Merge branch 'release-4.5.0' into trunk-minor

glotzerlab · Feb 13, 2024 · 235b8fa · 235b8fa
2 parents 2814777 + 7ce2ac1
commit 235b8fa
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Showing 16 changed files with 42 additions and 37 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.4.1
+current_version = 4.5.0
 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-]*)))?$
@@ -25,3 +25,5 @@ values =
 [bumpversion:file:hoomd/hpmc/external/user.py]
 
 [bumpversion:file:.github/ISSUE_TEMPLATE/bug_report.yml]
+
+[bumpversion:file:.github/ISSUE_TEMPLATE/release.md]
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: 4.4.1
+      placeholder: 4.5.0
     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.x.y'
+title: 'Release 4.5.0'
 labels: ''
 assignees: 'joaander'
 

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -70,7 +70,7 @@ jobs:
         run: tar -cvzf ${name}-${tag:1}.tar.gz ${name}-${tag:1}
 
       - name: Upload release files
-        uses: actions/upload-artifact@v3.1.3
+        uses: actions/upload-artifact@v4.3.1
         with:
           name: release
           path: |
@@ -84,7 +84,7 @@ jobs:
 
     steps:
       - name: Download artifacts
-        uses: actions/download-artifact@v3.0.2
+        uses: actions/download-artifact@v4.1.2
         with:
           name: release
 

diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Run stale action
-      uses: actions/stale@v8.0.0
+      uses: actions/stale@v9.0.0
       with:
         operations-per-run: 120
         delete-branch: true

diff --git a/.github/workflows/templates/release.yml b/.github/workflows/templates/release.yml
@@ -57,7 +57,7 @@ jobs:
         run: tar -cvzf ${name}-${tag:1}.tar.gz ${name}-${tag:1}
 
       - name: Upload release files
-        uses: actions/upload-artifact@v3.1.3
+        uses: actions/upload-artifact@v4.3.1
         with:
           name: release
           path: |
@@ -71,7 +71,7 @@ jobs:
 
     steps:
       - name: Download artifacts
-        uses: actions/download-artifact@v3.0.2
+        uses: actions/download-artifact@v4.1.2
         with:
           name: release
 

diff --git a/.github/workflows/templates/test.yml b/.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@v3.1.3
+      uses: actions/upload-artifact@v4.3.1
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: build.tar
         retention-days: 7
     - name: 'Upload install'
-      uses: actions/upload-artifact@v3.1.3
+      uses: actions/upload-artifact@v4.3.1
       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@v3.0.2
+      uses: actions/download-artifact@v4.1.2
       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@v3.0.2
+      uses: actions/download-artifact@v4.1.2
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar install
@@ -211,7 +211,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Use jetstream2-admin/start
-      uses: glotzerlab/jetstream2-admin/start@v1.2.3
+      uses: glotzerlab/jetstream2-admin/start@v1.2.4
       with:
         OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }}
         OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -52,7 +52,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Use jetstream2-admin/start
-      uses: glotzerlab/jetstream2-admin/start@v1.2.3
+      uses: glotzerlab/jetstream2-admin/start@v1.2.4
       with:
         OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }}
         OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }}
@@ -145,13 +145,13 @@ jobs:
     # Upload the tarballs. Retain the file for a limited time in case developers need to download
     # and run tests locally for further debugging.
     - name: 'Upload build'
-      uses: actions/upload-artifact@v3.1.3
+      uses: actions/upload-artifact@v4.3.1
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: build.tar
         retention-days: 7
     - name: 'Upload install'
-      uses: actions/upload-artifact@v3.1.3
+      uses: actions/upload-artifact@v4.3.1
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: install.tar
@@ -196,7 +196,7 @@ jobs:
         submodules: true
 
     - name: Download install
-      uses: actions/download-artifact@v3.0.2
+      uses: actions/download-artifact@v4.1.2
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar install
@@ -257,7 +257,7 @@ jobs:
         submodules: true
 
     - name: Download build
-      uses: actions/download-artifact@v3.0.2
+      uses: actions/download-artifact@v4.1.2
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar build
@@ -307,7 +307,7 @@ jobs:
         submodules: true
 
     - name: Download install
-      uses: actions/download-artifact@v3.0.2
+      uses: actions/download-artifact@v4.1.2
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar install
@@ -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@v3.1.3
+      uses: actions/upload-artifact@v4.3.1
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: build.tar
         retention-days: 7
     - name: 'Upload install'
-      uses: actions/upload-artifact@v3.1.3
+      uses: actions/upload-artifact@v4.3.1
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
         path: install.tar
@@ -485,7 +485,7 @@ jobs:
         submodules: true
 
     - name: Download install
-      uses: actions/download-artifact@v3.0.2
+      uses: actions/download-artifact@v4.1.2
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar install
@@ -555,7 +555,7 @@ jobs:
         submodules: true
 
     - name: Download build
-      uses: actions/download-artifact@v3.0.2
+      uses: actions/download-artifact@v4.1.2
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar build

diff --git a/.mailmap b/.mailmap
@@ -1,3 +1,4 @@
+
 Joshua A. Anderson <joaander@umich.edu> Joshua Anderson <joaander@umich.edu>
 Joshua A. Anderson <joaander@umich.edu> joaander <joaander@kuhn.engin.umich.edu>
 Joshua A. Anderson <joaander@umich.edu> test <test>
@@ -144,6 +145,7 @@ Sophie YouJung Lee <syjlee@umich.edu> Sophie YJL <syjlee@umich.edu>
 Yuan Zhou <yuanzhou@umich.edu> yuanzhou0827 <46976996+yuanzhou0827@users.noreply.github.com>
 Yuan Zhou <yuanzhou@umich.edu> yuanzhou <yuanzhou@umich.edu>
 Tobias Dwyer <ttdwyer@umich.edu> Tobias-Dwyer <55504950+Tobias-Dwyer@users.noreply.github.com>
+Tobias Dwyer <ttdwyer@umich.edu> Tobias-Dwyer <tobiasdwyer@gmail.com>
 Sophie YouJung Lee <syjlee@umich.edu> SophieYJL <44685431+syjlee@users.noreply.github.com>
 Sophie YouJung Lee <syjlee@umich.edu> Sophie Youjung Lee <syjlee@umich.edu>
 Jakin B. Delony <53496274+jbdelony@users.noreply.github.com> jbdelony <53496274+jbdelony@users.noreply.github.com>
@@ -177,3 +179,4 @@ Alex Lee <shihkual@umich.edu> shihkual <shihkual@umich.edu>
 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>
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-4.4.1.tar.gz`_.
+Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.5.0.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-4.4.1.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.4.1/hoomd-4.4.1.tar.gz
+.. _Download hoomd-4.5.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.5.0/hoomd-4.5.0.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/CMakeLists.txt b/CMakeLists.txt
@@ -14,7 +14,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "4.4.1")
+set(HOOMD_VERSION_RAW "4.5.0")
 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=4.4.1
+    $ conda install hoomd=4.5.0
 
 ``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=4.4.1=*gpu*" "cuda-version=12.0"
+    $ conda install "hoomd=4.5.0=*gpu*" "cuda-version=12.0"
 
 Similarly, you can force CPU only package installation with::
 
-    $ conda install "hoomd=4.4.1=*cpu*"
+    $ conda install "hoomd=4.5.0=*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/\
-            v4.4.1/hoomd/VectorMath.h
+            v4.5.0/hoomd/VectorMath.h
     .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.4.1/hoomd/BoxDim.h
+            v4.5.0/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/\
-            v4.4.1/hoomd/VectorMath.h
+            v4.5.0/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:: 4.4.1
+    .. deprecated:: 4.5.0
 
         ``num_cpu_threads >= 1`` is deprecated. Set ``num_cpu_threads = 1``.
 
@@ -543,7 +543,7 @@ def _attach_hook(self):
         if (isinstance(self._simulation.device, hoomd.device.CPU)
                 and self._simulation.device.num_cpu_threads > 1):
             warnings.warn(
-                "num_cpu_threads > 1 is deprecated since 4.4.1. "
+                "num_cpu_threads > 1 is deprecated since 4.5.0. "
                 "Use num_cpu_threads=1.",
                 FutureWarning,
                 stacklevel=1)

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 = '4.4.1'
-release = '4.4.1'
+version = '4.5.0'
+release = '4.5.0'
 
 language = 'en'
 

diff --git a/sphinx-doc/tutorial b/sphinx-doc/tutorial