Merge pull request #1917 from glotzerlab/release-4.9.0

joaander · web-flow · commit e93861af1dfe · 2024-10-29T15:44:36.000-04:00
Release 4.9.0
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.8.2
+current_version = 4.9.0
 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
@@ -60,7 +60,7 @@ body:
     attributes:
       label: HOOMD-blue version
       description: What version of HOOMD-blue are you using?
-      placeholder: 4.8.2
+      placeholder: 4.9.0
     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 4.8.2'
+title: 'Release 4.9.0'
 labels: ''
 assignees: 'joaander'
 
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -21,15 +21,9 @@ Resolves #???
 <!--- Please build the sphinx documentation and check that any changes to
       documentation display properly. -->
 
-## Change log
-
-<!-- Propose a change log entry. -->
-```
-
-```
-
 ## Checklist:
 
 - [ ] I have reviewed the [**Contributor Guidelines**](https://github.com/glotzerlab/hoomd-blue/blob/trunk-minor/CONTRIBUTING.rst).
 - [ ] I agree with the terms of the [**HOOMD-blue Contributor Agreement**](https://github.com/glotzerlab/hoomd-blue/blob/trunk-minor/ContributorAgreement.md).
 - [ ] My name is on the list of contributors (`sphinx-doc/credits.rst`) in the pull request source branch.
+- [ ] I have summarized these changes in `CHANGELOG.rst` following the established format.
diff --git a/.mailmap b/.mailmap
@@ -2,6 +2,7 @@
 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>
+Joshua A. Anderson <joaander@umich.edu> joaander <2197568+joaander@users.noreply.github.com>
 Jens Glaser <glaserj@ornl.gov> Jens Glaser <jsglaser@umich.edu>
 Jens Glaser <glaserj@ornl.gov> Jens Glaser <jglaser@umn.edu>
 Jens Glaser <glaserj@ornl.gov> Jens Glaser <jglaser@kidlogin2.nics.utk.edu>
@@ -183,3 +184,5 @@ Kieran Nehil-Puleo <nehilkieran@gmail.com> kierannp <nehilkieran@gmail.com>
 Cristina Butu <icb2114@columbia.edu> crisbutu <129013261+crisbutu@users.noreply.github.com>
 Joseph Burkhart <joaburkh@umich.edu> josephburkhart <joaburkh@umich.edu>
 Joseph Burkhart <joaburkh@umich.edu> Joseph Burkhart <61951318+josephburkhart@users.noreply.github.com>
+Calvin Condon <chcondon@umich.edu> Calvin Condon <145710053+chcondon@users.noreply.github.com>
+baho-cb <bargun2@illinois.edu> baho-cb <72244147+baho-cb@users.noreply.github.com>
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -19,7 +19,7 @@ Change Log
   ``hoomd.md.pair.aniso.PatchyGaussian``, ``hoomd.md.pair.aniso.PatchyLJ``,
   ``hoomd.md.pair.aniso.PatchyMie``, and ``hoomd.md.pair.aniso.PatchyYukawa``
   (`#1412 <https://github.com/glotzerlab/hoomd-blue/pull/1412>`__).
-* ``hoomd.hpmc.pair.LJGauss`` and ``hoomd.hpmc.pair.OPP``
+* Double-well potentials in HPMC: ``hoomd.hpmc.pair.LJGauss`` and ``hoomd.hpmc.pair.OPP``
   (`#1889 <https://github.com/glotzerlab/hoomd-blue/pull/1889>`__).
 * Mesh potentials: ``hoomd.md.mesh.bending.BendingRigidity``, ``hoomd.md.mesh.bending.Helfrich``,
   ``hoomd.md.mesh.conservation.Area``, ``hoomd.md.mesh.conservation.TriangleArea``, and
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -16,7 +16,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "4.8.2")
+set(HOOMD_VERSION_RAW "4.9.0")
 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/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -107,4 +107,4 @@ contributed to the code.
 Propose a change log entry
 __________________________
 
-Propose a short concise entry describing the change in the pull request description.
+Propose a concise entry describing the change in ``CHANGELOG.rst``.
diff --git a/INSTALLING.rst b/INSTALLING.rst
@@ -22,7 +22,7 @@ channel:
 
 .. code-block:: bash
 
-    micromamba install hoomd=4.8.2
+    micromamba install hoomd=4.9.0
 
 .. _conda-forge: https://conda-forge.org/docs/user/introduction.html
 
@@ -32,13 +32,13 @@ appropriate package. Override this and force the GPU enabled package installatio
 .. code-block:: bash
 
     export CONDA_OVERRIDE_CUDA="12.0"
-    micromamba install "hoomd=4.8.2=*gpu*" "cuda-version=12.0"
+    micromamba install "hoomd=4.9.0=*gpu*" "cuda-version=12.0"
 
 Similarly, you can force CPU-only package installation with:
 
 .. code-block:: bash
 
-    micromamba install "hoomd=4.8.2=*cpu*"
+    micromamba install "hoomd=4.9.0=*cpu*"
 
 .. note::
 
diff --git a/hoomd/hpmc/external/user.py b/hoomd/hpmc/external/user.py
@@ -85,9 +85,9 @@ class CPPExternalPotential(ExternalField):
         Your code *must* return a value.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.8.2/hoomd/VectorMath.h
+            v4.9.0/hoomd/VectorMath.h
     .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.8.2/hoomd/BoxDim.h
+            v4.9.0/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/\
-            v4.8.2/hoomd/VectorMath.h
+            v4.9.0/hoomd/VectorMath.h
 
     Note:
         Your code *must* return a value.
diff --git a/hoomd/md/mesh/bending.py b/hoomd/md/mesh/bending.py
@@ -17,6 +17,13 @@
 See Also:
    See the documentation in `hoomd.mesh.Mesh` for more information on the
    initialization of the mesh object.
+
+.. invisible-code-block: python
+
+    mesh = hoomd.mesh.Mesh()
+    mesh.types = ["mesh"]
+    mesh.triangulation = dict(type_ids = [0,0,0,0],
+          triangles = [[0,1,2],[0,2,3],[0,1,3],[1,2,3]])
 """
 
 from hoomd.md.mesh.potential import MeshPotential
@@ -51,9 +58,11 @@ class BendingRigidity(MeshPotential):
             * ``k`` (`float`, **required**) - bending stiffness
               :math:`[\mathrm{energy}]`
 
-    Examples::
+    .. rubric:: Example:
+
+    .. code-block:: python
 
-        bending_potential = mesh.bond.BendingRigidity(mesh)
+        bending_potential = hoomd.md.mesh.bending.BendingRigidity(mesh)
         bending_potential.params["mesh"] = dict(k=10.0)
     """
     _cpp_class_name = "BendingRigidityMeshForceCompute"
@@ -104,9 +113,13 @@ class Helfrich(MeshPotential):
             * ``k`` (`float`, **required**) - bending stiffness
               :math:`[\mathrm{energy}]`
 
-    Examples::
+    .. rubric:: Example:
+
+    .. skip: next if(hoomd.version.mpi_enabled)
+
+    .. code-block:: python
 
-        helfrich_potential = mesh.bond.Helfrich(mesh)
+        helfrich_potential = hoomd.md.mesh.bending.Helfrich(mesh)
         helfrich_potential.params["mesh"] = dict(k=10.0)
     """
     _cpp_class_name = "HelfrichMeshForceCompute"
diff --git a/hoomd/md/mesh/bond.py b/hoomd/md/mesh/bond.py
@@ -40,6 +40,13 @@
     U_i = \frac{1}{2} \sum_{k \in \mathrm{Neigh}(i)}U_{ik}(r)
 
 and similarly for virials.
+
+.. invisible-code-block: python
+
+    mesh = hoomd.mesh.Mesh()
+    mesh.types = ["mesh"]
+    mesh.triangulation = dict(type_ids = [0,0,0,0],
+          triangles = [[0,1,2],[0,2,3],[0,1,3],[1,2,3]])
 """
 
 from hoomd.md.mesh.potential import MeshPotential
@@ -68,7 +75,9 @@ class Harmonic(MeshPotential):
             * ``r0`` (`float`, **required**) - rest length
               :math:`[\mathrm{length}]`
 
-    Examples::
+    .. rubric:: Example:
+
+    .. code-block:: python
 
         harmonic = hoomd.md.mesh.bond.Harmonic(mesh)
         harmonic.params["mesh"] = dict(k=10.0, r0=1.0)
@@ -113,7 +122,9 @@ class FENEWCA(MeshPotential):
             * ``delta`` (`float`, **required**) - radial shift :math:`\Delta`
               :math:`[\mathrm{length}]`.
 
-    Examples::
+    .. rubric:: Example:
+
+    .. code-block:: python
 
         bond_potential = hoomd.md.mesh.bond.FENEWCA(mesh)
         bond_potential.params["mesh"] = dict(k=10.0, r0=1.0,
@@ -166,7 +177,9 @@ class Tether(MeshPotential):
             * ``l_max`` (`float`, **required**) - maximum bond length
               :math:`[\mathrm{length}]`
 
-    Examples::
+    .. rubric:: Example:
+
+    .. code-block:: python
 
         bond_potential = hoomd.md.mesh.bond.Tether(mesh)
         bond_potential.params["mesh"] = dict(k_b=10.0, l_min=0.9, l_c1=1.2,
diff --git a/hoomd/md/mesh/conservation.py b/hoomd/md/mesh/conservation.py
@@ -15,15 +15,21 @@
    See the documentation in `hoomd.mesh.Mesh` for more information on the
    initialization of the mesh object.
 
+.. invisible-code-block: python
+
+    mesh = hoomd.mesh.Mesh()
+    mesh.types = ["mesh"]
+    mesh.triangulation = dict(type_ids = [0,0,0,0],
+          triangles = [[0,1,2],[0,2,3],[0,1,3],[1,2,3]])
 """
 
-from hoomd.md.mesh.potential import MeshPotential, MeshConvervationPotential
+from hoomd.md.mesh.potential import MeshPotential, MeshConservationPotential
 from hoomd.data.typeparam import TypeParameter
 from hoomd.data.parameterdicts import TypeParameterDict
 from hoomd.logging import log
 
 
-class Area(MeshConvervationPotential):
+class Area(MeshConservationPotential):
     r"""Area conservation potential.
 
     `Area` specifies a global area conservation energy for each
@@ -53,9 +59,11 @@ class Area(MeshConvervationPotential):
             * ``A0`` (`float`, **required**) - targeted global surface area
               :math:`[\mathrm{length}]^2]`
 
-    Examples::
+    .. rubric:: Example:
+
+    .. code-block:: python
 
-        area_conservation_potential = mesh.conservation.Area(mesh)
+        area_conservation_potential = hoomd.md.mesh.conservation.Area(mesh)
         area_conservation_potential.params["mesh"] = dict(k=10.0, A0=250)
     """
     _cpp_class_name = "AreaConservationMeshForceCompute"
@@ -105,9 +113,12 @@ class TriangleArea(MeshPotential):
               of a single triangle in the mesh
               :math:`[\mathrm{length}]^2`
 
-    Examples::
+    .. rubric:: Example:
 
-        tringle_area_conservation_potential = mesh.conservation.TriangleArea(mesh)
+    .. code-block:: python
+
+        tringle_area_conservation_potential = \
+            hoomd.md.mesh.conservation.TriangleArea(mesh)
         tringle_area_conservation_potential.params["mesh"] = dict(k=10.0, A0=250)
     """
     _cpp_class_name = "TriangleAreaConservationMeshForceCompute"
@@ -125,7 +136,7 @@ def area(self):
         return self._cpp_obj.getArea()
 
 
-class Volume(MeshConvervationPotential):
+class Volume(MeshConservationPotential):
     r"""Volume conservation potential.
 
     :py:class:`Volume` specifies a volume constraint on the whole mesh
@@ -152,9 +163,11 @@ class Volume(MeshConvervationPotential):
             * ``V0`` (`float`, **required**) - target volume
               :math:`[\mathrm{length}^{3}]`
 
-    Examples::
+    .. rubric:: Example:
+
+    .. code-block:: python
 
-        volume = mesh.conservation.Volume(mesh)
+        volume = hoomd.md.mesh.conservation.Volume(mesh)
         volume.params["mesh"] = dict(k=10.0, V0=100)
     """
     _cpp_class_name = "VolumeConservationMeshForceCompute"
diff --git a/hoomd/md/mesh/potential.py b/hoomd/md/mesh/potential.py
@@ -72,10 +72,10 @@ def mesh(self, value):
         self._mesh = mesh
 
 
-class MeshConvervationPotential(MeshPotential):
+class MeshConservationPotential(MeshPotential):
     """Constructs the conservation potential applied to a mesh.
 
-    `MeshConvervationPotential` is the base class for global conservation
+    `MeshConservationPotential` is the base class for global conservation
     potentials applied to meshes.
 
     Warning:
diff --git a/hoomd/write/gsd_burst.py b/hoomd/write/gsd_burst.py
@@ -41,7 +41,7 @@ class Burst(GSD):
             when `hoomd.Simulation.run` is called. Defaults to ``False``.
         clear_whole_buffer_after_dump (bool): When ``True`` the buffer is
             emptied after calling `dump` each time. When ``False``, `dump`
-            removes frames from the buffer unil the ``end`` index. Defaults
+            removes frames from the buffer until the ``end`` index. Defaults
             to ``True``.
 
     Warning:
@@ -87,7 +87,7 @@ class Burst(GSD):
 
         clear_whole_buffer_after_dump (bool): When ``True`` the buffer is
             emptied after calling `dump` each time. When ``False``, `dump`
-            removes frames from the buffer unil the ``end`` index.
+            removes frames from the buffer until the ``end`` index.
 
             .. rubric:: Example:
 
diff --git a/sphinx-doc/conf.py b/sphinx-doc/conf.py
@@ -68,8 +68,8 @@
 copyright = f'2009-{year} The Regents of the University of Michigan'
 author = 'The Regents of the University of Michigan'
 
-version = '4.8.2'
-release = '4.8.2'
+version = '4.9.0'
+release = '4.9.0'
 
 language = 'en'
 
diff --git a/sphinx-doc/tutorial b/sphinx-doc/tutorial
@@ -1 +1 @@
-Subproject commit b3d5aa43c7b7fb98cc87b30153cfd777d9fd13c7
+Subproject commit 7a5cf4d38befe8490751af54d96b18961f0ac0ef

-Original file line number
+Diff line change
 Joshua A. Anderson <[email protected]> Joshua Anderson <[email protected]>
 Joshua A. Anderson <[email protected]> joaander <[email protected]>
 Joshua A. Anderson <[email protected]> test <test>
 +Joshua A. Anderson <[email protected]> joaander <[email protected]>
 Jens Glaser <[email protected]> Jens Glaser <[email protected]>
 Jens Glaser <[email protected]> Jens Glaser <[email protected]>
 Jens Glaser <[email protected]> Jens Glaser <[email protected]>
 Cristina Butu <[email protected]> crisbutu <[email protected]>
 Joseph Burkhart <[email protected]> josephburkhart <[email protected]>
 Joseph Burkhart <[email protected]> Joseph Burkhart <[email protected]>
 +Calvin Condon <[email protected]> Calvin Condon <[email protected]>
 +baho-cb <[email protected]> baho-cb <[email protected]>