changes

.github/workflows/tests.yaml

@@ -1,36 +1,42 @@
 name: Source Code Tests
+
 on: [push]
+
 permissions:
     contents: read
-jobs:
-    formatting:
-        runs-on: ubuntu-latest
-        steps:
-            - uses: actions/checkout@v3
-            - uses: actions/setup-python@v3
-              with:
-                  python-version: 3.9
-            - name: update pip
-              run: pip install --upgrade pip
-            - name: Install ruff
-              run: pip install ruff
-            - name: Run ruff
-              run: ruff check
 
+jobs:
     tests:
         runs-on: ubuntu-latest
+        strategy:
+            fail-fast: false
+            matrix:
+                python-version:
+                    - 3.8
+                    - 3.9
+                    - "3.10"
+                    - 3.11
+        name: test - ${{ matrix.python-version }}
         steps:
-            - uses: actions/checkout@v3
-            - uses: actions/setup-python@v3
+            - uses: actions/checkout@v4
+            - uses: actions/setup-python@v5
               with:
-                  python-version: 3.9
+                  python-version: ${{ matrix.python-version }}
             - name: update pip
               run: pip install --upgrade pip
+            # - name: Install ruff
+            # run: pip install ruff
+            # - name: Run ruff
+            # run: ruff check
             - name: Install graph-pes
               run: pip install -e ".[test]"
+            - name: Useful info
+              run: pip freeze
             - name: Run tests
               run: pytest --cov src --cov-report xml
             - name: Upload coverage reports to Codecov
               uses: codecov/codecov-action@v3
+              # only upload coverage reports for the first python version
+              if: matrix.python-version == '3.8'
               with:
                   token: ${{secrets.CODECOV_TOKEN}}

.gitignore

@@ -13,10 +13,16 @@ coverage.xml
 *.extxyz
 *.npz
 *.ipynb
+**/wandb
 
 .vscode
 .isort.cfg
 .DS_Store
 
 thoughts*
-TODO*
+TODO*
+
+results/
+lammps/
+dumps/
+**.cache

README.md

@@ -7,7 +7,7 @@ Under-the-hood, this relies on Pytorch/Geometric for efficient tensor operations
 Batteries are included:
 - **easy data manipulations** : see docs relating to `AtomicGraph`, intuitive batching, easy conversion from ase etc.
 - **easy construction of PES models** : implement `predict_local_energies` , easy to save, load and share
-- **useful primitives** : PerSpeciesParameter
+- **useful primitives** : PerElementParameter
 - **easy training** : forces, energies, well conditioned losses etc.
 - **analysis** : easy to plot, analyse and compare models
 

docs/source/models/nn.rst

@@ -2,10 +2,10 @@
 PyTorch Helpers
 ###############
 
-.. autoclass :: graph_pes.nn.PerSpeciesParameter()
+.. autoclass :: graph_pes.nn.PerElementParameter()
    :members:
 
-.. autoclass :: graph_pes.nn.PerSpeciesEmbedding
+.. autoclass :: graph_pes.nn.PerElementEmbedding
 
 .. autoclass :: graph_pes.nn.MLP
     :members: