From b7517534454333074cc3eff3cce5e896f78a1e37 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
Date: Mon, 17 Oct 2022 18:52:47 +0200
Subject: [PATCH 1/5] Fix TravisCI badge

---
 README.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/README.md b/README.md
index f40921c5..de079218 100644
--- a/README.md
+++ b/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.
 

From 4d968b73bb99f42ac54269b394b3ad048c6b9607 Mon Sep 17 00:00:00 2001
From: Abigail Afi Gbadago <38146824+AfiMaameDufie@users.noreply.github.com>
Date: Tue, 18 Oct 2022 10:14:57 +0000
Subject: [PATCH 2/5] Add clarity for installing dependencies and pip command
 for Graphviz (#304)

Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>
---
 CONTRIBUTING.md | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 567f0da3..0646b614 100644
--- a/CONTRIBUTING.md
+++ b/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

From f05e2658526fef727660cb9cdbf704a0cc9270f5 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 18 Oct 2022 12:18:32 +0200
Subject: [PATCH 3/5] add attribution for Mary Gathoni

---
 .zenodo.json | 2 +-
 AUTHORS.md   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.zenodo.json b/.zenodo.json
index a9aa97e9..ae6ae159 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -36,7 +36,7 @@
             "name": "Ngumih Fien"
 	},
 	{
-            "name": "gathoni-k"
+            "name": "Mary Gathoni"
 	},
 	{
             "name": "Henry Liu"
diff --git a/AUTHORS.md b/AUTHORS.md
index 6a2a3a58..49ca6978 100644
--- a/AUTHORS.md
+++ b/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

From 6bb00557a7577b6bbfca9d8e61d2651b5e8aa096 Mon Sep 17 00:00:00 2001
From: khaiyra <44167602+khaiyra@users.noreply.github.com>
Date: Tue, 18 Oct 2022 11:22:27 +0100
Subject: [PATCH 4/5] Display hello.js file as we do other files (#306)

---
 src/topics/using-containers.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/topics/using-containers.md b/src/topics/using-containers.md
index 8a9551b9..903e6fdc 100644
--- a/src/topics/using-containers.md
+++ b/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

From 09030ed6d2d94e0dc91a4d672effaf904c8c2936 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
Date: Tue, 18 Oct 2022 14:21:31 +0200
Subject: [PATCH 5/5] remove errant >

---
 .zenodo.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.zenodo.json b/.zenodo.json
index ae6ae159..b36b3818 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -15,7 +15,7 @@
             "name": "bamiwoaluko"
 	},
 	{
-            "orcid": "https://orcid.org/0000-0002-6206-4638%3E",
+            "orcid": "https://orcid.org/0000-0002-6206-4638",
             "name": "Benjamin Carr"
 	},
         {