Merge pull request #222 from kkovary/221-max_mols-fix

pass max_mols to Draw.MolsToGridImage

.github/workflows/code-check.yml

@@ -24,7 +24,7 @@ jobs:
 
       - name: Install black
         run: |
-          pip install black>=23
+          pip install black>=24
 
       - name: Lint
         run: black --check .

binder/environment.yml

@@ -38,7 +38,7 @@ dependencies:
   - pytest >=6.0
   - pytest-cov
   - pytest-xdist
-  - black >=23
+  - black >=24
   - jupyterlab
   - mypy
   - codecov

datamol/data/__init__.py

@@ -66,18 +66,15 @@ def open_datamol_data_file(
 
 
 @overload
-def freesolv(as_df: Literal[True] = True) -> pd.DataFrame:
-    ...
+def freesolv(as_df: Literal[True] = True) -> pd.DataFrame: ...
 
 
 @overload
-def freesolv(as_df: Literal[False] = False) -> List[Mol]:
-    ...
+def freesolv(as_df: Literal[False] = False) -> List[Mol]: ...
 
 
 @overload
-def freesolv(as_df: bool = True) -> Union[List[Mol], pd.DataFrame]:
-    ...
+def freesolv(as_df: bool = True) -> Union[List[Mol], pd.DataFrame]: ...
 
 
 def freesolv(as_df: bool = True) -> Union[List[Mol], pd.DataFrame]:
@@ -102,18 +99,17 @@ def freesolv(as_df: bool = True) -> Union[List[Mol], pd.DataFrame]:
 
 
 @overload
-def cdk2(as_df: Literal[True] = True, mol_column: Optional[str] = "mol") -> pd.DataFrame:
-    ...
+def cdk2(as_df: Literal[True] = True, mol_column: Optional[str] = "mol") -> pd.DataFrame: ...
 
 
 @overload
-def cdk2(as_df: Literal[False] = False, mol_column: Optional[str] = "mol") -> List[Mol]:
-    ...
+def cdk2(as_df: Literal[False] = False, mol_column: Optional[str] = "mol") -> List[Mol]: ...
 
 
 @overload
-def cdk2(as_df: bool = True, mol_column: Optional[str] = "mol") -> Union[List[Mol], pd.DataFrame]:
-    ...
+def cdk2(
+    as_df: bool = True, mol_column: Optional[str] = "mol"
+) -> Union[List[Mol], pd.DataFrame]: ...
 
 
 def cdk2(as_df: bool = True, mol_column: Optional[str] = "mol"):
@@ -130,20 +126,17 @@ def cdk2(as_df: bool = True, mol_column: Optional[str] = "mol"):
 
 
 @overload
-def solubility(as_df: Literal[True] = True, mol_column: Optional[str] = "mol") -> pd.DataFrame:
-    ...
+def solubility(as_df: Literal[True] = True, mol_column: Optional[str] = "mol") -> pd.DataFrame: ...
 
 
 @overload
-def solubility(as_df: Literal[False] = False, mol_column: Optional[str] = "mol") -> List[Mol]:
-    ...
+def solubility(as_df: Literal[False] = False, mol_column: Optional[str] = "mol") -> List[Mol]: ...
 
 
 @overload
 def solubility(
     as_df: bool = True, mol_column: Optional[str] = "mol"
-) -> Union[List[Mol], pd.DataFrame]:
-    ...
+) -> Union[List[Mol], pd.DataFrame]: ...
 
 
 def solubility(as_df: bool = True, mol_column: Optional[str] = "mol"):
@@ -184,13 +177,11 @@ def solubility(as_df: bool = True, mol_column: Optional[str] = "mol"):
 
 
 @overload
-def chembl_drugs(as_df: Literal[True] = True) -> pd.DataFrame:
-    ...
+def chembl_drugs(as_df: Literal[True] = True) -> pd.DataFrame: ...
 
 
 @overload
-def chembl_drugs(as_df: Literal[False] = False) -> List[Mol]:
-    ...
+def chembl_drugs(as_df: Literal[False] = False) -> List[Mol]: ...
 
 
 def chembl_drugs(as_df: bool = True) -> Union[List[Mol], pd.DataFrame]:
@@ -210,13 +201,11 @@ def chembl_drugs(as_df: bool = True) -> Union[List[Mol], pd.DataFrame]:
 
 
 @overload
-def chembl_samples(as_df: Literal[True] = True) -> pd.DataFrame:
-    ...
+def chembl_samples(as_df: Literal[True] = True) -> pd.DataFrame: ...
 
 
 @overload
-def chembl_samples(as_df: Literal[False] = False) -> List[Mol]:
-    ...
+def chembl_samples(as_df: Literal[False] = False) -> List[Mol]: ...
 
 
 def chembl_samples(as_df: bool = True) -> Union[List[Mol], pd.DataFrame]:

datamol/io.py

@@ -116,8 +116,7 @@ def read_sdf(
     max_num_mols: Optional[int] = ...,
     discard_invalid: bool = ...,
     n_jobs: Optional[int] = ...,
-) -> List[Mol]:
-    ...
+) -> List[Mol]: ...
 
 
 @overload
@@ -134,8 +133,7 @@ def read_sdf(
     max_num_mols: Optional[int] = ...,
     discard_invalid: bool = ...,
     n_jobs: Optional[int] = ...,
-) -> pd.DataFrame:
-    ...
+) -> pd.DataFrame: ...
 
 
 @overload
@@ -152,8 +150,7 @@ def read_sdf(
     max_num_mols: Optional[int] = ...,
     discard_invalid: bool = ...,
     n_jobs: Optional[int] = ...,
-) -> Union[List[Mol], pd.DataFrame]:
-    ...
+) -> Union[List[Mol], pd.DataFrame]: ...
 
 
 def read_sdf(

datamol/viz/_viz.py

@@ -3,6 +3,7 @@
 from typing import Tuple
 from typing import Optional
 from typing import Any
+from loguru import logger
 
 from rdkit.Chem import Draw
 
@@ -22,6 +23,7 @@ def to_image(
     highlight_bond: Optional[List[List[int]]] = None,
     outfile: Optional[str] = None,
     max_mols: int = 32,
+    max_mols_ipython: int = 50,
     copy: bool = True,
     indices: bool = False,
     bond_indices: bool = False,
@@ -44,6 +46,7 @@ def to_image(
         highlight_bond: The bonds to highlight.
         outfile: Path where to save the image (local or remote path).
         max_mols: The maximum number of molecules to display.
+        max_mols_ipython: The maximum number of molecules to display when running within an IPython environment.
         copy: Whether to copy the molecules or not.
         indices: Whether to draw the atom indices.
         bond_indices: Whether to draw the bond indices.
@@ -120,6 +123,18 @@ def to_image(
         else:
             _kwargs[k] = v
 
+    # Check if we are in a Jupyter notebook or IPython display context
+    # If so, conditionally add the maxMols argument
+    in_notebook = dm.viz.utils.is_ipython_session()
+
+    if in_notebook:
+        _kwargs["maxMols"] = max_mols_ipython
+        if max_mols > max_mols_ipython:
+            logger.warning(
+                f"You have set max_mols to {max_mols}, which is higher than max_mols_ipython ({max_mols_ipython}). "
+                "Consider increasing max_mols_ipython if you want to display all molecules in an IPython environment."
+            )
+
     image = Draw.MolsToGridImage(
         mols,
         legends=legends,

env.yml

@@ -38,7 +38,7 @@ dependencies:
   - pytest >=6.0
   - pytest-cov
   - pytest-xdist
-  - black >=23
+  - black >=24
   - ruff
   - jupyterlab
   - mypy