deepmd-gnn 0.1.0__tar.gz

deepmd_gnn-0.1.0/.clang-format

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+---
+BasedOnStyle: Google
+BinPackParameters: false
+InsertBraces: true

deepmd_gnn-0.1.0/.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

deepmd_gnn-0.1.0/.github/workflows/release.yaml

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+on:
+  push:
+    branches:
+      - master
+    tags:
+      - "v*"
+  pull_request:
+name: Build and release to pypi
+permissions:
+  contents: read
+jobs:
+  release-build:
+    name: Build and upload distributions
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: |
+            **/requirements*.txt
+            **/pyproject.toml
+      - name: Build dist
+        run: uv tool run --with build[uv] --from build python -m build --installer uv --sdist
+      - name: Upload release distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+  release-wheel:
+    name: Build wheels for cp${{ matrix.python }}-${{ matrix.platform_id }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          # linux-64
+          - os: ubuntu-latest
+            python: 312
+            platform_id: manylinux_x86_64
+          # macos-x86-64
+          - os: macos-13
+            python: 312
+            platform_id: macosx_x86_64
+          # macos-arm64
+          - os: macos-14
+            python: 312
+            platform_id: macosx_arm64
+          # win-64
+          - os: windows-2019
+            python: 312
+            platform_id: win_amd64
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: |
+            **/requirements*.txt
+            **/pyproject.toml
+        if: runner.os != 'Linux'
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.21
+        env:
+          CIBW_ARCHS: all
+          CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
+          CIBW_BUILD_FRONTEND: "build[uv]"
+      - uses: actions/upload-artifact@v4
+        with:
+          name: release-cibw-cp${{ matrix.python }}-${{ matrix.platform_id }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+  pypi-publish:
+    name: Release to pypi
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi_publish
+      url: https://pypi.org/p/python-template
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    needs:
+      - release-build
+      - release-wheel
+    permissions:
+      id-token: write
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+          pattern: release-*
+          path: dist/
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

deepmd_gnn-0.1.0/.github/workflows/test.yaml

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+name: Test Python package
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+env:
+  UV_SYSTEM_PYTHON: 1
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: |
+            **/requirements*.txt
+            **/pyproject.toml
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+      - name: Install dependencies
+        run: uv pip install nox[uv]
+      - name: Test with pytest
+        run: nox -db uv
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          use_oidc: ${{ !(github.event_name == 'pull_request' && github.event.pull_request.head.repo.fork) }}

deepmd_gnn-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+.ruff_cache/
+node_modules/
+deepmd_gnn/_version.py

deepmd_gnn-0.1.0/.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-json
+      - id: check-added-large-files
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-toml
+      - id: mixed-line-ending
+  # Python
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.4
+    hooks:
+      - id: ruff
+        args: ["--fix"]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.13.0"
+    hooks:
+      - id: mypy
+        additional_dependencies: []
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        types_or: [javascript, css, html, markdown, yaml]
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.23
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+  # C++
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v19.1.3
+    hooks:
+      - id: clang-format
+  # CMake
+  - repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: v0.6.13
+    hooks:
+      - id: cmake-format

deepmd_gnn-0.1.0/CMakeLists.txt

@@ -0,0 +1,68 @@
+cmake_minimum_required(VERSION 3.15)
+project(deepmd-gnn CXX)
+
+set(CMAKE_CXX_STANDARD 14)
+macro(set_if_higher VARIABLE VALUE)
+  # ${VARIABLE} is a variable name, not a string
+  if(${VARIABLE} LESS "${VALUE}")
+    set(${VARIABLE} ${VALUE})
+  endif()
+endmacro()
+
+# build cpp or python interfaces
+option(BUILD_CPP_IF "Build C++ interfaces" ON)
+option(BUILD_PY_IF "Build Python interfaces" OFF)
+option(USE_PT_PYTHON_LIBS "Use PyTorch Python libraries" OFF)
+
+if((NOT BUILD_PY_IF) AND (NOT BUILD_CPP_IF))
+  # nothing to do
+  message(FATAL_ERROR "Nothing to build.")
+endif()
+
+if(BUILD_CPP_IF
+   AND USE_PT_PYTHON_LIBS
+   AND NOT CMAKE_CROSSCOMPILING
+   AND NOT SKBUILD
+   OR "$ENV{CIBUILDWHEEL}" STREQUAL "1")
+  find_package(
+    Python
+    COMPONENTS Interpreter
+    REQUIRED)
+  execute_process(
+    COMMAND ${Python_EXECUTABLE} -c
+            "import torch;print(torch.utils.cmake_prefix_path)"
+    WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+    OUTPUT_VARIABLE PYTORCH_CMAKE_PREFIX_PATH
+    RESULT_VARIABLE PYTORCH_CMAKE_PREFIX_PATH_RESULT_VAR
+    ERROR_VARIABLE PYTORCH_CMAKE_PREFIX_PATH_ERROR_VAR
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  if(NOT ${PYTORCH_CMAKE_PREFIX_PATH_RESULT_VAR} EQUAL 0)
+    message(
+      FATAL_ERROR
+        "Cannot determine PyTorch CMake prefix path, error code: $PYTORCH_CMAKE_PREFIX_PATH_RESULT_VAR}, error message: ${PYTORCH_CMAKE_PREFIX_PATH_ERROR_VAR}"
+    )
+  endif()
+  list(APPEND CMAKE_PREFIX_PATH ${PYTORCH_CMAKE_PREFIX_PATH})
+endif()
+find_package(Torch REQUIRED)
+if(NOT Torch_VERSION VERSION_LESS "2.1.0")
+  set_if_higher(CMAKE_CXX_STANDARD 17)
+elseif(NOT Torch_VERSION VERSION_LESS "1.5.0")
+  set_if_higher(CMAKE_CXX_STANDARD 14)
+endif()
+string(REGEX MATCH "_GLIBCXX_USE_CXX11_ABI=([0-9]+)" CXXABI_PT_MATCH
+             "${TORCH_CXX_FLAGS}")
+if(CXXABI_PT_MATCH)
+  set(OP_CXX_ABI_PT ${CMAKE_MATCH_1})
+  message(STATUS "PyTorch CXX11 ABI: ${CMAKE_MATCH_1}")
+else()
+  # Maybe in macos/windows
+  set(OP_CXX_ABI_PT 0)
+endif()
+
+# define build type
+if((NOT DEFINED CMAKE_BUILD_TYPE) OR CMAKE_BUILD_TYPE STREQUAL "")
+  set(CMAKE_BUILD_TYPE release)
+endif()
+
+add_subdirectory(op)

deepmd_gnn-0.1.0/LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.