nerdd-module 0.2.0__tar.gz → 0.2.1__tar.gz

{nerdd-module-0.2.0 → nerdd-module-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nerdd-module
-Version: 0.2.0
+Version: 0.2.1
 Summary: Base package to create NERDD modules
 Home-page: https://github.com/molinfo-vienna/nerdd-module.git
 Maintainer: Steffen Hirte

nerdd-module-0.2.1/nerdd_module/__init__.py

@@ -0,0 +1,10 @@
+from .abstract_model import *
+from .cli import *
+from .config import *
+from .problem import *
+from .version import *
+from .polyfills import get_entry_points
+
+
+for entry_point in get_entry_points("nerdd-module.plugins"):
+    entry_point.load()

nerdd-module-0.2.1/nerdd_module/config/package_configuration.py

@@ -0,0 +1,31 @@
+from ..polyfills import files
+from .configuration import Configuration
+from .dict_configuration import DictConfiguration
+from .yaml_configuration import YamlConfiguration
+
+__all__ = ["PackageConfiguration"]
+
+
+class PackageConfiguration(Configuration):
+    def __init__(self, package):
+        super().__init__()
+
+        # get the resource directory
+        try:
+            root_dir = files(package)
+        except ModuleNotFoundError:
+            root_dir = None
+
+        if root_dir is None:
+            self.config = DictConfiguration({})
+        else:
+            # navigate to the config file
+            config_file = root_dir / "nerdd.yml"
+
+            if config_file is not None and config_file.exists():
+                self.config = YamlConfiguration(config_file, base_path=root_dir)
+            else:
+                self.config = DictConfiguration({})
+
+    def _get_dict(self):
+        return self.config.get_dict()

{nerdd-module-0.2.0 → nerdd-module-0.2.1}/nerdd_module/io/depth_first_explorer.py

@@ -38,7 +38,7 @@ class DepthFirstExplorer(Explorer):
         if readers is None:
             self.reader_registry = ReaderRegistry()
         else:
-            self.reader_registry = None
+            self.reader_registry = readers
 
         self.num_test_entries = num_test_entries
         self.threshold = threshold

{nerdd-module-0.2.0 → nerdd-module-0.2.1}/nerdd_module/io/file_reader.py

@@ -1,4 +1,5 @@
 import os
+from pathlib import Path
 from typing import Generator
 
 from .reader import MoleculeEntry, Reader
@@ -9,12 +10,20 @@ __all__ = ["FileReader"]
 
 @register_reader
 class FileReader(Reader):
-    def __init__(self):
+    def __init__(self, data_dir="."):
         super().__init__()
+        self.data_dir = Path(data_dir)
 
     def read(self, filename, explore) -> Generator[MoleculeEntry, None, None]:
-        if not isinstance(filename, str) or not os.path.exists(filename):
-            raise TypeError("input must be a valid filename")
+        assert isinstance(filename, str), "input must be a string"
+
+        try:
+            path = Path(filename).absolute()
+        except:
+            raise ValueError("input must be a valid path")
+
+        assert path.is_relative_to(self.data_dir), "input must be a relative path"
+        assert path.exists(), "input must be a valid file"
 
         with open(filename, "rb") as f:
             for entry in explore(f):

nerdd-module-0.2.1/nerdd_module/polyfills/__init__.py

@@ -0,0 +1,2 @@
+from .files import *
+from .get_entry_points import *

nerdd-module-0.2.1/nerdd_module/polyfills/files.py

@@ -0,0 +1,8 @@
+import sys
+
+__all__ = ["files"]
+
+if sys.version_info < (3, 9):
+    from importlib_resources import files
+else:
+    from importlib.resources import files

nerdd-module-0.2.0/nerdd_module/__init__.py → nerdd-module-0.2.1/nerdd_module/polyfills/get_entry_points.py

@@ -1,22 +1,15 @@
-from .abstract_model import *
-from .cli import *
-from .config import *
-from .problem import *
-from .version import *
+__all__ = ["get_entry_points"]
 
 # import entry_points from importlib.metadata or fall back to pkg_resources
+# TODO: add importlib_metadata as another option
 try:
     from importlib.metadata import entry_points
 
     def get_entry_points(group):
-        return entry_points().get(group, [])
+        return entry_points(group=group)
 
 except ImportError:
     import pkg_resources
 
     def get_entry_points(group):
         return pkg_resources.iter_entry_points(group)
-
-
-for entry_point in get_entry_points("nerdd-module.plugins"):
-    entry_point.load()

{nerdd-module-0.2.0 → nerdd-module-0.2.1}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nerdd-module
-Version: 0.2.0
+Version: 0.2.1
 Summary: Base package to create NERDD modules
 Home-page: https://github.com/molinfo-vienna/nerdd-module.git
 Maintainer: Steffen Hirte

{nerdd-module-0.2.0 → nerdd-module-0.2.1}/nerdd_module.egg-info/SOURCES.txt

@@ -38,6 +38,9 @@ nerdd_module/io/tar_reader.py
 nerdd_module/io/writer.py
 nerdd_module/io/writer_registry.py
 nerdd_module/io/zip_reader.py
+nerdd_module/polyfills/__init__.py
+nerdd_module/polyfills/files.py
+nerdd_module/polyfills/get_entry_points.py
 nerdd_module/preprocessing/__init__.py
 nerdd_module/preprocessing/check_valid_smiles.py
 nerdd_module/preprocessing/chembl_structure_pipeline.py

{nerdd-module-0.2.0 → nerdd-module-0.2.1}/setup.py

@@ -16,7 +16,7 @@ rdkit_requirement = ["rdkit>=2022.3.3"] if not rdkit_installed else []
 
 setup(
     name="nerdd-module",
-    version="0.2.0",
+    version="0.2.1",
     maintainer="Steffen Hirte",
     maintainer_email="steffen.hirte@univie.ac.at",
     packages=find_packages(),

{nerdd-module-0.2.0 → nerdd-module-0.2.1}/tests/steps/molecules.py

@@ -4,8 +4,7 @@ from hypothesis import settings
 from hypothesis import strategies as st
 from hypothesis_rdkit import mols
 from pytest_bdd import given, parsers
-from rdkit.Chem import MolFromSmiles, MolToInchi, MolToMolBlock, MolToSmiles
-from rdkit.Chem.Descriptors import MolWt
+from rdkit.Chem import MolToInchi, MolToMolBlock, MolToSmiles
 
 
 @given(

nerdd-module-0.2.0/nerdd_module/config/package_configuration.py

@@ -1,30 +0,0 @@
-try:
-    # works in python 3.9+
-    from importlib.resources import files
-except ImportError:
-    from importlib_resources import files
-
-from .configuration import Configuration
-from .dict_configuration import DictConfiguration
-from .yaml_configuration import YamlConfiguration
-
-__all__ = ["PackageConfiguration"]
-
-
-class PackageConfiguration(Configuration):
-    def __init__(self, package):
-        super().__init__()
-
-        # get the resource directory
-        root_dir = files(package)
-
-        # navigate to the config file
-        config_file = root_dir / "nerdd.yml"
-
-        if config_file is not None and config_file.exists():
-            self.config = YamlConfiguration(config_file, base_path=root_dir)
-        else:
-            self.config = DictConfiguration({})
-
-    def _get_dict(self):
-        return self.config.get_dict()