[med-svn] [Git][med-team/scoary][master] 5 commits: d/rules: enable build time tests; inspired from .travis.yml.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Dec 7 21:04:00 GMT 2022
Étienne Mollier pushed to branch master at Debian Med / scoary
Commits:
6348641f by Étienne Mollier at 2022-12-07T22:00:18+01:00
d/rules: enable build time tests; inspired from .travis.yml.
- - - - -
7909993f by Étienne Mollier at 2022-12-07T22:01:11+01:00
python3.11.patch: add; fix failure to open mode 'U' with python3.11.
- - - - -
aa98904a by Étienne Mollier at 2022-12-07T22:01:45+01:00
d/control: update test dependencies, notably remove nose.
Closes: #1018636
- - - - -
99457071 by Étienne Mollier at 2022-12-07T22:02:34+01:00
d/control: add myself to uploaders.
- - - - -
24d87a93 by Étienne Mollier at 2022-12-07T22:03:29+01:00
ready to upload to unstable.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/python3.11.patch
- + debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+scoary (1.6.16-5) unstable; urgency=medium
+
+ * d/rules: enable build time tests; inspired from .travis.yml.
+ * python3.11.patch: add; fix failure to open mode 'U' with python3.11.
+ * d/control: update test dependencies, notably remove nose.
+ (Closes: #1018636)
+ * d/control: add myself to uploaders.
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 07 Dec 2022 22:02:55 +0100
+
scoary (1.6.16-4) unstable; urgency=medium
* Fix watch file
=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
Source: scoary
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -8,7 +9,8 @@ Build-Depends: debhelper-compat (= 13),
python3-all,
python3-setuptools,
python3-scipy,
- python3-nose <!nocheck>
+ python3-ete3 <!nocheck>,
+ python3-six <!nocheck>
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/scoary
Vcs-Git: https://salsa.debian.org/med-team/scoary.git
=====================================
debian/patches/python3.11.patch
=====================================
@@ -0,0 +1,79 @@
+Description: fix invalid argument in open mode past python3.11.
+ Since python3, the universal newline mode 'U' has no effects.
+ Since python3.11, that mode is obsolete and its use raises:
+
+ Command: scoary.py -g scoary/exampledata/Gene_presence_absence.csv -t scoary/exa
+ mpledata/Tetracycline_resistance.csv -o Test1 --no-time
+ Traceback (most recent call last):
+ File "/<<PKGBUILDDIR>>/scoary.py", line 25, in <module>
+ methods.main()
+ File "/<<PKGBUILDDIR>>/scoary/methods.py", line 184, in main
+ with open(args.genes, "rU") as genes, \
+ ^^^^^^^^^^^^^^^^^^^^^^
+ ValueError: invalid mode: 'rU'
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2022-12-07
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- scoary.orig/scoary/methods.py
++++ scoary/scoary/methods.py
+@@ -181,15 +181,15 @@
+ cutoffs.pop(m,None)
+
+ # Start analysis
+- with open(args.genes, "rU") as genes, \
+- open(args.traits, "rU") as traits:
++ with open(args.genes, "r") as genes, \
++ open(args.traits, "r") as traits:
+
+ if args.restrict_to is not None:
+ # Note: Despite being a dictionary, the values of
+ # allowed_isolates are not currently used, only the keys
+ allowed_isolates = {isolate : "all"
+ for line in
+- open(args.restrict_to,"rU")
++ open(args.restrict_to,"r")
+ for isolate in line.rstrip().split(",")}
+ else:
+ # Despite the confusing name
+@@ -343,7 +343,7 @@
+
+ if writereducedset:
+ file = open(ReduceSet(genefile,delimiter, grabcols, startcol,
+- allowed_isolates,time,outdir),"rU")
++ allowed_isolates,time,outdir),"r")
+ csvfile = csv.reader(file, skipinitialspace=True,
+ delimiter=delimiter)
+ else:
+--- scoary.orig/scoary/vcf2scoary.py
++++ scoary/scoary/vcf2scoary.py
+@@ -100,7 +100,7 @@
+ if not os.path.isfile(args.vcf):
+ sys.exit("Unable to locate input file %s" % args.vcf)
+
+- with open(args.vcf,'rU') as vcffile, open(args.out,'w') as outfile:
++ with open(args.vcf,'r') as vcffile, open(args.out,'w') as outfile:
+ lines = csv.reader(vcffile, delimiter='\t', quotechar='"')
+ metainfo = {"##INFO" : {},
+ "##FILTER" : {},
+--- scoary.orig/tests/test_scoary_output.py
++++ scoary/tests/test_scoary_output.py
+@@ -20,7 +20,7 @@
+
+
+ for Test in ["1","2","4"]:
+- with open(os.getcwd() + "/Test" + Test + "/Tetracycline_resistance.results.csv" ,"rU") as resfile:
++ with open(os.getcwd() + "/Test" + Test + "/Tetracycline_resistance.results.csv" ,"r") as resfile:
+ tab = csv.reader(resfile, delimiter=",")
+ for i in range(2):
+ if i == 0:
+@@ -120,7 +120,7 @@
+ print("Not equal at Test %s col 17: %s %s" % (Test, data[17], str(reference[17])))
+ sys.exit(-1)
+
+-with open(os.getcwd() + "/mutations_presence_absence.csv" ,"rU") as vcfresfile:
++with open(os.getcwd() + "/mutations_presence_absence.csv" ,"r") as vcfresfile:
+ tab = csv.reader(vcfresfile, delimiter=",")
+ for i in range(2):
+ if i == 0:
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+python3.11.patch
=====================================
debian/rules
=====================================
@@ -8,5 +8,34 @@ export LC_ALL = C.UTF-8
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- echo "Test data are missing so we can not test"
+ # tests steps are described in .travis.yml
+ set -e \
+ ; for PYTHON3 in $(shell py3versions --supported) \
+ ; do \
+ $$PYTHON3 scoary.py \
+ -g scoary/exampledata/Gene_presence_absence.csv \
+ -t scoary/exampledata/Tetracycline_resistance.csv \
+ -o Test1 \
+ --no-time \
+ ; $$PYTHON3 scoary.py \
+ -g scoary/exampledata/Gene_presence_absence.csv \
+ -t scoary/exampledata/Tetracycline_resistance.csv \
+ --no_pairwise \
+ -o Test2 \
+ --no-time \
+ ; $$PYTHON3 scoary.py \
+ -g scoary/exampledata/Gene_presence_absence.csv \
+ -t scoary/exampledata/Tetracycline_resistance.csv \
+ -r scoary/exampledata/Restrict_to.csv \
+ -w -o Test3 --no-time \
+ ; $$PYTHON3 scoary.py \
+ -g scoary/exampledata/Gene_presence_absence.csv \
+ -t scoary/exampledata/Tetracycline_resistance.csv \
+ -p 0.01 1E-5 -c B EPW --collapse -m 50 -u \
+ -n scoary/exampledata/ExampleTree.nwk \
+ --threads 4 -o Test4 --no-time \
+ ; $$PYTHON3 scoary/vcf2scoary.py \
+ --force scoary/exampledata/Example.vcf \
+ ; $$PYTHON3 tests/test_scoary_output.py \
+ ; done
endif
View it on GitLab: https://salsa.debian.org/med-team/scoary/-/compare/10041f27ace4e2f155b8166a184855a760ea3049...24d87a93d2f9d981f16fbc42e2c3bcf0668aa3d1
--
View it on GitLab: https://salsa.debian.org/med-team/scoary/-/compare/10041f27ace4e2f155b8166a184855a760ea3049...24d87a93d2f9d981f16fbc42e2c3bcf0668aa3d1
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