Merge branch 'main' into docs

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+**/*.c
+
+# 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/

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: fix-encoding-pragma
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+      - id: check-json
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        args: ["--line-length", "88"]
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        args: ["--max-line-length=88", "--ignore=E203,W503"]

environment.yaml

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+name: mattersim
+channels:
+  - pyg
+  - pytorch
+  - conda-forge
+dependencies:
+  - python=3.9
+  - pytorch==1.11.0
+  - pytorch-sparse=0.6.15
+  - pytorch-scatter=2.0.9
+  - ca-certificates
+  - openssl
+  - numpy<2
+  - phonopy==2.14.0
+  - phono3py==2.3.0
+  - cython
+  - loguru
+  - pip:
+    - seekpath
+    - torch==1.11.0+cu113
+    - torchvision==0.12.0+cu113
+    - torchaudio==0.11.0
+    - --extra-index-url https://download.pytorch.org/whl/cu113

setup.py

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+# -*- coding: utf-8 -*-
+import numpy as np
+from setuptools import Extension, find_packages, setup
+from setuptools.command.build_ext import build_ext as _build_ext
+
+
+class build_ext(_build_ext):
+    def finalize_options(self):
+        _build_ext.finalize_options(self)
+        if self.distribution.ext_modules:
+            import pyximport
+
+            pyximport.install()
+
+
+setup(
+    name="mattersim",
+    version="1.0",
+    description=(
+        "MatterSim: MatterSim: A Deep Learning Atomistic Model Across "
+        "Elements, Temperatures and Pressures."
+    ),
+    author=(
+        "Han Yang, Chenxi Hu, Yichi Zhou, Xixian Liu, Yu Shi, Jielan Li, "
+        "Guanzhi Li, Zekun Chen, Shuizhou Chen, Claudio Zeni, Matthew Horton, "
+        "Robert Pinsler, Andrew Fowler, Daniel Zügner, Tian Xie, Jake Smith, "
+        "Lixin Sun, Qian Wang, Lingyu Kong, Chang Liu, Hongxia Hao, Ziheng Lu"
+    ),
+    author_email=(
+        "[email protected]; [email protected]; "
+        "[email protected]; [email protected];"
+    ),
+    python_requires=">=3.9",
+    packages=find_packages(where="src", include=["mattersim", "mattersim.*"]),
+    package_dir={"": "src"},
+    url="https://github.com/msr-ai4science/mattersim",
+    requires=[
+        "torch",
+    ],
+    install_requires=[
+        "ase>=3.23.0",
+        "Cython>=0.29.32",
+        "e3nn==0.5.0",
+        "numpy<2",
+        "pymatgen",
+        "torch_geometric==2.0.4",
+        "torch_runstats==0.2.0",
+        "torchmetrics>=0.10.0",
+        "torch-ema==0.3",
+        "opt_einsum_fx",
+        "pre-commit",
+        "Pathlib",
+        "pytest",
+        "pytest-testmon",
+        "azure-storage-blob",
+        "azure-identity",
+    ],
+    setup_requires=[
+        "Cython>=0.29.32",
+    ],
+    cmdclass={"build_ext": build_ext},
+    ext_modules=[
+        Extension(
+            "mattersim.datasets.utils.threebody_indices",
+            ["src/mattersim/datasets/utils/threebody_indices.pyx"],
+            include_dirs=[np.get_include()],
+        )
+    ],
+)