nerdd-module 0.3.20__tar.gz → 0.3.22__tar.gz

{nerdd_module-0.3.20 → nerdd_module-0.3.22}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nerdd-module
-Version: 0.3.20
+Version: 0.3.22
 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-0.3.20 → nerdd_module-0.3.22}/nerdd_module/config/package_configuration.py

@@ -19,23 +19,19 @@ class PackageConfiguration(Configuration):
         remaining_path = package_path[1:]
 
         # get the resource directory
-        try:
-            root_dir = files(package_root)
-        except ModuleNotFoundError:
-            root_dir = None
+        root_dir = files(package_root)
+        assert root_dir is not None
 
         self.config: Configuration = DictConfiguration({})
-        if root_dir is not None:
-            # navigate to the config file
-            config_file = root_dir.joinpath(*remaining_path, filename)
-
-            if config_file is not None and config_file.is_file():
-                logger.info(f"Found configuration file in package: {config_file}")
-                self.config = YamlConfiguration(
-                    config_file.open(), base_path=root_dir.joinpath(*remaining_path)
-                )
-            else:
-                self.config = DictConfiguration({})
+
+        # navigate to the config file
+        config_file = root_dir.joinpath(*remaining_path, filename)
+        assert config_file is not None and config_file.is_file()
+
+        logger.info(f"Found configuration file in package: {config_file}")
+        self.config = YamlConfiguration(
+            config_file.open(), base_path=root_dir.joinpath(*remaining_path)
+        )
 
     def _get_dict(self) -> dict:
         return self.config._get_dict()

{nerdd_module-0.3.20 → nerdd_module-0.3.22}/nerdd_module/config/search_yaml_configuration.py

@@ -12,7 +12,9 @@ logger = logging.getLogger(__name__)
 
 
 class SearchYamlConfiguration(DictConfiguration):
-    def __init__(self, start: str, base_path: Optional[str] = None) -> None:
+    def __init__(
+        self, start: str, base_path: Optional[str] = None, filename: str = "nerdd.yml"
+    ) -> None:
         # provide a default configuration if no configuration file is found
         config: Configuration = DictConfiguration({})
 
@@ -22,8 +24,8 @@ class SearchYamlConfiguration(DictConfiguration):
             # reached)
             leaf = start
             while True:
-                if os.path.isfile(os.path.join(leaf, "nerdd.yml")):
-                    default_config_file = os.path.join(leaf, "nerdd.yml")
+                if os.path.isfile(os.path.join(leaf, filename)):
+                    default_config_file = os.path.join(leaf, filename)
                     break
                 elif leaf == os.path.dirname(leaf):  # reached root
                     default_config_file = None

{nerdd_module-0.3.20 → nerdd_module-0.3.22}/nerdd_module/converters/__init__.py

@@ -4,4 +4,5 @@ from .converter_config import *
 from .mol_converter import *
 from .problem_list_converter import *
 from .representation_converter import *
+from .source_list_converter import *
 from .void_converter import *

nerdd_module-0.3.22/nerdd_module/converters/source_list_converter.py

@@ -0,0 +1,29 @@
+import logging
+from typing import Any
+
+from .converter import Converter
+from .converter_config import ConverterConfig
+
+__all__ = ["SourceListIdentityConverter", "SourceListConverter"]
+
+logger = logging.getLogger(__name__)
+
+
+class SourceListIdentityConverter(Converter):
+    def _convert(self, input: Any, context: dict) -> Any:
+        return input
+
+    config = ConverterConfig(
+        data_types="source_list",
+        output_formats=["pandas", "iterator", "record_list"],
+    )
+
+
+class SourceListConverter(Converter):
+    def _convert(self, input: Any, context: dict) -> Any:
+        return " / ".join(source for source in input)
+
+    config = ConverterConfig(
+        data_types="source_list",
+        output_formats=["csv", "sdf"],
+    )

{nerdd_module-0.3.20 → nerdd_module-0.3.22}/nerdd_module/model/simple_model.py

@@ -32,10 +32,9 @@ __all__ = ["SimpleModel"]
 class SimpleModel(Model):
     def __init__(self, preprocessing_steps: Iterable[Step] = []) -> None:
         super().__init__()
-        assert isinstance(preprocessing_steps, Iterable), (
-            f"Expected Iterable for argument preprocessing_steps, "
-            f"got {type(preprocessing_steps)}"
-        )
+        assert isinstance(
+            preprocessing_steps, Iterable
+        ), f"Expected Iterable for argument preprocessing_steps, got {type(preprocessing_steps)}"
         assert all(isinstance(step, Step) for step in preprocessing_steps), (
             f"Expected all elements of preprocessing_steps to be of type Step, "
             f"got {[type(step) for step in preprocessing_steps if not isinstance(step, Step)]}"
@@ -79,14 +78,6 @@ class SimpleModel(Model):
         pass
 
     def _get_base_config(self) -> Union[Configuration, dict]:
-        return {}
-
-    def _get_config(self) -> Configuration:
-        # get base configuration specified in this class
-        base_config = self._get_base_config()
-        if isinstance(base_config, dict):
-            base_config = DictConfiguration(base_config)
-
         # get the class of the nerdd module, e.g. <CypstrateModel>
         nerdd_module_class = self.__class__
 
@@ -97,17 +88,30 @@ class SimpleModel(Model):
         # get the root module name, e.g. "cypstrate"
         root_module = python_module.split(".")[0]
 
-        configs = [
-            DefaultConfiguration(self),
-            # TODO: remove "."
-            SearchYamlConfiguration(get_file_path_to_instance(self) or "."),
-            PackageConfiguration(f"{root_module}.data"),
-            # base config comes last -> highest priority
-            base_config,
-        ]
+        configs: List[Configuration] = []
+
+        try:
+            configs.append(  # TODO: remove "."
+                SearchYamlConfiguration(get_file_path_to_instance(self) or ".")
+            )
+        except Exception:
+            pass
+
+        try:
+            configs.append(PackageConfiguration(f"{root_module}.data", filename="nerdd.yml"))
+        except Exception:
+            pass
+
+        return MergedConfiguration(*configs)
+
+    def _get_config(self) -> Configuration:
+        # get base configuration specified in this class
+        base_config = self._get_base_config()
+        if isinstance(base_config, dict):
+            base_config = DictConfiguration(base_config)
 
         # add default properties mol_id, raw_input, etc.
-        task = MergedConfiguration(*configs).get_dict().task
+        task = base_config.get_dict().task
 
         # check whether we need to add to add a property "atom_id" or "derivative_id"
         task_based_property = []
@@ -138,7 +142,7 @@ class SimpleModel(Model):
             {
                 "name": "source",
                 "visible_name": "Source",
-                "type": "string",
+                "type": "source_list",
                 "visible": False,
             },
             {"name": "name", "visible_name": "Name", "type": "string"},
@@ -179,8 +183,9 @@ class SimpleModel(Model):
         ]
 
         configs = [
+            DefaultConfiguration(self),
             DictConfiguration({"result_properties": default_properties_start}),
-            *configs,
+            base_config,
             DictConfiguration({"result_properties": default_properties_end}),
         ]
 

{nerdd_module-0.3.20 → nerdd_module-0.3.22}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nerdd-module
-Version: 0.3.20
+Version: 0.3.22
 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-0.3.20 → nerdd_module-0.3.22}/nerdd_module.egg-info/SOURCES.txt

@@ -27,6 +27,7 @@ nerdd_module/converters/converter_config.py
 nerdd_module/converters/mol_converter.py
 nerdd_module/converters/problem_list_converter.py
 nerdd_module/converters/representation_converter.py
+nerdd_module/converters/source_list_converter.py
 nerdd_module/converters/void_converter.py
 nerdd_module/input/__init__.py
 nerdd_module/input/depth_first_explorer.py

{nerdd_module-0.3.20 → nerdd_module-0.3.22}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.20"
+version = "0.3.22"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = { file = "LICENSE" }