Merge pull request #1783 from glotzerlab/release-4.7.0

Release 4.7.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.6.0
+current_version = 4.7.0
 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: 4.6.0
+      placeholder: 4.7.0
     validations:
       required: true
   - type: markdown

.github/ISSUE_TEMPLATE/release.md

@@ -1,7 +1,7 @@
 ---
 name: Release checklist
 about: '[for maintainer use]'
-title: 'Release 4.6.0'
+title: 'Release 4.7.0'
 labels: ''
 assignees: 'joaander'
 

.github/workflows/release.yml

@@ -40,7 +40,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4.1.4
         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/upload-artifact@v4.3.1
+        uses: actions/upload-artifact@v4.3.3
         with:
           name: release
           path: |
@@ -84,7 +84,7 @@ jobs:
 
     steps:
       - name: Download artifacts
-        uses: actions/download-artifact@v4.1.4
+        uses: actions/download-artifact@v4.1.7
         with:
           name: release
 

.github/workflows/templates/release.yml

@@ -27,7 +27,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4.1.4
         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/upload-artifact@v4.3.1
+        uses: actions/upload-artifact@v4.3.3
         with:
           name: release
           path: |
@@ -71,7 +71,7 @@ jobs:
 
     steps:
       - name: Download artifacts
-        uses: actions/download-artifact@v4.1.4
+        uses: actions/download-artifact@v4.1.7
         with:
           name: release
 

.github/workflows/templates/test.yml

@@ -107,29 +107,29 @@ 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/upload-artifact@v4.3.1
+      uses: actions/upload-artifact@v4.3.3
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: build.tar
         retention-days: 7
     - name: 'Upload install'
-      uses: actions/upload-artifact@v4.3.1
+      uses: actions/upload-artifact@v4.3.3
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: install.tar
         retention-days: 7
 <% endset %>
 <% set download_build_steps %>
     - name: Download build
-      uses: actions/download-artifact@v4.1.4
+      uses: actions/download-artifact@v4.1.7
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar build
       run: << tar_command >> -xvf build.tar
 <% endset %>
 <% set download_install_steps %>
     - name: Download install
-      uses: actions/download-artifact@v4.1.4
+      uses: actions/download-artifact@v4.1.7
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar install
@@ -183,7 +183,7 @@ env:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.4
       with:
         path: code
         submodules: true
@@ -211,7 +211,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Use jetstream2-admin/start
-      uses: glotzerlab/jetstream2-admin/start@v1.2.4
+      uses: glotzerlab/jetstream2-admin/start@v1.2.5
       with:
         OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }}
         OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}

.github/workflows/test.yml

@@ -52,7 +52,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Use jetstream2-admin/start
-      uses: glotzerlab/jetstream2-admin/start@v1.2.4
+      uses: glotzerlab/jetstream2-admin/start@v1.2.5
       with:
         OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }}
         OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}
@@ -84,7 +84,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.4
       with:
         path: code
         submodules: true
@@ -145,13 +145,13 @@ jobs:
     # Upload the tarballs. Retain the file for a limited time in case developers need to download
     # and run tests locally for further debugging.
     - name: 'Upload build'
-      uses: actions/upload-artifact@v4.3.1
+      uses: actions/upload-artifact@v4.3.3
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: build.tar
         retention-days: 7
     - name: 'Upload install'
-      uses: actions/upload-artifact@v4.3.1
+      uses: actions/upload-artifact@v4.3.3
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: install.tar
@@ -190,13 +190,13 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.4
       with:
         path: code
         submodules: true
 
     - name: Download install
-      uses: actions/download-artifact@v4.1.4
+      uses: actions/download-artifact@v4.1.7
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar install
@@ -251,13 +251,13 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.4
       with:
         path: code
         submodules: true
 
     - name: Download build
-      uses: actions/download-artifact@v4.1.4
+      uses: actions/download-artifact@v4.1.7
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar build
@@ -301,13 +301,13 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.4
       with:
         path: code
         submodules: true
 
     - name: Download install
-      uses: actions/download-artifact@v4.1.4
+      uses: actions/download-artifact@v4.1.7
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar install
@@ -364,7 +364,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.4
       with:
         path: code
         submodules: true
@@ -425,13 +425,13 @@ 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/upload-artifact@v4.3.1
+      uses: actions/upload-artifact@v4.3.3
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: build.tar
         retention-days: 7
     - name: 'Upload install'
-      uses: actions/upload-artifact@v4.3.1
+      uses: actions/upload-artifact@v4.3.3
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: install.tar
@@ -479,13 +479,13 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.4
       with:
         path: code
         submodules: true
 
     - name: Download install
-      uses: actions/download-artifact@v4.1.4
+      uses: actions/download-artifact@v4.1.7
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar install
@@ -549,13 +549,13 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.4
       with:
         path: code
         submodules: true
 
     - name: Download build
-      uses: actions/download-artifact@v4.1.4
+      uses: actions/download-artifact@v4.1.7
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar build

.mailmap

@@ -180,3 +180,4 @@ Simone Ciarella <s.ciarella@tue.nl> Ciarella, S <s.ciarella@tue.nl>
 Simone Ciarella <s.ciarella@tue.nl> SCiarella <simoneciarella@gmail.com>
 Simone Ciarella <s.ciarella@tue.nl> SCiarella <58949181+SCiarella@users.noreply.github.com>
 Kieran Nehil-Puleo <nehilkieran@gmail.com> kierannp <nehilkieran@gmail.com>
+Cristina Butu <icb2114@columbia.edu> crisbutu <129013261+crisbutu@users.noreply.github.com>

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-4.6.0.tar.gz`_.
+Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.7.0.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-4.6.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.6.0/hoomd-4.6.0.tar.gz
+.. _Download hoomd-4.7.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.7.0/hoomd-4.7.0.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

@@ -7,6 +7,37 @@ Change Log
 4.x
 ---
 
+4.7.0 (2024-05-16)
+^^^^^^^^^^^^^^^^^^
+
+*Fixed*
+
+* ``md.methods.rattle.Brownian`` executes without causing a segmentation fault on the CPU with domain
+  decomposition (`#1748 <https://github.com/glotzerlab/hoomd-blue/pull/1748>`__).
+* Compile ``BoxDim.h`` without warnings
+  (`#1756 <https://github.com/glotzerlab/hoomd-blue/pull/1756>`__).
+* Do not compute dipole-dipole interactions that are not necessary
+  (`#1758 <https://github.com/glotzerlab/hoomd-blue/pull/1758>`__).
+* Correctly define the units of gamma in ``md.methods.Langevin``
+  (`#1771 <https://github.com/glotzerlab/hoomd-blue/pull/1771>`__).
+* Fix compile errors with external components that use the Expanded Mie potential
+  (`#1781 <https://github.com/glotzerlab/hoomd-blue/pull/1781>`__).
+* Allow HPMC pair potentials to be subclassed in external components
+  (`#1780 <https://github.com/glotzerlab/hoomd-blue/pull/1780>`__).
+
+*Added*
+
+* "How to tune move sizes in multicomponent HPMC systems" documentation page
+  (`#1750 <https://github.com/glotzerlab/hoomd-blue/pull/1750>`__).
+* ``hoomd.box.from_basis_vectors`` - construct a box from arbitrary basis vectors
+  (`#1769 <https://github.com/glotzerlab/hoomd-blue/pull/1769>`__).
+
+*Changed*
+
+* Make readthedocs builds more reproducible
+  (`#1758 <https://github.com/glotzerlab/hoomd-blue/pull/1758>`__).
+
+
 4.6.0 (2024-03-19)
 ^^^^^^^^^^^^^^^^^^
 

CMakeLists.txt

@@ -18,7 +18,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "4.6.0")
+set(HOOMD_VERSION_RAW "4.7.0")
 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=4.6.0
+    $ conda install hoomd=4.7.0
 
 ``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=4.6.0=*gpu*" "cuda-version=12.0"
+    $ conda install "hoomd=4.7.0=*gpu*" "cuda-version=12.0"
 
 Similarly, you can force CPU only package installation with::
 
-    $ conda install "hoomd=4.6.0=*cpu*"
+    $ conda install "hoomd=4.7.0=*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/\
-            v4.6.0/hoomd/VectorMath.h
+            v4.7.0/hoomd/VectorMath.h
     .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.6.0/hoomd/BoxDim.h
+            v4.7.0/hoomd/BoxDim.h
 
     .. rubric:: Example:
 

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/\
-            v4.6.0/hoomd/VectorMath.h
+            v4.7.0/hoomd/VectorMath.h
 
     Note:
         Your code *must* return a value.
@@ -343,7 +343,7 @@ class CPPPotentialUnion(CPPPotentialBase):
 
     CPPPotentialUnion uses threaded execution on multiple CPU cores.
 
-    .. deprecated:: 4.6.0
+    .. deprecated:: 4.7.0
 
         ``num_cpu_threads >= 1`` is deprecated. Set ``num_cpu_threads = 1``.