[med-svn] [Git][med-team/macs][master] 2 commits: d/rules: s/MACS2/MACS3/g for new major version.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Thu Dec 14 12:40:27 GMT 2023
Michael R. Crusoe pushed to branch master at Debian Med / macs
Commits:
96467dc2 by Michael R. Crusoe at 2023-12-14T13:26:53+01:00
d/rules: s/MACS2/MACS3/g for new major version.
- - - - -
dba8863c by Michael R. Crusoe at 2023-12-14T13:31:47+01:00
d/patches/simde: doesn't need forwarding
- - - - -
7 changed files:
- debian/changelog
- debian/copyright
- debian/lintian-overrides
- debian/manpages
- debian/patches/simde.patch
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -13,6 +13,8 @@ macs (3.0.0-1) UNRELEASED; urgency=medium
* d/copyright: MACS2/khash.h→MACS3/fermi-lite/khash.h
* d/clean: remove temp/ directory leftover from test execution.
Closes: #1047612
+ * d/rules: s/MACS2/MACS3/g for new major version.
+ * d/patches/simde: doesn't need forwarding
-- Michael R. Crusoe <crusoe at debian.org> Wed, 15 Nov 2023 20:44:36 +0100
=====================================
debian/copyright
=====================================
@@ -1,5 +1,5 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: MACS2
+Upstream-Name: MACS3
Source: https://github.com/macs3-project/MACS
Files: *
=====================================
debian/lintian-overrides
=====================================
@@ -1 +1 @@
-macs: manpage-has-errors-from-man usr/share/man/man1/macs2.1.gz 8: warning [p 1, 1.7i]: cannot adjust line
+macs: manpage-has-errors-from-man usr/share/man/man1/macs3.1.gz 8: warning [p 1, 1.7i]: cannot adjust line
=====================================
debian/manpages
=====================================
@@ -1,13 +1,13 @@
-debian/macs2.1
-debian/macs2_bdgbroadcall.1
-debian/macs2_bdgcmp.1
-debian/macs2_bdgdiff.1
-debian/macs2_bdgopt.1
-debian/macs2_bdgpeakcall.1
-debian/macs2_callpeak.1
-debian/macs2_cmbreps.1
-debian/macs2_filterdup.1
-debian/macs2_pileup.1
-debian/macs2_predictd.1
-debian/macs2_randsample.1
-debian/macs2_refinepeak.1
+debian/macs3.1
+debian/macs3_bdgbroadcall.1
+debian/macs3_bdgcmp.1
+debian/macs3_bdgdiff.1
+debian/macs3_bdgopt.1
+debian/macs3_bdgpeakcall.1
+debian/macs3_callpeak.1
+debian/macs3_cmbreps.1
+debian/macs3_filterdup.1
+debian/macs3_pileup.1
+debian/macs3_predictd.1
+debian/macs3_randsample.1
+debian/macs3_refinepeak.1
=====================================
debian/patches/simde.patch
=====================================
@@ -1,5 +1,6 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Tue, 14 Nov 2023 10:43:27 +0100
+Forwarded: not-needed
Description: Fix location of simde header
--- a/MACS3/fermi-lite/ksw.c
=====================================
debian/rules
=====================================
@@ -1,6 +1,6 @@
#!/usr/bin/make -f
-export PYBUILD_NAME=MACS2
+export PYBUILD_NAME=MACS3
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
include /usr/share/dpkg/default.mk
@@ -14,21 +14,21 @@ tagline=\- Model\-based Analysis for ChIP\-Sequencing
dh $@ --buildsystem=pybuild
override_dh_auto_build:
- for pyx in $$(find MACS2/ -name "*.pyx"); do \
+ for pyx in $$(find MACS3/ -name "*.pyx"); do \
rm -f $${pyx%%.pyx}.{h,c}; touch $${pyx}; done
dh_auto_build
- PYTHONPATH=./.pybuild/cpython3_$$(py3versions -v -d)_MACS2/build/ help2man \
+ PYTHONPATH=./.pybuild/cpython3_$$(py3versions -v -d)_MACS3/build/ help2man \
--no-discard-stderr --no-info \
- --name "macs2 ${tagline}" "python3 bin/macs2" > debian/macs2.1
+ --name "macs3 ${tagline}" "python3 bin/macs3" > debian/macs3.1
for subcommand in ${subcommands}; do printf \
- "[NAME]\nmacs2_$${subcommand} ${tagline}\n" \
- > debian/macs2_$${subcommand}-man-include; done
+ "[NAME]\nmac3_$${subcommand} ${tagline}\n" \
+ > debian/macs3_$${subcommand}-man-include; done
for subcommand in ${subcommands}; do \
- PYTHONPATH=./.pybuild/cpython3_$$(py3versions -v -d)_MACS2/build/ help2man \
+ PYTHONPATH=./.pybuild/cpython3_$$(py3versions -v -d)_MACS3/build/ help2man \
--no-discard-stderr --no-info --version-string="$(DEB_VERSION_UPSTREAM)" \
- --include debian/macs2_$${subcommand}-man-include \
- "python3 bin/macs2 $${subcommand}" > \
- debian/macs2_$${subcommand}.1; done
+ --include debian/macs3_$${subcommand}-man-include \
+ "python3 bin/macs3 $${subcommand}" > \
+ debian/macs3_$${subcommand}.1; done
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
@@ -36,7 +36,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
ifeq (,$(filter $(DEB_HOST_ARCH),arm64 ppc64el s390x))
cd test && for PY3VER in $(shell py3versions -vs); do \
export PATH=$(CURDIR)/build/scripts-$${PY3VER}:$$PATH \
- && export PYTHONPATH=$(CURDIR)/.pybuild/cpython3_$${PY3VER}_MACS2/build \
+ && export PYTHONPATH=$(CURDIR)/.pybuild/cpython3_$${PY3VER}_MACS3/build \
&& ./cmdlinetest macs$(DEB_VERSION)-$${PY3VER} ; done
endif
endif
=====================================
debian/tests/run-unit-test
=====================================
@@ -15,5 +15,5 @@ cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
cd $AUTOPKGTEST_TMP
gunzip *.gz
-macs2 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01
-macs2 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1
+macs3 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01
+macs3 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1
View it on GitLab: https://salsa.debian.org/med-team/macs/-/compare/eb8c4902c0b2a0251a1c4f0f73acfda7bf5dae1c...dba8863c0388b0a67a494ca81bebac8b0ab3e6ab
--
View it on GitLab: https://salsa.debian.org/med-team/macs/-/compare/eb8c4902c0b2a0251a1c4f0f73acfda7bf5dae1c...dba8863c0388b0a67a494ca81bebac8b0ab3e6ab
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