3.1.20211020155521

What's Changed

• cwltool.Dockerfile fix by @mr-c in #1549
• outdir can be any valid URI ; add test for this by @tetron in #1552
• GitHub Actions: Separate concurrency groups by @mr-c in #1553

Full Changelog: 3.1.20211019185001...3.1.20211020155521

3.1.20211014180718

What's Changed

• test with Python 3.10 by @mr-c in #1546
• support singularity-ce by @mr-c in #1547
• bump minimum setuptools & pip for py3.10 by @mr-c in #1548

Full Changelog: 3.1.20211004060744...3.1.20211014180718

3.1.20211004060744

What's Changed

• Remove temporary directories when cache dir is empty string ; by @kinow in #1541
  That also fixes #1542 (Intermediary outputs are not deleted after workflow completion)!

New Contributors to cwltool

• @kinow made their first contribution in #1541

Full Changelog: 3.1.20211001174446...3.1.20211004060744

cwltool 3.1.20211001174446 Fix erroneous URL encoding of final output filenames

fix

• Fix erroneous URL encoding of final output filenames (#1446) 96ebb49 @AlexTate @mr-c
  (thanks to @gmloose for the encouragement!)

misc

• MPIRequirement.process can be an expression directly: d1aa327 @mr-c
• delete unnecessary files 06baf76 @mr-c
• include more in sdist 80c8ee1 @mr-c
• No reason to include the draft-N schemas 3f725e9 @mr-c
• udocker: test with newer version (1.3.1) 9dd1027 @mr-c
• Increase resiliance of test_malformed_reqs 63c7c72 @mr-c

cwltool 3.1.20210922203925 ; fix for toil-cwl-runner & others

• trust given secondaryFiles if discover_secondaryFiles is False 478d45a @mr-c

This is needed for toil-cwl-runner (and others) as some secondaryFile expressions can modify other entries in a way that would cause them to not pass validation a second time

cwltool 3.1.20210922130607 ; revert relocation of default_make_tool initialization

revert relocation of default_make_tool initialization (Fixes: #1525) 2ca1a0d @mr-c
mypy: warn_unreachable = True a3cc4fc @mr-c
enable test_arguments_self on systems without docker a265968 @mr-c

cwltool 3.1.20210921111717 ; now with podman support!

New features:

• support (rootless) podman container engine 52e1ebe @mr-c
• Need nodejs? use podman or singularity in addition to docker bb6fe86 @mr-c

Fixes:

• CommandLineTool.arguments: correctly set $(self) 2b17b14 @mr-c
• fix add_file_or_directory_volume for singularity 7017990 @mr-c
• tweaks for testing with Singularity 3.4.x fbe4aa1 @mr-c
• cope with datetime objects 62d1e11 @mr-c
• subgraph: support long version of WorkflowStep[].out 5a1488b @mr-c
• pack: add $namespaces to the (efffective) root only (#1506) cd9fde3 @mr-c
• Fix #811 (SchemaDefRequirements not working in workflows) 8f9a9ef @ThomasHickman @mr-c
• Fix #816 (Any type in inner tool fails to run) (#1510) 23c5aab @ThomasHickman @mr-c
• schema-salad 8.2.20210914115719 fixed a bug c02bd92 @mr-c
• packing: treat the IDs of the outputs separately (#1501) 57f9be0 @mr-c

Improvements

• expression evaluation: better error messages b67a5e0 @mr-c
• (docs): grammar updates for README.rst (#1482) 952de68 @vladdoster
• more helpful message for "paths starting with '/' only permitted in CWL 1.2 and later" error @twigleingrid fed2086

Misc:

• Modernize Dockerfile; build and publish containers to quay.io a293c47 74994e5 (#1485) 1953cf6 462377e b7468c7 801a317
  8ef2512 f5e5700 45be161 da64403 9fc0f2c b9fca03 f4cc3d4 @mr-c
• Update ruamel-yaml requirement from <0.17.11,>=0.15 to >=0.15,<0.17.17 abb5a7f b1bc9cf 7fe6399 05fc01b @dependabot @mr-c
• codeql: follow best practices 5356a63 330ad30 @mr-c
• allow for spaces in the current working directory 3a419f1 @mr-c
• update lingering reference to galaxy-lib 3163e89 @mr-c
• Bump codecov/codecov-action from 1 to 2.0.3 45be161 f111cf1 @dependabot @mr-c
• skip broken version of importlib_metadata 99463af @mr-c
• parallelize all tests 48c9d0c @mr-c
• cleanup requests calculations ffb7513 @mr-c
• doc: explicit mention of node.js dependency during testing (#857) 0893cbe @fgeorgatos
• add command line options to the docs 661c5d5 reduce sphinx warnings 092dd9d add docs badge c014c36 @mr-c
• add registry to dockerPull references 6a7f35f @mr-c
• fix an assert message 4ccbdde @mr-c
• mypy: warn_unreachable = True a3cc4fc @mr-c

cwltool 3.1.20210816212154 — fix for validation of SchemaDefRequirement ; writable workdirs; and named-pipes

Validates file with SchemaDefRequirement (#1475) 1fb45c8 @tetron
Fix #1480: make writable workdir actually writable (#1481) 3cf62d8 @jdidion @mr-c
Allow files to be named pipes when toil-cwl-runner or other cwltool-using runners are doing streaming (#1469) 0e89055 @mhpopescu @mr-c

work around networkx issue so we don't install numpy, scipy and pandas by default 6f9b232 58238d3 0358a41 @tetron @mr-c
release-test: Check python3 (#1478) fa46c0a @tetron
Update rdflib requirement from <5.1,>=4.2.2 to >=4.2.2,<6.1 (#1474) cef7385 @dependabot
README: Sort and expand the badge collection (now with Conda badges!) 7094ede @mr-c

cwltool 3.1.20210628163208 ; --pack Operations, updated schema-salad for bug fix

Allow packing Operation records (#1467) ed9dd4c @jmfernandez
Update schema-salad dependency for bug fix (#1463) 56d5120 @tetron @mr-c

Bump mypy from 0.812 to 0.910 fcdd2c7 8da32f2 03ba4bb 75795bf @dependabot @mr-c
fix ruamel.yaml PendingDeprecationWarnings 79e2350 @mr-c
upgrade to Python 3.6+ syntax 83f5fb7 @mr-c
Update ruamel-yaml requirement from <0.17.10,>=0.15 to >=0.15,<0.17.11 8ec1eb7 @dependabot @mr-c

cwltool 3.1.20210616134059 --single-process flag

--single-step: fix typo ; add --single-process (#1444) d91e812 @mr-c
Dependencies updates 695a6fa 9c4d5f3 1cdc689 7a68ce4 be0869a 63a9d43 dc5381e @mr-c @dependabot