Editorial board guide
All you need to know about this GitHub repository
General rules
As an editor, try to work as much as possible on a different branch than the master branch. This can be on the elixir-europe rdm-toolkit repo or your own fork. Open a pull request if you want to merge your changes with the master branch. This way it is possible for other editors to give feedback on your changes. Typos or other small fixes can of course be done immediately on the master branch.
The google doc way of contributing
This process is sketched below.
Overview of the file structure in GitHub
The content of the website is built up using markdown files found in the pages directory. These markdown files are divided over subdirectories (your_role, your_domain, your_tasks…) for sorting reasons only.
The metadata/frontmatter of the markdown file
In order to render the markdown file to the website, it needs a specific frontmatter/metadata section in the top part of the file. This latter can look like:
---
title: Title of the page
---
Mandatory metadata/frontmatter:
title
: Specify here the page title. This will be the H1 title (replacing the top level title using the # in markdown )
Optional metadata/frontmatter:
-
summary
: By using this attribute it is possible to specify a summary which will be displayed under the page title. -
description
: Short sentence about the page starting with a lowercase. This sentence is visualized when pages are automatically listed as Related page. -
contributors
: List here all the contributors that helped in establishing the page, preferibly with their full name. Make sure that the person names that are listed can be found in the CONTRIBUTORS.yaml file in the _data directory if you want to link the GitHub ID and other contact information. Multiple contributors will be put in a list like this: [example1, example2]. -
coordinators
: List here the names of the people responsible for the content of the page. People responsible for the content of the National resources pages can be members of the ELIXIR data management network. Make sure that coordinators also listed as contributors incontributors
and CONTRIBUTORS.yaml. Multiple coordinators will be put in a list like this: [example1, example2]. -
search_exclude
: By setting this field to “true”, the page will not end up in the search results of the search bar.search_exclude: true
is the default for template pages. Make sure to delete this metadata field when creating a new page for contributors, before approving or before merging a pull request. -
sitemap
: let the page appear in the sitema.xml. Default: true -
no_robots
: by setting this field to true, the page will not end up in the search results of google or any other search engine. -
hide_sidebar
: When true, the sidebar will be hidden. Default: false. -
custom-editme
: This attribute can be used to specify an alternative file/link when clicked on the edit-me button. -
keywords
: List here all the keywords that can be used to find the page using the search box in the right-upper corner of the page. Multiple keywords are put in a list like this: [example1, example2]. -
sidebar
: Specify here an alternative sidebar. Default: main. -
toc
: When set to false, the table of contents at the beginning of the page will not be generated. -
affiliations
: List here all affiliations that made this page possible. This is especially used for tool assembly pages. Countries use the ISO 3166-1-alpha-2 notation, other affiliations must be present in the affiliations.yaml in the _data directory in order to work. -
page_id
: Unique identifier of a page. It is usually a shortened version of the page name or title, with small letters and spaces, or an acronym, with capital and small letters. Used to list Related pages. -
related_pages
: List here the page_id of RDMkit pages that you want to display as Related pages, grouped by section (Your tasks, Your domain, Tool assembly).If you want pages from the specific section (Your tasks, Your domain, Tool assembly) to be shown here as Related pages, list their
page_id
. If you want to list multiple related pages, make sure to put them in a list like this: [page_id1, page_id2]. The specific sections allowed in each page are specified in each page template. Please, do not add extra sections in the metadata of the page.related_pages: your_tasks: [page_id1, page_id2] your_domain: [page_id1, page_id2] tool_assembly: [page_id1, page_id2]
-
training
: List here training material relevant for the page. We recommend to add your training material in TeSS. However, you can also list here training material that is not yet present in TeSS. Each training item will be automatically added as an entry to the table in the All training resources page. If the registry is specified, please use one of the following: TeSS, Youtube, Zenodo or Carpentries.training: - name: Training in TeSS registry: TeSS url: https://tess.elixir-europe.org/search?q=data%20analysis - name: Training in TeSS registry: TeSS url: https://tess.elixir-europe.org/search?q=data%20analysis
-
faircookbook
: Here all relevant FAIR Cookbook recipes are listed. This is automaticity updated based on thefaircookbook_rdmkit_mapping.yml
mapping file. If you want to make a new link, please make a pull request against this file. Every week the changes of this mapping file are used to update the frontmatter of the corresponding markdown files. -
dsw
: Here all relevant Data Stewardship Wizard questions in the RDMkit knowledge model are listed. This is automaticity updated and can not be altered by humans! If you want to add a link you have to add the link towards the RDMkit page the the knowledge model on DSW. -
datatable
: use this attribute to activate the pagination + sorting + searching in tables
Markdown file naming
- Markdown files should be named without capitals and without spaces (replace them with underscores).
- Make sure that the markdown file has a unique name.
- If the markdown file is named example.md, the page will be found at https://rdmkit.elixir-europe.org/example.
- By default a page will not show up in the sidebar. In order to do so you will have to add the link towards the page to the
.yaml
file in the _data/sidebars directory or link towards it from another page. More info about this can be found on the find your page back section.
GitHub checks
With each PR or merge to the master, some checks are done using GitHub actions. One of them checks wether the website builds correctly. The other checks for changes in the tool/resource Excel table. When each of them fails, the PR will not be able to be merged. Click on the red dot/failed check to understand better what caused the fail.
Label, discuss and assign issues
- Check open issues regularly or enable notifications by clicking the “WATCH” icon in the top-right side of the GitHub repository.
- Assign labels to issues.
- Discuss who is going to be responsible for each issue with other editors and reviewers (via issue comments or other communication channels).
- Assign at least one editor/reviewer to the issue, who will discuss the possible content with the contributor.
- When a Pull Request (PR) or a draft PR related to an issue is created, link the PR to the issue.
More information about these topics can be found in the GitHub documentation:
Review pull requests
If contributors make a pull request to make changes, by default the editors that are responsible for files that will changed by the PR will be assigned and notified. All PR should be assigned to one of the editors. Before merging a PR, pages’ tags and keywords, and tools and resources’ tags should be checked and assigned according to the established tagging system.
Link a pull request to an issue
When you make a pull request resolving an issue, it is possible to link this pull request to that specific issue. This can be easily done by writing in the conversation of the PR: closes #number_of_issue
, or fixes #number_of_issue
or even resolves #number_of_issue
. This is definitely applicable when authors first open an issue announcing a change or requesting a new page, followed up by the pull request.
For more information about this topic please visit the GitHub documentation page.
Adding a new event
Add an event to the landing page by editing the events.yml
in the _data
directory in this repository. Use following attributes to define an event:
- name: Contentathon
startDate: 2021-06-23
startTime: '9:00'
endDate: 2021-06-24
endTime: 13:30 CET
description: We would like to invite you to highlight your set of data management tools as a tool assembly in the RDMkit and describe how to use it, so others can do the same. (two half days)
location: Online
Only name and startDate are mandatory attributes.
Adding a news item
Add a news item to the landing page by editing the news.yml
in the _data
directory in this repository. Use following attributes to define a news item:
- name: News title
date: 2021-06-23
description: A short description
All attributes are mandatory.
Create a new page
Simple way: using the GitHub interface
To generate a new page it is sufficient to simply copy the TEMPLATE file in the subdirectory and rename it. To copy a template you have to:
-
Go to the
TEMPLATE_
file of choice in the GitHub repo, every section has its own TEMPLATE file. For example the TEMPLATE_your_tasks.md file. - Click “Raw” on the GitHub page to open the file ‘as is’
-
Select and copy all the content.
- Go back to the main section were you want to make the new page, in our example this will be in /pages/your_tasks. Click on
Add file
on the right followed up byCreate new file
. -
Paste the copied content from the template.
- Name the file by choosing a unique self explaining short name without capitals and without spaces (replace them with underscores).
- Check the frontmatter/metadata of the markdown page:
- delete
search_exclude: true
attribute. - add the author names to the contributors list.
- optional: change the title into an appropriate one.
- delete
- Describe shortly which changes you made in the description of your commit below the page. Commit to the master branch by clicking
Commit new file
. - If the markdown file is named example.md the page will be rendered at https://rdmkit.elixir-europe.org/example. This link can be provided to the contributor through the issue.
Advanced: working on your own feature branch and pushing local changes
Just like with every change you want to make to this repo, it is possible to do this through Git by working on a local copy. For more information on how to do this, please read our working with Git page.
Find your newly added page back on the website
By default your page will not be linked in the sidebar on the website, or on the landing page, but it will exist as an orphan at https://rdmkit.elixir-europe.org/markdown_file_name. In order to prevent that people will not find the page back it is better to link towards it in the sidebar or get linked within an existing page.
Linking pages in the sidebar and frontpage
Make sure all pages are accessible from the navigation sidebar. Please, avoid generating sub-pages that are not directly accessible from the navigation sidebar.
This website supports multiple sidebars, the one in the main sections of the website is for example different from the one in the contribute section. Both of them are defined by .yaml
files in the _data/sidebars directory. Changing these yaml file will immediately impact the sidebars and the frontpage of the website. The sidebar supports multiple levels and each level in the hierarchy can contain a URL to a page within this website or an external URL.
The attributes that define the structure are:
title
: This is the text that will show up in the sidebar.url
: The URL to the internal page you want to link to. This is mostly in the form of: /markdown_file_name.html.external_url
: Use this instead of URL if you want to link to an external page.subitems
: to define a sublevel.
- title: Level_1_title
url: level_1_url
subitems:
- title: Level_2_title
url: level_2_url
Link page within existing page
Avoid manual linking to internal pages. If necessary, you can manually link to the pages like this:
If the markdown page is named example_1.md, you can link towards it using:
[Example 1](example_1)
Adding extra info to the contributors
Do you want that the GitHub picture of a contributor is shown next to their name? Or maybe you want that the name is clickable and links towards the GitHub page of that person? To enable this please add the name and the necessary metadata to the CONTRIBUTORS.yaml file in the _data directory like this:
Bert Droesbeke:
git: bedroesb
email: bedro@psb.ugent.be
orcid: 0000-0003-0522-5674
role: editor
affiliation: VIB-UGent
Adding an institution, infrastructure, project or funder
Institutions, projects, funders and infrastructures are listed in the affiliations.yml file. The info in this file is used on the support page in the about section, but also for the affiliations in tool assembly pages. Make sure you make use of the same name in those assembly pages. The yaml file has following syntax:
- name: VIB
image_url: /images/institutions/VIB-PSB.svg
pid: https://ror.org/03xrhmk39
expose: true
type: institution
url: https://www.psb.ugent.be/
name
: nameimage_url
: relative url towards the imagepid
: url including the unique identifier towards the page of the association on RORexpose
: true or false, when true this association will be shown in the about sectiontype
: can be any of these values: institution, funder, infrastructure or projecturl
: url towards the homepage of this association
The logos can be added to the /images/institutions, /images/projects, /images/infrastructures and /images/funders directory.
Related pages
Add “Related pages” to a page
RDMkit pages from the sections Your tasks, Your domain and Tool assembly can be displayed as “Related RDMkit pages” in a page, grouped by section.
Only pages from specific sections are allowed in each page (see image below), as pre-defined in the metadata of each template page. Please, do not add extra sections in the metadata of the page.
page_id | Related pages id: Data life cycle | Related pages id: Your tasks | Related pages id: Your role | Related pages id: Your domain | Related pages id: Tool assembly | Related pages visualised |
---|---|---|---|---|---|---|
Data life cycle | yes | Your tasks | ||||
Your tasks | yes | Tool assembly | ||||
Your role | yes | Your tasks | ||||
Your domain | yes | yes | Your tasks, Tool assembly | |||
Tool assembly | yes | yes | Your tasks, Your domain |
An overview of all RDMkit pages (belonging to the sections listed above) and their page_id
can be found in the Website overview page.
related_pages:
your_tasks: [page_id1, page_id2]
your_domain: [page_id1, page_id2]
tool_assembly: [page_id1, page_id2]
Page ID
To find out what the page_id
of an RDMkit page is, please check its metadata attribute page_id
at the top of the markdown file or the Website overview page.