common-workflow-language cwltool issues

common-workflow-language / cwltool

Common Workflow Language reference implementation

https://cwltool.readthedocs.io/

Apache License 2.0

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issues

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Replace .decode method with str(bytes, "utf-8")

#1998 tetron closed 5 months ago
2
build now uses the module name

#1997 mr-c closed 5 months ago
1
Update pytest requirement from <8.2,>=6.2 to >=6.2,<8.3

#1996 dependabot[bot] closed 5 months ago
2
Bump mypy from 1.9.0 to 1.10.0

#1995 dependabot[bot] closed 4 months ago
2
Update flake8-bugbear requirement from <24.3 to <24.5

#1994 dependabot[bot] closed 1 month ago
3
Update paths for the CWL v1.2 conformance tests now that 1.2.1 has been released.

#1993 mr-c closed 5 months ago
1
Update black requirement from ~=24.3 to ~=24.4

#1992 dependabot[bot] closed 4 months ago
4
podman nor singularity/apptainer support is experimental

#1991 mr-c closed 6 months ago
0
Galaxy-* 24.0.0

#1990 mr-c closed 6 months ago
1
Prov data input output

#1989 mr-c opened 6 months ago
4
Update galaxy-util requirement from <23.2 to <24.1

#1988 dependabot[bot] closed 6 months ago
2
Update galaxy-tool-util requirement from !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<23.3,>=22.1.2 to >=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1

#1987 dependabot[bot] closed 6 months ago
2
Update and Check loadListing for input dir provenance

#1986 ElderMedic closed 6 months ago
1
Update black requirement from ~=24.2 to ~=24.3

#1985 dependabot[bot] closed 6 months ago
1
pytest: use the worksteal scheduler and run on all logical cores, not just physical.

#1984 mr-c closed 6 months ago
1
biocontainers test is flaky, automatically retry it.

#1983 mr-c closed 6 months ago
1
Bump mypy from 1.8.0 to 1.9.0

#1982 dependabot[bot] closed 6 months ago
1
setuptools: silence package discovery warnings

#1981 mr-c closed 6 months ago
1
Update pytest requirement from <8.1,>=6.2 to >=6.2,<8.2

#1980 dependabot[bot] closed 7 months ago
1
patch dockerFile build

#1979 misterbrandonwalker closed 4 months ago
3
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

#1978 dependabot[bot] closed 7 months ago
1
Append "cwltool" to HTTP User-Agent string

#1977 svonworl closed 7 months ago
4
Update black requirement from ~=24.1 to ~=24.2

#1976 dependabot[bot] closed 7 months ago
1
Update flake8-bugbear requirement from <24.2 to <24.3

#1975 dependabot[bot] closed 7 months ago
1
Adding new choice to --on-error

#1974 AlexTate opened 8 months ago
2
Bump codecov/codecov-action from 3 to 4

#1973 dependabot[bot] closed 8 months ago
1
add the --shm-size parameter at runtime

#1972 lihl2014 closed 8 months ago
4
Update pytest requirement from <7.5,>=6.2 to >=6.2,<8.1

#1971 dependabot[bot] closed 8 months ago
1
Update black requirement from ~=23.12 to ~=24.1

#1970 dependabot[bot] closed 8 months ago
1
CWL Conditionals, when component doesn't handle condition when tool input parameter is a non-optional file with loadContents set to true

#1969 alexiswl opened 8 months ago
2
Bump actions/cache from 3 to 4

#1968 dependabot[bot] closed 8 months ago
1
Add CITATION.cff / codemeta.json file

#1967 mr-c opened 8 months ago
0
Update flake8-bugbear requirement from <23.13 to <24.2

#1966 dependabot[bot] closed 8 months ago
1
Added new test on loop

#1965 LanderOtto closed 8 months ago
1
Permit calling cwltool.main with preparsed args only even with provenance

#1964 davidjsherman closed 9 months ago
3
Calling cwltool.main() with preparsed args and provenance fails unless unparsed args are also provided

#1963 davidjsherman closed 9 months ago
4
Fix fast container job hangs

#1962 kuanyili closed 9 months ago
3
cwltool hangs running fast jobs in Podman

#1961 kuanyili closed 9 months ago
2
Bump mypy from 1.7.1 to 1.8.0

#1960 dependabot[bot] closed 9 months ago
1
Bump actions/upload-artifact from 3 to 4

#1959 dependabot[bot] closed 9 months ago
1
Bump github/codeql-action from 2 to 3

#1958 dependabot[bot] closed 9 months ago
1
Update black requirement from ~=23.11 to ~=23.12

#1957 dependabot[bot] closed 9 months ago
1
rename singularity image

#1956 misterbrandonwalker closed 9 months ago
2
remove galaxy-tool-util from build dependency

#1955 jfennick closed 9 months ago
1
remove redundant mypy-requirements.txt

#1954 mr-c closed 10 months ago
1
setup.py was missing spython install dependency

#1953 mr-c closed 10 months ago
1
Bump actions/setup-python from 4 to 5

#1952 dependabot[bot] closed 10 months ago
1
conformance tests: do so with the mypc compiled version of cwltool

#1951 mr-c closed 10 months ago
1
Update flake8-bugbear requirement from <23.12 to <23.13

#1950 dependabot[bot] closed 10 months ago
1
pathmapper: don't use temporary lists

#1949 mr-c closed 10 months ago
2

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