Add python 3.13 support (#59)

* Add python 3.13 to CI

* remove codecoverage

* reorganize the CI so that it supports different python versions via lockfiles

* fix path for CI testing

* fix CI variable

* fix publishpypi

* Address PR review comments.

* Add script to automatically update lockfiles.

* Automatically update lockfiles.

* Update GitHub Actions with dependabot.

* Remove unused links from README.

* Remove extra spaces between badges.

* Update change log.

* Remove overspecified version constraint.

---------

Co-authored-by: Joshua A. Anderson <joaander@umich.edu>

.github/workflows/dependabot.yml

@@ -0,0 +1,23 @@
+version: 2
+updates:
+- package-ecosystem: "github-actions"
+  directory: "/"
+  target-branch: trunk
+  schedule:
+    interval: "monthly"
+    time: "07:00"
+    timezone: "EST5EDT"
+  pull-request-branch-name:
+    separator: "-"
+  open-pull-requests-limit: 2
+  reviewers:
+  - joaander
+  groups:
+    actions-version:
+      applies-to: version-updates
+      patterns:
+      - '*'
+    actions-security:
+      applies-to: security-updates
+      patterns:
+      - '*'

.github/workflows/environments/requirements-build.in

@@ -0,0 +1 @@
+build

.github/workflows/requirements-build.txt → .github/workflows/environments/requirements-build.txt

@@ -1,8 +1,8 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile requirements-build.in
-build==1.1.1
+#    uv pip compile --python-version 3.13 --python-platform linux requirements-build.in
+build==1.2.2.post1
     # via -r requirements-build.in
 packaging==24.1
     # via build
-pyproject-hooks==1.1.0
+pyproject-hooks==1.2.0
     # via build

.github/workflows/environments/requirements-test-3.10.txt

@@ -0,0 +1,20 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.10 --python-platform linux requirements-test.in
+exceptiongroup==1.2.2
+    # via pytest
+iniconfig==2.0.0
+    # via pytest
+numpy==2.1.2
+    # via
+    #   -r requirements-test.in
+    #   scipy
+packaging==24.1
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pytest==8.3.3
+    # via -r requirements-test.in
+scipy==1.14.1
+    # via -r requirements-test.in
+tomli==2.0.2
+    # via pytest

.github/workflows/environments/requirements-test-3.11.txt

@@ -0,0 +1,16 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.11 --python-platform linux requirements-test.in
+iniconfig==2.0.0
+    # via pytest
+numpy==2.1.2
+    # via
+    #   -r requirements-test.in
+    #   scipy
+packaging==24.1
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pytest==8.3.3
+    # via -r requirements-test.in
+scipy==1.14.1
+    # via -r requirements-test.in

.github/workflows/environments/requirements-test-3.12.txt

@@ -0,0 +1,16 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.12 --python-platform linux requirements-test.in
+iniconfig==2.0.0
+    # via pytest
+numpy==2.1.2
+    # via
+    #   -r requirements-test.in
+    #   scipy
+packaging==24.1
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pytest==8.3.3
+    # via -r requirements-test.in
+scipy==1.14.1
+    # via -r requirements-test.in

.github/workflows/environments/requirements-test-3.13.txt

@@ -0,0 +1,16 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.13 --python-platform linux requirements-test.in
+iniconfig==2.0.0
+    # via pytest
+numpy==2.1.2
+    # via
+    #   -r requirements-test.in
+    #   scipy
+packaging==24.1
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pytest==8.3.3
+    # via -r requirements-test.in
+scipy==1.14.1
+    # via -r requirements-test.in

.github/workflows/environments/requirements-test-3.9.txt

@@ -0,0 +1,20 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.9 --python-platform linux requirements-test.in
+exceptiongroup==1.2.2
+    # via pytest
+iniconfig==2.0.0
+    # via pytest
+numpy==2.0.2
+    # via
+    #   -r requirements-test.in
+    #   scipy
+packaging==24.1
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pytest==8.3.3
+    # via -r requirements-test.in
+scipy==1.13.1
+    # via -r requirements-test.in
+tomli==2.0.2
+    # via pytest

.github/workflows/environments/requirements-test.in

@@ -0,0 +1,3 @@
+numpy
+pytest
+scipy

.github/workflows/environments/update-lockfiles.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+# Execute this script to update all lock files to the latest versions of dependencies.
+
+rm requirements*.txt
+
+for python_version in 3.9 3.10 3.11 3.12 3.13
+do
+    uv pip compile --python-version ${python_version} --python-platform linux requirements-test.in > requirements-test-${python_version}.txt
+done
+
+uv pip compile --python-version 3.13 --python-platform linux requirements-build.in > requirements-build.txt

.github/workflows/release.yaml

@@ -27,10 +27,9 @@ jobs:
       with:
         python-version: 3.12
     - name: Set up Python environment
-      uses: glotzerlab/workflows/setup-uv@5cfac9da9cb78e16ae97a9119b6fd13c1c2d6f5e # 0.1.0
+      uses: glotzerlab/workflows/setup-uv@e130dd2814c7db5635babe4427dedcbd5aab76d4 # 0.5.0
       with:
-        lockfile: ".github/workflows/requirements-build.txt"
-
+        lockfile: ".github/workflows/environments/requirements-build.txt"
     - name: Build wheel
       run: python3 -m build --outdir dist/ .
 

.github/workflows/unit_test.yaml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python: ["3.9", "3.10", "3.11", "3.12"]
+        python: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - name: Checkout
@@ -34,9 +34,9 @@ jobs:
       with:
         python-version: ${{ matrix.python }}
     - name: Set up Python environment
-      uses: glotzerlab/workflows/setup-uv@5cfac9da9cb78e16ae97a9119b6fd13c1c2d6f5e # 0.1.0
+      uses: glotzerlab/workflows/setup-uv@e130dd2814c7db5635babe4427dedcbd5aab76d4 # 0.5.0
       with:
-        lockfile: ".github/workflows/requirements-test.txt"
+        lockfile: ".github/workflows/environments/requirements-test-${{matrix.python}}.txt"
     - name: Run tests
       run: python3 -m pytest -v
 

.github/workflows/update-uv-lockfiles.yaml

@@ -0,0 +1,14 @@
+name: Update uv lockfiles
+
+on:
+  schedule:
+    - cron: '0 12 1 * *'
+
+  workflow_dispatch:
+
+jobs:
+  update:
+    uses: glotzerlab/workflows/.github/workflows/update-uv-lockfiles.yaml@e130dd2814c7db5635babe4427dedcbd5aab76d4 # 0.5.0
+    secrets: inherit
+    with:
+      branch: master

ChangeLog.rst

@@ -1,6 +1,19 @@
 The format is based on `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_.
 This project adheres to `Semantic Versioning <http://semver.org/spec/v2.0.0.html>`_.
 
+1.3.1 - not yet released
+------------------------
+
+Added
++++++
+
+* Test with Python 3.13.
+* Test with NumPy 2.0.
+
+Changed
++++++++
+
+* Require Python >=3.8
 
 v1.3.0 - 2020-06-18
 -------------------

README.rst

@@ -6,32 +6,18 @@ rowan
     :local:
 
 |ReadTheDocs|
-|CircleCI|
-|Codecov|
 |PyPI|
 |conda-forge|
-|Zenodo|
 |JOSS|
 
 .. |ReadTheDocs| image:: https://readthedocs.org/projects/rowan/badge/?version=latest
-    :target: http://rowan.readthedocs.io/en/latest/?badge=latest
-.. |CircleCI| image:: https://circleci.com/gh/glotzerlab/rowan.svg?style=svg
-    :target: https://circleci.com/gh/glotzerlab/rowan
-.. |Codecov| image:: https://codecov.io/gh/glotzerlab/rowan/branch/master/graph/badge.svg
-    :target: https://codecov.io/gh/glotzerlab/rowan
+   :target: http://rowan.readthedocs.io/en/latest/?badge=latest
 .. |PyPI| image:: https://img.shields.io/pypi/v/rowan.svg
-    :target: https://pypi.org/project/rowan/
+   :target: https://pypi.org/project/rowan/
 .. |conda-forge| image:: https://img.shields.io/conda/vn/conda-forge/rowan.svg
    :target: https://anaconda.org/conda-forge/rowan
-.. |Codacy| image:: https://api.codacy.com/project/badge/Grade/2ff6c23cb9be4f77827428a87e0e9cfc
-    :target: https://www.codacy.com/app/vramasub/rowan?utm_source=github.com&utm_medium=referral&utm_content=glotzerlab/rowan&utm_campaign=Badge_Grade
-.. |Zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1323676.svg
-    :target: https://doi.org/10.5281/zenodo.1323676
 .. |JOSS| image:: http://joss.theoj.org/papers/10.21105/joss.00787/status.svg
-    :target: https://doi.org/10.21105/joss.00787
-.. |pre-commit.ci| image:: https://results.pre-commit.ci/badge/github/glotzerlab/rowan/master.svg
-    :target: https://results.pre-commit.ci/latest/github/glotzerlab/rowan/master
-    :alt: pre-commit.ci status
+   :target: https://doi.org/10.21105/joss.00787
 
 Welcome to the documentation for rowan, a package for working with quaternions!
 Quaternions, which form a number system with various interesting properties, were originally developed for classical mechanics.
@@ -130,17 +116,6 @@ To run the packaged unit tests, execute the following line from the root of the
 
     python -m unittest discover tests
 
-To check test coverage, make sure the coverage module is installed:
-
-.. code-block:: bash
-
-    pip install coverage
-
-and then run the packaged unit tests with the coverage module:
-
-.. code-block:: bash
-
-    coverage run -m unittest discover tests
 
 Running Benchmarks
 ------------------

doc/conf.py

@@ -38,7 +38,6 @@
     "sphinx.ext.intersphinx",
     "sphinx.ext.doctest",
     "sphinx.ext.todo",
-    "sphinx.ext.coverage",
     "sphinx.ext.mathjax",
 ]
 

pyproject.toml

@@ -8,7 +8,7 @@ version = "1.3.0"
 description = "Perform quaternion operations using NumPy arrays"
 readme = "README.rst"
 license = { file = "LICENSE.txt" }
-requires-python = ">=3.8, <4"
+requires-python = ">=3.8"
 authors = [
     { name = "Vyas Ramasubramani", email = "vramasub@umich.edu" },
 ]