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

3.1.20231016170136

What's Changed

• No longer supporting Python 3.7 by @mr-c in #1901
• guard import fcntl for windows by @jfennick in #1914
• extend validation to the inputs of the top level proces by @mr-c in #1915
• silence spurious warning when validating some documents with "cwltool" extensions by @mr-c in #1921
• job loading: allow inputs named "id" by @mr-c in #1923

Deps

• Update galaxy-tool-util requirement from <23,>=22.1.2 to >=22.1.2,<24 by @dependabot in #1859
• Update black requirement from ~=23.7 to ~=23.9 by @dependabot in #1902
• Update flake8-bugbear requirement from <23.8 to <23.10 by @dependabot in #1909
• Bump docker/build-push-action from 4 to 5 by @dependabot in #1904
• Bump docker/setup-buildx-action from 2 to 3 by @dependabot in #1905
• Bump docker/setup-qemu-action from 2 to 3 by @dependabot in #1906
• Bump docker/login-action from 2 to 3 by @dependabot in #1907
• Bump mypy from 1.3.0 to 1.6.0 by @dependabot in #1862
• Remove packaging requirement by @dependabot in #1917
• Update black requirement from ~=22.0 to ~=23.9 by @dependabot in #1918
• default to testing with Python 3.12 by @mr-c in #1919

Misc

• switch to setuptools_scm by @mr-c in #1920
• release: fix target name by @mr-c in #1924
• release: set version via SCM variable by @mr-c in #1925

Full Changelog: 3.1.20230906142556...3.1.20231016170136

3.1.20230906142556

What's Changed

Dropped Python 3.6 support, brought back Python 3.7 support for this release only
Python 3.12 is now supported

• Fixed race condition which happens when a job runs "too fast", by @jmfernandez in #1890
• Propery locate podman images by @jmfernandez in #1891
• add cudaDeviceCount flag to the request requirements by @ndonyapour in #1895
• use nonlocal mem_tn variable by @jfennick in #1896
• start testing with Python 3.12 by @mr-c in #1882
• py version support policy, RHEL: only track full support releases by @mr-c in #1881
• Cope with narrower terminal by @mr-c in #1893
• release testing tweaks by @mr-c in #1900
• add back in Python 3.7 for one last release by @mr-c in #1898

Deps

• Update rdflib requirement from <6.4,>=4.2.2 to >=4.2.2,<7.1 by @dependabot in #1880
• Bump sphinx-rtd-theme from 1.2.2 to 1.3.0 by @dependabot in #1892
• bump minimum required schema_salad version to reflect reality. by @mr-c in #1894
• Bump actions/checkout from 3 to 4 by @dependabot in #1897

New Contributors

• @ndonyapour made their first contribution in #1895

Full Changelog: 3.1.20230719185429...3.1.20230906142556