[med-svn] [Git][med-team/pyscanfcs][master] 7 commits: d/rules: invoke dh_numpy3 to specify ABI compatibility.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Feb 8 19:05:41 GMT 2025
Étienne Mollier pushed to branch master at Debian Med / pyscanfcs
Commits:
9ea024e5 by Étienne Mollier at 2025-02-08T19:50:31+01:00
d/rules: invoke dh_numpy3 to specify ABI compatibility.
Closes: #1095282
- - - - -
9b3b869e by Étienne Mollier at 2025-02-08T19:51:12+01:00
numpy-2.0.patch: new: fix overflow issue raised by numpy 2.0.
Closes: #1095368
- - - - -
2bfb6016 by Étienne Mollier at 2025-02-08T19:51:47+01:00
d/rules: adjust python3 shebang for _version*.py.
- - - - -
8b171c5d by Étienne Mollier at 2025-02-08T19:53:05+01:00
d/u/metadata: reference upstream repository.
- - - - -
915d34d2 by Étienne Mollier at 2025-02-08T19:53:51+01:00
d/control: declare compliance to standards version 4.7.0.
- - - - -
b381d9c1 by Étienne Mollier at 2025-02-08T20:04:19+01:00
do-not-use-utf8x.patch: patch forwarded upstream.
- - - - -
91c86979 by Étienne Mollier at 2025-02-08T20:05:14+01:00
d/changelog: ready for upload to unstable.
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/patches/do-not-use-utf8x.patch
- + debian/patches/numpy-2.0.patch
- debian/patches/series
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+pyscanfcs (0.3.6+ds-5) unstable; urgency=medium
+
+ * Team upload.
+ * d/rules: invoke dh_numpy3 to specify ABI compatibility. (Closes: #1095282)
+ * numpy-2.0.patch: new: fix overflow issue raised by numpy 2.0.
+ (Closes: #1095368)
+ * d/rules: adjust python3 shebang for _version*.py.
+ * d/u/metadata: reference upstream repository.
+ * d/control: declare compliance to standards version 4.7.0.
+ * do-not-use-utf8x.patch: patch forwarded upstream.
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 08 Feb 2025 20:05:05 +0100
+
pyscanfcs (0.3.6+ds-4) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -25,7 +25,7 @@ Build-Depends: cython3,
texlive-latex-extra,
texlive-latex-recommended,
texlive-science
-Standards-Version: 4.6.1
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/pyscanfcs
Vcs-Git: https://salsa.debian.org/med-team/pyscanfcs.git
Homepage: https://fcs-analysis.github.io/PyScanFCS/
=====================================
debian/patches/do-not-use-utf8x.patch
=====================================
@@ -2,6 +2,8 @@ Description: use package [utf8] instead of [utf8x]
Author: Nilesh Patra <nilesh at debian.org>
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1016342
Last-Update: 2022-08-07
+Reviewed-By: Étienne Mollier <emollier at debian.org>
+Forwarded: https://github.com/FCS-analysis/PyScanFCS/pull/20
--- a/doc/PyScanFCS_doc.tex
+++ b/doc/PyScanFCS_doc.tex
@@ -3,7 +3,7 @@
=====================================
debian/patches/numpy-2.0.patch
=====================================
@@ -0,0 +1,28 @@
+Description: fix for numpy 2.0.
+ test_open_dat fails with numpy 2.0 and beyond with the following error:
+ .
+ # Make a 32 bit array
+ data = np.uint32(data16)
+ > data[occ] = data16[occ + 1] + data16[occ + 2] * 65536
+ E OverflowError: Python integer 65536 out of bounds for uint16
+ .
+ This change uses the freshly converted data array to uint32 for the
+ data concatenation instead of using the uint16 data16 array elements.
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1095368
+Forwarded: https://github.com/FCS-analysis/PyScanFCS/pull/19
+Last-Update: 2025-02-08
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- pyscanfcs.orig/pyscanfcs/openfile.py
++++ pyscanfcs/pyscanfcs/openfile.py
+@@ -95,7 +95,7 @@
+
+ # Make a 32 bit array
+ data = np.uint32(data16)
+- data[occ] = data16[occ + 1] + data16[occ + 2] * 65536
++ data[occ] = data[occ + 1] + data[occ + 2] * 65536
+
+ if callback is not None:
+ ret = callback(**cb_kwargs)
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
noDownloadOfDoc.patch
do-not-use-utf8x.patch
+numpy-2.0.patch
=====================================
debian/rules
=====================================
@@ -44,8 +44,13 @@ override_dh_auto_build:
convert -background "rgba(255,255,255,0)" -geometry 32x32 \
$(DOCDIR)/Images/PyScanFCS_icon.svg debian/pyscanfcs.xpm
dh_auto_build
+ # Provide an usual interpreter.
+ sed -i '1s@^#!/usr/bin/env python$$@#!/usr/bin/python3@' \
+ pyscanfcs/_version_save.py \
+ pyscanfcs/_version.py
override_dh_install:
+ dh_numpy3
dh_install
mv $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/pyscanfcs \
$(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/pyscanfcs_run
=====================================
debian/upstream/metadata
=====================================
@@ -9,3 +9,5 @@ Registry:
- Name: SciCrunch
Entry: NA
Bug-Database: https://github.com/paulmueller/PyScanFCS/issues
+Repository: https://github.com/FCS-analysis/PyScanFCS.git
+Repository-Browse: https://github.com/FCS-analysis/PyScanFCS
View it on GitLab: https://salsa.debian.org/med-team/pyscanfcs/-/compare/0899c3632bce06645de653138994ba20f4f94aac...91c869797f1506123baad2bc54bd158df15ecf51
--
View it on GitLab: https://salsa.debian.org/med-team/pyscanfcs/-/compare/0899c3632bce06645de653138994ba20f4f94aac...91c869797f1506123baad2bc54bd158df15ecf51
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