Separate environments

.github/workflows/ci.yml

@@ -21,103 +21,41 @@ 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}
+      - name: Run Talktorials
+        shell: bash -el {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 ${PACKAGE}/tests/
-
-      - name: Run tests
-        shell: bash -l {0}
-        run: |
-          PYTEST_ARGS="--nbval-lax --current-env --dist loadscope --numprocesses 2"
-
-          PYTEST_IGNORE_T001="--ignore=teachopencadd/talktorials/T001_query_chembl/talktorial.ipynb"
-          PYTEST_IGNORE_T018="--ignore=teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb"
-          PYTEST_IGNORE_T019="--ignore=teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb"
-          PYTEST_IGNORE_T020="--ignore=teachopencadd/talktorials/T020_md_analysis/talktorial.ipynb"
-          PYTEST_IGNORE_T035="--ignore=teachopencadd/talktorials/T035_graph_neural_networks/talktorial.ipynb"
-          PYTEST_IGNORE_T036="--ignore=teachopencadd/talktorials/T036_e3_equivariant_gnn/talktorial.ipynb"
-          PYTEST_IGNORE_T038="--ignore=teachopencadd/talktorials/T038_protein_ligand_interaction_prediction/talktorial.ipynb"
-
-          IGNORE="$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
-
-          pytest $PYTEST_ARGS teachopencadd/talktorials/ $IGNORE
+          python devtools/test_talktorials.py
 
   format:
-    name: Black
+    name: Talktorial Formatting
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - 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
 
   readmes:
-    name: READMEs
+    name: README consistency
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3

devtools/environment_a.yml

@@ -0,0 +1,16 @@
+name: teachopencadd-a
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=3.11
+  - jupyterlab
+  - notebook=7
+  - pandas=2.
+  - rdkit=2023.9
+  - chembl_webresource_client=0.10
+  - iprogress
+  - ipywidgets=8
+  - tqdm

devtools/environment_b.yml

@@ -0,0 +1,23 @@
+name: teachopencadd-b
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=3.11
+  - pip
+  - jupyterlab 
+  - numpy
+  - pandas=2.0
+  - rdkit
+  - pyarrow 
+  - ipywidgets 
+  - tqdm
+  - scikit-learn
+  - pdbfixer
+  - tensorflow
+  - seaborn
+  - biotite
+  - pip:
+    - ..

devtools/environment_c.yml

@@ -0,0 +1,30 @@
+name: teachopencadd-c
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=3.9
+  - jupyterlab
+  - pandas=2.1.4
+  - numpy
+  - notebook=7
+  - tqdm
+  - pyarrow
+  - ipywidgets=8
+  - matplotlib=3.8
+  - rdkit=2023.9
+  - opencadd
+  - pypdb=2
+  - redo=2
+  - nglview=3
+  - requests-cache
+  - bravado=11
+  - matplotlib-venn
+  - plip
+  - openbabel
+  - smina
+  - seaborn
+  - scikit-learn
+  - kissim

devtools/environment_d.yml

@@ -0,0 +1,15 @@
+name: teachopencadd-d
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=3.11
+  - jupyterlab
+  - notebook>=7
+  - rdkit=2023.9
+  - pandas>=2.1
+  - pyarrow
+  - nglview=3
+  - scikit-learn=1.4

devtools/environment_e.yml

@@ -0,0 +1,19 @@
+name: teachopencadd-e
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=3.9
+  - jupyterlab
+  - pandas=2.0
+  - notebook=7
+  - pyarrow
+  - rdkit=2022.9
+  - opencadd
+  - pypdb=2
+  - redo=2
+  - nglview=3
+  - numpy=1.21
+  - mdanalysis=2

devtools/environment_f.yml

@@ -0,0 +1,14 @@
+name: teachopencadd-e
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=3.11 
+  - jupyterlab 
+  - pandas
+  - pyarrow
+  - seaborn
+  - biotite
+  - scikit-learn

devtools/environment_g.yml

@@ -0,0 +1,21 @@
+name: teachopencadd-g
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - matplotlib
+  - numpy
+  - pandas
+  - pytorch
+  - tqdm
+  - pytorch_geometric
+  - torch-scatter
+  - scipy
+  - seaborn
+  - rdkit
+  - jupyterlab
+  - pyarrow
+  - nglview
+  - biotite
+  - pypdb
+  - chembl_webresource_client

devtools/environment_h.yml

@@ -0,0 +1,16 @@
+name: teachopencadd-h
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=3.11
+  - jupyterlab
+  - notebook=7
+  - pandas=2.1
+  - pyarrow
+  - nglview=3
+  - scikit-learn=1.4
+  - biopython
+  - bravado

devtools/environment_i.yml

@@ -0,0 +1,21 @@
+name: teachopencadd-i
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python = 3.12.1
+  - jupyterlab = 4.1.1
+  - numpy = 1.26.4
+  - pandas = 2.1.4  # not 2.2.x due to this problem in RDKit: https://github.com/rdkit/rdkit/pull/7165
+  - matplotlib = 3.8.2
+  - rdkit = 2023.09.5
+  - nglview = 3.1.1
+  - openbabel = 3.1.1
+  - biopandas = 0.4.1
+  - pypdb = 2.3
+  - mdanalysis = 2.7.0
+  - plip = 2.3.0
+  - smina = 2020.12.10
+  - requests = 2.31.0
+  - redo = 2.0.4
+  - ipywidgets = 8.1.2

devtools/test_configurations.yml

@@ -0,0 +1,60 @@
+environments:
+  - name: teachopencadd-a
+    file: environment_a.yml
+    notebooks:
+      - T001_query_chembl
+  - name: teachopencadd-b
+    file: environment_b.yml
+    notebooks:
+      - T002_compound_adme
+      - T003_compound_unwanted_substructures
+      - T004_compound_similarity
+      - T005_compound_clustering
+      - T006_compound_maximum_common_substructures
+      - T007_compound_activity_machine_learning
+      - T013_query_pubchem
+        #   - T019_md_simulation
+      - T021_one_hot_encoding
+      - T027_kinase_similarity_ligand_profile
+  - name: teachopencadd-c
+    file: environment_c.yml
+    notebooks:
+      - T008_query_pdb
+      - T012_query_klifs
+      - T014_binding_site_detection
+      - T015_protein_ligand_docking
+      - T016_protein_ligand_interactions
+      - T017_advanced_nglview_usage
+      - T023_what_is_a_kinase
+      - T025_kinase_similarity_kissim
+      - T026_kinase_similarity_ifp
+  - name: teachopencadd-d
+    file: environment_d.yml
+    notebooks:
+      - T009_compound_ensemble_pharmacophores
+  - name: teachopencadd-e
+    file: environment_e.yml
+    notebooks:
+      - T010_binding_site_comparison
+  - name: teachopencadd-f
+    file: environment_f.yml
+    notebooks:
+      - T024_kinase_similarity_sequence
+      - T028_kinase_similarity_compare_perspectiv
+  - name: teachopencadd-g
+    file: environment_g.yml
+    notebooks:
+      - T033_molecular_representations
+      - T034_recurrent_neural_networks
+      - T035_graph_neural_networks
+      - T036_e3_equivariant_gnn
+      - T037_uncertainty_estimation
+      - T038_protein_ligand_interaction_prediction
+  - name: teachopencadd-h
+    file: environment_h.yml
+    notebooks:
+      - T011_query_online_api_webservices
+  - name: teachopencadd-i
+    file: environment_i.yml
+    notebooks:
+      - T018_automated_cadd_pipeline