toil 6.1.0__tar.gz → 7.0.0__tar.gz

{toil-6.1.0 → toil-7.0.0}/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-7.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: toil
-Version: 6.1.0
+Version: 7.0.0
 Summary: Pipeline management software for clusters.
 Home-page: https://github.com/DataBiosphere/toil
 Author: Benedict Paten and the Toil community
@@ -29,31 +29,33 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: System :: Distributed Computing
 Classifier: Topic :: Utilities
 Requires-Python: >=3.8
+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: PyPubSub<5,>=4.0.3
 Requires-Dist: addict<2.5,>=2.2.1
-Requires-Dist: pytz>=2012
 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==3.1.20240508115724; 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"
@@ -71,15 +73,15 @@ 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==1.12.0; 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: flask-cors==4.0.1; extra == "server"
+Requires-Dist: gunicorn==22.0.0; 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"
@@ -88,14 +90,15 @@ Requires-Dist: htcondor<11,>=10.2.0.post1; sys_platform != "darwin" and extra ==
 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==3.1.20240508115724; 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"
@@ -109,15 +112,47 @@ 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==1.12.0; 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: flask-cors==4.0.1; extra == "all"
+Requires-Dist: gunicorn==22.0.0; 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"
+
+.. 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-7.0.0}/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-7.0.0/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-7.0.0}/requirements-cwl.txt

@@ -1,7 +1,7 @@
-cwltool==3.1.20240112164112
+cwltool==3.1.20240508115724
 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

{toil-6.1.0 → toil-7.0.0}/requirements-dev.txt

@@ -1,20 +1,24 @@
 pytest>=6.2.1,<9
-pytest-cov>=2.12.1,<5
+pytest-cov>=2.12.1,<6
 pytest-timeout>=1.4.2,<3
 stubserver>=1.1,<2
 setuptools>=65.5.1,<70
 sphinx>=7,<8
-sphinx-autoapi>=2.1.1,<3
-# astroid 3 won't work until some sphinx-autoapi release after 2.1.1
-astroid>=2.15,<3
+sphinx-autoapi>=3,<4
+astroid>=3,<4
 sphinx-autodoc-typehints>=1.24.0,<3
-sphinxcontrib-autoprogram==0.1.8
+sphinxcontrib-autoprogram==0.1.9
 cwltest>=2.2.20211116163652
-mypy==1.8.0
+mypy==1.10.0
+types-aws-xray-sdk
+types-boto<2.49.18.20240205
+types-Flask-Cors
 types-requests
+types-psutil
+types-python-dateutil
 types-setuptools
-types-boto<2.49.18.20240205
-types-pytz
+types-xmltodict
+backports.zoneinfo[tzdata];python_version<"3.9"
 flake8>=3.8.4,<8
 flake8-bugbear>=20.11.1,<25
 black
@@ -24,6 +28,7 @@ autoflake
 isort
 diff_cover
 lxml
-docutils>=0.16,<0.21
+docutils>=0.16,<0.22
 pyupgrade
 pytest-xdist
+build

{toil-6.1.0 → toil-7.0.0}/requirements-server.txt

@@ -1,8 +1,8 @@
 connexion[swagger-ui]>=2.10.0, <3
 flask>=2.0,<3
 werkzeug>=2.0,<3
-flask-cors==4.0.0
-gunicorn==21.2.0
+flask-cors==4.0.1
+gunicorn==22.0.0
 celery>=5.1.0, <6
 wes-service>=4.0.0, <5
 ruamel.yaml>=0.15,<0.19

{toil-6.1.0 → toil-7.0.0}/requirements-wdl.txt

@@ -1,3 +1,3 @@
-miniwdl==1.11.1
+miniwdl==1.12.0
 wdlparse==0.1.0
 graphlib-backport==1.0 ; python_version < '3.9'

{toil-6.1.0 → toil-7.0.0}/requirements.txt

@@ -1,15 +1,14 @@
 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
 PyPubSub >=4.0.3, <5
 addict>=2.2.1, <2.5
-pytz>=2012
 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-7.0.0}/setup.cfg

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

{toil-6.1.0 → toil-7.0.0}/setup.py

@@ -11,7 +11,6 @@
 # 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 imp
 import os
 import types
 from importlib.machinery import SourceFileLoader
@@ -19,6 +18,8 @@ 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):
     """
@@ -70,6 +71,8 @@ def run_setup():
     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',
@@ -138,16 +141,6 @@ def import_version():
             }))
         os.rename(f.name, 'src/toil/version.py')
 
-    # Unfortunately, we can't use a straight import here because that would also load the stuff
-    # defined in "src/toil/__init__.py" which imports modules from external dependencies that may
-    # yet to be installed when setup.py is invoked.
-    #
-    # This is also the reason we cannot switch from the "deprecated" imp library
-    # and use:
-    #     from importlib.machinery import SourceFileLoader
-    #     return SourceFileLoader('toil.version', path='src/toil/version.py').load_module()
-    #
-    # Because SourceFileLoader will error and load "src/toil/__init__.py" .
     loader = SourceFileLoader('toil.version', 'src/toil/version.py')
     mod = types.ModuleType(loader.name)
     loader.exec_module(mod)

{toil-6.1.0 → toil-7.0.0}/src/toil/__init__.py

@@ -22,7 +22,6 @@ from datetime import datetime
 from typing import TYPE_CHECKING, Optional, Tuple
 
 import requests
-from pytz import timezone
 
 from docker.errors import ImageNotFound
 from toil.lib.memoize import memoize
@@ -210,7 +209,7 @@ def customDockerInitCmd() -> str:
     private docker registries). Any single quotes are escaped and the command cannot contain a
     set of blacklisted chars (newline or tab).
 
-    :returns: The custom commmand, or an empty string is returned if the environment variable is not set.
+    :returns: The custom command, or an empty string is returned if the environment variable is not set.
     """
     command = lookupEnvVar(name='user-defined custom docker init command',
                            envName='TOIL_CUSTOM_DOCKER_INIT_COMMAND',
@@ -440,7 +439,6 @@ def logProcessContext(config: "Config") -> None:
 
 
 try:
-    from boto import provider
     from botocore.credentials import (JSONFileCache,
                                       RefreshableCredentials,
                                       create_credential_resolver)
@@ -477,234 +475,5 @@ try:
         """
         return datetime.strptime(s, datetime_format)
 
-
-    class BotoCredentialAdapter(provider.Provider):
-        """
-        Boto 2 Adapter to use AWS credentials obtained via Boto 3's credential finding logic.
-
-        This allows for automatic role assumption
-        respecting the Boto 3 config files, even when parts of the app still use
-        Boto 2.
-
-        This class also handles caching credentials in multi-process environments
-        to avoid loads of processes swamping the EC2 metadata service.
-        """
-
-        # TODO: We take kwargs because new boto2 versions have an 'anon'
-        # argument and we want to be future proof
-
-        def __init__(self, name, access_key=None, secret_key=None,
-                     security_token=None, profile_name=None, **kwargs):
-            """Create a new BotoCredentialAdapter."""
-            # TODO: We take kwargs because new boto2 versions have an 'anon'
-            # argument and we want to be future proof
-
-            if (name == 'aws' or name is None) and access_key is None and not kwargs.get('anon', False):
-                # We are on AWS and we don't have credentials passed along and we aren't anonymous.
-                # We will backend into a boto3 resolver for getting credentials.
-                # Make sure to enable boto3's own caching, so we can share that
-                # cache with pure boto3 code elsewhere in Toil.
-                # Keep synced with toil.lib.aws.session.establish_boto3_session
-                self._boto3_resolver = create_credential_resolver(Session(profile=profile_name), cache=JSONFileCache())
-            else:
-                # We will use the normal flow
-                self._boto3_resolver = None
-
-            # Pass along all the arguments
-            super().__init__(name, access_key=access_key,
-                                                        secret_key=secret_key, security_token=security_token,
-                                                        profile_name=profile_name, **kwargs)
-
-        def get_credentials(self, access_key=None, secret_key=None, security_token=None, profile_name=None):
-            """
-            Make sure our credential fields are populated.
-
-            Called by the base class constructor.
-            """
-            if self._boto3_resolver is not None:
-                # Go get the credentials from the cache, or from boto3 if not cached.
-                # We need to be eager here; having the default None
-                # _credential_expiry_time makes the accessors never try to refresh.
-                self._obtain_credentials_from_cache_or_boto3()
-            else:
-                # We're not on AWS, or they passed a key, or we're anonymous.
-                # Use the normal route; our credentials shouldn't expire.
-                super().get_credentials(access_key=access_key,
-                                                                   secret_key=secret_key, security_token=security_token,
-                                                                   profile_name=profile_name)
-
-        def _populate_keys_from_metadata_server(self):
-            """
-            Hack to catch _credential_expiry_time being too soon and refresh the credentials.
-
-            This override is misnamed; it's actually the only hook we have to catch
-            _credential_expiry_time being too soon and refresh the credentials. We
-            actually just go back and poke the cache to see if it feels like
-            getting us new credentials.
-
-            Boto 2 hardcodes a refresh within 5 minutes of expiry:
-            https://github.com/boto/boto/blob/591911db1029f2fbb8ba1842bfcc514159b37b32/boto/provider.py#L247
-
-            Boto 3 wants to refresh 15 or 10 minutes before expiry:
-            https://github.com/boto/botocore/blob/8d3ea0e61473fba43774eb3c74e1b22995ee7370/botocore/credentials.py#L279
-
-            So if we ever want to refresh, Boto 3 wants to refresh too.
-            """
-            # This should only happen if we have expiring credentials, which we should only get from boto3
-            if self._boto3_resolver is None:
-                raise RuntimeError("The Boto3 resolver should not be None.")
-
-            self._obtain_credentials_from_cache_or_boto3()
-
-        @retry()
-        def _obtain_credentials_from_boto3(self):
-            """
-            Fill our credential fields from Boto 3.
-
-            We know the current cached credentials are not good, and that we
-            need to get them from Boto 3. Fill in our credential fields
-            (_access_key, _secret_key, _security_token,
-            _credential_expiry_time) from Boto 3.
-            """
-            # We get a Credentials object
-            # <https://github.com/boto/botocore/blob/8d3ea0e61473fba43774eb3c74e1b22995ee7370/botocore/credentials.py#L227>
-            # or a RefreshableCredentials, or None on failure.
-            creds = self._boto3_resolver.load_credentials()
-
-            if creds is None:
-                try:
-                    resolvers = str(self._boto3_resolver.providers)
-                except:
-                    resolvers = "(Resolvers unavailable)"
-                raise RuntimeError("Could not obtain AWS credentials from Boto3. Resolvers tried: " + resolvers)
-
-            # Make sure the credentials actually has some credentials if it is lazy
-            creds.get_frozen_credentials()
-
-            # Get when the credentials will expire, if ever
-            if isinstance(creds, RefreshableCredentials):
-                # Credentials may expire.
-                # Get a naive UTC datetime like boto 2 uses from the boto 3 time.
-                self._credential_expiry_time = creds._expiry_time.astimezone(timezone('UTC')).replace(tzinfo=None)
-            else:
-                # Credentials never expire
-                self._credential_expiry_time = None
-
-            # Then, atomically get all the credentials bits. They may be newer than we think they are, but never older.
-            frozen = creds.get_frozen_credentials()
-
-            # Copy them into us
-            self._access_key = frozen.access_key
-            self._secret_key = frozen.secret_key
-            self._security_token = frozen.token
-
-        def _obtain_credentials_from_cache_or_boto3(self):
-            """
-            Get the cached credentials.
-
-            Or retrieve them from Boto 3 and cache them
-            (or wait for another cooperating process to do so) if they are missing
-            or not fresh enough.
-            """
-            cache_path = '~/.cache/aws/cached_temporary_credentials'
-            path = os.path.expanduser(cache_path)
-            tmp_path = path + '.tmp'
-            while True:
-                log.debug('Attempting to read cached credentials from %s.', path)
-                try:
-                    with open(path) as f:
-                        content = f.read()
-                        if content:
-                            record = content.split('\n')
-                            if len(record) != 4:
-                                raise RuntimeError("Number of cached credentials is not 4.")
-                            self._access_key = record[0]
-                            self._secret_key = record[1]
-                            self._security_token = record[2]
-                            self._credential_expiry_time = str_to_datetime(record[3])
-                        else:
-                            log.debug('%s is empty. Credentials are not temporary.', path)
-                            self._obtain_credentials_from_boto3()
-                            return
-                except OSError as e:
-                    if e.errno == errno.ENOENT:
-                        log.debug('Cached credentials are missing.')
-                        dir_path = os.path.dirname(path)
-                        if not os.path.exists(dir_path):
-                            log.debug('Creating parent directory %s', dir_path)
-                            try:
-                                # A race would be ok at this point
-                                os.makedirs(dir_path, exist_ok=True)
-                            except OSError as e2:
-                                if e2.errno == errno.EROFS:
-                                    # Sometimes we don't actually have write access to ~.
-                                    # We may be running in a non-writable Toil container.
-                                    # We should just go get our own credentials
-                                    log.debug('Cannot use the credentials cache because we are working on a read-only filesystem.')
-                                    self._obtain_credentials_from_boto3()
-                                else:
-                                    raise
-                    else:
-                        raise
-                else:
-                    if self._credentials_need_refresh():
-                        log.debug('Cached credentials are expired.')
-                    else:
-                        log.debug('Cached credentials exist and are still fresh.')
-                        return
-                # We get here if credentials are missing or expired
-                log.debug('Racing to create %s.', tmp_path)
-                # Only one process, the winner, will succeed
-                try:
-                    fd = os.open(tmp_path, os.O_CREAT | os.O_EXCL | os.O_WRONLY, 0o600)
-                except OSError as e:
-                    if e.errno == errno.EEXIST:
-                        log.debug('Lost the race to create %s. Waiting on winner to remove it.', tmp_path)
-                        while os.path.exists(tmp_path):
-                            time.sleep(0.1)
-                        log.debug('Winner removed %s. Trying from the top.', tmp_path)
-                    else:
-                        raise
-                else:
-                    try:
-                        log.debug('Won the race to create %s.  Requesting credentials from backend.', tmp_path)
-                        self._obtain_credentials_from_boto3()
-                    except:
-                        os.close(fd)
-                        fd = None
-                        log.debug('Failed to obtain credentials, removing %s.', tmp_path)
-                        # This unblocks the losers.
-                        os.unlink(tmp_path)
-                        # Bail out. It's too likely to happen repeatedly
-                        raise
-                    else:
-                        if self._credential_expiry_time is None:
-                            os.close(fd)
-                            fd = None
-                            log.debug('Credentials are not temporary.  Leaving %s empty and renaming it to %s.',
-                                      tmp_path, path)
-                            # No need to actually cache permanent credentials,
-                            # because we know we aren't getting them from the
-                            # metadata server or by assuming a role. Those both
-                            # give temporary credentials.
-                        else:
-                            log.debug('Writing credentials to %s.', tmp_path)
-                            with os.fdopen(fd, 'w') as fh:
-                                fd = None
-                                fh.write('\n'.join([
-                                    self._access_key,
-                                    self._secret_key,
-                                    self._security_token,
-                                    datetime_to_str(self._credential_expiry_time)]))
-                            log.debug('Wrote credentials to %s. Renaming to %s.', tmp_path, path)
-                        os.rename(tmp_path, path)
-                        return
-                    finally:
-                        if fd is not None:
-                            os.close(fd)
-
-
-    provider.Provider = BotoCredentialAdapter
-
 except ImportError:
     pass