[med-svn] [Git][med-team/pbsuite][master] 9 commits: routine-update: Standards-Version: 4.5.0
Andreas Tille
gitlab at salsa.debian.org
Sat Apr 18 07:41:40 BST 2020
Andreas Tille pushed to branch master at Debian Med / pbsuite
Commits:
f420b9bf by Andreas Tille at 2020-04-18T08:36:27+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
389447b9 by Andreas Tille at 2020-04-18T08:36:28+02:00
routine-update: debhelper-compat 12
- - - - -
04b2f9bb by Andreas Tille at 2020-04-18T08:36:35+02:00
routine-update: Secure URI in copyright format
- - - - -
a7569f3d by Andreas Tille at 2020-04-18T08:36:35+02:00
R-U: Trailing whitespace in debian/copyright
- - - - -
bf94ebd9 by Andreas Tille at 2020-04-18T08:36:35+02:00
routine-update: Add salsa-ci file
- - - - -
87399aad by Andreas Tille at 2020-04-18T08:36:36+02:00
routine-update: Rules-Requires-Root: no
- - - - -
2d254970 by Andreas Tille at 2020-04-18T08:36:36+02:00
debian/copyright: use spaces rather than tabs to start continuation lines..
Fixes: lintian: tab-in-license-text
See-also: https://lintian.debian.org/tags/tab-in-license-text.html
- - - - -
aa2abff4 by Andreas Tille at 2020-04-18T08:36:44+02:00
Set upstream metadata fields: Archive, Repository.
- - - - -
96d55ae3 by Andreas Tille at 2020-04-18T08:40:45+02:00
routine-update: Ready to upload to unstable
- - - - -
6 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/salsa-ci.yml
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+pbsuite (15.8.24+dfsg-5) unstable; urgency=medium
+
+ * Team upload.
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 12 (routine-update)
+ * Secure URI in copyright format (routine-update)
+ * Remove trailing whitespace in debian/copyright (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * debian/copyright: use spaces rather than tabs to start continuation
+ lines.
+ * Set upstream metadata fields: Archive, Repository.
+
+ -- Andreas Tille <tille at debian.org> Sat, 18 Apr 2020 08:36:45 +0200
+
pbsuite (15.8.24+dfsg-4) unstable; urgency=medium
* Switch to python3 (Closes: #937258).
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,13 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Olivier Sallou <osallou at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
dh-python,
python3-all
-Standards-Version: 4.2.0
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/pbsuite
Vcs-Git: https://salsa.debian.org/med-team/pbsuite.git
Homepage: http://sourceforge.net/projects/pb-jelly
+Rules-Requires-Root: no
Package: pbsuite
Architecture: all
@@ -28,7 +29,7 @@ Architecture: all
Section: python
Depends: ${misc:Depends},
${python3:Depends},
- python3-pysam (>= 0.8.0)
+ python3-pysam
Description: software for Pacific Biosciences sequencing data -- Python utilities
The PBSuite currently contains two projects created and maintained
by Adam English for analysis of Pacific Biosciences long-read
@@ -44,7 +45,7 @@ Depends: ${misc:Depends},
${python3:Depends},
python3-pbsuite-utils (= ${source:Version}),
python3-networkx,
- blasr (>= 5.3)
+ blasr
Description: genome assembly upgrading tool
PBJelly is a highly automated pipeline that aligns long sequencing
reads (such as PacBio RS reads or long 454 reads in fasta format)
@@ -59,12 +60,12 @@ Depends: ${misc:Depends},
${python3:Depends},
python3-pbsuite-utils (= ${source:Version}),
python3-pbbanana (= ${source:Version}),
- python3-pysam (>= 0.8.0),
+ python3-pysam,
python3-networkx,
python3-h5py,
python3-numpy,
python3-intervaltree-bio,
- blasr (>= 5.3),
+ blasr,
samtools
Recommends: pbdagcon
Description: genomic structural variation discovery
=====================================
debian/copyright
=====================================
@@ -1,14 +1,14 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: pbsuite
Source: http://sourceforge.net/p/pb-jelly/code-0/HEAD/tree/
Files-Excluded:
- bin/pbdagcon
- bin/sawriter
- pbsuite/*.pyc
- pbsuite/utils/*.pyc
- pbsuite/honey/*.pyc
- pbsuite/jelly/*.pyc
- pbsuite/banana/*.pyc
+ bin/pbdagcon
+ bin/sawriter
+ pbsuite/*.pyc
+ pbsuite/utils/*.pyc
+ pbsuite/honey/*.pyc
+ pbsuite/jelly/*.pyc
+ pbsuite/banana/*.pyc
Files: *
Copyright: 2013 Baylor College of Medicine
@@ -29,13 +29,13 @@ License: BSD-2-Clause
documentation and/or other materials provided with the distribution.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE HOLDERS OR
- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+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
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+Archive: SourceForge
Reference:
- Debian-package: pbhoney
Author: Adam C. English and William J. Salerno and Jeffery G. Reid
@@ -35,3 +36,4 @@ Registry:
Entry: NA
- Name: SciCrunch
Entry: NA
+Repository: https://svn.code.sf.net/p/pb-jelly/code-0/
View it on GitLab: https://salsa.debian.org/med-team/pbsuite/-/compare/ca2c825196ddf0c7701f219443d6061b3bc45ad8...96d55ae376e0e2329d166451557c56d1a7b0dab9
--
View it on GitLab: https://salsa.debian.org/med-team/pbsuite/-/compare/ca2c825196ddf0c7701f219443d6061b3bc45ad8...96d55ae376e0e2329d166451557c56d1a7b0dab9
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