Update and Check loadListing for input dir provenance#1986

Merged

ElderMedic merged 144 commits intocommon-workflow-language:prov_data_input_outputfrom

ElderMedic:prov_data_input_output

Mar 27, 2024

Commits on Jun 5, 2023

pass through QEMU_LD_PREFIX by default (#1849)
mr-c
authored

Commits on Jun 6, 2023

Update flake8-bugbear requirement from <23.6 to <23.7 (#1856)
dependabot[bot]
authored
gh-actions: keep running even if codecov upload fails (#1857)
mr-c
authored

Commits on Jun 13, 2023

Bump sphinx-rtd-theme from 1.2.1 to 1.2.2 (#1858)
dependabot[bot]
authored

Commits on Jun 24, 2023

Commits on Jun 27, 2023

*requirements.txt; remove spaces to enable re-use in other contexts
mr-c
committed

Commits on Jun 30, 2023

Commits on Jul 1, 2023

required outputs with secondaryFiles fix for containers (#1870)
mr-c
authored

Commits on Jul 19, 2023

enable pickling of cwltool.workflow.Workflow (#1878)
mr-c
authored

Commits on Aug 8, 2023

Commits on Aug 21, 2023

Fixed race condition which happens when a job runs "too fast",

jmfernandez
authored and
mr-c
committed

Commits on Aug 22, 2023

Bump sphinx-rtd-theme from 1.2.2 to 1.3.0

dependabot[bot]
authored and
mr-c
committed
Cope with narrower terminal
mr-c
committed
Use python3 in test CWL tool description
mr-c
committed

Commits on Aug 23, 2023

bump minimum required schema_salad version to reflect reality.
mr-c
committed

Commits on Aug 28, 2023

Use docker/podman/udocker inspect instead of docker images.

jmfernandez
authored and
mr-c
committed
Removed additional udocker/podman pull.

jmfernandez
authored and
mr-c
committed
Narrowed the exceptions to be caught, as of @mr-c indication.

jmfernandez
authored and
mr-c
committed
Possible workaround for some corner cases in `test_bad_userspace_runtime`

jmfernandez
authored and
mr-c
committed
Lowered overhead of metrics gathering

jmfernandez
authored and
mr-c
committed
Raised `timelimit` from 15 to 20, as it seems udocker needs more additional time.

jmfernandez
authored and
mr-c
committed
Job max memory usage gathering was happening only once, after the first second of the job running.

jmfernandez
authored and
mr-c
committed
Shelled popen was not implementing neither the timelimit nor the monitoring

jmfernandez
authored and
mr-c
committed

Commits on Aug 29, 2023

Fix resource allocation for CUDA

mr-c
and
ndonyapour
committed

Commits on Aug 31, 2023

use nonlocal mem_tn variable

jfennick
authored and
mr-c
committed

Commits on Sep 5, 2023

Bump actions/checkout from 3 to 4

dependabot[bot]
authored and
mr-c
committed

Commits on Sep 7, 2023

Revert "add back in Python 3.7 for one last release"
mr-c
committed

Commits on Sep 13, 2023

Update black requirement from ~=23.7 to ~=23.9

dependabot[bot]
authored and
mr-c
committed

Commits on Sep 18, 2023

Update flake8-bugbear requirement from <23.8 to <23.10

dependabot[bot]
authored and
mr-c
committed

Commits on Sep 27, 2023

guard `import fcntl` for windows

jfennick
authored and
mr-c
committed

Commits on Oct 2, 2023

extend validation to the inputs of the top level proces
mr-c
committed
Bump docker/build-push-action from 4 to 5

dependabot[bot]
authored and
mr-c
committed
Bump docker/setup-buildx-action from 2 to 3

dependabot[bot]
authored and
mr-c
committed
Bump docker/setup-qemu-action from 2 to 3

dependabot[bot]
authored and
mr-c
committed
Bump docker/login-action from 2 to 3

dependabot[bot]
authored and
mr-c
committed

Commits on Oct 11, 2023

Commits on Oct 13, 2023

Commits on Oct 16, 2023

Commits on Oct 18, 2023

Bump mypy from 1.6.0 to 1.6.1

dependabot[bot]
authored and
mr-c
committed
Update black requirement from ~=23.9 to ~=23.10

dependabot[bot]
authored and
mr-c
committed

Commits on Oct 24, 2023

Commits on Nov 13, 2023

skip cwl-utils 0.30
mr-c
committed

Commits on Nov 14, 2023

Update black requirement from ~=23.10 to ~=23.11

dependabot[bot]
authored and
mr-c
committed

Commits on Nov 15, 2023

Drop "Atomic" types in favor of recursive typedefs
mr-c
committed

Commits on Nov 23, 2023

Bump mypy from 1.6.1 to 1.7.1

dependabot[bot]
authored and
mr-c
committed
type updates for mypy 1.7.x
mr-c
committed
remove last usage of pkg_resources
mr-c
committed

Commits on Nov 28, 2023

Bump sphinx-rtd-theme from 1.3.0 to 2.0.0

dependabot[bot]
authored and
mr-c
committed
Update flake8-bugbear requirement from <23.10 to <23.12

dependabot[bot]
authored and
mr-c
committed

Commits on Dec 1, 2023

pathmapper: don't use temporary lists
mr-c
committed

Commits on Dec 4, 2023

Update flake8-bugbear requirement from <23.12 to <23.13

dependabot[bot]
authored and
mr-c
committed

Commits on Dec 5, 2023

Commits on Dec 6, 2023

Commits on Dec 7, 2023

setup.py was missing spython install dependency
mr-c
committed
Bump actions/setup-python from 4 to 5

dependabot[bot]
authored and
mr-c
committed

Commits on Dec 12, 2023

Update black requirement from ~=23.11 to ~=23.12

dependabot[bot]
authored and
mr-c
committed

Commits on Dec 14, 2023

Bump github/codeql-action from 2 to 3

dependabot[bot]
authored and
mr-c
committed

Commits on Dec 15, 2023

Bump actions/upload-artifact from 3 to 4

dependabot[bot]
authored and
mr-c
committed

Commits on Jan 3, 2024

Bump mypy from 1.7.1 to 1.8.0

dependabot[bot]
authored and
mr-c
committed
upgrade udocker version used for testing to 1.3.12
mr-c
committed
fix fast container job hangs

kuanyili
authored and
mr-c
committed

Commits on Jan 8, 2024

Unit test call cwltool.main with parsed args only, w/wo provenance

davidjsherman
authored and
mr-c
committed
cwltoo.main provenance does not require unparsed args

davidjsherman
authored and
mr-c
committed
rename singularity image (#1956)

misterbrandonwalker
and
Brandon Walker
authored
remove galaxy-tool-util from build dependency

jfennick
authored and
mr-c
committed
strip newline from version string; fix mypy error

jfennick
authored and
mr-c
committed

Commits on Jan 12, 2024

add test for scatter in loop (#1965)
LanderOtto
authored

Commits on Jan 18, 2024

Bump actions/cache from 3 to 4 (#1968)
dependabot[bot]
authored

Commits on Jan 26, 2024

Update black requirement from ~=23.12 to ~=24.1
dependabot[bot]
authored

Commits on Feb 1, 2024

Bump codecov/codecov-action from 3 to 4

dependabot[bot]
authored and
mr-c
committed
Fix codecov v4 configuration
mr-c
committed
add the --shm-size parameter at runtime (#1972)

authored

Commits on Feb 22, 2024

Update galaxy-tool-util requirement

dependabot[bot]
authored and
mr-c
committed

Commits on Feb 27, 2024

Update black requirement from ~=24.1 to ~=24.2

dependabot[bot]
authored and
mr-c
committed

Commits on Feb 28, 2024

Append "cwltool" to HTTP User-Agent string (#1977)

svonworl
and
mr-c
authored

Commits on Mar 4, 2024

Commits on Mar 14, 2024

Commits on Mar 22, 2024

Commits on Mar 26, 2024