[med-svn] [Git][med-team/python-biopython][master] 2 commits: d/control: adjust build-deps to be more cross-build friendly.

Sat Sep 14 12:38:52 BST 2024


Michael R. Crusoe pushed to branch master at Debian Med / python-biopython


Commits:
aaf8cfa7 by Michael R. Crusoe at 2024-09-14T13:36:14+02:00
d/control: adjust build-deps to be more cross-build friendly.

- - - - -
67df7659 by Michael R. Crusoe at 2024-09-14T13:38:33+02:00
Fix some of the DEP-3 patch metadata

- - - - -


8 changed files:

- debian/changelog
- debian/control
- debian/patches/croak-on-muscle5.patch
- debian/patches/fix-use-of-unversioned-python.patch
- debian/patches/muscle3.patch
- debian/patches/privacy_breach_ie9.patch
- debian/patches/reproduciblebuild.patch
- debian/patches/seqxml-parser.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -6,6 +6,8 @@ python-biopython (1.83+dfsg1-5) UNRELEASED; urgency=medium
   * Remove constraints unnecessary since bullseye (oldstable):
     + python3-biopython: Drop versioned constraint on ncbi-blast+ (>= 2.10.1-3)
       in Recommends.
+  * d/control: adjust build-deps to be more cross-build friendly.
+  * Fix some of the DEP-3 patch metadata
 
  -- Michael R. Crusoe <crusoe at debian.org>  Sat, 14 Sep 2024 09:51:48 +0200
 


=====================================
debian/control
=====================================
@@ -7,7 +7,8 @@ Section: python
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                dh-sequence-python3,
-               python3-all-dev,
+               python3-all-dev:native,
+               libpython3-all-dev,
                python3-numpy,
                flex,
                python3-reportlab (>= 4.0.4-1~) <!nocheck>,


=====================================
debian/patches/croak-on-muscle5.patch
=====================================
@@ -1,17 +1,17 @@
-From: =?utf-8?q?=C3=89tienne_Mollier?= <emollier at debian.org>
-Date: Sat, 14 Sep 2024 09:48:28 +0200
 Subject: raise runtime error when trying to use wrapper on muscle 5.
-
 Bug: https://github.com/biopython/biopython/issues/3902
-Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1009118
+Bug-Debian: https://bugs.debian.org/1009118
+From: =?utf-8?q?=C3=89tienne_Mollier?= <emollier at debian.org>
 Last-Update: 2022-11-24
 
+Date: Sat, 14 Sep 2024 09:48:28 +0200
+
 The muscle wrapper only supports muscle 3, and the biopython project is aiming
 to remove wrapper support in an upcoming version.  Port of the wrapping code
 to support both muscle versions will thus probably never happen.  The affected
 code section is due to disappear in an upcoming biopython version and it thus
 not forwarded upstream.
-Last-Update: 2022-11-24
+
 ---
  Bio/Align/Applications/_Muscle.py | 5 +++++
  1 file changed, 5 insertions(+)


=====================================
debian/patches/fix-use-of-unversioned-python.patch
=====================================
@@ -1,14 +1,12 @@
 From: =?utf-8?q?=C3=89tienne_Mollier?= <etienne.mollier at mailoo.org>
 Date: Sat, 14 Sep 2024 09:48:28 +0200
 Subject: fix use of unversioned 'python' interpreter
-
 Forwarded: not-needed
 Last-Update: 2020-09-09
 
 The Doc/Makefile uses python to evaluate the current version of the library in
 order to build the documentation, but the unversioned "python" interpreter is
 not available anymore, at least not in the build context.
-Last-Update: 2020-09-09
 ---
  Doc/Makefile | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)


=====================================
debian/patches/muscle3.patch
=====================================
@@ -1,7 +1,6 @@
 From: =?utf-8?q?=C3=89tienne_Mollier?= <emollier at debian.org>
 Date: Sat, 14 Sep 2024 09:48:28 +0200
 Subject: expect muscle3 as executable instead of muscle.
-
 Bug-Debian: https://bugs.debian.org/1009118
 Forwarded: not-needed
 Last-Update: 2022-11-24
@@ -12,7 +11,6 @@ with the biopython wrapper.
 
 Forwarding is not needed since wrappers are deprecated and due to be removed
 in an upcoming biopython version.
-Last-Update: 2022-11-24
 ---
  Bio/Align/Applications/_Muscle.py | 10 +++++++++-
  Tests/test_Muscle_tool.py         | 12 +++++++++---


=====================================
debian/patches/privacy_breach_ie9.patch
=====================================
@@ -1,7 +1,6 @@
 From: =?utf-8?q?=C3=89tienne_Mollier?= <etienne.mollier at mailoo.org>
 Date: Sat, 14 Sep 2024 09:48:28 +0200
 Subject: fix privacy breach with html5shiv
-
 Forwarded: not-needed
 Last-Update: 2020-09-11
 
@@ -9,7 +8,6 @@ Actually the script called is commented out, except when reading the page with
 Internet Explorer 9.  This patch makes sure the script is not called at all,
 even if it is very unlikely that HTML document installed in Debian will ever
 be read with this browser.
-Last-Update: 2020-09-11
 ---
  Doc/cookbook/Restriction/Restriction.html | 3 ---
  1 file changed, 3 deletions(-)


=====================================
debian/patches/reproduciblebuild.patch
=====================================
@@ -1,7 +1,6 @@
 From: =?utf-8?q?=C3=89tienne_Mollier?= <etienne.mollier at mailoo.org>
 Date: Sat, 14 Sep 2024 09:48:28 +0200
 Subject: make the build reproducible
-
 Forwarded: not-needed
 Last-Update: 2020-09-12
 
@@ -10,7 +9,6 @@ when the package was build, and wouldn't be too relevant in the document.
 Focusing on the version number would be a better approach here.  This patch is
 not needed upstream, as it would interfere with development releases, marked
 only with the version "dev", so would benefit of the date here.
-Last-Update: 2020-09-12
 ---
  Doc/Tutorial.tex | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)


=====================================
debian/patches/seqxml-parser.patch
=====================================
@@ -1,22 +1,20 @@
-From: Michiel de Hoon <mdehoon at tkx249.genome.gsc.riken.jp>
-Date: Sat, 14 Sep 2024 09:48:28 +0200
 Subject: Trying to figure out what is going wrong in the SeqXML parser
-MIME-Version: 1.0
-Content-Type: text/plain; charset="utf-8"
-Content-Transfer-Encoding: 8bit
-
-Origin: upstream, https://github.com/biopython/biopython/pull/4686
 Bug: https://github.com/biopython/biopython/issues/4640
-Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1064147
+Bug-Debian: https://bugs.debian.org/1064147
+Origin: upstream, https://github.com/biopython/biopython/pull/4686
+From: Michiel de Hoon <mdehoon at tkx249.genome.gsc.riken.jp>
 Reviewed-by: Étienne Mollier <emollier at debian.org>
 Last-Update: 2024-05-22
 
+Content-Transfer-Encoding: 8bit
+
  * using original block size
  * print data
  * print data
  * print data
  * print data
  * closing the parser on time does the trick
+
 ---
  Bio/SeqIO/SeqXmlIO.py | 3 ++-
  1 file changed, 2 insertions(+), 1 deletion(-)



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/b3524b225d8e88a23c57915f85a4d9cb419631af...67df7659a0ea084fd94d8543941e456a8d2b4909

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/b3524b225d8e88a23c57915f85a4d9cb419631af...67df7659a0ea084fd94d8543941e456a8d2b4909
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