Merge pull request #1840 from glotzerlab/release-4.8.0

Release 4.8.0
glotzerlab · Jul 15, 2024 · 1101041 · 1101041
2 parents 109a0e3 + 0c6de57
commit 1101041
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.7.0
+current_version = 4.8.0
 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-]*)))?$

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.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: 4.8.0
     validations:
       required: true
   - type: markdown

diff --git a/.github/ISSUE_TEMPLATE/release.md b/.github/ISSUE_TEMPLATE/release.md
@@ -1,7 +1,7 @@
 ---
 name: Release checklist
 about: '[for maintainer use]'
-title: 'Release 4.7.0'
+title: 'Release 4.8.0'
 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.

diff --git a/.mailmap b/.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]>
diff --git a/.pre-commit-config.yaml b/.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

diff --git a/BUILDING.rst b/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-4.8.0.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-4.7.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.7.0/hoomd-4.7.0.tar.gz
+.. _Download hoomd-4.8.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.8.0/hoomd-4.8.0.tar.gz
 .. _GitHub release: https://github.com/glotzerlab/hoomd-blue/releases
 .. _git book: https://git-scm.com/book
 .. _Git: https://git-scm.com/

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -7,22 +7,25 @@ Change Log
 4.x
 ---
 
-4.8.0 (not yet released)
-^^^^^^^^^^^^^^^^^^^^^^^^
+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 +42,23 @@ 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*
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -18,7 +18,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "4.7.0")
+set(HOOMD_VERSION_RAW "4.8.0")
 string(REGEX MATCH "(.*)\\.(.*)\\.(.*)$" _hoomd_version_match ${HOOMD_VERSION_RAW})
 set(HOOMD_VERSION_MAJOR ${CMAKE_MATCH_1})
 set(HOOMD_VERSION_MINOR ${CMAKE_MATCH_2})

diff --git a/INSTALLING.rst b/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=4.8.0
 
 .. _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=4.8.0=*gpu*" "cuda-version=12.0"
 
 Similarly, you can force CPU only package installation with::
 
-    $ mamba install "hoomd=4.7.0=*cpu*"
+    $ mamba install "hoomd=4.8.0=*cpu*"
 
 .. note::
 
@@ -42,7 +42,7 @@ Similarly, you can force CPU only package installation with::
 .. note::
 
     Run time compilation is no longer available on conda-forge builds starting with HOOMD-blue
-    4.7.0.
+    4.8.0.
 
 .. tip::
 

diff --git a/hoomd/hpmc/external/user.py b/hoomd/hpmc/external/user.py
@@ -85,9 +85,9 @@ class CPPExternalPotential(ExternalField):
         Your code *must* return a value.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.7.0/hoomd/VectorMath.h
+            v4.8.0/hoomd/VectorMath.h
     .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.7.0/hoomd/BoxDim.h
+            v4.8.0/hoomd/BoxDim.h
 
     .. rubric:: Example:
 

diff --git a/hoomd/hpmc/pair/user.py b/hoomd/hpmc/pair/user.py
@@ -76,7 +76,7 @@ class CPPPotentialBase(AutotunedObject):
                 HOOMD-blue source code.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.7.0/hoomd/VectorMath.h
+            v4.8.0/hoomd/VectorMath.h
 
     Note:
         Your code *must* return a value.
@@ -340,7 +340,7 @@ class CPPPotentialUnion(CPPPotentialBase):
 
     CPPPotentialUnion uses threaded execution on multiple CPU cores.
 
-    .. deprecated:: 4.7.0
+    .. deprecated:: 4.8.0
 
         ``num_cpu_threads >= 1`` is deprecated. Set ``num_cpu_threads = 1``.
 

diff --git a/sphinx-doc/conf.py b/sphinx-doc/conf.py
@@ -68,8 +68,8 @@
 copyright = f'2009-{year} The Regents of the University of Michigan'
 author = 'The Regents of the University of Michigan'
 
-version = '4.7.0'
-release = '4.7.0'
+version = '4.8.0'
+release = '4.8.0'
 
 language = 'en'