Merge pull request #214 from jeetsukumaran/update-citing

Update citing info
jeetsukumaran · Sep 23, 2024 · 49cf2cc · 49cf2cc
2 parents de9b9e1 + 94cb76c
commit 49cf2cc
Show file tree

Hide file tree

Showing 6 changed files with 67 additions and 26 deletions.
diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,39 @@
+cff-version: "1.2.0"
+authors:
+- family-names: Moreno
+  given-names: Matthew Andres
+  orcid: "https://orcid.org/0000-0003-4726-4479"
+- family-names: Holder
+  given-names: Mark T.
+  orcid: "https://orcid.org/0000-0001-5575-0536"
+- family-names: Sukumaran
+  given-names: Jeet
+  orcid: "https://orcid.org/0000-0002-9222-9608"
+doi: 10.5281/zenodo.13340136
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Moreno
+    given-names: Matthew Andres
+    orcid: "https://orcid.org/0000-0003-4726-4479"
+  - family-names: Holder
+    given-names: Mark T.
+    orcid: "https://orcid.org/0000-0001-5575-0536"
+  - family-names: Sukumaran
+    given-names: Jeet
+    orcid: "https://orcid.org/0000-0002-9222-9608"
+  date-published: 2024-09-23
+  doi: 10.21105/joss.06943
+  issn: 2475-9066
+  issue: 101
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 6943
+  title: "DendroPy 5: a mature Python library for phylogenetic
+    computing"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.06943"
+  volume: 9
+title: "DendroPy 5: a mature Python library for phylogenetic computing"
diff --git a/NOTICES.rst b/NOTICES.rst
@@ -1,9 +1,7 @@
 1.  If you use this work or any portion thereof in published work
     please cite it as:
 
-        Moreno, M. A., Sukumaran, J., and M. T. Holder. 2024.
-        DendroPy 5: a mature Python library for phylogenetic computing.
-        arXiv preprint arXiv:2405.14120. https://doi.org/10.48550/arXiv.2405.14120
+        Moreno, M. A., Holder, M. T., & Sukumaran, J. (2024). DendroPy 5: a mature Python library for phylogenetic computing. Journal of Open Source Software, 9(101), 6943, https://doi.org/10.21105/joss.06943
 
 2.  All DendroPy documentation, (non-logo) images and other media, as
     provided online or otherwise distributed, can be used in accordance with the

diff --git a/README.rst b/README.rst
@@ -92,22 +92,24 @@ Citing
 
 If you use any portion of DendroPy v5 in your research, please cite it as:
 
-      Moreno, M. A., Sukumaran, J., and M. T. Holder. 2024. DendroPy 5: a mature Python library for phylogenetic computing. arXiv preprint arXiv:2405.14120. https://doi.org/10.48550/arXiv.2405.14120
+      Moreno, M. A., Holder, M. T., & Sukumaran, J. (2024). DendroPy 5: a mature Python library for phylogenetic computing. Journal of Open Source Software, 9(101), 6943, https://doi.org/10.21105/joss.06943
 
 For BibTex users:
 
 .. code-block:: bibtex
 
-      @misc{dendropy5,
-         title = {DendroPy 5: a mature Python library for phylogenetic computing},
-         author = {Moreno,  Matthew Andres and Sukumaran,  Jeet and Holder,  Mark T.},
-         year = {2024},
-         keywords = {Populations and Evolution (q-bio.PE),  FOS: Biological sciences,  FOS: Biological sciences},
-         publisher = {arXiv},
-         doi = {10.48550/ARXIV.2405.14120},
-         url = {https://arxiv.org/abs/2405.14120},
-         copyright = {arXiv.org perpetual, non-exclusive license}
-      }
+  @misc{dendropy5,
+    doi = {10.21105/joss.06943},
+    url = {https://doi.org/10.21105/joss.06943},
+    year = {2024},
+  publisher = {The Open Journal},
+    volume = {9},
+    number = {101},
+    pages = {6943},
+    author = {Matthew Andres Moreno and Mark T. Holder and Jeet Sukumaran},
+    title = {DendroPy 5: a mature Python library for phylogenetic computing},
+    journal = {Journal of Open Source Software}
+  }
 
 Earlier DendroPy versions can be cited as:
 

diff --git a/docs/source/citation.inc b/docs/source/citation.inc
@@ -10,16 +10,18 @@ For BibTex users:
 
 .. code-block:: bibtex
 
-      @misc{dendropy5,
-         title = {DendroPy 5: a mature Python library for phylogenetic computing},
-         author = {Moreno,  Matthew Andres and Sukumaran,  Jeet and Holder,  Mark T.},
-         year = {2024},
-         keywords = {Populations and Evolution (q-bio.PE),  FOS: Biological sciences,  FOS: Biological sciences},
-         publisher = {arXiv},
-         doi = {10.48550/ARXIV.2405.14120},
-         url = {https://arxiv.org/abs/2405.14120},
-         copyright = {arXiv.org perpetual, non-exclusive license}
-      }
+  @misc{dendropy5,
+    doi = {10.21105/joss.06943},
+    url = {https://doi.org/10.21105/joss.06943},
+    year = {2024},
+  publisher = {The Open Journal},
+    volume = {9},
+    number = {101},
+    pages = {6943},
+    author = {Matthew Andres Moreno and Mark T. Holder and Jeet Sukumaran},
+    title = {DendroPy 5: a mature Python library for phylogenetic computing},
+    journal = {Journal of Open Source Software}
+  }
 
 Note that, in the interests of scientific reproducibility, in addition to noting the primary citation for DendroPy as given above in the reference section, you should note in the text of your publications (e.g., in the "Methods" section, or, at the very least, in the "Supplemental Materials" section) the specific version of DendroPy that you used (e.g., "DendroPy version 4.0.0, revision 78e6a63"). You can get useful information about your DendroPy installation by typing "``python -m dendropy``".
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -294,7 +294,7 @@ def setup(app):
 """ % (version, version)
 
 rst_prolog += """\
-.. |dendropy_citation| replace:: Moreno, M. A., Sukumaran, J., and M. T. Holder. 2024. DendroPy 5: a mature Python library for phylogenetic computing. arXiv preprint arXiv:2405.14120. https://doi.org/10.48550/arXiv.2405.14120
+.. |dendropy_citation| replace:: Moreno, M. A., Holder, M. T., & Sukumaran, J. (2024). DendroPy 5: a mature Python library for phylogenetic computing. Journal of Open Source Software, 9(101), 6943, https://doi.org/10.21105/joss.06943
 .. |dendropy_copyright| replace:: Copyright {copyright}. All rights reserved.
 .. |
 """.format(copyright=copyright)

diff --git a/src/dendropy/__init__.py b/src/dendropy/__init__.py
@@ -108,7 +108,7 @@
 __version__ = "5.0.2"
 __author__ = "Jeet Sukumaran and Mark T. Holder and Matthew Andres Moreno"
 __copyright__ = "Copyright 2010-2022 Jeet Sukumaran and Mark T. Holder."
-__citation__ = "Moreno, M. A., Sukumaran, J., and M. T. Holder. 2024. DendroPy 5: a mature Python library for phylogenetic computing. arXiv preprint arXiv:2405.14120. https://doi.org/10.48550/arXiv.2405.14120"
+__citation__ = "Moreno, M. A., Holder, M. T., & Sukumaran, J. (2024). DendroPy 5: a mature Python library for phylogenetic computing. Journal of Open Source Software, 9(101), 6943, https://doi.org/10.21105/joss.06943"
 PACKAGE_VERSION = __version__ # for backwards compatibility (with sate)
 
 def _get_revision_object():