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Merge pull request #115 from common-workflow-language/1.2.1_proposed
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1.2.1 has been approved by the following members of the CWL Leadership Team: 
- Michael R. Crusoe
- Peter Amstutz
- Stian Soiland-Reyes
- Jeff Gentry
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mr-c committed Jan 3, 2024
2 parents a507314 + 504ccbe commit ae6899d
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3 changes: 2 additions & 1 deletion .github/config/spellcheck.yml
Original file line number Diff line number Diff line change
Expand Up @@ -17,5 +17,6 @@ matrix:
ignores:
- :matches(code, pre)
sources:
- '**/*.md'
- '!env*/**|**/*.md'
- '!env*/**|!tests/**|*.yml'
default_encoding: utf-8
152 changes: 150 additions & 2 deletions .github/config/wordlist.txt
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@@ -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
Expand All @@ -54,25 +117,50 @@ implementors
initialworkdirrequirement
initialworkdirrequirements
inlinejavascriptrequirement
inplaceupdate
inplaceupdaterequirement
inputarrayschema
inputenumschema
inputbinding
inputformat
inputrecordfield
inputrecordschema
inputparameter
inputschema
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
Expand All @@ -84,43 +172,80 @@ nebojša
nekrutenko
networkaccess
neuro
nolinkcheck
ogc
onlinepubs
opengroup
operationinputparameter
operationoutputparameter
orcid
osx
outputarrayschema
outputbinding
outputenumschema
outputeval
outputformat
outputschema
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
Expand All @@ -132,24 +257,47 @@ 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
11 changes: 11 additions & 0 deletions .github/dependabot.yml
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@@ -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"
21 changes: 18 additions & 3 deletions .github/workflows/ci.yml
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Expand Up @@ -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
Expand All @@ -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
42 changes: 42 additions & 0 deletions .github/workflows/codeql.yml
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@@ -0,0 +1,42 @@
name: "CodeQL"

on:
push:
branches: [ "1.2.1_proposed", "main" ]
pull_request:
branches: [ "1.2.1_proposed" ]
schedule:
- cron: "32 15 * * 5"

jobs:
analyze:
name: Analyze
runs-on: ubuntu-latest
permissions:
actions: read
contents: read
security-events: write

strategy:
fail-fast: false
matrix:
language: [ javascript, python ]

steps:
- name: Checkout
uses: actions/checkout@v4

- name: Initialize CodeQL
uses: github/codeql-action/init@v2
with:
languages: ${{ matrix.language }}
queries: +security-and-quality

- name: Autobuild
uses: github/codeql-action/autobuild@v2
if: ${{ matrix.language == 'javascript' || matrix.language == 'python' }}

- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v2
with:
category: "/language:${{ matrix.language }}"
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