[med-svn] [Git][med-team/macs][master] 2 commits: add patch to force the use of Python3.

[Michael R. Crusoe (@crusoe)]

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 <crusoe at 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 <crusoe at 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
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