Merge pull request #1623 from glotzerlab/release-4.2.0

Release HOOMD-blue 4.2.0
glotzerlab · Sep 20, 2023 · 4184da2 · 4184da2
2 parents dfc4bef + 5ffc65b
commit 4184da2
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.1.0
+current_version = 4.2.0
 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: 4.1.0
+      placeholder: 4.2.0
     validations:
       required: true
   - type: markdown

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -40,7 +40,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3.5.3
+        uses: actions/checkout@v4.0.0
         with:
           fetch-depth: 0
           submodules: true
@@ -70,7 +70,7 @@ jobs:
         run: tar -cvzf ${name}-${tag:1}.tar.gz ${name}-${tag:1}
 
       - name: Upload release files
-        uses: actions/[email protected].2
+        uses: actions/[email protected].3
         with:
           name: release
           path: |

diff --git a/.github/workflows/templates/release.yml b/.github/workflows/templates/release.yml
@@ -27,7 +27,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3.5.3
+        uses: actions/checkout@v4.0.0
         with:
           fetch-depth: 0
           submodules: true
@@ -57,7 +57,7 @@ jobs:
         run: tar -cvzf ${name}-${tag:1}.tar.gz ${name}-${tag:1}
 
       - name: Upload release files
-        uses: actions/[email protected].2
+        uses: actions/[email protected].3
         with:
           name: release
           path: |

diff --git a/.github/workflows/templates/test.yml b/.github/workflows/templates/test.yml
@@ -105,13 +105,13 @@ env:
     # Upload the tarballs. Retain the file for a limited time in case developers need to download
     # and run tests locally for further debugging.
     - name: 'Upload build'
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: build.tar
         retention-days: 7
     - name: 'Upload install'
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: install.tar
@@ -181,7 +181,7 @@ env:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v3.5.3
+      uses: actions/checkout@v4.0.0
       with:
         path: code
         submodules: true

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -82,7 +82,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v3.5.3
+      uses: actions/checkout@v4.0.0
       with:
         path: code
         submodules: true
@@ -143,13 +143,13 @@ jobs:
     # Upload the tarballs. Retain the file for a limited time in case developers need to download
     # and run tests locally for further debugging.
     - name: 'Upload build'
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: build.tar
         retention-days: 7
     - name: 'Upload install'
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: install.tar
@@ -188,7 +188,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v3.5.3
+      uses: actions/checkout@v4.0.0
       with:
         path: code
         submodules: true
@@ -249,7 +249,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v3.5.3
+      uses: actions/checkout@v4.0.0
       with:
         path: code
         submodules: true
@@ -299,7 +299,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v3.5.3
+      uses: actions/checkout@v4.0.0
       with:
         path: code
         submodules: true
@@ -361,7 +361,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v3.5.3
+      uses: actions/checkout@v4.0.0
       with:
         path: code
         submodules: true
@@ -422,13 +422,13 @@ jobs:
     # Upload the tarballs. Retain the file for a limited time in case developers need to download
     # and run tests locally for further debugging.
     - name: 'Upload build'
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: build.tar
         retention-days: 7
     - name: 'Upload install'
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: install.tar
@@ -475,7 +475,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v3.5.3
+      uses: actions/checkout@v4.0.0
       with:
         path: code
         submodules: true
@@ -544,7 +544,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v3.5.3
+      uses: actions/checkout@v4.0.0
       with:
         path: code
         submodules: true

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-4.1.0.tar.gz`_.
+Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.2.0.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-4.1.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.1.0/hoomd-4.1.0.tar.gz
+.. _Download hoomd-4.2.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.2.0/hoomd-4.2.0.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
@@ -6,6 +6,51 @@ Change Log
 
 4.x
 ---
+4.2.0 (2024-09-20)
+^^^^^^^^^^^^^^^^^^
+
+*Fixed*
+
+* Make ``HDF5Log`` example more visible
+  (`#1602 <https://github.com/glotzerlab/hoomd-blue/pull/1602>`__).
+* Access valid GPU memory in ``hoomd.hpmc.update.Clusters``
+  (`#1607 <https://github.com/glotzerlab/hoomd-blue/pull/1607>`__).
+* Test suite passes on the ROCm GPU platform
+  (`#1607 <https://github.com/glotzerlab/hoomd-blue/pull/1607>`__).
+* Provide an error message when using ``md.external.field.Periodic`` in 2D
+  (`#1603 <https://github.com/glotzerlab/hoomd-blue/pull/1603>`__).
+* ``hoomd.write.GSD`` reports "File exists" in the exception description when using the ``'xb'``
+  mode and the file exists (`#1609 <https://github.com/glotzerlab/hoomd-blue/pull/1609>`__).
+* Write small numbers correctly in ``hoomd.write.Table``
+  (`#1617 <https://github.com/glotzerlab/hoomd-blue/pull/1617>`__).
+* Make examples in ``hoomd.md.methods.NVE`` and ``hoomd.md.methods.DisplacementCapped`` more visible
+  (`#1601 <https://github.com/glotzerlab/hoomd-blue/pull/1601>`__).
+
+*Added*
+
+* Documentation page: "How to apply arbitrary forces in MD"
+  (`#1610 <https://github.com/glotzerlab/hoomd-blue/pull/1610>`__).
+* Documentation page: "How to prevent particles from moving"
+  (`#1611 <https://github.com/glotzerlab/hoomd-blue/pull/1611>`__).
+* Documentation page: "How to minimize the potential energy of a system"
+  (`#1614 <https://github.com/glotzerlab/hoomd-blue/pull/1614>`__).
+* Documentation page: "How to continuously vary potential parameters"
+  (`#1612 <https://github.com/glotzerlab/hoomd-blue/pull/1612>`__).
+* Documentation page: "How to determine the most efficient device"
+  (`#1616 <https://github.com/glotzerlab/hoomd-blue/pull/1616>`__).
+* Documentation page: "How to choose the neighbor list buffer distance"
+  (`#1615 <https://github.com/glotzerlab/hoomd-blue/pull/1615>`__).
+* Documentation page: "How to compute the free energy of solids"
+  (`#1613 <https://github.com/glotzerlab/hoomd-blue/pull/1613>`__).
+* MPCD particle data is now available included in ``Snapshot``
+  (`#1580 <https://github.com/glotzerlab/hoomd-blue/pull/1580>`__).
+* Add variable parameters to ``hpmc.external.user.CPPExternalPotential``
+  (`#1608 <https://github.com/glotzerlab/hoomd-blue/pull/1608>`__).
+
+*Changed*
+
+* Removed the unused ``ExternalFieldComposite.h`` and all the related ``ExternalFieldComposite*``
+  (`#1604 <https://github.com/glotzerlab/hoomd-blue/pull/1604>`__).
 
 4.1.0 (2024-08-07)
 ^^^^^^^^^^^^^^^^^^

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -14,7 +14,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "4.1.0")
+set(HOOMD_VERSION_RAW "4.2.0")
 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
@@ -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=4.1.0
+    $ conda install hoomd=4.2.0
 
 ``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=4.1.0=*gpu*" "cuda-version=12.0"
+    $ conda install "hoomd=4.2.0=*gpu*" "cuda-version=12.0"
 
 Similarly, you can force CPU only package installation with::
 
-    $ conda install "hoomd=4.1.0=*cpu*"
+    $ conda install "hoomd=4.2.0=*cpu*"
 
 .. note::
 

diff --git a/hoomd/hpmc/external/user.py b/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/\
-            v4.1.0/hoomd/VectorMath.h
+            v4.2.0/hoomd/VectorMath.h
     .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.1.0/hoomd/BoxDim.h
+            v4.2.0/hoomd/BoxDim.h
 
     .. rubric:: Example:
 

diff --git a/hoomd/hpmc/pair/user.py b/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/\
-            v4.1.0/hoomd/VectorMath.h
+            v4.2.0/hoomd/VectorMath.h
 
     Note:
         Your code *must* return a value.

diff --git a/sphinx-doc/conf.py b/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 = '4.1.0'
-release = '4.1.0'
+version = '4.2.0'
+release = '4.2.0'
 
 language = 'en'
 

diff --git a/sphinx-doc/tutorial b/sphinx-doc/tutorial
+2 −2		.github/workflows/test.yml
+1 −0		.gitignore
+5 −5		00-Introducing-HOOMD-blue/01-The-Simulation-Object.ipynb
+2 −2		00-Introducing-HOOMD-blue/02-Performing-Hard-Particle-Monte-Carlo-Simulations.ipynb
+2 −2		00-Introducing-HOOMD-blue/03-Initializing-the-System-State.ipynb
+7 −7		00-Introducing-HOOMD-blue/04-Randomizing-the-System.ipynb
+17 −15		00-Introducing-HOOMD-blue/05-Compressing-the-System.ipynb
+10 −10		00-Introducing-HOOMD-blue/06-Equilibrating-the-System.ipynb
+10 −10		01-Introducing-Molecular-Dynamics/02-Initializing-a-Random-System.ipynb
+18 −18		01-Introducing-Molecular-Dynamics/03-Compressing-the-System.ipynb
+3 −3		02-Logging/00-index.ipynb
+464 −283		02-Logging/01-Logging-to-a-file.ipynb
+486 −492		02-Logging/02-Saving-Array-Quantities.ipynb
+6 −6		02-Logging/03-Storing-Particle-Shape.ipynb
+14 −13		02-Logging/04-Writing-Formatted-Output.ipynb
+4 −4		03-Parallel-Simulations-With-MPI/00-index.ipynb
+2 −2		03-Parallel-Simulations-With-MPI/01-Introduction-to-MPI.ipynb
+2 −2		03-Parallel-Simulations-With-MPI/02-Domain-Decomposition.ipynb
+5 −5		03-Parallel-Simulations-With-MPI/domain_decomposition.py
+3 −3		03-Parallel-Simulations-With-MPI/global_snapshot.py
+4 −4		03-Parallel-Simulations-With-MPI/lj_domain_error.py
+5 −5		03-Parallel-Simulations-With-MPI/lj_kinetic_energy.py
+6 −6		03-Parallel-Simulations-With-MPI/lj_partition.py
+6 −6		03-Parallel-Simulations-With-MPI/lj_performance.py
+5 −5		03-Parallel-Simulations-With-MPI/lj_trajectory.py
+3 −3		03-Parallel-Simulations-With-MPI/local_snapshot.py
+4 −4		04-Custom-Actions-In-Python/02-An-Initial-Custom-Action.ipynb
+7 −7		04-Custom-Actions-In-Python/03-Custom-Action-Features.ipynb
+11 −11		04-Custom-Actions-In-Python/04-Custom-Updater.ipynb
+12 −11		04-Custom-Actions-In-Python/05-Custom-Writer.ipynb
+10 −10		04-Custom-Actions-In-Python/06-Improving-Performance.ipynb
+17 −17		05-Organizing-and-Executing-Simulations/02-Executing-Simulations.ipynb
+38 −36		05-Organizing-and-Executing-Simulations/03-Continuing-Simulations.ipynb
+2 −2		05-Organizing-and-Executing-Simulations/04-Submitting-Cluster-Jobs.ipynb
+35 −34		05-Organizing-and-Executing-Simulations/project.py
+35 −34		05-Organizing-and-Executing-Simulations/project_partitioned.py
+16 −16		06-Modelling-Rigid-Bodies/01-Introduction-to-Rigid-Bodies.ipynb
+14 −13		06-Modelling-Rigid-Bodies/02-Running-Rigid-Body-Simulations.ipynb
+8 −8		07-Modelling-Patchy-Particles/02-Simulating-a-System-of-Patchy-Particles.ipynb