Cwltool

What's Changed
* add the --shm-size parameter at runtime by lihl2014 in https://github.com/common-workflow-language/cwltool/pull/1972
* Append "cwltool" to HTTP User-Agent string by svonworl in https://github.com/common-workflow-language/cwltool/pull/1977
* biocontainers test is flaky, automatically retry it. by mr-c in https://github.com/common-workflow-language/cwltool/pull/1983
* setuptools: silence package discovery warnings by mr-c in https://github.com/common-workflow-language/cwltool/pull/1981
* pytest: use the worksteal scheduler and run on all logical cores, not just physical. by mr-c in https://github.com/common-
workflow-language/cwltool/pull/1984
* podman nor singularity/apptainer support is experimental by mr-c in https://github.com/common-workflow-language/cwltool/pull/1991

Deps
* Bump actions/cache from 3 to 4 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1968
* Update black requirement from ~=23.12 to ~=24.1 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1970
* Update pytest requirement from <7.5,>=6.2 to >=6.2,<8.1 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1971
* Update pytest requirement from <8.1,>=6.2 to >=6.2,<8.2 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1980
* Update flake8-bugbear requirement from <23.13 to <24.2 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1966
* Update flake8-bugbear requirement from <24.2 to <24.3 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1975
* Bump codecov/codecov-action from 3 to 4 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1973
* Update galaxy-tool-util requirement from !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<23.2,>=22.1.2 to >=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<23.3 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1978
* Update black requirement from ~=24.1 to ~=24.2 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1976
* Bump mypy from 1.8.0 to 1.9.0 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1982
* Galaxy-* 24.0.0 by mr-c in https://github.com/common-workflow-language/cwltool/pull/1990
* Update black requirement from ~=24.2 to ~=24.3 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1985

New Contributors
* lihl2014 made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1972
* svonworl made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1977

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20240112164112...3.1.20240404144621

What's Changed

* Fix fast container job hangs by kuanyili in https://github.com/common-workflow-language/cwltool/pull/1962
* Permit calling cwltool.main with preparsed args only even with provenance by davidjsherman in https://github.com/common-workflow-language/cwltool/pull/1964
* rename singularity image by misterbrandonwalker in https://github.com/common-workflow-language/cwltool/pull/1956
* remove galaxy-tool-util from build dependency by jfennick in https://github.com/common-workflow-language/cwltool/pull/1955
* Added new test on loop by LanderOtto in https://github.com/common-workflow-language/cwltool/pull/1965

Deps
* Bump actions/setup-python from 4 to 5 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1952
* Update black requirement from ~=23.11 to ~=23.12 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1957
* Bump github/codeql-action from 2 to 3 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1958
* Bump actions/upload-artifact from 3 to 4 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1959
* Bump mypy from 1.7.1 to 1.8.0 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1960

New Contributors
* kuanyili made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1962
* LanderOtto made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1965

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20231207110929...3.1.20240112164112

What's Changed
* setup.py was missing spython install dependency by mr-c in https://github.com/common-workflow-language/cwltool/pull/1953
* conformance tests: do so with the mypc compiled version of cwltool by mr-c in https://github.com/common-workflow-language/cwltool/pull/1951

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20231206180100...3.1.20231207110929

What's Changed
* `--no-warnings` for even quieter output (errors only) by mr-c in https://github.com/common-workflow-language/cwltool/pull/1885
* pathmapper: don't use temporary lists by mr-c in https://github.com/common-workflow-language/cwltool/pull/1949
* a `toil-cwl-runner` user with many inputs of large "measurement set" directories had reported many hours to process `stage_files` and now [reports that this PR reduces that to several minutes](https://matrix.to/#/!sSMDDqTXkxpNofyjTR:gitter.im/$uD3IBa1uCvZy7bi9abforEYrRw2DALXFxbGaAifTY5o?via=gitter.im&via=matrix.org)!
* run the CWL v1.2.1 conformance tests by mr-c in https://github.com/common-workflow-language/cwltool/pull/1942
* add support for `dockerFile` with `--singularity` by misterbrandonwalker in https://github.com/common-workflow-language/cwltool/pull/1938
* fix compute_checksums during cache check for input File with literal default by mr-c in https://github.com/common-workflow-language/cwltool/pull/1776
* make running the conformance test more flexible by mr-c in https://github.com/common-workflow-language/cwltool/pull/1911

Misc
* remove last usage of pkg_resources by mr-c in https://github.com/common-workflow-language/cwltool/pull/1945
* Drop "Atomic" types in favor of recursive typedefs by mr-c in https://github.com/common-workflow-language/cwltool/pull/1943

Deps
* Bump mypy from 1.6.1 to 1.7.1 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1940
* Bump sphinx-rtd-theme from 1.3.0 to 2.0.0 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1948
* Update flake8-bugbear requirement from <23.10 to <23.12 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1947
* Update flake8-bugbear requirement from <23.12 to <23.13 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1950

New Contributors
* misterbrandonwalker made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1938

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20231114134824...3.1.20231206180100

What's Changed
* gh-actions: need newer setuptools to run setuptools_scm by mr-c in https://github.com/common-workflow-language/cwltool/pull/1932
* Update ruamel-yaml requirement from <0.18,>=0.16.0 to >=0.16.0,<0.19 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1934
* software dependencies: allow newer versions of galaxy-tool-util by mr-c in https://github.com/common-workflow-language/cwltool/pull/1936
* skip cwl-utils 0.30 by mr-c in https://github.com/common-workflow-language/cwltool/pull/1941
* Update black requirement from ~=23.10 to ~=23.11 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1939


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20231020140205...3.1.20231114134824

What's Changed
* fix the pickling error for IO objects by ndonyapour in https://github.com/common-workflow-language/cwltool/pull/1929
* gh-actions: record version before building container to publish to quay.io by mr-c in https://github.com/common-workflow-language/cwltool/pull/1931


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20231020113452...3.1.20231020140205