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Update latest main - #2073

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ElderMedic wants to merge 230 commits into
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Update latest main #2073
ElderMedic wants to merge 230 commits into
prov_data_input_outputfrom
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@ElderMedic

@ElderMedic ElderMedic commented Nov 21, 2024

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mr-c and others added 30 commits October 4, 2024 14:20
@mr-c
prepare for mypy 1.12
48cea18
@a-detiste
remove usage of ancient shellescape backport of Stdlib's shlex (#2041)
75e073c
@mr-c
setuptools is not a install requirement
04fd426
@mr-c
gh-actions: fail-fast false
0056ca5
@dependabot @mr-c
Bump sphinx-rtd-theme from 2.0.0 to 3.0.0
18b8fdf 
Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 2.0.0 to 3.0.0.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](readthedocs/sphinx_rtd_theme@2.0.0...3.0.0)

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

Signed-off-by: dependabot[bot] <support@github.com>
@GlassOfWhiskey @mr-c
Handle spurious ReceiveScatterOutput callbacks (#2051)
6970186 
This commit fixes #2003 by handling spurious, repeated callbacks of the
`receive_scatter_output` method of the `ReceiveScatterOutput` class. The
reason of multiple awakenings has not been investigated deeply, though.
In the future, a thorough examination of the `MultithreadedJobExecutor`
logic may be necessary.

---------

Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>
@mr-c
prepare for future mypy release and enable --local-partial-types now
83000ae
@dependabot @mr-c
Bump sphinx-rtd-theme from 3.0.0 to 3.0.1
c6ad93a 
Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 3.0.0 to 3.0.1.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](readthedocs/sphinx_rtd_theme@3.0.0...3.0.1)

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

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
Update black requirement from ~=24.8 to ~=24.10
82f37d5 
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@24.8.0...24.10.0)

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

Signed-off-by: dependabot[bot] <support@github.com>
@mr-c
Update lint-requirements.txt
1a2c939
@mr-c
Update lint-requirements.txt
83def6a
@mr-c
Drop Python 3.8
05af6c1
@mr-c
add more docs
a956766
@dependabot @mr-c
Bump mypy from 1.11.2 to 1.12.0
606ec26 
Bumps [mypy](https://github.com/python/mypy) from 1.11.2 to 1.12.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.11.2...v1.12.0)

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

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
Update rdflib requirement from <7.1,>=4.2.2 to >=4.2.2,<7.2
74a08ca 
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...7.1.0)

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

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
Bump mypy from 1.12.0 to 1.12.1 (#2057)
e3e6bf9 
* Bump mypy from 1.12.0 to 1.12.1

Bumps [mypy](https://github.com/python/mypy) from 1.12.0 to 1.12.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.12.0...v1.12.1)

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

Signed-off-by: dependabot[bot] <support@github.com>

* Update pyproject.toml

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>
@dependabot @mr-c
Bump mypy from 1.12.1 to 1.13.0 (#2058)
8dee8e9 
* Bump mypy from 1.12.1 to 1.13.0

Bumps [mypy](https://github.com/python/mypy) from 1.12.1 to 1.13.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.12.1...v1.13.0)

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

Signed-off-by: dependabot[bot] <support@github.com>

* Update pyproject.toml

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>
@mr-c
build binary wheels
e3f6cf7 
But don't publish them yet
@mr-c
binary wheels: only build on main and other optimizations
6cfef62 
- cibuildwheel: adjust pytest parallel execution
- cicircle: upgrade to ubuntu 24.04
- Stop building for musllinux_1_1
  pypa/manylinux#1629
  > musl libc 1.1 is EOL and Alpine Linux 3.12 also (support ended 2 years ago, May 1st, 2022).
@dependabot @mr-c
Update flake8-bugbear requirement from <24.9 to <24.11
d810958 
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...24.10.31)

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

Signed-off-by: dependabot[bot] <support@github.com>
@mr-c
cpu_count can be None, so fallback to 1
9cda157
@Brilator @mr-c
add note on docker platform issue (#2064)
ee30368 
Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>
@dependabot
Update ruamel-yaml requirement from <0.18,>=0.16.0 to >=0.16.0,<0.19 (#…
0b64935 
…2066)

Updates the requirements on [ruamel-yaml]() to permit the latest version.

---
updated-dependencies:
- dependency-name: ruamel-yaml
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@kmavrommatis @mr-c
use max_cores in taskQueue instead of system cores (#2038)
048eb55 
The class TascQueue accepts an argument `thread_count` that is used for the max size of a queue.

In the `MultithreadedJobExecutor `class there is a variable defined (`max_cores`) that is getting its value from the available cores of the machine. Further down in the same class when TaskQueue is called instead of using the `max_cores` it is using `psutil.cpu_count()`. 

I suggest to use  the self.max_cores in the call of TaskQueue in the file executor.py instead of psutil.cpu_count()

Use case:
when a job executor is setup as MultithreadedJobExecutor one can override the max_cores after the initialization of the object and limit the use to the specified cores.

Additional enhancement would be to include an argument to allow the use to provide the number of cores available for use

Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>
@sameeul @mr-c
Use "run" with singularity/apptainer instead of "exec", when possible
1557c8d 
Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>
@mr-c
conformances testing: no longer skip tests for singularity/apptainer
c3c92eb
@dependabot @mr-c
Bump codecov/codecov-action from 4 to 5
e4d42b8 
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](codecov/codecov-action@v4...v5)

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

Signed-off-by: dependabot[bot] <support@github.com>
@mr-c
make-template: fix type error
6c86caa
@mr-c
--no-warnings includes schema-salad; --validate should complain to st…
7fa57dd 
…dout
@sameeul
Append "_latest" to image id if no tag is present (#2085)
604fd12
arimu1 and others added 19 commits July 19, 2026 13:55
@arimu1 @claude @mr-c
Add regression test for boolean input with a default (#779)
a49e83f 
Issue #779 reported that a boolean input with `default: false` was
treated as a required CLI argument (`error: the following arguments
are required: --a_false`), while `default: true` worked fine.

This was fixed in 48e8afd (2019) when `required` became
`default is None and input_required`, but the behavior was never
locked down by a test and the issue stayed open.

Add a parametrized regression test in test_toolargparse.py covering
both `default: false` and `default: true`, asserting the generated
parser treats the input as optional and falls back to the declared
default. Verified the test fails against the pre-fix logic with the
exact error from the issue.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
@arimu1 @claude
@mr-c @cursoragent
Warn when 'format' is used on a non-File parameter (#1616, #607) (#2291)
f79659f 
* Warn when 'format' is used on a non-File parameter (#1616, #607)

`format` is only meaningful for File parameters, but cwltool silently
accepted it on Directory (and other) inputs/outputs, so validation
passed with no indication that the field would be ignored.

Emit a validation warning (pointing at the offending `format` line)
when a parameter declares `format` but its type does not contain a
File. File and File[] parameters are unaffected. A warning, rather
than a hard error, avoids breaking documents that currently carry a
harmless stray `format`.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Add fixtures and tests for File[], Directory[], and record types so
_type_contains_file's array and record branches are exercised. Also
accept string array items (e.g. items: File), which is the common
loaded form — matching only list items incorrectly warned on File[].

Co-authored-by: Cursor <cursoragent@cursor.com>

---------

Co-authored-by: arimu1 <19286898+arimu1@users.noreply.github.com>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Co-authored-by: Michael R. Crusoe <michael.crusoe@gmail.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
@mr-c
document the minimum Python version is 3.10, and the max supported is…
4b30e07 
… 3.14
@arimu1 @claude
Warn when 'baseCommand' is a single string with whitespace (#2240) (#…
1f6aa50 
…2292)

A CommandLineTool 'baseCommand' given as a single string with internal
whitespace (e.g. "tar xf" instead of [tar, xf]) is passed to the OS as one
program name, which almost never exists. --validate previously accepted it
silently. Emit a warning at construction time pointing at the offending line
and suggesting the list form. List- and single-word baseCommands are
unaffected.

Co-authored-by: arimu1 <19286898+arimu1@users.noreply.github.com>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
@dependabot
build(deps): bump zizmorcore/zizmor-action from 0.5.3 to 0.5.6 (#2274)
5fbea4d 
Bumps [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) from 0.5.3 to 0.5.6.
- [Release notes](https://github.com/zizmorcore/zizmor-action/releases)
- [Commits](zizmorcore/zizmor-action@b1d7e1f...5f14fd0)

---
updated-dependencies:
- dependency-name: zizmorcore/zizmor-action
  dependency-version: 0.5.6
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@mr-c
gh-actions: drop codeql, no longer free-of-charge
349ef7c
@dependabot @mr-c
build(deps): bump docker/build-push-action from 7.1.0 to 7.2.0
9038732 
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 7.1.0 to 7.2.0.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](docker/build-push-action@bcafcac...f9f3042)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-version: 7.2.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump docker/setup-buildx-action from 4.0.0 to 4.1.0
e949ab0 
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 4.0.0 to 4.1.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](docker/setup-buildx-action@4d04d5d...d7f5e7f)

---
updated-dependencies:
- dependency-name: docker/setup-buildx-action
  dependency-version: 4.1.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump docker/login-action from 4.1.0 to 4.2.0
8e282c8 
Bumps [docker/login-action](https://github.com/docker/login-action) from 4.1.0 to 4.2.0.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](docker/login-action@4907a6d...650006c)

---
updated-dependencies:
- dependency-name: docker/login-action
  dependency-version: 4.2.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@mr-c
dependabot: try increase-if-needed for Python deps
d00b7a8
@dependabot @mr-c
build(deps): bump codecov/codecov-action from 6.0.1 to 7.0.0
5020d83 
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 6.0.1 to 7.0.0.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](codecov/codecov-action@e79a696...fb8b358)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-version: 7.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump zizmorcore/zizmor-action from 0.5.6 to 0.6.0
dc6ee73 
Bumps [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) from 0.5.6 to 0.6.0.
- [Release notes](https://github.com/zizmorcore/zizmor-action/releases)
- [Commits](zizmorcore/zizmor-action@5f14fd0...6599ee8)

---
updated-dependencies:
- dependency-name: zizmorcore/zizmor-action
  dependency-version: 0.6.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump actions/setup-python from 6.2.0 to 6.3.0
55516b7 
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 6.2.0 to 6.3.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@a309ff8...ece7cb0)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: 6.3.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump docker/setup-qemu-action from 4.0.0 to 4.2.0
91f46ad 
Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 4.0.0 to 4.2.0.
- [Release notes](https://github.com/docker/setup-qemu-action/releases)
- [Commits](docker/setup-qemu-action@ce36039...96fe6ef)

---
updated-dependencies:
- dependency-name: docker/setup-qemu-action
  dependency-version: 4.2.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump actions/cache from 5.0.5 to 6.1.0
772f4da 
Bumps [actions/cache](https://github.com/actions/cache) from 5.0.5 to 6.1.0.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](actions/cache@27d5ce7...55cc834)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-version: 6.1.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump docker/login-action from 4.2.0 to 4.4.0
f94b7f3 
Bumps [docker/login-action](https://github.com/docker/login-action) from 4.2.0 to 4.4.0.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](docker/login-action@650006c...af1e73f)

---
updated-dependencies:
- dependency-name: docker/login-action
  dependency-version: 4.4.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump pypa/cibuildwheel from 3.4.1 to 4.1.0
b2859e2 
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 3.4.1 to 4.1.0.
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](pypa/cibuildwheel@8d2b08b...2947353)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-version: 4.1.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump docker/setup-buildx-action from 4.1.0 to 4.2.0
1ab37bb 
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 4.1.0 to 4.2.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](docker/setup-buildx-action@d7f5e7f...bb05f3f)

---
updated-dependencies:
- dependency-name: docker/setup-buildx-action
  dependency-version: 4.2.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump actions/checkout from 6.0.2 to 7.0.1
7e636cf 
Bumps [actions/checkout](https://github.com/actions/checkout) from 6.0.2 to 7.0.1.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@de0fac2...3d3c42e)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: 7.0.1
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
github-advanced-security[bot]
github-advanced-security AI found potential problems Jul 25, 2026
View reviewed changes
Comment thread .github/workflows/ci-tests.yml

steps:
- uses: actions/checkout@v4
- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v6
Comment thread .github/workflows/ci-tests.yml
- name: MyPy cache
if: ${{ matrix.step == 'mypy' }}
uses: actions/cache@v4
uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v5
Comment thread .github/workflows/ci-tests.yml

steps:
- uses: actions/checkout@v4
- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v6
Comment thread .github/workflows/ci-tests.yml
py-semver: "3.13"
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v6
Comment thread .github/workflows/ci-tests.yml

steps:
- uses: actions/checkout@v4
- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v6
Comment thread .github/workflows/wheels.yml
with:
fetch-depth: 0 # slow, but gets all the tags
persist-credentials: false
- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v6
Comment thread .github/workflows/wheels.yml
name: Build source distribution
runs-on: ubuntu-24.04
steps:
- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v6
Comment thread .github/workflows/wheels.yml
with:
fetch-depth: 0 # slow, but gets all the tags
persist-credentials: false
- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v6
Comment thread .github/workflows/wheels.yml
# macos-15-intel is an intel runner, macos-14 is apple silicon
os: [macos-15-intel, macos-14, macos-15]
steps:
- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v6
Comment thread .github/workflows/wheels.yml
with:
fetch-depth: 0 # slow, but gets all the tags
persist-credentials: false
- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v6
dependabot Bot and others added 6 commits July 25, 2026 12:35
@dependabot @mr-c
build(deps): bump docker/build-push-action from 7.2.0 to 7.3.0
e509262 
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 7.2.0 to 7.3.0.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](docker/build-push-action@f9f3042...53b7df9)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-version: 7.3.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump actions/setup-python from 6.3.0 to 7.0.0
c6153a9 
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 6.3.0 to 7.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@ece7cb0...5fda3b9)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: 7.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
@arimu1
Handle list-valued doc when rendering --tool-help (#2304)
ece97e1 
* Handle list-valued doc when rendering --tool-help

The CWL spec allows the doc/label fields to be either a single string
or an array of strings, but the --tool-help renderer assumed doc was
always a string when building the argparse description and per-input
help text. A list doc crashed rich with "Unable to get render width"
(or a TypeError from rich.markup.escape for input-level doc).

Normalize doc to a string (joining list entries with newlines) before
it reaches argparse/rich, in both generate_parser and add_argument.

Fixes #2100

* Normalize list-valued doc before add_argument, not inside it

The typeguard-enabled test env type-checks arguments at the call
boundary, so passing the raw ruamel CommentedSeq into add_argument()
failed on its 'description: str' annotation before the normalization
inside the function could run.

Move the doc_to_str() call up into generate_parser(), where the value
is read off the input, and restore add_argument() to escaping a plain
string.

* Let doc_to_str own the None case in generate_parser

The caller guarded doc against None before calling doc_to_str(), which
duplicated the check the helper already performs and left the helper's
own None branch unreachable from the public API.

Pass the raw value straight through and map the resulting empty string
back to None, so a tool without doc/label still gets description=None.

* fix(argparser): join list-valued doc without str() repack

Per review: use plain "\n".join(doc) inside the MutableSequence branch.

---------

Co-authored-by: arimu1 <19286898+arimu1@users.noreply.github.com>
@Sanjays2402 @mr-c
Give a meaningful error for an empty job order file
a56df27 
An empty input object file made schema-salad's Loader.fetch() raise a
bare StopIteration, which main() caught in its generic handler and
rendered as "I'm sorry, I couldn't load this CWL file" followed by an
empty error string, giving the user nothing to act on.

load_job_order() now catches StopIteration from resolve_ref and reports
that the input object file is empty, matching the existing
"not formatted correctly" error for malformed input objects.

Fixes #2043
@arimu1 @mr-c
Fix float/double inputs below 1e-6 truncating to 0 on the command line (
0a30d8d 
#2104)

Builder.tostr() converts scientific-notation floats to plain decimal
so they never appear as e.g. "1E-6" on the command line. To do this it
checked whether the ruamel-yaml scalar's Decimal representation used
"E" notation, and if so quantized it to the nearest integer
(dec_value.quantize(1)). That was fine for values like 1.23e5, which
are already whole numbers, but any small fractional value that needs
scientific notation to display (roughly abs(x) < 1e-6) got rounded
down to 0 instead of being expanded to its full decimal form. A float
input defaulting to 9.999e-7 was silently turned into "0" on the
command line.

Replace the integer quantize with a full-precision fixed-point format
(format(dec_value, "f")), which expands scientific notation to plain
decimal without discarding any digits. Whole numbers still render the
same ("123000", "1230000"); a float/double default of 9.999e-7 now
renders as "0.0000009999" instead of "0".

Extended the existing floats_small_and_large.cwl fixture with a float
and a double input defaulting to 9.999e-7 and updated
test_very_small_and_large_floats to assert on the full value.
@dependabot @mr-c
build(deps): bump docker/login-action from 4.4.0 to 4.5.1
5fc88d3 
Bumps [docker/login-action](https://github.com/docker/login-action) from 4.4.0 to 4.5.1.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](docker/login-action@af1e73f...abd2ef4)

---
updated-dependencies:
- dependency-name: docker/login-action
  dependency-version: 4.5.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
github-advanced-security[bot]
github-advanced-security AI found potential problems Aug 1, 2026
View reviewed changes
Comment thread .github/workflows/quay-publish.yml Fixed
dependabot Bot added 3 commits August 1, 2026 12:43
@dependabot @mr-c
build(deps): bump pypa/cibuildwheel from 4.1.0 to 4.1.1
a0dca37 
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 4.1.0 to 4.1.1.
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](pypa/cibuildwheel@2947353...4726cd3)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-version: 4.1.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump zizmorcore/zizmor-action from 0.6.0 to 0.6.1
b4c828c 
Bumps [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) from 0.6.0 to 0.6.1.
- [Release notes](https://github.com/zizmorcore/zizmor-action/releases)
- [Commits](zizmorcore/zizmor-action@6599ee8...6fc4b00)

---
updated-dependencies:
- dependency-name: zizmorcore/zizmor-action
  dependency-version: 0.6.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot @mr-c
build(deps): bump docker/login-action from 4.5.1 to 4.6.0
9b603df 
Bumps [docker/login-action](https://github.com/docker/login-action) from 4.5.1 to 4.6.0.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](docker/login-action@abd2ef4...dbcb813)

---
updated-dependencies:
- dependency-name: docker/login-action
  dependency-version: 4.6.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
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