4OSS

introductions

we introduce ourselves
participants introduce themselves
- who they are, where they work
- one top best practice for research software
expectations for the workshop
introduce Software Development Best Practices WG of ELIXIR tools platform, papers and 4OSS
exercise (in pairs): challanges when reusing someone elses research software
exercise (in pairs): challanges in making your own sofware open, what they did to make it easier for others to reuse their software
exercise (pairs)
- what are the fears of opening up the code?
- what are the fears of contributing to someones code?

start with empty README.md file
introduction to markdown
https://opensource.guide
exercise:
- what is the advantage of making code open from day one vs when having first ready version of the software?
- what are the disadvantages?
exercise:
- what is the minimum information necesary to document the software?
exercise:
- what is different audience of the documentation?
  - (end)users
    - novices
    - experts
  - developers
    - first time contributors
    - you one month later
  - collaborators
there are different kinds of documentation
- start with README.md
- there are (web) tools/plarforms that make it easier:
  - sphinx
  - readthedocs
release on github, connect to zenodo, get a DOI
what other files?
- CONTRIBUTING.md
- CITE.cff
  - why citation?
  - we need recognition for software and that will not happen if there is no way to cite software
- Code of Conduct
- requirements.txt/environment.yml
- CHANGELOG.md
- metadata description (codemeta, schema.org, requirements by different journals eg. SoftwareX)
- license
other ways to increase reusability of your software
- containers (biocontainers)
- packaging
computational notebooks (eg. Jupyter Notebook)

you need a license from day one
copyright vs license
reuse existing license
criteria for selecting the license
choosealicense.com
licenses and dependecies
- license conflicts
- relicensing
- dual licensing (academic and commercial use)

Discussion: What are the benefits of having external contributions in your project?
have you contributted to an external project?
- how did it happen?
Toby (owner) in the repo
- find a typo
- create and issue
- labels it "good first contribution"
Mateusz (collaborator)
- look at contribution guidelines
- fork
- fix the typo
- make a contribution
Toby
- merges
- thanks for contribution
- add the contributor to the contributors file
what is the governance (discussion)?
- responsibilities
- bdfl
- RFCs
be kind to the contributors and have the guidelines (CONTRIBUTING.md)
differnt kinds of documentation and their purpose
- email
- issues
- wiki
- stack overflow
- gitter / slack / etc
- irc

why is discoverability of your software important
- have you ever tried to find softare used in a paper? How easy was it?
what is metadata?
- why structured metadata (machine readibility)?
- if you have structured citation info (.cff) you can pull all the citation info
- example of metadata in R package (http://r-pkgs.had.co.nz/description.html)
controlled vocabularies, ontologies etc
- dublin core
- schema.org
- codemata
- EDAM ontology
software registries/repositories
- GitHub
- zenodo
- Bio.tools
- research software directory
FAIR software
- top 10 FAIR software things