Michael R. Crusoe pushed to branch master at Debian Med / cwltool
Commits: 9a31f8d0 by Michael R. Crusoe at 2023-08-21T17:01:16+02:00 Whoops, fix debian release number - - - - - 6158522d by Michael R. Crusoe at 2023-08-22T15:30:02+02:00 d/control: Update breaks for Toil to be less than 5.11.0. - - - - - 462dbf08 by Michael R. Crusoe at 2023-08-22T15:33:42+02:00 d/test/run-tests: cleanup temp directory automatically. - - - - - 4c7724d1 by Michael R. Crusoe at 2023-08-22T16:20:58+02:00 debian/patches/test_relax_whitespace_check: add patch to fix a test that was having issues with varying terminal widths. - - - - - 0d7f4ed8 by Michael R. Crusoe at 2023-08-22T16:20:58+02:00 d/control: add jq to build-deps to enable another test. - - - - - be764ac4 by Michael R. Crusoe at 2023-08-22T16:23:14+02:00 routine-update: Ready to upload to unstable - - - - - 7 changed files: - debian/changelog - debian/control - debian/patches/python3 - debian/patches/series - + debian/patches/test_relax_whitespace_check - debian/tests/control - debian/tests/run-tests Changes: ===================================== debian/changelog ===================================== @@ -1,13 +1,18 @@ cwltool (3.1.20230719185429-2) unstable; urgency=medium - * d/control: require setuptools, not distutilts + * d/control: Update breaks for Toil to be less than 5.11.0. + * d/test/run-tests: cleanup temp directory automatically. + * debian/patches/test_relax_whitespace_check: add patch to fix a test + that was having issues with varying terminal widths. + * d/control: add jq to build-deps to enable another test. - -- Michael R. Crusoe <[email protected]> Mon, 21 Aug 2023 14:31:32 +0200 + -- Michael R. Crusoe <[email protected]> Tue, 22 Aug 2023 16:23:14 +0200 cwltool (3.1.20230719185429-1) unstable; urgency=medium * New upstream version * d/control: add build-dep on python3-importlib-resources + * d/control: require setuptools, not distutilts -- Michael R. Crusoe <[email protected]> Tue, 08 Aug 2023 20:49:27 +0200 ===================================== debian/control ===================================== @@ -34,6 +34,7 @@ Build-Depends: debhelper-compat (= 13), python3-argcomplete <!nocheck> <!nodoc>, python3-typing-extensions <!nocheck> <!nodoc>, nodejs <!nocheck>, + jq <!nocheck>, help2man Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/cwltool @@ -52,7 +53,7 @@ Depends: ${python3:Depends}, python3-setuptools Recommends: nodejs Suggests: podman | docker.io | singularity-container -Breaks: toil (<< 5.6) +Breaks: toil (<< 5.12.0) Provides: cwl-runner Description: Common Workflow Language reference implementation This is the reference implementation of the Common Workflow Language ===================================== debian/patches/python3 ===================================== @@ -1,6 +1,7 @@ -Author: Michael R. Crusoe <[email protected]> -Description: Use python3 in test CWL tool description -Forwarded: not-needed +From: Michael R. Crusoe <[email protected]> +Subject: Use python3 in test CWL tool description +Forwarded: https://github.com/common-workflow-language/cwltool/pull/1893 + --- cwltool.orig/tests/wf/echo.cwl +++ cwltool/tests/wf/echo.cwl @@ -21,4 +21,4 @@ ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ disable_prov python3 +test_relax_whitespace_check ===================================== debian/patches/test_relax_whitespace_check ===================================== @@ -0,0 +1,14 @@ +From: Michael R. Crusoe <[email protected]> +Subject: Cope with narrower terminal +Forwarded: https://github.com/common-workflow-language/cwltool/pull/1893 + +--- cwltool.orig/tests/test_examples.py ++++ cwltool/tests/test_examples.py +@@ -1850,6 +1850,7 @@ + ] + ) + assert exit_code == 1, stderr ++ stderr = re.sub(r"\n\s+", " ", stderr) + stderr = re.sub(r"\s\s+", " ", stderr) + assert "Tool definition failed validation:" in stderr + assert ( ===================================== debian/tests/control ===================================== @@ -1,3 +1,3 @@ Tests: run-tests -Depends: @, python3-pytest-xdist, python3-pytest-mock, python3-pytest-runner, nodejs, curl, python3-mock, procps, python3-pytest (>> 6.2) +Depends: @, python3-pytest-xdist, python3-pytest-mock, python3-pytest-runner, nodejs, curl, python3-mock, procps, python3-pytest (>> 6.2), jq Restrictions: allow-stderr ===================================== debian/tests/run-tests ===================================== @@ -1,19 +1,18 @@ -#!/bin/sh -ex +#!/bin/bash +set -ex -pkg=packagename -if [ "$AUTOPKGTEST_TMP" = "" ] ; then - AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) +pkg=cwltool + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + # shellcheck disable=SC2064 + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM fi cd "$AUTOPKGTEST_TMP" export HOME=${AUTOPKGTEST_TMP} -SKIPS= -# if [ "$(id -u)" -eq 0 ]; then -# SKIPS="-k 'not TestUdocker and not test_use_metadata'" -# else -# SKIPS="-k 'not test_use_metadata'" -# fi py.test-3 --numprocesses=auto --ignore=cwltool/schemas -rs \ --ignore=/usr/lib/python3/dist-packages/cwltool/tests/test_http_input.py \ -k 'not (test_udocker_usage_should_not_write_cid_file or test_udocker_should_display_memory_usage or test_udocker_nobanner)' \ View it on GitLab: https://salsa.debian.org/med-team/cwltool/-/compare/eb9250b596120ded1c96c4046c44639de6e0cbaa...be764ac4a3e1b30133b883bfacf9f553be5858e5 -- View it on GitLab: https://salsa.debian.org/med-team/cwltool/-/compare/eb9250b596120ded1c96c4046c44639de6e0cbaa...be764ac4a3e1b30133b883bfacf9f553be5858e5 You're receiving this email because of your account on salsa.debian.org.
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