Merge branch 'main' into release-5.0

.github/workflows/ci.yaml

@@ -179,8 +179,9 @@ jobs:
     - name: Generate coverage report
       run: |
         python3 -m pytest tests/unittests --cov=tests --cov-report=xml
-    - uses: codecov/codecov-action@v3
+    - uses: codecov/codecov-action@v4
       with:
+        token: ae13d715-bae4-4e6d-9dce-f47e7d7c7c01
         flags: unittests # optional
         fail_ci_if_error: true # optional (default = false)
         verbose: true # optional (default = false)

AUTHORS.rst

@@ -1,4 +1,5 @@
-Jeet Sukumaran <[email protected]>
-Mark T. Holder <[email protected]>
+- Jeet Sukumaran <[email protected]>
+- Mark T. Holder <[email protected]>
+- Matthew Andres Moreno <[email protected]>
 
 Find a comprehensive, up-to-date listing of project contributors `here <https://github.com/jeetsukumaran/DendroPy/graphs/contributors>`_.

README.rst

@@ -7,11 +7,11 @@
    :target: https://github.com/jeetsukumaran/DendroPy
    :alt: DendroPy wordmark
 
-+--------------------+-+---------------------+-+---------------------+
-| *automated tests:* | | *package version:*  | | *documentation:*    |
-|                    | |                     | |                     |
-| |CI|               | | |PyPI|              | | |Docs|              |
-+--------------------+-+---------------------+-+---------------------+
++--------------------+-+---------------------+-+---------------------+-+-------------------+
+| *automated tests:* | | *package version:*  | | *documentation:*    | | *test coverage:*  |
+|                    | |                     | |                     | |                   |
+| |CI|               | | |PyPI|              | | |Docs|              | | |Coverage|        |
++--------------------+-+---------------------+-+---------------------+-+-------------------+
 
 .. |CI| image:: https://github.com/jeetsukumaran/DendroPy/actions/workflows/ci.yaml/badge.svg
    :target: https://github.com/jeetsukumaran/DendroPy/actions/workflows/ci.yaml
@@ -22,7 +22,10 @@
 .. |Docs| image:: https://github.com/jeetsukumaran/DendroPy/actions/workflows/pages/pages-build-deployment/badge.svg
    :target: https://jeetsukumaran.github.io/DendroPy/
    :alt: Documentation Status
-.. |nbsp| unicode:: 0xA0 
+.. |Coverage| image:: https://codecov.io/gh/jeetsukumaran/DendroPy/graph/badge.svg?token=JwMfFOpBBD
+   :target: https://codecov.io/gh/jeetsukumaran/DendroPy
+   :alt: codecov coverage
+.. |nbsp| unicode:: 0xA0
    :trim:
 
 .. raw:: html
@@ -79,6 +82,13 @@ This includes:
 
 and more.
 
+Citing
+======
+
+If you use this library or any portion thereof in published work, please cite it as:
+
+      Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26: 1569-1571.
+
 License and Warranty
 ====================
 

src/dendropy/application/sumlabels.py

@@ -18,7 +18,7 @@
 ##############################################################################
 
 """
-Marge labels of splits/branches from different input trees onto corresponding
+Merge labels of splits/branches from different input trees onto corresponding
 splits/branches of a single tree.
 """