carpentries-incubator · agitter · Jan 14, 2020 · Jan 9, 2020 · Jan 9, 2020 · Jan 9, 2020
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -2,10 +2,9 @@
 layout: page
 title: "Contributor Code of Conduct"
 ---
-As contributors and maintainers of this project,
-we pledge to follow the [Carpentry Code of Conduct][coc].
+Workshop participants, contributors, and maintainers of this project pledge to follow the [Carpentry Code of Conduct][coc].
 
-Instances of abusive, harassing, or otherwise unacceptable behavior
-may be reported by following our [reporting guidelines][coc-reporting].
+Because this workshop is not an official Carpentries workshop, instances of abusive, harassing, or otherwise unacceptable behavior may be reported using the Contact link below instead of the 
+Carpentries incident report form.
 
 {% include links.md %}
diff --git a/LICENSE.md b/LICENSE.md
@@ -3,6 +3,16 @@ layout: page
 title: "Licenses"
 root: .
 ---
+## ml4bio Licenses
+
+The content of the ml4bio workshop is made available under the [Creative Commons Attribution 4.0 International Public License][cc-by-human] by the Gitter Lab.
+The [ml4bio software](https://github.com/gitter-lab/ml4bio) is made available under the [MIT license](https://github.com/gitter-lab/ml4bio/blob/master/LICENSE).
+The [ml4bio guides](https://github.com/gitter-lab/ml-bio-workshop/tree/master/guide) contain [images from third-party sources](https://github.com/gitter-lab/ml-bio-workshop/blob/master/figures/third_party_figures), as noted in the image links and guide references.
+See the linked original image sources for their licenses and terms of reuse.
+
+The ml4bio workshop is derived from materials, software, and templates from [The Carpentries](https://carpentries.org/).
+See below for The Carpentries licensing information.
+
 ## Instructional Material
 
 All Software Carpentry, Data Carpentry, and Library Carpentry instructional material is

diff --git a/Makefile b/Makefile
@@ -66,6 +66,8 @@ RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
 RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))
 
 # Lesson source files in the order they appear in the navigation menu.
+# Some unused *.md files have been renamed *.md.unused so they are not displayed
+# Remove the '.unused' suffix to include this content
 MARKDOWN_SRC = \
   index.md \
   CODE_OF_CONDUCT.md \

diff --git a/_config.yml b/_config.yml
@@ -7,7 +7,7 @@
 # dc: Data Carpentry
 # lc: Library Carpentry
 # cp: Carpentries (to use for instructor traning for instance)
-carpentry: "dc"
+carpentry: "cp"
 
 # Overall title for pages.
 title: "Machine Learning for Biology"
@@ -39,6 +39,7 @@ carpentries_site: "https://carpentries.org/"
 dc_site: "http://datacarpentry.org"
 example_repo: "https://github.com/carpentries/lesson-example"
 example_site: "https://carpentries.github.io/lesson-example"
+gitter_site: "https://www.biostat.wisc.edu/~gitter/index.html"
 lc_site: "https://librarycarpentry.org/"
 swc_github: "https://github.com/swcarpentry"
 swc_pages: "https://swcarpentry.github.io"

diff --git a/_extras/about.md b/_extras/about.md
@@ -1,5 +1,5 @@
 ---
-title: About ml4bio
+title: About ml4bio software
 ---
 {% include links.md %}
 
@@ -21,7 +21,7 @@ This is a popular general purpose machine learning package.
 When you use the ml4bio graphical interface, it calls functions in scikit-learn to train classifiers and make predictions.
 
 ### Advanced users
-Advanced users who already have Python installed can install the [required packages](../scripts/README.md) through pip.
+Advanced users who already have Python installed can install the [required packages](https://github.com/gitter-lab/ml-bio-workshop/blob/master/scripts/README.md) through pip.
 Then launch ml4bio from the command line with the command `ml4bio`.
 
 ### A quick tour

diff --git a/_extras/discuss.md → _extras/discuss.md.unused b/_extras/discuss.md → _extras/discuss.md.unused
diff --git a/_extras/guide.md → _extras/guide.md.unused b/_extras/guide.md → _extras/guide.md.unused
diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html
@@ -7,23 +7,26 @@
 <footer>
   <div class="row">
     <div class="col-md-6 copyright" align="left">
+    Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
+	by <a href="{{ site.gitter_site }}">the Gitter Lab</a>
+	<br>
 	{% if site.carpentry == "swc" %}
-	Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
+	Website template licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
 	by <a href="{{ site.carpentries_site }}">The Carpentries</a>
         <br>
-        Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2016–2018
+        Website template licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2016–2018
 	by <a href="{{ site.swc_site }}">Software Carpentry Foundation</a>
 	{% elsif site.carpentry == "dc" %}
-	Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
+	Website template licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
 	by <a href="{{ site.carpentries_site }}">The Carpentries</a>
         <br>
-        Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2016–2018
+        Website template licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2016–2018
 	by <a href="{{ site.dc_site }}">Data Carpentry</a>
 	{% elsif site.carpentry == "lc" %}
-	Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2016–{{ 'now' | date: "%Y" }}
+	Website template licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2016–{{ 'now' | date: "%Y" }}
 	by <a href="{{ site.lc_site }}">Library Carpentry</a>
 	{% elsif site.carpentry == "cp" %}
-	Licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
+	Website template licensed under <a href="{{ site.cc_by_human }}">CC-BY 4.0</a> 2018–{{ 'now' | date: "%Y" }}
 	by <a href="{{ site.carpentries_site }}">The Carpentries</a>
 	{% endif %}
     </div>
@@ -38,7 +41,7 @@
 	/
 	<a href="{{ repo_url }}/blob/{{ source_branch }}/CONTRIBUTING.md" data-checker-ignore>Contributing</a>
 	/
-	<a href="{{ repo_url }}/">Source</a>
+	<a href="{{ repo_url }}/tree/{{ source_branch }}">Source</a>
 	/
 	<a href="{{ repo_url }}/blob/{{ source_branch }}/CITATION" data-checker-ignore>Cite</a>
 	/

diff --git a/_includes/navbar.html b/_includes/navbar.html
@@ -14,23 +14,31 @@
         <span class="icon-bar"></span>
       </button>
 
-      {% comment %} Select what logo to display. {% endcomment %}
+      {% comment %} Select what logo to display. Commented out until ml4bio has a custom logo. {% endcomment %}
       {% if site.carpentry == "swc" %}
+      {% comment %}
       <a href="{{ site.swc_site }}" class="pull-left">
         <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/swc-icon-blue.svg %}" alt="Software Carpentry logo" />
       </a>
+      {% endcomment %}
       {% elsif site.carpentry == "dc" %}
+      {% comment %}
       <a href="{{ site.dc_site }}" class="pull-left">
         <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/dc-icon-black.svg %}" alt="Data Carpentry logo" />
       </a>
+      {% endcomment %}
       {% elsif site.carpentry == "lc" %}
+      {% comment %}
       <a href="{{ site.lc_site }}" class="pull-left">
         <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/lc-icon-black.svg %}" alt="Library Carpentry logo" />
       </a>
+      {% endcomment %}
       {% elsif site.carpentry == "cp" %}
+      {% comment %}
       <a href="{{ site.carpentries_site }}" class="pull-left">
         <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/cp-logo-blue.svg %}" alt="The Carpentries logo" />
       </a>
+      {% endcomment %}
       {% endif %}
 
       {% comment %} Always show link to home page. {% endcomment %}
@@ -77,10 +85,10 @@
         <li><a href="{{ relative_root_path }}{% link LICENSE.md %}">License</a></li>
 	{% if page.source %}
 	{% if page.source == "Rmd" %}
-	<li><a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
+	<li><a href="{{repo_url}}/edit/{{ source_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
 	{% endif %}
 	{% else %}
-	<li><a href="{{repo_url}}/edit/{{ default_branch}}/{{page.path}}" data-checker-ignore>Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
+	<li><a href="{{repo_url}}/edit/{{ source_branch}}/{{page.path}}" data-checker-ignore>Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
 	{% endif %}
       </ul>
       <form class="navbar-form navbar-right" role="search" id="search" onsubmit="google_search(); return false;">

diff --git a/reference.md b/reference.md
@@ -1,9 +1,12 @@
 ---
 layout: reference
+title: "References"
 ---
 
-## Glossary
+## Glossary and other resources
 
-The [Google machine learning glossary](https://developers.google.com/machine-learning/glossary) and our [guides](https://github.com/gitter-lab/ml-bio-workshop/tree/master/guide) define common machine learning terms.
+The [Google machine learning glossary](https://developers.google.com/machine-learning/glossary) and [ml4bio guides](https://github.com/gitter-lab/ml-bio-workshop/tree/master/guide) define common machine learning terms.
+
+The [Elements of AI](https://course.elementsofai.com/) course presents general introductory materials to machine learning and related topics.
 
 {% include links.md %}
diff --git a/setup.md b/setup.md
@@ -3,17 +3,17 @@ title: Setup
 ---
 # Software overview
 
-### Setup and launch the ML4Bio software
+### Setup and launch the ml4bio software
 
 > #### Questions
 >
-> 1.   What do I need to run the ML4Bio software?
-> 2.   How do I download the ML4Bio workshop materials?
+> 1.   What do I need to run the ml4bio software?
+> 2.   How do I download the ml4bio workshop materials?
 >
 > #### Objectives
 >
-> 1.   Provide instructions for installing the ML4Bio software.
-> 2.   Explain the ML4Bio software environment
+> 1.   Provide instructions for installing the ml4bio software.
+> 2.   Explain the ml4bio software environment
 
 ### Overview
 
@@ -25,16 +25,16 @@ title: Setup
 >
 > 1.   Explain how the software works through an example.
 
-There are three main steps to prepare for the ML4Bio workshop:
+There are three main steps to prepare for the ml4bio workshop:
 1. [Download the workshop materials](#download-the-ml4bio-materials)
 2. [Install the Anaconda Python distribution](#install-python)
-3. [Install the ML4Bio software](#launch-the-ml4bio-software)
+3. [Install the ml4bio software](#launch-the-ml4bio-software)
 
 See the [troubleshooting](#troubleshooting) if you run into problems during the installation.
-If you already have Python installed and do not want to use Anaconda, download the ML4Bio materials and proceed to the [advanced](#advanced-users) instructions.
+If you already have Python installed and do not want to use Anaconda, download the ml4bio materials and proceed to the [advanced](#advanced-users) instructions.
 
-### Download the ML4Bio materials
-To download the ML4Bio materials, visit <https://github.com/gitter-lab/ml-bio-workshop/>.
+### Download the ml4bio materials
+To download the ml4bio materials, visit <https://github.com/gitter-lab/ml-bio-workshop/>.
 Click the `Clone or download` button followed by `Download ZIP`.
 
 <p align="center">
@@ -43,10 +43,10 @@ Click the `Clone or download` button followed by `Download ZIP`.
 
 Save the file `ml-bio-workshop-master.zip` and then open that location on your computer.
 Extract the zip file and open the folder `ml-bio-workshop-master`, which has the same contents as <https://github.com/gitter-lab/ml-bio-workshop/>.
-You are now ready to install the Python dependencies needed to run the ML4Bio software and follow the workshop exercises.
+You are now ready to install the Python dependencies needed to run the ml4bio software and follow the workshop exercises.
 
 ### Install Python
-ML4Bio requires Python and several other Python packages.
+ml4bio requires Python and several other Python packages.
 The easiest way to install Python and the correct version of these packages is through [Anaconda](https://anaconda.com/), a Python distribution.
 If you do not have Anaconda installed, please visit <https://www.anaconda.com/download/> to download and install the Python 3.x version (for example, 3.7).
 **We recommend letting the Anaconda installer add Anaconda to your computer's `PATH` environment variable so that it is easily accessible from the command line.**
@@ -58,9 +58,9 @@ If you do not have Anaconda installed, please visit <https://www.anaconda.com/do
 This will also make Anaconda your primary Python distribution.
 See the [Carpentries Anaconda installation instructions](http://carpentries.github.io/workshop-template/#python) for a step-by-step guide and video on how to install Anaconda for your operating system.
 
-### Launch the ML4Bio software
+### Launch the ml4bio software
 After you install Anaconda, return to the unzipped `ml-bio-workshop-master` directory and open the `scripts` subdirectory.
-There are wrapper scripts that will run ML4Bio inside a [conda environment](#software-environment-details).
+There are wrapper scripts that will run ml4bio inside a [conda environment](#software-environment-details).
 If the environment does not already exist, it will be created.
 This can take 5-10 minutes and requires internet connectivity to download the Python packages.
 - For **Windows**, launch the `install_launch_windows.bat` script.
@@ -77,14 +77,14 @@ For Windows, launch the Anaconda Prompt (formerly Anaconda Command Prompt) and t
 For Linux or Mac OS, open the terminal and navigate to the `ml-bio-workshop-master/scripts` directory.
 Then, enter the name of the script for your operating system.
 
-Visit the [software guide](software.md) to learn more about the ML4Bio software functionality.
-See the [software environment details](#software-environment-details) for more information about how the ML4Bio software works.
+Visit the [software guide](software.md) to learn more about the ml4bio software functionality.
+See the [software environment details](#software-environment-details) for more information about how the ml4bio software works.
 
 ### Troubleshooting
 You must extract the contents of the `ml-bio-workshop-master.zip` workshop materials file.
 Even though you may be able to browse the compressed directory to inspect the files, the software installation will not work until the file is unzipped.
 
-Launching ML4Bio from the command line can resolve many common problems related to Anaconda and how it was installed.
+Launching ml4bio from the command line can resolve many common problems related to Anaconda and how it was installed.
 
 If you did not add Anaconda to your `PATH` during installation and would like to, follow these instructions for Windows 10:
 - Start -> Type "Path" -> Edit environment variables for your account
@@ -95,17 +95,15 @@ This warning can be ignored.
 
 See also known [software warnings](../scripts/README.md#warnings) that can be safely ignored.
 
-### Updating ML4Bio
-New versions of the ML4Bio software will be periodically released through [PyPI](https://pypi.org/project/ml4bio/).
+### Updating ml4bio
+New versions of the ml4bio software will be periodically released through [PyPI](https://pypi.org/project/ml4bio/).
 The [release notes](https://github.com/gitter-lab/ml4bio/releases) describe the changes in each new version.
-To install the latest version of ML4Bio, run the appropriate update script for your operating system:
+To install the latest version of ml4bio, run the appropriate update script for your operating system:
 - `update_ml4bio_windows.bat`
 - `update_ml4bio_mac.command`
 - `update_ml4bio_linux.sh`
 
 Run these scripts in the same manner as the install scripts above.
 
 
-
-
 {% include links.md %}