Merge pull request #2 from TU-Delft-DCC/create-resources

Add resources

fair4rs/_toc.yml

@@ -12,6 +12,7 @@ parts:
 - caption: Seminars
   chapters:
   - file: 1-intro
+    title: Week 1 - Introduction
   - url: https://coderefinery.github.io/2023-03-21-workshop/
     title: Week 2 - CodeRefinery workshop
   - url: https://coderefinery.github.io/2023-03-21-workshop/
@@ -33,5 +34,7 @@ parts:
 
 - caption: Resources
   chapters:
+  - url: https://tu-delft-dcc.github.io/software/project_cards.html
+    title: FAIR cards
   - file: resources
     title: Resources

fair4rs/resources.md

@@ -1,2 +1,96 @@
-# References
+# Resources
 
+## General resources
+
+- CodeRefinery lessons: https://coderefinery.github.io/
+- Software Carpentry lessons: https://software-carpentry.org/lessons/
+- The Turing Way: https://the-turing-way.netlify.app/
+- FAIR software: https://fair-software.nl/
+- TU Delft DCC Guides: https://tu-delft-dcc.github.io/
+
+## Resources per topics
+
+### FAIR research software
+- [Introducing the FAIR principles for research software](https://www.nature.com/articles/s41597-022-01710-x)
+- https://fair-software.nl
+- [Publishing data and code at TU Delft](https://zenodo.org/record/7674963#.ZBNM6XbMKUk)
+- [Blog Anton Akhmerov (Applied Sciences)](https://quantumtinkerer.tudelft.nl/blog/demand-data-for-review/)
+
+#### Software Management Plans
+- [eScience Center - Practical Guide to Software Management Plans](https://zenodo.org/record/7248877)
+- [Software Sustainability Institute - Checklist for an SMP](https://zenodo.org/record/2159713#.ZBNOCnbMKUl)
+
+### Version control with git
+- [Code Refinery Git lesson](https://coderefinery.github.io/git-intro/)
+- [Code Refinery lesson](https://coderefinery.github.io/git-collaborative/)
+- [Pro Git book](https://git-scm.com/book/en/v2)
+- [DCC Guides - Branch management](https://tu-delft-dcc.github.io/software/git/branch_management.html)
+- [The Turing Way - Version control for data](https://the-turing-way.netlify.app/reproducible-research/vcs/vcs-data.html)
+- [Templates for .gitignore](https://github.com/github/gitignore)
+
+### Project planning and management
+- [GitHub boards](https://docs.github.com/en/issues/organizing-your-work-with-project-boards/managing-project-boards/about-project-boards)
+- [Build Better Scientific Software - Better Planning blogs](https://bssw.io/items?category=better-planning)
+- [GitFlow original blog post by Vincent Driessen](https://nvie.com/posts/a-successful-git-branching-model/)
+- [Gitflow process](http://datasift.github.io/gitflow/IntroducingGitFlow.html)
+
+### Licenses
+- [TU Delft - Research Software Policy](https://zenodo.org/record/4629662#.ZCwWVnZBzuo)
+- [TU Delft - Guidelines on Research Software](https://doi.org/10.5281/zenodo.4629635)
+- [The Turing Way - Software Licenses](https://the-turing-way.netlify.app/reproducible-research/licensing/licensing-software.html)
+
+### Reproducible environments
+- [Code Refinery lesson](https://coderefinery.github.io/reproducible-research/)
+- [The Turing Way - Reproducible environments](https://the-turing-way.netlify.app/reproducible-research/renv.html)
+
+#### Conda
+- [Conda cheat sheet](https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdfs)
+- [Faster conda alternative: Mamba](https://mamba.readthedocs.io/en/latest/)
+- [Pin exact versions with conda-lock](https://github.com/conda/conda-lock)
+
+#### Matlab
+- [Find your Matlab dependencies](https://nl.mathworks.com/help/matlab/ref/matlab.codetools.requiredfilesandproducts.html)
+- [Matlab Dependency Analyzer](https://nl.mathworks.com/help/matlab/matlab_prog/analyze-project-dependencies.html)
+
+#### Containers
+- [Introduction to Docker containers](https://carpentries-incubator.github.io/docker-introduction/)
+- [The Turing Way - containerized workflow](https://the-turing-way.netlify.app/reproducible-research/renv/renv-containers.html)
+- [Ditching Docker Hub: serve research software with GHCR + Zenodo](https://blog.esciencecenter.nl/ditching-docker-hub-serve-research-software-with-ghcr-zenodo-2e47b8c93d88)
+
+### Documentation
+- [Code Refinery lesson - Documentation](https://coderefinery.github.io/documentation/)
+- [Quarto](https://quarto.org/)
+- [Myst parser](https://myst-parser.readthedocs.io/en/latest/)
+- [CITATION.cff reference](https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md)
+
+#### Sphinx
+- [Theme gallery](https://sphinx-themes.org/)
+- [Jupyerbook](https://jupyterbook.org/en/stable/intro.html)
+- [Code Refinery lesson - Deploying documentation](https://coderefinery.github.io/documentation/gh_workflow/)
+
+#### Examples of contributing guidelines
+- [Contributing guide](https://github.com/cncf/project-template/blob/main/CONTRIBUTING.md)
+- [eScience Center - matchms](https://github.com/matchms/matchms/blob/master/CONTRIBUTING.md)
+
+### Code quality
+- [The Turing Way - code quality](https://the-turing-way.netlify.app/reproducible-research/code-quality.html)
+- [Code Refinery lesson on modular code](https://coderefinery.github.io/modular-type-along/)
+- [EOSC documentation](https://www.eosc-synergy.eu/for-developers/)
+- [OpenSSF Best Practices Badge](https://bestpractices.coreinfrastructure.org/en)
+- [Utrecht University - Code quality](https://utrechtuniversity.github.io/workshop-computational-reproducibility/slides/slides_code-quality.html#1)
+- [Clean code by Uncle Bob](https://gist.github.com/wojteklu/73c6914cc446146b8b533c0988cf8d29)
+- [SonarCloud - Getting started](https://docs.sonarcloud.io/getting-started/overview/)
+- [Repository Badges](https://shields.io/)
+
+#### Testing
+- [Code Refinery lesson - Testing](https://coderefinery.github.io/testing/)
+- [The Turing Way - Testing](https://the-turing-way.netlify.app/reproducible-research/testing.html)
+- [Code Refinery - Automated testing](https://coderefinery.github.io/testing/continuous-integration/)
+
+#### Reviewing code
+- [The Turing Way - Code reviewing process](https://the-turing-way.netlify.app/reproducible-research/reviewing.html)
+- [Example of a review process](https://www.youtube.com/watch?v=Kxxr1UdXTmI)
+
+#### Refactoring
+- [Best practices for refactoring code for Python](https://www.freecodecamp.org/news/best-practices-for-refactoring-code/)
+- [What is refactoring?](https://refactoring.guru/refactoring/what-is-refactoring)