[med-svn] [Git][med-team/bcbio][master] 6 commits: Drop python3-seqcluster from Build-Depends and downgrade from Recommends to Suggests
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Dec 10 15:03:17 GMT 2023
Andreas Tille pushed to branch master at Debian Med / bcbio
Commits:
dc284531 by Andreas Tille at 2023-02-07T09:52:59+01:00
Drop python3-seqcluster from Build-Depends and downgrade from Recommends to Suggests
- - - - -
49e5916c by Andreas Tille at 2023-02-07T10:14:08+01:00
Fix lintian-overrides about script-with-language-extension
- - - - -
db383802 by Andreas Tille at 2023-02-07T10:58:39+01:00
DEP3
- - - - -
5c4207e9 by Andreas Tille at 2023-02-07T11:03:41+01:00
Upload to unstable
- - - - -
e7f3c276 by Andreas Tille at 2023-02-07T11:06:46+01:00
Do not ship empty manpage
- - - - -
e201be54 by Andreas Tille at 2023-12-10T16:02:58+01:00
Use pytest instead of node
- - - - -
10 changed files:
- debian/bcbio.lintian-overrides
- debian/bcbio.manpages
- debian/changelog
- debian/control
- debian/patches/add_installed_dir_paths.patch
- debian/patches/cnvkitPath.patch
- debian/patches/hts_nim_tools.patch
- debian/patches/pytest2to3.patch
- debian/patches/pythonpaths.patch
- debian/rules
Changes:
=====================================
debian/bcbio.lintian-overrides
=====================================
@@ -1,8 +1,4 @@
# Better not mess with the community that expects these binaries
# just like they are.
-bcbio: script-with-language-extension usr/bin/bcbio_fastq_umi_prep.py
-bcbio: script-with-language-extension usr/bin/bcbio_nextgen.py
-bcbio: script-with-language-extension usr/bin/bcbio_prepare_samples.py
-bcbio: script-with-language-extension usr/bin/bcbio_setup_genome.py
-bcbio: script-with-language-extension usr/bin/cwltool2wdl.py
+bcbio: script-with-language-extension
=====================================
debian/bcbio.manpages
=====================================
@@ -1 +1,2 @@
-build/man/bcbio_nextgen.1
+# FIXME: This manpage is empty
+# build/man/bcbio_nextgen.1
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+bcbio (1.2.9-3) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Drop python3-seqcluster from Build-Depends and downgrade from
+ Recommends to Suggests
+ * Fix lintian-overrides about script-with-language-extension
+ * DEP3
+ * Do not ship empty manpage
+ * Use pytest instead of node
+ Closes: #1018312
+
+ -- Andreas Tille <tille at debian.org> Tue, 07 Feb 2023 10:58:48 +0100
+
bcbio (1.2.9-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -48,11 +48,10 @@ Build-Depends: debhelper-compat (= 13),
python3-cyvcf2 <!nocheck>,
python3-geneimpacts <!nocheck>,
python3-logbook <!nocheck>,
- python3-nose <!nocheck>,
python3-requests <!nocheck>,
python3-pytest <!nocheck>,
python3-pytest-mock <!nocheck>,
- python3-seqcluster <!nocheck>,
+# python3-seqcluster <!nocheck>,
pythonpy <!nocheck>,
rapmap <!nocheck>,
rna-star <!nocheck>,
@@ -115,7 +114,7 @@ Recommends: cnvkit,
python3-geneimpacts,
python3-h5py,
python3-pyvcf,
- python3-seqcluster,
+# python3-seqcluster,
python3-statsmodels,
python3-tabulate,
r-other-wasabi,
@@ -128,7 +127,8 @@ Recommends: cnvkit,
Suggests: bcbio-doc,
python3-bioblend,
python3-dnapilib,
- python3-msgpack
+ python3-msgpack,
+ python3-seqcluster
Description: library for analysing high-throughput sequencing data
This package installs the Python 3 libraries of the bcbio-nextgen
toolkit implementing best-practice pipelines for fully automated high
=====================================
debian/patches/add_installed_dir_paths.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Möller
+Last-Update: 2019-04-14 16:41:16 +0200
+Description: Enable finding installed modules at build time test
+
Index: bcbio/tests/run_tests.sh
===================================================================
--- bcbio.orig/tests/run_tests.sh
=====================================
debian/patches/cnvkitPath.patch
=====================================
@@ -1,3 +1,10 @@
+Author: Steffen Moeller
+Last-Update: 2020-11-14 22:30:48 +0100
+Description: Deal with renamed cnvkit binary
+FIXME: Probably we should rather provide /usr/bin/cnvkit.py in cnvkit package
+ since we decided to diverge from Debian Policy in
+ https://lists.debian.org/debian-med/2018/06/msg00043.html
+
Index: bcbio/bcbio/structural/cnvkit.py
===================================================================
--- bcbio.orig/bcbio/structural/cnvkit.py
=====================================
debian/patches/hts_nim_tools.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2020-11-13 23:16:13 +0100
+Description: Use dash ('-') in file name of hts-nim-tools binary
+
Index: bcbio/bcbio/bam/readstats.py
===================================================================
--- bcbio.orig/bcbio/bam/readstats.py
=====================================
debian/patches/pytest2to3.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2020-11-13 23:16:13 +0100
+Description: Use Python3
+
Index: bcbio/tests/run_tests.sh
===================================================================
--- bcbio.orig/tests/run_tests.sh
=====================================
debian/patches/pythonpaths.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2020-11-13 23:16:13 +0100
+Description: Fix interpreter name to python3
+
Index: bcbio/scripts/bcbio_fastq_umi_prep.py
===================================================================
--- bcbio.orig/scripts/bcbio_fastq_umi_prep.py
=====================================
debian/rules
=====================================
@@ -2,10 +2,8 @@
export DH_VERBOSE = 1
export PYBUILD_NAME=bcbio
-export PYBUILD_DISABLE=test # not quite ready
export PYBUILD_TEST_ARGS= -p no:cacheprovider -p no:stepwise -k 'not S3 and not rnaseq and not fusion and not srnaseq and not chipseq and not install_required and not devel and not template and not hla and not combo'
-
%:
dh $@ --with python3,sphinxdoc --buildsystem=pybuild
View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/797da3afb5d78c3a887f509a4d0b36733df81235...e201be54f1a17f0e6841a6cb65e8a0b0eae48c5e
--
View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/797da3afb5d78c3a887f509a4d0b36733df81235...e201be54f1a17f0e6841a6cb65e8a0b0eae48c5e
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