Merge branch 'trunk-minor' into trunk-major

glotzerlab · May 16, 2024 · c93e034 · c93e034
2 parents ce65b59 + be621be
commit c93e034
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diff --git a/.bumpversion.cfg b/.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-]*)))?$

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: 4.6.0
+      placeholder: 4.7.0
     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 4.6.0'
+title: 'Release 4.7.0'
 labels: ''
 assignees: 'joaander'
 

diff --git a/.github/dependabot.yaml b/.github/dependabot.yaml
@@ -0,0 +1,29 @@
+version: 2
+updates:
+- package-ecosystem: "pip"
+  directory: "/"
+  target-branch: trunk-patch
+  schedule:
+    interval: "monthly"
+    time: "07:00"
+    timezone: "EST5EDT"
+  pull-request-branch-name:
+    separator: "-"
+  open-pull-requests-limit: 2
+  reviewers:
+  - joaander
+  groups:
+    pip-version:
+      applies-to: version-updates
+      patterns:
+      - '*'
+      update-types:
+      - minor
+      - patch
+    pip-security:
+      applies-to: security-updates
+      patterns:
+      - '*'
+      update-types:
+      - minor
+      - patch
diff --git a/.github/workflows/release.yml b/.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
 

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@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
 

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@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 }}

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@v1.2.4
+      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

diff --git a/.mailmap b/.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>
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -71,15 +71,15 @@ repos:
     - --keep-after=.. include
     - --comment-prefix=..
 - repo: https://github.com/kynan/nbstripout
-  rev: 0.6.1
+  rev: 0.7.1
   hooks:
     - id: nbstripout
 - repo: https://github.com/google/yapf
   rev: 'v0.40.2'
   hooks:
   - id: yapf
 - repo: https://github.com/PyCQA/flake8
-  rev: '6.1.0'
+  rev: '7.0.0'
   hooks:
   - id: flake8
     additional_dependencies:
@@ -97,7 +97,7 @@ repos:
         ^hoomd/metal/
       )
 - repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v17.0.6
+  rev: v18.1.2
   hooks:
   - id: clang-format
     types_or: [c, c++, cuda, inc]

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -11,7 +11,7 @@ sphinx:
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.12"
 
 submodules:
   include: all
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-4.6.0.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/

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -26,6 +26,37 @@ Removed:
 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)
 ^^^^^^^^^^^^^^^^^^