From 8f0b0f3eb12d1dd39a1858de4299276412f5605b Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 16 May 2024 08:55:23 -0400 Subject: [PATCH 1/6] 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 3ce3cbb84e..4ab997a6aa 160000 --- a/sphinx-doc/tutorial +++ b/sphinx-doc/tutorial @@ -1 +1 @@ -Subproject commit 3ce3cbb84eb2153817ac95673ada816e4489e782 +Subproject commit 4ab997a6aae536a172529100df3a56cad2ee14d4 From b906ca7b78551d441c02c1f5f263b5f1007fc1ce Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 16 May 2024 09:03:52 -0400 Subject: [PATCH 2/6] Bump action versions. --- .github/workflows/release.yml | 6 ++--- .github/workflows/templates/release.yml | 6 ++--- .github/workflows/templates/test.yml | 12 ++++----- .github/workflows/test.yml | 34 ++++++++++++------------- 4 files changed, 29 insertions(+), 29 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 570857670a..eaba8faca3 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -40,7 +40,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v4.1.1 + uses: actions/checkout@v4.1.4 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@v4.3.1 + uses: actions/upload-artifact@v4.3.3 with: name: release path: | @@ -84,7 +84,7 @@ jobs: steps: - name: Download artifacts - uses: actions/download-artifact@v4.1.4 + uses: actions/download-artifact@v4.1.7 with: name: release diff --git a/.github/workflows/templates/release.yml b/.github/workflows/templates/release.yml index 54d44e3c82..21223260fa 100644 --- a/.github/workflows/templates/release.yml +++ b/.github/workflows/templates/release.yml @@ -27,7 +27,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v4.1.1 + uses: actions/checkout@v4.1.4 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@v4.3.1 + uses: actions/upload-artifact@v4.3.3 with: name: release path: | @@ -71,7 +71,7 @@ jobs: steps: - name: Download artifacts - uses: actions/download-artifact@v4.1.4 + uses: actions/download-artifact@v4.1.7 with: name: release diff --git a/.github/workflows/templates/test.yml b/.github/workflows/templates/test.yml index 12434fbdc3..bf7f5e6370 100644 --- a/.github/workflows/templates/test.yml +++ b/.github/workflows/templates/test.yml @@ -107,13 +107,13 @@ 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@v4.3.1 + uses: actions/upload-artifact@v4.3.3 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} path: build.tar retention-days: 7 - name: 'Upload install' - uses: actions/upload-artifact@v4.3.1 + uses: actions/upload-artifact@v4.3.3 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} path: install.tar @@ -121,7 +121,7 @@ env: <% endset %> <% set download_build_steps %> - name: Download build - uses: actions/download-artifact@v4.1.4 + uses: actions/download-artifact@v4.1.7 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar build @@ -129,7 +129,7 @@ env: <% endset %> <% set download_install_steps %> - name: Download install - uses: actions/download-artifact@v4.1.4 + uses: actions/download-artifact@v4.1.7 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar install @@ -183,7 +183,7 @@ env: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.1.1 + uses: actions/checkout@v4.1.4 with: path: code submodules: true @@ -211,7 +211,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Use jetstream2-admin/start - uses: glotzerlab/jetstream2-admin/start@v1.2.4 + uses: glotzerlab/jetstream2-admin/start@v1.2.5 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 17c52ce64e..f1f62a94ad 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -52,7 +52,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Use jetstream2-admin/start - uses: glotzerlab/jetstream2-admin/start@v1.2.4 + uses: glotzerlab/jetstream2-admin/start@v1.2.5 with: OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }} OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }} @@ -84,7 +84,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.1.1 + uses: actions/checkout@v4.1.4 with: path: code submodules: true @@ -145,13 +145,13 @@ jobs: # Upload the tarballs. Retain the file for a limited time in case developers need to download # and run tests locally for further debugging. - name: 'Upload build' - uses: actions/upload-artifact@v4.3.1 + uses: actions/upload-artifact@v4.3.3 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} path: build.tar retention-days: 7 - name: 'Upload install' - uses: actions/upload-artifact@v4.3.1 + uses: actions/upload-artifact@v4.3.3 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} path: install.tar @@ -190,13 +190,13 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.1.1 + uses: actions/checkout@v4.1.4 with: path: code submodules: true - name: Download install - uses: actions/download-artifact@v4.1.4 + uses: actions/download-artifact@v4.1.7 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar install @@ -251,13 +251,13 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.1.1 + uses: actions/checkout@v4.1.4 with: path: code submodules: true - name: Download build - uses: actions/download-artifact@v4.1.4 + uses: actions/download-artifact@v4.1.7 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar build @@ -301,13 +301,13 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.1.1 + uses: actions/checkout@v4.1.4 with: path: code submodules: true - name: Download install - uses: actions/download-artifact@v4.1.4 + uses: actions/download-artifact@v4.1.7 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar install @@ -364,7 +364,7 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.1.1 + uses: actions/checkout@v4.1.4 with: path: code submodules: true @@ -425,13 +425,13 @@ jobs: # Upload the tarballs. Retain the file for a limited time in case developers need to download # and run tests locally for further debugging. - name: 'Upload build' - uses: actions/upload-artifact@v4.3.1 + uses: actions/upload-artifact@v4.3.3 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} path: build.tar retention-days: 7 - name: 'Upload install' - uses: actions/upload-artifact@v4.3.1 + uses: actions/upload-artifact@v4.3.3 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} path: install.tar @@ -479,13 +479,13 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.1.1 + uses: actions/checkout@v4.1.4 with: path: code submodules: true - name: Download install - uses: actions/download-artifact@v4.1.4 + uses: actions/download-artifact@v4.1.7 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar install @@ -549,13 +549,13 @@ jobs: run: ( shopt -s dotglob nullglob; rm -rf ./* ) shell: bash - name: Checkout - uses: actions/checkout@v4.1.1 + uses: actions/checkout@v4.1.4 with: path: code submodules: true - name: Download build - uses: actions/download-artifact@v4.1.4 + uses: actions/download-artifact@v4.1.7 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar build From 46752e4d810ab5151c5cf995ef8a32dd66fcf0f9 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 16 May 2024 09:05:39 -0400 Subject: [PATCH 3/6] Update mailmap. --- .mailmap | 1 + 1 file changed, 1 insertion(+) diff --git a/.mailmap b/.mailmap index 8ba4cf3ae8..fa92936a82 100644 --- a/.mailmap +++ b/.mailmap @@ -180,3 +180,4 @@ Simone Ciarella Ciarella, S 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> From 1cc8b54ce34b9178fe8bbf76ca82befcad992d7e Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 16 May 2024 09:37:44 -0400 Subject: [PATCH 4/6] Update change log. --- CHANGELOG.rst | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index a477cb2563..107ecdb986 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -7,6 +7,37 @@ Change Log 4.x --- +4.7.0 (2024-05-17) +^^^^^^^^^^^^^^^^^^ + +*Fixed* + +* ``md.methods.rattle.Brownian`` executes without causing a segmentation fault on the CPU with domain + decomposition (`#1748 `__). +* Compile ``BoxDim.h`` without warnings + (`#1756 `__). +* Do not compute dipole-dipole interactions that are not necessary + (`#1758 `__). +* Correctly define the units of gamma in ``md.methods.Langevin`` + (`#1771 `__). +* Fix compile errors with external components that use the Expanded Mie potential + (`#1781 `__). +* Allow HPMC pair potentials to be subclassed in external components + (`#1780 `__). + +*Added* + +* "How to tune move sizes in multicomponent HPMC systems" documentation page + (`#1750 `__). +* ``hoomd.box.from_basis_vectors`` - construct a box from arbitrary basis vectors + (`#1769 `__). + +*Changed* + +* Make readthedocs builds more reproducible + (`#1758 `__). + + 4.6.0 (2024-03-19) ^^^^^^^^^^^^^^^^^^ From 99ea11b0fe7eae0aac31ec54e5a3a5e35e24ab0f Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 16 May 2024 09:43:59 -0400 Subject: [PATCH 5/6] Bump version to 4.7.0 --- .bumpversion.cfg | 2 +- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/ISSUE_TEMPLATE/release.md | 2 +- BUILDING.rst | 4 ++-- CMakeLists.txt | 2 +- INSTALLING.rst | 6 +++--- hoomd/hpmc/external/user.py | 4 ++-- hoomd/hpmc/pair/user.py | 4 ++-- sphinx-doc/conf.py | 4 ++-- 9 files changed, 15 insertions(+), 15 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 638d0c932f..54ef82c222 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 4.6.0 +current_version = 4.7.0 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 889d2be696..8505b540f9 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: 4.6.0 + placeholder: 4.7.0 validations: required: true - type: markdown diff --git a/.github/ISSUE_TEMPLATE/release.md b/.github/ISSUE_TEMPLATE/release.md index dc505b8ef8..1ee80f45de 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 4.6.0' +title: 'Release 4.7.0' labels: '' assignees: 'joaander' diff --git a/BUILDING.rst b/BUILDING.rst index 2247b0df49..b87f19dcf6 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-4.6.0.tar.gz`_. +Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.7.0.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-4.6.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.6.0/hoomd-4.6.0.tar.gz +.. _Download hoomd-4.7.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.7.0/hoomd-4.7.0.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 3c2535fa22..03751e5512 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -18,7 +18,7 @@ add_subdirectory (CMake) ################################ ## Version information -set(HOOMD_VERSION_RAW "4.6.0") +set(HOOMD_VERSION_RAW "4.7.0") 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 d2bff5add1..1c92a7b6ed 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=4.6.0 + $ conda install hoomd=4.7.0 ``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=4.6.0=*gpu*" "cuda-version=12.0" + $ conda install "hoomd=4.7.0=*gpu*" "cuda-version=12.0" Similarly, you can force CPU only package installation with:: - $ conda install "hoomd=4.6.0=*cpu*" + $ conda install "hoomd=4.7.0=*cpu*" .. note:: diff --git a/hoomd/hpmc/external/user.py b/hoomd/hpmc/external/user.py index 139e5a9fca..c9ad202bb3 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/\ - v4.6.0/hoomd/VectorMath.h + v4.7.0/hoomd/VectorMath.h .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\ - v4.6.0/hoomd/BoxDim.h + v4.7.0/hoomd/BoxDim.h .. rubric:: Example: diff --git a/hoomd/hpmc/pair/user.py b/hoomd/hpmc/pair/user.py index e59b79923f..e153eac46a 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/\ - v4.6.0/hoomd/VectorMath.h + v4.7.0/hoomd/VectorMath.h Note: Your code *must* return a value. @@ -343,7 +343,7 @@ class CPPPotentialUnion(CPPPotentialBase): CPPPotentialUnion uses threaded execution on multiple CPU cores. - .. deprecated:: 4.6.0 + .. deprecated:: 4.7.0 ``num_cpu_threads >= 1`` is deprecated. Set ``num_cpu_threads = 1``. diff --git a/sphinx-doc/conf.py b/sphinx-doc/conf.py index ca682c0fcf..1914069262 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 = '4.6.0' -release = '4.6.0' +version = '4.7.0' +release = '4.7.0' language = 'en' From ff4c6d4d5b4a10dc4e8ad8335e095dbb2ebbb4df Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Thu, 16 May 2024 09:45:13 -0400 Subject: [PATCH 6/6] Fix release date. --- CHANGELOG.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 107ecdb986..26e918446c 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -7,7 +7,7 @@ Change Log 4.x --- -4.7.0 (2024-05-17) +4.7.0 (2024-05-16) ^^^^^^^^^^^^^^^^^^ *Fixed*