Merge pull request #1 from common-workflow-language/gh-pages

Merge recent updates from carpentry repo

Author: tobyhodges

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,9 @@
+Please delete the text below before submitting your contribution. 
+
+---
+
+Thanks for contributing! If this contribution is for instructor training, please send an email to [email protected] with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  
+
+Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck ([email protected]).  
+
+---

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,9 @@
+Please delete the text below before submitting your contribution. 
+
+---
+
+Thanks for contributing! If this contribution is for instructor training, please send an email to [email protected] with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  
+
+Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck ([email protected]).  
+
+---

AUTHORS

@@ -0,0 +1 @@
+FIXME: list authors' names and email addresses.

CITATION

@@ -0,0 +1 @@
+FIXME: describe how to cite this lesson.

CONDUCT.md

@@ -10,35 +10,8 @@ updating documentation,
 submitting pull requests or patches,
 and other activities.
 
-We are committed to making participation in this project a harassment-free experience for everyone,
-regardless of level of experience,
-gender,
-gender identity and expression,
-sexual orientation,
-disability,
-personal appearance,
-body size,
-race,
-ethnicity,
-age,
-or religion.
+The CWL Project is dedicated to providing a harassment-free experience for everyone, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, age, race, or religion. We do not tolerate harassment of participants in any form.
 
-Examples of unacceptable behavior by participants include the use of sexual language or imagery,
-derogatory comments or personal attacks,
-trolling,
-public or private harassment,
-insults,
-or other unprofessional conduct.
+This code of conduct applies to all CWL Project spaces, including the Google Group, the Gitter chat room, the Google Hangouts chats, both online and off. Anyone who violates this code of conduct may be sanctioned or expelled from these spaces at the discretion of the leadership team.
 
-Project maintainers have the right and responsibility to remove, edit, or reject
-comments, commits, code, wiki edits, issues, and other contributions
-that are not aligned to this Code of Conduct.
-Project maintainers who do not follow the Code of Conduct may be removed from the project team.
-
-Instances of abusive, harassing, or otherwise unacceptable behavior
-may be reported by opening an issue or contacting one or more of the project maintainers.
-
-This Code of Conduct is adapted from
-the [Contributor Covenant][contrib-covenant] Version 1.0.0.
-
-[contrib-covenant]: http://contributor-covenant.org/
+For more details, see our https://github.com/common-workflow-language/common-workflow-language/blob/master/CODE_OF_CONDUCT.md

CONTRIBUTING.md

@@ -0,0 +1,150 @@
+# Contributing
+
+The [Common Workflow Language project](cwl-site) is an open source project,
+and we welcome contributions of all kinds:
+new lessons,
+fixes to existing material,
+bug reports,
+and reviews of proposed changes are all welcome.
+
+## Contributor Agreement
+
+By contributing,
+you agree that we may redistribute your work under [our license](LICENSE.md).
+In exchange,
+we will address your issues and/or assess your change proposal as promptly as we can,
+and help you become a member of our community.
+Everyone involved in the [Common Workflow Language project](cwl-site)
+agrees to abide by our [code of conduct](CONDUCT.md).
+
+## How to Contribute
+
+The easiest way to get started is to file an issue
+to tell us about a spelling mistake,
+some awkward wording,
+or a factual error.
+This is a good way to introduce yourself
+and to meet some of our community members.
+
+1.  If you do not have a [GitHub][github] account,
+    you can [send us comments by email][contact].
+    However,
+    we will be able to respond more quickly if you use one of the other methods described below.
+
+2.  If you have a [GitHub][github] account,
+    or are willing to [create one][github-join],
+    but do not know how to use Git,
+    you can report problems or suggest improvements by [creating an issue][issues].
+    This allows us to assign the item to someone
+    and to respond to it in a threaded discussion.
+
+3.  If you are comfortable with Git,
+    and would like to add or change material,
+    you can submit a pull request (PR).
+    Instructions for doing this are [included below](#using-github).
+
+## Where to Contribute
+
+1.  If you wish to change this lesson,
+    please work in <https://github.com/common-workflow-language/user_guide>,
+    which can be viewed at <https://swcarpentry.github.io/FIXME>.
+
+2.  If you wish to change the example lesson,
+    please work in <https://github.com/swcarpentry/lesson-example>,
+    which documents the format of our lessons
+    and can be viewed at <https://swcarpentry.github.io/lesson-example>.
+
+3.  If you wish to change the template used for workshop websites,
+    please work in <https://github.com/swcarpentry/workshop-template>.
+    The home page of that repository explains how to set up workshop websites,
+    while the extra pages in <https://swcarpentry.github.io/workshop-template>
+    provide more background on our design choices.
+
+4.  If you wish to change CSS style files, tools,
+    or HTML boilerplate for lessons or workshops stored in `_includes` or `_layouts`,
+    please work in <https://github.com/swcarpentry/styles>.
+
+## What to Contribute
+
+There are many ways to contribute,
+from writing new exercises and improving existing ones
+to updating or filling in the documentation
+and and submitting [bug reports][issues]
+about things that don't work, aren't clear, or are missing.
+If you are looking for ideas,
+please see [the list of issues for this repository][issues],
+or the issues for [Common Workflow Language](cwl-issues) project itself.
+
+Comments on issues and reviews of pull requests are just as welcome:
+we are smarter together than we are on our own.
+Reviews from novices and newcomers are particularly valuable:
+it's easy for people who have been using these lessons for a while
+to forget how impenetrable some of this material can be,
+so fresh eyes are always welcome.
+
+<!--
+## What *Not* to Contribute
+
+Our lessons already contain more material than we can cover in a typical workshop,
+so we are usually *not* looking for more concepts or tools to add to them.
+As a rule,
+if you want to introduce a new idea,
+you must (a) estimate how long it will take to teach
+and (b) explain what you would take out to make room for it.
+The first encourages contributors to be honest about requirements;
+the second, to think hard about priorities.
+
+We are also not looking for exercises or other material that only run on one platform.
+Our workshops typically contain a mixture of Windows, Mac OS X, and Linux users;
+in order to be usable,
+our lessons must run equally well on all three.
+-->
+## Using GitHub
+
+If you choose to contribute via GitHub,
+you may want to look at
+[How to Contribute to an Open Source Project on GitHub][how-contribute].
+In brief:
+
+1.  The published copy of the lesson is in the `gh-pages` branch of the repository
+    (so that GitHub will regenerate it automatically).
+    Please create all branches from that,
+    and merge the [master repository][repo]'s `gh-pages` branch into your `gh-pages` branch
+    before starting work.
+    Please do *not* work directly in your `gh-pages` branch,
+    since that will make it difficult for you to work on other contributions.
+
+2.  We use [GitHub flow][github-flow] to manage changes:
+    1.  Create a new branch in your desktop copy of this repository for each significant change.
+    2.  Commit the change in that branch.
+    3.  Push that branch to your fork of this repository on GitHub.
+    4.  Submit a pull request from that branch to the [master repository][repo].
+    5.  If you receive feedback,
+        make changes on your desktop and push to your branch on GitHub:
+        the pull request will update automatically.
+
+Each lesson has two maintainers who review issues and pull requests
+or encourage others to do so.
+The maintainers are community volunteers,
+and have final say over what gets merged into the lesson.
+
+## Other Resources
+
+General discussion of [Common Workflow Language](cwl-site) project
+happens on the [discussion mailing list][discuss-list],
+which everyone is welcome to join.
+
+[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
+[dc-lessons]: http://datacarpentry.org/lessons/
+[dc-site]: http://datacarpentry.org/
+[discuss-list]: https://groups.google.com/forum/#!forum/common-workflow-language
+[github]: http://github.com
+[github-flow]: https://guides.github.com/introduction/flow/
+[github-join]: https://github.com/join
+[how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
+[issues]: https://github.com/common-workflow-language/user_guide/issues
+[repo]: https://github.com/common-workflow-language/user_guide
+[swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
+[swc-lessons]: http://software-carpentry.org/lessons/
+[swc-site]: http://software-carpentry.org/
+[cwl-site]: http://www.commonwl.org/

LICENSE.md

@@ -5,8 +5,12 @@ permalink: /license/
 ---
 ## Instructional Material
 
-All Software Carpentry and Data Carpentry instructional material is
-made available under the [Creative Commons Attribution
+This material is derived from a framework created by the Software Carpentry
+and Data Carpentry projects under the [Creative Commons Attribution
+license][cc-by-human].
+
+All Common Workflow Language project instructional material and changes
+to the structure are also made available under the [Creative Commons Attribution
 license][cc-by-human]. The following is a human-readable summary of
 (and not a substitute for) the [full legal text of the CC BY 4.0
 license][cc-by-legal].
@@ -24,9 +28,9 @@ license terms.
 Under the following terms:
 
 * **Attribution**---You must give appropriate credit (mentioning that
-  your work is derived from work that is Copyright © Software
-  Carpentry and, where practical, linking to
-  http://software-carpentry.org/), provide a [link to the
+  your work is derived from work that is Copyright © the Common Workflow
+  Language project, and Copyright © Software Carpentry, and, where practical, linking to
+  http://www.commonwl.org/ and http://software-carpentry.org/), provide a [link to the
   license][cc-by-human], and indicate if changes were made. You may do
   so in any reasonable manner, but not in any way that suggests the
   licensor endorses you or your use.
@@ -48,28 +52,15 @@ Notices:
 ## Software
 
 Except where otherwise noted, the example programs and other software
-provided by Software Carpentry and Data Carpentry are made available under the
+provided by Common Workflow Language project are made available under the
 [OSI][osi]-approved
-[MIT license][mit-license].
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+[Apache 2.0 license][apache-2.0-license].
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
 
 ## Trademark
 
@@ -78,6 +69,6 @@ are registered trademarks of [NumFOCUS][numfocus].
 
 [cc-by-human]: https://creativecommons.org/licenses/by/4.0/
 [cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
-[mit-license]: http://opensource.org/licenses/mit-license.html
+[apache-2.0-license]: https://opensource.org/licenses/Apache-2.0
 [numfocus]: http://numfocus.org/
 [osi]: http://opensource.org

README.md

@@ -0,0 +1,6 @@
+
+WIP re-structuring and expansion of the CWL v1.0 user guide
+
+http://www.commonwl.org/v1.0/UserGuide.html
+which is built from
+https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/UserGuide.yml

_config.yml

@@ -0,0 +1,73 @@
+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this ("swc", "dc", "lc", or "cwl")?
+carpentry: "cwl"
+
+# Overall title for pages.
+title: "Lesson Title"
+
+# Contact.  This *must* include the protocol: if it's an email
+# address, it must look like "mailto:[email protected]",
+# or if it's a URL, "https://gitter.im/username/ProjectName".
+contact: "mailto:[email protected]"
+
+#------------------------------------------------------------
+# Generic settings (should not need to change).
+#------------------------------------------------------------
+
+# What kind of thing is this ("workshop" or "lesson")?
+kind: "lesson"
+
+# Magic to make URLs resolve both locally and on GitHub.
+# See https://help.github.com/articles/repository-metadata-on-github-pages/.
+repository: <USERNAME>/<PROJECT>
+
+# Sites.
+amy_site: "https://amy.software-carpentry.org/workshops"
+dc_site: "http://datacarpentry.org"
+swc_github: "https://github.com/swcarpentry"
+swc_site: "https://software-carpentry.org"
+swc_pages: "https://swcarpentry.github.io"
+lc_site: "http://librarycarpentry.github.io/"
+template_repo: "https://github.com/swcarpentry/styles"
+example_repo: "https://github.com/swcarpentry/lesson-example"
+example_site: "https://swcarpentry.github.com/lesson-example"
+workshop_repo: "https://github.com/swcarpentry/workshop-template"
+workshop_site: "https://swcarpentry.github.io/workshop-template"
+training_site: "https://swcarpentry.github.io/instructor-training"
+
+# Surveys.
+pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id="
+post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id="
+training_post_survey: "https://www.surveymonkey.com/r/post-instructor-training"
+
+# Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am).
+start_time: 0
+
+# Specify that things in the episodes collection should be output.
+collections:
+  episodes:
+    output: true
+    permalink: /:path/
+  extras:
+    output: true
+
+# Set the default layout for things in the episodes collection.
+defaults:
+  - values:
+      root: ..
+  - scope:
+      path: ""
+      type: episodes
+    values:
+      layout: episode
+
+# Files and directories that are not to be copied.
+exclude:
+  - Makefile
+  - bin
+
+# Turn off built-in syntax highlighting.
+highlighter: false

_episodes/01-introduction.md

@@ -0,0 +1,15 @@
+---
+title: "Introduction"
+teaching: 0
+exercises: 0
+questions:
+- "Key question"
+objectives:
+- "First objective."
+keypoints:
+- "First key point."
+---
+Content here
+
+{% include links.md %}
+