From be38b92f79e68621d2133ef4d0139a93695cbb4e Mon Sep 17 00:00:00 2001 From: Jaro Camphuijsen Date: Tue, 23 Sep 2025 17:14:02 +0200 Subject: [PATCH 01/12] Convert CITATION.md to CITATION.cff --- CITATION.cff | 85 ++++++++++++++++++++++++++++++++++++++++++++++++++++ CITATION.md | 3 -- 2 files changed, 85 insertions(+), 3 deletions(-) create mode 100644 CITATION.cff delete mode 100644 CITATION.md diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 000000000..3ede7650f --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,85 @@ +# This CITATION.cff file was generated with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! + +cff-version: 1.2.0 +title: Intermediate Research Software Development Skills (Python) +message: >- + If you use this dataset, please cite it using the metadata + from this file. +type: dataset +authors: + - given-names: Aleksandra + family-names: Nenadic + - given-names: Steve + family-names: Crouch + - given-names: Thomas + family-names: Kiley + - given-names: Raniere + family-names: Silva + - given-names: François + family-names: Michonneau + - given-names: Maxim + family-names: Belkin + - given-names: James + family-names: Graham + - given-names: Greg + family-names: Wilson + - given-names: Matthew + family-names: Bluteau + - given-names: Toby + family-names: Hodges + - given-names: Zhian + family-names: Kamvar + - given-names: Sven + family-names: Burg + name-particle: van der + - given-names: Abby + family-names: Cabunoc Mayes + - given-names: Jacalyn + family-names: Laird + - given-names: Sarah + family-names: Stevens + - given-names: Katrin + family-names: Leinweber + - given-names: Erin + family-names: Becker + - given-names: João + family-names: Rodrigues + - given-names: Douglas + family-names: Lowe + - given-names: Aman + family-names: Goel + - given-names: Matt + family-names: Graham + - given-names: Deveraj + family-names: Gopinathan + - given-names: Jaro + family-names: Camphuijsen + orcid: 'https://orcid.org/0000-0002-8928-7831' + - given-names: Giulia + family-names: Crocioni + - given-names: William + family-names: Close +identifiers: + - type: doi + value: 10.5281/zenodo.6532056 + description: Zenodo +repository-code: >- + https://github.com/carpentries-incubator/python-intermediate-development +url: >- + https://carpentries-incubator.github.io/python-intermediate-development/ +abstract: >- + This is an intermediate-level course in collaborative + research software engineering and development skills, + using Python as an example language. It teaches these + skills in a way that mimics a typical software development + process working as a part of a team, starting from an + existing piece of software. +keywords: + - Python + - Software Development + - Carpentries +license: CC-BY-4.0 +commit: 9c4db4c870d9b9cdf85f84f032b7341cbd8cb387 +version: beta-July2025 +date-released: '2025-07-30' diff --git a/CITATION.md b/CITATION.md deleted file mode 100644 index 272385194..000000000 --- a/CITATION.md +++ /dev/null @@ -1,3 +0,0 @@ -Cite as: - -Aleksandra Nenadic, Steve Crouch, Thomas Kiley, Raniere Silva, François Michonneau, Maxim Belkin, James Graham, Greg Wilson, Matthew Bluteau, Toby Hodges, Zhian N. Kamvar, Sven van der Burg, Abby Cabunoc Mayes, JacalynLaird, Sarah Stevens, Katrin Leinweber, Erin Becker, João Rodrigues, Douglas Lowe, Aman Goel, Matt Graham, Deveraj Gopinathan, Jaro Camphuijsen, … William L. Close. (2024). carpentries-incubator/python-intermediate-development: beta-Nov2024 (beta-Nov2024). Zenodo. https://doi.org/10.5281/zenodo.16606960 From f1ebd512b7da4900afd9d09da05944eed76bb8e8 Mon Sep 17 00:00:00 2001 From: Jaro Camphuijsen Date: Tue, 23 Sep 2025 17:14:40 +0200 Subject: [PATCH 02/12] Remove AUTHORS file for storing duplicate information --- AUTHORS | 10 ---------- 1 file changed, 10 deletions(-) delete mode 100644 AUTHORS diff --git a/AUTHORS b/AUTHORS deleted file mode 100644 index 8fc00bec6..000000000 --- a/AUTHORS +++ /dev/null @@ -1,10 +0,0 @@ -* [Steve Crouch](https://github.com/steve-crouch) -* [Aleksandra Nenadic](https://github.com/anenadic) -* [James Graham](https://github.com/jag1g13) -* [Martin Robinson](https://github.com/martinjrobins) -* [Sam Mangham](https://github.com/smangham) -* [Jacalyn Laird](https://github.com/JacalynLaird) -* [Thomas Kiley](https://github.com/thomaskileyukaea) -* [Matthew Bluteau](https://github.com/bielsnohr) -* [Sven van der Burg](https://github.com/svenvanderburg) -* [Giulia Crocioni](https://github.com/gcroci2) From b26594f24a8c3e05461cafddaeeee5689281ae95 Mon Sep 17 00:00:00 2001 From: Douglas Lowe <10961945+douglowe@users.noreply.github.com> Date: Tue, 28 Oct 2025 08:53:17 +0000 Subject: [PATCH 03/12] correct readme link to citation file --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 92ac9ed2c..edd8d119a 100644 --- a/README.md +++ b/README.md @@ -97,7 +97,7 @@ under the [MIT licence][mit-license]. For more information, see [LICENSE.md](LIC ## Citation -To cite this lesson, please consult with [CITATION](CITATION). +To cite this lesson, please consult [CITATION.cff](CITATION.cff). ## Contact From 4fff7330f8ce3e7587d5399bde20818a42a5f8c5 Mon Sep 17 00:00:00 2001 From: Matthew <6177028+bielsnohr@users.noreply.github.com> Date: Tue, 9 Dec 2025 10:11:58 +0000 Subject: [PATCH 04/12] Add ORCID for most maintainers in CITATION.cff --- CITATION.cff | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 3ede7650f..c5983ba9d 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -12,6 +12,7 @@ authors: family-names: Nenadic - given-names: Steve family-names: Crouch + orcid: 'https://orcid.org/0000-0001-8985-6814' - given-names: Thomas family-names: Kiley - given-names: Raniere @@ -26,6 +27,7 @@ authors: family-names: Wilson - given-names: Matthew family-names: Bluteau + orcid: 'https://orcid.org/0000-0001-9498-8475' - given-names: Toby family-names: Hodges - given-names: Zhian @@ -47,6 +49,7 @@ authors: family-names: Rodrigues - given-names: Douglas family-names: Lowe + orcid: 'https://orcid.org/0000-0002-1248-3594' - given-names: Aman family-names: Goel - given-names: Matt From 33f668eeae3e5933cfc3fa18fe5d9c98f30eebf9 Mon Sep 17 00:00:00 2001 From: Aleksandra Nenadic Date: Tue, 9 Dec 2025 10:44:09 +0000 Subject: [PATCH 05/12] Add Aleks's orcid --- CITATION.cff | 1 + 1 file changed, 1 insertion(+) diff --git a/CITATION.cff b/CITATION.cff index c5983ba9d..6a9fceaed 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -10,6 +10,7 @@ type: dataset authors: - given-names: Aleksandra family-names: Nenadic + orcid: 'https://orcid.org/0000-0002-2269-3894' - given-names: Steve family-names: Crouch orcid: 'https://orcid.org/0000-0001-8985-6814' From f62aee375fe8789fab3afa734a15ec5aea38b3d2 Mon Sep 17 00:00:00 2001 From: Aleksandra Nenadic Date: Tue, 9 Dec 2025 10:47:09 +0000 Subject: [PATCH 06/12] Update paper.bib --- paper.bib | 52 +++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 47 insertions(+), 5 deletions(-) diff --git a/paper.bib b/paper.bib index 523432940..0467b0aab 100644 --- a/paper.bib +++ b/paper.bib @@ -1,6 +1,48 @@ -@misc{ssi-international-rse-survey-2018, - title={SSI International RSE Survey 2018: What do we know about RSEs?}, - author={Philippe, Olivier and Hammitzsch, Martin and Janosch, Stephan and van der Walt, Anelda and van Werkhoven, Ben and Hettrick, Simon and Katz, Daniel S. and Leinweber, Katrin and Gesing, Sandra and Druskat, Stephan and Henwood, Scott and May, Nicholas R. and Lohani, Nooriyah P. and Sinha, Manodeep} - year={2018}, - url={https://zenodo.org/records/2585783} +@software{aleksandra_nenadic_2025_16606960, + author = {Aleksandra Nenadic and + Steve Crouch and + Thomas Kiley and + Matthew and + James Graham and + Toby Hodges and + Sven van der Burg and + JacalynLaird and + Sarah Stevens and + Douglas Lowe and + Sam Mangham and + Frank Löffler and + Sander van Rijn and + Giulia Crocioni and + Harry Saunders and + Tom Neep and + Renato Alves and + Daniel S. Katz and + Aman Goel and + wk9874 and + Jen Reeve and + gkmurphy and + Yuriy Sverchkov and + shartleybham-acuk and + gadgil48 and + Olexandr Konovalov and + Martin Robinson and + Kristian Zarębski and + k-collie and + Jonathan Guyer}, + title = {carpentries-incubator/python-intermediate- + development: beta-July2025 + }, + month = jul, + year = 2025, + publisher = {Zenodo}, + version = {beta-July2025}, + doi = {10.5281/zenodo.16606960}, + url = {https://doi.org/10.5281/zenodo.16606960}, + swhid = {swh:1:dir:4e163afdc5932d261104cb14711a1b74f3830e93 + ;origin=https://doi.org/10.5281/zenodo.6532056;vis + it=swh:1:snp:c533704377fc2ff7bd185837b8a4da705e9f3 + 81e;anchor=swh:1:rel:ccaf7af66378454acc2fb3232edb0 + 4f78d050dde;path=carpentries-incubator-python- + intermediate-development-9c4db4c + }, } From ecdf162c91bdefd026e2f577caeff57dae4dca13 Mon Sep 17 00:00:00 2001 From: Matt Graham Date: Tue, 23 Dec 2025 10:49:04 +0000 Subject: [PATCH 07/12] Adding ORCiDs and updating details for MG and DG --- CITATION.cff | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 6a9fceaed..b22faf41f 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -53,10 +53,12 @@ authors: orcid: 'https://orcid.org/0000-0002-1248-3594' - given-names: Aman family-names: Goel - - given-names: Matt + - given-names: Matthew M. family-names: Graham - - given-names: Deveraj + orcid: 'https://orcid.org/0000-0001-9104-7960' + - given-names: Devaraj family-names: Gopinathan + orcid: 'https://orcid.org/0000-0002-0490-3229' - given-names: Jaro family-names: Camphuijsen orcid: 'https://orcid.org/0000-0002-8928-7831' From eed058dc106ab46fd8b1dd2e4584744ef2ed83c3 Mon Sep 17 00:00:00 2001 From: Jaro Camphuijsen Date: Wed, 11 Feb 2026 16:59:31 +0100 Subject: [PATCH 08/12] Add Sven's and Giulia's orcid --- CITATION.cff | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index b22faf41f..3da773d4d 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -36,6 +36,7 @@ authors: - given-names: Sven family-names: Burg name-particle: van der + orcid: 'https://orcid.org/0000-0003-1250-6968' - given-names: Abby family-names: Cabunoc Mayes - given-names: Jacalyn @@ -64,6 +65,7 @@ authors: orcid: 'https://orcid.org/0000-0002-8928-7831' - given-names: Giulia family-names: Crocioni + orcid: 'https://orcid.org/0000-0002-0823-0121' - given-names: William family-names: Close identifiers: From 171d7493838d0c3a0e4836d8be78f594bd89c2fc Mon Sep 17 00:00:00 2001 From: Jaro Camphuijsen Date: Wed, 11 Feb 2026 17:02:24 +0100 Subject: [PATCH 09/12] Add missing names from AUTHORS file --- CITATION.cff | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 3da773d4d..879258b2e 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -39,6 +39,10 @@ authors: orcid: 'https://orcid.org/0000-0003-1250-6968' - given-names: Abby family-names: Cabunoc Mayes + - given-names: Martin + family-names: Robinson + - given-names: Sam + family-names: Mangham - given-names: Jacalyn family-names: Laird - given-names: Sarah From c9052e8feb60344c3d3751b635fb348476ad3bcf Mon Sep 17 00:00:00 2001 From: Aleksandra Nenadic Date: Tue, 24 Feb 2026 10:33:56 +0000 Subject: [PATCH 10/12] Apply suggestion from @bielsnohr Co-authored-by: Matthew <6177028+bielsnohr@users.noreply.github.com> --- paper.bib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paper.bib b/paper.bib index 0467b0aab..e80095d47 100644 --- a/paper.bib +++ b/paper.bib @@ -2,7 +2,7 @@ @software{aleksandra_nenadic_2025_16606960 author = {Aleksandra Nenadic and Steve Crouch and Thomas Kiley and - Matthew and + Matthew Bluteau and James Graham and Toby Hodges and Sven van der Burg and From bab12ae51f9fa91519f4d434c29bd44b3d61e10d Mon Sep 17 00:00:00 2001 From: Jaro Camphuijsen Date: Tue, 24 Feb 2026 12:13:30 +0100 Subject: [PATCH 11/12] Add missing authors from zenodo entry/paper.bib --- CITATION.cff | 34 +++++++++++++++++++++++++++++++++- 1 file changed, 33 insertions(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index 879258b2e..58f0ff44e 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -72,6 +72,39 @@ authors: orcid: 'https://orcid.org/0000-0002-0823-0121' - given-names: William family-names: Close + - given-names: Frank + family-names: Löffler + - given-names: Sander + family-names: Rijn + name-particle: van + - given-names: Harry + family-names: Saunders + - given-names: Matthew + family-names: Field + - given-names: Sanket + family-names: Gadgil + - given-names: Kristian + family-names: Zarębski + - given-names: Kingsley + family-names: Collie + - given-names: Tom + family-names: Neep + - given-names: Renato + family-names: Alves + - given-names: Daniel + family-names: Katz + - given-names: Jen + family-names: Reeve + - given-names: G.K. + family-names: Murphy + - given-names: Yuriy + family-names: Sverchkov + - given-names: S. + family-names: Hartley + - given-names: Olexandr + family-names: Konovalov + - given-names: Jonathan + family-names: Guyer identifiers: - type: doi value: 10.5281/zenodo.6532056 @@ -92,6 +125,5 @@ keywords: - Software Development - Carpentries license: CC-BY-4.0 -commit: 9c4db4c870d9b9cdf85f84f032b7341cbd8cb387 version: beta-July2025 date-released: '2025-07-30' From c466409cf09200ad99a9e48278e1fa3efe9bcc3c Mon Sep 17 00:00:00 2001 From: Jaro Camphuijsen Date: Tue, 24 Feb 2026 15:18:33 +0100 Subject: [PATCH 12/12] Update paper.bib, generated from citation.cff with github interface button and add including doi --- paper.bib | 56 ++++++++----------------------------------------------- 1 file changed, 8 insertions(+), 48 deletions(-) diff --git a/paper.bib b/paper.bib index e80095d47..bdf8af465 100644 --- a/paper.bib +++ b/paper.bib @@ -1,48 +1,8 @@ -@software{aleksandra_nenadic_2025_16606960, - author = {Aleksandra Nenadic and - Steve Crouch and - Thomas Kiley and - Matthew Bluteau and - James Graham and - Toby Hodges and - Sven van der Burg and - JacalynLaird and - Sarah Stevens and - Douglas Lowe and - Sam Mangham and - Frank Löffler and - Sander van Rijn and - Giulia Crocioni and - Harry Saunders and - Tom Neep and - Renato Alves and - Daniel S. Katz and - Aman Goel and - wk9874 and - Jen Reeve and - gkmurphy and - Yuriy Sverchkov and - shartleybham-acuk and - gadgil48 and - Olexandr Konovalov and - Martin Robinson and - Kristian Zarębski and - k-collie and - Jonathan Guyer}, - title = {carpentries-incubator/python-intermediate- - development: beta-July2025 - }, - month = jul, - year = 2025, - publisher = {Zenodo}, - version = {beta-July2025}, - doi = {10.5281/zenodo.16606960}, - url = {https://doi.org/10.5281/zenodo.16606960}, - swhid = {swh:1:dir:4e163afdc5932d261104cb14711a1b74f3830e93 - ;origin=https://doi.org/10.5281/zenodo.6532056;vis - it=swh:1:snp:c533704377fc2ff7bd185837b8a4da705e9f3 - 81e;anchor=swh:1:rel:ccaf7af66378454acc2fb3232edb0 - 4f78d050dde;path=carpentries-incubator-python- - intermediate-development-9c4db4c - }, -} +@misc{Nenadic_Intermediate_Research_Software_2025, +author = {Nenadic, Aleksandra and Crouch, Steve and Kiley, Thomas and Silva, Raniere and Michonneau, François and Belkin, Maxim and Graham, James and Wilson, Greg and Bluteau, Matthew and Hodges, Toby and Kamvar, Zhian and van der Burg, Sven and Cabunoc Mayes, Abby and Robinson, Martin and Mangham, Sam and Laird, Jacalyn and Stevens, Sarah and Leinweber, Katrin and Becker, Erin and Rodrigues, João and Lowe, Douglas and Goel, Aman and Graham, Matthew M. and Gopinathan, Devaraj and Camphuijsen, Jaro and Crocioni, Giulia and Close, William and Löffler, Frank and van Rijn, Sander and Saunders, Harry and Field, Matthew and Gadgil, Sanket and Zarębski, Kristian and Collie, Kingsley and Neep, Tom and Alves, Renato and Katz, Daniel and Reeve, Jen and Murphy, G.K. and Sverchkov, Yuriy and Hartley, S. and Konovalov, Olexandr and Guyer, Jonathan}, +month = jul, +title = {{Intermediate Research Software Development Skills (Python)}}, +url = {https://github.com/carpentries-incubator/python-intermediate-development}, +year = {2025}, +doi = {10.5281/zenodo.16606960} +} \ No newline at end of file