[med-svn] [khmer] branch master updated (8ea7186 -> 9a3304b)
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to branch master in repository khmer. from 8ea7186 Merge branch 'upstream' new 9a3304b rc3 The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/changelog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [khmer] 01/01: rc3
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch master in repository khmer. commit 9a3304b30e24266573eab450f0fe538ad4df2a42 Author: Michael R. Crusoe Date: Tue Aug 11 20:12:09 2015 -0700 rc3 --- debian/changelog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index 5983c59..958d0b7 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,4 +1,4 @@ -khmer (2.0~rc2+dfsg-1) UNRELEASED; urgency=low +khmer (2.0~rc3+dfsg-1) UNRELEASED; urgency=low * Initial upload (Closes: #777688) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [khmer] branch upstream updated (abe8250 -> 7483ff8)
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to branch upstream in repository khmer. from abe8250 Imported Upstream version 2.0~rc2+dfsg new 7483ff8 Imported Upstream version 2.0~rc3+dfsg The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: .gitignore | 2 + ChangeLog | 160 +++- Makefile | 14 +- TODO | 10 - doc/dev/coding-guidelines-and-review.rst | 36 +- doc/dev/scripts-and-sandbox.rst| 3 +- doc/user/scripts.rst | 3 - doc/whats-new-2.0.rst | 32 +- khmer/__init__.py | 130 +-- khmer/_khmer.cc| 361 +++- khmer/_version.py | 4 +- khmer/kfile.py | 53 +- khmer/khmer_args.py| 369 +--- khmer/khmer_logger.py | 53 ++ khmer/thread_utils.py | 12 +- khmer/utils.py | 15 +- lib/Makefile | 4 +- lib/counting.cc| 75 +- lib/counting.hh| 46 +- lib/hashbits.cc| 122 +-- lib/hashbits.hh| 98 +-- lib/hashtable.cc | 450 ++ lib/hashtable.hh | 171 +--- lib/hllcounter.cc | 19 +- lib/hllcounter.hh | 2 + lib/khmer.hh | 4 + lib/kmer_hash.cc | 67 ++ lib/kmer_hash.hh | 211 + lib/labelhash.cc | 2 +- lib/read_aligner.cc| 76 +- lib/read_parsers.cc| 15 + lib/read_parsers.hh| 2 + lib/subset.cc | 483 +++--- lib/subset.hh | 18 +- lib/traversal.cc | 118 +++ lib/traversal.hh | 56 ++ oxli/__init__.py | 6 +- oxli/build_graph.py| 44 +- oxli/functions.py | 135 --- sandbox/README.rst | 6 +- sandbox/assembly-diff-2.py | 2 +- sandbox/assembly-diff.py | 4 +- sandbox/bloom-count-intersection.py| 61 -- sandbox/bloom-count.py | 2 +- sandbox/build-sparse-graph.py | 2 +- sandbox/calc-error-profile.py | 2 +- sandbox/calc-median-distribution.py| 2 +- sandbox/collect-reads.py | 16 +- sandbox/collect-variants.py| 4 +- sandbox/correct-reads.py | 30 +- sandbox/count-kmers-single.py | 26 +- sandbox/count-kmers.py | 24 +- sandbox/error-correct-pass2.py | 2 +- sandbox/estimate_optimal_hash.py | 3 +- sandbox/fasta-to-abundance-hist.py | 2 +- sandbox/filter-below-abund.py | 2 +- sandbox/filter-median-and-pct.py | 2 +- sandbox/filter-median.py | 2 +- sandbox/find-high-abund-kmers.py | 2 +- sandbox/graph-size.py | 2 +- sandbox/hi-lo-abundance-by-position.py | 2 +- sandbox/multi-rename.py| 7 +- sandbox/normalize-by-median-pct.py | 4 +- sandbox/optimal_args_hashbits.py | 20 +- sandbox/print-stoptags.py | 2 +- sandbox/print-tagset.py| 2 +- sandbox/readaligner_pairhmm_train.py | 2 +- sandbox/saturate-by-median.py | 34 +- sandbox/slice-reads-by-coverage.py | 4 +- sandbox/stoptag-abundance-hist.py | 2 +- sandbox/stoptags-by-position.py| 2 +- sandbox/subset-report.py | 2 +- sandbox/sweep-files.py | 8 +
[med-svn] [khmer] branch master updated (e2ed6fe -> 8ea7186)
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to branch master in repository khmer. from e2ed6fe include missing SphinxDoc depends adds abe8250 Imported Upstream version 2.0~rc2+dfsg new 7483ff8 Imported Upstream version 2.0~rc3+dfsg new 8ea7186 Merge branch 'upstream' The 2 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: .gitignore | 2 + ChangeLog | 160 +++- Makefile | 14 +- TODO | 10 - doc/dev/coding-guidelines-and-review.rst | 36 +- doc/dev/scripts-and-sandbox.rst| 3 +- doc/user/scripts.rst | 3 - doc/whats-new-2.0.rst | 32 +- khmer/__init__.py | 130 +-- khmer/_khmer.cc| 361 +++- khmer/_version.py | 4 +- khmer/kfile.py | 53 +- khmer/khmer_args.py| 369 +--- khmer/khmer_logger.py | 53 ++ khmer/thread_utils.py | 12 +- khmer/utils.py | 15 +- lib/Makefile | 4 +- lib/counting.cc| 75 +- lib/counting.hh| 46 +- lib/hashbits.cc| 122 +-- lib/hashbits.hh| 98 +-- lib/hashtable.cc | 450 ++ lib/hashtable.hh | 171 +--- lib/hllcounter.cc | 19 +- lib/hllcounter.hh | 2 + lib/khmer.hh | 4 + lib/kmer_hash.cc | 67 ++ lib/kmer_hash.hh | 211 + lib/labelhash.cc | 2 +- lib/read_aligner.cc| 76 +- lib/read_parsers.cc| 15 + lib/read_parsers.hh| 2 + lib/subset.cc | 483 +++--- lib/subset.hh | 18 +- lib/traversal.cc | 118 +++ lib/traversal.hh | 56 ++ oxli/__init__.py | 6 +- oxli/build_graph.py| 44 +- oxli/functions.py | 135 --- sandbox/README.rst | 6 +- sandbox/assembly-diff-2.py | 2 +- sandbox/assembly-diff.py | 4 +- sandbox/bloom-count-intersection.py| 61 -- sandbox/bloom-count.py | 2 +- sandbox/build-sparse-graph.py | 2 +- sandbox/calc-error-profile.py | 2 +- sandbox/calc-median-distribution.py| 2 +- sandbox/collect-reads.py | 16 +- sandbox/collect-variants.py| 4 +- sandbox/correct-reads.py | 30 +- sandbox/count-kmers-single.py | 26 +- sandbox/count-kmers.py | 24 +- sandbox/error-correct-pass2.py | 2 +- sandbox/estimate_optimal_hash.py | 3 +- sandbox/fasta-to-abundance-hist.py | 2 +- sandbox/filter-below-abund.py | 2 +- sandbox/filter-median-and-pct.py | 2 +- sandbox/filter-median.py | 2 +- sandbox/find-high-abund-kmers.py | 2 +- sandbox/graph-size.py | 2 +- sandbox/hi-lo-abundance-by-position.py | 2 +- sandbox/multi-rename.py| 7 +- sandbox/normalize-by-median-pct.py | 4 +- sandbox/optimal_args_hashbits.py | 20 +- sandbox/print-stoptags.py | 2 +- sandbox/print-tagset.py| 2 +- sandbox/readaligner_pairhmm_train.py | 2 +- sandbox/saturate-by-median.py | 34 +- sandbox/slice-reads-by-coverage.py | 4 +- sandbox/stoptag-abundance-hist.py | 2 +- sandbox/stoptags-by-position.py| 2 +- sandbox/subset-repo
[med-svn] [khmer] branch pristine-tar updated (582c882 -> c892456)
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to branch pristine-tar in repository khmer. from 582c882 pristine-tar data for khmer_2.0~rc2+dfsg.orig.tar.xz new c892456 pristine-tar data for khmer_2.0~rc3+dfsg.orig.tar.xz The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: khmer_2.0~rc3+dfsg.orig.tar.xz.delta | Bin 0 -> 27657 bytes khmer_2.0~rc3+dfsg.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) create mode 100644 khmer_2.0~rc3+dfsg.orig.tar.xz.delta create mode 100644 khmer_2.0~rc3+dfsg.orig.tar.xz.id -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [khmer] 01/01: pristine-tar data for khmer_2.0~rc3+dfsg.orig.tar.xz
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch pristine-tar in repository khmer. commit c89245645d6d960cb19183229f7bdc7ccc8a39eb Author: Michael R. Crusoe Date: Tue Aug 11 20:04:21 2015 -0700 pristine-tar data for khmer_2.0~rc3+dfsg.orig.tar.xz --- khmer_2.0~rc3+dfsg.orig.tar.xz.delta | Bin 0 -> 27657 bytes khmer_2.0~rc3+dfsg.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/khmer_2.0~rc3+dfsg.orig.tar.xz.delta b/khmer_2.0~rc3+dfsg.orig.tar.xz.delta new file mode 100644 index 000..81a94e0 Binary files /dev/null and b/khmer_2.0~rc3+dfsg.orig.tar.xz.delta differ diff --git a/khmer_2.0~rc3+dfsg.orig.tar.xz.id b/khmer_2.0~rc3+dfsg.orig.tar.xz.id new file mode 100644 index 000..630c2e9 --- /dev/null +++ b/khmer_2.0~rc3+dfsg.orig.tar.xz.id @@ -0,0 +1 @@ +c4fdc29c072cc5c317f3b868c2e66dd74d019ffe -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [khmer] 02/02: Merge branch 'upstream'
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch master in repository khmer. commit 8ea7186da036ab103314519dcd03883a0f4b9978 Merge: e2ed6fe 7483ff8 Author: Michael R. Crusoe Date: Tue Aug 11 20:10:58 2015 -0700 Merge branch 'upstream' .gitignore | 2 + ChangeLog | 160 +++- Makefile | 14 +- TODO | 10 - doc/dev/coding-guidelines-and-review.rst | 36 +- doc/dev/scripts-and-sandbox.rst| 3 +- doc/user/scripts.rst | 3 - doc/whats-new-2.0.rst | 32 +- khmer/__init__.py | 130 +-- khmer/_khmer.cc| 361 +++- khmer/_version.py | 4 +- khmer/kfile.py | 53 +- khmer/khmer_args.py| 369 +--- khmer/khmer_logger.py | 53 ++ khmer/thread_utils.py | 12 +- khmer/utils.py | 15 +- lib/Makefile | 4 +- lib/counting.cc| 75 +- lib/counting.hh| 46 +- lib/hashbits.cc| 122 +-- lib/hashbits.hh| 98 +-- lib/hashtable.cc | 450 ++ lib/hashtable.hh | 171 +--- lib/hllcounter.cc | 19 +- lib/hllcounter.hh | 2 + lib/khmer.hh | 4 + lib/kmer_hash.cc | 67 ++ lib/kmer_hash.hh | 211 + lib/labelhash.cc | 2 +- lib/read_aligner.cc| 76 +- lib/read_parsers.cc| 15 + lib/read_parsers.hh| 2 + lib/subset.cc | 483 +++--- lib/subset.hh | 18 +- lib/traversal.cc | 118 +++ lib/traversal.hh | 56 ++ oxli/__init__.py | 6 +- oxli/build_graph.py| 44 +- oxli/functions.py | 135 --- sandbox/README.rst | 6 +- sandbox/assembly-diff-2.py | 2 +- sandbox/assembly-diff.py | 4 +- sandbox/bloom-count-intersection.py| 61 -- sandbox/bloom-count.py | 2 +- sandbox/build-sparse-graph.py | 2 +- sandbox/calc-error-profile.py | 2 +- sandbox/calc-median-distribution.py| 2 +- sandbox/collect-reads.py | 16 +- sandbox/collect-variants.py| 4 +- sandbox/correct-reads.py | 30 +- sandbox/count-kmers-single.py | 26 +- sandbox/count-kmers.py | 24 +- sandbox/error-correct-pass2.py | 2 +- sandbox/estimate_optimal_hash.py | 3 +- sandbox/fasta-to-abundance-hist.py | 2 +- sandbox/filter-below-abund.py | 2 +- sandbox/filter-median-and-pct.py | 2 +- sandbox/filter-median.py | 2 +- sandbox/find-high-abund-kmers.py | 2 +- sandbox/graph-size.py | 2 +- sandbox/hi-lo-abundance-by-position.py | 2 +- sandbox/multi-rename.py| 7 +- sandbox/normalize-by-median-pct.py | 4 +- sandbox/optimal_args_hashbits.py | 20 +- sandbox/print-stoptags.py | 2 +- sandbox/print-tagset.py| 2 +- sandbox/readaligner_pairhmm_train.py | 2 +- sandbox/saturate-by-median.py | 34 +- sandbox/slice-reads-by-coverage.py | 4 +- sandbox/stoptag-abundance-hist.py | 2 +- sandbox/stoptags-by-position.py| 2 +- sandbox/subset-report.py | 2 +- sandbox/sweep-files.py | 8 +- sandbox/sweep-out-reads-with-contigs.py| 4 +- sandbox/sweep-reads.py | 8 +- sandbox/sweep-reads2.py| 6 +- sandbox/sweep-reads3.py
[med-svn] [khmer] annotated tag upstream/2.0_rc3+dfsg created (now d9dcf4f)
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to annotated tag upstream/2.0_rc3+dfsg in repository khmer. at d9dcf4f (tag) tagging 7483ff8d0a0efb83da513a3dc90f5fc8de9358f1 (commit) replaces upstream/2.0_rc2+dfsg tagged by Michael R. Crusoe on Tue Aug 11 20:04:21 2015 -0700 - Log - Upstream version 2.0~rc3+dfsg Michael R. Crusoe (1): Imported Upstream version 2.0~rc3+dfsg --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] branch master updated (8574ffb -> 923a2d8)
This is an automated email from the git hooks/post-receive script. afif-guest pushed a change to branch master in repository python-pbcore. from 8574ffb Fix changelog file name new 1da9767 Fix configuration of autopkgtests new 923a2d8 Update changelog The 2 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/changelog | 6 ++ debian/tests/control | 4 ++-- 2 files changed, 8 insertions(+), 2 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] 01/02: Fix configuration of autopkgtests
This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository python-pbcore. commit 1da97678b713b0ff79090fdec9dd6381dca88726 Author: Afif Elghraoui Date: Tue Aug 11 19:37:50 2015 -0700 Fix configuration of autopkgtests --- debian/tests/control | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/debian/tests/control b/debian/tests/control index 5ef6767..2026779 100644 --- a/debian/tests/control +++ b/debian/tests/control @@ -1,3 +1,3 @@ -Test-Command: nosetests -v tests -Depends: python-pbcore-data, python-nose +Test-Command: nosetests -v +Depends: python-pbcore, python-nose Restrictions: allow-stderr -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] 02/02: Update changelog
This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository python-pbcore. commit 923a2d8f013a87ebca3e36227c707feca5751482 Author: Afif Elghraoui Date: Tue Aug 11 19:39:55 2015 -0700 Update changelog --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index 8d904e3..057ddba 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,6 +1,12 @@ python-pbcore (1.2.2+dfsg1-1) UNRELEASED; urgency=medium * Imported Upstream version 1.2.1+dfsg1 + * Install upstream-provided convenience scripts + * Refresh patches + * Install upstream changelog and readme in main package (not doc package) + * Enable build-time testing + * Configure autopkgtests + * Drop nonfunctional Python3 package and merge data package with main one -- Afif Elghraoui Mon, 03 Aug 2015 23:43:39 -0700 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [khmer] 02/04: added missing leading /
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch master in repository khmer. commit 24b5543626b71a33d83d862c31431da17ef7246b Author: Michael R. Crusoe Date: Tue Aug 11 21:15:28 2015 -0400 added missing leading / --- debian/khmer-common.postinst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/khmer-common.postinst b/debian/khmer-common.postinst index 30f33a7..e5e2fa3 100644 --- a/debian/khmer-common.postinst +++ b/debian/khmer-common.postinst @@ -1,2 +1,2 @@ -cd usr/share/file && file --compile khmer +cd /usr/share/file && file --compile khmer #DEBHELPER# -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [khmer] branch master updated (ff75b29 -> e2ed6fe)
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to branch master in repository khmer. from ff75b29 Add test of liboxli-dev install new 496f708 ubuntu fixes new 24b5543 added missing leading / new 0599ec4 add file dep new e2ed6fe include missing SphinxDoc depends The 4 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/control | 10 +- debian/khmer-common.postinst | 2 +- debian/khmer-common.postrm | 2 +- debian/patches/get_version | 2 +- debian/rules | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [khmer] 01/04: ubuntu fixes
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository khmer.
commit 496f70894111e2f5b2f952421ec83d7f8421c8f7
Author: Michael R. Crusoe
Date: Tue Aug 11 20:01:47 2015 -0400
ubuntu fixes
---
debian/patches/get_version | 2 +-
debian/rules | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/debian/patches/get_version b/debian/patches/get_version
index 00d1237..3d9e9a4 100644
--- a/debian/patches/get_version
+++ b/debian/patches/get_version
@@ -23,7 +23,7 @@
-del versioneer
-sys.path.remove('../')
+release = subprocess.check_output(
-+['sh', '-c', 'cd ..; dpkg-parsechangelog -S Version'])
++['sh', '-c', 'cd ..; dpkg-parsechangelog --show-field Version'])
+release = release.decode('utf-8')
+
diff --git a/debian/rules b/debian/rules
index 99e95fc..98b2edf 100755
--- a/debian/rules
+++ b/debian/rules
@@ -30,7 +30,7 @@ override_dh_auto_test:
override_dh_auto_clean:
- dh_auto_clean
+ #dh_auto_clean
rm -f khmer/*.so
rm -f debian/*.1
cd lib && $(MAKE) clean
--
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[med-svn] [khmer] 03/04: add file dep
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository khmer.
commit 0599ec47932e16ba89dada4f2c8267d6d7e6f08c
Author: Michael R. Crusoe
Date: Tue Aug 11 21:21:07 2015 -0400
add file dep
---
debian/control | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/debian/control b/debian/control
index 9b223b3..c782b67 100644
--- a/debian/control
+++ b/debian/control
@@ -27,7 +27,8 @@ X-Python-Version: 3.4
Package: khmer-common
Architecture: any
Multi-Arch: same
-Depends: ${misc:Depends},
+Depends: file,
+${misc:Depends},
${shlibs:Depends}
Description: common files for the khmer project tools
khmer is a library and suite of command line tools for working with DNA
--
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[med-svn] [khmer] 04/04: include missing SphinxDoc depends
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository khmer.
commit e2ed6fe567ab73cb80387a4188d720a6ef87f6d1
Author: Michael R. Crusoe
Date: Tue Aug 11 21:28:43 2015 -0400
include missing SphinxDoc depends
and another missing slash
---
debian/control | 7 +++
debian/khmer-common.postinst | 2 +-
debian/khmer-common.postrm | 2 +-
3 files changed, 5 insertions(+), 6 deletions(-)
diff --git a/debian/control b/debian/control
index c782b67..3b6e8c1 100644
--- a/debian/control
+++ b/debian/control
@@ -29,7 +29,8 @@ Architecture: any
Multi-Arch: same
Depends: file,
${misc:Depends},
- ${shlibs:Depends}
+ ${shlibs:Depends},
+ ${sphinxdoc:Depends}
Description: common files for the khmer project tools
khmer is a library and suite of command line tools for working with DNA
sequence. It is primarily aimed at short-read sequencing data such as that
@@ -48,8 +49,7 @@ Depends: khmer-common,
python3-screed (<< 1.0),
${misc:Depends},
${shlibs:Depends},
- ${python3:Depends},
- ${sphinxdoc:Depends}
+ ${python3:Depends}
Description: in-memory DNA sequence kmer counting, filtering & graph traversal
khmer is a library and suite of command line tools for working with DNA
sequence. It is primarily aimed at short-read sequencing data such as that
@@ -79,7 +79,6 @@ Section: libdevel
Depends: khmer-common,
${shlibs:Depends},
${misc:Depends}
-Pre-Depends: ${misc:Pre-Depends}
Description: in-memory DNA sequence analysis dev library
khmer is a library and suite of command line tools for working with DNA
sequence. It is primarily aimed at short-read sequencing data such as that
diff --git a/debian/khmer-common.postinst b/debian/khmer-common.postinst
index e5e2fa3..21bac8f 100644
--- a/debian/khmer-common.postinst
+++ b/debian/khmer-common.postinst
@@ -1,2 +1,2 @@
-cd /usr/share/file && file --compile khmer
+cd /usr/share/file && file -m khmer --compile
#DEBHELPER#
diff --git a/debian/khmer-common.postrm b/debian/khmer-common.postrm
index 1d65e43..f391f80 100644
--- a/debian/khmer-common.postrm
+++ b/debian/khmer-common.postrm
@@ -1,2 +1,2 @@
-rm -f usr/share/file/khmer.mgc
+rm -f /usr/share/file/khmer.mgc
#DEBHELPER#
--
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/srv/git.debian.org/git/debian-med/khmer.git
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[med-svn] [khmer] branch master updated (c76d6be -> ff75b29)
This is an automated email from the git hooks/post-receive script. daube-guest pushed a change to branch master in repository khmer. from c76d6be try setting the PYTHONPATH new ff75b29 Add test of liboxli-dev install The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/tests/control | 4 ++-- debian/tests/test-liboxli-dev | 14 ++ 2 files changed, 16 insertions(+), 2 deletions(-) create mode 100644 debian/tests/test-liboxli-dev -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [khmer] 01/01: Add test of liboxli-dev install
This is an automated email from the git hooks/post-receive script. daube-guest pushed a commit to branch master in repository khmer. commit ff75b29347d37ede58b1b7ce6857fc0a67cbf3a1 Author: Kevin Murray Date: Wed Aug 12 09:48:18 2015 +1000 Add test of liboxli-dev install --- debian/tests/control | 4 ++-- debian/tests/test-liboxli-dev | 14 ++ 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/debian/tests/control b/debian/tests/control index d2aa55a..4692703 100644 --- a/debian/tests/control +++ b/debian/tests/control @@ -1,3 +1,3 @@ -Tests: run-unit-test -Depends: @ +Tests: run-unit-test, test-liboxli-dev +Depends: @, @builddeps@ Restrictions: allow-stderr diff --git a/debian/tests/test-liboxli-dev b/debian/tests/test-liboxli-dev new file mode 100644 index 000..7560e03 --- /dev/null +++ b/debian/tests/test-liboxli-dev @@ -0,0 +1,14 @@ +#!/bin/bash + +c++ -o test-prog-static \ +lib/test-compile.cc \ +/usr/lib/`dpkg-architecture -qDEB_HOST_MULTIARCH`/liboxli.a + +./test-prog-static + +c++ -o test-prog-dynamic lib/test-compile.cc -loxli + +./test-prog-dynamic + + +rm -f test-prog-* -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r19915 - in trunk/packages/sumaclust/trunk/debian: . patches
Author: tille Date: 2015-08-11 13:05:05 + (Tue, 11 Aug 2015) New Revision: 19915 Modified: trunk/packages/sumaclust/trunk/debian/changelog trunk/packages/sumaclust/trunk/debian/patches/hardening.patch Log: Upload to new Modified: trunk/packages/sumaclust/trunk/debian/changelog === --- trunk/packages/sumaclust/trunk/debian/changelog 2015-08-11 12:30:05 UTC (rev 19914) +++ trunk/packages/sumaclust/trunk/debian/changelog 2015-08-11 13:05:05 UTC (rev 19915) @@ -1,5 +1,5 @@ -sumaclust (1.0.10-1) UNRELEASED; urgency=medium +sumaclust (1.0.10-1) unstable; urgency=medium - * Initial upload to Debian (Closes: #???) + * Initial upload to Debian (Closes: #795176) - -- Andreas Tille Thu, 06 Aug 2015 15:30:54 +0200 + -- Andreas Tille Tue, 11 Aug 2015 14:59:19 +0200 Modified: trunk/packages/sumaclust/trunk/debian/patches/hardening.patch === --- trunk/packages/sumaclust/trunk/debian/patches/hardening.patch 2015-08-11 12:30:05 UTC (rev 19914) +++ trunk/packages/sumaclust/trunk/debian/patches/hardening.patch 2015-08-11 13:05:05 UTC (rev 19915) @@ -2,14 +2,14 @@ Last-Update: Wed, 05 Aug 2015 17:54:58 +0200 Description: Propagate hardening options a/Makefile -+++ b/Makefile -@@ -28,7 +28,7 @@ all: $(EXEC) +--- a/global.mk b/global.mk +@@ -10,7 +10,7 @@ LIBFILE = ./sumalibs/libfile/libfile.a + LIBUTILS = ./sumalibs/libutils/libutils.a + + CC=gcc +-LDFLAGS= ++LDFLAGS:=$(LDFLAGS) + + ifeq ($(CC),gcc) - LFLAGS = -fopenmp - else --LFLAGS = -+LFLAGS = $(LDFLAGS) - endif - - sumaclust: $(SUMACLUST_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS) ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r19914 - in trunk/packages: . sumaclust sumaclust/trunk sumaclust/trunk/debian sumaclust/trunk/debian/patches sumaclust/trunk/debian/source
Author: tille
Date: 2015-08-11 12:30:05 + (Tue, 11 Aug 2015)
New Revision: 19914
Added:
trunk/packages/sumaclust/
trunk/packages/sumaclust/trunk/
trunk/packages/sumaclust/trunk/debian/
trunk/packages/sumaclust/trunk/debian/changelog
trunk/packages/sumaclust/trunk/debian/compat
trunk/packages/sumaclust/trunk/debian/control
trunk/packages/sumaclust/trunk/debian/copyright
trunk/packages/sumaclust/trunk/debian/doc-base
trunk/packages/sumaclust/trunk/debian/docs
trunk/packages/sumaclust/trunk/debian/install
trunk/packages/sumaclust/trunk/debian/manpages
trunk/packages/sumaclust/trunk/debian/patches/
trunk/packages/sumaclust/trunk/debian/patches/hardening.patch
trunk/packages/sumaclust/trunk/debian/patches/series
trunk/packages/sumaclust/trunk/debian/rules
trunk/packages/sumaclust/trunk/debian/source/
trunk/packages/sumaclust/trunk/debian/source/format
trunk/packages/sumaclust/trunk/debian/sumaclust.1
trunk/packages/sumaclust/trunk/debian/watch
Log:
Inject sumaclust
Added: trunk/packages/sumaclust/trunk/debian/changelog
===
--- trunk/packages/sumaclust/trunk/debian/changelog
(rev 0)
+++ trunk/packages/sumaclust/trunk/debian/changelog 2015-08-11 12:30:05 UTC
(rev 19914)
@@ -0,0 +1,5 @@
+sumaclust (1.0.10-1) UNRELEASED; urgency=medium
+
+ * Initial upload to Debian (Closes: #???)
+
+ -- Andreas Tille Thu, 06 Aug 2015 15:30:54 +0200
Added: trunk/packages/sumaclust/trunk/debian/compat
===
--- trunk/packages/sumaclust/trunk/debian/compat
(rev 0)
+++ trunk/packages/sumaclust/trunk/debian/compat2015-08-11 12:30:05 UTC
(rev 19914)
@@ -0,0 +1 @@
+9
Added: trunk/packages/sumaclust/trunk/debian/control
===
--- trunk/packages/sumaclust/trunk/debian/control
(rev 0)
+++ trunk/packages/sumaclust/trunk/debian/control 2015-08-11 12:30:05 UTC
(rev 19914)
@@ -0,0 +1,27 @@
+Source: sumaclust
+Maintainer: Debian Med Packaging Team
+Uploaders: Tim Booth ,
+ Andreas Tille
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/sumaclust/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/sumaclust/trunk/
+Homepage: http://metabarcoding.org/sumaclust
+
+Package: sumaclust
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: fast and exact clustering of genomic sequences
+ With the development of next-generation sequencing, efficient tools are
+ needed to handle millions of sequences in reasonable amounts of time.
+ Sumaclust is a program developed by the LECA. Sumaclust aims to cluster
+ sequences in a way that is fast and exact at the same time. This tool
+ has been developed to be adapted to the type of data generated by DNA
+ metabarcoding, i.e. entirely sequenced, short markers. Sumaclust
+ clusters sequences using the same clustering algorithm as UCLUST and CD-
+ HIT. This algorithm is mainly useful to detect the 'erroneous' sequences
+ created during amplification and sequencing protocols, deriving from
+ 'true' sequences.
Added: trunk/packages/sumaclust/trunk/debian/copyright
===
--- trunk/packages/sumaclust/trunk/debian/copyright
(rev 0)
+++ trunk/packages/sumaclust/trunk/debian/copyright 2015-08-11 12:30:05 UTC
(rev 19914)
@@ -0,0 +1,519 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Céline Mercier
+Source: https://git.metabarcoding.org/obitools/sumaclust
+
+Files: *
+Copyright: 2013-2015 Tiayyba Riaz
+ Celine Mercier
+Eric Coissac
+License: CeCILL-2
+
+Files: debian/*
+Copyright: 2015 Andreas Tille
+License: CeCILL-2
+
+License: CeCILL-2
+ CeCILL FREE SOFTWARE LICENSE AGREEMENT
+ .
+Notice
+ .
+ This Agreement is a Free Software license agreement that is the result
+ of discussions between its authors in order to ensure compliance with
+ the two main principles guiding its drafting:
+ .
+* firstly, compliance with the principles governing the distribution
+ of Free Software: access to source code, broad rights granted to
+ users,
+* secondly, the election of a governing law, French law, with which
+ it is conformant, both as regards the law of torts and
+ intellectual property law, and the protection that it offers to
+ both authors and holders of the economic rights over software.
+ .
+ The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+ license are:
+ .
+ Commissariat à l'Energie Atomique - CEA, a public scientific, technical
+ and indu
[med-svn] r19913 - trunk/packages/sumatra/trunk/debian
Author: tille Date: 2015-08-11 12:15:35 + (Tue, 11 Aug 2015) New Revision: 19913 Modified: trunk/packages/sumatra/trunk/debian/sumatra.1 Log: File was heavily edited Modified: trunk/packages/sumatra/trunk/debian/sumatra.1 === --- trunk/packages/sumatra/trunk/debian/sumatra.1 2015-08-11 09:12:10 UTC (rev 19912) +++ trunk/packages/sumatra/trunk/debian/sumatra.1 2015-08-11 12:15:35 UTC (rev 19913) @@ -1,4 +1,3 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.1. .TH SUMATRA "1" "August 2015" "sumatra 1.0.03" "User Commands" .SH NAME sumatra \- fast and exact comparison and clustering of sequences ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r19912 - trunk/packages/sortmerna/trunk/debian
Author: tille Date: 2015-08-11 09:12:10 + (Tue, 11 Aug 2015) New Revision: 19912 Added: trunk/packages/sortmerna/trunk/debian/doc-base trunk/packages/sortmerna/trunk/debian/lintian-overrides Modified: trunk/packages/sortmerna/trunk/debian/changelog trunk/packages/sortmerna/trunk/debian/copyright trunk/packages/sortmerna/trunk/debian/rules Log: Upload to new Modified: trunk/packages/sortmerna/trunk/debian/changelog === --- trunk/packages/sortmerna/trunk/debian/changelog 2015-08-09 07:53:57 UTC (rev 19911) +++ trunk/packages/sortmerna/trunk/debian/changelog 2015-08-11 09:12:10 UTC (rev 19912) @@ -1,4 +1,4 @@ -sortmerna (2.0-1) UNRELEASED; urgency=medium +sortmerna (2.0-1) unstable; urgency=medium * Initial upload to Debian (Closes: #794607) Modified: trunk/packages/sortmerna/trunk/debian/copyright === --- trunk/packages/sortmerna/trunk/debian/copyright 2015-08-09 07:53:57 UTC (rev 19911) +++ trunk/packages/sortmerna/trunk/debian/copyright 2015-08-11 09:12:10 UTC (rev 19912) @@ -46,20 +46,6 @@ 2015 Andreas Tille License: LGPL-3+ -License: LGPL-3+ - SortMeRNA is free software: you can redistribute it and/or modify - it under the terms of the GNU Lesser General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - . - SortMeRNA is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU Lesser General Public License for more details. - . - On Debian systems you can find a copy of the GNU Lesser General - Public License in /usr/share/common-licenses/LGPL. - Files: src/ssw.c Copyright: 2012-1015 Boston College. Mengyao Zhao @@ -83,3 +69,18 @@ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +License: LGPL-3+ + SortMeRNA is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + . + SortMeRNA is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + . + On Debian systems you can find a copy of the GNU Lesser General + Public License in /usr/share/common-licenses/LGPL. + Added: trunk/packages/sortmerna/trunk/debian/doc-base === --- trunk/packages/sortmerna/trunk/debian/doc-base (rev 0) +++ trunk/packages/sortmerna/trunk/debian/doc-base 2015-08-11 09:12:10 UTC (rev 19912) @@ -0,0 +1,20 @@ +Document: sortmerna +Title: SortMeRNA User Manual +Author: Evguenia Kopylova +Abstract: tool for filtering, mapping and OTU-picking NGS reads + SortMeRNA is a biological sequence analysis tool for filtering, mapping and + OTU-picking NGS reads. The core algorithm is based on approximate seeds and + allows for fast and sensitive analyses of nucleotide sequences. The main + application of SortMeRNA is filtering rRNA from metatranscriptomic data. + Additional applications include OTU-picking and taxonomy assignation available + through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1). + SortMeRNA takes as input a file of reads (fasta or fastq format) and one or + multiple rRNA database file(s), and sorts apart rRNA and rejected reads into + two files specified by the user. Optionally, it can provide high quality local + alignments of rRNA reads against the rRNA database. SortMeRNA works with + Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and + BLAST-like alignments. +Section: Science/Biology + +Format: pdf +Files: /usr/share/doc/sortmerna/SortMeRNA-User-Manual-2.0.pdf Added: trunk/packages/sortmerna/trunk/debian/lintian-overrides === --- trunk/packages/sortmerna/trunk/debian/lintian-overrides (rev 0) +++ trunk/packages/sortmerna/trunk/debian/lintian-overrides 2015-08-11 09:12:10 UTC (rev 19912) @@ -0,0 +1,2 @@ +# no intend to change the original copyright text +sortmerna: spelling-error-in-copyright offical official Modified: trunk/packages/sortmerna/trunk/debian/rules === --- trunk/packages/sortmerna/trunk/debian/rules 2015-08-09 07:53:57 UTC (rev 19911) +++ trunk/packages/sortmerna/trunk/debian/rules 2015-08-11 09:12:10 UTC (rev 19912) @@ -35,3 +35,6 @@ dh_fixperms find
[med-svn] [beast-mcmc] tag debian/jessie/1.8.2_754b844-1_bpo8+1 created (now 5b08e5d)
This is an automated email from the git hooks/post-receive script. tille pushed a change to tag debian/jessie/1.8.2_754b844-1_bpo8+1 in repository beast-mcmc. at 5b08e5d (commit) This tag includes the following new commits: new 5b08e5d Backport to Jessie The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beast-mcmc.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [beast-mcmc] 01/01: Backport to Jessie
This is an automated email from the git hooks/post-receive script. tille pushed a commit to tag debian/jessie/1.8.2_754b844-1_bpo8+1 in repository beast-mcmc. commit 5b08e5df5f0e30536472c5ee463bc9e0d174ca5c Author: Andreas Tille Date: Mon Aug 3 13:48:46 2015 +0200 Backport to Jessie --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index f6b62bf..3a38fed 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +beast-mcmc (1.8.2~754b844-1~bpo8+1) jessie-backports; urgency=medium + + * Backport to Jessie + + -- Andreas Tille Mon, 03 Aug 2015 13:47:04 +0200 + beast-mcmc (1.8.2~754b844-1) unstable; urgency=medium * New upstream version -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beast-mcmc.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] annotated tag upstream/1.2.2+dfsg1 created (now 42e81e8)
This is an automated email from the git hooks/post-receive script. afif-guest pushed a change to annotated tag upstream/1.2.2+dfsg1 in repository python-pbcore. at 42e81e8 (tag) tagging cd3bf3529d696597f98846c32c28999d5534aea3 (commit) replaces upstream/1.2.1+dfsg1 tagged by Afif Elghraoui on Mon Aug 10 22:55:58 2015 -0700 - Log - Upstream version 1.2.2+dfsg1 Afif Elghraoui (1): Imported Upstream version 1.2.2+dfsg1 --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] 06/11: Update version in changelog
This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository python-pbcore. commit 30c724c74b4e39d7136ad0d399b6589bbcfff98c Author: Afif Elghraoui Date: Mon Aug 10 23:03:43 2015 -0700 Update version in changelog --- debian/changelog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index 6a91817..8d904e3 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,4 +1,4 @@ -python-pbcore (1.2.1+dfsg1-1) UNRELEASED; urgency=medium +python-pbcore (1.2.2+dfsg1-1) UNRELEASED; urgency=medium * Imported Upstream version 1.2.1+dfsg1 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] 01/01: pristine-tar data for python-pbcore_1.2.2+dfsg1.orig.tar.xz
This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch pristine-tar in repository python-pbcore. commit c37d5f7512331b5db4aa4b9f7b03b9bfad5ec125 Author: Afif Elghraoui Date: Mon Aug 10 22:55:58 2015 -0700 pristine-tar data for python-pbcore_1.2.2+dfsg1.orig.tar.xz --- python-pbcore_1.2.2+dfsg1.orig.tar.xz.delta | Bin 0 -> 6771 bytes python-pbcore_1.2.2+dfsg1.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/python-pbcore_1.2.2+dfsg1.orig.tar.xz.delta b/python-pbcore_1.2.2+dfsg1.orig.tar.xz.delta new file mode 100644 index 000..a6567b2 Binary files /dev/null and b/python-pbcore_1.2.2+dfsg1.orig.tar.xz.delta differ diff --git a/python-pbcore_1.2.2+dfsg1.orig.tar.xz.id b/python-pbcore_1.2.2+dfsg1.orig.tar.xz.id new file mode 100644 index 000..28b6f3e --- /dev/null +++ b/python-pbcore_1.2.2+dfsg1.orig.tar.xz.id @@ -0,0 +1 @@ +3189bd42a887815132f04632454dd1e45ba9c7d0 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] 11/11: Fix changelog file name
This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository python-pbcore. commit 8574ffb7c9ae1217cffca79f08004c3cfd5e7712 Author: Afif Elghraoui Date: Tue Aug 11 00:47:43 2015 -0700 Fix changelog file name --- debian/python-pbcore.docs | 1 - debian/rules | 1 + 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/python-pbcore.docs b/debian/python-pbcore.docs index e4044c6..b43bf86 100644 --- a/debian/python-pbcore.docs +++ b/debian/python-pbcore.docs @@ -1,2 +1 @@ README.md -CHANGELOG.org diff --git a/debian/rules b/debian/rules index 9b7e7de..e265831 100755 --- a/debian/rules +++ b/debian/rules @@ -23,6 +23,7 @@ override_dh_install: mkdir -p $(SCRIPTSDIR) mv $(DESTDIR)/usr/bin/.open $(SCRIPTSDIR)/open mv $(DESTDIR)/usr/bin/dataset.py $(SCRIPTSDIR)/ + mv CHANGELOG.org $(DESTDIR)/usr/share/doc/$(DEB_SOURCE)/changelog override_dh_installdocs: dh_installdocs -X _source -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] 05/11: Merge tag 'upstream/1.2.2+dfsg1'
This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository python-pbcore. commit 74b076bf4fc88417a1b0d53d0e7cf0e4fa25d035 Merge: 10a2a68 cd3bf35 Author: Afif Elghraoui Date: Mon Aug 10 22:55:58 2015 -0700 Merge tag 'upstream/1.2.2+dfsg1' Upstream version 1.2.2+dfsg1 CHANGELOG.org |7 + bin/dataset.py |2 + pbcore/__init__.py |2 +- pbcore/data/Makefile |7 + pbcore/data/datasets/__init__.py |6 +- pbcore/data/datasets/alignment.dataset.xml |8 + .../datasets/m150430_142051_Mon_p1_b25.sts.xml |1 + ...10071048255001823136404221563_s1_p0.sts.xml |1 + pbcore/data/datasets/pbalchemysim0.reference.xml | 79 +- pbcore/data/datasets/subreadSetWithStats.xml | 1139 +++- pbcore/io/FastaIO.py |2 +- pbcore/io/align/PacBioBamIndex.py | 83 +- pbcore/io/dataset/DataSetIO.py | 1400 ++-- pbcore/io/dataset/DataSetMembers.py| 206 ++- pbcore/io/dataset/DataSetReader.py | 233 ++-- pbcore/io/dataset/DataSetValidator.py | 53 +- pbcore/io/dataset/DataSetWriter.py | 19 +- pbcore/io/dataset/EntryPoints.py | 53 +- pbcore/util/ToolRunner.py |3 + tests/test_pbdataset.py| 205 ++- tests/test_pbdataset_subtypes.py | 174 ++- 21 files changed, 2996 insertions(+), 687 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] 01/01: Set up debian/rules for running the tests as pybuild intended
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch topic/pybuild-intended-testsetup
in repository python-pbcore.
commit faa6f7e31296e230f4fe4546911efd5bb5b06d87
Author: Afif Elghraoui
Date: Wed Aug 5 01:43:11 2015 -0700
Set up debian/rules for running the tests as pybuild intended
This is how pybuild was supposed to work. Unfortunately,
the PYTHONPATH does not get set correctly and the tests all
fail because they can't find the package module.
See:
https://lists.debian.org/debian-python/2015/07/msg00062.html
Example of a crazy workaround:
https://lists.debian.org/debian-python/2014/05/msg00148.html
---
debian/rules | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/debian/rules b/debian/rules
index 0865054..cf19a6a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -5,6 +5,9 @@ include /usr/share/dpkg/default.mk
export PYBUILD_NAME = pbcore
+export PYBUILD_TEST_NOSE = 1
+export PYBUILD_TEST_ARGS = {dir}/tests
+
%:
LC_ALL=C.UTF-8 dh $@ --with python2,python3 --buildsystem=pybuild
@@ -18,5 +21,3 @@ override_dh_installdocs:
get-orig-source:
uscan --verbose --force-download --repack --rename --compression xz
-# test requires the package itself to be installed...
-override_dh_auto_test:
--
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[med-svn] [python-pbcore] 10/11: Install upstream changelog and readme in main package (not doc package)
This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository python-pbcore. commit b20eeb0e92d9071855754e547346b2a7bc780ff6 Author: Afif Elghraoui Date: Tue Aug 11 00:36:20 2015 -0700 Install upstream changelog and readme in main package (not doc package) --- debian/python-pbcore-doc.install | 2 -- debian/python-pbcore.docs| 2 ++ 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/debian/python-pbcore-doc.install b/debian/python-pbcore-doc.install index d7d167f..72d7b2c 100644 --- a/debian/python-pbcore-doc.install +++ b/debian/python-pbcore-doc.install @@ -1,3 +1 @@ doc/_build/htmlusr/share/doc/python-pbcore -README.md usr/share/doc/python-pbcore -CHANGELOG.org usr/share/doc/python-pbcore diff --git a/debian/python-pbcore.docs b/debian/python-pbcore.docs new file mode 100644 index 000..e4044c6 --- /dev/null +++ b/debian/python-pbcore.docs @@ -0,0 +1,2 @@ +README.md +CHANGELOG.org -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] 09/11: Refresh patch
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-pbcore.
commit 16e3ec543e01d66bda8caebdf688a1f0d5853d3e
Author: Afif Elghraoui
Date: Tue Aug 11 00:35:10 2015 -0700
Refresh patch
---
debian/patches/enable-build-time-testing.patch | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/debian/patches/enable-build-time-testing.patch
b/debian/patches/enable-build-time-testing.patch
index 9cdbd64..01e6fc7 100644
--- a/debian/patches/enable-build-time-testing.patch
+++ b/debian/patches/enable-build-time-testing.patch
@@ -20,6 +20,6 @@ Last-Update: 2015-08-06
},
zip_safe = False,
+test_suite = 'nose.collector',
+ entry_points = { "console_scripts" : [ ".open =
pbcore.io.opener:entryPoint" ] },
+ scripts=['bin/dataset.py'],
install_requires=[
- 'h5py >= 2.0.1',
- 'numpy >= 1.7.1',
--
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[med-svn] [python-pbcore] branch upstream updated (716f5d3 -> cd3bf35)
This is an automated email from the git hooks/post-receive script. afif-guest pushed a change to branch upstream in repository python-pbcore. from 716f5d3 Imported Upstream version 1.2.1+dfsg1 new cd3bf35 Imported Upstream version 1.2.2+dfsg1 The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: CHANGELOG.org |7 + bin/dataset.py |2 + pbcore/__init__.py |2 +- pbcore/data/Makefile |7 + pbcore/data/datasets/__init__.py |6 +- pbcore/data/datasets/alignment.dataset.xml |8 + .../datasets/m150430_142051_Mon_p1_b25.sts.xml |1 + ...10071048255001823136404221563_s1_p0.sts.xml |1 + pbcore/data/datasets/pbalchemysim0.reference.xml | 79 +- pbcore/data/datasets/subreadSetWithStats.xml | 1139 +++- pbcore/io/FastaIO.py |2 +- pbcore/io/align/PacBioBamIndex.py | 83 +- pbcore/io/dataset/DataSetIO.py | 1400 ++-- pbcore/io/dataset/DataSetMembers.py| 206 ++- pbcore/io/dataset/DataSetReader.py | 233 ++-- pbcore/io/dataset/DataSetValidator.py | 53 +- pbcore/io/dataset/DataSetWriter.py | 19 +- pbcore/io/dataset/EntryPoints.py | 53 +- pbcore/util/ToolRunner.py |3 + tests/test_pbdataset.py| 205 ++- tests/test_pbdataset_subtypes.py | 174 ++- 21 files changed, 2996 insertions(+), 687 deletions(-) create mode 100644 pbcore/data/datasets/m150430_142051_Mon_p1_b25.sts.xml create mode 100755 pbcore/data/datasets/m150616_053259_ethan_c10071048255001823136404221563_s1_p0.sts.xml -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] 02/11: Remove executable bit from installed h5 data files
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-pbcore.
commit 68a3ebb3258d7b7c0856cb9705b24a31f673f1ab
Author: Afif Elghraoui
Date: Mon Aug 10 22:52:56 2015 -0700
Remove executable bit from installed h5 data files
---
debian/rules | 1 +
1 file changed, 1 insertion(+)
diff --git a/debian/rules b/debian/rules
index ad7edae..2a26bbd 100755
--- a/debian/rules
+++ b/debian/rules
@@ -4,6 +4,7 @@ DPKG_EXPORT_BUILDFLAGS = 1
include /usr/share/dpkg/default.mk
export PYBUILD_NAME = pbcore
+export PYBUILD_AFTER_INSTALL = chmod -x
{destdir}/{install_dir}/pbcore/data/*.h5
%:
LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
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[med-svn] [python-pbcore] branch pristine-tar updated (f3a0c52 -> c37d5f7)
This is an automated email from the git hooks/post-receive script. afif-guest pushed a change to branch pristine-tar in repository python-pbcore. from f3a0c52 pristine-tar data for python-pbcore_1.2.1+dfsg1.orig.tar.xz new c37d5f7 pristine-tar data for python-pbcore_1.2.2+dfsg1.orig.tar.xz The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: python-pbcore_1.2.2+dfsg1.orig.tar.xz.delta | Bin 0 -> 6771 bytes python-pbcore_1.2.2+dfsg1.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) create mode 100644 python-pbcore_1.2.2+dfsg1.orig.tar.xz.delta create mode 100644 python-pbcore_1.2.2+dfsg1.orig.tar.xz.id -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] 08/11: Install upstream-provided convenience scripts
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-pbcore.
commit fcb7bb9e78700aa63605bc2a44a7c31daad61740
Author: Afif Elghraoui
Date: Tue Aug 11 00:30:10 2015 -0700
Install upstream-provided convenience scripts
---
debian/README.Debian | 13 +
debian/patches/remove-convenience-script.patch | 21 -
debian/patches/series | 1 -
debian/rules | 9 +
4 files changed, 22 insertions(+), 22 deletions(-)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 000..48e8cc8
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,13 @@
+python-pbcore for Debian
+
+
+The software as provided by PacBio makes two scripts available on the
+system path:
+
+* dataset.py
+* .open
+
+These have been made available instead in /usr/share/doc/python-pbcore/scripts/
+and .open has been renamed to open (so that it is no longer hidden).
+
+ -- Afif Elghraoui , Tue, 11 Aug 2015 00:19:59 -0700
diff --git a/debian/patches/remove-convenience-script.patch
b/debian/patches/remove-convenience-script.patch
deleted file mode 100644
index 6282ad9..000
--- a/debian/patches/remove-convenience-script.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Description: Remove convenience scripts ".open" and "dataset.py"
- I am not quite sure what .open does, but it puts a file named
- ".open" in /usr/bin, which is quite strange. The upstream changelog
- indicates that this script is for convenience, so I am removing it
- for the time being. I may later put these two scripts in /usr/share/
- or /usr/share/doc
-Author: Afif Elghraoui
-Last-Update: 2015-08-05
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
python-pbcore.orig/setup.py
-+++ python-pbcore/setup.py
-@@ -30,8 +30,6 @@
-'data/datasets/yieldtest/*.*']
-},
- zip_safe = False,
--entry_points = { "console_scripts" : [ ".open =
pbcore.io.opener:entryPoint" ] },
--scripts=['bin/dataset.py'],
- install_requires=[
- 'h5py >= 2.0.1',
- 'numpy >= 1.7.1',
diff --git a/debian/patches/series b/debian/patches/series
index 8f4e122..57f5ddc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
-remove-convenience-script.patch
doc-theme.patch
enable-build-time-testing.patch
diff --git a/debian/rules b/debian/rules
index 169f433..9b7e7de 100755
--- a/debian/rules
+++ b/debian/rules
@@ -8,6 +8,9 @@ export PYBUILD_AFTER_INSTALL = \
chmod -x {destdir}/{install_dir}/pbcore/data/*.h5 \
{destdir}/{install_dir}/pbcore/data/datasets/*.xml
+DESTDIR = $(CURDIR)/debian/$(DEB_SOURCE)
+SCRIPTSDIR = $(DESTDIR)/usr/share/doc/$(DEB_SOURCE)/scripts
+
%:
LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
@@ -15,6 +18,12 @@ override_dh_auto_build:
dh_auto_build
$(MAKE) doc
+override_dh_install:
+ dh_install
+ mkdir -p $(SCRIPTSDIR)
+ mv $(DESTDIR)/usr/bin/.open $(SCRIPTSDIR)/open
+ mv $(DESTDIR)/usr/bin/dataset.py $(SCRIPTSDIR)/
+
override_dh_installdocs:
dh_installdocs -X _source
--
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[med-svn] [python-pbcore] 01/11: Drop non-functional python3 package
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-pbcore.
commit dafea9c3a095d483965d16cef85465861fefb3c4
Author: Afif Elghraoui
Date: Mon Aug 10 21:50:39 2015 -0700
Drop non-functional python3 package
It needed quite a bit of work and is not supported upstream at
the moment [1]. This also removes the need to split the data
package, so that has been dropped as well.
1. https://github.com/PacificBiosciences/pbcore/issues/18
---
debian/control | 46 +++---
debian/patches/enable-build-time-testing.patch | 6 ++--
debian/patches/remove-convenience-script.patch | 4 +--
debian/patches/series | 1 -
debian/patches/support-python3.patch | 38 -
debian/python-pbcore-data.install | 1 -
debian/python-pbcore.links | 1 -
debian/python-pbcore.pyremove | 1 -
debian/python3-pbcore.links| 1 -
debian/python3-pbcore.pyremove | 1 -
debian/rules | 5 +--
debian/tests/control | 8 ++---
12 files changed, 12 insertions(+), 101 deletions(-)
diff --git a/debian/control b/debian/control
index e15cd42..1b18d06 100644
--- a/debian/control
+++ b/debian/control
@@ -11,16 +11,9 @@ Build-Depends: debhelper (>= 9),
python-h5py (>= 2.0.1),
python-numpy (>= 1.7.1),
python-pysam (>= 0.8.1),
- python3-all,
- python3-setuptools,
- python3-nose,
- python3-h5py (>= 2.0.1),
- python3-numpy (>= 1.7.1),
- python3-pysam (>= 0.8.1),
python-sphinx
Standards-Version: 3.9.6
X-Python-Version: >= 2.7
-X-Python3-Version: >= 3.2
Homepage: https://github.com/PacificBiosciences/pbcore
Vcs-Git: git://anonscm.debian.org/debian-med/python-pbcore.git
Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-pbcore.git
@@ -28,47 +21,16 @@ Vcs-Browser:
http://anonscm.debian.org/cgit/debian-med/python-pbcore.git
Package: python-pbcore
Architecture: all
Depends: ${misc:Depends},
-${python:Depends},
-python-six
-Suggests: python-pbcore-doc
-Description: Python library for processing PacBio data files (Python 2)
+${python:Depends}
+Suggests: python-pbcore-doc (= ${source:Version})
+Description: Python library for processing PacBio data files
The pbcore package provides Python modules for processing Pacific Biosciences
data files and building PacBio bioinformatics applications. These modules
include tools to read/write PacBio data formats, sample data files for
testing and debugging, base classes, and utilities for building bioinformatics
applications.
.
- This package is part of the SMRTAnalysis suite. It provides the Python2
- module
-
-Package: python3-pbcore
-Architecture: all
-Depends: ${misc:Depends},
-${python3:Depends},
-python3-six
-Suggests: python-pbcore-doc
-Description: Python library for processing PacBio data files (Python 3)
- The pbcore package provides Python modules for processing Pacific Biosciences
- data files and building PacBio bioinformatics applications. These modules
- include tools to read/write PacBio data formats, sample data files for
- testing and debugging, base classes, and utilities for building bioinformatics
- applications.
- .
- This package is part of the SMRTAnalysis suite. It provides the Python3
- module.
-
-Package: python-pbcore-data
-Architecture: all
-Depends: ${misc:Depends}
-Description: Python library for processing PacBio data files (data)
- The pbcore package provides Python modules for processing Pacific Biosciences
- data files and building PacBio bioinformatics applications. These modules
- include tools to read/write PacBio data formats, sample data files for
- testing and debugging, base classes, and utilities for building bioinformatics
- applications.
- .
- pbcore is part of the SMRTAnalysis suite. This package provides sample
- data files.
+ This package is part of the SMRTAnalysis suite.
Package: python-pbcore-doc
Architecture: all
diff --git a/debian/patches/enable-build-time-testing.patch
b/debian/patches/enable-build-time-testing.patch
index 88c722b..9cdbd64 100644
--- a/debian/patches/enable-build-time-testing.patch
+++ b/debian/patches/enable-build-time-testing.patch
@@ -12,12 +12,12 @@ Last-Update: 2015-08-06
description-file = README.md
+[nosetests]
+verbosity=2
-+where=temptests
++where=tests
--- python-pbcore.orig/setup.py
+++ python-pbcore/setup.py
-@@ -29,6 +29,7 @@
+@@ -30,6 +30,7 @@
+'data/datasets/yieldtest/*.*']
},
- use_2to3 = True,
zip_safe = False,
+test_suite = 'nose.collector',
install_requires=[
diff --git a/debian
[med-svn] [python-pbcore] 07/11: Remove executable bit from non-executable file
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-pbcore.
commit b3b09484fd3f9496bfe26668714979d962716cbb
Author: Afif Elghraoui
Date: Mon Aug 10 23:31:12 2015 -0700
Remove executable bit from non-executable file
---
debian/rules | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/debian/rules b/debian/rules
index 2a26bbd..169f433 100755
--- a/debian/rules
+++ b/debian/rules
@@ -4,7 +4,9 @@ DPKG_EXPORT_BUILDFLAGS = 1
include /usr/share/dpkg/default.mk
export PYBUILD_NAME = pbcore
-export PYBUILD_AFTER_INSTALL = chmod -x
{destdir}/{install_dir}/pbcore/data/*.h5
+export PYBUILD_AFTER_INSTALL = \
+ chmod -x {destdir}/{install_dir}/pbcore/data/*.h5 \
+ {destdir}/{install_dir}/pbcore/data/datasets/*.xml
%:
LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
--
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[med-svn] [python-pbcore] branch topic/pybuild-intended-testsetup created (now faa6f7e)
This is an automated email from the git hooks/post-receive script. afif-guest pushed a change to branch topic/pybuild-intended-testsetup in repository python-pbcore. at faa6f7e Set up debian/rules for running the tests as pybuild intended This branch includes the following new commits: new faa6f7e Set up debian/rules for running the tests as pybuild intended The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] branch master updated (b6a9edd -> 8574ffb)
This is an automated email from the git hooks/post-receive script. afif-guest pushed a change to branch master in repository python-pbcore. from b6a9edd Add override for clean target in d/rules new dafea9c Drop non-functional python3 package new 68a3ebb Remove executable bit from installed h5 data files new 10a2a68 Install upstream readme and changelog files new cd3bf35 Imported Upstream version 1.2.2+dfsg1 new 74b076b Merge tag 'upstream/1.2.2+dfsg1' new 30c724c Update version in changelog new b3b0948 Remove executable bit from non-executable file new fcb7bb9 Install upstream-provided convenience scripts new 16e3ec5 Refresh patch new b20eeb0 Install upstream changelog and readme in main package (not doc package) new 8574ffb Fix changelog file name The 11 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: CHANGELOG.org |7 + bin/dataset.py |2 + debian/README.Debian | 13 + debian/changelog |2 +- debian/control | 46 +- debian/patches/enable-build-time-testing.patch | 10 +- debian/patches/remove-convenience-script.patch | 21 - debian/patches/series |2 - debian/patches/support-python3.patch | 38 - debian/python-pbcore-data.install |1 - debian/python-pbcore.docs |1 + debian/python-pbcore.links |1 - debian/python-pbcore.pyremove |1 - debian/python3-pbcore.links|1 - debian/python3-pbcore.pyremove |1 - debian/rules | 18 +- debian/tests/control |8 +- pbcore/__init__.py |2 +- pbcore/data/Makefile |7 + pbcore/data/datasets/__init__.py |6 +- pbcore/data/datasets/alignment.dataset.xml |8 + .../datasets/m150430_142051_Mon_p1_b25.sts.xml |1 + ...10071048255001823136404221563_s1_p0.sts.xml |1 + pbcore/data/datasets/pbalchemysim0.reference.xml | 79 +- pbcore/data/datasets/subreadSetWithStats.xml | 1139 +++- pbcore/io/FastaIO.py |2 +- pbcore/io/align/PacBioBamIndex.py | 83 +- pbcore/io/dataset/DataSetIO.py | 1400 ++-- pbcore/io/dataset/DataSetMembers.py| 206 ++- pbcore/io/dataset/DataSetReader.py | 233 ++-- pbcore/io/dataset/DataSetValidator.py | 53 +- pbcore/io/dataset/DataSetWriter.py | 19 +- pbcore/io/dataset/EntryPoints.py | 53 +- pbcore/util/ToolRunner.py |3 + tests/test_pbdataset.py| 205 ++- tests/test_pbdataset_subtypes.py | 174 ++- 36 files changed, 3036 insertions(+), 811 deletions(-) create mode 100644 debian/README.Debian delete mode 100644 debian/patches/remove-convenience-script.patch delete mode 100644 debian/patches/support-python3.patch delete mode 100644 debian/python-pbcore-data.install create mode 100644 debian/python-pbcore.docs delete mode 100644 debian/python-pbcore.links delete mode 100644 debian/python-pbcore.pyremove delete mode 100644 debian/python3-pbcore.links delete mode 100644 debian/python3-pbcore.pyremove create mode 100644 pbcore/data/datasets/m150430_142051_Mon_p1_b25.sts.xml create mode 100755 pbcore/data/datasets/m150616_053259_ethan_c10071048255001823136404221563_s1_p0.sts.xml -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [python-pbcore] 03/11: Install upstream readme and changelog files
This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository python-pbcore. commit 10a2a6818e87d5c9104f5429d663bfa8587aa45c Author: Afif Elghraoui Date: Mon Aug 10 22:53:29 2015 -0700 Install upstream readme and changelog files --- debian/python-pbcore-doc.install | 2 ++ 1 file changed, 2 insertions(+) diff --git a/debian/python-pbcore-doc.install b/debian/python-pbcore-doc.install index 72d7b2c..d7d167f 100644 --- a/debian/python-pbcore-doc.install +++ b/debian/python-pbcore-doc.install @@ -1 +1,3 @@ doc/_build/htmlusr/share/doc/python-pbcore +README.md usr/share/doc/python-pbcore +CHANGELOG.org usr/share/doc/python-pbcore -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [khmer] branch master updated (2fe66a6 -> c76d6be)
This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to branch master in repository khmer. from 2fe66a6 do not track symbols new c76d6be try setting the PYTHONPATH The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/rules | 8 1 file changed, 4 insertions(+), 4 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [khmer] 01/01: try setting the PYTHONPATH
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
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commit c76d6be5e8408a1251e9ff161ac75d2766445779
Author: Michael R. Crusoe
Date: Mon Aug 10 20:23:25 2015 -0700
try setting the PYTHONPATH
---
debian/rules | 8
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/debian/rules b/debian/rules
index 710071d..99e95fc 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,7 +1,6 @@
#!/usr/bin/make -f
export DH_VERBOSE=1
export PYBUILD_NAME=khmer
-export PYBUILD_SYSTEM=distutils
export PYBUILD_INSTALL_ARGS='--install-scripts=/usr/lib/khmer/bin'
export PYBUILD_DESTDIR_python3=debian/khmer
@@ -23,10 +22,11 @@ override_dh_auto_build:
cd lib && $(MAKE) clean all
override_dh_auto_test:
+ dh_auto_install
PYBUILD_SYSTEM=custom \
- PYBUILD_TEST_ARGS="cd {dir}; {interpreter} setup.py develop --user; \
- {interpreter} setup.py nosetests \
- --attr '!known_failing,!jenkins,!huge'" dh_auto_test
+ PYBUILD_TEST_ARGS="cd {dir}; export
PATH={destdir}/usr/lib/khmer/bin:$$PATH ; \
+ cd {build_dir}; {interpreter} -m nose --attr \
+ '!known_failing,!jenkins,!huge'" dh_auto_test
override_dh_auto_clean:
--
Alioth's /usr/local/bin/git-commit-notice on
/srv/git.debian.org/git/debian-med/khmer.git
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