cwltool 3.1.20210521105815 update minimum required version of schema_salad to grab bugfix

update minimum required version of schema_salad 9ffdfe5 @rupertnash

cwltool 3.1.20210426140515 fix for SoftwareRequirement & environment modules; and more!

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 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

cwltool 3.0.2021031914372: --single-step; auto-kill spawn Docker containers

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

cwltool 3.0.20210124104916: upgrade acceptable rdflib version

upgrade acceptable rdflib version 5bdb3d3 @mr-c
upgraded pytest 5f30c8e 2a922ab @mr-c

3.0.20201203173111

• When collecting output, now correctly looks for loadListing in outputBinding
• Fix a long standing issue where empty, unused, randomly named temporary directories would be created and not cleaned up, cluttering up the user's file system.

cwltool 3.0.20201121085451 Fix for parallel execution; cwltool-in-docker.sh

Parallel execution uses thread pool to avoid leaking resources. #1367 by @tetron with support from @mr-c
Fix cwltool-in-docker.sh to accept DOCKER_HOST #1372 by @tom-tan with shellchecking by @mr-c
Add fs_access for unknown URIs in relocateOutputs() _realpath(). #1376 by @DailyDreaming

cwltool 3.0.20201117141248 : recursive_resolve_and_validate_document() added for Galaxy

Added recursive_resolve_and_validate_document #1375 by @simleo

3.0.20201116114821: --tmpdir-prefix & --tmp-outdir-prefix fixed!

Added argcomplete support to cwltool #1362 by @lucasace
fix timeout message #1366 by @pvanheus
unify and fix tempdir creation logic #1374 by @mr-c

The following are #BioHackEU20 contributions:
support opaque resources better (for Galaxy) #1363 by @mr-c
switch to autoapi for docs generation #1368 by @mr-c
new function to convert CWL Expression with string interpolation from $() style to ${} style #1371 by @mr-c

PEP 561 compatibility

For users of Python type hints (via mypy or others), the cwltool module now advertises that our code comes with PEP 484 type hints

"add PEP 561 compatibility" (#1355) by @mr-c

Hello Python 3.9, goodbye Python 3.5!

Fix algorithm for generating output names when output names clash (#1342) by @pvanheus
allow pytest version 6 and other build cleanups (#1345) by @mr-c
Drop support/testing/CI for Python 3.5 (#1346) by @mr-c
Python 3.9 testing (#1352) by @mr-c

• upgrade to mypy 0.790
  Singularity: Support both --userns error messages (#1350) by @jonathanxu18
  (also removes --pid when using --userns with Signularity, for better Singularity in Kubernetes support)