CI: integrating more talktorials

devtools/environment_a.yml

@@ -13,4 +13,3 @@ dependencies:
   - chembl_webresource_client=0.10
   - iprogress
   - ipywidgets=8
-  - 

devtools/environment_b.yml

@@ -15,5 +15,9 @@ dependencies:
   - ipywidgets 
   - tqdm
   - scikit-learn
+  - pdbfixer
+  - tensorflow
+  - seaborn
+  - biotite
   - pip:
     - ..

devtools/environment_c.yml

@@ -8,6 +8,7 @@ dependencies:
   - python=3.9
   - jupyterlab
   - pandas=2.1.4
+  - numpy
   - notebook=7
   - tqdm
   - pyarrow
@@ -21,3 +22,9 @@ dependencies:
   - requests-cache
   - bravado=11
   - matplotlib-venn
+  - plip
+  - openbabel
+  - smina
+  - seaborn
+  - scikit-learn
+  - kissim

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/test_configurations.yml

@@ -1,8 +1,8 @@
 environments:
-  #- name: teachopencadd-a
-    #file: environment_a.yml
-    #notebooks:
-      #- T001_query_chembl
+  - name: teachopencadd-a
+    file: environment_a.yml
+    notebooks:
+      - T001_query_chembl
   - name: teachopencadd-b
     file: environment_b.yml
     notebooks:
@@ -13,12 +13,21 @@ environments:
       - 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:
@@ -27,3 +36,10 @@ environments:
     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
+# MISSING: T011 T018

devtools/test_talktorials.py

@@ -2,12 +2,20 @@
 import sys
 import subprocess
 import pathlib
+import platform
 import yaml
 
 HERE = pathlib.Path().absolute()
 PYTEST_ARGS = "--nbval-lax --nbval-current-env --dist loadscope --numprocesses 4"
 
 
+def setup_mamba():
+    if platform.system() == "Windows":
+        subprocess.run("conda config --add channels conda-forge".split(), check=True)
+        subprocess.run("conda update -n base --all".split(), check=True)
+        subprocess.run("conda install -n base mamba".split(), check=True)
+
+
 def create_conda_environment(env_file, env_name):
     # Create Conda environment from environment file
     env_path = HERE / "devtools" / env_file
@@ -45,10 +53,14 @@ def main():
         env_file = environment["file"]
         notebooks = environment["notebooks"]
 
+        print("Set up mamba")
+        setup_mamba()
+
         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}'...")
+        print(f"\n".join(" - " + nb for nb in notebooks))
         res = test_notebooks(notebooks, env_name)
         success = success and res