Cwltool

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

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

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

update minimum required version of schema_salad 9ffdfe5 rupertnash

Breaking change: MS Windows support has been dropped in favor of WSL 2, as previously announced 99c8f1a 337edaa mr-c

Major re-working of software requirements and environments, including environment modules and Singularity; all thanks to rupertnash in response to [SoftwareRequirement: environment modules changes to env not propagating to tool](https://github.com/common-workflow-language/cwltool/issues/1377) 26530dc 3758687 29b66ed bdb20fa efda9e3 420b69f 782d5f4 9dc966e df79fd0 3f6b455 a89c329 82030b5 725174e a523c2f 4248e07 7bdc74d (rupertnash with some help from mr-c)

Empty `hints` or `requriments` now produce a sensible error message a3e3a57 mr-c

Replace distutils.spawn usage 14c3f8f KushalBeniwal

New functionality

Kill Docker container if --cidfile is specified (996) 828e48a michael-kotliar
--single-step to extract/run a single step 667943c mr-c
Detect some types of bad URLs for the job/cwl inputs 39496f3 mr-c

Bug fixes:

Fixed singularity user namespace feature detection (1419) 8bdc152 jmfernandez
add unicode regex for paths and fix path encoding (1420) 0053a86 Panaetius
Secondaryfile deps (1416) 22a1fd2 tetron

Developer friendliness:

Enable CI via GitHub Actions (1411) 506ac9d 3a32a8f 193c575 0b78dec abac575 rupertnash (many thanks!)
make unit tests run in-process for speed (1392) 10c2cb6 dbde435 rupertnash
upgrade to py3.6+ syntax 9c702a9 mr-c

Miscellaneous:

Update installation instructions dd99739 mr-c
fix wrong URL in udocker example 72733d9 mr-c
Add Debian package badges ab713b6 mr-c
upgrade to mypy 0.800 be00beb mr-c
minimum setuptools & pip versions for Python3.9 ea6273d mr-c
Add missing interpreter lines f288e67 mr-c
increase checkout depth for codecov.io e9ee415 mr-c
Consolidate our typeshed (1417) 322d16c mr-c
release-test, tox, makefile: converge with schema_salad 83a489e mr-c