[med-svn] [snakemake] branch upstream updated (1881744 -> a51fb0f)

[Kevin Murray]

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

daube-guest pushed a change to branch upstream
in repository snakemake.

      from  1881744   New upstream version 3.8.2+dfsg
       new  a51fb0f   New upstream version 3.9.0+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:
 CHANGELOG.md                                       |  15 ++
 biglogo.pdf                                        | Bin 0 -> 3806 bytes
 biglogo.png                                        | Bin 0 -> 17334 bytes
 biglogo.svg                                        | 141 +++++++++++
 bitbucket-pipelines.yml                            |   1 -
 environment.yml                                    |   4 +
 setup.py                                           |  12 +-
 snakemake/__init__.py                              |  47 +++-
 snakemake/common.py                                |  10 +
 snakemake/conda.py                                 |  50 ++++
 snakemake/dag.py                                   |  22 +-
 snakemake/exceptions.py                            |   8 +
 snakemake/executors.py                             | 131 ++++++----
 snakemake/futures.py                               |  36 ---
 snakemake/io.py                                    |  98 ++++++--
 snakemake/jobs.py                                  |  56 ++++-
 snakemake/logging.py                               |  53 ++--
 snakemake/parser.py                                | 110 ++++----
 snakemake/persistence.py                           |  20 +-
 snakemake/remote/HTTP.py                           |  14 +-
 snakemake/remote/__init__.py                       |   4 +-
 snakemake/report.py                                |  46 ++--
 snakemake/rules.py                                 |  53 +++-
 snakemake/scheduler.py                             |  18 +-
 snakemake/script.py                                | 160 +++++++-----
 snakemake/shell.py                                 |   8 +-
 snakemake/version.py                               |   4 +-
 snakemake/workflow.py                              |  45 +++-
 snakemake/wrapper.py                               |  38 ++-
 tests/test01/Snakefile                             |   2 +-
 tests/test05/Snakefile                             |   4 +
 tests/test09/Snakefile                             |   3 +
 tests/test13/Snakefile                             |   4 +
 tests/test14/Snakefile.nonstandard                 |   4 +
 tests/test_ancient/Snakefile                       |  28 +++
 .../test_ancient/expected-results/A                |   0
 .../test_ancient/expected-results/B                |   0
 tests/test_ancient/expected-results/C              |   1 +
 tests/test_ancient/expected-results/D              |   1 +
 tests/test_conda/Snakefile                         |  11 +
 tests/test_conda/expected-results/test0.out        | 279 +++++++++++++++++++++
 tests/test_conda/expected-results/test1.out        | 279 +++++++++++++++++++++
 tests/test_conda/expected-results/test2.out        | 279 +++++++++++++++++++++
 tests/test_conda/test-env.yaml                     |   4 +
 tests/test_delete_output/Snakefile                 |  52 +++-
 .../hg19.fa => tests/test_delete_output/nosuchfile |   0
 tests/test_get_log_both/test.out                   |   2 -
 tests/test_get_log_complex/test.out                |   2 -
 tests/test_get_log_stderr/test.out                 |   2 -
 tests/test_get_log_stdout/test.out                 |   2 -
 tests/test_issue381/Snakefile                      |  21 ++
 .../cufflinks/hg19.fa => tests/test_issue381/a.in  |   0
 .../test_issue381/expected-results/b.out           |   0
 tests/test_persistent_dict/Snakefile               |  44 ++--
 tests/test_rule_defined_in_for_loop/Snakefile      |  12 +
 .../expected-results/iteration-01.txt              |   0
 .../expected-results/iteration-02.txt              |   0
 .../test_rule_defined_in_for_loop/iteration-01.txt |   0
 tests/test_wrapper/Snakefile                       |   7 +
 tests/test_wrapper/expected-results/test.vcf.gz    | Bin 0 -> 438 bytes
 tests/test_wrapper/test.vcf                        |  15 ++
 tests/tests.py                                     |  44 +++-
 62 files changed, 1915 insertions(+), 391 deletions(-)
 create mode 100644 biglogo.pdf
 create mode 100644 biglogo.png
 create mode 100644 biglogo.svg
 create mode 100644 snakemake/conda.py
 delete mode 100644 snakemake/futures.py
 create mode 100644 tests/test_ancient/Snakefile
 copy examples/cufflinks/hg19.fa => tests/test_ancient/expected-results/A (100%)
 copy examples/cufflinks/hg19.fa => tests/test_ancient/expected-results/B (100%)
 create mode 100644 tests/test_ancient/expected-results/C
 create mode 100644 tests/test_ancient/expected-results/D
 create mode 100644 tests/test_conda/Snakefile
 create mode 100644 tests/test_conda/expected-results/test0.out
 create mode 100644 tests/test_conda/expected-results/test1.out
 create mode 100644 tests/test_conda/expected-results/test2.out
 create mode 100644 tests/test_conda/test-env.yaml
 copy examples/cufflinks/hg19.fa => tests/test_delete_output/nosuchfile (100%)
 delete mode 100644 tests/test_get_log_both/test.out
 delete mode 100644 tests/test_get_log_complex/test.out
 delete mode 100644 tests/test_get_log_stderr/test.out
 delete mode 100644 tests/test_get_log_stdout/test.out
 create mode 100644 tests/test_issue381/Snakefile
 copy examples/cufflinks/hg19.fa => tests/test_issue381/a.in (100%)
 copy examples/cufflinks/hg19.fa => tests/test_issue381/expected-results/b.out (100%)
 create mode 100644 tests/test_rule_defined_in_for_loop/Snakefile
 copy examples/cufflinks/hg19.fa => tests/test_rule_defined_in_for_loop/expected-results/iteration-01.txt (100%)
 copy examples/cufflinks/hg19.fa => tests/test_rule_defined_in_for_loop/expected-results/iteration-02.txt (100%)
 copy examples/cufflinks/hg19.fa => tests/test_rule_defined_in_for_loop/iteration-01.txt (100%)
 create mode 100644 tests/test_wrapper/Snakefile
 create mode 100644 tests/test_wrapper/expected-results/test.vcf.gz
 create mode 100644 tests/test_wrapper/test.vcf

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snakemake.git