Documentation fixes

.github/workflows/test.yaml

@@ -95,6 +95,38 @@ jobs:
         - config: [gcc, 11, -py, 310, -mpi, -tbb]
         - config: [gcc, 10, -py, 310, -mpi, -tbb]
 
+  check-links:
+    name: "Check links"
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check out repo
+      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      with:
+        submodules: true
+    - name: Set up Python
+      uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
+      with:
+        python-version: "3.12"
+    - name: Setup uv
+      uses: glotzerlab/workflows/setup-uv@5cfac9da9cb78e16ae97a9119b6fd13c1c2d6f5e # 0.1.0
+    - name: Install dependencies
+      run: uv pip install -r sphinx-doc/requirements.txt --system
+    - name: Install tools
+      run: sudo apt-get install pandoc
+    - name: Build Sphinx Docs
+      run: sphinx-build -b html sphinx-doc doc_build
+    - name: Link Checker
+      id: lychee
+      uses: lycheeverse/lychee-action@2b973e86fc7b1f6b36a93795fe2c9c6ae1118621  # v1.10.0
+      with:
+        args: -n
+              --exclude-path 'sphinx-doc/_templates/page.html'
+              --exclude-path 'hoomd/extern'
+              --exclude https://glotzerlab.engin.umich.edu
+              --exclude doi.org
+              './**/*.md' './**/*.html' './**/*.rst'
+        fail: true
+
   tests_complete:
     name: Unit test
     if: always()

ARCHITECTURE.md

@@ -19,19 +19,15 @@ Each minor and major release of HOOMD-blue at a minimum supports:
 ### Continuous integration
 
 [Github Actions] performs continuous integration testing on HOOMD-blue. GitHub
-Actions compiles HOOMD-blue, runs the unit tests, and and reports the
+Actions compiles HOOMD-blue, runs the unit tests, and reports the
 status to GitHub pull requests. A number of parallel builds test a variety of
 compiler and build configurations as defined above.
 
 Visit the [workflows] page to find recent builds. The pipeline configuration
-files are in [.github/workflows/] and are built from Jinja templates in
-[.github/workflows/templates/] using `make_workflows.py` which is automatically
-run by `pre-commit`. To make changes to the workflows, edit the templates.
+files are in `.github/workflows/`.
 
 [GitHub Actions]: https://docs.github.com/en/actions
 [workflows]: https://github.com/glotzerlab/hoomd-blue/actions
-[.github/workflows/]: .github/workflows/
-[.github/workflows/templates/]: .github/workflows/templates/
 
 ## Build system
 
@@ -398,7 +394,7 @@ classes is automated through previously described classes.
 
 HOOMD-blue version 3 allows for much more interaction with Python objects within
 its C++ core. One feature is custom actions (see the tutorial
-https://hoomd-blue.readthedocs.io/en/latest/tutorial/03-Custom-Actions-In-Python/00-index.html
+https://hoomd-blue.readthedocs.io/en/latest/tutorial/04-Custom-Actions-In-Python/00-index.html
 or API documentation for more introductory information). When using custom
 actions internally for HOOMD, the classes `hoomd.custom._InternalAction` and one
 of the `hoomd.custom._InternalOperation` subclasses are to be used. They allow

README.md

@@ -3,7 +3,7 @@
 [![Citing HOOMD](https://img.shields.io/badge/cite-hoomd-blue.svg)](https://hoomd-blue.readthedocs.io/en/latest/citing.html)
 [![conda-forge](https://img.shields.io/conda/vn/conda-forge/hoomd.svg?style=flat)](https://anaconda.org/conda-forge/hoomd)
 [![conda-forge Downloads](https://img.shields.io/conda/dn/conda-forge/hoomd.svg?style=flat)](https://anaconda.org/conda-forge/hoomd)
-[![GitHub Actions](https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yml/badge.svg?branch=trunk-patch)](https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yml)
+[![GitHub Actions](https://github.com/glotzerlab/hoomd-blue/actions/workflows//test.yaml/badge.svg?branch=trunk-patch)](https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yaml)
 [![Read the Docs](https://img.shields.io/readthedocs/hoomd-blue/latest.svg)](https://hoomd-blue.readthedocs.io/en/latest/?badge=latest)
 [![Contributors](https://img.shields.io/github/contributors-anon/glotzerlab/hoomd-blue.svg?style=flat)](https://hoomd-blue.readthedocs.io/en/latest/credits.html)
 [![License](https://img.shields.io/badge/license-BSD--3--Clause-green.svg)](LICENSE)

hoomd/data/array.py

@@ -720,7 +720,7 @@ class HOOMDGPUArray(_NoGPU):
 
 The HOOMDGPUArray object exposes a GPU data buffer using
 `__cuda_array_interface__
-<https://numba.pydata.org/numba-doc/latest/cuda/cuda_array_interface.html>`_.
+<https://nvidia.github.io/numba-cuda/user/cuda_array_interface.html>`_.
 This class provides buffer access through a context manager to prevent invalid
 memory accesses (`hoomd.State.gpu_local_snapshot`). To avoid errors, use arrays
 only within the relevant context manager. For example:
@@ -755,7 +755,7 @@ class HOOMDGPUArray(_NoGPU):
     Packages like Numba and PyTorch can use `HOOMDGPUArray` without CuPy
     installed. Any package that supports version 2 of the
     `__cuda_array_interface__
-    <https://numba.pydata.org/numba-doc/latest/cuda/cuda_array_interface.html>`_
+    <https://nvidia.github.io/numba-cuda/user/cuda_array_interface.html>`_
     should support the direct use of `HOOMDGPUArray` objects.
 
 """

hoomd/md/bond.py

@@ -279,7 +279,7 @@ class Tether(Bond):
     The tethered network is described in Refs. `Gompper, G. & Kroll, D. M.
     Statistical Mechanics of Membranes and Surfaces 2nd edn (eds Nelson, D. R.
     et al.) 359-426 (World Scientific, 2004)
-    <https://www.worldscientific.com/worldscibooks/10.1142/5473>`__ and
+    <https://doi.org/10.1142/5473>`__ and
     `Noguchi, H. & Gompper, G., Phys. Rev. E 72 011901 (2005)
     <https://link.aps.org/doi/10.1103/PhysRevE.72.011901>`__.
 

hoomd/md/constrain.py

@@ -77,7 +77,7 @@ class Distance(Constraint):
 
     Where :math:`i` and :math:`j` are the the particle tags in the
     ``constraint_group`` and :math:`d_{ij}` is the constraint distance as given
-    by the `system state <hoomd.State>`_.
+    by the system state.
 
     The method sets the second derivative of the Lagrange multipliers with
     respect to time to zero, such that both the distance constraints and their

sphinx-doc/_templates/page.html

@@ -30,7 +30,7 @@
 </div>
 <div class="bottom-of-page">
   <div class="left-details">
-    <p>Development of {{ project }} is led by the <a href="https://glotzerlab.engin.umich.edu">Glotzer Group</a> at the <a href="https://umich.edu">University of Michigan</a> (supported by NSF DMR 1808342) with many <a href="credits.html">external contributions</a>.
+    <p>Development of {{ project }} is led by the <a href="https://glotzerlab.engin.umich.edu">Glotzer Group</a> at the <a href="https://umich.edu">University of Michigan</a> (supported by NSF DMR 1808342) with many <a href="{{ pathto('credits') }}">external contributions</a>.
     </p>
 
     {%- if show_copyright %}

sphinx-doc/index.rst

@@ -21,8 +21,8 @@ HOOMD-blue
         :target: https://anaconda.org/conda-forge/hoomd
     .. |conda-forge-Downloads| image:: https://img.shields.io/conda/dn/conda-forge/hoomd.svg?style=flat
         :target: https://anaconda.org/conda-forge/hoomd
-    .. |GitHub Actions| image:: https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yml/badge.svg?branch=trunk-patch
-        :target: https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yml
+    .. |GitHub Actions| image:: https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yaml/badge.svg?branch=trunk-patch
+        :target: https://github.com/glotzerlab/hoomd-blue/actions/workflows/test.yaml
     .. |Contributors| image:: https://img.shields.io/github/contributors-anon/glotzerlab/hoomd-blue.svg?style=flat
         :target: https://hoomd-blue.readthedocs.io/en/latest/credits.html
     .. |License| image:: https://img.shields.io/badge/license-BSD--3--Clause-green.svg

sphinx-doc/license.rst

@@ -9,7 +9,7 @@ License
 Libraries
 ---------
 
-**HOOMD:** HOOMD-blue is a continuation of the HOOMD project (http://www.ameslab.gov/hoomd/). The code from the original project is used under the following license::
+**HOOMD:** HOOMD-blue is a continuation of the HOOMD project. The code from the original project is used under the following license::
 
     Highly Optimized Object-Oriented Molecular Dynamics (HOOMD) Open
     Source Software License
@@ -122,7 +122,7 @@ following license::
     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
     SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-`CUB <http://nvlabs.github.io/cub/>`_, used under the following license::
+`CUB <https://nvidia.github.io/cccl/cub/>`_, used under the following license::
 
     Copyright (c) 2011, Duane Merrill.  All rights reserved.
     Copyright (c) 2011-2016, NVIDIA CORPORATION.  All rights reserved.

sphinx-doc/migrating.rst

@@ -292,9 +292,9 @@ HOOMD v3 removes old APIs, unused functionality, and features better served by o
    * - ``deprecated.init.read_xml``
      - `Simulation.create_state_from_gsd`
    * - ``deprecated.init.create_random``
-     - `mBuild <https://mosdef-hub.github.io/mbuild/>`_, `packmol <https://www.ime.unicamp.br/~martinez/packmol/userguide.shtml>`_, or user script.
+     - `mBuild <https://github.com/mosdef-hub/mbuild/>`_, `packmol <https://www.ime.unicamp.br/~martinez/packmol/userguide.shtml>`_, or user script.
    * - ``deprecated.init.create_random_polymers``
-     - `mBuild <https://mosdef-hub.github.io/mbuild/>`_, `packmol <https://www.ime.unicamp.br/~martinez/packmol/userguide.shtml>`_, or user script.
+     - `mBuild <https://github.com/mosdef-hub/mbuild/>`_, `packmol <https://www.ime.unicamp.br/~martinez/packmol/userguide.shtml>`_, or user script.
 
 :py:mod:`hoomd.hpmc`:
 

sphinx-doc/style.rst

@@ -34,7 +34,7 @@ Tools
   * With these plugins:
 
     * `pep8-naming <https://github.com/PyCQA/pep8-naming>`_
-    * `flake8-docstrings <https://gitlab.com/pycqa/flake8-docstrings>`_
+    * `flake8-docstrings <https://pypi.org/project/flake8-docstrings/>`_
     * `flake8-rst-docstrings <https://github.com/peterjc/flake8-rst-docstrings>`_
 
   * Configure flake8 in your editor to see violations on save.