From af3cd784b4d6f6c262e5a3bd70f3d357bc919a70 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 19 Sep 2023 11:16:00 -0400 Subject: [PATCH 1/5] Update change log. --- CHANGELOG.rst | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 09c5443764..871fc54e6c 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,51 @@ Change Log 4.x --- +4.2.0 (2024-09-20) +^^^^^^^^^^^^^^^^^^ + +*Fixed* + +* Make ``HDF5Log`` example more visible + (`#1602 `__). +* Access valid GPU memory in ``hoomd.hpmc.update.Clusters`` + (`#1607 `__). +* Test suite passes on the ROCm GPU platform + (`#1607 `__). +* Provide an error message when using ``md.external.field.Periodic`` in 2D + (`#1603 `__). +* ``hoomd.write.GSD`` reports "File exists" in the exception description when using the ``'xb'`` + mode and the file exists (`#1609 `__). +* Write small numbers correctly in ``hoomd.write.Table`` + (`#1617 `__). +* Make examples in ``hoomd.md.methods.NVE`` and ``hoomd.md.methods.DisplacementCapped`` more visible + (`#1601 `__). + +*Added* + +* How-to documentation page: "How to apply arbitrary forces in MD" + (`#1610 `__). +* MPCD particle data is now available included in ``Snapshot`` + (`#1580 `__). +* Documentation page: "How to prevent particles from moving" + (`#1611 `__). +* Documentation page: "How to minimize the potential energy of a system" + (`#1614 `__). +* Documentation page: "How to continuously vary potential parameters" + (`#1612 `__). +* Documentation page: "How to determine the most efficient device" + (`#1616 `__). +* Add variable parameters to ``hpmc.external.user.CPPExternalPotential`` + (`#1608 `__). +* Documentation page: "How to choose the neighbor list buffer distance" + (`#1615 `__). +* How-to documentation page: "How to compute the free energy of solids" + (`#1613 `__). + +*Changed* + +* Removed the unused ``ExternalFieldComposite.h`` and all the related ``ExternalFieldComposite*`` + (`#1604 `__). 4.1.0 (2024-08-07) ^^^^^^^^^^^^^^^^^^ From 1806283c93629c63322f9c0d460989ba1ac73b1a Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 19 Sep 2023 11:17:56 -0400 Subject: [PATCH 2/5] 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 d363bef246..85fad94614 160000 --- a/sphinx-doc/tutorial +++ b/sphinx-doc/tutorial @@ -1 +1 @@ -Subproject commit d363bef2465643c6a13933d7f55c9e3d0d51498f +Subproject commit 85fad94614a41f1a5108777ee5484a73d84fdf84 From 50a78450715ef41933a1fec49563fea2c180e689 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 19 Sep 2023 11:19:56 -0400 Subject: [PATCH 3/5] Revise change log. --- CHANGELOG.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 871fc54e6c..6a8abea4ae 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -28,10 +28,8 @@ Change Log *Added* -* How-to documentation page: "How to apply arbitrary forces in MD" +* Documentation page: "How to apply arbitrary forces in MD" (`#1610 `__). -* MPCD particle data is now available included in ``Snapshot`` - (`#1580 `__). * Documentation page: "How to prevent particles from moving" (`#1611 `__). * Documentation page: "How to minimize the potential energy of a system" @@ -40,12 +38,14 @@ Change Log (`#1612 `__). * Documentation page: "How to determine the most efficient device" (`#1616 `__). -* Add variable parameters to ``hpmc.external.user.CPPExternalPotential`` - (`#1608 `__). * Documentation page: "How to choose the neighbor list buffer distance" (`#1615 `__). -* How-to documentation page: "How to compute the free energy of solids" +* Documentation page: "How to compute the free energy of solids" (`#1613 `__). +* MPCD particle data is now available included in ``Snapshot`` + (`#1580 `__). +* Add variable parameters to ``hpmc.external.user.CPPExternalPotential`` + (`#1608 `__). *Changed* From d49e67ade5ff8dec96eec50b1193818fe5ea7da5 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 19 Sep 2023 11:24:13 -0400 Subject: [PATCH 4/5] Update actions versions. --- .github/workflows/release.yml | 4 ++-- .github/workflows/templates/release.yml | 4 ++-- .github/workflows/templates/test.yml | 6 +++--- .github/workflows/test.yml | 22 +++++++++++----------- 4 files changed, 18 insertions(+), 18 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 7333c12a07..e60e81fb9c 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -40,7 +40,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3.5.3 + uses: actions/checkout@v4.0.0 with: fetch-depth: 0 submodules: true @@ -70,7 +70,7 @@ jobs: run: tar -cvzf ${name}-${tag:1}.tar.gz ${name}-${tag:1} - name: Upload release files - uses: actions/upload-artifact@v3.1.2 + uses: actions/upload-artifact@v3.1.3 with: name: release path: | diff --git a/.github/workflows/templates/release.yml b/.github/workflows/templates/release.yml index ba1fab6036..a3e646a6cf 100644 --- a/.github/workflows/templates/release.yml +++ b/.github/workflows/templates/release.yml @@ -27,7 +27,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3.5.3 + uses: actions/checkout@v4.0.0 with: fetch-depth: 0 submodules: true @@ -57,7 +57,7 @@ jobs: run: tar -cvzf ${name}-${tag:1}.tar.gz ${name}-${tag:1} - name: Upload release files - uses: actions/upload-artifact@v3.1.2 + uses: actions/upload-artifact@v3.1.3 with: name: release path: | diff --git a/.github/workflows/templates/test.yml b/.github/workflows/templates/test.yml index 8e3cb0f9c4..e721d1a382 100644 --- a/.github/workflows/templates/test.yml +++ b/.github/workflows/templates/test.yml @@ -105,13 +105,13 @@ env: # Upload the tarballs. Retain the file for a limited time in case developers need to download # and run tests locally for further debugging. - name: 'Upload build' - uses: actions/upload-artifact@v3.1.2 + uses: actions/upload-artifact@v3.1.3 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} path: build.tar retention-days: 7 - name: 'Upload install' - uses: actions/upload-artifact@v3.1.2 + uses: actions/upload-artifact@v3.1.3 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} path: install.tar @@ -181,7 +181,7 @@ env: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v3.5.3 + uses: actions/checkout@v4.0.0 with: path: code submodules: true diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index fd97d52155..e1a99fd5d0 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -82,7 +82,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v3.5.3 + uses: actions/checkout@v4.0.0 with: path: code submodules: true @@ -143,13 +143,13 @@ jobs: # Upload the tarballs. Retain the file for a limited time in case developers need to download # and run tests locally for further debugging. - name: 'Upload build' - uses: actions/upload-artifact@v3.1.2 + uses: actions/upload-artifact@v3.1.3 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} path: build.tar retention-days: 7 - name: 'Upload install' - uses: actions/upload-artifact@v3.1.2 + uses: actions/upload-artifact@v3.1.3 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} path: install.tar @@ -188,7 +188,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v3.5.3 + uses: actions/checkout@v4.0.0 with: path: code submodules: true @@ -249,7 +249,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v3.5.3 + uses: actions/checkout@v4.0.0 with: path: code submodules: true @@ -299,7 +299,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v3.5.3 + uses: actions/checkout@v4.0.0 with: path: code submodules: true @@ -361,7 +361,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v3.5.3 + uses: actions/checkout@v4.0.0 with: path: code submodules: true @@ -422,13 +422,13 @@ jobs: # Upload the tarballs. Retain the file for a limited time in case developers need to download # and run tests locally for further debugging. - name: 'Upload build' - uses: actions/upload-artifact@v3.1.2 + uses: actions/upload-artifact@v3.1.3 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} path: build.tar retention-days: 7 - name: 'Upload install' - uses: actions/upload-artifact@v3.1.2 + uses: actions/upload-artifact@v3.1.3 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} path: install.tar @@ -475,7 +475,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v3.5.3 + uses: actions/checkout@v4.0.0 with: path: code submodules: true @@ -544,7 +544,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v3.5.3 + uses: actions/checkout@v4.0.0 with: path: code submodules: true From 5ffc65bf9fc89bb9425eb62fc9d5ea75c2257b35 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 19 Sep 2023 11:28:16 -0400 Subject: [PATCH 5/5] Bump version to 4.2.0. --- .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 0025a25354..112e8fbbd3 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 4.1.0 +current_version = 4.2.0 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 93c4650388..6e9df7fdf9 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: 4.1.0 + placeholder: 4.2.0 validations: required: true - type: markdown diff --git a/BUILDING.rst b/BUILDING.rst index fac8e2a771..8ce6b44b55 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-4.1.0.tar.gz`_. +Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.2.0.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-4.1.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.1.0/hoomd-4.1.0.tar.gz +.. _Download hoomd-4.2.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.2.0/hoomd-4.2.0.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 28d7d80584..3832d9f2c6 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -14,7 +14,7 @@ add_subdirectory (CMake) ################################ ## Version information -set(HOOMD_VERSION_RAW "4.1.0") +set(HOOMD_VERSION_RAW "4.2.0") 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 f85cbe09b1..fb8e296736 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=4.1.0 + $ conda install hoomd=4.2.0 ``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=4.1.0=*gpu*" "cuda-version=12.0" + $ conda install "hoomd=4.2.0=*gpu*" "cuda-version=12.0" Similarly, you can force CPU only package installation with:: - $ conda install "hoomd=4.1.0=*cpu*" + $ conda install "hoomd=4.2.0=*cpu*" .. note:: diff --git a/hoomd/hpmc/external/user.py b/hoomd/hpmc/external/user.py index cccb5866ea..f037507333 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/\ - v4.1.0/hoomd/VectorMath.h + v4.2.0/hoomd/VectorMath.h .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\ - v4.1.0/hoomd/BoxDim.h + v4.2.0/hoomd/BoxDim.h .. rubric:: Example: diff --git a/hoomd/hpmc/pair/user.py b/hoomd/hpmc/pair/user.py index a0befe0688..e8eca353f8 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/\ - v4.1.0/hoomd/VectorMath.h + v4.2.0/hoomd/VectorMath.h Note: Your code *must* return a value. diff --git a/sphinx-doc/conf.py b/sphinx-doc/conf.py index 7edfa376cb..596104921f 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 = '4.1.0' -release = '4.1.0' +version = '4.2.0' +release = '4.2.0' language = 'en'