PIG 24 - Authorship policy#
Authors: Bruno Khélifi, Thomas Vuillaume
Created: May 25th, 2022
Accepted: Oct. 20th, 2022
Discussion: GH 3970
Given that the Gammapy library is more widely used by the community, a proper citation of the project including a policy about the authorship is necessary. This PIG addresses this issue by setting an authorship policy for the Gammapy project for each type of products (releases, papers and conferences).
Gammapy started in 2013 and is now widely used in scientific publications. A proper citation scheme with correct authorship allows:
a proper citation of the used Gammapy release,
a proper recognition of the achieved work of any contributor,
compliance with the FAIR principles for Research Software (FAIR4RS).
This PIG aims to set up the project policy about authorship for our publication and releases.
Given the fact that Gammapy is licensed under a 3-clause BSD style license (see gammapy/LICENSE.rst), Gammapy can be used and even modified for a science project. For this modified version, the proposed authorship policy of this PIG is not applicable but the general citation scheme should be applied.
This PIG is structured as follows: a reminder of our general citation scheme that was up-to-now only given orally and on our web pages; then, the authorship policy is given for each of the products associated with Gammapy, namely the intermediate releases, the Long Term Support (LTS) releases, the general Gammapy papers, and the contributions to the conference.
When Gammapy is used for any publication, contribution to conferences or software, authors should properly cite Gammapy. It is asked to cite the DOI of the used Gammapy version as well as the associated paper (e.g. the latest LTS release).
As the Gammapy community fully supports Open Science, we strongly encourage authors using Gammapy to follow the FAIR4RS principles and to allow the reproducibility of their results. As consequence, we suggest always mentioning the Zenodo DOI or the HAL SWHID identifier (associated with the Software Heritage archive) of the used release of Gammapy.
This citation scheme with these two references will be given on our web pages.
The Gammapy references contain a list of authors that requires to be updated with time according to a general policy. This section defines who is a contributor to Gammapy and the policy for each type of product.
Definition of a Contributor#
Contributions to Gammapy can be made in different ways:
contributing to gammapy source code,
contributing to its documentation (rst pages, docstring, gammapy-webpage),
contributing to code reviews, maintenance, deployment and DeVops,
contributing to our associated projects (gammapy-benchmarks, etc),
organizing communication, e.g. hands-on sessions, schools, social media,
coordinating the project.
Contributions on any of the aforementioned aspects make a user as official Gammapy contributor.
Many of these contributions are tracked using the git history. However, the use of personal data is regulated in Europe and one should have the authorisation of users to be cited with their personal information for publications (their full name is mandatory, and, if any, their affiliation and their ORCID number). For this reason, we propose to use the Developer Certificate of Origin (DCO, see the text in here) for each commit. Its acceptation by contributors will permit to:
certify that a user wrote or otherwise has the right to submit a code under our open source licence,
allow our project to use their personal data for the contributions’ record (ie for releases).
README.md will contain a Contributing section explaining that the project follows this DCO that will be
given in a new
CONTRIBUTING.md file, as well as a link to this PIG.
For practical reasons, it is strongly advised that the contributors use always the same GitHub account with a valid full name, to synchronise their git email addresses with their GitHub addresses, to have a unique ORCID identifier and store it into their GitHub user profile for commodity, and inform the developers of any change of affiliation or email address.
Each Gammapy release should be associated with an updated list of authors that will be public on repository (Zenodo and HAL/SWH). This section is about feature releases. Bug releases will have as list of authors the one of its associated feature release whose rules are described here, plus the potentiel additional contributors.
The list of authors is composed of people who contributed to the current release code by accepting the DCO. The history of merged pull requests will be used as starting point. Other type of contributions (see _contributor) could be added during a dedicated call (see below).
The order of the authors is first ‘The Gammapy team’, followed by the list of contributors in alphabetical order:
The Gammapy team: aa, bb, cc, ...
As mentioned in the PIG 23, the publication of a release is preceded by a code freeze period. With its announcement, a call will be made to contributors to update their personal information (e.g. their affiliation) under their sole responsibility. This call will also permit to add any additional author into the list for their special contribution (e.g. on communication). The Project Managers and Lead Developers will have the duty to examine such request and to update accordingly the author list data . In case of conflict, the Gammapy Coordination Committee will be the final decision maker.
Long Term Support releases#
The list of authors is composed of the union of all the contributors of the releases realised since the last LTS release. As the Coordination Committee provides a long term support of the project, their members will be de-facto co-authors.
The order of the authors is first ‘The Gammapy team’, followed by the list of contributors in alphabetical order.
Like for the common releases, a period of code freeze is used to make a call to update the personal information of contributors, as well as to submit a request of co-authorship for special contributions. The same rules and methods as for the standard releases are applied here.
For the first LTS release, the V1.0, all contributors from the beginning of the project will be co-authors by default. As the DCO has not be applied for the past contributions, the best will be done to contact all contributors in order to exercise their right to sign it (“OptIn” scheme), to update their personal information, and to add authors with special contributions. The order of the authors is ‘The Gammapy team’, followed by the list of contributors in alphabetical order.
General Gammapy publications#
This product aims to describe the project and/or the library as a whole and will be most of the time associated with the publication of an LTS release. As it targets a wide community, the following scheme is used.
- List of authors
a/ By default, ‘The Gammapy team’ is mentioned first, then the Lead Developers, then the past Lead Developers since the last general Gammapy publication, then the list of contributors of each release since the last Gammapy publication.
b/ If the editorial rules of the targeted journal permit it, the scheme used by the Astropy project (e.g. Astropy V2.0) should be used in priority:
‘The Gammapy team’, and the list of primary paper contributors in order of contribution agreed per consensus with the development team, as ‘(Primary Paper Contributors)’,
the members of the Coordination Committee, as ‘(Gammapy Coordination Committee)’,
the list of contributors of the associated LTS ordered by alphabetical order, as ‘(Gammapy Contributors)’
In this case, a comment on the author list composition should be added. Extracted from the Astropy project, one can precise:
“The author list has three parts: the authors that made significant contributions to the writing of the paper, the members of the Gammapy Project Coordination Committee, and contributors to the Gammapy Project in alphabetical order. The position in the author list does not correspond to contributions to the Gammapy Project as a whole. A more complete list of contributors to the core package can be found in the package repository and at the Gammapy team webpage.”
- Corresponding author
It is the ‘Gammapy Coordination Committee’, associated with its usual mailing list (GAMMAPY-COORDINATION-L@IN2P3.FR).
One has the freedom to precisely mention acknowledgements associated with the publication. In practice, it is recommended to precise the grants or fellowships given to some authors. One should in any case always acknowledge the Astropy project, to which we are affiliated, and our mandatory external libraries (e.g. numpy, scipy, matplotlib, iminuit). Our web pages will contain a section with some standard sentence(s) on which one could make a reference.
Contribution in conferences#
The section is about any contribution in conferences (a talk, a poster and their associated proceedings) related to the Gammapy project itself. It does not concern a technical or scientific work that uses Gammapy as an open library. In this case, the citation scheme of Gammapy should be used by these authors.
As the length of the author list is generally a constrain, the author list is reduced to the short list of contributors for the conference, followed by ‘The Gammapy team’ associated with a link to the Gammapy team webpage:
oo, ff, tt, for `the Gammapy team <https://gammapy.org/team.html>`_
If there is a corresponding author, the ‘Gammapy Coordination Committee’ associated with its usual mailing list, is used. Concerning the acknowledgement, the Astropy project should always be mentioned, and if possible our mandatory external libraries.
Depending on the software repository, different metadata files are used in the eco-system of Open Source research software and are mandatory.
CITATION.cff is used by Zenodo and GitHub. Its format should follow the rules set up by the
Citation File Format project. A GitHub
Action can be used to automatically check the compliance with the latest format. At the date of this PIG, there is no
official scheme to handle current and past affiliations, that might be needed for LTS releases for example (see the
CFF project Issue #268).
In the affiliation string, one could add a past affiliation as precised below, but with a risk that Zenodo or tools
CITATION.cff to make the
codemeta.json does not process correctly this double affiliation.
authors: - family-names: XXX given-names: "YYYY Z." affiliation: "Lab AA, XX; Past: Lab BB, YY" email: firstname.lastname@example.org orcid: "https://orcid.org/0000-0000-0000-0000"
It offers a more detailed description of a software than the one into
CITATION.cff, that is focused on authors.
Definition of the Maintainer#
In the codemeta format, a specific field, a Maintainer, can be filled. Usually, a software maintainer or package maintainer is one or more people who build source code into a binary package for distribution, commit patches, or organize code in a source repository. And in case of issue, this person can be contacted to fix a broken deposit.
For Gammapy, by default, the maintainers are the Lead Developers. If in the future a task is dedicated to the creation of a release, the maintainer will be the person in charge of this task. The name or the names of the maintainers will be filled by the Lead Developers.
Today, the tool offered by GitHub to sign the DCO is to add the extra parameter
-s to each git commit. Users have to
be aware of that and get used of it. For the reviewers, a github CI can be used to check quickly if a contributor has
signed the DCO. This method will be used for the moment. If there is any other method that avoids this extra parameter,
one will naturally consider it.
In order to respect these rules, some automation is required to create the list of contributors. One could use the Python library Tributors. This library uses the GitHub API to determine the list of contributors, which is written in the format associated with codemeta.json, citation.cff, zenodo.json. This kind of library allows then two requirements: retrieve automatically the list of contributors from GitHub and write the authors list in all the needed formats.
Collection of the personal information of authors#
CITATION.cff file will be used as the main file to be maintained, while the
codemeta.json will be
automatically created from it. For any release, the former should be carefully updated and systematically a review
should be organised by the dev team.
In order to maintain updated data about authors for the LTS releases and LTS papers, a new file could be used with
LTS_AUTHORS.cff. The decision will be made in a dedicated PR.
The data collected from the git history are not sufficient for any publication. Most of the contributors must give their affiliation as stipulated by their working contract. Also, the ORCID number is a relatively new type of information, recommended to be used in the context of the Open Science movement, but it is not mandatory. However, one needs to collect this information to build the authors lists, in a safe and fair way.
In this purpose, one could use the public user profile of the GitHub platform. They are public data, but one should be aware that they might not be complete and/or up-to-date. As mentioned earlier, it is recommended to fill correctly this GitHub profile to help the dev team to pre-fill the metadata files.
One should note that the GitHub profile does not contain a field associated with the ORCID identifier. However, one could also retrieve the ORCID identifier of a contributor with the ORCID API (e.g. How-To-1 or How-To-2).
In any case, a specific Python script located in the main Gammapy repository had to be written such that the authors’ order follows these rules. In this case, integration within a GitHub action could be possible.
In this context, one could technically use an other cff file as maintenance file to store the personal data of users that have signed the DCO.
A second script should be settled in order to create the list of authors associated
to the latest LTS in HTML format that could be inserted in the team section for our general
web page. This script would read one of the metadata files (e.g.
citation.cff) to create
It is important to note that the list of personal information might change from one editor to an other. For the code deposits in Zenodo, SWH, etc, the data follow standards of Open Science and scripts can be settled. For publications, the editors have frequently their own scheme and adaptations will be made on the case by case.
As mentioned here, the authors list will be reviewed for any publication, for safety and to allow OptIn/OptOut requests.
Handling of conference material#
Conference contributions (Proceedings, Posters, …) could be developed in dedicated repositories in the Gammapy Github organization, as well as the author list.
One could ask CTAO software coordinators (ie ACADA, DPPS, SUSS) if such rules can be used by them also, even if the The Gammapy project is independent. In the same spirit, advice could be asked to people of the ESCAPE project via our corresponding person. And finally, one could mention the existence of these rules and ask for advice to the Astropy project.
These requests to the Astropy community and CTAO for recommendations and preferences either remained un-responded or did not lead to objections at the current time.
After the addition of comments and proposals, the PIG is accepted by the dev team and the CC. The choice of practical implementation of such scheme will be made in dedicated pull requests.