Backport formatting fixes (#210)

* add missing newlines in code samples (#207)

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

Co-authored-by: Francis Charette-Migneault <[email protected]>

Author: mr-c

.github/config/spellcheck.yml

@@ -0,0 +1,21 @@
+matrix:
+- name: Markdown
+  aspell:
+    lang: en
+    ignore-case: true
+  dictionary:
+    encoding: utf-8
+    wordlists:
+      - .github/config/wordlist.txt
+  pipeline:
+  - pyspelling.filters.markdown:
+  - pyspelling.filters.html:
+      comments: true
+      attributes:
+      - title
+      - alt
+      ignores:
+      - :matches(code, pre)
+  sources:
+  - '**/*.md'
+  default_encoding: utf-8

.github/config/wordlist.txt

@@ -0,0 +1,155 @@
+acyclic
+amstutz
+arvados
+auditability
+avro
+backchannel
+backrub
+basedir
+bnf
+bogdan
+checkpoint
+checkpointing
+chilton
+cisphobia
+classname
+commandlinetool
+commandlinetools
+commonwl
+complextype
+coreutils
+ctbrown
+curii
+curoverse
+cwl
+cwltest
+cwltool
+cwlversion
+cyclic
+dataflow
+dev
+dockerrequirement
+doubleq
+dsl
+dusenbery
+edu
+eg
+envvarrequirement
+expressionlib
+expressiontool
+expressiontools
+filesystem
+freedesktop
+gavrilovic
+ghose
+gitter
+gmail
+hervé
+https
+ietf
+implementer
+implementers
+implementor
+implementors
+initialworkdirrequirement
+initialworkdirrequirements
+inlinejavascriptrequirement
+inplaceupdaterequirement
+inputparameter
+institut
+invocab
+iri
+jmchilton
+json
+junit
+kaushik
+ld
+lexicographically
+linkmerge
+lookahead
+maccallum
+macos
+mebibyte
+mebibytes
+ménager
+metaschema
+misgendering
+mrc
+multipleinputfeaturerequirement
+multithreaded
+namespace
+namespaces
+nebojsa
+nebojša
+nekrutenko
+networkaccess
+neuro
+onlinepubs
+opengroup
+orcid
+osx
+outputsource
+petermac
+pickvalue
+posix
+pre
+preprocess
+preprocessed
+preprocessing
+psu
+publically
+pvanheus
+rdf
+recurse
+repo
+reproducibility
+resourcerequirement
+routable
+runtime
+sbgenomics
+scatterfeaturerequirement
+schemadefrequirement
+schemaorg
+schemas
+secondaryfiles
+secondaryfilesdsl
+shellcommandrequirement
+singleq
+softwarepackage
+softwarerequirement
+soiland
+stepinputexpressionrequirement
+stian
+subdirectory
+subprocess
+subprocesses
+subscope
+subscoped
+subshell
+substep
+substring
+substrings
+subtype
+subtypes
+subworkflow
+subworkflowrequirement
+superset
+svg
+tijanic
+tijanić
+toc
+tooltimelimit
+transcode
+txt
+uc
+ucdavis
+untrusted
+uri
+utf
+vandewege
+virtualenv
+walkthrough
+wdl
+whitespace
+xdg
+yaml

.github/workflows/ci.yml

@@ -8,7 +8,7 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
+    branches: [ main, 1.2.1_proposed ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:

.github/workflows/cwltool.yml

@@ -0,0 +1,29 @@
+name: test_with_cwltool
+
+# Controls when the action will run.
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main, 1.2.1_proposed ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  test_with_cwltool:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.9.x'
+      
+      - name: Setup prerequirements
+        run: pip install cwltest cwltool
+      
+      - name: Run tests against the reference runner
+        run: ./run_test.sh RUNNER=cwltool "EXTRA=--parallel --relax-path-checks" -j$(nproc)

.github/workflows/spellcheck.yml

@@ -0,0 +1,21 @@
+name: Spellcheck Action
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main, 1.2.1_proposed ]
+  workflow_dispatch:
+
+jobs:
+  build:
+    # https://github.com/marketplace/actions/github-spellcheck-action
+    # To run locally, `pip install pyspelling`, followed by
+    # `pyspelling -c .github/config/spellcheck.yml`.
+    name: Spellcheck
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - uses: rojopolis/[email protected]
+        name: Spellcheck
+        with:
+          config_path: .github/config/spellcheck.yml

CODE_OF_CONDUCT.md

@@ -43,7 +43,7 @@ except as necessary to protect vulnerable people from intentional abuse.
  - Publication of non-harassing private communication.
 
 The CWL Project prioritizes marginalized people’s safety over privileged
-people’s comfort. The CWL Leadeship Team will not act on complaints regarding:
+people’s comfort. The CWL Leadership Team will not act on complaints regarding:
 
  - ‘Reverse’ -isms, including ‘reverse racism,’ ‘reverse sexism,’ and ‘cisphobia’
  - Reasonable communication of boundaries, such as “leave me alone,” “go away,” or

CONFORMANCE_TESTS.md

@@ -184,7 +184,7 @@ Likewise, please do not test the `path` for `class: File` and `class: Directory`
 
 To add a new conformance test:
 1. Ensure the CWL document you have tests the desired feature or aspect.
-2. All `CommandLineTool`s need a software container (via `DockerRequirement`) for better reproducibility, preferrably under `hints`.
+2. All `CommandLineTool`s need a software container (via `DockerRequirement`) for better reproducibility, preferably under `hints`.
      Please limit your container usage to the following: 
      - `dockerPull: docker.io/alpine:latest`
      - `dockerPull: docker.io/bash:4.4`

CommandLineTool.yml

@@ -143,7 +143,7 @@ $graph:
   doc: |
 
     When listed under `inputBinding` in the input schema, the term
-    "value" refers to the the corresponding value in the input object.  For
+    "value" refers to the corresponding value in the input object.  For
     binding objects listed in `CommandLineTool.arguments`, the term "value"
     refers to the effective value after evaluating `valueFrom`.
 
@@ -201,7 +201,7 @@ $graph:
       type: string?
       doc: |
         Join the array elements into a single string with the elements
-        separated by by `itemSeparator`.
+        separated by `itemSeparator`.
     - name: valueFrom
       type:
         - "null"
@@ -455,7 +455,7 @@ $graph:
     - name: inputBinding
       type: CommandLineBinding?
       doc: |
-        Describes how to turns the input parameters of a process into
+        Describes how to turn the input parameters of a process into
         command line arguments.
       jsonldPredicate: "cwl:inputBinding"
 
@@ -859,7 +859,7 @@ $graph:
         One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s
         identifying resources for installing or enabling the software named in
         the `package` field. Implementations may provide resolvers which map
-        these software identifer IRIs to some configuration action; or they can
+        these software identifier IRIs to some configuration action; or they can
         use only the name from the `package` field on a best effort basis.
 
         For example, the IRI https://packages.debian.org/bowtie could
@@ -871,19 +871,19 @@ $graph:
         software installation or selection mechanism.
         Using [RRID](https://www.identifiers.org/rrid/) as an example:
         https://identifiers.org/rrid/RRID:SCR_005476
-        could be fulfilled using the above mentioned Debian or bioconda
-        package, a local installation managed by [Environement Modules](http://modules.sourceforge.net/),
+        could be fulfilled using the above-mentioned Debian or bioconda
+        package, a local installation managed by [Environment Modules](https://modules.sourceforge.net/),
         or any other mechanism the platform chooses. IRIs can also be from
-        identifer sources that are discipline specific yet still system
+        identifier sources that are discipline specific yet still system
         independent. As an example, the equivalent [ELIXIR Tools and Data
         Service Registry](https://bio.tools) IRI to the previous RRID example is
         https://bio.tools/tool/bowtie2/version/2.2.8.
         If supported by a given registry, implementations are encouraged to
-        query these system independent sofware identifier IRIs directly for
+        query these system independent software identifier IRIs directly for
         links to packaging systems.
 
         A site specific IRI can be listed as well. For example, an academic
-        computing cluster using Environement Modules could list the IRI
+        computing cluster using Environment Modules could list the IRI
         `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that
         `module load bowtie-tbb/1.1.2` should be executed to make available
         `bowtie` version 1.1.2 compiled with the TBB library prior to running
@@ -1234,7 +1234,7 @@ $graph:
     For implementations that support reusing output from past work (on
     the assumption that same code and same input produce same
     results), control whether to enable or disable the reuse behavior
-    for a particular tool or step (to accomodate situations where that
+    for a particular tool or step (to accommodate situations where that
     assumption is incorrect).  A reused step is not executed but
     instead returns the same output as the original execution.
 
@@ -1269,7 +1269,7 @@ $graph:
     may apply their own security policies to restrict what is
     accessible by the tool.
 
-    Enabling network access does not imply a publically routable IP
+    Enabling network access does not imply a publicly routable IP
     address or the ability to accept inbound connections.
 
   fields:
@@ -1302,7 +1302,7 @@ $graph:
     read-only in every step.
 
     Workflow steps which modify a file must produce the modified file
-    as output.  Downstream steps which futher process the file must
+    as output.  Downstream steps which further process the file must
     use the output of previous steps, and not refer to a common input
     (this is necessary for both ordering and correctness).