From 9b5db17abd0f5eddde8fb02c4cee6b1f03d7c1b5 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 6 Jun 2023 14:52:24 -0400 Subject: [PATCH 1/7] Update change log. --- CHANGELOG.rst | 24 ++++++++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index ecc43db3e7..89cb2d2fd9 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,11 +4,11 @@ Change Log ========== -v4.x ----- +4.x +--- -v4.0.0 (not yet released) -^^^^^^^^^^^^^^^^^^^^^^^^^ +4.0.0 (2023-06-06) +^^^^^^^^^^^^^^^^^^ *Fixed* @@ -18,6 +18,8 @@ v4.0.0 (not yet released) (`#1548 `__). * Work around cases where Python's garbage collector fails to collect ``Operation`` objects (`#1457 `__). +* Incorrect behavior with ``hpmc.external.user.CPPExternalPotential`` in MPI domain decomposition + simulations (`#1562 `__). *Added* @@ -38,6 +40,16 @@ v4.0.0 (not yet released) (`#1541 `__). * More descriptive error messages when calling ``Simulation.run`` (`#1552 `__). +* `hoomd.Snapshot.from_gsd_frame` - convert a `gsd.hoomd.Frame` object to `hoomd.Snapshot` + (`#1559 `__). +* `hoomd.device.NoticeFile` - a file-like object that writes to `hoomd.device.Device.notice` + (`#1449 `__). +* `hoomd.write.Burst` - selective high-frequency frame writing to GSD files + (`#1543 `__). +* Support LLVM 16 + (`#1568 `__). +* More detailed status message for found CUDA libraries + (`#1566 `__). *Changed* @@ -68,12 +80,16 @@ v4.0.0 (not yet released) (`#1538 `__). * No longer test with GCC 7-8, Python 3.6-3.7, or Clang 6-9) (`#1544 `__). +* Improved error messages with NVRTC compiled code + (`#1567 `__). *Deprecated* * ``Scalar``, ``Scalar2``, ``Scalar3``, and ``Scalar4`` data types. Use ``LongReal[N]`` instead in new code (`#355 `__). +* ``hoomd.Snapshot.from_gsd_snapshot`` - use `hoomd.Snapshot.from_gsd_frame` + (`#1559 `__). *Removed* From 3a0a399042689679ffc738aa810a9b5c64810317 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 6 Jun 2023 14:54:06 -0400 Subject: [PATCH 2/7] Update release issue template. --- .github/ISSUE_TEMPLATE/release.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/ISSUE_TEMPLATE/release.md b/.github/ISSUE_TEMPLATE/release.md index fa207ecd19..39c8c1d8c8 100644 --- 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 v3.x.y' +title: 'Release 4.x.y' labels: '' assignees: 'joaander' From 508c51a9accea9294dffbd77d3e5692bfa679741 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 6 Jun 2023 14:55:06 -0400 Subject: [PATCH 3/7] Bump tutorial submodule. --- sphinx-doc/tutorial | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sphinx-doc/tutorial b/sphinx-doc/tutorial index 7dd1638274..174c26e5cb 160000 --- a/sphinx-doc/tutorial +++ b/sphinx-doc/tutorial @@ -1 +1 @@ -Subproject commit 7dd1638274fd854a135e8cd6365b4cd6e053b2b9 +Subproject commit 174c26e5cbd9887001e1eccc9adcce7f4ee91c7a From 51b8800450c232b667ee16d64b95af6bcc1f4f7e Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 6 Jun 2023 15:05:22 -0400 Subject: [PATCH 4/7] Combine duplicate committers. --- .mailmap | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.mailmap b/.mailmap index 3738e3c2a0..25bfdeecb9 100644 --- a/.mailmap +++ b/.mailmap @@ -72,6 +72,7 @@ Alyssa Travitz Ross Smith Tim Moore Tim Moore Tim Moore Tim Moore +Tim Moore mtimc Aaron Keys Brandon Denis Smith Brandon Denis Smith Igor Morozov @@ -127,6 +128,7 @@ Peter Schwendeman Peter S. Schwendeman Philipp Schönhöfer Philipp Schönhöfer Philipp Schönhöfer SchoeniPhlippsn Philipp Schönhöfer Philipp Schönhöfer +Philipp Schönhöfer SchoeniPhlippsn Tommy Waltmann tommy-waltmann Tommy Waltmann tommy-waltmann Tommy Waltmann tommy-waltmann @@ -158,3 +160,9 @@ Chris Jones Melody Zhang Melody Zhang <114299909+melodyyzh@users.noreply.github.com> Jen Bradley Jen Bradley <55467578+janbridley@users.noreply.github.com> Jen Bradley janbridley +Martin Girard MartinGirard <80533099+MartinGirard@users.noreply.github.com> +Martin Girard martin +Ignacio Blanco Varela Ignacio Blanco Varela <83680829+iblanco11981870@users.noreply.github.com> +Domagoj Fijan Domagoj Fijan +Domagoj Fijan Domagoj Fijan <50439291+DomFijan@users.noreply.github.com> +Adrien Chen Adrien Chen <72541752+cantfindname@users.noreply.github.com> From 53157ed82bef66304711551492633fd6c6de390b Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 6 Jun 2023 15:08:49 -0400 Subject: [PATCH 5/7] Bump version to 4.0.0. --- .bumpversion.cfg | 2 +- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- BUILDING.rst | 4 ++-- CMakeLists.txt | 2 +- hoomd/hpmc/external/user.py | 4 ++-- hoomd/hpmc/pair/user.py | 2 +- sphinx-doc/conf.py | 4 ++-- 7 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index cf87d3945f..03c0cfa72b 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 3.11.0 +current_version = 4.0.0 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/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 1960d74312..ee6f6ef16d 100644 --- 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: 3.11.0 + placeholder: 4.0.0 validations: required: true - type: markdown diff --git a/BUILDING.rst b/BUILDING.rst index d90222623e..8ce40423ed 100644 --- 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-v3.11.0.tar.gz`_. +Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-v4.0.0.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-v3.11.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v3.11.0/hoomd-v3.11.0.tar.gz +.. _Download hoomd-v4.0.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.0.0/hoomd-v4.0.0.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/CMakeLists.txt b/CMakeLists.txt index 45210a268a..ff5d1715ea 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -14,7 +14,7 @@ add_subdirectory (CMake) ################################ ## Version information -set(HOOMD_VERSION_RAW "3.11.0") +set(HOOMD_VERSION_RAW "4.0.0") 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/hoomd/hpmc/external/user.py b/hoomd/hpmc/external/user.py index 2d0bfa0832..36f6442737 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/\ - v3.11.0/hoomd/VectorMath.h + v4.0.0/hoomd/VectorMath.h .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\ - v3.11.0/hoomd/BoxDim.h + v4.0.0/hoomd/BoxDim.h Example: .. code-block:: python diff --git a/hoomd/hpmc/pair/user.py b/hoomd/hpmc/pair/user.py index b391ed421a..5b87336d0b 100644 --- a/hoomd/hpmc/pair/user.py +++ b/hoomd/hpmc/pair/user.py @@ -75,7 +75,7 @@ class CPPPotentialBase(AutotunedObject): HOOMD-blue source code. .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\ - v3.11.0/hoomd/VectorMath.h + v4.0.0/hoomd/VectorMath.h Note: Your code *must* return a value. diff --git a/sphinx-doc/conf.py b/sphinx-doc/conf.py index 6d4d45740f..19b7639841 100644 --- a/sphinx-doc/conf.py +++ b/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 = '3.11.0' -release = '3.11.0' +version = '4.0.0' +release = '4.0.0' language = 'en' From 42b0858aa239f0bedb54301aeb91b9071c9896d9 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 6 Jun 2023 15:15:38 -0400 Subject: [PATCH 6/7] Find HOOMD-blue 4.0.0 in example plugin. --- example_plugins/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/example_plugins/CMakeLists.txt b/example_plugins/CMakeLists.txt index 940a842edd..75af19ed7d 100644 --- a/example_plugins/CMakeLists.txt +++ b/example_plugins/CMakeLists.txt @@ -6,7 +6,7 @@ CMAKE_MINIMUM_REQUIRED(VERSION 3.9 FATAL_ERROR) project(example_plugins LANGUAGES C CXX) # Find the installed HOOMD -find_package(HOOMD 3.0.0 REQUIRED) +find_package(HOOMD 4.0.0 REQUIRED) message(STATUS "Found HOOMD ${HOOMD_VERSION}: ${HOOMD_INSTALL_PREFIX}/${PYTHON_SITE_INSTALL_DIR}") From 17dc0671cdbcbd0658410cbbe76723673799602f Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 6 Jun 2023 15:46:58 -0400 Subject: [PATCH 7/7] Provide modern Python version as a placeholder. --- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index ee6f6ef16d..d62d3825f3 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -73,7 +73,7 @@ body: attributes: label: Python version description: What version of Python are you using? - placeholder: 3.10.6 + placeholder: 3.11.3 validations: required: true - type: markdown