Michael R. Crusoe pushed to branch master at Debian Med / macs
Commits: 5b4d0846 by Michael R. Crusoe at 2024-02-23T17:02:29+01:00 add patch to force the use of Python3. - - - - - 1ee064da by Michael R. Crusoe at 2024-02-23T17:02:30+01:00 d/control: add build-dep on bc for the tests. - - - - - 4 changed files: - debian/changelog - debian/control - + debian/patches/python3 - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -27,6 +27,8 @@ macs (3.0.1-1) UNRELEASED; urgency=medium 16.18.3 checking hmmratac hmmratac_yeast500k_load_hmm_model_accessible_regions.gappedPeak 16.18.4 checking hmmratac hmmratac_yeast500k_load_training_regions_accessible_regions.gappedPeak * d/patch/no_install_depends_cython.patch removed, applied upstream. + * add patch to force the use of Python3. + * d/control: add build-dep on bc for the tests. -- Michael R. Crusoe <cru...@debian.org> Fri, 23 Feb 2024 14:26:24 +0100 ===================================== debian/control ===================================== @@ -17,7 +17,8 @@ Build-Depends: debhelper-compat (= 13), libsimde-dev, cython3, help2man, - procps + procps, + bc Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/macs Vcs-Git: https://salsa.debian.org/med-team/macs.git ===================================== debian/patches/python3 ===================================== @@ -0,0 +1,36 @@ +From: Michael R. Crusoe <cru...@debian.org> +Subject: explictly use Python version 3 +Forwarded: https://github.com/macs3-project/MACS/pull/623 +--- macs.orig/test/cmdlinetest ++++ macs/test/cmdlinetest +@@ -280,7 +280,7 @@ + # the similar using jaccard index + if [[ "$fq" == *.bed || "$fq" == *.gappedPeak || "$fq" == *.narrowPeak || "$fq" == *.bed12 ]]; then + # for peaks, we will use our jaccard index script to check +- ji=$(python ./jaccard.py "$fq" "$fs") ++ ji=$(python3 ./jaccard.py "$fq" "$fs") + # Compare the output value + if (( $(echo "$ji > 0.99" | bc -l) )); then + echo " ... success! Results are different but Jaccard Index is $ji (>0.99)" +--- macs.orig/test/cmdlinetest-nohmmratac ++++ macs/test/cmdlinetest-nohmmratac +@@ -280,7 +280,7 @@ + # the similar using jaccard index + if [[ "$fq" == *.bed || "$fq" == *.gappedPeak || "$fq" == *.narrowPeak || "$fq" == *.bed12 ]]; then + # for peaks, we will use our jaccard index script to check +- ji=$(python ./jaccard.py "$fq" "$fs") ++ ji=$(python3 ./jaccard.py "$fq" "$fs") + # Compare the output value + if (( $(echo "$ji > 0.99" | bc -l) )); then + echo " ... success! Results are different but Jaccard Index is $ji (>0.99)" +--- macs.orig/test/pyprofile ++++ macs/test/pyprofile +@@ -21,7 +21,7 @@ + CMD=${CMD[@]: 1} + + # run CMD with cProfile +-python -m cProfile -o $PROF $CMD ++python3 -m cProfile -o $PROF $CMD + + # brief the profile + ./pyprofile_stat $PROF tottime > ${PROF/.prof/}.tottime ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ +python3 keep_debug simde.patch View it on GitLab: https://salsa.debian.org/med-team/macs/-/compare/4b0afdebec23eef182dd363ff8023e10a84a716b...1ee064daf6a894783b157c69644703a491a3d5d1 -- View it on GitLab: https://salsa.debian.org/med-team/macs/-/compare/4b0afdebec23eef182dd363ff8023e10a84a716b...1ee064daf6a894783b157c69644703a491a3d5d1 You're receiving this email because of your account on salsa.debian.org.
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