Merge pull request #126 from datamol-org/tutos

Tutos

.github/workflows/doc.yml

@@ -17,26 +17,17 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Setup conda
-        # see https://github.com/mamba-org/provision-with-micromamba/issues/54
-        uses: mamba-org/provision-with-micromamba@755a9542150cc9dedd1c1dd95b963460ec320939
+        uses: mamba-org/provision-with-micromamba@main
         with:
-          environment-file: false
+          environment-file: env.yml
+          environment-name: datamol
           cache-downloads: true
 
-      - name: Install Dependencies
-        run: |
-          micromamba activate
-          micromamba create -n datamol -f env.yml
-
       - name: Install library
-        run: |
-          micromamba activate datamol
-          python -m pip install .
+        run: python -m pip install --no-deps .
 
       - name: Deploy the doc
         run: |
-          micromamba activate datamol
-
           echo "Configure git"
           git config --global user.name 'hadim'
           git config --global user.email '[email protected]'

.github/workflows/test.yml

@@ -30,38 +30,20 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Setup conda
-        # see https://github.com/mamba-org/provision-with-micromamba/issues/54
-        uses: mamba-org/provision-with-micromamba@755a9542150cc9dedd1c1dd95b963460ec320939
+        uses: mamba-org/provision-with-micromamba@main
         with:
-          environment-file: false
+          environment-file: env.yml
+          environment-name: datamol
           cache-downloads: true
-
-      - name: Setup conda env
-        run: |
-          micromamba activate
-
-          # Patch the conda env file to specify the Python and RDKit version
-          micromamba install -c conda-forge --yes pyyaml
-
-          python .github/patch_conda_env.py --env env.yml -d \
-            python="${{ matrix.python-version }}" \
-            rdkit="${{ matrix.rdkit-version }}" \
-            > env-patched.yml
-
-      - name: Install Dependencies
-        run: |
-          micromamba activate
-          micromamba create -n datamol -f env-patched.yml
+          extra-specs: |
+            python=${{ matrix.python-version }}
+            rdkit=${{ matrix.rdkit-version }}
 
       - name: Install library
-        run: |
-          micromamba activate datamol
-          python -m pip install -e .  # `-e` required for correct `coverage` run.
+        run: python -m pip install --no-deps -e . # `-e` required for correct `coverage` run.
 
       - name: Run tests
-        run: |
-          micromamba activate datamol
-          pytest
+        run: pytest
 
       - name: Codecov Upload
         uses: codecov/codecov-action@v1
@@ -74,8 +56,4 @@ jobs:
           env_vars: ${{ matrix.os }},${{ matrix.python-version }},${{ matrix.rdkit-version }}
 
       - name: Test building the doc
-        run: |
-          micromamba activate datamol
-
-          # Build and serve the doc
-          mkdocs build
+        run: mkdocs build

datamol/__init__.py

@@ -69,8 +69,6 @@
 
 from . import fragment
 from . import scaffold
-from . import reactions
-from . import actions
 from . import molar
 from . import descriptors
 from . import predictors