qupled 1.3.2__cp310-cp310-macosx_14_0_arm64.whl

qupled/__init__.py

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+

qupled/database.py

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+import io
+import json
+import struct
+from datetime import datetime
+from enum import Enum
+from collections.abc import Callable
+
+import numpy as np
+import sqlalchemy as sql
+from sqlalchemy.dialects.sqlite import insert as sqlite_insert
+import blosc2
+
+from . import mpi
+
+
+class DataBaseHandler:
+    """
+    DataBaseHandler is a class for managing a SQLite database that stores information
+    about runs, inputs, and results. It provides methods for inserting, retrieving,
+    and deleting data, as well as managing the database schema."
+    """
+
+    DEFAULT_DATABASE_NAME = "qupled.db"
+    RUN_TABLE_NAME = "runs"
+    INPUT_TABLE_NAME = "inputs"
+    RESULT_TABLE_NAME = "results"
+
+    class TableKeys(Enum):
+        COUPLING = "coupling"
+        DATE = "date"
+        DEGENERACY = "degeneracy"
+        NAME = "name"
+        PRIMARY_KEY = "id"
+        RUN_ID = "run_id"
+        STATUS = "status"
+        THEORY = "theory"
+        TIME = "time"
+        VALUE = "value"
+
+    class RunStatus(Enum):
+        RUNNING = "STARTED"
+        SUCCESS = "SUCCESS"
+        FAILED = "FAILED"
+
+    INT_TO_RUN_STATUS = {
+        0: RunStatus.SUCCESS,
+        1: RunStatus.FAILED,
+    }
+
+    def __init__(self, database_name: str | None = None):
+        """
+        Initializes the DataBaseHandler instance.
+
+        Args:
+            database_name (str | None, optional): The name of the database file. If not provided,
+                the default database name (`DEFAULT_DATABASE_NAME`) will be used.
+
+        Attributes:
+            database_name (str): The name of the database file being used.
+            engine (sqlalchemy.engine.Engine): The SQLAlchemy engine connected to the SQLite database.
+            table_metadata (sqlalchemy.MetaData): Metadata object for managing table schemas.
+            run_table (sqlalchemy.Table): The table schema for storing run information.
+            input_table (sqlalchemy.Table): The table schema for storing input data.
+            result_table (sqlalchemy.Table): The table schema for storing result data.
+            run_id (int | None): The ID of the current run, or None if no run is active.
+        """
+        self.database_name = (
+            database_name if database_name is not None else self.DEFAULT_DATABASE_NAME
+        )
+        self.engine = sql.create_engine(f"sqlite:///{self.database_name}")
+        # Enforce foreign keys in sqlite
+        DataBaseHandler._set_sqlite_pragma(self.engine)
+        self.table_metadata = sql.MetaData()
+        self.run_table = self._build_run_table()
+        self.input_table = self._build_inputs_table()
+        self.result_table = self._build_results_table()
+        self.run_id: int | None = None
+
+    @mpi.MPI.run_only_on_root
+    def insert_run(self, inputs):
+        """
+        Inserts a new run into the database by storing the provided inputs and results.
+
+        Args:
+            inputs (object): An object containing the input data for the run.
+                             The attributes of this object will be converted to a dictionary.
+            results (object): An object containing the result data for the run.
+                              The attributes of this object will be converted to a dictionary.
+
+        """
+        self._insert_run(inputs, self.RunStatus.RUNNING)
+        self.insert_inputs(inputs.__dict__)
+
+    @mpi.MPI.run_only_on_root
+    def insert_inputs(self, inputs: dict[str, any]):
+        """
+        Inserts input data into the database for the current run.
+
+        Args:
+            inputs (dict[str, any]): A dictionary containing input data to be inserted.
+                The keys represent column names, and the values represent the data
+                to be stored in the corresponding columns.
+
+        Raises:
+            ValueError: If `run_id` is None, indicating that no run is currently active.
+
+        Notes:
+            - The input data is serialized to JSON format before being inserted into
+              the database.
+            - The insertion is performed using the `_insert_from_dict` method, which
+              maps the input values using the `sql_mapping` function.
+        """
+        if self.run_id is not None:
+            sql_mapping = lambda value: (self._to_json(value))
+            self._insert_from_dict(self.input_table, inputs, sql_mapping)
+
+    @mpi.MPI.run_only_on_root
+    def insert_results(self, results: dict[str, any]):
+        """
+        Inserts the given results into the database table associated with this instance.
+
+        Args:
+            results (dict[str, any]): A dictionary where the keys are column names
+                and the values are the corresponding data to be inserted.
+
+        Notes:
+            - This method requires that `self.run_id` is not None; otherwise, no insertion will occur.
+            - The values in the `results` dictionary are converted to bytes using the `_to_bytes` method
+              before being inserted into the database.
+        """
+        if self.run_id is not None:
+            sql_mapping = lambda value: (self._to_bytes(value))
+            self._insert_from_dict(self.result_table, results, sql_mapping)
+
+    def inspect_runs(self) -> list[dict[str, any]]:
+        """
+        Retrieve and inspect all runs from the database.
+
+        This method executes a SQL SELECT statement on the `run_table` and retrieves
+        all rows. Each row is converted into a dictionary where the keys are the column
+        names and the values are the corresponding data.
+
+        Returns:
+            list[dict[str, any]]: A list of dictionaries, each representing a row
+            from the `run_table`. The keys in the dictionary correspond to the column
+            names, and the values are the respective data for each column.
+        """
+        statement = sql.select(self.run_table)
+        rows = self._execute(statement).mappings().all()
+        return [{key: row[key] for key in row.keys()} for row in rows]
+
+    def update_run_status(self, status: int) -> None:
+        """
+        Updates the status of a run in the database.
+
+        Args:
+            status (int): The new status code to update the run with. If the status
+                          code is not found in the INT_TO_RUN_STATUS mapping, the
+                          status will default to RunStatus.FAILED.
+
+        Returns:
+            None
+        """
+        if self.run_id is not None:
+            new_status = self.INT_TO_RUN_STATUS.get(status, self.RunStatus.FAILED)
+            statement = (
+                sql.update(self.run_table)
+                .where(
+                    self.run_table.c[self.TableKeys.PRIMARY_KEY.value] == self.run_id
+                )
+                .values({self.TableKeys.STATUS.value: new_status.value})
+            )
+            self._execute(statement)
+
+    def get_run(
+        self,
+        run_id: int,
+        input_names: list[str] | None = None,
+        result_names: list[str] | None = None,
+    ) -> dict:
+        """
+        Retrieve a run's data, including its inputs and results, from the database.
+
+        Args:
+            run_id (int): The unique identifier of the run to retrieve.
+            input_names (list[str] | None): A list of input names to filter the inputs
+                associated with the run. If None, all inputs are retrieved.
+            result_names (list[str] | None): A list of result names to filter the results
+                associated with the run. If None, all results are retrieved.
+
+        Returns:
+            dict: A dictionary containing the run's data, inputs, and results. The structure is:
+                {
+                    "RUN_TABLE_NAME": {<run_data>},
+                    "INPUT_TABLE_NAME": [<inputs>],
+                    "RESULT_TABLE_NAME": [<results>]
+                If the run is not found, an empty dictionary is returned.
+        """
+        statement = sql.select(self.run_table).where(
+            self.run_table.c[self.TableKeys.PRIMARY_KEY.value] == run_id
+        )
+        result = self._execute(statement).mappings().first()
+        if result is not None:
+            run_data = {key: result[key] for key in result.keys()}
+            inputs = self.get_inputs(run_id, names=input_names)
+            results = self.get_results(run_id, names=result_names)
+            return {
+                self.RUN_TABLE_NAME: run_data,
+                self.INPUT_TABLE_NAME: inputs,
+                self.RESULT_TABLE_NAME: results,
+            }
+        else:
+            return {}
+
+    def get_inputs(self, run_id: int, names: list[str] | None = None) -> dict:
+        """
+        Retrieve input data for a specific run ID from the input table.
+
+        Args:
+            run_id (int): The unique identifier for the run whose inputs are to be retrieved.
+            names (list[str] | None): A list of input names to filter the results. If None, all inputs are retrieved.
+
+        Returns:
+            dict: A dictionary containing the input data, where keys are input names and values are the corresponding data.
+        """
+        sql_mapping = lambda value: (self._from_json(value))
+        return self._get(self.input_table, run_id, names, sql_mapping)
+
+    def get_results(self, run_id: int, names: list[str] | None = None) -> dict:
+        """
+        Retrieve results from the database for a specific run ID and optional list of names.
+
+        Args:
+            run_id (int): The unique identifier for the run whose results are to be retrieved.
+            names (list[str] | None): A list of column names to filter the results. If None, all columns are retrieved.
+
+        Returns:
+            dict: A dictionary containing the retrieved results, where the keys are column names and the values
+                  are the corresponding data, processed using the `_from_bytes` method.
+        """
+        sql_mapping = lambda value: (self._from_bytes(value))
+        return self._get(self.result_table, run_id, names, sql_mapping)
+
+    @mpi.MPI.synchronize_ranks
+    @mpi.MPI.run_only_on_root
+    def delete_run(self, run_id: int) -> None:
+        """
+        Deletes a run entry from the database based on the provided run ID.
+
+        Args:
+            run_id (int): The unique identifier of the run to be deleted.
+
+        Returns:
+            None
+        """
+        condition = self.run_table.c[self.TableKeys.PRIMARY_KEY.value] == run_id
+        statement = sql.delete(self.run_table).where(condition)
+        self._execute(statement)
+
+    def _build_run_table(self):
+        """
+        Builds the SQLAlchemy table object for the "runs" table in the database.
+
+        This method defines the schema for the "runs" table, including its columns,
+        data types, constraints, and metadata. The table includes the following columns:
+
+        - PRIMARY_KEY: An auto-incrementing integer that serves as the primary key.
+        - THEORY: A string representing the theory associated with the run (non-nullable).
+        - COUPLING: A float representing the coupling value (non-nullable).
+        - DEGENERACY: A float representing the degeneracy value (non-nullable).
+        - DATE: A string representing the date of the run (non-nullable).
+        - TIME: A string representing the time of the run (non-nullable).
+        - STATUS: A string representing the status of the run (non-nullable).
+
+        After defining the table schema, the method creates the table in the database
+        using the `_create_table` method.
+
+        Returns:
+            sqlalchemy.Table: The constructed SQLAlchemy table object for the "runs" table.
+        """
+        table = sql.Table(
+            self.RUN_TABLE_NAME,
+            self.table_metadata,
+            sql.Column(
+                self.TableKeys.PRIMARY_KEY.value,
+                sql.Integer,
+                primary_key=True,
+                autoincrement=True,
+            ),
+            sql.Column(
+                self.TableKeys.THEORY.value,
+                sql.String,
+                nullable=False,
+            ),
+            sql.Column(
+                self.TableKeys.COUPLING.value,
+                sql.Float,
+                nullable=False,
+            ),
+            sql.Column(
+                self.TableKeys.DEGENERACY.value,
+                sql.Float,
+                nullable=False,
+            ),
+            sql.Column(
+                self.TableKeys.DATE.value,
+                sql.String,
+                nullable=False,
+            ),
+            sql.Column(
+                self.TableKeys.TIME.value,
+                sql.String,
+                nullable=False,
+            ),
+            sql.Column(self.TableKeys.STATUS.value, sql.String, nullable=False),
+        )
+        self._create_table(table)
+        return table
+
+    def _build_inputs_table(self) -> sql.Table:
+        """
+        Builds and returns the SQLAlchemy Table object for the inputs table.
+
+        This method constructs a table definition for storing input data, using
+        the predefined table name and a JSON column type.
+
+        Returns:
+            sql.Table: The SQLAlchemy Table object representing the inputs table.
+        """
+        return self._build_data_table(self.INPUT_TABLE_NAME, sql.JSON)
+
+    def _build_results_table(self) -> sql.Table:
+        """
+        Constructs and returns the results table for the database.
+
+        This method creates a SQL table with the name specified by
+        `RESULTS_TABLE_NAME` and a column of type `LargeBinary` to store
+        binary data.
+
+        Returns:
+            sql.Table: The constructed results table.
+        """
+        return self._build_data_table(self.RESULT_TABLE_NAME, sql.LargeBinary)
+
+    def _build_data_table(self, table_name, sql_data_type) -> sql.Table:
+        """
+        Builds and creates a SQLAlchemy table with the specified name and data type.
+
+        This method defines a table schema with the following columns:
+        - `RUN_ID`: An integer column that acts as a foreign key referencing the primary key
+          of the runs table. It is non-nullable and enforces cascading deletes.
+        - `NAME`: A string column that is non-nullable.
+        - `VALUE`: A column with a data type specified by the `sql_data_type` parameter,
+          which can be nullable.
+
+        The table also includes a composite primary key constraint on the `RUN_ID` and `NAME` columns.
+
+        After defining the table schema, the method creates the table in the database
+        if it does not already exist.
+
+        Args:
+            table_name (str): The name of the table to be created.
+            sql_data_type (sqlalchemy.types.TypeEngine): The SQLAlchemy data type for the `VALUE` column.
+
+        Returns:
+            sqlalchemy.Table: The created SQLAlchemy table object.
+        """
+        table = sql.Table(
+            table_name,
+            self.table_metadata,
+            sql.Column(
+                self.TableKeys.RUN_ID.value,
+                sql.Integer,
+                sql.ForeignKey(
+                    f"{self.RUN_TABLE_NAME}.{self.TableKeys.PRIMARY_KEY.value}",
+                    ondelete="CASCADE",
+                ),
+                nullable=False,
+            ),
+            sql.Column(
+                self.TableKeys.NAME.value,
+                sql.String,
+                nullable=False,
+            ),
+            sql.Column(
+                self.TableKeys.VALUE.value,
+                sql_data_type,
+                nullable=True,
+            ),
+            sql.PrimaryKeyConstraint(
+                self.TableKeys.RUN_ID.value, self.TableKeys.NAME.value
+            ),
+        )
+        self._create_table(table)
+        return table
+
+    @mpi.MPI.synchronize_ranks
+    @mpi.MPI.run_only_on_root
+    def _create_table(self, table):
+        table.create(self.engine, checkfirst=True)
+
+    @mpi.MPI.run_only_on_root
+    def _insert_run(self, inputs: any, status: RunStatus):
+        """
+        Inserts a new run entry into the database.
+
+        Args:
+            inputs (any): An object containing the input data for the run.
+                          Expected attributes include:
+                          - theory: Theoretical data to be serialized into JSON.
+                          - coupling: Coupling data to be serialized into JSON.
+                          - degeneracy: Degeneracy data to be serialized into JSON.
+
+        Side Effects:
+            - Updates the `self.run_id` attribute with the primary key of the newly inserted run.
+
+        Notes:
+            - The current date and time are automatically added to the entry.
+            - The input data is serialized into JSON format before insertion.
+        """
+        now = datetime.now()
+        data = {
+            self.TableKeys.THEORY.value: inputs.theory,
+            self.TableKeys.COUPLING.value: inputs.coupling,
+            self.TableKeys.DEGENERACY.value: inputs.degeneracy,
+            self.TableKeys.DATE.value: now.date().isoformat(),
+            self.TableKeys.TIME.value: now.time().isoformat(),
+            self.TableKeys.STATUS.value: status.value,
+        }
+        statement = sql.insert(self.run_table).values(data)
+        result = self._execute(statement)
+        if run_id := result.inserted_primary_key:
+            self.run_id = run_id[0]
+
+    @staticmethod
+    def _set_sqlite_pragma(engine):
+        """
+        Configures the SQLite database engine to enforce foreign key constraints.
+
+        This function sets up a listener for the "connect" event on the provided
+        SQLAlchemy engine. When a new database connection is established, it executes
+        the SQLite PRAGMA statement to enable foreign key support.
+
+        Args:
+            engine (sqlalchemy.engine.Engine): The SQLAlchemy engine instance to configure.
+
+        Notes:
+            SQLite does not enforce foreign key constraints by default. This function
+            ensures that foreign key constraints are enabled for all connections made
+            through the provided engine.
+        """
+
+        @sql.event.listens_for(engine, "connect")
+        def _set_pragma(dbapi_connection, connection_record):
+            cursor = dbapi_connection.cursor()
+            cursor.execute("PRAGMA foreign_keys=ON")
+            cursor.close()
+
+    @mpi.MPI.run_only_on_root
+    def _insert_from_dict(
+        self, table, data: dict[str, any], sql_mapping: Callable[[any], any]
+    ) -> None:
+        """
+        Inserts data into a specified table by mapping values through a provided SQL mapping function.
+
+        Args:
+            table (str): The name of the table where the data will be inserted.
+            data (dict[str, any]): A dictionary containing column names as keys and their corresponding values.
+            sql_mapping (Callable[[any], any]): A function that maps input values to their SQL-compatible representations.
+
+        Returns:
+            None
+        """
+        for name, value in data.items():
+            if mapped_value := sql_mapping(value):
+                self._insert(table, name, mapped_value)
+
+    @mpi.MPI.run_only_on_root
+    def _insert(self, table: sql.Table, name: str, value: any):
+        """
+        Inserts a record into the specified SQL table or updates it if a conflict occurs.
+
+        Args:
+            table (sql.Table): The SQLAlchemy Table object representing the target table.
+            name (str): The name of the record to insert or update.
+            value (any): The value associated with the record.
+
+        Behavior:
+            - If a record with the same `RUN_ID` and `NAME` already exists in the table,
+              the `VALUE` field of the existing record will be updated.
+            - If no such record exists, a new record will be inserted.
+
+        Raises:
+            Any exceptions raised by the `_execute` method during the execution of the SQL statement.
+        """
+        data = {
+            self.TableKeys.RUN_ID.value: self.run_id,
+            self.TableKeys.NAME.value: name,
+            self.TableKeys.VALUE.value: value,
+        }
+        statement = (
+            sqlite_insert(table)
+            .values(data)
+            .on_conflict_do_update(
+                index_elements=[
+                    self.TableKeys.RUN_ID.value,
+                    self.TableKeys.NAME.value,
+                ],
+                set_={self.TableKeys.VALUE.value: value},
+            )
+        )
+        self._execute(statement)
+
+    def _get(
+        self,
+        table: sql.Table,
+        run_id: int,
+        names: list[str] | None,
+        sql_mapping: Callable[[any], any],
+    ) -> dict:
+        """
+        Retrieve data from a specified SQL table based on a run ID and optional list of names.
+
+        Args:
+            table (sql.Table): The SQLAlchemy Table object to query.
+            run_id (int): The run ID to filter the data.
+            names (list[str] | None): An optional list of names to filter the data. If None, no name filtering is applied.
+            sql_mapping (Callable[[any], any]): A callable to transform the SQL value into the desired format.
+
+        Returns:
+            dict: A dictionary where the keys are the names from the table and the values are the transformed values
+                  obtained by applying `sql_mapping` to the corresponding SQL values.
+
+        """
+        conditions = [table.c[self.TableKeys.RUN_ID.value] == run_id]
+        if names is not None:
+            conditions.append(table.c[self.TableKeys.NAME.value].in_(names))
+        statement = sql.select(table).where(*conditions)
+        rows = self._execute(statement).mappings().all()
+        return {
+            row[self.TableKeys.NAME.value]: sql_mapping(row[self.TableKeys.VALUE.value])
+            for row in rows
+        }
+
+    def _execute(self, statement) -> sql.CursorResult[any]:
+        """
+        Executes a given SQL statement using the database engine.
+
+        This method establishes a connection to the database, executes the provided
+        SQL statement, and returns the result.
+
+        Args:
+            statement: The SQL statement to be executed.
+
+        Returns:
+            sql.CursorResult[any]: The result of the executed SQL statement.
+        """
+        with self.engine.begin() as connection:
+            result = connection.execute(statement)
+            return result
+
+    def _to_bytes(self, data: float | np.ndarray) -> bytes | None:
+        """
+        Converts a float or a NumPy array into a bytes representation.
+
+        Parameters:
+            data (float | np.ndarray): The input data to be converted. It can be either
+                a float or a NumPy array.
+
+        Returns:
+            bytes | None: The bytes representation of the input data if it is a float
+                or a NumPy array. Returns None if the input data type is unsupported.
+        """
+        if isinstance(data, float):
+            return struct.pack("d", data)
+        elif isinstance(data, np.ndarray):
+            arr_bytes = io.BytesIO()
+            np.save(arr_bytes, data)
+            compressed_arr_bytes = blosc2.compress(arr_bytes.getvalue())
+            return compressed_arr_bytes
+        else:
+            return None
+
+    def _from_bytes(self, data: bytes) -> float | np.ndarray | None:
+        """
+        Converts a byte sequence into a float, a NumPy array, or None.
+
+        This method attempts to interpret the input byte sequence as either:
+        - A double-precision floating-point number if the length of the data is 8 bytes.
+        - A NumPy array if the data represents a serialized array.
+        - Returns None if the conversion fails.
+
+        Args:
+            data (bytes): The byte sequence to be converted.
+
+        Returns:
+            float | np.ndarray | None: The converted value as a float, a NumPy array,
+            or None if the conversion is unsuccessful.
+        """
+        try:
+            if len(data) == 8:
+                return struct.unpack("d", data)[0]
+            else:
+                decompressed_data = blosc2.decompress(data)
+                arr_bytes = io.BytesIO(decompressed_data)
+                return np.load(arr_bytes, allow_pickle=False)
+        except Exception:
+            return None
+
+    def _to_json(self, data: any) -> json:
+        """
+        Converts the given data to a JSON-formatted string.
+
+        Args:
+            data (any): The data to be converted to JSON.
+
+        Returns:
+            str: A JSON-formatted string representation of the data if conversion is successful.
+            None: If an error occurs during the conversion process.
+        """
+        try:
+            return json.dumps(data)
+        except:
+            return None
+
+    def _from_json(self, data: json) -> any:
+        """
+        Converts a JSON-formatted string into a Python object.
+
+        Args:
+            data (json): A JSON-formatted string to be deserialized.
+
+        Returns:
+            any: The deserialized Python object if the input is valid JSON.
+                 Returns None if deserialization fails.
+        """
+        try:
+            return json.loads(data)
+        except:
+            return None

qupled/esa.py

@@ -0,0 +1,27 @@
+from __future__ import annotations
+
+from . import hf
+from . import native
+
+
+class ESA(hf.HF):
+    """
+    Class used to solve the ESA scheme.
+    """
+
+    def __init__(self):
+        super().__init__()
+        self.results: hf.Result = hf.Result()
+        # Undocumented properties
+        self.native_scheme_cls = native.ESA
+
+
+class Input(hf.Input):
+    """
+    Class used to manage the input for the :obj:`qupled.esa.ESA` class.
+    """
+
+    def __init__(self, coupling: float, degeneracy: float):
+        super().__init__(coupling, degeneracy)
+        # Undocumented default values
+        self.theory = "ESA"