[med-svn] [Git][med-team/cnvkit][master] 5 commits: d/patches/spelling: forwarded upstream.

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / cnvkit


Commits:
a9d2318c by Michael R. Crusoe at 2024-03-05T10:18:30+01:00
d/patches/spelling: forwarded upstream.

- - - - -
a2349549 by Michael R. Crusoe at 2024-03-05T10:18:31+01:00
d/control: build the PEP-517 way with pybuild-plugin-pyproject.

- - - - -
61a43c61 by Michael R. Crusoe at 2024-03-05T10:18:31+01:00
d/control: also run the built-in tests as autopkgtests.

- - - - -
af8fcbe4 by Michael R. Crusoe at 2024-03-05T10:21:44+01:00
d/rules: move items into d/clean.

- - - - -
3168dd1e by Michael R. Crusoe at 2024-03-05T10:53:08+01:00
d/tests: skip-not-installable for s390x and others where python3- pysam isn't available.

- - - - -


9 changed files:

- debian/changelog
- debian/clean
- debian/control
- debian/patches/no-py-ext
- debian/patches/python3compat.patch
- debian/patches/spelling
- debian/rules
- + debian/tests/autopkgtest-pkg-pybuild.conf
- debian/tests/control


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+cnvkit (0.9.10-2) UNRELEASED; urgency=medium
+
+  * d/patches/spelling: forwarded upstream.
+  * d/control: build the PEP-517 way with pybuild-plugin-pyproject.
+  * d/control: also run the built-in tests as autopkgtests.
+  * d/rules: move items into d/clean.
+  * d/tests: skip-not-installable for s390x and others where python3-
+    pysam isn't available.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Tue, 05 Mar 2024 10:11:04 +0100
+
 cnvkit (0.9.10-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/clean
=====================================
@@ -1,2 +1,7 @@
 debian/*.1
 debian/*.include
+test/p2-20-metrics.tsv
+test/p2-5_5-metrics.tsv
+test/p2-9_2-metrics.tsv
+test/build/
+CNVkit.egg-info/


=====================================
debian/control
=====================================
@@ -9,6 +9,7 @@ Build-Depends: debhelper-compat (= 13),
                dh-sequence-python3,
                python3-all,
                python3-setuptools,
+               pybuild-plugin-pyproject,
                python3-pytest <!nocheck>,
                python3-pyfaidx <!nocheck>,
                python3-biopython <!nocheck>,
@@ -27,6 +28,7 @@ Vcs-Browser: https://salsa.debian.org/med-team/cnvkit
 Vcs-Git: https://salsa.debian.org/med-team/cnvkit.git
 Homepage: https://cnvkit.readthedocs.org
 Rules-Requires-Root: no
+Testsuite: autopkgtest-pkg-pybuild
 
 Package: cnvkit
 Architecture: amd64 arm64 ppc64el


=====================================
debian/patches/no-py-ext
=====================================
@@ -1,8 +1,9 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Author: Michael R. Crusoe <crusoe at debian.org>
 Description: Remove .py extensions as per Debian policy
   This patch is deactivated since this is differently organised in upstream
   code and inside Debian Med we decided to derive from policy (see
      https://lists.debian.org/debian-med/2018/06/msg00043.html)
+Forwarded: not-needed
 
 --- a/pyproject.toml
 +++ b/pyproject.toml


=====================================
debian/patches/python3compat.patch
=====================================
@@ -1,4 +1,5 @@
 Description: enable building with Python3
+Forwarded: not-needed
 --- a/test/test_cnvlib.py
 +++ b/test/test_cnvlib.py
 @@ -1,4 +1,4 @@


=====================================
debian/patches/spelling
=====================================
@@ -1,5 +1,6 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
+From: Michael R. Crusoe <crusoe at debian.org>
 Subject: Fix typos
+Forwarded: https://github.com/etal/cnvkit/pull/873
 --- a/cnvlib/commands.py
 +++ b/cnvlib/commands.py
 @@ -272,7 +272,7 @@ P_batch.add_argument(


=====================================
debian/rules
=====================================
@@ -18,7 +18,4 @@ override_dh_auto_install:
 
 override_dh_auto_clean:
 	cd test && ${MAKE} clean || /bin/true
-#	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/autopkgtest-pkg-pybuild.conf
=====================================
@@ -0,0 +1 @@
+extra_restrictions = skip-not-installable


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
 Tests: run-unit-test
 Depends: @, poppler-utils
-Restrictions: allow-stderr
+Restrictions: allow-stderr, skip-not-installable



View it on GitLab: https://salsa.debian.org/med-team/cnvkit/-/compare/44fa2541b54f329634ccc759f976206d32533d68...3168dd1e4cbc82032f4f24d474459dfb8c1160d1

-- 
View it on GitLab: https://salsa.debian.org/med-team/cnvkit/-/compare/44fa2541b54f329634ccc759f976206d32533d68...3168dd1e4cbc82032f4f24d474459dfb8c1160d1
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