Andreas Tille pushed to branch master at Debian Med / resfinder
Commits: 352027b4 by Andreas Tille at 2020-12-04T22:44:23+01:00 Install Python modules - - - - - 181976df by Andreas Tille at 2020-12-04T23:10:32+01:00 Set path in testscript, do not install trash - - - - - 8d0a15dd by Andreas Tille at 2020-12-04T23:12:12+01:00 Fix syntax - - - - - 5dfddc29 by Andreas Tille at 2020-12-04T23:33:18+01:00 Work arround not-executable test script - - - - - 7 changed files: - debian/changelog - + debian/patches/fix_path_in_testscript.patch - + debian/patches/fix_syntax.patch - + debian/patches/series - debian/resfinder.install - debian/rules - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -3,8 +3,6 @@ resfinder (4.0.1-1) UNRELEASED; urgency=medium * New upstream version * debhelper-compat 13 (routine-update) * resfinder.py is now run_resfinder.py - TODO: No idea how to properly test the package, asked upstream in - https://bitbucket.org/genomicepidemiology/resfinder/issues/31/how-to-properly-test-resfinder -- Andreas Tille <[email protected]> Sat, 03 Oct 2020 12:00:25 +0200 ===================================== debian/patches/fix_path_in_testscript.patch ===================================== @@ -0,0 +1,51 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Sat, 03 Oct 2020 12:00:25 +0200 +Description: run_resfinder.py is in PATH + +--- a/tests/functional_tests.py ++++ b/tests/functional_tests.py +@@ -70,7 +70,7 @@ class ResFinderRunTest(unittest.TestCase + # She therefore runs resfinder cmd line. + + # First Maria checks out the documentation. +- procs = run("python3 ../run_resfinder.py -h", shell=True, stdout=PIPE, ++ procs = run("run_resfinder.py -h", shell=True, stdout=PIPE, + check=True) + output = procs.stdout.decode() + self.assertIn("--help", output) +@@ -81,7 +81,7 @@ class ResFinderRunTest(unittest.TestCase + test1_dir = run_test_dir + "/" + test_names[0] + os.makedirs(test1_dir) + # Then she runs run_resfinder with her first isolate. +- cmd_acquired = ("python3 " + self.dir_res + "/run_resfinder.py" ++ cmd_acquired = ("run_resfinder.py" + + " -ifa " + test_data[test_names[0]] + + " -o " + test1_dir + + " -s 'Escherichia coli'" +@@ -139,7 +139,7 @@ class ResFinderRunTest(unittest.TestCase + os.makedirs(test2_dir, exist_ok=False) + + # Then she runs run_resfinder with her first isolate. +- cmd_acquired = ("python3 " + self.dir_res + "/run_resfinder.py" ++ cmd_acquired = ("run_resfinder.py" + + " -ifq " + test_data[test_names[1]] + + " -o " + test2_dir + + " -s 'Escherichia coli'" +@@ -196,7 +196,7 @@ class ResFinderRunTest(unittest.TestCase + os.makedirs(test3_dir) + + # Then she runs run_resfinder with her first isolate. +- cmd_point = ("python3 " + self.dir_res + "/run_resfinder.py" ++ cmd_point = ("run_resfinder.py" + + " -ifa " + test_data[test_names[2]] + + " -o " + test3_dir + + " -s 'Escherichia coli'" +@@ -240,7 +240,7 @@ class ResFinderRunTest(unittest.TestCase + os.makedirs(test4_dir, exist_ok=False) + + # Then she runs run_resfinder with her first isolate. +- cmd_acquired = ("python3 " + self.dir_res + "/run_resfinder.py" ++ cmd_acquired = ("run_resfinder.py" + + " -ifq " + test_data[test_names[3]] + + " -o " + test4_dir + + " -s 'Escherichia coli'" ===================================== debian/patches/fix_syntax.patch ===================================== @@ -0,0 +1,15 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Sat, 03 Oct 2020 12:00:25 +0200 +Description: Fix syntax + +--- a/cge/resfinder.py ++++ b/cge/resfinder.py +@@ -424,7 +424,7 @@ class ResFinder(CGEFinder): + """ + """ + # Check if databases and config file are correct/correponds +- if databases is '': ++ if databases == '': + sys.exit("Input Error: No database was specified!\n") + elif databases is None: + # Choose all available databases from the config file ===================================== debian/patches/series ===================================== @@ -0,0 +1,2 @@ +fix_path_in_testscript.patch +fix_syntax.patch ===================================== debian/resfinder.install ===================================== @@ -1 +1,3 @@ *.py usr/share/resfinder +cge usr/share/resfinder +scripts usr/share/resfinder ===================================== debian/rules ===================================== @@ -3,5 +3,9 @@ %: dh $@ --with python3 +override_dh_install: + dh_install + find debian -name trash -type d | xargs rm -rf + override_dh_installman: dh_installman --language=C ===================================== debian/tests/run-unit-test ===================================== @@ -15,4 +15,4 @@ cd "${AUTOPKGTEST_TMP}" gunzip -r * -python3 unit_tests.py +python3 functional_tests.py View it on GitLab: https://salsa.debian.org/med-team/resfinder/-/compare/19f0c5e316810b942e7cd24f3ad95d09550b95a3...5dfddc299f3f20dbf1650934eb4baa79e5303652 -- View it on GitLab: https://salsa.debian.org/med-team/resfinder/-/compare/19f0c5e316810b942e7cd24f3ad95d09550b95a3...5dfddc299f3f20dbf1650934eb4baa79e5303652 You're receiving this email because of your account on salsa.debian.org.
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