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Merge branch 'master' of github.com:elixir-europe/rdmkit into pr/vild…
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bedroesb committed Sep 16, 2024
2 parents 6a5448f + 3a7a632 commit b766125
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2 changes: 2 additions & 0 deletions .github/workflows/jekyll.yml
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Expand Up @@ -55,10 +55,12 @@ jobs:
JEKYLL_BUILD_BRANCH: ${{ github.ref_name }}
JEKYLL_ENV: ${{ steps.name.outputs.jekyll_env }}
JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }}

- name: Upload artifact
uses: actions/upload-pages-artifact@v1


deploy:
runs-on: ubuntu-latest
needs: build
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14 changes: 5 additions & 9 deletions .github/workflows/tool_list_conversion.yml
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Expand Up @@ -22,10 +22,10 @@ jobs:
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install pyyaml requests python-frontmatter
pip install ruamel.yaml requests python-frontmatter
- name: Run tool table 2 yaml
run: |
python var/conversions.py
python var/tools_validator.py
registry-lookup:
if: |
Expand All @@ -49,15 +49,11 @@ jobs:
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install pyyaml requests python-frontmatter
pip install ruamel.yaml requests python-frontmatter
- name: Run tool table 2 yaml
- name: Run regsitry lookup for the tools file
run: |
python var/conversions.py --reg --username ${{ secrets.FAIRSHARING_USERNAME }} --password "${{ secrets.FAIRSHARING_PASSWORD }}"
- name: Fetch country names with corresponding iso
run: |
python var/country_list.py
python var/tools_validator.py --reg --username ${{ secrets.FAIRSHARING_USERNAME }} --password "${{ secrets.FAIRSHARING_PASSWORD }}"
- name: Update markdown pages with DSW links
run: |
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14 changes: 7 additions & 7 deletions CODEOWNERS
Validating CODEOWNERS rules …
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Expand Up @@ -5,18 +5,18 @@
* @bedroesb

# Contribute
/pages/contribute @floradanna @pinarpink @bedroesb
/pages/contribute @floradanna @bedroesb
/pages/contribute/copyright.md @martin-nc
/pages/contribute/style_guide.md @martin-nc
CONTRIBUTING.md @floradanna @pinarpink
CONTRIBUTING.md @floradanna

# Different Sections
/pages/your_tasks @DanFaria @floradanna @nazeeefa
/pages/your_role @smza @pinarpink
/pages/data_life_cycle @wittigue @floradanna @smza
/pages/your_tasks @floradanna @nazeeefa @marikapop @diana-pilvar
/pages/your_role @smza @GilOliveira
/pages/data_life_cycle @wittigue @floradanna @smza @marikapop
/pages/tool_assembly @korbinib @bianchini88
/pages/your_domain @DanFaria @pinarpink @bianchini88 @lauportell
/pages/national_resources @lauportell @nazeeefa
/pages/your_domain @bianchini88 @lauportell @GilOliveira
/pages/national_resources @lauportell @nazeeefa @diana-pilvar

#About
/pages/about/about.md @frederikcoppens @CaroleGoble
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2 changes: 1 addition & 1 deletion CODE_OF_CONDUCT.md
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Expand Up @@ -52,7 +52,7 @@ As such, we do not tolerate behaviour that is disrespectful to our community mem
We do not tolerate discrimination or harassment based on characteristics that include, but are not limited to: gender identity and expression, sexual orientation, disability, physical appearance, body size, citizenship, nationality, ethnic or social origin, pregnancy, familial status, veteran status, genetic information, religion or belief (or lack thereof), membership of a national minority, property, age, education, socio-economic status, technical choices, and experience level.

Everyone who participates in the RDMkit activities is required to conform to this Code of Conduct.
This Code of Conduct applies to all spaces managed by the Turing Way project including, but not limited to, in person focus groups and workshops, and communications online via GitHub.
This Code of Conduct applies to all spaces managed by the RDMkit including, but not limited to, in person focus groups and workshops, and communications online via GitHub.
By participating, contributors indicate their acceptance of the procedures by which the RDMkit project core development team resolves any Code of Conduct incidents, which may include storage and processing of their personal information.

### 2.1 Expected behaviour
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21 changes: 16 additions & 5 deletions Gemfile
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@@ -1,8 +1,19 @@
source "https://rubygems.org"
source 'https://rubygems.org'

# GitHub pages dependencies
gem 'github-pages', group: :jekyll_plugins
gem 'elixir-toolkit-theme-plugins', '~> 0.1.10'
gem 'webrick', '~> 1.7'
gem 'jekyll', '~> 4.3.1'
gem 'jemoji', '~> 0.13.0'
gem 'kramdown-parser-gfm', '~> 1.1'
gem 'jekyll-octicons'

# Webrick needed for Ruby v3.0+ compatibility
gem "webrick"
group :jekyll_plugins do
gem 'jekyll-redirect-from', '~> 0.16.0'
gem 'jekyll-sitemap', '~> 1.4'
gem 'jekyll-github-metadata', '~> 2.15'
gem 'jekyll-relative-links', '~> 0.6'
gem 'jekyll-seo-tag', '~> 2.8'
gem 'jekyll-scholar', '~> 7.1.3'
gem 'jekyll-remote-theme'
end

16 changes: 9 additions & 7 deletions README.md
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@@ -1,4 +1,4 @@
[![Converting the tool and resource table](https://github.com/elixir-europe/rdmkit/workflows/Converting%20the%20tool%20and%20resource%20table/badge.svg)](https://github.com/elixir-europe/rdmkit/actions?query=workflow%3A%22Converting+the+tool+and+resource+table%22) [![Jekyll site CI](https://github.com/elixir-europe/rdmkit/workflows/Jekyll%20site%20CI/badge.svg)](https://github.com/elixir-europe/rdmkit/actions?query=workflow%3A%22Jekyll+site+CI%22) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5110061.svg)](https://doi.org/10.5281/zenodo.5110061) [![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
[![Validation of the tools and page metadata](https://github.com/elixir-europe/rdmkit/actions/workflows/tool_list_conversion.yml/badge.svg)](https://github.com/elixir-europe/rdmkit/actions/workflows/tool_list_conversion.yml) [![Jekyll site CI](https://github.com/elixir-europe/rdmkit/workflows/Jekyll%20site%20CI/badge.svg)](https://github.com/elixir-europe/rdmkit/actions?query=workflow%3A%22Jekyll+site+CI%22) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5110061.svg)](https://doi.org/10.5281/zenodo.5110061) [![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)

<img src="https://raw.githubusercontent.com/elixir-europe/rdmkit/master/assets/img/RDMkit_logo.svg" alt="RDMkit logo" width="450"/>

Expand Down Expand Up @@ -26,10 +26,10 @@ Do you want to help with this project? Please check out following pages for more

Do you which to contact the editors of this project? Use [rdm-editors@elixir-europe.org](mailto:rdm-editors@elixir-europe.org )

If you want to build the website locally, please have a look at our [tutorial](working_with_git#the-advantage-of-working-locally-previewing-your-changes-through-your-web-browser).
If you want to build the website locally, please have a look at our [Git tutorial](https://rdmkit.elixir-europe.org/working_with_git).


## RDMkit is an ELIXIR Converge project
## RDMkit is an ELIXIR product

ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers. All the ELIXIR National nodes and the special EMBL-EBI node have come to support data management within the Nodes and for data stewards, researchers and institutional data managers. The idea is to support data management at the point of creation and enable data to be "FAIR by Design". The development of a Research Data Management Kit will provide researchers with a strategy to manage their data to international standards.

Expand All @@ -40,10 +40,12 @@ The process documents and data are made available under a CC-BY license. Softwar

## Acknowledgements

The RDMkit is supported by:
- ELIXIR-CONVERGE https://elixir-europe.org/about-us/how-funded/eu-projects/converge
- Contributions from the 23 ELIXIR Nodes
The RDMkit was supported by [ELIXIR-CONVERGE](https://elixir-europe.org/about-us/how-funded/eu-projects/converge) and it is coordinated by [ELIXIR Europe](https://elixir-europe.org/) and [NIH](https://www.nih.gov/).

### Custom icons

We would like to thank Xènia Pérez Sitjà for creating the custom icons for the RDMkit. Her work has added to the visual appeal and usability of our toolkit.

<br>
<br>
<a href="https://elixir-europe.org/about-us/how-funded/eu-projects/converge"><img src="https://raw.githubusercontent.com/elixir-europe/rdmkit/master/assets/img/converge_logo.svg" width="15%"></a>
<a href="https://elixir-europe.org/about-us/how-funded/eu-projects/converge"><img src="https://raw.githubusercontent.com/elixir-europe/rdmkit/master/assets/img/elixir_logo_inverted.svg" width="15%"></a>
168 changes: 168 additions & 0 deletions _bibliography/nature_custom.csl
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@@ -0,0 +1,168 @@
<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-GB">
<info>
<title>Nature</title>
<id>http://www.zotero.org/styles/nature</id>
<link href="http://www.zotero.org/styles/nature" rel="self"/>
<link href="http://www.nature.com/nature/authors/gta/index.html#a5.4" rel="documentation"/>
<link href="http://www.nature.com/srep/publish/guidelines#references" rel="documentation"/>
<author>
<name>Michael Berkowitz</name>
<email>mberkowi@gmu.edu</email>
</author>
<category citation-format="numeric"/>
<category field="science"/>
<category field="generic-base"/>
<issn>0028-0836</issn>
<eissn>1476-4687</eissn>
<updated>2022-07-01T16:03:34+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<macro name="title">
<choose>
<if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<text variable="title" font-style="italic" text-case="title"/>
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<text variable="title"/>
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<macro name="author">
<names variable="author">
<name sort-separator=", " delimiter=", " and="symbol" initialize-with=". " delimiter-precedes-last="never" name-as-sort-order="all"/>
<label form="short" prefix=", "/>
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<macro name="access">
<choose>
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<else-if variable="DOI">
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</choose>
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<choose>
<if type="dataset software" match="any">
<text variable="DOI" prefix="https://doi.org/"/>
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<choose>
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<group delimiter=" ">
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<if variable="genre" match="any">
<text variable="genre" text-case="capitalize-first"/>
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<text term="article" text-case="capitalize-first"/>
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<text term="at"/>
<choose>
<if variable="DOI" match="any">
<text variable="DOI" prefix="https://doi.org/"/>
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<else>
<text variable="URL"/>
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<date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
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</else-if>
<else-if type="dataset software" match="any">
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<text variable="publisher"/>
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<else-if type="report webpage post post-weblog" match="any">
<group delimiter=" ">
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<date variable="issued" prefix="(" suffix=")">
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<macro name="container-title">
<choose>
<if type="article-journal">
<text variable="container-title" font-style="italic" form="short"/>
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<text variable="container-title" font-style="italic"/>
</else>
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<macro name="editor">
<choose>
<if type="chapter paper-conference" match="any">
<names variable="editor" prefix="(" suffix=")">
<label form="short" suffix=" "/>
<name and="symbol" delimiter-precedes-last="never" initialize-with=". " name-as-sort-order="all"/>
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<macro name="volume">
<choose>
<if type="article-journal" match="any">
<text variable="volume" font-weight="bold" suffix=","/>
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<else>
<group delimiter=" ">
<label variable="volume" form="short"/>
<text variable="volume"/>
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<citation collapse="citation-number">
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<key variable="citation-number"/>
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<layout vertical-align="sup" delimiter=",">
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<bibliography et-al-min="6" et-al-use-first="1" second-field-align="flush" entry-spacing="0" line-spacing="2">
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<text macro="editor"/>
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