Merge pull request #240 from ga4gh-beacon/website-docs

Website docs update

Author: costero-e

README.md

@@ -1,4 +1,4 @@
-# Unified repository for Beacon v2 Code & Documentation
+# Unified repository for Beacon Code & Documentation
 
 ## Description
 
@@ -8,7 +8,7 @@ This repository is a unified repository representing the different parts of the
 * [models](models)
 * Beacon v2 Documentation
     - authoritive source already in this repository [`/docs`](docs)
-    - rendered version through [here](https://beacon-project.io/beacon-v2/) (alternative address is [docs.genomebeacons.org](https://docs.genomebeacons.org))
+    - rendered version through [here](https://genomebeacons.org/beacon-v2/) (alternative address is [docs.genomebeacons.org](https://docs.genomebeacons.org))
 
 As with other schema projects, here we separate between the schema source files (in `src`; JSON-Schema written in YAML) and the generated versions for referencing. The current setup allows already the direct referencing of the generated JSON schemas. Examples:
 

bin/_jsonref2json.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-#   Script to dereference JSON $ref in Beacon v2 Models schemas
+#   Script to dereference JSON $ref in Beacon Models schemas
 #
 #    ------------ DEPRECATED ------------
 #   *******************************************************

docs/FAQ.md

@@ -1,2 +1,2 @@
 This directory contains the Beacon documentation. The files here are rendered through
-MkDocs and available at [beacon-project.io/beacon-v2/](https://beacon-project.io/beacon-v2/).
+MkDocs and available at [genomebeacons.org/beacon-v2/](https://genomebeacons.org/beacon-v2/).

docs/README.md

@@ -1,7 +1,7 @@
 # Beacon "Flavours"
 
 !!! Note "About UI"
-    Most of the information that you will find here is related to the [Beacon v2 specification](/). For that reason, the examples are shown as REST API requests/responses in the form of [JSON](https://www.json.org/json-en.html). If you are only interested in using beacon with a **graphical interface** please visit the [implementations](implementations-options.md) page.
+    Most of the information that you will find here is related to the [Beacon {{config.beacon_major_version}} specification](/). For that reason, the examples are shown as REST API requests/responses in the form of [JSON](https://www.json.org/json-en.html). If you are only interested in using beacon with a **graphical interface** please visit the [implementations](implementations-options.md) page.
 
 While the original Beacon v1 only provided Boolean (_i.e._ **YES/NO**) responses
 on queries for the existence of specific genomic variants, Beacon v2 is a flexible
@@ -24,9 +24,10 @@ with a _true_ or _false_ value when queried for the existence of some data in a
 a _Count Response_ Beacon only returns aggregate information, _i.e._ the number of matched
 entries (e.g. genomic variants), a feature also part of the Beacon v1 protocol.
 
-However, in contrast to earlier versions, in Beacon v2 _in principle_ a beaconized resource
-may implement all types of query options (e.g. combinations of various filters and
-genomic query parameters) but still only offer a Boolean and optionally Count response.
+However, in contrast to earlier versions, in Beacon {{config.beacon_major_version}}
+_in principle_ a beaconized resource may implement all types of query options
+(e.g. combinations of various filters and genomic query parameters) but still
+only offer a Boolean and optionally Count response.
 
 Also, all Beacons _should_ implement the _Boolean Response_ format as fallback option and
 handle extended options depending on the user's authentication status.
@@ -84,6 +85,5 @@ Information about the different data delivery options can be found here:
 
 
 
-
 [^1]: Privacy protecting as in "reasonably protecting by design but not immune to complex
 re-identification attacks".

docs/beacon-flavours.md

@@ -5,6 +5,23 @@ of the Beacon project site(s) as well as with overarching repository organizatio
 
 ## Changes
 
+### 2024-08-08: [genomebeacons.org](https://genomebeacons.org) now default Beacon domain
+
+We have now migrated towards general use fo the `genomebeacons.org` domain for
+Beacon-related services and documentation. The main addresses are:
+
+* [genomebeacons.org](https://genomebeacons.org) - main site for information, news ...
+* [docs.genomebeacons.org](https://docs.genomebeacons.org) - documentation site for API development and implementations
+
+In due course we will disentangle the current pages and purge the more general Beacon
+information from [docs.genomebeacons.org](https://docs.genomebeacons.org). A start
+has been made with the **F**requently **A**sked **Q**uestions section which is now under
+[genomebeacons.org/FAQ](https://genomebeacons.org/FAQ).
+
+The old domain [beacon-project.io](https://beacon-project.io) still exists but
+is only used for forwarding.
+
+
 ### 2023-06-12: Restructured and extended documentation
 
 * new separation of navigation areas into "Introducing Beacon", "Using Beacons",
@@ -102,7 +119,7 @@ to `beacon-v2`.
 
 * Reorganization of navigation
 * Deleted page `implement-and-deploy.md`
-* Added pages: [What is Beacon v2](what-is-beacon-v2.md) and [Implementation options](implementations-options.md)
+* Added pages: [What is Beacon](what-is-beacon-v2.md) and [Implementation options](implementations-options.md)
 * [Filters](filters.md) Page Updated
 
 ### 2022-03-18: Macros and Variables for Documentation pages
@@ -120,9 +137,9 @@ The `mkdocs-macros-plugin` has been activated, allowing the use of site-wide var
 
 ### 2022-03-14: Documentation in Repository
 
-As of today the new/emerging Beacon v2 documentation is meintained in this repository. We're testing rendered versions (same text/code base) through Github actions ([here](https://beacon-project.io/beacon-v2/)) and [ReadTheDocs](https://beacon-v2-unity.readthedocs.io/en/latest/).
+As of today the new/emerging Beacon v2 documentation is meintained in this repository. We're testing rendered versions (same text/code base) through Github actions ([here](https://genomebeacons.org/beacon-v2/)) and [ReadTheDocs](https://beacon-v2-unity.readthedocs.io/en/latest/).
 
-* [x] testing of [ReadTheDocs version](https://beacon-v2-unity.readthedocs.io/) vs. a [`material` themed build](https://beacon-project.io/beacon-v2/)
+* [x] testing of [ReadTheDocs version](https://beacon-v2-unity.readthedocs.io/) vs. a [`material` themed build](https://genomebeacons.org/beacon-v2/)
 * [x] created and linked [docs.genomebeacons.org](https://docs.genomebeacons.org)
 sub-domain to the Github hosted version of the rendered documentation
 * [x] merging of previous separate documentation repository content from _beacon-v2-schema-documentation_

docs/changes-todo.md

@@ -2,6 +2,9 @@
 
 The development of Beacon code and documentation happens in the [`beacon-v2` repository](https://github.com/ga4gh-beacon/beacon-v2).
 
+[![Branch Structure](img/Beacon2API_branch_decision_tree.png)](img/Beacon2API_branch_decision_tree.png)
+
+
 ## Core branches
 
 ### `main`
@@ -44,6 +47,8 @@ Some of the instances of the schema were missing attributes and other aspects th
 
 <b>Current status:</b><span style="color:blue">Waiting for PR to be accepted.</span>
 
+
+
 ## Feature and subfeature branches
 
 The feature branches are the branches that bring a lot of changes together to change some specific part of the specifications. They can be composed by different subfeature branches that commit to them or just have one single working branch. The feature branches commit to the `develop` branch as they are the changes that will lead beacon to be upgraded to a new version. The subfeature branches commit to their parent feature branch, as they are a microchange of all the aspects that have to change in a new feature that is being developed. The branches are named as the main purpose of them, so it is made very clear what is the working area of them and the subfeature branches add the name of the feature branch they belong as a prefix followed by an underscore. The list of these feature branches with their subfeature branches is the one shown next:

docs/code-organization.md

@@ -5,4 +5,5 @@ and Health [**GA4GH**](https://ga4gh.org). Since 2016 Beacon development has bee
 organized through projects supported by ELIXIR with additional contributions from
 outside organizations and individual developers and implementers.
 
-==TBD==
+The easiest way to contribute to Beacon development - or to enquire about or 
+request additional features - is through the project's Github{{config.repo_icon}} [issues]({{config.repo_url}}/issues) and [discussions]({{config.repo_url}}/discussions).

docs/contribute.md

@@ -3,7 +3,7 @@
 }
 
 .md-grid {
-  max-width: 1024px; 
+  max-width: 1200px; 
 }
 
 .md-header__source {