Cwltool

What's Changed
* test with Python 3.10 by mr-c in https://github.com/common-workflow-language/cwltool/pull/1546
* support singularity-ce by mr-c in https://github.com/common-workflow-language/cwltool/pull/1547
* bump minimum setuptools & pip for py3.10 by mr-c in https://github.com/common-workflow-language/cwltool/pull/1548

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20211004060744...3.1.20211014180718

What's Changed
* Remove temporary directories when cache dir is empty string ; by kinow in https://github.com/common-workflow-language/cwltool/pull/1541
That also fixes 1542 (Intermediary outputs are not deleted after workflow completion)!

New Contributors to cwltool
* kinow made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1541

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20211001174446...3.1.20211004060744

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

- 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

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

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