[med-svn] [Git][med-team/toil][master] 9 commits: d/rules, d/control, d/patches/intersphinx: Fix some sphinx warnings, ignore the rest.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Tue Jan 23 14:10:10 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / toil
Commits:
3fe2b405 by Michael R. Crusoe at 2024-01-23T12:49:57+01:00
d/rules,d/control, d/patches/intersphinx: Fix some sphinx warnings, ignore the rest.
- - - - -
aa2c967c by Michael R. Crusoe at 2024-01-23T12:55:06+01:00
fix version-related patches
- - - - -
9124c0ed by Michael R. Crusoe at 2024-01-23T13:08:50+01:00
Add patch to avoid need for ruamel.yaml.string package.
- - - - -
39ed38b7 by Michael R. Crusoe at 2024-01-23T13:22:30+01:00
Add patch to allow for older configarparser version.
- - - - -
e7f4cc56 by Michael R. Crusoe at 2024-01-23T13:35:59+01:00
Ignore the new test_cactus_integration
- - - - -
bc3543d3 by Michael R. Crusoe at 2024-01-23T14:23:52+01:00
Enhance avoid_boto patch
- - - - -
6dc496b0 by Michael R. Crusoe at 2024-01-23T14:48:30+01:00
d/patches: updated metatdata
- - - - -
c834ba79 by Michael R. Crusoe at 2024-01-23T14:48:30+01:00
d/copyright: upstream removed wdl_functions.py
- - - - -
b0097841 by Michael R. Crusoe at 2024-01-23T15:06:16+01:00
Add patch to remove use of distutils by copying in strtobool().
- - - - -
20 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/atomic_copy_as_alternative.patch
- debian/patches/avoid_boto
- + debian/patches/avoid_ruamel_yaml_string_dep.patch
- debian/patches/debianize_docs
- + debian/patches/goodbye_distutils
- + debian/patches/intersphinx
- − debian/patches/python3.12.patch
- debian/patches/python3_in_doc.patch
- − debian/patches/remove-python3-mock.patch
- debian/patches/series
- debian/patches/setting_version.patch
- + debian/patches/soften-configargparser-deps
- debian/patches/soften-cwltool-dep.patch
- debian/patches/soften-mesos-deps
- − debian/patches/soften-pydocker-dep
- debian/rules
- debian/tests/run-unit-tests
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
toil (6.0.0-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Team upload.
* New upstream version
Closes: #1058195
@@ -13,6 +14,17 @@ toil (6.0.0-1) UNRELEASED; urgency=medium
* Build-Depends: python3-configargparse
* Soften versioned dependency from cwltool
+ [ Michael R. Crusoe ]
+ * d/rules,d/control, d/patches/intersphinx: Fix some sphinx warnings, ignore
+ the rest.
+ * Add patch to avoid need for ruamel.yaml.string package.
+ * Add patch to allow for older configarparser version.
+ * Ignore the new test_cactus_integration
+ * Enhance avoid_boto patch
+ * d/patches: updated metatdata
+ * d/copyright: upstream removed wdl_functions.py
+ * Add patch to remove use of distutils by copying in strtobool().
+
-- Andreas Tille <tille at debian.org> Tue, 12 Dec 2023 16:57:57 +0100
toil (5.12.0-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -28,7 +28,8 @@ Build-Depends: debhelper-compat (= 13),
python3-sphinx-autoapi <!nodoc>,
python3-sphinx-autodoc-typehints <!nodoc>,
python3-sphinxcontrib.autoprogram <!nodoc>,
- python3-pubsub <!nodoc>
+ python3-pubsub <!nodoc>,
+ python3-doc <!nodoc>
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/toil
Vcs-Git: https://salsa.debian.org/med-team/toil.git
=====================================
debian/copyright
=====================================
@@ -32,10 +32,6 @@ Files: docs/vendor/sphinxcontrib/fulltoc.py
Copyright: 2012, New Dream Network, LLC (DreamHost)
License: Apache-2.0
-Files: src/toil/wdl/wdl_functions.py
-Copyright: 2015, Broad Institute, Inc.
-License: BSD-3-clause
-
Files: debian/*
Copyright: 2017 Steffen Moeller <moeller at debian.org>
License: Apache-2.0
@@ -74,28 +70,3 @@ License: Expat
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.
-
-License: BSD-3-clause
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- .
- * Redistributions of source code must retain the above copyright notice, this
- list of conditions and the following disclaimer.
- .
- * Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
- .
- * Neither the name Broad Institute, Inc. nor the names of its
- contributors may be used to endorse or promote products derived from
- this software without specific prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
- FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF T
=====================================
debian/patches/atomic_copy_as_alternative.patch
=====================================
@@ -2,6 +2,7 @@ Description: os.link does not work with debci based setup and hence default to a
when it does not work as intended
Author: Nilesh Patra <nilesh at debian.org>
Last-Update: 2022-03-10
+Forwarded: not-needed
--- a/src/toil/jobStores/fileJobStore.py
+++ b/src/toil/jobStores/fileJobStore.py
@@ -557,13 +557,16 @@ class FileJobStore(AbstractJobStore):
=====================================
debian/patches/avoid_boto
=====================================
@@ -1,8 +1,9 @@
From: Michael R. Crusoe <crusoe at debian.org>
Subject: avoid an unnecessary mypy_boto3_s3 import
---- a/src/toil/jobStores/aws/utils.py
-+++ b/src/toil/jobStores/aws/utils.py
-@@ -17,13 +17,12 @@ import logging
+Forwarded: https://github.com/DataBiosphere/toil/pull/4763
+--- toil.orig/src/toil/jobStores/aws/utils.py
++++ toil/src/toil/jobStores/aws/utils.py
+@@ -17,13 +17,12 @@
import os
import types
from ssl import SSLError
@@ -17,7 +18,7 @@ Subject: avoid an unnecessary mypy_boto3_s3 import
from toil.lib.aws import session
from toil.lib.aws.utils import connection_reset, get_bucket_region
-@@ -36,6 +35,8 @@ from toil.lib.retry import (DEFAULT_DELA
+@@ -36,6 +35,8 @@
get_error_status,
old_retry,
retry)
@@ -26,7 +27,7 @@ Subject: avoid an unnecessary mypy_boto3_s3 import
logger = logging.getLogger(__name__)
-@@ -290,7 +291,7 @@ class ServerSideCopyProhibitedError(Runt
+@@ -290,7 +291,7 @@
error=ClientError,
error_codes=[404, 500, 502, 503, 504]
)])
@@ -35,7 +36,7 @@ Subject: avoid an unnecessary mypy_boto3_s3 import
srcBucketName: str,
srcKeyName: str,
srcKeyVersion: str,
-@@ -346,7 +347,7 @@ def copyKeyMultipart(resource: S3Service
+@@ -346,7 +347,7 @@
# not wherever the bucket virtual hostnames go.
source_region = get_bucket_region(srcBucketName)
source_client = cast(
@@ -44,3 +45,48 @@ Subject: avoid an unnecessary mypy_boto3_s3 import
session.client(
's3',
region_name=source_region,
+--- toil.orig/src/toil/test/jobStores/jobStoreTest.py
++++ toil/src/toil/test/jobStores/jobStoreTest.py
+@@ -40,7 +40,6 @@
+ from toil.jobStores.abstractJobStore import (NoSuchFileException,
+ NoSuchJobException)
+ from toil.jobStores.fileJobStore import FileJobStore
+-from toil.lib.aws.utils import create_s3_bucket, get_object_for_url
+ from toil.lib.io import mkdtemp
+ from toil.lib.memoize import memoize
+ from toil.lib.retry import retry
+@@ -1463,6 +1462,7 @@
+
+ def _hashTestFile(self, url: str) -> str:
+ from toil.jobStores.aws.jobStore import AWSJobStore
++ from toil.lib.aws.utils import get_object_for_url
+ str(AWSJobStore) # to prevent removal of that import
+ key = get_object_for_url(urlparse.urlparse(url), existing=True)
+ contents = key.get().get('Body').read()
+@@ -1471,7 +1471,7 @@
+ def _createExternalStore(self):
+ """A S3.Bucket instance is returned"""
+ from toil.jobStores.aws.jobStore import establish_boto3_session
+- from toil.lib.aws.utils import retry_s3
++ from toil.lib.aws.utils import retry_s3, create_s3_bucket
+
+ resource = establish_boto3_session().resource(
+ "s3", region_name=self.awsRegion()
+--- toil.orig/src/toil/test/lib/test_ec2.py
++++ toil/src/toil/test/lib/test_ec2.py
+@@ -20,7 +20,6 @@
+ feed_flatcar_ami_release,
+ flatcar_release_feed_amis,
+ get_flatcar_ami)
+-from toil.lib.aws.session import establish_boto3_session
+ from toil.test import ToilTest, needs_aws_ec2, needs_online
+
+ logger = logging.getLogger(__name__)
+@@ -59,6 +58,7 @@
+ class AMITest(ToilTest):
+ @classmethod
+ def setUpClass(cls):
++ from toil.lib.aws.session import establish_boto3_session
+ session = establish_boto3_session(region_name='us-west-2')
+ cls.ec2_client = session.client('ec2')
+
=====================================
debian/patches/avoid_ruamel_yaml_string_dep.patch
=====================================
@@ -0,0 +1,52 @@
+From 893aa9b3295400829a86054cab028635e9bd2dd2 Mon Sep 17 00:00:00 2001
+From: "Michael R. Crusoe" <michael.crusoe at gmail.com>
+Date: Mon, 22 Jan 2024 14:58:45 +0100
+Subject: remove ruamel.yaml.string dependency for a simpler solution
+Forwarded: https://github.com/DataBiosphere/toil/pull/4760
+---
+ requirements.txt | 1 -
+ src/toil/common.py | 14 ++++++++------
+ 2 files changed, 8 insertions(+), 7 deletions(-)
+
+--- toil.orig/requirements.txt
++++ toil/requirements.txt
+@@ -11,6 +11,5 @@
+ enlighten>=1.5.2, <2
+ configargparse>=1.5.3,<2
+ ruamel.yaml>=0.15
+-ruamel.yaml.string>=0.1.1
+ pyyaml>=6,<7
+ typing-extensions>=4.6.2, <5
+--- toil.orig/src/toil/common.py
++++ toil/src/toil/common.py
+@@ -23,6 +23,7 @@
+ import time
+ import uuid
+ import warnings
++from io import StringIO
+
+ from ruamel.yaml import YAML
+ from ruamel.yaml.comments import CommentedMap
+@@ -580,15 +581,16 @@
+ with AtomicFileCreate(filepath) as temp_path:
+ with open(temp_path, "w") as f:
+ f.write("config_version: 1.0\n")
+- yaml = YAML(typ=['rt', 'string'])
++ yaml = YAML(typ='rt')
+ for data in all_data:
+ if "config_version" in data:
+ del data["config_version"]
+- for line in yaml.dump_to_string(data).split("\n"): # type: ignore[attr-defined]
+- if line:
+- f.write("#")
+- f.write(line)
+- f.write("\n")
++ with StringIO() as data_string:
++ yaml.dump(data, data_string)
++ for line in data_string.readline():
++ if line:
++ f.write("#")
++ f.write(f"{line}\n")
+
+
+ def parser_with_common_options(
=====================================
debian/patches/debianize_docs
=====================================
@@ -1,9 +1,9 @@
Author: Michael R. Crusoe <crusoe at debian.org>
Description: Update docs to reflect a local install
Forwarded: not-needed
---- a/docs/index.rst
-+++ b/docs/index.rst
-@@ -29,7 +29,6 @@ If using Toil for your research, please
+--- toil.orig/docs/index.rst
++++ toil/docs/index.rst
+@@ -29,7 +29,6 @@
.. toctree::
:caption: Getting Started
@@ -11,9 +11,28 @@ Forwarded: not-needed
gettingStarted/quickStart
.. toctree::
---- a/docs/gettingStarted/quickStart.rst
-+++ b/docs/gettingStarted/quickStart.rst
-@@ -50,11 +50,11 @@ Running CWL workflows using Toil is easy
+--- toil.orig/docs/gettingStarted/quickStart.rst
++++ toil/docs/gettingStarted/quickStart.rst
+@@ -13,18 +13,6 @@
+ workflows that are portable across multiple workflow engines and platforms.
+ Running CWL workflows using Toil is easy.
+
+-#. First ensure that Toil is installed with the
+- ``cwl`` extra (see :ref:`extras`)::
+-
+- (venv) $ pip install 'toil[cwl]'
+-
+- This installs the ``toil-cwl-runner`` executable.
+-
+- .. note::
+-
+- Don't actually type ``(venv) $`` in at the beginning of each command. This is intended only to remind the user that
+- they should have their :ref:`virtual environment <venvPrep>` running.
+-
+ #. Copy and paste the following code block into ``example.cwl``:
+
+ .. code-block:: yaml
+@@ -50,11 +38,11 @@
#. To run the workflow simply enter ::
@@ -27,7 +46,7 @@ Forwarded: not-needed
Hello world!
-@@ -84,13 +84,6 @@ Running a basic WDL workflow
+@@ -84,13 +72,6 @@
The `Workflow Description Language`_ (WDL) is another emerging language for writing workflows that are portable across multiple workflow engines and platforms.
Running WDL workflows using Toil is still in alpha, and currently experimental. Toil currently supports basic workflow syntax (see :ref:`wdl` for more details and examples). Here we go over running a basic WDL helloworld workflow.
@@ -41,7 +60,7 @@ Forwarded: not-needed
#. Copy and paste the following code block into ``wdl-helloworld.wdl``::
workflow write_simple_file {
-@@ -110,11 +103,11 @@ Running WDL workflows using Toil is stil
+@@ -110,11 +91,11 @@
#. To run the workflow simply enter ::
@@ -55,90 +74,86 @@ Forwarded: not-needed
Hello world!
This will, like the CWL example above, use the ``single_machine`` batch system
-@@ -134,17 +127,15 @@ Running a basic Python workflow
+@@ -144,7 +125,7 @@
- In addition to workflow languages like CWL and WDL, Toil supports running workflows written against its Python API.
-
--An example Toil Python workflow can be run with just three steps:
--
--1. Install Toil (see :ref:`installation-ref`)
-+An example Toil Python workflow can be run with just two steps:
+ 3. Specify the name of the :ref:`job store <jobStoreOverview>` and run the workflow::
--2. Copy and paste the following code block into a new file called ``helloWorld.py``:
-+1. Copy and paste the following code block into a new file called ``helloWorld.py``:
-
- .. literalinclude:: ../../src/toil/test/docs/scripts/tutorial_helloworld.py
-
--3. Specify the name of the :ref:`job store <jobStoreOverview>` and run the workflow::
-+2. Specify the name of the :ref:`job store <jobStoreOverview>` and run the workflow::
-
-- (venv) $ python helloWorld.py file:my-job-store
-+ (venv) $ python3 helloWorld.py file:my-job-store
+- (venv) $ python3 helloWorld.py file:my-job-store
++ $ python3 helloWorld.py file:my-job-store
For something beyond a "Hello, world!" example, refer to :ref:`runningDetail`.
-@@ -169,7 +160,7 @@ Running the example
+@@ -169,7 +150,7 @@
#. Run it with the default settings::
-- (venv) $ python sort.py file:jobStore
-+ $ python sort.py file:jobStore
+- (venv) $ python3 sort.py file:jobStore
++ $ python3 sort.py file:jobStore
The workflow created a file called ``sortedFile.txt`` in your current directory.
Have a look at it and notice that it contains a whole lot of sorted lines!
-@@ -186,7 +177,7 @@ Running the example
+@@ -186,7 +167,7 @@
3. Run with custom options::
-- (venv) $ python sort.py file:jobStore \
-+ $ python sort.py file:jobStore \
+- (venv) $ python3 sort.py file:jobStore \
++ $ python3 sort.py file:jobStore \
--numLines=5000 \
--lineLength=10 \
--overwriteOutput=True \
-@@ -305,7 +296,7 @@ in addition to messages from the batch s
+@@ -305,7 +286,7 @@
with the ``--logLevel`` flag. For example, to only log ``CRITICAL`` level
messages to the screen::
-- (venv) $ python sort.py file:jobStore \
-+ $ python sort.py file:jobStore \
+- (venv) $ python3 sort.py file:jobStore \
++ $ python3 sort.py file:jobStore \
--logLevel=critical \
--overwriteOutput=True
-@@ -331,7 +322,7 @@ example (the first line of ``down()``):
+@@ -331,7 +312,7 @@
When we run the pipeline, Toil will show a detailed failure log with a traceback::
-- (venv) $ python sort.py file:jobStore
-+ $ python sort.py file:jobStore
+- (venv) $ python3 sort.py file:jobStore
++ $ python3 sort.py file:jobStore
...
---TOIL WORKER OUTPUT LOG---
...
-@@ -353,13 +344,13 @@ that a job store of the same name alread
+@@ -353,13 +334,13 @@
failure, the job store is preserved so that the workflow can be restarted,
starting from the previously failed jobs. We can restart the pipeline by running ::
-- (venv) $ python sort.py file:jobStore \
-+ $ python sort.py file:jobStore \
+- (venv) $ python3 sort.py file:jobStore \
++ $ python3 sort.py file:jobStore \
--restart \
--overwriteOutput=True
We can also change the number of times Toil will attempt to retry a failed job::
-- (venv) $ python sort.py file:jobStore \
-+ $ python sort.py file:jobStore \
+- (venv) $ python3 sort.py file:jobStore \
++ $ python3 sort.py file:jobStore \
--retryCount 2 \
--restart \
--overwriteOutput=True
-@@ -373,7 +364,7 @@ line 30, or remove it, and then run
+@@ -373,7 +354,7 @@
::
-- (venv) $ python sort.py file:jobStore \
-+ $ python sort.py file:jobStore \
+- (venv) $ python3 sort.py file:jobStore \
++ $ python3 sort.py file:jobStore \
--restart \
--overwriteOutput=True
-@@ -412,13 +403,13 @@ Also! Remember to use the :ref:`destroy
+@@ -401,7 +382,7 @@
+
+ #. Launch a cluster in AWS using the :ref:`launchCluster` command::
+
+- (venv) $ toil launch-cluster <cluster-name> \
++ $ toil launch-cluster <cluster-name> \
+ --clusterType kubernetes \
+ --keyPairName <AWS-key-pair-name> \
+ --leaderNodeType t2.medium \
+@@ -412,13 +393,13 @@
#. Copy ``helloWorld.py`` to the ``/tmp`` directory on the leader node using the :ref:`rsyncCluster` command::
@@ -154,7 +169,7 @@ Forwarded: not-needed
Note that this command will log you in as the ``root`` user.
-@@ -439,7 +430,7 @@ Also! Remember to use the :ref:`destroy
+@@ -439,7 +420,7 @@
#. Use the :ref:`destroyCluster` command to destroy the cluster::
@@ -163,7 +178,16 @@ Forwarded: not-needed
Note that this command will destroy the cluster leader
node and any resources created to run the job, including the S3 bucket.
-@@ -467,12 +458,12 @@ Also! Remember to use the :ref:`destroy
+@@ -457,7 +438,7 @@
+
+ #. First launch a node in AWS using the :ref:`launchCluster` command::
+
+- (venv) $ toil launch-cluster <cluster-name> \
++ $ toil launch-cluster <cluster-name> \
+ --clusterType kubernetes \
+ --keyPairName <AWS-key-pair-name> \
+ --leaderNodeType t2.medium \
+@@ -467,12 +448,12 @@
#. Copy ``example.cwl`` and ``example-job.yaml`` from the :ref:`CWL example <cwlquickstart>` to the node using
the :ref:`rsyncCluster` command::
@@ -179,7 +203,7 @@ Forwarded: not-needed
#. Once on the leader node, command line tools such as ``kubectl`` will be available to you. It's also a good idea to
update and install the following::
-@@ -503,7 +494,7 @@ Also! Remember to use the :ref:`destroy
+@@ -503,7 +484,7 @@
#. Finally, log out of the leader node and from your local computer, destroy the cluster::
@@ -188,7 +212,16 @@ Forwarded: not-needed
.. _awscactus:
-@@ -559,11 +550,11 @@ Also! Remember to use the :ref:`destroy
+@@ -543,7 +524,7 @@
+
+ #. Launch a cluster using the :ref:`launchCluster` command::
+
+- (venv) $ toil launch-cluster <cluster-name> \
++ $ toil launch-cluster <cluster-name> \
+ --provisioner <aws, gce> \
+ --keyPairName <key-pair-name> \
+ --leaderNodeType <type> \
+@@ -559,11 +540,11 @@
When using AWS, setting the environment variable eliminates having to specify the ``--zone`` option
for each command. This will be supported for GCE in the future. ::
@@ -202,7 +235,7 @@ Forwarded: not-needed
$ mkdir /root/cact_ex
$ exit
-@@ -572,18 +563,18 @@ Also! Remember to use the :ref:`destroy
+@@ -572,18 +553,18 @@
`here <https://github.com/ComparativeGenomicsToolkit/cactus#seqfile-the-input-file>`__), organisms' genome sequence
files in FASTA format, and configuration files (e.g. blockTrim1.xml, if desired), up to the leader node::
=====================================
debian/patches/goodbye_distutils
=====================================
@@ -0,0 +1,71 @@
+commit 656ad9be65ff281786926dfd5b4e8350f414aa3e
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Date: Tue Jan 23 14:59:04 2024 +0100
+Subject: remove use of distutils by copying in strtobool()
+Forwarded: https://github.com/DataBiosphere/toil/pull/4765
+
+ Copied code is MIT licensed
+
+ https://github.com/pypa/distutils/blob/fb5c5704962cd3f40c69955437da9a88f4b28567/distutils/util.py#L340
+ https://github.com/pypa/distutils/blob/fb5c5704962cd3f40c69955437da9a88f4b28567/LICENSE
+
+diff --git a/src/toil/lib/conversions.py b/src/toil/lib/conversions.py
+index 2a8d5a848..9e896b65d 100644
+--- a/src/toil/lib/conversions.py
++++ b/src/toil/lib/conversions.py
+@@ -128,3 +128,19 @@ def hms_duration_to_seconds(hms: str) -> float:
+ seconds += float(vals_to_convert[2])
+
+ return seconds
++
++
++def strtobool(val):
++ """Convert a string representation of truth to true (1) or false (0).
++
++ True values are 'y', 'yes', 't', 'true', 'on', and '1'; false values
++ are 'n', 'no', 'f', 'false', 'off', and '0'. Raises ValueError if
++ 'val' is anything else.
++ """
++ val = val.lower()
++ if val in ("y", "yes", "t", "true", "on", "1"):
++ return 1
++ elif val in ("n", "no", "f", "false", "off", "0"):
++ return 0
++ else:
++ raise ValueError("invalid truth value {!r}".format(val))
+diff --git a/src/toil/options/common.py b/src/toil/options/common.py
+index 47d0ab763..d2003ab06 100644
+--- a/src/toil/options/common.py
++++ b/src/toil/options/common.py
+@@ -2,13 +2,12 @@ import os
+ from argparse import ArgumentParser, Action, _AppendAction
+ from typing import Any, Optional, Union, Type, Callable, List, Dict, TYPE_CHECKING
+
+-from distutils.util import strtobool
+ from configargparse import SUPPRESS
+ import logging
+
+ from ruamel.yaml import YAML
+
+-from toil.lib.conversions import bytes2human, human2bytes
++from toil.lib.conversions import bytes2human, human2bytes, strtobool
+
+ from toil.batchSystems.options import add_all_batchsystem_options
+ from toil.provisioners import parse_node_types
+diff --git a/src/toil/utils/toilDebugFile.py b/src/toil/utils/toilDebugFile.py
+index 3ce5052ba..b8abcea4b 100644
+--- a/src/toil/utils/toilDebugFile.py
++++ b/src/toil/utils/toilDebugFile.py
+@@ -17,11 +17,11 @@ import logging
+ import os.path
+ import sys
+ from typing import Optional
+-from distutils.util import strtobool
+
+ from toil.common import Config, Toil, parser_with_common_options
+ from toil.jobStores.fileJobStore import FileJobStore
+ from toil.lib.resources import glob
++from toil.lib.conversions import strtobool
+ from toil.statsAndLogging import set_logging_from_options
+
+ logger = logging.getLogger(__name__)
=====================================
debian/patches/intersphinx
=====================================
@@ -0,0 +1,14 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Link to the offline Python docs.
+Forwarded: not-needed
+--- toil.orig/docs/conf.py
++++ toil/docs/conf.py
+@@ -71,7 +71,7 @@
+ ]
+
+ intersphinx_mapping = {
+- "python": ("https://docs.python.org/3", None),
++ "python": ("https://docs.python.org/3", f"/usr/share/doc/python{sys.version_info.major}.{sys.version_info.minor}/html/objects.inv"),
+ "cwltool": ("https://cwltool.readthedocs.io/en/latest/", None),
+ }
+
=====================================
debian/patches/python3.12.patch deleted
=====================================
@@ -1,37 +0,0 @@
-Description: Pytho3.12 does not feature imp any more
-Bug-Debian: https://bugs.debian.org/1058195
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 12 Dec 2023 16:57:57 +0100
-
---- a/setup.py
-+++ b/setup.py
-@@ -11,8 +11,8 @@
- # 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 subprocess
- from tempfile import NamedTemporaryFile
-
- from setuptools import find_packages, setup
-@@ -64,9 +64,11 @@ def run_setup():
- extras_require['htcondor:sys_platform!="darwin"'] = get_requirements("htcondor")
- extras_require["all"] = all_reqs
-
-+ command = r"grep '^distVersion *=' src/toil/version.py | sed 's/^distVersion *= *[^0-9]\([0-9][-.0-9a-f]\+\).\.*$/\1/'"
-+ distversion=subprocess.check_output(command, shell=True, text=True).strip()
- setup(
- name='toil',
-- version=version.distVersion,
-+ version=distversion,
- description='Pipeline management software for clusters.',
- author='Benedict Paten and the Toil community',
- author_email='toil-community at googlegroups.com',
-@@ -149,5 +151,5 @@ def import_version():
- return imp.load_source('toil.version', 'src/toil/version.py')
-
-
--version = import_version()
-+#version = import_version()
- run_setup()
=====================================
debian/patches/python3_in_doc.patch
=====================================
@@ -1,10 +1,16 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 23 Jun 2022 10:34:56 +0200
-Description: Make sure the doc applies to Debian installations with Python3
+From: Andreas Tille <tille at debian.org>
+Last-Update: 2024-01-23
+Subject: Make sure the doc applies to Debian installations with Python3
+Forwarded: https://github.com/DataBiosphere/toil/pull/4764
---- a/docs/gettingStarted/quickStart.rst
-+++ b/docs/gettingStarted/quickStart.rst
-@@ -139,7 +139,7 @@ An example Toil Python workflow can be r
+--- toil.orig/docs/gettingStarted/quickStart.rst
++++ toil/docs/gettingStarted/quickStart.rst
+@@ -144,11 +144,11 @@
+
+ 3. Specify the name of the :ref:`job store <jobStoreOverview>` and run the workflow::
+
+- (venv) $ python helloWorld.py file:my-job-store
++ (venv) $ python3 helloWorld.py file:my-job-store
For something beyond a "Hello, world!" example, refer to :ref:`runningDetail`.
@@ -13,25 +19,25 @@ Description: Make sure the doc applies to Debian installations with Python3
.. _runningDetail:
-@@ -160,7 +160,7 @@ Running the example
+@@ -169,7 +169,7 @@
#. Run it with the default settings::
-- $ python sort.py file:jobStore
-+ $ python3 sort.py file:jobStore
+- (venv) $ python sort.py file:jobStore
++ (venv) $ python3 sort.py file:jobStore
The workflow created a file called ``sortedFile.txt`` in your current directory.
Have a look at it and notice that it contains a whole lot of sorted lines!
-@@ -177,7 +177,7 @@ Running the example
+@@ -186,7 +186,7 @@
3. Run with custom options::
-- $ python sort.py file:jobStore \
-+ $ python3 sort.py file:jobStore \
+- (venv) $ python sort.py file:jobStore \
++ (venv) $ python3 sort.py file:jobStore \
--numLines=5000 \
--lineLength=10 \
--overwriteOutput=True \
-@@ -282,7 +282,7 @@ Kubernetes the worker processes will typ
+@@ -291,7 +291,7 @@
boilerplate ensures that the pipeline is only started once---on the leader---but
not when its job functions are imported and executed on the individual workers.
@@ -40,50 +46,50 @@ Description: Make sure the doc applies to Debian installations with Python3
arguments for the workflow which includes both Toil's and ones defined inside
``sort.py``. A complete explanation of Toil's arguments can be
found in :ref:`commandRef`.
-@@ -296,7 +296,7 @@ in addition to messages from the batch s
+@@ -305,7 +305,7 @@
with the ``--logLevel`` flag. For example, to only log ``CRITICAL`` level
messages to the screen::
-- $ python sort.py file:jobStore \
-+ $ python3 sort.py file:jobStore \
+- (venv) $ python sort.py file:jobStore \
++ (venv) $ python3 sort.py file:jobStore \
--logLevel=critical \
--overwriteOutput=True
-@@ -322,7 +322,7 @@ example (the first line of ``down()``):
+@@ -331,7 +331,7 @@
When we run the pipeline, Toil will show a detailed failure log with a traceback::
-- $ python sort.py file:jobStore
-+ $ python3 sort.py file:jobStore
+- (venv) $ python sort.py file:jobStore
++ (venv) $ python3 sort.py file:jobStore
...
---TOIL WORKER OUTPUT LOG---
...
-@@ -344,13 +344,13 @@ that a job store of the same name alread
+@@ -353,13 +353,13 @@
failure, the job store is preserved so that the workflow can be restarted,
starting from the previously failed jobs. We can restart the pipeline by running ::
-- $ python sort.py file:jobStore \
-+ $ python3 sort.py file:jobStore \
+- (venv) $ python sort.py file:jobStore \
++ (venv) $ python3 sort.py file:jobStore \
--restart \
--overwriteOutput=True
We can also change the number of times Toil will attempt to retry a failed job::
-- $ python sort.py file:jobStore \
-+ $ python3 sort.py file:jobStore \
+- (venv) $ python sort.py file:jobStore \
++ (venv) $ python3 sort.py file:jobStore \
--retryCount 2 \
--restart \
--overwriteOutput=True
-@@ -364,7 +364,7 @@ line 30, or remove it, and then run
+@@ -373,7 +373,7 @@
::
-- $ python sort.py file:jobStore \
-+ $ python3 sort.py file:jobStore \
+- (venv) $ python sort.py file:jobStore \
++ (venv) $ python3 sort.py file:jobStore \
--restart \
--overwriteOutput=True
-@@ -415,7 +415,7 @@ Also! Remember to use the :ref:`destroy
+@@ -424,7 +424,7 @@
#. Run the workflow on the cluster::
@@ -92,9 +98,9 @@ Description: Make sure the doc applies to Debian installations with Python3
In this particular case, we create an S3 bucket called ``my-S3-bucket`` in
the ``us-west-2`` availability zone to store intermediate job results.
---- a/docs/running/cloud/amazon.rst
-+++ b/docs/running/cloud/amazon.rst
-@@ -147,7 +147,7 @@ all you need to do is specify the prefix
+--- toil.orig/docs/running/cloud/amazon.rst
++++ toil/docs/running/cloud/amazon.rst
+@@ -147,7 +147,7 @@
To run the sort example :ref:`sort example <sortExample>` with the AWS job store you would type ::
@@ -103,7 +109,7 @@ Description: Make sure the doc applies to Debian installations with Python3
.. _installProvisioner:
-@@ -360,7 +360,7 @@ are good to start running workflows. ::
+@@ -360,7 +360,7 @@
Now we can run the workflow: ::
@@ -112,7 +118,7 @@ Description: Make sure the doc applies to Debian installations with Python3
--batchSystem kubernetes \
aws:<region>:<job-store-name>
-@@ -430,7 +430,7 @@ If a job is not specified to be preempti
+@@ -430,7 +430,7 @@
are available, unless the workflow is run with the ``--defaultPreemptible`` flag. The ``--defaultPreemptible`` flag will allow
jobs without an explicit ``preemptible`` requirement to run on preemptible machines. For example::
@@ -121,7 +127,7 @@ Description: Make sure the doc applies to Debian installations with Python3
--batchSystem kubernetes \
--defaultPreemptible
-@@ -506,7 +506,7 @@ non-preemptible nodes of that type were
+@@ -506,7 +506,7 @@
#. Run the workflow with in-workflow autoscaling, specifying a provisioner and node types and counts as workflow arguments: ::
@@ -130,9 +136,9 @@ Description: Make sure the doc applies to Debian installations with Python3
--provisioner aws \
--nodeTypes c3.large \
--maxNodes 2 \
---- a/docs/running/cloud/gce.rst
-+++ b/docs/running/cloud/gce.rst
-@@ -58,7 +58,7 @@ To use the Google Job Store you will nee
+--- toil.orig/docs/running/cloud/gce.rst
++++ toil/docs/running/cloud/gce.rst
+@@ -58,7 +58,7 @@
Then to run the sort example with the Google job store you would type ::
@@ -141,7 +147,7 @@ Description: Make sure the doc applies to Debian installations with Python3
Running a Workflow with Autoscaling
-----------------------------------
-@@ -93,7 +93,7 @@ need to explicitly specify the ``--provi
+@@ -93,7 +93,7 @@
#. Run the workflow::
@@ -150,9 +156,9 @@ Description: Make sure the doc applies to Debian installations with Python3
--provisioner gce \
--batchSystem mesos \
--nodeTypes n1-standard-2 \
---- a/docs/appendices/deploy.rst
-+++ b/docs/appendices/deploy.rst
-@@ -70,7 +70,7 @@ both Python and Toil are assumed to be p
+--- toil.orig/docs/appendices/deploy.rst
++++ toil/docs/appendices/deploy.rst
+@@ -70,7 +70,7 @@
We can now run our workflow::
@@ -161,7 +167,7 @@ Description: Make sure the doc applies to Debian installations with Python3
.. important::
-@@ -79,9 +79,9 @@ We can now run our workflow::
+@@ -79,9 +79,9 @@
.. warning::
@@ -173,7 +179,7 @@ Description: Make sure the doc applies to Debian installations with Python3
doesn't work either as it installs the project as a Python ``.egg`` which is
also not currently supported by Toil (though it `could be`_ in the future).
-@@ -143,7 +143,7 @@ The following shell session illustrates
+@@ -143,7 +143,7 @@
└── main.py
3 directories, 5 files
@@ -182,7 +188,7 @@ Description: Make sure the doc applies to Debian installations with Python3
.. _package: https://docs.python.org/2/tutorial/modules.html#packages
-@@ -151,7 +151,7 @@ Here the workflow entry point module ``m
+@@ -151,7 +151,7 @@
is part of a package called ``util``, in a subdirectory of the current
directory. Additional functionality is in a separate module called
``util.sort.quick`` which corresponds to ``util/sort/quick.py``. Because we
@@ -191,7 +197,7 @@ Description: Make sure the doc applies to Debian installations with Python3
root directory of the hierarchy–``my_project`` in this case–and copy all Python
modules underneath it to each worker. The ``-m`` option is documented `here`_
-@@ -160,7 +160,7 @@ modules underneath it to each worker. Th
+@@ -160,7 +160,7 @@
When ``-m`` is passed, Python adds the current working directory to
``sys.path``, the list of root directories to be considered when resolving a
module name like ``workflow.main``. Without that added convenience we'd have to
@@ -200,7 +206,7 @@ Description: Make sure the doc applies to Debian installations with Python3
means that Toil can detect the root directory of the invoked module's package
hierarchy even if it isn't the current working directory. In other words we
could do this::
-@@ -168,7 +168,7 @@ could do this::
+@@ -168,7 +168,7 @@
$ cd my_project
$ export PYTHONPATH="$PWD"
$ cd /some/other/dir
@@ -209,9 +215,35 @@ Description: Make sure the doc applies to Debian installations with Python3
Also note that the root directory itself must not be package, i.e. must not
contain an ``__init__.py``.
---- a/docs/running/cliOptions.rst
-+++ b/docs/running/cliOptions.rst
-@@ -59,8 +59,8 @@ Running Toil workflows requires a file p
+--- toil.orig/docs/running/cliOptions.rst
++++ toil/docs/running/cliOptions.rst
+@@ -11,7 +11,7 @@
+
+ Or a Toil Python workflow::
+
+- $ python example.py --help
++ $ python3 example.py --help
+
+ For a basic toil workflow, Toil has one mandatory argument, the job store. All other arguments are optional.
+
+@@ -41,14 +41,14 @@
+
+ After editing the config file, you can run Toil with its settings by passing it on the command line::
+
+- $ python example.py --config=[filename].yaml
++ $ python3 example.py --config=[filename].yaml
+
+ Alternatively, you can edit the default config file, which is located at ``$HOME/.toil/default.yaml``
+
+ If CLI options are used in addition to the configuration file, the CLI options will overwrite the configuration file
+ options. For example::
+
+- $ python example.py --config=[filename].yaml --defaultMemory 80Gi
++ $ python3 example.py --config=[filename].yaml --defaultMemory 80Gi
+
+ This will result in a default memory per job of 80GiB no matter what is in the configuration file provided.
+
+@@ -59,8 +59,8 @@
For ``toil-cwl-runner`` and ``toil-wdl-runner`` a job store can often be selected automatically or can be specified with the ``--jobStore`` option; Toil Python workflows generally require the job store as a positional command line argument.
To use the :ref:`Python quickstart <pyquickstart>` example,
if you're on a node that has a large **/scratch** volume, you can specify that the jobstore be created there by
@@ -222,9 +254,9 @@ Description: Make sure the doc applies to Debian installations with Python3
Syntax for specifying different job stores:
---- a/docs/running/cloud/clusterUtils.rst
-+++ b/docs/running/cloud/clusterUtils.rst
-@@ -58,7 +58,7 @@ that toil does not delete the job store,
+--- toil.orig/docs/running/cloud/clusterUtils.rst
++++ toil/docs/running/cloud/clusterUtils.rst
+@@ -58,7 +58,7 @@
An example of this would be running the following::
@@ -233,7 +265,7 @@ Description: Make sure the doc applies to Debian installations with Python3
Where ``discoverfiles.py`` is the following:
-@@ -112,7 +112,7 @@ Status Command
+@@ -112,7 +112,7 @@
Continuing the example from the stats section above, if we ran our workflow with the command ::
@@ -242,9 +274,9 @@ Description: Make sure the doc applies to Debian installations with Python3
We could interrogate our jobstore with the status command, for example::
---- a/docs/contributing/contributing.rst
-+++ b/docs/contributing/contributing.rst
-@@ -66,7 +66,7 @@ Often it is simpler to use pytest direct
+--- toil.orig/docs/contributing/contributing.rst
++++ toil/docs/contributing/contributing.rst
+@@ -66,7 +66,7 @@
This usually works as expected, but some tests need some manual preparation. To run a specific test with pytest,
use the following::
@@ -253,9 +285,9 @@ Description: Make sure the doc applies to Debian installations with Python3
For more information, see the `pytest documentation`_.
---- a/docs/gettingStarted/install.rst
-+++ b/docs/gettingStarted/install.rst
-@@ -27,7 +27,7 @@ If not already present, please install t
+--- toil.orig/docs/gettingStarted/install.rst
++++ toil/docs/gettingStarted/install.rst
+@@ -27,7 +27,7 @@
And create a virtual environment called ``venv`` somewhere convenient, usch as under ``~``::
@@ -264,3 +296,14 @@ Description: Make sure the doc applies to Debian installations with Python3
.. _pip: https://pip.readthedocs.io/en/latest/installing/
+--- toil.orig/docs/running/hpcEnvironments.rst
++++ toil/docs/running/hpcEnvironments.rst
+@@ -24,7 +24,7 @@
+ For example, to run the sort example :ref:`sort example <sortExample>` on Slurm, assuming you are currently in a shared directory, you would type, on the cluster head node::
+
+ $ mkdir -p logs
+- $ python sort.py ./store --batchSystem slurm --batchLogsDir ./logs
++ $ python3 sort.py ./store --batchSystem slurm --batchLogsDir ./logs
+
+ Slurm Tips
+ ~~~~~~~~~~
=====================================
debian/patches/remove-python3-mock.patch deleted
=====================================
@@ -1,14 +0,0 @@
-From: Alexandre Detiste <tchet at debian.org>
-Subject: remove extraneous dependency on python3-mock
-
---- a/Makefile
-+++ b/Makefile
-@@ -259,7 +259,7 @@
- clean: clean_develop clean_sdist clean_docs
-
- check_build_reqs:
-- @(python -c 'import mock; import pytest' && which sphinx-build >/dev/null) \
-+ @(python -c 'import pytest' && which sphinx-build >/dev/null) \
- || ( printf "$(red)Build requirements are missing. Run 'make prepare' to install them.$(normal)\n" ; false )
-
- prepare: check_venv
=====================================
debian/patches/series
=====================================
@@ -1,11 +1,12 @@
+goodbye_distutils
+python3_in_doc.patch
+soften-configargparser-deps
+avoid_ruamel_yaml_string_dep.patch
+intersphinx
setting_version.patch
no_galaxy_lib
debianize_docs
soften-mesos-deps
-soften-pydocker-dep
atomic_copy_as_alternative.patch
-python3_in_doc.patch
avoid_boto
-# python3.12.patch
-# remove-python3-mock.patch
soften-cwltool-dep.patch
=====================================
debian/patches/setting_version.patch
=====================================
@@ -2,7 +2,7 @@ Description: Fixing version.py that is variable and required
Author: Steffen Moeller <moeller at debian.org>
Bug-Debian: https://bugs.debian.org/851365
Forwarded: not-needed
-Last-Update: 2020-05-07
+Last-Update: 2024-01-23
Generated by running `python version_template.py` from a git checkout of the
source to the tag corresponding to the release
@@ -11,16 +11,18 @@ As of Toil 5.7.0 the `cwltool_version` field is set in requirements-cwl.txt, ple
copy/update that field manually
--- /dev/null
+++ toil/src/toil/version.py
-@@ -0,0 +1,12 @@
-+baseVersion = '5.12.0'
+@@ -0,0 +1,14 @@
++baseVersion = '6.0.0'
+cgcloudVersion = '1.6.0a1.dev393'
-+version = '5.12.0-6d5a5b83b649cd8adf34a5cfe89e7690c95189d3'
-+distVersion = '5.12.0'
-+exactPython = 'python3'
++version = '6.0.0-0e2a07a20818e593bfdfde3cc51ca4ad809fde96'
++cacheTag = 'cache-local-py3.11'
++mainCacheTag = 'cache-master-py3.11'
++distVersion = '6.0.0'
++exactPython = 'python3.11'
+python = 'python3.11'
-+dockerTag = '5.12.0-6d5a5b83b649cd8adf34a5cfe89e7690c95189d3-py3.11'
-+currentCommit = '6d5a5b83b649cd8adf34a5cfe89e7690c95189d3'
++dockerTag = '6.0.0-0e2a07a20818e593bfdfde3cc51ca4ad809fde96-py3.11'
++currentCommit = '0e2a07a20818e593bfdfde3cc51ca4ad809fde96'
+dockerRegistry = 'quay.io/ucsc_cgl'
+dockerName = 'toil'
+dirty = False
-+cwltool_version = '3.1.20230601100705'
++cwltool_version = '3.1.20240112164112'
=====================================
debian/patches/soften-configargparser-deps
=====================================
@@ -0,0 +1,14 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Older configargparser is good enough
+Forwarded: not-needed
+--- toil.orig/requirements.txt
++++ toil/requirements.txt
+@@ -9,7 +9,7 @@
+ addict>=2.2.1, <2.5
+ pytz>=2012
+ enlighten>=1.5.2, <2
+-configargparse>=1.7,<2
++configargparse>=1.5.3,<2
+ ruamel.yaml>=0.15
+ ruamel.yaml.string>=0.1.1
+ pyyaml>=6,<7
=====================================
debian/patches/soften-cwltool-dep.patch
=====================================
@@ -1,20 +1,12 @@
Description: Soften versioned dependency from cwltool
Author: Andreas Tille <tille at debian.org>
Last-Update: Tue, 12 Dec 2023 16:57:57 +0100
-
---- a/requirements-cwl.txt
-+++ b/requirements-cwl.txt
+Forwarded: not-needed
+--- toil.orig/requirements-cwl.txt
++++ toil/requirements-cwl.txt
@@ -1,4 +1,4 @@
-cwltool==3.1.20240112164112
-+cwltool
++cwltool>=3.1.20240112164112
schema-salad>=8.4.20230128170514,<9
ruamel.yaml>=0.15,<=0.18.3
ruamel.yaml.clib>=0.2.6
---- a/src/toil/version.py
-+++ b/src/toil/version.py
-@@ -9,4 +9,4 @@ currentCommit = '6d5a5b83b649cd8adf34a5c
- dockerRegistry = 'quay.io/ucsc_cgl'
- dockerName = 'toil'
- dirty = False
--cwltool_version = '3.1.20230601100705'
-+# cwltool_version = '3.1.20230601100705'
=====================================
debian/patches/soften-mesos-deps
=====================================
@@ -1,13 +1,13 @@
Author: Michael R. Crusoe <crusoe at debian.org>
Subject: Skip addict
Forwarded: not-needed
---- a/requirements.txt
-+++ b/requirements.txt
-@@ -6,7 +6,6 @@ urllib3>=1.26.0,<3
+--- toil.orig/requirements.txt
++++ toil/requirements.txt
+@@ -6,7 +6,6 @@
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
+ configargparse>=1.5.3,<2
=====================================
debian/patches/soften-pydocker-dep deleted
=====================================
@@ -1,13 +0,0 @@
-Author: Michael R. Crusoe <crusoe at debian.org>
-Description: Allow for use of python3-docker package
-Forwarded: not-needed
---- a/requirements.txt
-+++ b/requirements.txt
-@@ -1,6 +1,6 @@
- dill>=0.3.2, <0.4
- requests>=2, <3
--docker>=3.7.2, <8
-+docker
- # Work around https://github.com/docker/docker-py/issues/3113
- urllib3>=1.26.0,<3
- python-dateutil
=====================================
debian/rules
=====================================
@@ -12,7 +12,7 @@ export PYBUILD_DISABLE_python2=1
override_dh_auto_build:
dh_auto_build
- PYTHONPATH=$(CURDIR)/src http_proxy='127.0.0.1:9' $(MAKE) -C docs man
+ PYTHONPATH=$(CURDIR)/src $(MAKE) -C docs man SPHINXOPTS=""
override_dh_auto_install:
dh_auto_install
@@ -23,7 +23,7 @@ override_dh_auto_install:
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
PYBUILD_SYSTEM=custom \
- PYBUILD_TEST_ARGS='HOME={home_dir} {interpreter} setup.py develop --user && PYTHONPATH={dir}/src:$$PYTHONPATH PATH={home_dir}/.local/bin/:$$PATH TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True {interpreter} -m pytest -n auto --dist loadscope -vv -W ignore --ignore src/toil/test/lib/aws/test_s3.py --ignore src/toil/test/provisioners/aws/awsProvisionerTest.py --ignore src/toil/test/wdl/wdltoil_test.py --ignore src/toil/test/cwl/cwlTest.py --ignore src/toil/test/src/promisedRequirementTest.py --ignore src/toil/test/lib/test_ec2.py --ignore src/toil/test/batchSystems/batchSystemTest.py --ignore src/toil/test/lib/aws/test_iam.py -k "not (test_bioconda or test_run_conformance or testImportFtpFile or ToilWdlIntegrationTest or SortTest or testCwlexample or testVirtualEnv or ToilDocumentationTest or test_cwl_toil_kill or testImportReadFileCompatibility or CleanWorkDirTest or DeferredFunctionTest or WdlToilTest)" {dir}/src/toil/test' \
+ PYBUILD_TEST_ARGS='HOME={home_dir} {interpreter} setup.py develop --user && PYTHONPATH={dir}/src:$$PYTHONPATH PATH={home_dir}/.local/bin/:$$PATH TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True {interpreter} -m pytest -n auto --dist loadscope -vv -W ignore --ignore src/toil/test/lib/aws/test_s3.py --ignore src/toil/test/provisioners/aws/awsProvisionerTest.py --ignore src/toil/test/wdl/wdltoil_test.py --ignore src/toil/test/cwl/cwlTest.py --ignore src/toil/test/src/promisedRequirementTest.py --ignore src/toil/test/lib/test_ec2.py --ignore src/toil/test/batchSystems/batchSystemTest.py --ignore src/toil/test/lib/aws/test_iam.py -k "not (test_bioconda or test_run_conformance or testImportFtpFile or ToilWdlIntegrationTest or SortTest or testCwlexample or testVirtualEnv or ToilDocumentationTest or test_cwl_toil_kill or testImportReadFileCompatibility or CleanWorkDirTest or DeferredFunctionTest or WdlToilTest or test_cactus_integration)" {dir}/src/toil/test' \
dh_auto_test
endif
=====================================
debian/tests/run-unit-tests
=====================================
@@ -10,7 +10,7 @@ TMPDIR=${HOME}/tmp TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True python3 -m pytest
--junit-xml=$AUTOPKGTEST_ARTIFACTS/toil-tests-junit.xml \
-vv -rs -W ignore -k "not (test_bioconda or AWSJobStoreTest or \
awsjobstoretest or testCwlexample or CWLv10Test or CWLv11Test or \
- CWLv12Test or AWSAutoscaleTest or AWSStaticAutoscaleTest or \
+ CWLv12Test or AWSAutoscaleTest or AWSStaticAutoscaleTest or test_cactus_integration or \
AWSManagedAutoscaleTest or AWSAutoscaleTestMultipleNodeTypes or \
AWSRestartTest or PreemptableDeficitCompensationTest or ToilDocumentationTest \
or test_cwl_toil_kill or testImportReadFileCompatibility or testBuiltIn \
View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/1d71375e81a55d1057ef2d40bdbcaf97731b72ae...b009784137295bb990a091b5161d41bc08fe6447
--
View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/1d71375e81a55d1057ef2d40bdbcaf97731b72ae...b009784137295bb990a091b5161d41bc08fe6447
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