common-workflow-language/cwltool: 3.1.20260108082145

What's Changed Drop Python 3.9 support by @mr-c in https://github.com/common-workflow-language/cwltool/pull/2159 Discard undeclared fields from cwl.output.json by @GlassOfWhiskey in https://github.com/common-workflow-language/cwltool/pull/2177 Improve --parallel --singularity by @mr-c in https://github.com/common-workflow-language/cwltool/pull/2187 --parallel execution limits by @mr-c in https://github.com/common-workflow-language/cwltool/pull/2189 Fix use of extensions in $graph by @mr-c in https://github.com/common-workflow-language/cwltool/pull/2181 Singularity, caching, and docker monitor tweaks by @mr-c in https://github.com/common-workflow-language/cwltool/pull/2190 Reorganize the command line groups & add environment variables table by @mr-c in https://github.com/common-workflow-language/cwltool/pull/2194 handle singularity/apptainer sandbox images by @natthan-pigoux in https://github.com/common-workflow-language/cwltool/pull/2166 ProcessGenerator: match Input/Output schema to ExpressionTool by @mr-c in https://github.com/common-workflow-language/cwltool/pull/2198 Suppress erroneous warnings for pickValue by @LanderOtto in https://github.com/common-workflow-language/cwltool/pull/2197 printrdf: also include the input values by @mr-c in https://github.com/common-workflow-language/cwltool/pull/2186 Tests Added new loop test by @LanderOtto in https://github.com/common-workflow-language/cwltool/pull/2188 Deps Update pytest requirement from <8.5,>=6.2 to >=6.2,<9.1 by @dependabot[bot] in https://github.com/common-workflow-language/cwltool/pull/2176 Bump pypa/cibuildwheel from 3.2 to 3.3 by @dependabot[bot] in https://github.com/common-workflow-language/cwltool/pull/2178 Bump actions/checkout from 5 to 6 by @dependabot[bot] in https://github.com/common-workflow-language/cwltool/pull/2180 Update rdflib requirement from <7.5,>=4.2.2 to >=4.2.2,<7.6 by @dependabot[bot] in https://github.com/common-workflow-language/cwltool/pull/2183 build(deps): bump actions/upload-artifact from 5 to 6 by @dependabot[bot] in https://github.com/common-workflow-language/cwltool/pull/2193 Bump mypy from 1.18.2 to 1.19.1 by @dependabot[bot] in https://github.com/common-workflow-language/cwltool/pull/2185 build(deps): bump actions/cache from 4 to 5 by @dependabot[bot] in https://github.com/common-workflow-language/cwltool/pull/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 https://github.com/common-workflow-language/cwltool/pull/2196 build(deps): update galaxy-util requirement from <25.1 to <25.2 by @dependabot[bot] in https://github.com/common-workflow-language/cwltool/pull/2195 build(deps): update ruamel-yaml requirement from <0.19,>=0.16.0 to >=0.16.0,<0.20 by @dependabot[bot] in https://github.com/common-workflow-language/cwltool/pull/2199 New Contributors @natthan-pigoux made their first contribution in https://github.com/common-workflow-language/cwltool/pull/2166 Full Changelog: https://github.com/common-workflow-language/cwltool/compare/3.1.20251031082601...3.1.20260108082145