Finalize documentation (again!)

docs/index.md

@@ -12,7 +12,7 @@ micromamba install -c conda-forge medchem
 
 ## Getting Started
 
-The best way to get started is by going through the tutorials.
+The best way to get started is by going through [**the tutorials**](./tutorials/Basic_Concepts.ipynb).
 
 ## Usage Notice
 

docs/tutorials/Catalogs.ipynb

@@ -711,6 +711,16 @@
     "matches = [custom_catalog.HasMatch(x) for x in mols]\n",
     "dm.to_image(mols, legends=[f\"Match: {x}\" for x in matches])\n"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "dcef48d4",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "\n",
+    "-- The End :-)"
+   ]
   }
  ],
  "metadata": {

docs/tutorials/Chemical_Groups.ipynb

@@ -588,12 +588,14 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4f369694",
+   "cell_type": "markdown",
+   "id": "f446e5b2",
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "source": [
+    "---\n",
+    "\n",
+    "-- The End :-)"
+   ]
   }
  ],
  "metadata": {

docs/tutorials/Constraints_Filtering.ipynb

@@ -515,6 +515,16 @@
     "\n",
     "dm.to_image(mols, legends=legends)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2021dfa2",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "\n",
+    "-- The End :-)"
+   ]
   }
  ],
  "metadata": {

docs/tutorials/Functional_API.ipynb

@@ -9121,12 +9121,12 @@
   },
   {
    "cell_type": "markdown",
-   "id": "51768c29",
+   "id": "8713cdbb",
    "metadata": {},
    "source": [
     "---\n",
     "\n",
-    "The End!"
+    "-- The End :-)"
    ]
   }
  ],

docs/tutorials/Medchem_Query_Language.ipynb

@@ -1135,6 +1135,16 @@
     "  - OR operator : `OR` or `|` or `||` or `or`\n",
     "  - NOT operator : `NOT` or `!` or `~` or `not`\n"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a851c80b",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "\n",
+    "-- The End :-)"
+   ]
   }
  ],
  "metadata": {

docs/tutorials/Medchem_Rules.ipynb

@@ -1654,6 +1654,16 @@
     "# Apply rule #2\n",
     "rule_2(mol)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "eb05d65b",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "\n",
+    "-- The End :-)"
+   ]
   }
  ],
  "metadata": {

docs/tutorials/Molecular_Complexity.ipynb

@@ -1466,6 +1466,16 @@
     "\n",
     "dm.to_image(data[\"mol\"].tolist(), legends=legends, mol_size=(300, 200))"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "165a451d",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "\n",
+    "-- The End :-)"
+   ]
   }
  ],
  "metadata": {

docs/tutorials/Structural_Filters.ipynb

@@ -3126,6 +3126,16 @@
     "\n",
     "results.head()"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3bae7171",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "\n",
+    "-- The End :-)"
+   ]
   }
  ],
  "metadata": {

docs/tutorials/data/Drug_Prodrug_pairs.csv

@@ -0,0 +1,8 @@
+Drug,Drug SMILES,Prodrug,Prodrug SMILES
+Gabapentin,O=C(O)CC1(CN)CCCCC1,Gabapentin enacarbil,CC(C)C(=O)OC(C)OC(=O)NCC1(CCCCC1)CC(=O)O
+Dabigatran,CN1C2=C(C=C(C=C2)C(=O)N(CCC(=O)O)C3=CC=CC=N3)N=C1CNC4=CC=C(C=C4)C(=N)N,Dabigatran etexilate,CCCCCCOC(=O)N=C(C1=CC=C(C=C1)NCC2=NC3=C(N2C)C=CC(=C3)C(=O)N(CCC(=O)OCC)C4=CC=CC=N4)N
+Sofosbuvir,OP(OC[C@@H]1[C@@H](O)[C@@](C)(F)[C@H](N2C=CC(NC2=O)=O)O1)(O)=O,Sofosbuvir,C[C@@H](C(=O)OC(C)C)N[P@](=O)(OC[C@@H]1[C@H]([C@@]([C@@H](O1)N2C=CC(=O)NC2=O)(C)F)O)OC3=CC=CC=C3
+Tedizolid,O=C4O[C@H](CN4c3cc(F)c(c1ccc(nc1)c2nn(nn2)C)cc3)CO,Tedizolid phosphate,CN1N=NC(=N1)C1=CC=C(C=N1)C1=CC=C(C=C1F)N1C[C@H](COP(O)(O)=O)OC1=O
+Isavuconazole,C[C@H]([C@](c1c(F)ccc(F)c1)(O)Cn2ncnc2)c3scc(c4ccc(C#N)cc4)n3,Isavuconazonium,C[C@H]([C@](c1c(F)ccc(F)c1)(O)Cn2nc[n+](C(OC(N(c3ncccc3COC(CNC)=O)C)=O)C)c2)c4scc(c5ccc(C#N)cc5)n4
+Aripiprazole,Clc4cccc(N3CCN(CCCCOc2ccc1c(NC(=O)CC1)c2)CC3)c4Cl,Aripiprazole lauroxil,CCCCCCCCCCCC(=O)OCN1C(=O)CCC2=C1C=C(C=C2)OCCCCN3CCN(CC3)C4=C(C(=CC=C4)Cl)Cl
+ACT-333679,CC(N(C1=CN=C(C2=CC=CC=C2)C(C3=CC=CC=C3)=N1)CCCCOCC(O)=O)C,Selexipag,CC(C)N(CCCCOCC(=O)NS(=O)(=O)C)C1=CN=C(C(=N1)C2=CC=CC=C2)C3=CC=CC=C3

mkdocs.yml

@@ -14,7 +14,6 @@ strict: true
 
 nav:
   - Overview: index.md
-  - CLI: cli.md
   - Tutorials:
       - Basic Concepts: tutorials/Basic_Concepts.ipynb
       - Functional API: tutorials/Functional_API.ipynb
@@ -25,6 +24,7 @@ nav:
       - Medchem Query Language: tutorials/Medchem_Query_Language.ipynb
       - Molecular Complexity: tutorials/Molecular_Complexity.ipynb
       - Constraints Filtering: tutorials/Constraints_Filtering.ipynb
+  - CLI: cli.md
   - API:
       - medchem.rules: api/medchem.rules.md
       - medchem.structural: api/medchem.structural.md

tests/test_notebooks.py

@@ -12,6 +12,10 @@
 NOTEBOOK_PATHS = sorted(list(TUTORIALS_DIR.glob("*.ipynb")))
 NOTEBOOK_PATHS = list(filter(lambda x: x.name not in DISABLE_NOTEBOOKS, NOTEBOOK_PATHS))
 
+# Discard some notebooks
+NOTEBOOKS_TO_DISCARD = ["Basic_Concepts.ipynb"]
+NOTEBOOK_PATHS = list(filter(lambda x: x.name not in NOTEBOOKS_TO_DISCARD, NOTEBOOK_PATHS))
+
 
 @pytest.mark.parametrize("nb_path", NOTEBOOK_PATHS, ids=[str(n.name) for n in NOTEBOOK_PATHS])
 def test_notebook(nb_path):