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)

Now supports the ratified and release vrsion of CWL v1.2

Add v1.2 stable release (#1334) by @tetron

upgrade to JSHint 2.12.0 (MIT license) @mr-c

Support CWL v1.2.0-dev5

Permit fractional storage values in ResourceRequirement (#1327) by @tetron

• Make sure parallel executor sets tmpdirSize and outdirSize

The road to CWL 1.2

Since the last github release:

• New experimental extension MPIRequirement (#1276)
• Support for 1.2.0-dev4 (#1315) (#1324)
• Packing handles mixed document versions in a workflow (#1320)
• Improved --print-dot output (#1316)
• Fix string interpolation and backslash escaping to match 1.2 spec. (#1309)

cwltool 3.0.20200530110633 CWL v1.2.0-dev3 , mypyc support, and more!

Fixed typo in docker.py #1269 by @hknust
Support CWL v1.2.0 dev3 ("only_non_null" -> "the_only_non_null") #1273 by @mr-c
Allow specification of file object in sec expression #1233 by @illusional
cope with unmovable files left over from Docker+IWDR #1282 by @mr-c
Remove schema_salad mention from tox.ini #1288 by @mr-c
Use schema_salad.avro.schema.Name according to docs #1281 by @rupertnash
Restore udocker feature #1293 by @mr-c
Upgrade to new mypy; get codebase compatible with mypyc #1294 by @mr-c
Rework types to use "Any" less often #1299 by @mr-c

cwltool 3.0.20200324120055 small tweaks to support toil-cwl-runner

#1265

cwltool 3.0.20200317203547: Conditionals, abstract operations, v1.2-dev2 and more!

Conditionals! #1222 @tetron
abstract operation #1255 @tetron
Use non-flat badges with the commonwl icon for conformance badges #1244 @tom-tan
Add doc field message to the output of --help #1248 @tom-tan
docker: change from --volume to --mount #1251 @mccalluc
explain who provides cwltool #1245 @mr-c
Update fragments in index #1256 @tetron
Ensure pack() produces original documents, not internally updated #1259 @tetron
Add test for packing a fragment of a document & fix. #1261 @tetron
Bump to 1.2.0-dev2 #1262 @tetron

cwltool 2.0.20200126090152 Allow turning off caching of downloaded documents

--pack: allow inputs/outputs named "name" #1239 @mr-c
run conformance tests using Travis #1237 @mr-c
Allow turning off caching of downloaded documents #1242 @tetron

cwltool 2.0.20200122124526 increase max. ruaml.yaml version to 0.16.5

max ruamel.yaml is 0.16.5; update mypy #1236 @mr-c