Merge remote-tracking branch 'origin/main' into release

.zenodo.json

@@ -15,7 +15,7 @@
             "name": "bamiwoaluko"
 	},
 	{
-            "orcid": "https://orcid.org/0000-0002-6206-4638>",
+            "orcid": "https://orcid.org/0000-0002-6206-4638",
             "name": "Benjamin Carr"
 	},
         {
@@ -36,7 +36,7 @@
             "name": "Ngumih Fien"
 	},
 	{
-            "name": "gathoni-k"
+            "name": "Mary Gathoni"
 	},
 	{
             "name": "Henry Liu"

AUTHORS.md

@@ -8,7 +8,7 @@ Thank you to the following contributors (in alphabetical order by user name):
 * Eugene Miloslavsky (@emiloslavsky)
 * Robin Long (@longr) <https://orcid.org/0000-0003-2249-645X>
 * Ngumih Fien (@Fienne)
-* @gathoni-k
+* Mary Gathoni (@gathoni-k)
 * Henry Liu (@HenryLiu0)
 * Marijke J. van Baren (@Jeltje)
 * @jessMaia

CONTRIBUTING.md

@@ -102,14 +102,21 @@ tool. You must have a recent version of Python 3.6+ installed to build the proje
 locally. It is also recommended having `make` (otherwise look at the commands used
 in `Makefile`).
 
+The `dot` program from Graphviz is needed to render some of the diagrams.
+
+* For Debian/Ubuntu users:
+```bash
+sudo apt get install graphviz
+```
+* For non-Debian/Ubuntu users, follow the directions at [the GraphViz download site](https://graphviz.org/download).
 ```bash
 # Create and activate a virtual environment
 python -m venv venv
 source venv/bin/activate
 # update the version of pip, setuptools, and wheel
 (venv) pip install -U pip setuptools wheel
-# Install the dependencies in your virtual environment
-(venv) pip install .[all]
+# Install all the dependencies in your virtual environment.
+(venv) pip install ".[all]"
 # Create the HTML to visualize locally
 (venv) make html
 (venv) open _build/index.html

README.md

@@ -1,7 +1,6 @@
 [![DOI for the latest version](https://zenodo.org/badge/89621457.svg)](https://zenodo.org/badge/latestdoi/89621457)
 
-[![Syntax Check](https://travis-ci.org/common-workflow-language/user_guide.svg?branch=main)](https://travis-ci.org/common-workflow-language/user_guide)
-
+[![Syntax Check](https://app.travis-ci.com/common-workflow-language/user_guide.svg?branch=main)](https://app.travis-ci.com/common-workflow-language/user_guide)
 
 This is the source of the official user guide for the Common Workflow Language standards.
 

src/topics/using-containers.md

@@ -52,8 +52,10 @@ used a container called `node:slim`.
 Provide a "hello.js" and invoke `cwltool` providing the tool description and the
 input object on the command line:
 
-```{code-block} console
-$ echo "console.log(\"Hello World\");" > hello.js
+```{literalinclude} /_includes/cwl/using-containers/hello.js
+:language: javascript
+:caption: "`hello.js`"
+:name: hello.js
 ```
 
 ```{runcmd} cwltool docker.cwl docker-job.yml