From 3fa199dd3ab8e5ce90df7a6a61fa7ed975b1bc9c Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 23 Oct 2023 10:32:51 -0400 Subject: [PATCH 1/6] Update change log. --- CHANGELOG.rst | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 61398b680f..0a484614a4 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,35 @@ Change Log 4.x --- + +4.3.0 (2024-10-24) +^^^^^^^^^^^^^^^^^^ + +*Fixed* + +* ``md.alchemy.methods.NVT`` now evolves the elements provided in ``alchemical_dof`` + (`#1633 `__). +* More consistent notice messages regarding MPI ranks used in GPU selection + (`#1635 `__). +* ``hoomd.hpmc.compute.SDF`` computes correct pressures with patchy potentials. + (`#1636 `__). + +*Added* + +* Support GCC 13 + (`#1634 `__). +* Support Python 3.12 + (`#1634 `__). +* ``tau`` parameter to ``hoomd.md.methods.thermostats.Bussi`` + (`#1619 `__). + +*Changed* + +* Revise class documentation. + (`#1628 `__). +* Add more code snippets to the class documentation + (`#1628 `__). + 4.2.1 (2024-10-02) ^^^^^^^^^^^^^^^^^^ From dde36868c1c63753b54b6b19d177dc31bb00cbee Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 23 Oct 2023 10:47:35 -0400 Subject: [PATCH 2/6] Revise release checklist. --- .github/ISSUE_TEMPLATE/release.md | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/release.md b/.github/ISSUE_TEMPLATE/release.md index 39c8c1d8c8..8c14ba67f3 100644 --- a/.github/ISSUE_TEMPLATE/release.md +++ b/.github/ISSUE_TEMPLATE/release.md @@ -7,15 +7,9 @@ assignees: 'joaander' --- -Release checklist: +Minor and major releases: - [ ] Update tutorial submodule. -- [ ] Update change log. - - ``git log --format=oneline --first-parent `git log -n 1 --pretty=format:%H -- CHANGELOG.rst`...`` - - [milestone](https://github.com/glotzerlab/hoomd-blue/milestones) -- [ ] Check readthedocs build, especially change log formatting. - - [Build status](https://readthedocs.org/projects/hoomd-blue/builds/) - - [Output](https://hoomd-blue.readthedocs.io/en/latest/) - [ ] 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 @@ -24,8 +18,16 @@ Release checklist: Add entries to `.mailmap` to remove duplicates. - [ ] Run [hoomd-benchmarks](https://github.com/glotzerlab/hoomd-benchmarks), check for performance regressions with the previous release, and post the tables in the release pull request. +- [ ] Run [hoomd-validation](https://github.com/glotzerlab/hoomd-validation). + +All releases: + +- [ ] Update change log. + - ``git log --format=oneline --first-parent `git log -n 1 --pretty=format:%H -- CHANGELOG.rst`...`` + - [milestone](https://github.com/glotzerlab/hoomd-blue/milestones) +- [ ] Check readthedocs build, especially change log formatting. - [ ] Run *bumpversion*. - [ ] Tag and push. - [ ] Update conda-forge recipe. -- [ ] Update glotzerlab-software. +- [ ] Update *glotzerlab-software*. - [ ] Announce release on mailing list. From f183c6740ff819ad0235299b9a44031351ffac28 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 23 Oct 2023 10:51:32 -0400 Subject: [PATCH 3/6] Update tutorial submodule. --- sphinx-doc/tutorial | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sphinx-doc/tutorial b/sphinx-doc/tutorial index 85fad94614..b58fe8262b 160000 --- a/sphinx-doc/tutorial +++ b/sphinx-doc/tutorial @@ -1 +1 @@ -Subproject commit 85fad94614a41f1a5108777ee5484a73d84fdf84 +Subproject commit b58fe8262b3956164e6e578f17ee2125e6786f73 From 3d8c4b7569128384af66ffcc4b0c46e7eb1e9c17 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 23 Oct 2023 10:57:49 -0400 Subject: [PATCH 4/6] Update actions versions. --- .github/workflows/release.yml | 2 +- .github/workflows/templates/release.yml | 2 +- .github/workflows/templates/test.yml | 4 ++-- .github/workflows/test.yml | 16 ++++++++-------- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 6e45bb932b..b7d1de0b31 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -40,7 +40,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v4.0.0 + uses: actions/checkout@v4.1.1 with: fetch-depth: 0 submodules: true diff --git a/.github/workflows/templates/release.yml b/.github/workflows/templates/release.yml index a3e646a6cf..2e4ed52f0f 100644 --- a/.github/workflows/templates/release.yml +++ b/.github/workflows/templates/release.yml @@ -27,7 +27,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v4.0.0 + uses: actions/checkout@v4.1.1 with: fetch-depth: 0 submodules: true diff --git a/.github/workflows/templates/test.yml b/.github/workflows/templates/test.yml index e721d1a382..aa5585ed67 100644 --- a/.github/workflows/templates/test.yml +++ b/.github/workflows/templates/test.yml @@ -181,7 +181,7 @@ env: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.0.0 + uses: actions/checkout@v4.1.1 with: path: code submodules: true @@ -209,7 +209,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Use jetstream2-admin/start - uses: glotzerlab/jetstream2-admin/start@v1.2.2 + uses: glotzerlab/jetstream2-admin/start@v1.2.3 with: OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }} OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }} diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 3863a6358b..a9acd9a661 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -50,7 +50,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Use jetstream2-admin/start - uses: glotzerlab/jetstream2-admin/start@v1.2.2 + uses: glotzerlab/jetstream2-admin/start@v1.2.3 with: OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }} OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }} @@ -82,7 +82,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.0.0 + uses: actions/checkout@v4.1.1 with: path: code submodules: true @@ -188,7 +188,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.0.0 + uses: actions/checkout@v4.1.1 with: path: code submodules: true @@ -249,7 +249,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.0.0 + uses: actions/checkout@v4.1.1 with: path: code submodules: true @@ -299,7 +299,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.0.0 + uses: actions/checkout@v4.1.1 with: path: code submodules: true @@ -362,7 +362,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.0.0 + uses: actions/checkout@v4.1.1 with: path: code submodules: true @@ -477,7 +477,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.0.0 + uses: actions/checkout@v4.1.1 with: path: code submodules: true @@ -547,7 +547,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.0.0 + uses: actions/checkout@v4.1.1 with: path: code submodules: true From bb36a83fd63515848eb7d207dbbaf333e4b89879 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 23 Oct 2023 11:00:44 -0400 Subject: [PATCH 5/6] Update mailmap. --- .mailmap | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.mailmap b/.mailmap index 9a4a28cf7b..fe2a8069f0 100644 --- a/.mailmap +++ b/.mailmap @@ -171,3 +171,6 @@ Domagoj Fijan Domagoj Fijan Domagoj Fijan Domagoj Fijan <50439291+DomFijan@users.noreply.github.com> Adrien Chen Adrien Chen <72541752+cantfindname@users.noreply.github.com> Antonia Statt <49729189+astatt@users.noreply.github.com> Antonia Statt <> +Alex Lee Alex +Alex Lee shihkual <89434748+shihkual@users.noreply.github.com> +Alex Lee shihkual From a985796f555a73930f99d0f10d21dbbd3ca57a86 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 23 Oct 2023 11:01:42 -0400 Subject: [PATCH 6/6] Bump version to 4.3.0. --- .bumpversion.cfg | 2 +- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- BUILDING.rst | 4 ++-- CMakeLists.txt | 2 +- INSTALLING.rst | 6 +++--- hoomd/hpmc/external/user.py | 4 ++-- hoomd/hpmc/pair/user.py | 2 +- sphinx-doc/conf.py | 4 ++-- 8 files changed, 13 insertions(+), 13 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 96e9e0fd98..d31be046a4 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 4.2.1 +current_version = 4.3.0 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 447376705c..68163e7d82 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: 4.2.1 + placeholder: 4.3.0 validations: required: true - type: markdown diff --git a/BUILDING.rst b/BUILDING.rst index 5ab69aeaa4..b7834b6687 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-4.2.1.tar.gz`_. +Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.3.0.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-4.2.1.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.2.1/hoomd-4.2.1.tar.gz +.. _Download hoomd-4.3.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.3.0/hoomd-4.3.0.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 e7e0f8cf18..d7bac294cb 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -14,7 +14,7 @@ add_subdirectory (CMake) ################################ ## Version information -set(HOOMD_VERSION_RAW "4.2.1") +set(HOOMD_VERSION_RAW "4.3.0") 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 24e5cb9cbf..a4e49febfb 100644 --- a/INSTALLING.rst +++ b/INSTALLING.rst @@ -24,17 +24,17 @@ Conda package **HOOMD-blue** is available on conda-forge_ on the *linux-64*, *osx-64*, and *osx-arm64* platforms. Install the ``hoomd`` package from the conda-forge_ channel into a conda environment:: - $ conda install hoomd=4.2.1 + $ conda install hoomd=4.3.0 ``conda`` auto-detects whether your system has a GPU and attempts to install the appropriate package. Override this and force the GPU enabled package installation with:: $ export CONDA_OVERRIDE_CUDA="12.0" - $ conda install "hoomd=4.2.1=*gpu*" "cuda-version=12.0" + $ conda install "hoomd=4.3.0=*gpu*" "cuda-version=12.0" Similarly, you can force CPU only package installation with:: - $ conda install "hoomd=4.2.1=*cpu*" + $ conda install "hoomd=4.3.0=*cpu*" .. note:: diff --git a/hoomd/hpmc/external/user.py b/hoomd/hpmc/external/user.py index af5ca3dc4e..1e6bad88e6 100644 --- a/hoomd/hpmc/external/user.py +++ b/hoomd/hpmc/external/user.py @@ -84,9 +84,9 @@ class CPPExternalPotential(ExternalField): Your code *must* return a value. .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\ - v4.2.1/hoomd/VectorMath.h + v4.3.0/hoomd/VectorMath.h .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\ - v4.2.1/hoomd/BoxDim.h + v4.3.0/hoomd/BoxDim.h .. rubric:: Example: diff --git a/hoomd/hpmc/pair/user.py b/hoomd/hpmc/pair/user.py index 7f3a050aaa..bb41a78a0d 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/\ - v4.2.1/hoomd/VectorMath.h + v4.3.0/hoomd/VectorMath.h Note: Your code *must* return a value. diff --git a/sphinx-doc/conf.py b/sphinx-doc/conf.py index c6f4e2c46b..4485bbb091 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 = '4.2.1' -release = '4.2.1' +version = '4.3.0' +release = '4.3.0' language = 'en'