Merge branch 'master' into graph_plots

.github/workflows/build.yaml

@@ -22,8 +22,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9, "3.10"]
-        torch: [1.13.0, 2.1.0, 2.2.0]
+        python-version: [3.8, 3.9, "3.10", "3.11"]
+        torch: [1.13.0, 2.1.0, 2.2.0, 2.3.0, 2.4.0]
     # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
     defaults:
       run:
@@ -33,28 +33,33 @@ jobs:
         uses: actions/checkout@v3
         # See: https://github.com/marketplace/actions/setup-miniconda
       - name: Setup miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           miniforge-variant: Mambaforge
           channels: "conda-forge, salilab, pytorch, pyg"
           python-version: ${{ matrix.python-version }}
           use-mamba: true
+      - name: Install setuptools
+        run: pip install setuptools==69.5.1
       - name: Install Boost 1.7.3 (for DSSP)
         run: conda install -c anaconda libboost=1.73.0
       - name: Install DSSP
         run: conda install dssp -c salilab
       - name: Install mmseqs
         run: mamba install -c conda-forge -c bioconda mmseqs2
-      - name: Install PyTorch
-        #run: mamba install -c pytorch pytorch==${{matrix.torch}} cpuonly
-        run: pip install torch==${{matrix.torch}}+cpu -f https://download.pytorch.org/whl/torch_stable.html
+      - name: Install PyTorch (1.13.0)
+        if: matrix.torch == '1.13.0'
+        run: pip install torch==${{matrix.torch}}+cpu --extra-index-url https://download.pytorch.org/whl/cpu
+      - name: Install PyTorch (2.0+)
+        if: matrix.torch != '1.13.0'
+        run: pip install torch==${{matrix.torch}} -f https://download.pytorch.org/whl/cpu
       - name: Install PyG
         #run: mamba install -c pyg pyg
         run: pip install torch_geometric
       - name: Install torch-cluster
         #run: mamba install pytorch-cluster -c pyg
-        run: pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-${{matrix.torch}}+cpu.html
+        run: pip install torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-${{matrix.torch}}+cpu.html
       - name: Install BLAST
         run: sudo apt install ncbi-blast+
       - name: Install Graphein
@@ -68,4 +73,4 @@ jobs:
       - name: Run unit tests and generate coverage report
         run: pytest .
       - name: Test notebook execution
-        run: pytest --nbval-lax notebooks/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb" --ignore-glob="notebooks/foldcomp.ipynb"
+        run: pytest --nbval-lax notebooks/ --nbval-current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb" --ignore-glob="notebooks/foldcomp.ipynb" --ignore-glob="notebooks/grn_tutorial.ipynb"

.github/workflows/code-tests-docker.yaml

@@ -1,6 +1,13 @@
 name: Code tests (docker)
 
-on: [pull_request]
+on:
+  pull_request:
+      paths-ignore:
+      - "README.md"
+      - "CHANGELOG.md"
+      - "CONTRIBUTORS.md"
+      - "CONTRIBUTING.md"
+      - "docs/**"
 
 jobs:
   code-tests-docker:
@@ -38,7 +45,7 @@ jobs:
       - name: Build Docker container
         # if: steps.cache-environment.outputs.cache-hit != 'true'
         run: |
-          docker-compose -f docker-compose.cpu.yml up -d --build
+          docker compose -f docker-compose.cpu.yml up -d --build
 
       - name: Install Graphein (Docker)
         run: |
@@ -50,7 +57,7 @@ jobs:
 
       - name: Run example notebooks (Docker)
         run: |
-          docker exec $(docker ps -q) bash -c 'grep -l smoke_test notebooks/*.ipynb | pytest --nbval-lax --current-env'
+          docker exec $(docker ps -q) bash -c 'grep -l smoke_test notebooks/*.ipynb | pytest --nbval-lax --nbval-current-env'
 
       - name: Upload code coverage
         run: |

.github/workflows/minimal__install.yaml

@@ -34,7 +34,7 @@ jobs:
         uses: actions/checkout@v3
         # See: https://github.com/marketplace/actions/setup-miniconda
       - name: Setup miniconda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           miniforge-variant: Mambaforge
@@ -50,4 +50,4 @@ jobs:
       - name: Run unit tests and generate coverage report
         run: pytest . --ignore-glob="tests/protein/tensor" --ignore="tests/ml/test_conversion.py" --ignore="tests/ml/test_torch_geometric_dataset.py"
       - name: Test notebook execution
-        run: pytest --nbval-lax notebooks/ --current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/higher_order_graphs.ipynb" --ignore-glob="notebooks/protein_graph_analytics.ipynb" --ignore-glob="notebooks/subgraphing_tutorial.ipynb" --ignore-glob="notebooks/splitting_a_dataset.ipynb" --ignore-glob="notebooks/protein_tensors.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb" --ignore-glob="notebooks/foldcomp.ipynb" --ignore-glob="notebooks/creating_datasets_from_the_pdb.ipynb"
+        run: pytest --nbval-lax notebooks/ --nbval-current-env --ignore-glob="notebooks/dataloader_tutorial.ipynb" --ignore-glob="notebooks/higher_order_graphs.ipynb" --ignore-glob="notebooks/protein_graph_analytics.ipynb" --ignore-glob="notebooks/subgraphing_tutorial.ipynb" --ignore-glob="notebooks/splitting_a_dataset.ipynb" --ignore-glob="notebooks/protein_tensors.ipynb" --ignore-glob="notebooks/datasets_and_dataloaders.ipynb" --ignore-glob="notebooks/foldcomp.ipynb" --ignore-glob="notebooks/creating_datasets_from_the_pdb.ipynb" --ignore-glob="notebooks/grn_tutorial.ipynb"

.pre-commit-config.yaml

@@ -2,14 +2,14 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 24.3.0
+    rev: 24.8.0
     hooks:
     - id: black
 -   repo: https://github.com/pre-commit/pre-commit-hooks

.requirements/base.in

@@ -1,14 +1,16 @@
-pandas<2.0.0
-biopandas>=0.5.0.dev0
+pandas
+biopandas>=0.5.1
 biopython
 bioservices>=1.10.0
+cpdb-protein==0.2.0
+cython
 deepdiff
 loguru
 looseversion
 matplotlib>=3.4.3
 multipledispatch
 networkx
-numpy<1.24.0
+numpy<2
 pandas
 plotly
 pydantic