[med-svn] [paleomix] branch master updated (b96def7 -> 41f9c71)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository paleomix.

      from  b96def7   Add missing license statement
       new  1067366   New upstream version 1.2.12
       new  7993529   Updated version 1.2.12 from 'upstream/1.2.12'
       new  57b14a1   New upstream version
       new  d092f07   Standards-Version: 4.1.1
       new  392d73f   Drop patches replaced by upstream code
       new  75429a1   Exclude one test that strangely fails
       new  41f9c71   Exclude test in d/rules rather than in patch

The 7 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 +
 CHANGES.md                                      | 109 +++++-
 INSTALL.rst                                     |   4 +
 README.rst                                      |  16 +-
 debian/changelog                                |   8 +
 debian/control                                  |   2 +-
 debian/patches/exclude_failing_test.patch       |  44 +++
 debian/patches/fix_makefile_test.patch          |  39 ---
 debian/patches/series                           |   3 +-
 debian/patches/work_around_os.getlogin.patch    |  35 --
 debian/rules                                    |   2 +
 docs/bam_pipeline/requirements.rst              |   6 +-
 docs/conf.py                                    |  28 +-
 docs/index.rst                                  |  14 +-
 docs/yaml.rst                                   | 164 ++++++++-
 docs/zonkey_pipeline/index.rst                  |  11 +-
 paleomix/__init__.py                            |   2 +-
 paleomix/atomiccmd/builder.py                   |  81 +++--
 paleomix/atomiccmd/command.py                   |   8 +-
 paleomix/atomiccmd/pprint.py                    | 102 +++---
 paleomix/common/formats/fasta.py                |  16 +-
 paleomix/common/makefile.py                     |  20 ++
 paleomix/common/testing.py                      |   6 +-
 paleomix/common/vcffilter.py                    |   3 +-
 paleomix/common/vcfwrap.py                      |  15 +-
 paleomix/common/versions.py                     |  77 +++--
 paleomix/main.py                                |   4 +
 paleomix/node.py                                | 100 +++---
 paleomix/nodes/bowtie2.py                       |  31 +-
 paleomix/nodes/bwa.py                           |  41 +--
 paleomix/nodes/commands.py                      |  73 ++--
 paleomix/nodes/mapdamage.py                     |  38 +-
 paleomix/nodes/picard.py                        | 233 ++++++-------
 paleomix/nodes/samtools.py                      |  27 +-
 paleomix/nodes/validation.py                    | 252 ++++++++------
 paleomix/pipeline.py                            |   4 +-
 paleomix/tools/bam_pipeline/makefile.py         | 105 +++---
 paleomix/tools/bam_pipeline/mkfile.py           |   6 +-
 paleomix/tools/bam_pipeline/nodes.py            |  73 ++--
 paleomix/tools/bam_pipeline/parts/lane.py       |   9 +-
 paleomix/tools/bam_pipeline/parts/library.py    |  40 ++-
 paleomix/tools/bam_pipeline/parts/prefix.py     | 102 ++++--
 paleomix/tools/bam_pipeline/parts/statistics.py |  20 +-
 paleomix/tools/bam_pipeline/pipeline.py         |  46 ++-
 paleomix/tools/bam_stats/common.py              |   2 +-
 paleomix/tools/cleanup.py                       |  42 ++-
 paleomix/tools/dupcheck.py                      |  93 +++++
 paleomix/tools/rmdup_collapsed.py               | 315 ++++++++++-------
 paleomix/tools/zonkey/config.py                 |  18 +-
 paleomix/tools/zonkey/pipeline.py               |  17 +-
 paleomix/ui.py                                  |  10 +-
 setup.py                                        |   2 +-
 tests/.coveragerc                               |  11 +
 tests/README.md                                 |   4 +
 tests/atomiccmd_test/builder_test.py            |  75 +++-
 tests/atomiccmd_test/command_test.py            | 213 +++++++-----
 tests/atomiccmd_test/pprint_test.py             | 439 ++++++++++++++----------
 tests/atomiccmd_test/sets_test.py               |  18 +-
 tests/common_tests/fileutils_test.py            |  10 +-
 tests/common_tests/makefile_test.py             | 216 ++++++++++--
 tests/common_tests/versions_tests.py            | 118 +++++--
 tests/run                                       |  27 --
 tests/setup.sh                                  |  15 +
 tox.ini                                         |   4 +-
 64 files changed, 2342 insertions(+), 1328 deletions(-)
 create mode 100644 INSTALL.rst
 create mode 100644 debian/patches/exclude_failing_test.patch
 delete mode 100644 debian/patches/fix_makefile_test.patch
 delete mode 100644 debian/patches/work_around_os.getlogin.patch
 create mode 100644 paleomix/tools/dupcheck.py
 create mode 100644 tests/.coveragerc
 create mode 100644 tests/README.md
 delete mode 100755 tests/run
 create mode 100755 tests/setup.sh

-- 
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