"""Project Io registration convenience functions.
Note
----
The [call-arg] type error would be raised since the base methods doesn't have a ``**kwargs``
argument, but we rather ignore this error here, than adding ``**kwargs`` to the base method
and causing an [override] type error in the plugins implementation.
"""
from __future__ import annotations
from dataclasses import dataclass
from pathlib import Path
from typing import TYPE_CHECKING
from typing import TypeVar
from tabulate import tabulate
from glotaran.io.interface import ProjectIoInterface
from glotaran.plugin_system.base_registry import __PluginRegistry
from glotaran.plugin_system.base_registry import add_instantiated_plugin_to_registry
from glotaran.plugin_system.base_registry import get_method_from_plugin
from glotaran.plugin_system.base_registry import get_plugin_from_registry
from glotaran.plugin_system.base_registry import is_registered_plugin
from glotaran.plugin_system.base_registry import methods_differ_from_baseclass_table
from glotaran.plugin_system.base_registry import registered_plugins
from glotaran.plugin_system.base_registry import set_plugin
from glotaran.plugin_system.base_registry import show_method_help
from glotaran.plugin_system.io_plugin_utils import bool_table_repr
from glotaran.plugin_system.io_plugin_utils import inferr_file_format
from glotaran.plugin_system.io_plugin_utils import not_implemented_to_value_error
from glotaran.plugin_system.io_plugin_utils import protect_from_overwrite
from glotaran.utils.ipython import MarkdownStr
if TYPE_CHECKING:
from typing import Any
from typing import Callable
from typing import Literal
from glotaran.model import Model
from glotaran.parameter import ParameterGroup
from glotaran.project import Result
from glotaran.project import Scheme
from glotaran.typing import StrOrPath
ProjectIoMethods = TypeVar(
"ProjectIoMethods",
Literal["load_model"],
Literal["save_model"],
Literal["load_parameters"],
Literal["save_parameters"],
Literal["load_scheme"],
Literal["save_scheme"],
Literal["load_result"],
Literal["save_result"],
)
[docs]@dataclass
class SavingOptions:
"""A collection of options for result saving."""
data_filter: list[str] | None = None
data_format: Literal["nc"] = "nc"
parameter_format: Literal["csv"] = "csv"
report: bool = True
SAVING_OPTIONS_DEFAULT = SavingOptions()
SAVING_OPTIONS_MINIMAL = SavingOptions(data_filter=["fitted_data", "residual"], report=False)
PROJECT_IO_METHODS = (
"load_model",
"save_model",
"load_parameters",
"save_parameters",
"load_scheme",
"save_scheme",
"load_result",
"save_result",
)
[docs]def register_project_io(
format_names: str | list[str],
) -> Callable[[type[ProjectIoInterface]], type[ProjectIoInterface]]:
"""Register project io plugins to one or more formats.
Decorate a project io plugin class with ``@register_project_io(format_name|[*format_names])``
to add it to the registry.
Parameters
----------
format_names : str | list[str]
Name of the project io plugin under which it is registered.
Returns
-------
Callable[[type[ProjectIoInterface]], type[ProjectIoInterface]]
Inner decorator function.
Examples
--------
>>> @register_project_io("my_format_1")
... class MyProjectIo1(ProjectIoInterface):
... pass
>>> @register_project_io(["my_format_1", "my_format_1_alias"])
... class MyProjectIo2(ProjectIoInterface):
... pass
"""
def wrapper(cls: type[ProjectIoInterface]) -> type[ProjectIoInterface]:
add_instantiated_plugin_to_registry(
plugin_register_keys=format_names,
plugin_class=cls,
plugin_registry=__PluginRegistry.project_io,
plugin_set_func_name="set_project_plugin",
)
return cls
return wrapper
[docs]def set_project_plugin(
format_name: str,
full_plugin_name: str,
) -> None:
"""Set the plugin used for a specific project format.
This function is useful when you want to resolve conflicts of installed plugins
or overwrite the plugin used for a specific format.
Effected functions:
- :func:`load_model`
- :func:`save_model`
- :func:`load_parameters`
- :func:`save_parameters`
- :func:`load_scheme`
- :func:`save_scheme`
- :func:`load_result`
- :func:`save_result`
Parameters
----------
format_name : str
Format name used to refer to the plugin when used for ``save`` and ``load`` functions.
full_plugin_name : str
Full name (import path) of the registered plugin.
"""
set_plugin(
plugin_register_key=format_name,
full_plugin_name=full_plugin_name,
plugin_registry=__PluginRegistry.project_io,
)
[docs]def get_project_io(format_name: str) -> ProjectIoInterface:
"""Retrieve a data io plugin from the project_io registry.
Parameters
----------
format_name : str
Name of the data io plugin under which it is registered.
Returns
-------
ProjectIoInterface
Project io plugin instance.
"""
return get_plugin_from_registry(
plugin_register_key=format_name,
plugin_registry=__PluginRegistry.project_io,
not_found_error_message=(
f"Unknown Project Io format {format_name!r}. "
f"Known formats are: {known_project_formats()}"
),
)
[docs]@not_implemented_to_value_error
def load_model(file_name: StrOrPath, format_name: str = None, **kwargs: Any) -> Model:
"""Create a Model instance from the specs defined in a file.
Parameters
----------
file_name : StrOrPath
File containing the model specs.
format_name : str
Format the file is in, if not provided it will be inferred from the file extension.
**kwargs: Any
Additional keyword arguments passes to the ``load_model`` implementation
of the project io plugin.
Returns
-------
Model
Model instance created from the file.
"""
io = get_project_io(format_name or inferr_file_format(file_name))
model = io.load_model(Path(file_name).as_posix(), **kwargs) # type: ignore[call-arg]
model.source_path = Path(file_name).as_posix()
return model
[docs]@not_implemented_to_value_error
def save_model(
model: Model,
file_name: StrOrPath,
format_name: str = None,
*,
allow_overwrite: bool = False,
update_source_path: bool = True,
**kwargs: Any,
) -> None:
"""Save a :class:`Model` instance to a spec file.
Parameters
----------
model: Model
:class:`Model` instance to save to specs file.
file_name : StrOrPath
File to write the model specs to.
format_name : str
Format the file should be in, if not provided it will be inferred from the file extension.
allow_overwrite : bool
Whether or not to allow overwriting existing files, by default False
update_source_path: bool
Whether or not to update the ``source_path`` attribute to ``file_name`` when saving.
by default True
**kwargs : Any
Additional keyword arguments passes to the ``save_model`` implementation
of the project io plugin.
"""
protect_from_overwrite(file_name, allow_overwrite=allow_overwrite)
io = get_project_io(format_name or inferr_file_format(file_name, needs_to_exist=False))
io.save_model( # type: ignore[call-arg]
file_name=Path(file_name).as_posix(),
model=model,
**kwargs,
)
if update_source_path is True:
model.source_path = Path(file_name).as_posix()
[docs]@not_implemented_to_value_error
def load_parameters(file_name: StrOrPath, format_name: str = None, **kwargs) -> ParameterGroup:
"""Create a :class:`ParameterGroup` instance from the specs defined in a file.
Parameters
----------
file_name : StrOrPath
File containing the parameter specs.
format_name : str
Format the file is in, if not provided it will be inferred from the file extension.
**kwargs: Any
Additional keyword arguments passes to the ``load_parameters`` implementation
of the project io plugin.
Returns
-------
ParameterGroup
:class:`ParameterGroup` instance created from the file.
"""
io = get_project_io(format_name or inferr_file_format(file_name))
parameters = io.load_parameters( # type: ignore[call-arg]
Path(file_name).as_posix(),
**kwargs,
)
parameters.source_path = Path(file_name).as_posix()
return parameters
[docs]@not_implemented_to_value_error
def save_parameters(
parameters: ParameterGroup,
file_name: StrOrPath,
format_name: str = None,
*,
allow_overwrite: bool = False,
update_source_path: bool = True,
**kwargs: Any,
) -> None:
"""Save a :class:`ParameterGroup` instance to a spec file.
Parameters
----------
parameters : ParameterGroup
:class:`ParameterGroup` instance to save to specs file.
file_name : StrOrPath
File to write the parameter specs to.
format_name : str
Format the file should be in, if not provided it will be inferred from the file extension.
allow_overwrite : bool
Whether or not to allow overwriting existing files, by default False
update_source_path: bool
Whether or not to update the ``source_path`` attribute to ``file_name`` when saving.
by default True
**kwargs : Any
Additional keyword arguments passes to the ``save_parameters`` implementation
of the project io plugin.
"""
protect_from_overwrite(file_name, allow_overwrite=allow_overwrite)
io = get_project_io(format_name or inferr_file_format(file_name, needs_to_exist=False))
io.save_parameters( # type: ignore[call-arg]
file_name=Path(file_name).as_posix(),
parameters=parameters,
**kwargs,
)
if update_source_path is True:
parameters.source_path = Path(file_name).as_posix()
[docs]@not_implemented_to_value_error
def load_scheme(file_name: StrOrPath, format_name: str = None, **kwargs: Any) -> Scheme:
"""Create a :class:`Scheme` instance from the specs defined in a file.
Parameters
----------
file_name : StrOrPath
File containing the parameter specs.
format_name : str
Format the file is in, if not provided it will be inferred from the file extension.
**kwargs : Any
Additional keyword arguments passes to the ``load_scheme`` implementation
of the project io plugin.
Returns
-------
Scheme
:class:`Scheme` instance created from the file.
"""
io = get_project_io(format_name or inferr_file_format(file_name))
scheme = io.load_scheme(Path(file_name).as_posix(), **kwargs) # type: ignore[call-arg]
scheme.source_path = Path(file_name).as_posix()
return scheme
[docs]@not_implemented_to_value_error
def save_scheme(
scheme: Scheme,
file_name: StrOrPath,
format_name: str = None,
*,
allow_overwrite: bool = False,
update_source_path: bool = True,
**kwargs: Any,
) -> None:
"""Save a :class:`Scheme` instance to a spec file.
Parameters
----------
scheme : Scheme
:class:`Scheme` instance to save to specs file.
file_name : StrOrPath
File to write the scheme specs to.
format_name : str
Format the file should be in, if not provided it will be inferred from the file extension.
allow_overwrite : bool
Whether or not to allow overwriting existing files, by default False
update_source_path: bool
Whether or not to update the ``source_path`` attribute to ``file_name`` when saving.
by default True
**kwargs : Any
Additional keyword arguments passes to the ``save_scheme`` implementation
of the project io plugin.
"""
protect_from_overwrite(file_name, allow_overwrite=allow_overwrite)
io = get_project_io(format_name or inferr_file_format(file_name, needs_to_exist=False))
io.save_scheme( # type: ignore[call-arg]
file_name=Path(file_name).as_posix(),
scheme=scheme,
**kwargs,
)
if update_source_path is True:
scheme.source_path = Path(file_name).as_posix()
[docs]@not_implemented_to_value_error
def load_result(result_path: StrOrPath, format_name: str = None, **kwargs: Any) -> Result:
"""Create a :class:`Result` instance from the specs defined in a file.
Parameters
----------
result_path : StrOrPath
Path containing the result data.
format_name : str
Format the result is in, if not provided and it is a file
it will be inferred from the file extension.
**kwargs : Any
Additional keyword arguments passes to the ``load_result`` implementation
of the project io plugin.
Returns
-------
Result
:class:`Result` instance created from the saved format.
"""
io = get_project_io(format_name or inferr_file_format(result_path))
result = io.load_result(Path(result_path).as_posix(), **kwargs) # type: ignore[call-arg]
result.source_path = Path(result_path).as_posix()
return result
[docs]@not_implemented_to_value_error
def save_result(
result: Result,
result_path: StrOrPath,
format_name: str = None,
*,
allow_overwrite: bool = False,
update_source_path: bool = True,
**kwargs: Any,
) -> list[str] | None:
"""Write a :class:`Result` instance to a spec file.
Parameters
----------
result : Result
:class:`Result` instance to write.
result_path : StrOrPath
Path to write the result data to.
format_name : str
Format the result should be saved in, if not provided and it is a file
it will be inferred from the file extension.
allow_overwrite : bool
Whether or not to allow overwriting existing files, by default False
update_source_path: bool
Whether or not to update the ``source_path`` attribute to ``result_path`` when saving.
by default True
**kwargs : Any
Additional keyword arguments passes to the ``save_result`` implementation
of the project io plugin.
Returns
-------
list[str] | None
List of file paths which were saved.
"""
protect_from_overwrite(result_path, allow_overwrite=allow_overwrite)
io = get_project_io(
format_name or inferr_file_format(result_path, needs_to_exist=False, allow_folder=True)
)
paths = io.save_result( # type: ignore[call-arg]
result_path=Path(result_path).as_posix(),
result=result,
**kwargs,
)
if update_source_path is True:
result.source_path = Path(result_path).as_posix()
return paths
[docs]def get_project_io_method(format_name: str, method_name: ProjectIoMethods) -> Callable[..., Any]:
"""Retrieve implementation of project io functionality for the format 'format_name'.
This allows to get the proper help and autocomplete for the function,
which is especially valuable if the function provides additional options.
Parameters
----------
format_name : str
Format the dataloader should be able to read.
method_name : {'load_model', 'write_model', 'load_parameters', 'write_parameters',\
'load_scheme', 'write_scheme', 'load_result', 'write_result'}
Method name, e.g. load_model.
Returns
-------
Callable[..., Any]
The function which is called in the background by the convenience functions.
.. # noqa: DAR103 method_name
"""
io = get_project_io(format_name)
return get_method_from_plugin(io, method_name)
[docs]def show_project_io_method_help(format_name: str, method_name: ProjectIoMethods) -> None:
"""Show help for the implementation of project io plugin methods.
Parameters
----------
format_name : str
Format the method should support.
method_name : {'load_model', 'write_model', 'load_parameters', 'write_parameters',\
'load_scheme', 'write_scheme', 'load_result', 'write_result'}
Method name.
.. # noqa: DAR103 method_name
.. # noqa: DAR101
"""
io = get_project_io(format_name)
show_method_help(io, method_name)
[docs]def project_io_plugin_table(
*, plugin_names: bool = False, full_names: bool = False
) -> MarkdownStr:
"""Return registered project io plugins and which functions they support as markdown table.
This is especially useful when you work with new plugins.
Parameters
----------
plugin_names : bool
Whether or not to add the names of the plugins to the table.
full_names : bool
Whether to display the full names the plugins are
registered under as well.
Returns
-------
MarkdownStr
Markdown table of project io plugins.
"""
table_data = methods_differ_from_baseclass_table(
PROJECT_IO_METHODS,
known_project_formats(full_names=full_names),
get_project_io,
ProjectIoInterface,
plugin_names=plugin_names,
)
header_values = ["Format name", *PROJECT_IO_METHODS]
if plugin_names:
header_values.append("Plugin name")
headers = tuple(map(lambda x: f"__{x}__", header_values))
return MarkdownStr(
tabulate(
bool_table_repr(table_data), tablefmt="github", headers=headers, stralign="center"
)
)