Merge pull request #1989 from glotzerlab/release-5.0.1

Release 5.0.1
glotzerlab · Jan 20, 2025 · 665633e · 665633e
2 parents 2307cc1 + c2b6fb9
commit 665633e
Show file tree

Hide file tree

Showing 1,074 changed files with 1,083 additions and 1,081 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 5.0.0
+current_version = 5.0.1
 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
@@ -60,7 +60,7 @@ body:
     attributes:
       label: HOOMD-blue version
       description: What version of HOOMD-blue are you using?
-      placeholder: 5.0.0
+      placeholder: 5.0.1
     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 5.0.0'
+title: 'Release 5.0.1'
 labels: ''
 assignees: 'joaander'
 

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -9,7 +9,7 @@ sphinx:
   fail_on_warning: true
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
     python: "3.12"
 

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -4,15 +4,17 @@ Change Log
 5.x
 ---
 
-5.0.1 (not yet released)
-^^^^^^^^^^^^^^^^^^^^^^^^
+5.0.1 (2025-01-20)
+^^^^^^^^^^^^^^^^^^
 
 *Fixed*
 
 * Prevent ``missing 1 required positional argument: 'kT'`` errors when using NEC integrators
-  (`#1965 <https://github.com/glotzerlab/hoomd-blue/pull/1965>`__)
+  (`#1965 <https://github.com/glotzerlab/hoomd-blue/pull/1965>`__).
 * Note the current version of CUDA in the micromamba installation instructions
-  (`#1972 <https://github.com/glotzerlab/hoomd-blue/pull/1972>`__)
+  (`#1972 <https://github.com/glotzerlab/hoomd-blue/pull/1972>`__).
+* Provide a navigation bar on the 404 not found page in the documentation
+  (`#1986 <https://github.com/glotzerlab/hoomd-blue/pull/1986>`__).
 
 
 5.0.0 (2024-12-02)

diff --git a/CMake/hoomd/test.cc b/CMake/hoomd/test.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 int main(int argc, char **argv)

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -16,7 +16,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "5.0.0")
+set(HOOMD_VERSION_RAW "5.0.1")
 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
@@ -22,7 +22,7 @@ channel:
 
 .. code-block:: bash
 
-    micromamba install hoomd=5.0.0
+    micromamba install hoomd=5.0.1
 
 .. _conda-forge: https://conda-forge.org/docs/user/introduction.html
 
@@ -32,7 +32,7 @@ appropriate package. Override this and force the GPU enabled package installatio
 .. code-block:: bash
 
     export CONDA_OVERRIDE_CUDA="12.6"
-    micromamba install "hoomd=5.0.0=*gpu*" "cuda-version=12.6"
+    micromamba install "hoomd=5.0.1=*gpu*" "cuda-version=12.6"
 
 .. note::
 
@@ -43,7 +43,7 @@ Similarly, you can force CPU-only package installation with:
 
 .. code-block:: bash
 
-    micromamba install "hoomd=5.0.0=*cpu*"
+    micromamba install "hoomd=5.0.1=*cpu*"
 
 .. note::
 

diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,4 @@
-Copyright (c) 2009-2024 The Regents of the University of Michigan.
+Copyright (c) 2009-2025 The Regents of the University of Michigan.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/hoomd/AABB.h b/hoomd/AABB.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "HOOMDMath.h"

diff --git a/hoomd/AABBTree.h b/hoomd/AABBTree.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "HOOMDMath.h"

diff --git a/hoomd/Action.cc b/hoomd/Action.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "Action.h"

diff --git a/hoomd/Action.h b/hoomd/Action.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #pragma once

diff --git a/hoomd/Analyzer.cc b/hoomd/Analyzer.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file Analyzer.cc

diff --git a/hoomd/Analyzer.h b/hoomd/Analyzer.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file Analyzer.h

diff --git a/hoomd/ArrayView.h b/hoomd/ArrayView.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file ArrayView.h

diff --git a/hoomd/Autotuned.cc b/hoomd/Autotuned.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "Autotuned.h"

diff --git a/hoomd/Autotuned.h b/hoomd/Autotuned.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #pragma once

diff --git a/hoomd/Autotuner.h b/hoomd/Autotuner.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 // inclusion guard

diff --git a/hoomd/BondedGroupData.cc b/hoomd/BondedGroupData.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file BondedGroupData.h

diff --git a/hoomd/BondedGroupData.cu b/hoomd/BondedGroupData.cu
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "BondedGroupData.cuh"

diff --git a/hoomd/BondedGroupData.cuh b/hoomd/BondedGroupData.cuh
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file BondedGroupData.cuh

diff --git a/hoomd/BondedGroupData.h b/hoomd/BondedGroupData.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file BondedGroupData.h

diff --git a/hoomd/BoxDim.h b/hoomd/BoxDim.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file BoxDim.h

diff --git a/hoomd/BoxResizeUpdater.cc b/hoomd/BoxResizeUpdater.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file BoxResizeUpdater.cc

diff --git a/hoomd/BoxResizeUpdater.h b/hoomd/BoxResizeUpdater.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file BoxResizeUpdater.h

diff --git a/hoomd/BoxResizeUpdaterGPU.cc b/hoomd/BoxResizeUpdaterGPU.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file BoxResizeUpdater.cc

diff --git a/hoomd/BoxResizeUpdaterGPU.cu b/hoomd/BoxResizeUpdaterGPU.cu
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "BoxResizeUpdaterGPU.cuh"

diff --git a/hoomd/BoxResizeUpdaterGPU.cuh b/hoomd/BoxResizeUpdaterGPU.cuh
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "hoomd/HOOMDMath.h"

diff --git a/hoomd/BoxResizeUpdaterGPU.h b/hoomd/BoxResizeUpdaterGPU.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file BoxResizeUpdater.h

diff --git a/hoomd/CachedAllocator.h b/hoomd/CachedAllocator.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file CachedAllocator.h

diff --git a/hoomd/CellList.cc b/hoomd/CellList.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file CellList.cc

diff --git a/hoomd/CellList.h b/hoomd/CellList.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "HOOMDMath.h"

diff --git a/hoomd/CellListGPU.cc b/hoomd/CellListGPU.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file CellListGPU.cc

diff --git a/hoomd/CellListGPU.cu b/hoomd/CellListGPU.cu
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "CellListGPU.cuh"

diff --git a/hoomd/CellListGPU.cuh b/hoomd/CellListGPU.cuh
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #ifndef __CELLLISTGPU_CUH__

diff --git a/hoomd/CellListGPU.h b/hoomd/CellListGPU.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "Autotuner.h"

diff --git a/hoomd/CellListStencil.cc b/hoomd/CellListStencil.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file CellListStencil.cc

diff --git a/hoomd/CellListStencil.h b/hoomd/CellListStencil.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "CellList.h"

diff --git a/hoomd/ClockSource.cc b/hoomd/ClockSource.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file ClockSource.cc

diff --git a/hoomd/ClockSource.h b/hoomd/ClockSource.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file ClockSource.h

diff --git a/hoomd/Communicator.cc b/hoomd/Communicator.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file Communicator.cc

diff --git a/hoomd/Communicator.h b/hoomd/Communicator.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file Communicator.h

diff --git a/hoomd/CommunicatorGPU.cc b/hoomd/CommunicatorGPU.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file CommunicatorGPU.cc

diff --git a/hoomd/CommunicatorGPU.cu b/hoomd/CommunicatorGPU.cu
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file CommunicatorGPU.cu

diff --git a/hoomd/CommunicatorGPU.cuh b/hoomd/CommunicatorGPU.cuh
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file CommunicatorGPU.cuh

diff --git a/hoomd/CommunicatorGPU.h b/hoomd/CommunicatorGPU.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file CommunicatorGPU.h

diff --git a/hoomd/Compute.cc b/hoomd/Compute.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "Compute.h"

diff --git a/hoomd/Compute.h b/hoomd/Compute.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "Action.h"

diff --git a/hoomd/DCDDumpWriter.cc b/hoomd/DCDDumpWriter.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file DCDDumpWriter.cc

diff --git a/hoomd/DCDDumpWriter.h b/hoomd/DCDDumpWriter.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #ifndef __DCDDUMPWRITER_H__

diff --git a/hoomd/DomainDecomposition.cc b/hoomd/DomainDecomposition.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file DomainDecomposition.cc

diff --git a/hoomd/DomainDecomposition.h b/hoomd/DomainDecomposition.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file DomainDecomposition.h

diff --git a/hoomd/ExecutionConfiguration.cc b/hoomd/ExecutionConfiguration.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "ExecutionConfiguration.h"

diff --git a/hoomd/ExecutionConfiguration.h b/hoomd/ExecutionConfiguration.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #ifndef __EXECUTION_CONFIGURATION__

diff --git a/hoomd/Filesystem.h b/hoomd/Filesystem.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file Filesystem.h

diff --git a/hoomd/ForceCompute.cc b/hoomd/ForceCompute.cc
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 /*! \file ForceCompute.cc

diff --git a/hoomd/ForceCompute.h b/hoomd/ForceCompute.h
@@ -1,4 +1,4 @@
-// Copyright (c) 2009-2024 The Regents of the University of Michigan.
+// Copyright (c) 2009-2025 The Regents of the University of Michigan.
 // Part of HOOMD-blue, released under the BSD 3-Clause License.
 
 #include "Compute.h"