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Changes upstreamed while packaging libkhmer for Debian #1148

Merged
merged 20 commits into from
Jul 31, 2015
Merged

Changes upstreamed while packaging libkhmer for Debian #1148

merged 20 commits into from
Jul 31, 2015

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kdm9
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@kdm9 kdm9 commented Jul 6, 2015

Misc changes @mr-c & I though should be upstreamed

This was referenced Jul 6, 2015
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@kdm9 kdm9 force-pushed the fix/debian-libkhmer-upstreaming branch from 5e53d92 to 038f415 Compare July 8, 2015 12:07
@mr-c
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mr-c commented Jul 8, 2015

@kdmurray91 I'm going to leave feedback on the Debian packaging here, for lack of better place

Since we haven't published the release candidate on GitHub you can't use uscan to download & exclude files & repack.

Looks like the way to work around that is:

wget https://github.com/dib-lab/khmer/archive/v2.0-rc1.tar.gz
mk-origtargz v2.0-rc1.tar.gz --repack --compression xz --version 2.0rc1+dfsg

& update the ChangeLog to use the matching version (with 'dfsg' in it)

debian/control: Should build-depend on python3-screed (>= 0.9,<< 1.0); strip out other python(2) and replace with python3.

Why liboxli2 ?

debian/rules: remove "export PYBUILD_AFTER_INSTALL" paragraph as that has been fixed in 2.0

Don't add/change files directly to the upstream (khmer) code. Add them using quilt :-)

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mr-c commented Jul 8, 2015

Feel free to bring your commits into the master branch.

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mr-c commented Jul 15, 2015

Seems fine to me; as I don't personally use that Makefile I'm happy to leave it up to you, @blahah, and @luizirber

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mr-c commented Jul 31, 2015

Checklist?

@kdm9
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kdm9 commented Jul 31, 2015

  • Is it mergeable?
  • Did it pass the tests?
  • If it introduces new functionality in scripts/ is it tested?
    Check for code coverage with make clean diff-cover
  • Is it well formatted? Look at make pep8, make diff_pylint_report,
    make cppcheck, and make doc output. Use make format and manual
    fixing as needed.
  • Did it change the command-line interface? Only additions are allowed
    without a major version increment. Changing file formats also requires a
    major version number increment.
  • Is it documented in the ChangeLog?
    http://en.wikipedia.org/wiki/Changelog#Format
  • Was a spellchecker run on the source code and documentation after
    changes were made?
  • Is the Copyright year up to date?

kdm9 added 18 commits July 31, 2015 11:12
@kdm9
Install lib headers to $PREFIX/include/oxli
3a1b78c
@kdm9
Fix libtest target of root makefile
c24133c 
Headers should be installed to $PREFIX/include/oxli
@kdm9
Revamp C/CXXFlags in lib/makefile
3a8c06d
@kdm9
Rewrite lib/Makefile with debian-related stuff
99f4b4b 
- Add USE_SYSTEM_ZLIB and USE_SYSTEM_LIBBZ2 flags to disable code under
  third-party/
- Allow C/CPP/LD/CXXFLAGS to be overwridden, e.g. by dpkg-buildflags
- Misc makefile formatting and fixes
@kdm9
lib/Makefile: Parse major and minor versions
f9e683c
@kdm9
Add SONAME flags, name OSX lib .dylib, use LDFLAGS
831924f
@kdm9
Actually use the SONAME_FLAGS during compilation
4df5308
@kdm9
Allow overriding of VERSION in makefile
634682f
@kdm9
Fix disabling of bundled third party libs
ebb6db2
@kdm9
Always use common flags in lib/Makefile
1739524
@kdm9
s/khmer/oxli as appropriate in lib/makefile
cd8122b
@kdm9
Rename liboxli pkgconfig file
b5dda64
@kdm9
Unset *FLAGS before building the libary in jenkins
d995a3f
@kdm9
Fix test of C++ lib installation & compile
8e60e7a
@kdm9
Only compile libary once in jenkins-build.sh
5e0cc92
@kdm9
Update library name in package config file
b874659
@kdm9
Hard-code ABI version in lib/Makefile
3c0e6a8
@kdm9
Fix rebase, remove internal metrics code
9b317b4 
Accidentally re-added the metrics code while conflict-popping
@kdm9 kdm9 force-pushed the fix/debian-libkhmer-upstreaming branch from d8369dc to 9b317b4 Compare July 31, 2015 01:18
@kdm9
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kdm9 commented Jul 31, 2015

Ready for review @mr-c et al.

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mr-c commented Jul 31, 2015

LGTM, thanks!

mr-c added a commit that referenced this pull request Jul 31, 2015
@mr-c
Merge pull request #1148 from dib-lab/fix/debian-libkhmer-upstreaming
8c2f8d3 
Changes upstreamed while packaging `libkhmer` for Debian
@mr-c mr-c merged commit 8c2f8d3 into master Jul 31, 2015
@mr-c mr-c deleted the fix/debian-libkhmer-upstreaming branch August 5, 2015 00:20
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@kdm9 @mr-c