nerdd-module 0.3.45__tar.gz → 0.3.47__tar.gz

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.45
+Version: 0.3.47
 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-0.3.45 → nerdd_module-0.3.47}/nerdd_module/input/depth_first_explorer.py

@@ -85,11 +85,9 @@ class DepthFirstExplorer(Explorer):
 
                 if (
                     score > best_score
-                    # if the score is the same, prefer the reader with higher ratio
-                    # of valid entries
+                    # if the score is the same, prefer the reader with higher ratio of valid entries
                     or (score == best_score and ratio > best_ratio)
-                    # if the ratio is the same, prefer the reader with less invalid
-                    # results
+                    # if the ratio is the same, prefer the reader with less invalid results
                     or (
                         score == best_score
                         and ratio == best_ratio

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/nerdd_module/input/inchi_reader.py

@@ -12,8 +12,9 @@ __all__ = ["InchiReader"]
 
 
 class InchiReader(StreamReader):
-    def __init__(self) -> None:
+    def __init__(self, max_length_inchi: int = 10_000) -> None:
         super().__init__()
+        self._max_length_inchi = max_length_inchi
 
     def _read_stream(self, input_stream: Any, explore: ExploreCallable) -> Iterator[MoleculeEntry]:
         # suppress RDKit warnings
@@ -27,6 +28,23 @@ class InchiReader(StreamReader):
                 if line.strip().startswith("#"):
                     continue
 
+                # avoid long InChI strings, because they might take veeeeery long to parse
+                if len(line) > self._max_length_inchi:
+                    errors = [
+                        Problem(
+                            "line_too_long",
+                            f"Line exceeds max length of {self._max_length_inchi} characters",
+                        )
+                    ]
+                    yield MoleculeEntry(
+                        raw_input=line.strip("\n")[: self._max_length_inchi - 3] + "...",
+                        input_type="inchi",
+                        source=("raw_input",),
+                        mol=None,
+                        errors=errors,
+                    )
+                    continue
+
                 try:
                     mol = MolFromInchi(line, sanitize=False)
                 except:  # noqa: E722 (allow bare except, because RDKit is unpredictable)
@@ -46,10 +64,12 @@ class InchiReader(StreamReader):
                 )
 
     def __repr__(self) -> str:
-        return "InchiReader()"
+        return f"InchiReader(max_length_inchi={self._max_length_inchi})"
 
     config = ReaderConfig(
         examples=[
-            "InChI=1S/C18H16O3/c1-2-13(12-8-4-3-5-9-12)16-17(19)14-10-6-7-11-15(14)21-18(16)20/h3-11,13,19H,2H2,1H3"
+            # (this is one InChI string, split into two lines)
+            "InChI=1S/C18H16O3/c1-2-13(12-8-4-3-5-9-12)16-17(19)14-10-6-7-11-15(14)21-18(16)20"
+            "/h3-11,13,19H,2H2,1H3"
         ]
     )

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/nerdd_module/input/list_reader.py

@@ -1,5 +1,5 @@
-from io import BytesIO, StringIO
-from typing import Any, BinaryIO, Iterable, Iterator
+from io import IOBase
+from typing import Any, Iterable, Iterator
 
 from .reader import ExploreCallable, MoleculeEntry, Reader
 
@@ -12,7 +12,7 @@ class ListReader(Reader):
 
     def read(self, input_iterable: Any, explore: ExploreCallable) -> Iterator[MoleculeEntry]:
         assert isinstance(input_iterable, Iterable) and not isinstance(
-            input_iterable, (str, bytes, BytesIO, StringIO, BinaryIO)
+            input_iterable, (str, bytes, IOBase)
         ), f"input must be an iterable, but is {type(input_iterable)}"
 
         for entry in input_iterable:

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/nerdd_module/input/sdf_reader.py

@@ -11,7 +11,7 @@ __all__ = ["SdfReader"]
 
 
 class SdfReader(StreamReader):
-    def __init__(self, max_num_lines_mol_block: int = 10000) -> None:
+    def __init__(self, max_num_lines_mol_block: int = 10_000) -> None:
         super().__init__()
         self.max_num_lines_mol_block = max_num_lines_mol_block
 

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/nerdd_module/input/smiles_reader.py

@@ -12,8 +12,9 @@ __all__ = ["SmilesReader"]
 
 
 class SmilesReader(StreamReader):
-    def __init__(self) -> None:
+    def __init__(self, max_length_smiles: int = 10_000) -> None:
         super().__init__()
+        self._max_length_smiles = max_length_smiles
 
     def _read_stream(self, input_stream: Any, explore: ExploreCallable) -> Iterator[MoleculeEntry]:
         # suppress RDKit warnings
@@ -27,6 +28,23 @@ class SmilesReader(StreamReader):
                 if line.strip().startswith("#"):
                     continue
 
+                # avoid long smiles strings, because they might take veeeeery long to parse
+                if len(line) > self._max_length_smiles:
+                    errors = [
+                        Problem(
+                            "line_too_long",
+                            f"Line exceeds max length of {self._max_length_smiles} characters",
+                        )
+                    ]
+                    yield MoleculeEntry(
+                        raw_input=line.strip("\n")[: self._max_length_smiles - 3] + "...",
+                        input_type="smiles",
+                        source=("raw_input",),
+                        mol=None,
+                        errors=errors,
+                    )
+                    continue
+
                 try:
                     mol = MolFromSmiles(line, sanitize=False)
                 except:  # noqa: E722 (allow bare except, because RDKit is unpredictable)
@@ -56,6 +74,6 @@ class SmilesReader(StreamReader):
                 )
 
     def __repr__(self) -> str:
-        return "SmilesReader()"
+        return f"SmilesReader(max_length={self._max_length_smiles})"
 
     config = ReaderConfig(examples=["C1=NC2=C(N1COCCO)N=C(NC2=O)N"])

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/nerdd_module/input/string_reader.py

@@ -11,9 +11,12 @@ class StringReader(Reader):
         super().__init__()
 
     def read(self, input: Any, explore: ExploreCallable) -> Iterator[MoleculeEntry]:
-        assert isinstance(input, str)
+        assert isinstance(input, (str, bytes))
 
-        with BytesIO(input.encode("utf-8")) as f:
+        if isinstance(input, str):
+            input = input.encode("utf-8")
+
+        with BytesIO(input) as f:
             yield from explore(f)
 
     def __repr__(self) -> str:

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/nerdd_module/tests/checks.py

@@ -46,7 +46,7 @@ def check_column_value_equality(subset, column_name, expected_value):
     # try to convert to float if possible
     try:
         expected_value = literal_eval(expected_value)
-    except:
+    except:  # noqa: E722
         pass
 
     if expected_value is None:
@@ -72,7 +72,7 @@ def check_column_value_inequality(subset, column_name, forbidden_value):
     # try to convert to float if possible
     try:
         forbidden_value = literal_eval(forbidden_value)
-    except:
+    except:  # noqa: E722
         pass
 
     if forbidden_value is None:
@@ -156,13 +156,13 @@ def check_conditional_column_value(
     # try to convert to float if possible
     try:
         expected_value = literal_eval(expected_value)
-    except:
+    except:  # noqa: E722
         pass
 
     # same for condition value
     try:
         condition_value = literal_eval(condition_value)
-    except:
+    except:  # noqa: E722
         pass
 
     # condition value can be (none) to indicate None

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/nerdd_module/tests/files.py

@@ -39,9 +39,7 @@ def representation_files(molecules, input_type, num_files):
     # choose num_files-1 numbers to split the representations into num_files parts
     # the while loop makes sure that each part contains at least one valid molecule
     while True:
-        split_indices = np.random.choice(
-            len(representations), size=num_files - 1, replace=False
-        )
+        split_indices = np.random.choice(len(representations), size=num_files - 1, replace=False)
         split_indices = np.sort(split_indices)
 
         # split the representations
@@ -57,13 +55,16 @@ def representation_files(molecules, input_type, num_files):
     # write the representations to files
     representations_files = []
 
-    for _, split_representation in enumerate(split_representations):
+    for split_representation in split_representations:
         with NamedTemporaryFile("w", delete=False) as f:
             for representation in split_representation:
+                # write representation
                 if representation is None:
                     f.write("None")
                 else:
                     f.write(representation)
+
+                # write separator
                 if input_type in ["smiles", "inchi"]:
                     f.write("\n")
                 elif input_type == "mol_block":

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/nerdd_module/tests/models/AtomicMassModel.py

@@ -8,7 +8,9 @@ allowed_versions = ["mol_ids", "mols", "iterator", "error"]
 
 
 class AtomicMassModel(Model):
-    def __init__(self, preprocessing_steps=[Sanitize()], version="mol_ids", **kwargs):
+    def __init__(self, preprocessing_steps=None, version="mol_ids", **kwargs):
+        if preprocessing_steps is None:
+            preprocessing_steps = [Sanitize()]
         assert (
             version in allowed_versions
         ), f"version must be one of {allowed_versions}, got {version}"
@@ -64,5 +66,3 @@ class AtomicMassModel(Model):
                 {"name": "mass", "type": "float", "level": "atom"},
             ],
         }
-
-

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/nerdd_module/tests/models/MolWeightModel.py

@@ -9,7 +9,9 @@ allowed_versions = ["order_based", "mol_ids", "mols", "iterator", "error"]
 
 
 class MolWeightModel(Model):
-    def __init__(self, preprocessing_steps=[Sanitize()], version="order_based", **kwargs):
+    def __init__(self, preprocessing_steps=None, version="order_based", **kwargs):
+        if preprocessing_steps is None:
+            preprocessing_steps = [Sanitize()]
         assert (
             version in allowed_versions
         ), f"version must be one of {allowed_versions}, got {version}"
@@ -48,4 +50,4 @@ class MolWeightModel(Model):
             "result_properties": [
                 {"name": "weight", "type": "float"},
             ],
-        }
+        }

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/nerdd_module/tests/predictions.py

@@ -21,7 +21,8 @@ def mol_weight_model(version):
 
 @when(
     parsers.parse(
-        "the mol weight model (version '{version}') generates predictions for the molecule representations"
+        "the mol weight model (version '{version}') generates predictions for the molecule "
+        "representations"
     ),
     target_fixture="predictions",
 )
@@ -36,7 +37,8 @@ def predictions_mol_weight_model(representations, version, multiplier):
 
 @when(
     parsers.parse(
-        "the atomic mass model (version '{version}') generates predictions for the molecule representations"
+        "the atomic mass model (version '{version}') generates predictions for the molecule "
+        "representations"
     ),
     target_fixture="predictions",
 )
@@ -48,6 +50,7 @@ def predictions_atomic_mass_model(representations, version, multiplier):
         output_format="record_list",
     )
 
+
 @when(
     "all results are considered",
     target_fixture="subset",
@@ -55,6 +58,7 @@ def predictions_atomic_mass_model(representations, version, multiplier):
 def all_results(predictions):
     return predictions
 
+
 @when(
     "the subset of the result where the input was not None is considered",
     target_fixture="subset",
@@ -63,10 +67,11 @@ def subset_without_input_none(predictions):
     # remove None entries
     return [p for p in predictions if p["input_mol"] is not None]
 
+
 @when(
     "the subset of the result where the preprocessed mol was not None is considered",
     target_fixture="subset",
 )
 def subset_without_preprocessed_none(predictions):
     # remove None entries
-    return [p for p in predictions if p["preprocessed_mol"] is not None]
+    return [p for p in predictions if p["preprocessed_mol"] is not None]

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/nerdd_module/tests/representations.py

@@ -1,3 +1,6 @@
+import re
+from functools import reduce
+
 import numpy as np
 from hypothesis import given as hgiven
 from hypothesis import seed, settings
@@ -5,10 +8,9 @@ from hypothesis import strategies as st
 from hypothesis_rdkit import mols
 from pytest_bdd import given, parsers
 from rdkit.Chem import MolToInchi, MolToMolBlock, MolToSmiles
-from ..polyfills import BlockLogs
 from rdkit.Chem.rdMolDescriptors import CalcExactMolWt
-import re
-from functools import reduce
+
+from ..polyfills import BlockLogs
 
 
 @given(parsers.parse("a random seed set to {seed:d}"), target_fixture="random_seed")
@@ -38,7 +40,9 @@ def representations_from_molecules(molecules, input_type):
     elif input_type == "inchi":
         converter = MolToInchi
     elif input_type == "rdkit_mol":
-        converter = lambda mol: mol
+
+        def converter(mol):
+            return mol
     else:
         raise ValueError(f"Unknown input_type: {input_type}")
 
@@ -49,9 +53,7 @@ def representations_from_molecules(molecules, input_type):
 
 
 @given(
-    parsers.re(
-        r"a list of (?P<num>\d+) random molecules(?:, where(?P<conditions>[\s\S]*))?"
-    ),
+    parsers.re(r"a list of (?P<num>\d+) random molecules(?:, where(?P<conditions>[\s\S]*))?"),
     target_fixture="molecules",
 )
 def molecules(num, conditions, random_seed=0):
@@ -61,6 +63,7 @@ def molecules(num, conditions, random_seed=0):
     maps = []
 
     if conditions is not None:
+
         def filter_weight(min_weight, max_weight):
             min_weight = float(min_weight)
             max_weight = float(max_weight)
@@ -76,15 +79,19 @@ def molecules(num, conditions, random_seed=0):
 
         expressions = [
             # filters are functions that return True if the molecule should be kept
-            ("filter", r"each mol has a weight between (?P<min_weight>\d+) and (?P<max_weight>\d+)", filter_weight),
+            (
+                "filter",
+                r"each mol has a weight between (?P<min_weight>\d+) and (?P<max_weight>\d+)",
+                filter_weight,
+            ),
             # maps are functions that modify the molecule
-            ("map", r"(?P<num_none>\d+) entries are None", map_to_none)
+            ("map", r"(?P<num_none>\d+) entries are None", map_to_none),
         ]
 
         conditions_list = [c for c in conditions.split("\n") if c.strip() != ""]
 
         for condition in conditions_list:
-            for kind, expression, f in expressions:
+            for kind, expression, f in expressions:  # noqa: B007
                 # conditions might be a markdown list (starting with a star character)
                 expression = r"\s*(\*\s*)?" + expression + r"\s*"
 
@@ -92,7 +99,7 @@ def molecules(num, conditions, random_seed=0):
                 if match:
                     params = match.groupdict()
                     break
-            
+
             assert match is not None, f"Could not parse condition: {condition}"
 
             if kind == "filter":
@@ -102,8 +109,11 @@ def molecules(num, conditions, random_seed=0):
             else:
                 raise ValueError(f"Unknown kind: {kind}")
 
-    filter_func = lambda mol: all(f(mol) for f in filters)
-    map_func = lambda ms: reduce(lambda ms, f: f(ms), maps, ms)
+    def filter_func(mol):
+        return all(f(mol) for f in filters)
+
+    def map_func(ms):
+        return reduce(lambda ms, f: f(ms), maps, ms)
 
     result = None
 

{nerdd_module-0.3.45 → nerdd_module-0.3.47}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nerdd-module
-Version: 0.3.45
+Version: 0.3.47
 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-0.3.45 → nerdd_module-0.3.47}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.45"
+version = "0.3.47"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = "BSD-3-Clause"
@@ -105,7 +105,6 @@ patterns = ["*.py", "*.feature", "pyproject.toml"]
 
 [tool.ruff]
 line-length = 100
-extend-exclude = ["tests", "nerdd_module/tests"]
 
 [tool.ruff.lint]
 select = [