Merge branch 'master' of github.com:elixir-europe/rdmkit into demo

elixir-europe · Jun 27, 2023 · f02f39d · f02f39d
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diff --git a/_data/sidebars/contribute.yml b/_data/sidebars/contribute.yml
@@ -19,10 +19,14 @@ subitems:
     url: /markdown_cheat_sheet
   - title: Page metadata
     url: /page_metadata
-  - title: Editorial board guide
-    url: /editorial_board_guide
-  - title: Editors checklist
-    url: /editors_checklist
+  - title: For editors
+    subitems:
+    - title: Editorial board guide
+      url: /editorial_board_guide
+    - title: Editors checklist
+      url: /editors_checklist
+    - title: Preview changes
+      url: /preview_changes
   - title: Code of Conduct
     url: /CODE_OF_CONDUCT
   - title: List of page IDs

diff --git a/images/change_branch.png b/images/change_branch.png
diff --git a/images/commit_new_branch.png b/images/commit_new_branch.png
diff --git a/images/create_pr_from_fork.png b/images/create_pr_from_fork.png
diff --git a/images/deploy_using_gh_actions.png b/images/deploy_using_gh_actions.png
diff --git a/images/sync_branch.png b/images/sync_branch.png
diff --git a/images/your_own_fork.png b/images/your_own_fork.png
diff --git a/pages/contribute/preview_changes.md b/pages/contribute/preview_changes.md
@@ -0,0 +1,66 @@
+---
+title: Preview changes
+summary: Use your own fork to preview changes on the website.
+---
+
+## Introduction
+
+This guide is mainly targeted at editors who have more rights than other contributors. Other contributors who want to preview their changes on their fork can skip towards the GitHub pages section right away.
+
+
+## Make changes on your fork
+
+As an editor with editing rights, changes made by clicking on the pencil icon will be committed to a branch on the main website itself. This is not a problem in normal circumstances, but when one wants to preview changes on one's own fork, this is not wanted.
+
+### 1. Make sure you have forked the main branch
+
+Click on the 'fork' button in the right top corner to find out. If a fork is present under your personal GitHub ID, click on it. 
+
+{% include image.html file="your_own_fork.png" alt="Your own fork" %}
+
+
+Make sure you are in the `main` branch of your fork seen in the left top corner.
+
+{% include image.html file="change_branch.png" alt="Change branch on GitHUb" %}
+
+
+### 2. Make sure your fork is up to date
+
+Click on the 'sync fork' button to make sure you have the latest changes of the main branch in your fork. 'Update branch'.
+
+{% include image.html file="sync_branch.png" alt="Click on the sync fork button." %}
+
+
+### 3. Make changes
+
+You can go to a folder and create a new file, or edit an existing file. See [Contributing using GitHub](/github_way) and [Creating a new page](/editorial_board_guide#create-a-new-page) for more information.
+
+### 4. Commit to a new branch
+
+This step is important. Make sure to commit to a new feature branch which you name in a logical way. 
+
+{% include image.html file="commit_new_branch.png" alt="Propose changes on GitHub" %}
+
+
+## Preview your changes using GitHub Actions
+
+- Go to Settings > Pages and enable GitHub Actions as a source
+- Go to Environments > github-pages and remove the rule under Deployment branches if you want to deploy other branches than master via Workflow Dispatch (manually triggered action)
+- Enable GitHub Actions (and use Workflow Dispatch)
+
+{% include image.html file="deploy_using_gh_actions.png" alt="Got to the settings tab in your repo to enable GitHub pages" %}
+
+
+## Open a Pull Request (PR) with you changes
+
+Got to your newly created branch and click 'Contribute'. This will create a PR to the main repository.
+
+{% include image.html file="create_pr_from_fork.png" alt="Create new PR from fork." %}
+
+You can always make changes after the creation of this pull request by going to the files changed tab 
+
+{% include image.html file="files_changed_github.png" alt="Files changed tab on GitHub" %}
+
+and clicking on the 3 dots to edit the file again. Changes made this way will become visible in your preview automatically after a few minutes.
+
+{% include image.html file="3_dots_github.png" alt="File change options on GitHub" %}
diff --git a/pages/your_tasks/machine_actionability.md b/pages/your_tasks/machine_actionability.md
@@ -210,7 +210,7 @@ Vocabularies and ontologies are meant for describing concepts and relationships
   "alternateName": "Jaguar"
   }
   ```
-* Metadata schemas and checklists can be found within [RDA curated list of Life Sciences metadata standards](https://rd-alliance.github.io/metadata-directory/subjects/life-sciences.html) or among standards in [Fairsharing.org](https://fairsharing.org/standards/).
+* Metadata schemas and checklists can be found within [RDA curated list of Life Sciences metadata standards](https://rdamsc.bath.ac.uk) or among standards in [Fairsharing.org](https://fairsharing.org/standards/).
 * Examples of standard (meta)data schemas, in different formats, in Life Sciences: 
   * [ISA-JSON (.json) and ISA-TAB (.txt)](https://isa-specs.readthedocs.io/en/latest/) - generic metadata framework originally created to describe information about multi-omics experiments.
   * [MAGE-TAB](https://www.ebi.ac.uk/arrayexpress/help/magetab_spec.html) (.txt) - MicroArray Gene Expression Tabular. The format has been developed and adopted by the functional genomics community.