Merge branch 'main' into delaunay

Author: gbg141

.github/workflows/lint.yml

@@ -11,4 +11,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - uses: chartboost/ruff-action@v1
+      - uses: chartboost/ruff-action@v1
+        with:
+          src: './modules'

.github/workflows/test_codebase.yml

@@ -27,34 +27,31 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.10", "3.11"]
-        torch-version: [2.0.1]
-        include:
-          - torch-version: 2.0.1
+        python-version: [3.11.3]
 
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{matrix.python-version}}
+        uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
-          cache-dependency-path: '**/pyproject.toml'
+          python-version: ${{matrix.python-version}}
 
-      - name: Install PyTorch ${{ matrix.torch-version }}+cpu
-        run: |
-          pip install --upgrade pip setuptools wheel
-          pip install torch==${{ matrix.torch-version}} --extra-index-url https://download.pytorch.org/whl/cpu
-          pip install torch-scatter -f https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html
-          pip install torch-sparse -f https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html
-          pip install torch-cluster -f https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html
-          pip show pip
-      - name: Install main package
+      - uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{matrix.os}}-${{matrix.python-version}}-${{ hashFiles('pyproject.toml') }}
+
+      - name: Install dependencies
         run: |
-          pip install -e .[all]
-      - name: Run tests for codebase [pytest]
+          python -m pip install --upgrade pip
+          pip install pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          source env_setup.sh
+
+      - name: Test with pytest
         run: |
           pytest -n 2 --cov --cov-report=xml:coverage.xml test/transforms/feature_liftings test/transforms/liftings
+          pytest test/tutorials/test_tutorials.py
       - name: Upload coverage
         uses: codecov/codecov-action@v3
         with:

.github/workflows/test_tutorials.yml

@@ -17,25 +17,12 @@ repos:
       - id: trailing-whitespace
       - id: requirements-txt-fixer
 
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
     hooks:
-      - id: black-jupyter
+      - id: ruff-format
 
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id : isort
-        args : ["--profile=black", "--filter-files"]
-
-  #- repo: https://github.com/asottile/blacken-docs
-  #  rev: 1.13.0
-  #  hooks:
-  #  -   id: blacken-docs
-  #      additional_dependencies: [black==23.3.0]
-
-  # - repo: https://github.com/pycqa/flake8
-  #   rev: 6.0.0
+  # - repo: https://github.com/numpy/numpydoc
+  #   rev: v1.6.0
   #   hooks:
-  #   -   id: flake8
-  #       additional_dependencies: [flake8-docstrings, Flake8-pyproject]
+  #     - id: numpydoc-validation

.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+data_domain: graph
+data_type: QM9
+data_name: QM9
+data_dir: datasets/${data_domain}/${data_type}
+#data_split_dir: ${oc.env:PROJECT_ROOT}/datasets/data_splits/${data_name}
+
+# Dataset parameters
+num_features: 11
+num_classes: 1
+task: regression
+loss_type: mse
+monitor_metric: mae
+task_level: graph
+

configs/datasets/QM9.yaml

@@ -0,0 +1,12 @@
+data_domain: graph
+data_type: toy_dataset
+data_name: manual_mol
+data_dir: datasets/${data_domain}/${data_type}
+
+# Dataset parameters
+num_features: 1
+num_classes: 2
+task: classification
+loss_type: cross_entropy
+monitor_metric: accuracy
+task_level: node

configs/datasets/manual_mol.yaml

@@ -0,0 +1,5 @@
+in_channels: null # This will be set by the dataset
+hidden_channels: 32
+out_channels: null # This will be set by the dataset
+n_layers: 2
+negative_slope: 0.2

configs/models/combinatorial/hmc.yaml

@@ -0,0 +1,7 @@
+transform_type: 'lifting'
+transform_name: "CombinatorialRingCloseAtomsLifting"
+max_cell_length: null
+preserve_edge_attr: True
+feature_lifting: ProjectionSum
+
+threshold_distance: 1.5

configs/transforms/liftings/graph2combinatorial/ring_close_atoms_lifting.yaml

@@ -0,0 +1,6 @@
+transform_type: 'lifting'
+transform_name: "SimplicialGraphInducedLifting"
+complex_dim: 3
+preserve_edge_attr: False
+signed: True
+feature_lifting: ProjectionSum

configs/transforms/liftings/graph2simplicial/graph_induced_lifting.yaml

@@ -0,0 +1,3 @@
+transform_type: "lifting"
+transform_name: "SimplicialLineLifting"
+feature_lifting: ProjectionSum