geometallurgy 0.4.12__py3-none-any.whl → 0.4.13__py3-none-any.whl

elphick/geomet/validate.py.hide

@@ -1,176 +1,176 @@
-"""
-Classes to support validation of block model files.
-"""
-
-import logging
-import tempfile
-from abc import ABC, abstractmethod
-from concurrent.futures import ThreadPoolExecutor
-from concurrent.futures import as_completed
-from pathlib import Path
-from typing import Optional
-
-import pandas as pd
-
-from elphick.geomet.readers import ParquetFileReader, OMFFileReader
-from elphick.geomet.utils.components import is_compositional
-
-
-#
-# class FileValidator(ABC):
-#     def __init__(self, file_path: Path, schema_path: Optional[Path] = None,
-#                  lazy_validation: bool = True,
-#                  negative_to_nan_threshold: float = 0):
-#         if not file_path.exists():
-#             raise ValueError(f"File does not exist: {file_path}")
-#         self._logger = logging.getLogger(self.__class__.__name__)
-#         self.file_path = file_path
-#         self.schema_path = schema_path
-#         self.schema: DataFrameSchema = DataFrameSchema({}) if schema_path is None else pandera.io.from_yaml(schema_path)
-#         self.lazy_validation = lazy_validation
-#         self.negative_to_nan_threshold = negative_to_nan_threshold
-#
-#         self.report: Optional[dict] = None
-#
-#     @abstractmethod
-#     def validate(self):
-#         pass
-#
-#     def create_schema_file(self, schema_output_path: Path):
-#         """
-#         Create an inferred schema file from the file being validated
-#         Args:
-#             schema_output_path: The output path for the schema file
-#
-#         Returns:
-#
-#         """
-#
-#         df = self.read_column()
-#
-#         with open(schema_output_path, 'w') as f:
-#             yaml.dump(self.schema.to_yaml(), f)
-
-
-class BaseProcessor(ABC):
-    """
-    To support columnar processing of large datasets, the BaseProcessor class provides a framework for processing
-    data by column. The process method will process the data by column if a file_path is provided, or the entire
-    dataset if data is provided.
-    """
-
-    def __init__(self, file_path: Optional[Path] = None, data: Optional[pd.DataFrame] = None, **kwargs):
-        self.logger = logging.getLogger(self.__class__.__name__)
-        if file_path is None and data is None:
-            raise ValueError("Either file_path or data must be provided.")
-        self.file_path = file_path
-        self.data = data
-        self.temp_files = []
-
-        if self.file_path.suffix == '.parquet':
-            self.reader: ParquetFileReader = ParquetFileReader(self.file_path)
-        elif self.file_path.suffix == '.omf':
-            self.reader: OMFFileReader = OMFFileReader(self.file_path, **kwargs)
-        else:
-            raise ValueError(f"Unsupported file format: {self.file_path.suffix}")
-
-    @property
-    def composition_variables(self) -> list[str]:
-        """
-        Detect columns that contain composition data
-
-        Returns:
-            A list of column names that contain composition data
-        """
-        res = None
-        if self.reader.variables_in_file:
-            res = list(is_compositional(self.reader.variables_in_file, strict=False).keys())
-        return res
-
-    def process(self, num_workers: Optional[int] = 1, **kwargs):
-        if self.data is None:
-            with ThreadPoolExecutor(max_workers=num_workers, thread_name_prefix='geomet-processor') as executor:
-                futures = {executor.submit(self._process_variable, variable, **kwargs): variable for variable in
-                           self.reader.variables_in_file}
-                results = {}
-                for future in as_completed(futures):
-                    variable = futures[future]
-                    try:
-                        results[variable] = future.result()
-                    except Exception as exc:
-                        print(f'{variable} generated an exception: {exc}')
-        else:
-            results = self._process_data()
-        return results
-
-    @abstractmethod
-    def _process_variable(self, column, **kwargs):
-        pass
-
-    @abstractmethod
-    def _process_data(self):
-        pass
-
-
-class PreProcessor(BaseProcessor):
-    def __init__(self, file_path: Optional[Path] = None, data: Optional[pd.DataFrame] = None, **kwargs):
-        """
-        Preprocess data before validation.
-        For large datasets where memory may be constrained, file_path will provide processing by columns.
-        If data is provided, the entire dataset already in memory will be processed.
-        Args:
-            file_path: The optional path to the file to be preprocessed.
-            data: The optional DataFrame to be preprocessed.
-        """
-
-        super().__init__(file_path, data, **kwargs)
-
-    def process(self, negative_to_nan_threshold: Optional[float] = -1,
-                not_detected_assays_threshold: Optional[float] = 0.5,
-                max_workers=1):
-        super().process(max_workers=max_workers, negative_to_nan_threshold=negative_to_nan_threshold,
-                        not_detected_assays_threshold=not_detected_assays_threshold)
-
-    def _process_variable(self, column, **kwargs):
-        data = pd.read_parquet(self.file_path, columns=[column])
-        processed_data = self._process_data(data)
-        temp_file = tempfile.NamedTemporaryFile(delete=False)
-        processed_data.to_parquet(temp_file.name)
-        self.temp_files.append(temp_file)
-
-    def _process_data(self) -> pd.DataFrame:
-        # Preprocessing logic here
-        return data
-
-
-class Validator(BaseProcessor):
-    def __init__(self, file_path: Optional[Path] = None, data: Optional[pd.DataFrame] = None, **kwargs):
-        """
-        Validate the data using a pandera schema.
-        For large datasets where memory may be constrained file_path will provide processing by columns.
-        If data is provided, the entire dataset already in memory will be processed.
-        Args:
-            file_path: The optional path to the file to be preprocessed.
-            data: The optional DataFrame to be preprocessed.
-        """
-        super().__init__(file_path, data, **kwargs)
-
-    def process(self):
-        if self.data is None:
-            columns = get_parquet_columns(self.file_path)
-            with ThreadPoolExecutor() as executor:
-                for column in columns:
-                    executor.submit(self._process_variable, column)
-        else:
-            self._process_data()
-
-    def _process_variable(self, column):
-        data = pd.read_parquet(self.file_path, columns=[column])
-        processed_data = self._process_data(data)
-        temp_file = tempfile.NamedTemporaryFile(delete=False)
-        processed_data.to_parquet(temp_file.name)
-        self.temp_files.append(temp_file)
-
-    def _process_data(self, data):
-        # Validation logic here
-        return data
+"""
+Classes to support validation of block model files.
+"""
+
+import logging
+import tempfile
+from abc import ABC, abstractmethod
+from concurrent.futures import ThreadPoolExecutor
+from concurrent.futures import as_completed
+from pathlib import Path
+from typing import Optional
+
+import pandas as pd
+
+from elphick.geomet.readers import ParquetFileReader, OMFFileReader
+from elphick.geomet.utils.components import is_compositional
+
+
+#
+# class FileValidator(ABC):
+#     def __init__(self, file_path: Path, schema_path: Optional[Path] = None,
+#                  lazy_validation: bool = True,
+#                  negative_to_nan_threshold: float = 0):
+#         if not file_path.exists():
+#             raise ValueError(f"File does not exist: {file_path}")
+#         self._logger = logging.getLogger(self.__class__.__name__)
+#         self.file_path = file_path
+#         self.schema_path = schema_path
+#         self.schema: DataFrameSchema = DataFrameSchema({}) if schema_path is None else pandera.io.from_yaml(schema_path)
+#         self.lazy_validation = lazy_validation
+#         self.negative_to_nan_threshold = negative_to_nan_threshold
+#
+#         self.report: Optional[dict] = None
+#
+#     @abstractmethod
+#     def validate(self):
+#         pass
+#
+#     def create_schema_file(self, schema_output_path: Path):
+#         """
+#         Create an inferred schema file from the file being validated
+#         Args:
+#             schema_output_path: The output path for the schema file
+#
+#         Returns:
+#
+#         """
+#
+#         df = self.read_column()
+#
+#         with open(schema_output_path, 'w') as f:
+#             yaml.dump(self.schema.to_yaml(), f)
+
+
+class BaseProcessor(ABC):
+    """
+    To support columnar processing of large datasets, the BaseProcessor class provides a framework for processing
+    data by column. The process method will process the data by column if a file_path is provided, or the entire
+    dataset if data is provided.
+    """
+
+    def __init__(self, file_path: Optional[Path] = None, data: Optional[pd.DataFrame] = None, **kwargs):
+        self.logger = logging.getLogger(self.__class__.__name__)
+        if file_path is None and data is None:
+            raise ValueError("Either file_path or data must be provided.")
+        self.file_path = file_path
+        self.data = data
+        self.temp_files = []
+
+        if self.file_path.suffix == '.parquet':
+            self.reader: ParquetFileReader = ParquetFileReader(self.file_path)
+        elif self.file_path.suffix == '.omf':
+            self.reader: OMFFileReader = OMFFileReader(self.file_path, **kwargs)
+        else:
+            raise ValueError(f"Unsupported file format: {self.file_path.suffix}")
+
+    @property
+    def composition_variables(self) -> list[str]:
+        """
+        Detect columns that contain composition data
+
+        Returns:
+            A list of column names that contain composition data
+        """
+        res = None
+        if self.reader.variables_in_file:
+            res = list(is_compositional(self.reader.variables_in_file, strict=False).keys())
+        return res
+
+    def process(self, num_workers: Optional[int] = 1, **kwargs):
+        if self.data is None:
+            with ThreadPoolExecutor(max_workers=num_workers, thread_name_prefix='geomet-processor') as executor:
+                futures = {executor.submit(self._process_variable, variable, **kwargs): variable for variable in
+                           self.reader.variables_in_file}
+                results = {}
+                for future in as_completed(futures):
+                    variable = futures[future]
+                    try:
+                        results[variable] = future.result()
+                    except Exception as exc:
+                        print(f'{variable} generated an exception: {exc}')
+        else:
+            results = self._process_data()
+        return results
+
+    @abstractmethod
+    def _process_variable(self, column, **kwargs):
+        pass
+
+    @abstractmethod
+    def _process_data(self):
+        pass
+
+
+class PreProcessor(BaseProcessor):
+    def __init__(self, file_path: Optional[Path] = None, data: Optional[pd.DataFrame] = None, **kwargs):
+        """
+        Preprocess data before validation.
+        For large datasets where memory may be constrained, file_path will provide processing by columns.
+        If data is provided, the entire dataset already in memory will be processed.
+        Args:
+            file_path: The optional path to the file to be preprocessed.
+            data: The optional DataFrame to be preprocessed.
+        """
+
+        super().__init__(file_path, data, **kwargs)
+
+    def process(self, negative_to_nan_threshold: Optional[float] = -1,
+                not_detected_assays_threshold: Optional[float] = 0.5,
+                max_workers=1):
+        super().process(max_workers=max_workers, negative_to_nan_threshold=negative_to_nan_threshold,
+                        not_detected_assays_threshold=not_detected_assays_threshold)
+
+    def _process_variable(self, column, **kwargs):
+        data = pd.read_parquet(self.file_path, columns=[column])
+        processed_data = self._process_data(data)
+        temp_file = tempfile.NamedTemporaryFile(delete=False)
+        processed_data.to_parquet(temp_file.name)
+        self.temp_files.append(temp_file)
+
+    def _process_data(self) -> pd.DataFrame:
+        # Preprocessing logic here
+        return data
+
+
+class Validator(BaseProcessor):
+    def __init__(self, file_path: Optional[Path] = None, data: Optional[pd.DataFrame] = None, **kwargs):
+        """
+        Validate the data using a pandera schema.
+        For large datasets where memory may be constrained file_path will provide processing by columns.
+        If data is provided, the entire dataset already in memory will be processed.
+        Args:
+            file_path: The optional path to the file to be preprocessed.
+            data: The optional DataFrame to be preprocessed.
+        """
+        super().__init__(file_path, data, **kwargs)
+
+    def process(self):
+        if self.data is None:
+            columns = get_parquet_columns(self.file_path)
+            with ThreadPoolExecutor() as executor:
+                for column in columns:
+                    executor.submit(self._process_variable, column)
+        else:
+            self._process_data()
+
+    def _process_variable(self, column):
+        data = pd.read_parquet(self.file_path, columns=[column])
+        processed_data = self._process_data(data)
+        temp_file = tempfile.NamedTemporaryFile(delete=False)
+        processed_data.to_parquet(temp_file.name)
+        self.temp_files.append(temp_file)
+
+    def _process_data(self, data):
+        # Validation logic here
+        return data

{geometallurgy-0.4.12.dist-info → geometallurgy-0.4.13.dist-info}/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2024 Greg Elphick
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2024 Greg Elphick
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{geometallurgy-0.4.12.dist-info → geometallurgy-0.4.13.dist-info}/METADATA

@@ -1,26 +1,28 @@
 Metadata-Version: 2.1
 Name: geometallurgy
-Version: 0.4.12
+Version: 0.4.13
 Summary: Tools for the geometallurgist
 Home-page: https://github.com/elphick/geometallurgy
 Author: Greg
 Author-email: 11791585+elphick@users.noreply.github.com
-Requires-Python: >=3.9,<3.13
+Requires-Python: >=3.10,<3.13
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Provides-Extra: all
 Provides-Extra: blockmodel
-Provides-Extra: map
+Provides-Extra: spatial
 Provides-Extra: validation
-Requires-Dist: folium (>=0.16.0,<0.17.0) ; extra == "map"
+Requires-Dist: folium (>=0.16.0,<0.17.0) ; extra == "spatial"
+Requires-Dist: omfpandas (>=0.8.1,<0.9.0) ; extra == "blockmodel"
 Requires-Dist: omfvista (>=0.3.0) ; extra == "blockmodel"
 Requires-Dist: pandas (>=1.0)
 Requires-Dist: pandera[io] (>=0.19.3,<0.21.0) ; extra == "validation"
 Requires-Dist: periodictable (>=1.7.0,<2.0.0)
 Requires-Dist: plotly (>=5.22.0,<6.0.0)
 Requires-Dist: pyarrow (>=16.1.0,<18.0.0)
+Requires-Dist: rioxarray (>=0.18.2,<0.19.0) ; extra == "spatial"
 Project-URL: Documentation, https://elphick.github.io/geometallurgy
 Project-URL: Repository, https://github.com/elphick/geometallurgy
 Description-Content-Type: text/markdown

geometallurgy-0.4.13.dist-info/RECORD

@@ -0,0 +1,49 @@
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