doc updates, workflow updates

.github/workflows/doc.yml

@@ -32,7 +32,7 @@ jobs:
 
       - name: Install library
         run: |
-          python -m pip install --no-deps .
+          python -m pip install --no-deps --no-build-isolation .
           pip install typer-cli
 
       - name: Configure git

.github/workflows/release.yml

@@ -99,7 +99,7 @@ jobs:
           git push origin "${{ inputs.release-version }}"
 
       - name: Install library
-        run: python -m pip install --no-deps .
+        run: python -m pip install --no-deps --no-build-isolation .
 
       - name: Build the wheel and sdist
         run: python -m build --no-isolation

.github/workflows/test.yml

@@ -52,7 +52,7 @@ jobs:
             pytorch=${{ matrix.pytorch-version }}
 
       - name: Install library
-        run: python -m pip install --no-deps -e . # `-e` required for correct `coverage` run.
+        run: python -m pip install --no-deps --no-build-isolation -e . # `-e` required for correct `coverage` run.
 
       - name: Install test dependencies
         run: micromamba install -c conda-forge pytdc  # Required to run the `test_finetuning.py`

README.md

@@ -59,7 +59,7 @@ mamba env create -f env.yml -n graphium
 # To force the CUDA version to 11.2, or any other version you prefer, use the following command:
 # CONDA_OVERRIDE_CUDA=11.2 mamba env create -f env.yml -n graphium
 
-# Activate the mamba environment containing graphium's dependencies
+# Activate the mamba environment containing Graphium's dependencies
 mamba activate graphium
 
 # Install Graphium in dev mode

docs/contribute.md

@@ -13,9 +13,11 @@ Use [`mamba`](https://github.com/mamba-org/mamba), a preferred alternative to co
 # Install Graphium's dependencies in a new environment named `graphium`
 mamba env create -f env.yml -n graphium
 
-# Install Graphium in dev mode
+# Activate the mamba environment containing graphium's dependencies
 mamba activate graphium
-pip install --no-deps -e .
+
+# Install Graphium in dev mode
+pip install --no-deps --no-build-isolation -e .
 ```
 
 ## Build the documentation
@@ -24,5 +26,6 @@ You can build and serve the documentation locally with:
 
 ```bash
 # Build and serve the doc
+doxygen Doxyfile
 mkdocs serve
 ```

graphium/graphium_cpp/README.md

@@ -25,16 +25,16 @@ mamba install graphium -c conda-forge
 ## Installation for developers 
 To install `graphium_cpp` (and `graphium`) locally, refer to these steps:
 ```
-# Install graphium's dependencies in a new environment named `graphium`
+# Install Graphium's dependencies in a new environment named `graphium`
 mamba env create -f env.yml -n graphium
 
 # To force the CUDA version to 11.2, or any other version you prefer, use the following command:
 # CONDA_OVERRIDE_CUDA=11.2 mamba env create -f env.yml -n graphium
 
-# Activate the mamba environment containing graphium's dependencies
+# Activate the mamba environment containing Graphium's dependencies
 mamba activate graphium
 
-# Install graphium in dev mode
+# Install Graphium in dev mode
 pip install --no-deps --no-build-isolation -e .
 
 # On every change to graphium_cpp code, reinstall the package