Merge pull request #1747 from glotzerlab/release-4.6.0

Release 4.6.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.5.0
+current_version = 4.6.0
 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: 4.5.0
+      placeholder: 4.6.0
     validations:
       required: true
   - type: markdown

.github/ISSUE_TEMPLATE/release.md

@@ -1,7 +1,7 @@
 ---
 name: Release checklist
 about: '[for maintainer use]'
-title: 'Release 4.5.0'
+title: 'Release 4.6.0'
 labels: ''
 assignees: 'joaander'
 
@@ -16,6 +16,7 @@ Minor and major releases:
 - [ ] Check for new or duplicate contributors since the last release:
   `comm -13 (git log $(git describe --tags --abbrev=0) --format="%aN <%aE>" | sort | uniq | psub) (git log --format="%aN <%aE>" | sort | uniq | psub)`.
   Add entries to `.mailmap` to remove duplicates.
+- [ ] Ensure that added features have Sybil examples.
 - [ ] Run [hoomd-benchmarks](https://github.com/glotzerlab/hoomd-benchmarks), check for performance
   regressions with the previous release, and post the tables in the release pull request.
 - [ ] Run [hoomd-validation](https://github.com/glotzerlab/hoomd-validation).

.github/workflows/release.yml

@@ -84,12 +84,12 @@ jobs:
 
     steps:
       - name: Download artifacts
-        uses: actions/[email protected].2
+        uses: actions/[email protected].4
         with:
           name: release
 
       - name: Create release
-        uses: softprops/action-gh-release@v0.1.15
+        uses: softprops/action-gh-release@v2.0.2
         if: startsWith(github.ref, 'refs/tags/v')
         with:
           files: "*.tar.gz"

.github/workflows/templates/release.yml

@@ -71,12 +71,12 @@ jobs:
 
     steps:
       - name: Download artifacts
-        uses: actions/[email protected].2
+        uses: actions/[email protected].4
         with:
           name: release
 
       - name: Create release
-        uses: softprops/action-gh-release@v0.1.15
+        uses: softprops/action-gh-release@v2.0.2
         if: startsWith(github.ref, 'refs/tags/v')
         with:
           files: "*.tar.gz"

.github/workflows/templates/test.yml

@@ -121,15 +121,15 @@ env:
 <% endset %>
 <% set download_build_steps %>
     - name: Download build
-      uses: actions/[email protected].2
+      uses: actions/[email protected].4
       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/[email protected].2
+      uses: actions/[email protected].4
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar install

.github/workflows/test.yml

@@ -196,7 +196,7 @@ jobs:
         submodules: true
 
     - name: Download install
-      uses: actions/[email protected].2
+      uses: actions/[email protected].4
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar install
@@ -257,7 +257,7 @@ jobs:
         submodules: true
 
     - name: Download build
-      uses: actions/[email protected].2
+      uses: actions/[email protected].4
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar build
@@ -307,7 +307,7 @@ jobs:
         submodules: true
 
     - name: Download install
-      uses: actions/[email protected].2
+      uses: actions/[email protected].4
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar install
@@ -485,7 +485,7 @@ jobs:
         submodules: true
 
     - name: Download install
-      uses: actions/[email protected].2
+      uses: actions/[email protected].4
       with:
         name: install-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar install
@@ -555,7 +555,7 @@ jobs:
         submodules: true
 
     - name: Download build
-      uses: actions/[email protected].2
+      uses: actions/[email protected].4
       with:
         name: build-${{ join(matrix.config, '_') }}-${{ github.sha }}
     - name: Untar build

.ignore

@@ -1 +1,2 @@
+!.github
 hoomd/extern

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-4.5.0.tar.gz`_.
+Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.6.0.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-4.5.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.5.0/hoomd-4.5.0.tar.gz
+.. _Download hoomd-4.6.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.6.0/hoomd-4.6.0.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 +7,49 @@ Change Log
 4.x
 ---
 
+4.6.0 (2024-03-19)
+^^^^^^^^^^^^^^^^^^
+
+*Fixed*
+
+* ``create_state_from_gsd`` reads bond/angle/dihedral/improper/pair types when there are no
+  corresponding groups (`#1729 <https://github.com/glotzerlab/hoomd-blue/pull/1729>`__).
+
+*Added*
+
+* ``hoomd.variant.box.BoxVariant`` - Describe boxes that change as a function of timestep
+  (`#1685 <https://github.com/glotzerlab/hoomd-blue/pull/1685>`__).
+* ``hoomd.variant.box.Constant`` - A constant box
+  (`#1685 <https://github.com/glotzerlab/hoomd-blue/pull/1685>`__).
+* ``hoomd.variant.box.Interpolate`` - Linearly interpolate between two boxes
+  (`#1685 <https://github.com/glotzerlab/hoomd-blue/pull/1685>`__).
+* ``hoomd.variant.box.InverseVolumeRamp`` - Linearly ramp the inverse volume of the system
+  (`#1685 <https://github.com/glotzerlab/hoomd-blue/pull/1685>`__).
+* ``hoomd.hpmc.update.QuickCompress`` now accepts a ``hoomd.variant.box.BoxVariant`` object for
+  `target_box` (`#1736 <https://github.com/glotzerlab/hoomd-blue/pull/1736>`__).
+* ``box`` argument to ``hoomd.update.BoxResize`` that accepts a ``hoomd.variant.box.BoxVariant``
+  (`#1740 <https://github.com/glotzerlab/hoomd-blue/pull/1740>`__).
+* ``hoomd.hpmc.pair.Union`` computes pair potentials between unions of points. Replaces
+  ``CPPPotentialUnion`` (`#1725 <https://github.com/glotzerlab/hoomd-blue/pull/1725>`__).
+* ``hoomd.hpmc.pair.Step`` - A step function potential
+  (`#1732 <https://github.com/glotzerlab/hoomd-blue/pull/1732>`__).
+* ``hoomd.hpmc.pair.AngularStep`` - Angular patches on particles with step function interactions
+  (e.g. Kern-Frenkel) (`#1728 <https://github.com/glotzerlab/hoomd-blue/pull/1728>`__).
+
+*Changed*
+
+* Use ``FindPython`` on modern CMake installations. You may need to adjust build scripts
+  in cases where the new behavior does not exactly match the old (i.e. use
+  ``-DPython_EXECUTABLE`` in place of ``-DPYTHON_EXECUTABLE``)
+  (`#1730 <https://github.com/glotzerlab/hoomd-blue/pull/1730>`__).
+* External components must switch from ``pybind11_add_module`` to ``hoomd_add_module``
+  (`#1730 <https://github.com/glotzerlab/hoomd-blue/pull/1730>`__).
+
+*Deprecated*
+
+* ``box1``, ``box2``, and ``variant`` arguments to ``hoomd.update.BoxResize``
+  (`#1740 <https://github.com/glotzerlab/hoomd-blue/pull/1740>`__).
+
 4.5.0 (2024-02-13)
 ^^^^^^^^^^^^^^^^^^
 

CMakeLists.txt

@@ -18,7 +18,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "4.5.0")
+set(HOOMD_VERSION_RAW "4.6.0")
 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=4.5.0
+    $ conda install hoomd=4.6.0
 
 ``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=4.5.0=*gpu*" "cuda-version=12.0"
+    $ conda install "hoomd=4.6.0=*gpu*" "cuda-version=12.0"
 
 Similarly, you can force CPU only package installation with::
 
-    $ conda install "hoomd=4.5.0=*cpu*"
+    $ conda install "hoomd=4.6.0=*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/\
-            v4.5.0/hoomd/VectorMath.h
+            v4.6.0/hoomd/VectorMath.h
     .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.5.0/hoomd/BoxDim.h
+            v4.6.0/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/\
-            v4.5.0/hoomd/VectorMath.h
+            v4.6.0/hoomd/VectorMath.h
 
     Note:
         Your code *must* return a value.
@@ -245,7 +245,7 @@ def __init__(self, r_cut, code, param_array):
         self.code = code
 
         warnings.warn(
-            "CPPPotential is deprecated since 4.5.0. "
+            "CPPPotential is deprecated since 4.6.0. "
             "Use a hpmc.pair.Pair potential.",
             FutureWarning,
             stacklevel=2)
@@ -343,7 +343,7 @@ class CPPPotentialUnion(CPPPotentialBase):
 
     CPPPotentialUnion uses threaded execution on multiple CPU cores.
 
-    .. deprecated:: 4.5.0
+    .. deprecated:: 4.6.0
 
         ``num_cpu_threads >= 1`` is deprecated. Set ``num_cpu_threads = 1``.
 
@@ -528,7 +528,7 @@ def __init__(self, r_cut_constituent, code_constituent, r_cut_isotropic,
         self.code_isotropic = code_isotropic
 
         warnings.warn(
-            "CPPPotentialUnion is deprecated since 4.5.0. "
+            "CPPPotentialUnion is deprecated since 4.6.0. "
             "Use a hpmc.pair.Pair potential.",
             FutureWarning,
             stacklevel=2)
@@ -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 4.5.0. "
+                "num_cpu_threads > 1 is deprecated since 4.6.0. "
                 "Use num_cpu_threads=1.",
                 FutureWarning,
                 stacklevel=1)

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 = '4.5.0'
-release = '4.5.0'
+version = '4.6.0'
+release = '4.6.0'
 
 language = 'en'