From f433c6d6e0defce881bc9dbb4aaab9d9db8be75e Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 09:22:49 -0400 Subject: [PATCH 01/23] Add nanobind to pyproject.toml. --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index e2353d6d9..e647c8cbe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["setuptools", "wheel", "numpy>=2.0.0rc1", "cython>=3.0.2", "scikit-build>=0.17.3", "cmake"] +requires = ["setuptools", "wheel", "numpy>=2.0.0rc1", "cython>=3.0.2", "scikit-build>=0.17.3", "cmake", "nanobind>=2.0.0"] build-backend = "setuptools.build_meta" [project] From 1d518d090d5b5407da880768bdb9fd9c637a4c06 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 09:23:25 -0400 Subject: [PATCH 02/23] Attempt to run style check action. --- .github/workflows/env-files/environment.yaml | 2 + .../workflows/env-files/py310-conda-lock.yml | 2891 ++++++++++------- .../workflows/env-files/py311-conda-lock.yml | 2610 ++++++++++----- .../workflows/env-files/py312-conda-lock.yml | 2666 ++++++++++----- .../workflows/env-files/py39-conda-lock.yml | 2606 ++++++++++----- .github/workflows/style_check.yml | 28 +- 6 files changed, 7109 insertions(+), 3694 deletions(-) diff --git a/.github/workflows/env-files/environment.yaml b/.github/workflows/env-files/environment.yaml index e8a1037a9..bfd3e7db4 100644 --- a/.github/workflows/env-files/environment.yaml +++ b/.github/workflows/env-files/environment.yaml @@ -4,6 +4,7 @@ channels: dependencies: - python==3.12 + - cppcheck - tbb - tbb-devel - ninja @@ -14,6 +15,7 @@ dependencies: - matplotlib - numpy - pillow + - pre-commit - pytest - rowan - scikit-build diff --git a/.github/workflows/env-files/py310-conda-lock.yml b/.github/workflows/env-files/py310-conda-lock.yml index 7a081632a..004d8abc5 100644 --- a/.github/workflows/env-files/py310-conda-lock.yml +++ b/.github/workflows/env-files/py310-conda-lock.yml @@ -13,10 +13,10 @@ version: 1 metadata: content_hash: - 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name: zstd diff --git a/.github/workflows/env-files/py311-conda-lock.yml b/.github/workflows/env-files/py311-conda-lock.yml index 182b143e3..ea552ddde 100644 --- a/.github/workflows/env-files/py311-conda-lock.yml +++ b/.github/workflows/env-files/py311-conda-lock.yml @@ -13,10 +13,10 @@ version: 1 metadata: content_hash: - osx-arm64: 1b80c4b9bce63d706e13275a010441b3ecdb233a657b52141f7f77b1e61863e7 - osx-64: 5b1e996fe9f5b0af19c709404d9a7bcf1adbd4fb9627c45243bb6c5f7c92f87e - linux-64: 30a52f9b086684683d3cd51e84d6faf101a5ab829ff04a49a944f0d22ce7e366 - win-64: 8db74bbcc6e369ff74a32ac878a9790757e587698dfa932ed3b22569f2163cc3 + osx-arm64: 8aee7186dee490ab6c47a4b9567db5f775e12109a53c67c6e424c0dccd06609b + osx-64: 7ceec95c625491478fa5be077b82f2eb15895ddeb84bb1131bfa40390dfb758c + linux-64: 9688d5fb9d4c9d7670c724b1f966d631894fb27b6356792863e0b63f63f3655e + win-64: 7e96e14e48954a17dca467c46ad3ffb1d0264c358b4ab124d182e4be079eb191 channels: - url: conda-forge used_env_vars: [] @@ -53,19 +53,19 @@ package: category: main optional: false - 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name: zstd diff --git a/.github/workflows/env-files/py39-conda-lock.yml b/.github/workflows/env-files/py39-conda-lock.yml index b537709a8..53aa604a8 100644 --- a/.github/workflows/env-files/py39-conda-lock.yml +++ b/.github/workflows/env-files/py39-conda-lock.yml @@ -13,10 +13,10 @@ version: 1 metadata: content_hash: - osx-arm64: 3e572aec6491a567ea0423707b44842763261653c20489833b48e9eeeff566c5 - osx-64: c2f6e528ec88a21cb888f2b77be304c1346daf6272c6e36b15cc5f24a2b03a43 - linux-64: 08411e8c9c2b748004829dd4d16bc8de731b5eb6ad05724da40e4f5d95729417 - win-64: 9492902b2c7db80d8e97b38bca80997d76436044845b4f2510f6012345c81c15 + osx-arm64: 8a3e2ab59a9fc10151c1f2a086d05ba4b221edaaf811c2955a7b9c939e62e0cf + osx-64: acf3502088fa5eda7d72ab02f7e52e6d4b2226ea9a31f1417f31d86ba9b616bd + linux-64: 65de55ad2cd8f6a63bc10642005429165fed34c1bc5914e4e0af60dc685ed88b + win-64: de7f8cb8448f01f3a616816e140a5b56df7217df67b3eff0df39a6c3fa3534b2 channels: - url: conda-forge used_env_vars: [] @@ -53,19 +53,19 @@ package: category: main optional: false - 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name: zstd diff --git a/.github/workflows/style_check.yml b/.github/workflows/style_check.yml index 0ac4c9658..e4b812010 100644 --- a/.github/workflows/style_check.yml +++ b/.github/workflows/style_check.yml @@ -5,35 +5,37 @@ concurrency: cancel-in-progress: true on: - # Trigger on pull requests. pull_request: - # Trigger on pushes to main push: branches: - "main" - # Trigger on request. workflow_dispatch: +defaults: + run: + shell: bash -leo pipefail {0} + jobs: clang-tidy: name: Check C++ Code Style - runs-on: ubuntu-latest - container: - image: glotzerlab/ci:2021.11-clang10_py38 + runs-on: ubuntu-20.04 steps: - - uses: actions/checkout@v4.1.6 + - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7 with: submodules: true - - name: Install pre-commit - run: python3 -m pip install pre-commit + - name: Create Python Environment + uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822 # v1.9.0 + with: + micromamba-version: '1.5.8-0' + environment-name: test + environment-file: .github/workflows/env-files/py312-conda-lock.yml - name: Build freud and export compile commands run: | - # glotzerlab ci containers do not come with scikit-build installed - # this install can be removed once scikit-build is in the container - python3 -m pip install scikit-build - python3 setup.py build_ext --inplace -- -DCMAKE_EXPORT_COMPILE_COMMANDS=True + uv pip install --no-build-isolation --no-deps -ve . + env: + CMAKE_ARGS: "-DCMAKE_EXPORT_COMPILE_COMMANDS=True" - name: Execute clang-tidy and cppcheck run: | pre-commit run cppcheck --all-files --hook-stage=manual From ea1102e4f12deb73c3003429a96df114cc2a91bf Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 09:36:59 -0400 Subject: [PATCH 03/23] Use static_cast. --- cpp/box/export_Box.cc | 46 +++++++++++++++++++++---------------------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/cpp/box/export_Box.cc b/cpp/box/export_Box.cc index 562796f38..188006e5b 100644 --- a/cpp/box/export_Box.cc +++ b/cpp/box/export_Box.cc @@ -11,8 +11,8 @@ void makeAbsolute(std::shared_ptr box, nb_array> ve nb_array> out) { unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = (vec3*) (vecs.data()); - vec3* out_data = (vec3*) (out.data()); + vec3* vecs_data = static_cast*>(vecs.data()); + vec3* out_data = static_cast*>(out.data()); box->makeAbsolute(vecs_data, Nvecs, out_data); } @@ -20,8 +20,8 @@ void makeFractional(std::shared_ptr box, nb_array> nb_array> out) { unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = (vec3*) (vecs.data()); - vec3* out_data = (vec3*) (out.data()); + vec3* vecs_data = static_cast*>(vecs.data()); + vec3* out_data = static_cast*>(out.data()); box->makeFractional(vecs_data, Nvecs, out_data); } @@ -29,8 +29,8 @@ void getImages(std::shared_ptr box, nb_array> vecs, nb_array> images) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = (vec3*) (vecs.data()); - vec3* images_data = (vec3*) (images.data()); + vec3* vecs_data = static_cast*>(vecs.data()); + vec3* images_data = static_cast*>(images.data()); box->getImages(vecs_data, Nvecs, images_data); } @@ -38,17 +38,17 @@ void wrap(std::shared_ptr box, nb_array> vecs, nb_array> out) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = (vec3*) (vecs.data()); - vec3* out_data = (vec3*) (out.data()); + vec3* vecs_data = static_cast*>(vecs.data()); + vec3* out_data = static_cast*>(out.data()); box->wrap(vecs_data, Nvecs, out_data); } void unwrap(std::shared_ptr box, nb_array vecs, nb_array images, nb_array out) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = (vec3*) (vecs.data()); - vec3* images_data = (vec3*) (images.data()); - vec3* out_data = (vec3*) (out.data()); + vec3* vecs_data = static_cast*>(vecs.data()); + vec3* images_data = static_cast*>(images.data()); + vec3* out_data = static_cast*>(out.data()); box->unwrap(vecs_data, images_data, Nvecs, out_data); } @@ -56,8 +56,8 @@ std::vector centerOfMass(std::shared_ptr box, nb_array vecs, nb_array> masses) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = (vec3*) (vecs.data()); - float* masses_data = (float*) (masses.data()); + vec3* vecs_data = static_cast*>(vecs.data()); + float* masses_data = static_cast(masses.data()); auto com = box->centerOfMass(vecs_data, Nvecs, masses_data); return {com.x, com.y, com.z}; } @@ -65,8 +65,8 @@ std::vector centerOfMass(std::shared_ptr box, nb_array vecs, void center(std::shared_ptr box, nb_array vecs, nb_array> masses) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = (vec3*) (vecs.data()); - float* masses_data = (float*) (masses.data()); + vec3* vecs_data = static_cast*>(vecs.data()); + float* masses_data = static_cast(masses.data()); box->center(vecs_data, Nvecs, masses_data); } @@ -74,10 +74,10 @@ void computeDistances(std::shared_ptr box, nb_array query_points, nb nb_array> distances) { const unsigned int n_query_points = query_points.shape(0); - vec3* query_points_data = (vec3*) (query_points.data()); + vec3* query_points_data = static_cast*>(query_points.data()); const unsigned int n_points = points.shape(0); - vec3* points_data = (vec3*) (points.data()); - float* distances_data = (float*) (distances.data()); + vec3* points_data = static_cast*>(points.data()); + float* distances_data = static_cast(distances.data()); if (n_query_points != n_points) { throw std::invalid_argument("The number of query points and points must match."); @@ -89,18 +89,18 @@ void computeAllDistances(std::shared_ptr box, nb_array query_points, nb_array> distances) { const unsigned int n_query_points = query_points.shape(0); - vec3* query_points_data = (vec3*) (query_points.data()); + vec3* query_points_data = static_cast*>(query_points.data()); const unsigned int n_points = points.shape(0); - vec3* points_data = (vec3*) (points.data()); - float* distances_data = (float*) (distances.data()); + vec3* points_data = static_cast*>(points.data()); + float* distances_data = static_cast(distances.data()); box->computeAllDistances(query_points_data, n_query_points, points_data, n_points, distances_data); } void contains(std::shared_ptr box, nb_array points, nb_array> contains_mask) { const unsigned int n_points = points.shape(0); - vec3* points_data = (vec3*) (points.data()); - bool* contains_mask_data = (bool*) (contains_mask.data()); + vec3* points_data = static_cast*>(points.data()); + bool* contains_mask_data = static_cast(contains_mask.data()); box->contains(points_data, n_points, contains_mask_data); } From 77a495a6f5fa6c5d6551454b7d1a9a9253fb7c23 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 09:43:50 -0400 Subject: [PATCH 04/23] Add nanobind to unit test environment. --- .github/workflows/env-files/environment.yaml | 1 + .../workflows/env-files/py310-conda-lock.yml | 56 +++++++++++++++++-- .../workflows/env-files/py311-conda-lock.yml | 56 +++++++++++++++++-- .../workflows/env-files/py312-conda-lock.yml | 56 +++++++++++++++++-- .../workflows/env-files/py39-conda-lock.yml | 56 +++++++++++++++++-- 5 files changed, 209 insertions(+), 16 deletions(-) diff --git a/.github/workflows/env-files/environment.yaml b/.github/workflows/env-files/environment.yaml index bfd3e7db4..5f0f9891d 100644 --- a/.github/workflows/env-files/environment.yaml +++ b/.github/workflows/env-files/environment.yaml @@ -13,6 +13,7 @@ dependencies: - dynasor - gsd - matplotlib + - nanobind>=2.0 - numpy - pillow - pre-commit diff --git a/.github/workflows/env-files/py310-conda-lock.yml b/.github/workflows/env-files/py310-conda-lock.yml index 004d8abc5..7609cf16a 100644 --- a/.github/workflows/env-files/py310-conda-lock.yml +++ b/.github/workflows/env-files/py310-conda-lock.yml @@ -13,10 +13,10 @@ version: 1 metadata: content_hash: - 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name: ncurses version: '6.5' manager: conda diff --git a/.github/workflows/env-files/py311-conda-lock.yml b/.github/workflows/env-files/py311-conda-lock.yml index ea552ddde..2fb3ebe20 100644 --- a/.github/workflows/env-files/py311-conda-lock.yml +++ b/.github/workflows/env-files/py311-conda-lock.yml @@ -13,10 +13,10 @@ version: 1 metadata: content_hash: - osx-arm64: 8aee7186dee490ab6c47a4b9567db5f775e12109a53c67c6e424c0dccd06609b - osx-64: 7ceec95c625491478fa5be077b82f2eb15895ddeb84bb1131bfa40390dfb758c - linux-64: 9688d5fb9d4c9d7670c724b1f966d631894fb27b6356792863e0b63f63f3655e - win-64: 7e96e14e48954a17dca467c46ad3ffb1d0264c358b4ab124d182e4be079eb191 + osx-arm64: 371845dfed193f8e2c5bd84f67c999680ec7c09c8f926cc96129136c3c69e251 + osx-64: e92869c0cd433fe777f02a014fd5ab836336677a36a9013f68a8e8f99038b824 + linux-64: 3c49aa4b6769dc88ffeee52b0e181a01255c9c313328905516daad1b85ce2f89 + win-64: 5fddc6705b086ad21a9f0f5997164f00add479d542ae0849abe3a764ae06233a channels: - url: conda-forge used_env_vars: [] @@ -6390,6 +6390,54 @@ package: sha256: c39cdd1a5829aeffc611f789bdfd4dbd4ce1aa829c73d728defec180b5265d91 category: main optional: false +- name: nanobind + version: 2.0.0 + manager: conda + platform: linux-64 + dependencies: + python: '>=3.8' + url: https://conda.anaconda.org/conda-forge/noarch/nanobind-2.0.0-pyhd8ed1ab_1.conda + hash: + md5: eb27b425a215c7ddfb03f1547897e467 + sha256: e98e30de46985b78c34083e00b4accf2fb7ebb382f58f8d0f10125cfdc1d3f48 + category: main + optional: false +- name: nanobind + version: 2.0.0 + manager: conda + platform: osx-64 + dependencies: + python: '>=3.8' + url: https://conda.anaconda.org/conda-forge/noarch/nanobind-2.0.0-pyhd8ed1ab_1.conda + hash: + md5: eb27b425a215c7ddfb03f1547897e467 + sha256: e98e30de46985b78c34083e00b4accf2fb7ebb382f58f8d0f10125cfdc1d3f48 + category: main + optional: false +- name: nanobind + version: 2.0.0 + manager: conda + platform: osx-arm64 + dependencies: + python: '>=3.8' + url: https://conda.anaconda.org/conda-forge/noarch/nanobind-2.0.0-pyhd8ed1ab_1.conda + hash: + md5: eb27b425a215c7ddfb03f1547897e467 + sha256: e98e30de46985b78c34083e00b4accf2fb7ebb382f58f8d0f10125cfdc1d3f48 + category: main + optional: false +- name: nanobind + version: 2.0.0 + manager: conda + platform: win-64 + dependencies: + python: '>=3.8' + url: https://conda.anaconda.org/conda-forge/noarch/nanobind-2.0.0-pyhd8ed1ab_1.conda + hash: + md5: eb27b425a215c7ddfb03f1547897e467 + sha256: e98e30de46985b78c34083e00b4accf2fb7ebb382f58f8d0f10125cfdc1d3f48 + category: main + optional: false - 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name: ncurses version: '6.5' manager: conda From 423f497f8585d542aba2edeb2127af7ddcab7fc8 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 09:44:02 -0400 Subject: [PATCH 05/23] Convert readthedocs build to pip. --- .readthedocs.yaml | 6 +++--- doc/readthedocs-env.yml | 1 + 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 1149cb926..4f360ab1a 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,13 +1,13 @@ version: 2 build: - os: ubuntu-22.04 + os: ubuntu-24.04 tools: - python: "mambaforge-4.10" + python: "mambaforge-23.11" conda: environment: doc/readthedocs-env.yml python: install: - - method: setuptools + - method: pip path: . submodules: include: all diff --git a/doc/readthedocs-env.yml b/doc/readthedocs-env.yml index a9068317c..d89a00f27 100644 --- a/doc/readthedocs-env.yml +++ b/doc/readthedocs-env.yml @@ -9,6 +9,7 @@ dependencies: - cython==3.0.10 - tbb==2021.12.0 - tbb-devel==2021.12.0 + - nanobind==2.0.0 - numpy==1.26.4 - rowan==1.3.0.post1 - scipy==1.13.1 From b48ac3e68d4b37ed77edb8c0ecefa35ec9595395 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 09:52:46 -0400 Subject: [PATCH 06/23] Use reinterpret_cast --- cpp/box/export_Box.cc | 46 +++++++++++++++++++++---------------------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/cpp/box/export_Box.cc b/cpp/box/export_Box.cc index 188006e5b..7617a5005 100644 --- a/cpp/box/export_Box.cc +++ b/cpp/box/export_Box.cc @@ -11,8 +11,8 @@ void makeAbsolute(std::shared_ptr box, nb_array> ve nb_array> out) { unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = static_cast*>(vecs.data()); - vec3* out_data = static_cast*>(out.data()); + vec3* vecs_data = reinterpret_cast*>(vecs.data()); + vec3* out_data = reinterpret_cast*>(out.data()); box->makeAbsolute(vecs_data, Nvecs, out_data); } @@ -20,8 +20,8 @@ void makeFractional(std::shared_ptr box, nb_array> nb_array> out) { unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = static_cast*>(vecs.data()); - vec3* out_data = static_cast*>(out.data()); + vec3* vecs_data = reinterpret_cast*>(vecs.data()); + vec3* out_data = reinterpret_cast*>(out.data()); box->makeFractional(vecs_data, Nvecs, out_data); } @@ -29,8 +29,8 @@ void getImages(std::shared_ptr box, nb_array> vecs, nb_array> images) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = static_cast*>(vecs.data()); - vec3* images_data = static_cast*>(images.data()); + vec3* vecs_data = reinterpret_cast*>(vecs.data()); + vec3* images_data = reinterpret_cast*>(images.data()); box->getImages(vecs_data, Nvecs, images_data); } @@ -38,17 +38,17 @@ void wrap(std::shared_ptr box, nb_array> vecs, nb_array> out) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = static_cast*>(vecs.data()); - vec3* out_data = static_cast*>(out.data()); + vec3* vecs_data = reinterpret_cast*>(vecs.data()); + vec3* out_data = reinterpret_cast*>(out.data()); box->wrap(vecs_data, Nvecs, out_data); } void unwrap(std::shared_ptr box, nb_array vecs, nb_array images, nb_array out) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = static_cast*>(vecs.data()); - vec3* images_data = static_cast*>(images.data()); - vec3* out_data = static_cast*>(out.data()); + vec3* vecs_data = reinterpret_cast*>(vecs.data()); + vec3* images_data = reinterpret_cast*>(images.data()); + vec3* out_data = reinterpret_cast*>(out.data()); box->unwrap(vecs_data, images_data, Nvecs, out_data); } @@ -56,8 +56,8 @@ std::vector centerOfMass(std::shared_ptr box, nb_array vecs, nb_array> masses) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = static_cast*>(vecs.data()); - float* masses_data = static_cast(masses.data()); + vec3* vecs_data = reinterpret_cast*>(vecs.data()); + float* masses_data = reinterpret_cast(masses.data()); auto com = box->centerOfMass(vecs_data, Nvecs, masses_data); return {com.x, com.y, com.z}; } @@ -65,8 +65,8 @@ std::vector centerOfMass(std::shared_ptr box, nb_array vecs, void center(std::shared_ptr box, nb_array vecs, nb_array> masses) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = static_cast*>(vecs.data()); - float* masses_data = static_cast(masses.data()); + vec3* vecs_data = reinterpret_cast*>(vecs.data()); + float* masses_data = reinterpret_cast(masses.data()); box->center(vecs_data, Nvecs, masses_data); } @@ -74,10 +74,10 @@ void computeDistances(std::shared_ptr box, nb_array query_points, nb nb_array> distances) { const unsigned int n_query_points = query_points.shape(0); - vec3* query_points_data = static_cast*>(query_points.data()); + vec3* query_points_data = reinterpret_cast*>(query_points.data()); const unsigned int n_points = points.shape(0); - vec3* points_data = static_cast*>(points.data()); - float* distances_data = static_cast(distances.data()); + vec3* points_data = reinterpret_cast*>(points.data()); + float* distances_data = reinterpret_cast(distances.data()); if (n_query_points != n_points) { throw std::invalid_argument("The number of query points and points must match."); @@ -89,18 +89,18 @@ void computeAllDistances(std::shared_ptr box, nb_array query_points, nb_array> distances) { const unsigned int n_query_points = query_points.shape(0); - vec3* query_points_data = static_cast*>(query_points.data()); + vec3* query_points_data = reinterpret_cast*>(query_points.data()); const unsigned int n_points = points.shape(0); - vec3* points_data = static_cast*>(points.data()); - float* distances_data = static_cast(distances.data()); + vec3* points_data = reinterpret_cast*>(points.data()); + float* distances_data = reinterpret_cast(distances.data()); box->computeAllDistances(query_points_data, n_query_points, points_data, n_points, distances_data); } void contains(std::shared_ptr box, nb_array points, nb_array> contains_mask) { const unsigned int n_points = points.shape(0); - vec3* points_data = static_cast*>(points.data()); - bool* contains_mask_data = static_cast(contains_mask.data()); + vec3* points_data = reinterpret_cast*>(points.data()); + bool* contains_mask_data = reinterpret_cast(contains_mask.data()); box->contains(points_data, n_points, contains_mask_data); } From bf82c812eb60739cb35b2238650074a5121abe47 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 09:54:43 -0400 Subject: [PATCH 07/23] Force usage of clang-tidy-10 For compatibility to existing code checks. A later PR can bump this by changing the version of clang-tidy in .pre-commit.yaml and the github actions runner version in style_check.yml. --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e6abc2ea2..f27832801 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -94,7 +94,7 @@ repos: - id: clang-tidy stages: [manual] # Requires clang-tidy. name: clang-tidy - entry: clang-tidy + entry: clang-tidy-10 language: system types: [c++] # Exclude external files. Also exclude AABB.h because it uses intrinsics From 53602d196534ad006c862a618f95d0419ac5ad9d Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 10:21:17 -0400 Subject: [PATCH 08/23] Fix pre-commit failures. --- freud/__init__.py | 8 ++++---- freud/box.py | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/freud/__init__.py b/freud/__init__.py index 59154b7c0..92a1f1491 100644 --- a/freud/__init__.py +++ b/freud/__init__.py @@ -1,10 +1,10 @@ # Copyright (c) 2010-2024 The Regents of the University of Michigan # This file is from the freud project, released under the BSD 3-Clause License. -from . import ( # cluster,; data,; density,; diffraction,; environment,; interface,; locality,; msd,; order,; pmft, - box, - parallel, -) + +# cluster,; data,; density,; diffraction,; environment,; interface,; locality,;; msd,; +# order,; pmft, +from . import box, parallel from .box import Box # from .locality import AABBQuery, LinkCell, NeighborList diff --git a/freud/box.py b/freud/box.py index 8b583f791..ec52aab7a 100644 --- a/freud/box.py +++ b/freud/box.py @@ -143,7 +143,7 @@ def yz(self, value): self._cpp_obj.setTiltFactorYZ(value) def __eq__(self, other): - if type(other) != freud.box.Box: + if type(other) is not freud.box.Box: return False return ( self.Lx == other.Lx From b44209e293a630c2857d697864cf7e1dbd691d17 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 10:22:29 -0400 Subject: [PATCH 09/23] Test only converted modules. --- .github/workflows/run_tests.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index 70034a901..d084a5c1f 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -59,7 +59,10 @@ jobs: - name: Run Tests run: | - pytest tests/ -v + # Enable tests only for nanobind-converted modules + pytest tests/test_box_Box.py -v + pytest tests/test_parallel.py -v + # pytest tests/ -v tests_complete: name: All tests From 9e850657512d89db1f1af1ea3f28bba654d670db Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 10:28:24 -0400 Subject: [PATCH 10/23] Show cppcheck and clang-tidy output. --- .github/workflows/style_check.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/style_check.yml b/.github/workflows/style_check.yml index e4b812010..b3a435d36 100644 --- a/.github/workflows/style_check.yml +++ b/.github/workflows/style_check.yml @@ -38,5 +38,5 @@ jobs: CMAKE_ARGS: "-DCMAKE_EXPORT_COMPILE_COMMANDS=True" - name: Execute clang-tidy and cppcheck run: | - pre-commit run cppcheck --all-files --hook-stage=manual - pre-commit run clang-tidy --all-files --hook-stage=manual + pre-commit run cppcheck --all-files --hook-stage=manual -v + pre-commit run clang-tidy --all-files --hook-stage=manual -v From 2c0c79eff72bfef817c37e93109fc865e34d095f Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 10:29:49 -0400 Subject: [PATCH 11/23] Test only active modules in cibuildwheel. --- .github/workflows/build_wheels.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index d79ad1c54..8f6ea29c9 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -113,7 +113,9 @@ jobs: scipy==${{ matrix.python.oldest_scipy }} gsd==${{ matrix.python.oldest_gsd }} matplotlib==${{ matrix.python.oldest_matplotlib }} - CIBW_TEST_COMMAND: "cd {package}/tests && pytest . -v --log-level=DEBUG" + # Test only the currently ported modules + CIBW_TEST_COMMAND: "cd {package}/tests && pytest test_box_Box.py test_parallel.py -v --log-level=DEBUG" + # CIBW_TEST_COMMAND: "cd {package}/tests && pytest . -v --log-level=DEBUG" - uses: actions/upload-artifact@v4.3.3 with: From 20444153af296f90b2272cdf5240d4c399a075ad Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 10:40:56 -0400 Subject: [PATCH 12/23] Make INSTALL_RPATH_USE_LINK_PATH global for cibuildwheel. --- .github/workflows/build_wheels.yml | 4 ++-- cpp/box/CMakeLists.txt | 2 +- cpp/parallel/CMakeLists.txt | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index 8f6ea29c9..e9a16efb9 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -96,8 +96,8 @@ jobs: CIBW_ARCHS: auto64 # Configure environment variables. - CIBW_ENVIRONMENT_LINUX: "CMAKE_PREFIX_PATH=/project/tbb LD_LIBRARY_PATH=/project/tbb/lib/intel64/gcc4.8:$LD_LIBRARY_PATH" - CIBW_ENVIRONMENT_MACOS: "CMAKE_PREFIX_PATH=/Users/runner/work/freud/freud/tbb:/Users/runner/work/tbb-install LD_LIBRARY_PATH=/Users/runner/work/freud/freud/tbb/lib/intel64/gcc4.8:$LD_LIBRARY_PATH" + CIBW_ENVIRONMENT_LINUX: "CMAKE_PREFIX_PATH=/project/tbb LD_LIBRARY_PATH=/project/tbb/lib/intel64/gcc4.8:$LD_LIBRARY_PATH CMAKE_ARGS=-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=True" + CIBW_ENVIRONMENT_MACOS: "CMAKE_PREFIX_PATH=/Users/runner/work/freud/freud/tbb:/Users/runner/work/tbb-install LD_LIBRARY_PATH=/Users/runner/work/freud/freud/tbb/lib/intel64/gcc4.8:$LD_LIBRARY_PATH CMAKE_ARGS=-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=True" MACOSX_DEPLOYMENT_TARGET: "10.14" # Set up TBB. diff --git a/cpp/box/CMakeLists.txt b/cpp/box/CMakeLists.txt index 2aa003ea8..78808beb1 100644 --- a/cpp/box/CMakeLists.txt +++ b/cpp/box/CMakeLists.txt @@ -8,7 +8,7 @@ else() set_target_properties(_box PROPERTIES INSTALL_RPATH "\$ORIGIN") endif() -if(_using_conda OR DEFINED ENV{CIBUILDWHEEL}) +if(_using_conda) set_target_properties(_box PROPERTIES INSTALL_RPATH_USE_LINK_PATH True) endif() diff --git a/cpp/parallel/CMakeLists.txt b/cpp/parallel/CMakeLists.txt index 6be11854b..5c6af0059 100644 --- a/cpp/parallel/CMakeLists.txt +++ b/cpp/parallel/CMakeLists.txt @@ -7,7 +7,7 @@ else() set_target_properties(_parallel PROPERTIES INSTALL_RPATH "\$ORIGIN") endif() -if(_using_conda OR DEFINED ENV{CIBUILDWHEEL}) +if(_using_conda) set_target_properties(_parallel PROPERTIES INSTALL_RPATH_USE_LINK_PATH True) endif() From 34390880d67fb1c0a823761a2b8293ed47556ab9 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 11:06:19 -0400 Subject: [PATCH 13/23] Remove unused LD_LIBRARY_PATH. --- .github/workflows/build_wheels.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index e9a16efb9..8181fb257 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -97,7 +97,7 @@ jobs: # Configure environment variables. CIBW_ENVIRONMENT_LINUX: "CMAKE_PREFIX_PATH=/project/tbb LD_LIBRARY_PATH=/project/tbb/lib/intel64/gcc4.8:$LD_LIBRARY_PATH CMAKE_ARGS=-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=True" - CIBW_ENVIRONMENT_MACOS: "CMAKE_PREFIX_PATH=/Users/runner/work/freud/freud/tbb:/Users/runner/work/tbb-install LD_LIBRARY_PATH=/Users/runner/work/freud/freud/tbb/lib/intel64/gcc4.8:$LD_LIBRARY_PATH CMAKE_ARGS=-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=True" + CIBW_ENVIRONMENT_MACOS: "CMAKE_PREFIX_PATH=/Users/runner/work/freud/freud/tbb:/Users/runner/work/tbb-install CMAKE_ARGS=-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=True" MACOSX_DEPLOYMENT_TARGET: "10.14" # Set up TBB. From 9ae18f2433074bab44db940acdb11c6a0976c45f Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 11:06:30 -0400 Subject: [PATCH 14/23] Check the directory structure after install -e. --- .github/workflows/style_check.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/style_check.yml b/.github/workflows/style_check.yml index b3a435d36..bc3dc06f6 100644 --- a/.github/workflows/style_check.yml +++ b/.github/workflows/style_check.yml @@ -36,6 +36,7 @@ jobs: uv pip install --no-build-isolation --no-deps -ve . env: CMAKE_ARGS: "-DCMAKE_EXPORT_COMPILE_COMMANDS=True" + - run: ls -lR - name: Execute clang-tidy and cppcheck run: | pre-commit run cppcheck --all-files --hook-stage=manual -v From 8a0abead5564ad9e71799d8f3a0c45ffda53c1ea Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 11:17:22 -0400 Subject: [PATCH 15/23] Bring back deprecated setup.py usage. --- .github/workflows/style_check.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/style_check.yml b/.github/workflows/style_check.yml index bc3dc06f6..db8a51d8e 100644 --- a/.github/workflows/style_check.yml +++ b/.github/workflows/style_check.yml @@ -33,7 +33,9 @@ jobs: environment-file: .github/workflows/env-files/py312-conda-lock.yml - name: Build freud and export compile commands run: | - uv pip install --no-build-isolation --no-deps -ve . + python3 setup.py build_ext --inplace + # TODO: switch to this command after migrating to scikit-build-core + # uv pip install --no-build-isolation --no-deps -ve . env: CMAKE_ARGS: "-DCMAKE_EXPORT_COMPILE_COMMANDS=True" - run: ls -lR From 19efa4cac3eb2c7338d1c6cdedcc559d2c502da5 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 11:36:09 -0400 Subject: [PATCH 16/23] Install a matching version of cppcheck. --- .github/workflows/env-files/environment.yaml | 3 +- .../workflows/env-files/py310-conda-lock.yml | 217 +----------------- .../workflows/env-files/py311-conda-lock.yml | 217 +----------------- .../workflows/env-files/py312-conda-lock.yml | 217 +----------------- .../workflows/env-files/py39-conda-lock.yml | 217 +----------------- .github/workflows/style_check.yml | 9 +- .pre-commit-config.yaml | 1 + 7 files changed, 51 insertions(+), 830 deletions(-) diff --git a/.github/workflows/env-files/environment.yaml b/.github/workflows/env-files/environment.yaml index 5f0f9891d..f8b29552d 100644 --- a/.github/workflows/env-files/environment.yaml +++ b/.github/workflows/env-files/environment.yaml @@ -4,7 +4,8 @@ channels: dependencies: - python==3.12 - - cppcheck + # TODO: Update to a newer cppcheck and adjust all C++ code to meet the new style guidlines + - cppcheck<2.0.0 # [linux64] - tbb - tbb-devel - ninja diff --git a/.github/workflows/env-files/py310-conda-lock.yml b/.github/workflows/env-files/py310-conda-lock.yml index 7609cf16a..b7ac3c9c4 100644 --- a/.github/workflows/env-files/py310-conda-lock.yml +++ b/.github/workflows/env-files/py310-conda-lock.yml @@ -13,10 +13,10 @@ version: 1 metadata: content_hash: - osx-arm64: c8b6ea3602dde99b079b3c95e7b46b1ce7c84b8ac86318db69397caa790a1dbf - osx-64: c6229e72813a938805730c03fc8afb49827d24cf07b43554953b123e41aeca60 - linux-64: 891f63143875788728a60dc22321d2a128a5786b273d9dab68efd466846b4c2b - win-64: 9fdc6d38c76d0a95ab4377a6abb1b6d2c801018273b2cc5bae5b80eabe541983 + osx-arm64: b05f323d66bb920a32d8f5b4f20e15540a9c53474885ea4e5553b5b529886868 + osx-64: 1fd160245e6551edc96bd36441dfa523b66a15958e3acfc57646107c2faf0c47 + linux-64: c7266e65cbac0a36d5af739700ea3773b69da43cc7f4138343a236275f5c9322 + win-64: 99ec5b5b7ea82dbc5b450d97b16256dd1be7c906fd1fbc1f06200e70855fdc5f channels: - url: conda-forge used_env_vars: [] @@ -1083,76 +1083,17 @@ package: category: main optional: false - 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md5: 735aed8d8520133135b66466e0e3388b - sha256: 20f7c68ff11637aed77fd774224b81c1c6ba5f96189fa66ca3ad965ce70ba523 + md5: d61bba75ab4825d84f0d90b6ebc98681 + sha256: 75174a05c0ffbe5f86fdc02f5c18594c0871605d3975ecf0857689c4c1147e4e category: main optional: false - name: cycler @@ -6984,43 +6925,6 @@ package: sha256: 8f35c244b1631a4f31fb1d66ab6e1d9bfac0ca9b679deced1112c7225b3ad138 category: main optional: false -- name: pcre - version: '8.45' - manager: conda - platform: osx-64 - dependencies: - libcxx: '>=11.1.0' - url: https://conda.anaconda.org/conda-forge/osx-64/pcre-8.45-he49afe7_0.tar.bz2 - hash: - md5: 0526850419e04ac003bc0b65a78dc4cc - sha256: 8002279cf4084fbf219f137c2bdef2825d076a5a57a14d1d922d7c5fa7872a5c - category: main - optional: false -- name: pcre - version: '8.45' - manager: conda - platform: osx-arm64 - dependencies: - libcxx: '>=11.1.0' - url: https://conda.anaconda.org/conda-forge/osx-arm64/pcre-8.45-hbdafb3b_0.tar.bz2 - hash: - md5: 500758f2515ae07c640d255c11afc19f - sha256: f2e0c4ae3306f94851eea2318c6d26d24f8e191e329ddd256a612cd1184c5737 - category: main - optional: false -- name: pcre - version: '8.45' - manager: conda - platform: win-64 - dependencies: - vc: '>=14.1,<15.0a0' - vs2015_runtime: '>=14.16.27012' - url: https://conda.anaconda.org/conda-forge/win-64/pcre-8.45-h0e60522_0.tar.bz2 - hash: - md5: 3cd3948bb5de74ebef93b6be6d8cf0d5 - sha256: 2ee62337b921b2d60a87aa9a91bf34bc855a0bbf6a5642ec66a7a175a772be6d - category: main - optional: false - name: pcre2 version: '10.44' manager: conda @@ -7483,54 +7387,6 @@ package: sha256: 88429d3c889604dc4be9133a82a3e9857e34f76fa2d28f91fadfeb8f030ff09e category: main optional: false -- name: pygments - version: 2.18.0 - manager: conda - platform: linux-64 - dependencies: - python: '>=3.8' - url: https://conda.anaconda.org/conda-forge/noarch/pygments-2.18.0-pyhd8ed1ab_0.conda - hash: - md5: b7f5c092b8f9800150d998a71b76d5a1 - sha256: 78267adf4e76d0d64ea2ffab008c501156c108bb08fecb703816fb63e279780b - category: main - optional: false -- name: pygments - version: 2.18.0 - manager: conda - platform: osx-64 - dependencies: - python: '>=3.8' - url: https://conda.anaconda.org/conda-forge/noarch/pygments-2.18.0-pyhd8ed1ab_0.conda - hash: - md5: b7f5c092b8f9800150d998a71b76d5a1 - sha256: 78267adf4e76d0d64ea2ffab008c501156c108bb08fecb703816fb63e279780b - category: main - optional: false -- name: pygments - version: 2.18.0 - manager: conda - platform: osx-arm64 - dependencies: - python: '>=3.8' - url: https://conda.anaconda.org/conda-forge/noarch/pygments-2.18.0-pyhd8ed1ab_0.conda - hash: - md5: b7f5c092b8f9800150d998a71b76d5a1 - sha256: 78267adf4e76d0d64ea2ffab008c501156c108bb08fecb703816fb63e279780b - category: main - optional: false -- name: pygments - version: 2.18.0 - manager: conda - platform: win-64 - dependencies: - python: '>=3.8' - url: https://conda.anaconda.org/conda-forge/noarch/pygments-2.18.0-pyhd8ed1ab_0.conda - hash: - md5: b7f5c092b8f9800150d998a71b76d5a1 - sha256: 78267adf4e76d0d64ea2ffab008c501156c108bb08fecb703816fb63e279780b - category: main - optional: false - 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url: https://conda.anaconda.org/conda-forge/win-64/tinyxml2-10.0.0-h63175ca_0.conda - hash: - md5: 353cf648e0d3165c9f9c8adbe7c9d05d - sha256: 76ba12053a358d5c4b07ac3a8eb1cc3282df5cada273fc625fc2211e48082036 - category: main - optional: false - name: tk version: 8.6.13 manager: conda diff --git a/.github/workflows/style_check.yml b/.github/workflows/style_check.yml index db8a51d8e..cfebf1ce5 100644 --- a/.github/workflows/style_check.yml +++ b/.github/workflows/style_check.yml @@ -38,8 +38,7 @@ jobs: # uv pip install --no-build-isolation --no-deps -ve . env: CMAKE_ARGS: "-DCMAKE_EXPORT_COMPILE_COMMANDS=True" - - run: ls -lR - - name: Execute clang-tidy and cppcheck - run: | - pre-commit run cppcheck --all-files --hook-stage=manual -v - pre-commit run clang-tidy --all-files --hook-stage=manual -v + - name: cppcheck + run: pre-commit run cppcheck --all-files --hook-stage=manual -v + - name: clang-tidy + run: pre-commit run clang-tidy --all-files --hook-stage=manual -v diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f27832801..53348bd25 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -94,6 +94,7 @@ repos: - id: clang-tidy stages: [manual] # Requires clang-tidy. name: clang-tidy + # TODO: Update to a newer clang-tidy and adjust all C++ code to meet the new style guidlines. entry: clang-tidy-10 language: system types: [c++] From 1aca1d3c6f6db7644aef903520efce5b07bd5034 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 12:10:10 -0400 Subject: [PATCH 17/23] Fix some clang-tidy warnings. --- cpp/box/export_Box.cc | 69 ++++++++++++++++++++++--------------------- 1 file changed, 35 insertions(+), 34 deletions(-) diff --git a/cpp/box/export_Box.cc b/cpp/box/export_Box.cc index 7617a5005..68bf274f9 100644 --- a/cpp/box/export_Box.cc +++ b/cpp/box/export_Box.cc @@ -7,77 +7,77 @@ namespace nb = nanobind; namespace freud { namespace box { namespace wrap { -void makeAbsolute(std::shared_ptr box, nb_array> vecs, +void makeAbsolute(const std::shared_ptr& box, nb_array> vecs, nb_array> out) { unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = reinterpret_cast*>(vecs.data()); - vec3* out_data = reinterpret_cast*>(out.data()); + auto vecs_data = reinterpret_cast*>(vecs.data()); + auto out_data = reinterpret_cast*>(out.data()); box->makeAbsolute(vecs_data, Nvecs, out_data); } -void makeFractional(std::shared_ptr box, nb_array> vecs, +void makeFractional(const std::shared_ptr& box, nb_array> vecs, nb_array> out) { unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = reinterpret_cast*>(vecs.data()); - vec3* out_data = reinterpret_cast*>(out.data()); + auto vecs_data = reinterpret_cast*>(vecs.data()); + auto out_data = reinterpret_cast*>(out.data()); box->makeFractional(vecs_data, Nvecs, out_data); } -void getImages(std::shared_ptr box, nb_array> vecs, +void getImages(const std::shared_ptr& box, nb_array> vecs, nb_array> images) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = reinterpret_cast*>(vecs.data()); - vec3* images_data = reinterpret_cast*>(images.data()); + auto vecs_data = reinterpret_cast*>(vecs.data()); + auto images_data = reinterpret_cast*>(images.data()); box->getImages(vecs_data, Nvecs, images_data); } -void wrap(std::shared_ptr box, nb_array> vecs, +void wrap(const std::shared_ptr& box, nb_array> vecs, nb_array> out) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = reinterpret_cast*>(vecs.data()); - vec3* out_data = reinterpret_cast*>(out.data()); + auto vecs_data = reinterpret_cast*>(vecs.data()); + auto out_data = reinterpret_cast*>(out.data()); box->wrap(vecs_data, Nvecs, out_data); } -void unwrap(std::shared_ptr box, nb_array vecs, nb_array images, nb_array out) +void unwrap(const std::shared_ptr& box, nb_array vecs, nb_array images, nb_array out) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = reinterpret_cast*>(vecs.data()); - vec3* images_data = reinterpret_cast*>(images.data()); - vec3* out_data = reinterpret_cast*>(out.data()); + auto vecs_data = reinterpret_cast*>(vecs.data()); + auto images_data = reinterpret_cast*>(images.data()); + auto out_data = reinterpret_cast*>(out.data()); box->unwrap(vecs_data, images_data, Nvecs, out_data); } -std::vector centerOfMass(std::shared_ptr box, nb_array vecs, +std::vector centerOfMass(const std::shared_ptr& box, nb_array vecs, nb_array> masses) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = reinterpret_cast*>(vecs.data()); - float* masses_data = reinterpret_cast(masses.data()); + auto vecs_data = reinterpret_cast*>(vecs.data()); + auto masses_data = reinterpret_cast(masses.data()); auto com = box->centerOfMass(vecs_data, Nvecs, masses_data); return {com.x, com.y, com.z}; } -void center(std::shared_ptr box, nb_array vecs, nb_array> masses) +void center(const std::shared_ptr& box, nb_array vecs, nb_array> masses) { const unsigned int Nvecs = vecs.shape(0); - vec3* vecs_data = reinterpret_cast*>(vecs.data()); - float* masses_data = reinterpret_cast(masses.data()); + auto vecs_data = reinterpret_cast*>(vecs.data()); + auto masses_data = reinterpret_cast(masses.data()); box->center(vecs_data, Nvecs, masses_data); } -void computeDistances(std::shared_ptr box, nb_array query_points, nb_array points, +void computeDistances(const std::shared_ptr& box, nb_array query_points, nb_array points, nb_array> distances) { const unsigned int n_query_points = query_points.shape(0); - vec3* query_points_data = reinterpret_cast*>(query_points.data()); + auto query_points_data = reinterpret_cast*>(query_points.data()); const unsigned int n_points = points.shape(0); - vec3* points_data = reinterpret_cast*>(points.data()); - float* distances_data = reinterpret_cast(distances.data()); + auto points_data = reinterpret_cast*>(points.data()); + auto distances_data = reinterpret_cast(distances.data()); if (n_query_points != n_points) { throw std::invalid_argument("The number of query points and points must match."); @@ -85,22 +85,23 @@ void computeDistances(std::shared_ptr box, nb_array query_points, nb box->computeDistances(query_points_data, n_query_points, points_data, n_points, distances_data); } -void computeAllDistances(std::shared_ptr box, nb_array query_points, nb_array points, - nb_array> distances) +void computeAllDistances(const std::shared_ptr& box, nb_array query_points, + nb_array points, nb_array> distances) { const unsigned int n_query_points = query_points.shape(0); - vec3* query_points_data = reinterpret_cast*>(query_points.data()); + auto query_points_data = reinterpret_cast*>(query_points.data()); const unsigned int n_points = points.shape(0); - vec3* points_data = reinterpret_cast*>(points.data()); - float* distances_data = reinterpret_cast(distances.data()); + auto points_data = reinterpret_cast*>(points.data()); + auto distances_data = reinterpret_cast(distances.data()); box->computeAllDistances(query_points_data, n_query_points, points_data, n_points, distances_data); } -void contains(std::shared_ptr box, nb_array points, nb_array> contains_mask) +void contains(const std::shared_ptr& box, nb_array points, + nb_array> contains_mask) { const unsigned int n_points = points.shape(0); - vec3* points_data = reinterpret_cast*>(points.data()); - bool* contains_mask_data = reinterpret_cast(contains_mask.data()); + auto points_data = reinterpret_cast*>(points.data()); + auto contains_mask_data = reinterpret_cast(contains_mask.data()); box->contains(points_data, n_points, contains_mask_data); } From dd7ddeb31715aa26b26de75e22e0103ac7fbbdd7 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 12:25:39 -0400 Subject: [PATCH 18/23] Fix compile errors. --- cpp/box/export_Box.cc | 46 +++++++++++++++++++++---------------------- cpp/box/export_Box.h | 22 ++++++++++----------- 2 files changed, 34 insertions(+), 34 deletions(-) diff --git a/cpp/box/export_Box.cc b/cpp/box/export_Box.cc index 68bf274f9..5e40a80c1 100644 --- a/cpp/box/export_Box.cc +++ b/cpp/box/export_Box.cc @@ -11,8 +11,8 @@ void makeAbsolute(const std::shared_ptr& box, nb_array> out) { unsigned int Nvecs = vecs.shape(0); - auto vecs_data = reinterpret_cast*>(vecs.data()); - auto out_data = reinterpret_cast*>(out.data()); + auto* vecs_data = reinterpret_cast*>(vecs.data()); + auto* out_data = reinterpret_cast*>(out.data()); box->makeAbsolute(vecs_data, Nvecs, out_data); } @@ -20,8 +20,8 @@ void makeFractional(const std::shared_ptr& box, nb_array> out) { unsigned int Nvecs = vecs.shape(0); - auto vecs_data = reinterpret_cast*>(vecs.data()); - auto out_data = reinterpret_cast*>(out.data()); + auto* vecs_data = reinterpret_cast*>(vecs.data()); + auto* out_data = reinterpret_cast*>(out.data()); box->makeFractional(vecs_data, Nvecs, out_data); } @@ -29,8 +29,8 @@ void getImages(const std::shared_ptr& box, nb_array nb_array> images) { const unsigned int Nvecs = vecs.shape(0); - auto vecs_data = reinterpret_cast*>(vecs.data()); - auto images_data = reinterpret_cast*>(images.data()); + auto* vecs_data = reinterpret_cast*>(vecs.data()); + auto* images_data = reinterpret_cast*>(images.data()); box->getImages(vecs_data, Nvecs, images_data); } @@ -38,17 +38,17 @@ void wrap(const std::shared_ptr& box, nb_array> vec nb_array> out) { const unsigned int Nvecs = vecs.shape(0); - auto vecs_data = reinterpret_cast*>(vecs.data()); - auto out_data = reinterpret_cast*>(out.data()); + auto* vecs_data = reinterpret_cast*>(vecs.data()); + auto* out_data = reinterpret_cast*>(out.data()); box->wrap(vecs_data, Nvecs, out_data); } void unwrap(const std::shared_ptr& box, nb_array vecs, nb_array images, nb_array out) { const unsigned int Nvecs = vecs.shape(0); - auto vecs_data = reinterpret_cast*>(vecs.data()); - auto images_data = reinterpret_cast*>(images.data()); - auto out_data = reinterpret_cast*>(out.data()); + auto* vecs_data = reinterpret_cast*>(vecs.data()); + auto* images_data = reinterpret_cast*>(images.data()); + auto* out_data = reinterpret_cast*>(out.data()); box->unwrap(vecs_data, images_data, Nvecs, out_data); } @@ -56,8 +56,8 @@ std::vector centerOfMass(const std::shared_ptr& box, nb_array nb_array> masses) { const unsigned int Nvecs = vecs.shape(0); - auto vecs_data = reinterpret_cast*>(vecs.data()); - auto masses_data = reinterpret_cast(masses.data()); + auto* vecs_data = reinterpret_cast*>(vecs.data()); + auto* masses_data = reinterpret_cast(masses.data()); auto com = box->centerOfMass(vecs_data, Nvecs, masses_data); return {com.x, com.y, com.z}; } @@ -65,8 +65,8 @@ std::vector centerOfMass(const std::shared_ptr& box, nb_array void center(const std::shared_ptr& box, nb_array vecs, nb_array> masses) { const unsigned int Nvecs = vecs.shape(0); - auto vecs_data = reinterpret_cast*>(vecs.data()); - auto masses_data = reinterpret_cast(masses.data()); + auto* vecs_data = reinterpret_cast*>(vecs.data()); + auto* masses_data = reinterpret_cast(masses.data()); box->center(vecs_data, Nvecs, masses_data); } @@ -74,10 +74,10 @@ void computeDistances(const std::shared_ptr& box, nb_array query_poi nb_array> distances) { const unsigned int n_query_points = query_points.shape(0); - auto query_points_data = reinterpret_cast*>(query_points.data()); + auto* query_points_data = reinterpret_cast*>(query_points.data()); const unsigned int n_points = points.shape(0); - auto points_data = reinterpret_cast*>(points.data()); - auto distances_data = reinterpret_cast(distances.data()); + auto* points_data = reinterpret_cast*>(points.data()); + auto* distances_data = reinterpret_cast(distances.data()); if (n_query_points != n_points) { throw std::invalid_argument("The number of query points and points must match."); @@ -89,10 +89,10 @@ void computeAllDistances(const std::shared_ptr& box, nb_array query_ nb_array points, nb_array> distances) { const unsigned int n_query_points = query_points.shape(0); - auto query_points_data = reinterpret_cast*>(query_points.data()); + auto* query_points_data = reinterpret_cast*>(query_points.data()); const unsigned int n_points = points.shape(0); - auto points_data = reinterpret_cast*>(points.data()); - auto distances_data = reinterpret_cast(distances.data()); + auto* points_data = reinterpret_cast*>(points.data()); + auto* distances_data = reinterpret_cast(distances.data()); box->computeAllDistances(query_points_data, n_query_points, points_data, n_points, distances_data); } @@ -100,8 +100,8 @@ void contains(const std::shared_ptr& box, nb_array points, nb_array> contains_mask) { const unsigned int n_points = points.shape(0); - auto points_data = reinterpret_cast*>(points.data()); - auto contains_mask_data = reinterpret_cast(contains_mask.data()); + auto* points_data = reinterpret_cast*>(points.data()); + auto* contains_mask_data = reinterpret_cast(contains_mask.data()); box->contains(points_data, n_points, contains_mask_data); } diff --git a/cpp/box/export_Box.h b/cpp/box/export_Box.h index fcf319691..477eef081 100644 --- a/cpp/box/export_Box.h +++ b/cpp/box/export_Box.h @@ -13,32 +13,32 @@ namespace freud { namespace box { namespace wrap { template> using nb_array = nanobind::ndarray; -void makeAbsolute(std::shared_ptr box, nb_array> vecs, +void makeAbsolute(const std::shared_ptr& box, nb_array> vecs, nb_array> out); -void makeFractional(std::shared_ptr box, nb_array> vecs, +void makeFractional(const std::shared_ptr& box, nb_array> vecs, nb_array> out); -void getImages(std::shared_ptr box, nb_array> vecs, +void getImages(const std::shared_ptr& box, nb_array> vecs, nb_array> images); -void wrap(std::shared_ptr box, nb_array> vecs, +void wrap(const std::shared_ptr& box, nb_array> vecs, nb_array> out); -void unwrap(std::shared_ptr box, nb_array vecs, nb_array images, nb_array out); +void unwrap(const std::shared_ptr& box, nb_array vecs, nb_array images, nb_array out); -std::vector centerOfMass(std::shared_ptr box, nb_array vecs, +std::vector centerOfMass(const std::shared_ptr& box, nb_array vecs, nb_array> masses); -void center(std::shared_ptr box, nb_array vecs, nb_array> masses); +void center(const std::shared_ptr& box, nb_array vecs, nb_array> masses); -void computeDistances(std::shared_ptr box, nb_array query_points, nb_array points, +void computeDistances(const std::shared_ptr& box, nb_array query_points, nb_array points, nb_array> distances); -void computeAllDistances(std::shared_ptr box, nb_array query_points, nb_array points, - nb_array> distances); +void computeAllDistances(const std::shared_ptr& box, nb_array query_points, + nb_array points, nb_array> distances); -void contains(std::shared_ptr box, nb_array points, +void contains(const std::shared_ptr& box, nb_array points, nb_array> contains_mask); }; }; }; // namespace freud::box::wrap From f584adeb7b6d32cfdfdd917f59e8800b96f27a57 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 13:40:37 -0400 Subject: [PATCH 19/23] Fix more clang-tidy errors. --- cpp/box/Box.h | 5 +++-- cpp/order/SolidLiquid.cc | 2 +- cpp/order/SolidLiquid.h | 2 +- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/cpp/box/Box.h b/cpp/box/Box.h index df0d61e51..cd9fb04b9 100644 --- a/cpp/box/Box.h +++ b/cpp/box/Box.h @@ -367,7 +367,7 @@ class Box * \param masses Optional array of masses, of length Nvecs * \return Center of mass as a vec3 */ - vec3 centerOfMass(vec3* vecs, size_t Nvecs, const float* masses) const + vec3 centerOfMass(vec3* vecs, size_t Nvecs, const float* masses = nullptr) const { // This roughly follows the implementation in // https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions @@ -379,7 +379,7 @@ class Box vec3 phase(constants::TWO_PI * makeFractional(vecs[i])); vec3> xi(std::polar(float(1.0), phase.x), std::polar(float(1.0), phase.y), std::polar(float(1.0), phase.z)); - float mass = masses[i]; + float mass = (masses != nullptr) ? masses[i] : float(1.0); total_mass += mass; xi_mean += std::complex(mass, 0) * xi; } @@ -426,6 +426,7 @@ class Box void computeDistances(const vec3* query_points, const unsigned int n_query_points, const vec3* points, const unsigned int n_points, float* distances) const { + assert(query_points == n_points); util::forLoopWrapper(0, n_query_points, [&](size_t begin, size_t end) { for (size_t i = begin; i < end; ++i) { diff --git a/cpp/order/SolidLiquid.cc b/cpp/order/SolidLiquid.cc index 3f403a8e5..330f4d19a 100644 --- a/cpp/order/SolidLiquid.cc +++ b/cpp/order/SolidLiquid.cc @@ -94,7 +94,7 @@ void SolidLiquid::compute(const freud::locality::NeighborList* nlist, neighbor_count_filter[bond] = (m_number_of_connections[i] >= m_solid_threshold && m_number_of_connections[j] >= m_solid_threshold); } - freud::locality::NeighborList solid_neighbor_nlist(solid_nlist); + freud::locality::NeighborList& solid_neighbor_nlist(solid_nlist); solid_neighbor_nlist.filter(neighbor_count_filter.cbegin()); // Find clusters of solid-like particles diff --git a/cpp/order/SolidLiquid.h b/cpp/order/SolidLiquid.h index 5a70fbaee..65e080e70 100644 --- a/cpp/order/SolidLiquid.h +++ b/cpp/order/SolidLiquid.h @@ -8,7 +8,7 @@ #include #include -#include "Cluster.h" +#include "../cluster/Cluster.h" #include "ManagedArray.h" #include "NeighborList.h" #include "Steinhardt.h" From a5e0e9a1edaf332fbe2a0853c476dd708fa781f5 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 13:41:46 -0400 Subject: [PATCH 20/23] Do not fail fast. --- .github/workflows/run_tests.yml | 1 + cpp/box/Box.h | 2 +- cpp/box/export_Box.cc | 2 ++ 3 files changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index d084a5c1f..c3e83c97c 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -26,6 +26,7 @@ jobs: name: Unit test [py${{ matrix.python }} ${{ matrix.os }}] runs-on: ${{ matrix.os }} strategy: + fail-fast: false matrix: os: [ubuntu-latest] python: ['39', '310', '311', '312'] diff --git a/cpp/box/Box.h b/cpp/box/Box.h index cd9fb04b9..d86237b3f 100644 --- a/cpp/box/Box.h +++ b/cpp/box/Box.h @@ -426,7 +426,7 @@ class Box void computeDistances(const vec3* query_points, const unsigned int n_query_points, const vec3* points, const unsigned int n_points, float* distances) const { - assert(query_points == n_points); + assert(n_query_points == n_points); util::forLoopWrapper(0, n_query_points, [&](size_t begin, size_t end) { for (size_t i = begin; i < end; ++i) { diff --git a/cpp/box/export_Box.cc b/cpp/box/export_Box.cc index 5e40a80c1..54142dc16 100644 --- a/cpp/box/export_Box.cc +++ b/cpp/box/export_Box.cc @@ -1,6 +1,8 @@ // Copyright (c) 2010-2024 The Regents of the University of Michigan // This file is from the freud project, released under the BSD 3-Clause License. +#include + #include "export_Box.h" namespace nb = nanobind; From 5751c6d3a8ceaef0c14065515e3d8e136774d3fe Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 14:13:03 -0400 Subject: [PATCH 21/23] Use NB_STATIC on windows. --- CMakeLists.txt | 7 +++++++ cpp/CMakeLists.txt | 4 +++- cpp/box/CMakeLists.txt | 2 +- cpp/parallel/CMakeLists.txt | 2 +- 4 files changed, 12 insertions(+), 3 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index d1bca9668..520848989 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -59,6 +59,13 @@ if(nanobind_FOUND) "[${nanobind_DIR},${nanobind_VERSION}]") endif() +# shared nanobind linking seems broken on windows for unknown reasons +if(WIN32) + set(freud_nanobind_linking "NB_STATIC") +else() + set(freud_nanobind_linking "NB_SHARED") +endif() + # Fail fast if users have not cloned submodules. if(NOT WIN32) string(ASCII 27 Esc) diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt index 892541546..e081ae75e 100644 --- a/cpp/CMakeLists.txt +++ b/cpp/CMakeLists.txt @@ -65,4 +65,6 @@ add_subdirectory(parallel) # add_subdirectory(locality) add_subdirectory(order) add_subdirectory(pmft) # add_subdirectory(util) -install(TARGETS nanobind DESTINATION freud) +if(NOT WIN32) + install(TARGETS nanobind DESTINATION freud) +endif() diff --git a/cpp/box/CMakeLists.txt b/cpp/box/CMakeLists.txt index 78808beb1..b61bac398 100644 --- a/cpp/box/CMakeLists.txt +++ b/cpp/box/CMakeLists.txt @@ -1,5 +1,5 @@ # create the target and add the needed properties -nanobind_add_module(_box NB_SHARED module-box.cc export_Box.cc) +nanobind_add_module(_box ${freud_nanobind_linking} module-box.cc export_Box.cc) target_link_libraries(_box PUBLIC libfreud) if(APPLE) diff --git a/cpp/parallel/CMakeLists.txt b/cpp/parallel/CMakeLists.txt index 5c6af0059..e938ca5a0 100644 --- a/cpp/parallel/CMakeLists.txt +++ b/cpp/parallel/CMakeLists.txt @@ -1,4 +1,4 @@ -nanobind_add_module(_parallel NB_SHARED module-parallel.cc) +nanobind_add_module(_parallel ${freud_nanobind_linking} module-parallel.cc) target_link_libraries(_parallel PUBLIC libfreud) if(APPLE) From 6f6a4082372f7c5a4a4663a56927ad755c72cf34 Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 14:28:13 -0400 Subject: [PATCH 22/23] Attempt to fix assert. --- cpp/box/Box.h | 1 + cpp/box/export_Box.cc | 2 -- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/cpp/box/Box.h b/cpp/box/Box.h index d86237b3f..e1e77e2e6 100644 --- a/cpp/box/Box.h +++ b/cpp/box/Box.h @@ -5,6 +5,7 @@ #define BOX_H #include +#include #include #include #include diff --git a/cpp/box/export_Box.cc b/cpp/box/export_Box.cc index 54142dc16..5e40a80c1 100644 --- a/cpp/box/export_Box.cc +++ b/cpp/box/export_Box.cc @@ -1,8 +1,6 @@ // Copyright (c) 2010-2024 The Regents of the University of Michigan // This file is from the freud project, released under the BSD 3-Clause License. -#include - #include "export_Box.h" namespace nb = nanobind; From 4b44cf48a8245d0df99599c01d7c8e4d38f7a07c Mon Sep 17 00:00:00 2001 From: "Joshua A. Anderson" Date: Mon, 24 Jun 2024 14:36:53 -0400 Subject: [PATCH 23/23] clang-tidy knows that assert is used only in debug mode. Remove n_points from the argument list. --- cpp/box/Box.h | 4 +--- cpp/box/export_Box.cc | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/cpp/box/Box.h b/cpp/box/Box.h index e1e77e2e6..b6840c0d3 100644 --- a/cpp/box/Box.h +++ b/cpp/box/Box.h @@ -5,7 +5,6 @@ #define BOX_H #include -#include #include #include #include @@ -425,9 +424,8 @@ class Box query_point (overwritten in place). */ void computeDistances(const vec3* query_points, const unsigned int n_query_points, - const vec3* points, const unsigned int n_points, float* distances) const + const vec3* points, float* distances) const { - assert(n_query_points == n_points); util::forLoopWrapper(0, n_query_points, [&](size_t begin, size_t end) { for (size_t i = begin; i < end; ++i) { diff --git a/cpp/box/export_Box.cc b/cpp/box/export_Box.cc index 5e40a80c1..85544eb9e 100644 --- a/cpp/box/export_Box.cc +++ b/cpp/box/export_Box.cc @@ -82,7 +82,7 @@ void computeDistances(const std::shared_ptr& box, nb_array query_poi { throw std::invalid_argument("The number of query points and points must match."); } - box->computeDistances(query_points_data, n_query_points, points_data, n_points, distances_data); + box->computeDistances(query_points_data, n_query_points, points_data, distances_data); } void computeAllDistances(const std::shared_ptr& box, nb_array query_points,