docs: restructure docs and update branding

.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] |

docs/guides/guide-contributor/general-guidelines.md → docs/contribute/general-guidelines.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.,

docs/guides/guide-contributor/index.md → docs/contribute/index.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/language-specific/python.md → docs/contribute/language-specific/python.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

docs/guides/guide-contributor/managing-projects.md → docs/contribute/managing-projects.md

@@ -12,7 +12,7 @@ root directory:
 
 - **README** in file `README.md`
 - **Code of Conduct** in file `CODE_OF_CONDUCT.md` (can link to the [Code of
-  Conduct](../../about/code-of-conduct.md) on this page)
+  Conduct](../about/code-of-conduct.md) on this page)
 - **Contributing guidelines** in file `CONTRIBUTING.md` (can link to the
   [contributor guide](index.md) on this page)
 - **License** in file `LICENSE`
@@ -88,7 +88,7 @@ sections (fill in with "Coming soon" if not yet available):
 - **Versioning**: Information on how the project is versioned
 - **Contributing**: Guidelines on how to contribute to the project, with links
     to the [contributing guidelines](index.md) and our
-    [code of conduct](../../about/code-of-conduct.md)
+    [code of conduct](../about/code-of-conduct.md)
 - **Contact**: Information on how to contact the project leads
 
 ### Hosted documentation

docs/guides/guide-contributor/workflow.md → docs/contribute/workflow.md

@@ -3,17 +3,17 @@
 To start working with us, please follow these simple steps:
 
 1. Join [:custom-github-black: GitHub][github-join].
-2. Check out our [repositories][elixir-cloud-aai-github] and [open
-   issues][elixir-cloud-aai-issues].
-3. Join our [:custom-slack: Slack board][elixir-cloud-aai-slack] (please [let us
-   know](../../about/contact.md) if the link expired).
-4. Join the [`#oss-community`][elixir-cloud-aai-slack-channel-oss] and leave
+2. Check out our [repositories][elixir-on-cloud-github] and [open
+   issues][elixir-on-cloud-issues].
+3. Join our [:custom-slack: Slack board][elixir-on-cloud-slack] (please [let us
+   know](../about/contact.md) if the link expired).
+4. Join the [`#oss-community`][elixir-on-cloud-slack-channel-oss] and leave
    a short message about yourself. Please include (1) your relevant skills and
    experience level, (2) your GitHub username, (3) your email address (e.g.,
    for calendar invitations), and (4) the repositories or issues you are most
    interested in. If you can't decide, no problem, just indicate that you are
    open to work on anything and we will suggest some issues for you.
-5. Once we have added you to our [GitHub organization][elixir-cloud-aai-github],
+5. Once we have added you to our [GitHub organization][elixir-on-cloud-github],
    you can assign yourself to an issue.
 6. Please carefully read the [guidelines](general-guidelines.md) below, as well
    as any relevant [language-specific guidelines](language-specific/index.md).
@@ -25,7 +25,7 @@ To start working with us, please follow these simple steps:
 
     If you do not want to share your GitHub username and/or your email address
     in the public channel, please send a direct message to a
-    [project lead][elixir-cloud-aai-contributors] instead.
+   [project lead][elixir-on-cloud-contributors] instead.
 
 !!! note "Always work on issues"
 

docs/guides/guide-user/index.md → docs/general/ga4gh_cloud.md

@@ -1,14 +1,4 @@
-# User guide
-
-## Introduction
-
-Welcome to the user documentation for the ELIXIR Cloud & AAI ecosystem. With
-this powerful set of services, you'll be able to easily access cloud resources
-and send analysis pipelines to your data with just a few simple commands.
-Imagine being able to run complex genomic analyses on massive datasets without
-worrying about infrastructure limitations or having to manage complex server
-environments. The GA4GH Cloud APIs give you access to powerful tools and
-resources that allow you to focus on your research goals, not IT.
+# GA4GH Cloud Workstream
 
 The GA4GH (Global Alliance for Genomics and Health) cloud [APIs][ga4gh-cloud]
 are a set of standard APIs that provide a common interface for accessing
@@ -24,20 +14,11 @@ while the TES API allows you to execute individual tasks within those
 workflows. The DRS API provides a way to access and download genomic data, and
 the TRS API enables the discovery of genomic analysis tools.
 
-Whether you are a bioinformatician or a data scientist, this documentation will
+Whether you are a bioinformatician or a data scientist, this site will
 provide you with all the information you need to start using ELIXIR's GA4GH
 cloud services ecosystem and harness the power of cloud computing for your
 genomic data analysis needs. Let's get started!
 
-## ELIXIR Cloud & AAI deployments
-
-The ELIXIR Cloud & AAI group manages different services and appliocations as
-part of the ELIXIR cloud framework. Currently, these services are temporarily
-listed in a dedicated [services list applications][elixir-cloud-services].  In
-the mid-term, all services instances will be registered in the [ELIXIR Cloud
-Registry][elixir-cloud-registry], an implementation of the [GA4GH Service
-Registry API][ga4gh-service-registry].
-
 ## Task Execution Service (TES)
 
 The GA4GH [TES][ga4gh-tes] specification is a standard interface that enables
@@ -100,6 +81,7 @@ plugins {
 ```
 
 ## Workflow Execution Service (WES)
+
 The GA4GH [WES][ga4gh-wes] is a standard specification protocol for executing
 and monitoring bioinformatics workflows. It allows researchers to easily
 execute and manage complex analysis pipelines across multiple computing
@@ -128,14 +110,14 @@ specification are:
 The GA4GH [DRS][ga4gh-drs] API provides a standard set of data retrieval methods
 to access genomic and related health data across different repositories.
 It allows researchers to simplify and standardize data retrieval in cloud-based
-environements. Some key features like Standardized data access that offers a consistent
-API for retrieving datasets. Cloud-agnostic means that it works accross different
+environments. Some key features like Standardized data access that offers a consistent
+API for retrieving datasets. Cloud-agnostic means that it works across different
 cloud infrastructures. Two use cases for the GA4GH DRS:
 
 - Scenario 1: A researcher wants to run an analysis pipeline on a dataset without
   worrying about where the data physically resides. The researcher uses a DRS ID
   to request the dataset. DRS resolves the ID to the actual storage location and
-  provides signed URLs or access tokens and the pipeline retrievess the data
+  provides signed URLs or access tokens and the pipeline retrieves the data
   seamlessly, regardless of the underlying cloud or storage system.
 
 - Scenario 2: A pharmaceutical company is collaborating with hospitals to analyze
@@ -147,7 +129,7 @@ cloud infrastructures. Two use cases for the GA4GH DRS:
 ## Tool Registry Service (TRS)
 
 The GA4GH [TRS][ga4gh-trs] API provides a standard mechanism to list, search and
-register tools and worflows across different platforms and cloud environments.
+register tools and workflows across different platforms and cloud environments.
 It supports workflows written in CWL, WDL, Nextflow, Galaxy, Snakemake.
 Here are examples of two use cases:
 
@@ -163,4 +145,4 @@ Here are examples of two use cases:
   exome data for rare disease diagnosis. The pipeline queries a TRS registry to find
   the latest version of tools (like VEP or GATK), retrieves the workflow descriptor
   and container images. Finally, the pipeline executes the tools in a secure,
-  compliant environment.
+  compliant environment.

docs/general/index.md

@@ -0,0 +1,14 @@
+# General
+
+This section provides the cross-cutting context for the ELIXIR-on-Cloud ecosystem: the standards we align with, the constraints that matter (especially for sensitive data), and practical narratives that connect researchers, data providers, and service operators.
+
+## In this section
+
+- [GA4GH Cloud Workstream](ga4gh_cloud.md)
+  Introduces the GA4GH cloud APIs that enable interoperable, federated analysis across providers. It gives background and examples for core standards used throughout this documentation (WES, TES, DRS, TRS) and how they fit into real workflows.
+
+- [Processing Sensitive Data](sensitive_data.md)
+  Summarizes key requirements and scenarios for working with sensitive human data in cloud contexts, including relevant legal/regulatory frameworks (e.g., GDPR, EHDS) and typical secure analysis environments (TEE/SPE/TRE).
+
+- [User Stories](user_stories.md)
+  Collects user stories that describe common journeys (access to services, access to data, and running analyses). Use these to align expectations between researchers, service providers, and data controllers.

docs/guides/guide-user/user_stories.md → docs/general/user_stories.md

@@ -27,4 +27,4 @@ With the elixir cloud activities, we support the development of cloud services t
 
 ## Analysis
 
-**As a researcher, I can run a specific data analysis workflow on an external dataset in the cloud, so that I can integrate the results into my research activities.** The GA4GH standardizes the execution of workflows and workflow tasks in the cloud via the specification of the [Workflow Execution Service (WES)](https://www.ga4gh.org/product/workflow-execution-service-wes/) and the [Task Execution Service (TES)](https://www.ga4gh.org/product/task-execution-service-tes/) respectively. The ELIXIR on cloud project supports the execution of workflows and tasks by developing tools and providing guidance for researchers ([user-guide](https://elixir-cloud-aai.github.io/guides/guide-user/)). A user can trigger the execution of a workflow via a WES implementation. Once the workflow has been successfully completed, the resulting data can be used by the researcher for further activities.
+**As a researcher, I can run a specific data analysis workflow on an external dataset in the cloud, so that I can integrate the results into my research activities.** The GA4GH standardizes the execution of workflows and workflow tasks in the cloud via the specification of the [Workflow Execution Service (WES)](https://www.ga4gh.org/product/workflow-execution-service-wes/) and the [Task Execution Service (TES)](https://www.ga4gh.org/product/task-execution-service-tes/) respectively. The ELIXIR-on-cloud project supports the execution of workflows and tasks by developing tools and providing guidance for researchers ([user guide](../sandbox/index.md)). A user can trigger the execution of a workflow via a WES implementation. Once the workflow has been successfully completed, the resulting data can be used by the researcher for further activities.