Merge pull request #762 from malariagen/update-citation

Include package-wide citation notes

Author: ahernank

README.md

@@ -128,6 +128,17 @@ the documentation via GitHub Actions.
 The version switcher for the documentation can then be updated by
 modifying the `docs/source/_static/switcher.json` file accordingly.
 
+## Citation
+
+If you use the `malariagen_data` package in a publication
+or include any of its functions or code in other materials (_e.g._ training resources),
+please cite: [doi.org/10.5281/zenodo.11173411](doi.org/10.5281/zenodo.11173411)
+
+Some functions may require additional citations to acknowledge specific contributions. These are indicated in the description for each relevant function.
+
+For any questions, please feel free to contact us at: [[email protected]](mailto:[email protected])
+
+
 ## Sponsorship
 
 This project is currently supported by the following grants:

malariagen_data/anoph/dipclust.py

@@ -47,7 +47,7 @@ def __init__(
         summary=""""
         Hierarchically cluster diplotypes in region and produce an interactive plot.
 
-        If you use this function in a publication, please cite the original manuscript: doi.org/10.1093/molbev/msae140
+        If you use this function in a publication, please cite both this package and the original manuscript: doi.org/10.1093/molbev/msae140
         """,
     )
     def plot_diplotype_clustering(
@@ -598,7 +598,7 @@ def _insert_dipclust_snp_trace(
         summary=""""
         Perform diplotype clustering, annotated with heterozygosity, gene copy number and amino acid variants.
 
-        If you use this function in a publication, please cite the original manuscript: doi.org/10.1093/molbev/msae140
+        If you use this function in a publication, please cite both this package and the original manuscript: doi.org/10.1093/molbev/msae140
         """,
         parameters=dict(
             heterozygosity="Plot heterozygosity track.",