From 372b7e3e1a425749b3e0e6ad651c6ec61e35bd98 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 11 Jul 2024 18:21:19 -0400 Subject: [PATCH 1/5] Update change log. --- CHANGELOG.rst | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 73f3695582..e72404f182 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -7,14 +7,15 @@ Change Log 4.x --- -4.8.0 (not yet released) -^^^^^^^^^^^^^^^^^^^^^^^^ +4.8.0 (2024-07-11) +^^^^^^^^^^^^^^^^^^ *Added* * ``hoomd.mpcd`` reimplements the MPCD method for simulating hydrodynamic interactions. See the migrating page for an overview and individual class and method documentation for more information (`#1784 `__). +* MPCD tutorial. * Support numpy 2.0 (`#1797 `__) * ``hoomd.hpmc.external.External`` provides an abstract interface to external potentials @@ -23,7 +24,9 @@ Change Log (`#1811 `__). * ``HPMCIntegrator.external_potentials`` sets the list of external potentials applied to the system (`#1811 `__). - +* ``hpmc.pair.ExpandedGaussian`` computes the expanded Gaussian pair potential in HPMC + (`#1817 `__). + *Changed* * Miscellaneous documentation improvements @@ -39,6 +42,8 @@ Change Log `#1816 `__). * Ensure that Gaussian-type pair potentials have positive sigma values (`#1810 `__). +* Demonstrate ``Step`` and ``AngularStep`` in the tutorial "Modelling Patchy Particles". +* Fixed typos in all tutorials. *Fixed* From 1f72d56de555dc5464ce9da84806dbd158e870d1 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 11 Jul 2024 18:29:45 -0400 Subject: [PATCH 2/5] Action versions are now managed by depdendabot. --- .github/ISSUE_TEMPLATE/release.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/release.md b/.github/ISSUE_TEMPLATE/release.md index 1e19a760ca..e85c809080 100644 --- a/.github/ISSUE_TEMPLATE/release.md +++ b/.github/ISSUE_TEMPLATE/release.md @@ -10,9 +10,6 @@ assignees: 'joaander' Minor and major releases: - [ ] Update tutorial submodule. -- [ ] Update actions versions. - - See current actions usage with: `rg --no-filename --hidden uses: | awk '{$1=$1;print}' | sort | uniq` - - Use global search and replace to update them to the latest tags - [ ] Check for new or duplicate contributors since the last release: `comm -13 (git log $(git describe --tags --abbrev=0) --format="%aN <%aE>" | sort | uniq | psub) (git log --format="%aN <%aE>" | sort | uniq | psub)`. Add entries to `.mailmap` to remove duplicates. From e69924da603b296d930ef22b6f53a47199af42e9 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 11 Jul 2024 18:31:05 -0400 Subject: [PATCH 3/5] Remove duplicate users with mailmap. --- .mailmap | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.mailmap b/.mailmap index fa92936a82..3ca56b59f6 100644 --- a/.mailmap +++ b/.mailmap @@ -181,3 +181,5 @@ Simone Ciarella SCiarella Simone Ciarella SCiarella <58949181+SCiarella@users.noreply.github.com> Kieran Nehil-Puleo kierannp Cristina Butu crisbutu <129013261+crisbutu@users.noreply.github.com> +Joseph Burkhart josephburkhart +Joseph Burkhart Joseph Burkhart <61951318+josephburkhart@users.noreply.github.com> From d412da93c75b5e6a839c7340774e948c213ad22e Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 11 Jul 2024 18:41:30 -0400 Subject: [PATCH 4/5] Bump version to 4.8.0. --- .bumpversion.cfg | 2 +- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/ISSUE_TEMPLATE/release.md | 2 +- .pre-commit-config.yaml | 3 --- BUILDING.rst | 4 ++-- CHANGELOG.rst | 2 +- CMakeLists.txt | 2 +- INSTALLING.rst | 8 ++++---- hoomd/hpmc/external/user.py | 4 ++-- hoomd/hpmc/pair/user.py | 4 ++-- sphinx-doc/conf.py | 4 ++-- 11 files changed, 17 insertions(+), 20 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 54ef82c222..ed36e28d25 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 4.7.0 +current_version = 4.8.0 commit = False tag = False parse = ^(?P0|[1-9]\d*)\.(?P0|[1-9]\d*)\.(?P0|[1-9]\d*)(?:-(?P(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))(?:\.(?P0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)))?$ diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 574170a8e8..af95105c5a 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: 4.7.0 + placeholder: 4.8.0 validations: required: true - type: markdown diff --git a/.github/ISSUE_TEMPLATE/release.md b/.github/ISSUE_TEMPLATE/release.md index e85c809080..80ffd816cc 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 4.7.0' +title: 'Release 4.8.0' labels: '' assignees: 'joaander' diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5b810b2fe1..8cced4d134 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -28,9 +28,6 @@ repos: - id: check-yaml exclude: (?:^.github/workflows/templates) # templates are not properly formatted yaml - id: check-case-conflict - - id: fix-encoding-pragma - args: - - --remove - id: mixed-line-ending - repo: https://github.com/glotzerlab/fix-license-header rev: v0.3.2 diff --git a/BUILDING.rst b/BUILDING.rst index a8132f25dc..fe351cc9e2 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-4.7.0.tar.gz`_. +Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.8.0.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-4.7.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.7.0/hoomd-4.7.0.tar.gz +.. _Download hoomd-4.8.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.8.0/hoomd-4.8.0.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/CHANGELOG.rst b/CHANGELOG.rst index e72404f182..6f34efa3fc 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -26,7 +26,7 @@ Change Log (`#1811 `__). * ``hpmc.pair.ExpandedGaussian`` computes the expanded Gaussian pair potential in HPMC (`#1817 `__). - + *Changed* * Miscellaneous documentation improvements diff --git a/CMakeLists.txt b/CMakeLists.txt index 5e2ddffbec..17d693471b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -18,7 +18,7 @@ add_subdirectory (CMake) ################################ ## Version information -set(HOOMD_VERSION_RAW "4.7.0") +set(HOOMD_VERSION_RAW "4.8.0") 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/INSTALLING.rst b/INSTALLING.rst index ec9d3cc16d..6f28249581 100644 --- a/INSTALLING.rst +++ b/INSTALLING.rst @@ -20,7 +20,7 @@ Serial CPU and single GPU builds *linux-64*, *osx-64*, and *osx-arm64* platforms. Install the ``hoomd`` package from the conda-forge_ channel into a conda environment:: - $ mamba install hoomd=4.7.0 + $ mamba install hoomd=4.8.0 .. _conda-forge: https://conda-forge.org/docs/user/introduction.html @@ -28,11 +28,11 @@ channel into a conda environment:: package. Override this and force the GPU enabled package installation with:: $ export CONDA_OVERRIDE_CUDA="12.0" - $ mamba install "hoomd=4.7.0=*gpu*" "cuda-version=12.0" + $ mamba install "hoomd=4.8.0=*gpu*" "cuda-version=12.0" Similarly, you can force CPU only package installation with:: - $ mamba install "hoomd=4.7.0=*cpu*" + $ mamba install "hoomd=4.8.0=*cpu*" .. note:: @@ -42,7 +42,7 @@ Similarly, you can force CPU only package installation with:: .. note:: Run time compilation is no longer available on conda-forge builds starting with HOOMD-blue - 4.7.0. + 4.8.0. .. tip:: diff --git a/hoomd/hpmc/external/user.py b/hoomd/hpmc/external/user.py index 5d767b56bc..24a92bca1a 100644 --- 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/\ - v4.7.0/hoomd/VectorMath.h + v4.8.0/hoomd/VectorMath.h .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\ - v4.7.0/hoomd/BoxDim.h + v4.8.0/hoomd/BoxDim.h .. rubric:: Example: diff --git a/hoomd/hpmc/pair/user.py b/hoomd/hpmc/pair/user.py index 39a8e271aa..99d4e430f6 100644 --- 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/\ - v4.7.0/hoomd/VectorMath.h + v4.8.0/hoomd/VectorMath.h Note: Your code *must* return a value. @@ -340,7 +340,7 @@ class CPPPotentialUnion(CPPPotentialBase): CPPPotentialUnion uses threaded execution on multiple CPU cores. - .. deprecated:: 4.7.0 + .. deprecated:: 4.8.0 ``num_cpu_threads >= 1`` is deprecated. Set ``num_cpu_threads = 1``. diff --git a/sphinx-doc/conf.py b/sphinx-doc/conf.py index 271e3e9ac0..a03066a5ca 100644 --- 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 = '4.7.0' -release = '4.7.0' +version = '4.8.0' +release = '4.8.0' language = 'en' From 0c6de579c4fdb2d9037f89d100ab5e445a5d859d Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 15 Jul 2024 05:38:55 -0400 Subject: [PATCH 5/5] Reword change log. --- CHANGELOG.rst | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 6f34efa3fc..0eb8deb2b9 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -20,8 +20,8 @@ Change Log (`#1797 `__) * ``hoomd.hpmc.external.External`` provides an abstract interface to external potentials (`#1811 `__). -* ``hoomd.hpmc.external.Linear`` computes linear potential as a function of the distance from a point to a plane - (`#1811 `__). +* ``hoomd.hpmc.external.Linear`` computes the potential as a linear function of the distance from a + point to a plane (`#1811 `__). * ``HPMCIntegrator.external_potentials`` sets the list of external potentials applied to the system (`#1811 `__). * ``hpmc.pair.ExpandedGaussian`` computes the expanded Gaussian pair potential in HPMC @@ -43,13 +43,13 @@ Change Log * Ensure that Gaussian-type pair potentials have positive sigma values (`#1810 `__). * Demonstrate ``Step`` and ``AngularStep`` in the tutorial "Modelling Patchy Particles". -* Fixed typos in all tutorials. +* Fixed typographical errors in all tutorials. *Fixed* -* Issue a proper error message when ``ALJ.shape`` is not set for all particle types +* Issue the proper error message when ``ALJ.shape`` is not set for all particle types (`#1808 `__). -* Correctly apply brownian torque when elements of the inertia tensor are 0 +* Correctly apply Brownian torque when elements of the inertia tensor are 0 (`#1825 `__). @@ -57,8 +57,8 @@ Change Log * ``HPMCIntegrator.external_potential`` - use ``HPMCIntegrator.external_potentials`` (`#1811 `__). -* ``hoomd.hpmc.external.user.CPPExternalPotential`` - use ``hoomd.hpmc.external.Linear`` or write a custom component in C++ - (`#1811 `__). +* ``hoomd.hpmc.external.user.CPPExternalPotential`` - use ``hoomd.hpmc.external.Linear`` or write a + custom component in C++ (`#1811 `__). *Removed*