Automated publications

.gitignore

@@ -23,3 +23,6 @@ Thumbs.db
 *~
 .env
 .env.*.local
+
+uv.lock
+.local/*

data/publications.yaml

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+publication-dois:
+- 10.1038/s41597-025-05503-w
+- 10.48550/arXiv.2507.03674
+- 10.48550/arXiv.2504.07824
+- 10.2196/63343
+- 10.1002/hipo.70028
+- 10.1007/s12021-024-09665-7
+- 10.1038/s41592-023-02145-x
+- 10.1038/s41597-024-03629-x
+- 10.1093/gigascience/giae009
+- 10.1101/2024.04.29.24306516
+- 10.1162/imag_a_00103
+- 10.1176/appi.ajp.20230249
+- 10.1186/s12984-024-01309-w
+- 10.1371/journal.pdig.0000516
+- 10.1371/journal.pone.0295069
+- 10.21105/joss.05839
+- 10.3389/fninf.2024.1376022
+- 10.52294/001c.123059
+- 10.1016/j.neuroimage.2022.119807
+- 10.1038/s41562-023-01647-0
+- 10.1038/s41597-023-01946-1
+- 10.1038/s41598-022-25306-y
+- 10.1101/2023.08.01.551505
+- 10.1101/2023.08.16.552472
+- 10.1159/000530358
+- 10.21203/rs.3.rs-2649734/v1
+- 10.3389/fnhum.2023.1237651
+- 10.3389/fnimg.2022.1098604
+- 10.3389/fnimg.2023.1099301
+- 10.3389/fninf.2023.1174156
+- 10.3389/fnins.2023.1233416
+- 10.1148/radiol.230096
+- 10.1007/s10548-022-00935-8
+- 10.1007/s12021-021-09557-0
+- 10.1016/j.neuroimage.2022.119612
+- 10.1016/j.neuroimage.2022.119623
+- 10.1016/j.neuron.2021.11.017
+- 10.1038/s41398-022-02211-6
+- 10.1038/s41592-022-01681-2
+- 10.1038/s41597-022-01682-y
+- 10.1038/s41598-022-19356-5
+- 10.1093/gigascience/giac013
+- 10.1148/radiol.210385
+- 10.12688/f1000research.108008.2
+- 10.1371/journal.pcbi.1009651
+- 10.3389/fnhum.2022.749767
+- 10.7554/eLife.79277
+- 10.1002/hbm.25351
+- 10.1007/s12021-020-09509-0
+- 10.1007/s12021-021-09517-8
+- 10.1007/s12021-021-09522-x
+- 10.1007/s12021-021-09533-8
+- 10.1016/j.mex.2021.101595
+- 10.1016/j.neuroimage.2021.118683
+- 10.1016/j.neuron.2021.04.001
+- 10.1016/j.nicl.2021.102790
+- 10.1038/s41597-021-01033-3
+- 10.1038/s41598-021-87069-2
+- 10.1038/s41598-021-94733-0
+- 10.1093/gigascience/giaa155
+- 10.1093/gigascience/giab055
+- 10.12688/f1000research.25306.2
+- 10.1515/nf-2020-0037
+- 10.21105/joss.03262
+- 10.2196/22369
+- 10.7554/eLife.71774
+- 10.7554/eLife.72129
+- 10.1002/lio2.354
+- 10.1016/j.neuroimage.2019.116330
+- 10.1016/j.nicl.2020.102240
+- 10.1016/j.nicl.2020.102242
+- 10.1016/j.nicl.2020.102266
+- 10.1038/s41586-020-2314-9
+- 10.1038/s41596-020-0327-3
+- 10.1038/s41597-020-0486-7
+- 10.1101/2020.11.23.20235945
+- 10.1146/annurev-neuro-100119-110036
+- 10.12688/f1000research.24544.1
+- 10.1016/j.neulet.2019.01.037
+- 10.1016/j.neuroimage.2019.116091
+- 10.1038/s41597-019-0031-8
+- 10.12688/mniopenres.12772.2
+- 10.1371/journal.pone.0210028
+- 10.21105/joss.01294
+- 10.3233/JPD-191775
+- 10.3389/fninf.2019.00001
+- 10.3389/fninf.2019.00003
+- 10.7554/eLife.48932
+- 10.1007/s12021-018-9379-8
+- 10.1038/sdata.2018.29
+- 10.1093/database/bay130
+- 10.1093/gigascience/giy077
+- 10.1109/TMI.2018.2831261
+- 10.3389/fnins.2018.00727
+- 10.7554/eLife.36652
+- 10.1007/s12021-017-9331-3
+- 10.1007/s12021-017-9335-z
+- 10.1038/nn.4500
+- 10.1038/nn.4550
+- 10.1038/nrn.2016.167
+- 10.1038/sdata.2017.59
+- 10.1093/cercor/bhx030
+- 10.12688/f1000research.10783.2
+- 10.1371/journal.pcbi.1005209
+- 10.1371/journal.pcbi.1005350
+- 10.1016/j.neuron.2016.04.030
+- 10.1038/sdata.2016.102
+- 10.1038/sdata.2016.44
+- 10.1073/pnas.1608282113
+- 10.1093/gerona/glw236
+- 10.3389/fninf.2016.00034

pyproject.toml

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+[project]
+name = "repronim-publications"
+version = "0.1.0"
+description = "Scripts for generating ReproNim publications from DOIs"
+requires-python = ">=3.10"
+dependencies = [
+    "citeproc-py[full]>=0.9.0",
+    "pyyaml>=6.0",
+    "duecredit>=0.9.0",
+]

scripts/README.md

@@ -0,0 +1,12 @@
+# Publication Generation
+
+Regenerate publications from DOIs in `data/publications.yaml`:
+
+Run from the root of this repo:
+
+```bash
+datalad run -m "Generate publications from DOIs" \
+  --input data/publications.yaml \
+  --output content/about/publications.md \
+  "uv run python scripts/generate_publications.py"
+```

scripts/generate_publications.py

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+#!/usr/bin/env python3
+"""
+Generate publications.md from list of DOIs using duecredit/citeproc-py.
+
+This script reads DOIs from data/publications.yaml and generates
+formatted citations in APA style, writing to content/about/publications.md
+"""
+
+import sys
+import yaml
+from pathlib import Path
+from duecredit.io import format_bibtex, import_doi, BibTeX
+
+
+def fetch_citation(doi):
+    """
+    Fetch and format a single citation from a DOI.
+
+    Args:
+        doi: DOI string (e.g., "10.1038/s41597-025-05503-w")
+
+    Returns:
+        Formatted citation string in APA style, or None if fetch failed
+    """
+    try:
+        # Add https://doi.org/ prefix if not present
+        doi_url = doi if doi.startswith('http') else f'https://doi.org/{doi}'
+
+        # Fetch citation data and format as APA
+        bibtex_data = BibTeX(import_doi(doi_url))
+        citation = format_bibtex(bibtex_data, style='apa')
+
+        return citation
+    except Exception as e:
+        print(f"Warning: Failed to fetch DOI {doi}: {e}", file=sys.stderr)
+        return None
+
+
+def generate_publications_markdown(dois, output_path):
+    """
+    Generate the publications markdown file from a list of DOIs.
+
+    Args:
+        dois: List of DOI strings
+        output_path: Path to write the generated markdown file
+    """
+    # Frontmatter for the markdown file
+    frontmatter = """---
+Title: ReproNim Publications
+linkTitle: "Publications"
+type: docs
+weight: 60
+---
+"""
+
+    citations = []
+    failed_dois = []
+
+    print(f"Fetching {len(dois)} publications...")
+
+    for i, doi in enumerate(dois, 1):
+        print(f"  [{i}/{len(dois)}] Fetching {doi}...", end=' ')
+        citation = fetch_citation(doi)
+
+        if citation:
+            citations.append(citation)
+            print("✓")
+        else:
+            failed_dois.append(doi)
+            print("✗")
+
+    # Write the markdown file
+    with open(output_path, 'w') as f:
+        f.write(frontmatter)
+
+        for i, citation in enumerate(citations, 1):
+            f.write(f"{i}. {citation}\n\n")
+
+    print(f"\nGenerated {len(citations)} citations to {output_path}")
+
+    if failed_dois:
+        print(f"\nWarning: {len(failed_dois)} DOIs failed to fetch:")
+        for doi in failed_dois:
+            print(f"  - {doi}")
+
+
+def main():
+    # Paths
+    repo_root = Path(__file__).parent.parent
+    doi_yaml = repo_root / 'data' / 'publications.yaml'
+    output_md = repo_root / 'content' / 'about' / 'publications.md'
+
+    # Load DOIs from YAML
+    print(f"Loading DOIs from: {doi_yaml}")
+    with open(doi_yaml, 'r') as f:
+        data = yaml.safe_load(f)
+        dois = data.get('publication-dois', [])
+
+    if not dois:
+        print("Error: No DOIs found in publications.yaml", file=sys.stderr)
+        sys.exit(1)
+
+    # Optional: limit number of DOIs for testing (use first argument)
+    if len(sys.argv) > 1:
+        limit = int(sys.argv[1])
+        print(f"Testing mode: processing first {limit} DOIs only")
+        dois = dois[:limit]
+
+    # Generate publications
+    generate_publications_markdown(dois, output_md)
+
+    print("\nDone! To add new publications:")
+    print(f"  1. Add DOI to {doi_yaml}")
+    print(f"  2. Run: uv run python scripts/generate_publications.py")
+
+
+if __name__ == '__main__':
+    main()