fix #8749 (#8835)

Co-authored-by: ptosco <paolo.tosco@novartis.com>

Scripts/gen_rdkit_stubs/__init__.py

@@ -1,5 +1,6 @@
 import sys
 import os
+import glob
 import builtins
 import importlib
 import re
@@ -14,6 +15,8 @@ logger = logging.getLogger(__name__)
 
 
 WORKER_SCRIPT = "worker.py"
+PATCH_DIR = "patch"
+PATCH_EXT = ".diff"
 IMPORT_MODULES = re.compile(r"^\s*import\s+(.*)$")
 FROM_IMPORT_MODULES = re.compile(r"^\s*from\s+(\S+)\s+import\s+(.*)$")
 PYI_TO_PY = re.compile(r"\.pyi$")
@@ -67,6 +70,26 @@ def find_rdkit_include_path():
             rdkit_include_path = None
     return rdkit_include_path
 
+def apply_patch(tempdir, patch_file):
+    """Apply a patch file to the corresponding stub file."""
+    cmd = ["git", "--git-dir=", "apply", patch_file]
+    proc = subprocess.run(cmd, cwd=tempdir, capture_output=True)
+    if proc.returncode:
+        msg = proc.stderr.decode("utf-8") or "(no error message)"
+        cmd_as_str = " ".join(cmd)
+        logger.critical(f"Failed to apply patch {patch_file};\n\"{cmd_as_str}\" failed with:\n{msg}")
+
+def patch_stubs(tempdir, src_entry):
+    """Patch the stubs in src_entry if a diff fail is available."""
+    patch_dir = os.path.join(os.path.dirname(__file__), PATCH_DIR)
+    if not os.path.isdir(patch_dir):
+        return
+    for pyi in glob.glob(os.path.join(src_entry, "**/*.pyi")):
+        pyi_rel = os.path.relpath(pyi, tempdir)
+        patch_file = os.path.join(patch_dir, pyi_rel + PATCH_EXT)
+        if os.path.exists(patch_file):
+            apply_patch(tempdir, patch_file)
+
 def copy_stubs(src_entry, outer_dirs):
     """Copy src_entry to each directory in outer_dirs.
     If src_entry is a directory it will be recursively copied.
@@ -183,6 +206,7 @@ def generate_stubs_internal(modules, outer_dirs, args):
         if concat_out and args.verbose:
             logger.warning(concat_out)
         if os.path.isdir(src_dir):
+            patch_stubs(tempdir, src_dir)
             for f in os.listdir(src_dir):
                 src_entry = os.path.join(src_dir, f)
                 if os.path.exists(src_entry):

Scripts/gen_rdkit_stubs/patch/rdkit/Chem/inchi.pyi.diff

@@ -0,0 +1,70 @@
+--- a/rdkit/Chem/inchi.pyi	2025-09-29 14:01:41.137282007 +0200
++++ b/rdkit/Chem/inchi.pyi	2025-09-29 14:26:05.297333355 +0200
+@@ -1,16 +1,19 @@
+ from __future__ import annotations
+ import logging as logging
++from rdkit.Chem import rdchem
++import rdkit.Chem.rdchem
+ from rdkit.Chem import rdinchi
+-import rdkit.RDLogger
+ from rdkit import RDLogger
++import rdkit.RDLogger
++import typing as typing
+ __all__: list = ['MolToInchiAndAuxInfo', 'MolToInchi', 'MolBlockToInchiAndAuxInfo', 'MolBlockToInchi', 'MolFromInchi', 'InchiReadWriteError', 'InchiToInchiKey', 'MolToInchiKey', 'GetInchiVersion', 'INCHI_AVAILABLE']
+ class InchiReadWriteError(Exception):
+     pass
+-def InchiToInchiKey(inchi):
++def InchiToInchiKey(inchi: str) -> typing.Optional[str]:
+     """
+     Return the InChI key for the given InChI string. Return None on error
+     """
+-def MolBlockToInchi(molblock, options = '', logLevel = None, treatWarningAsError = False):
++def MolBlockToInchi(molblock: str, options: str = '', logLevel: typing.Optional[int] = None, treatWarningAsError: bool = False) -> str:
+     """
+     Returns the standard InChI string for a mol block
+     
+@@ -26,7 +29,7 @@
+         the standard InChI string returned by InChI API for the input molecule
+         
+     """
+-def MolBlockToInchiAndAuxInfo(molblock, options = '', logLevel = None, treatWarningAsError = False):
++def MolBlockToInchiAndAuxInfo(molblock: str, options: str = '', logLevel: typing.Optional[int] = None, treatWarningAsError: bool = False) -> typing.Tuple[str, str]:
+     """
+     Returns the standard InChI string and InChI auxInfo for a mol block
+     
+@@ -43,7 +46,7 @@
+         InChI API, in that order, for the input molecule
+         
+     """
+-def MolFromInchi(inchi, sanitize = True, removeHs = True, logLevel = None, treatWarningAsError = False):
++def MolFromInchi(inchi: str, sanitize: bool = True, removeHs: bool = True, logLevel: typing.Optional[int] = None, treatWarningAsError: bool = False) -> typing.Optional[rdkit.Chem.rdchem.Mol]:
+     """
+     Construct a molecule from a InChI string
+     
+@@ -62,7 +65,7 @@
+         a rdkit.Chem.rdchem.Mol instance
+         
+     """
+-def MolToInchi(mol, options = '', logLevel = None, treatWarningAsError = False):
++def MolToInchi(mol: rdkit.Chem.rdchem.Mol, options: str = '', logLevel: typing.Optional[int] = None, treatWarningAsError: bool = False) -> str:
+     """
+     Returns the standard InChI string for a molecule
+     
+@@ -78,7 +81,7 @@
+         the standard InChI string returned by InChI API for the input molecule
+         
+     """
+-def MolToInchiAndAuxInfo(mol, options = '', logLevel = None, treatWarningAsError = False):
++def MolToInchiAndAuxInfo(mol: rdkit.Chem.rdchem.Mol, options: str = '', logLevel: typing.Optional[int] = None, treatWarningAsError: bool = False) -> typing.Tuple[str, str]:
+     """
+     Returns the standard InChI string and InChI auxInfo for a molecule
+     
+@@ -95,7 +98,7 @@
+         InChI API, in that order, for the input molecule
+         
+     """
+-def MolToInchiKey(mol, options = ''):
++def MolToInchiKey(mol: rdkit.Chem.rdchem.Mol, options: str = '') -> typing.Optional[str]:
+     """
+     Returns the standard InChI key for a molecule
+     

Scripts/gen_rdkit_stubs/worker.py

@@ -74,4 +74,6 @@ if __name__ == "__main__":
             print(str(e))
     finally:
         sys.argv = stored_argv
-    gen_rdkit_stubs.copy_stubs(os.path.join(args.tempdir, *args.module_name.split(".")), args.outer_dirs)
+    src_path = os.path.join(args.tempdir, *args.module_name.split("."))
+    gen_rdkit_stubs.patch_stubs(args.tempdir, src_path)
+    gen_rdkit_stubs.copy_stubs(src_path, args.outer_dirs)