title: "Contributor Code of Conduct"
---
As contributors and maintainers of this project,
-we pledge to follow the [Carpentry Code of Conduct][coc].
+we pledge to follow the [Arvados Code of Conduct][coc].
Instances of abusive, harassing, or otherwise unacceptable behavior
-may be reported by following our [reporting guidelines][coc-reporting].
+may be reported by contacting [Curii Corporation][coc-reporting].
{% include links.md %}
+---
+layout: page
+title: "Contributing"
+---
# Contributing
-[The Carpentries][c-site] ([Software Carpentry][swc-site], [Data Carpentry][dc-site], and [Library Carpentry][lc-site]) are open source projects,
+[Arvados](https://arvados.org) 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.
+The source to this lesson can be found at [git.arvados.org/rnaseq-cwl-training.git](https://git.arvados.org/rnaseq-cwl-training.git/), it is also
+mirrored at <https://github.com/common-workflow-lab/rnaseq-cwl-training>.
+
## Contributor Agreement
By contributing,
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 Carpentries][c-site]
+Everyone involved
agrees to abide by our [code of conduct](CODE_OF_CONDUCT.md).
## How to Contribute
## Where to Contribute
1. If you wish to change this lesson,
- please work in <https://github.com/swcarpentry/FIXME>,
- 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/carpentries/lesson-example>,
- which documents the format of our lessons
- and can be viewed at <https://carpentries.github.io/lesson-example>.
-
-3. If you wish to change the template used for workshop websites,
- please work in <https://github.com/carpentries/workshop-template>.
- The home page of that repository explains how to set up workshop websites,
- while the extra pages in <https://carpentries.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/carpentries/styles>.
+ please make a pull request against <https://github.com/common-workflow-lab/rnaseq-cwl-training>.
## What to Contribute
and submitting [bug reports][issues]
about things that do not work, aren not clear, or are missing.
If you are looking for ideas, please see the 'Issues' tab for
-a list of issues associated with this repository,
-or you may also look at the issues for [Data Carpentry][dc-issues],
-[Software Carpentry][swc-issues], and [Library Carpentry][lc-issues] projects.
+a list of issues associated with this repository.
Comments on issues and reviews of pull requests are just as welcome:
we are smarter together than we are on our own.
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, macOS, 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].
-To manage changes, we follow [GitHub flow][github-flow].
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.
To use the web interface for contributing to a lesson:
---
## Instructional Material
-All Software Carpentry, Data Carpentry, and Library Carpentry instructional material is
+All instructional material is
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
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 © Arvados Project and, where practical, linking to
+ http://arvados.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.
## Software
Except where otherwise noted, the example programs and other software
-provided by Software Carpentry and Data Carpentry are made available under the
-[OSI][osi]-approved
-[MIT license][mit-license].
+provided in Arvados documentation and training are made available under the
+[OSI][osi]-approved [Apache 2.0 license](https://opensource.org/licenses/Apache-2.0).
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
## Trademark
-"Software Carpentry" and "Data Carpentry" and their respective logos
-are registered trademarks of [Community Initiatives][CI].
+"Arvados" is a registered trademarks of [Curii Corporation][curii].
[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
[mit-license]: https://opensource.org/licenses/mit-license.html
[ci]: http://communityin.org/
[osi]: https://opensource.org
+[curii]: https://curii.com
$(sort $(wildcard _episodes/*.md)) \
reference.md \
$(sort $(wildcard _extras/*.md)) \
- LICENSE.md
+ LICENSE.md \
+ CONTRIBUTING.md
# Generated lesson files in the order they appear in the navigation menu.
HTML_DST = \
# Life cycle stage of the lesson
# See this page for more details: https://cdh.carpentries.org/the-lesson-life-cycle.html
# Possible values: "pre-alpha", "alpha", "beta", "stable"
-life_cycle: "beta"
+life_cycle: "stable"
#------------------------------------------------------------
# Generic settings (should not need to change).
<footer>
<div class="row">
<div class="col-md-6 license" id="license-info" align="left">
- {% if site.carpentry == "swc" %}
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
- 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" }}
- 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
- 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" }}
- 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" }}
- by <a href="{{ site.carpentries_site }}">The Carpentries</a>
- {% endif %}
+ by <a href="https://curii.com">Curii Corporation</a>
</div>
<div class="col-md-6 help-links" align="right">
- {% if page.source %}
- {% if page.source == "Rmd" %}
- <a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Edit on GitHub</a>
- {% endif %}
- {% else %}
- <a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path}}" data-checker-ignore>Edit on GitHub</a>
- {% endif %}
- /
- <a href="{{ repo_url }}/blob/{{ source_branch }}/CONTRIBUTING.md" data-checker-ignore>Contributing</a>
- /
- <a href="{{ repo_url }}/">Source</a>
+ <a href="{{ relative_root_path }}{% link CONTRIBUTING.md %}" data-checker-ignore>Contributing</a>
/
- <a href="{{ repo_url }}/blob/{{ source_branch }}/CITATION" data-checker-ignore>Cite</a>
+ <a href="https://git.arvados.org/rnaseq-cwl-training.git/">Source</a>
/
<a href="mailto:{{ site.email }}">Contact</a>
</div>
[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
[ci]: http://communityin.org/
-[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
-[coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html
+[coc-reporting]: mailto:info@curii.com
+[coc]: https://git.arvados.org/arvados.git/blob/HEAD:/CODE_OF_CONDUCT.md
[concept-maps]: https://carpentries.github.io/instructor-training/05-memory/
[contrib-covenant]: https://contributor-covenant.org/
[contributing]: {{ repo_url }}/blob/{{ source_branch }}/CONTRIBUTING.md
[lesson-reference]: {{ relative_root_path }}{% link reference.md %}
[lesson-setup]: {{ relative_root_path }}{% link setup.md %}
[mit-license]: https://opensource.org/licenses/mit-license.html
+[apache-license]: https://opensource.org/licenses/Apache-2.0
[morea]: https://morea-framework.github.io/
[numfocus]: https://numfocus.org/
[osi]: https://opensource.org
</button>
{% comment %} Select what logo to display. {% endcomment %}
- {% if site.carpentry == "swc" %}
- <a href="{{ site.swc_site }}" class="pull-left">
+ <a href="https://doc.arvados.org" class="pull-left">
<img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/swc-icon-blue.svg %}" alt="Software Carpentry logo" />
</a>
- {% elsif site.carpentry == "dc" %}
- <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>
- {% elsif site.carpentry == "lc" %}
- <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>
- {% elsif site.carpentry == "cp" %}
- <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>
- {% endif %}
{% comment %} Always show link to home page. {% endcomment %}
<a class="navbar-brand" href="{{ relative_root_path }}{% link index.md %}">Home</a>
{% comment %} Always show license. {% endcomment %}
<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>
- {% 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>
- {% endif %}
+ <li><a href="{{ relative_root_path }}{% link CONTRIBUTING.md %}">Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
</ul>
<form class="navbar-form navbar-right" role="search" id="search" onsubmit="google_search(); return false;">
<div class="form-group">
---
This training will walk you through the development of a
-best-practices CWL workflow. At the conclusion of this training, you
+best-practices Common Workflow Language (CWL) workflow. At the conclusion of this training, you
should have a grasp of the essential components of a workflow, and
have a basis for learning more.
projects / rnaseq-cwl-training.git / commitdiff