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add type hints #62

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merged 5 commits into from Apr 13, 2016

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mr-c commented Apr 7, 2016

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mr-c commented Apr 7, 2016

@tetron ready for review; thanks!

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mr-c commented Apr 13, 2016

Thank you @tetron for the out of band code-review!

@mr-c mr-c merged commit b77c6ef into master Apr 13, 2016

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@mr-c mr-c deleted the types branch Apr 13, 2016

tetron added a commit that referenced this pull request Jul 23, 2017

Provide line numbers in error messages (#62)
* Line number reporting WIP

* Handle line number tracking $import expansion of lists and idmaps.

* Break long lines.

* Formatting bullets, indentation.

* Add tests of validation error reporting.

* type cleanups

* Better error reporting on link checking.

* Add missing sourceline.py

* Fix tests, typing, add tests for validation errors.

* Bump version.

* Print error validation messages for manual audit.

tetron added a commit that referenced this pull request Mar 20, 2018

Squashed 'cwltool/schemas/' changes from 0f28896..0d75172e
0d75172e Refactor to fix secondaryFiles on record fields, consolidate fields, use new subscope feature.
005c9c91 Spec clarification for #331
9ce6f8c8 Add explicit defaults for some fields.
fd9861b0 Synchronize with v1.0.2
e239d5b8 Merge pull request #647 from common-workflow-language/dnanexus
81f1bb98 Add Geet's ORCID
5d980b1f Add DNAnexus to supporting organizations list
1b71ddc7 Merge pull request #646 from wtsi-hgi/array-of-strings-job-files-input
ebd63119 Make array-of-strings-job.yml take in an array of files
83650a5b Merge pull request #645 from common-workflow-language/fix_run_test_help
83e899d9 fix help formatting
0ca7e798 Merge pull request #642 from common-workflow-language/IBM
839ec690 Add IBM to the supporting organizations list
47fe0f2c Merge pull request #639 from common-workflow-language/enhancement/test-dyn-iwdr
cfbc7b8e Merge pull request #638 from common-workflow-language/fix/valuefrom-constant
9c2c4fee Do not assume output file is present in dynamic iwdr test
89b2b782 Add DockerRequirement for `python` command in valueFrom-constant.cwl
000a889d Merge pull request #623 from common-workflow-language/new-test/valuefrom-constant
b5f0f5b7 Merge pull request #625 from common-workflow-language/new-test/any-compatibility
fb520d21 Merge pull request #612 from common-workflow-language/multInpReq
76b9b775 Merge pull request #620 from common-workflow-language/new-test/empty-array-input
155fdc45 Merge pull request #634 from common-workflow-language/new-test/concat-vf
6bb22505 Merge branch 'master' of github.com:common-workflow-language/common-workflow-language into new-test/valuefrom-constant
06c54e04 copy test for empty array input to v1.0
ec9cf54d Add test for empty array input
068c1ad5 Merge pull request #611 from common-workflow-language/step-level-resourcereq-test
f734e8d1 remove unneeded linkMerge to match Rabix behaviour
e8d3f6ae Merge branch 'master' of github.com:common-workflow-language/common-workflow-language into step-level-resourcereq-test
a4b1bf84 Add test for two concatenated expressions in valueFrom
c101119a Merge pull request #626 from common-workflow-language/workflow_with_dynreq
af9e0736 Merge branch 'master' into workflow_with_dynreq
06cd7d33 Merge pull request #628 from common-workflow-language/exit_code_tests
791886b8 don't use path for false
8d2a2977 test for alternative success exit codes
9c398386 test having a dynamics resoure requirement as part of a workflow
e22e0523 Testing Any type compatibility in outputSource
ffe52883 Add test for valueFrom with constant value overriding array inputs
91f108df Merge pull request #618 from common-workflow-language/test_with_classname
63dbb6d3 explain EXTRA
a33e9eee Merge pull request #607 from common-workflow-language/clarify_basename-fields-job.yml
31c68fde fix non v1.0 testing
e7a3e568 Merge branch 'master' into step-level-resourcereq-test
2889ba91 Add test for step-level ResourceRequirement for v1.0
1ea31342 Allow passing --classname to cwltest, improve --help
a8728791 Merge pull request #615 from common-workflow-language/avoid_unstrictjs
56776751 Merge pull request #610 from common-workflow-language/boolean-empty-inputbinding-test
e9d559bc Merge branch 'master' into boolean-empty-inputbinding-test
e21ee6ee Merge pull request #616 from common-workflow-language/new-test/staging-optional-file
b9c52371 Merge pull request #613 from common-workflow-language/wc-test-portability
8b4e1eb7 Merge pull request #614 from common-workflow-language/staging-writable-dir
74261a6d Test for expression engine with self reference to null input
e14a5d29 Add test for empty not-null boolean inputBinding
c0984113 Add test for MultipleInputFeatureReq if source is a single-item list
ecd8e2bd Ensure the staged directory is writable
62f74816 modify template use to avoid with(), which violates strict mode
619fdad9 Add test for staging a writable directory inside Docker
2141724c Replace `wc` with `cat` for test of command execution with standard streams redirection
42d37d04 Add test for step-level ResourceRequirement
9c34c2a5 Update basename-fields-job.yml
3b747ab9 Merge pull request #601 from common-workflow-language/hmenager-patch-1
4a0a558c Merge pull request #603 from cjfields/patch-1
e0309c49 Add PBS/Torque support for Toil
7b831fe0 Merge pull request #602 from common-workflow-language/cwl-emacs
0bff6183 Add links to blog post about cwl-emacs
89b5390d correct typo in travis file
103006b3 Merge pull request #598 from mdmiller53/patch-2
7b7ea1cf Update README.md
35a371d7 Merge pull request #594 from common-workflow-language/recursive-input-directory-test-fix
49b503ca basename not required to be in output
2a393205 Merge pull request #589 from common-workflow-language/nested-dir-test-fix
b3b9d1f5 Fix conformance test, directory needs to be marked writable in order to write to it!
2ee358c7 Merge pull request #580 from common-workflow-language/cease_building_old_userguide
85009292 Merge pull request #586 from common-workflow-language/cwl_output_singular
10a3ddf0 cwl.output.json is singular
0814764e Merge pull request #585 from bmeg/workflow-default
d728efde Adding conformance test for #592
cd93e026 stop building old user guide
c4a3085f Merge pull request #578 from common-workflow-language/cromwell_ci
1ad1276e link to CI testing of Cromwell
77ef9829 Merge pull request #570 from common-workflow-language/IWDR_nested
74d6f3a5 Test InitialWorkDirRequirement with a nested directory structure from another step
c2489659 Merge pull request #577 from common-workflow-language/test_glob_order
9111c888 Merge pull request #557 from otiai10/master
739d3d6d Merge pull request #576 from common-workflow-language/biostars_tag
1687baae fix capitalization of 'post'
daca82a1 Merge pull request #574 from common-workflow-language/citation_update
8ca65e26 test for POSIX glob behavior
ea485c46 Explicitly link to the Biostars post form
fb4f92fe synchronize with http://www.commonwl.org/#Citation
1fe86e5b Merge pull request #573 from common-workflow-language/reana
41a69b2c Add REANA to the list
dd0813f3 CWL files under `v1.0/examples` are no longer to be tested
97173a98 Merge pull request #542 from common-workflow-language/mr-c-patch-1
504fb7e3 Merge pull request #544 from common-workflow-language/jp_link
97c7e362 clarify JP link
7a7d27a7 Merge pull request #549 from common-workflow-language/embl_abr
53c52230 Merge pull request #567 from common-workflow-language/intelliJ
95fcd1df Correct links to IntelliJ/JetBrains CWL plugin
3e98cab3 Merge pull request #560 from common-workflow-language/mv_Hello
9ccd71c9 Move Hell.java
8b99a846 Merge pull request #558 from manabuishii/move_test_files
915d49f8 Move files under v1.0/ for conformance test
fcb4ed86 re-arrange
c6e3f151 Add status badge of itself
21de641b Test myself by using schema_salad
c888cb48 Add EMBL-ABR
a83ab96d Merge pull request #548 from otiai10/master
4e28adab Enable testing without cd to the repository
7bd0d7ea Add JP link
6d77fa69 Removed extraneous baseCommand
d126e152 Merge pull request #536 from common-workflow-language/mr-c-patch-1
702afe31 Merge pull request #539 from stellargo/patch-1
b04007b2 remove link to user guide, add link to stable ver.
2482b66f draft-3/README.md: Link address changed
6bc4368c Clarify citation, link to citeulike
c6bc1288 Merge pull request #535 from common-workflow-language/remove_draft3_userguide
26d650b8 Remove draft-3 userguide and link to the new URL
ffe182e8 Merge pull request #534 from common-workflow-language/cwl-software
8433a910 Prepopulate github/google links with search query
d08e37b2 Add tricks for searching Github / Google for CWL.
b49f7bc4 Merge pull request #533 from common-workflow-language/cwl-software
af2eedb7 Remove language column whoops
d5125033 remove spurious [
b6e47a23 Remove 'language' column.  Make explicit SDK section.
811deca0 Fix links
bfdde7ff Swap columns
6a91db53 Separate language/platform support columns.
96a0c9ae Add note about github searching trick.  Add yacle and cerise.
eb1e0cdc Add Cromwell, CWL libraries for various languages.
f2031e4a Update and rearrange software section
612414eb Merge pull request #528 from cure/master
43d67d0d Run all v1.0 tests that use a Debian Docker image with the debian:stretch-slim image instead of a debian:8 or debian:wheezy.
0c8f9ddf Merge pull request #524 from jmchilton/fix_dir3
8b0a8905 Merge pull request #526 from tom-tan/fix-typo
33603758 Fix indent in the example of stdout
92ee6abc Merge pull request #512 from common-workflow-language/update_contribs
2100e7f6 Fix doc for dir3.cwl test.
0e1ac178 Merge pull request #520 from michael-kotliar/master
9cbe3743 Update link for Airflow
55208187 Merge pull request #509 from common-workflow-language/typo42
a66b295b ORCID for John Kern
01fc1084 ORCIDs: Josh Randall, Mark Robinson, & Tom Morris
51a5b048 add Marc Fiume's ORCID; https for orcid.org links
f253f3a2 ORCIDs for Ward & James
a3e9d38c Merge pull request #511 from common-workflow-language/link_new_userguide
ca83f2d6 ORCID for Gaurav
e3862128 add CWL advisors, leadership team, some ORCIDS
813bf044 remove old user guide, link to the new one
d53c4983 XDF_DATA_HOME -> XD**G**_DATA_HOME
1eb152b4 Merge pull request #508 from common-workflow-language/full-citation
f7be9835 Provide full citation details
76bd4fd4 Merge pull request #506 from common-workflow-language/broken-valueFrom
67567438 Fix merge conflict.
15252f40 Merge pull request #507 from common-workflow-language/literal-without-docker
18e902ac remove Docker mention in docstring
c04b2c6f Test file literal as input without Docker
e2fa9668 Merge pull request #505 from common-workflow-language/broken-valueFrom
9c0d75bc Add conformance test for valueFrom on a scatter parameter, from https://github.com/dleehr/broken-valueFrom
165b5130 Merge pull request #503 from mccalluc/patch-1
e142260c missing back-tick causes misformatting
7f510ec7 Merge pull request #498 from common-workflow-language/no-location-secondary
67b4d608 Merge pull request #499 from common-workflow-language/fix-dynresreq
5351b234 Tweak dynresreq test, remove 'basename' check and remove newline from special_file.
ba99368e Bump couple additional references to v1.0.2
08c09893 Merge pull request #496 from common-workflow-language/no-location-secondary
d7732801 Merge pull request #497 from common-workflow-language/dynresreqs
e1ab24bc test for dyn res reqs
e9a869f2 Bump spec to v1.0.2.  Expand secondaryFile tests to include expressions returning lists and directories in secondaryFiles.
66ef5a09 Fix conformance test entry.
1ed4f764 Specify that nameroot and nameext must be present for secondaryFile eval as well.
28ce0407 Update spec.
95001104 Revise secondaryFile conformance test to use basename and path instead of location.
ffd2dbf Merge pull request #487 from common-workflow-language/1.0.1-text
6a28a1a Update text to v1.0.1.
2674c57 Merge pull request #410 from common-workflow-language/v1.0-errata
351d032 Merge remote-tracking branch 'origin/clarify-package' into v1.0-errata
a4e9eb6 Adjust core request in bwa command line test from 4 to 2.
a5b1032 Merge branch 'empty-writable-dir' into v1.0-errata
28cdbec Clarify behavior of `entryname`
1c57443 Add note that command line arguments must not be shell intepreted except when shellQuote: false.
d0420dd Merge branch 'StarvingMarvin-empty-scatter' into v1.0-errata
f6a71a0 Merge branch 'empty-scatter' of https://github.com/StarvingMarvin/common-workflow-language into StarvingMarvin-empty-scatter
0ad5a58 Merge branch 'shellchar' into v1.0-errata
ab4a189 Merge branch 'michael-kotliar-master' into v1.0-errata
0e225b5 Merge branch 'master' of https://github.com/michael-kotliar/common-workflow-language into michael-kotliar-master
9026a00 Merge branch 'michael-kotliar-static_checker_bug' into v1.0-errata
4294b6d Merge branch 'static_checker_bug' of https://github.com/michael-kotliar/common-workflow-language into michael-kotliar-static_checker_bug
eb12fae Update to v1.0.1 version in text.  Update release notes.
e0bf631 Merge remote-tracking branch 'origin/output-format-fix' into v1.0-errata
444d892 Expanded discussion of File and Directory types.
4a8215c Merge pull request #481 from kapilkd13/container-correction
b8e57da clarify the format field on outputs
a486e91 Add conformance test that files in initialworkdir have $(inputs) in $(outdir).
cb782b7 Merge branch 'undu-basename-fields' into v1.0-errata
8526423 Merge branch 'basename-fields' of https://github.com/undu/common-workflow-language into undu-basename-fields
1166ea4 Clarify interpretation of secondaryFiles on inputs.
c645e3b Add test executing compound document with absolute identifiers.
13f35aa Add clarification about scattering over empty arrays.
1234c09 Update generation of documentation for schema salad.
cc78562 Merge schema salad commit '7ea7dcf92e5782c4aca844f1e98d2d9550e07aae' into v1.0-errata
4e24494 Test that missing parameters are explicitly set to null.
0b31629 Merge branch 'gijzelaerr-recursive_directory' into v1.0-errata
71efb7b Merge branch 'recursive_directory' of https://github.com/gijzelaerr/common-workflow-language
51a5dd6 Test use default value on step input parameter with empty source.
7751643 Conformance tests for default value behavior.
345c449 Clarify that default values apply prior to scattering and evaluating valueFrom.
d200b3f Typo fix EMACScript -> ECMAScript
619314b Clarify that all input parameters must be `null` if not assigned.  Clarify that `default` applies when the paramater value is `null`.
19e53aa List v1.0.1 errata.
0829bd0 Fix mistake in discussion of extracting field names from workflow step ids.
cdc31b5 Add note that writable: true applies recursively.
4afaff7 Add note that files in InitialWorkDir must have path in output directory.
05c11fa Add note that recursive subworkflows is not allowed.
0477abc Bump to version 1.0.1. Add change of treatment `default` field as errata.
e287937 adding docker container: test 52, rev command is not posix compliant
13d31ae adding docker container: test 51, rev command is not posix compliant
c50c150 Merge pull request #480 from kapilkd13/gitattributes
d94a88f adding .fasta file to gitattributes
30bc3d7 Merge pull request #479 from kapilkd13/container-correction
62fac93 Docker container added: test 89 inlinejs.cwl
e18a107 Merge pull request #477 from common-workflow-language/yank-last-draft-ref
9da1f4b Merge pull request #474 from kapilkd13/gitattributes
0d859c8 Merge pull request #478 from common-workflow-language/correct-softreq-usage
68bce59 remove unused test file
a2a8a08 remove last unneeded draft-N ref in v1.0 docs
1c24a42 Merge pull request #469 from common-workflow-language/cwltest-j
b83f419 fix: change nameext test to include the dot
66296ad new: add conformance test for nameroot and nameext
557bd4f Merge pull request #475 from kapilkd13/container-correction
f30c103 adding docker container hint, test 72: stagefile.cwl
739562c adding docker container hint, test 42: search.cwl
68d85c8 adding Docker Container, test 4:cat1-testcli.cwl
3125ddf added docker container, test no 3: tmap-tool.cwl
b1ac8d7 added python conatiner as hints in test 2: binding-test.cwl
d11bf77 adding git attributes file to keep LF line endings for correct sha on windows system instead of CRLF
8f26c9b Merge pull request #460 from common-workflow-language/expr-tests
88df8ef Merge pull request #473 from common-workflow-language/fix-v1.1-path
ef1c87b fix path to conformance tests for optional default File
9e003bc Add support for cwltest -j to run_test.sh
7ea7dcf Merge pull request #118 from common-workflow-language/manu-chroma-patch-1
bde8dfb pin upper version of ruamel.yaml package
4d1c3ff Merge pull request #117 from common-workflow-language/better-bump
a8c3fde oops
b3c579f a better bump of the version (mea culpa)
fa93acc Merge pull request #109 from manu-chroma/modernize
52c054e 3.6 too!
a8903de setup.py: change version, uncomment classifiers for py3
d9bdc8b setup.py: cleanup
7748526 schema.py: fix some types, remove redundant str
b2a5a26 bump ruamel version, put upper bound on ruamel in setup.py
3d60033 mypy_requirements.txt: bump mypy version
a1f697b ref_resolver.py: mypy: use Text instead of unicode
669ebfc remove redundant condition with typing package
6b3d068 typeshed/3: add stubs(autogen) for avro-python3
8672a5c sourceline.py: replace AnyStr with Text type
740e235 mypy: turn off warn for unused ignore in --py3
4f0ad4f tox: separate out mypy targets for py2 and py3
d16c0e5 move cachecontrol stub files to typshed/2and3/
ad05e61 minor changes in rdflib stub files to make them compatible with mypy in py3 mode and move to typshed/2and3/ directory
65e583c mypy: some improvements in type annotations
f051f49 typesheds/2.7: remove stub files which already come with mypy==0.511
1d11190 Makefile: add target for mypy without --py2 flag
c6c88f1 add mypy.ini and ignore all ruamel.yaml package errors
2850043 makedoc.py: pass unicode string mintune markdown function
963ea3f mypy: add typeshed/2and3 in mypypath
62cbece add stub file for mistune package author = "Aleksandr Slepchenkov" email = "Sl.aleksandr28@gmail.com"
4958ebf use Text type where ever Union[str, unicode] is expected
d16a308 mypy: remove redundant ignore type annotations
090c1ba mypy: use latest stable version of mypy - use update ruamel.yaml package which includes more mypy annotations
67d7481 use same import pattern for six.urllib accross the codebase - also, re-ogranise six lib imports
150730c py3 fix: use six StringIO import
0773e44 fix urlparse using six in tests and schema_salad core; no automated fixers
6a11b16 mypy type annotations fix: replace unicode -> Text
8b6f9b3 Apply Python3 modernize transforms
1eb19b6 use typing>=3.5.3
b0b1f14 disable git version tagging to avoid testing conflicts with cwltool
ff000db setup.py: add six as explicit dependency
c66a3f9 tests: remove redundant parentheses in print statements
b1605e3 fix: use six integer_types and string_types in place of int and basestring
29dcb7f tox.ini: fix bugs, enable flake8 linting for all python versions
5efed90 tox.ini: re-write file, include unit tests for all supported versions of python - enable more python3 versions on travis for unit testing
508c8d3 setup.py: bump version to '3.0'
9874d11 use same import pattern for six.urllib accross the codebase - also, re-ogranise six lib imports
d23c804 tests: use assertEqual() inplace assertEquals()
3095597 fix: use six.integer_types to handle int, long incompatibles
965378f .tox.ini: turn on python3 unit testing
7ee4848 .gitignore: add more local folders
4d3c6de fix: use list of dict keys to iterate, fix flake8 warnings - py3 compatibility
916aaa1 py3: use six.moves.urllib instead of urllib
9108c7b fix: minor: py3 compatibility wrt avro
cec0213 setup.py: install different version of avro in case of py3 runtime
3704c98 py3 fix: use six StringIO import
e795ac9 fix: make regex command python3 compatible
b4273f2 fix urlparse using six in tests and schema_salad core; no automated fixers
df685ea modernize tests
e9bb3ec mypy type annotations fix: replace unicode -> Text
3080c69 Apply Python3 modernize transforms
caec629 Merge pull request #116 from manu-chroma/master
5a76bb6 create mypy_requirements.txt for mypy related deps
ba88f5e add mypy, typed-ast dependency in requirements.txt
b61311c Makefile: pin mypy, typed-ast version for jenkins make target
9d9317e Merge pull request #114 from manu-chroma/master
8372fe2 Merge branch 'master' into master
d370602 Merge pull request #115 from common-workflow-language/skip_schemas
e39018a Optional skip_schemas
99eae75 Add conformance test for static_checker
9bcc4f1 Add tests for $(null) and .length on arrays.
961986b cleanup
6a582c3 refactor flatten function. move to utils.py
3bba34e minor refactor: create utils.py
1acdac4 Add test for MultipleInputFeatureRequirement
5b3863a Merge pull request #112 from common-workflow-language/tweak-cov
ffc3367 exclude tests from coverage report
f4fe77f added v1.0 jobs, and fixed v1.1 paths
35dc6c5 spec clarification and tests for empty scatter
fefed51 Merge remote-tracking branch 'upstream/master'
5b0b019 Validation fix.  Must raise exception when raise_ex is true and record class (#107)
424ad78 Fix for self-colliding ids on $import (#102)
8a6eaff Validating Ids for duplicate Issue#56 (#98)
a560ef3 Pass through logger to capture warnings. (#101)
c3cd5b5 Merge remote-tracking branch 'upstream/master'
ca9218e Merge pull request #99 from manu-chroma/master
a63f75f schema_salad/tests: add tests for cli args testing: --version, empty args - fix return condition in main()
04c6784 schema_salad/main.py: --version now correctly prints version
61c2203 Merge pull request #100 from manu-chroma/test_patch
a082ab5 schema_salad/tests: use print() in tests
00ad407 Merge branch 'master' of https://github.com/common-workflow-language/common-workflow-language
0114153 In vocab flag (#97)
39516e5 Add map and typedsl resolution documentation. (#96)
0b76655 Merge pull request #92 from kapilkd13/master
c00ad4c Merge branch 'master' into master
2114715 Merge pull request #93 from common-workflow-language/mypy-0.501
f1d824d Don't switch to mypy v0.501 yet
8ab39f9 Upgrade to mypy v0.501 --strict
4f4fe73 added instalation from source instructions
d2d7b1e added a warning message when error is being ignored
a808742 Add tests that ShellCommandRequirement quote properly.
4573403 Add test to ensure that arguments containing shell directives are not interpreted and that `shellQuote: false` has no effect when ShellCommandRequirement is not in effect.
1e05b44 Set publicID when passing plain data to RDF parser. (#91)
2b98c03 Test case for creating empty writable directory using InitialWorkDirRequirement
15c0ab8 Relax strict checking foreign properties (#90)
3a7cf29 Merge pull request #89 from tjelvar-olsson/master
f16c1a8 Add more directory fallbacks Loader session
50d0361 Make ref_resolver.Loader more fault tolerant
7522a24 Make split_frag optional in converting fileuri. (#88)
d736a0e capture stdout and write to file
c9fd6b9 write test result to file
878a74f Merge pull request #87 from common-workflow-language/release-update
6209496 newer pip dependency
05b82f1 add link and writable check
0347b8e Merge pull request #85 from chapmanb/debug-fixes
5c4ef60 Merge branch 'master' into debug-fixes
286001f Merge pull request #86 from common-workflow-language/mypy-470
9676ea8 track mypy rename
e47f4e6 Improve debugging: missing filename and bad lists
2c6f26b implement feedback
e334b74 first try
bee8bf1 Merge pull request #84 from common-workflow-language/mypy0.470
822c8c1 upgrade to mypy 0.470
42f4bdd Fix performance regression in schema loading by stripping ruamel.yaml metadata, (#83)
d21fa84 Expand uris in $schemas in resolve_all(). (#82)
55018dd Bump version to 2.2 (#81)
b883526 Bugfix to uri_file_path. (#80)
0c7cc02 Remove pathlib2 because it is only used for one thing but creates dependency issues. (#79)
f31369c Merge pull request #78 from common-workflow-language/explict-include
f34d4ac explicitly include MD files & fix release test
c1cf3e9 Merge pull request #77 from common-workflow-language/simplify-manifest
a2e4236 simply the manifest
5d04ddb Merge pull request #76 from common-workflow-language/ensure-test-paths
a37b623 ensure all test data is loaded flexibly
6a02920 Merge pull request #75 from common-workflow-language/adjust-manifest
cefb22e Merge branch 'master' into adjust-manifest
dd496a1 Include all relevant files so tests work post installation
8edfbc2 Bugfix resolving references to document fragments. (#74)
a3ba891 Relax ruamel.yaml version pin. (#73)
a5bbb36 Ensure keys are sorted when generated CommentedMap from a regular dict. (#72)
ebdf27d Merge pull request #71 from common-workflow-language/pip-conflict-checker
2aecb05 Merge branch 'master' into pip-conflict-checker
999d689 Merge pull request #70 from psafont/win32
01af23d Fix typing
7a793ac drop html5lib pin, add pip-conflict-check
0e616d1 Fix types
ad742f3 Manage pathlib and pathlib2 for all python versions
cb754df Make url2pathname args compatible with python3
da751f7 Don't assume the type of ref
f302f5f Fix a couple of test cases
0c0e4cc Added pathlib2 requirement
159541c Paths and URIs conversions are more generalized
9a9d639 Tweak cmap to better propagate filename down. (#69)
5a15c58 merge 1.21 changes into salad 2.0 (#68)
a1db0ac Merge pull request #67 from common-workflow-language/mr-c-patch-1
56ac12b Link to v1.0 specs
beed46d Merge pull request #65 from common-workflow-language/mobile-friendly
1e0f6a5 set the meta viewport tag
f0b88d0 Bump major version number, because of backwards-incompatible changes. (#63)
8ac4540 Provide line numbers in error messages (#62)
c045684 make example IRIs links; update v1.1 text
419fed3 link to IRI wikipage; update example modules IRI.
68c53bf Clarify SoftwareRequirement spec fields
8454546 Bugfix for validating "class" field. (#61)
01dd303 Optimize validate (#60)
423e48b Merge pull request #58 from common-workflow-language/quiet-external-schema
f2d86c1 Merge branch 'master' into quiet-external-schema
f6744ad Merge pull request #53 from common-workflow-language/check-file-support-http
1728fd4 fix types
823f378 Merge remote-tracking branch 'origin/master' into check-file-support-http
9b6a6be demote log about external schema
b1d7b69 Support http/https existence check (using HTTP HEAD) in check_file.

git-subtree-dir: cwltool/schemas
git-subtree-split: 0d75172ee6e5951dda7a3f8b5d84eb8f9749c9a5

tetron added a commit that referenced this pull request Apr 16, 2018

Squashed 'cwltool/schemas/' changes from 0f28896..721aa892
721aa892 Remove "Workspace", "BatchQueue" and "acceptList" based on feedback.
146f545d be more precise and use a briefer name
4a36b4b7 Add Workspace, TimeLimit, BatchQueue, WorkReuse and NetworkAccess to schema.
46091d30 Merge pull request #665 from common-workflow-language/new_rabix_lead
eebceefd Update to the new Rabix lead
f96bca69 Merge pull request #633 from wtsi-hgi/parameter-like-reference-parsing
e1308521 Merge pull request #624 from common-workflow-language/new-test/trailing-newline
46b40226 Merge pull request #660 from common-workflow-language/v1.1.0-fix-wf-bindings
9f979e91 break out Changlogs into seperate sections and cross-link them.
e7b87b5e descriptions for {in,out}putBinding
c30b27a1 diverse CLT changelog updates
566a735c Changelog: the `doc` field may be an array of strings.
ea9faa89 Fix userguide.  Fix schema table of contents ordering (a bit).
0bc210a9 sync some fixes
28218d9f Fix doc for CommandInputParameter.inputBinding
c373b9fc Be more specific that loadContents in inputBinding (and inputBinding on WorkflowInputParameter) will go away in v2.0
1646a398 Merge pull request #659 from common-workflow-language/cern
40086a12 Add CommandLineBindable
2bf64e89 Add inputBinding to CommandInputRecordField.
e1e3cc1a Add Tibor Simko; CERN
dfdb1467 Merge pull request #656 from common-workflow-language/mr-c-patch-1
9cb8f9c8 Revert accidental change
f9d95cbd Refactor loadContents to be available on InputParameter, WorkflowStepInput, CommandOutputBinding.  Note that InputBinding on WorkflowInputParameter is deprecated.  Add conformance tests.
d6780795 More cleanup to deprecate inputBinding and remove outputBinding from Workflow parameters.
e1091653 Merge commit '9c21375acac04407b672f3e3c55e5ea7eca0b591' into v1.1.0-fix-wf-bindings
9c21375a Squashed 'v1.1.0-dev1/salad/' changes from 98a5bea..27c20e8
2346c52d Deprecate inputBinding from Workflow and ExpressionTool
9cb4d3c2 Merge pull request #636 from common-workflow-language/v1.1.0-wip
e86e8e5b Refactor 'format' field so array can only be used to describe input, not output.
1ab449b0 * Add negative conformance tests for file format checking.
0e98c3d4 Added changelog summary for changes so far in this branch.
0313fae2 Add test format field on output.
26482cc7 Add 'doc' field to InputSchema
b38788cb Add doc field to record
2f8906d1 Conformance tests for secondaryFiles on input and output record fields.
54ef74ee Conformance tests for secondaryFiles on record fields.
42132253 Merge pull request #278 from common-workflow-language/v1.0-cwl-runner-proposal
c055af45 Fix site generation
ca7cba78 rename conflicting steps
836187e9 drop --user from Travis
9b111b59 misc
53ad516b Restore stdin shortcut test.
4e307e36 Sync with v1.0 tests
aee2fbbe Refactor to fix secondaryFiles on record fields, consolidate fields, use new subscope feature.
53b626aa Spec clarification for #331
064f8bff Add explicit defaults for some fields.
8d96c02c Synchronize with v1.0.2
78efaef7 Merge remote-tracking branch 'origin/master' into v1.0-cwl-runner-proposal
370c52fc document output format
6178438c Merge pull request #635 from common-workflow-language/categorize_tests
3d4893e0 tag the tests
e239d5b8 Merge pull request #647 from common-workflow-language/dnanexus
81f1bb98 Add Geet's ORCID
5d980b1f Add DNAnexus to supporting organizations list
1b71ddc7 Merge pull request #646 from wtsi-hgi/array-of-strings-job-files-input
ebd63119 Make array-of-strings-job.yml take in an array of files
83650a5b Merge pull request #645 from common-workflow-language/fix_run_test_help
83e899d9 fix help formatting
0ca7e798 Merge pull request #642 from common-workflow-language/IBM
839ec690 Add IBM to the supporting organizations list
47fe0f2c Merge pull request #639 from common-workflow-language/enhancement/test-dyn-iwdr
cfbc7b8e Merge pull request #638 from common-workflow-language/fix/valuefrom-constant
9c2c4fee Do not assume output file is present in dynamic iwdr test
89b2b782 Add DockerRequirement for `python` command in valueFrom-constant.cwl
000a889d Merge pull request #623 from common-workflow-language/new-test/valuefrom-constant
b5f0f5b7 Merge pull request #625 from common-workflow-language/new-test/any-compatibility
fb520d21 Merge pull request #612 from common-workflow-language/multInpReq
76b9b775 Merge pull request #620 from common-workflow-language/new-test/empty-array-input
155fdc45 Merge pull request #634 from common-workflow-language/new-test/concat-vf
6bb22505 Merge branch 'master' of github.com:common-workflow-language/common-workflow-language into new-test/valuefrom-constant
06c54e04 copy test for empty array input to v1.0
ec9cf54d Add test for empty array input
068c1ad5 Merge pull request #611 from common-workflow-language/step-level-resourcereq-test
f734e8d1 remove unneeded linkMerge to match Rabix behaviour
e8d3f6ae Merge branch 'master' of github.com:common-workflow-language/common-workflow-language into step-level-resourcereq-test
57e2a0ec Remove reference to parameter-reference.cwl
3128b673 Move parameter-reference test to inline-js
602e077f Add prefix to parameter-reference
a4b1bf84 Add test for two concatenated expressions in valueFrom
36644bc7 Add output to parameter-reference.cwl conformance test
98f62660 change parameter-reference type from string to boolean
ad3c1640 Conformance test for parameter-reference-like javascript
c101119a Merge pull request #626 from common-workflow-language/workflow_with_dynreq
af9e0736 Merge branch 'master' into workflow_with_dynreq
06cd7d33 Merge pull request #628 from common-workflow-language/exit_code_tests
791886b8 don't use path for false
8d2a2977 test for alternative success exit codes
9c398386 test having a dynamics resoure requirement as part of a workflow
e22e0523 Testing Any type compatibility in outputSource
16456581 add version
4e2a75fb Add test for trailing whitespace in file entries of InitialWorkDir
ffe52883 Add test for valueFrom with constant value overriding array inputs
91f108df Merge pull request #618 from common-workflow-language/test_with_classname
63dbb6d3 explain EXTRA
a33e9eee Merge pull request #607 from common-workflow-language/clarify_basename-fields-job.yml
31c68fde fix non v1.0 testing
e7a3e568 Merge branch 'master' into step-level-resourcereq-test
2889ba91 Add test for step-level ResourceRequirement for v1.0
1ea31342 Allow passing --classname to cwltest, improve --help
a8728791 Merge pull request #615 from common-workflow-language/avoid_unstrictjs
56776751 Merge pull request #610 from common-workflow-language/boolean-empty-inputbinding-test
e9d559bc Merge branch 'master' into boolean-empty-inputbinding-test
e21ee6ee Merge pull request #616 from common-workflow-language/new-test/staging-optional-file
b9c52371 Merge pull request #613 from common-workflow-language/wc-test-portability
8b4e1eb7 Merge pull request #614 from common-workflow-language/staging-writable-dir
74261a6d Test for expression engine with self reference to null input
e14a5d29 Add test for empty not-null boolean inputBinding
c0984113 Add test for MultipleInputFeatureReq if source is a single-item list
ecd8e2bd Ensure the staged directory is writable
62f74816 modify template use to avoid with(), which violates strict mode
619fdad9 Add test for staging a writable directory inside Docker
2141724c Replace `wc` with `cat` for test of command execution with standard streams redirection
42d37d04 Add test for step-level ResourceRequirement
9c34c2a5 Update basename-fields-job.yml
c93718d6 fix travis
8f5e8523 Merge remote-tracking branch 'origin/master' into v1.0-cwl-runner-proposal
3b747ab9 Merge pull request #601 from common-workflow-language/hmenager-patch-1
4a0a558c Merge pull request #603 from cjfields/patch-1
e0309c49 Add PBS/Torque support for Toil
7b831fe0 Merge pull request #602 from common-workflow-language/cwl-emacs
0bff6183 Add links to blog post about cwl-emacs
89b5390d correct typo in travis file
103006b3 Merge pull request #598 from mdmiller53/patch-2
7b7ea1cf Update README.md
35a371d7 Merge pull request #594 from common-workflow-language/recursive-input-directory-test-fix
49b503ca basename not required to be in output
2a393205 Merge pull request #589 from common-workflow-language/nested-dir-test-fix
b3b9d1f5 Fix conformance test, directory needs to be marked writable in order to write to it!
2ee358c7 Merge pull request #580 from common-workflow-language/cease_building_old_userguide
85009292 Merge pull request #586 from common-workflow-language/cwl_output_singular
10a3ddf0 cwl.output.json is singular
0814764e Merge pull request #585 from bmeg/workflow-default
d728efde Adding conformance test for #592
cd93e026 stop building old user guide
c4a3085f Merge pull request #578 from common-workflow-language/cromwell_ci
1ad1276e link to CI testing of Cromwell
77ef9829 Merge pull request #570 from common-workflow-language/IWDR_nested
74d6f3a5 Test InitialWorkDirRequirement with a nested directory structure from another step
c2489659 Merge pull request #577 from common-workflow-language/test_glob_order
9111c888 Merge pull request #557 from otiai10/master
739d3d6d Merge pull request #576 from common-workflow-language/biostars_tag
1687baae fix capitalization of 'post'
daca82a1 Merge pull request #574 from common-workflow-language/citation_update
8ca65e26 test for POSIX glob behavior
ea485c46 Explicitly link to the Biostars post form
fb4f92fe synchronize with http://www.commonwl.org/#Citation
1fe86e5b Merge pull request #573 from common-workflow-language/reana
41a69b2c Add REANA to the list
dd0813f3 CWL files under `v1.0/examples` are no longer to be tested
97173a98 Merge pull request #542 from common-workflow-language/mr-c-patch-1
504fb7e3 Merge pull request #544 from common-workflow-language/jp_link
97c7e362 clarify JP link
7a7d27a7 Merge pull request #549 from common-workflow-language/embl_abr
53c52230 Merge pull request #567 from common-workflow-language/intelliJ
95fcd1df Correct links to IntelliJ/JetBrains CWL plugin
3e98cab3 Merge pull request #560 from common-workflow-language/mv_Hello
9ccd71c9 Move Hell.java
8b99a846 Merge pull request #558 from manabuishii/move_test_files
915d49f8 Move files under v1.0/ for conformance test
fcb4ed86 re-arrange
c6e3f151 Add status badge of itself
21de641b Test myself by using schema_salad
c888cb48 Add EMBL-ABR
a83ab96d Merge pull request #548 from otiai10/master
4e28adab Enable testing without cd to the repository
7bd0d7ea Add JP link
6d77fa69 Removed extraneous baseCommand
d126e152 Merge pull request #536 from common-workflow-language/mr-c-patch-1
702afe31 Merge pull request #539 from stellargo/patch-1
b04007b2 remove link to user guide, add link to stable ver.
2482b66f draft-3/README.md: Link address changed
6bc4368c Clarify citation, link to citeulike
c6bc1288 Merge pull request #535 from common-workflow-language/remove_draft3_userguide
26d650b8 Remove draft-3 userguide and link to the new URL
ffe182e8 Merge pull request #534 from common-workflow-language/cwl-software
8433a910 Prepopulate github/google links with search query
d08e37b2 Add tricks for searching Github / Google for CWL.
b49f7bc4 Merge pull request #533 from common-workflow-language/cwl-software
af2eedb7 Remove language column whoops
d5125033 remove spurious [
b6e47a23 Remove 'language' column.  Make explicit SDK section.
811deca0 Fix links
bfdde7ff Swap columns
6a91db53 Separate language/platform support columns.
96a0c9ae Add note about github searching trick.  Add yacle and cerise.
eb1e0cdc Add Cromwell, CWL libraries for various languages.
f2031e4a Update and rearrange software section
612414eb Merge pull request #528 from cure/master
43d67d0d Run all v1.0 tests that use a Debian Docker image with the debian:stretch-slim image instead of a debian:8 or debian:wheezy.
0c8f9ddf Merge pull request #524 from jmchilton/fix_dir3
8b0a8905 Merge pull request #526 from tom-tan/fix-typo
33603758 Fix indent in the example of stdout
92ee6abc Merge pull request #512 from common-workflow-language/update_contribs
2100e7f6 Fix doc for dir3.cwl test.
0e1ac178 Merge pull request #520 from michael-kotliar/master
9cbe3743 Update link for Airflow
55208187 Merge pull request #509 from common-workflow-language/typo42
a66b295b ORCID for John Kern
01fc1084 ORCIDs: Josh Randall, Mark Robinson, & Tom Morris
51a5b048 add Marc Fiume's ORCID; https for orcid.org links
f253f3a2 ORCIDs for Ward & James
a3e9d38c Merge pull request #511 from common-workflow-language/link_new_userguide
ca83f2d6 ORCID for Gaurav
e3862128 add CWL advisors, leadership team, some ORCIDS
813bf044 remove old user guide, link to the new one
d53c4983 XDF_DATA_HOME -> XD**G**_DATA_HOME
1eb152b4 Merge pull request #508 from common-workflow-language/full-citation
f7be9835 Provide full citation details
76bd4fd4 Merge pull request #506 from common-workflow-language/broken-valueFrom
67567438 Fix merge conflict.
15252f40 Merge pull request #507 from common-workflow-language/literal-without-docker
18e902ac remove Docker mention in docstring
c04b2c6f Test file literal as input without Docker
e2fa9668 Merge pull request #505 from common-workflow-language/broken-valueFrom
9c0d75bc Add conformance test for valueFrom on a scatter parameter, from https://github.com/dleehr/broken-valueFrom
165b5130 Merge pull request #503 from mccalluc/patch-1
e142260c missing back-tick causes misformatting
7f510ec7 Merge pull request #498 from common-workflow-language/no-location-secondary
67b4d608 Merge pull request #499 from common-workflow-language/fix-dynresreq
5351b234 Tweak dynresreq test, remove 'basename' check and remove newline from special_file.
ba99368e Bump couple additional references to v1.0.2
08c09893 Merge pull request #496 from common-workflow-language/no-location-secondary
d7732801 Merge pull request #497 from common-workflow-language/dynresreqs
e1ab24bc test for dyn res reqs
e9a869f2 Bump spec to v1.0.2.  Expand secondaryFile tests to include expressions returning lists and directories in secondaryFiles.
66ef5a09 Fix conformance test entry.
1ed4f764 Specify that nameroot and nameext must be present for secondaryFile eval as well.
28ce0407 Update spec.
95001104 Revise secondaryFile conformance test to use basename and path instead of location.
6732dafb Merge remote-tracking branch 'origin/master' into v1.0-cwl-runner-proposal
ffd2dbf Merge pull request #487 from common-workflow-language/1.0.1-text
6a28a1a Update text to v1.0.1.
2674c57 Merge pull request #410 from common-workflow-language/v1.0-errata
351d032 Merge remote-tracking branch 'origin/clarify-package' into v1.0-errata
a4e9eb6 Adjust core request in bwa command line test from 4 to 2.
a5b1032 Merge branch 'empty-writable-dir' into v1.0-errata
28cdbec Clarify behavior of `entryname`
1c57443 Add note that command line arguments must not be shell intepreted except when shellQuote: false.
d0420dd Merge branch 'StarvingMarvin-empty-scatter' into v1.0-errata
f6a71a0 Merge branch 'empty-scatter' of https://github.com/StarvingMarvin/common-workflow-language into StarvingMarvin-empty-scatter
0ad5a58 Merge branch 'shellchar' into v1.0-errata
ab4a189 Merge branch 'michael-kotliar-master' into v1.0-errata
0e225b5 Merge branch 'master' of https://github.com/michael-kotliar/common-workflow-language into michael-kotliar-master
9026a00 Merge branch 'michael-kotliar-static_checker_bug' into v1.0-errata
4294b6d Merge branch 'static_checker_bug' of https://github.com/michael-kotliar/common-workflow-language into michael-kotliar-static_checker_bug
eb12fae Update to v1.0.1 version in text.  Update release notes.
e0bf631 Merge remote-tracking branch 'origin/output-format-fix' into v1.0-errata
444d892 Expanded discussion of File and Directory types.
4a8215c Merge pull request #481 from kapilkd13/container-correction
b8e57da clarify the format field on outputs
a486e91 Add conformance test that files in initialworkdir have $(inputs) in $(outdir).
cb782b7 Merge branch 'undu-basename-fields' into v1.0-errata
8526423 Merge branch 'basename-fields' of https://github.com/undu/common-workflow-language into undu-basename-fields
1166ea4 Clarify interpretation of secondaryFiles on inputs.
c645e3b Add test executing compound document with absolute identifiers.
13f35aa Add clarification about scattering over empty arrays.
1234c09 Update generation of documentation for schema salad.
cc78562 Merge schema salad commit '7ea7dcf92e5782c4aca844f1e98d2d9550e07aae' into v1.0-errata
4e24494 Test that missing parameters are explicitly set to null.
0b31629 Merge branch 'gijzelaerr-recursive_directory' into v1.0-errata
71efb7b Merge branch 'recursive_directory' of https://github.com/gijzelaerr/common-workflow-language
51a5dd6 Test use default value on step input parameter with empty source.
7751643 Conformance tests for default value behavior.
345c449 Clarify that default values apply prior to scattering and evaluating valueFrom.
d200b3f Typo fix EMACScript -> ECMAScript
619314b Clarify that all input parameters must be `null` if not assigned.  Clarify that `default` applies when the paramater value is `null`.
19e53aa List v1.0.1 errata.
0829bd0 Fix mistake in discussion of extracting field names from workflow step ids.
cdc31b5 Add note that writable: true applies recursively.
4afaff7 Add note that files in InitialWorkDir must have path in output directory.
05c11fa Add note that recursive subworkflows is not allowed.
0477abc Bump to version 1.0.1. Add change of treatment `default` field as errata.
e287937 adding docker container: test 52, rev command is not posix compliant
13d31ae adding docker container: test 51, rev command is not posix compliant
c50c150 Merge pull request #480 from kapilkd13/gitattributes
d94a88f adding .fasta file to gitattributes
30bc3d7 Merge pull request #479 from kapilkd13/container-correction
62fac93 Docker container added: test 89 inlinejs.cwl
e18a107 Merge pull request #477 from common-workflow-language/yank-last-draft-ref
9da1f4b Merge pull request #474 from kapilkd13/gitattributes
0d859c8 Merge pull request #478 from common-workflow-language/correct-softreq-usage
68bce59 remove unused test file
a2a8a08 remove last unneeded draft-N ref in v1.0 docs
1c24a42 Merge pull request #469 from common-workflow-language/cwltest-j
b83f419 fix: change nameext test to include the dot
66296ad new: add conformance test for nameroot and nameext
557bd4f Merge pull request #475 from kapilkd13/container-correction
f30c103 adding docker container hint, test 72: stagefile.cwl
739562c adding docker container hint, test 42: search.cwl
68d85c8 adding Docker Container, test 4:cat1-testcli.cwl
3125ddf added docker container, test no 3: tmap-tool.cwl
b1ac8d7 added python conatiner as hints in test 2: binding-test.cwl
d11bf77 adding git attributes file to keep LF line endings for correct sha on windows system instead of CRLF
8f26c9b Merge pull request #460 from common-workflow-language/expr-tests
88df8ef Merge pull request #473 from common-workflow-language/fix-v1.1-path
ef1c87b fix path to conformance tests for optional default File
9e003bc Add support for cwltest -j to run_test.sh
7ea7dcf Merge pull request #118 from common-workflow-language/manu-chroma-patch-1
bde8dfb pin upper version of ruamel.yaml package
4d1c3ff Merge pull request #117 from common-workflow-language/better-bump
a8c3fde oops
b3c579f a better bump of the version (mea culpa)
fa93acc Merge pull request #109 from manu-chroma/modernize
52c054e 3.6 too!
a8903de setup.py: change version, uncomment classifiers for py3
d9bdc8b setup.py: cleanup
7748526 schema.py: fix some types, remove redundant str
b2a5a26 bump ruamel version, put upper bound on ruamel in setup.py
3d60033 mypy_requirements.txt: bump mypy version
a1f697b ref_resolver.py: mypy: use Text instead of unicode
669ebfc remove redundant condition with typing package
6b3d068 typeshed/3: add stubs(autogen) for avro-python3
8672a5c sourceline.py: replace AnyStr with Text type
740e235 mypy: turn off warn for unused ignore in --py3
4f0ad4f tox: separate out mypy targets for py2 and py3
d16c0e5 move cachecontrol stub files to typshed/2and3/
ad05e61 minor changes in rdflib stub files to make them compatible with mypy in py3 mode and move to typshed/2and3/ directory
65e583c mypy: some improvements in type annotations
f051f49 typesheds/2.7: remove stub files which already come with mypy==0.511
1d11190 Makefile: add target for mypy without --py2 flag
c6c88f1 add mypy.ini and ignore all ruamel.yaml package errors
2850043 makedoc.py: pass unicode string mintune markdown function
963ea3f mypy: add typeshed/2and3 in mypypath
62cbece add stub file for mistune package author = "Aleksandr Slepchenkov" email = "Sl.aleksandr28@gmail.com"
4958ebf use Text type where ever Union[str, unicode] is expected
d16a308 mypy: remove redundant ignore type annotations
090c1ba mypy: use latest stable version of mypy - use update ruamel.yaml package which includes more mypy annotations
67d7481 use same import pattern for six.urllib accross the codebase - also, re-ogranise six lib imports
150730c py3 fix: use six StringIO import
0773e44 fix urlparse using six in tests and schema_salad core; no automated fixers
6a11b16 mypy type annotations fix: replace unicode -> Text
8b6f9b3 Apply Python3 modernize transforms
1eb19b6 use typing>=3.5.3
b0b1f14 disable git version tagging to avoid testing conflicts with cwltool
ff000db setup.py: add six as explicit dependency
c66a3f9 tests: remove redundant parentheses in print statements
b1605e3 fix: use six integer_types and string_types in place of int and basestring
29dcb7f tox.ini: fix bugs, enable flake8 linting for all python versions
5efed90 tox.ini: re-write file, include unit tests for all supported versions of python - enable more python3 versions on travis for unit testing
508c8d3 setup.py: bump version to '3.0'
9874d11 use same import pattern for six.urllib accross the codebase - also, re-ogranise six lib imports
d23c804 tests: use assertEqual() inplace assertEquals()
3095597 fix: use six.integer_types to handle int, long incompatibles
965378f .tox.ini: turn on python3 unit testing
7ee4848 .gitignore: add more local folders
4d3c6de fix: use list of dict keys to iterate, fix flake8 warnings - py3 compatibility
916aaa1 py3: use six.moves.urllib instead of urllib
9108c7b fix: minor: py3 compatibility wrt avro
cec0213 setup.py: install different version of avro in case of py3 runtime
3704c98 py3 fix: use six StringIO import
e795ac9 fix: make regex command python3 compatible
b4273f2 fix urlparse using six in tests and schema_salad core; no automated fixers
df685ea modernize tests
e9bb3ec mypy type annotations fix: replace unicode -> Text
3080c69 Apply Python3 modernize transforms
caec629 Merge pull request #116 from manu-chroma/master
5a76bb6 create mypy_requirements.txt for mypy related deps
ba88f5e add mypy, typed-ast dependency in requirements.txt
b61311c Makefile: pin mypy, typed-ast version for jenkins make target
9d9317e Merge pull request #114 from manu-chroma/master
8372fe2 Merge branch 'master' into master
d370602 Merge pull request #115 from common-workflow-language/skip_schemas
e39018a Optional skip_schemas
99eae75 Add conformance test for static_checker
9bcc4f1 Add tests for $(null) and .length on arrays.
961986b cleanup
6a582c3 refactor flatten function. move to utils.py
3bba34e minor refactor: create utils.py
1acdac4 Add test for MultipleInputFeatureRequirement
5b3863a Merge pull request #112 from common-workflow-language/tweak-cov
ffc3367 exclude tests from coverage report
f4fe77f added v1.0 jobs, and fixed v1.1 paths
35dc6c5 spec clarification and tests for empty scatter
fefed51 Merge remote-tracking branch 'upstream/master'
5b0b019 Validation fix.  Must raise exception when raise_ex is true and record class (#107)
424ad78 Fix for self-colliding ids on $import (#102)
8a6eaff Validating Ids for duplicate Issue#56 (#98)
a560ef3 Pass through logger to capture warnings. (#101)
c3cd5b5 Merge remote-tracking branch 'upstream/master'
ca9218e Merge pull request #99 from manu-chroma/master
a63f75f schema_salad/tests: add tests for cli args testing: --version, empty args - fix return condition in main()
04c6784 schema_salad/main.py: --version now correctly prints version
61c2203 Merge pull request #100 from manu-chroma/test_patch
a082ab5 schema_salad/tests: use print() in tests
00ad407 Merge branch 'master' of https://github.com/common-workflow-language/common-workflow-language
0114153 In vocab flag (#97)
39516e5 Add map and typedsl resolution documentation. (#96)
0b76655 Merge pull request #92 from kapilkd13/master
c00ad4c Merge branch 'master' into master
2114715 Merge pull request #93 from common-workflow-language/mypy-0.501
f1d824d Don't switch to mypy v0.501 yet
8ab39f9 Upgrade to mypy v0.501 --strict
4f4fe73 added instalation from source instructions
d2d7b1e added a warning message when error is being ignored
a808742 Add tests that ShellCommandRequirement quote properly.
4573403 Add test to ensure that arguments containing shell directives are not interpreted and that `shellQuote: false` has no effect when ShellCommandRequirement is not in effect.
1e05b44 Set publicID when passing plain data to RDF parser. (#91)
2b98c03 Test case for creating empty writable directory using InitialWorkDirRequirement
15c0ab8 Relax strict checking foreign properties (#90)
3a7cf29 Merge pull request #89 from tjelvar-olsson/master
f16c1a8 Add more directory fallbacks Loader session
50d0361 Make ref_resolver.Loader more fault tolerant
7522a24 Make split_frag optional in converting fileuri. (#88)
d736a0e capture stdout and write to file
c9fd6b9 write test result to file
878a74f Merge pull request #87 from common-workflow-language/release-update
6209496 newer pip dependency
05b82f1 add link and writable check
0347b8e Merge pull request #85 from chapmanb/debug-fixes
5c4ef60 Merge branch 'master' into debug-fixes
286001f Merge pull request #86 from common-workflow-language/mypy-470
9676ea8 track mypy rename
e47f4e6 Improve debugging: missing filename and bad lists
2c6f26b implement feedback
e334b74 first try
bee8bf1 Merge pull request #84 from common-workflow-language/mypy0.470
822c8c1 upgrade to mypy 0.470
42f4bdd Fix performance regression in schema loading by stripping ruamel.yaml metadata, (#83)
d21fa84 Expand uris in $schemas in resolve_all(). (#82)
55018dd Bump version to 2.2 (#81)
b883526 Bugfix to uri_file_path. (#80)
0c7cc02 Remove pathlib2 because it is only used for one thing but creates dependency issues. (#79)
f31369c Merge pull request #78 from common-workflow-language/explict-include
f34d4ac explicitly include MD files & fix release test
c1cf3e9 Merge pull request #77 from common-workflow-language/simplify-manifest
a2e4236 simply the manifest
5d04ddb Merge pull request #76 from common-workflow-language/ensure-test-paths
a37b623 ensure all test data is loaded flexibly
6a02920 Merge pull request #75 from common-workflow-language/adjust-manifest
cefb22e Merge branch 'master' into adjust-manifest
dd496a1 Include all relevant files so tests work post installation
8edfbc2 Bugfix resolving references to document fragments. (#74)
a3ba891 Relax ruamel.yaml version pin. (#73)
a5bbb36 Ensure keys are sorted when generated CommentedMap from a regular dict. (#72)
ebdf27d Merge pull request #71 from common-workflow-language/pip-conflict-checker
2aecb05 Merge branch 'master' into pip-conflict-checker
999d689 Merge pull request #70 from psafont/win32
01af23d Fix typing
7a793ac drop html5lib pin, add pip-conflict-check
0e616d1 Fix types
ad742f3 Manage pathlib and pathlib2 for all python versions
cb754df Make url2pathname args compatible with python3
da751f7 Don't assume the type of ref
f302f5f Fix a couple of test cases
0c0e4cc Added pathlib2 requirement
159541c Paths and URIs conversions are more generalized
9a9d639 Tweak cmap to better propagate filename down. (#69)
5a15c58 merge 1.21 changes into salad 2.0 (#68)
a1db0ac Merge pull request #67 from common-workflow-language/mr-c-patch-1
56ac12b Link to v1.0 specs
beed46d Merge pull request #65 from common-workflow-language/mobile-friendly
1e0f6a5 set the meta viewport tag
f0b88d0 Bump major version number, because of backwards-incompatible changes. (#63)
8ac4540 Provide line numbers in error messages (#62)
c045684 make example IRIs links; update v1.1 text
419fed3 link to IRI wikipage; update example modules IRI.
68c53bf Clarify SoftwareRequirement spec fields
c2383bbd attempt at shipping cwl-runner.cwl
8454546 Bugfix for validating "class" field. (#61)
01dd303 Optimize validate (#60)
5a218794 rename toolfile to processfile & clarify
24dff784 clarify meaning of stdout, stderr
4a420989 drop implementation specific options
70d3543e add error code for unimplemented features
003fd482 drop conformance & basedir, clarify stdout
824c7057 add v1.0 cwl-runner interface
423e48b Merge pull request #58 from common-workflow-language/quiet-external-schema
f2d86c1 Merge branch 'master' into quiet-external-schema
f6744ad Merge pull request #53 from common-workflow-language/check-file-support-http
1728fd4 fix types
823f378 Merge remote-tracking branch 'origin/master' into check-file-support-http
9b6a6be demote log about external schema
b1d7b69 Support http/https existence check (using HTTP HEAD) in check_file.

git-subtree-dir: cwltool/schemas
git-subtree-split: 721aa89275b3e5f09354b7926f8cb6291c3d834e
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