3.1.20260108082145

What's Changed

• Drop Python 3.9 support by @mr-c in #2159
• Discard undeclared fields from cwl.output.json by @GlassOfWhiskey in #2177
• Improve --parallel --singularity by @mr-c in #2187
• --parallel execution limits by @mr-c in #2189
• Fix use of extensions in $graph by @mr-c in #2181
• Singularity, caching, and docker monitor tweaks by @mr-c in #2190
• Reorganize the command line groups & add environment variables table by @mr-c in #2194
• handle singularity/apptainer sandbox images by @natthan-pigoux in #2166
• ProcessGenerator: match Input/Output schema to ExpressionTool by @mr-c in #2198
• Suppress erroneous warnings for pickValue by @LanderOtto in #2197
• printrdf: also include the input values by @mr-c in #2186

Tests

• Added new loop test by @LanderOtto in #2188

Deps

• Update pytest requirement from <8.5,>=6.2 to >=6.2,<9.1 by @dependabot[bot] in #2176
• Bump pypa/cibuildwheel from 3.2 to 3.3 by @dependabot[bot] in #2178
• Bump actions/checkout from 5 to 6 by @dependabot[bot] in #2180
• Update rdflib requirement from <7.5,>=4.2.2 to >=4.2.2,<7.6 by @dependabot[bot] in #2183
• build(deps): bump actions/upload-artifact from 5 to 6 by @dependabot[bot] in #2193
• Bump mypy from 1.18.2 to 1.19.1 by @dependabot[bot] in #2185
• build(deps): bump actions/cache from 4 to 5 by @dependabot[bot] in #2191
• build(deps): update galaxy-tool-util requirement from !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<25.1,>=22.1.2 to >=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<25.2 by @dependabot[bot] in #2196
• build(deps): update galaxy-util requirement from <25.1 to <25.2 by @dependabot[bot] in #2195
• build(deps): update ruamel-yaml requirement from <0.19,>=0.16.0 to >=0.16.0,<0.20 by @dependabot[bot] in #2199

New Contributors

• @natthan-pigoux made their first contribution in #2166

Full Changelog: 3.1.20251031082601...3.1.20260108082145

3.1.20251031082601

Python 3.9

This is the last release of cwltool with Python 3.9 support, as per our Python support version policy.

What's Changed

• 2X faster startup, defer galaxy-* imports to when needed by @mr-c in #2155
• support Pydot versions before 3.0 by @mr-c in #2157
• more docstrings by @mr-c in #2158
• CUDA: if no nvidia-smi program, don't complain so loudly. by @mr-c in #2160

Deps

• Bump pydantic from 2.12.0a1 to 2.12.0b1 by @dependabot[bot] in #2156
• Bump github/codeql-action from 3 to 4 by @dependabot[bot] in #2161
• Bump pydantic from 2.12.0b1 to 2.12.0 by @dependabot[bot] in #2162
• Update rdflib requirement from <7.3,>=4.2.2 to >=4.2.2,<7.4 by @dependabot[bot] in #2168
• Bump actions/upload-artifact from 4 to 5 by @dependabot[bot] in #2169
• Update rdflib requirement from <7.4,>=4.2.2 to >=4.2.2,<7.5 by @dependabot[bot] in #2172

Full Changelog: 3.1.20250925164626...3.1.20251031082601

3.1.20250925164626

In memory of @tetron , RIP

What's Changed

• support Python 3.14 by @mr-c in #2144
• py3.14 newer pydantic by @mr-c in #2146
• github actions cibw: unpin to just minor version tag, not the full patch number by @dependabot[bot] in https://github.com/
  /pull/2138

Deps

• Bump pypa/cibuildwheel from 3.0.1 to 3.1.0 by @dependabot[bot] in #2137
• Bump mypy from 1.17.0 to 1.17.1 by @dependabot[bot] in #2140
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #2142
• cibw 3.1.x by @mr-c in #2145
• Update setuptools-scm requirement from <9,>=8.0.4 to >=8.0.4,<10 by @dependabot[bot] in #2148
• Update setuptools-scm[toml] requirement from <9,>=8.0.4 to >=8.0.4,<10 by @dependabot[bot] in #2147
• Bump actions/setup-python from 5 to 6 by @dependabot[bot] in #2149
• Update rdflib requirement from <7.2,>=4.2.2 to >=4.2.2,<7.3 by @dependabot[bot] in #2153
• Bump mypy from 1.17.1 to 1.18.2 by @dependabot[bot] in #2152
• Bump pypa/cibuildwheel from 3.1 to 3.2 by @dependabot[bot] in #2154

Full Changelog: 3.1.20250715140722...3.1.20250925164626

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