  | 
+ mbpoll                                    |     67 | {simulations}                                                       | 
+ giac                                      |     55 | {mathematics}                                                       | 
+ muparser                                  |     47 | {mathematics-dev}                                                   | 
+ imview                                    |     45 | {viewing}                                                           | 
+ guiqwt                                    |     39 | {numericalcomputation,viewing}                                      | 
  setzer                                    |     36 | {typesetting}                                                       | 
  pyzo                                      |     33 | {numericalcomputation}                                              | 
- persalys                                  |     31 | {statistics,mathematics,engineering}                                | 
+ persalys                                  |     32 | {statistics,mathematics,engineering}                                | 
  apophenia                                 |     30 | {statistics}                                                        | 
- sardana                                   |     28 | {dataacquisition}                                                   | 
- teem                                      |     28 | {imageanalysis}                                                     | 
+ sardana                                   |     29 | {dataacquisition}                                                   | 
+ teem                                      |     29 | {imageanalysis}                                                     | 
  colpack                                   |     25 | {numericalcomputation}                                              | 
- flann                                     |     25 | {mathematics-dev,engineering-dev}                                   | 
  ntl                                       |     25 | {mathematics-dev}                                                   | 
+ palp                                      |     25 | {mathematics}                                                       | 
+ persalys                                  |     25 | {mathematics,engineering,statistics}                                | 
  adolc                                     |     24 | {numericalcomputation}                                              | 
  feedgnuplot                               |     24 | {viewing}                                                           | 
+ flann                                     |     24 | {mathematics-dev,engineering-dev}                                   | 
  lxi-tools                                 |     24 | {dataacquisition,engineering}                                       | 
- palp                                      |     24 | {mathematics}                                                       | 
- persalys                                  |     24 | {mathematics,engineering,statistics}                                | 
  sketch                                    |     24 | {typesetting}                                                       | 
  arduino-mk                                |     22 | {robotics}                                                          | 
  coinor-symphony                           |     21 | {logic,mathematics,numericalcomputation}                            | 
@@ -37,42 +37,42 @@ Last-Update: Wed, 01 Jul 2026 01:42:04 +0000
  getdp                                     |     20 | {mathematics,simulations,engineering}                               | 
  python-escript                            |     20 | {simulations,numericalcomputation,engineering}                      | 
  dune-uggrid                               |     19 | {mathematics-dev}                                                   | 
- libmatio                                  |     18 | {mathematics-dev}                                                   | 
+ libmatio                                  |     19 | {mathematics-dev}                                                   | 
  ppl                                       |     18 | {numericalcomputation}                                              | 
  toulbar2                                  |     18 | {mathematics,numericalcomputation,physics,logic}                    | 
  eccodes                                   |     17 | {meteorology-dev}                                                   | 
+ libcvd                                    |     17 | {imageanalysis}                                                     | 
  libm4ri                                   |     17 | {mathematics-dev}                                                   | 
  xygrib                                    |     17 | {meteorology}                                                       | 
- eccodes                                   |     16 | {meteorology,meteorology-dev}                                       | 
  fftw                                      |     16 | {mathematics-dev,meteorology-dev,physics-dev}                       | 
- libcvd                                    |     16 | {imageanalysis}                                                     | 
- flintqs                                   |     15 | {mathematics}                                                       | 
+ flintqs                                   |     16 | {mathematics}                                                       | 
+ eccodes                                   |     15 | {meteorology,meteorology-dev}                                       | 
  libvigraimpex                             |     15 | {imageanalysis-dev,machine-learning}                                | 
  grads                                     |     14 | {meteorology}                                                       | 
+ gts                                       |     14 | {viewing-dev}                                                       | 
+ ipe-tools                                 |     14 | {typesetting}                                                       | 
  picosat                                   |     14 | {logic}                                                             | 
  psurface                                  |     14 | {numericalcomputation}                                              | 
+ sat4j                                     |     14 | {logic}                                                             | 
  debian-science                            |     13 | {machine-learning,neuroscience-cognitive}                           | 
  debian-science                            |     13 | {machine-learning,nanoscale-physics,economics,physics}              | 
- gts                                       |     13 | {viewing-dev}                                                       | 
- ipe-tools                                 |     13 | {typesetting}                                                       | 
  jeuclid                                   |     13 | {viewing,typesetting}                                               | 
  matlab-support                            |     13 | {mathematics,numericalcomputation}                                  | 
  mseed2sac                                 |     13 | {dataacquisition-dev}                                               | 
- sat4j                                     |     13 | {logic}                                                             | 
  bossa                                     |     12 | {devices}                                                           | 
- debian-science                            |     12 | {electrophysiology}                                                 | 
  debian-science                            |     12 | {tools}                                                             | 
+ debian-science                            |     12 | {electrophysiology}                                                 | 
  opencascade                               |     11 | {simulations}                                                       | 
+ rubiks                                    |     11 | {mathematics,geometry}                                              | 
  vdt                                       |     11 | {mathematics-dev}                                                   | 
  alberta                                   |     10 | {engineering-dev}                                                   | 
  feff85exafs                               |     10 | {chemistry}                                                         | 
- rubiks                                    |     10 | {mathematics,geometry}                                              | 
  cliquer                                   |      9 | {mathematics-dev}                                                   | 
  cliquer                                   |      9 | {mathematics}                                                       | 
  lrcalc                                    |      9 | {mathematics-dev}                                                   | 
- pcl                                       |      9 | {robotics-dev}                                                      | 
  chemical-structures                       |      8 | {chemistry}                                                         | 
  libitpp                                   |      8 | {engineering-dev,mathematics-dev}                                   | 
+ pcl                                       |      8 | {robotics-dev}                                                      | 
  ros-vcstool                               |      8 | {robotics-dev}                                                      | 
  apertium                                  |      7 | {linguistics}                                                       | 
  fftw                                      |      7 | {meteorology-dev,physics-dev,mathematics-dev}                       | 
@@ -136,8 +136,8 @@ Last-Update: Wed, 01 Jul 2026 01:42:04 +0000
  trilinos                                  |      3 | {mathematics-dev,physics-dev,engineering-dev}                       | 
  apertium-apy                              |      2 | {linguistics}                                                       | 
  clipper                                   |      2 | {nanoscale-physics-dev}                                             | 
- coda                                      |      2 | {meteorology}                                                       | 
  coda                                      |      2 | {meteorology-dev}                                                   | 
+ coda                                      |      2 | {meteorology}                                                       | 
  coinor-bonmin                             |      2 | {mathematics}                                                       | 
  cqrlib                                    |      2 | {mathematics-dev}                                                   | 
  cvector                                   |      2 | {mathematics-dev}                                                   | 
@@ -151,17 +151,17 @@ Last-Update: Wed, 01 Jul 2026 01:42:04 +0000
  libgtkdatabox                             |      2 | {engineering-dev,viewing-dev}                                       | 
  liborigin2                                |      2 | {viewing-dev}                                                       | 
  libtnt                                    |      2 | {mathematics-dev}                                                   | 
+ makedepf90                                |      2 | {meteorology-dev}                                                   | 
  meshsdfilter                              |      2 | {mathematics-dev}                                                   | 
  mmdb                                      |      2 | {nanoscale-physics-dev,highenergy-physics-dev}                      | 
  mpi4py-fft                                |      2 | {mathematics-dev}                                                   | 
  ncrystal                                  |      2 | {nanoscale-physics-dev,highenergy-physics-dev}                      | 
  neartree                                  |      2 | {numericalcomputation,mathematics-dev}                              | 
  nrn-iv                                    |      2 | {biology}                                                           | 
- odc                                       |      2 | {meteorology}                                                       | 
  odc                                       |      2 | {meteorology-dev}                                                   | 
+ odc                                       |      2 | {meteorology}                                                       | 
  openmesh                                  |      2 | {mathematics-dev}                                                   | 
  quadrule                                  |      2 | {mathematics-dev}                                                   | 
- ros-ros-environment                       |      2 | {robotics-dev}                                                      | 
  scram                                     |      2 | {engineering}                                                       | 
  silo-llnl                                 |      2 | {engineering}                                                       | 
  ssm                                       |      2 | {nanoscale-physics-dev}                                             | 
@@ -193,14 +193,14 @@ Last-Update: Wed, 01 Jul 2026 01:42:04 +0000
  looptools                                 |      1 | {highenergy-physics}                                                | 
  looptools                                 |      1 | {highenergy-physics-dev}                                            | 
  magics++                                  |      1 | {meteorology-dev}                                                   | 
- makedepf90                                |      1 | {meteorology-dev}                                                   | 
- metkit                                    |      1 | {meteorology-dev}                                                   | 
  metkit                                    |      1 | {meteorology}                                                       | 
+ metkit                                    |      1 | {meteorology-dev}                                                   | 
  metview                                   |      1 | {meteorology}                                                       | 
  nrn-mod2c                                 |      1 | {biology}                                                           | 
  openctm                                   |      1 | {physics-dev}                                                       | 
  python-escript                            |      1 | {numericalcomputation,engineering,simulations}                      | 
  ros-collada-urdf                          |      1 | {robotics}                                                          | 
+ ros-ros-environment                       |      1 | {robotics-dev}                                                      | 
  schroedinger-coordgenlibs                 |      1 | {nanoscale-physics-dev,chemistry}                                   | 
  tulip                                     |      1 | {viewing-dev}                                                       | 
  amgcl                                     |      0 | {mathematics-dev}                                                   | 
@@ -228,8 +228,8 @@ Last-Update: Wed, 01 Jul 2026 01:42:04 +0000
  cg3                                       |      0 | {linguistics}                                                       | 
  clhep                                     |      0 | {highenergy-physics-dev}                                            | 
  coda                                      |      0 | {meteorology-dev}                                                   | 
- debian-science                            |      0 | {physics}                                                           | 
  debian-science                            |      0 | {electrophysiology}                                                 | 
+ debian-science                            |      0 | {physics}                                                           | 
  dune-grid-glue                            |      0 | {mathematics-dev}                                                   | 
  etsf-io                                   |      0 | {nanoscale-physics-dev}                                             | 
  fastjet                                   |      0 | {highenergy-physics-dev}                                            | 
@@ -244,8 +244,8 @@ Last-Update: Wed, 01 Jul 2026 01:42:04 +0000
  mbt                                       |      0 | {linguistics}                                                       | 
  mbtserver                                 |      0 | {linguistics}                                                       | 
  mctc-lib                                  |      0 | {highenergy-physics-dev,nanoscale-physics-dev}                      | 
- metis-edf                                 |      0 | {engineering-dev}                                                   | 
  metis-edf                                 |      0 | {engineering,numericalcomputation}                                  | 
+ metis-edf                                 |      0 | {engineering-dev}                                                   | 
  opengv                                    |      0 | {geometry}                                                          | 
  openigtlink                               |      0 | {robotics-dev}                                                      | 
  qrupdate                                  |      0 | {mathematics-dev}                                                   | 


=====================================
outdated_med-packages.txt
=====================================
The diff for this file was not included because it is too large.

=====================================
python-team-tests.txt
=====================================
@@ -1,114 +1,114 @@
-Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
+Last-Update: Wed, 01 Jul 2026 13:42:06 +0000
 
      Source                             | Vote   |                          Tags                          
 ----------------------------------------+--------+--------------------------------------------------------
- python-repoze.lru                      |   7427 | 
- netifaces                              |   5172 | 
- sortedcontainers                       |   4145 | 
- python-babel                           |   4062 | 
- python-babel                           |   3703 | 
- ghp-import                             |   3077 | 
- python-lunr                            |   3066 | 
- python-zopfli                          |   3016 | 
- python-outcome                         |   2719 | 
- python-gssapi                          |   2694 | 
+ python-repoze.lru                      |   7408 | 
+ netifaces                              |   5165 | 
+ sortedcontainers                       |   4158 | 
+ python-babel                           |   4073 | 
+ python-babel                           |   3723 | 
+ ghp-import                             |   3071 | 
+ python-lunr                            |   3059 | 
+ python-zopfli                          |   3023 | 
+ python-outcome                         |   2720 | 
+ python-gssapi                          |   2704 | 
  python-greenlet                        |   2538 | 
- humanfriendly                          |   2389 | 
- python-invoke                          |   2147 | 
- hyperlink                              |   1885 | 
+ humanfriendly                          |   2384 | 
+ python-invoke                          |   2148 | 
+ hyperlink                              |   1870 | 
  python-mysqldb                         |   1797 | 
- alabaster                              |   1690 | 
- python-hyperframe                      |   1626 | 
- websocket-client                       |   1583 | 
- python-hpack                           |   1479 | 
- python-linux-procfs                    |   1446 | 
- python-notify2                         |   1425 | 
- python-gbinder                         |   1286 | 
- pdfarranger                            |   1134 | 
- python-rsa                             |   1029 | 
- menulibre                              |    931 | 
- python-requests-oauthlib               |    927 | 
- python-webob                           |    780 | 
- python-geoip                           |    770 | 
- django-stronghold                      |    742 | 
+ alabaster                              |   1695 | 
+ python-hyperframe                      |   1633 | 
+ websocket-client                       |   1591 | 
+ python-hpack                           |   1483 | 
+ python-linux-procfs                    |   1440 | 
+ python-notify2                         |   1429 | 
+ python-gbinder                         |   1289 | 
+ pdfarranger                            |   1148 | 
+ python-rsa                             |   1018 | 
+ menulibre                              |    935 | 
+ python-requests-oauthlib               |    925 | 
+ python-webob                           |    771 | 
+ python-geoip                           |    769 | 
+ django-stronghold                      |    750 | 
  python-pandocfilters                   |    622 | 
- powerline                              |    616 | 
- powerline                              |    611 | 
- powerline                              |    578 | 
- kazam                                  |    500 | 
- python-gevent                          |    495 | 
+ powerline                              |    617 | 
+ powerline                              |    612 | 
+ powerline                              |    587 | 
+ python-gevent                          |    501 | 
+ kazam                                  |    499 | 
  python-ewmh                            |    481 | 
- intelhex                               |    432 | 
- python-pyu2f                           |    420 | 
- autopep8                               |    397 | 
- asn1crypto                             |    392 | 
- python-et-xmlfile                      |    379 | 
- catfish                                |    323 | 
- pytoolconfig                           |    315 | 
- pyenv                                  |    289 | 
+ intelhex                               |    431 | 
+ python-pyu2f                           |    406 | 
+ autopep8                               |    400 | 
+ asn1crypto                             |    394 | 
+ python-et-xmlfile                      |    382 | 
+ catfish                                |    332 | 
+ pytoolconfig                           |    317 | 
+ pyenv                                  |    288 | 
  spf-engine                             |    254 | 
- python-text-unidecode                  |    247 | 
- python-utmp                            |    236 | 
+ python-text-unidecode                  |    251 | 
+ python-utmp                            |    235 | 
  spf-engine                             |    232 | 
- python-keyutils                        |    221 | 
+ python-keyutils                        |    220 | 
  gaupol                                 |    218 | 
- python-ldap3                           |    216 | 
- python-smmap                           |    206 | 
+ python-ldap3                           |    215 | 
+ python-smmap                           |    208 | 
  python-mimeparse                       |    179 | 
- dockerpty                              |    172 | 
- httpie                                 |    150 | 
- python-rfc6555                         |    145 | 
- smem                                   |    145 | 
- video-downloader                       |    142 | 
- python-ntlm-auth                       |    141 | 
+ dockerpty                              |    169 | 
+ httpie                                 |    151 | 
+ python-rfc6555                         |    147 | 
+ python-ntlm-auth                       |    144 | 
+ smem                                   |    143 | 
+ video-downloader                       |    141 | 
  python-consul                          |    140 | 
+ python-i3ipc                           |    139 | 
  autokey                                |    138 | 
- python-toml                            |    137 | 
- python-i3ipc                           |    134 | 
+ python-toml                            |    138 | 
  kivy                                   |    133 | 
- python-pyaml-env                       |    130 | 
- nodeenv                                |    124 | 
+ python-pyaml-env                       |    133 | 
+ nodeenv                                |    125 | 
  timekpr-next                           |    116 | 
- python-click-repl                      |    109 | 
+ python-click-repl                      |    108 | 
  notebook-shim                          |     96 | 
- pymediainfo                            |     92 | 
+ pymediainfo                            |     93 | 
  lollypop                               |     88 | 
- mugshot                                |     87 | 
+ sphinx-inline-tabs                     |     88 | 
+ datalad                                |     86 | 
+ mugshot                                |     86 | 
  pacparser                              |     85 | 
- sphinx-inline-tabs                     |     85 | 
- pssh                                   |     83 | 
- datalad                                |     81 | 
- python-colour                          |     80 | 
- mypaint                                |     76 | 
- fabric                                 |     75 | 
- datalad                                |     73 | 
- python-zombie-imp                      |     69 | 
- funcparserlib                          |     68 | 
+ pssh                                   |     81 | 
+ python-colour                          |     79 | 
+ datalad                                |     77 | 
+ fabric                                 |     74 | 
+ mypaint                                |     74 | 
+ funcparserlib                          |     70 | 
+ python-zombie-imp                      |     68 | 
  sphinx-copybutton                      |     67 | 
- python-looseversion                    |     66 | 
- python-scp                             |     64 | 
+ python-looseversion                    |     65 | 
+ python-scp                             |     65 | 
  show-in-file-manager                   |     64 | 
- ueberzug                               |     64 | 
- python-casttube                        |     63 | 
- numpy-stl                              |     61 | 
+ python-casttube                        |     62 | 
+ smartypants                            |     61 | 
  sshtunnel                              |     61 | 
- smartypants                            |     60 | 
- pymacaroons                            |     58 | 
- nwg-displays                           |     57 | 
- itstool                                |     54 | 
- mitmproxy                              |     54 | 
+ ueberzug                               |     61 | 
+ numpy-stl                              |     60 | 
+ pymacaroons                            |     60 | 
+ nwg-displays                           |     59 | 
+ itstool                                |     56 | 
+ autotiling                             |     52 | 
+ mitmproxy                              |     52 | 
  trac                                   |     52 | 
- autotiling                             |     51 | 
- python3-onelogin-saml2                 |     49 | 
- pyenv                                  |     43 | 
+ python3-onelogin-saml2                 |     48 | 
+ pyenv                                  |     42 | 
  certipy                                |     41 | 
  jupyterhub                             |     39 | 
  pamela                                 |     39 | 
- pywavelets                             |     36 | 
  mysql-connector-python                 |     35 | 
- pyquery                                |     34 | 
+ pyquery                                |     35 | 
+ pywavelets                             |     35 | 
  spf-engine                             |     34 | 
- python-slip10                          |     33 | 
+ python-slip10                          |     32 | 
  hatchling                              |     31 | 
  typogrify                              |     30 | 
  python-statsd                          |     29 | 
@@ -118,65 +118,65 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  sphinxcontrib-blockdiag                |     27 | 
  python-priority                        |     26 | 
  python-scrypt                          |     26 | 
- pylibmc                                |     25 | 
- fabric                                 |     24 | 
+ pylibmc                                |     24 | 
  pymacs                                 |     24 | 
  python-zstd                            |     24 | 
- sphinxcontrib-seqdiag                  |     24 | 
  enlighten                              |     23 | 
+ fabric                                 |     23 | 
  membernator                            |     23 | 
+ sphinxcontrib-seqdiag                  |     23 | 
  pssh                                   |     22 | 
  python-rangehttpserver                 |     22 | 
- backoff                                |     21 | 
- python-translationstring               |     20 | 
+ backoff                                |     20 | 
  pithos                                 |     19 | 
  powerline-gitstatus                    |     19 | 
+ python-translationstring               |     19 | 
+ rst2pdf                                |     19 | 
  enzyme                                 |     18 | 
  flask-principal                        |     18 | 
  python-demjson                         |     18 | 
  python-pem                             |     18 | 
- rst2pdf                                |     18 | 
  subliminal                             |     18 | 
  toot                                   |     18 | 
+ kivy                                   |     17 | 
  python-pysubs2                         |     17 | 
  python-sdnotify                        |     17 | 
- censys                                 |     16 | 
  clustershell                           |     16 | 
  mopidy-mpd                             |     16 | 
  policyd-rate-limit                     |     16 | 
- python-hupper                          |     16 | 
+ censys                                 |     15 | 
+ gtextfsm                               |     15 | 
  jschema-to-python                      |     15 | 
- kivy                                   |     15 | 
  mistune0                               |     15 | 
+ parfive                                |     15 | 
+ pykwalify                              |     15 | 
+ python-args                            |     15 | 
  python-dataset                         |     15 | 
+ python-hupper                          |     15 | 
  python-sarif-python-om                 |     15 | 
  subliminal                             |     15 | 
+ alot                                   |     14 | 
+ cppman                                 |     14 | 
  dnsdiag                                |     14 | 
- gtextfsm                               |     14 | 
- parfive                                |     14 | 
  pwntools                               |     14 | 
- pykwalify                              |     14 | 
- python-args                            |     14 | 
  python-py-zipkin                       |     14 | 
- alot                                   |     13 | 
- cppman                                 |     13 | 
  datalad-container                      |     13 | 
  micropython-mpremote                   |     13 | 
  mopidy-local                           |     13 | 
- python-clint                           |     12 | 
+ python-clint                           |     13 | 
  python-pyalsa                          |     12 | 
  sphinxcontrib-actdiag                  |     12 | 
  sphinxcontrib-nwdiag                   |     12 | 
  gmplot                                 |     11 | 
  pytest-runner                          |     11 | 
+ python-pygal                           |     11 | 
+ sphinxcontrib-log-cabinet              |     11 | 
+ unearth                                |     11 | 
  django-environ                         |     10 | 
  python-dbussy                          |     10 | 
  python-halo                            |     10 | 
  python-nmea2                           |     10 | 
  python-numpysane                       |     10 | 
- python-pygal                           |     10 | 
- sphinxcontrib-log-cabinet              |     10 | 
- unearth                                |     10 | 
  dbf                                    |      9 | 
  flask-security                         |      9 | 
  junos-eznc                             |      9 | 
@@ -187,48 +187,52 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  httpcode                               |      8 | 
  python-envs                            |      8 | 
  python-openstep-plist                  |      8 | 
- speg                                   |      8 | 
+ sphinxcontrib-images                   |      8 | 
  todoman                                |      8 | 
  beanquery                              |      7 | 
+ clustershell                           |      7 | 
+ dask-sphinx-theme                      |      7 | 
  debiancontributors                     |      7 | 
  drf-yasg-nonfree                       |      7 | 
  flask-paranoid                         |      7 | 
  hachoir                                |      7 | 
  librouteros                            |      7 | 
  pyp                                    |      7 | 
- pyparallel                             |      7 | 
+ pysequoia                              |      7 | 
  python-aiohttp-security                |      7 | 
  python-crcelk                          |      7 | 
  python-drf-spectacular-sidecar-nonfree |      7 | 
- python-ethtool                         |      7 | 
  python-setuptools-git                  |      7 | 
  python-versioneer                      |      7 | 
  slimit                                 |      7 | 
- sphinxcontrib-images                   |      7 | 
+ speg                                   |      7 | 
  sphinx-intl                            |      7 | 
  txt2tags                               |      7 | 
- azote                                  |      6 | 
- clustershell                           |      6 | 
+ flask-session                          |      6 | 
+ pyparallel                             |      6 | 
+ pytaglib                               |      6 | 
  python-kyotocabinet                    |      6 | 
  python-pyrss2gen                       |      6 | 
  sphinxcontrib-globalsubs               |      6 | 
  tuna                                   |      6 | 
  zabbix-cli                             |      6 | 
+ azote                                  |      5 | 
+ bootstrap-flask                        |      5 | 
  btchip-python                          |      5 | 
- dask-sphinx-theme                      |      5 | 
+ extension-helpers                      |      5 | 
  fava                                   |      5 | 
- flask-session                          |      5 | 
  graphql-relay                          |      5 | 
  mypy-protobuf                          |      5 | 
  numpy-stl                              |      5 | 
  pyfltk                                 |      5 | 
- pytaglib                               |      5 | 
+ python-deepmerge                       |      5 | 
+ python-ethtool                         |      5 | 
  python-overpy                          |      5 | 
  python-xdo                             |      5 | 
  speaklater                             |      5 | 
+ sphinx-design                          |      5 | 
  aiomysql                               |      4 | 
  ansi                                   |      4 | 
- bootstrap-flask                        |      4 | 
  cram                                   |      4 | 
  flask-api                              |      4 | 
  imap-tools                             |      4 | 
@@ -239,23 +243,16 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  proglog                                |      4 | 
  pycrc                                  |      4 | 
  pylint-common                          |      4 | 
- pysequoia                              |      4 | 
- python-deepmerge                       |      4 | 
- python-imageio-ffmpeg                  |      4 | 
  python-netfilterqueue                  |      4 | 
  python-simpy                           |      4 | 
  ruff                                   |      4 | 
  securestring                           |      4 | 
  smem                                   |      4 | 
- sphinx-design                          |      4 | 
  trac-accountmanager                    |      4 | 
  wikitrans                              |      4 | 
- aiocache                               |      3 | 
- aiomcache                              |      3 | 
  django-sass                            |      3 | 
  drf-extensions                         |      3 | 
  drf-haystack                           |      3 | 
- extension-helpers                      |      3 | 
  flask-flatpages                        |      3 | 
  flufl.testing                          |      3 | 
  htmlmin                                |      3 | 
@@ -266,16 +263,19 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  namecheap                              |      3 | 
  pyjokes                                |      3 | 
  pynliner                               |      3 | 
+ pyrad                                  |      3 | 
  python-cookies                         |      3 | 
+ python-imageio-ffmpeg                  |      3 | 
  python-imgviz                          |      3 | 
  python-urlobject                       |      3 | 
  sorl-thumbnail                         |      3 | 
  traittypes                             |      3 | 
  voltron                                |      3 | 
  wikitrans                              |      3 | 
+ aiocache                               |      2 | 
+ aiomcache                              |      2 | 
  django-jinja                           |      2 | 
  django-paintstore                      |      2 | 
- django-pglocks                         |      2 | 
  django-redis-sessions                  |      2 | 
  django-shortuuidfield                  |      2 | 
  dotdrop                                |      2 | 
@@ -295,10 +295,10 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  painintheapt                           |      2 | 
  panoramisk                             |      2 | 
  pdudaemon                              |      2 | 
+ purl                                   |      2 | 
  pyina                                  |      2 | 
  pyjunitxml                             |      2 | 
  pynag                                  |      2 | 
- pyrad                                  |      2 | 
  pytest-black                           |      2 | 
  python-biplist                         |      2 | 
  python-broadlink                       |      2 | 
@@ -338,6 +338,7 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  django-ajax-selects                    |      1 | 
  django-bitfield                        |      1 | 
  django-ldapdb                          |      1 | 
+ django-pglocks                         |      1 | 
  django-render-block                    |      1 | 
  django-rq                              |      1 | 
  django-templated-email                 |      1 | 
@@ -354,9 +355,9 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  jpy                                    |      1 | 
  mkdocs-macros-plugin                   |      1 | 
  mopidy-mpris                           |      1 | 
+ myst-nb                                |      1 | 
  pcpp                                   |      1 | 
  pdudaemon                              |      1 | 
- purl                                   |      1 | 
  pycallgraph                            |      1 | 
  pydataverse                            |      1 | 
  pydenticon                             |      1 | 
@@ -369,7 +370,6 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  python-aio-pika                        |      1 | 
  python-ansicolors                      |      1 | 
  python-brother-ql                      |      1 | 
- python-calendarweek                    |      1 | 
  python-calendra                        |      1 | 
  python-dirq                            |      1 | 
  python-django-adminsortable            |      1 | 
@@ -377,7 +377,6 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  python-django-push-notifications       |      1 | 
  python-django-registration             |      1 | 
  python-dnsq                            |      1 | 
- python-easy-ansi                       |      1 | 
  python-ephemeral-port-reserve          |      1 | 
  python-expiringdict                    |      1 | 
  python-fluent-logger                   |      1 | 
@@ -482,7 +481,6 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  mssql-django                           |      0 | 
  mwoauth                                |      0 | 
  mypaint                                |      0 | 
- myst-nb                                |      0 | 
  nbgitpuller                            |      0 | 
  niri-companion                         |      0 | 
  okasha                                 |      0 | 
@@ -523,6 +521,7 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  python-bottle-cork                     |      0 | 
  python-btrees                          |      0 | 
  python-bumpfontversion                 |      0 | 
+ python-calendarweek                    |      0 | 
  python-certstream                      |      0 | 
  python-chartkick                       |      0 | 
  python-chevron                         |      0 | 
@@ -532,6 +531,7 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  python-django-casclient                |      0 | 
  python-django-registration             |      0 | 
  python-doubly-py-linked-list           |      0 | 
+ python-easy-ansi                       |      0 | 
  python-einx                            |      0 | 
  python-ewmh                            |      0 | 
  python-flanker                         |      0 | 
@@ -614,7 +614,8 @@ Last-Update: Wed, 01 Jul 2026 01:42:05 +0000
  python-asyncprawcore                   |     -1 | 
  python-ledger-bitcoin                  |     -1 | 
  python-mercadopago                     |     -1 | 
+ python-plantuml                        |     -1 | 
  s3ql                                   |     -1 | 
  trac-tickettemplate                    |     -1 | 
-(630 rows)
+(631 rows)
 



View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/052f400f15c445de1bceae3b4cb027a8f6c23bd7

-- 
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/052f400f15c445de1bceae3b4cb027a8f6c23bd7
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From gitlab at salsa.debian.org  Wed Jul  1 18:16:09 2026
From: gitlab at salsa.debian.org (Gilles Filippini (@pini))
Date: Wed, 01 Jul 2026 17:16:09 +0000
Subject: [med-svn] [Git][med-team/unifrac-tools][master] 5 commits:
 python3.patch: fix remaining python calls
Message-ID: <6a454b597b290_55bea42b5437396b8@godard.mail>



Gilles Filippini pushed to branch master at Debian Med / unifrac-tools


Commits:
34f81756 by Gilles Filippini at 2026-07-01T18:57:17+02:00
python3.patch: fix remaining python calls

- - - - -
221fcd39 by Gilles Filippini at 2026-07-01T18:59:43+02:00
soname.patch: fix typo

(or maybe a misunderstanding about how globs work)

- - - - -
66dea109 by Gilles Filippini at 2026-07-01T19:01:14+02:00
baseline.patch: tentative fix after messed-up refresh

- - - - -
97dc8831 by Gilles Filippini at 2026-07-01T19:02:32+02:00
hdf5: fix messed-up patch

- - - - -
5d6710ab by Gilles Filippini at 2026-07-01T19:03:41+02:00
d/rules: prevent deletion of debian/tmp after build

- - - - -


5 changed files:

- debian/patches/baseline.patch
- debian/patches/enable_linking_to_shared_hdf5_lib.patch
- debian/patches/python3.patch
- debian/patches/soname.patch
- debian/rules


Changes:

=====================================
debian/patches/baseline.patch
=====================================
@@ -5,8 +5,10 @@ Forwarded: not-needed
 Last-Update: 2023-07-26
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/src/Makefile
-+++ b/src/Makefile
+Index: unifrac-tools-1.6.1/src/Makefile
+===================================================================
+--- unifrac-tools-1.6.1.orig/src/Makefile
++++ unifrac-tools-1.6.1/src/Makefile
 @@ -123,46 +123,6 @@ ifndef NOGPU
     endif
  endif
@@ -54,15 +56,16 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  ifeq (,$(findstring pgi,$(COMPILER)))
      ifeq ($(PERFORMING_CONDA_BUILD),False)
  	# basically, not gcc
---- a/combined/libssu.c
-+++ b/combined/libssu.c
-@@ -48,6 +48,9 @@ static const char *ssu_get_lib_name() {
-       has_v4 = false;
-     }
-    }
-+#else
-+   ssu="libssu_cpu_basic.so";
-+#endif
- 
-    const char *ssu = "unknown"; // just to have a default
-    if (has_v4) {
+Index: unifrac-tools-1.6.1/combined/libssu.c
+===================================================================
+--- unifrac-tools-1.6.1.orig/combined/libssu.c
++++ unifrac-tools-1.6.1/combined/libssu.c
+@@ -24,7 +24,7 @@
+ /* Must be before the include of ssu_ld */
+ #ifndef BASIC_ONLY
+ static const char *ssu_get_lib_name() {
+-#if defined(__x86_64__)
++#if defined (__i386__) || defined(__x86_64__)
+    __builtin_cpu_init ();
+    bool has_v2  = __builtin_cpu_supports ("x86-64-v2");
+    bool has_v3  = __builtin_cpu_supports ("x86-64-v3");


=====================================
debian/patches/enable_linking_to_shared_hdf5_lib.patch
=====================================
@@ -6,22 +6,16 @@ Description: Enable linking to shared hdf5 library
 Forwarded: not-needed
 FIXME: Aaron, please review the changes
 
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -2,6 +2,7 @@
- 
- PLATFORM := $(shell uname -s)
- COMPILER := $(shell (h5c++ -v 2>&1) | tr A-Z a-z )
-+CPPFLAGS += -shlib
- 
- ifeq ($(BUILD_VARIANT),)
- 	SSU = ssu
-@@ -172,7 +173,7 @@ $(FPD): faithpd.cpp api.hpp $(PREFIX)/li
+Index: unifrac-tools-1.6.1/src/Makefile
+===================================================================
+--- unifrac-tools-1.6.1.orig/src/Makefile
++++ unifrac-tools-1.6.1/src/Makefile
+@@ -172,7 +172,7 @@ $(FPD): faithpd.cpp api.hpp $(PREFIX)/li
  
  lib$(SSU).so: tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)
  #	h5c++ $(LDDFLAGS) -o lib$(SSU).so tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 $(SKBBLIB) -L$(PREFIX)/lib -noshlib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
 -	h5c++ $(LDDFLAGS) -o lib$(SSU).so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,lib$(SSU).so.0 $(SKBBLIB) -L$(PREFIX)/lib -noshlib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
-+	h5c++ $(LDDFLAGS) -o lib$(SSU).so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -Wl,-soname,lib$(SSU).so.0 $(SKBBLIB) -L$(PREFIX)/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
++	h5c++ -shlib $(LDDFLAGS) -o lib$(SSU).so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -Wl,-soname,lib$(SSU).so.0 $(SKBBLIB) -L$(PREFIX)/lib
  	ln -sf lib$(SSU).so.0 lib$(SSU).so
  	# FIXME: Should build static lib as well
  	# $(CXX) $(LDDFLAGS) -o libssu.a tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 $(BLASLIB) -L$(PREFIX)/lib


=====================================
debian/patches/python3.patch
=====================================
@@ -3,8 +3,28 @@ Last-Update: 2022-10-10
 Description: Call Python3
 Forwarded: not-needed
 
---- a/ci/crawford_test.sh
-+++ b/ci/crawford_test.sh
+Index: unifrac-tools-1.6.1/ci/crawford_test.sh
+===================================================================
+--- unifrac-tools-1.6.1.orig/ci/crawford_test.sh
++++ unifrac-tools-1.6.1/ci/crawford_test.sh
+@@ -17,7 +17,7 @@ cat test.ssu.exp |awk '{printf("%s %.4f
+ 
+ exp=$($MD5 test.dm.f4 | awk '{ print $1 }')
+ obs=$($MD5 test.ssu.exp.f4 | awk '{ print $1 }')
+-python -c "assert '${obs}' == '${exp}'"
++python3 -c "assert '${obs}' == '${exp}'"
+ 
+ ssu -i crawford.biom -t crawford.tre -o test.vaw.dm -m unweighted_fp64 --vaw
+ 
+@@ -27,7 +27,7 @@ cat test.ssu_vaw.exp |awk '{printf("%s %
+ 
+ exp=$($MD5 test.dm.f4 | awk '{ print $1 }')
+ obs=$($MD5 test.ssu.exp.f4 | awk '{ print $1 }')
+-python -c "assert '${obs}' == '${exp}'"
++python3 -c "assert '${obs}' == '${exp}'"
+ 
+ ssu -i crawford.biom -t crawford.tre -o test.dm.start0.stop3 -m unweighted_fp64 --mode partial --start 0 --stop 3
+ ssu -i crawford.biom -t crawford.tre -o test.dm.start3.stop5 -m unweighted_fp64 --mode partial --start 3 --stop 5
 @@ -35,12 +35,12 @@ ssu -i crawford.biom -t crawford.tre -o
  
  exp=$($MD5 test.dm | awk '{ print $1 }')


=====================================
debian/patches/soname.patch
=====================================
@@ -3,8 +3,10 @@ Last-Update: 2022-07-26
 Description: Create SONAME for libssu
 Forwarded: not-needed
 
---- a/src/Makefile
-+++ b/src/Makefile
+Index: unifrac-tools-1.6.1/src/Makefile
+===================================================================
+--- unifrac-tools-1.6.1.orig/src/Makefile
++++ unifrac-tools-1.6.1/src/Makefile
 @@ -211,7 +211,11 @@ $(FPD): faithpd.cpp api.hpp $(PREFIX)/li
  	h5c++ $(CPPFLAGS) $(EXEFLAGS) faithpd.cpp -o $@ -l$(SSU)
  
@@ -23,7 +25,7 @@ Forwarded: not-needed
  
  install_lib: lib$(SSU).so
 -	for f in lib$(SSU).so ; do rm -f "${PREFIX}/lib/$${f}"; cp "$${f}" ${PREFIX}/lib/; done
-+	for f in lib$(SSU).so ; do rm -f "${PREFIX}/lib/$${f}"; cp -a "$${f}*" ${PREFIX}/lib/; done
++	for f in lib$(SSU).so ; do rm -f "${PREFIX}/lib/$${f}"; cp -a "$${f}"* ${PREFIX}/lib/; done
  
  
  install_lib_acc: $(UNIFRAC_ACC_SHLIBS)


=====================================
debian/rules
=====================================
@@ -18,14 +18,15 @@ override_dh_auto_build:
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	export PATH=${PATH}:$(CURDIR)/debian/tmp/usr/bin ; \
+	export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:$(CURDIR)/debian/tmp/usr/lib ; \
 	cd ci ; \
 	./crawford_test.sh
 endif
 
-override_dh_auto_install:
-	mkdir -p $(CURDIR)/debian/tmp/usr/bin
-	mkdir -p $(CURDIR)/debian/tmp/usr/lib
-	dh_auto_install -- PREFIX=$(CURDIR)/debian/tmp/usr
+override_dh_prep:;
+	dh_prep -Xtmp
+
+override_dh_auto_install:;
 
 override_dh_install:
 	chrpath -d debian/tmp/usr/bin/ssu



View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/6295f42c390df38d1598576dc91ef4c4b12c5c5b...5d6710abf179d34f592728c857921ad572f1c570

-- 
View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/6295f42c390df38d1598576dc91ef4c4b12c5c5b...5d6710abf179d34f592728c857921ad572f1c570
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From gitlab at salsa.debian.org  Wed Jul  1 19:46:10 2026
From: gitlab at salsa.debian.org (Rebecca N. Palmer (@rnpalmer-guest))
Date: Wed, 01 Jul 2026 18:46:10 +0000
Subject: [med-svn] [Git][med-team/snakemake][debian-v7] 2 commits: remove
 duplicate metadata
Message-ID: <6a45607247dd7_55b947fec437625a3@godard.mail>



Rebecca N. Palmer pushed to branch debian-v7 at Debian Med / snakemake


Commits:
3b95bb9a by Rebecca N. Palmer at 2026-07-01T19:42:00+01:00
remove duplicate metadata

- - - - -
da0b5f80 by Rebecca N. Palmer at 2026-07-01T19:45:40+01:00
Re-enable R/rpy2 tests.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/rules
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+snakemake (7.32.4-12) UNRELEASED; urgency=medium
+
+  * Re-enable R/rpy2 tests.
+
+ -- Rebecca N. Palmer <rebecca_palmer at zoho.com>  Wed, 01 Jul 2026 19:45:01 +0100
+
 snakemake (7.32.4-11) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -40,6 +40,7 @@ Build-Depends:
  python3-requests,
  python3-requests-mock <!nocheck>,
  python3-retry,
+ python3-rpy2 <!nocheck>,
  python3-pytest-mock <!nocheck>,
  python3-setuptools,
  python3-smart-open,
@@ -54,6 +55,7 @@ Build-Depends:
  python3-wrapt,
  python3-yaml,
  python3-yte <!nocheck>,
+ r-cran-rmarkdown <!nocheck>,
  stress <!nocheck>,
 Vcs-Browser: https://salsa.debian.org/med-team/snakemake
 Vcs-Git: https://salsa.debian.org/med-team/snakemake.git
@@ -87,7 +89,6 @@ Recommends:
  imagemagick,
  python3-pytz,
  python3-yappi,
- python3-rpy2,
 # for the templating and reports features
  python3-jinja2,
  python3-pygments,


=====================================
debian/rules
=====================================
@@ -8,7 +8,7 @@ export PYBUILD_DESTDIR=debian/snakemake
 # copy the tests and run them from there to avoid having to clean up after them
 export PYBUILD_BEFORE_TEST=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir}
 export PYBUILD_AFTER_TEST=rm -fr {build_dir}/bin {build_dir}/tests
-export PYBUILD_TEST_ARGS=python{version} -m pytest -o faulthandler_timeout=60 -v {build_dir}/tests/test*.py -k 'not (test_cwl or test_cwl_singularity or test_url_include or test_wrapper or test_issue1083 or test_github_issue78 or test_container or test_singularity or test_singularity_conda or test_convert_to_cwl or test_report or test_report_zip or test_archive or test_jupyter_notebook or test_conda or test_upstream_conda or test_conda_custom_prefix or test_script or test_issue635 or test_issue1093 or test_default_resources or test_default_remote or test_remote or test_output_file_cache_remote or test_tibanna or test_module_complex or test_module_complex2 or test_module_with_script or test_module_report or test_modules_meta_wrapper or test_tes or test_deploy_script or test_deploy_hashing or test_peppy or test_modules_peppy or test_report_display_code or test_wrapper_local_git_prefix or test_github_issue1396 or test_az_batch_executor or test_modules_prefix or test_ancient or test_github_issue1062 or test_symlink_time_handling or test_env_modules or test_github_issue1460 or test_rule_inheritance_globals or test_prebuilt_conda_script or test_persistent_dict or test_issue328 or test_pipes_fail or test_pipes or test_multicomp_group_jobs or test_group_job_resources_with_pipe or test_converting_path_for_r_script)'
+export PYBUILD_TEST_ARGS=python{version} -m pytest -o faulthandler_timeout=60 -v {build_dir}/tests/test*.py -k 'not (test_cwl or test_cwl_singularity or test_url_include or test_wrapper or test_issue1083 or test_github_issue78 or test_container or test_singularity or test_singularity_conda or test_convert_to_cwl or test_report or test_report_zip or test_archive or test_jupyter_notebook or test_conda or test_upstream_conda or test_conda_custom_prefix or test_script or test_issue635 or test_issue1093 or test_default_resources or test_default_remote or test_remote or test_output_file_cache_remote or test_tibanna or test_module_complex or test_module_complex2 or test_module_with_script or test_module_report or test_modules_meta_wrapper or test_tes or test_deploy_script or test_deploy_hashing or test_peppy or test_modules_peppy or test_report_display_code or test_wrapper_local_git_prefix or test_github_issue1396 or test_az_batch_executor or test_modules_prefix or test_ancient or test_github_issue1062 or test_symlink_time_handling or test_env_modules or test_github_issue1460 or test_rule_inheritance_globals or test_prebuilt_conda_script or test_persistent_dict or test_issue328 or test_pipes_fail or test_pipes or test_multicomp_group_jobs or test_group_job_resources_with_pipe)'
 
 # Skipped because they download executables (which is forbidden in Debian buildd and debci)
 # Snakefile/snakemake-wrapper/CWL scripts: test_cwl, test_cwl_singularity, test_url_include, test_wrapper, test_wrapper_local_git_prefix, test_module_with_script, test_module_report, test_module_complex(2), test_modules_meta_wrapper
@@ -38,9 +38,6 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -o faulthandler_timeout=60 -v
 # needs Azure credentials: test_az_batch_executor
 # flaky (these are run in autopkgtest but get 3 tries there) test_pipes_fail, test_pipes, test_multicomp_group_jobs, test_group_job_resources_with_pipe
 
-# skipped to avoid R instability from removing the snakemake package
-# test_converting_path_for_r_script
-
 export PATH:=$(shell pybuild --print build_dir --interpreter python3 --name $(PYBUILD_NAME))/bin:$(PATH)
 
 # Force the use of python3's sphinx-build.


=====================================
debian/upstream/metadata
=====================================
@@ -18,5 +18,3 @@ Registry:
   Entry: SCR_003475
 Repository: https://github.com/snakemake/snakemake.git
 Repository-Browse: https://github.com/snakemake/snakemake
-Repository: https://github.com/snakemake/snakemake.git
-Repository-Browse: https://github.com/snakemake/snakemake



View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/f5ee9a60b8086da55b118761fbe1b90761f534d2...da0b5f80a6b0b865af2f714025b951917f4e3dee

-- 
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/f5ee9a60b8086da55b118761fbe1b90761f534d2...da0b5f80a6b0b865af2f714025b951917f4e3dee
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From gitlab at salsa.debian.org  Wed Jul  1 21:53:53 2026
From: gitlab at salsa.debian.org (Rebecca N. Palmer (@rnpalmer-guest))
Date: Wed, 01 Jul 2026 20:53:53 +0000
Subject: [med-svn] [Git][med-team/snakemake][debian-v7] Fix config schema
 loading from local files. (Closes: #1141070)
Message-ID: <6a457e616d8b5_55b15b0b98381518e@godard.mail>



Rebecca N. Palmer pushed to branch debian-v7 at Debian Med / snakemake


Commits:
2316ca65 by Rebecca N. Palmer at 2026-07-01T21:32:36+01:00
Fix config schema loading from local files. (Closes: #1141070)

- - - - -


4 changed files:

- debian/changelog
- debian/patches/series
- + debian/patches/urljoin_slashes.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,6 +1,7 @@
 snakemake (7.32.4-12) UNRELEASED; urgency=medium
 
   * Re-enable R/rpy2 tests.
+  * Fix config schema loading from local files. (Closes: #1141070)
 
  -- Rebecca N. Palmer <rebecca_palmer at zoho.com>  Wed, 01 Jul 2026 19:45:01 +0100
 


=====================================
debian/patches/series
=====================================
@@ -23,3 +23,4 @@ test_extra_time.patch
 no_pkg_resources.patch
 numpy2compat.patch
 graphviz_compat.patch
+urljoin_slashes.patch


=====================================
debian/patches/urljoin_slashes.patch
=====================================
@@ -0,0 +1,17 @@
+Description: Include the /// in file: config URLs
+
+Author: Rebecca N. Palmer <rebecca_palmer at zoho.com>
+Bug-Debian: https://bugs.debian.org/1141070
+Forwarded: no
+
+--- snakemake-7.32.4.orig/snakemake/utils.py
++++ snakemake-7.32.4/snakemake/utils.py
+@@ -68,7 +68,7 @@ def validate(data, schema, set_default=T
+     schema = _load_configfile(source, filetype="Schema")
+     if isinstance(schemafile, LocalSourceFile):
+         resolver = RefResolver(
+-            urljoin("file:", schemafile.get_path_or_uri()),
++            urljoin("file://", schemafile.get_path_or_uri()),
+             schema,
+             handlers={
+                 "file": lambda uri: _load_configfile(re.sub("^file://", "", uri))


=====================================
debian/rules
=====================================
@@ -47,7 +47,9 @@ export SPHINXBUILD=/usr/share/sphinx/scripts/python3/sphinx-build
 	dh $@ --with sphinxdoc --buildsystem=pybuild
 
 # LC_ALL is for reproducibility
+# the first python3 is a test related to #1141070 (in trixie/python3.13, both of these get a triple slash)
 execute_after_dh_auto_build:
+	python3 -c "import urllib.parse;print(urllib.parse.urljoin('file:','/b/a.html'),urllib.parse.urljoin('file://','/b/a.html'))"
 	PYTHONPATH=$(shell pybuild --print build_dir --interpreter python3) \
 	cd docs && LC_ALL=C.UTF-8 LANGUAGE=C.UTF-8 make html
 



View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/2316ca65fe222a35f23ab26ae1799e0ba6e31824

-- 
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From gitlab at salsa.debian.org  Wed Jul  1 22:10:46 2026
From: gitlab at salsa.debian.org (Rebecca N. Palmer (@rnpalmer-guest))
Date: Wed, 01 Jul 2026 21:10:46 +0000
Subject: [med-svn] [Git][med-team/snakemake][debian-v7] remove temporary
 test, record its findings
Message-ID: <6a4582562f30f_55bea42b5438186f5@godard.mail>



Rebecca N. Palmer pushed to branch debian-v7 at Debian Med / snakemake


Commits:
d7c72f0e by Rebecca N. Palmer at 2026-07-01T22:10:28+01:00
remove temporary test, record its findings

- - - - -


3 changed files:

- debian/changelog
- debian/patches/urljoin_slashes.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,9 +1,10 @@
-snakemake (7.32.4-12) UNRELEASED; urgency=medium
+snakemake (7.32.4-12) unstable; urgency=medium
 
   * Re-enable R/rpy2 tests.
-  * Fix config schema loading from local files. (Closes: #1141070)
+  * Make config schema loading from local files
+    Python 3.14 compatible. (Closes: #1141070)
 
- -- Rebecca N. Palmer <rebecca_palmer at zoho.com>  Wed, 01 Jul 2026 19:45:01 +0100
+ -- Rebecca N. Palmer <rebecca_palmer at zoho.com>  Wed, 01 Jul 2026 22:06:28 +0100
 
 snakemake (7.32.4-11) unstable; urgency=medium
 


=====================================
debian/patches/urljoin_slashes.patch
=====================================
@@ -1,5 +1,7 @@
 Description: Include the /// in file: config URLs
 
+Python 3.14 no longer automatically does this
+
 Author: Rebecca N. Palmer <rebecca_palmer at zoho.com>
 Bug-Debian: https://bugs.debian.org/1141070
 Forwarded: no


=====================================
debian/rules
=====================================
@@ -47,9 +47,7 @@ export SPHINXBUILD=/usr/share/sphinx/scripts/python3/sphinx-build
 	dh $@ --with sphinxdoc --buildsystem=pybuild
 
 # LC_ALL is for reproducibility
-# the first python3 is a test related to #1141070 (in trixie/python3.13, both of these get a triple slash)
 execute_after_dh_auto_build:
-	python3 -c "import urllib.parse;print(urllib.parse.urljoin('file:','/b/a.html'),urllib.parse.urljoin('file://','/b/a.html'))"
 	PYTHONPATH=$(shell pybuild --print build_dir --interpreter python3) \
 	cd docs && LC_ALL=C.UTF-8 LANGUAGE=C.UTF-8 make html
 



View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/d7c72f0e2d4c84c421bf79d781e63b6e49622f1e

-- 
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/d7c72f0e2d4c84c421bf79d781e63b6e49622f1e
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From gitlab at salsa.debian.org  Wed Jul  1 22:37:58 2026
From: gitlab at salsa.debian.org (Alexandre Detiste (@detiste-guest))
Date: Wed, 01 Jul 2026 21:37:58 +0000
Subject: [med-svn] [Git][python-team/packages/python-easydev][master] 6
 commits: drop build-dep on python3-poetry, python3-poetry-core is enough
Message-ID: <6a4588b628513_55b94cca443826868@godard.mail>



Alexandre Detiste pushed to branch master at Debian Python Team / packages / python-easydev


Commits:
d494ad7f by Alexandre Detiste at 2026-07-01T23:35:52+02:00
drop build-dep on python3-poetry, python3-poetry-core is enough

- - - - -
e1c294fe by Alexandre Detiste at 2026-07-01T22:36:07+01:00
Remove redundant Priority: optional from source stanza.

Changes-By: lintian-brush
Fixes: lintian: source: redundant-priority-optional-field
See-also: https://lintian.debian.org/tags/redundant-priority-optional-field.html

- - - - -
d854a67d by Alexandre Detiste at 2026-07-01T22:36:07+01:00
Update standards version to 4.7.4, no changes needed.

Upgrade checklist verified:
 4.6.2 ? 4.7.0:
  * Package does not use dpkg-divert
 4.7.0 ? 4.7.1:
  * Package does not install to non-/usr paths
 4.7.3 ? 4.7.4:
  * Package is not in non-free-firmware

Changes-By: lintian-brush
Fixes: lintian: source: ancient-standards-version 4.6.2 (released 2022-12-17) (current is 4.7.4.1)
See-also: https://lintian.debian.org/tags/ancient-standards-version.html

- - - - -
fc8ee1f9 by Alexandre Detiste at 2026-07-01T23:36:41+02:00
drop "Rules-Requires-Root: no": it is the default now

- - - - -
54872afb by Alexandre Detiste at 2026-07-01T23:37:18+02:00
rewrite d/watch in v5 format

- - - - -
c00c81fa by Alexandre Detiste at 2026-07-01T23:37:52+02:00
release

- - - - -


3 changed files:

- debian/changelog
- debian/control
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+python-easydev (0.13.3+dfsg1-3) unstable; urgency=medium
+
+  * Team upload.
+  * Drop build-dep on python3-poetry, python3-poetry-core is enough
+  * Remove redundant Priority: optional from source stanza.
+  * Update standards version to 4.7.4, no changes needed.
+  * Drop "Rules-Requires-Root: no": it is the default now
+  * Rewrite d/watch in v5 format
+
+ -- Alexandre Detiste <tchet at debian.org>  Wed, 01 Jul 2026 23:37:35 +0200
+
 python-easydev (0.13.3+dfsg1-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -3,12 +3,10 @@ Maintainer: Debian Python Team <team+python at tracker.debian.org>
 Uploaders: Olivier Sallou <osallou at debian.org>
 Section: python
 Testsuite: autopkgtest-pkg-pybuild
-Priority: optional
 Build-Depends: debhelper-compat (= 13),
                dh-sequence-python3,
                pybuild-plugin-pyproject,
                python3-all,
-               python3-poetry,
                python3-poetry-core,
                python3-platformdirs,
                python3-colorlog,
@@ -17,11 +15,10 @@ Build-Depends: debhelper-compat (= 13),
                python3-pytest,
                python3-pytest-cov,
                python3-pytest-mock,
-Standards-Version: 4.6.2
+Standards-Version: 4.7.4
 Vcs-Browser: https://salsa.debian.org/python-team/packages/python-easydev
 Vcs-Git: https://salsa.debian.org/python-team/packages/python-easydev.git
 Homepage: https://easydev-python.readthedocs.io/en/latest/
-Rules-Requires-Root: no
 
 Package: python3-easydev
 Architecture: all


=====================================
debian/watch
=====================================
@@ -1,3 +1,8 @@
-version=4
-opts="repacksuffix=+dfsg1,dversionmangle=auto,repack,compression=xz" \
-  https://github.com/cokelaer/easydev/tags  (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
+Version: 5
+
+Source: https://github.com/cokelaer/easydev/tags
+Matching-Pattern: (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
+Compression: xz
+Dversionmangle: auto
+Repack: yes
+Repacksuffix: +dfsg1



View it on GitLab: https://salsa.debian.org/python-team/packages/python-easydev/-/compare/be2ca1bbd5b628d20c2755594b99be839a9b57ff...c00c81fa5a4d2f11f424220d089a268cf84831d7

-- 
View it on GitLab: https://salsa.debian.org/python-team/packages/python-easydev/-/compare/be2ca1bbd5b628d20c2755594b99be839a9b57ff...c00c81fa5a4d2f11f424220d089a268cf84831d7
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From gitlab at salsa.debian.org  Wed Jul  1 22:56:49 2026
From: gitlab at salsa.debian.org (Rebecca N. Palmer (@rnpalmer-guest))
Date: Wed, 01 Jul 2026 21:56:49 +0000
Subject: [med-svn] [Git][med-team/snakemake] Pushed new tag debian/7.32.4-12
Message-ID: <6a458d21b2458_55b15eb08d838297df@godard.mail>



Rebecca N. Palmer pushed new tag debian/7.32.4-12 at Debian Med / snakemake

-- 
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/tree/debian/7.32.4-12
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From gitlab at salsa.debian.org  Wed Jul  1 23:52:23 2026
From: gitlab at salsa.debian.org (Alexandre Detiste (@detiste-guest))
Date: Wed, 01 Jul 2026 22:52:23 +0000
Subject: [med-svn] [Git][python-team/packages/python-easydev] Pushed new tag
 debian/0.13.3+dfsg1-3
Message-ID: <6a459a271b6e2_55b15b0b9838410b@godard.mail>



Alexandre Detiste pushed new tag debian/0.13.3+dfsg1-3 at Debian Python Team / packages / python-easydev

-- 
View it on GitLab: https://salsa.debian.org/python-team/packages/python-easydev/-/tree/debian/0.13.3+dfsg1-3
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From gitlab at salsa.debian.org  Thu Jul  2 02:42:23 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 01:42:23 +0000
Subject: [med-svn] [Git][med-team/community/helper-scripts][master]
 automatic update
Message-ID: <6a45c1ffa4180_55b15eb08d83850726@godard.mail>



Andreas Tille pushed to branch master at Debian Med / community / helper-scripts


Commits:
3180f92b by Andreas Tille at 2026-07-02T01:42:18+00:00
automatic update

- - - - -


4 changed files:

- debian-med-tests.txt
- debian-science-tests.txt
- outdated_med-packages.txt
- python-team-tests.txt


Changes:

=====================================
debian-med-tests.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Wed, 01 Jul 2026 13:42:03 +0000
+Last-Update: Thu, 02 Jul 2026 01:42:03 +0000
 
  Source                        | Vote   | Tasks                                      |                                 Tags                                 
 -------------------------------+--------+--------------------------------------------+----------------------------------------------------------------------


=====================================
debian-science-tests.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Wed, 01 Jul 2026 13:42:05 +0000
+Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
 
        Source                              | Vote   |             Tasks                                                   |                          Tags                          
 -------------------------------------------+--------+---------------------------------------------------------------------+--------------------------------------------------------


=====================================
outdated_med-packages.txt
=====================================
The diff for this file was not included because it is too large.

=====================================
python-team-tests.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Wed, 01 Jul 2026 13:42:06 +0000
+Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
 
      Source                             | Vote   |                          Tags                          
 ----------------------------------------+--------+--------------------------------------------------------



View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/3180f92b7a5229caa9b393b29127deb7e322e3fd

-- 
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From gitlab at salsa.debian.org  Thu Jul  2 13:41:22 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 12:41:22 +0000
Subject: [med-svn] [Git][med-team/unifrac-tools][master] 2 commits: No need
 to use dh-exec any more
Message-ID: <6a465c724a56b_55b1145199039531e1@godard.mail>



Andreas Tille pushed to branch master at Debian Med / unifrac-tools


Commits:
97db599e by Andreas Tille at 2026-07-02T12:10:33+02:00
No need to use dh-exec any more

- - - - -
9fdc69e3 by Andreas Tille at 2026-07-02T13:32:50+02:00
Symlink for libsso.so

- - - - -


4 changed files:

- debian/changelog
- debian/libssu-dev.install
- debian/libssu0.install
- debian/patches/enable_linking_to_shared_hdf5_lib.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -9,6 +9,7 @@ unifrac-tools (1.6.1-1) UNRELEASED; urgency=medium
   * Drop 'Rules-Requires-Root: no' from d/control (routine-update)
   * Build-Depends: libskbb-dev
   * Reformat the Last-Update date as ISO YYYY-MM-DD.
+  * No need to use dh-exec any more
 
   [ Gilles Filippini ]
   * Fix FTBFS against HDF5 2.1.0


=====================================
debian/libssu-dev.install
=====================================
@@ -1,3 +1,2 @@
-#! /usr/bin/dh-exec
 /usr/include/unifrac
 usr/lib/*.so	usr/lib/${DEB_HOST_MULTIARCH}/


=====================================
debian/libssu0.install
=====================================
@@ -1,2 +1 @@
-#! /usr/bin/dh-exec
 usr/lib/*.so.*	usr/lib/${DEB_HOST_MULTIARCH}/


=====================================
debian/patches/enable_linking_to_shared_hdf5_lib.patch
=====================================
@@ -6,10 +6,8 @@ Description: Enable linking to shared hdf5 library
 Forwarded: not-needed
 FIXME: Aaron, please review the changes
 
-Index: unifrac-tools-1.6.1/src/Makefile
-===================================================================
---- unifrac-tools-1.6.1.orig/src/Makefile
-+++ unifrac-tools-1.6.1/src/Makefile
+--- a/src/Makefile
++++ b/src/Makefile
 @@ -172,7 +172,7 @@ $(FPD): faithpd.cpp api.hpp $(PREFIX)/li
  
  lib$(SSU).so: tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)
@@ -19,3 +17,19 @@ Index: unifrac-tools-1.6.1/src/Makefile
  	ln -sf lib$(SSU).so.0 lib$(SSU).so
  	# FIXME: Should build static lib as well
  	# $(CXX) $(LDDFLAGS) -o libssu.a tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 $(BLASLIB) -L$(PREFIX)/lib
+--- a/combined/Makefile
++++ b/combined/Makefile
+@@ -20,10 +20,11 @@ libssu.o: libssu.c
+ 	$(CC) $(CPPFLAGS) $(CFLAGS) -c libssu.c -fPIC
+ 
+ libssu.so: libssu.o
+-	$(CC) -shared -o libssu.so libssu.o -fPIC -ldl $(LDFLAGS)
++	$(CC) -shared -o libssu.so.0 libssu.o -fPIC -ldl -Wl,-soname,libssu.so.0 $(LDFLAGS)
++	ln -sf libssu.so.0 libssu.so
+ 
+ install: libssu.so
+-	rm -f ${PREFIX}/lib/libssu.so; cp libssu.so ${PREFIX}/lib/
++	rm -f ${PREFIX}/lib/libssu.so; cp -a libssu.so* ${PREFIX}/lib/
+ 
+ clean:
+ 	rm -f libssu.o



View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/5d6710abf179d34f592728c857921ad572f1c570...9fdc69e335bee6ec08650a720892b306ecb331bc

-- 
View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/5d6710abf179d34f592728c857921ad572f1c570...9fdc69e335bee6ec08650a720892b306ecb331bc
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From gitlab at salsa.debian.org  Thu Jul  2 14:01:17 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 13:01:17 +0000
Subject: [med-svn] [Git][med-team/unifrac-tools][master] 2 commits: Verify
 that new upstream version builds with shuffle=reverse
Message-ID: <6a46611d45dd2_55be8cd5083955973@godard.mail>



Andreas Tille pushed to branch master at Debian Med / unifrac-tools


Commits:
45ac7f43 by Andreas Tille at 2026-07-02T14:53:10+02:00
Verify that new upstream version builds with shuffle=reverse

- - - - -
decef882 by Andreas Tille at 2026-07-02T15:00:28+02:00
Upload to unstable

- - - - -


1 changed file:

- debian/changelog


Changes:

=====================================
debian/changelog
=====================================
@@ -1,8 +1,9 @@
-unifrac-tools (1.6.1-1) UNRELEASED; urgency=medium
+unifrac-tools (1.6.1-1) unstable; urgency=medium
 
   [ Andreas Tille ]
-  * d/watch: version=5
   * New upstream version
+    Closes: #1105659
+  * d/watch: version=5
   * Standards-Version: 4.7.4 (routine-update)
   * Reflow Uploaders field (cme)
   * Remove Priority field (cme)
@@ -15,7 +16,7 @@ unifrac-tools (1.6.1-1) UNRELEASED; urgency=medium
   * Fix FTBFS against HDF5 2.1.0
     Closes: #1139615
 
- -- Andreas Tille <tille at debian.org>  Tue, 16 Jun 2026 22:24:42 +0200
+ -- Andreas Tille <tille at debian.org>  Thu, 02 Jul 2026 14:53:58 +0200
 
 unifrac-tools (1.4-3) unstable; urgency=medium
 



View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/9fdc69e335bee6ec08650a720892b306ecb331bc...decef8824c31cdbdfeb47b500f96303df0dc5863

-- 
View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/9fdc69e335bee6ec08650a720892b306ecb331bc...decef8824c31cdbdfeb47b500f96303df0dc5863
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From gitlab at salsa.debian.org  Thu Jul  2 14:01:21 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 13:01:21 +0000
Subject: [med-svn] [Git][med-team/unifrac-tools] Pushed new tag
 debian/1.6.1-1
Message-ID: <6a4661212054_55b109773443956225@godard.mail>



Andreas Tille pushed new tag debian/1.6.1-1 at Debian Med / unifrac-tools

-- 
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From gitlab at salsa.debian.org  Thu Jul  2 14:42:28 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 13:42:28 +0000
Subject: [med-svn] [Git][med-team/community/helper-scripts][master]
 automatic update
Message-ID: <6a466ac49f6fb_55b14c3e68c405392b@godard.mail>



Andreas Tille pushed to branch master at Debian Med / community / helper-scripts


Commits:
d7941a3d by Andreas Tille at 2026-07-02T13:42:18+00:00
automatic update

- - - - -


4 changed files:

- debian-med-tests.txt
- debian-science-tests.txt
- outdated_med-packages.txt
- python-team-tests.txt


Changes:

=====================================
debian-med-tests.txt
=====================================
@@ -1,26 +1,27 @@
-Last-Update: Thu, 02 Jul 2026 01:42:03 +0000
+Last-Update: Thu, 02 Jul 2026 13:42:03 +0000
 
  Source                        | Vote   | Tasks                                      |                                 Tags                                 
 -------------------------------+--------+--------------------------------------------+----------------------------------------------------------------------
- dicomscope                    |     24 | {imaging}                                  | 
- jebl2                         |     13 | {bio-dev}                                  | 
+ dicomscope                    |     25 | {imaging}                                  | 
+ jebl2                         |     14 | {bio-dev}                                  | 
+ biojava-live                  |     13 | {bio-dev}                                  | 
  adun.app                      |     12 | {bio}                                      | 
- biojava-live                  |     12 | {bio-dev}                                  | 
  icb-utils                     |     12 | {bio-dev}                                  | 
  mrtrix3                       |     12 | {imaging}                                  | 
- oscar                         |     12 | {tools,practice,data}                      | 
  orthanc-gdcm                  |     11 | {imaging}                                  | 
+ oscar                         |     11 | {tools,practice,data}                      | 
  sight                         |     11 | {imaging}                                  | 
  gnumed-server                 |     10 | {covid-19,practice}                        | 
  embassy-domsearch             |      9 | {cloud,bio}                                | 
  pixelmed                      |      9 | {imaging}                                  | 
+ embassy-domainatrix           |      8 | {cloud,bio}                                | 
+ embassy-domalign              |      8 | {cloud,bio}                                | 
+ saint                         |      8 | {bio}                                      | 
  ants                          |      7 | {imaging}                                  | 
- embassy-domainatrix           |      7 | {cloud,bio}                                | 
- embassy-domalign              |      7 | {cloud,bio}                                | 
- saint                         |      7 | {bio}                                      | 
  sight                         |      7 | {imaging}                                  | 
  bart-view                     |      6 | {imaging}                                  | 
  beast-mcmc                    |      6 | {bio,bio-phylogeny}                        | 
+ biojava6-live                 |      6 | {bio-dev}                                  | 
  dextractor                    |      6 | {bio,covid-19}                             | 
  ipig                          |      6 | {bio}                                      | 
  libjloda-java                 |      6 | {bio-dev}                                  | 
@@ -32,12 +33,12 @@ Last-Update: Thu, 02 Jul 2026 01:42:03 +0000
  proalign                      |      6 | {bio,bio-phylogeny}                        | 
  sga                           |      6 | {bio}                                      | 
  sprai                         |      6 | {bio}                                      | 
- biojava6-live                 |      5 | {bio-dev}                                  | 
  bio-tradis                    |      5 | {bio,bio-dev}                              | 
  fastml                        |      5 | {bio}                                      | 
  libdivsufsort                 |      5 | {bio-dev}                                  | 
  phyutility                    |      5 | {cloud,bio}                                | 
  piler                         |      5 | {bio}                                      | 
+ rambo-k                       |      5 | {bio}                                      | 
  rtax                          |      5 | {bio,cloud}                                | 
  runcircos-gui                 |      5 | {bio}                                      | 
  sibsim4                       |      5 | {bio,cloud}                                | 
@@ -50,8 +51,8 @@ Last-Update: Thu, 02 Jul 2026 01:42:03 +0000
  lamarc                        |      4 | {bio}                                      | 
  libminc                       |      4 | {imaging-dev}                              | 
  mauve-aligner                 |      4 | {bio}                                      | 
+ plasmidid                     |      4 | {bio,covid-19}                             | 
  pscan-chip                    |      4 | {bio}                                      | 
- rambo-k                       |      4 | {bio}                                      | 
  rdp-alignment                 |      4 | {bio}                                      | 
  savvy                         |      4 | {bio}                                      | 
  surankco                      |      4 | {bio}                                      | 
@@ -63,7 +64,6 @@ Last-Update: Thu, 02 Jul 2026 01:42:03 +0000
  mhap                          |      3 | {bio-ngs,bio}                              | 
  pigx-rnaseq                   |      3 | {bio,covid-19}                             | 
  placnet                       |      3 | {bio}                                      | 
- plasmidid                     |      3 | {bio,covid-19}                             | 
  plasmidseeker                 |      3 | {bio}                                      | 
  skesa                         |      3 | {bio}                                      | 
  soapaligner                   |      3 | {bio}                                      | 


=====================================
debian-science-tests.txt
=====================================
@@ -1,167 +1,168 @@
-Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
+Last-Update: Thu, 02 Jul 2026 13:42:05 +0000
 
        Source                              | Vote   |             Tasks                                                   |                          Tags                          
 -------------------------------------------+--------+---------------------------------------------------------------------+--------------------------------------------------------
- gts                                       |   5491 | {viewing}                                                           | 
- nltk                                      |   3182 | {linguistics}                                                       | 
- libaec                                    |    396 | {meteorology-dev}                                                   | 
- spacenavd                                 |    279 | {tools}                                                             | 
+ gts                                       |   5477 | {viewing}                                                           | 
+ nltk                                      |   3161 | {linguistics}                                                       | 
+ libaec                                    |    397 | {meteorology-dev}                                                   | 
+ spacenavd                                 |    278 | {tools}                                                             | 
  opencascade                               |    232 | {simulations}                                                       | 
- armadillo                                 |    195 | {mathematics-dev}                                                   | 
- open-coarrays                             |    159 | {meteorology-dev}                                                   | 
- arpack                                    |    106 | {mathematics-dev}                                                   | 
- refmac-dictionary                         |     75 | {highenergy-physics-dev,chemistry}                                  | 
- mbpoll                                    |     67 | {simulations}                                                       | 
- giac                                      |     55 | {mathematics}                                                       | 
- muparser                                  |     47 | {mathematics-dev}                                                   | 
+ armadillo                                 |    200 | {mathematics-dev}                                                   | 
+ open-coarrays                             |    158 | {meteorology-dev}                                                   | 
+ arpack                                    |    108 | {mathematics-dev}                                                   | 
+ refmac-dictionary                         |     74 | {highenergy-physics-dev,chemistry}                                  | 
+ mbpoll                                    |     66 | {simulations}                                                       | 
+ giac                                      |     52 | {mathematics}                                                       | 
+ muparser                                  |     51 | {mathematics-dev}                                                   | 
  imview                                    |     45 | {viewing}                                                           | 
- guiqwt                                    |     39 | {numericalcomputation,viewing}                                      | 
+ guiqwt                                    |     38 | {numericalcomputation,viewing}                                      | 
  setzer                                    |     36 | {typesetting}                                                       | 
+ persalys                                  |     33 | {statistics,mathematics,engineering}                                | 
  pyzo                                      |     33 | {numericalcomputation}                                              | 
- persalys                                  |     32 | {statistics,mathematics,engineering}                                | 
- apophenia                                 |     30 | {statistics}                                                        | 
- sardana                                   |     29 | {dataacquisition}                                                   | 
  teem                                      |     29 | {imageanalysis}                                                     | 
- colpack                                   |     25 | {numericalcomputation}                                              | 
+ apophenia                                 |     28 | {statistics}                                                        | 
+ sardana                                   |     28 | {dataacquisition}                                                   | 
+ colpack                                   |     26 | {numericalcomputation}                                              | 
+ persalys                                  |     26 | {mathematics,engineering,statistics}                                | 
+ adolc                                     |     25 | {numericalcomputation}                                              | 
+ flann                                     |     25 | {mathematics-dev,engineering-dev}                                   | 
  ntl                                       |     25 | {mathematics-dev}                                                   | 
  palp                                      |     25 | {mathematics}                                                       | 
- persalys                                  |     25 | {mathematics,engineering,statistics}                                | 
- adolc                                     |     24 | {numericalcomputation}                                              | 
- feedgnuplot                               |     24 | {viewing}                                                           | 
- flann                                     |     24 | {mathematics-dev,engineering-dev}                                   | 
  lxi-tools                                 |     24 | {dataacquisition,engineering}                                       | 
  sketch                                    |     24 | {typesetting}                                                       | 
  arduino-mk                                |     22 | {robotics}                                                          | 
+ feedgnuplot                               |     22 | {viewing}                                                           | 
  coinor-symphony                           |     21 | {logic,mathematics,numericalcomputation}                            | 
  debian-science                            |     20 | {physics,machine-learning,economics,mathematics,nanoscale-physics}  | 
- getdp                                     |     20 | {mathematics,simulations,engineering}                               | 
+ dune-uggrid                               |     20 | {mathematics-dev}                                                   | 
+ libmatio                                  |     20 | {mathematics-dev}                                                   | 
  python-escript                            |     20 | {simulations,numericalcomputation,engineering}                      | 
- dune-uggrid                               |     19 | {mathematics-dev}                                                   | 
- libmatio                                  |     19 | {mathematics-dev}                                                   | 
- ppl                                       |     18 | {numericalcomputation}                                              | 
+ getdp                                     |     19 | {mathematics,simulations,engineering}                               | 
+ fftw                                      |     18 | {mathematics-dev,meteorology-dev,physics-dev}                       | 
+ libcvd                                    |     18 | {imageanalysis}                                                     | 
+ libm4ri                                   |     18 | {mathematics-dev}                                                   | 
  toulbar2                                  |     18 | {mathematics,numericalcomputation,physics,logic}                    | 
  eccodes                                   |     17 | {meteorology-dev}                                                   | 
- libcvd                                    |     17 | {imageanalysis}                                                     | 
- libm4ri                                   |     17 | {mathematics-dev}                                                   | 
+ ppl                                       |     17 | {numericalcomputation}                                              | 
  xygrib                                    |     17 | {meteorology}                                                       | 
- fftw                                      |     16 | {mathematics-dev,meteorology-dev,physics-dev}                       | 
  flintqs                                   |     16 | {mathematics}                                                       | 
+ libvigraimpex                             |     16 | {imageanalysis-dev,machine-learning}                                | 
  eccodes                                   |     15 | {meteorology,meteorology-dev}                                       | 
- libvigraimpex                             |     15 | {imageanalysis-dev,machine-learning}                                | 
+ gts                                       |     15 | {viewing-dev}                                                       | 
+ picosat                                   |     15 | {logic}                                                             | 
+ sat4j                                     |     15 | {logic}                                                             | 
  grads                                     |     14 | {meteorology}                                                       | 
- gts                                       |     14 | {viewing-dev}                                                       | 
- ipe-tools                                 |     14 | {typesetting}                                                       | 
- picosat                                   |     14 | {logic}                                                             | 
  psurface                                  |     14 | {numericalcomputation}                                              | 
- sat4j                                     |     14 | {logic}                                                             | 
- debian-science                            |     13 | {machine-learning,neuroscience-cognitive}                           | 
  debian-science                            |     13 | {machine-learning,nanoscale-physics,economics,physics}              | 
- jeuclid                                   |     13 | {viewing,typesetting}                                               | 
- matlab-support                            |     13 | {mathematics,numericalcomputation}                                  | 
- mseed2sac                                 |     13 | {dataacquisition-dev}                                               | 
+ ipe-tools                                 |     13 | {typesetting}                                                       | 
+ alberta                                   |     12 | {engineering-dev}                                                   | 
  bossa                                     |     12 | {devices}                                                           | 
+ debian-science                            |     12 | {machine-learning,neuroscience-cognitive}                           | 
  debian-science                            |     12 | {tools}                                                             | 
  debian-science                            |     12 | {electrophysiology}                                                 | 
+ jeuclid                                   |     12 | {viewing,typesetting}                                               | 
+ mseed2sac                                 |     12 | {dataacquisition-dev}                                               | 
+ rubiks                                    |     12 | {mathematics,geometry}                                              | 
+ vdt                                       |     12 | {mathematics-dev}                                                   | 
+ matlab-support                            |     11 | {mathematics,numericalcomputation}                                  | 
  opencascade                               |     11 | {simulations}                                                       | 
- rubiks                                    |     11 | {mathematics,geometry}                                              | 
- vdt                                       |     11 | {mathematics-dev}                                                   | 
- alberta                                   |     10 | {engineering-dev}                                                   | 
  feff85exafs                               |     10 | {chemistry}                                                         | 
+ lrcalc                                    |     10 | {mathematics-dev}                                                   | 
  cliquer                                   |      9 | {mathematics-dev}                                                   | 
- cliquer                                   |      9 | {mathematics}                                                       | 
- lrcalc                                    |      9 | {mathematics-dev}                                                   | 
  chemical-structures                       |      8 | {chemistry}                                                         | 
+ cliquer                                   |      8 | {mathematics}                                                       | 
+ fftw                                      |      8 | {meteorology-dev,physics-dev,mathematics-dev}                       | 
+ iml                                       |      8 | {mathematics-dev}                                                   | 
+ libhomfly                                 |      8 | {mathematics-dev}                                                   | 
  libitpp                                   |      8 | {engineering-dev,mathematics-dev}                                   | 
+ newmat                                    |      8 | {mathematics-dev}                                                   | 
  pcl                                       |      8 | {robotics-dev}                                                      | 
+ rheolef                                   |      8 | {mathematics}                                                       | 
  ros-vcstool                               |      8 | {robotics-dev}                                                      | 
+ rw                                        |      8 | {mathematics-dev}                                                   | 
+ sagemath-database-conway-polynomials      |      8 | {mathematics}                                                       | 
  apertium                                  |      7 | {linguistics}                                                       | 
- fftw                                      |      7 | {meteorology-dev,physics-dev,mathematics-dev}                       | 
- iml                                       |      7 | {mathematics-dev}                                                   | 
- libhomfly                                 |      7 | {mathematics-dev}                                                   | 
+ gf2x                                      |      7 | {mathematics-dev}                                                   | 
+ libmatheval                               |      7 | {mathematics}                                                       | 
+ libxsmm                                   |      7 | {mathematics-dev}                                                   | 
  lttoolbox                                 |      7 | {linguistics}                                                       | 
- newmat                                    |      7 | {mathematics-dev}                                                   | 
- rheolef                                   |      7 | {mathematics}                                                       | 
- rw                                        |      7 | {mathematics-dev}                                                   | 
- sagemath-database-conway-polynomials      |      7 | {mathematics}                                                       | 
  toon                                      |      7 | {numericalcomputation}                                              | 
+ auto-07p                                  |      6 | {mathematics}                                                       | 
  cg3                                       |      6 | {linguistics}                                                       | 
- gf2x                                      |      6 | {mathematics-dev}                                                   | 
+ coinmp                                    |      6 | {numericalcomputation,mathematics-dev,logic}                        | 
+ form                                      |      6 | {mathematics}                                                       | 
  hdf-eos4                                  |      6 | {meteorology-dev}                                                   | 
  hdf-eos5                                  |      6 | {meteorology-dev}                                                   | 
  libccp4                                   |      6 | {nanoscale-physics-dev}                                             | 
- libmatheval                               |      6 | {mathematics}                                                       | 
- libxsmm                                   |      6 | {mathematics-dev}                                                   | 
+ libm4rie                                  |      6 | {mathematics-dev}                                                   | 
+ lrcalc                                    |      6 | {mathematics}                                                       | 
  ncl                                       |      6 | {meteorology}                                                       | 
- ros-rosconsole                            |      6 | {robotics-dev}                                                      | 
  uctodata                                  |      6 | {linguistics}                                                       | 
- coinmp                                    |      5 | {numericalcomputation,mathematics-dev,logic}                        | 
+ debian-science                            |      5 | {statistics,economics,nanoscale-physics,physics}                    | 
  dxsamples                                 |      5 | {nanoscale-physics}                                                 | 
- form                                      |      5 | {mathematics}                                                       | 
  libcvd                                    |      5 | {imageanalysis-dev}                                                 | 
  libgctp                                   |      5 | {meteorology-dev}                                                   | 
+ liblbfgs                                  |      5 | {mathematics-dev}                                                   | 
  liblxi                                    |      5 | {dataacquisition-dev,engineering-dev}                               | 
- libm4rie                                  |      5 | {mathematics-dev}                                                   | 
- lrcalc                                    |      5 | {mathematics}                                                       | 
+ libmatheval                               |      5 | {mathematics-dev}                                                   | 
+ libzn-poly                                |      5 | {mathematics-dev}                                                   | 
  metar                                     |      5 | {meteorology}                                                       | 
  ncl                                       |      5 | {meteorology-dev}                                                   | 
+ polylib                                   |      5 | {mathematics}                                                       | 
  python-aws-xray-sdk                       |      5 | {dataacquisition-dev}                                               | 
  python-cdo                                |      5 | {meteorology}                                                       | 
+ ratpoints                                 |      5 | {mathematics-dev}                                                   | 
+ ros-rosconsole                            |      5 | {robotics-dev}                                                      | 
+ spfft                                     |      5 | {nanoscale-physics-dev,meteorology-dev,mathematics-dev,physics-dev} | 
  urdfdom-headers                           |      5 | {robotics-dev}                                                      | 
- auto-07p                                  |      4 | {mathematics}                                                       | 
- debian-science                            |      4 | {statistics,economics,nanoscale-physics,physics}                    | 
+ veccore                                   |      5 | {mathematics-dev}                                                   | 
+ boolector                                 |      4 | {logic}                                                             | 
+ debian-science                            |      4 | {nanoscale-physics-dev}                                             | 
  ecbuild                                   |      4 | {meteorology-dev}                                                   | 
  hfst                                      |      4 | {linguistics}                                                       | 
  libcgns                                   |      4 | {engineering-dev}                                                   | 
- liblbfgs                                  |      4 | {mathematics-dev}                                                   | 
- libmatheval                               |      4 | {mathematics-dev}                                                   | 
- libzn-poly                                |      4 | {mathematics-dev}                                                   | 
- polylib                                   |      4 | {mathematics}                                                       | 
- ratpoints                                 |      4 | {mathematics-dev}                                                   | 
+ qd                                        |      4 | {mathematics-dev}                                                   | 
  silo-llnl                                 |      4 | {engineering-dev}                                                   | 
- spfft                                     |      4 | {nanoscale-physics-dev,meteorology-dev,mathematics-dev,physics-dev} | 
+ trilinos                                  |      4 | {mathematics-dev,physics-dev,engineering-dev}                       | 
  ucto                                      |      4 | {linguistics}                                                       | 
- veccore                                   |      4 | {mathematics-dev}                                                   | 
  vlfeat                                    |      4 | {imageanalysis-dev}                                                 | 
  xppaut                                    |      4 | {neuroscience-modeling}                                             | 
- boolector                                 |      3 | {logic}                                                             | 
  cdftools                                  |      3 | {meteorology}                                                       | 
- debian-science                            |      3 | {nanoscale-physics-dev}                                             | 
+ coinor-bonmin                             |      3 | {mathematics}                                                       | 
+ cqrlib                                    |      3 | {mathematics-dev}                                                   | 
+ cvector                                   |      3 | {mathematics-dev}                                                   | 
  dxflib                                    |      3 | {engineering-dev}                                                   | 
  fckit                                     |      3 | {meteorology-dev}                                                   | 
  frog                                      |      3 | {linguistics}                                                       | 
  gadap                                     |      3 | {meteorology-dev}                                                   | 
+ gemmlowp                                  |      3 | {mathematics-dev}                                                   | 
  hpcc                                      |      3 | {distributedcomputing,numericalcomputation}                         | 
+ libdogleg                                 |      3 | {mathematics-dev}                                                   | 
+ libtnt                                    |      3 | {mathematics-dev}                                                   | 
+ meshsdfilter                              |      3 | {mathematics-dev}                                                   | 
+ mpi4py-fft                                |      3 | {mathematics-dev}                                                   | 
+ neartree                                  |      3 | {numericalcomputation,mathematics-dev}                              | 
+ openmesh                                  |      3 | {mathematics-dev}                                                   | 
  openstereogram                            |      3 | {tools}                                                             | 
- qd                                        |      3 | {mathematics-dev}                                                   | 
- trilinos                                  |      3 | {mathematics-dev,physics-dev,engineering-dev}                       | 
+ quadrule                                  |      3 | {mathematics-dev}                                                   | 
  apertium-apy                              |      2 | {linguistics}                                                       | 
  clipper                                   |      2 | {nanoscale-physics-dev}                                             | 
- coda                                      |      2 | {meteorology-dev}                                                   | 
  coda                                      |      2 | {meteorology}                                                       | 
- coinor-bonmin                             |      2 | {mathematics}                                                       | 
- cqrlib                                    |      2 | {mathematics-dev}                                                   | 
- cvector                                   |      2 | {mathematics-dev}                                                   | 
+ coda                                      |      2 | {meteorology-dev}                                                   | 
  debian-science                            |      2 | {psychophysics}                                                     | 
+ dimbl                                     |      2 | {linguistics}                                                       | 
  fckit                                     |      2 | {meteorology}                                                       | 
  fpzip                                     |      2 | {meteorology}                                                       | 
- gemmlowp                                  |      2 | {mathematics-dev}                                                   | 
  hfst-ospell                               |      2 | {linguistics}                                                       | 
  iapws                                     |      2 | {meteorology}                                                       | 
- libdogleg                                 |      2 | {mathematics-dev}                                                   | 
  libgtkdatabox                             |      2 | {engineering-dev,viewing-dev}                                       | 
  liborigin2                                |      2 | {viewing-dev}                                                       | 
- libtnt                                    |      2 | {mathematics-dev}                                                   | 
  makedepf90                                |      2 | {meteorology-dev}                                                   | 
- meshsdfilter                              |      2 | {mathematics-dev}                                                   | 
  mmdb                                      |      2 | {nanoscale-physics-dev,highenergy-physics-dev}                      | 
- mpi4py-fft                                |      2 | {mathematics-dev}                                                   | 
  ncrystal                                  |      2 | {nanoscale-physics-dev,highenergy-physics-dev}                      | 
- neartree                                  |      2 | {numericalcomputation,mathematics-dev}                              | 
  nrn-iv                                    |      2 | {biology}                                                           | 
- odc                                       |      2 | {meteorology-dev}                                                   | 
  odc                                       |      2 | {meteorology}                                                       | 
- openmesh                                  |      2 | {mathematics-dev}                                                   | 
- quadrule                                  |      2 | {mathematics-dev}                                                   | 
+ odc                                       |      2 | {meteorology-dev}                                                   | 
  scram                                     |      2 | {engineering}                                                       | 
  silo-llnl                                 |      2 | {engineering}                                                       | 
  ssm                                       |      2 | {nanoscale-physics-dev}                                             | 
@@ -174,7 +175,6 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  cylc-flow                                 |      1 | {meteorology}                                                       | 
  debian-science                            |      1 | {neuroscience-cognitive}                                            | 
  debian-science                            |      1 | {economics}                                                         | 
- dimbl                                     |      1 | {linguistics}                                                       | 
  drslib                                    |      1 | {meteorology}                                                       | 
  dune-functions                            |      1 | {mathematics-dev}                                                   | 
  dune-localfunctions                       |      1 | {mathematics-dev}                                                   | 
@@ -244,8 +244,8 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  mbt                                       |      0 | {linguistics}                                                       | 
  mbtserver                                 |      0 | {linguistics}                                                       | 
  mctc-lib                                  |      0 | {highenergy-physics-dev,nanoscale-physics-dev}                      | 
- metis-edf                                 |      0 | {engineering,numericalcomputation}                                  | 
  metis-edf                                 |      0 | {engineering-dev}                                                   | 
+ metis-edf                                 |      0 | {engineering,numericalcomputation}                                  | 
  opengv                                    |      0 | {geometry}                                                          | 
  openigtlink                               |      0 | {robotics-dev}                                                      | 
  qrupdate                                  |      0 | {mathematics-dev}                                                   | 


=====================================
outdated_med-packages.txt
=====================================
The diff for this file was not included because it is too large.

=====================================
python-team-tests.txt
=====================================
@@ -1,204 +1,201 @@
-Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
+Last-Update: Thu, 02 Jul 2026 13:42:07 +0000
 
      Source                             | Vote   |                          Tags                          
 ----------------------------------------+--------+--------------------------------------------------------
- python-repoze.lru                      |   7408 | 
- netifaces                              |   5165 | 
- sortedcontainers                       |   4158 | 
- python-babel                           |   4073 | 
- python-babel                           |   3723 | 
- ghp-import                             |   3071 | 
- python-lunr                            |   3059 | 
- python-zopfli                          |   3023 | 
- python-outcome                         |   2720 | 
- python-gssapi                          |   2704 | 
- python-greenlet                        |   2538 | 
- humanfriendly                          |   2384 | 
- python-invoke                          |   2148 | 
- hyperlink                              |   1870 | 
- python-mysqldb                         |   1797 | 
- alabaster                              |   1695 | 
- python-hyperframe                      |   1633 | 
- websocket-client                       |   1591 | 
- python-hpack                           |   1483 | 
- python-linux-procfs                    |   1440 | 
- python-notify2                         |   1429 | 
- python-gbinder                         |   1289 | 
- pdfarranger                            |   1148 | 
- python-rsa                             |   1018 | 
- menulibre                              |    935 | 
- python-requests-oauthlib               |    925 | 
- python-webob                           |    771 | 
- python-geoip                           |    769 | 
+ python-repoze.lru                      |   7381 | 
+ netifaces                              |   5176 | 
+ sortedcontainers                       |   4149 | 
+ python-babel                           |   4078 | 
+ python-babel                           |   3722 | 
+ ghp-import                             |   3050 | 
+ python-lunr                            |   3039 | 
+ python-zopfli                          |   2997 | 
+ python-gssapi                          |   2719 | 
+ python-outcome                         |   2717 | 
+ python-greenlet                        |   2523 | 
+ humanfriendly                          |   2383 | 
+ python-invoke                          |   2153 | 
+ hyperlink                              |   1852 | 
+ python-mysqldb                         |   1799 | 
+ alabaster                              |   1701 | 
+ python-hyperframe                      |   1641 | 
+ websocket-client                       |   1580 | 
+ python-hpack                           |   1489 | 
+ python-linux-procfs                    |   1447 | 
+ python-notify2                         |   1422 | 
+ python-gbinder                         |   1287 | 
+ pdfarranger                            |   1152 | 
+ python-rsa                             |   1016 | 
+ menulibre                              |    936 | 
+ python-requests-oauthlib               |    927 | 
+ python-webob                           |    779 | 
+ python-geoip                           |    757 | 
  django-stronghold                      |    750 | 
- python-pandocfilters                   |    622 | 
- powerline                              |    617 | 
- powerline                              |    612 | 
- powerline                              |    587 | 
- python-gevent                          |    501 | 
- kazam                                  |    499 | 
- python-ewmh                            |    481 | 
+ python-pandocfilters                   |    620 | 
+ powerline                              |    619 | 
+ powerline                              |    614 | 
+ powerline                              |    594 | 
+ kazam                                  |    502 | 
+ python-gevent                          |    499 | 
+ python-ewmh                            |    483 | 
  intelhex                               |    431 | 
  python-pyu2f                           |    406 | 
- autopep8                               |    400 | 
- asn1crypto                             |    394 | 
- python-et-xmlfile                      |    382 | 
- catfish                                |    332 | 
- pytoolconfig                           |    317 | 
- pyenv                                  |    288 | 
- spf-engine                             |    254 | 
- python-text-unidecode                  |    251 | 
+ autopep8                               |    402 | 
+ asn1crypto                             |    399 | 
+ python-et-xmlfile                      |    384 | 
+ catfish                                |    334 | 
+ pytoolconfig                           |    316 | 
+ pyenv                                  |    290 | 
+ python-text-unidecode                  |    256 | 
+ spf-engine                             |    256 | 
  python-utmp                            |    235 | 
- spf-engine                             |    232 | 
- python-keyutils                        |    220 | 
- gaupol                                 |    218 | 
- python-ldap3                           |    215 | 
- python-smmap                           |    208 | 
- python-mimeparse                       |    179 | 
- dockerpty                              |    169 | 
- httpie                                 |    151 | 
+ spf-engine                             |    235 | 
+ python-ldap3                           |    223 | 
+ python-keyutils                        |    218 | 
+ gaupol                                 |    213 | 
+ python-smmap                           |    209 | 
+ python-mimeparse                       |    181 | 
+ dockerpty                              |    175 | 
+ httpie                                 |    149 | 
  python-rfc6555                         |    147 | 
- python-ntlm-auth                       |    144 | 
- smem                                   |    143 | 
- video-downloader                       |    141 | 
+ smem                                   |    142 | 
  python-consul                          |    140 | 
- python-i3ipc                           |    139 | 
- autokey                                |    138 | 
+ python-ntlm-auth                       |    139 | 
+ video-downloader                       |    139 | 
  python-toml                            |    138 | 
+ autokey                                |    137 | 
+ python-i3ipc                           |    136 | 
+ python-pyaml-env                       |    134 | 
  kivy                                   |    133 | 
- python-pyaml-env                       |    133 | 
- nodeenv                                |    125 | 
- timekpr-next                           |    116 | 
- python-click-repl                      |    108 | 
- notebook-shim                          |     96 | 
+ nodeenv                                |    126 | 
+ timekpr-next                           |    117 | 
+ python-click-repl                      |    115 | 
  pymediainfo                            |     93 | 
- lollypop                               |     88 | 
- sphinx-inline-tabs                     |     88 | 
+ notebook-shim                          |     92 | 
+ lollypop                               |     90 | 
+ mugshot                                |     88 | 
  datalad                                |     86 | 
- mugshot                                |     86 | 
  pacparser                              |     85 | 
- pssh                                   |     81 | 
- python-colour                          |     79 | 
+ sphinx-inline-tabs                     |     83 | 
+ pssh                                   |     82 | 
+ python-colour                          |     78 | 
  datalad                                |     77 | 
- fabric                                 |     74 | 
- mypaint                                |     74 | 
- funcparserlib                          |     70 | 
- python-zombie-imp                      |     68 | 
+ fabric                                 |     76 | 
+ mypaint                                |     76 | 
+ funcparserlib                          |     69 | 
+ python-zombie-imp                      |     67 | 
  sphinx-copybutton                      |     67 | 
- python-looseversion                    |     65 | 
  python-scp                             |     65 | 
- show-in-file-manager                   |     64 | 
- python-casttube                        |     62 | 
- smartypants                            |     61 | 
+ python-looseversion                    |     64 | 
+ show-in-file-manager                   |     63 | 
+ smartypants                            |     62 | 
+ python-casttube                        |     61 | 
  sshtunnel                              |     61 | 
- ueberzug                               |     61 | 
- numpy-stl                              |     60 | 
  pymacaroons                            |     60 | 
- nwg-displays                           |     59 | 
+ numpy-stl                              |     59 | 
+ ueberzug                               |     59 | 
+ nwg-displays                           |     58 | 
  itstool                                |     56 | 
- autotiling                             |     52 | 
  mitmproxy                              |     52 | 
  trac                                   |     52 | 
+ autotiling                             |     51 | 
  python3-onelogin-saml2                 |     48 | 
  pyenv                                  |     42 | 
  certipy                                |     41 | 
  jupyterhub                             |     39 | 
  pamela                                 |     39 | 
- mysql-connector-python                 |     35 | 
  pyquery                                |     35 | 
  pywavelets                             |     35 | 
+ mysql-connector-python                 |     34 | 
  spf-engine                             |     34 | 
- python-slip10                          |     32 | 
- hatchling                              |     31 | 
+ python-slip10                          |     31 | 
+ hatchling                              |     30 | 
  typogrify                              |     30 | 
  python-statsd                          |     29 | 
  dkimpy-milter                          |     28 | 
- persepolis                             |     28 | 
- ruff                                   |     27 | 
- sphinxcontrib-blockdiag                |     27 | 
+ persepolis                             |     27 | 
  python-priority                        |     26 | 
- python-scrypt                          |     26 | 
+ ruff                                   |     26 | 
+ sphinxcontrib-blockdiag                |     26 | 
+ fabric                                 |     24 | 
+ membernator                            |     24 | 
  pylibmc                                |     24 | 
  pymacs                                 |     24 | 
+ python-scrypt                          |     24 | 
  python-zstd                            |     24 | 
  enlighten                              |     23 | 
- fabric                                 |     23 | 
- membernator                            |     23 | 
  sphinxcontrib-seqdiag                  |     23 | 
  pssh                                   |     22 | 
- python-rangehttpserver                 |     22 | 
- backoff                                |     20 | 
- pithos                                 |     19 | 
+ backoff                                |     21 | 
+ python-rangehttpserver                 |     21 | 
+ pithos                                 |     20 | 
  powerline-gitstatus                    |     19 | 
  python-translationstring               |     19 | 
  rst2pdf                                |     19 | 
  enzyme                                 |     18 | 
  flask-principal                        |     18 | 
- python-demjson                         |     18 | 
- python-pem                             |     18 | 
+ python-sdnotify                        |     18 | 
  subliminal                             |     18 | 
  toot                                   |     18 | 
  kivy                                   |     17 | 
+ mopidy-mpd                             |     17 | 
+ python-demjson                         |     17 | 
  python-pysubs2                         |     17 | 
- python-sdnotify                        |     17 | 
  clustershell                           |     16 | 
- mopidy-mpd                             |     16 | 
  policyd-rate-limit                     |     16 | 
+ python-dataset                         |     16 | 
+ python-pem                             |     16 | 
  censys                                 |     15 | 
+ cppman                                 |     15 | 
  gtextfsm                               |     15 | 
  jschema-to-python                      |     15 | 
  mistune0                               |     15 | 
- parfive                                |     15 | 
  pykwalify                              |     15 | 
  python-args                            |     15 | 
- python-dataset                         |     15 | 
  python-hupper                          |     15 | 
+ python-py-zipkin                       |     15 | 
  python-sarif-python-om                 |     15 | 
  subliminal                             |     15 | 
  alot                                   |     14 | 
- cppman                                 |     14 | 
+ datalad-container                      |     14 | 
  dnsdiag                                |     14 | 
+ mopidy-local                           |     14 | 
+ parfive                                |     14 | 
  pwntools                               |     14 | 
- python-py-zipkin                       |     14 | 
- datalad-container                      |     13 | 
  micropython-mpremote                   |     13 | 
- mopidy-local                           |     13 | 
  python-clint                           |     13 | 
  python-pyalsa                          |     12 | 
+ python-pygal                           |     12 | 
  sphinxcontrib-actdiag                  |     12 | 
  sphinxcontrib-nwdiag                   |     12 | 
  gmplot                                 |     11 | 
- pytest-runner                          |     11 | 
- python-pygal                           |     11 | 
- sphinxcontrib-log-cabinet              |     11 | 
  unearth                                |     11 | 
  django-environ                         |     10 | 
+ pytest-runner                          |     10 | 
  python-dbussy                          |     10 | 
  python-halo                            |     10 | 
  python-nmea2                           |     10 | 
  python-numpysane                       |     10 | 
+ sphinxcontrib-log-cabinet              |     10 | 
  dbf                                    |      9 | 
  flask-security                         |      9 | 
  junos-eznc                             |      9 | 
+ pysequoia                              |      9 | 
  python-gnuplotlib                      |      9 | 
  python-inotify                         |      9 | 
  trac-wysiwyg                           |      9 | 
  west                                   |      9 | 
+ debiancontributors                     |      8 | 
  httpcode                               |      8 | 
  python-envs                            |      8 | 
  python-openstep-plist                  |      8 | 
- sphinxcontrib-images                   |      8 | 
  todoman                                |      8 | 
  beanquery                              |      7 | 
  clustershell                           |      7 | 
- dask-sphinx-theme                      |      7 | 
- debiancontributors                     |      7 | 
  drf-yasg-nonfree                       |      7 | 
  flask-paranoid                         |      7 | 
- hachoir                                |      7 | 
  librouteros                            |      7 | 
  pyp                                    |      7 | 
- pysequoia                              |      7 | 
  python-aiohttp-security                |      7 | 
  python-crcelk                          |      7 | 
  python-drf-spectacular-sidecar-nonfree |      7 | 
@@ -206,36 +203,37 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  python-versioneer                      |      7 | 
  slimit                                 |      7 | 
  speg                                   |      7 | 
+ sphinxcontrib-images                   |      7 | 
  sphinx-intl                            |      7 | 
- txt2tags                               |      7 | 
+ dask-sphinx-theme                      |      6 | 
  flask-session                          |      6 | 
+ hachoir                                |      6 | 
+ mypy-protobuf                          |      6 | 
  pyparallel                             |      6 | 
  pytaglib                               |      6 | 
  python-kyotocabinet                    |      6 | 
  python-pyrss2gen                       |      6 | 
  sphinxcontrib-globalsubs               |      6 | 
  tuna                                   |      6 | 
+ txt2tags                               |      6 | 
  zabbix-cli                             |      6 | 
+ aiomysql                               |      5 | 
  azote                                  |      5 | 
  bootstrap-flask                        |      5 | 
  btchip-python                          |      5 | 
- extension-helpers                      |      5 | 
  fava                                   |      5 | 
  graphql-relay                          |      5 | 
- mypy-protobuf                          |      5 | 
  numpy-stl                              |      5 | 
  pyfltk                                 |      5 | 
- python-deepmerge                       |      5 | 
  python-ethtool                         |      5 | 
  python-overpy                          |      5 | 
  python-xdo                             |      5 | 
  speaklater                             |      5 | 
- sphinx-design                          |      5 | 
- aiomysql                               |      4 | 
+ wikitrans                              |      5 | 
  ansi                                   |      4 | 
  cram                                   |      4 | 
+ extension-helpers                      |      4 | 
  flask-api                              |      4 | 
- imap-tools                             |      4 | 
  jpylyzer                               |      4 | 
  mopidy-alsamixer                       |      4 | 
  namecheap                              |      4 | 
@@ -243,13 +241,16 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  proglog                                |      4 | 
  pycrc                                  |      4 | 
  pylint-common                          |      4 | 
+ pyrad                                  |      4 | 
+ python-deepmerge                       |      4 | 
  python-netfilterqueue                  |      4 | 
  python-simpy                           |      4 | 
+ python-urlobject                       |      4 | 
  ruff                                   |      4 | 
  securestring                           |      4 | 
  smem                                   |      4 | 
+ sphinx-design                          |      4 | 
  trac-accountmanager                    |      4 | 
- wikitrans                              |      4 | 
  django-sass                            |      3 | 
  drf-extensions                         |      3 | 
  drf-haystack                           |      3 | 
@@ -257,17 +258,17 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  flufl.testing                          |      3 | 
  htmlmin                                |      3 | 
  humanfriendly                          |      3 | 
- kconfiglib                             |      3 | 
+ imap-tools                             |      3 | 
  mopidy-internetarchive                 |      3 | 
  mopidy-podcast                         |      3 | 
  namecheap                              |      3 | 
  pyjokes                                |      3 | 
  pynliner                               |      3 | 
- pyrad                                  |      3 | 
  python-cookies                         |      3 | 
  python-imageio-ffmpeg                  |      3 | 
  python-imgviz                          |      3 | 
- python-urlobject                       |      3 | 
+ python-openshift                       |      3 | 
+ s3ql                                   |      3 | 
  sorl-thumbnail                         |      3 | 
  traittypes                             |      3 | 
  voltron                                |      3 | 
@@ -276,6 +277,7 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  aiomcache                              |      2 | 
  django-jinja                           |      2 | 
  django-paintstore                      |      2 | 
+ django-pglocks                         |      2 | 
  django-redis-sessions                  |      2 | 
  django-shortuuidfield                  |      2 | 
  dotdrop                                |      2 | 
@@ -283,6 +285,7 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  flask-paginate                         |      2 | 
  fypp                                   |      2 | 
  htmlmin                                |      2 | 
+ kconfiglib                             |      2 | 
  magic-wormhole-mailbox-server          |      2 | 
  mercurial-evolve                       |      2 | 
  mopidy-podcast-itunes                  |      2 | 
@@ -295,7 +298,6 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  painintheapt                           |      2 | 
  panoramisk                             |      2 | 
  pdudaemon                              |      2 | 
- purl                                   |      2 | 
  pyina                                  |      2 | 
  pyjunitxml                             |      2 | 
  pynag                                  |      2 | 
@@ -313,13 +315,13 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  python-networkmanager                  |      2 | 
  python-noise                           |      2 | 
  python-offtrac                         |      2 | 
- python-openshift                       |      2 | 
  python-pgmagick                        |      2 | 
  python-pyout                           |      2 | 
  python-simpy                           |      2 | 
  python-webdavclient                    |      2 | 
  python-zc.customdoctests               |      2 | 
- s3ql                                   |      2 | 
+ sphinxcontrib-emojicodes               |      2 | 
+ sphinx-markdown-tables                 |      2 | 
  testrepository                         |      2 | 
  trac-customfieldadmin                  |      2 | 
  trac-roadmap                           |      2 | 
@@ -338,7 +340,6 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  django-ajax-selects                    |      1 | 
  django-bitfield                        |      1 | 
  django-ldapdb                          |      1 | 
- django-pglocks                         |      1 | 
  django-render-block                    |      1 | 
  django-rq                              |      1 | 
  django-templated-email                 |      1 | 
@@ -355,9 +356,9 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  jpy                                    |      1 | 
  mkdocs-macros-plugin                   |      1 | 
  mopidy-mpris                           |      1 | 
- myst-nb                                |      1 | 
  pcpp                                   |      1 | 
  pdudaemon                              |      1 | 
+ purl                                   |      1 | 
  pycallgraph                            |      1 | 
  pydataverse                            |      1 | 
  pydenticon                             |      1 | 
@@ -366,7 +367,6 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  pypass                                 |      1 | 
  pyseq                                  |      1 | 
  pyssim                                 |      1 | 
- pytest-expect                          |      1 | 
  python-aio-pika                        |      1 | 
  python-ansicolors                      |      1 | 
  python-brother-ql                      |      1 | 
@@ -403,9 +403,7 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  resistor-decoder                       |      1 | 
  slimit                                 |      1 | 
  soundcraft-utils                       |      1 | 
- sphinxcontrib-emojicodes               |      1 | 
  sphinx-favicon                         |      1 | 
- sphinx-markdown-tables                 |      1 | 
  sphinxtesters                          |      1 | 
  testrepository                         |      1 | 
  trac-httpauth                          |      1 | 
@@ -481,6 +479,7 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  mssql-django                           |      0 | 
  mwoauth                                |      0 | 
  mypaint                                |      0 | 
+ myst-nb                                |      0 | 
  nbgitpuller                            |      0 | 
  niri-companion                         |      0 | 
  okasha                                 |      0 | 
@@ -510,6 +509,7 @@ Last-Update: Thu, 02 Jul 2026 01:42:04 +0000
  pypass                                 |      0 | 
  pyprind                                |      0 | 
  pysquashfsimage                        |      0 | 
+ pytest-expect                          |      0 | 
  python3-simpleobsws                    |      0 | 
  python-aiohttp-security                |      0 | 
  python-aio-pika                        |      0 | 



View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/d7941a3d95e5f1676d84abeffa9d3a9a954d293f

-- 
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From gitlab at salsa.debian.org  Thu Jul  2 15:00:41 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 14:00:41 +0000
Subject: [med-svn] [Git][med-team/unifrac-tools][master] Build reproducibly
Message-ID: <6a466f09aa71c_55bea410ec406749f@godard.mail>



Andreas Tille pushed to branch master at Debian Med / unifrac-tools


Commits:
c0dae05d by Andreas Tille at 2026-07-02T16:00:34+02:00
Build reproducibly

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/reproducible-build.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+unifrac-tools (1.6.1-2) UNRELEASED; urgency=medium
+
+  * Build reproducibly
+
+ -- Andreas Tille <tille at debian.org>  Thu, 02 Jul 2026 16:00:27 +0200
+
 unifrac-tools (1.6.1-1) unstable; urgency=medium
 
   [ Andreas Tille ]


=====================================
debian/patches/reproducible-build.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-07-02
+Description: Build reproducibly
+
+--- a/src/ssu_generate_helper.py
++++ b/src/ssu_generate_helper.py
+@@ -234,7 +234,7 @@ def print_body(method,lines,nmspace):
+             line = lines[i]
+             i+=1
+         
+-        for ft in ftypes:
++        for ft in sorted(ftypes):
+             print_func_args(method,ftype,nmspace,fname,ft,fargs)
+             print('');
+ 


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ soname.patch
 baseline.patch
 enable_linking_to_shared_hdf5_lib.patch
 hardening.patch
+reproducible-build.patch



View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/commit/c0dae05d3f3392787f768751fa4136f49bee7bec

-- 
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From gitlab at salsa.debian.org  Thu Jul  2 15:57:46 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 14:57:46 +0000
Subject: [med-svn] [Git][med-team/unifrac-tools][master] Forwarded patch
Message-ID: <6a467c6a19939_55b14c7a718408379d@godard.mail>



Andreas Tille pushed to branch master at Debian Med / unifrac-tools


Commits:
3d007400 by Andreas Tille at 2026-07-02T16:57:29+02:00
Forwarded patch

- - - - -


1 changed file:

- debian/patches/reproducible-build.patch


Changes:

=====================================
debian/patches/reproducible-build.patch
=====================================
@@ -1,6 +1,7 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Update: 2026-07-02
 Description: Build reproducibly
+Forwarded: https://github.com/biocore/unifrac-binaries/issues/87
 
 --- a/src/ssu_generate_helper.py
 +++ b/src/ssu_generate_helper.py



View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/commit/3d0074001a51d3467b720a9389771e8c6af14931

-- 
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From gitlab at salsa.debian.org  Thu Jul  2 16:07:48 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 15:07:48 +0000
Subject: [med-svn] [Git][med-team/gwyddion][master] Fix FTBFS against HDF5
 2.1.0 Closes: #1139602
Message-ID: <6a467ec473e33_55b14a5328c40855f3@godard.mail>



Andreas Tille pushed to branch master at Debian Med / gwyddion


Commits:
8ee8fead by Andreas Tille at 2026-07-02T17:07:35+02:00
Fix FTBFS against HDF5 2.1.0 Closes: #1139602

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/hdf5-2.1.0.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+gwyddion (3.10-7) UNRELEASED; urgency=medium
+
+  [ Gilles Filippini ]
+  * Fix FTBFS against HDF5 2.1.0
+    Closes: #1139602
+
+ -- Andreas Tille <tille at debian.org>  Thu, 02 Jul 2026 17:06:33 +0200
+
 gwyddion (3.10-6) unstable; urgency=medium
 
   * Rename -dev and -doc package to not use the version number


=====================================
debian/patches/hdf5-2.1.0.patch
=====================================
@@ -0,0 +1,92 @@
+Author: Gilles Filippini <pini at debian.org>
+Last-Update: 2026-06-10
+Bug-Debian: https://bugs.debian.org/1139602
+Description: Fix FTBFS against HDF5 2.1.0
+
+Index: gwyddion-3.10/configure
+===================================================================
+--- gwyddion-3.10.orig/configure
++++ gwyddion-3.10/configure
+@@ -25841,7 +25841,7 @@ esac
+             esac
+             done
+ 
+-            HDF5_LIBS="$HDF5_LIBS -lhdf5"
++            HDF5_LIBS="$HDF5_LIBS -lhdf5_serial"
+             { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: yes (version $HDF5_VERSION)" >&5
+ printf "%s\n" "yes (version $HDF5_VERSION)" >&6; }
+ 
+@@ -25862,14 +25862,14 @@ else case e in #(
+ esac
+ fi
+ 
+-                        { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for H5free_memory in -lhdf5" >&5
+-printf %s "checking for H5free_memory in -lhdf5... " >&6; }
++                        { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for H5free_memory in -lhdf5_serial" >&5
++printf %s "checking for H5free_memory in -lhdf5_serial... " >&6; }
+ if test ${ac_cv_lib_hdf5_H5free_memory+y}
+ then :
+   printf %s "(cached) " >&6
+ else case e in #(
+   e) ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lhdf5  $LIBS"
++LIBS="-lhdf5_serial  $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -25917,14 +25917,14 @@ fi
+             { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: Unable to compile HDF5 test program" >&5
+ printf "%s\n" "$as_me: WARNING: Unable to compile HDF5 test program" >&2;}
+             fi
+-                        { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for main in -lhdf5_hl" >&5
+-printf %s "checking for main in -lhdf5_hl... " >&6; }
++                        { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for main in -lhdf5_serial_hl" >&5
++printf %s "checking for main in -lhdf5_serial_hl... " >&6; }
+ if test ${ac_cv_lib_hdf5_hl_main+y}
+ then :
+   printf %s "(cached) " >&6
+ else case e in #(
+   e) ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lhdf5_hl  $LIBS"
++LIBS="-lhdf5_serial_hl  $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -25953,7 +25953,7 @@ fi
+ printf "%s\n" "$ac_cv_lib_hdf5_hl_main" >&6; }
+ if test "x$ac_cv_lib_hdf5_hl_main" = xyes
+ then :
+-  HDF5_LIBS="$HDF5_LIBS -lhdf5_hl"
++  HDF5_LIBS="$HDF5_LIBS -lhdf5_serial_hl"
+ fi
+ 
+             ac_cv_lib_hdf5_hl=ac_cv_lib_hdf5_hl_main
+Index: gwyddion-3.10/m4/gwy-hdf5.m4
+===================================================================
+--- gwyddion-3.10.orig/m4/gwy-hdf5.m4
++++ gwyddion-3.10/m4/gwy-hdf5.m4
+@@ -157,7 +157,14 @@ HDF5 support is being disabled (equivale
+             esac
+             done
+ 
+-            HDF5_LIBS="$HDF5_LIBS -lhdf5"
++            HDF5_INFIX=
++            case "$HDF5_LIBS" in
++                -lhdf5_*)
++                    HDF5_INFIX="${HDF5_LIBS#-lhdf5_}"
++                    HDF5_INFIX="_${HDF5_INFIX%%_*}"
++                    ;;
++            esac
++            HDF5_LIBS="$HDF5_LIBS -lhdf5$HDF5_INFIX"
+             AC_MSG_RESULT([yes (version $[HDF5_VERSION])])
+ 
+             dnl See if we can compile
+@@ -176,7 +183,7 @@ HDF5 support is being disabled (equivale
+             AC_MSG_WARN([Unable to compile HDF5 test program])
+             fi
+             dnl Look for HDF5's high level library
+-            AC_CHECK_LIB([hdf5_hl],[main],[HDF5_LIBS="$HDF5_LIBS -lhdf5_hl"],[],[])
++            AC_CHECK_LIB([hdf5_hl],[main],[HDF5_LIBS="$HDF5_LIBS -lhdf5${HDF5_INFIX}_hl"],[],[])
+             ac_cv_lib_hdf5_hl=ac_cv_lib_hdf5_hl_main
+ 
+             CC=$gwy_hdf5_save_CC


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+hdf5-2.1.0.patch
 launcher.patch
 skip_test.patch
 flaky.patch



View it on GitLab: https://salsa.debian.org/med-team/gwyddion/-/commit/8ee8fead2184760c907f551e7fb173b9668b845a

-- 
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From gitlab at salsa.debian.org  Thu Jul  2 18:07:17 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 17:07:17 +0000
Subject: [med-svn] [Git][med-team/gwyddion][master] 8 commits: New upstream
 version
Message-ID: <6a469ac556c3d_55b142067a041352d9@godard.mail>



Andreas Tille pushed to branch master at Debian Med / gwyddion


Commits:
94e10415 by Andreas Tille at 2026-07-02T17:08:15+02:00
New upstream version

- - - - -
64abe3be by Andreas Tille at 2026-07-02T17:08:16+02:00
New upstream version 3.11
- - - - -
5069a328 by Andreas Tille at 2026-07-02T17:08:30+02:00
Update upstream source from tag 'upstream/3.11'

Update to upstream version '3.11'
with Debian dir 7a2102e12d9e522d6067fc06921f0415b5ba0a15
- - - - -
75633fdf by Andreas Tille at 2026-07-02T17:13:18+02:00
Changes made by cme

- - - - -
cc72f2fb by Andreas Tille at 2026-07-02T18:34:35+02:00
Make sure modules/preview.h will be found

- - - - -
bf2327b9 by Andreas Tille at 2026-07-02T18:54:05+02:00
d/copyright: review

- - - - -
992126a7 by Andreas Tille at 2026-07-02T18:56:53+02:00
Add d/lrc.config

- - - - -
0abc7937 by Andreas Tille at 2026-07-02T19:02:42+02:00
Upload to unstable

- - - - -


675 changed files:

- Makefile.in
- NEWS
- aclocal.m4
- autogen.sh
- build-aux/Makefile.in
- build-aux/compile
- build-aux/config.rpath
- build-aux/depcomp
- build-aux/install-sh
- build-aux/missing
- build-aux/tap-driver.sh
- build-aux/test-driver
- configure
- configure.ac
- data/Makefile.in
- data/glmaterials/Makefile.in
- data/gradients/Makefile.in
- data/gwyddion3.spec.in
- data/gwyddion3.vim
- data/net.gwyddion.Gwyddion3.appdata.xml
- debian/changelog
- debian/control
- debian/copyright
- + debian/lrc.config
- + debian/patches/fix_AM_CPPFLAGS.patch
- debian/patches/hdf5-2.1.0.patch
- debian/patches/series
- debian/patches/skip_test.patch
- debian/rules
- devel-docs/Makefile.in
- devel-docs/libgwyapp/Makefile.in
- + devel-docs/libgwyapp/html/GwyAppDataWindow.html
- devel-docs/libgwyapp/html/GwyAppGraphWindow.html
- devel-docs/libgwyapp/html/GwyAppImageWindow.html
- devel-docs/libgwyapp/html/GwyDataChooser.html
- devel-docs/libgwyapp/html/GwyDialog.html
- + devel-docs/libgwyapp/html/GwyFunctionList.html
- devel-docs/libgwyapp/html/GwyLogBrowser.html
- devel-docs/libgwyapp/html/GwyParamDef.html
- devel-docs/libgwyapp/html/GwyParamResource.html
- devel-docs/libgwyapp/html/GwyParamTable.html
- devel-docs/libgwyapp/html/GwyParams.html
- devel-docs/libgwyapp/html/GwyPlainTool.html
- devel-docs/libgwyapp/html/GwyResourceEditor.html
- devel-docs/libgwyapp/html/GwyResultsExport.html
- devel-docs/libgwyapp/html/GwyTool.html
- devel-docs/libgwyapp/html/ModuleTutorial.html
- devel-docs/libgwyapp/html/annotation-glossary.html
- devel-docs/libgwyapp/html/api-index-all.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-beyond.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-file.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-graph.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-install.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-minimal.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-overview.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-process.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-tool.html
- devel-docs/libgwyapp/html/index.html
- devel-docs/libgwyapp/html/libgwyapp-Application.html
- devel-docs/libgwyapp/html/libgwyapp-Curve-map-modules.html
- devel-docs/libgwyapp/html/libgwyapp-Data-browser.html
- devel-docs/libgwyapp/html/libgwyapp-File-module-utils.html
- devel-docs/libgwyapp/html/libgwyapp-File-modules.html
- devel-docs/libgwyapp/html/libgwyapp-Graph-modules.html
- devel-docs/libgwyapp/html/libgwyapp-module-process.html ? devel-docs/libgwyapp/html/libgwyapp-Image-modules.html
- devel-docs/libgwyapp/html/libgwyapp-Log.html
- devel-docs/libgwyapp/html/libgwyapp-Module-browser.html
- devel-docs/libgwyapp/html/libgwyapp-Module-loader.html
- devel-docs/libgwyapp/html/libgwyapp-Module-utilties.html
- + devel-docs/libgwyapp/html/libgwyapp-Recent-functions.html
- devel-docs/libgwyapp/html/libgwyapp-Synth-module-utils.html
- devel-docs/libgwyapp/html/libgwyapp-Synthetic-data-modules.html
- devel-docs/libgwyapp/html/libgwyapp-Tool-modules.html
- devel-docs/libgwyapp/html/libgwyapp-Volume-data-modules.html
- devel-docs/libgwyapp/html/libgwyapp-XYZ-data-modules.html
- devel-docs/libgwyapp/html/libgwyapp-data.html
- devel-docs/libgwyapp/html/libgwyapp-filelist.html
- devel-docs/libgwyapp/html/libgwyapp-menu.html
- devel-docs/libgwyapp/html/libgwyapp-modules.html
- devel-docs/libgwyapp/html/libgwyapp-settings.html
- devel-docs/libgwyapp/html/libgwyapp-utils.html
- devel-docs/libgwyapp/html/libgwyapp-wait.html
- devel-docs/libgwyapp/html/libgwyapp.devhelp2
- devel-docs/libgwyapp/libgwyapp-docs.xml
- devel-docs/libgwyddion/Makefile.in
- devel-docs/libgwyddion/html/DataProcess.html
- devel-docs/libgwyddion/html/GwyBrick.html
- devel-docs/libgwyddion/html/GwyCDLine.html
- devel-docs/libgwyddion/html/GwyField.html
- devel-docs/libgwyddion/html/GwyGLMaterial.html
- devel-docs/libgwyddion/html/GwyGradient.html
- devel-docs/libgwyddion/html/GwyGrainValue.html
- devel-docs/libgwyddion/html/GwyLine.html
- devel-docs/libgwyddion/html/GwyNield.html
- devel-docs/libgwyddion/html/GwyTriangulation.html
- devel-docs/libgwyddion/html/api-index-all.html
- devel-docs/libgwyddion/html/index.html
- devel-docs/libgwyddion/html/libgwyddion-Correction.html
- devel-docs/libgwyddion/html/libgwyddion-Distance-transform.html
- devel-docs/libgwyddion/html/libgwyddion-Enums.html
- devel-docs/libgwyddion/html/libgwyddion-Fractals.html
- devel-docs/libgwyddion/html/libgwyddion-Grain-quantities.html
- devel-docs/libgwyddion/html/libgwyddion-grains.html ? devel-docs/libgwyddion/html/libgwyddion-Grains.html
- devel-docs/libgwyddion/html/libgwyddion-Serialisation-utils.html
- devel-docs/libgwyddion/html/libgwyddion-Statistics.html
- devel-docs/libgwyddion/html/libgwyddion-Version.html
- devel-docs/libgwyddion/html/libgwyddion-Watershed.html
- devel-docs/libgwyddion/html/libgwyddion-filters.html
- devel-docs/libgwyddion/html/libgwyddion.devhelp2
- devel-docs/libgwyui/Makefile.am
- devel-docs/libgwyui/Makefile.in
- devel-docs/libgwyui/html/ColorWidgets.html
- devel-docs/libgwyui/html/GraphWidgets.html
- devel-docs/libgwyui/html/GwyAdjustBar.html
- devel-docs/libgwyui/html/GwyCellRendererGradient.html
- devel-docs/libgwyui/html/GwyColorAxis.html
- devel-docs/libgwyui/html/GwyColorButton.html
- devel-docs/libgwyui/html/GwyColorDialog.html
- devel-docs/libgwyui/html/GwyColorEditor.html
- devel-docs/libgwyui/html/GwyColorSwatch.html
- devel-docs/libgwyui/html/GwyColorWheel.html
- devel-docs/libgwyui/html/GwyCorrelTable.html
- devel-docs/libgwyui/html/GwyDataView.html
- devel-docs/libgwyui/html/GwyDataViewLayer.html
- devel-docs/libgwyui/html/GwyDataWindow.html
- devel-docs/libgwyui/html/GwyFitTable.html
- devel-docs/libgwyui/html/GwyGradientSwatch.html
- devel-docs/libgwyui/html/GwyGraphArea.html
- devel-docs/libgwyui/html/GwyGraphAxis.html
- devel-docs/libgwyui/html/GwyGraphCorner.html
- devel-docs/libgwyui/html/GwyGraphCurveDialog.html
- devel-docs/libgwyui/html/GwyGraphCurveModel.html
- devel-docs/libgwyui/html/GwyGraphCurves.html
- devel-docs/libgwyui/html/GwyGraphModel.html
- devel-docs/libgwyui/html/GwyGraphWindow.html
- devel-docs/libgwyui/html/GwyInventoryStore.html
- devel-docs/libgwyui/html/GwyNullStore.html
- devel-docs/libgwyui/html/GwyRuler.html
- devel-docs/libgwyui/html/GwySensitivityGroup.html
- devel-docs/libgwyui/html/GwyShader.html
- + devel-docs/libgwyui/html/GwyShrinkWrap.html
- devel-docs/libgwyui/html/GwyVectorLayer.html
- devel-docs/libgwyui/html/WidgetUtilities.html
- devel-docs/libgwyui/html/api-index-all.html
- + devel-docs/libgwyui/html/gtk-quit.png
- devel-docs/libgwyui/html/index.html
- + devel-docs/libgwyui/html/libgwyui-Cairo-drawing-utils.html
- devel-docs/libgwyui/html/libgwyui-Checkboxes.html
- devel-docs/libgwyui/html/libgwyui-Combo-boxes.html
- devel-docs/libgwyui/html/libgwyui-GwyGrainValueTreeView.html
- devel-docs/libgwyui/html/libgwyui-Icons.html
- devel-docs/libgwyui/html/libgwyui-Option-menus.html
- devel-docs/libgwyui/html/libgwyui-Pixbuf-rendering.html
- devel-docs/libgwyui/html/libgwyui-Radiobuttons.html
- devel-docs/libgwyui/html/libgwyui-Widget-utilities.html
- devel-docs/libgwyui/html/libgwyui-gwyui.html
- devel-docs/libgwyui/html/libgwyui.devhelp2
- devel-docs/libgwyui/libgwyui-docs.xml
- gwyddion/Makefile.am
- gwyddion/Makefile.in
- gwyddion/about.c
- + gwyddion/file-handling.c
- gwyddion/gwyddion.c
- gwyddion/gwyddion.h
- gwyddion/release.h
- + gwyddion/shortcut-editor.c
- gwyddion/splash.c
- gwyddion/toolbox-editor.c
- gwyddion/toolbox-spec.c
- gwyddion/toolbox.c
- gwyddion/toolbox.h
- gwyddion/toolbox.xml
- gwyddion3.spec
- libgwyapp/GwyApp-3.10.gir ? libgwyapp/GwyApp-3.11.gir
- libgwyapp/Makefile.am
- libgwyapp/Makefile.in
- + libgwyapp/app-data-window.c
- + libgwyapp/app-data-window.h
- libgwyapp/app-graph-window.c
- libgwyapp/app-graph-window.h
- libgwyapp/app-image-window.c
- libgwyapp/app-image-window.h
- libgwyapp/app.c
- libgwyapp/app.h
- libgwyapp/change-preview-cmap.c
- libgwyapp/change-preview-volume.c
- libgwyapp/change-preview-xyz.c
- libgwyapp/data-browser--gui.c
- libgwyapp/data-browser-internal.h
- libgwyapp/data-browser.c
- libgwyapp/data-browser.h
- libgwyapp/dialog.c
- libgwyapp/dialog.h
- libgwyapp/file-chooser.c
- libgwyapp/file-chooser.h
- libgwyapp/file.c
- libgwyapp/filelist.c
- + libgwyapp/function-list.c
- + libgwyapp/function-list.h
- libgwyapp/glmaterial-editor.h
- libgwyapp/gradient-editor.c
- libgwyapp/gwyapp.c
- libgwyapp/gwyapp.h
- libgwyapp/gwyplaintool.c
- libgwyapp/gwyplaintool.h
- libgwyapp/gwytool.c
- libgwyapp/gwytool.h
- libgwyapp/help.c
- libgwyapp/log-browser.c
- libgwyapp/log.c
- libgwyapp/menu-recent-files.c
- libgwyapp/menu.c
- libgwyapp/menu.h
- libgwyapp/meta-browser.c
- libgwyapp/module-browser.h
- libgwyapp/module-cmap.c
- libgwyapp/module-cmap.h
- libgwyapp/module-process.c ? libgwyapp/module-image.c
- libgwyapp/module-process.h ? libgwyapp/module-image.h
- libgwyapp/module-internal.h
- libgwyapp/module-loader.c
- libgwyapp/module-loader.h
- libgwyapp/module-utils-synth.h
- libgwyapp/module-utils.c
- libgwyapp/module-volume.c
- libgwyapp/module-volume.h
- libgwyapp/module-xyz.c
- libgwyapp/module-xyz.h
- libgwyapp/param-def.c
- libgwyapp/param-def.h
- libgwyapp/param-internal.h
- libgwyapp/param-table.c
- libgwyapp/param-table.h
- + libgwyapp/recent-funcs.c
- modules/synth/preview.h ? libgwyapp/recent-funcs.h
- libgwyapp/resource-editor.c
- libgwyapp/resource-editor.h
- libgwyapp/results-export.h
- libgwyapp/sanity.h
- libgwyapp/settings.c
- libgwyapp/wait.c
- libgwyddion/Gwyddion-3.10.gir ? libgwyddion/Gwyddion-3.11.gir
- libgwyddion/Makefile.in
- libgwyddion/brick.c
- libgwyddion/brick.h
- libgwyddion/cdline.h
- libgwyddion/dict.h
- libgwyddion/distance-transform.c
- libgwyddion/enums.c
- libgwyddion/field.c
- libgwyddion/field.h
- libgwyddion/filters--convdeconv.c
- libgwyddion/filters.c
- libgwyddion/gl-material.h
- libgwyddion/gradient.h
- libgwyddion/grain-quantities.c
- libgwyddion/grain-quantities.h
- libgwyddion/grain-value.c
- libgwyddion/grain-value.h
- libgwyddion/grains.c
- libgwyddion/internal.h
- libgwyddion/inttrans.c
- libgwyddion/lawn.h
- libgwyddion/line.c
- libgwyddion/line.h
- libgwyddion/nield.c
- libgwyddion/nield.h
- libgwyddion/nl-fitter.c
- libgwyddion/scatter.c
- libgwyddion/scatter.h
- libgwyddion/selection.h
- libgwyddion/serializable-utils.h
- libgwyddion/triangulation.h
- libgwyddion/types.c
- libgwyddion/utils.h
- libgwyddion/version.h
- libgwyddion/watershed.c
- libgwyddion/xyz.h
- libgwyui/GwyUI-3.10.gir ? libgwyui/GwyUI-3.11.gir
- libgwyui/Makefile.am
- libgwyui/Makefile.in
- libgwyui/adjust-bar.c
- libgwyui/adjust-bar.h
- libgwyui/cairo-utils.c
- libgwyui/cairo-utils.h
- libgwyui/color-axis.h
- libgwyui/color-button.c
- libgwyui/color-button.h
- libgwyui/color-dialog.c
- libgwyui/color-dialog.h
- libgwyui/color-editor.c
- libgwyui/color-editor.h
- libgwyui/color-swatch.h
- libgwyui/color-wheel.c
- libgwyui/color-wheel.h
- libgwyui/correl-table.h
- libgwyui/data-view-layer.h
- libgwyui/data-view.c
- libgwyui/data-view.h
- libgwyui/data-window.c
- libgwyui/data-window.h
- libgwyui/fit-table.c
- libgwyui/fit-table.h
- libgwyui/gradient-swatch.h
- libgwyui/graph-area.h
- libgwyui/graph-axis-dialog.c
- libgwyui/graph-axis.h
- libgwyui/graph-corner.h
- libgwyui/graph-curve-dialog.c
- libgwyui/graph-curve-model.c
- libgwyui/graph-curve-model.h
- libgwyui/graph-curves.h
- libgwyui/graph-internal.h
- libgwyui/graph-key-dialog.c
- libgwyui/graph-key.c
- libgwyui/graph-model.h
- libgwyui/graph-utils.c
- libgwyui/graph-utils.h
- libgwyui/graph-window-measure-dialog.c
- libgwyui/graph-window.c
- libgwyui/graph-window.h
- libgwyui/gwyglwindow.c
- libgwyui/gwyglwindow.h
- libgwyui/gwyui.h
- libgwyui/icons.c
- libgwyui/inventory-store.h
- libgwyui/layer-line.c
- libgwyui/layer-point.c
- libgwyui/null-store.h
- libgwyui/option-menus.c
- libgwyui/pixbuf-render.h
- libgwyui/ruler.h
- libgwyui/sci-text.c
- libgwyui/shader.h
- + libgwyui/shrink-wrap.c
- + libgwyui/shrink-wrap.h
- libgwyui/types.c
- libgwyui/types.h
- libgwyui/utils.c
- libgwyui/utils.h
- libgwyui/vector-layer.c
- libgwyui/vector-layer.h
- m4/Makefile.am
- m4/Makefile.in
- + m4/gettext-build-to-host.m4
- + m4/gettext-host-cpu-c-abi.m4
- m4/iconv.m4 ? m4/gettext-iconv.m4
- + m4/gettext-intlmacosx.m4
- + m4/gettext-lib-ld.m4
- + m4/gettext-lib-link.m4
- + m4/gettext-lib-prefix.m4
- m4/nls.m4 ? m4/gettext-nls.m4
- m4/po.m4 ? m4/gettext-po.m4
- m4/progtest.m4 ? m4/gettext-progtest.m4
- m4/gettext.m4
- modules/Makefile.am
- modules/Makefile.in
- modules/cmap/Makefile.in
- modules/cmap/cmap_align.c
- modules/cmap/cmap_asciiexport.c
- modules/cmap/cmap_crop.c
- modules/cmap/cmap_cutter.c
- modules/cmap/cmap_extractcurve.c
- modules/cmap/cmap_fdfit.c
- modules/cmap/cmap_fit.c
- modules/cmap/cmap_fztofd.c
- modules/cmap/cmap_linestat.c
- modules/cmap/cmap_lockin.c
- modules/cmap/cmap_polylevel.c
- modules/cmap/cmap_possearch.c
- modules/cmap/cmap_rename.c
- modules/cmap/cmap_simplemech.c
- modules/cmap/cmap_sinebg.c
- modules/cmap/cmap_volumize.c
- modules/file/Makefile.in
- modules/file/accurell.c
- modules/file/asciiexport.c
- modules/file/formats3d.c
- modules/file/gwyfile.c
- modules/file/gxyzffile.c
- modules/file/hdf5/Makefile.in
- modules/file/hdf5/fusionscope.c
- modules/file/hdf5/gxsm4.c
- modules/file/hdf5/veloxemd.c
- modules/file/hdrimage.c
- modules/file/imgexport.c
- modules/file/nmmxyz.c
- modules/file/openexr.cc
- modules/file/pixmap.c
- modules/file/rawfile.c
- modules/file/rawgraph.c
- modules/file/rmitmd.c
- modules/file/xyzexport.c
- modules/graph/Makefile.in
- modules/graph/graph_cd.c
- modules/graph/graph_cut.c
- modules/graph/graph_export_ascii.c
- modules/graph/graph_export_image.c
- modules/graph/graph_fit.c
- modules/graph/graph_fztofd.c
- modules/graph/graph_logscale.c
- modules/graph/graph_measure_period.c
- modules/graph/graph_peaks.c
- modules/graph/graph_polylevel.c
- modules/graph/graph_sfuncs.c
- modules/graph/graph_simplemech.c
- modules/graph/graph_sinebg.c
- modules/graph/graph_stats.c
- modules/graph/graph_terraces.c
- modules/process/Makefile.am ? modules/image/Makefile.am
- modules/process/Makefile.in ? modules/image/Makefile.in
- modules/process/acf2d.c ? modules/image/acf2d.c
- modules/process/angle_dist.c ? modules/image/angle_dist.c
- modules/process/arc-revolve.c ? modules/image/arc-revolve.c
- modules/process/arithmetic.c ? modules/image/arithmetic.c
- modules/process/averaging.c ? modules/image/averaging.c
- modules/process/basicops.c ? modules/image/basicops.c
- modules/process/binning.c ? modules/image/binning.c
- modules/process/blockstep.c ? modules/image/blockstep.c
- modules/process/calibrate.c ? modules/image/calibrate.c
- modules/process/classify.c ? modules/image/classify.c
- modules/process/coerce.c ? modules/image/coerce.c
- modules/process/convolution-filter.h ? modules/image/convolution-filter.h
- modules/process/convolution_filter.c ? modules/image/convolution_filter.c
- modules/process/convolve.c ? modules/image/convolve.c
- modules/process/correct_affine.c ? modules/image/correct_affine.c
- modules/process/correct_perspective.c ? modules/image/correct_perspective.c
- modules/process/crosscor.c ? modules/image/crosscor.c
- modules/process/curvature.c ? modules/image/curvature.c
- modules/process/cwt.c ? modules/image/cwt.c
- modules/process/ddd.c ? modules/image/ddd.c
- modules/process/deconvolve.c ? modules/image/deconvolve.c
- modules/process/displfield.c ? modules/image/displfield.c
- modules/process/drift.c ? modules/image/drift.c
- modules/process/dwt.c ? modules/image/dwt.c
- modules/process/dwtanisotropy.c ? modules/image/dwtanisotropy.c
- modules/process/edge.c ? modules/image/edge.c
- modules/process/entropy.c ? modules/image/entropy.c
- modules/process/extend.c ? modules/image/extend.c
- modules/process/extract_path.c ? modules/image/extract_path.c
- modules/process/facet-level.c ? modules/image/facet-level.c
- modules/process/facet_analysis.c ? modules/image/facet_analysis.c
- modules/process/facet_measure.c ? modules/image/facet_measure.c
- modules/process/fft.c ? modules/image/fft.c
- modules/process/fft_filter_1d.c ? modules/image/fft_filter_1d.c
- modules/process/fft_filter_2d.c ? modules/image/fft_filter_2d.c
- modules/process/fit-shape.c ? modules/image/fit-shape.c
- modules/process/flatten_base.c ? modules/image/flatten_base.c
- modules/process/fraccor.c ? modules/image/fraccor.c
- modules/process/fractal.c ? modules/image/fractal.c
- modules/process/freq_split.c ? modules/image/freq_split.c
- modules/process/gaussian_step.c ? modules/image/gaussian_step.c
- modules/process/good_profile.c ? modules/image/good_profile.c
- modules/process/gradient.c ? modules/image/gradient.c
- modules/process/grain_cross.c ? modules/image/grain_cross.c
- modules/process/grain_dist.c ? modules/image/grain_dist.c
- modules/process/grain_edge.c ? modules/image/grain_edge.c
- modules/process/grain_filter.c ? modules/image/grain_filter.c
- modules/process/grain_makesel.c ? modules/image/grain_makesel.c
- modules/process/grain_mark.c ? modules/image/grain_mark.c
- modules/process/grain_number.c ? modules/image/grain_number.c
- modules/process/grain_stat.c ? modules/image/grain_stat.c
- modules/process/grain_summary.c ? modules/image/grain_summary.c
- modules/process/grain_wshed.c ? modules/image/grain_wshed.c
- modules/process/hertz.c ? modules/image/hertz.c
- modules/process/hough.c ? modules/image/hough.c
- modules/process/process.c ? modules/image/image.c
- modules/process/immerse.c ? modules/image/immerse.c
- modules/process/indent_analyze.c ? modules/image/indent_analyze.c
- modules/process/laplace.c ? modules/image/laplace.c
- modules/process/latsim.c ? modules/image/latsim.c
- modules/process/level.c ? modules/image/level.c
- modules/process/level_grains.c ? modules/image/level_grains.c
- modules/process/linecorrect.c ? modules/image/linecorrect.c
- modules/process/linematch.c ? modules/image/linematch.c
- modules/process/local_contrast.c ? modules/image/local_contrast.c
- modules/process/logistic.c ? modules/image/logistic.c
- modules/process/mark_disconn.c ? modules/image/mark_disconn.c
- modules/process/mark_with.c ? modules/image/mark_with.c
- modules/process/mask_distribute.c ? modules/image/mask_distribute.c
- modules/process/mask_edt.c ? modules/image/mask_edt.c
- modules/process/mask_morph.c ? modules/image/mask_morph.c
- modules/process/mask_noisify.c ? modules/image/mask_noisify.c
- modules/process/mask_shift.c ? modules/image/mask_shift.c
- modules/process/maskcor.c ? modules/image/maskcor.c
- modules/process/maskops.c ? modules/image/maskops.c
- modules/process/mcrop.c ? modules/image/mcrop.c
- modules/process/measure_lattice.c ? modules/image/measure_lattice.c
- modules/process/median-bg.c ? modules/image/median-bg.c
- modules/process/merge.c ? modules/image/merge.c
- modules/process/mfm_field.c ? modules/image/mfm_field.c
- modules/process/mfm_findshift.c ? modules/image/mfm_findshift.c
- modules/process/mfm_recalc.c ? modules/image/mfm_recalc.c
- modules/process/mfm_shift.c ? modules/image/mfm_shift.c
- modules/process/mfmops.h ? modules/image/mfmops.h
- modules/process/multiprofile.c ? modules/image/multiprofile.c
- modules/process/neural.c ? modules/image/neural.c
- modules/process/neuraldata.h ? modules/image/neuraldata.h
- modules/process/otsu_threshold.c ? modules/image/otsu_threshold.c
- modules/process/outliers.c ? modules/image/outliers.c
- modules/process/pfm.c ? modules/image/pfm.c
- modules/process/pid.c ? modules/image/pid.c
- modules/process/polydistort.c ? modules/image/polydistort.c
- modules/process/polylevel.c ? modules/image/polylevel.c
- modules/process/presentationops.c ? modules/image/presentationops.c
- modules/process/psdf2d.c ? modules/image/psdf2d.c
- modules/process/psdf_logphi.c ? modules/image/psdf_logphi.c
- modules/process/psf-fit.c ? modules/image/psf-fit.c
- modules/process/psf.c ? modules/image/psf.c
- modules/process/ptranslate.c ? modules/image/ptranslate.c
- modules/process/rank-filter.c ? modules/image/rank-filter.c
- modules/process/rank.c ? modules/image/rank.c
- modules/process/raveraging.c ? modules/image/raveraging.c
- modules/process/relate.c ? modules/image/relate.c
- modules/process/reorder.c ? modules/image/reorder.c
- modules/process/resample.c ? modules/image/resample.c
- modules/process/rotate.c ? modules/image/rotate.c
- modules/process/scale.c ? modules/image/scale.c
- modules/process/scars.c ? modules/image/scars.c
- modules/process/semsim.c ? modules/image/semsim.c
- modules/process/shade.c ? modules/image/shade.c
- modules/process/slope_dist.c ? modules/image/slope_dist.c
- modules/process/smm.c ? modules/image/smm.c
- modules/process/smm_apply.c ? modules/image/smm_apply.c
- modules/process/sphere-revolve.c ? modules/image/sphere-revolve.c
- modules/process/stitch.c ? modules/image/stitch.c
- modules/process/straighten_path.c ? modules/image/straighten_path.c
- modules/process/terracefit.c ? modules/image/terracefit.c
- modules/process/threshold.c ? modules/image/threshold.c
- modules/process/tilt.c ? modules/image/tilt.c
- modules/process/tip_blind.c ? modules/image/tip_blind.c
- modules/process/tip_model.c ? modules/image/tip_model.c
- modules/process/tipops.c ? modules/image/tipops.c
- modules/process/tipshape.c ? modules/image/tipshape.c
- modules/process/trimmed-mean.c ? modules/image/trimmed-mean.c
- modules/process/volumize.c ? modules/image/volumize.c
- modules/process/volumize_layers.c ? modules/image/volumize_layers.c
- modules/process/wpour_mark.c ? modules/image/wpour_mark.c
- modules/process/wrapvalue.c ? modules/image/wrapvalue.c
- modules/process/xydenoise.c ? modules/image/xydenoise.c
- modules/process/xyz_channels.c ? modules/image/xyz_channels.c
- modules/process/xyzize.c ? modules/image/xyzize.c
- modules/process/zero_crossing.c ? modules/image/zero_crossing.c
- modules/process/preview.h ? modules/preview.h
- modules/pygwy/Makefile.in
- modules/synth/Makefile.am
- modules/synth/Makefile.in
- modules/synth/annealing.c
- modules/synth/ballistic.c
- + modules/synth/chaining.c
- modules/synth/columnar.c
- modules/synth/cpde.c
- modules/synth/deposit.c
- modules/synth/diffusion.c
- modules/synth/discs.c
- modules/synth/domains.c
- modules/synth/dunes.c
- modules/synth/fbrownian.c
- modules/synth/fibres.c
- modules/synth/fourier.c
- modules/synth/lattice.c
- modules/synth/linenoise.c
- modules/synth/mfm_current.c
- modules/synth/mfm_parallel.c
- modules/synth/noise.c
- modules/synth/objects.c
- modules/synth/pattern.c
- modules/synth/phases.c
- modules/synth/pileup.c
- modules/synth/plateaus.c
- modules/synth/residue.c
- modules/synth/roddeposit.c
- modules/synth/synth.c
- modules/synth/waves.c
- modules/synth/wetfront.c
- modules/tools/Makefile.in
- modules/tools/corrlen.c
- modules/tools/crop.c
- modules/tools/grainmeasure.c
- modules/tools/icolorange.c
- modules/tools/linestats.c
- modules/tools/maskedit.c
- modules/tools/profile.c
- modules/tools/readvalue.c
- modules/tools/roughness.c
- modules/tools/rprofile.c
- modules/tools/selectionmanager.c
- modules/tools/sfunctions.c
- modules/tools/stats.c
- modules/volume/Makefile.in
- modules/volume/volume_1dfft.c
- modules/volume/volume_addframe.c
- modules/volume/volume_arithmetic.c
- modules/volume/volume_asciiexport.c
- modules/volume/volume_calibrate.c
- modules/volume/volume_cluster.c
- modules/volume/volume_crop.c
- modules/volume/volume_drift.c
- modules/volume/volume_equiplane.c
- modules/volume/volume_fdfit.c
- modules/volume/volume_flattenbase.c
- modules/volume/volume_lawnize.c
- modules/volume/volume_linelevel.c
- modules/volume/volume_linestat.c
- modules/volume/volume_localdetect.c
- modules/volume/volume_mfmrecalc.c
- modules/volume/volume_planestat.c
- modules/volume/volume_psf.c
- modules/volume/volume_removeframe.c
- modules/volume/volume_rephase.c
- modules/volume/volume_scars.c
- modules/volume/volume_slice.c
- modules/volume/volume_strayfield.c
- modules/volume/volume_swaxes.c
- modules/volume/volume_xyarithmetic.c
- modules/volume/volume_xystitch.c
- modules/volume/volume_zcal.c
- modules/volume/volume_zposlevel.c
- modules/xyz/Makefile.am
- modules/xyz/Makefile.in
- modules/xyz/xyz.c
- modules/xyz/xyz_crop.c
- + modules/xyz/xyz_fft.c
- modules/xyz/xyz_level.c
- modules/xyz/xyz_merge.c
- modules/xyz/xyz_raster.c
- modules/xyz/xyz_reduce.c
- modules/xyz/xyz_relate.c
- modules/xyz/xyz_split.c
- + modules/xyz/xyz_tcrop.c
- modules/xyz/xyz_tcut.c
- modules/xyz/xyz_valueops.c
- modules/xyz/xyz_volumize.c
- modules/xyz/xyz_zdrift.c
- + pixmaps/16x16/actions/gtk-quit.png
- pixmaps/Makefile.am
- pixmaps/Makefile.in
- pixmaps/src/Makefile.in
- po/Makefile.in.in
- po/POTFILES.in
- po/cs.gmo
- po/cs.po
- po/de.gmo
- po/de.po
- po/en_GB.gmo
- po/en_GB.po
- po/es.gmo
- po/es.po
- po/fr.gmo
- po/fr.po
- po/gwyddion.pot
- po/it.gmo
- po/it.po
- po/ja.gmo
- po/ja.po
- po/ko.gmo
- po/ko.po
- po/pt_BR.gmo
- po/pt_BR.po
- + po/remove-potcdate.sed
- ? po/remove-potcdate.sin
- po/ru.gmo
- po/ru.po
- tests/Makefile.in
- tests/graph-curve-model.c
- tests/nield.c
- tests/scatter.c
- tests/test-list.c
- tests/test-list.h
- tests/test-list.txt
- thumbnailer/Makefile.in
- thumbnailer/gwyddion3-thumbnailer.c
- utils/Makefile.in
- utils/dump-modules.c
- utils/update-langs.py


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/gwyddion/-/compare/8ee8fead2184760c907f551e7fb173b9668b845a...0abc79371ad7126961ce9a5e1eb5de3bda9bb3e7

-- 
View it on GitLab: https://salsa.debian.org/med-team/gwyddion/-/compare/8ee8fead2184760c907f551e7fb173b9668b845a...0abc79371ad7126961ce9a5e1eb5de3bda9bb3e7
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From gitlab at salsa.debian.org  Thu Jul  2 18:07:19 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 17:07:19 +0000
Subject: [med-svn] [Git][med-team/gwyddion][pristine-tar] pristine-tar data
 for gwyddion_3.11.orig.tar.xz
Message-ID: <6a469ac7a6ec5_55bfcdb44135556@godard.mail>



Andreas Tille pushed to branch pristine-tar at Debian Med / gwyddion


Commits:
4dd41ca6 by Andreas Tille at 2026-07-02T17:08:30+02:00
pristine-tar data for gwyddion_3.11.orig.tar.xz

- - - - -


3 changed files:

- + gwyddion_3.11.orig.tar.xz.asc
- + gwyddion_3.11.orig.tar.xz.delta
- + gwyddion_3.11.orig.tar.xz.id


Changes:

=====================================
gwyddion_3.11.orig.tar.xz.asc
=====================================
@@ -0,0 +1,7 @@
+-----BEGIN PGP SIGNATURE-----
+
+iHUEABYKAB0WIQR3gXqRQUQpJt3j5eVtQYLngjLYSwUCaj00hAAKCRBtQYLngjLY
+SzeuAQDXyh3oOV+WPp8S8Pcu8gASx1916ZYvgmAQ2HwX1wFl1wEA3PrpaJDet/z7
+vhJRc08i1Tdb5gYWN5sCfhoBSvHkhQM=
+=AOaY
+-----END PGP SIGNATURE-----


=====================================
gwyddion_3.11.orig.tar.xz.delta
=====================================
Binary files /dev/null and b/gwyddion_3.11.orig.tar.xz.delta differ


=====================================
gwyddion_3.11.orig.tar.xz.id
=====================================
@@ -0,0 +1 @@
+f770a45048d96aa0289a77beece4a50924c13682



View it on GitLab: https://salsa.debian.org/med-team/gwyddion/-/commit/4dd41ca67d85ef5118f1f1c28c90fa6a4f2c0215

-- 
View it on GitLab: https://salsa.debian.org/med-team/gwyddion/-/commit/4dd41ca67d85ef5118f1f1c28c90fa6a4f2c0215
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From gitlab at salsa.debian.org  Thu Jul  2 18:07:21 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 17:07:21 +0000
Subject: [med-svn] [Git][med-team/gwyddion] Pushed new tag debian/3.11-1
Message-ID: <6a469ac9d96e7_55b15eb08d8413584b@godard.mail>



Andreas Tille pushed new tag debian/3.11-1 at Debian Med / gwyddion

-- 
View it on GitLab: https://salsa.debian.org/med-team/gwyddion/-/tree/debian/3.11-1
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From gitlab at salsa.debian.org  Thu Jul  2 18:07:26 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 17:07:26 +0000
Subject: [med-svn] [Git][med-team/gwyddion][upstream] New upstream version
 3.11
Message-ID: <6a469ace32066_55b82c2ed441361d7@godard.mail>



Andreas Tille pushed to branch upstream at Debian Med / gwyddion


Commits:
64abe3be by Andreas Tille at 2026-07-02T17:08:16+02:00
New upstream version 3.11
- - - - -


666 changed files:

- Makefile.in
- NEWS
- aclocal.m4
- autogen.sh
- build-aux/Makefile.in
- build-aux/compile
- build-aux/config.rpath
- build-aux/depcomp
- build-aux/install-sh
- build-aux/missing
- build-aux/tap-driver.sh
- build-aux/test-driver
- configure
- configure.ac
- data/Makefile.in
- data/glmaterials/Makefile.in
- data/gradients/Makefile.in
- data/gwyddion3.spec.in
- data/gwyddion3.vim
- data/net.gwyddion.Gwyddion3.appdata.xml
- devel-docs/Makefile.in
- devel-docs/libgwyapp/Makefile.in
- + devel-docs/libgwyapp/html/GwyAppDataWindow.html
- devel-docs/libgwyapp/html/GwyAppGraphWindow.html
- devel-docs/libgwyapp/html/GwyAppImageWindow.html
- devel-docs/libgwyapp/html/GwyDataChooser.html
- devel-docs/libgwyapp/html/GwyDialog.html
- + devel-docs/libgwyapp/html/GwyFunctionList.html
- devel-docs/libgwyapp/html/GwyLogBrowser.html
- devel-docs/libgwyapp/html/GwyParamDef.html
- devel-docs/libgwyapp/html/GwyParamResource.html
- devel-docs/libgwyapp/html/GwyParamTable.html
- devel-docs/libgwyapp/html/GwyParams.html
- devel-docs/libgwyapp/html/GwyPlainTool.html
- devel-docs/libgwyapp/html/GwyResourceEditor.html
- devel-docs/libgwyapp/html/GwyResultsExport.html
- devel-docs/libgwyapp/html/GwyTool.html
- devel-docs/libgwyapp/html/ModuleTutorial.html
- devel-docs/libgwyapp/html/annotation-glossary.html
- devel-docs/libgwyapp/html/api-index-all.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-beyond.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-file.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-graph.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-install.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-minimal.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-overview.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-process.html
- devel-docs/libgwyapp/html/gwymodule-tutorial-tool.html
- devel-docs/libgwyapp/html/index.html
- devel-docs/libgwyapp/html/libgwyapp-Application.html
- devel-docs/libgwyapp/html/libgwyapp-Curve-map-modules.html
- devel-docs/libgwyapp/html/libgwyapp-Data-browser.html
- devel-docs/libgwyapp/html/libgwyapp-File-module-utils.html
- devel-docs/libgwyapp/html/libgwyapp-File-modules.html
- devel-docs/libgwyapp/html/libgwyapp-Graph-modules.html
- devel-docs/libgwyapp/html/libgwyapp-module-process.html ? devel-docs/libgwyapp/html/libgwyapp-Image-modules.html
- devel-docs/libgwyapp/html/libgwyapp-Log.html
- devel-docs/libgwyapp/html/libgwyapp-Module-browser.html
- devel-docs/libgwyapp/html/libgwyapp-Module-loader.html
- devel-docs/libgwyapp/html/libgwyapp-Module-utilties.html
- + devel-docs/libgwyapp/html/libgwyapp-Recent-functions.html
- devel-docs/libgwyapp/html/libgwyapp-Synth-module-utils.html
- devel-docs/libgwyapp/html/libgwyapp-Synthetic-data-modules.html
- devel-docs/libgwyapp/html/libgwyapp-Tool-modules.html
- devel-docs/libgwyapp/html/libgwyapp-Volume-data-modules.html
- devel-docs/libgwyapp/html/libgwyapp-XYZ-data-modules.html
- devel-docs/libgwyapp/html/libgwyapp-data.html
- devel-docs/libgwyapp/html/libgwyapp-filelist.html
- devel-docs/libgwyapp/html/libgwyapp-menu.html
- devel-docs/libgwyapp/html/libgwyapp-modules.html
- devel-docs/libgwyapp/html/libgwyapp-settings.html
- devel-docs/libgwyapp/html/libgwyapp-utils.html
- devel-docs/libgwyapp/html/libgwyapp-wait.html
- devel-docs/libgwyapp/html/libgwyapp.devhelp2
- devel-docs/libgwyapp/libgwyapp-docs.xml
- devel-docs/libgwyddion/Makefile.in
- devel-docs/libgwyddion/html/DataProcess.html
- devel-docs/libgwyddion/html/GwyBrick.html
- devel-docs/libgwyddion/html/GwyCDLine.html
- devel-docs/libgwyddion/html/GwyField.html
- devel-docs/libgwyddion/html/GwyGLMaterial.html
- devel-docs/libgwyddion/html/GwyGradient.html
- devel-docs/libgwyddion/html/GwyGrainValue.html
- devel-docs/libgwyddion/html/GwyLine.html
- devel-docs/libgwyddion/html/GwyNield.html
- devel-docs/libgwyddion/html/GwyTriangulation.html
- devel-docs/libgwyddion/html/api-index-all.html
- devel-docs/libgwyddion/html/index.html
- devel-docs/libgwyddion/html/libgwyddion-Correction.html
- devel-docs/libgwyddion/html/libgwyddion-Distance-transform.html
- devel-docs/libgwyddion/html/libgwyddion-Enums.html
- devel-docs/libgwyddion/html/libgwyddion-Fractals.html
- devel-docs/libgwyddion/html/libgwyddion-Grain-quantities.html
- devel-docs/libgwyddion/html/libgwyddion-grains.html ? devel-docs/libgwyddion/html/libgwyddion-Grains.html
- devel-docs/libgwyddion/html/libgwyddion-Serialisation-utils.html
- devel-docs/libgwyddion/html/libgwyddion-Statistics.html
- devel-docs/libgwyddion/html/libgwyddion-Version.html
- devel-docs/libgwyddion/html/libgwyddion-Watershed.html
- devel-docs/libgwyddion/html/libgwyddion-filters.html
- devel-docs/libgwyddion/html/libgwyddion.devhelp2
- devel-docs/libgwyui/Makefile.am
- devel-docs/libgwyui/Makefile.in
- devel-docs/libgwyui/html/ColorWidgets.html
- devel-docs/libgwyui/html/GraphWidgets.html
- devel-docs/libgwyui/html/GwyAdjustBar.html
- devel-docs/libgwyui/html/GwyCellRendererGradient.html
- devel-docs/libgwyui/html/GwyColorAxis.html
- devel-docs/libgwyui/html/GwyColorButton.html
- devel-docs/libgwyui/html/GwyColorDialog.html
- devel-docs/libgwyui/html/GwyColorEditor.html
- devel-docs/libgwyui/html/GwyColorSwatch.html
- devel-docs/libgwyui/html/GwyColorWheel.html
- devel-docs/libgwyui/html/GwyCorrelTable.html
- devel-docs/libgwyui/html/GwyDataView.html
- devel-docs/libgwyui/html/GwyDataViewLayer.html
- devel-docs/libgwyui/html/GwyDataWindow.html
- devel-docs/libgwyui/html/GwyFitTable.html
- devel-docs/libgwyui/html/GwyGradientSwatch.html
- devel-docs/libgwyui/html/GwyGraphArea.html
- devel-docs/libgwyui/html/GwyGraphAxis.html
- devel-docs/libgwyui/html/GwyGraphCorner.html
- devel-docs/libgwyui/html/GwyGraphCurveDialog.html
- devel-docs/libgwyui/html/GwyGraphCurveModel.html
- devel-docs/libgwyui/html/GwyGraphCurves.html
- devel-docs/libgwyui/html/GwyGraphModel.html
- devel-docs/libgwyui/html/GwyGraphWindow.html
- devel-docs/libgwyui/html/GwyInventoryStore.html
- devel-docs/libgwyui/html/GwyNullStore.html
- devel-docs/libgwyui/html/GwyRuler.html
- devel-docs/libgwyui/html/GwySensitivityGroup.html
- devel-docs/libgwyui/html/GwyShader.html
- + devel-docs/libgwyui/html/GwyShrinkWrap.html
- devel-docs/libgwyui/html/GwyVectorLayer.html
- devel-docs/libgwyui/html/WidgetUtilities.html
- devel-docs/libgwyui/html/api-index-all.html
- + devel-docs/libgwyui/html/gtk-quit.png
- devel-docs/libgwyui/html/index.html
- + devel-docs/libgwyui/html/libgwyui-Cairo-drawing-utils.html
- devel-docs/libgwyui/html/libgwyui-Checkboxes.html
- devel-docs/libgwyui/html/libgwyui-Combo-boxes.html
- devel-docs/libgwyui/html/libgwyui-GwyGrainValueTreeView.html
- devel-docs/libgwyui/html/libgwyui-Icons.html
- devel-docs/libgwyui/html/libgwyui-Option-menus.html
- devel-docs/libgwyui/html/libgwyui-Pixbuf-rendering.html
- devel-docs/libgwyui/html/libgwyui-Radiobuttons.html
- devel-docs/libgwyui/html/libgwyui-Widget-utilities.html
- devel-docs/libgwyui/html/libgwyui-gwyui.html
- devel-docs/libgwyui/html/libgwyui.devhelp2
- devel-docs/libgwyui/libgwyui-docs.xml
- gwyddion/Makefile.am
- gwyddion/Makefile.in
- gwyddion/about.c
- + gwyddion/file-handling.c
- gwyddion/gwyddion.c
- gwyddion/gwyddion.h
- gwyddion/release.h
- + gwyddion/shortcut-editor.c
- gwyddion/splash.c
- gwyddion/toolbox-editor.c
- gwyddion/toolbox-spec.c
- gwyddion/toolbox.c
- gwyddion/toolbox.h
- gwyddion/toolbox.xml
- gwyddion3.spec
- libgwyapp/GwyApp-3.10.gir ? libgwyapp/GwyApp-3.11.gir
- libgwyapp/Makefile.am
- libgwyapp/Makefile.in
- + libgwyapp/app-data-window.c
- + libgwyapp/app-data-window.h
- libgwyapp/app-graph-window.c
- libgwyapp/app-graph-window.h
- libgwyapp/app-image-window.c
- libgwyapp/app-image-window.h
- libgwyapp/app.c
- libgwyapp/app.h
- libgwyapp/change-preview-cmap.c
- libgwyapp/change-preview-volume.c
- libgwyapp/change-preview-xyz.c
- libgwyapp/data-browser--gui.c
- libgwyapp/data-browser-internal.h
- libgwyapp/data-browser.c
- libgwyapp/data-browser.h
- libgwyapp/dialog.c
- libgwyapp/dialog.h
- libgwyapp/file-chooser.c
- libgwyapp/file-chooser.h
- libgwyapp/file.c
- libgwyapp/filelist.c
- + libgwyapp/function-list.c
- + libgwyapp/function-list.h
- libgwyapp/glmaterial-editor.h
- libgwyapp/gradient-editor.c
- libgwyapp/gwyapp.c
- libgwyapp/gwyapp.h
- libgwyapp/gwyplaintool.c
- libgwyapp/gwyplaintool.h
- libgwyapp/gwytool.c
- libgwyapp/gwytool.h
- libgwyapp/help.c
- libgwyapp/log-browser.c
- libgwyapp/log.c
- libgwyapp/menu-recent-files.c
- libgwyapp/menu.c
- libgwyapp/menu.h
- libgwyapp/meta-browser.c
- libgwyapp/module-browser.h
- libgwyapp/module-cmap.c
- libgwyapp/module-cmap.h
- libgwyapp/module-process.c ? libgwyapp/module-image.c
- libgwyapp/module-process.h ? libgwyapp/module-image.h
- libgwyapp/module-internal.h
- libgwyapp/module-loader.c
- libgwyapp/module-loader.h
- libgwyapp/module-utils-synth.h
- libgwyapp/module-utils.c
- libgwyapp/module-volume.c
- libgwyapp/module-volume.h
- libgwyapp/module-xyz.c
- libgwyapp/module-xyz.h
- libgwyapp/param-def.c
- libgwyapp/param-def.h
- libgwyapp/param-internal.h
- libgwyapp/param-table.c
- libgwyapp/param-table.h
- + libgwyapp/recent-funcs.c
- modules/synth/preview.h ? libgwyapp/recent-funcs.h
- libgwyapp/resource-editor.c
- libgwyapp/resource-editor.h
- libgwyapp/results-export.h
- libgwyapp/sanity.h
- libgwyapp/settings.c
- libgwyapp/wait.c
- libgwyddion/Gwyddion-3.10.gir ? libgwyddion/Gwyddion-3.11.gir
- libgwyddion/Makefile.in
- libgwyddion/brick.c
- libgwyddion/brick.h
- libgwyddion/cdline.h
- libgwyddion/dict.h
- libgwyddion/distance-transform.c
- libgwyddion/enums.c
- libgwyddion/field.c
- libgwyddion/field.h
- libgwyddion/filters--convdeconv.c
- libgwyddion/filters.c
- libgwyddion/gl-material.h
- libgwyddion/gradient.h
- libgwyddion/grain-quantities.c
- libgwyddion/grain-quantities.h
- libgwyddion/grain-value.c
- libgwyddion/grain-value.h
- libgwyddion/grains.c
- libgwyddion/internal.h
- libgwyddion/inttrans.c
- libgwyddion/lawn.h
- libgwyddion/line.c
- libgwyddion/line.h
- libgwyddion/nield.c
- libgwyddion/nield.h
- libgwyddion/nl-fitter.c
- libgwyddion/scatter.c
- libgwyddion/scatter.h
- libgwyddion/selection.h
- libgwyddion/serializable-utils.h
- libgwyddion/triangulation.h
- libgwyddion/types.c
- libgwyddion/utils.h
- libgwyddion/version.h
- libgwyddion/watershed.c
- libgwyddion/xyz.h
- libgwyui/GwyUI-3.10.gir ? libgwyui/GwyUI-3.11.gir
- libgwyui/Makefile.am
- libgwyui/Makefile.in
- libgwyui/adjust-bar.c
- libgwyui/adjust-bar.h
- libgwyui/cairo-utils.c
- libgwyui/cairo-utils.h
- libgwyui/color-axis.h
- libgwyui/color-button.c
- libgwyui/color-button.h
- libgwyui/color-dialog.c
- libgwyui/color-dialog.h
- libgwyui/color-editor.c
- libgwyui/color-editor.h
- libgwyui/color-swatch.h
- libgwyui/color-wheel.c
- libgwyui/color-wheel.h
- libgwyui/correl-table.h
- libgwyui/data-view-layer.h
- libgwyui/data-view.c
- libgwyui/data-view.h
- libgwyui/data-window.c
- libgwyui/data-window.h
- libgwyui/fit-table.c
- libgwyui/fit-table.h
- libgwyui/gradient-swatch.h
- libgwyui/graph-area.h
- libgwyui/graph-axis-dialog.c
- libgwyui/graph-axis.h
- libgwyui/graph-corner.h
- libgwyui/graph-curve-dialog.c
- libgwyui/graph-curve-model.c
- libgwyui/graph-curve-model.h
- libgwyui/graph-curves.h
- libgwyui/graph-internal.h
- libgwyui/graph-key-dialog.c
- libgwyui/graph-key.c
- libgwyui/graph-model.h
- libgwyui/graph-utils.c
- libgwyui/graph-utils.h
- libgwyui/graph-window-measure-dialog.c
- libgwyui/graph-window.c
- libgwyui/graph-window.h
- libgwyui/gwyglwindow.c
- libgwyui/gwyglwindow.h
- libgwyui/gwyui.h
- libgwyui/icons.c
- libgwyui/inventory-store.h
- libgwyui/layer-line.c
- libgwyui/layer-point.c
- libgwyui/null-store.h
- libgwyui/option-menus.c
- libgwyui/pixbuf-render.h
- libgwyui/ruler.h
- libgwyui/sci-text.c
- libgwyui/shader.h
- + libgwyui/shrink-wrap.c
- + libgwyui/shrink-wrap.h
- libgwyui/types.c
- libgwyui/types.h
- libgwyui/utils.c
- libgwyui/utils.h
- libgwyui/vector-layer.c
- libgwyui/vector-layer.h
- m4/Makefile.am
- m4/Makefile.in
- + m4/gettext-build-to-host.m4
- + m4/gettext-host-cpu-c-abi.m4
- m4/iconv.m4 ? m4/gettext-iconv.m4
- + m4/gettext-intlmacosx.m4
- + m4/gettext-lib-ld.m4
- + m4/gettext-lib-link.m4
- + m4/gettext-lib-prefix.m4
- m4/nls.m4 ? m4/gettext-nls.m4
- m4/po.m4 ? m4/gettext-po.m4
- m4/progtest.m4 ? m4/gettext-progtest.m4
- m4/gettext.m4
- modules/Makefile.am
- modules/Makefile.in
- modules/cmap/Makefile.in
- modules/cmap/cmap_align.c
- modules/cmap/cmap_asciiexport.c
- modules/cmap/cmap_crop.c
- modules/cmap/cmap_cutter.c
- modules/cmap/cmap_extractcurve.c
- modules/cmap/cmap_fdfit.c
- modules/cmap/cmap_fit.c
- modules/cmap/cmap_fztofd.c
- modules/cmap/cmap_linestat.c
- modules/cmap/cmap_lockin.c
- modules/cmap/cmap_polylevel.c
- modules/cmap/cmap_possearch.c
- modules/cmap/cmap_rename.c
- modules/cmap/cmap_simplemech.c
- modules/cmap/cmap_sinebg.c
- modules/cmap/cmap_volumize.c
- modules/file/Makefile.in
- modules/file/accurell.c
- modules/file/asciiexport.c
- modules/file/formats3d.c
- modules/file/gwyfile.c
- modules/file/gxyzffile.c
- modules/file/hdf5/Makefile.in
- modules/file/hdf5/fusionscope.c
- modules/file/hdf5/gxsm4.c
- modules/file/hdf5/veloxemd.c
- modules/file/hdrimage.c
- modules/file/imgexport.c
- modules/file/nmmxyz.c
- modules/file/openexr.cc
- modules/file/pixmap.c
- modules/file/rawfile.c
- modules/file/rawgraph.c
- modules/file/rmitmd.c
- modules/file/xyzexport.c
- modules/graph/Makefile.in
- modules/graph/graph_cd.c
- modules/graph/graph_cut.c
- modules/graph/graph_export_ascii.c
- modules/graph/graph_export_image.c
- modules/graph/graph_fit.c
- modules/graph/graph_fztofd.c
- modules/graph/graph_logscale.c
- modules/graph/graph_measure_period.c
- modules/graph/graph_peaks.c
- modules/graph/graph_polylevel.c
- modules/graph/graph_sfuncs.c
- modules/graph/graph_simplemech.c
- modules/graph/graph_sinebg.c
- modules/graph/graph_stats.c
- modules/graph/graph_terraces.c
- modules/process/Makefile.am ? modules/image/Makefile.am
- modules/process/Makefile.in ? modules/image/Makefile.in
- modules/process/acf2d.c ? modules/image/acf2d.c
- modules/process/angle_dist.c ? modules/image/angle_dist.c
- modules/process/arc-revolve.c ? modules/image/arc-revolve.c
- modules/process/arithmetic.c ? modules/image/arithmetic.c
- modules/process/averaging.c ? modules/image/averaging.c
- modules/process/basicops.c ? modules/image/basicops.c
- modules/process/binning.c ? modules/image/binning.c
- modules/process/blockstep.c ? modules/image/blockstep.c
- modules/process/calibrate.c ? modules/image/calibrate.c
- modules/process/classify.c ? modules/image/classify.c
- modules/process/coerce.c ? modules/image/coerce.c
- modules/process/convolution-filter.h ? modules/image/convolution-filter.h
- modules/process/convolution_filter.c ? modules/image/convolution_filter.c
- modules/process/convolve.c ? modules/image/convolve.c
- modules/process/correct_affine.c ? modules/image/correct_affine.c
- modules/process/correct_perspective.c ? modules/image/correct_perspective.c
- modules/process/crosscor.c ? modules/image/crosscor.c
- modules/process/curvature.c ? modules/image/curvature.c
- modules/process/cwt.c ? modules/image/cwt.c
- modules/process/ddd.c ? modules/image/ddd.c
- modules/process/deconvolve.c ? modules/image/deconvolve.c
- modules/process/displfield.c ? modules/image/displfield.c
- modules/process/drift.c ? modules/image/drift.c
- modules/process/dwt.c ? modules/image/dwt.c
- modules/process/dwtanisotropy.c ? modules/image/dwtanisotropy.c
- modules/process/edge.c ? modules/image/edge.c
- modules/process/entropy.c ? modules/image/entropy.c
- modules/process/extend.c ? modules/image/extend.c
- modules/process/extract_path.c ? modules/image/extract_path.c
- modules/process/facet-level.c ? modules/image/facet-level.c
- modules/process/facet_analysis.c ? modules/image/facet_analysis.c
- modules/process/facet_measure.c ? modules/image/facet_measure.c
- modules/process/fft.c ? modules/image/fft.c
- modules/process/fft_filter_1d.c ? modules/image/fft_filter_1d.c
- modules/process/fft_filter_2d.c ? modules/image/fft_filter_2d.c
- modules/process/fit-shape.c ? modules/image/fit-shape.c
- modules/process/flatten_base.c ? modules/image/flatten_base.c
- modules/process/fraccor.c ? modules/image/fraccor.c
- modules/process/fractal.c ? modules/image/fractal.c
- modules/process/freq_split.c ? modules/image/freq_split.c
- modules/process/gaussian_step.c ? modules/image/gaussian_step.c
- modules/process/good_profile.c ? modules/image/good_profile.c
- modules/process/gradient.c ? modules/image/gradient.c
- modules/process/grain_cross.c ? modules/image/grain_cross.c
- modules/process/grain_dist.c ? modules/image/grain_dist.c
- modules/process/grain_edge.c ? modules/image/grain_edge.c
- modules/process/grain_filter.c ? modules/image/grain_filter.c
- modules/process/grain_makesel.c ? modules/image/grain_makesel.c
- modules/process/grain_mark.c ? modules/image/grain_mark.c
- modules/process/grain_number.c ? modules/image/grain_number.c
- modules/process/grain_stat.c ? modules/image/grain_stat.c
- modules/process/grain_summary.c ? modules/image/grain_summary.c
- modules/process/grain_wshed.c ? modules/image/grain_wshed.c
- modules/process/hertz.c ? modules/image/hertz.c
- modules/process/hough.c ? modules/image/hough.c
- modules/process/process.c ? modules/image/image.c
- modules/process/immerse.c ? modules/image/immerse.c
- modules/process/indent_analyze.c ? modules/image/indent_analyze.c
- modules/process/laplace.c ? modules/image/laplace.c
- modules/process/latsim.c ? modules/image/latsim.c
- modules/process/level.c ? modules/image/level.c
- modules/process/level_grains.c ? modules/image/level_grains.c
- modules/process/linecorrect.c ? modules/image/linecorrect.c
- modules/process/linematch.c ? modules/image/linematch.c
- modules/process/local_contrast.c ? modules/image/local_contrast.c
- modules/process/logistic.c ? modules/image/logistic.c
- modules/process/mark_disconn.c ? modules/image/mark_disconn.c
- modules/process/mark_with.c ? modules/image/mark_with.c
- modules/process/mask_distribute.c ? modules/image/mask_distribute.c
- modules/process/mask_edt.c ? modules/image/mask_edt.c
- modules/process/mask_morph.c ? modules/image/mask_morph.c
- modules/process/mask_noisify.c ? modules/image/mask_noisify.c
- modules/process/mask_shift.c ? modules/image/mask_shift.c
- modules/process/maskcor.c ? modules/image/maskcor.c
- modules/process/maskops.c ? modules/image/maskops.c
- modules/process/mcrop.c ? modules/image/mcrop.c
- modules/process/measure_lattice.c ? modules/image/measure_lattice.c
- modules/process/median-bg.c ? modules/image/median-bg.c
- modules/process/merge.c ? modules/image/merge.c
- modules/process/mfm_field.c ? modules/image/mfm_field.c
- modules/process/mfm_findshift.c ? modules/image/mfm_findshift.c
- modules/process/mfm_recalc.c ? modules/image/mfm_recalc.c
- modules/process/mfm_shift.c ? modules/image/mfm_shift.c
- modules/process/mfmops.h ? modules/image/mfmops.h
- modules/process/multiprofile.c ? modules/image/multiprofile.c
- modules/process/neural.c ? modules/image/neural.c
- modules/process/neuraldata.h ? modules/image/neuraldata.h
- modules/process/otsu_threshold.c ? modules/image/otsu_threshold.c
- modules/process/outliers.c ? modules/image/outliers.c
- modules/process/pfm.c ? modules/image/pfm.c
- modules/process/pid.c ? modules/image/pid.c
- modules/process/polydistort.c ? modules/image/polydistort.c
- modules/process/polylevel.c ? modules/image/polylevel.c
- modules/process/presentationops.c ? modules/image/presentationops.c
- modules/process/psdf2d.c ? modules/image/psdf2d.c
- modules/process/psdf_logphi.c ? modules/image/psdf_logphi.c
- modules/process/psf-fit.c ? modules/image/psf-fit.c
- modules/process/psf.c ? modules/image/psf.c
- modules/process/ptranslate.c ? modules/image/ptranslate.c
- modules/process/rank-filter.c ? modules/image/rank-filter.c
- modules/process/rank.c ? modules/image/rank.c
- modules/process/raveraging.c ? modules/image/raveraging.c
- modules/process/relate.c ? modules/image/relate.c
- modules/process/reorder.c ? modules/image/reorder.c
- modules/process/resample.c ? modules/image/resample.c
- modules/process/rotate.c ? modules/image/rotate.c
- modules/process/scale.c ? modules/image/scale.c
- modules/process/scars.c ? modules/image/scars.c
- modules/process/semsim.c ? modules/image/semsim.c
- modules/process/shade.c ? modules/image/shade.c
- modules/process/slope_dist.c ? modules/image/slope_dist.c
- modules/process/smm.c ? modules/image/smm.c
- modules/process/smm_apply.c ? modules/image/smm_apply.c
- modules/process/sphere-revolve.c ? modules/image/sphere-revolve.c
- modules/process/stitch.c ? modules/image/stitch.c
- modules/process/straighten_path.c ? modules/image/straighten_path.c
- modules/process/terracefit.c ? modules/image/terracefit.c
- modules/process/threshold.c ? modules/image/threshold.c
- modules/process/tilt.c ? modules/image/tilt.c
- modules/process/tip_blind.c ? modules/image/tip_blind.c
- modules/process/tip_model.c ? modules/image/tip_model.c
- modules/process/tipops.c ? modules/image/tipops.c
- modules/process/tipshape.c ? modules/image/tipshape.c
- modules/process/trimmed-mean.c ? modules/image/trimmed-mean.c
- modules/process/volumize.c ? modules/image/volumize.c
- modules/process/volumize_layers.c ? modules/image/volumize_layers.c
- modules/process/wpour_mark.c ? modules/image/wpour_mark.c
- modules/process/wrapvalue.c ? modules/image/wrapvalue.c
- modules/process/xydenoise.c ? modules/image/xydenoise.c
- modules/process/xyz_channels.c ? modules/image/xyz_channels.c
- modules/process/xyzize.c ? modules/image/xyzize.c
- modules/process/zero_crossing.c ? modules/image/zero_crossing.c
- modules/process/preview.h ? modules/preview.h
- modules/pygwy/Makefile.in
- modules/synth/Makefile.am
- modules/synth/Makefile.in
- modules/synth/annealing.c
- modules/synth/ballistic.c
- + modules/synth/chaining.c
- modules/synth/columnar.c
- modules/synth/cpde.c
- modules/synth/deposit.c
- modules/synth/diffusion.c
- modules/synth/discs.c
- modules/synth/domains.c
- modules/synth/dunes.c
- modules/synth/fbrownian.c
- modules/synth/fibres.c
- modules/synth/fourier.c
- modules/synth/lattice.c
- modules/synth/linenoise.c
- modules/synth/mfm_current.c
- modules/synth/mfm_parallel.c
- modules/synth/noise.c
- modules/synth/objects.c
- modules/synth/pattern.c
- modules/synth/phases.c
- modules/synth/pileup.c
- modules/synth/plateaus.c
- modules/synth/residue.c
- modules/synth/roddeposit.c
- modules/synth/synth.c
- modules/synth/waves.c
- modules/synth/wetfront.c
- modules/tools/Makefile.in
- modules/tools/corrlen.c
- modules/tools/crop.c
- modules/tools/grainmeasure.c
- modules/tools/icolorange.c
- modules/tools/linestats.c
- modules/tools/maskedit.c
- modules/tools/profile.c
- modules/tools/readvalue.c
- modules/tools/roughness.c
- modules/tools/rprofile.c
- modules/tools/selectionmanager.c
- modules/tools/sfunctions.c
- modules/tools/stats.c
- modules/volume/Makefile.in
- modules/volume/volume_1dfft.c
- modules/volume/volume_addframe.c
- modules/volume/volume_arithmetic.c
- modules/volume/volume_asciiexport.c
- modules/volume/volume_calibrate.c
- modules/volume/volume_cluster.c
- modules/volume/volume_crop.c
- modules/volume/volume_drift.c
- modules/volume/volume_equiplane.c
- modules/volume/volume_fdfit.c
- modules/volume/volume_flattenbase.c
- modules/volume/volume_lawnize.c
- modules/volume/volume_linelevel.c
- modules/volume/volume_linestat.c
- modules/volume/volume_localdetect.c
- modules/volume/volume_mfmrecalc.c
- modules/volume/volume_planestat.c
- modules/volume/volume_psf.c
- modules/volume/volume_removeframe.c
- modules/volume/volume_rephase.c
- modules/volume/volume_scars.c
- modules/volume/volume_slice.c
- modules/volume/volume_strayfield.c
- modules/volume/volume_swaxes.c
- modules/volume/volume_xyarithmetic.c
- modules/volume/volume_xystitch.c
- modules/volume/volume_zcal.c
- modules/volume/volume_zposlevel.c
- modules/xyz/Makefile.am
- modules/xyz/Makefile.in
- modules/xyz/xyz.c
- modules/xyz/xyz_crop.c
- + modules/xyz/xyz_fft.c
- modules/xyz/xyz_level.c
- modules/xyz/xyz_merge.c
- modules/xyz/xyz_raster.c
- modules/xyz/xyz_reduce.c
- modules/xyz/xyz_relate.c
- modules/xyz/xyz_split.c
- + modules/xyz/xyz_tcrop.c
- modules/xyz/xyz_tcut.c
- modules/xyz/xyz_valueops.c
- modules/xyz/xyz_volumize.c
- modules/xyz/xyz_zdrift.c
- + pixmaps/16x16/actions/gtk-quit.png
- pixmaps/Makefile.am
- pixmaps/Makefile.in
- pixmaps/src/Makefile.in
- po/Makefile.in.in
- po/POTFILES.in
- po/cs.gmo
- po/cs.po
- po/de.gmo
- po/de.po
- po/en_GB.gmo
- po/en_GB.po
- po/es.gmo
- po/es.po
- po/fr.gmo
- po/fr.po
- po/gwyddion.pot
- po/it.gmo
- po/it.po
- po/ja.gmo
- po/ja.po
- po/ko.gmo
- po/ko.po
- po/pt_BR.gmo
- po/pt_BR.po
- + po/remove-potcdate.sed
- ? po/remove-potcdate.sin
- po/ru.gmo
- po/ru.po
- tests/Makefile.in
- tests/graph-curve-model.c
- tests/nield.c
- tests/scatter.c
- tests/test-list.c
- tests/test-list.h
- tests/test-list.txt
- thumbnailer/Makefile.in
- thumbnailer/gwyddion3-thumbnailer.c
- utils/Makefile.in
- utils/dump-modules.c
- utils/update-langs.py


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/gwyddion/-/commit/64abe3befecb504afe4130cca39cbf33b708cd9f

-- 
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From gitlab at salsa.debian.org  Thu Jul  2 18:07:27 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Thu, 02 Jul 2026 17:07:27 +0000
Subject: [med-svn] [Git][med-team/gwyddion] Pushed new tag upstream/3.11
Message-ID: <6a469acf62be4_55b17471028413648d@godard.mail>



Andreas Tille pushed new tag upstream/3.11 at Debian Med / gwyddion

-- 
View it on GitLab: https://salsa.debian.org/med-team/gwyddion/-/tree/upstream/3.11
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From gitlab at salsa.debian.org  Fri Jul  3 02:42:20 2026
From: gitlab at salsa.debian.org (Andreas Tille (@tille))
Date: Fri, 03 Jul 2026 01:42:20 +0000
Subject: [med-svn] [Git][med-team/community/helper-scripts][master]
 automatic update
Message-ID: <6a47137cad6e4_55b1747102842641ad@godard.mail>



Andreas Tille pushed to branch master at Debian Med / community / helper-scripts


Commits:
32c49043 by Andreas Tille at 2026-07-03T01:42:16+00:00
automatic update

- - - - -


4 changed files:

- debian-med-tests.txt
- debian-science-tests.txt
- outdated_med-packages.txt
- python-team-tests.txt


Changes:

=====================================
debian-med-tests.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Thu, 02 Jul 2026 13:42:03 +0000
+Last-Update: Fri, 03 Jul 2026 01:42:04 +0000
 
  Source                        | Vote   | Tasks                                      |                                 Tags                                 
 -------------------------------+--------+--------------------------------------------+----------------------------------------------------------------------


=====================================
debian-science-tests.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Thu, 02 Jul 2026 13:42:05 +0000
+Last-Update: Fri, 03 Jul 2026 01:42:04 +0000
 
        Source                              | Vote   |             Tasks                                                   |                          Tags                          
 -------------------------------------------+--------+---------------------------------------------------------------------+--------------------------------------------------------


=====================================
outdated_med-packages.txt
=====================================
The diff for this file was not included because it is too large.

=====================================
python-team-tests.txt
=====================================
@@ -1,4 +1,4 @@
-Last-Update: Thu, 02 Jul 2026 13:42:07 +0000
+Last-Update: Fri, 03 Jul 2026 01:42:04 +0000
 
      Source                             | Vote   |                          Tags                          
 ----------------------------------------+--------+--------------------------------------------------------



View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/32c490437004980f89ad63bf46dc4556ea229cca

-- 
View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/32c490437004980f89ad63bf46dc4556ea229cca
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