Recovery commit

.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflow/lint.yml

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+name: Linting and code formatting
+
+on: []
+  # Trigger the workflow on push or pull request,
+  # but only for the main branch
+  # push:
+  #   branches: []
+  # pull_request:
+  #   branches: []
+
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Setup
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8.10
+      - name: Get cache
+        uses: actions/cache@v2
+        with:
+          path: /opt/hostedtoolcache/Python/3.8.10/x64/lib/python3.8/site-packages
+          # Look to see if there is a cache hit for the corresponding requirements file
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+
+      # Install packages
+      - name: Install packages required for installation
+        run: python -m pip install --upgrade pip setuptools wheel
+      - name: Install dependencies
+        run: pip install -r requirements.txt
+
+      # Check code
+      - name: Check formatting with yapf
+        run: python -m yapf --style=.style.yapf --diff --recursive .
+#      - name: Lint with flake8
+#        run: flake8 --config=.flake8 .
+#      - name: Check type annotations with mypy
+#        run: mypy --config-file=.mypy.ini .
+
+      - name: Test with pytest
+        run: python -m pytest tests

.github/workflow/pre-commit.yaml

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+name: Pre-Commit Checks
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - uses: pre-commit/action@v3.0.0

.github/workflow/unittest.yaml

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+name: unit tests
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pytest-container:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+
+      - name: Install requirements
+        run: |
+          pip install -U pip
+          pip install .[dev]
+
+      - name: Log installed environment
+        run: |
+          python3 -m pip freeze
+
+      - name: Run unit tests
+        run: |
+          pytest tests

.github/workflows/lint.yml

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+name: Linting and code formatting
+
+on: []
+  # Trigger the workflow on push or pull request,
+  # but only for the main branch
+  # push:
+  #   branches: []
+  # pull_request:
+  #   branches: []
+
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Setup
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8.10
+      - name: Get cache
+        uses: actions/cache@v2
+        with:
+          path: /opt/hostedtoolcache/Python/3.8.10/x64/lib/python3.8/site-packages
+          # Look to see if there is a cache hit for the corresponding requirements file
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+
+      # Install packages
+      - name: Install packages required for installation
+        run: python -m pip install --upgrade pip setuptools wheel
+      - name: Install dependencies
+        run: pip install -r requirements.txt
+
+      # Check code
+      - name: Check formatting with yapf
+        run: python -m yapf --style=.style.yapf --diff --recursive .
+#      - name: Lint with flake8
+#        run: flake8 --config=.flake8 .
+#      - name: Check type annotations with mypy
+#        run: mypy --config-file=.mypy.ini .
+
+      - name: Test with pytest
+        run: python -m pytest tests

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+build/
+*.egg-info/
+
+# pytest
+.pytest_cache/
+
+# mypy
+.mypy_cache/
+
+# IDE
+.idea/
+.vscode/
+*.txt
+*.log
+*.out
+
+# Distribution
+dist/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# DS_Store
+.DS_Store
+*.models
+*.pt
+/wandb
+*.xyz
+/checkpoints
+*.model
+/results
+/logs
+
+# plots
+*.png
+*.gif
+
+cache_files/
+creat_links.sh

.mypy.ini

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+[mypy]
+# Platform configuration
+python_version = 3.8
+
+# Untyped definitions and calls
+check_untyped_defs = True
+
+[mypy-mace.tools.torch_geometric.*]
+ignore_errors = True
+
+[mypy-mace.tools.scatter]
+ignore_errors = True
+
+[mypy-setuptools.*]
+ignore_missing_imports = True
+
+[mypy-e3nn.*]
+ignore_missing_imports = True
+
+[mypy-scipy.*]
+ignore_missing_imports = True
+
+[mypy-ase.*]
+ignore_missing_imports = True
+
+[mypy-prettytable.*]
+ignore_missing_imports = True
+
+[mypy-torch_ema.*]
+ignore_missing_imports = True
+
+[mypy-matplotlib.*]
+ignore_missing_imports = True
+
+[mypy-pandas.*]
+ignore_missing_imports = True
+
+[mypy-opt_einsum.*]
+ignore_missing_imports = True

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 23.12.1
+    hooks:
+      - id: black
+        name: Black Formating
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: Sort imports
+
+  # Failing - to be investigated separately
+  # - repo: local
+  #   hooks:
+  #     - id: pylint
+  #       name: Pylint Checks
+  #       entry: pylint
+  #       language: system
+  #       types: [python]
+  #       args:
+  #         [
+  #           "--rcfile=pyproject.toml", 
+  #           "mace", 
+  #           "tests", 
+  #           "scripts"
+  #         ]  
+
+  # - repo: local
+  #   hooks:
+  #     - id: mypy
+  #       name: mypy type checks
+  #       entry: mypy
+  #       language: system
+  #       types: [python]
+  #       args:
+  #         [
+  #           --config-file=.mypy.ini,
+  #           mace,
+  #           tests,
+  #           scripts
+  #         ]
+

LICENSE.md

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+MIT License
+
+Copyright (c) 2022 ACEsuit/mace
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.