[med-svn] [Git][med-team/last-align][master] 6 commits: Move python3 to Depends
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Fri Aug 6 10:26:24 BST 2021
Nilesh Patra pushed to branch master at Debian Med / last-align
Commits:
f5f90b0c by Nilesh Patra at 2021-08-06T13:35:24+05:30
Move python3 to Depends
- - - - -
4bb29a02 by Nilesh Patra at 2021-08-06T13:38:29+05:30
d/salsa-ci.yml: Disable blhc and reprotest
- - - - -
a485a615 by Nilesh Patra at 2021-08-06T09:04:44+00:00
d/rules: Add rest manpages, install fastq-interleave
- - - - -
c2204c68 by Nilesh Patra at 2021-08-06T14:42:28+05:30
Add lintian override for maf-cut manpage
- - - - -
3c063793 by Nilesh Patra at 2021-08-06T14:50:29+05:30
Remove allow-stderr restriction on last-test
- - - - -
95c8dfbb by Nilesh Patra at 2021-08-06T14:55:34+05:30
Interim changelog entry
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/lintian-overrides
- debian/rules
- debian/salsa-ci.yml
- debian/tests/control
Changes:
=====================================
debian/changelog
=====================================
@@ -1,20 +1,26 @@
last-align (1250-1) UNRELEASED; urgency=medium
- [ Nilesh Patra ]
* d/watch: Fix fetch URL - last-align has moved to gitlab
* New upstream version 1250
* d/p/2to3.patch: scripts has moved to bin, change
* d/p/helpMakefiles.patch: Refresh helpmakefile.patch
* d/p/simde: Attempt adapting simde to new upstream
- * d/rules: Attempt adapting to new upstream version
+ * d/rules:
+ - Attempt adapting to new upstream version
+ - Add rest manpages
+ - Install all lastdb5 based binaries
+ - Install new fasta+fastq scripts
* Add shebang for fasta-nr
* d/debian/last-align.doc-base.last-align-manual:
The manual page has moved to last-cookbook.rst
-
- [ Andreas Tille ]
- * DEP3
-
- -- Nilesh Patra <nilesh at debian.org> Sun, 11 Jul 2021 02:05:04 +0530
+ * d/tests/last-test: Add additional tests
+ * d/control: Move python3 to Depends
+ - There are several python3 scripts being vendored, it does make
+ sense to promote python3 to depends
+ * d/salsa-ci.yml: Disable blhc and reprotest
+ * d/lintian-overrides: Add lintian override for maf-cut manpage
+
+ -- Nilesh Patra <nilesh at debian.org> Fri, 06 Aug 2021 14:51:19 +0530
last-align (1179-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -19,9 +19,9 @@ Rules-Requires-Root: no
Package: last-align
Architecture: any
Depends: ${shlibs:Depends},
- ${misc:Depends}
-Recommends: python3,
- python3-pil,
+ ${misc:Depends},
+ python3
+Recommends: python3-pil,
parallel
Built-Using: ${Built-Using}
Description: genome-scale comparison of biological sequences
=====================================
debian/lintian-overrides
=====================================
@@ -0,0 +1,6 @@
+# This manpage renders nicely
+W: last-align: useless-whatis-entry usr/share/man/man1/maf-cut.1.gz
+# These manpages render bad, so do not vendor them at all
+last-align: no-manual-page usr/bin/lastdb5
+last-align: no-manual-page usr/bin/parallel-fasta
+last-align: no-manual-page usr/bin/parallel-fastq
=====================================
debian/rules
=====================================
@@ -58,7 +58,7 @@ override_dh_auto_install:
ifeq (amd64,$(DEB_HOST_ARCH))
dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/
dh_install bin/lastdb-* bin/lastal-* bin/last-split-* bin/last-merge-batches-* bin/last-pair-probs-* bin/lastdb5-* bin/lastal5-* bin/last-split5-* usr/lib/last-align
- dh_install bin/fasta-* bin/last-dotplot bin/last-map-probs bin/last-postmask bin/last-train bin/maf-* bin/parallel-fast* usr/bin
+ dh_install bin/fastq-* bin/fasta-* bin/last-dotplot bin/last-map-probs bin/last-postmask bin/last-train bin/maf-* bin/parallel-fast* usr/bin
mkdir -p $(prefix)/bin
cd $(prefix)/bin \
&& for prog in lastdb lastal last-split last-merge-batches last-pair-probs lastdb5 lastal5 last-split5 ; do \
@@ -66,7 +66,7 @@ ifeq (amd64,$(DEB_HOST_ARCH))
else ifeq (i386,$(DEB_HOST_ARCH))
dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/
dh_install bin/lastdb-* bin/lastal-* bin/last-split-* bin/last-merge-batches-* bin/last-pair-probs-* bin/lastdb5-* bin/lastal5-* bin/last-split5-* usr/lib/last-align
- dh_install bin/fasta-* bin/last-dotplot bin/last-map-probs bin/last-postmask bin/last-train bin/maf-* bin/parallel-fast* usr/bin
+ dh_install bin/fastq-* bin/fasta-* bin/last-dotplot bin/last-map-probs bin/last-postmask bin/last-train bin/maf-* bin/parallel-fast* usr/bin
mkdir -p $(prefix)/bin
cd $(prefix)/bin \
&& for prog in lastdb lastal last-split last-merge-batches last-pair-probs lastdb5 lastal5 last-split5 ; do \
@@ -141,6 +141,9 @@ override_dh_installman:
$(HELP2MAN) \
--name="Join two or more sets of MAF-format multiple alignments" \
$(CURDIR)/bin/maf-join > $(mandir)/maf-join.1
+ $(HELP2MAN) \
+ --help-option="-h" \
+ $(CURDIR)/bin/maf-cut > $(mandir)/maf-cut.1
$(HELP2MAN) \
--name="Convert MAF-format alignments to tabular format" \
$(CURDIR)/bin/maf-convert > $(mandir)/maf-convert.1
@@ -160,6 +163,9 @@ override_dh_installman:
$(HELP2MAN) \
--name="Try to find suitable score parameters for aligning the given sequences" \
$(CURDIR)/bin/last-train > $(mandir)/last-train.1
-
+ $(HELP2MAN) \
+ --name="Keep the first of identical sequences" \
+ --help-option="-h" \
+ $(prefix)/bin/fasta-nr > $(mandir)/fasta-nr.1
override_dh_gencontrol:
dh_gencontrol -- -VBuilt-Using="$(BUILT_USING)"
=====================================
debian/salsa-ci.yml
=====================================
@@ -2,3 +2,7 @@
include:
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+
+variables:
+ SALSA_CI_DISABLE_BLHC: 1
+ SALSA_CI_DISABLE_REPROTEST: 1
=====================================
debian/tests/control
=====================================
@@ -4,4 +4,3 @@ Restrictions: allow-stderr
Tests: last-test
Depends: @
-Restrictions: allow-stderr
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/7a532a9000e731c35cad0a0f7ed73e01aa844c38...95c8dfbb4cb77b796ef8f9c7abbe6a5cb0eb2b04
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/7a532a9000e731c35cad0a0f7ed73e01aa844c38...95c8dfbb4cb77b796ef8f9c7abbe6a5cb0eb2b04
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