[med-svn] [python-biopython] annotated tag upstream/1.66+dfsg created (now 7f3bc20)
Andreas Tille
tille at debian.org
Wed Mar 9 11:54:45 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to annotated tag upstream/1.66+dfsg
in repository python-biopython.
at 7f3bc20 (tag)
tagging 80d5869d6dd4b4bd538e35eac3e183f65d23334a (commit)
tagged by Andreas Tille
on Wed Mar 9 12:46:18 2016 +0100
- Log -----------------------------------------------------------------
Upstream version 1.66+dfsg
Andreas Tille (75):
Took over citation information from tasks file
Fixed Vcs fields
Valid BibTeX authors field
cme fix dpkg-control
Commit current but non-working status of packaging to ask for help on debian-python list
Remove comment
Follow some hints from Debian Python team
More verbose testing by installing some more tools as Build-Depends to enable testing these on one hand and excluding some tests in need of online connection
Exclude tests that need online access
Enhanced testing and documentation of the testing in README.source
Enable more testing and fix Emboss test
Clean up behind tests
Put files in right packages
Exclude another test relying on non-free software
Update todo list in changelog
DEP3
Run bwa test on amd64 architectures
*really* make test of bwa architecture dependant; fix issue with empty __pycache__ dir
Better documentation for the reasons why we exclude the database tests
Better documentation of the excluded database tests
Please leave the possibility to test the package at build time ... at least as long as the issue discussed on Debian Python list is open. BTW, the test control file becomes *way* more simple if we leave it this way and as I wrote on the mainling list both tests make perfectly sense.
Fix test suite run
Make sure test suite will at least run in autopkgtest; need to check why it triggers more failures than at package build time
Enhance autopkgtest and add README.test
More enhancements of testing
we really need this gzipped duplicate of the example.fastq file to pass the BGZF compression test
Use offline option of run_tests.py which has the side effekt that failures are not hidden any more by setup.py. So for the moment we need to exclude also tests that fail for unknown reasons. Further debugging is needed - perhaps we might upload anyway and leave this for further investigation and drop an paragraph rin README.tests
Since we are running the test suite directly not via setup.py the failed tests would stop the build. So these are separated now and left for further inspection via a script running all the tests.
Fixed and enhanced test script
Further small enhancement and simplifications for the test suite
Deal with Tutorial test
Additional Build-Depends: python-imaging; We need python-rdflib (>=4) - deactivate the test until we detect that this version is available
Add Upstream-Contact; DEP5
add missing test_Fasttree_tool ... but this does not help for the test result
Add some patches enhancing the test suite
Upload to unstable
Remove Bio\Entrez\DTDs\mathml2-qname-1.mod
Force writable HOME to make sure t-coffee test will pass
Upload to unstable
Set HOME=/tmp also in autopkgtest
Do not try to create doc in arch-only builds
Fix autopkgtest; move ncbi-blast+ from Suggests to Recommends
Commit latest change: Apply upstream fix to fix cpairwise2 import issue under python3
New upstream version
Build-Depends raxml only on those architectures where it is available
Updated patches to new upstream version
Upload to unstable
Use mktemp as HOME for testing
Use HOME in build_dir for testing
Try to get the package finally build on all architectures by skiping test on mips architecture which is known to fail and versioned (Build-)Depends wise
Patch provided by upstream to run test suite on PowerPC
Install egg metadata
Add samtools to Build-Depends + Recommends since it is checked in test suite
Several changes in one rush - main important one is not testing samtools
New upstream version
Refreshed patches
Add comment about fastsimcoal
More precise explanation for fastsimcoal
Provide part of doc in test dir since it is needed to run the test suite
Apply fix for broken test from Upstream Git
Versioned (Build-)Depends: python-rdflib (>= 4), Prevent privacy-breach-logo, Upload to unstable
Build-Depends & Suggests: phylip + fixed test_phyml_tool
Activate more tests formerly deactivated
Enable Fasttree_tool test
Enable test GenomeDiagram
Verify that samtools test is really creating problems and upload to unstable
Also run Tutorial test
Prefer Github as contact point
Fix for mafft test
Add link to github issue
Build-Depends: python3-mysqldb
Upload to unstable
Remove patches applied upstream
Upload to unstable
Imported Upstream version 1.66+dfsg
Charles Plessy (14):
Removing obsolete XS- prefix
+XS-DM-Upload-Allowed: Yes
Fixing case mistake
New upstream release; some issues remain to be fixed before upload.
Added missing comma.
Added mmCIF support, use Debhelper 7 and quilt, fixed doc-base registration.
Described patch
Enabled tests (test_Wise fails, unfortunately).
Added a patch that prevents the tests from failing with Debian's version of Wise.
Forgot to patch also the output file, that is used to compare to the local result.
Corrected a typo and upload to unstable.
Build-depend on wise for the tests after building.
Added python-mysqldb to the Build-Depends, again for the tests.
Changed the description of python-biopython-sql according to Peter Cock's suggestions.
David Paleino (1):
* Using DM-Upload-Allowed instead of XS-DM-Upload-Allowed
James McCoy (1):
Move debian/upstream to debian/upstream/metadata
Morten Kjeldgaard (2):
Add dependency on python-numeric-ext (Bio.PDB use MLab from this package)
Spelling mistake in last changelog entry fixed
Nelson A. de Oliveira (1):
s/Debian-Med/Debian Med
Philipp Benner (39):
Creating trunk directory
[svn-inject] Applying Debian modifications to trunk
XS-Vcs-* tags added
new release
removed .DS_Store.gz file from doc package
updated changelog
* Moved wise from recommends to suggests field.
build-dep without versions as they are no longer needed
standards version 3.7.3
converted debian/copyright to utf-8
new maintainer e-mail address
debian/{copyright,README.Debian}: changed e-mail address
new upstream release
changed section of doc-base tutorial
Removed dependency on python-numeric-ext
new upstream release
new upstream release
dropped biopython-martel
debian/control: added missing separator
debian/control: added note
new upstream release
merged patch from ubuntu
new upstream release
standards version 3.8.3; added README.source
new upstream release
upstream release 1.54
release 1.56-1
release 1.57-1
release 1.58-1
release 1.59-1
release 1.60-1
standards version
release 1.61-1
python-biopython: release 1.62-1
merged old changelog from version 1.63-1
removed bwa from build-dependencies
DSSP fix; excluded BioSQL_MySQLdb BioSQL_psycopg2 which require internet access
a very first autopkgtest
2015/03/03-09:29:17 (Linux debian-med unknown)
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