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 <[email protected]> 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 <[email protected]> Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1016342 Last-Update: 2022-08-07 +Reviewed-By: Étienne Mollier <[email protected]> +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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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