Merge pull request #14 from common-workflow-language/refresh_from_1.2.1-proposed

refresh from 1.2.1-proposed

Author: mr-c

.github/config/spellcheck.yml

@@ -17,5 +17,6 @@ matrix:
       ignores:
       - :matches(code, pre)
   sources:
-  - '**/*.md'
+  - '!env*/**|**/*.md'
+  - '!env*/**|!tests/**|*.yml'
   default_encoding: utf-8

.github/config/wordlist.txt

@@ -1,51 +1,114 @@
 acyclic
 amstutz
+arrayschema
 arvados
 auditability
+autogenerated
 avro
 backchannel
 backrub
+basecommand
 basedir
+basename
+basetypesdoc
+bioconda
+bioinformatics
 bnf
 bogdan
+bowtie
+changelog
+charette
 checkpoint
 checkpointing
+checksums
 chilton
 cisphobia
 classname
+cmd
+commandinputarrayschema
+commandinputenumschema
+commandinputparameter
+commandinputrecordfield
+commandinputrecordschema
+commandinputschema
+commandlinebindable
+commandlinebinding
 commandlinetool
+commandlinetooldoc
 commandlinetools
+commandoutputarrayschema
+commandoutputbinding
+commandoutputenumschema
+commandoutputparameter
+commandoutputrecordfield
+commandoutputrecordschema
 commonwl
+conformant
+contrib
 complextype
+coresMin
 coreutils
+cpus
+crossproduct
+cryptographic
 ctbrown
 curii
-curoverse
 cwl
 cwltest
 cwltool
+cwltype
 cwlversion
 cyclic
 dataflow
+deserialize
 dev
+dirent
+docafter
+docchild
+dockerfile
+dockerimport
+dockerload
+dockeroutputdirectory
+dockerpull
 dockerrequirement
+documentroot
+docparent
+doi
+dotproduct
 doubleq
 dsl
 dusenbery
 edu
 eg
+enablereuse
+entryname
+enum
+enumschema
+entrypoint
+envdef
+environmentdef
+envname
+envvalue
 envvarrequirement
 expressionlib
+expressionplaceholder
 expressiontool
+expressiontooloutputparameter
 expressiontools
+fieldbase
+filenameABCDEFG
 filesystem
 freedesktop
 gavrilovic
+geoscience
 ghose
 gitter
+globbing
 gmail
+gunzip
 hervé
 https
+iana
 ietf
 implementer
 implementers
@@ -54,25 +117,51 @@ implementors
 initialworkdirrequirement
 initialworkdirrequirements
 inlinejavascriptrequirement
+inplaceupdate
 inplaceupdaterequirement
+inputarrayschema
+inputenumschema
+inputbinding
+inputformat
+inputrecordfield
+inputrecordschema
 inputparameter
+inputschema
+inputsink
 institut
+interoperable
 invocab
+ioschema
+ipv
 iri
+itemseparator
 jmchilton
 json
+jsonldpredicate
 junit
 kaushik
+kib
 ld
 lexicographically
 linkmerge
+linkmergemethod
+loadcontents
+loadlisting
+loadlistingenum
+loadlistingrequirement
+localhost
 lookahead
+loopback
 maccallum
 macos
+mappredicate
+mapsubject
 mebibyte
 mebibytes
 ménager
+metacharacters
 metaschema
+migneault
 misgendering
 mrc
 multipleinputfeaturerequirement
@@ -84,43 +173,81 @@ nebojša
 nekrutenko
 networkaccess
 neuro
+nolinkcheck
+ogc
 onlinepubs
 opengroup
+operationinputparameter
+operationoutputparameter
 orcid
 osx
+outputarrayschema
+outputbinding
+outputenumschema
+outputeval
+outputformat
+outputschema
+outputsink
 outputsource
+outputparameter
+outputrecordfield
+outputrecordschema
+parsers
+pathname
 petermac
 pickvalue
+pickvaluemethod
 posix
 pre
 preprocess
 preprocessed
 preprocessing
+primitivetype
+processrequirement
 psu
-publically
 pvanheus
 rdf
+rdfs
+recordfield
+recordschema
 recurse
+refscope
 repo
 reproducibility
+resolvers
 resourcerequirement
 routable
+rrid
 runtime
+saladversion
 sbgenomics
 scatterfeaturerequirement
+scattermethod
 schemadefrequirement
 schemaorg
 schemas
+scr
 secondaryfiles
+secondaryfileschema
 secondaryfilesdsl
+semver
 shellcommandrequirement
 singleq
+sld
+specializeto
+specializefrom
 softwarepackage
 softwarerequirement
 soiland
+stderr
+stdin
+stdout
 stepinputexpressionrequirement
 stian
+streamable
+subdirectories
 subdirectory
+subnet
 subprocess
 subprocesses
 subscope
@@ -132,24 +259,47 @@ substrings
 subtype
 subtypes
 subworkflow
+subworkflows
+subworkflowfeaturerequirement
 subworkflowrequirement
 superset
 svg
+symlink
+tbb
+testcase
 tijanic
 tijanić
+timelimit
 toc
 tooltimelimit
 transcode
 txt
+typedef
+typedsl
+undeploy
+unserialized
 uc
 ucdavis
+udocker
+underspecified
 untrusted
+updatable
 uri
 utf
+valuefrom
 vandewege
 virtualenv
+virtualized
 walkthrough
 wdl
 whitespace
+workflowdoc
+workflowinputparameter
+workflowoutputparameter
+workflowstep
+workflowstepinput
+workflowstepoutput
+workreuse
 xdg
 yaml
+yml

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/ci.yml

@@ -18,14 +18,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.8.x'
 
       - name: Setup prerequirements
-        run: pip install cwltest schema-salad[pycodegen]
+        run: pip install cwltest 'schema-salad[pycodegen]'
 
       - name: Download schema for conformance_tests.yaml
         run: curl -LO https://raw.githubusercontent.com/common-workflow-language/cwltest/main/cwltest/cwltest-schema.yml
@@ -35,3 +35,18 @@ jobs:
 
       - name: Validate CWL documents
         run: ./run_test.sh --self
+
+  validate_json:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.8.x'
+
+      - name: Validate JSON schema document
+        run: |
+          pip install -r ./requirements-jsonschema-test.txt
+          pytest tests/json_schema

.github/workflows/codeql.yml

@@ -24,7 +24,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v2

.github/workflows/cwltool.yml

@@ -14,16 +14,23 @@ on:
 jobs:
   test_with_cwltool:
     runs-on: ubuntu-latest
-
+    env:
+      CWLTOOL_OPTIONS: "--parallel --relax-path-checks --enable-dev"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.9.x'
-      
+
       - name: Setup prerequirements
-        run: pip install cwltest "https://github.com/common-workflow-language/cwltool/archive/refs/heads/cwl-v1.3.zip"
-      
+        run: pip install "cwltest>=2.3" pytest-xdist "git+https://github.com/common-workflow-language/[email protected]#egg=cwltool"
+
+      - name: Copy in cwltool-specific configuration for the cwltest pytest plugin
+        run: cp "$(python -c 'from cwltool.tests.util import get_data; print(get_data("tests/cwl-conformance/cwltool-conftest.py"))')" conftest.py
+
+      - name: Copy conformance test index to .cwltest.yaml
+        run: cp conformance_tests.yaml conformance_tests.cwltest.yaml
+
       - name: Run tests against the reference runner
-        run: ./run_test.sh RUNNER=cwltool "EXTRA=--parallel --relax-path-checks --enable-dev" -j$(nproc)
+        run: python -m pytest conformance_tests.cwltest.yaml -n auto -rs