From 3725453be633d1d95bf94cea8c41289abc0acebf Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 13 Feb 2024 11:28:20 -0500 Subject: [PATCH 1/4] 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 d02a778efa..eff1ec718a 160000 --- a/sphinx-doc/tutorial +++ b/sphinx-doc/tutorial @@ -1 +1 @@ -Subproject commit d02a778efa3280d80f357f150421c6b60024465d +Subproject commit eff1ec718a6648c3934cc180f93cafaf8bbe0e2d From eaa53a7abfb65413789bb8d12bdf53b294e5a422 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 13 Feb 2024 11:32:23 -0500 Subject: [PATCH 2/4] Update actions versions. --- .github/workflows/release.yml | 4 ++-- .github/workflows/stale.yml | 2 +- .github/workflows/templates/release.yml | 4 ++-- .github/workflows/templates/test.yml | 10 +++++----- .github/workflows/test.yml | 20 ++++++++++---------- 5 files changed, 20 insertions(+), 20 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index b7d1de0b31..e56adf0407 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -70,7 +70,7 @@ jobs: run: tar -cvzf ${name}-${tag:1}.tar.gz ${name}-${tag:1} - name: Upload release files - uses: actions/upload-artifact@v3.1.3 + uses: actions/upload-artifact@v4.3.1 with: name: release path: | @@ -84,7 +84,7 @@ jobs: steps: - name: Download artifacts - uses: actions/download-artifact@v3.0.2 + uses: actions/download-artifact@v4.1.2 with: name: release diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml index 23832bd175..e3c8161c7b 100644 --- a/.github/workflows/stale.yml +++ b/.github/workflows/stale.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Run stale action - uses: actions/stale@v8.0.0 + uses: actions/stale@v9.0.0 with: operations-per-run: 120 delete-branch: true diff --git a/.github/workflows/templates/release.yml b/.github/workflows/templates/release.yml index 2e4ed52f0f..a4e507aaae 100644 --- a/.github/workflows/templates/release.yml +++ b/.github/workflows/templates/release.yml @@ -57,7 +57,7 @@ jobs: run: tar -cvzf ${name}-${tag:1}.tar.gz ${name}-${tag:1} - name: Upload release files - uses: actions/upload-artifact@v3.1.3 + uses: actions/upload-artifact@v4.3.1 with: name: release path: | @@ -71,7 +71,7 @@ jobs: steps: - name: Download artifacts - uses: actions/download-artifact@v3.0.2 + uses: actions/download-artifact@v4.1.2 with: name: release diff --git a/.github/workflows/templates/test.yml b/.github/workflows/templates/test.yml index ed56c9c88d..b9c6e695c5 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@v3.1.3 + uses: actions/upload-artifact@v4.3.1 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} path: build.tar retention-days: 7 - name: 'Upload install' - uses: actions/upload-artifact@v3.1.3 + uses: actions/upload-artifact@v4.3.1 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@v3.0.2 + uses: actions/download-artifact@v4.1.2 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@v3.0.2 + uses: actions/download-artifact@v4.1.2 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar install @@ -211,7 +211,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Use jetstream2-admin/start - uses: glotzerlab/jetstream2-admin/start@v1.2.3 + uses: glotzerlab/jetstream2-admin/start@v1.2.4 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 a4a51f59c9..f84a637f4e 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@v1.2.3 + uses: glotzerlab/jetstream2-admin/start@v1.2.4 with: OS_APPLICATION_CREDENTIAL_ID: ${{ secrets.OS_APPLICATION_CREDENTIAL_ID }} OS_APPLICATION_CREDENTIAL_SECRET: ${{ secrets.OS_APPLICATION_CREDENTIAL_SECRET }} @@ -145,13 +145,13 @@ jobs: # Upload the tarballs. Retain the file for a limited time in case developers need to download # and run tests locally for further debugging. - name: 'Upload build' - uses: actions/upload-artifact@v3.1.3 + uses: actions/upload-artifact@v4.3.1 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} path: build.tar retention-days: 7 - name: 'Upload install' - uses: actions/upload-artifact@v3.1.3 + uses: actions/upload-artifact@v4.3.1 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} path: install.tar @@ -196,7 +196,7 @@ jobs: submodules: true - name: Download install - uses: actions/download-artifact@v3.0.2 + uses: actions/download-artifact@v4.1.2 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar install @@ -257,7 +257,7 @@ jobs: submodules: true - name: Download build - uses: actions/download-artifact@v3.0.2 + uses: actions/download-artifact@v4.1.2 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar build @@ -307,7 +307,7 @@ jobs: submodules: true - name: Download install - uses: actions/download-artifact@v3.0.2 + uses: actions/download-artifact@v4.1.2 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar install @@ -425,13 +425,13 @@ jobs: # Upload the tarballs. Retain the file for a limited time in case developers need to download # and run tests locally for further debugging. - name: 'Upload build' - uses: actions/upload-artifact@v3.1.3 + uses: actions/upload-artifact@v4.3.1 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} path: build.tar retention-days: 7 - name: 'Upload install' - uses: actions/upload-artifact@v3.1.3 + uses: actions/upload-artifact@v4.3.1 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} path: install.tar @@ -485,7 +485,7 @@ jobs: submodules: true - name: Download install - uses: actions/download-artifact@v3.0.2 + uses: actions/download-artifact@v4.1.2 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar install @@ -555,7 +555,7 @@ jobs: submodules: true - name: Download build - uses: actions/download-artifact@v3.0.2 + uses: actions/download-artifact@v4.1.2 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar build From 900cb9473268a4387c37f64124af120325756cd9 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 13 Feb 2024 12:24:46 -0500 Subject: [PATCH 3/4] Update mailmap. --- .mailmap | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.mailmap b/.mailmap index f29d148ba4..8ba4cf3ae8 100644 --- a/.mailmap +++ b/.mailmap @@ -1,3 +1,4 @@ + Joshua A. Anderson Joshua Anderson Joshua A. Anderson joaander Joshua A. Anderson test @@ -144,6 +145,7 @@ Sophie YouJung Lee Sophie YJL Yuan Zhou yuanzhou0827 <46976996+yuanzhou0827@users.noreply.github.com> Yuan Zhou yuanzhou Tobias Dwyer Tobias-Dwyer <55504950+Tobias-Dwyer@users.noreply.github.com> +Tobias Dwyer Tobias-Dwyer Sophie YouJung Lee SophieYJL <44685431+syjlee@users.noreply.github.com> Sophie YouJung Lee Sophie Youjung Lee Jakin B. Delony <53496274+jbdelony@users.noreply.github.com> jbdelony <53496274+jbdelony@users.noreply.github.com> @@ -177,3 +179,4 @@ Alex Lee shihkual Simone Ciarella Ciarella, S Simone Ciarella SCiarella Simone Ciarella SCiarella <58949181+SCiarella@users.noreply.github.com> +Kieran Nehil-Puleo kierannp From 7ce2ac1e6fd300ea97186668484064726241f271 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 13 Feb 2024 13:00:59 -0500 Subject: [PATCH 4/4] Bump version to 4.5.0. --- .bumpversion.cfg | 4 +++- .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 | 6 +++--- sphinx-doc/conf.py | 4 ++-- 9 files changed, 18 insertions(+), 16 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 98b170bf5b..20f07d9820 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 4.4.1 +current_version = 4.5.0 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-]*)))?$ @@ -25,3 +25,5 @@ values = [bumpversion:file:hoomd/hpmc/external/user.py] [bumpversion:file:.github/ISSUE_TEMPLATE/bug_report.yml] + +[bumpversion:file:.github/ISSUE_TEMPLATE/release.md] diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index e5ab65cdca..9ad881efc2 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: 4.4.1 + placeholder: 4.5.0 validations: required: true - type: markdown diff --git a/.github/ISSUE_TEMPLATE/release.md b/.github/ISSUE_TEMPLATE/release.md index 1821609a5a..6155bc2784 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.x.y' +title: 'Release 4.5.0' labels: '' assignees: 'joaander' diff --git a/BUILDING.rst b/BUILDING.rst index 4e6196112f..4dbbadc366 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-4.4.1.tar.gz`_. +Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.5.0.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-4.4.1.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.4.1/hoomd-4.4.1.tar.gz +.. _Download hoomd-4.5.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.5.0/hoomd-4.5.0.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 cbbb7e4907..3852a353af 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -14,7 +14,7 @@ add_subdirectory (CMake) ################################ ## Version information -set(HOOMD_VERSION_RAW "4.4.1") +set(HOOMD_VERSION_RAW "4.5.0") 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 7a50846c75..192bfa948a 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=4.4.1 + $ conda install hoomd=4.5.0 ``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=4.4.1=*gpu*" "cuda-version=12.0" + $ conda install "hoomd=4.5.0=*gpu*" "cuda-version=12.0" Similarly, you can force CPU only package installation with:: - $ conda install "hoomd=4.4.1=*cpu*" + $ conda install "hoomd=4.5.0=*cpu*" .. note:: diff --git a/hoomd/hpmc/external/user.py b/hoomd/hpmc/external/user.py index 6016a4bf06..72415d8d09 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/\ - v4.4.1/hoomd/VectorMath.h + v4.5.0/hoomd/VectorMath.h .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\ - v4.4.1/hoomd/BoxDim.h + v4.5.0/hoomd/BoxDim.h .. rubric:: Example: diff --git a/hoomd/hpmc/pair/user.py b/hoomd/hpmc/pair/user.py index 6ce11c4336..bc648d2f4c 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/\ - v4.4.1/hoomd/VectorMath.h + v4.5.0/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:: 4.4.1 + .. deprecated:: 4.5.0 ``num_cpu_threads >= 1`` is deprecated. Set ``num_cpu_threads = 1``. @@ -543,7 +543,7 @@ def _attach_hook(self): if (isinstance(self._simulation.device, hoomd.device.CPU) and self._simulation.device.num_cpu_threads > 1): warnings.warn( - "num_cpu_threads > 1 is deprecated since 4.4.1. " + "num_cpu_threads > 1 is deprecated since 4.5.0. " "Use num_cpu_threads=1.", FutureWarning, stacklevel=1) diff --git a/sphinx-doc/conf.py b/sphinx-doc/conf.py index 5b2803bf1a..97dd4a01ab 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 = '4.4.1' -release = '4.4.1' +version = '4.5.0' +release = '4.5.0' language = 'en'