[med-svn] [Git][med-team/bcbio][master] 2 commits: routine-update: Standards-Version: 4.6.2

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / bcbio


Commits:
cb269b87 by Andreas Tille at 2023-12-10T16:12:06+01:00
routine-update: Standards-Version: 4.6.2

- - - - -
853bd873 by Andreas Tille at 2023-12-10T16:13:12+01:00
[skip ci] routine-update: Build-Depends: s/dh-python/dh-sequence-python3/

- - - - -


3 changed files:

- debian/changelog
- debian/control
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -8,6 +8,8 @@ bcbio (1.2.9-3) UNRELEASED; urgency=medium
   * Do not ship empty manpage
   * Use pytest instead of node
     Closes: #1018312
+  * Standards-Version: 4.6.2 (routine-update)
+  * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
 
  -- Andreas Tille <tille at debian.org>  Tue, 07 Feb 2023 10:58:48 +0100
 


=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Testsuite: autopkgtest-pkg-python
 XS-Autobuild: no
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               dh-python,
+               dh-sequence-python3,
                python3-all,
                python3-setuptools,
                python3-gffutils,
@@ -14,7 +14,6 @@ Build-Depends: debhelper-compat (= 13),
                python3-pandas,
                python3-pybedtools,
                python3-pysam,
-               python3-pyvcf,
                python3-toolz,
                python3-tornado,
                python3-yaml,
@@ -81,7 +80,7 @@ Build-Depends: debhelper-compat (= 13),
                libhts-dev <!nocheck>,
 # documentation
                python3-sphinx
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/bcbio
 Vcs-Git: https://salsa.debian.org/med-team/bcbio.git
 Homepage: https://github.com/bcbio/bcbio-nextgen
@@ -113,7 +112,6 @@ Recommends: cnvkit,
             python3-arrow,
             python3-geneimpacts,
             python3-h5py,
-            python3-pyvcf,
 #            python3-seqcluster,
             python3-statsmodels,
             python3-tabulate,
@@ -124,8 +122,7 @@ Recommends: cnvkit,
             snpeff,
             vcfanno,
             vt
-Suggests: bcbio-doc,
-          python3-bioblend,
+Suggests: python3-bioblend,
           python3-dnapilib,
           python3-msgpack,
           python3-seqcluster
@@ -173,7 +170,6 @@ Recommends: bcftools,
 Suggests: toil,
           cwltool,
           kallisto,
-          bcbio-doc,
 # still missing lumpy-sv,
 # still missing manta,
 # non-free, install manually: novoalign,


=====================================
debian/rules
=====================================
@@ -5,7 +5,7 @@ export PYBUILD_NAME=bcbio
 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
+	dh $@ --with sphinxdoc --buildsystem=pybuild
 
 override_dh_auto_build:
 	dh_auto_build



View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/e201be54f1a17f0e6841a6cb65e8a0b0eae48c5e...853bd873ac91ca67b0f271c6a4f7e7b8e152fd24

-- 
View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/compare/e201be54f1a17f0e6841a6cb65e8a0b0eae48c5e...853bd873ac91ca67b0f271c6a4f7e7b8e152fd24
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