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

3.1.20240112164112

What's Changed

• Fix fast container job hangs by @kuanyili in #1962
• Permit calling cwltool.main with preparsed args only even with provenance by @davidjsherman in #1964
• rename singularity image by @misterbrandonwalker in #1956
• remove galaxy-tool-util from build dependency by @jfennick in #1955
• Added new test on loop by @LanderOtto in #1965

Deps

• Bump actions/setup-python from 4 to 5 by @dependabot in #1952
• Update black requirement from ~=23.11 to ~=23.12 by @dependabot in #1957
• Bump github/codeql-action from 2 to 3 by @dependabot in #1958
• Bump actions/upload-artifact from 3 to 4 by @dependabot in #1959
• Bump mypy from 1.7.1 to 1.8.0 by @dependabot in #1960

New Contributors

• @kuanyili made their first contribution in #1962
• @LanderOtto made their first contribution in #1965

Full Changelog: 3.1.20231207110929...3.1.20240112164112

3.1.20231207110929

What's Changed

• setup.py was missing spython install dependency by @mr-c in #1953
• conformance tests: do so with the mypc compiled version of cwltool by @mr-c in #1951

Full Changelog: 3.1.20231206180100...3.1.20231207110929

3.1.20231206180100

What's Changed

• --no-warnings for even quieter output (errors only) by @mr-c in #1885
• pathmapper: don't use temporary lists by @mr-c in #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!
• run the CWL v1.2.1 conformance tests by @mr-c in #1942
• add support for dockerFile with --singularity by @misterbrandonwalker in #1938
• fix compute_checksums during cache check for input File with literal default by @mr-c in #1776
• make running the conformance test more flexible by @mr-c in #1911

Misc

• remove last usage of pkg_resources by @mr-c in #1945
• Drop "Atomic" types in favor of recursive typedefs by @mr-c in #1943

Deps

• Bump mypy from 1.6.1 to 1.7.1 by @dependabot in #1940
• Bump sphinx-rtd-theme from 1.3.0 to 2.0.0 by @dependabot in #1948
• Update flake8-bugbear requirement from <23.10 to <23.12 by @dependabot in #1947
• Update flake8-bugbear requirement from <23.12 to <23.13 by @dependabot in #1950

New Contributors

• @misterbrandonwalker made their first contribution in #1938

Full Changelog: 3.1.20231114134824...3.1.20231206180100

3.1.20231114134824

What's Changed

• gh-actions: need newer setuptools to run setuptools_scm by @mr-c in #1932
• Update ruamel-yaml requirement from <0.18,>=0.16.0 to >=0.16.0,<0.19 by @dependabot in #1934
• software dependencies: allow newer versions of galaxy-tool-util by @mr-c in #1936
• skip cwl-utils 0.30 by @mr-c in #1941
• Update black requirement from ~=23.10 to ~=23.11 by @dependabot in #1939

Full Changelog: 3.1.20231020140205...3.1.20231114134824

3.1.20231020140205

What's Changed

• fix the pickling error for IO objects by @ndonyapour in #1929
• gh-actions: record version before building container to publish to quay.io by @mr-c in #1931

Full Changelog: 3.1.20231020113452...3.1.20231020140205

3.1.20231020113452

What's Changed

• temporarily downgrade galaxy-tool-util to workaround issue with newer conda by @mr-c in #1930

Deps

• Bump mypy from 1.6.0 to 1.6.1 by @dependabot in #1927
• Update black requirement from ~=23.9 to ~=23.10 by @dependabot in #1926

Full Changelog: 3.1.20231016170136...3.1.20231020113452