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Merge branch 'develop' into bioimage_deposition
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proccaserra authored Oct 7, 2024
2 parents d0d4a87 + 4d67642 commit 9a1d3da
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145 changes: 145 additions & 0 deletions .github/ISSUE_TEMPLATE/recipe_template.yml
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name: Recipe Template
description: Please use this template to submit your new recipes
title: "Recipe title"
body:
- type: markdown
attributes:
value: |
Thanks for providing content for the FAIR Cookbook!
- type: dropdown
id: recipe-type
attributes:
label: Recipe Type
multiple: true
description:
options:
- Background information
- Experience Report / Applied Example
- Guidance
- Hands-on
- Inventory
- Technical Guidance
- Other
validations:
required: true
- type: dropdown
id: audience
attributes:
label: Audience
multiple: true
description: Who is your target audience?
options:
- Bioinformatician
- Chemoinformatician
- Data Consumer
- Data Curator
- Data Engineer
- Data Manager
- Data Producer
- Data Scientist
- Data Steward
- Everyone
- Funder
- Ontologist
- Principal Investigator
- Procurement Officer
- Software Engineer
- Software Developer
- System Administrator
- Terminology Manager
validations:
required: false
- type: dropdown
id: executable_code
attributes:
label: Executable Code
description: Does your recipe have executable codes?
options:
- "Yes"
- "No"
validations:
required: false
- type: textarea
id: main_objectives
attributes:
label: Main Objectives
description: Please explain the main objective of the recipe.
validations:
required: true
- type: textarea
id: graphical_overview
attributes:
label: Graphical Overview
description: If you have a graphical overview, please upload it. Tip, You can attach files by clicking this area to highlight it and then dragging files in.
validations:
required: false
- type: textarea
id: requirements
attributes:
label: Requirements
description: Please specify the technical and knowledge requirements to implement this recipe.
validations:
required: false
- type: textarea
id: fairification_objectives
attributes:
label: FAIRification Objectives, Inputs and Outputs
description: Examples of objectives are "formatting" and "text annotation". An example of input is "Waters MS format". An example of output is "mzML".
validations:
required: true
- type: textarea
id: data-standards
attributes:
label: Table of Data Standards
description: An example of "Data Formats" is "mzML". An example of "Terminologies" is "PSI-MS".
validations:
required: false
- type: textarea
id: introduction
attributes:
label: Introduction
description:
validations:
required: true
- type: textarea
id: ingredients
attributes:
label: Ingredients
description: Add a list of tools and software required to implement the recipe.
validations:
required: false
- type: textarea
id: body
attributes:
label: Recipe body or step-by-step guidance
description:
validations:
required: true
- type: textarea
id: conclusion
attributes:
label: Conclusion
description:
validations:
required: true
- type: textarea
id: read_next
attributes:
label: What to read next?
description:
validations:
required: false
- type: textarea
id: references
attributes:
label: References
description:
validations:
required: true
- type: textarea
id: authors
attributes:
label: Authors
description:
validations:
required: true
2 changes: 1 addition & 1 deletion _config.yml
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Expand Up @@ -9,7 +9,7 @@ exclude_patterns : [.github/*, README.md, venv/*, node_modules/*, _co
# Execution settings
execute:
execute_notebooks : off # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off")
cache : "" # A path to the jupyter cache that will be used to store execution artifacs. Defaults to `_build/.jupyter_cache/`
cache : "" # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/`
exclude_patterns : [] # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time)

#######################################################################################
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6 changes: 3 additions & 3 deletions _ext/global_variables_fairplus.py
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Expand Up @@ -206,7 +206,7 @@
"Hannah" : { "github_handle" : "HEHurst", "name" : "Hannah Hurst", "orcid" : "", "affiliation" : "EMBL-EBI", "type_of_affiliation" : "academia", "elixir_node" : "embl" },
"Herman" : { "github_handle" : "", "name" : "Herman Van Vlijmen", "orcid" : "0000-0002-1915-3141", "affiliation" : "Janssen", "type_of_affiliation" : "efpia", "elixir_node" : "" },
"Ibrahim" : { "github_handle" : "iemam", "name" : "Ibrahim Emam", "orcid" : "0000-0002-7561-2787", "affiliation" : "Imperial College London", "type_of_affiliation" : "academia", "elixir_node" : "UK" },
"Isuru" : { "github_handle" : "tburdett", "name" : "Isuru Liyanage", "orcid" : "0000-0002-4839-5158", "affiliation" : "EMBL-EBI", "type_of_affiliation" : "academia", "elixir_node" : "embl" },
"Isuru" : { "github_handle" : "", "name" : "Isuru Liyanage", "orcid" : "0000-0002-4839-5158", "affiliation" : "EMBL-EBI", "type_of_affiliation" : "academia", "elixir_node" : "embl" },
"Ines" : { "github_handle" : "imsachaves", "name" : "Inês Chaves", "orcid" : "0000-0001-7569-3495", "affiliation" : "ITQB, NOVA University of Lisbon", "type_of_affiliation" : "academia", "elixir_node" : "PT" },
"Isabel" : { "github_handle" : "", "name" : "Isabel Kemmer", "orcid" : "0000-0002-8799-4671", "affiliation" : "Euro-BioImaging ERIC", "type_of_affiliation" : "academia", "elixir_node" : "" },
"Jean" : { "github_handle" : "", "name" : "Jean-Marc Neefs", "orcid" : "", "affiliation" : "Janssen", "type_of_affiliation" : "efpia", "elixir_node" : "" },
Expand All @@ -224,7 +224,7 @@
"Mark" : { "github_handle" : "", "name" : "Mark Ibberson", "orcid" : "0000-0003-3152-5670", "affiliation" : "SIB", "type_of_affiliation" : "academia", "elixir_node" : "CH" },
"Martin" : { "github_handle" : "", "name" : "Martin Cook", "orcid" : "", "affiliation" : "Elixir Europe", "type_of_affiliation" : "academia", "elixir_node" : "CH" },
"Melanie" : { "github_handle" : "mcourtot", "name" : "Melanie Courtot", "orcid" : "0000-0002-9551-6370", "affiliation" : "EMBL-EBI", "type_of_affiliation" : "academia", "elixir_node" : "UK" },
"Mike" : { "github_handle" : "mikedarcy", "name" : "Mike d'Arcy", "orcid" : "0000-0003-2280-917X", "affiliation" : "University of Southern California", "type_of_affiliation" : "academia", "elixir_node" : "embl" },
"Mike" : { "github_handle" : "mikedarcy", "name" : "Mike d'Arcy", "orcid" : "0000-0003-2280-917X", "affiliation" : "University of Southern California", "type_of_affiliation" : "academia", "elixir_node" : "" },
"NickJuty" : { "github_handle" : "nsjuty", "name" : "Nick Juty", "orcid" : "0000-0002-2036-8350", "affiliation" : "University of Manchester", "type_of_affiliation" : "academia", "elixir_node" : "UK" },
"NickLynch" : { "github_handle" : "nicklynch", "name" : "Nick Lynch", "orcid" : "0000-0002-8997-5298", "affiliation" : "OpenPhacts", "type_of_affiliation" : "sme", "elixir_node" : "" },
"Nicolas" : { "github_handle" : "", "name" : "Nicolas Francillonne", "orcid" : "", "affiliation" : "Université Paris-Saclay, INRAE, BioinfOmics", "type_of_affiliation" : "academia", "elixir_node" : "FR" },
Expand All @@ -237,7 +237,7 @@
"Philippe" : { "github_handle" : "proccaserra", "name" : "Philippe Rocca-Serra", "orcid" : "0000-0001-9853-5668", "affiliation" : "University of Oxford", "type_of_affiliation" : "academia", "elixir_node" : "UK" },
"Ratnesh" : { "github_handle" : "", "name" : "Ratnesh Sahay", "orcid" : "", "affiliation" : "Astra-Zeneca", "type_of_affiliation" : "efpia", "elixir_node" : "" },
"Robert" : { "github_handle" : "robertgiessmann", "name" : "Robert Giessmann", "orcid" : "0000-0002-0254-1500", "affiliation" : "Bayer AG", "type_of_affiliation" : "efpia", "elixir_node" : "" },
"Ronald" : { "github_handle" : "ronaldcornet", "name" : "Ronald Cornet", "orcid" : "0000-0002-1704-5980", "affiliation" : "Amsterdam UMC", "type_of_affiliation" : "academia", "elixir_node" : "" },
"Ronald" : { "github_handle" : "ronaldcornet", "name" : "Ronald Cornet", "orcid" : "0000-0002-1704-5980", "affiliation" : "Amsterdam UMC", "type_of_affiliation" : "academia", "elixir_node" : "NL" },
"Rudi" : { "github_handle" : "rverbeec", "name" : "Rudi Verbeeck", "orcid" : "0000-0001-5445-6095", "affiliation" : "Janssen", "type_of_affiliation" : "efpia", "elixir_node" : "" },
"Salvador" : { "github_handle" : "scapella", "name" : "Salvador Capella Gutierrez", "orcid" : "0000-0002-0309-604X", "affiliation" : "Barcelona Supercomputing Centre", "type_of_affiliation" : "academia", "elixir_node" : "ES" },
"Scott" : { "github_handle" : "", "name" : "Scott Lusher", "orcid" : "", "affiliation" : "Janssen", "type_of_affiliation" : "efpia", "elixir_node" : "" },
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