Merge pull request #1296 from glotzerlab/release-v3.0.1

Release v3.0.1

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.0
+current_version = 3.0.1
 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-]*)))?$

.mailmap

@@ -149,3 +149,4 @@ Fengyi Gao <[email protected]> Fengyi Gao <[email protected]>
 Alain Kadar <[email protected]> AlainKadar <[email protected]>
 Raymond Asare <[email protected]> rayasare <[email protected]>
 Marco Klement <[email protected]> Marco Klement, M.Sc <[email protected]>
+Chris Jones <[email protected]> <[email protected]>

CHANGELOG.rst

@@ -7,6 +7,18 @@ Change Log
 v3.x
 ----
 
+v3.0.1 (2022-04-08)
+^^^^^^^^^^^^^^^^^^^
+
+*Fixed*:
+
+* Display status of ``trunk-patch`` branch in the GitHub actions badge.
+* Add ``EvaluatorPairTable.h`` to installation directory.
+* Add ``hoomd.filter.Rigid`` to the documentation.
+* Prevent ``TypeError: 'bool' object is not iterable`` errors when comparing ``Tag`` filters with
+  different lengths arrays.
+* ``Simulation.tps`` and ``Simulation.walltime`` update every step of the run.
+
 v3.0.0 (2022-03-22)
 ^^^^^^^^^^^^^^^^^^^
 

CMakeLists.txt

@@ -14,7 +14,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "3.0.0")
+set(HOOMD_VERSION_RAW "3.0.1")
 string(REGEX MATCH "(.*)\\.(.*)\\.(.*)$" _hoomd_version_match ${HOOMD_VERSION_RAW})
 set(HOOMD_VERSION_MAJOR ${CMAKE_MATCH_1})
 set(HOOMD_VERSION_MINOR ${CMAKE_MATCH_2})

hoomd/hpmc/external/user.py

@@ -67,9 +67,9 @@ class CPPExternalPotential(ExternalField):
         Your code *must* return a value.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v3.0.0/hoomd/VectorMath.h
+            v3.0.1/hoomd/VectorMath.h
     .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v3.0.0/hoomd/BoxDim.h
+            v3.0.1/hoomd/BoxDim.h
 
     Example:
         .. code-block:: python

hoomd/hpmc/pair/user.py

@@ -76,7 +76,7 @@ class CPPPotentialBase(_HOOMDBaseObject):
                 HOOMD-blue source code.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v3.0.0/hoomd/VectorMath.h
+            v3.0.1/hoomd/VectorMath.h
 
     Note:
         Your code *must* return a value.

hoomd/pytest/test_simulation.py

@@ -1,6 +1,8 @@
 # Copyright (c) 2009-2022 The Regents of the University of Michigan.
 # Part of HOOMD-blue, released under the BSD 3-Clause License.
 
+import time
+
 import hoomd
 import numpy as np
 import pytest
@@ -18,6 +20,16 @@
                               reason="gsd Python package was not found.")
 
 
+class SleepUpdater(hoomd.custom.Action):
+
+    def act(self, timestep):
+        time.sleep(1e-6 * timestep)
+
+    @classmethod
+    def wrapped(cls):
+        return hoomd.update.CustomUpdater(1, cls())
+
+
 def make_gsd_snapshot(hoomd_snapshot):
     s = gsd.hoomd.Snapshot()
     for attr in dir(hoomd_snapshot):
@@ -126,6 +138,7 @@ def test_tps(simulation_factory, two_particle_snapshot_factory):
     sim.operations.writers.append(
         hoomd.write.CustomWriter(action=list_writer,
                                  trigger=hoomd.trigger.Periodic(1)))
+    sim.operations += SleepUpdater.wrapped()
     sim.run(10)
     tps = list_writer.data
     assert len(np.unique(tps)) > 1
@@ -142,9 +155,10 @@ def test_walltime(simulation_factory, two_particle_snapshot_factory):
     sim.operations.writers.append(
         hoomd.write.CustomWriter(action=list_writer,
                                  trigger=hoomd.trigger.Periodic(1)))
+    sim.operations += SleepUpdater.wrapped()
     sim.run(10)
     walltime = list_writer.data
-    assert all(a > b for a, b in zip(walltime[1:], walltime[:-1]))
+    assert all(a >= b for a, b in zip(walltime[1:], walltime[:-1]))
 
 
 def test_timestep(simulation_factory, lattice_snapshot_factory):

sphinx-doc/conf.py

@@ -56,8 +56,8 @@
 copyright = f'2009-{ year } The Regents of the University of Michigan'
 author = 'The Regents of the University of Michigan'
 
-version = '3.0.0'
-release = '3.0.0'
+version = '3.0.1'
+release = '3.0.1'
 
 language = None