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 <[email protected]> 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 <[email protected]. Uploaders: Olivier Sallou <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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