toil 6.1.0__tar.gz → 8.0.0__tar.gz

{toil-6.1.0 → toil-8.0.0}/LICENSE

@@ -202,3 +202,28 @@
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
    limitations under the License.
+
+All code in this repository excluding src/toil/statsAndLogging.py::install_log_color is under the Apache License as outlined directly above.
+Some code in src/toil/statsAndLogging.py::install_log_color is under the MiniWDL MIT License as outlined directly below.
+
+MIT License
+
+Copyright (c) 2018 Chan Zuckerberg Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{toil-6.1.0 → toil-8.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: toil
-Version: 6.1.0
+Version: 8.0.0
 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
@@ -28,36 +29,40 @@ 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
-Requires-Dist: requests<3,>=2
+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<7,>=6.1.0
 Requires-Dist: PyPubSub<5,>=4.0.3
 Requires-Dist: addict<2.5,>=2.2.1
-Requires-Dist: pytz>=2012
+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
 Provides-Extra: aws
-Requires-Dist: boto<3,>=2.48.0; extra == "aws"
-Requires-Dist: boto3-stubs[boto3,iam,s3,sdb,sts]<2,>=1.28.3.post2; 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"
-Requires-Dist: moto<5,>=4.1.11; extra == "aws"
+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==3.1.20240112164112; 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<23; extra == "cwl"
-Requires-Dist: galaxy-util<23; extra == "cwl"
+Requires-Dist: galaxy-tool-util<25; extra == "cwl"
+Requires-Dist: galaxy-util<25; extra == "cwl"
 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
@@ -65,59 +70,104 @@ 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==1.11.1; 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==4.0.0; extra == "server"
-Requires-Dist: gunicorn==21.2.0; 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==5.0.0; 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
-Requires-Dist: boto<3,>=2.48.0; extra == "all"
-Requires-Dist: boto3-stubs[boto3,iam,s3,sdb,sts]<2,>=1.28.3.post2; extra == "all"
+Requires-Dist: boto3-stubs[autoscaling,boto3,ec2,iam,s3,sdb,sts]<2,>=1.28.3.post2; extra == "all"
 Requires-Dist: mypy-boto3-iam<2,>=1.28.3.post2; extra == "all"
-Requires-Dist: moto<5,>=4.1.11; extra == "all"
-Requires-Dist: cwltool==3.1.20240112164112; 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==3.1.20250110105449; extra == "all"
 Requires-Dist: schema-salad<9,>=8.4.20230128170514; extra == "all"
-Requires-Dist: galaxy-tool-util<23; extra == "all"
-Requires-Dist: galaxy-util<23; extra == "all"
+Requires-Dist: galaxy-tool-util<25; extra == "all"
+Requires-Dist: galaxy-util<25; extra == "all"
 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==1.11.1; 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==4.0.0; extra == "all"
-Requires-Dist: gunicorn==21.2.0; 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==5.0.0; 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://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 is a scalable, efficient, cross-platform (Linux & macOS) pipeline management system,
+written entirely in Python, and designed around the principles of functional
+programming. It supports running workflows written in either Common Workflow Language (`CWL`_) 1.0-1.2 or 
+Workflow Description Language (`WDL`_) 1.0-1.1, as well as having its own rich Python API for writing workflows against. 
+It supports running workflows locally on your system (e.g. a laptop), on an HPC cluster, or in the cloud. 
+
+* Check the `website`_ for a description of Toil and its features.
+* Full documentation for the latest stable release can be found at
+  `Read the Docs`_.
+* Please subscribe to low-volume `announce`_ mailing list so we keep you informed
+* Google Groups discussion `forum`_
+* See our occasional `blog`_ for tutorials. 
+* Use `biostars`_ channel for discussion.
+
+.. _website: http://toil.ucsc-cgl.org/
+.. _Read the Docs: https://toil.readthedocs.io/en/latest
+.. _announce: https://groups.google.com/forum/#!forum/toil-announce
+.. _forum: https://groups.google.com/forum/#!forum/toil-community
+.. _blog: https://toilpipelines.wordpress.com/
+.. _biostars: https://www.biostars.org/t/toil/
+.. _CWL: https://www.commonwl.org/
+.. _WDL: https://openwdl.org/
+
+Notes:
+
+* Toil moved from https://github.com/BD2KGenomics/toil to https://github.com/DataBiosphere/toil on July 5th, 2018.
+* Toil dropped Python 2.7 support on February 13, 2020 (the last working py2.7 version is 3.24.0).

{toil-6.1.0 → toil-8.0.0}/README.rst

@@ -4,7 +4,9 @@
 
 Toil is a scalable, efficient, cross-platform (Linux & macOS) pipeline management system,
 written entirely in Python, and designed around the principles of functional
-programming.
+programming. It supports running workflows written in either Common Workflow Language (`CWL`_) 1.0-1.2 or 
+Workflow Description Language (`WDL`_) 1.0-1.1, as well as having its own rich Python API for writing workflows against. 
+It supports running workflows locally on your system (e.g. a laptop), on an HPC cluster, or in the cloud. 
 
 * Check the `website`_ for a description of Toil and its features.
 * Full documentation for the latest stable release can be found at
@@ -20,8 +22,10 @@ programming.
 .. _forum: https://groups.google.com/forum/#!forum/toil-community
 .. _blog: https://toilpipelines.wordpress.com/
 .. _biostars: https://www.biostars.org/t/toil/
+.. _CWL: https://www.commonwl.org/
+.. _WDL: https://openwdl.org/
 
 Notes:
 
 * Toil moved from https://github.com/BD2KGenomics/toil to https://github.com/DataBiosphere/toil on July 5th, 2018.
-* Toil dropped python 2.7 support on February 13, 2020 (last working py2.7 version is 3.24.0).
+* Toil dropped Python 2.7 support on February 13, 2020 (the last working py2.7 version is 3.24.0).

toil-8.0.0/requirements-aws.txt

@@ -0,0 +1,5 @@
+boto3-stubs[s3,sdb,iam,sts,boto3,ec2,autoscaling]>=1.28.3.post2, <2
+mypy-boto3-iam>=1.28.3.post2, <2 # Need to force .post1 to be replaced
+mypy-boto3-s3>=1.28.3.post2, <2
+moto>=5.0.3, <6
+ec2_metadata<3

{toil-6.1.0 → toil-8.0.0}/requirements-cwl.txt

@@ -1,8 +1,9 @@
-cwltool==3.1.20240112164112
+cwltool==3.1.20250110105449
 schema-salad>=8.4.20230128170514,<9
-galaxy-tool-util<23
-galaxy-util<23
+galaxy-tool-util<25
+galaxy-util<25
 ruamel.yaml>=0.15,<=0.19
 ruamel.yaml.clib>=0.2.6
 networkx!=2.8.1,<4
 CacheControl[filecache]
+cwl-utils>=0.36

toil-8.0.0/requirements-dev.txt

@@ -0,0 +1,34 @@
+pytest>=6.2.1,<9
+pytest-cov>=2.12.1,<7
+pytest-timeout>=1.4.2,<3
+stubserver>=1.1,<2
+setuptools>=65.5.1,<76
+sphinx>=7,<9
+sphinx-autoapi>=3.2.1,<4
+astroid>=3,<4
+sphinx-autodoc-typehints>=1.24.0,<4
+sphinxcontrib-autoprogram==0.1.9
+cwltest>=2.2.20211116163652
+mypy==1.15.0
+types-aws-xray-sdk
+types-boto<2.49.18.20241020
+types-Flask-Cors
+types-requests
+types-psutil>=6.1.0.20241102
+types-python-dateutil
+types-setuptools
+types-xmltodict
+flake8>=3.8.4,<8
+flake8-bugbear>=20.11.1,<25
+black
+isort
+pydocstyle
+autoflake
+isort
+diff_cover
+lxml
+docutils>=0.16,<0.22
+pyupgrade
+pytest-xdist
+build
+check-jsonschema

toil-8.0.0/requirements-htcondor.txt

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

{toil-6.1.0 → toil-8.0.0}/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-8.0.0/requirements-server.txt

@@ -0,0 +1,8 @@
+connexion[swagger-ui]>=2.10.0, <4
+flask>=2.0,<4
+werkzeug>=2.0,<4
+flask-cors==5.0.0
+gunicorn==23.0.0
+celery>=5.1.0, <6
+wes-service>=4.0.0, <5
+ruamel.yaml>=0.15,<0.19

{toil-6.1.0 → toil-8.0.0}/requirements-wdl.txt

@@ -1,3 +1,3 @@
-miniwdl==1.11.1
+miniwdl==1.12.1
 wdlparse==0.1.0
 graphlib-backport==1.0 ; python_version < '3.9'

{toil-6.1.0 → toil-8.0.0}/requirements.txt

@@ -1,15 +1,15 @@
 dill>=0.3.2, <0.4
-requests>=2, <3
+requests<=2.31.0
 docker>=6.1.0, <8
-# Work around https://github.com/docker/docker-py/issues/3113
 urllib3>=1.26.0,<3
 python-dateutil
-psutil >= 3.0.1, <6
+psutil >= 6.1.0, < 7
 PyPubSub >=4.0.3, <5
 addict>=2.2.1, <2.5
-pytz>=2012
+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

{toil-6.1.0 → toil-8.0.0}/setup.cfg

@@ -33,6 +33,7 @@ markers =
 	wes_server
 	cwl_small_log_dir
 	cwl_small
+	wdl
 
 [flake8]
 max-line-length = 88

toil-8.0.0/setup.py

@@ -0,0 +1,166 @@
+# Copyright (C) 2015-2021 Regents of the University of California
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+import os
+import types
+from importlib.machinery import SourceFileLoader
+from tempfile import NamedTemporaryFile
+
+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.
+
+    Uses the appropriate requirements-extra.txt, or the main requirements.txt
+    if no extra is specified.
+    """
+    filename = f"requirements-{extra}.txt" if extra else "requirements.txt"
+
+    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()
+        ]
+
+
+def run_setup():
+    """
+    Call setup().
+
+    This function exists so the setup() invocation preceded more internal functionality.
+    The `version` module is imported dynamically by import_version() below.
+    """
+    install_requires = get_requirements()
+
+    extras_require = {}
+    # htcondor is not supported by apple
+    # this is tricky to conditionally support in 'all' due
+    # to how wheels work, so it is not included in all and
+    # must be explicitly installed as an extra
+    all_reqs = []
+
+    non_htcondor_extras = [
+        "aws",
+        "cwl",
+        "encryption",
+        "google",
+        "kubernetes",
+        "wdl",
+        "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")
+    all_reqs += get_requirements("mesos")
+    extras_require["all"] = all_reqs
+    setup(
+        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",
+        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 :: 3.9",
+            "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=">=3.9",
+        install_requires=install_requires,
+        extras_require=extras_require,
+        package_dir={"": "src"},
+        packages=find_packages(where="src"),
+        package_data={
+            "": ["*.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",
+            ]
+        },
+    )
+
+
+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"):
+        for req in get_requirements("cwl"):
+            # Determine cwltool version from requirements file
+            if req.startswith("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")
+    mod = types.ModuleType(loader.name)
+    loader.exec_module(mod)
+    return mod
+
+
+version = import_version()
+run_setup()