[med-svn] [Git][med-team/cwltool][master] 4 commits: routine-update: New upstream version
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Sat Sep 7 12:50:07 BST 2024
Michael R. Crusoe pushed to branch master at Debian Med / cwltool
Commits:
f379c2a7 by Michael R. Crusoe at 2024-09-07T13:38:51+02:00
routine-update: New upstream version
- - - - -
66264524 by Michael R. Crusoe at 2024-09-07T13:38:52+02:00
New upstream version 3.1.20240708091337
- - - - -
453b01d4 by Michael R. Crusoe at 2024-09-07T13:38:57+02:00
Update upstream source from tag 'upstream/3.1.20240708091337'
Update to upstream version '3.1.20240708091337'
with Debian dir f82516307938a74869e4611423517b6dc4d4c23f
- - - - -
7c6c698e by Michael R. Crusoe at 2024-09-07T13:39:14+02:00
routine-update: Ready to upload to unstable
- - - - -
13 changed files:
- .github/workflows/quay-publish.yml
- PKG-INFO
- cwltool.egg-info/PKG-INFO
- cwltool.egg-info/requires.txt
- cwltool/_version.py
- cwltool/cwlprov/ro.py
- cwltool/job.py
- debian/changelog
- lint-requirements.txt
- mypy-requirements.txt
- pyproject.toml
- setup.py
- test-requirements.txt
Changes:
=====================================
.github/workflows/quay-publish.yml
=====================================
@@ -38,7 +38,7 @@ jobs:
username: ${{ secrets.REGISTRY_USERNAME }}
password: ${{ secrets.REGISTRY_PASSWORD }}
- name: Build and publish cwltool_module image to Quay
- uses: docker/build-push-action at v5
+ uses: docker/build-push-action at v6
with:
context: .
file: cwltool.Dockerfile
@@ -49,7 +49,7 @@ jobs:
cache-from: type=gha
cache-to: type=gha,mode=max
- name: Build and publish cwltool image to Quay
- uses: docker/build-push-action at v5
+ uses: docker/build-push-action at v6
with:
context: .
file: cwltool.Dockerfile
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: cwltool
-Version: 3.1.20240508115724
+Version: 3.1.20240708091337
Summary: Common workflow language reference implementation
Home-page: https://github.com/common-workflow-language/cwltool
Download-URL: https://github.com/common-workflow-language/cwltool
@@ -50,8 +50,8 @@ Requires-Dist: pyparsing!=3.0.2
Requires-Dist: cwl-utils>=0.32
Requires-Dist: spython>=0.3.0
Provides-Extra: deps
-Requires-Dist: galaxy-tool-util!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1,>=22.1.2; extra == "deps"
-Requires-Dist: galaxy-util<24.1; extra == "deps"
+Requires-Dist: galaxy-tool-util!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.2,>=22.1.2; extra == "deps"
+Requires-Dist: galaxy-util<24.2; extra == "deps"
#############################################################################################
``cwltool``: The reference reference implementation of the Common Workflow Language standards
=====================================
cwltool.egg-info/PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: cwltool
-Version: 3.1.20240508115724
+Version: 3.1.20240708091337
Summary: Common workflow language reference implementation
Home-page: https://github.com/common-workflow-language/cwltool
Download-URL: https://github.com/common-workflow-language/cwltool
@@ -50,8 +50,8 @@ Requires-Dist: pyparsing!=3.0.2
Requires-Dist: cwl-utils>=0.32
Requires-Dist: spython>=0.3.0
Provides-Extra: deps
-Requires-Dist: galaxy-tool-util!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1,>=22.1.2; extra == "deps"
-Requires-Dist: galaxy-util<24.1; extra == "deps"
+Requires-Dist: galaxy-tool-util!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.2,>=22.1.2; extra == "deps"
+Requires-Dist: galaxy-util<24.2; extra == "deps"
#############################################################################################
``cwltool``: The reference reference implementation of the Common Workflow Language standards
=====================================
cwltool.egg-info/requires.txt
=====================================
@@ -18,5 +18,5 @@ spython>=0.3.0
importlib_resources>=1.4
[deps]
-galaxy-tool-util!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1,>=22.1.2
-galaxy-util<24.1
+galaxy-tool-util!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.2,>=22.1.2
+galaxy-util<24.2
=====================================
cwltool/_version.py
=====================================
@@ -12,5 +12,5 @@ __version__: str
__version_tuple__: VERSION_TUPLE
version_tuple: VERSION_TUPLE
-__version__ = version = '3.1.20240508115724'
-__version_tuple__ = version_tuple = (3, 1, 20240508115724)
+__version__ = version = '3.1.20240708091337'
+__version_tuple__ = version_tuple = (3, 1, 20240708091337)
=====================================
cwltool/cwlprov/ro.py
=====================================
@@ -106,6 +106,7 @@ class ResearchObject:
return f"ResearchObject <{self.ro_uuid}> in <{self.folder}>"
def _initialize(self) -> None:
+ """Initialize the bagit folder structure."""
for research_obj_folder in (
METADATA,
DATA,
@@ -359,6 +360,7 @@ class ResearchObject:
return uri
def _ro_annotations(self) -> List[Annotation]:
+ """Append base RO and provenance annotations to the list of annotations."""
annotations: List[Annotation] = []
annotations.append(
{
@@ -414,6 +416,7 @@ class ResearchObject:
def _authored_by(self) -> Optional[AuthoredBy]:
authored_by: AuthoredBy = {}
+ """Returns the authoredBy metadata if it was supplied on CLI"""
if self.orcid:
authored_by["orcid"] = self.orcid
if self.full_name:
@@ -542,6 +545,7 @@ class ResearchObject:
checksum_file.write(line)
def _add_to_bagit(self, rel_path: str, **checksums: str) -> None:
+ """Compute file size and checksums and adds to bagit manifest."""
if PurePosixPath(rel_path).is_absolute():
raise ValueError(f"rel_path must be relative: {rel_path}")
lpath = os.path.join(self.folder, local_path(rel_path))
=====================================
cwltool/job.py
=====================================
@@ -913,7 +913,7 @@ class ContainerCommandLineJob(JobBase, metaclass=ABCMeta):
self.name,
int((max_mem_percent / 100 * max_mem) / (2**20)),
)
- if cleanup_cidfile:
+ if cleanup_cidfile and os.path.exists(cidfile):
os.remove(cidfile)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+cwltool (3.1.20240708091337-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Michael R. Crusoe <crusoe at debian.org> Sat, 07 Sep 2024 13:39:14 +0200
+
cwltool (3.1.20240508115724-1) unstable; urgency=medium
* New upstream version
=====================================
lint-requirements.txt
=====================================
@@ -1,3 +1,3 @@
flake8-bugbear<24.3
-black~=24.3
+black~=24.4
codespell
=====================================
mypy-requirements.txt
=====================================
@@ -1,9 +1,9 @@
-mypy==1.10.0 # also update pyproject.toml
+mypy==1.10.1 # also update pyproject.toml
ruamel.yaml>=0.16.0,<0.19
cwl-utils>=0.32
types-requests
types-setuptools
types-psutil
types-mock
-galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1
-galaxy-util<24.1
+galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.2
+galaxy-util<24.2
=====================================
pyproject.toml
=====================================
@@ -2,7 +2,7 @@
requires = [
"setuptools>=45",
"setuptools_scm[toml]>=8.0.4,<9",
- "mypy==1.10.0", # also update mypy-requirements.txt
+ "mypy==1.10.1", # also update mypy-requirements.txt
"types-requests",
"types-psutil",
"importlib_resources>=1.4;python_version<'3.9'",
=====================================
setup.py
=====================================
@@ -141,8 +141,8 @@ setup(
],
extras_require={
"deps": [
- "galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1",
- "galaxy-util <24.1",
+ "galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.2",
+ "galaxy-util <24.2",
],
},
python_requires=">=3.8, <4",
=====================================
test-requirements.txt
=====================================
@@ -8,6 +8,6 @@ mock>=2.0.0
pytest-mock>=1.10.0
pytest-cov
arcp>=0.2.0
--rrequirements.txt
-galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1
-galaxy-util<24.1
+-r requirements.txt
+galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.2
+galaxy-util<24.2
View it on GitLab: https://salsa.debian.org/med-team/cwltool/-/compare/1be37337b522a67877e10e4236202ded30aa8dbc...7c6c698e9b7f0213d57aba9f8dcd8a2ffb10cd97
--
View it on GitLab: https://salsa.debian.org/med-team/cwltool/-/compare/1be37337b522a67877e10e4236202ded30aa8dbc...7c6c698e9b7f0213d57aba9f8dcd8a2ffb10cd97
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