3.1.20220117131913

What's Changed

• Drop Python 3.6 by @mr-c in #1593
• adjustment for docker build by @mr-c in #1595

Full Changelog: 3.1.20220116183622...3.1.20220117131913

3.1.20220116183622

New Features

• Initial support CUDARequirement extension by @tetron in #1581
• allow additional pathname characters in strict mode by @mr-c in #1579
• _terminate_processes for non-docker processes, like nodejs by @mr-c in #1577
• Add helpful error message when a program is terminated by a (Unix) signal, such as a segfault by @gmloose in #1569

Bug fixes

• expand stdin shortcut even when an ID is preset by @mr-c in #1592
• Fix --print-targets to pass inherited reqs. by @mr-c in #1580
• Protect ruamel from blank comment strings when making templates by @leipzig in #1390

What's Changed

• WSL2 clarification by @mr-c in #1567
• remove unnecessary encodes by @mr-c in #1575
• add better string representation for Process objects by @mr-c in #1571
• Remove noisy exception when the monitored process exits quickly by @mr-c in #1584
• Update how to setup pip environment by @manabuishii in #1017
• remove an Any type hint by @mr-c in #1587
• GA: simplify pip caching by @mr-c in #1589

Dependency updates

• Bump mypy from 0.910 to 0.920 by @dependabot in #1574
• Update rdflib requirement from <6.1,>=4.2.2 to >=4.2.2,<6.2 by @dependabot in #1576
• Bump mypy from 0.920 to 0.921 by @dependabot in #1578
• Bump mypy from 0.921 to 0.930 by @dependabot in #1582
• Update ruamel-yaml requirement from <0.17.18,>=0.15 to >=0.15,<0.17.20 by @dependabot in #1583
• Update ruamel-yaml requirement from <0.17.20,>=0.15 to >=0.15,<0.17.21 by @dependabot in #1585
• Bump mypy from 0.930 to 0.931 by @dependabot in #1588

New Contributors

• @gmloose made their first contribution in #1569
• @manabuishii made their first contribution in #1017
• @leipzig made their first contribution in #1390

Full Changelog: 3.1.20211107152837...3.1.20220116183622

3.1.20211107152837

What's Changed

• --print-targets: support embedded step processess by @mr-c in #1564
• --print-input-deps: support secondaryFile resolution by @mr-c in #1565

Misc

• Update README by @ALuesink in #1561
• Update ruamel-yaml requirement from <0.17.17,>=0.15 to >=0.15,<0.17.18 by @dependabot in #1559
• cwltool.Dockerfile: only install one version of pyparsing by @mr-c in #1562

New Contributors

• @ALuesink made their first contribution in #1561

Full Changelog: 3.1.20211104071347...3.1.20211107152837

3.1.20211104071347

What's Changed

• Call fsaccess.realpath before comparing paths in _relocate. by @tetron in #1560
  (Also bumps minimum schema-salad version to 8.2.20211104054942)

Full Changelog: 3.1.20211103193132...3.1.20211104071347

3.1.20211103193132

What's Changed

• Bump eWaterCycle/setup-singularity from 6 to 7 by @dependabot in #1554
• skip pyparsing 3.x to fix pydot; rdflib's sparql parsing by @mr-c in #1557
• detect circular workflow dependencies by @lijiayong in #1543
• --single-process inherit reqs & hints; support sub-workflows by @mr-c in #1558

Full Changelog: 3.1.20211020155521...3.1.20211103193132

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