From 016df8b0a2bc1807bdb496ff77ac0e17e557e556 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Fri, 8 Apr 2022 07:15:29 -0400 Subject: [PATCH 1/6] v3.0.1 change log. --- CHANGELOG.rst | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 5a269f1b79..a4142a9d00 100644 --- a/CHANGELOG.rst +++ b/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) ^^^^^^^^^^^^^^^^^^^ From a7bce8eba2f4b806c1f52d493db1fdd461670a94 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Fri, 8 Apr 2022 07:18:48 -0400 Subject: [PATCH 2/6] Resolve duplicate contributors in mailmap. --- .mailmap | 1 + 1 file changed, 1 insertion(+) diff --git a/.mailmap b/.mailmap index 7a5fe6acb0..225b330141 100644 --- a/.mailmap +++ b/.mailmap @@ -149,3 +149,4 @@ Fengyi Gao Fengyi Gao Alain Kadar AlainKadar <73320455+AlainKadar@users.noreply.github.com> Raymond Asare rayasare Marco Klement Marco Klement, M.Sc +Chris Jones From 4db2b2ee5bfcb9ecc859e98e9cd0c7d69e103bd8 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Fri, 8 Apr 2022 07:55:47 -0400 Subject: [PATCH 3/6] Bump version to v3.0.1. --- .bumpversion.cfg | 2 +- CMakeLists.txt | 2 +- hoomd/hpmc/external/user.py | 4 ++-- hoomd/hpmc/pair/user.py | 2 +- sphinx-doc/conf.py | 4 ++-- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 6c96f32ad7..e150b0bde7 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 3.0.0 +current_version = 3.0.1 commit = False tag = False parse = ^(?P0|[1-9]\d*)\.(?P0|[1-9]\d*)\.(?P0|[1-9]\d*)(?:-(?P(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))(?:\.(?P0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)))?$ diff --git a/CMakeLists.txt b/CMakeLists.txt index 726ff9f91a..cf276f472a 100644 --- a/CMakeLists.txt +++ b/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}) diff --git a/hoomd/hpmc/external/user.py b/hoomd/hpmc/external/user.py index 5a27632f28..e85014471e 100644 --- a/hoomd/hpmc/external/user.py +++ b/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 diff --git a/hoomd/hpmc/pair/user.py b/hoomd/hpmc/pair/user.py index 622f00ed40..1dd2de6550 100644 --- a/hoomd/hpmc/pair/user.py +++ b/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. diff --git a/sphinx-doc/conf.py b/sphinx-doc/conf.py index f97b3baed3..952fca469d 100644 --- a/sphinx-doc/conf.py +++ b/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 From d4eb80cd4d3c10609a2b0b2b2f0e369dc48fc3a8 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Fri, 8 Apr 2022 10:41:30 -0400 Subject: [PATCH 4/6] Fix failing walltime test. --- hoomd/pytest/test_simulation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hoomd/pytest/test_simulation.py b/hoomd/pytest/test_simulation.py index 7abf4cde21..0309181bce 100644 --- a/hoomd/pytest/test_simulation.py +++ b/hoomd/pytest/test_simulation.py @@ -144,7 +144,7 @@ def test_walltime(simulation_factory, two_particle_snapshot_factory): trigger=hoomd.trigger.Periodic(1))) 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): From 8c6e8cc9d6efeb4f5995d22b0865e729f0349934 Mon Sep 17 00:00:00 2001 From: Brandon Butler Date: Fri, 8 Apr 2022 11:00:46 -0400 Subject: [PATCH 5/6] Ensure TPS and Walltime vary more than clock resolution Fixes tests for Simulation --- hoomd/pytest/test_simulation.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/hoomd/pytest/test_simulation.py b/hoomd/pytest/test_simulation.py index 0309181bce..eb02070652 100644 --- a/hoomd/pytest/test_simulation.py +++ b/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: + + 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 @@ -142,6 +155,7 @@ 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])) From 8e596785a8643e4461b609467598c9560b34302a Mon Sep 17 00:00:00 2001 From: Brandon Butler Date: Fri, 8 Apr 2022 12:36:40 -0400 Subject: [PATCH 6/6] Add missing Action inheritance for SleepUpdater --- hoomd/pytest/test_simulation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hoomd/pytest/test_simulation.py b/hoomd/pytest/test_simulation.py index eb02070652..e60fcbc74c 100644 --- a/hoomd/pytest/test_simulation.py +++ b/hoomd/pytest/test_simulation.py @@ -20,7 +20,7 @@ reason="gsd Python package was not found.") -class SleepUpdater: +class SleepUpdater(hoomd.custom.Action): def act(self, timestep): time.sleep(1e-6 * timestep)