[med-svn] [Git][med-team/circlator][master] 3 commits: Do not run build-time tests by hand, rely on pybuild; copy test dir to...

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / circlator


Commits:
02f433f1 by Nilesh Patra at 2023-12-03T03:02:20+05:30
Do not run build-time tests by hand, rely on pybuild; copy test dir to {build_dir}/circlator before testing

- - - - -
c203e6de by Nilesh Patra at 2023-12-03T03:03:51+05:30
Replace LooseVersion usage with packaging.version.parse (Closes: #1056234)

- - - - -
270329ba by Nilesh Patra at 2023-12-03T03:04:44+05:30
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/remove-distutils.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+circlator (1.5.6-11) unstable; urgency=medium
+
+  * Team Upload.
+  * Do not run build-time tests by hand, rely on pybuild; copy test
+    dir to {build_dir}/circlator before testing
+  * Replace LooseVersion usage with packaging.version.parse (Closes: #1056234)
+
+ -- Nilesh Patra <nilesh at debian.org>  Sun, 03 Dec 2023 03:04:05 +0530
+
 circlator (1.5.6-10) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -7,6 +7,7 @@ Build-Depends: debhelper-compat (= 13),
                dh-sequence-python3,
                python3-all,
                python3-setuptools,
+               python3-packaging,
                python3-openpyxl,
                python3-jdcal,
                python3-pysam,


=====================================
debian/patches/remove-distutils.patch
=====================================
@@ -0,0 +1,58 @@
+--- a/circlator/program.py
++++ b/circlator/program.py
+@@ -2,7 +2,7 @@
+ import os
+ import re
+ import subprocess
+-from distutils.version import LooseVersion
++from packaging.version import parse
+ from circlator import common
+ 
+ 
+@@ -79,14 +79,14 @@
+         v = self.version
+         if v is None:
+             return None
+-        return LooseVersion(v) >= LooseVersion(min_version)
++        return parse(v) >= parse(min_version)
+ 
+ 
+     def version_at_most(self, max_version):
+         v = self.version
+         if v is None:
+             return None
+-        return LooseVersion(v) <= LooseVersion(max_version)
++        return parse(v) <= parse(max_version)
+ 
+ 
+     def exe(self):
+--- a/circlator/start_fixer.py
++++ b/circlator/start_fixer.py
+@@ -2,7 +2,7 @@
+ import shutil
+ import copy
+ import tempfile
+-from distutils.version import LooseVersion
++from packaging.version import parse
+ import pyfastaq
+ import pymummer
+ import circlator
+@@ -180,7 +180,7 @@
+         if (total_contig_length < 20000):
+             # prodigal needs -p meta option for sequences less than 20000
+             # annoyingly newer version of prodigal has different -p option!
+-            if LooseVersion(prodigal.version) >= LooseVersion('3.0'):
++            if parse(prodigal.version) >= parse('3.0'):
+                 p_option = "-p anon"
+             else:
+                 p_option = "-p meta"
+--- a/setup.py
++++ b/setup.py
+@@ -21,6 +21,7 @@
+         'pyfastaq >= 3.12.1',
+         'pysam >= 0.8.1',
+         'pymummer>=0.9.0',
++        'packaging'
+     ],
+     license='GPLv3',
+     classifiers=[


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 fix_canu_detection.patch
 switch-to-pytest.patch
 split_canu_tests
+remove-distutils.patch


=====================================
debian/rules
=====================================
@@ -4,15 +4,12 @@
 include /usr/share/dpkg/default.mk
 
 export LC_ALL=C.UTF-8
+export PYBUILD_BEFORE_TEST=cp -av circlator/tests {build_dir}/circlator/
+export PYBUILD_TEST_ARGS=circlator/tests
 
 %:
 	dh $@ --buildsystem=pybuild
 
-override_dh_auto_test:
-ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-	PYTHONPATH=$(CURDIR) pytest-3 -v circlator/tests
-endif
-
 override_dh_installexamples:
 	dh_installexamples
 	cd debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples && tar caf data.tar.xz data --owner=0 --group=0 --numeric-owner --sort=name --mode=a+rX,og-w && rm -rf data



View it on GitLab: https://salsa.debian.org/med-team/circlator/-/compare/f38953ac18ca60949b25bd41e4d70a2d96105c87...270329badf9cc4cc4b8dd8bdc74872d7a11bbd0f

-- 
View it on GitLab: https://salsa.debian.org/med-team/circlator/-/compare/f38953ac18ca60949b25bd41e4d70a2d96105c87...270329badf9cc4cc4b8dd8bdc74872d7a11bbd0f
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