Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Modified with Calire feedback: change repo name, add info on landing page, change footer #15

Merged
merged 1 commit into from
Apr 22, 2024
Merged

Modified with Calire feedback: change repo name, add info on landing page, change footer #15

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .github/workflows/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ In theory, all this could be done at deployment, but I wanted to make sure that

A series of QA checks run on the documentation.

The checks can be started manually from the ![workflow page](https://github.com/nesi/agdr-docs-concept/actions/workflows/checks.yml/badge.svg),
The checks can be started manually from the ![workflow page](https://github.com/nesi/agdr-docs/actions/workflows/checks.yml/badge.svg),
select the target branch, give the pattern of files to include, and select which checks you want done.

Checks will also be run on any _non main_ branch pushes. All checks will be run, but only on _changed_ files.
Expand Down
2 changes: 1 addition & 1 deletion .vscode/includes.code-snippets
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
// Place your agdr-docs-concept workspace snippets here. Each snippet is defined under a snippet name and has a scope, prefix, body and
// Place your agdr-docs workspace snippets here. Each snippet is defined under a snippet name and has a scope, prefix, body and
// description. Add comma separated ids of the languages where the snippet is applicable in the scope field. If scope
// is left empty or omitted, the snippet gets applied to all languages. The prefix is what is
// used to trigger the snippet and the body will be expanded and inserted. Possible variables are:
Expand Down
6 changes: 3 additions & 3 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# agdr-docs-concept
Proof of Concept for Mkdocs based AGDR support pages.
# agdr-docs
Mkdocs based AGDR support pages.

[AGDR support files example](https://nesi.github.io/agdr-docs-concept/docs/index.md)
[AGDR support files example](https://nesi.github.io/agdr-docs/docs/index.md)
20 changes: 10 additions & 10 deletions docs/CONTRIBUTING.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
---

Check warning on line 1 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check page meta

meta_missing_description 

Missing 'description' from front matter.

Check warning on line 1 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check page meta

minimum_tags 

'tags' property in meta is missing or malformed.
title: Contributing
---

**[CLICK TO VIEW THIS PAGE RENDERED IN MKDOCS](https://nesi.github.io/agdr-docs-concept/CONTRIBUTING)**{ .hidden }
**[CLICK TO VIEW THIS PAGE RENDERED IN MKDOCS](https://nesi.github.io/agdr-docs/CONTRIBUTING)**{ .hidden }

Check warning on line 5 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check Spelling

spelling 

Word 'MKDOCS' is misspelled.

!!! prerequisite "See also"
- For examples of markdown use, [see FORMAT](FORMAT.md).
- For information about page creation, [see NEWPAGE](NEWPAGE.md).

Check warning on line 9 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check Spelling

spelling 

Word 'NEWPAGE' is misspelled.

Check warning on line 9 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check Spelling

spelling 

Word 'NEWPAGE' is misspelled.

Any changes made should be merged via a pull request.

Expand All @@ -16,14 +16,14 @@

## Major edits through GitHub

This repository has been configured to be usable with [GitHub Codespaces](https://github.com/features/codespaces).

Check warning on line 19 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check Spelling

spelling 

Word 'Codespaces' is misspelled.
It allows accessing a full featured preconfigured development environment remotely, without installing anything on your local machine.

Check warning on line 20 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check Spelling

spelling 

Word 'preconfigured' is misspelled.

Clicking on the following link will open a VS Code instance ready to be used with the latest version of the documentation files.

[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nesi/agdr-docs-concept?quickstart=1)
[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nesi/agdr-docs?quickstart=1)

Check warning on line 24 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check Spelling

spelling 

Word 'Codespaces' is misspelled.

## Local Development Environment

Check warning on line 26 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check page meta

walk_toc 

Header 'Local Development Environment' is too long.  Try to keep it under 32 characters to avoid word wrapping in the toc.

A local development environment is not required to make doc edits, but if you are making lots of changes, the real time rendering can be quite helpful.

Expand All @@ -34,8 +34,8 @@
Clone this repository and create a Python virtual environment using:

```sh
git clone https://github.com/nesi/agdr-docs-concept.git
cd agdr-docs-concept
git clone https://github.com/nesi/agdr-docs.git
cd agdr-docs
python -m venv .venv
source .venv/bin/activate
pip3 install -r requirements.txt
Expand Down Expand Up @@ -64,23 +64,23 @@

#### Recommended Extensions

When opening the workspace for the first time, you should be prompted to install the <a href="https://github.com/nesi/agdr-docs-concept/blob/main/.vscode/extensions.json">Recommended VS Code Plugins</a>.
When opening the workspace for the first time, you should be prompted to install the <a href="https://github.com/nesi/agdr-docs/blob/main/.vscode/extensions.json">Recommended VS Code Plugins</a>.

#### Snippets

`ctrl` + `space` can be used to aid by auto-completing.

e.g. starting to type an image include `![my image](` then pressing `ctrl` + `space` will show all the valid paths.

Custom snippets can be added in <a href="https://github.com/nesi/agdr-docs-concept/blob/main/.vscode/includes.code-snippets.json">`../.vscode/includes.code-snippets`</a>
Custom snippets can be added in <a href="https://github.com/nesi/agdr-docs/blob/main/.vscode/includes.code-snippets.json">`../.vscode/includes.code-snippets`</a>

#### Tasks

Some of the same checks run during the GitHub CI, can also be run in VS Code.

This is shown with word underlining, and in the 'PROBLEMS' tab in the terminal.

Tasks allow continuous checks to be run in the background, these can be defined in <a href="https://github.com/nesi/agdr-docs-concept/blob/main/.vscode/tasks.json">`../.vscode/tasks.json`</a>, also include in <a href="https://github.com/nesi/agdr-docs-concept/blob/main/.vscode/settings.json">`../.vscode/settings.json`</a> in order to trigger on save.
Tasks allow continuous checks to be run in the background, these can be defined in <a href="https://github.com/nesi/agdr-docs/blob/main/.vscode/tasks.json">`../.vscode/tasks.json`</a>, also include in <a href="https://github.com/nesi/agdr-docs/blob/main/.vscode/settings.json">`../.vscode/settings.json`</a> in order to trigger on save.

## Making a Merge Request

Expand All @@ -103,7 +103,7 @@
CI checks will run on your branch, you can check them under 'Actions'
Might be worth having a quick look at these before making a pull request.

Make a pull [request](https://github.com/nesi/agdr-docs-concept/pulls)
Make a pull [request](https://github.com/nesi/agdr-docs/pulls)

Assign a reviewer if you wish.

Expand All @@ -115,15 +115,15 @@

Clicking on the 'Files Changed' tab, will give a convenient diff of the changes, as well as inline errors identified by the CI checks.

If some of the CI checks failed (make sure they are not important ones), you will have to click the `Merge without waiting for requirements to be met (bypass branch protections)` button before proceeding with the merge.

Check warning on line 118 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check Prose

strunk_white.composition 

'Try 'trifling' instead of 'not important'.'

Feel free to raise an issue, make a proposal or [add words to the dictionary](#adding-words-to-dictionary) if you feel you are being unfairly targeted by the CI checks.

## Update Remote Assets

Certain files need to be fetched from other repos for up to date info. This will be automated, but for not the proccess is manual.

Check warning on line 124 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check Spelling

spelling 

Word 'proccess' is misspelled.

1. Run the [![Fetch Remote Assets](https://github.com/nesi/agdr-docs-concept/actions/workflows/fetch_includes.yml/badge.svg?branch=main&event=workflow_run)](https://github.com/nesi/agdr-docs-concept/actions/workflows/fetch_includes.yml) workflow in this repo.
1. Run the [![Fetch Remote Assets](https://github.com/nesi/agdr-docs/actions/workflows/fetch_includes.yml/badge.svg?branch=main&event=workflow_run)](https://github.com/nesi/agdr-docs/actions/workflows/fetch_includes.yml) workflow in this repo.
2. A branch `new-assets` will be created, which can be merged into main.

## Adding Words to Dictionary
Expand All @@ -132,8 +132,8 @@

1. Visit the [NeSI Word List](https://github.com/nesi/nesi-wordlist), follow the instructions there on adding words.
2. Once changes to the word list have been merged, return to this repo and run [update remote assets](#update-remote-assets).
3. You should see your new words in the [Dictionary](assets/glossary/dictionary.txt) if your words included a definition, they will also be in the <a href="https://github.com/nesi/agdr-docs-concept/blob/main/overrides/Glossary.md">Glossary</a>.
3. You should see your new words in the [Dictionary](assets/glossary/dictionary.txt) if your words included a definition, they will also be in the <a href="https://github.com/nesi/agdr-docs/blob/main/overrides/Glossary.md">Glossary</a>.

## Raise an issue

*Not documented at the moment (TODO)*

Check warning on line 139 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check Prose

annotations.misc 

'Annotation left in text.'

Check warning on line 139 in docs/CONTRIBUTING.md

View workflow job for this annotation

GitHub Actions / Check Spelling

spelling 

Word 'TODO' is misspelled.
2 changes: 1 addition & 1 deletion docs/FORMAT.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
---

Check warning on line 1 in docs/FORMAT.md

View workflow job for this annotation

GitHub Actions / Check page meta

meta_missing_description 

Missing 'description' from front matter.

Check warning on line 1 in docs/FORMAT.md

View workflow job for this annotation

GitHub Actions / Check page meta

minimum_tags 

'tags' property in meta is missing or malformed.
title: Formatting
---

**[CLICK TO VIEW THIS PAGE RENDERED IN MKDOCS](https://nesi.github.io/agdr-docs-concept/FORMAT/)**{ .hidden }
**[CLICK TO VIEW THIS PAGE RENDERED IN MKDOCS](https://nesi.github.io/agdr-docs/FORMAT/)**{ .hidden }

Check warning on line 5 in docs/FORMAT.md

View workflow job for this annotation

GitHub Actions / Check Spelling

spelling 

Word 'MKDOCS' is misspelled.

!!! prerequisite "See also"
- To learn how you can contribute, [see CONTRIBUTING](CONTRIBUTING.md).
- For information about page creation, [see NEWPAGE](NEWPAGE.md).

Check warning on line 9 in docs/FORMAT.md

View workflow job for this annotation

GitHub Actions / Check Spelling

spelling 

Word 'NEWPAGE' is misspelled.

This page is an overview of the Markdown syntax supported in this documentation.

Expand Down Expand Up @@ -106,8 +106,8 @@
Wheeee
```

Consider making a Admonition collapsable-open (`???+`) if it is particularly long.

Check warning on line 109 in docs/FORMAT.md

View workflow job for this annotation

GitHub Actions / Check Prose

spelling.able_ible 

'-able vs. -ible. 'collapsible' is the preferred spelling.'
An Admonition **shouldn't be made collapsable-closed** (`???`) unless it has been given an **optional title explaining it's contents**.

Check warning on line 110 in docs/FORMAT.md

View workflow job for this annotation

GitHub Actions / Check Prose

spelling.able_ible 

'-able vs. -ible. 'collapsible' is the preferred spelling.'

### Admonition Flavours

Expand Down Expand Up @@ -270,7 +270,7 @@
Try to avoid putting links on ambiguous words, e.g.

=== "Bad"
View the software homepage [here](https://www.example.com).

Check warning on line 273 in docs/FORMAT.md

View workflow job for this annotation

GitHub Actions / Check page meta

click_here 

Don't use 'here' for link text, impedes accessability.

```md
View the homepage [here](https://www.example.com).
Expand Down Expand Up @@ -385,7 +385,7 @@
Macros allow use of [Jinja filter syntax](https://jinja.palletsprojects.com/en/3.1.x/templates/) _inside the markdown files_ allowing for much more flexible templating.
More details can be found on the [mkdocs-macros-plugin page](https://mkdocs-macros-plugin.readthedocs.io/).

### Includes

Check warning on line 388 in docs/FORMAT.md

View workflow job for this annotation

GitHub Actions / Check page meta

walk_toc 

Header 'Includes' is a useless only-child. Give it siblings or remove it.

The macro plugin allows the use of 'includes', here is an example.

Expand Down
2 changes: 1 addition & 1 deletion docs/MACROS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
**[CLICK TO VIEW THIS PAGE RENDERED IN MKDOCS](https://nesi.github.io/agdr-docs-concept/MACROS/)**{ .hidden }
**[CLICK TO VIEW THIS PAGE RENDERED IN MKDOCS](https://nesi.github.io/agdr-docs/MACROS/)**{ .hidden }

Check warning on line 1 in docs/MACROS.md

View workflow job for this annotation

GitHub Actions / Check page meta

meta.parse 

Meta block missing or malformed.

Check failure on line 1 in docs/MACROS.md

View workflow job for this annotation

GitHub Actions / Check page meta

misc 

'children'

# Info about macros

Expand Down
2 changes: 1 addition & 1 deletion docs/NEWPAGE.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
---

Check warning on line 1 in docs/NEWPAGE.md

View workflow job for this annotation

GitHub Actions / Check page meta

meta_missing_description 

Missing 'description' from front matter.

Check warning on line 1 in docs/NEWPAGE.md

View workflow job for this annotation

GitHub Actions / Check page meta

minimum_tags 

'tags' property in meta is missing or malformed.
title: Create a new page
---

**[CLICK TO VIEW THIS PAGE RENDERED IN MKDOCS](https://nesi.github.io/agdr-docs-concept/NEWPAGE/)**{ .hidden }
**[CLICK TO VIEW THIS PAGE RENDERED IN MKDOCS](https://nesi.github.io/agdr-docs/NEWPAGE/)**{ .hidden }

!!! prerequisite "See also"
- To learn how you can contribute, [see CONTRIBUTING](CONTRIBUTING.md).
Expand Down
9 changes: 8 additions & 1 deletion docs/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,14 @@
layout: default
---

# [Aotearoa Genomic Data Repository](https://data.agdr.org.nz/)
# [Aotearoa Genomic Data Repository](https://data.agdr.org.nz/){:target="_blank"}

The Aotearoa Genomic Data Repository provides secure within-nation storage, management and sharing of non-human genomic data generated from biological and environmental samples originating in Aotearoa New Zealand. This resource has been developed to follow the principles of Māori Data Sovereignty, and to enable kaitiakitanga (guardianship), so that iwi, hapū and whānau (tribes, kinship groups and families) can effectively exercise their responsibilities as guardians over biological entities that are taonga (precious or treasured).
While the repository is designed to facilitate the sharing of data — making it findable by researchers and interoperable with data held in other genomic repositories — the decision-making process regarding who can access the data is entirely in the hands of those holding kaitiakitanga over each data set.

Check warning on line 8 in docs/index.md

View workflow job for this annotation

GitHub Actions / Check Prose

cliches.garner 

''decision-making process' is cliché.'

More information about the design and operating principles of the Aotearoa Genomic Data Repository can be found in our recent publication: [doi.org/10.1111/1755-0998.13866](https://doi.org/10.1111/1755-0998.13866){:target="_blank"}.

The repository has been jointly developed by Genomics Aotearoa and NeSI, and is an evolving project to which we are still adding functionality, so you will see ongoing improvements as we implement new features.

## Recent activity

Expand Down
4 changes: 2 additions & 2 deletions mkdocs.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,12 +35,12 @@ plugins:
verbose: false
include_dir: overrides
repo_name: GitHub
repo_url: https://github.com/nesi/agdr-docs-concept
repo_url: https://github.com/nesi/agdr-docs
edit_uri: edit/main/docs/
site_description: AGDR
site_dir: public
site_name: AGDR
site_url: https://github.com/nesi/agdr-docs-concept
site_url: https://github.com/nesi/agdr-docs
extra_css:
- assets/stylesheets/footer.css
- assets/stylesheets/my.css
Expand Down
12 changes: 1 addition & 11 deletions overrides/partials/footer.html
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,17 +1,7 @@
<footer class="md-footer">
<div id="new-footer">
<div id="partners">
<div id="logos">
<a href="https://nesi.org.nz" class="nesi-footer-logo" target="_blank"><img alt="" src="https://www.nesi.org.nz/sites/default/files/LogoNeSI-footer.png"></a>
<a href="http://www.mbie.govt.nz/" target="_blank"><img alt="" src="https://www.nesi.org.nz/sites/default/files/media/LogoMBIE.png"></a>
<a href="https://www.auckland.ac.nz/" target="_blank"><img alt="" src="https://www.nesi.org.nz/sites/default/files/media/LogoUoA.png"></a>
<a href="https://www.niwa.co.nz/" target="_blank"><img alt="" src="https://www.nesi.org.nz/sites/default/files/media/LogoNIWA.png"></a>
<a href="https://www.otago.ac.nz/" target="_blank"><img alt="" src="https://www.nesi.org.nz/sites/default/files/media/LogoUoO.png"></a>
<a href="http://www.landcareresearch.co.nz/" target="_blank"><img alt="" src="https://www.nesi.org.nz/sites/default/files/LogoManaakiWhenuaLandcareResearch.png"></a>
</div>
</div>
<div id="inner">
<span id="links"><a href="https://www.nesi.org.nz/copyright" target="_blank">Copyright © <span id="year">2023</span> · New Zealand eScience Infrastructure</a> | <a href="https://www.nesi.org.nz//disclaimer" target="_blank">Disclaimer</a> | <a href="https://www.nesi.org.nz//privacy" target="_blank">Privacy</a>
<span id="links"><a href="https://www.nesi.org.nz/copyright" target="_blank">Copyright © <span id="year">2024</span> · New Zealand eScience Infrastructure</a> | <a href="https://www.nesi.org.nz//disclaimer" target="_blank">Disclaimer</a> | <a href="https://www.nesi.org.nz//privacy" target="_blank">Privacy</a>
</span>
</div>
</div>
Expand Down
Loading