[med-svn] [Git][med-team/python-biopython][master] 6 commits: d/changelog: hevea change closes #1036174.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / python-biopython


Commits:
23818f07 by Étienne Mollier at 2023-07-09T16:57:11+02:00
d/changelog: hevea change closes #1036174.

Gbp-Dch: ignore

- - - - -
1932350b by Lukas Märdian at 2023-07-09T17:07:52+02:00
avoid the python3-renderpm dependency

The python3-renderpm binary package got dropped by its (new)
maintainer since src:python-reportlab 4.0.4-1.  This makes
python-biopython's build- & autopkgtests fail.

Closes: #1039565

- - - - -
813409fa by Étienne Mollier at 2023-07-09T17:31:53+02:00
d/rules: disable install-doc target with nodoc profile.

This should address the remaining ftbfs when building biopython with
the nodoc build profile spotted while discussing on #1036174.

- - - - -
f4fb5f29 by Étienne Mollier at 2023-07-09T17:40:10+02:00
d/control: enable numpy outside nocheck build profile.

- - - - -
3f92cedf by Étienne Mollier at 2023-07-09T17:41:43+02:00
d/*.lintian-overrides: make the spelling override more generic.

It is now independent of the python3 version and shared objects
architecture.

- - - - -
95b72c44 by Étienne Mollier at 2023-07-09T17:49:03+02:00
ready to upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/python3-biopython.lintian-overrides
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,8 +1,18 @@
-python-biopython (1.80+dfsg-5) UNRELEASED; urgency=medium
+python-biopython (1.80+dfsg-5) unstable; urgency=medium
 
+  [ Andreas Tille ]
   * Drop nocheck profile from hevea since its also needed to create doc
+    (Closes: #1036174)
+
+  [ Lukas Märdian ]
+  * avoid the python3-renderpm dependency (Closes: #1039565)
+
+  [ Étienne Mollier ]
+  * d/rules: disable install-doc target with nodoc profile.
+  * d/control: enable numpy outside nocheck build profile.
+  * d/*.lintian-overrides: make the spelling override more generic.
 
- -- Andreas Tille <tille at debian.org>  Wed, 17 May 2023 07:30:21 +0200
+ -- Étienne Mollier <emollier at debian.org>  Sun, 09 Jul 2023 17:48:34 +0200
 
 python-biopython (1.80+dfsg-4) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -10,7 +10,7 @@ Priority: optional
 Build-Depends: debhelper-compat (= 13),
                dh-python,
                python3-all-dev,
-               python3-numpy <!nocheck>,
+               python3-numpy,
                flex,
                python3-reportlab <!nocheck>,
                hevea,
@@ -37,7 +37,6 @@ Build-Depends: debhelper-compat (= 13),
                python3-mmtf <!nocheck>,
                python3-pil <!nocheck>,
                python3-rdflib <!nocheck>,
-               python3-renderpm <!nocheck>,
                python3-psycopg2 <!nocheck>,
                python3-pygments <!nocheck>,
                python3-scipy <!nocheck>,
@@ -58,7 +57,6 @@ Architecture: any
 Depends: ${python3:Depends},
          ${shlibs:Depends},
          ${misc:Depends},
-         python3-renderpm,
          python3-reportlab,
          w3c-sgml-lib
 Recommends: python-biopython-doc (= ${source:Version}),


=====================================
debian/python3-biopython.lintian-overrides
=====================================
@@ -1,3 +1,2 @@
 # The affected word doesn't show up when scanning the source code.
-python3-biopython: spelling-error-in-binary ment meant [usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-310-x86_64-linux-gnu.so]
-python3-biopython: spelling-error-in-binary ment meant [usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-311-x86_64-linux-gnu.so]
+python3-biopython: spelling-error-in-binary ment meant [usr/lib/python3/dist-packages/Bio/Align/_aligners.cpython-3*.so]


=====================================
debian/rules
=====================================
@@ -25,7 +25,7 @@ EXCLUDENONFREE=PAML_tools EmbossPhylipNew
 
 # avoid testing tools that are not packaged for Debian yet (or will never be packaged since they might be outdated)
 # This would not trigger a failure but bloats the build log with irrelevant noise
-EXCLUDENOTPACKAGED=MSAProbs_tool NACCESS_tool PopGen_GenePop PopGen_GenePop_EasyController XXmotif_tool PDB_ResidueDepth mmtf mmtf_online
+EXCLUDENOTPACKAGED=MSAProbs_tool NACCESS_tool PopGen_GenePop PopGen_GenePop_EasyController XXmotif_tool PDB_ResidueDepth mmtf mmtf_online GraphicsBitmaps
 
 # avoid amd64 only tools on other architectures
 ifeq ($(BUILDARCH),amd64)
@@ -62,7 +62,9 @@ override_dh_auto_clean:
 
 override_dh_auto_build:
 	dh_auto_build
+ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS)))
 	cd Doc && make
+endif
 
 override_dh_auto_install:
 	dh_auto_install
@@ -99,6 +101,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 endif
 
 override_dh_installdocs-indep:
+ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS)))
 	dh_installdocs -i
 	find debian -name __pycache__ -type d | xargs rm -rf
 	find debian -name example.fastq.gz
@@ -114,6 +117,7 @@ override_dh_installdocs-indep:
 	find debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc -name "*.aux" -delete
 	find debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc -name "*.lyx" -delete
 	find debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc -type d -empty -delete
+endif
 
 override_dh_fixperms:
 	dh_fixperms



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/a3031bff6e26f44b3c15b43ea7c71e6056484c67...95b72c445ba0b285d92afb89066c4f96cfec36e5

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/a3031bff6e26f44b3c15b43ea7c71e6056484c67...95b72c445ba0b285d92afb89066c4f96cfec36e5
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