Automated publications

[asmacdo]

Closes #89

This change means we can keep a list of dois in data/publications.yaml and publications.md can be automatically generated. (Currently done with a manual step, documented in the README)

This works as-is, remaining TODOs:

• needs CI to automatically regenerate publications.md if data/publications.yaml changes and push a new change
  • Audit failure behavior, probably if any citations fail to render we should error out instead of just printing warnings
• Audit format: we lost some formatting, ie no italics and doi links are longer. may need a post processing step or a different style from citeproc-py.
• Alternative location for pyproject.toml? May not belong in the root, since overall this is not a python project.

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[dnkennedy]

Couple comments, related to the differences between this and the original, and my opinion:

• I would like the article title and journal name to be italicized,
• Current shows 1 author initial, original showed at least 2 (perhaps more?); I think I like the multiple initials (ie. D.N. Kennedy as opposed to D. Kennedy)
• There seems to be an extra period '.' after the authors, before the title, I think that should not be there.

I can try to invoke these updates.

[asmacdo]

Ive written a short script to test out various styles that we can choose from. (there are a LOT of them!)

Additionally, duecredit doesn't currently render italics, since it outputs plaintext instead of html. That turned out to be an easy enhancement, so I've added the ability to choose formatters here duecredit/duecredit#260

So below, we have various styles, rendered with and without html.

Note: the double period might be an issue with citeproc-py but I wasn't able to quickly track down.

./compare_styles.py

# /home/austin/devel/repronim.org/scripts/compare_styles.py
#!/usr/bin/env python3
"""Compare citation styles for sample DOIs."""

from duecredit.io import import_doi, BibTeX, format_bibtex

# Sample DOIs from publications.yaml
SAMPLE_DOIS = [
    "10.1038/s41597-025-05503-w",
    "10.1038/s41592-023-02145-x",
    "10.1007/s12021-024-09665-7",
]

STYLES = [
    "apa",
    "nature",
    "harvard-cite-them-right",
    "vancouver",
    "chicago-author-date",
]

FORMATTERS = ["plain", "html"]


def main():
    print("Fetching BibTeX data for sample DOIs...\n")
    bibtex_data = {}
    for doi in SAMPLE_DOIS:
        try:
            doi_url = f"https://doi.org/{doi}"
            data = BibTeX(import_doi(doi_url))
            bibtex_data[doi] = data
            print(f"✓ {doi}")
        except Exception as e:
            print(f"✗ {doi}: {e}")

    print("\n" + "=" * 80)
    print("STYLE COMPARISON (PLAIN vs HTML)")
    print("=" * 80)

    for style in STYLES:
        print(f"\n### {style.upper()} ###\n")
        for formatter in FORMATTERS:
            print(f"**{formatter.upper()}**\n")
            for doi, bibtex in bibtex_data.items():
                try:
                    citation = format_bibtex(bibtex, style=style, formatter=formatter)
                    print(f"{citation}\n")
                except Exception as e:
                    print(f"Error formatting {doi}: {e}\n")
            print()
        print("-" * 80)


if __name__ == "__main__":
    main()

Output

================================================================================
STYLE COMPARISON (PLAIN vs HTML)

APA

PLAIN

Rorden, C., Béranger, B., Cheng, H., Clemence, M., Debacker, C., Fernandez, B., Halchenko, Y. O., Harms, M. P., Holla, B., Innis, I., Kuijer, J. P. A., Levitas, D., Litinas, K., Luci, J., Newman-Norlund, R., Peltier, S., Rehwald, W., Reid, R. I., Rogers, B., … Morgan, P. S.. (2025). DICOM datasets for reproducible neuroimaging research across manufacturers and software versions. Scientific Data, 12(1). https://doi.org/10.1038/s41597-025-05503-w

Renton, A. I., Dao, T. T., Johnstone, T., Civier, O., Sullivan, R. P., White, D. J., Lyons, P., Slade, B. M., Abbott, D. F., Amos, T. J., Bollmann, S., Botting, A., Campbell, M. E. J., Chang, J., Close, T. G., Dörig, M., Eckstein, K., Egan, G. F., Evas, S., … Bollmann, S.. (2024). Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nature Methods, 21(5), 804–808. https://doi.org/10.1038/s41592-023-02145-x

Szczepanik, M., Wagner, A. S., Heunis, S., Waite, L. K., Eickhoff, S. B., & Hanke, M.. (2024). Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort. Neuroinformatics, 22(4), 635–645. https://doi.org/10.1007/s12021-024-09665-7

HTML

Rorden, C., Béranger, B., Cheng, H., Clemence, M., Debacker, C., Fernandez, B., Halchenko, Y. O., Harms, M. P., Holla, B., Innis, I., Kuijer, J. P. A., Levitas, D., Litinas, K., Luci, J., Newman-Norlund, R., Peltier, S., Rehwald, W., Reid, R. I., Rogers, B., … Morgan, P. S.. (2025). DICOM datasets for reproducible neuroimaging research across manufacturers and software versions. Scientific Data, 12(1). https://doi.org/10.1038/s41597-025-05503-w

Renton, A. I., Dao, T. T., Johnstone, T., Civier, O., Sullivan, R. P., White, D. J., Lyons, P., Slade, B. M., Abbott, D. F., Amos, T. J., Bollmann, S., Botting, A., Campbell, M. E. J., Chang, J., Close, T. G., Dörig, M., Eckstein, K., Egan, G. F., Evas, S., … Bollmann, S.. (2024). Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nature Methods, 21(5), 804–808. https://doi.org/10.1038/s41592-023-02145-x

Szczepanik, M., Wagner, A. S., Heunis, S., Waite, L. K., Eickhoff, S. B., & Hanke, M.. (2024). Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort. Neuroinformatics, 22(4), 635–645. https://doi.org/10.1007/s12021-024-09665-7

---

NATURE

PLAIN

1.Rorden, C.. DICOM datasets for reproducible neuroimaging research across manufacturers and software versions. Scientific Data 12, (2025).

1.Renton, A. I.. Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nature Methods 21, 804–808 (2024).

1.Szczepanik, M.. Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort. Neuroinformatics 22, 635–645 (2024).

HTML

1.Rorden, C.. DICOM datasets for reproducible neuroimaging research across manufacturers and software versions. Scientific Data 12, (2025).

1.Renton, A. I.. Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nature Methods 21, 804–808 (2024).

1.Szczepanik, M.. Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort. Neuroinformatics 22, 635–645 (2024).

---

HARVARD-CITE-THEM-RIGHT

PLAIN

Rorden, C. (2025) ‘DICOM datasets for reproducible neuroimaging research across manufacturers and software versions’, Scientific Data, 12(1). doi:10.1038/s41597-025-05503-w.

Renton, A.I. (2024) ‘Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging’, Nature Methods, 21(5), pp. 804–808. doi:10.1038/s41592-023-02145-x.

Szczepanik, M. (2024) ‘Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort’, Neuroinformatics, 22(4), pp. 635–645. doi:10.1007/s12021-024-09665-7.

HTML

Rorden, C. (2025) ‘DICOM datasets for reproducible neuroimaging research across manufacturers and software versions’, Scientific Data, 12(1). doi:10.1038/s41597-025-05503-w.

Renton, A.I. (2024) ‘Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging’, Nature Methods, 21(5), pp. 804–808. doi:10.1038/s41592-023-02145-x.

Szczepanik, M. (2024) ‘Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort’, Neuroinformatics, 22(4), pp. 635–645. doi:10.1007/s12021-024-09665-7.

---

VANCOUVER

PLAIN

1. Rorden C, Béranger B, Cheng H, Clemence M, Debacker C, Fernandez B, et al.. DICOM datasets for reproducible neuroimaging research across manufacturers and software versions. Scientific Data. 2025Jul;12(1).

2. Renton AI, Dao TT, Johnstone T, Civier O, Sullivan RP, White DJ, et al.. Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nature Methods. 2024Jan;21(5):804–8.

3. Szczepanik M, Wagner AS, Heunis S, Waite LK, Eickhoff SB, Hanke M. Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort. Neuroinformatics. 2024May;22(4):635–45.

HTML

1. Rorden C, Béranger B, Cheng H, Clemence M, Debacker C, Fernandez B, et al.. DICOM datasets for reproducible neuroimaging research across manufacturers and software versions. Scientific Data. 2025Jul;12(1).

2. Renton AI, Dao TT, Johnstone T, Civier O, Sullivan RP, White DJ, et al.. Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. Nature Methods. 2024Jan;21(5):804–8.

3. Szczepanik M, Wagner AS, Heunis S, Waite LK, Eickhoff SB, Hanke M. Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort. Neuroinformatics. 2024May;22(4):635–45.

---

CHICAGO-AUTHOR-DATE

PLAIN

Rorden, Christopher, Benoît Béranger, Hu Cheng, Matthew Clemence, Clément Debacker, Brice Fernandez, Yaroslav O. Halchenko, et al.. 2025. “DICOM Datasets for Reproducible Neuroimaging Research Across Manufacturers and Software Versions”. Scientific Data 12 (1). https://doi.org/10.1038/s41597-025-05503-w.

Renton, Angela I., Thuy T. Dao, Tom Johnstone, Oren Civier, Ryan P. Sullivan, David J. White, Paris Lyons, et al.. 2024. “Neurodesk: An Accessible, Flexible and Portable Data Analysis Environment for Reproducible Neuroimaging”. Nature Methods 21 (5): 804–8. https://doi.org/10.1038/s41592-023-02145-x.

Szczepanik, Michał, Adina S. Wagner, Stephan Heunis, Laura K. Waite, Simon B. Eickhoff, and Michael Hanke. 2024. “Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort”. Neuroinformatics 22 (4): 635–45. https://doi.org/10.1007/s12021-024-09665-7.

HTML

Rorden, Christopher, Benoît Béranger, Hu Cheng, Matthew Clemence, Clément Debacker, Brice Fernandez, Yaroslav O. Halchenko, et al.. 2025. “DICOM Datasets for Reproducible Neuroimaging Research Across Manufacturers and Software Versions”. Scientific Data 12 (1). https://doi.org/10.1038/s41597-025-05503-w.

Renton, Angela I., Thuy T. Dao, Tom Johnstone, Oren Civier, Ryan P. Sullivan, David J. White, Paris Lyons, et al.. 2024. “Neurodesk: An Accessible, Flexible and Portable Data Analysis Environment for Reproducible Neuroimaging”. Nature Methods 21 (5): 804–8. https://doi.org/10.1038/s41592-023-02145-x.

Szczepanik, Michał, Adina S. Wagner, Stephan Heunis, Laura K. Waite, Simon B. Eickhoff, and Michael Hanke. 2024. “Teaching Research Data Management with DataLad: A Multi-year, Multi-domain Effort”. Neuroinformatics 22 (4): 635–45. https://doi.org/10.1007/s12021-024-09665-7.