nerdd-module 0.3.14__tar.gz → 0.3.15__tar.gz

{nerdd_module-0.3.14 → nerdd_module-0.3.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nerdd-module
-Version: 0.3.14
+Version: 0.3.15
 Summary: Base package to create NERDD modules
 Author-email: Steffen Hirte <steffen.hirte@univie.ac.at>
 Maintainer-email: Steffen Hirte <steffen.hirte@univie.ac.at>

{nerdd_module-0.3.14 → nerdd_module-0.3.15}/nerdd_module/converters/mol_converter.py

@@ -15,7 +15,7 @@ class MolConverter(Converter):
         if self.output_format == "sdf" and self.result_property.name != "input_mol":
             # in an SDF, the main molecule (input_mol) can be a Mol object
             return Converter.HIDE
-        elif self.output_format in ["pandas", "record_list", "iterator"]:
+        elif self.output_format in ["sdf", "pandas", "record_list", "iterator"]:
             return input
 
     config = ConverterConfig(

{nerdd_module-0.3.14 → nerdd_module-0.3.15}/nerdd_module/input/inchi_reader.py

@@ -2,8 +2,8 @@ from codecs import getreader
 from typing import Any, Iterator
 
 from rdkit.Chem import MolFromInchi
-from rdkit.rdBase import BlockLogs
 
+from ..polyfills import BlockLogs
 from ..problem import Problem
 from .reader import ExploreCallable, MoleculeEntry, Reader
 from .reader_config import ReaderConfig
@@ -47,7 +47,7 @@ class InchiReader(Reader):
                     errors = []
 
                 yield MoleculeEntry(
-                    raw_input=line,
+                    raw_input=line.strip("\n"),
                     input_type="inchi",
                     source=("raw_input",),
                     mol=mol,

{nerdd_module-0.3.14 → nerdd_module-0.3.15}/nerdd_module/input/sdf_reader.py

@@ -2,8 +2,8 @@ from codecs import getreader
 from typing import Any, Iterator
 
 from rdkit.Chem import MolFromMolBlock
-from rdkit.rdBase import BlockLogs
 
+from ..polyfills import BlockLogs
 from ..problem import Problem
 from .reader import ExploreCallable, MoleculeEntry, Reader
 
@@ -59,7 +59,7 @@ class SdfReader(Reader):
                         errors = []
 
                     yield MoleculeEntry(
-                        raw_input=mol_block,
+                        raw_input=mol_block.strip("\n"),
                         input_type="mol_block",
                         source=("raw_input",),
                         mol=mol,

{nerdd_module-0.3.14 → nerdd_module-0.3.15}/nerdd_module/input/smiles_reader.py

@@ -2,8 +2,8 @@ from codecs import getreader
 from typing import Any, Iterator
 
 from rdkit.Chem import MolFromSmiles
-from rdkit.rdBase import BlockLogs
 
+from ..polyfills import BlockLogs
 from ..problem import Problem
 from .reader import ExploreCallable, MoleculeEntry, Reader
 from .reader_config import ReaderConfig
@@ -57,7 +57,7 @@ class SmilesReader(Reader):
                     errors = []
 
                 yield MoleculeEntry(
-                    raw_input=line,
+                    raw_input=line.strip("\n"),
                     input_type="smiles",
                     source=("raw_input",),
                     mol=mol,

{nerdd_module-0.3.14 → nerdd_module-0.3.15}/nerdd_module/polyfills/__init__.py

@@ -1,3 +1,4 @@
+from .block_logs import *
 from .files import *
 from .get_entry_points import *
 from .literal import *

nerdd_module-0.3.15/nerdd_module/polyfills/block_logs.py

@@ -0,0 +1,45 @@
+from typing import Optional, Protocol, Type
+
+from rdkit.rdBase import BlockLogs as OriginalBlockLogs
+
+__all__ = ["BlockLogs"]
+
+
+class BlockLogsProtocol(Protocol):
+    def __init__(self) -> None: ...
+    def __enter__(self) -> "BlockLogsProtocol": ...
+
+    def __exit__(
+        self,
+        exc_type: Optional[Type[BaseException]],
+        exc_val: Optional[BaseException],
+        exc_tb: Optional[Type[BaseException]],
+    ) -> None: ...
+
+
+BlockLogs: Type[BlockLogsProtocol]
+
+if hasattr(OriginalBlockLogs, "__enter__"):
+    BlockLogs = OriginalBlockLogs
+else:
+    # We would like to use
+    #   with BlockLogs(): ...
+    # but this does not work with old versions of RDKit. Therefore, we create an instance of
+    # BlockLogs that will suppress log messages as long as it exists. When it is deleted (in the
+    # "__exit__" block), logs are enabled again.
+    class CustomBlockLogs:
+        block_logs: Optional[OriginalBlockLogs] = None
+
+        def __enter__(self) -> BlockLogsProtocol:
+            self.block_logs = OriginalBlockLogs()
+            return self
+
+        def __exit__(
+            self,
+            exc_type: Optional[Type[BaseException]],
+            exc_val: Optional[BaseException],
+            exc_tb: Optional[Type[BaseException]],
+        ) -> None:
+            del self.block_logs
+
+    BlockLogs = CustomBlockLogs

{nerdd_module-0.3.14 → nerdd_module-0.3.15}/nerdd_module/preprocessing/chembl_structure_pipeline.py

@@ -2,8 +2,8 @@ import warnings
 from typing import List, Optional, Tuple
 
 from rdkit.Chem import Mol
-from rdkit.rdBase import BlockLogs
 
+from ..polyfills import BlockLogs
 from ..problem import Problem
 from .preprocessing_step import PreprocessingStep
 
@@ -15,22 +15,16 @@ warnings.filterwarnings(
 )
 
 # We check if chembl_structure_pipeline is installed. Since importing this library already logs
-# messages, we suppress them using RDKit's BlockLogs. We would like to use
-#   with BlockLogs(): ...
-# but this does not work with old versions of RDKit. Therefore, we create an instance of
-# BlockLogs that will suppress log messages as long as it exists. When it is deleted (in the
-# "finally" block), logs are enabled again.
-block_logs = BlockLogs()
-try:
-    from chembl_structure_pipeline import get_parent_mol, standardize_mol
-
-    import_error = None
-except ImportError as e:
-    # raise ImportError later when using this class
-    # --> this allows to use the rest of the package without chembl_structure_pipeline
-    import_error = e
-finally:
-    del block_logs
+# messages, we suppress them using RDKit's BlockLogs.
+with BlockLogs():
+    try:
+        from chembl_structure_pipeline import get_parent_mol, standardize_mol
+
+        import_error = None
+    except ImportError as e:
+        # raise ImportError later when using this class
+        # --> this allows to use the rest of the package without chembl_structure_pipeline
+        import_error = e
 
 __all__ = ["GetParentMolWithCsp", "StandardizeWithCsp"]
 

{nerdd_module-0.3.14 → nerdd_module-0.3.15}/nerdd_module/tests/representations.py

@@ -6,7 +6,7 @@ from hypothesis import strategies as st
 from hypothesis_rdkit import mols  # type: ignore
 from pytest_bdd import given, parsers
 from rdkit.Chem import MolToInchi, MolToMolBlock, MolToSmiles
-from rdkit.rdBase import BlockLogs
+from ..polyfills import BlockLogs
 
 
 @given(parsers.parse("a random seed set to {seed:d}"), target_fixture="random_seed")

{nerdd_module-0.3.14 → nerdd_module-0.3.15}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nerdd-module
-Version: 0.3.14
+Version: 0.3.15
 Summary: Base package to create NERDD modules
 Author-email: Steffen Hirte <steffen.hirte@univie.ac.at>
 Maintainer-email: Steffen Hirte <steffen.hirte@univie.ac.at>

{nerdd_module-0.3.14 → nerdd_module-0.3.15}/nerdd_module.egg-info/SOURCES.txt

@@ -62,6 +62,7 @@ nerdd_module/output/record_list_writer.py
 nerdd_module/output/sdf_writer.py
 nerdd_module/output/writer.py
 nerdd_module/polyfills/__init__.py
+nerdd_module/polyfills/block_logs.py
 nerdd_module/polyfills/files.py
 nerdd_module/polyfills/get_entry_points.py
 nerdd_module/polyfills/literal.py

{nerdd_module-0.3.14 → nerdd_module-0.3.15}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.14"
+version = "0.3.15"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = { file = "LICENSE" }