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Remove superfluous logger setup. #431

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Remove superfluous logger setup. #431

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c7cf177
Remove superfluous logger setup.
johanneskoester Mar 5, 2019
e592c57
Allow to restrict bioconductor-skeleton update to data packages.
johanneskoester Mar 6, 2019
77589a9
Merge branch 'master' into fix-logger-setup
johanneskoester Mar 7, 2019
a7e8add
Merge branch 'master' into fix-logger-setup
epruesse Mar 18, 2019
aab4559
Merge branch 'master' into fix-logger-setup
epruesse Mar 18, 2019
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10 changes: 7 additions & 3 deletions bioconda_utils/bioconductor_skeleton.py
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Original file line number Diff line number Diff line change
Expand Up @@ -874,7 +874,7 @@ def write_recipe_recursive(proj, seen_dependencies, recipe_dir, config, force,

def write_recipe(package, recipe_dir, config, force=False, bioc_version=None,
pkg_version=None, versioned=False, recursive=False, seen_dependencies=None,
packages=None, skip_if_in_channels=None):
packages=None, skip_if_in_channels=None, only_datapkgs=False):
"""
Write the meta.yaml and build.sh files. If the package is detected to be
a data package (bsed on the detected URL from Bioconductor), then also
Expand Down Expand Up @@ -922,6 +922,11 @@ def write_recipe(package, recipe_dir, config, force=False, bioc_version=None,
"""
config = utils.load_config(config)
proj = BioCProjectPage(package, bioc_version, pkg_version, packages=packages)

if only_datapkgs and not proj.is_data_package:
logger.info("Skipping non-data package {}".format(proj.package))
return

logger.info('Making recipe for: {}'.format(package))

if seen_dependencies is None:
Expand Down Expand Up @@ -972,7 +977,7 @@ def write_recipe(package, recipe_dir, config, force=False, bioc_version=None,
):
proj.build_number = int(current_build_number) + 1
if 'extra' in current_meta:
exclude = set(['final', 'copy_test_source_files'])
exclude = set(['final', 'copy_test_source_files', 'parent_recipe'])
proj.extra = {x: y for x, y in current_meta['extra'].items() if x not in exclude}

with open(os.path.join(recipe_dir, 'meta.yaml'), 'w') as fout:
Expand Down Expand Up @@ -1002,7 +1007,6 @@ def write_recipe(package, recipe_dir, config, force=False, bioc_version=None,
proj.bioconductor_tarball_url,
bioarchive_url(proj.package, proj.version, proj.bioc_version),
cargoport_url(proj.package, proj.version, proj.bioc_version),
proj.cargoport_url
]
if u is not None
]
Expand Down
7 changes: 5 additions & 2 deletions bioconda_utils/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -675,11 +675,13 @@ def dependent(recipe_folder, config, restrict=False,
@arg('--skip-if-in-channels', nargs='*', help="""When --recursive is used, it will build
*all* recipes. Use this argument to skip recursive building for packages
that already exist in the packages listed here.""")
@arg('--only-datapkgs', action='store_true', help="""Only consider data packages.
To be used in combination with 'update-all-packages'.""")
@enable_logging('debug')
def bioconductor_skeleton(
recipe_folder, config, package, versioned=False, force=False,
pkg_version=None, bioc_version=None, recursive=False,
skip_if_in_channels=['conda-forge', 'bioconda']):
skip_if_in_channels=['conda-forge', 'bioconda'], only_datapkgs=False):
"""
Build a Bioconductor recipe. The recipe will be created in the `recipes`
directory and will be prefixed by "bioconductor-". If `--recursive` is set,
Expand Down Expand Up @@ -710,7 +712,8 @@ def bioconductor_skeleton(
_bioconductor_skeleton.write_recipe(
k, recipe_folder, config, force=True, bioc_version=bioc_version,
pkg_version=v['Version'], versioned=versioned, packages=packages,
skip_if_in_channels=skip_if_in_channels)
skip_if_in_channels=skip_if_in_channels,
only_datapkgs=only_datapkgs)
except:
problems.append(k)
if len(problems):
Expand Down