Merge branch 'trunk-minor' into asymmetric_sinusoidal_channel

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.7.0
+current_version = 4.8.2
 commit = False
 tag = False
 parse = ^(?P<major>0|[1-9]\d*)\.(?P<minor>0|[1-9]\d*)\.(?P<patch>0|[1-9]\d*)(?:-(?P<prerelease>(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))(?:\.(?P<number>0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)))?$

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -62,7 +62,7 @@ body:
     attributes:
       label: HOOMD-blue version
       description: What version of HOOMD-blue are you using?
-      placeholder: 4.7.0
+      placeholder: 4.8.2
     validations:
       required: true
   - type: markdown

.github/ISSUE_TEMPLATE/release.md

@@ -1,7 +1,7 @@
 ---
 name: Release checklist
 about: '[for maintainer use]'
-title: 'Release 4.7.0'
+title: 'Release 4.8.2'
 labels: ''
 assignees: 'joaander'
 
@@ -10,9 +10,6 @@ assignees: 'joaander'
 Minor and major releases:
 
 - [ ] Update tutorial submodule.
-- [ ] Update actions versions.
-  - See current actions usage with: `rg --no-filename --hidden uses: | awk '{$1=$1;print}' | sort | uniq`
-  - Use global search and replace to update them to the latest tags
 - [ ] Check for new or duplicate contributors since the last release:
   `comm -13 (git log $(git describe --tags --abbrev=0) --format="%aN <%aE>" | sort | uniq | psub) (git log --format="%aN <%aE>" | sort | uniq | psub)`.
   Add entries to `.mailmap` to remove duplicates.

.github/workflows/build_and_test.yaml

@@ -118,7 +118,7 @@ jobs:
         apt-get update
         apt-get install git --yes
     - name: Checkout
-      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       with:
         path: code
         submodules: true
@@ -203,13 +203,13 @@ jobs:
       run: tar --use-compress-program='zstd -10 -T0' -cvf install.tar install
 
     - name: 'Upload build'
-      uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+      uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
       with:
         name: build-${{ inputs.config }}-${{ github.sha }}
         path: build.tar
         retention-days: 7
     - name: 'Upload install'
-      uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+      uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
       with:
         name: install-${{ inputs.config }}-${{ github.sha }}
         path: install.tar
@@ -233,7 +233,7 @@ jobs:
         apt-get update
         apt-get install git --yes
     - name: Checkout
-      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       with:
         path: code
 
@@ -254,7 +254,7 @@ jobs:
         echo "$MAMBA_ROOT_PREFIX/envs/test/bin" >> $GITHUB_PATH
 
     - name: Download install
-      uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+      uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
       with:
         name: install-${{ inputs.config }}-${{ github.sha }}
     - name: Untar install
@@ -312,7 +312,7 @@ jobs:
         echo "LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu" >> $GITHUB_ENV
 
     - name: Download build
-      uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+      uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
       with:
         name: build-${{ inputs.config }}-${{ github.sha }}
     - name: Untar build

.github/workflows/release.yaml

@@ -31,7 +31,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       with:
         fetch-depth: 0
         submodules: true
@@ -67,7 +67,7 @@ jobs:
       run: tar -cvJf ${name}-${tag:1}.tar.xz ${name}-${tag:1}
 
     - name: Upload release files
-      uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+      uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
       with:
         name: release
         path: |
@@ -81,12 +81,12 @@ jobs:
 
     steps:
     - name: Download artifacts
-      uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+      uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
       with:
         name: release
 
     - name: Create release
-      uses: softprops/action-gh-release@69320dbe05506a9a39fc8ae11030b214ec2d1f87 # v2.0.5
+      uses: softprops/action-gh-release@a74c6b72af54cfa997e81df42d94703d6313a2d0 # v2.0.6
       if: startsWith(github.ref, 'refs/tags/v')
       with:
         files: "*.tar.*"

.github/workflows/stale.yaml

@@ -8,4 +8,4 @@ on:
 
 jobs:
   stale:
-    uses: glotzerlab/workflows/.github/workflows/stale.yaml@5cfac9da9cb78e16ae97a9119b6fd13c1c2d6f5e # 0.1.0
+    uses: glotzerlab/workflows/.github/workflows/stale.yaml@ea2e25d07af862a1c696a932c2bd6b242d142049 # 0.2.0

.github/workflows/test.yaml

@@ -17,7 +17,7 @@ on:
 jobs:
   start_action_runners:
     name: Start
-    uses: glotzerlab/jetstream2-admin/.github/workflows/start.yaml@c89b62aa89f7886318edb166bc0500cfc658f24f # v1.3.0
+    uses: glotzerlab/jetstream2-admin/.github/workflows/start.yaml@98f840ba341f72bf412100f2180d38c06e792b84 # v1.3.1
     secrets: inherit
 
   typical:
@@ -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()

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

@@ -0,0 +1,14 @@
+name: Update conda lockfiles
+
+on:
+  schedule:
+    - cron: '0 12 1 * *'
+
+  workflow_dispatch:
+
+jobs:
+  update:
+    uses: glotzerlab/workflows/.github/workflows/update-conda-lockfiles.yaml@ea2e25d07af862a1c696a932c2bd6b242d142049 # 0.2.0
+    secrets: inherit
+    with:
+      branch: trunk-patch

.mailmap

@@ -181,3 +181,5 @@ Simone Ciarella <[email protected]> SCiarella <[email protected]>
 Simone Ciarella <[email protected]> SCiarella <[email protected]>
 Kieran Nehil-Puleo <[email protected]> kierannp <[email protected]>
 Cristina Butu <[email protected]> crisbutu <[email protected]>
+Joseph Burkhart <[email protected]> josephburkhart <[email protected]>
+Joseph Burkhart <[email protected]> Joseph Burkhart <[email protected]>

.pre-commit-config.yaml

@@ -28,9 +28,6 @@ repos:
   - id: check-yaml
     exclude: (?:^.github/workflows/templates) # templates are not properly formatted yaml
   - id: check-case-conflict
-  - id: fix-encoding-pragma
-    args:
-    - --remove
   - id: mixed-line-ending
 - repo: https://github.com/glotzerlab/fix-license-header
   rev: v0.3.2

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

BUILDING.rst

@@ -145,7 +145,7 @@ Clone using Git_::
 
    $ git clone --recursive https://github.com/glotzerlab/hoomd-blue
 
-Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.7.0.tar.gz`_.
+Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.8.2.tar.gz`_.
 
 .. seealso::
 
@@ -158,7 +158,7 @@ Release tarballs are also available as `GitHub release`_ assets: `Download hoomd
     Execute ``git submodule update --init`` to fetch the submodules each time you switch branches
     and the submodules show as modified.
 
-.. _Download hoomd-4.7.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.7.0/hoomd-4.7.0.tar.gz
+.. _Download hoomd-4.8.2.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.8.2/hoomd-4.8.2.tar.gz
 .. _GitHub release: https://github.com/glotzerlab/hoomd-blue/releases
 .. _git book: https://git-scm.com/book
 .. _Git: https://git-scm.com/

CHANGELOG.rst

@@ -7,22 +7,49 @@ Change Log
 4.x
 ---
 
-4.8.0 (not yet released)
-^^^^^^^^^^^^^^^^^^^^^^^^
+4.8.2 (2024-07-23)
+^^^^^^^^^^^^^^^^^^
+
+Fixed:
+
+* Correct citation to Langevin piston paper
+  (`#1849 <https://github.com/glotzerlab/hoomd-blue/pull/1849>`__).
+* External walls, external fields, and constrains can now be implemented via external plugins
+  (`#1849 <https://github.com/glotzerlab/hoomd-blue/pull/1849>`__).
+* Prevent compile errors with ``-DENABLE_GPU=on -DHOOMD_GPU_PLATFORM=HIP``
+  (`#1851 <https://github.com/glotzerlab/hoomd-blue/pull/1851>`__).
+* Prevent ``/usr/lib64/slurm/auth_munge.so: undefined symbol: slurm_conf`` error on Purdue Anvil
+  (`#1850 <https://github.com/glotzerlab/hoomd-blue/pull/1850>`__).
+
+4.8.1 (2024-07-18)
+^^^^^^^^^^^^^^^^^^
+
+Fixed:
+
+* Prevent illegal instruction when accessing 0 length snapshot arrays
+  (`#1846 <https://github.com/glotzerlab/hoomd-blue/pull/1846>`__)
+* Fix MPCD compiler warning.
+  (`#1845 <https://github.com/glotzerlab/hoomd-blue/pull/1845>`__)
+
+4.8.0 (2024-07-11)
+^^^^^^^^^^^^^^^^^^
 
 *Added*
 
 * ``hoomd.mpcd`` reimplements the MPCD method for simulating hydrodynamic interactions.
   See the migrating page for an overview and individual class and method documentation for more
   information (`#1784 <https://github.com/glotzerlab/hoomd-blue/pull/1784>`__).
+* MPCD tutorial.
 * Support numpy 2.0
   (`#1797 <https://github.com/glotzerlab/hoomd-blue/pull/1797>`__)
 * ``hoomd.hpmc.external.External`` provides an abstract interface to external potentials
   (`#1811 <https://github.com/glotzerlab/hoomd-blue/pull/1811>`__).
-* ``hoomd.hpmc.external.Linear`` computes linear potential as a function of the distance from a point to a plane
-  (`#1811 <https://github.com/glotzerlab/hoomd-blue/pull/1811>`__).
+* ``hoomd.hpmc.external.Linear`` computes the potential as a linear function of the distance from a
+  point to a plane (`#1811 <https://github.com/glotzerlab/hoomd-blue/pull/1811>`__).
 * ``HPMCIntegrator.external_potentials`` sets the list of external potentials applied to the system
   (`#1811 <https://github.com/glotzerlab/hoomd-blue/pull/1811>`__).
+* ``hpmc.pair.ExpandedGaussian`` computes the expanded Gaussian pair potential in HPMC
+  (`#1817 <https://github.com/glotzerlab/hoomd-blue/pull/1817>`__).
 
 *Changed*
 
@@ -39,21 +66,23 @@ Change Log
   `#1816 <https://github.com/glotzerlab/hoomd-blue/pull/1816>`__).
 * Ensure that Gaussian-type pair potentials have positive sigma values
   (`#1810 <https://github.com/glotzerlab/hoomd-blue/pull/1810>`__).
+* Demonstrate ``Step`` and ``AngularStep`` in the tutorial "Modelling Patchy Particles".
+* Fixed typographical errors in all tutorials.
 
 *Fixed*
 
-* Issue a proper error message when ``ALJ.shape`` is not set for all particle types
+* Issue the proper error message when ``ALJ.shape`` is not set for all particle types
   (`#1808 <https://github.com/glotzerlab/hoomd-blue/pull/1808>`__).
-* Correctly apply brownian torque when elements of the inertia tensor are 0
+* Correctly apply Brownian torque when elements of the inertia tensor are 0
   (`#1825 <https://github.com/glotzerlab/hoomd-blue/pull/1825>`__).
 
 
 *Deprecated*
 
 * ``HPMCIntegrator.external_potential`` - use ``HPMCIntegrator.external_potentials``
   (`#1811 <https://github.com/glotzerlab/hoomd-blue/pull/1811>`__).
-* ``hoomd.hpmc.external.user.CPPExternalPotential`` - use ``hoomd.hpmc.external.Linear`` or write a custom component in C++
-  (`#1811 <https://github.com/glotzerlab/hoomd-blue/pull/1811>`__).
+* ``hoomd.hpmc.external.user.CPPExternalPotential`` - use ``hoomd.hpmc.external.Linear`` or write a
+  custom component in C++ (`#1811 <https://github.com/glotzerlab/hoomd-blue/pull/1811>`__).
 
 *Removed*
 

CMakeLists.txt

@@ -18,7 +18,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "4.7.0")
+set(HOOMD_VERSION_RAW "4.8.2")
 string(REGEX MATCH "(.*)\\.(.*)\\.(.*)$" _hoomd_version_match ${HOOMD_VERSION_RAW})
 set(HOOMD_VERSION_MAJOR ${CMAKE_MATCH_1})
 set(HOOMD_VERSION_MINOR ${CMAKE_MATCH_2})
@@ -104,7 +104,13 @@ else ()
 option(BUILD_HPMC "Build the hpmc package" off)
 endif()
 option(BUILD_METAL "Build the metal package" on)
+
+if (ENABLE_GPU AND HOOMD_GPU_PLATFORM STREQUAL "HIP")
+message("Defaulting BUILD_MPCD=off due to HIP GPU platform.")
+option(BUILD_MPCD "Build the mpcd package" off)
+else()
 option(BUILD_MPCD "Build the mpcd package" ${BUILD_MD})
+endif()
 
 # Optionally use TBB for threading
 option(ENABLE_TBB "Enable support for Threading Building Blocks (TBB)" off)

INSTALLING.rst

@@ -20,19 +20,19 @@ Serial CPU and single GPU builds
 *linux-64*, *osx-64*, and *osx-arm64* platforms. Install the ``hoomd`` package from the conda-forge_
 channel into a conda environment::
 
-    $ mamba install hoomd=4.7.0
+    $ mamba install hoomd=4.8.2
 
 .. _conda-forge: https://conda-forge.org/docs/user/introduction.html
 
 ``conda`` auto-detects whether your system has a GPU and attempts to install the appropriate
 package. Override this and force the GPU enabled package installation with::
 
     $ export CONDA_OVERRIDE_CUDA="12.0"
-    $ mamba install "hoomd=4.7.0=*gpu*" "cuda-version=12.0"
+    $ mamba install "hoomd=4.8.2=*gpu*" "cuda-version=12.0"
 
 Similarly, you can force CPU only package installation with::
 
-    $ mamba install "hoomd=4.7.0=*cpu*"
+    $ mamba install "hoomd=4.8.2=*cpu*"
 
 .. note::
 

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)