volkamerlab · mbackenkoehler · Jan 26, 2024 · Jan 26, 2024 · Jan 26, 2024 · Jan 29, 2024
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -21,97 +21,47 @@ jobs:
       matrix:
         cfg:
           - os: ubuntu-latest
-            python-version: "3.8"
-          - os: ubuntu-latest
-            python-version: "3.9"
           - os: macos-latest
-            python-version: "3.8"
           - os: windows-latest
-            python-version: "3.8"
 
     env:
-      PYVER: ${{ matrix.cfg.python-version }}
       PACKAGE: teachopencadd
 
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        uses: actions/checkout@v4
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: ${{ matrix.cfg.python-version }}
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
           activate-environment: teachopencadd
           environment-file: devtools/test_env.yml
 
-      - name: Additional info about the build
-        shell: bash
-        run: |
-          uname -a
-          df -h
-          ulimit -a
-
-      - name: Install package
-        shell: bash -l {0}
-        run: |
-          pip install . --no-deps -vv
-
-      - name: Environment Information
-        shell: bash -l {0}
-        run: |
-          conda info --all
-          conda list
-
-      - name: Test CLI
-        shell: bash -l {0}
-        run: |
-          teachopencadd -h
-          pytest -v --cov=${PACKAGE} --cov-report=xml --color=yes ${PACKAGE}/tests/
-
-      - name: Run tests
-        shell: bash -l {0}
+      - name: Run Talktorials
+        shell: bash -el {0}
         run: |
-          PYTEST_ARGS="--nbval-lax --current-env --dist loadscope --numprocesses 2"
+          python devtools/test_talktorials.py
 
-          PYTEST_IGNORE_T001="--ignore=teachopencadd/talktorials/T001_query_chembl/talktorial.ipynb"
-          PYTEST_IGNORE_T018="--ignore=teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb"
-          PYTEST_IGNORE_T019="--ignore=teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb"
-          PYTEST_IGNORE_T020="--ignore=teachopencadd/talktorials/T020_md_analysis/talktorial.ipynb"
-          PYTEST_IGNORE_T035="--ignore=teachopencadd/talktorials/T035_graph_neural_networks/talktorial.ipynb"
-          PYTEST_IGNORE_T036="--ignore=teachopencadd/talktorials/T036_e3_equivariant_gnn/talktorial.ipynb"
-          PYTEST_IGNORE_T038="--ignore=teachopencadd/talktorials/T038_protein_ligand_interaction_prediction/talktorial.ipynb"
-
-          IGNORE="$PYTEST_IGNORE_T001"
-
-          if [ "$RUNNER_OS" == "Windows" ]; then
-            # Ignore T019 under Windows, see https://github.com/volkamerlab/teachopencadd/issues/313
-            IGNORE="$IGNORE $PYTEST_IGNORE_T019"
-            IGNORE="$IGNORE $PYTEST_IGNORE_T035"
-            IGNORE="$IGNORE $PYTEST_IGNORE_T036"
-            IGNORE="$IGNORE $PYTEST_IGNORE_T038"
-          fi
-
-          if [ "$RUNNER_OS" == "Linux" ]; then
-            IGNORE="$IGNORE $PYTEST_IGNORE_T018" # see 385
-          fi
-
-          if [ "$RUNNER_OS" == "macOS" ]; then
-            IGNORE="$IGNORE $PYTEST_IGNORE_T018" # see 385
-            IGNORE="$IGNORE $PYTEST_IGNORE_T019"
-            IGNORE="$IGNORE $PYTEST_IGNORE_T035" # may cause kernel dying in pytest
-            IGNORE="$IGNORE $PYTEST_IGNORE_T036" # may cause kernel dying in pytest
-          fi
+      - name: Cache Conda packages
+        uses: actions/cache@v3
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-
+          restore-keys: |
+            ${{ runner.os }}-conda-
 
-          pytest $PYTEST_ARGS teachopencadd/talktorials/ $IGNORE
 
   format:
     name: Black
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v3
       - name: Install format dependencies
-        run: python -m pip install black-nb shyaml
+        run: python -m pip install 'black<23.1.0' black-nb shyaml
       - name: Run black-nb
         run: |
           black-nb -l 99 --check teachopencadd/talktorials/T*/talktorial.ipynb
@@ -120,7 +70,7 @@ jobs:
     name: READMEs
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v3
       - name: Install nbformat
         run: python -m pip install nbformat shyaml

diff --git a/devtools/environment_a.yml b/devtools/environment_a.yml
@@ -0,0 +1,18 @@
+name: teachopencadd-a
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=3.11
+  - jupyterlab
+  - notebook=7
+  - pandas=2
+  - pyarrow 
+  - numpy
+  - rdkit=2023.9
+  - chembl_webresource_client=0.10
+  - iprogress
+  - ipywidgets=8
+  - tqdm
diff --git a/devtools/test_env.yml b/devtools/test_env.yml
@@ -3,72 +3,4 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python>=3.8
-  - pip
-  - jupyterlab>=3
-  # Workaround for jupyterlab, see https://github.com/volkamerlab/teachopencadd/issues/310
-  - jsonschema>=4.3.0
-  - nglview>=3
-  # Workaround for nglview, see https://github.com/volkamerlab/teachopencadd/issues/262
-  - ipywidgets<=7.75
-  - jupyter_client<=7.4.9
-  # New numpy version 1.2.4 too young, e.g. caused
-  # https://github.com/volkamerlab/teachopencadd/issues/299
-  - numpy<1.24
-  - scikit-learn
-  # API changed after v2.6, see https://github.com/volkamerlab/teachopencadd/issues/265
-  - tensorflow<=2.6
-  - seaborn
-  - matplotlib-venn
-  - bravado
-  - requests
-  - requests-cache
-  - redo
-  - suds-community
-  - beautifulsoup4
-  - chembl_webresource_client
-  - pypdb
-  - biopython<=1.77
-  - biopandas
-  - rdkit
-  - openbabel
-  - opencadd
-  - biotite>=0.34.0
-  - smina
-  - mdanalysis>=1.0.0
-  - mdtraj
-  - plip
-  - openmm
-  - mkl < 2022
-  - pytorch::pytorch==1.13.0
-  #- pyg::pyg==2.2.0  # installed manually for now
-  # Dependency not included, see https://github.com/volkamerlab/teachopencadd/issues/313
-  # - openmmforcefields
-  - pdbfixer
-  - tqdm
-  - lxml
-  - kissim
-  ## CI tests
-  - pytest
-  - pytest-xdist
-  - pytest-cov
-  - nbval
-  - shyaml
-  # Workaround for https://github.com/sphinx-doc/sphinx/issues/10289
-  - jinja2==3.0.3
-  ## Docs
-  - sphinx
-  - sphinx-material
-  - nbsphinx
-  - recommonmark
-  - sphinx-autodoc-typehints
-  - sphinx-copybutton
-  - sphinx-gallery
-  - autodocsumm
-  - pip:
-      - black-nb
-      - nbsphinx-link
-      - sphinxext-opengraph
-      - deepchem
-      # TeachOpenCADD itself
-      - ../
+  - pyyaml
diff --git a/devtools/test_talktorials.py b/devtools/test_talktorials.py
@@ -0,0 +1,69 @@
+import os
+import sys
+import subprocess
+import pathlib
+import yaml
+
+HERE = pathlib.Path().absolute()
+
+
+def create_conda_environment(env_file, env_name):
+    # Create Conda environment from environment file
+    env_path = HERE / "devtools" / env_file
+    assert env_path.exists(), f"No environment file {env_path} found."
+    # subprocess.run(f'mamba env remove -n {env_name}', check=False)
+    subprocess.run(
+        f"mamba env create -f {env_path} -n {env_name} -q".split(), check=True
+    )
+    subprocess.run(
+        f"mamba install -n {env_name} pytest pytest-xdist nbval -c conda-forge -y -q".split(),
+        check=True,
+    )
+
+
+def deactivate_conda_environment():
+    # Deactivate Conda environment
+    subprocess.run(["conda", "deactivate"], shell=True, check=True)
+
+
+def test_notebooks(notebooks, env_name):
+    # Run tests on Jupyter notebooks
+    success = True
+    for notebook in notebooks:
+        talktorial_path = (
+            HERE / "teachopencadd" / "talktorials" / notebook / "talktorial.ipynb"
+        )
+        assert talktorial_path.exists(), f"Talktorial {notebook} not found."
+        res = subprocess.run(
+            f"conda run -n {env_name} pytest --nbval {talktorial_path}".split()
+        )
+        success = (res == 0) and success
+    return success
+
+
+def main():
+    # Load configuration from YAML file
+    with open("tests.yml", "r") as file:
+        config = yaml.safe_load(file)
+
+    success = True
+    for environment in config["environments"]:
+        env_name = environment["name"]
+        env_file = environment["file"]
+        notebooks = environment["notebooks"]
+
+        print(f"Setting up Conda environment '{env_name}'...")
+        create_conda_environment(env_file, env_name)
+
+        print(f"Running tests on Jupyter notebooks for environment '{env_name}'...")
+        success = success and test_notebooks(notebooks, env_name)
+
+    return success
+
+
+if __name__ == "__main__":
+    success = main()
+    if success:
+        sys.exit(os.EX_OK)
+    else:
+        sys.exit(os.EX_SOFTWARE)
diff --git a/teachopencadd/talktorials/T001_query_chembl/environment.yml b/teachopencadd/talktorials/T001_query_chembl/environment.yml
@@ -0,0 +1 @@
+../../../devtools/environment_a.yml