Software Licenses & Copyright

Important: I AM NOT A LAWYER!

AKA: IANAL

Copyright

Facts and ideas are not copyrightable.

Expressions of ideas are copyrightable.

Copyright Examples

Game rules are not copyrightable (chess, Go, football, Dungeons & Dragons).

Expressions of game rules are copyrightable.

Copyright Examples 2

A function that computes standard deviation of values: name choices and concept of the function are not copyrightable.

The std() code actually computes the standard deviation is copyrightable.

Basic Copyright

"Right of First Publication": copyright automatically goes to the first creator of any creative work

(Even if not explicitly specified)

Consequence: if you post software to GitHub without an explicit license, then you own the copyright—even if openly and publicly visible.

By default, no one else is legally allowed to use or modify your work.

Software Licenses

All software codes you make publicly available should be accompanied by a software license describing the terms by which others may use and/or modify your code.

Public Domain

Alternatively, you can put work into the public domain: "This work has been placed in the public domain."

Free for anyone and everyone to use and modify.

Literature examples: Sherlock Holmes, Frankenstein

(There are some tricky issues internationally, however.)

Software Licenses

Kinds of software licenses: proprietary, and free/open source (FOSS, FLOSS, OSS)

Pick an existing license. Do not create your own.

Software Licenses

FOSS categories: permissive, and "copyleft"

Permissive licenses: BSD 3-clause, MIT; allow further distribution under any license

Copyleft licenses: GPL; require modifications to be shared under the same license ("viral")

https://choosealicense.com

Open Source Initiative licenses

Which license to use?

When in doubt, use a permissive license like the BSD 3-clause or MIT licenses.

Copyrighting other creative works: Creative Commons

• BY: Attribution
• SA: ShareAlike
• ND: NoDerivatives
• NC: NonCommercial

Licenses: CC BY, CC BY-SA, CC BY-NC, CC BY-NC-NC

Choose a license

Beyond copyright & licenses

Patents: cover ideas and concepts; modern issues with "patent trolls"

Trademarks: symbols that represent a business or organization

Export control: government may forbid the transfer of source code (and data, ideas) to another country or foreign national without permission

HIPAA compliance: software that deals with human patients must be anonymized

Long story short: pick a license when creating a project, and put as LICENSE.txt in your repo.

We've talked about best practices:

• Version control / collaboration
• Licensing
• Packaging / distribution
• Documentation

Is that it?

How to make your software citable?

Add a CITATION.cff file:

                            cff-version: 1.2.0
                            message: "Please cite the following works when using this software."
                            type: software
                            title: Title
                            abstract: Title
                            authors:
                            - family-names: ...
                              given-names: ...
                              orcid: ...
                              affiliation: ...
                            doi: ...
                            repository-code: ...
                            url: ...
                            keywords: ...
                            license: ...
                        

For research, need one more step: archiving software (or data)

Consider: what if you use/cite software, and someone modifies it?

Zenodo + GitHub = ❤️

Zenodo can be connected to GitHub, and set to automatically archive releases

Live demo time... connecting GitHub to Zenodo

Recommended workflow:

• git tag -a v0.0.1 -m "version 0.0.1"
• git push origin --tags
• Go to GitHub repo -> Releases -> v0.0.1
• Create release from tag
• Grab the DOI from Zenodo!

Citing software & data is important.

Our research results depend on software and data—different versions of software and data change our answers.

Without proper citations, your work is not reproducible.

Also, academia relies on citations for credit. (for better or worse)

Software citation principles

How to cite?

Name/description

Author(s)/developer(s)

DOI or other persistent identifier

Version number/commit hash

Location (e.g., GitHub repo)

(If there’s a paper describing it, cite that too)

Where to cite?

In the text with the references/bibliography.

KE Niemeyer, NJ Curtis, & CJ Sung. “pyJac: analytical Jacobian generator for chemical kinetics” (2017) Computer Physics Communications, 215:188–203. https://doi.org/10.1016/j.cpc.2017.02.004

Reproducibility: Repro-packs

Lorena Barba describes “reproducibility packages” associated with papers, with figures shared under CC-BY license:

“For every figure that presents some result, we bundle the files needed to reproduce it — input or configuration files used to run the simulation(s) behind the result; code to process raw data into derived data; and scripts to create output graphs — and deposit them together with the figure into an open-data repository, such as Figshare. Figshare assigns the bundle a DOI, which we then include in the figure caption so readers can easily find the data and re-create the result.”

My practice:

1. Produce a single repro-pack for an entire paper, which contains:
   • Python plotting scripts and associated results data
   • Figures (PDFs for plots, always)
   • Any other relevant data: input files, configuration files, etc.
2. Upload to Figshare/Zenodo under CC-BY license
3. Cite using the resulting DOI in the associated paper(s)

Benefits

Improving reproducibility and impact of your work

Reviewers will love you with this one great trick!

It also lets you reuse your figures without violating the journal copyright. (Yes, when published, the journal owns the paper and everything in it that isn’t licensed from somewhere else.)

How to cite/mention

JOSS: Journal of Open Source Software

Developer-friendly journal for research software packages

Affiliate of Open Source Initiative

Open access & no fees

“If you've already licensed your code and have good documentation then we expect that it should take less than an hour to prepare and submit your paper to JOSS.”

JOSS paper submission

JOSS reviews