toil 7.0.0__tar.gz → 8.1.0b1__tar.gz

{toil-7.0.0 → toil-8.1.0b1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: toil
-Version: 7.0.0
+Version: 8.1.0b1
 Summary: Pipeline management software for clusters.
 Home-page: https://github.com/DataBiosphere/toil
 Author: Benedict Paten and the Toil community
@@ -16,10 +16,11 @@ Classifier: Natural Language :: English
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
 Classifier: Operating System :: POSIX :: Linux
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Astronomy
@@ -28,7 +29,7 @@ Classifier: Topic :: Scientific/Engineering :: Information Analysis
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: System :: Distributed Computing
 Classifier: Topic :: Utilities
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: dill<0.4,>=0.3.2
@@ -36,15 +37,17 @@ Requires-Dist: requests<=2.31.0
 Requires-Dist: docker<8,>=6.1.0
 Requires-Dist: urllib3<3,>=1.26.0
 Requires-Dist: python-dateutil
-Requires-Dist: psutil<6,>=3.0.1
+Requires-Dist: psutil<8,>=6.1.0
 Requires-Dist: PyPubSub<5,>=4.0.3
 Requires-Dist: addict<2.5,>=2.2.1
+Requires-Dist: backports.zoneinfo[tzdata]; python_version < "3.9"
 Requires-Dist: enlighten<2,>=1.5.2
 Requires-Dist: configargparse<2,>=1.7
 Requires-Dist: ruamel.yaml>=0.15
 Requires-Dist: pyyaml<7,>=6
 Requires-Dist: typing-extensions<5,>=4.6.2
 Requires-Dist: coloredlogs<16,>=15
+Requires-Dist: prompt_toolkit<4,>=3.0
 Provides-Extra: aws
 Requires-Dist: boto3-stubs[autoscaling,boto3,ec2,iam,s3,sdb,sts]<2,>=1.28.3.post2; extra == "aws"
 Requires-Dist: mypy-boto3-iam<2,>=1.28.3.post2; extra == "aws"
@@ -52,7 +55,7 @@ Requires-Dist: mypy-boto3-s3<2,>=1.28.3.post2; extra == "aws"
 Requires-Dist: moto<6,>=5.0.3; extra == "aws"
 Requires-Dist: ec2_metadata<3; extra == "aws"
 Provides-Extra: cwl
-Requires-Dist: cwltool==3.1.20240508115724; extra == "cwl"
+Requires-Dist: cwltool==3.1.20250110105449; extra == "cwl"
 Requires-Dist: schema-salad<9,>=8.4.20230128170514; extra == "cwl"
 Requires-Dist: galaxy-tool-util<25; extra == "cwl"
 Requires-Dist: galaxy-util<25; extra == "cwl"
@@ -60,6 +63,7 @@ Requires-Dist: ruamel.yaml<=0.19,>=0.15; extra == "cwl"
 Requires-Dist: ruamel.yaml.clib>=0.2.6; extra == "cwl"
 Requires-Dist: networkx!=2.8.1,<4; extra == "cwl"
 Requires-Dist: CacheControl[filecache]; extra == "cwl"
+Requires-Dist: cwl-utils>=0.36; extra == "cwl"
 Provides-Extra: encryption
 Requires-Dist: pynacl<2,>=1.4.0; extra == "encryption"
 Provides-Extra: google
@@ -67,26 +71,26 @@ Requires-Dist: apache-libcloud<3,>=2.2.1; extra == "google"
 Requires-Dist: google-cloud-storage<=2.8.0,>=2; extra == "google"
 Requires-Dist: google-auth<3,>=2.18.1; extra == "google"
 Provides-Extra: kubernetes
-Requires-Dist: kubernetes<22,>=12.0.1; extra == "kubernetes"
+Requires-Dist: kubernetes<33,>=12.0.1; extra == "kubernetes"
 Requires-Dist: kubernetes-stubs==v22.6.0post1; extra == "kubernetes"
 Requires-Dist: types-urllib3; extra == "kubernetes"
 Requires-Dist: types-PyYAML; extra == "kubernetes"
 Requires-Dist: idna>=2; extra == "kubernetes"
 Provides-Extra: wdl
-Requires-Dist: miniwdl==1.12.0; extra == "wdl"
+Requires-Dist: miniwdl==1.12.1; extra == "wdl"
 Requires-Dist: wdlparse==0.1.0; extra == "wdl"
 Requires-Dist: graphlib-backport==1.0; python_version < "3.9" and extra == "wdl"
 Provides-Extra: server
-Requires-Dist: connexion[swagger-ui]<3,>=2.10.0; extra == "server"
-Requires-Dist: flask<3,>=2.0; extra == "server"
-Requires-Dist: werkzeug<3,>=2.0; extra == "server"
-Requires-Dist: flask-cors==4.0.1; extra == "server"
-Requires-Dist: gunicorn==22.0.0; extra == "server"
+Requires-Dist: connexion[swagger-ui]<4,>=2.10.0; extra == "server"
+Requires-Dist: flask<4,>=2.0; extra == "server"
+Requires-Dist: werkzeug<4,>=2.0; extra == "server"
+Requires-Dist: flask-cors==5.0.1; extra == "server"
+Requires-Dist: gunicorn==23.0.0; extra == "server"
 Requires-Dist: celery<6,>=5.1.0; extra == "server"
 Requires-Dist: wes-service<5,>=4.0.0; extra == "server"
 Requires-Dist: ruamel.yaml<0.19,>=0.15; extra == "server"
 Provides-Extra: htcondor
-Requires-Dist: htcondor<11,>=10.2.0.post1; sys_platform != "darwin" and extra == "htcondor"
+Requires-Dist: htcondor<25,>=23.6.0; sys_platform != "darwin" and extra == "htcondor"
 Provides-Extra: mesos
 Requires-Dist: pymesos<0.4,>=0.3.15; python_version < "3.11" and extra == "mesos"
 Provides-Extra: all
@@ -95,7 +99,7 @@ Requires-Dist: mypy-boto3-iam<2,>=1.28.3.post2; extra == "all"
 Requires-Dist: mypy-boto3-s3<2,>=1.28.3.post2; extra == "all"
 Requires-Dist: moto<6,>=5.0.3; extra == "all"
 Requires-Dist: ec2_metadata<3; extra == "all"
-Requires-Dist: cwltool==3.1.20240508115724; extra == "all"
+Requires-Dist: cwltool==3.1.20250110105449; extra == "all"
 Requires-Dist: schema-salad<9,>=8.4.20230128170514; extra == "all"
 Requires-Dist: galaxy-tool-util<25; extra == "all"
 Requires-Dist: galaxy-util<25; extra == "all"
@@ -103,27 +107,43 @@ Requires-Dist: ruamel.yaml<=0.19,>=0.15; extra == "all"
 Requires-Dist: ruamel.yaml.clib>=0.2.6; extra == "all"
 Requires-Dist: networkx!=2.8.1,<4; extra == "all"
 Requires-Dist: CacheControl[filecache]; extra == "all"
+Requires-Dist: cwl-utils>=0.36; extra == "all"
 Requires-Dist: pynacl<2,>=1.4.0; extra == "all"
 Requires-Dist: apache-libcloud<3,>=2.2.1; extra == "all"
 Requires-Dist: google-cloud-storage<=2.8.0,>=2; extra == "all"
 Requires-Dist: google-auth<3,>=2.18.1; extra == "all"
-Requires-Dist: kubernetes<22,>=12.0.1; extra == "all"
+Requires-Dist: kubernetes<33,>=12.0.1; extra == "all"
 Requires-Dist: kubernetes-stubs==v22.6.0post1; extra == "all"
 Requires-Dist: types-urllib3; extra == "all"
 Requires-Dist: types-PyYAML; extra == "all"
 Requires-Dist: idna>=2; extra == "all"
-Requires-Dist: miniwdl==1.12.0; extra == "all"
+Requires-Dist: miniwdl==1.12.1; extra == "all"
 Requires-Dist: wdlparse==0.1.0; extra == "all"
 Requires-Dist: graphlib-backport==1.0; python_version < "3.9" and extra == "all"
-Requires-Dist: connexion[swagger-ui]<3,>=2.10.0; extra == "all"
-Requires-Dist: flask<3,>=2.0; extra == "all"
-Requires-Dist: werkzeug<3,>=2.0; extra == "all"
-Requires-Dist: flask-cors==4.0.1; extra == "all"
-Requires-Dist: gunicorn==22.0.0; extra == "all"
+Requires-Dist: connexion[swagger-ui]<4,>=2.10.0; extra == "all"
+Requires-Dist: flask<4,>=2.0; extra == "all"
+Requires-Dist: werkzeug<4,>=2.0; extra == "all"
+Requires-Dist: flask-cors==5.0.1; extra == "all"
+Requires-Dist: gunicorn==23.0.0; extra == "all"
 Requires-Dist: celery<6,>=5.1.0; extra == "all"
 Requires-Dist: wes-service<5,>=4.0.0; extra == "all"
 Requires-Dist: ruamel.yaml<0.19,>=0.15; extra == "all"
 Requires-Dist: pymesos<0.4,>=0.3.15; python_version < "3.11" and extra == "all"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+.. image:: https://flat.badgen.net/https/ucsc-ci.com/api/v4/projects/3/jobs/artifacts/master/raw/badges1.2/required.json%3Fjob=cwl_badge?icon=commonwl&label=CWL%201.2%20Conformance
+   :alt: Toil CWL 1.2 Conformance Badge
+   :target: https://github.com/common-workflow-language/cwl-v1.2/blob/main/CONFORMANCE_TESTS.md
 
 .. image:: https://badges.gitter.im/bd2k-genomics-toil/Lobby.svg
    :alt: Join the chat at https://gitter.im/bd2k-genomics-toil/Lobby

{toil-7.0.0 → toil-8.1.0b1}/README.rst

@@ -1,3 +1,7 @@
+.. image:: https://flat.badgen.net/https/ucsc-ci.com/api/v4/projects/3/jobs/artifacts/master/raw/badges1.2/required.json%3Fjob=cwl_badge?icon=commonwl&label=CWL%201.2%20Conformance
+   :alt: Toil CWL 1.2 Conformance Badge
+   :target: https://github.com/common-workflow-language/cwl-v1.2/blob/main/CONFORMANCE_TESTS.md
+
 .. image:: https://badges.gitter.im/bd2k-genomics-toil/Lobby.svg
    :alt: Join the chat at https://gitter.im/bd2k-genomics-toil/Lobby
    :target: https://gitter.im/bd2k-genomics-toil/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge

{toil-7.0.0 → toil-8.1.0b1}/requirements-cwl.txt

@@ -1,4 +1,4 @@
-cwltool==3.1.20240508115724
+cwltool==3.1.20250110105449
 schema-salad>=8.4.20230128170514,<9
 galaxy-tool-util<25
 galaxy-util<25
@@ -6,3 +6,4 @@ ruamel.yaml>=0.15,<=0.19
 ruamel.yaml.clib>=0.2.6
 networkx!=2.8.1,<4
 CacheControl[filecache]
+cwl-utils>=0.36

{toil-7.0.0 → toil-8.1.0b1}/requirements-dev.txt

@@ -1,24 +1,23 @@
 pytest>=6.2.1,<9
-pytest-cov>=2.12.1,<6
+pytest-cov>=2.12.1,<7
 pytest-timeout>=1.4.2,<3
 stubserver>=1.1,<2
-setuptools>=65.5.1,<70
-sphinx>=7,<8
-sphinx-autoapi>=3,<4
+setuptools>=65.5.1,<77
+sphinx>=7,<9
+sphinx-autoapi>=3.2.1,<4
 astroid>=3,<4
-sphinx-autodoc-typehints>=1.24.0,<3
+sphinx-autodoc-typehints>=1.24.0,<4
 sphinxcontrib-autoprogram==0.1.9
 cwltest>=2.2.20211116163652
-mypy==1.10.0
+mypy==1.15.0
 types-aws-xray-sdk
-types-boto<2.49.18.20240205
+types-boto<2.49.18.20241020
 types-Flask-Cors
 types-requests
-types-psutil
+types-psutil>=6.1.0.20241102
 types-python-dateutil
 types-setuptools
 types-xmltodict
-backports.zoneinfo[tzdata];python_version<"3.9"
 flake8>=3.8.4,<8
 flake8-bugbear>=20.11.1,<25
 black
@@ -32,3 +31,4 @@ docutils>=0.16,<0.22
 pyupgrade
 pytest-xdist
 build
+check-jsonschema

toil-8.1.0b1/requirements-htcondor.txt

@@ -0,0 +1 @@
+htcondor>=23.6.0,<25

{toil-7.0.0 → toil-8.1.0b1}/requirements-kubernetes.txt

@@ -1,4 +1,4 @@
-kubernetes>=12.0.1, <22
+kubernetes>=12.0.1, <33
 # Nobody ever published stubs that support Python back to before 3.9, until
 # version 22.6.0 of the Kubernetes module. So we have to use the mismatched
 # stubs.

toil-8.1.0b1/requirements-server.txt

@@ -0,0 +1,8 @@
+connexion[swagger-ui]>=2.10.0, <4
+flask>=2.0,<4
+werkzeug>=2.0,<4
+flask-cors==5.0.1
+gunicorn==23.0.0
+celery>=5.1.0, <6
+wes-service>=4.0.0, <5
+ruamel.yaml>=0.15,<0.19

{toil-7.0.0 → toil-8.1.0b1}/requirements-wdl.txt

@@ -1,3 +1,3 @@
-miniwdl==1.12.0
+miniwdl==1.12.1
 wdlparse==0.1.0
 graphlib-backport==1.0 ; python_version < '3.9'

{toil-7.0.0 → toil-8.1.0b1}/requirements.txt

@@ -3,12 +3,14 @@ requests<=2.31.0
 docker>=6.1.0, <8
 urllib3>=1.26.0,<3
 python-dateutil
-psutil >= 3.0.1, <6
+psutil >= 6.1.0, < 8
 PyPubSub >=4.0.3, <5
 addict>=2.2.1, <2.5
+backports.zoneinfo[tzdata];python_version<"3.9"
 enlighten>=1.5.2, <2
 configargparse>=1.7,<2
 ruamel.yaml>=0.15
 pyyaml>=6,<7
 typing-extensions>=4.6.2, <5
 coloredlogs>=15,<16
+prompt_toolkit>=3.0,<4

{toil-7.0.0 → toil-8.1.0b1}/setup.py

@@ -21,6 +21,7 @@ from setuptools import find_packages, setup
 SETUP_DIR = os.path.dirname(__file__)
 README = os.path.join(SETUP_DIR, "README.rst")
 
+
 def get_requirements(extra=None):
     """
     Load the requirements for the given extra.
@@ -32,7 +33,9 @@ def get_requirements(extra=None):
 
     with open(filename) as fp:
         # Parse out as one per line, dropping comments
-        return [l.split('#')[0].strip() for l in fp.readlines() if l.split('#')[0].strip()]
+        return [
+            l.split("#")[0].strip() for l in fp.readlines() if l.split("#")[0].strip()
+        ]
 
 
 def run_setup():
@@ -58,90 +61,102 @@ def run_setup():
         "google",
         "kubernetes",
         "wdl",
-        "server"
+        "server",
     ]
     for extra in non_htcondor_extras:
         extras_require[extra] = get_requirements(extra)
         all_reqs += extras_require[extra]
     # We exclude htcondor from "all" because it can't be on Mac
     extras_require['htcondor:sys_platform!="darwin"'] = get_requirements("htcondor")
-    extras_require['mesos'] = get_requirements("mesos")
+    extras_require["mesos"] = get_requirements("mesos")
     all_reqs += get_requirements("mesos")
     extras_require["all"] = all_reqs
     setup(
-        name='toil',
+        name="toil",
         version=version.distVersion,
         long_description=open(README).read(),
         long_description_content_type="text/x-rst",
-        description='Pipeline management software for clusters.',
-        author='Benedict Paten and the Toil community',
-        author_email='toil-community@googlegroups.com',
+        description="Pipeline management software for clusters.",
+        author="Benedict Paten and the Toil community",
+        author_email="toil-community@googlegroups.com",
         url="https://github.com/DataBiosphere/toil",
         classifiers=[
-          'Development Status :: 5 - Production/Stable',
-          'Environment :: Console',
-          'Intended Audience :: Developers',
-          'Intended Audience :: Science/Research',
-          'Intended Audience :: Healthcare Industry',
-          'License :: OSI Approved :: Apache Software License',
-          'Natural Language :: English',
-          'Operating System :: MacOS :: MacOS X',
-          'Operating System :: POSIX',
-          'Operating System :: POSIX :: Linux',
-          'Programming Language :: Python :: 3.8',
-          'Programming Language :: Python :: 3.9',
-          'Programming Language :: Python :: 3.10',
-          'Programming Language :: Python :: 3.11',
-          'Topic :: Scientific/Engineering',
-          'Topic :: Scientific/Engineering :: Bio-Informatics',
-          'Topic :: Scientific/Engineering :: Astronomy',
-          'Topic :: Scientific/Engineering :: Atmospheric Science',
-          'Topic :: Scientific/Engineering :: Information Analysis',
-          'Topic :: Scientific/Engineering :: Medical Science Apps.',
-          'Topic :: System :: Distributed Computing',
-          'Topic :: Utilities'],
+            "Development Status :: 5 - Production/Stable",
+            "Environment :: Console",
+            "Intended Audience :: Developers",
+            "Intended Audience :: Science/Research",
+            "Intended Audience :: Healthcare Industry",
+            "License :: OSI Approved :: Apache Software License",
+            "Natural Language :: English",
+            "Operating System :: MacOS :: MacOS X",
+            "Operating System :: POSIX",
+            "Operating System :: POSIX :: Linux",
+            "Programming Language :: Python :: 3.9",
+            "Programming Language :: Python :: 3.10",
+            "Programming Language :: Python :: 3.11",
+            "Programming Language :: Python :: 3.12",
+            "Programming Language :: Python :: 3.13",
+            "Topic :: Scientific/Engineering",
+            "Topic :: Scientific/Engineering :: Bio-Informatics",
+            "Topic :: Scientific/Engineering :: Astronomy",
+            "Topic :: Scientific/Engineering :: Atmospheric Science",
+            "Topic :: Scientific/Engineering :: Information Analysis",
+            "Topic :: Scientific/Engineering :: Medical Science Apps.",
+            "Topic :: System :: Distributed Computing",
+            "Topic :: Utilities",
+        ],
         license="Apache License v2.0",
-        python_requires=">=3.8",
+        python_requires=">=3.9",
         install_requires=install_requires,
         extras_require=extras_require,
-        package_dir={'': 'src'},
-        packages=find_packages(where='src'),
+        package_dir={"": "src"},
+        packages=find_packages(where="src"),
         package_data={
-            '': ['*.yml', '*.yaml', 'cloud-config', '*.cwl'],
+            "": ["*.yml", "*.yaml", "cloud-config", "*.cwl"],
         },
         # Unfortunately, the names of the entry points are hard-coded elsewhere in the code base so
         # you can't just change them here. Luckily, most of them are pretty unique strings, and thus
         # easy to search for.
         entry_points={
-            'console_scripts': [
-                'toil = toil.utils.toilMain:main',
-                '_toil_worker = toil.worker:main',
-                'cwltoil = toil.cwl.cwltoil:cwltoil_was_removed [cwl]',
-                'toil-cwl-runner = toil.cwl.cwltoil:main [cwl]',
-                'toil-wdl-runner = toil.wdl.wdltoil:main [wdl]',
-                'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main [server]',
-                '_toil_mesos_executor = toil.batchSystems.mesos.executor:main [mesos]',
-                '_toil_contained_executor = toil.batchSystems.contained_executor:executor']})
+            "console_scripts": [
+                "toil = toil.utils.toilMain:main",
+                "_toil_worker = toil.worker:main",
+                "cwltoil = toil.cwl.cwltoil:cwltoil_was_removed [cwl]",
+                "toil-cwl-runner = toil.cwl.cwltoil:main [cwl]",
+                "toil-wdl-runner = toil.wdl.wdltoil:main [wdl]",
+                "toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main [server]",
+                "_toil_mesos_executor = toil.batchSystems.mesos.executor:main [mesos]",
+                "_toil_contained_executor = toil.batchSystems.contained_executor:executor",
+            ]
+        },
+    )
 
 
 def import_version():
     """Return the module object for src/toil/version.py, generate from the template if required."""
-    if not os.path.exists('src/toil/version.py'):
+    if not os.path.exists("src/toil/version.py"):
         for req in get_requirements("cwl"):
             # Determine cwltool version from requirements file
             if req.startswith("cwltool=="):
-                cwltool_version = req[len("cwltool=="):]
+                cwltool_version = req[len("cwltool==") :]
                 break
         # Use the template to generate src/toil/version.py
         import version_template
-        with NamedTemporaryFile(mode='w', dir='src/toil', prefix='version.py.', delete=False) as f:
-            f.write(version_template.expand_(others={
-                # expose the dependency versions that we may need to access in Toil
-                'cwltool_version': cwltool_version,
-            }))
-        os.rename(f.name, 'src/toil/version.py')
-
-    loader = SourceFileLoader('toil.version', 'src/toil/version.py')
+
+        with NamedTemporaryFile(
+            mode="w", dir="src/toil", prefix="version.py.", delete=False
+        ) as f:
+            f.write(
+                version_template.expand_(
+                    others={
+                        # expose the dependency versions that we may need to access in Toil
+                        "cwltool_version": cwltool_version,
+                    }
+                )
+            )
+        os.rename(f.name, "src/toil/version.py")
+
+    loader = SourceFileLoader("toil.version", "src/toil/version.py")
     mod = types.ModuleType(loader.name)
     loader.exec_module(mod)
     return mod