Package: snakemake / 5.24.1-2

Metadata

Package Version Patches format
snakemake 5.24.1-2 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
0001 Use the inbuild sphinx.ext.napoleon.patch | (download)

docs/conf.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 use the inbuild sphinx.ext.napoleon

Removes the dependency on sphinxcontrib.napoleon, which is now part of
sphinx proper, as sphinx.ext.napoleon.

local_javascript.patch | (download)

docs/conf.py | 3 3 + 0 - 0 !
docs/index.rst | 40 9 + 31 - 0 !
docs/project_info/citations.rst | 5 1 + 4 - 0 !
snakemake/gui.html | 10 5 + 5 - 0 !
4 files changed, 18 insertions(+), 40 deletions(-)

 use local javascript etc for privacy

Some of the badge images legally could be replaced with local copies,
but this would appear to be a live status when it isn't
(or a per-version status that is easy to forget to update),
so use text links instead

0003 Compat fix.patch | (download)

tests/test_symlink_time_handling/Snakefile | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 compat fix


0006 restore bin.patch | (download)

bin/snakemake | 6 6 + 0 - 0 !
1 file changed, 6 insertions(+)

 version 3.9.1 is lacking snakemake executable - using the
 binary that results from build process as quilt patch at the former location


0008 remove_sphinx.ext.patch | (download)

docs/conf.py | 3 1 + 2 - 0 !
1 file changed, 1 insertion(+), 2 deletions(-)

 remove sphinxext which spoils doc generation
0009 skip test without google cloud sdk.patch | (download)

tests/test_google_lifesciences.py | 6 5 + 1 - 0 !
tests/test_remote_gs/Snakefile | 30 17 + 13 - 0 !
2 files changed, 22 insertions(+), 14 deletions(-)

 skip tests that depend on google-cloud-sdk if not installed

This is not currently in Debian - see RFP #759578.

python3.patch | (download)

tests/test_delete_all_output/Snakefile | 8 4 + 4 - 0 !
tests/test_linting.py | 2 1 + 1 - 0 !
tests/test_list_untracked/Snakefile | 2 1 + 1 - 0 !
tests/test_profile/Snakefile | 2 1 + 1 - 0 !
tests/test_tibanna.py | 2 1 + 1 - 0 !
tests/tests.py | 4 2 + 2 - 0 !
6 files changed, 10 insertions(+), 10 deletions(-)

 use python 3 in subprocess calls

TODO - are any of the ones in snakemake/script.py:execute_script a problem?

workaround_sphinx_issue.patch | (download)

docs/conf.py | 2 2 + 0 - 0 !
1 file changed, 2 insertions(+)

 exclude common.py:lazy_property from documentation

Needed as Sphinx 2 can't process it

This is obviously not an ideal fix, but it's an internal class with little
documentation to begin with:
https://snakemake.readthedocs.io/en/stable/api_reference/internal/snakemake.html#snakemake.common.lazy_property

Also exclude Flask.request due to
https://github.com/sphinx-doc/sphinx/issues/7516

remove_ccbysa_snippets.patch | (download)

snakemake/io.py | 13 1 + 12 - 0 !
snakemake/remote/S3Mocked.py | 24 9 + 15 - 0 !
snakemake/utils.py | 42 17 + 25 - 0 !
tests/test_static_remote/S3MockedForStaticTest.py | 23 9 + 14 - 0 !
4 files changed, 36 insertions(+), 66 deletions(-)

 remove code from stack overflow

Stack Overflow content is CC-BY-SA licensed,
which this package is not supposed to be.  These snippets may be
too small to be copyrightable, but removing them to be safe.