From 61fbadbdcb17a21d42c668db57e3163e67836901 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 14 Dec 2021 11:16:48 -0500 Subject: [PATCH 1/6] Update change log --- CHANGELOG.rst | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 3959ab622a..82d11fadc6 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,6 +4,27 @@ Change Log v3.x ---- +v3.0.0-beta.12 (2021-12-15) +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +*Added* + +* Support simulations with arbitrarily large or small scales (within the limits of the floating + point representation). + +*Changed* + +* Report full error message in the exception reasons. +* Improved documentation. +* [breaking]: ``buffer`` is now a required argument when constructing a neighbor list. +* [breaking]: ``force_tol``, ``angmom_tol``, and ``energy_tol`` are now required arguments to + ``md.minimize.FIRE`` + +*Fixed* + +* Allow neighbor lists to store more than ``2**32-1`` total neighbors. +* Return expected parameter values instead of ``NaN`` when potential parameters are set to 0. + v3.0.0-beta.11 (2021-11-18) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ From e9007cb48c73b6214bc5de14f4cb0c4b3ed47aea Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 14 Dec 2021 11:23:01 -0500 Subject: [PATCH 2/6] Update GitHub actions. --- .github/workflows/release.yml | 4 ++-- .github/workflows/templates/release.yml | 4 ++-- .github/workflows/templates/test.yml | 8 ++++---- .github/workflows/test.yml | 18 +++++++++--------- 4 files changed, 17 insertions(+), 17 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 66e63e007a..68fef51cf9 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -67,7 +67,7 @@ jobs: run: tar -cvzf ${name}-${tag}.tar.gz ${name}-${tag} - name: Upload release files - uses: actions/upload-artifact@v2.2.4 + uses: actions/upload-artifact@v2.3.0 with: name: release path: | @@ -81,7 +81,7 @@ jobs: steps: - name: Download artifacts - uses: actions/download-artifact@v2.0.10 + uses: actions/download-artifact@v2.1.0 with: name: release diff --git a/.github/workflows/templates/release.yml b/.github/workflows/templates/release.yml index b5f4094f82..767ab8419a 100644 --- a/.github/workflows/templates/release.yml +++ b/.github/workflows/templates/release.yml @@ -53,7 +53,7 @@ jobs: run: tar -cvzf ${name}-${tag}.tar.gz ${name}-${tag} - name: Upload release files - uses: actions/upload-artifact@v2.2.4 + uses: actions/upload-artifact@v2.3.0 with: name: release path: | @@ -67,7 +67,7 @@ jobs: steps: - name: Download artifacts - uses: actions/download-artifact@v2.0.10 + uses: actions/download-artifact@v2.1.0 with: name: release diff --git a/.github/workflows/templates/test.yml b/.github/workflows/templates/test.yml index ee48f0dca3..32f226f408 100644 --- a/.github/workflows/templates/test.yml +++ b/.github/workflows/templates/test.yml @@ -84,13 +84,13 @@ 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@v2.2.4 + uses: actions/upload-artifact@v2.3.0 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} path: build.tar retention-days: 7 - name: 'Upload install' - uses: actions/upload-artifact@v2.2.4 + uses: actions/upload-artifact@v2.3.0 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} path: install.tar @@ -98,7 +98,7 @@ env: <% endset %> <% set download_build_steps %> - name: Download build - uses: actions/download-artifact@v2.0.10 + uses: actions/download-artifact@v2.1.0 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar build @@ -106,7 +106,7 @@ env: <% endset %> <% set download_install_steps %> - name: Download install - uses: actions/download-artifact@v2.0.10 + uses: actions/download-artifact@v2.1.0 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar install diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index b1f1f23f4a..c49a3d958b 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -100,13 +100,13 @@ 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@v2.2.4 + uses: actions/upload-artifact@v2.3.0 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} path: build.tar retention-days: 7 - name: 'Upload install' - uses: actions/upload-artifact@v2.2.4 + uses: actions/upload-artifact@v2.3.0 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} path: install.tar @@ -133,7 +133,7 @@ jobs: run: rm -rf ./* - name: Download install - uses: actions/download-artifact@v2.0.10 + uses: actions/download-artifact@v2.1.0 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar install @@ -176,7 +176,7 @@ jobs: run: rm -rf ./* - name: Download build - uses: actions/download-artifact@v2.0.10 + uses: actions/download-artifact@v2.1.0 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar build @@ -213,7 +213,7 @@ jobs: run: rm -rf ./* - name: Download install - uses: actions/download-artifact@v2.0.10 + uses: actions/download-artifact@v2.1.0 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar install @@ -289,13 +289,13 @@ 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@v2.2.4 + uses: actions/upload-artifact@v2.3.0 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} path: build.tar retention-days: 7 - name: 'Upload install' - uses: actions/upload-artifact@v2.2.4 + uses: actions/upload-artifact@v2.3.0 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} path: install.tar @@ -332,7 +332,7 @@ jobs: run: rm -rf ./* - name: Download install - uses: actions/download-artifact@v2.0.10 + uses: actions/download-artifact@v2.1.0 with: name: install-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar install @@ -385,7 +385,7 @@ jobs: run: rm -rf ./* - name: Download build - uses: actions/download-artifact@v2.0.10 + uses: actions/download-artifact@v2.1.0 with: name: build-${{ join(matrix.config, '_') }}-${{ github.sha }} - name: Untar build From 66a2ba6aa8fd337a1cd7806292d12fac15cc9285 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 14 Dec 2021 11:23:45 -0500 Subject: [PATCH 3/6] Bump version to 3.0.0-beta.12. --- .bumpversion.cfg | 6 +++--- CMakeLists.txt | 2 +- hoomd/hpmc/external/user.py | 4 ++-- hoomd/hpmc/pair/user.py | 2 +- sphinx-doc/conf.py | 4 ++-- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 2b97b71dc4..13c152461e 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,14 +1,14 @@ [bumpversion] -current_version = 3.0.0-beta.11 +current_version = 3.0.0-beta.12 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-]*)))?$ -serialize = +serialize = {major}.{minor}.{patch}-{prerelease}.{number} {major}.{minor}.{patch} [bumpversion:part:prerelease] -values = +values = beta rc diff --git a/CMakeLists.txt b/CMakeLists.txt index 9f41960583..c34b310088 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -14,7 +14,7 @@ add_subdirectory (CMake) ################################ ## Version information -set(HOOMD_VERSION_RAW "3.0.0-beta.11") +set(HOOMD_VERSION_RAW "3.0.0-beta.12") 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/hoomd/hpmc/external/user.py b/hoomd/hpmc/external/user.py index 660e696675..2c8a9b7754 100644 --- a/hoomd/hpmc/external/user.py +++ b/hoomd/hpmc/external/user.py @@ -60,9 +60,9 @@ class CPPExternalPotential(_HOOMDBaseObject): Your code *must* return a value. .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\ - v3.0.0-beta.11/hoomd/VectorMath.h + v3.0.0-beta.12/hoomd/VectorMath.h .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\ - v3.0.0-beta.11/hoomd/BoxDim.h + v3.0.0-beta.12/hoomd/BoxDim.h Example: .. code-block:: python diff --git a/hoomd/hpmc/pair/user.py b/hoomd/hpmc/pair/user.py index 609e29ad33..f2982b3cb8 100644 --- a/hoomd/hpmc/pair/user.py +++ b/hoomd/hpmc/pair/user.py @@ -68,7 +68,7 @@ class CPPPotentialBase(_HOOMDBaseObject): HOOMD-blue source code. .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\ - v3.0.0-beta.11/hoomd/VectorMath.h + v3.0.0-beta.12/hoomd/VectorMath.h Note: Your code *must* return a value. diff --git a/sphinx-doc/conf.py b/sphinx-doc/conf.py index e272b086c1..050909ee6e 100644 --- a/sphinx-doc/conf.py +++ b/sphinx-doc/conf.py @@ -51,8 +51,8 @@ copyright = '2009-2021 The Regents of the University of Michigan' author = 'The Regents of the University of Michigan' -version = '3.0.0-beta.11' -release = '3.0.0-beta.11' +version = '3.0.0-beta.12' +release = '3.0.0-beta.12' language = None From f875a577d02d41d9a8a16979f9ebfa5b6ab62ad5 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 14 Dec 2021 16:30:58 +0000 Subject: [PATCH 4/6] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .bumpversion.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 13c152461e..585e465add 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -3,12 +3,12 @@ current_version = 3.0.0-beta.12 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-]*)))?$ -serialize = +serialize = {major}.{minor}.{patch}-{prerelease}.{number} {major}.{minor}.{patch} [bumpversion:part:prerelease] -values = +values = beta rc From 527dd79d2090d7c2e0b195c4519580c2096e87ad Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 14 Dec 2021 11:56:25 -0500 Subject: [PATCH 5/6] Update tutorial. --- sphinx-doc/tutorial | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sphinx-doc/tutorial b/sphinx-doc/tutorial index 92038ecc81..5a5e4e11e9 160000 --- a/sphinx-doc/tutorial +++ b/sphinx-doc/tutorial @@ -1 +1 @@ -Subproject commit 92038ecc811ca450acd3c2912eb818c4ebece06b +Subproject commit 5a5e4e11e96397b761e90b27983cc38e2fb1a324 From 7f12e1fd9bbcd0c993839f336edf9b227bfa5d0d Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Tue, 14 Dec 2021 12:35:22 -0500 Subject: [PATCH 6/6] Update change log. --- CHANGELOG.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 82d11fadc6..0d69e114b7 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,7 +4,7 @@ Change Log v3.x ---- -v3.0.0-beta.12 (2021-12-15) +v3.0.0-beta.12 (2021-12-14) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ *Added* @@ -14,7 +14,7 @@ v3.0.0-beta.12 (2021-12-15) *Changed* -* Report full error message in the exception reasons. +* Report full error details in the exception message. * Improved documentation. * [breaking]: ``buffer`` is now a required argument when constructing a neighbor list. * [breaking]: ``force_tol``, ``angmom_tol``, and ``energy_tol`` are now required arguments to