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Update and Check loadListing for input dir provenance #1986

Merged
merged 144 commits into from
Mar 27, 2024
Merged

Update and Check loadListing for input dir provenance #1986

merged 144 commits into from
Mar 27, 2024

Commits on Jun 5, 2023

  1. pass through QEMU_LD_PREFIX by default (common-workflow-language#1849) 

    For systems using qemu-user-static to run foreign binaries outside of
containers
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Commits on Jun 6, 2023

  1. Update flake8-bugbear requirement from <23.6 to <23.7 (common-workflo… 

    …w-language#1856)

Updates the requirements on [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) to permit the latest version.
- [Release notes](https://github.com/PyCQA/flake8-bugbear/releases)
- [Commits](PyCQA/flake8-bugbear@16.4.1...23.6.5)

---
updated-dependencies:
- dependency-name: flake8-bugbear
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
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  2. gh-actions: keep running even if codecov upload fails (common-workflo… 

    …w-language#1857)
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Commits on Jun 13, 2023

  1. Bump sphinx-rtd-theme from 1.2.1 to 1.2.2 (common-workflow-language#1858 

    )

Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.1 to 1.2.2.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](readthedocs/sphinx_rtd_theme@1.2.1...1.2.2)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
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Commits on Jun 24, 2023

  1. dockerfile: pin graphviz to before 8.x

    @mr-c
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  2. pin to compatible galaxy-util

    @mr-c
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  3. Update pytest requirement from <7.4,>=6.2 to >=6.2,<7.5 

    Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@6.2.0...7.4.0)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
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Commits on Jun 27, 2023

  1. *requirements.txt; remove spaces to enable re-use in other contexts 

    Like `pip install $(grep -v mypy mypy-requirements.txt)`
    @mr-c
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Commits on Jun 30, 2023

  1. confirm enhanced TypeDSL from Schema Salad v1.3 doesn't leak through

    @mr-c
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  2. tox: skip py3.6 for lint

    @mr-c
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Commits on Jul 1, 2023

  1. required outputs with secondaryFiles fix for containers (common-workf… 

    …low-language#1870)

* required outputs with secondaryFiles fix for containers

* improve error message

* leave no files behind
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Commits on Jul 11, 2023

  1. Update flake8-bugbear requirement from <23.7 to <23.8 (common-workflo… 

    …w-language#1877)

Updates the requirements on [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) to permit the latest version.
- [Release notes](https://github.com/PyCQA/flake8-bugbear/releases)
- [Commits](PyCQA/flake8-bugbear@16.4.1...23.7.10)

---
updated-dependencies:
- dependency-name: flake8-bugbear
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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  2. Update Python version support document; drop Python 3.7 (EOL) (common… 

    …-workflow-language#1872)

* refresh python version support

* CI: Drop Python 3.7 from testing
    @mr-c
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  3. Update black requirement from ~=23.3 to ~=23.7 

    Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@23.3.0...23.7.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:production
...

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  4. drop py3.7 lint checks

    @mr-c
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Commits on Jul 19, 2023

  1. enable pickling of cwltool.workflow.Workflow (common-workflow-languag… 

    …e#1878)
    @mr-c
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Commits on Aug 8, 2023

  1. start testing with Python 3.12

    @mr-c
    mr-c committed Aug 8, 2023
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  2. formatting fix

    @mr-c
    mr-c committed Aug 8, 2023
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Commits on Aug 14, 2023

  1. py version support policy: latest from Debian stable or Ubuntu LTS 

    Allow for any supported version of Python, not just the default Python version

Stop tracking RHEL

This would mean that we can then drop Python 3.6 support
    @mr-c
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  2. code: drop Python 3.6-3.7 support

    @mr-c
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  3. drop msvcrt: we don't support MS Windows anyhow

    @mr-c
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  4. Update rdflib requirement from <6.4,>=4.2.2 to >=4.2.2,<7.1 

    Updates the requirements on [rdflib](https://github.com/RDFLib/rdflib) to permit the latest version.
- [Release notes](https://github.com/RDFLib/rdflib/releases)
- [Changelog](https://github.com/RDFLib/rdflib/blob/main/CHANGELOG.md)
- [Commits](RDFLib/rdflib@4.2.2...7.0.0)

---
updated-dependencies:
- dependency-name: rdflib
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
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Commits on Aug 21, 2023

  1. Fixed race condition which happens when a job runs "too fast", 

    When a podman process finishes even before reaching the monitoring
method, a deadlock happens, as no one is updating `process.returncode`
and spawned process is in zombie state (so, no signal is sent).

This fix adds a `process.poll()` call, so it gives the chance to fill in
`process.returncode`.
    @jmfernandez @mr-c
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Commits on Aug 22, 2023

  1. Bump sphinx-rtd-theme from 1.2.2 to 1.3.0 

    Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.2 to 1.3.0.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](readthedocs/sphinx_rtd_theme@1.2.2...1.3.0)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot @mr-c
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  2. Cope with narrower terminal

    @mr-c
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  3. Use python3 in test CWL tool description

    @mr-c
    mr-c committed Aug 22, 2023
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Commits on Aug 23, 2023

  1. bump minimum required schema_salad version to reflect reality.

    @mr-c
    mr-c committed Aug 23, 2023
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Commits on Aug 28, 2023

  1. Use docker/podman/udocker inspect instead of docker images. 

    This approach avoids the issue about podman using "canonical"
image tags just using the "inspect" subcommand.
    @jmfernandez @mr-c
    jmfernandez authored and mr-c committed Aug 28, 2023
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  2. Removed additional udocker/podman pull. 

    This udocker/podman pull command was being done even when
`--disable-pull` parameter is passed to `cwltool`, and it
should not be needed, as all container image pulls should
have happened at this point.
    @jmfernandez @mr-c
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  3. Narrowed the exceptions to be caught, as of @mr-c indication. 

    Also, cosmetic changes to fix some flake8 complaints.
    @jmfernandez @mr-c
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  4. Possible workaround for some corner cases in `test_bad_userspace_runt… 

    …ime`
    @jmfernandez @mr-c
    jmfernandez authored and mr-c committed Aug 28, 2023
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  5. Lowered overhead of metrics gathering

    @jmfernandez @mr-c
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  6. Raised timelimit from 15 to 20, as it seems udocker needs more addi… 

    …tional time.
    @jmfernandez @mr-c
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  7. Job max memory usage gathering was happening only once, after the fir… 

    …st second of the job running.
    @jmfernandez @mr-c
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  8. Shelled popen was not implementing neither the timelimit nor the moni… 

    …toring
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Commits on Aug 29, 2023

  1. Fix resource allocation for CUDA 

    Co-authored-by: Nazanin Donyapour <[email protected]>
    @mr-c @ndonyapour
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Commits on Aug 31, 2023

  1. use nonlocal mem_tn variable

    @jfennick @mr-c
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Commits on Sep 5, 2023

  1. Bump actions/checkout from 3 to 4 

    Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v3...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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Commits on Sep 6, 2023

  1. add back in Python 3.7 for one last release

    @mr-c
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  2. release: preinstall udocker so that test_udocker_should_display_memor… 

    …y_usage doesn't timeout
    @mr-c
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  3. release: testenv4 isn't needed

    @mr-c
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  4. release: bump minimum setuptools version slightly to match Debian 11 … 

    …('bullseye').
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Commits on Sep 7, 2023

  1. Revert "add back in Python 3.7 for one last release" 

    This reverts commit 6c32ae5.
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Commits on Sep 13, 2023

  1. Update black requirement from ~=23.7 to ~=23.9 

    Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@23.7.0...23.9.1)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:production
...

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Commits on Sep 18, 2023

  1. Update flake8-bugbear requirement from <23.8 to <23.10 

    Updates the requirements on [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) to permit the latest version.
- [Release notes](https://github.com/PyCQA/flake8-bugbear/releases)
- [Commits](PyCQA/flake8-bugbear@16.4.1...23.9.16)

---
updated-dependencies:
- dependency-name: flake8-bugbear
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
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Commits on Sep 27, 2023

  1. guard import fcntl for windows

    @jfennick @mr-c
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Commits on Oct 2, 2023

  1. extend validation to the inputs of the top level proces

    @mr-c
    mr-c committed Oct 2, 2023
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  2. Bump docker/build-push-action from 4 to 5 

    Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4 to 5.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](docker/build-push-action@v4...v5)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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  3. Bump docker/setup-buildx-action from 2 to 3 

    Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2 to 3.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](docker/setup-buildx-action@v2...v3)

---
updated-dependencies:
- dependency-name: docker/setup-buildx-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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  4. Bump docker/setup-qemu-action from 2 to 3 

    Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 2 to 3.
- [Release notes](https://github.com/docker/setup-qemu-action/releases)
- [Commits](docker/setup-qemu-action@v2...v3)

---
updated-dependencies:
- dependency-name: docker/setup-qemu-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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  5. Bump docker/login-action from 2 to 3 

    Bumps [docker/login-action](https://github.com/docker/login-action) from 2 to 3.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](docker/login-action@v2...v3)

---
updated-dependencies:
- dependency-name: docker/login-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
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Commits on Oct 11, 2023

  1. Bump mypy from 1.3.0 to 1.6.0 

    Bumps [mypy](https://github.com/python/mypy) from 1.3.0 to 1.6.0.
- [Commits](python/mypy@v1.3.0...v1.6.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
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  2. bump minimum ruamel.yaml to 0.16

    @mr-c
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  3. pin to packaging<22 due to cwl-utils

    @mr-c
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  4. pin black to 22.x due to clash with galaxy-utils

    @mr-c
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  5. fix codespell-discovered typos

    @mr-c
    mr-c committed Oct 11, 2023
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  6. mypy 1.6.0 fixes, test new type inference

    @mr-c
    mr-c committed Oct 11, 2023
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  7. remove packaging requirement

    @mr-c
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  8. Update black requirement from ~=22.0 to ~=23.9 

    Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@22.1.0...23.9.1)

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  9. default to testing with Python 3.12

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Commits on Oct 12, 2023

  1. Update galaxy-tool-util requirement from <23,>=22.1.2 to >=22.1.2,<24 

    Updates the requirements on [galaxy-tool-util](https://github.com/galaxyproject/galaxy) to permit the latest version.
- [Release notes](https://github.com/galaxyproject/galaxy/releases)
- [Commits](galaxyproject/galaxy@galaxy-tool-util-22.1.3...v23.0.1)

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  2. conda deps: increase debugging

    @mr-c
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  3. deps: turn on logging

    @mr-c
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  4. software dependencies: make directory before calling galaxy.tool_util… 

    ….deps()
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  5. tox: set a $HOME value, helps conda install

    @mr-c
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  6. switch to setuptools_scm

    @mr-c
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  7. tests: fix warnings

    @mr-c
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  8. cwlprov: fix snapshots for locations with plus signs

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Commits on Oct 13, 2023

  1. silence spurious warning when validating some documents with "cwltool… 

    …" extensions
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  2. job loading: allow inputs named "id" 

    Co-authored-by: Simon Gene Gottlieb <[email protected]>
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Commits on Oct 16, 2023

  1. release: fix target name

    @mr-c
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  2. release: set version via SCM variable

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Commits on Oct 18, 2023

  1. Bump mypy from 1.6.0 to 1.6.1 

    Bumps [mypy](https://github.com/python/mypy) from 1.6.0 to 1.6.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.6.0...v1.6.1)

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  2. Update black requirement from ~=23.9 to ~=23.10 

    Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@23.9.0...23.10.0)

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Commits on Oct 20, 2023

  1. Revert "Update galaxy-tool-util requirement from <23,>=22.1.2 to >=22… 

    ….1.2,<24"

This reverts commit 9144a78.
    @mr-c
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  2. fix the pickling error for IO objects

    @ndonyapour @mr-c
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  3. gh-actions: record version before building container to publish to qu… 

    …ay.io
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  4. gh-actions: need newer setuptools to run setuptools_scm

    @mr-c
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Commits on Oct 24, 2023

  1. Update ruamel-yaml requirement from <0.18,>=0.16.0 to >=0.16.0,<0.19 

    Updates the requirements on [ruamel-yaml](https://sourceforge.net/p/ruamel-yaml/code/ci/default/tree) to permit the latest version.

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  2. software dependencies: allow newer versions of galaxy-tool-util 

    Skip the known broken versions (23.0.1 - 23.0.5)
    @mr-c
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Commits on Nov 13, 2023

  1. skip cwl-utils 0.30

    @mr-c
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Commits on Nov 14, 2023

  1. Update black requirement from ~=23.10 to ~=23.11 

    Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@23.10.0...23.11.0)

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...

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Commits on Nov 15, 2023

  1. Drop "Atomic" types in favor of recursive typedefs

    @mr-c
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Commits on Nov 23, 2023

  1. Bump mypy from 1.6.1 to 1.7.1 

    Bumps [mypy](https://github.com/python/mypy) from 1.6.1 to 1.7.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.6.1...v1.7.1)

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  2. type updates for mypy 1.7.x

    @mr-c
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  3. remove last usage of pkg_resources

    @mr-c
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Commits on Nov 28, 2023

  1. Bump sphinx-rtd-theme from 1.3.0 to 2.0.0 

    Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.3.0 to 2.0.0.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](readthedocs/sphinx_rtd_theme@1.3.0...2.0.0)

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  2. Update flake8-bugbear requirement from <23.10 to <23.12 

    Updates the requirements on [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) to permit the latest version.
- [Release notes](https://github.com/PyCQA/flake8-bugbear/releases)
- [Commits](PyCQA/flake8-bugbear@16.4.1...23.11.26)

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Commits on Dec 1, 2023

  1. pathmapper: don't use temporary lists 

    Should speed up items_exclude_children() a bit
    @mr-c
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Commits on Dec 4, 2023

  1. Update flake8-bugbear requirement from <23.12 to <23.13 

    Updates the requirements on [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) to permit the latest version.
- [Release notes](https://github.com/PyCQA/flake8-bugbear/releases)
- [Commits](PyCQA/flake8-bugbear@16.4.1...23.12.2)

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Commits on Dec 5, 2023

  1. gh-actions: preserve conformance tests XML results

    @mr-c
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  2. gh-actions: set conformance test git target based upon CWL version

    @mr-c
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  3. gh-actions: double quote variable to silence actionlint/shellcheck

    @mr-c
    mr-c committed Dec 5, 2023
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  4. gh-actions: --relax-path-checks for CWL v1.2 checks

    @mr-c
    mr-c committed Dec 5, 2023
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  5. support colons in paths on Singularity 3.9+/Apptainer 1.0+

    @mr-c
    mr-c committed Dec 5, 2023
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  6. require the new cwl-utils release

    @mr-c
    mr-c committed Dec 5, 2023
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  7. --no-warnings for even quieter output (errors only)

    @mr-c
    mr-c committed Dec 5, 2023
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  8. singularity: support dockerFile (common-workflow-language#1938) 

    * allow user to set temp dir with APPTAINER_TMPDIR
* singularity build: automatically try fakeroot mode if proot is missing

---------

Co-authored-by: Brandon Walker <[email protected]>
Co-authored-by: Michael R. Crusoe <[email protected]>
    @misterbrandonwalker @mr-c
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  9. make conformance test more flexible

    @mr-c
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Commits on Dec 6, 2023

  1. fix compute_checksums for literal files

    @mr-c
    mr-c committed Dec 6, 2023
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  2. conformance tests: do so with the mypc compiled version of cwltool

    @mr-c
    mr-c committed Dec 6, 2023
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Commits on Dec 7, 2023

  1. setup.py was missing spython install dependency

    @mr-c
    mr-c committed Dec 7, 2023
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  2. Bump actions/setup-python from 4 to 5 

    Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4...v5)

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Commits on Dec 12, 2023

  1. Update black requirement from ~=23.11 to ~=23.12 

    Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@23.11.0...23.12.0)

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Commits on Dec 14, 2023

  1. Bump github/codeql-action from 2 to 3 

    Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](github/codeql-action@v2...v3)

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Commits on Dec 15, 2023

  1. Bump actions/upload-artifact from 3 to 4 

    Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](actions/upload-artifact@v3...v4)

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Commits on Jan 3, 2024

  1. Bump mypy from 1.7.1 to 1.8.0 

    Bumps [mypy](https://github.com/python/mypy) from 1.7.1 to 1.8.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.7.1...v1.8.0)

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  2. upgrade udocker version used for testing to 1.3.12

    @mr-c
    mr-c committed Jan 3, 2024
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  3. fix fast container job hangs 

    Starting from Podman 4.4.0, cidfile is removed along with the container.

Always return if container is terminated so we don't stuck in the loop
waiting for a file which has already been removed.
    @kuanyili @mr-c
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Commits on Jan 8, 2024

  1. Unit test call cwltool.main with parsed args only, w/wo provenance

    @davidjsherman @mr-c
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  2. cwltoo.main provenance does not require unparsed args

    @davidjsherman @mr-c
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  3. rename singularity image (common-workflow-language#1956) 

    Co-authored-by: Brandon Walker <[email protected]>
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  4. remove galaxy-tool-util from build dependency

    @jfennick @mr-c
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  5. strip newline from version string; fix mypy error

    @jfennick @mr-c
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Commits on Jan 12, 2024

  1. add test for scatter in loop (common-workflow-language#1965)

    @LanderOtto
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Commits on Jan 18, 2024

  1. Bump actions/cache from 3 to 4 (common-workflow-language#1968) 

    Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](actions/cache@v3...v4)

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Commits on Jan 26, 2024

  1. Update black requirement from ~=23.12 to ~=24.1 

    Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@23.12.0...24.1.0)

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Commits on Jan 29, 2024

  1. apply black 2024 formatting

    @mr-c
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  2. ignore black 2024 formatting commit

    @mr-c
    mr-c committed Jan 29, 2024
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  3. Merge pull request common-workflow-language#1970 from common-workflow… 

    …-language/dependabot/pip/black-approx-eq-24.1

Update black requirement from ~=23.12 to ~=24.1
    @mr-c
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  4. Update pytest requirement from <7.5,>=6.2 to >=6.2,<8.1 

    Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@6.2.0...8.0.0)

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  dependency-type: direct:production
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  5. Update flake8-bugbear requirement from <23.13 to <24.2 

    Updates the requirements on [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) to permit the latest version.
- [Release notes](https://github.com/PyCQA/flake8-bugbear/releases)
- [Commits](PyCQA/flake8-bugbear@16.4.1...24.1.15)

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  6. address flake8-bugbear suggestions

    @mr-c
    mr-c committed Jan 29, 2024
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Commits on Feb 1, 2024

  1. Bump codecov/codecov-action from 3 to 4 

    Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](codecov/codecov-action@v3...v4)

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  dependency-type: direct:production
  update-type: version-update:semver-major
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  2. Fix codecov v4 configuration

    @mr-c
    mr-c committed Feb 1, 2024
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  3. add the --shm-size parameter at runtime (common-workflow-language#1972) 

    Co-authored-by: lihl <lihl@1123>
Co-authored-by: Michael R. Crusoe <[email protected]>
    @lihl2014 @mr-c
    3 people authored Feb 1, 2024
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Commits on Feb 22, 2024

  1. Update galaxy-tool-util requirement 

    Updates the requirements on [galaxy-tool-util](https://github.com/galaxyproject/galaxy) to permit the latest version.
- [Release notes](https://github.com/galaxyproject/galaxy/releases)
- [Commits](galaxyproject/galaxy@galaxy-tool-util-22.1.3...v23.2.1)

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Commits on Feb 27, 2024

  1. Update black requirement from ~=24.1 to ~=24.2 

    Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@24.1.0...24.2.0)

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Commits on Feb 28, 2024

  1. Append "cwltool" to HTTP User-Agent string (common-workflow-language#… 

    …1977)

Also appends the program name, if not "cwltool"

Should work for calrissian, reana-cwl-runner, and arvados-cwl-runner, but not
toil-cwl-runner which doesn't call the cwltool.main.main() function.

Probably works for streamflow, but I haven't tested that.

---------

Co-authored-by: Michael R. Crusoe <[email protected]>
    @svonworl @mr-c
    svonworl and mr-c authored Feb 28, 2024
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Commits on Mar 4, 2024

  1. Update pytest requirement from <8.1,>=6.2 to >=6.2,<8.2 

    Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@6.2.0...8.1.0)

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- dependency-name: pytest
  dependency-type: direct:production
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  2. conformance testing: set cwltest 2.5 as minimum version for Pytest 8.… 

    …1.x compat.
    @mr-c
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  3. Update flake8-bugbear requirement from <24.2 to <24.3 

    Updates the requirements on [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) to permit the latest version.
- [Release notes](https://github.com/PyCQA/flake8-bugbear/releases)
- [Commits](PyCQA/flake8-bugbear@16.4.1...24.2.6)

---
updated-dependencies:
- dependency-name: flake8-bugbear
  dependency-type: direct:production
...

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Commits on Mar 11, 2024

  1. Bump mypy from 1.8.0 to 1.9.0 (common-workflow-language#1982) 

    * Bump mypy from 1.8.0 to 1.9.0

Bumps [mypy](https://github.com/python/mypy) from 1.8.0 to 1.9.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.8.0...1.9.0)

---
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- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

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* Update pyproject.toml

---------

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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  2. biocontainers test is flaky, automatically retry it.

    @mr-c
    mr-c committed Mar 11, 2024
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  3. setuptools: silence package discovery warnings

    @mr-c
    mr-c committed Mar 11, 2024
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  4. Makefile: check-python3 is unneeded, call python3 explictly. 

    the "dist", "clean", and "release-test" targets don't need a virtualenv
so as long as there is a python3 on the PATH they will work
    @mr-c
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  5. biocontainer tests: use version corresponding to v2 Docker Image Format

    @mr-c
    mr-c committed Mar 11, 2024
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  6. pytest: use the worksteal scheduler and run on all logical cores, not… 

    … just physical.
    @mr-c
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Commits on Mar 14, 2024

  1. Merge branch 'main' into prov_data_input_output for updates

    Changlin committed Mar 14, 2024
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  2. fix merge err

    Changlin committed Mar 14, 2024
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Commits on Mar 22, 2024

  1. fix loadListing of dir for prov

    Changlin committed Mar 22, 2024
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  2. misc change of comments

    Changlin committed Mar 22, 2024
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Commits on Mar 26, 2024

  1. fix text, remove vscode space files

    Changlin committed Mar 26, 2024
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  2. remove redundant texts

    Changlin committed Mar 26, 2024
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