Code

1.2.1 proposed#115

Code

Merged

mr-c merged 129 commits intomaincommon-workflow-language/cwl-v1.2:mainfrom 1.2.1_proposedcommon-workflow-language/cwl-v1.2:1.2.1_proposedCopy head branch name to clipboardJan 3, 2024

+6,757-58,689

Commits

Commits on Oct 9, 2021

• all Requirement classes should be static strings

  mr-c

  committed
  7b4b85e

  Copy full SHA for 7b4b85e

• all Process classes should also be static strings

  mr-c

  committed
  74b3ff4

  Copy full SHA for 74b3ff4

• More defaults (#68)

  Show description for 48475cd
  mr-c

  committed
  48475cd

  Copy full SHA for 48475cd

• Update cwloutput-nolimit.cwl

  mr-c

  committed
  596e811

  Copy full SHA for 596e811

• metaschema: clean up & sync

  mr-c

  committed
  9939cde

  Copy full SHA for 9939cde

• fix formatting of SecondaryFileSchema.pattern

  mr-c

  committed
  4e7b6bd

  Copy full SHA for 4e7b6bd

• explicitly allow an int where we allow a long

  mr-c

  committed
  f44d7c3

  Copy full SHA for f44d7c3

• metaschema: clean up & sync

  mr-c

  committed
  c4ebcec

  Copy full SHA for c4ebcec

• Clarify $() and ${}

  

  kinow

  authored and

  mr-c

  committed
  0eca666

  Copy full SHA for 0eca666

• Fewer containers (#129)

  Show description for 13ea3d1
  mr-c

  committed
  13ea3d1

  Copy full SHA for 13ea3d1

• Adjust behavior of command_input_file_expression (#128)

  Show description for 3b85afc
  

  tetron

  and

  mr-c

  committed
  3b85afc

  Copy full SHA for 3b85afc

• CI: less checks

  mr-c

  committed
  ed8b990

  Copy full SHA for ed8b990

• List who the publisher is

  mr-c

  committed
  0af8fc9

  Copy full SHA for 0af8fc9

Commits on Oct 10, 2021

• Update README.md

  mr-c

  authored
  de4177e

  Copy full SHA for de4177e

Commits on Oct 28, 2021

• Fix typo in SchemaDefRequirement section

  

  kinow

  authored and

  mr-c

  committed
  f97fb94

  Copy full SHA for f97fb94

• CI: add pycodegen extra to schema-salad

  mr-c

  committed
  beb4cb6

  Copy full SHA for beb4cb6

Commits on Nov 22, 2021

• Fix typo: $schema to $schemas

  

  tom-tan

  authored and

  mr-c

  committed
  8615de9

  Copy full SHA for 8615de9

Commits on Nov 26, 2021

• Clarify parameter reference: null and array length (#64)

  Show description for 236af6f
  pvanheus

  authored
  236af6f

  Copy full SHA for 236af6f

Commits on Nov 30, 2021

• Environement → Environment

  mr-c

  authored
  f7b9740

  Copy full SHA for f7b9740

Commits on Dec 6, 2021

• Confirm that File.size is in bytes

  Show description for 381302c
  mr-c

  authored
  381302c

  Copy full SHA for 381302c

Commits on Dec 10, 2021

• Test for literal directory with literal subdirectory.

  Show description for 60a9635
  mr-c

  committed
  60a9635

  Copy full SHA for 60a9635

Commits on Dec 23, 2021

• File.location: fix formatting of schemas

  mr-c

  committed
  130516a

  Copy full SHA for 130516a

• Test that colons are allowed in several places

  mr-c

  committed
  c0c31c5

  Copy full SHA for c0c31c5

Commits on Jan 25, 2022

• make workflow output types optional; addresses #146, #147 (#149)

  Show description for 04477a8
  

  John Didion

  and

  mr-c

  authored
  04477a8

  Copy full SHA for 04477a8

• Fix typo s/defualt/default

  

  kinow

  authored and

  mr-c

  committed
  abc8c45

  Copy full SHA for abc8c45

Commits on Jan 26, 2022

• Merge remote-tracking branch 'origin/main' into 1.2.1_proposed

  mr-c

  committed
  7590e5e

  Copy full SHA for 7590e5e

Commits on Feb 5, 2022

• s/compatability/compatibility

  

  kinow

  authored and

  mr-c

  committed
  80b87ae

  Copy full SHA for 80b87ae

Commits on Feb 23, 2022

• Allow records with defaults to be accepted, also type longs

  mr-c

  committed
  0a4c51c

  Copy full SHA for 0a4c51c

Commits on Feb 24, 2022

• Test for outputEval on a record type itself, not its fields

  mr-c

  committed
  5551e59

  Copy full SHA for 5551e59

Commits on Apr 26, 2022

• Add test that changing basename with an ExpressionTool (#158)

  Show description for b962666
  tetron

  authored
  b962666

  Copy full SHA for b962666

Commits on May 2, 2022

• Fix a few typos (automatic IDE spellchecker)

  

  kinow

  authored and

  mr-c

  committed
  d38ef4a

  Copy full SHA for d38ef4a

• Remove duplicate test

  

  kinow

  authored and

  mr-c

  committed
  f0edcc4

  Copy full SHA for f0edcc4

Commits on May 3, 2022

• Use main branch

  

  kinow

  authored and

  mr-c

  committed
  cef8fb7

  Copy full SHA for cef8fb7

Commits on May 4, 2022

• Adding a test to verify that runtime.outdir can be used with output glob

  

  kinow

  authored and

  mr-c

  committed
  5abc3d3

  Copy full SHA for 5abc3d3

Commits on May 6, 2022

• Adding GH Action spell check to the CI

  

  kinow

  authored and

  mr-c

  committed
  e22b916

  Copy full SHA for e22b916

• Remove unused test files

  

  kinow

  authored and

  mr-c

  committed
  d100782

  Copy full SHA for d100782

Commits on May 7, 2022

• Fix Spellcheck action YAML syntax (mea culpa)

  

  kinow

  authored and

  mr-c

  committed
  64968dc

  Copy full SHA for 64968dc

Commits on May 14, 2022

• Add note about cwl-upgrader in the Workflow changelog

  

  kinow

  authored and

  mr-c

  committed
  edd90f0

  Copy full SHA for edd90f0

• Fix tags for conformance tests

  

  tom-tan

  authored and

  mr-c

  committed
  99fcaf4

  Copy full SHA for 99fcaf4

Commits on May 16, 2022

• Add extra description of run field

  

  tom-tan

  authored and

  mr-c

  committed
  3bdc596

  Copy full SHA for 3bdc596

Commits on May 20, 2022

• Fix -l to list tests without cwl-runner (#174)

  tom-tan

  authored
  99ec14b

  Copy full SHA for 99ec14b

• Fix tags for workfows

  

  tom-tan

  authored and

  mr-c

  committed
  1d09972

  Copy full SHA for 1d09972

Commits on May 21, 2022

• Add missing label field

  

  tom-tan

  authored and

  mr-c

  committed
  033ed18

  Copy full SHA for 033ed18

Commits on May 27, 2022

• Update links used in concepts

  

  kinow

  authored and

  mr-c

  committed
  9bd4657

  Copy full SHA for 9bd4657

Commits on Jun 7, 2022

• Remove stray backtick

  

  kinow

  authored and

  mr-c

  committed
  a59b4d3

  Copy full SHA for a59b4d3

• Add link to Direntry entryname and fix typo

  

  kinow

  authored and

  mr-c

  committed
  29385c0

  Copy full SHA for 29385c0

Commits on Jun 21, 2022

• Add new test for chained commands, update the specification wording

  

  kinow

  authored and

  mr-c

  committed
  50dfc6b

  Copy full SHA for 50dfc6b

• Update the doc and use "true" as base command for the metadata test

  

  kinow

  authored and

  mr-c

  committed
  34b2117

  Copy full SHA for 34b2117

• Add glossary and clarification on opaque strings and identifiers

  

  kinow

  authored and

  mr-c

  committed
  f05f8bc

  Copy full SHA for f05f8bc

• Mention that we can refer to workflow level inputs in output parameter outputSource (#178)

  kinow

  authored
  8b7a2d8

  Copy full SHA for 8b7a2d8

Commits on Jun 23, 2022

• Add test for SchemaDefRequirement with a workflow and the types containing an $import statement. Used example written by @jeremiahsavage (thanks!)

  

  kinow

  authored and

  mr-c

  committed
  f1f1002

  Copy full SHA for f1f1002

• Merge pull request #176 from tom-tan/add-record-order-test

  Show description for 86972f0
  tom-tan

  authored
  86972f0

  Copy full SHA for 86972f0

• Add a conformance test for InlineJavascriptRequirement with an input record (#170)

  kinow

  authored
  6edb7a9

  Copy full SHA for 6edb7a9

• Add a conformance test for MultipleInputFeatureRequirement on Workflow outputs (#169)

  kinow

  authored
  d3c77ef

  Copy full SHA for d3c77ef

• Move label to id (#182)

  tom-tan

  authored
  60523c2

  Copy full SHA for 60523c2

• Added nested scatter conformance tests (#155)

  GlassOfWhiskey

  authored
  350f0ba

  Copy full SHA for 350f0ba

Commits on Jul 17, 2022

• typos (#194)

  Show description for 8c52930
  

  gertjandemulder

  and

  mr-c

  authored
  8c52930

  Copy full SHA for 8c52930

Commits on Jul 28, 2022

• Clarify process id field ($graph only) (#166)

  kinow

  authored
  6f15395

  Copy full SHA for 6f15395

Commits on Aug 31, 2022

• Schema fixes/clarifications that came up working on codegen (#196)

  tetron

  authored
  e15d7b7

  Copy full SHA for e15d7b7

Commits on Sep 6, 2022

• Add inheritable process requirements for CLT (#198)

  tom-tan

  authored
  f8f4dfe

  Copy full SHA for f8f4dfe

Commits on Sep 7, 2022

• Add tests for relative reference in cwl.output.json (#199)

  Show description for 5332d8c
  

  tetron

  and

  mr-c

  authored
  5332d8c

  Copy full SHA for 5332d8c

Commits on Sep 11, 2022

• Add File/Directory to WorkflowStepInput 'default' (#201)

  tetron

  authored
  9b091ed

  Copy full SHA for 9b091ed

Commits on Oct 20, 2022

• test case for hash marks in file names (#159)

  Show description for f0f9bc2
  

  tetron

  and

  mr-c

  authored
  f0f9bc2

  Copy full SHA for f0f9bc2

Commits on Nov 2, 2022

• fix typos spotted across docs (#205)

  Show description for f916947
  

  fmigneault

  and

  mr-c

  authored
  f916947

  Copy full SHA for f916947

Commits on Nov 5, 2022

• add missing newlines in code samples (#207)

  fmigneault

  authored
  e1205d5

  Copy full SHA for e1205d5

• fix over-indented list interpreted as code + typo (#208)

  fmigneault

  authored
  ebb9aa6

  Copy full SHA for ebb9aa6

Commits on Nov 7, 2022

• add code format to parameter references table definitions (fixes #206) (#209)

  fmigneault

  authored
  5951b8f

  Copy full SHA for 5951b8f

Commits on Nov 10, 2022

• Add CodeQL workflow for GitHub code scanning (#211)

  Show description for 59c3bea
  

  lgtm-com[bot]

  and

  lgtm-migrator

  authored
  59c3bea

  Copy full SHA for 59c3bea

Commits on Dec 2, 2022

• fix typo in ResourceRequirement.coresMin description (#214)

  fmigneault

  authored
  e4bb3bf

  Copy full SHA for e4bb3bf

Commits on Dec 4, 2022

• fix workflow scatter typos (#215)

  fmigneault

  authored
  ad6f77c

  Copy full SHA for ad6f77c

Commits on Dec 29, 2022

• Two tests were accidently still specifying v1.0 (#217)

  mr-c

  authored
  f6172e5

  Copy full SHA for f6172e5

Commits on Jan 25, 2023

• Increase the timeout in the time limit test

  Show description for f79146f
  

  tetron

  authored and

  mr-c

  committed
  f79146f

  Copy full SHA for f79146f

Commits on Feb 13, 2023

• Create dependabot.yml

  mr-c

  authored
  bcf1d89

  Copy full SHA for bcf1d89

• Added conformance tests for File and Directory glob

  Show description for fd53d9d
  

  GlassOfWhiskey

  authored and

  mr-c

  committed
  fd53d9d

  Copy full SHA for fd53d9d

• add hyperlinks to intent definition

  mr-c

  committed
  83c7208

  Copy full SHA for 83c7208

• Bump rojopolis/spellcheck-github-actions from 0.23.0 to 0.29.0

  Show description for 020e70d
  

  dependabot[bot]

  authored and

  mr-c

  committed
  020e70d

  Copy full SHA for 020e70d

• Bump actions/setup-python from 2 to 4

  Show description for c15357a
  

  dependabot[bot]

  authored and

  mr-c

  committed
  c15357a

  Copy full SHA for c15357a

• Bump actions/checkout from 2 to 3

  Show description for d1c2e2c
  

  dependabot[bot]

  authored and

  mr-c

  committed
  d1c2e2c

  Copy full SHA for d1c2e2c

• ci: use cwltest pytest plugin for better speed

  mr-c

  committed
  7052da7

  Copy full SHA for 7052da7

Commits on Feb 27, 2023

• Bump rojopolis/spellcheck-github-actions from 0.29.0 to 0.30.0

  Show description for bd5d12f
  

  dependabot[bot]

  authored and

  mr-c

  committed
  bd5d12f

  Copy full SHA for bd5d12f

Commits on Mar 3, 2023

• Fixed MacOS X compatibility for wc-tool

  

  GlassOfWhiskey

  authored and

  mr-c

  committed
  5411b8c

  Copy full SHA for 5411b8c

Commits on Apr 14, 2023

• Document that ExpressionTool outputs are always valid

  Show description for e136888
  

  GlassOfWhiskey

  authored and

  mr-c

  committed
  e136888

  Copy full SHA for e136888

Commits on Apr 17, 2023

• add render script

  mr-c

  committed
  192bb32

  Copy full SHA for 192bb32

• Merge remote-tracking branch 'origin/main' into 1.2.1_proposed

  mr-c

  committed
  e750ef2

  Copy full SHA for e750ef2

• install cwltool when rendering

  mr-c

  committed
  2bb40f5

  Copy full SHA for 2bb40f5

• also lockfile

  mr-c

  committed
  a75fbcb

  Copy full SHA for a75fbcb

• render: skip docker

  mr-c

  committed
  e8508f8

  Copy full SHA for e8508f8

Commits on Apr 18, 2023

• render: re-use git checkout

  mr-c

  committed
  c928c98

  Copy full SHA for c928c98

Commits on Apr 19, 2023

• official IANA media types for CWL documents

  Show description for 92d0acd
  mr-c

  committed
  92d0acd

  Copy full SHA for 92d0acd

• spelling: check YAML docs

  mr-c

  committed
  37a44af

  Copy full SHA for 37a44af

Commits on Apr 21, 2023

• Fixes #193

  

  GlassOfWhiskey

  authored and

  mr-c

  committed
  979accf

  Copy full SHA for 979accf

• Substitute URI with IRI in docs

  

  GlassOfWhiskey

  authored and

  mr-c

  committed
  63d4784

  Copy full SHA for 63d4784

Commits on May 8, 2023

• Add tests for decimal representation of very big and very small numbers

  Show description for 4f9b346
  mr-c

  committed
  4f9b346

  Copy full SHA for 4f9b346

• ci: add codespell check

  mr-c

  committed
  cbbf982

  Copy full SHA for cbbf982

• sync metaschema

  mr-c

  committed
  3d01afe

  Copy full SHA for 3d01afe

Commits on May 9, 2023

• typos

  mr-c

  committed
  146f6fb

  Copy full SHA for 146f6fb

Commits on May 10, 2023

• Fix typo {} vs ()

  Show description for ad91c84
  mr-c

  committed
  ad91c84

  Copy full SHA for ad91c84

Commits on Jun 5, 2023

• Bump rojopolis/spellcheck-github-actions from 0.30.0 to 0.32.0

  Show description for 3eeddca
  

  dependabot[bot]

  authored and

  mr-c

  committed
  3eeddca

  Copy full SHA for 3eeddca

• Bump codespell-project/actions-codespell from 1.0 to 2.0

  Show description for 1529286
  

  dependabot[bot]

  authored and

  mr-c

  committed
  1529286

  Copy full SHA for 1529286

• Update requirements.txt

  mr-c

  committed
  2a06a42

  Copy full SHA for 2a06a42

• Update requirements.txt

  mr-c

  committed
  f64fec0

  Copy full SHA for f64fec0

• All loadContents tests are required

  Show description for 4a715dd
  mr-c

  committed
  4a715dd

  Copy full SHA for 4a715dd

• default_with_falsey_value (#48)

  mr-c

  authored
  d50fad0

  Copy full SHA for d50fad0

Commits on Jun 19, 2023

• Bump rojopolis/spellcheck-github-actions from 0.32.0 to 0.33.0 (#257)

  Show description for c9d4ade
  dependabot[bot]

  authored
  c9d4ade

  Copy full SHA for c9d4ade

Commits on Jul 10, 2023

• Increase the time limits of this test and add a note. (#260)

  Show description for c2ac7e3
  

  tetron

  and

  mr-c

  authored
  c2ac7e3

  Copy full SHA for c2ac7e3

Commits on Jul 17, 2023

• Bump rojopolis/spellcheck-github-actions from 0.33.0 to 0.33.1 (#261)

  Show description for 53ea13c
  dependabot[bot]

  authored
  53ea13c

  Copy full SHA for 53ea13c

Commits on Jul 19, 2023

• fix run_tests indents + gitignore IDE/python files

  

  fmigneault

  authored and

  mr-c

  committed
  dc098f0

  Copy full SHA for dc098f0

• add CWL JSON schema + 'json_schema_invalid' tag (closes #253) + validation tests (2 failed related to #251)

  

  fmigneault

  authored and

  mr-c

  committed
  1612321

  Copy full SHA for 1612321

Commits on Jul 24, 2023

• changelog for 7b4b85...350f0b

  mr-c

  committed
  1ce7236

  Copy full SHA for 1ce7236

• json_output_{path,location}_relative: remove need for ShellCommandRequirement

  mr-c

  committed
  9351742

  Copy full SHA for 9351742

• changelog 350f0b...1612321

  mr-c

  committed
  180486e

  Copy full SHA for 180486e

• address review comments

  mr-c

  committed
  fa6d28f

  Copy full SHA for fa6d28f

Commits on Aug 17, 2023

• add conformance test for nested types in SchemaDefRequirement

  Show description for f368628
  

  jdidion

  and

  mr-c

  committed
  f368628

  Copy full SHA for f368628

Commits on Aug 21, 2023

• remove last references to Python 2

  mr-c

  committed
  5f84b9a

  Copy full SHA for 5f84b9a

• add explicit docker repository where missing

  Show description for df6fd28
  mr-c

  committed
  df6fd28

  Copy full SHA for df6fd28

• test for parameter references in CommandLineTool.arguments

  Show description for 01f2ee6
  mr-c

  committed
  01f2ee6

  Copy full SHA for 01f2ee6

• gh-actions: split out JSON schema validation

  mr-c

  committed
  63d914b

  Copy full SHA for 63d914b

Commits on Aug 28, 2023

• update the changelogs through 01f2ee6.

  mr-c

  committed
  c6c9be6

  Copy full SHA for c6c9be6

Commits on Aug 29, 2023

• add missing Any? and Any[]? CWL types to JSON schema

  

  fmigneault

  authored and

  mr-c

  committed
  1aa4a87

  Copy full SHA for 1aa4a87

• add missing ruamel.yaml package for JSON schema tests

  

  fmigneault

  authored and

  mr-c

  committed
  c0cc7bb

  Copy full SHA for c0cc7bb

Commits on Sep 7, 2023

• tests: conditionals: add 2 missing doc strings

  mr-c

  committed
  a4e0aa4

  Copy full SHA for a4e0aa4

• record_order_with_input_bindings had wrong tag

  mr-c

  committed
  5f4a24c

  Copy full SHA for 5f4a24c

Commits on Sep 11, 2023

• Bump actions/checkout from 3 to 4

  Show description for 31bda22
  

  dependabot[bot]

  authored and

  mr-c

  committed
  31bda22

  Copy full SHA for 31bda22

Commits on Oct 2, 2023

• Bump rojopolis/spellcheck-github-actions from 0.33.1 to 0.34.0

  Show description for cf52780
  

  dependabot[bot]

  authored and

  mr-c

  committed
  cf52780

  Copy full SHA for cf52780

Commits on Oct 30, 2023

• address review comments

  Show description for bd9e228
  

  mr-c

  and

  tetron

  committed
  bd9e228

  Copy full SHA for bd9e228

• spelling fix

  mr-c

  committed
  28803b0

  Copy full SHA for 28803b0

• json tests: adapt to newer ruamel.yaml

  mr-c

  committed
  0d538a0

  Copy full SHA for 0d538a0

Commits on Nov 20, 2023

• Bump rojopolis/spellcheck-github-actions from 0.34.0 to 0.35.0

  Show description for 1606e54
  

  dependabot[bot]

  authored and

  mr-c

  committed
  1606e54

  Copy full SHA for 1606e54

Commits on Dec 11, 2023

• Bump actions/setup-python from 4 to 5

  Show description for 504ccbe
  

  dependabot[bot]

  authored and

  mr-c

  committed
  504ccbe

  Copy full SHA for 504ccbe