Merge pull request #1639 from glotzerlab/release-4.3.0

Release 4.3.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.2.1
+current_version = 4.3.0
 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: 4.2.1
+      placeholder: 4.3.0
     validations:
       required: true
   - type: markdown

.github/ISSUE_TEMPLATE/release.md

@@ -7,15 +7,9 @@ assignees: 'joaander'
 
 ---
 
-Release checklist:
+Minor and major releases:
 
 - [ ] Update tutorial submodule.
-- [ ] Update change log.
-  - ``git log --format=oneline --first-parent `git log -n 1 --pretty=format:%H -- CHANGELOG.rst`...``
-  - [milestone](https://github.com/glotzerlab/hoomd-blue/milestones)
-- [ ] Check readthedocs build, especially change log formatting.
-  - [Build status](https://readthedocs.org/projects/hoomd-blue/builds/)
-  - [Output](https://hoomd-blue.readthedocs.io/en/latest/)
 - [ ] 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
@@ -24,8 +18,16 @@ Release checklist:
   Add entries to `.mailmap` to remove duplicates.
 - [ ] Run [hoomd-benchmarks](https://github.com/glotzerlab/hoomd-benchmarks), check for performance
   regressions with the previous release, and post the tables in the release pull request.
+- [ ] Run [hoomd-validation](https://github.com/glotzerlab/hoomd-validation).
+
+All releases:
+
+- [ ] Update change log.
+  - ``git log --format=oneline --first-parent `git log -n 1 --pretty=format:%H -- CHANGELOG.rst`...``
+  - [milestone](https://github.com/glotzerlab/hoomd-blue/milestones)
+- [ ] Check readthedocs build, especially change log formatting.
 - [ ] Run *bumpversion*.
 - [ ] Tag and push.
 - [ ] Update conda-forge recipe.
-- [ ] Update glotzerlab-software.
+- [ ] Update *glotzerlab-software*.
 - [ ] Announce release on mailing list.

.github/workflows/release.yml

@@ -40,7 +40,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4.0.0
+        uses: actions/checkout@v4.1.1
         with:
           fetch-depth: 0
           submodules: true

.github/workflows/templates/release.yml

@@ -27,7 +27,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4.0.0
+        uses: actions/checkout@v4.1.1
         with:
           fetch-depth: 0
           submodules: true

.github/workflows/templates/test.yml

@@ -181,7 +181,7 @@ env:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.0.0
+      uses: actions/checkout@v4.1.1
       with:
         path: code
         submodules: true
@@ -209,7 +209,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Use jetstream2-admin/start
-      uses: glotzerlab/jetstream2-admin/[email protected].2
+      uses: glotzerlab/jetstream2-admin/[email protected].3
       with:
         OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }}
         OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}

.github/workflows/test.yml

@@ -50,7 +50,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Use jetstream2-admin/start
-      uses: glotzerlab/jetstream2-admin/[email protected].2
+      uses: glotzerlab/jetstream2-admin/[email protected].3
       with:
         OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }}
         OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}
@@ -82,7 +82,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.0.0
+      uses: actions/checkout@v4.1.1
       with:
         path: code
         submodules: true
@@ -188,7 +188,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.0.0
+      uses: actions/checkout@v4.1.1
       with:
         path: code
         submodules: true
@@ -249,7 +249,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.0.0
+      uses: actions/checkout@v4.1.1
       with:
         path: code
         submodules: true
@@ -299,7 +299,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.0.0
+      uses: actions/checkout@v4.1.1
       with:
         path: code
         submodules: true
@@ -362,7 +362,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.0.0
+      uses: actions/checkout@v4.1.1
       with:
         path: code
         submodules: true
@@ -477,7 +477,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.0.0
+      uses: actions/checkout@v4.1.1
       with:
         path: code
         submodules: true
@@ -547,7 +547,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.0.0
+      uses: actions/checkout@v4.1.1
       with:
         path: code
         submodules: true

.mailmap

@@ -171,3 +171,6 @@ Domagoj Fijan <[email protected]> Domagoj Fijan <[email protected]>
 Domagoj Fijan <[email protected]> Domagoj Fijan <[email protected]>
 Adrien Chen <[email protected]> Adrien Chen <[email protected]>
 Antonia Statt <[email protected]> Antonia Statt <>
+Alex Lee <[email protected]> Alex <[email protected]>
+Alex Lee <[email protected]> shihkual <[email protected]>
+Alex Lee <[email protected]> shihkual <[email protected]>

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-4.2.1.tar.gz`_.
+Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.3.0.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-4.2.1.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.2.1/hoomd-4.2.1.tar.gz
+.. _Download hoomd-4.3.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.3.0/hoomd-4.3.0.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

@@ -6,6 +6,35 @@ Change Log
 
 4.x
 ---
+
+4.3.0 (2024-10-24)
+^^^^^^^^^^^^^^^^^^
+
+*Fixed*
+
+* ``md.alchemy.methods.NVT`` now evolves the elements provided in ``alchemical_dof``
+  (`#1633 <https://github.com/glotzerlab/hoomd-blue/pull/1633>`__).
+* More consistent notice messages regarding MPI ranks used in GPU selection
+  (`#1635 <https://github.com/glotzerlab/hoomd-blue/pull/1635>`__).
+* ``hoomd.hpmc.compute.SDF`` computes correct pressures with patchy potentials.
+  (`#1636 <https://github.com/glotzerlab/hoomd-blue/pull/1636>`__).
+
+*Added*
+
+* Support GCC 13
+  (`#1634 <https://github.com/glotzerlab/hoomd-blue/pull/1634>`__).
+* Support Python 3.12
+  (`#1634 <https://github.com/glotzerlab/hoomd-blue/pull/1634>`__).
+* ``tau`` parameter to ``hoomd.md.methods.thermostats.Bussi``
+  (`#1619 <https://github.com/glotzerlab/hoomd-blue/pull/1619>`__).
+
+*Changed*
+
+* Revise class documentation.
+  (`#1628 <https://github.com/glotzerlab/hoomd-blue/pull/1628>`__).
+* Add more code snippets to the class documentation
+  (`#1628 <https://github.com/glotzerlab/hoomd-blue/pull/1628>`__).
+
 4.2.1 (2024-10-02)
 ^^^^^^^^^^^^^^^^^^
 

CMakeLists.txt

@@ -14,7 +14,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "4.2.1")
+set(HOOMD_VERSION_RAW "4.3.0")
 string(REGEX MATCH "(.*)\\.(.*)\\.(.*)$" _hoomd_version_match ${HOOMD_VERSION_RAW})
 set(HOOMD_VERSION_MAJOR ${CMAKE_MATCH_1})
 set(HOOMD_VERSION_MINOR ${CMAKE_MATCH_2})

INSTALLING.rst

@@ -24,17 +24,17 @@ Conda package
 **HOOMD-blue** is available on conda-forge_ on the *linux-64*, *osx-64*, and *osx-arm64* platforms.
 Install the ``hoomd`` package from the conda-forge_ channel into a conda environment::
 
-    $ conda install hoomd=4.2.1
+    $ conda install hoomd=4.3.0
 
 ``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"
-    $ conda install "hoomd=4.2.1=*gpu*" "cuda-version=12.0"
+    $ conda install "hoomd=4.3.0=*gpu*" "cuda-version=12.0"
 
 Similarly, you can force CPU only package installation with::
 
-    $ conda install "hoomd=4.2.1=*cpu*"
+    $ conda install "hoomd=4.3.0=*cpu*"
 
 .. note::
 

hoomd/hpmc/external/user.py

@@ -84,9 +84,9 @@ class CPPExternalPotential(ExternalField):
         Your code *must* return a value.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.2.1/hoomd/VectorMath.h
+            v4.3.0/hoomd/VectorMath.h
     .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.2.1/hoomd/BoxDim.h
+            v4.3.0/hoomd/BoxDim.h
 
     .. rubric:: Example:
 

hoomd/hpmc/pair/user.py

@@ -75,7 +75,7 @@ class CPPPotentialBase(AutotunedObject):
                 HOOMD-blue source code.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.2.1/hoomd/VectorMath.h
+            v4.3.0/hoomd/VectorMath.h
 
     Note:
         Your code *must* return a value.

sphinx-doc/conf.py

@@ -63,8 +63,8 @@
 copyright = f'2009-{ year } The Regents of the University of Michigan'
 author = 'The Regents of the University of Michigan'
 
-version = '4.2.1'
-release = '4.2.1'
+version = '4.3.0'
+release = '4.3.0'
 
 language = 'en'