[med-svn] [Git][med-team/cnvkit][master] 2 commits: Do not rename cnvkit.py to cnvkit any more

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / cnvkit


Commits:
4f2ab0d2 by Andreas Tille at 2023-07-05T17:08:11+02:00
Do not rename cnvkit.py to cnvkit any more

- - - - -
94962fde by Andreas Tille at 2023-07-05T17:39:55+02:00
Fix installation of *.py scripts; TODO: manpages

- - - - -


8 changed files:

- + debian/NEWS
- debian/changelog
- debian/cnvkit.links
- + debian/install
- + debian/lintian-overrides
- debian/manpages
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/NEWS
=====================================
@@ -0,0 +1,10 @@
+cnvkit (0.9.10-1) unstable; urgency=medium
+
+  As per the discussion in
+     https://lists.debian.org/debian-med/2018/06/msg00043.html
+  and
+     https://lists.debian.org/debian-med/2023/07/msg00002.html
+  the main executable is now named cvnkit.py which is not following
+  the suggestion of Debian Policy to drop the .py extension any more.
+
+ -- Andreas Tille <tille at debian.org>  Tue, 04 Jul 2023 12:04:48 +0200


=====================================
debian/changelog
=====================================
@@ -1,10 +1,10 @@
-cnvkit (0.9.10-1) UNRELEASED; urgency=medium
+cnvkit (0.9.10-1) unstable; urgency=medium
 
   * Team upload.
   * New upstream version
   * Standards-Version: 4.6.2 (routine-update)
 
- -- Andreas Tille <tille at debian.org>  Tue, 04 Jul 2023 11:37:27 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 04 Jul 2023 12:04:48 +0200
 
 cnvkit (0.9.9-2) unstable; urgency=medium
 


=====================================
debian/cnvkit.links
=====================================
@@ -1 +1 @@
-usr/bin/cnvkit	usr/lib/debian-med/bin/cnvkit.py
+#usr/bin/cnvkit	usr/lib/debian-med/bin/cnvkit.py


=====================================
debian/install
=====================================
@@ -0,0 +1 @@
+scripts/*.sh	usr/bin


=====================================
debian/lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+# as well as debian/NEWS
+cnvkit: script-with-language-extension [usr/bin/cnvkit.py]


=====================================
debian/manpages
=====================================
@@ -1 +1 @@
-debian/*.1
+#debian/*.1


=====================================
debian/rules
=====================================
@@ -8,27 +8,13 @@ include /usr/share/dpkg/pkg-info.mk
 %:
 	dh $@ --with python3 --buildsystem=pybuild
 
-override_dh_auto_build:
-	[ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted build
-	if [ -f scripts/cnv_annotate.py ]; then \
-	  cd scripts && for script in *.py; do \
-	                  mv $${script} cnvkit-$${script%%.py}; \
-	                done; \
-	fi
-	dh_auto_build
-	cd scripts && for script in cnvkit-*; do \
-	                mv $${script} $${script##cnvkit-}.py; \
-	              done
-	mv cnvkit cnvkit.py
-
 override_dh_auto_install:
-	[ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted install
-	if [ -f scripts/cnv_annotate.py ]; then \
-	  cd scripts && for script in *.py; do \
-	                  mv $${script} cnvkit-$${script%%.py}; \
-	                done; \
-	fi
+	for script in `find scripts -name "*.py"` ; do \
+	    dh_install $${script} /usr/bin; \
+	done
 	dh_auto_install
+
+_override_dh_installman:
 	help2man --no-info --version-option=version \
 		--name="a command-line toolkit for copy number analysis." \
 		./cnvkit > debian/cnvkit.1
@@ -37,12 +23,12 @@ override_dh_auto_install:
 		--version-string=${DEB_VERSION_UPSTREAM} --help-option='-h' \
 		./cnvkit-reference2targets --name='Extract target and antitarget BED files from a CNVkit reference file.' \
 		> ../debian/cnvkit-reference2targets.1;
-	cd scripts && for script in cnvkit-*; do \
-	                mv $${script} $${script##cnvkit-}.py; \
-	              done
-	mv cnvkit cnvkit.py
+#	cd scripts && for script in cnvkit-*; do \
+#	                mv $${script} $${script##cnvkit-}.py; \
+#	              done
+#	mv cnvkit cnvkit.py
 
-override_dh_auto_test:
+_override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	cd test && ${MAKE}
 	cd test && ${MAKE} clean || /bin/true
@@ -51,7 +37,7 @@ endif
 
 override_dh_auto_clean:
 	cd test && ${MAKE} clean || /bin/true
-	if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi
+#	if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi
 	dh_auto_clean
 	rm -rf test/p2-20-metrics.tsv test/p2-5_5-metrics.tsv test/p2-9_2-metrics.tsv
 	rm -rf test/build CNVkit.egg-info


=====================================
debian/tests/run-unit-test
=====================================
@@ -13,6 +13,6 @@ cp -arL /usr/share/doc/${pkg}/examples/data "${AUTOPKGTEST_TMP}/"
 cd "${AUTOPKGTEST_TMP}"
 find . -name "*.gz" -exec gunzip \{\} \;
 cd test
-make cnvkit=/usr/bin/cnvkit
+make
 
 echo "PASS"



View it on GitLab: https://salsa.debian.org/med-team/cnvkit/-/compare/557f248c1515ca1fd96e1803a87e9f91bf26d6ac...94962fde7fb97c144785c4dbaa8851d826130b11

-- 
View it on GitLab: https://salsa.debian.org/med-team/cnvkit/-/compare/557f248c1515ca1fd96e1803a87e9f91bf26d6ac...94962fde7fb97c144785c4dbaa8851d826130b11
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