[med-svn] [Git][med-team/circlator][master] 8 commits: d/control: Spades is optional, therefore bump it down to a Recommends, and...
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Fri Aug 18 13:24:55 BST 2023
Michael R. Crusoe pushed to branch master at Debian Med / circlator
Commits:
cd14c230 by Michael R. Crusoe at 2023-08-18T13:51:59+02:00
d/control: Spades is optional, therefore bump it down to a Recommends, and switch the binary package to Architecture: All
- - - - -
3efecd3d by Michael R. Crusoe at 2023-08-18T13:51:59+02:00
autopkgtests: run for each Python version
- - - - -
19e3efac by Michael R. Crusoe at 2023-08-18T13:51:59+02:00
d/upstream/metadata: add link to the GitHub repo
- - - - -
7260c2f1 by Michael R. Crusoe at 2023-08-18T14:18:45+02:00
d/patches/split_canu_tests & d/tests/run-unit-test: allow for testing without spades
- - - - -
80c6bc8f by Michael R. Crusoe at 2023-08-18T14:18:45+02:00
routine-update: Standards-Version: 4.6.2
- - - - -
7202ae69 by Michael R. Crusoe at 2023-08-18T14:18:45+02:00
routine-update: Build-Depends: s/dh-python/dh-sequence-python3/
- - - - -
8cb69f98 by Michael R. Crusoe at 2023-08-18T14:18:46+02:00
Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
- - - - -
c7e798b0 by Michael R. Crusoe at 2023-08-18T14:18:46+02:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/split_canu_tests
- debian/rules
- debian/tests/control
- debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+circlator (1.5.6-8) unstable; urgency=medium
+
+ * Team upload.
+ * d/control: Spades is optional, therefore bump it down to a Recommends, and
+ switch the binary package to Architecture: All
+ * autopkgtests: run for each Python version
+ * d/upstream/metadata: add link to the GitHub repo
+ * d/patches/split_canu_tests & d/tests/run-unit-test: allow for
+ testing without spades
+ * Standards-Version: 4.6.2 (routine-update)
+ * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+ * Use secure URI in Homepage field.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Fri, 18 Aug 2023 13:58:28 +0200
+
circlator (1.5.6-7) unstable; urgency=medium
* Fix watch file (no idea why version 1.5.6 vanished upstream)
=====================================
debian/control
=====================================
@@ -4,36 +4,35 @@ Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- dh-python,
+ dh-sequence-python3,
python3-all,
python3-setuptools,
python3-openpyxl,
python3-jdcal,
- fastaq,
python3-pysam,
python3-pymummer,
-# Test-Depends:
- python3-pytest,
- spades,
- bwa,
- prodigal,
- canu (<< 1.8+dfsg-1) | canu (>= 1.8+dfsg-2)
-Standards-Version: 4.6.1
+ python3-pytest <!nocheck>,
+ fastaq <!nocheck>,
+ spades <!nocheck>,
+ bwa <!nocheck>,
+ prodigal <!nocheck>,
+ canu <!nocheck>
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/circlator
Vcs-Git: https://salsa.debian.org/med-team/circlator.git
-Homepage: http://sanger-pathogens.github.io/circlator/
+Homepage: https://sanger-pathogens.github.io/circlator/
Rules-Requires-Root: no
Package: circlator
-Architecture: amd64
+Architecture: all
Depends: ${misc:Depends},
${python3:Depends},
prodigal,
bwa,
mummer,
samtools,
- spades,
canu
+Recommends: spades
Description: circularize genome assemblies
Circlator is a tool to automate assembly circularization for bacterial and
small eukaryotic genomes and produce accurate linear representations of
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
fix_canu_detection.patch
switch-to-pytest.patch
+split_canu_tests
=====================================
debian/patches/split_canu_tests
=====================================
@@ -0,0 +1,26 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Allow for testing without spades installed
+
+--- circlator.orig/circlator/tests/assemble_test.py
++++ circlator/circlator/tests/assemble_test.py
+@@ -9,7 +9,7 @@
+ data_dir = os.path.join(modules_dir, 'tests', 'data')
+
+
+-class TestAssemble(unittest.TestCase):
++class TestAssembleSpades(unittest.TestCase):
+ def setUp(self):
+ self.tmp_assemble_dir = 'tmp.assemble_test'
+ self.assembler = assemble.Assembler(
+@@ -62,6 +62,11 @@
+ self.assertEqual(cmd_start + ' -o out -t 2 -k 41 --careful --only-assembler', self.assembler._make_spades_command(41, 'out'))
+
+
++class TestAssembleCanu(unittest.TestCase):
++ def setUp(self):
++ self.tmp_assemble_dir = 'tmp.assemble_test'
++
++
+ def test_make_canu_command(self):
+ '''test _make_canu_command'''
+ tmp_assemble_dir = 'tmp.assemble_test'
=====================================
debian/rules
=====================================
@@ -6,7 +6,7 @@ include /usr/share/dpkg/default.mk
export LC_ALL=C.UTF-8
%:
- dh $@ --with python3 --buildsystem=pybuild
+ dh $@ --buildsystem=pybuild
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, python3-pytest, python3-all
+Depends: @, spades [amd64], python3-pytest, python3-all
Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -15,6 +15,13 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
tar xaf data.tar.xz
-sed -i "s/data_dir = os.path.join(modules_dir, 'tests', 'data')/data_dir = os.path.join(os.getcwd(), 'data')/" *.py
+sed -i "s/data_dir = os.path.join(modules_dir, 'tests', 'data')/data_dir = os.path.join(os.getcwd(), 'data')/" ./*.py
-python3 -m pytest -v
+for py in $(py3versions --supported 2> /dev/null)
+do
+ if eval dpkg-architecture --is amd64 ; then
+ ${py} -m pytest -v
+ else
+ ${py} -m pytest -v -k 'not (test_build_spades_kmers or test_make_spades_command)'
+ fi
+done
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Repository: https://github.com/sanger-pathogens/circlator.git
+Repository-Browse: https://github.com/sanger-pathogens/circlator
Bug-Database: https://github.com/sanger-pathogens/circlator/issues
Bug-Submit: https://github.com/sanger-pathogens/circlator/issues/new
Reference:
View it on GitLab: https://salsa.debian.org/med-team/circlator/-/compare/0b0cdbf46695fbba0e3264ac47e1e159757543a9...c7e798b08104ba912ee1b0499795088c88c9bda2
--
View it on GitLab: https://salsa.debian.org/med-team/circlator/-/compare/0b0cdbf46695fbba0e3264ac47e1e159757543a9...c7e798b08104ba912ee1b0499795088c88c9bda2
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