Merge branch 'main' into hanwen/PBC_AL

duartegroup · Nov 25, 2024 · e23f8ef · e23f8ef
2 parents 37bf174 + 4bd5c1f
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1 @@
+a5e89e407dd5b4ac988138af6870262d3a9e43fa # apply ruff formatter
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,12 @@
+---
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      gha-dependencies:
+        patterns:
+          - '*'
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -4,6 +4,9 @@ on:
   push:
   pull_request:
 
+env:
+  FORCE_COLOR: 1
+
 jobs:
   pre-commit:
     env:
@@ -15,4 +18,4 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Run pre-commit
-        uses: pre-commit/[email protected].0
+        uses: pre-commit/[email protected].1
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -6,25 +6,28 @@ on:
     branches: [main]
   pull_request:
 
+env:
+  FORCE_COLOR: 1
+
 jobs:
   test:
     name: GAP (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
-    
+
     strategy:
       fail-fast: true
       matrix:
-        os: ["ubuntu-latest"]
+        os: ["ubuntu-22.04"]
         python-version: ["3.9"]
-      
+
     defaults:
       run:
         shell: bash -l {0}
-        
+
     steps:
     - uses: actions/checkout@v4
-        
-    - uses: mamba-org/setup-micromamba@v1
+
+    - uses: mamba-org/setup-micromamba@v2
       with:
         # the create command looks like this:
         # `micromamba create -n test-env python=3.9 -f environment.yml`
@@ -38,27 +41,75 @@ jobs:
       run: ./install_gap.sh
 
     - name: Test basic install
-      run: pytest
+      run: pytest --cov=mlptrain -k "not test_openmm"
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+          flags: python-${{ matrix.python-version }}
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: duartegroup/mlp-train
+
+  test-ace:
+    name: ACE (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: true
+      matrix:
+        os: ["ubuntu-22.04"]
+        python-version: ["3.9"]
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: julia-actions/setup-julia@v2
+      with:
+        version: '1.6'
+
+    - uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-file: environment_ace.yml
+        environment-name: gha-test-env
+        cache-environment: true
+        create-args: >-
+          python=${{ matrix.python-version }}
 
+    - name: ACE install
+      run: ./install_ace.sh
+
+    - name: Test ACE
+      run: pytest --cov=mlptrain -k "not test_openmm"
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+          flags: python-${{ matrix.python-version }}-ace
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: duartegroup/mlp-train
 
   test-mace:
     name: MACE (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
-    
+
     strategy:
       fail-fast: true
       matrix:
-        os: ["ubuntu-latest"]
+        os: ["ubuntu-22.04"]
         python-version: ["3.9"]
-      
+
     defaults:
       run:
         shell: bash -l {0}
-        
+
     steps:
     - uses: actions/checkout@v4
-        
-    - uses: mamba-org/setup-micromamba@v1
+
+    - uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: environment_mace.yml
         environment-name: gha-test-env
@@ -70,4 +121,11 @@ jobs:
       run: ./install_mace.sh
 
     - name: Test MACE install
-      run: pytest
+      run: pytest --cov=mlptrain
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+          flags: python-${{ matrix.python-version }}-mace
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: duartegroup/mlp-train
diff --git a/.gitignore b/.gitignore
@@ -5,5 +5,5 @@ dist/
 *DS_store
 **/__pycache__/
 **/__MACOSX/
-.coverage
-.pytest_cache
+.coverage*
+.pytest_cache
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,13 +10,14 @@ repos:
       - id: check-shebang-scripts-are-executable
       - id: check-added-large-files
         args: ['--maxkb=500', '--enforce-all']
-        exclude: mlptrain/sampling/tests/data.zip
+        exclude: tests/data/data.zip
       - id: check-yaml
       - id: check-toml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.3
+    rev: v0.2.1
     hooks:
       - id: ruff
         args: [--show-source, --fix]
+      - id: ruff-format
diff --git a/README.md b/README.md
@@ -1,8 +1,9 @@
-[![Test with pytest](https://github.com/duartegroup/mlp-train/actions/workflows/pytest.yml/badge.svg?event=push)](https://github.com/duartegroup/mlp-train/actions/workflows/pytest.yml)
+[![DOI](https://img.shields.io/badge/doi-10.6084/m9.figshare.25816864.v1-blue.svg?style=flat&labelColor=whitesmoke&logo=data%3Aimage%2Fpng%3Bbase64%2CiVBORw0KGgoAAAANSUhEUgAAAB8AAAAfCAYAAAAfrhY5AAAJsklEQVR42qWXd1DTaRrHf%2BiB2Hdt5zhrAUKz4IKEYu9IGiGFFJJQ0gkJCAKiWFDWBRdFhCQUF3UVdeVcRQEBxUI3yY9iEnQHb3bdW1fPubnyz%2F11M7lvEHfOQee2ZOYzPyDv%2B3yf9%2Fk95YX4fx%2BltfUt08GcFEuPR4U9hDDZ%2FVngIlhb%2FSiI6InkTgLzgDcgfvtnovhH4BzoVlrbwr55QnhCtBW4QHXnFrZbPBaQoBh4%2FSYH2EnpBEtqcDMVzB93wA%2F8AFwa23XFGcc8CkT3mxz%2BfXWtq9T9IQlLIXYEuHojudb%2BCM7Hgdq8ydi%2FAHiBXyY%2BLjwFlAEnS6Jnar%2FvnQVhvdzasad0eKvWZKe8hvDB2ofLZ%2FZEcWsh%2BhyIuyO5Bxs2iZIE4nRv7NWAb0EO8AC%2FWPxjYAWuOEX2MSXZVgPxzmRL3xKz3ScGpx6p6QnOx4mDIFqO0w6Q4fEhO5IzwxlSwyD2FYHzwAW%2BAZ4fEsf74gCumykwNHskLM7taQxLYjjIyy8MUtraGhTWdkfhkFJqtvuVl%2F9l2ZquDfEyrH8B0W06nnpH3JtIyRGpH1iJ6SfxDIHjRXHJmdQjLpfHeN54gnfFx4W9QRnovx%2FN20aXZeTD2J84hn3%2BqoF2Tqr14VqTPUCIcP%2B5%2Fly4qC%2BUL3sYxSvNj1NwsVYPsWdMUfomsdkYm3Tj0nbV0N1wRKwFe1MgKACDIBdMAhPE%2FwicwNWxll8Ag40w%2BFfhibJkGHmutjYeQ8gVlaN%2BjO51nDysa9TwNUFMqaGbKdRJZFfOJSp6mkRKsv0rRIpEVWjAvyFkxNOEpwvcAVPfEe%2Bl8ojeNTx3nXLBcWRrYGxSRjDEk0VlpxYrbe1ZmaQ5xuT0u3r%2B2qe5j0J5uytiZPGsRL2Jm32AldpxPUNJ3jmmsN4x62z1cXrbedXBQf2yvIFCeZrtyicZZG2U2nrrBJzYorI2EXLrvTfCSB43s41PKEvbZDEfQby6L4JTj%2FfIwam%2B4%2BwucBu%2BDgNK05Nle1rSt9HvR%2FKPC4U6LTfvUIaip1mjIa8fPzykii23h2eanT57zQ7fsyYH5QjywwlooAUcAdOh5QumgTHx6aAO7%2FL52eaQNEShrxfhL6albEDmfhGflrsT4tps8gTHNOJbeDeBlt0WJWDHSgxs6cW6lQqyg1FpD5ZVDfhn1HYFF1y4Eiaqa18pQf3zzYMBhcanlBjYfgWNayAf%2FASOgklu8bmgD7hADrk4cRlOL7NSOewEcbqSmaivT33QuFdHXj5sdvjlN5yMDrAECmdgDWG2L8P%2BAKLs9ZLZ7dJda%2BB4Xl84t7QvnKfvpXJv9obz2KgK8dXyqISyV0sXGZ0U47hOA%2FAiigbEMECJxC9aoKp86re5O5prxOlHkcksutSQJzxZRlPZmrOKhsQBF5zEZKybUC0vVjG8PqOnhOq46qyDTDnj5gZBriWCk4DvXrudQnXQmnXblebhAC2cCB6zIbM4PYgGl0elPSgIf3iFEA21aLdHYLHUQuVkpgi02SxFdrG862Y8ymYGMvXDzUmiX8DS5vKZyZlGmsSgQqfLub5RyLNS4zfDiZc9Edzh%2FtCE%2BX8j9k%2FqWB071rcZyMImne1SLkL4GRw4UPHMV3jjwEYpPG5uW5fAEot0aTSJnsGAwHJi2nvF1Y5OIqWziVCQd5NT7t6Q8guOSpgS%2Fa1dSRn8JGGaCD3BPXDyQRG4Bqhu8XrgAp0yy8DMSvvyVXDgJcJTcr1wQ2BvFKf65jqhvmxXUuDpGBlRvV36XvGjQzLi8KAKT2lYOnmxQPGorURSV0NhyTIuIyqOmKTMhQ%2BieEsgOgpc4KBbfDM4B3SIgFljvfHF6cef7qpyLBXAiQcXvg5l3Iunp%2FWv4dH6qFziO%2BL9PbrimQ9RY6MQphEfGUpOmma7KkGzuS8sPUFnCtIYcKCaI9EXo4HlQLgGrBjbiK5EqMj2AKWt9QWcIFMtnVvQVDQV9lXJJqdPVtUQpbh6gCI2Ov1nvZts7yYdsnvRgxiWFOtNJcOMVLn1vgptVi6qrNiFOfEjHCDB3J%2BHDLqUB77YgQGwX%2Fb1eYna3hGKdlqJKIyiE4nSbV8VFgxmxR4b5mVkkeUhMgs5YTi4ja2XZ009xJRHdkfwMi%2BfocaancuO7h%2FMlcLOa0V%2FSw6Dq47CumRQAKhgbOP8t%2BMTjuxjJGhXCY6XpmDDFqWlVYbQ1aDJ5Cptdw4oLbf3Ck%2BdWkVP0LpH7s9XLPXI%2FQX8ws%2Bj2In63IcRvOOo%2BTTjiN%2BlssfRsanW%2B3REVKoavBOAPTXABW4AL7e4NygHdpAKBscmlDh9Jysp4wxbnUNna3L3xBvyE1jyrGIkUHaqQMuxhHElV6oj1picvgL1QEuS5PyZTEaivqh5vUCKJqOuIgPFGESns8kyFk7%2FDxyima3cYxi%2FYOQCj%2F%2B9Ms2Ll%2Bhn4FmKnl7JkGXQGDKDAz9rUGL1TIlBpuJr9Be2JjK6qPzyDg495UxXYF7JY1qKimw9jWjF0iV6DRIqE%2B%2FeWG0J2ofmZTk0mLYVd4GLiFCOoKR0Cg727tWq981InYynvCuKW43aXgEjofVbxIqrm0VL76zlH3gQzWP3R3Bv9oXxclrlO7VVtgBRpSP4hMFWJ8BrUSBCJXC07l40X4jWuvtc42ofNCxtlX2JH6bdeojXgTh5TxOBKEyY5wvBE%2BACh8BtOPNPkApjoxi5h%2B%2FFMQQNpWvZaMH7MKFu5Ax8HoCQdmGkJrtnOiLHwD3uS5y8%2F2xTSDrE%2F4PT1yqtt6vGe8ldMBVMEPd6KwqiYECHDlfbvzphcWP%2BJiZuL5swoWQYlS%2Br7Yu5mNUiGD2retxBi9fl6RDGn4Ti9B1oyYy%2BMP5G87D%2FCpRlvdnuy0PY6RC8BzTA40NXqckQ9TaOUDywkYsudxJzPgyDoAWn%2BB6nEFbaVxxC6UXjJiuDkW9TWq7uRBOJocky9iMfUhGpv%2FdQuVVIuGjYqACbXf8aa%2BPeYNIHZsM7l4s5gAQuUAzRUoT51hnH3EWofXf2vkD5HJJ33vwE%2FaEWp36GHr6GpMaH4AAPuqM5eabH%2FhfG9zcCz4nN6cPinuAw6IHwtvyB%2FdO1toZciBaPh25U0ducR2PI3Zl7mokyLWKkSnEDOg1x5fCsJE9EKhH7HwFNhWMGMS7%2BqxyYsbHHRUDUH4I%2FAheQY7wujJNnFUH4KdCju83riuQeHU9WEqNzjsJFuF%2FdTDAZ%2FK7%2F1WaAU%2BAWymT59pVMT4g2AxcwNa0XEBDdBDpAPvgDIH73R25teeuAF5ime2Ul0OUIiG4GpSAEJeYW9wDTf43wfwHgHLKJoPznkwAAAABJRU5ErkJggg%3D%3D)](https://doi.org/10.6084/m9.figshare.25816864.v1)
+[![pytest CI](https://github.com/duartegroup/mlp-train/actions/workflows/pytest.yml/badge.svg?event=push)](https://github.com/duartegroup/mlp-train/actions/workflows/pytest.yml)
+[![codecov](https://codecov.io/gh/duartegroup/mlp-train/branch/main/graph/badge.svg)](https://codecov.io/gh/duartegroup/mlp-train)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![License](https://img.shields.io/badge/License-MIT%202.0-blue.svg)](https://opensource.org/licenses/mit)
-[![GitHub issues](https://img.shields.io/github/issues/duartegroup/mlp-train.svg)](https://github.com/duartegroup/mlp-train/issues)
 
 # mlp-train
 General machine learning potentials (MLP) training for molecular systems in gas phase and solution
@@ -15,7 +16,7 @@ Available models:
 
 ## Install
 
-Each model is installed into individual conda environment:
+Each model is installed into an individual conda environment:
 
 ```
 # Install GAP
@@ -32,14 +33,19 @@ Each model is installed into individual conda environment:
 
 - Units are: distance (Å), energy (eV), force (eV Å$`^{-1}`$), time (fs)
 
-## Using with OpenMM (Experimental!)
+## Using with OpenMM
 
 The OpenMM backend only works with MACE at the moment. The necessary dependencies are installed automatically via conda:
 
-```console
+```
 ./install_mace.sh
 ```
 
+Depending on your machine, you might need to prefix the command above with something like `CONDA_OVERRIDE_CUDA="11.2"` in two scenarios:
+
+- To ensure an environment that is compatible with your CUDA driver.
+- To force CUDA builds to be installed, even if the installation is being done from a CPU-only machine. This is typical in a situation where you are installing from a head node without GPUs but intend to run on GPUs and want to install the CUDA builds.
+
 You should now be able to run `water_openmm.py` in `./examples` or run the jupyter notebook on Google Colab [`water_openmm_colab.ipynb`](./examples/water_openmm_colab.ipynb).
 
 You can use OpenMM during active learning by passing the keyword argument `md_program="OpenMM"` to the `al_train` method.

diff --git a/environment.yml b/environment.yml
@@ -13,11 +13,13 @@ dependencies:
   - cython
   - dscribe=2.0
   - matplotlib-base
-  - numpy
-  - pytest
+  - numpy<2
+  - pytest=8
+  - pytest-cov=5
   - py-plumed
   - scipy
   - xtb
+  - scikit-learn
   - pip:
     - quippy-ase # GAP
     - ase@git+https://gitlab.com/ase/ase.git@f2615a6e9a # For PLUMED
diff --git a/environment_ace.yml b/environment_ace.yml
@@ -13,11 +13,13 @@ dependencies:
   - cython
   - dscribe=2.0
   - matplotlib-base
-  - numpy
-  - pytest
+  - numpy<2
+  - pytest=8
+  - pytest-cov=5
   - py-plumed
   - scipy
   - xtb
+  - scikit-learn
   - pip:
     - julia   # Python-Julia integration (this will not install Julia itself!)
     - pyjulip@git+https://github.com/casv2/pyjulip.git@72280a6ac3 # Integration with ACE

diff --git a/environment_mace.yml b/environment_mace.yml
@@ -15,26 +15,18 @@ dependencies:
   - dscribe=2.0
   - matplotlib-base
   - numpy
-  - pytest
+  - pytest=8
+  - pytest-cov=5
   - py-plumed
   - scipy
   - xtb
-  # MACE dependencies
-  - pytorch=2.0
-  - openmm-torch=1.1
-  - torchvision
-  - torchaudio
-  - torch-ema
-  # TODO: You might also need CUDA-specific libraries,
-  # but that depends on CUDA version
-  # https://pytorch.org/get-started/locally/
-  # - pytorch-cuda=11.8
-  # - pytorch-cuda=12.1
+  - scikit-learn
+  - openmm
+  - openmm-torch
+  - nnpops
+  - openmm-ml
+  - git
+  - openmm-ml
   - pip:
-    # e3nn is available on conda as well, but it is a dependency of mace
-    # so needs to be installed together.
-    - e3nn
-    - mace@git+https://github.com/ACEsuit/[email protected]
-    # The upstream PR to openmm-ml has not been merged yet: https://github.com/openmm/openmm-ml/pull/61)
-    - openmmml@git+https://github.com/sef43/openmm-ml.git@mace
     - ase@git+https://gitlab.com/ase/ase.git@f2615a6e9a # For PLUMED
+    - mace-torch
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		a5e89e407dd5b4ac988138af6870262d3a9e43fa # apply ruff formatter