From 303b02f27581316d8a67fa95d71f89f4760a2ad6 Mon Sep 17 00:00:00 2001 From: natnesi <111834566+natnesi@users.noreply.github.com> Date: Mon, 22 Apr 2024 20:20:41 +0000 Subject: [PATCH] Modified with Calire feedback: change repo name, add info on landing page, change footer --- .github/workflows/README.md | 2 +- .vscode/includes.code-snippets | 2 +- README.md | 6 +++--- docs/CONTRIBUTING.md | 20 ++++++++++---------- docs/FORMAT.md | 2 +- docs/MACROS.md | 2 +- docs/NEWPAGE.md | 2 +- docs/index.md | 9 ++++++++- mkdocs.yml | 4 ++-- overrides/partials/footer.html | 12 +----------- 10 files changed, 29 insertions(+), 32 deletions(-) diff --git a/.github/workflows/README.md b/.github/workflows/README.md index 8117826..f999795 100644 --- a/.github/workflows/README.md +++ b/.github/workflows/README.md @@ -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. diff --git a/.vscode/includes.code-snippets b/.vscode/includes.code-snippets index 3f02793..f595ae5 100644 --- a/.vscode/includes.code-snippets +++ b/.vscode/includes.code-snippets @@ -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: diff --git a/README.md b/README.md index d5764e9..2e19148 100644 --- a/README.md +++ b/README.md @@ -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) diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index 3323c64..45ef190 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -2,7 +2,7 @@ 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 } !!! prerequisite "See also" - For examples of markdown use, [see FORMAT](FORMAT.md). @@ -21,7 +21,7 @@ It allows accessing a full featured preconfigured development environment remote 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) ## Local Development Environment @@ -34,8 +34,8 @@ You will need to have Python **3.10** or later installed on your computer. 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 @@ -64,7 +64,7 @@ You can use any IDE you want, but various tools have been configured for use wit #### Recommended Extensions -When opening the workspace for the first time, you should be prompted to install the Recommended VS Code Plugins. +When opening the workspace for the first time, you should be prompted to install the Recommended VS Code Plugins. #### Snippets @@ -72,7 +72,7 @@ When opening the workspace for the first time, you should be prompted to install 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 `../.vscode/includes.code-snippets` +Custom snippets can be added in `../.vscode/includes.code-snippets` #### Tasks @@ -80,7 +80,7 @@ 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 `../.vscode/tasks.json`, also include in `../.vscode/settings.json` in order to trigger on save. +Tasks allow continuous checks to be run in the background, these can be defined in `../.vscode/tasks.json`, also include in `../.vscode/settings.json` in order to trigger on save. ## Making a Merge Request @@ -103,7 +103,7 @@ git push origin 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. @@ -123,7 +123,7 @@ Feel free to raise an issue, make a proposal or [add words to the dictionary](#a 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. -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 @@ -132,7 +132,7 @@ If the CI is failing the spellcheck phase, and you believe the identified words 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 Glossary. +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 Glossary. ## Raise an issue diff --git a/docs/FORMAT.md b/docs/FORMAT.md index 627bf0d..c568709 100644 --- a/docs/FORMAT.md +++ b/docs/FORMAT.md @@ -2,7 +2,7 @@ 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 } !!! prerequisite "See also" - To learn how you can contribute, [see CONTRIBUTING](CONTRIBUTING.md). diff --git a/docs/MACROS.md b/docs/MACROS.md index 7bc7990..5df088c 100644 --- a/docs/MACROS.md +++ b/docs/MACROS.md @@ -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 } # Info about macros diff --git a/docs/NEWPAGE.md b/docs/NEWPAGE.md index 58dd62e..45f6f8e 100644 --- a/docs/NEWPAGE.md +++ b/docs/NEWPAGE.md @@ -2,7 +2,7 @@ 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). diff --git a/docs/index.md b/docs/index.md index a29fcd2..1f24d5e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -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. + +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 diff --git a/mkdocs.yml b/mkdocs.yml index 6925306..f2c2c59 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -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 diff --git a/overrides/partials/footer.html b/overrides/partials/footer.html index cd02ee9..53b56ca 100644 --- a/overrides/partials/footer.html +++ b/overrides/partials/footer.html @@ -1,17 +1,7 @@