3.1.20250715140722

What's Changed

• Various cleanups to make the docs better. by @mr-c in #2093
• Add missing cwl-runner refs by @mr-c in #2095
• move hints vs. requirements specific error checking earlier by @mr-c in #2103
• ProcessGenerator: allow for pickling by @mr-c in #2113
• Step name callback by @tetron in #2109
• Fix pydot tests by @lkk7 in #2019
• musllinux wheels nodejs fix by @mr-c in #2127
• galaxy upgrade 25.1 by @mr-c in #2130
• propagate writable attribute to secondaryfiles by @mr-c in #2133
• Improve environmental variable caching by @stxue1 in #2101

Deps

• Update black requirement from ==24.* to ==25.* by @dependabot[bot] in #2094
• Bump mypy from 1.14.1 to 1.15.0 by @dependabot[bot] in #2096
• Bump mypy from 1.15.0 to 1.16.0 by @dependabot[bot] in #2119
• Bump mypy from 1.16.0 to 1.16.1 by @dependabot[bot] in #2125
• Bump mypy from 1.16.1 to 1.17.0 by @dependabot[bot] in #2135
• gh-actions: remove one last usage of the now-deprecated Ubuntu 20.04 by @mr-c in #2097
• Update galaxy-util requirement from <24.2 to <24.3 by @dependabot[bot] in #2098
• Update galaxy-tool-util requirement from !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.2,>=22.1.2 to >=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.3 by @dependabot[bot] in #2099
• Bump pypa/cibuildwheel from 2.22.0 to 2.23.3 by @dependabot[bot] in #2117
• Bump cibuildwheel from 2.22.0 to 2.23.3 by @dependabot[bot] in #2116
• Bump pypa/cibuildwheel from 2.23.3 to 3.0.0 by @dependabot[bot] in #2122
• Bump pypa/cibuildwheel from 3.0.0 to 3.0.1 by @dependabot[bot] in #2132
• Update pytest requirement from <8.4,>=6.2 to >=6.2,<8.5 by @dependabot[bot] in #2121
• Update bagit requirement from <1.9,>=1.6.4 to >=1.6.4,<1.10 by @dependabot[bot] in #2123
• cibw: Disable building PyPy wheels on all platforms by @mr-c in #2134

New Contributors

• @lkk7 made their first contribution in #2019

Full Changelog: 3.1.20250110105449...3.1.20250715140722

3.1.20250110105449

What's Changed

• docs: render the CLI groups too by @mr-c in #2089
• Change caching pathmapper to respect the pathmapper factory by @stxue1 in #2092

Deps

• Bump mypy from 1.13.0 to 1.14.0 by @dependabot in #2090
• Bump mypy from 1.14.0 to 1.14.1 by @dependabot in #2091

New Contributors

• @stxue1 made their first contribution in #2092

Full Changelog: 3.1.20241217163858...3.1.20250110105449

3.1.20241217163858

What's Changed

• make-template: fix type error by @mr-c in #2078
• --no-warnings includes schema-salad; --validate should complain to stdout by @mr-c in #2084
• Append "_latest" to image id if no tag is present by @sameeul in #2085
• Fix cwltool:Loop extension definition by @GlassOfWhiskey in #2081
• argparse: colorize the --help output with rich-argparse by @mr-c in #2080
• Refactored ProvenanceProfile definition by @fmigneault in #2082
• singularity: improve testing on version 4.x+ by @mr-c in #2088

Deps

• Bump codecov/codecov-action from 4 to 5 by @dependabot in #2070
• Update flake8-bugbear requirement from <24.11 to <24.13 by @dependabot in #2086
• Bump cibuildwheel from 2.21.3 to 2.22.0 by @dependabot in #2077
• Bump sphinx-rtd-theme from 3.0.1 to 3.0.2 by @dependabot in #2069
• Bump pypa/cibuildwheel from 2.21.3 to 2.22.0 by @dependabot in #2076

Full Changelog: 3.1.20241112140730...3.1.20241217163858

3.1.20241112140730

What's Changed

• use max_cores in taskQueue instead of system cores by @kmavrommatis in #2038

• Use "run" with singularity/apptainer instead of "exec", when possible by @sameeul in #2065

• add note on docker macOS platform issue by @Brilator in #2064

• cpu_count can be None, so fallback to 1 by @mr-c in #2063

• conformance testing: no longer skip tests for singularity/apptainer by @mr-c in #2067

• cibuildwheel: adjust pytest parallel execution ; drop musllinux_1_1 by @mr-c in #2061

Deps

• Update ruamel-yaml requirement from <0.18,>=0.16.0 to >=0.16.0,<0.19 by @dependabot in #2066
• Update flake8-bugbear requirement from <24.9 to <24.11 by @dependabot in #2062

New Contributors

• @Brilator made their first contribution in #2064
• @kmavrommatis made their first contribution in #2038
• @sameeul made their first contribution in #2065

Full Changelog: 3.1.20241024121129...3.1.20241112140730

3.1.20241024121129

From this release onwards, cwltool requires Python 3.9+

What's Changed

• Remove Python 3.8 support by @mr-c in #2047
• Handle spurious ReceiveScatterOutput callbacks by @GlassOfWhiskey in #2051
• prepare for future mypy release and enable --local-partial-types now by @mr-c in #2052
• CI: build binary wheels by @mr-c in #2059

Deps

• Bump sphinx-rtd-theme from 3.0.0 to 3.0.1 by @dependabot in #2053
• Update black requirement from ~=24.8 to ==24.* by @dependabot in #2050
• Bump mypy from 1.11.2 to 1.12.0 by @dependabot in #2054
• Update rdflib requirement from <7.1,>=4.2.2 to >=4.2.2,<7.2 by @dependabot in #2055
• Bump mypy from 1.12.0 to 1.12.1 by @dependabot in #2057
• Bump mypy from 1.12.1 to 1.13.0 by @dependabot in #2058

Full Changelog: 3.1.20241007082533...3.1.20241024121129

3.1.20241007082533

What's Changed

• Updated outputMethod values by @GlassOfWhiskey in #2042
• prepare for mypy 1.12 by @mr-c in #2046

Deps

• remove usage of ancient shellescape backport of Stdlib's shlex by @a-detiste in #2041
• setuptools is not a install requirement by @mr-c in #2048
• Bump sphinx-rtd-theme from 2.0.0 to 3.0.0 by @dependabot in #2049

New Contributors

• @a-detiste made their first contribution in #2041

Full Changelog: 3.1.20240909164951...3.1.20241007082533

3.1.20240909164951

What's Changed

• cwl v1.3.0-dev1 native loop support by @GlassOfWhiskey in #1779
• Start running the draft CWL v1.3.0 conformance tests by @mr-c in #2022
• Conformance testing, skip a bad cwltest release by @mr-c in #2017
• Added new loop test by @LanderOtto in #2006
• removing duplicate "reference" by @danielskatz in #2030
• Support array of integers and floats as command argument parameters by @tom-tan in #2037
• Explicitly support Python 3.13; add to CI matrix by @mr-c in https://github.com/common-workflow-language/cwltool/pul
• fix loadContents for File[] by @fmigneault in #2036

Deps

• Requires schema-salad >=8.7 for MapSchema validation by @tetron in #2024
• skip pydot 3.x+ for now by @mr-c in #2020
• Update pytest requirement from <8.3,>=6.2 to >=6.2,<8.4 by @dependabot in #2025
• Bump mypy from 1.10.1 to 1.11.1 by @dependabot in #2028
• Bump mypy from 1.11.1 to 1.11.2 by @dependabot in #2035
• Update black requirement from ~=24.4 to ~=24.8 by @dependabot in #2029
• Update flake8-bugbear requirement from <24.3 to <24.9 by @dependabot in #2032
  l/2040

New Contributors

• @danielskatz made their first contribution in #2030

Full Changelog: 3.1.20240708091337...3.1.20240909164951

3.1.20240708091337

What's Changed

• Support Podman version 5.x which autodeletes the cidfiles by @mr-c in #2016
• Use uv compatible syntax in test-requirements.txt by @hauntsaninja in #2012
• Add docstrings to functions in ro.py by @AGoetzee in #2002

Deps

• Update black requirement from ~=24.3 to ~=24.4 by @dependabot in #1992
• Bump docker/build-push-action from 5 to 6 by @dependabot in #2008
• Update galaxy-util requirement from <24.1 to <24.2 by @dependabot in #2015
• Bump mypy from 1.10.0 to 1.10.1 by @dependabot in #2009
• Update galaxy-tool-util requirement from !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1,>=22.1.2 to !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,>=24.1.1,<24.2 by @dependabot in #2014

New Contributors

• @AGoetzee made their first contribution in #2002
• @hauntsaninja made their first contribution in #2012

Full Changelog: 3.1.20240508115724...3.1.20240708091337

3.1.20240508115724

What's Changed

• Replace .decode method with str(bytes, "utf-8") by @tetron in #1998
• Update paths for the CWL v1.2 conformance tests now that 1.2.1 has been released. by @mr-c in #1993
• build now uses the module name by @mr-c in #1997
• Update pytest requirement from <8.2,>=6.2 to >=6.2,<8.3 by @dependabot in #1996
• patch dockerFile build by @misterbrandonwalker in #1979

Full Changelog: 3.1.20240404144621...3.1.20240508115724

3.1.20240404144621

What's Changed

• add the --shm-size parameter at runtime by @lihl2014 in #1972
• Append "cwltool" to HTTP User-Agent string by @svonworl in #1977
• biocontainers test is flaky, automatically retry it. by @mr-c in #1983
• setuptools: silence package discovery warnings by @mr-c in #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 #1991

Deps

• Bump actions/cache from 3 to 4 by @dependabot in #1968
• Update black requirement from ~=23.12 to ~=24.1 by @dependabot in #1970
• Update pytest requirement from <7.5,>=6.2 to >=6.2,<8.1 by @dependabot in #1971
• Update pytest requirement from <8.1,>=6.2 to >=6.2,<8.2 by @dependabot in #1980
• Update flake8-bugbear requirement from <23.13 to <24.2 by @dependabot in #1966
• Update flake8-bugbear requirement from <24.2 to <24.3 by @dependabot in #1975
• Bump codecov/codecov-action from 3 to 4 by @dependabot in #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 #1978
• Update black requirement from ~=24.1 to ~=24.2 by @dependabot in #1976
• Bump mypy from 1.8.0 to 1.9.0 by @dependabot in #1982
• Galaxy-* 24.0.0 by @mr-c in #1990
• Update black requirement from ~=24.2 to ~=24.3 by @dependabot in #1985

New Contributors

• @lihl2014 made their first contribution in #1972
• @svonworl made their first contribution in #1977

Full Changelog: 3.1.20240112164112...3.1.20240404144621