docs: restructure docs and update branding (#35)

Co-authored-by: Sven Twardziok <sven.twardziok@bih-charite.de>

Author: svedziok

.gitignore

@@ -1,3 +1,5 @@
 site/
 _site/
-.venv
+.venv
+.notes
+.codespell*

README.md

@@ -1,6 +1,6 @@
 # Documentation Hub
 
-Documentation for ELIXIR Cloud & AAI project.
+Documentation for the ELIXIR-on-Cloud project.
 
 ## Development
 

custom_theme/404.html

@@ -13,7 +13,7 @@
 
 
 
-        <title>ELIXIR::GA4GH Cloud Docs</title>
+        <title>ELIXIR-on-Cloud Docs</title>
 
 
 
@@ -75,7 +75,7 @@
 
 <header class="md-header" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="/." title="ELIXIR::GA4GH Cloud Docs" class="md-header__button md-logo" aria-label="ELIXIR::GA4GH Cloud Docs" data-md-component="logo">
+    <a href="/." title="ELIXIR-on-Cloud Docs" class="md-header__button md-logo" aria-label="ELIXIR-on-Cloud Docs" data-md-component="logo">
 
   <img src="/images/logo.256px.png" alt="logo">
 
@@ -87,7 +87,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            ELIXIR::GA4GH Cloud Docs
+            ELIXIR-on-Cloud Docs
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -172,12 +172,12 @@
 
 <nav class="md-nav md-nav--primary" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="/." title="ELIXIR::GA4GH Cloud Docs" class="md-nav__button md-logo" aria-label="ELIXIR::GA4GH Cloud Docs" data-md-component="logo">
+    <a href="/." title="ELIXIR-on-Cloud Docs" class="md-nav__button md-logo" aria-label="ELIXIR-on-Cloud Docs" data-md-component="logo">
 
   <img src="/images/logo.256px.png" alt="logo">
 
     </a>
-    ELIXIR::GA4GH Cloud Docs
+    ELIXIR-on-Cloud Docs
   </label>
 
     <div class="md-nav__source">

docs/about/code-of-conduct.md

@@ -1,4 +1,4 @@
-# ELIXIR Cloud & AAI Code of Conduct
+# ELIXIR-on-Cloud Code of Conduct
 
 ## Our Pledge
 

docs/about/contact.md

@@ -9,8 +9,8 @@ Get in touch with us through one of the following methods:
 
 | Method                 | Use it for |
 | --- | --- |
-| [:custom-github-black:   Issue trackers][elixir-cloud-aai-github] | Report bugs, suggest features or discuss existing issues; please try to create issues in the most relevant repository (or repositories); as an example, find [here][issue-tracker-example] the issue tracker for the repository containing this documentation |
-| [:custom-slack:   Slack][elixir-cloud-aai-slack] | Work closely together with us, e.g., if you would like to contribute or integrate your services or infrastructure with us |
-| [:custom-twitter:   Twitter][elixir-cloud-aai-twitter] | Include us in your tweets; note that our Twitter account is silent for now, i.e., as an organization, we do not tweet ourselves |
-| [:custom-forum-black:   Q&A forum][elixir-cloud-aai-forum] | Ask public Q&A style questions that can be answered by or discussed with us or anyone else |
-| [:custom-email:   Email][elixir-cloud-aai-email] | First contact for collaborations or any other private communication; for continuous communication, please join our [Slack board][elixir-cloud-aai-slack] |
+| [:custom-github-black:   Issue trackers][elixir-on-cloud-github] | Report bugs, suggest features or discuss existing issues; please try to create issues in the most relevant repository (or repositories); as an example, find [here][issue-tracker-example] the issue tracker for the repository containing this documentation |
+| [:custom-slack:   Slack][elixir-on-cloud-slack] | Work closely together with us, e.g., if you would like to contribute or integrate your services or infrastructure with us |
+| [:custom-twitter:   Twitter][elixir-on-cloud-twitter] | Include us in your tweets; note that our Twitter account is silent for now, i.e., as an organization, we do not tweet ourselves |
+| [:custom-forum-black:   Q&A forum][elixir-on-cloud-forum] | Ask public Q&A style questions that can be answered by or discussed with us or anyone else |
+| [:custom-email:   Email][elixir-on-cloud-email] | First contact for collaborations or any other private communication; for continuous communication, please join our [Slack board][elixir-on-cloud-slack] |

…ide-contributor/PULL_REQUEST_TEMPLATE.md docs/contribute/PULL_REQUEST_TEMPLATE.mddocs/guides/guide-contributor/PULL_REQUEST_TEMPLATE.md renamed to docs/contribute/PULL_REQUEST_TEMPLATE.md docs/guides/guide-contributor/PULL_REQUEST_TEMPLATE.md renamed to docs/contribute/PULL_REQUEST_TEMPLATE.md

@@ -17,8 +17,8 @@ of your ability.
 
 Please use the comment functions available on GitHub to discuss issues and
 pull requests. For all other communications please refer to the communication
-channels listed in the [contact](../../about/contact.md) section. In
-particular, use the [chat][elixir-cloud-aai-slack] to discuss project ideas,
+channels listed in the [contact](../about/contact.md) section. In
+particular, use the [chat][elixir-on-cloud-slack] to discuss project ideas,
 get help on a problem, or any other informal discussion that does not need to
 be preserved as part of the repository you are working on.
 
@@ -59,7 +59,7 @@ that code changes are always merged into protected branches via pull requests
 that will undergo one or more rounds of review and testing. The schema below
 visualizes this process.
 
-[![GitHub Flow](../../images/github_flow.svg)][github-flow]
+[![GitHub Flow](../images/github_flow.svg)][github-flow]
 
 1. [Create a "feature branch"][git-branch] from the development branch; use the
    `feature/my-feature` naming pattern to name your feature branch, e.g.,

…/guide-contributor/general-guidelines.md docs/contribute/general-guidelines.mddocs/guides/guide-contributor/general-guidelines.md renamed to docs/contribute/general-guidelines.md docs/guides/guide-contributor/general-guidelines.md renamed to docs/contribute/general-guidelines.md

@@ -3,7 +3,7 @@
 Great to see you here - we would be delighted to have you join our team! So if
 you are interested, just read on for information on how to contribute.
 
-If you don't know what [ELIXIR][elixir] [Cloud & AAI][elixir-cloud-aai] is all
+If you don't know what [ELIXIR-on-Cloud][elixir-on-cloud] is all
 about, follow the link or check out these documentation pages. Otherwise,
 please read on to find out more about the general topics you can help us with,
 our core values, what we can offer you and what we expect from contributors.
@@ -61,23 +61,23 @@ We offer you
   experts with diverse technical and cultural backgrounds
 - the opportunity to tackle modern, highly relevant technical challenges on the
   way to personalized medicine and genome-scale analytics in the cloud
-- support, feedback and appreciation for your work, as well as involvment in
+- support, feedback and appreciation for your work, as well as involvement in
   and influence on policy decisions proportional to the level of your
   engagement
 - networking opportunities within the [ELIXIR][elixir] and [GA4GH][ga4gh]
   communities, with many opinion leaders in academia and the tech industry
 
 !!! note "Regular contributors"
 
-    Check out the additional [exiciting opportunities](#opportunities) for
+  Check out the additional [exciting opportunities](#opportunities) for
     regular contributors!
 
 ## Our expectations
 
 If all of that sounds tempting and you are still interested to contribute, we
 would only expect you to please
 
-- respect our [Code of Conduct](../../about/code-of-conduct.md)
+- respect our [Code of Conduct](../about/code-of-conduct.md)
 - make an effort to adhere to good coding practices and our [contribution
 guidelines] (we will of course help you with that!)
 - communicate clearly and openly with us with regard to any issues that you
@@ -130,10 +130,10 @@ projects they were working on):
 
 ### Hackathons
 
-We regularly lead [ELIXIR][elixir] [Cloud & AAI][elixir-cloud-aai]-related
+We regularly lead [ELIXIR-on-Cloud][elixir-on-cloud]-related
 projects at various (bio)hackathons. These are always fun events and often a
 highlight of the year! Check our [news
-page][elixir-cloud-aai-news] for any upcoming events. If you are interested in
+page][elixir-on-cloud-news] for any upcoming events. If you are interested in
 attending a hackathon, please reach out to us. In some cases, we may be able
 to procure funding for contributors.
 

docs/guides/guide-contributor/index.md docs/contribute/index.mddocs/guides/guide-contributor/index.md renamed to docs/contribute/index.md

@@ -6,7 +6,7 @@ section.
 ## Python version
 
 For any _new_ projects, please use one of the two most recent [Python minor
-versions][py-downloads], exclusing pre-releases. For existing projects, use the
+versions][py-downloads], excluding pre-releases. For existing projects, use the
 Python version used throughout the project (mentioned in `pyproject.toml`).
 
 ## Packaging, build system & dependencies