diff --git a/cyclops/evaluate/metrics/utils.py b/cyclops/evaluate/metrics/utils.py index 3c4bbc8f6..2a39a7dc4 100644 --- a/cyclops/evaluate/metrics/utils.py +++ b/cyclops/evaluate/metrics/utils.py @@ -135,7 +135,7 @@ def common_input_checks_and_format( def sigmoid(arr: npt.ArrayLike) -> npt.NDArray[np.float_]: """Sigmoid function.""" arr = np.asanyarray(arr) - return 1 / (1 + np.exp(-arr)) + return 1 / (1 + np.exp(-arr)) # type: ignore def check_topk(top_k: int, type_preds: str, type_target: str, n_classes: int) -> None: diff --git a/cyclops/query/interface.py b/cyclops/query/interface.py index c1dddfb04..07e9b508a 100644 --- a/cyclops/query/interface.py +++ b/cyclops/query/interface.py @@ -25,7 +25,7 @@ class QueryInterface: Parameters ---------- - database: cyclops.orm.Database + database Database object to create ORM, and query data. query: cyclops.query.util.TableTypes The query. diff --git a/cyclops/query/ops.py b/cyclops/query/ops.py index 672212ff9..c643e799c 100644 --- a/cyclops/query/ops.py +++ b/cyclops/query/ops.py @@ -1,17 +1,20 @@ -"""Low-level query operations. +"""Query operations. -This module contains query operation modules such which can be used in high-level query -API functions specific to datasets. +This module contains query operations. You can use query operations instead of SQL +code to filter rows using conditions, join tables, etc. """ from __future__ import annotations import logging +import operator import typing -from abc import ABC, abstractmethod +from abc import abstractmethod +from collections import OrderedDict from dataclasses import dataclass, field from datetime import datetime, timedelta +from itertools import islice import sqlalchemy from sqlalchemy import and_, cast, extract, func, literal_column, or_, select @@ -63,19 +66,20 @@ class JoinArgs: Parameters ---------- - join_table: cyclops.query.util.TableTypes + join_table Table to join. - on: list of str or tuple, optional - on_to_type: list of type, optional + on + Column(s) to join on. + on_to_type A list of types to which to convert the on columns before joining. Useful when two columns have the same values but in different format, e.g., strings of int. - cond: BinaryExpression, optional + cond Condition on which to join to tables. - table_cols: str or list of str, optional + table_cols Filters to keep only these columns from the table. - join_table_cols: + join_table_cols Filters to keep only these columns from the join_table. - isouter: + isouter Flag to say if the join is a left outer join. """ @@ -103,48 +107,402 @@ def __post_init__(self) -> None: self.join_table_cols = to_list_optional(self.join_table_cols) -class QueryOp(ABC): - """Base type for query operations.""" +def _addindent(s_: str, num_spaces: int = 4) -> str: + """Add spaces to a string. + + Parameters + ---------- + s_ + String to add spaces to. + num_spaces + Number of spaces to add. + + Returns + ------- + str + String with spaces added. + + """ + s = s_.split("\n") + if len(s) == 1: + return s_ + first = s.pop(0) + s = [(num_spaces * " ") + line for line in s] + s = "\n".join(s) # type: ignore + + return first + "\n" + s # type: ignore + + +class QueryOp: + """Base class for query operations.""" + + _ops: typing.Dict[str, "QueryOp"] + + def __init__(self, *args: typing.Any, **kwargs: typing.Any) -> None: + """Initialize the object.""" + super().__setattr__("_ops", OrderedDict()) @abstractmethod def __call__(self, *args: typing.Any, **kwargs: typing.Any) -> Subquery: """Implement a calling function.""" pass + def add_op(self, name: str, op_: "QueryOp") -> None: + """Add a child operation to the current query operation. + + The query op can be accessed as an attribute using the given name. + + Parameters + ---------- + name + Name of the child op. The child op can be accessed from this op using + the given name + op_ + Child op to be added to the parent query op. + + """ + if not isinstance(op_, QueryOp) and op_ is not None: + raise TypeError("{} is not a QueryOp subclass".format(str(op_))) + if not isinstance(name, str): + raise TypeError("Query op name should be a string") + if hasattr(self, name) and name not in self._ops: + raise KeyError("Attribute '{}' already exists".format(name)) + if "." in name: + raise KeyError('Query op name can\'t contain ".", got: {}'.format(name)) + if name == "": + raise KeyError('Query op name can\'t be empty string ""') + self._ops[name] = op_ + + def ops(self) -> typing.Iterator["QueryOp"]: + """Return an iterator over the child operations. + + Returns + ------- + typing.Iterator[QueryOp] + Iterator over the child operations. + + """ + for _, op_ in self._ops.items(): + yield op_ + + def _get_name(self) -> str: + """Get the name of the query op. + + Returns + ------- + str + Name of the query op. + + """ + return self.__class__.__name__ + + def __setattr__(self, name: str, value: "QueryOp") -> None: + """Set an attribute. -class Sequential: + Parameters + ---------- + name + Name of the attribute. + value + Value of the attribute. + + """ + ops = self.__dict__.get("_ops") + if isinstance(value, QueryOp): + if ops is None: + raise AttributeError("Can't assign op before QueryOp.__init__() call") + ops[name] = value + elif ops is not None and name in ops: + if value is not None: + raise TypeError( + "Cannot assign '{}' as child op '{}' " "(QueryOp or None expected)", + ) + ops[name] = value + else: + super().__setattr__(name, value) + + def extra_repr(self) -> str: + """Set the extra representation of the query op. + + To print customized extra information, you should re-implement + this method in your own query ops. Both single-line and multi-line + strings are acceptable. + + Returns + ------- + str + Extra representation of the query op. + + """ + return "" + + def __repr__(self) -> str: + """Return the string representation of the query op. + + Returns + ------- + str + String representation of the query op. + + """ + extra_lines = [] + extra_repr = self.extra_repr() + if extra_repr: + extra_lines = extra_repr.split("\n") + child_lines = [] + for key, op_ in self._ops.items(): + mod_str = repr(op_) + mod_str = _addindent(mod_str, 2) + child_lines.append("(" + key + "): " + mod_str) + lines = extra_lines + child_lines + main_str = self._get_name() + "(" + if lines: + if len(extra_lines) == 1 and not child_lines: + main_str += extra_lines[0] + else: + main_str += "\n " + "\n ".join(lines) + "\n" + main_str += ")" + + return main_str + + +def _chain_ops( + query: Subquery, + ops: typing.Iterator[QueryOp], +) -> Subquery: + """Chain query ops. + + Parameters + ---------- + query + Query to chain the ops to. + ops + Query ops to chain. + + Returns + ------- + Subquery + Query with the ops chained. + + """ + for op_ in ops: + if isinstance(op_, Sequential): + query = _chain_ops(query, op_.ops()) + elif isinstance(op_, QueryOp): + query = op_(query) + + return query + + +class Sequential(QueryOp): """Sequential query operations class. - Chains a list of sequential query operations and executes the final query on a - table. + Chains a sequence of query operations and executes the final query on a table. """ - def __init__(self, *ops: typing.Sequence[typing.Any]) -> None: - """Initialize the Sequential class. + @typing.overload + def __init__(self, *ops: QueryOp) -> None: + ... + + @typing.overload + def __init__(self, ops: typing.List[QueryOp]) -> None: + ... + + @typing.overload + def __init__(self, op: OrderedDict[str, QueryOp]) -> None: + ... + + def __init__(self, *args: QueryOp) -> None: # type: ignore + """Initialize the class. Parameters ---------- - ops: tuple of QueryOp or Sequential or list of QueryOp - Query operations to be chained. + args + Query operations to be chained sequentially. """ - self.ops = ops + super().__init__() + if len(args) == 1 and isinstance(args[0], OrderedDict): + for key, op_ in args[0].items(): + self.add_op(key, op_) + elif len(args) == 1 and isinstance(args[0], list): + for idx, op_ in enumerate(args[0]): + self.add_op(str(idx), op_) + else: + for idx, op_ in enumerate(args): + self.add_op(str(idx), op_) + + def __len__(self) -> int: + """Return the number of query ops in the Sequential. + + Returns + ------- + int + Number of query ops in the Sequential. + + """ + return len(self._ops) + + def __iter__(self) -> typing.Iterator[QueryOp]: + """Return an iterator over the query ops. + + Returns + ------- + typing.Iterator[QueryOp] + Iterator over the query ops. - def _chain_ops( + """ + return iter(self._ops.values()) + + def __add__(self, other: "Sequential") -> "Sequential": + """Add two Sequential objects. + + Parameters + ---------- + other + Sequential object to be added. + + Returns + ------- + Sequential + Sequential object with the two Sequential objects chained. + + """ + if isinstance(other, Sequential): + ret = Sequential() + for op_ in self: + ret.append(op_) + for op_ in other: + ret.append(op_) + return ret + raise ValueError( + "Add operator supports only objects " + "of Sequential class, but {} is given.".format(str(type(other))), + ) + + def __iadd__(self, other: "Sequential") -> "Sequential": + """Add two Sequential objects inplace. + + Parameters + ---------- + other + Sequential object to be added. + + Returns + ------- + Sequential + Sequential object with the two Sequential objects chained. + + """ + if isinstance(other, Sequential): + offset = len(self) + for i, op_ in enumerate(other): + self.add_op(str(i + offset), op_) + return self + raise ValueError( + "Add operator supports only objects " + "of Sequential class, but {} is given.".format(str(type(other))), + ) + + def _get_item_by_idx( self, - query: Subquery, - ops: typing.Sequence[typing.Any], - ) -> Subquery: - for op_ in ops: - if isinstance(op_, Sequential): - query = self._chain_ops(query, op_.ops) - if isinstance(op_, list): - query = self._chain_ops(query, op_) - if isinstance(op_, QueryOp): - query = op_(query) - - return query + iterator: typing.Iterator[typing.Any], + idx: int, + ) -> typing.Any: + """Get the idx-th item of the iterator. + + Parameters + ---------- + iterator + Iterator to get the item from. + idx + Index of the item to get. + + Returns + ------- + QueryOp + The idx-th item of the iterator. + + """ + size = len(self) + idx = operator.index(idx) + if not -size <= idx < size: + raise IndexError("index {} is out of range".format(idx)) + idx %= size + + return next(islice(iterator, idx, None)) + + def __getitem__( + self, + idx: typing.Union[slice, int], + ) -> typing.Any: + """Get the idx-th item of the sequential query op. + + Parameters + ---------- + idx + Index of the item to get. + + Returns + ------- + Sequential or QueryOp + The idx-th item of the sequential query op. + + """ + if isinstance(idx, slice): + return self.__class__(OrderedDict(list(self._ops.items())[idx])) + + return self._get_item_by_idx(self._ops.values(), idx) # type: ignore + + def __setitem__(self, idx: int, op_: QueryOp) -> None: + """Set the idx-th item of the sequential query op. + + Parameters + ---------- + idx + Index of the item to set. + op_ + Query op to set. + + """ + key: str = self._get_item_by_idx(self._ops.keys(), idx) # type: ignore + return setattr(self, key, op_) + + def __delitem__(self, idx: typing.Union[slice, int]) -> None: + """Delete the idx-th item of the sequential query op. + + Parameters + ---------- + idx + Index of the item to delete. + + """ + if isinstance(idx, slice): + for key in list(self._ops.keys())[idx]: + delattr(self, key) + else: + key = self._get_item_by_idx(self._ops.keys(), idx) # type: ignore + delattr(self, key) + str_indices = [str(i) for i in range(len(self._ops))] + self._ops = OrderedDict(list(zip(str_indices, self._ops.values()))) + + def append(self, op_: QueryOp) -> "Sequential": + """Append a given query op to the end. + + Parameters + ---------- + op_ + Query op to append. + + Returns + ------- + Sequential + Sequential object with the query op appended. + + """ + self.add_op(str(len(self)), op_) + return self @table_params_to_type(Subquery) def __call__(self, table: TableTypes) -> Subquery: @@ -152,7 +510,7 @@ def __call__(self, table: TableTypes) -> Subquery: Parameters ---------- - table: TableTypes + table Table to be queried. Returns @@ -161,7 +519,7 @@ def __call__(self, table: TableTypes) -> Subquery: Query result after chaining the query operations. """ - return self._chain_ops(table, self.ops) + return _chain_ops(table, self.ops()) def _append_if_missing( @@ -173,11 +531,11 @@ def _append_if_missing( Parameters ---------- - table : cyclops.query.util.TableTypes + table Table on which to perform the operation. - keep_cols: str or list of str, optional + keep_cols Columns to keep. - force_include_cols: str or list of str, optional + force_include_cols Columns to include (forcefully). """ @@ -198,8 +556,15 @@ def _none_add(obj1: typing.Any, obj2: typing.Any) -> typing.Any: Parameters ---------- - obj1: typing.Any - obj2: typing.Any + obj1 + First object to add. + obj2 + Second object to add. + + Returns + ------- + typing.Any + Result of adding the two objects. """ if obj1 is None: @@ -219,11 +584,11 @@ def _process_checks( Parameters ---------- - table : cyclops.query.util.TableTypes + table Table on which to perform the operation. - cols: str or list of str, optional + cols Columns to check. - timestamp_cols: str or list of str, optional + timestamp_cols Timestamp columns to check. Returns @@ -247,17 +612,16 @@ def _process_checks( return table -@dataclass class FillNull(QueryOp): """Fill NULL values with a given value. Parameters ---------- - cols: str or list of str + cols Columns to fill. - fill_values: typing.Any or list of typing.Any + fill_values Value(s) to fill with. - new_col_names: str or list of str, optional + new_col_names New column name(s) for the filled columns. If not provided, Examples @@ -268,9 +632,16 @@ class FillNull(QueryOp): """ - cols: typing.Union[str, typing.List[str]] - fill_values: typing.Union[typing.Any, typing.List[typing.Any]] - new_col_names: typing.Optional[typing.Union[str, typing.List[str]]] = None + def __init__( + self, + cols: typing.Union[str, typing.List[str]], + fill_values: typing.Union[typing.Any, typing.List[typing.Any]], + new_col_names: typing.Optional[typing.Union[str, typing.List[str]]] = None, + ) -> None: + super().__init__() + self.cols = cols + self.fill_values = fill_values + self.new_col_names = new_col_names def __call__(self, table: TableTypes) -> Subquery: """Fill NULL values with a given value. @@ -313,7 +684,6 @@ def __call__(self, table: TableTypes) -> Subquery: return table -@dataclass class Drop(QueryOp): """Drop some columns. @@ -329,7 +699,9 @@ class Drop(QueryOp): """ - cols: typing.Union[str, typing.List[str]] + def __init__(self, cols: typing.Union[str, typing.List[str]]) -> None: + super().__init__() + self.cols = cols def __call__(self, table: TableTypes) -> Subquery: """Process the table. @@ -402,7 +774,9 @@ class Substring(QueryOp): to be extracted. start_index: int Start index of substring. - stop_index: str + stop_index: int + Stop index of substring. + new_col_name: str, optional Name of the new column with extracted substring. Examples @@ -414,7 +788,7 @@ class Substring(QueryOp): col: str start_index: int stop_index: int - new_col_label: str + new_col_label: typing.Optional[str] = None def __call__(self, table: TableTypes) -> Subquery: """Process the table. @@ -431,15 +805,18 @@ def __call__(self, table: TableTypes) -> Subquery: Processed table. """ - table = _process_checks(table, cols=self.col) - return select( + table = _process_checks(table, cols=self.col, cols_not_in=self.new_col_label) + + return apply_to_columns( table, - func.substr( - get_column(table, self.col), + self.col, + lambda x: func.substr( + process_column(x, to_str=True), self.start_index, self.stop_index, - ).label(self.new_col_label), - ).subquery() + ), + new_col_labels=self.new_col_label, + ) @dataclass @@ -907,8 +1284,6 @@ class AddDeltaColumn(QueryOp): ---------- add_to: str or list of str Column names specifying to which columns is being added. - add: Column - Column object of type interval. negative: bool, optional Subtract the object rather than adding. new_col_labels: str or list of str, optional @@ -934,6 +1309,7 @@ def __init__( **delta_kwargs: typing.Any, ) -> None: """Initialize.""" + super().__init__() self.add_to = add_to self.negative = negative self.new_col_labels = new_col_labels @@ -1142,6 +1518,7 @@ def __init__( isouter: typing.Optional[bool] = False, ) -> None: """Initialize.""" + super().__init__() if on is not None and cond is not None: raise ValueError("Cannot specify both the 'on' and 'cond' arguments.") @@ -1268,6 +1645,7 @@ def __init__( **cond_kwargs: typing.Any, ) -> None: """Initialize.""" + super().__init__() self.col = col self.value = value self.not_ = not_ @@ -1350,6 +1728,7 @@ def __init__( **cond_kwargs: typing.Any, ) -> None: """Initialize.""" + super().__init__() self.col = col self.value = value self.equal = equal @@ -1434,6 +1813,7 @@ def __init__( **cond_kwargs: typing.Any, ) -> None: """Initialize.""" + super().__init__() self.col = col self.value = value self.equal = equal @@ -1577,6 +1957,7 @@ def __init__( **cond_kwargs: typing.Any, ) -> None: """Initialize.""" + super().__init__() self.col = col self.values = values self.not_ = not_ @@ -1664,6 +2045,7 @@ def __init__( **cond_kwargs: typing.Any, ) -> None: """Initialize.""" + super().__init__() self.col = col self.substrings = to_list(substrings) self.any_ = any_ @@ -1740,6 +2122,7 @@ def __init__( **cond_kwargs: typing.Any, ) -> None: """Initialize.""" + super().__init__() self.col = col self.string = string self.not_ = not_ @@ -1819,6 +2202,7 @@ def __init__( **cond_kwargs: typing.Any, ) -> None: """Initialize.""" + super().__init__() self.col = col self.string = string self.not_ = not_ @@ -2209,8 +2593,8 @@ class Or(QueryOp): Parameters ---------- - ops: QueryOp or List[QueryOp] - Query ops to combine. + cond_ops: QueryOp or List[QueryOp] + Condition Query ops to combine. Examples -------- @@ -2218,7 +2602,7 @@ class Or(QueryOp): """ - ops: typing.Union[QueryOp, typing.List[QueryOp]] + cond_ops: typing.Union[QueryOp, typing.List[QueryOp]] def __call__(self, table: TableTypes, return_cond: bool = False) -> Subquery: """Process the table. @@ -2236,9 +2620,9 @@ def __call__(self, table: TableTypes, return_cond: bool = False) -> Subquery: Processed table. """ - if isinstance(self.ops, QueryOp): - return self.ops(table, return_cond=return_cond) - cond = or_(*[op(table, return_cond=True) for op in self.ops]) + if isinstance(self.cond_ops, QueryOp): + return self.cond_ops(table, return_cond=return_cond) + cond = or_(*[op(table, return_cond=True) for op in self.cond_ops]) if return_cond: return cond @@ -2260,7 +2644,7 @@ class And(QueryOp): """ - ops: typing.Union[QueryOp, typing.List[QueryOp]] + cond_ops: typing.Union[QueryOp, typing.List[QueryOp]] def __call__(self, table: TableTypes, return_cond: bool = False) -> Subquery: """Process the table. @@ -2278,9 +2662,9 @@ def __call__(self, table: TableTypes, return_cond: bool = False) -> Subquery: Processed table. """ - if isinstance(self.ops, QueryOp): - return self.ops(table, return_cond=return_cond) - cond = and_(*[op(table, return_cond=True) for op in self.ops]) + if isinstance(self.cond_ops, QueryOp): + return self.cond_ops(table, return_cond=return_cond) + cond = and_(*[op(table, return_cond=True) for op in self.cond_ops]) if return_cond: return cond diff --git a/cyclops/query/util.py b/cyclops/query/util.py index ef7bd1304..3d646a17f 100644 --- a/cyclops/query/util.py +++ b/cyclops/query/util.py @@ -1,7 +1,5 @@ """Utility functions for querying.""" -# mypy: ignore-errors - import logging from dataclasses import dataclass from functools import wraps @@ -67,49 +65,7 @@ class DBTable: TABLE_OBJECTS = [Table, Select, Subquery, DBTable] TableTypes = Union[Select, Subquery, Table, DBTable] - - -def ckwarg(kwargs: dict, kwarg: str): - """Get the value of a conditional keyword argument. - - A keyword argument may or may not be specified in some - keyword arguments. If specified, return the value, - otherwise return None. - - Parameters - ---------- - kwargs: dict - Process keyword arguments. - kwarg: str - The keyword argument of interest. - - Returns - ------- - any, optional - The value of the keyword argument if it exists, otherwise None. - - """ - if kwarg in kwargs: - return kwargs[kwarg] - return None - - -def remove_kwargs(process_kwargs: dict, kwargs: Union[str, List[str]]): - """Remove some keyword arguments from process_kwargs if they exist. - - Parameters - ---------- - process_kwargs: dict - Process keyword arguments. - kwargs: str or list of str - The keyword arguments to remove should they exist. - - """ - kwargs = to_list(kwargs) - for kwarg in kwargs: - if kwarg in process_kwargs: - del process_kwargs[kwarg] - return process_kwargs +CastableTypes = Union[Date, DateTime, Float, Integer, Interval, String] def _to_subquery(table: TableTypes) -> Subquery: @@ -176,7 +132,10 @@ def _to_select(table: TableTypes) -> Select: ) -def param_types_to_type(relevant_types: List[Any], to_type_fn: Callable) -> Callable: +def param_types_to_type( + relevant_types: List[Any], + to_type_fn: Callable[..., Any], +) -> Callable[..., Any]: """Convert TableTypes parameters to a specified type. A decorator which processes a function's arguments by taking all @@ -197,16 +156,16 @@ def param_types_to_type(relevant_types: List[Any], to_type_fn: Callable) -> Call """ - def decorator(func_: Callable) -> Callable: + def decorator(func_: Callable[..., Any]) -> Callable[..., Any]: """Decorate function to convert TableTypes parameters to a specified type.""" @wraps(func_) - def wrapper_func(*args, **kwargs) -> Callable: + def wrapper_func(*args: Any, **kwargs: Any) -> Any: # Convert relevant arguments. - args = list(args) - for i, arg in enumerate(args): + args_list = list(args) + for i, arg in enumerate(args_list): if type(arg) in relevant_types: - args[i] = to_type_fn(arg) + args_list[i] = to_type_fn(arg) # Convert relevant keyword arguments. kwargs = dict(kwargs) @@ -214,14 +173,14 @@ def wrapper_func(*args, **kwargs) -> Callable: if type(kwarg) in relevant_types: kwargs[key] = to_type_fn(kwarg) - return func_(*tuple(args), **kwargs) + return func_(*tuple(args_list), **kwargs) return wrapper_func return decorator -def table_params_to_type(to_type: TableTypes) -> Callable: +def table_params_to_type(to_type: TableTypes) -> Callable[..., Any]: """Decorate to convert TableTypes params to a specified type. Parameters @@ -254,7 +213,7 @@ def table_params_to_type(to_type: TableTypes) -> Callable: def get_column( table: TableTypes, col: str, -): +) -> Column: """Extract a column object from a table by name. Parameters @@ -274,7 +233,7 @@ def get_column( if col not in col_names: raise ValueError(f"Table does not contain column {col}") - return table.c[col_names.index(col)] + return table.c[col_names.index(col)] # type: ignore @table_params_to_type(Subquery) @@ -303,7 +262,7 @@ def filter_columns( for col in cols: if col not in col_names: continue - filtered.append(table.c[col_names.index(col)]) + filtered.append(table.c[col_names.index(col)]) # type: ignore return select(filtered).subquery() @@ -312,7 +271,7 @@ def filter_columns( def get_columns( table: TableTypes, cols: Union[str, List[str]], -): +) -> List[Column]: """Extract a number of columns from the table. Parameters @@ -332,7 +291,7 @@ def get_columns( @table_params_to_type(Subquery) -def get_column_names(table: TableTypes): +def get_column_names(table: TableTypes) -> List[str]: """Extract column names from a table. Parameters @@ -346,7 +305,7 @@ def get_column_names(table: TableTypes): The table column names. """ - return [c.name for c in table.columns] + return [c.name for c in table.columns] # type: ignore @table_params_to_type(Subquery) @@ -354,7 +313,7 @@ def has_columns( table: TableTypes, cols: Union[str, List[str]], raise_error: bool = False, -): +) -> bool: """Check whether a table has all of the specified columns. Parameters @@ -385,7 +344,10 @@ def has_columns( @table_params_to_type(Subquery) -def assert_table_has_columns(*args, **kwargs) -> Callable: +def assert_table_has_columns( + *args: Any, + **kwargs: Any, +) -> Callable[[TableTypes], TableTypes]: """Assert that TableTypes params have the necessary columns. assert_table_has_columns(["A", "B"], None) is equivalent to @@ -409,9 +371,11 @@ def assert_table_has_columns(*args, **kwargs) -> Callable: """ - def decorator(func_: Callable) -> Callable: + def decorator( + func_: Callable[..., Any], + ) -> Callable[..., Any]: @wraps(func_) - def wrapper_func(*fn_args, **fn_kwargs) -> Callable: + def wrapper_func(*fn_args: Any, **fn_kwargs: Any) -> Any: # Check only the table arguments table_args = [i for i in fn_args if isinstance(i, Subquery)] @@ -438,7 +402,7 @@ def wrapper_func(*fn_args, **fn_kwargs) -> Callable: return wrapper_func - return decorator + return decorator # type: ignore @table_params_to_type(Subquery) @@ -465,11 +429,11 @@ def drop_columns( """ drop_cols = get_columns(table, drop_cols) - return select(*[c for c in table.c if c not in drop_cols]).subquery() + return select(*[c for c in table.c if c not in drop_cols]).subquery() # type: ignore @table_params_to_type(Subquery) -def rename_columns(table: TableTypes, rename_map: dict) -> Subquery: +def rename_columns(table: TableTypes, rename_map: Dict[str, str]) -> Subquery: """Rename a table's columns. Rename the table's columns according to a dictionary of strings, @@ -491,7 +455,7 @@ def rename_columns(table: TableTypes, rename_map: dict) -> Subquery: return select( *[ c.label(rename_map[c.name]) if c.name in rename_map else c - for c in table.columns + for c in table.columns # type: ignore ], ).subquery() @@ -529,7 +493,7 @@ def reorder_columns(table: TableTypes, cols: List[str]) -> Subquery: # Reorder the columns. new_cols = [] for col in new_order: - new_cols.append(table.c[old_order.index(col)]) + new_cols.append(table.c[old_order.index(col)]) # type: ignore return select(*new_cols).subquery() @@ -540,7 +504,7 @@ def apply_to_columns( col_names: Union[str, List[str]], funcs: Union[ Callable[[sqlalchemy.sql.schema.Column], sqlalchemy.sql.schema.Column], - List[Callable], + List[Callable[[sqlalchemy.sql.schema.Column], sqlalchemy.sql.schema.Column]], ], new_col_labels: Optional[Union[str, List[str]]] = None, ) -> Subquery: @@ -768,7 +732,7 @@ def equals( value: Any, lower: bool = True, trim: bool = True, - **kwargs: Dict[str, bool], + **kwargs: bool, ) -> BinaryExpression: """Condition that a column has some value. @@ -810,7 +774,7 @@ def greater_than( lower: bool = True, trim: bool = True, equal: bool = False, - **kwargs: Dict[str, bool], + **kwargs: bool, ) -> BinaryExpression: """Condition that a column is greater than some value. @@ -861,7 +825,7 @@ def less_than( lower: bool = True, trim: bool = True, equal: bool = False, - **kwargs: Dict[str, bool], + **kwargs: bool, ) -> BinaryExpression: """Condition that a column is less than some value. @@ -987,7 +951,7 @@ def has_substring( col: Column, substring: Any, lower: bool = True, - **kwargs: Dict[str, bool], + **kwargs: bool, ) -> BinaryExpression: """Condition that a column has some substring. @@ -1020,7 +984,7 @@ def starts_with( value: Any, lower: bool = True, trim: bool = True, - **kwargs: Dict[str, bool], + **kwargs: bool, ) -> BinaryExpression: """Condition that a column starts with some value/string. @@ -1057,7 +1021,7 @@ def ends_with( value: Any, lower: bool = True, trim: bool = True, - **kwargs: Dict[str, bool], + **kwargs: bool, ) -> BinaryExpression: """Condition that a column ends with some value/string. @@ -1094,7 +1058,7 @@ def in_( lst: List[Any], lower: bool = True, trim: bool = True, - **kwargs: Dict[str, bool], + **kwargs: bool, ) -> BinaryExpression: """Condition that a column value is in a list of values. @@ -1131,8 +1095,8 @@ def _check_column_type( table: TableTypes, cols: Union[str, List[str]], types: Union[Any, List[Any]], - raise_error=False, -): + raise_error: bool = False, +) -> bool: """Check whether some columns are each one of a number of types. Parameters @@ -1175,8 +1139,8 @@ def _check_column_type( def check_timestamp_columns( table: TableTypes, cols: Union[str, List[str]], - raise_error=False, -): + raise_error: bool = False, +) -> bool: """Check whether some columns are Date or DateTime columns. Parameters @@ -1232,7 +1196,7 @@ def get_delta_column( """ - def get_col_or_none(col): + def get_col_or_none(col: Optional[str] = None) -> Optional[Column]: """If col is not None, get interval column from names.""" return None if col is None else get_column(table, col) diff --git a/cyclops/report/report.py b/cyclops/report/report.py index 25b54ead1..c0b8d1576 100644 --- a/cyclops/report/report.py +++ b/cyclops/report/report.py @@ -182,8 +182,7 @@ def log_descriptor( KeyError If the given section name is not valid. ValueError - If the given name conflicts with a defined class in the `model_card` - module. + If the given name conflicts with a defined class in the `model_card` module. Examples -------- diff --git a/docs/source/conf.py b/docs/source/conf.py index 534be55a1..5ca5984ce 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -58,6 +58,7 @@ autosectionlabel_prefix_document = True copybutton_prompt_text = r">>> |\.\.\. " copybutton_prompt_is_regexp = True +nbsphinx_execute = "never" intersphinx_mapping = { "python": ("https://docs.python.org/3.9/", None), diff --git a/docs/source/tutorials/eicu/query_api.ipynb b/docs/source/tutorials/eicu/query_api.ipynb index b9a2bb39e..a51ff85eb 100644 --- a/docs/source/tutorials/eicu/query_api.ipynb +++ b/docs/source/tutorials/eicu/query_api.ipynb @@ -74,10 +74,8 @@ "outputs": [], "source": [ "ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"hospitaldischargeyear\", 2014),\n", - " qo.ConditionEquals(\"gender\", \"Female\"),\n", - " ],\n", + " qo.ConditionEquals(\"hospitaldischargeyear\", 2014),\n", + " qo.ConditionEquals(\"gender\", \"Female\"),\n", ")\n", "patients = querier.eicu_crd.patient(ops=ops).run(limit=100)\n", "print(f\"{len(patients)} rows extracted!\")" @@ -102,17 +100,9 @@ }, "outputs": [], "source": [ - "ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"hospitaldischargeyear\", 2015),\n", - " ],\n", - ")\n", + "ops = qo.ConditionEquals(\"hospitaldischargeyear\", 2015)\n", "patients = querier.eicu_crd.patient(ops=ops)\n", - "diagnosis_ops = qo.Sequential(\n", - " [\n", - " qo.ConditionSubstring(\"diagnosisstring\", \"schizophrenia\"),\n", - " ],\n", - ")\n", + "diagnosis_ops = qo.ConditionSubstring(\"diagnosisstring\", \"schizophrenia\")\n", "diagnoses = querier.eicu_crd.diagnosis(\n", " join=qo.JoinArgs(\n", " join_table=patients.query,\n", @@ -142,19 +132,13 @@ "source": [ "hospitals = querier.eicu_crd.hospital()\n", "ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"hospitaldischargeyear\", 2015),\n", - " qo.ConditionEquals(\"teachingstatus\", True),\n", - " ],\n", + " qo.ConditionEquals(\"hospitaldischargeyear\", 2015),\n", + " qo.ConditionEquals(\"teachingstatus\", True),\n", ")\n", "patients = querier.eicu_crd.patient(\n", " join=qo.JoinArgs(join_table=hospitals.query, on=\"hospitalid\"), ops=ops,\n", ")\n", - "lab_ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"labname\", \"potassium\"),\n", - " ],\n", - ")\n", + "lab_ops = qo.ConditionEquals(\"labname\", \"potassium\")\n", "labs = querier.eicu_crd.lab(\n", " join=qo.JoinArgs(\n", " join_table=patients.query,\n", @@ -183,17 +167,11 @@ "outputs": [], "source": [ "ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"hospitaldischargeyear\", 2014),\n", - " qo.ConditionEquals(\"gender\", \"Female\"),\n", - " ],\n", + " qo.ConditionEquals(\"hospitaldischargeyear\", 2014),\n", + " qo.ConditionEquals(\"gender\", \"Female\"),\n", ")\n", "patients = querier.eicu_crd.patient(ops=ops)\n", - "medications_ops = qo.Sequential(\n", - " [\n", - " qo.ConditionSubstring(\"drugname\", \"glucose\"),\n", - " ],\n", - ")\n", + "medications_ops = qo.ConditionSubstring(\"drugname\", \"glucose\")\n", "medications = querier.eicu_crd.medication(\n", " join=qo.JoinArgs(join_table=patients.query, on=\"patientunitstayid\"),\n", " ops=medications_ops,\n", diff --git a/docs/source/tutorials/gemini/query_api.ipynb b/docs/source/tutorials/gemini/query_api.ipynb index e0790d849..d09e41064 100644 --- a/docs/source/tutorials/gemini/query_api.ipynb +++ b/docs/source/tutorials/gemini/query_api.ipynb @@ -112,12 +112,10 @@ ], "source": [ "ops = qo.Sequential(\n", - " [\n", - " qo.OrderBy(\n", - " [\"patient_id_hashed\", \"discharge_date_time\"], ascending=[True, False],\n", - " ),\n", - " qo.Distinct(\"patient_id_hashed\"),\n", - " ],\n", + " qo.OrderBy(\n", + " [\"patient_id_hashed\", \"discharge_date_time\"], ascending=[True, False],\n", + " ),\n", + " qo.Distinct(\"patient_id_hashed\"),\n", ")\n", "encounters_qi = querier.public.ip_administrative(ops=ops)\n", "encounters = encounters_qi.run()\n", @@ -156,10 +154,8 @@ ], "source": [ "ops = qo.Sequential(\n", - " [\n", - " qo.ConditionAfterDate(\"discharge_date_time\", \"2015-04-01\"),\n", - " qo.ConditionBeforeDate(\"discharge_date_time\", \"2016-03-31\"),\n", - " ],\n", + " qo.ConditionAfterDate(\"discharge_date_time\", \"2015-04-01\"),\n", + " qo.ConditionBeforeDate(\"discharge_date_time\", \"2016-03-31\"),\n", ")\n", "encounters_qi = querier.get_interface(encounters_qi.query, ops=ops)\n", "encounters = encounters_qi.run()\n", @@ -281,12 +277,10 @@ "encounter_ops = qo.ConditionEquals(\"hospital_id\", \"SMH\")\n", "encounters_qi = querier.public.ip_administrative(ops=encounter_ops)\n", "lab_ops = qo.Sequential(\n", - " [\n", - " qo.ConditionAfterDate(\"sample_collection_date_time\", \"2015-04-01\"),\n", - " qo.ConditionBeforeDate(\"sample_collection_date_time\", \"2015-05-31\"),\n", - " qo.ConditionSubstring(\"lab_test_name_mapped\", \"sodium\"),\n", - " qo.GroupByAggregate(\"hospital_id\", {\"hospital_id\": (\"count\", \"count\")}),\n", - " ],\n", + " qo.ConditionAfterDate(\"sample_collection_date_time\", \"2015-04-01\"),\n", + " qo.ConditionBeforeDate(\"sample_collection_date_time\", \"2015-05-31\"),\n", + " qo.ConditionSubstring(\"lab_test_name_mapped\", \"sodium\"),\n", + " qo.GroupByAggregate(\"hospital_id\", {\"hospital_id\": (\"count\", \"count\")}),\n", ")\n", "lab_qi = querier.public.lab(\n", " ops=lab_ops, join=qo.JoinArgs(join_table=encounters_qi.query, on=\"genc_id\"),\n", diff --git a/docs/source/tutorials/mimiciii/query_api.ipynb b/docs/source/tutorials/mimiciii/query_api.ipynb index 56b97f04c..eba11d290 100644 --- a/docs/source/tutorials/mimiciii/query_api.ipynb +++ b/docs/source/tutorials/mimiciii/query_api.ipynb @@ -74,10 +74,8 @@ "outputs": [], "source": [ "ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"expire_flag\", 1),\n", - " qo.ConditionEquals(\"gender\", \"M\"),\n", - " ],\n", + " qo.ConditionEquals(\"expire_flag\", 1),\n", + " qo.ConditionEquals(\"gender\", \"M\"),\n", ")\n", "patients = querier.mimiciii.patients(ops=ops).run(limit=100)\n", "print(f\"{len(patients)} rows extracted!\")" @@ -102,16 +100,8 @@ }, "outputs": [], "source": [ - "ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"gender\", \"F\"),\n", - " ],\n", - ")\n", - "diagnoses_ops = qo.Sequential(\n", - " [\n", - " qo.ConditionSubstring(\"long_title\", \"gastroenteritis\"),\n", - " ],\n", - ")\n", + "ops = qo.ConditionEquals(\"gender\", \"F\")\n", + "diagnoses_ops = qo.ConditionSubstring(\"long_title\", \"gastroenteritis\")\n", "patients = querier.mimiciii.patients(ops=ops)\n", "admissions = querier.mimiciii.admissions(\n", " join=qo.JoinArgs(join_table=patients.query, on=\"subject_id\"),\n", @@ -143,17 +133,9 @@ }, "outputs": [], "source": [ - "ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"gender\", \"F\"),\n", - " ],\n", - ")\n", + "ops = qo.ConditionEquals(\"gender\", \"F\")\n", "patients = querier.mimiciii.patients(ops=ops)\n", - "lab_ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"label\", \"potassium\"),\n", - " ],\n", - ")\n", + "lab_ops = qo.ConditionEquals(\"label\", \"potassium\")\n", "labs = querier.labevents(ops=lab_ops).run(limit=100)\n", "print(f\"{len(labs)} rows extracted!\")" ] @@ -175,17 +157,11 @@ }, "outputs": [], "source": [ - "ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"gender\", \"M\"),\n", - " ],\n", - ")\n", + "ops = qo.ConditionEquals(\"gender\", \"M\")\n", "chartevents_ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"dbsource\", \"carevue\"),\n", - " qo.ConditionEquals(\"label\", \"AaDO2\"),\n", - " qo.ConditionLessThan(\"valuenum\", 20),\n", - " ],\n", + " qo.ConditionEquals(\"dbsource\", \"carevue\"),\n", + " qo.ConditionEquals(\"label\", \"AaDO2\"),\n", + " qo.ConditionLessThan(\"valuenum\", 20),\n", ")\n", "patients = querier.mimiciii.patients(ops=ops)\n", "chart_events = querier.chartevents(ops=chartevents_ops).run(limit=100)\n", diff --git a/docs/source/tutorials/mimiciv/query_api.ipynb b/docs/source/tutorials/mimiciv/query_api.ipynb index e70aa1c2a..eeccf1c32 100644 --- a/docs/source/tutorials/mimiciv/query_api.ipynb +++ b/docs/source/tutorials/mimiciv/query_api.ipynb @@ -75,10 +75,8 @@ "source": [ "patients = querier.patients()\n", "ops = qo.Sequential(\n", - " [\n", - " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", - " qo.ConditionAfterDate(\"admittime\", \"2021-01-01\"),\n", - " ],\n", + " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", + " qo.ConditionAfterDate(\"admittime\", \"2021-01-01\"),\n", ")\n", "admissions = querier.mimiciv_hosp.admissions(\n", " join=qo.JoinArgs(join_table=patients.query, on=\"subject_id\"),\n", @@ -103,16 +101,12 @@ "outputs": [], "source": [ "diagnoses_ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"icd_version\", 10),\n", - " qo.ConditionSubstring(\"long_title\", \"schizophrenia\"),\n", - " ],\n", + " qo.ConditionEquals(\"icd_version\", 10),\n", + " qo.ConditionSubstring(\"long_title\", \"schizophrenia\"),\n", ")\n", "admissions_ops = qo.Sequential(\n", - " [\n", - " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", - " qo.ConditionInYears(\"admittime\", \"2015\"),\n", - " ],\n", + " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", + " qo.ConditionInYears(\"admittime\", \"2015\"),\n", ")\n", "patients = querier.patients()\n", "admissions = querier.mimiciv_hosp.admissions(\n", @@ -145,16 +139,12 @@ "outputs": [], "source": [ "admissions_ops = qo.Sequential(\n", - " [\n", - " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", - " qo.ConditionInYears(\"admittime\", \"2015\"),\n", - " ],\n", + " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", + " qo.ConditionInYears(\"admittime\", \"2015\"),\n", ")\n", "diagnoses_ops = qo.Sequential(\n", - " [\n", - " qo.ConditionEquals(\"icd_version\", 9),\n", - " qo.ConditionRegexMatch(\"long_title\", r\"(?=.*schizophrenia)(?=.*chronic)\"),\n", - " ],\n", + " qo.ConditionEquals(\"icd_version\", 9),\n", + " qo.ConditionRegexMatch(\"long_title\", r\"(?=.*schizophrenia)(?=.*chronic)\"),\n", ")\n", "patients = querier.patients()\n", "admissions = querier.mimiciv_hosp.admissions(\n", @@ -187,12 +177,10 @@ "outputs": [], "source": [ "admissions_ops = qo.Sequential(\n", - " [\n", - " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", - " qo.ConditionInYears(\"admittime\", \"2015\"),\n", - " ],\n", + " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", + " qo.ConditionInYears(\"admittime\", \"2015\"),\n", ")\n", - "chartevents_ops = qo.Sequential([qo.ConditionEquals(\"category\", \"Routine Vital Signs\")])\n", + "chartevents_ops = qo.ConditionEquals(\"category\", \"Routine Vital Signs\")\n", "patients = querier.patients()\n", "admissions = querier.mimiciv_hosp.admissions(\n", " join=qo.JoinArgs(join_table=patients.query, on=\"subject_id\"),\n", @@ -224,12 +212,10 @@ "outputs": [], "source": [ "admissions_ops = qo.Sequential(\n", - " [\n", - " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", - " qo.ConditionInYears(\"admittime\", \"2009\"),\n", - " ],\n", + " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", + " qo.ConditionInYears(\"admittime\", \"2009\"),\n", ")\n", - "labevents_ops = qo.Sequential([qo.ConditionEquals(\"label\", \"hemoglobin\")])\n", + "labevents_ops = qo.ConditionEquals(\"label\", \"hemoglobin\")\n", "patients = querier.patients()\n", "admissions = querier.mimiciv_hosp.admissions(\n", " join=qo.JoinArgs(join_table=patients.query, on=\"subject_id\"),\n", @@ -263,10 +249,8 @@ "outputs": [], "source": [ "admissions_ops = qo.Sequential(\n", - " [\n", - " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", - " qo.ConditionInYears(\"admittime\", \"2009\"),\n", - " ],\n", + " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", + " qo.ConditionInYears(\"admittime\", \"2009\"),\n", ")\n", "patients = querier.patients()\n", "admissions = querier.mimiciv_hosp.admissions(\n", @@ -293,7 +277,7 @@ }, { "cell_type": "markdown", - "id": "801c5ec5-6c7e-44af-8fb7-275d66ca82b0", + "id": "9550ba62-c128-4259-a075-0cbd9c70b662", "metadata": {}, "source": [ "## Example 7. Get all female patient encounters from year 2015, and return as dask dataframe (lazy evaluation) with 4 partitions (batches) aggregated based on `subject_id`." @@ -307,12 +291,10 @@ "outputs": [], "source": [ "admissions_ops = qo.Sequential(\n", - " [\n", - " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", - " qo.ConditionInYears(\"admittime\", \"2015\"),\n", - " qo.Cast(\"gender\", \"str\"),\n", - " qo.ConditionEquals(\"gender\", \"F\"),\n", - " ],\n", + " qo.AddDeltaColumn([\"admittime\", \"dischtime\"], years=\"anchor_year_difference\"),\n", + " qo.ConditionInYears(\"admittime\", \"2015\"),\n", + " qo.Cast(\"gender\", \"str\"),\n", + " qo.ConditionEquals(\"gender\", \"F\"),\n", ")\n", "patients = querier.patients()\n", "admissions = querier.mimiciv_hosp.admissions(\n", diff --git a/poetry.lock b/poetry.lock index 7a7d3561c..5cdf35e3a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -161,18 +161,16 @@ files = [ [[package]] name = "alembic" -version = "1.11.3" +version = "1.12.0" description = "A database migration tool for SQLAlchemy." optional = false python-versions = ">=3.7" files = [ - {file = "alembic-1.11.3-py3-none-any.whl", hash = "sha256:d6c96c2482740592777c400550a523bc7a9aada4e210cae2e733354ddae6f6f8"}, - {file = "alembic-1.11.3.tar.gz", hash = "sha256:3db4ce81a9072e1b5aa44c2d202add24553182672a12daf21608d6f62a8f9cf9"}, + {file = "alembic-1.12.0-py3-none-any.whl", hash = "sha256:03226222f1cf943deee6c85d9464261a6c710cd19b4fe867a3ad1f25afda610f"}, + {file = "alembic-1.12.0.tar.gz", hash = "sha256:8e7645c32e4f200675e69f0745415335eb59a3663f5feb487abfa0b30c45888b"}, ] [package.dependencies] -importlib-metadata = {version = "*", markers = "python_version < \"3.9\""} -importlib-resources = {version = "*", markers = "python_version < \"3.9\""} Mako = "*" SQLAlchemy = ">=1.3.0" typing-extensions = ">=4" @@ -182,77 +180,78 @@ tz = ["python-dateutil"] [[package]] name = "alibi" -version = "0.8.0" +version = "0.9.4" description = "Algorithms for monitoring and explaining machine learning models" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - 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"pytest-cov", "pytest-mock (>=3.3)", "zest.releaser"] -[[package]] -name = "unidecode" -version = "1.3.6" -description = "ASCII transliterations of Unicode text" -optional = false -python-versions = ">=3.5" -files = [ - {file = "Unidecode-1.3.6-py3-none-any.whl", hash = "sha256:547d7c479e4f377b430dd91ac1275d593308dce0fc464fb2ab7d41f82ec653be"}, - {file = "Unidecode-1.3.6.tar.gz", hash = "sha256:fed09cf0be8cf415b391642c2a5addfc72194407caee4f98719e40ec2a72b830"}, -] - [[package]] name = "uri-template" version = "1.3.0" @@ -7851,13 +7938,13 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake [[package]] name = "uritools" -version = "4.0.1" +version = "4.0.2" description = "URI parsing, classification and composition" optional = false -python-versions = "~=3.7" +python-versions = ">=3.7" files = [ - {file = "uritools-4.0.1-py3-none-any.whl", hash = "sha256:d122d394ed6e6e15ac0fddba6a5b19e9fa204e7797507815cbfb0e1455ac0475"}, - {file = "uritools-4.0.1.tar.gz", hash = "sha256:efc5c3a6de05404850685a8d3f34da8476b56aa3516fbf8eff5c8704c7a2826f"}, + {file = "uritools-4.0.2-py3-none-any.whl", hash = "sha256:607b15eae1e7b69a120f463a7d98f91a56671e1ab92aae13f8e1f25c017fe60e"}, + {file = "uritools-4.0.2.tar.gz", hash = "sha256:04df2b787d0eb76200e8319382a03562fbfe4741fd66c15506b08d3b8211d573"}, ] [[package]] @@ -7898,13 +7985,13 @@ standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)", [[package]] name = "virtualenv" -version = "20.24.3" +version = "20.24.4" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.7" files = [ - {file = "virtualenv-20.24.3-py3-none-any.whl", hash = "sha256:95a6e9398b4967fbcb5fef2acec5efaf9aa4972049d9ae41f95e0972a683fd02"}, - {file = "virtualenv-20.24.3.tar.gz", hash = "sha256:e5c3b4ce817b0b328af041506a2a299418c98747c4b1e68cb7527e74ced23efc"}, + {file = "virtualenv-20.24.4-py3-none-any.whl", hash = "sha256:29c70bb9b88510f6414ac3e55c8b413a1f96239b6b789ca123437d5e892190cb"}, + {file = "virtualenv-20.24.4.tar.gz", hash = "sha256:772b05bfda7ed3b8ecd16021ca9716273ad9f4467c801f27e83ac73430246dca"}, ] [package.dependencies] @@ -7913,7 +8000,7 @@ filelock = ">=3.12.2,<4" platformdirs = ">=3.9.1,<4" [package.extras] -docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx (>=7.0.1)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] +docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] [[package]] @@ -8094,6 +8181,20 @@ MarkupSafe = ">=2.1.1" [package.extras] watchdog = ["watchdog"] +[[package]] +name = "wheel" +version = "0.41.2" +description = "A built-package format for Python" +optional = false +python-versions = ">=3.7" +files = [ + {file = "wheel-0.41.2-py3-none-any.whl", hash = "sha256:75909db2664838d015e3d9139004ee16711748a52c8f336b52882266540215d8"}, + {file = "wheel-0.41.2.tar.gz", hash = "sha256:0c5ac5ff2afb79ac23ab82bab027a0be7b5dbcf2e54dc50efe4bf507de1f7985"}, +] + +[package.extras] +test = ["pytest (>=6.0.0)", "setuptools (>=65)"] + [[package]] name = "widgetsnbextension" version = "4.0.8" @@ -8524,5 +8625,5 @@ report = ["category-encoders", "kaleido", "pillow", "plotly", "pybtex", "pydanti [metadata] lock-version = "2.0" -python-versions = ">=3.8, <3.11" -content-hash = "9d5b2b1ddc430a72a1841a7adb2be6cb4d050e3b8502338ed80dea5c63da7ee7" +python-versions = ">=3.9, <3.12" +content-hash = "8a67fe016988f44a8fa9cca5e3ca3f0ffdbf9f734cea1c6671dcc654e5804612" diff --git a/pyproject.toml b/pyproject.toml index 89006c91d..79e397246 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,29 +12,29 @@ packages = [ readme = "README.md" [tool.poetry.dependencies] -python = ">=3.8, <3.11" +python = ">=3.9, <3.12" pandas = "^1.4.1" -numpy = "<=1.23.0" +numpy = "^1.23.0" datasets = "^2.10.1" psutil = "^5.9.4" pyarrow = "^11.0.0" -monai = { version = "1.1.0", extras = ["itk"] } +monai = { version = "^1.1.0", extras = ["itk"] } dask = { version = "^2022.9.1", extras = ["dataframe"] } -psycopg2 = { version = "2.9.6", optional = true } +psycopg2 = { version = "^2.9.6", optional = true } hydra-core = { version = "^1.2.0", optional = true } SQLAlchemy = { version = "^1.4.32, <2.0", optional = true } scikit-learn = { version = "^1.2.2", optional = true } torch = { version = "^1.11.0", optional = true } -torchxrayvision = { version = "^0.0.37", optional = true } +torchxrayvision = { version = "^1.2.0", optional = true } xgboost = { version = "^1.5.2", optional = true } -alibi = { version = "^0.8.0", optional = true, extras = ["shap"] } -alibi-detect = { version = "^0.10.4", optional = true, extras = ["torch"] } -llvmlite = { version = "0.38.0", optional = true } +alibi = { version = "^0.9.4", optional = true, extras = ["shap"] } +alibi-detect = { version = "^0.11.4", optional = true, extras = ["torch"] } +llvmlite = { version = "^0.40.0", optional = true } pydantic = { version = "^1.10.11", optional = true } -spdx-tools = { version = "0.8.0a2", optional = true } +spdx-tools = { version = "^0.8.1", optional = true } pybtex = { version = "^0.24.0", optional = true } -kaleido = { version = "^0.2.1", optional = true } +kaleido = { version = "0.2.1", optional = true } scour = { version = "^0.38.2", optional = true } category-encoders = { version = "^2.6.1", optional = true } plotly = { version = "^5.7.0", optional = true } @@ -49,15 +49,15 @@ SQLAlchemy = "^1.4.32, <2.0" hydra-core = "^1.2.0" scikit-learn = "^1.2.2" torch = "^1.11.0" -torchxrayvision = "^0.0.37" +torchxrayvision = "^1.2.0" xgboost = "^1.5.2" -alibi = { version = "^0.8.0", extras = ["shap"] } -alibi-detect = { version = "^0.10.4", extras = ["torch"] } -llvmlite = "0.38.0" +alibi = { version = "^0.9.4", extras = ["shap"] } +alibi-detect = { version = "^0.11.4", extras = ["torch"] } +llvmlite = "^0.40.0" [tool.poetry.group.report.dependencies] pydantic = "^1.10.11" -spdx-tools = "0.8.0a2" +spdx-tools = "^0.8.1" pybtex = "^0.24.0" kaleido = "0.2.1" scour = "^0.38.2" @@ -78,11 +78,11 @@ ruff = "^0.0.286" [tool.poetry.group.docs.dependencies] numpydoc = "^1.2" -Sphinx = "^4.4.0" -sphinx-rtd-theme = "1.1.1" -sphinxcontrib-apidoc = "^0.3.0" -sphinx-autodoc-typehints = "^1.18.1" -myst-parser = "^0.18.0" +sphinx = "^7.2.5" +sphinx-rtd-theme = "^2.0.0rc2" +sphinxcontrib-apidoc = "^0.4.0" +sphinx-autodoc-typehints = "^1.24.0" +myst-parser = "^2.0.0" sphinx-copybutton = "^0.5.0" sphinx-autoapi = "^2.0.0" nbsphinx = "^0.8.11" diff --git a/tests/cyclops/query/test_ops.py b/tests/cyclops/query/test_ops.py index 1f56c8724..01e72ea2b 100644 --- a/tests/cyclops/query/test_ops.py +++ b/tests/cyclops/query/test_ops.py @@ -516,9 +516,7 @@ def test_union(visits_input): def test_sequential(visits_input): """Test Sequential.""" substr_op = Sequential( - [ - Substring("visit_concept_name", 0, 4, "visit_concept_name_substr"), - ], + Substring("visit_concept_name", 0, 4, "visit_concept_name_substr"), ) operations = [ Literal(33, "const"), diff --git a/tests/cyclops/query/test_util.py b/tests/cyclops/query/test_util.py index cf69846ca..5e0b0fb6b 100644 --- a/tests/cyclops/query/test_util.py +++ b/tests/cyclops/query/test_util.py @@ -10,7 +10,6 @@ _check_column_type, _to_select, _to_subquery, - ckwarg, drop_columns, ends_with, equals, @@ -25,7 +24,6 @@ process_column, process_elem, process_list, - remove_kwargs, rename_columns, reorder_columns, starts_with, @@ -47,12 +45,6 @@ def test__check_column_type(test_table): assert _check_column_type(test_table, ["b"], Integer, raise_error=True) -def test_ckwarg(): - """Test ckwarg.""" - assert ckwarg({"arg1": 1}, "arg1") == 1 - assert ckwarg({"arg1": 1}, "arg2") is None - - def test_ends_with(): """Test ends_with.""" test_col = column("a") @@ -70,13 +62,6 @@ def test_starts_with(): ) -def test_remove_kwargs(): - """Test remove_kwargs.""" - kwargs = {"arg1": 1, "arg2": 2, "arg3": 3} - assert "arg2" not in remove_kwargs(kwargs, "arg2") - assert "arg1" not in remove_kwargs(kwargs, ["arg2", "arg1"]) - - def test__to_subquery(): """Test _to_subquery fn.""" assert isinstance(_to_subquery(select().subquery()), Subquery)