update citations as an action rather in the package

.github/workflows/run_citations.yml

@@ -0,0 +1,31 @@
+name: Update citations upon CITATION.cff changes
+
+on:
+  push:
+    paths:
+      - CITATION.cff
+
+jobs:
+  update-citations:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          # use customized version of cffconvert
+          pip install git+https://github.com/alexlancaster/cffconvert.git@combine_features#egg=cffconvert",
+    
+    uses: ./.github/workflows/update_citations.yml  # reference the reusable workflow
+    with:
+      CITATION_DIR: 'src/PyPop/citation'
+      INIT_FILE: 'src/PyPop/__init__.py'
+

.github/workflows/update_citations.yml

@@ -0,0 +1,46 @@
+name: Update citation files
+
+on:
+  workflow_call: # This allows the workflow to be triggered by another workflow
+    inputs:
+      CITATION_DIR:
+        description: 'Directory for citations'
+        required: true
+        default: 'src/PyPop/citation'
+      INIT_FILE:
+        description: 'Path to the init file'
+        required: true
+        default: 'src/PyPop/__init__.py'
+
+jobs:
+  update-citation:
+    steps:
+      - name: Extract citation formats
+        id: extract_formats
+        run: |
+          python -c "
+import ast
+with open('${{ inputs.INIT_FILE }}) as f:
+    contents = f.read()
+citation_output_formats = next((node.value.elts for node in ast.walk(ast.parse(contents)) if isinstance(node, ast.Assign) and node.targets[0].id == 'citation_output_formats'), [])
+formats = ','.join([str(elem.value) for elem in citation_output_formats])
+print(f'::set-output name=formats::{formats}')
+        "
+
+      - name: Copy CITATION.cff to citation directory
+        run: |
+          cp CITATION.cff ${{ inputs.CITATION_DIR }}/CITATION.cff
+
+      - name: Generate citation files
+        run: |
+          formats="${{ steps.extract_formats.outputs.formats }}"
+          IFS=',' read -r -a formats_array <<< "$formats"
+          for format in "${formats_array[@]}"; do
+            cffconvert --infile CITATION.cff --outfile "${{ inputs.CITATION_DIR }}/citation.${format}" --format "$format"
+          done
+
+      - name: Commit and push changes
+        uses: EndBug/add-and-commit@v9
+        with:
+          message: "Auto-update citation files based on CITATION.cff"
+          add: "${{ inputs.CITATION_DIR }}/*"

src/PyPop/citation/CITATION.cff

@@ -0,0 +1,88 @@
+cff-version: 1.2.0
+message: >-
+  If you use this software, please cite both the software itself, as well as the
+  article Lancaster AK et al. (2024) <a
+  href=\"https://doi.org/10.3389/fimmu.2024.1378512\">PyPop: A mature
+  open-source software pipeline for population genomics</a>. <i>Front.
+  Immunol.</i> <b>15</b>:1378512. doi: 10.3389/fimmu.2024.1378512
+abstract: >-
+  PyPop for Population Genomics (PyPop) is a Python program for processing
+  genotype and allele data and running population genetic analyses, including
+  conformity to Hardy-Weinberg expectations; tests for balancing or directional
+  selection; estimates of haplotype frequencies and measures and tests of
+  significance for linkage disequilibrium (LD).&nbsp;Output of analyses are
+  stored in XML format for maximum downstream flexibility. PyPop also has an
+  internal facility for additionally aggregating the output XML and generating
+  output tab-separated (TSV) files, as well as default plain text files for each
+  population. Although it can be run on any kind of genotype data, it has
+  additional support for analyzing population genotype with allelic nomenclature
+  from the human leukocyte antigen (HLA) region.
+authors:
+  - family-names: Lancaster
+    given-names: Alexander K.
+    orcid: https://orcid.org/0000-0002-0002-9263
+    affiliation: Amber Biology LLC and Ronin Institute
+  - family-names: Nelson
+    given-names: Mark P.
+    affiliation: University of California, Berkeley
+  - family-names: Single
+    given-names: Richard
+    orcid: https://orcid.org/0000-0001-6054-6505
+    affiliation: University of Vermont
+  - family-names: Solberg
+    given-names: Owen
+    orcid: https://orcid.org/0000-0003-3060-9709
+  - family-names: Tsai
+    given-names: Yingsu
+    affiliation: University of California, Berkeley
+    orcid: https://orcid.org/0009-0006-0162-6066
+  - family-names: Meyer
+    given-names: Diogo
+    orcid: https://orcid.org/0000-0002-7155-5674
+    affiliation: University of São Paulo
+  - family-names: Webster
+    given-names: Gordon
+    affiliation: Amber Biology LLC
+    orcid: https://orcid.org/0009-0009-2862-0467
+  - family-names: Mariani
+    given-names: Michael P.
+    orcid: https://orcid.org/0000-0001-5852-0517
+    affiliation: Mariani Systems LLC and University of Vermont
+  - family-names: Sochat
+    given-names: Vanessa
+    orcid: https://orcid.org/0000-0002-4387-3819
+    affiliation: Lawrence Livermore National Laboratory
+  - family-names: Kornel
+    given-names: Karl
+    orcid: https://orcid.org/0000-0001-5847-5330
+    affiliation: Stanford Research Computing Center
+  - family-names: Spaaks
+    given-names: Jurriaan H.
+    orcid: https://orcid.org/0000-0002-7064-4069
+    affiliation: Netherlands eScience Center
+  - family-names: Mack
+    given-names: Steven J.
+    orcid: https://orcid.org/0000-0001-9820-9547
+    affiliation: University of California, San Francisco
+  - family-names: Thomson
+    given-names: Glenys
+    orcid: https://orcid.org/0000-0001-5235-4159
+    affiliation: University of California, Berkeley
+title: 'PyPop: Python for Population Genomics'
+url: http://pypop.org/
+repository-artifact: https://pypi.org/project/pypop-genomics/
+repository-code: https://github.com/alexlancaster/pypop
+type: software
+keywords:
+  - population genetics
+  - population genomics
+  - bioinformatics
+  - computational biology
+  - evolutionary biology
+  - Human leukocyte antigen
+  - Major histocompatibility complex
+  - HLA
+  - MHC
+license: GPL-2.0-or-later
+version: v1.1.1
+doi: 10.5281/zenodo.13742984