App classes

Properties and methods of the app base classes.

`scinexus.composable.AppBase`

Bases: Generic[T, R]

Base for all app types. Provides call, repr, etc.

Raises:

Type Description

TypeError

If a subclass defines any method name reserved by the app framework. The reserved names depend on the app type.

All app types: __call__, __repr__, __str__, __new__, __copy__, __eq__, _validate_data_type, as_completed, check_data_type, _get_citations, citations, bib.

Composable apps (GENERIC, LOADER, WRITER) additionally: __add__, disconnect, input.

Writer apps additionally: apply_to, set_logger.

`bib` `property`

BibTeX formatted string of citations for this app and all composed input apps.

`check_data_type` `property` `writable`

toggle whether the type of input data matches the defined compatible types

Notes

If False, and an invalid data type is passed, the error will still be caught, but in a potentially less informative way. For instance "'NoneType' object has no attribute 'blah'"

`citations` `property`

Citations for this app and all composed input apps.

`as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)`

invokes self composable function on the provided data store

Parameters:

Name	Type	Description	Default
`dstore`	`DataStoreABC \| Iterable[Any] \| str`	a path, list of paths, or DataStore to which the process will be applied.	required
`parallel`	`bool`	run in parallel, according to arguments in par_kwargs. If True, the last step of the composable function serves as the master process, with earlier steps being executed in parallel for each member of dstore.	`False`
`par_kw`	`dict[str, Any] \| None`	dict of values for configuring parallel execution.	`None`
`id_from_source`	`GetIdFuncType \| None`	extracts a unique identifier from each input. If not provided, defaults to the function registered via `scinexus.data_store.set_id_from_source`, falling back to `scinexus.data_store.get_unique_id`.	`None`
`show_progress`	`bool \| Progress`	controls progress bar display. Pass `True` for the default progress bar, `False` to disable, or a `Progress` instance for a custom backend.	`False`

Notes

If run in parallel, this instance serves as the master object and aggregates results. If run in serial, results are returned in the same order as provided.

`scinexus.composable.ComposableApp`

Bases: AppBase[T, R]

Adds add for LOADER/GENERIC.

Raises:

Type	Description
`TypeError`	If a subclass defines any method name reserved by the app framework: `__call__`, `__repr__`, `__str__`, `__new__`, `__copy__`, `__eq__`, `_validate_data_type`, `as_completed`, `check_data_type`, `_get_citations`, `citations`, `bib`, `__add__`, `disconnect`, `input`.

`bib` `property`

BibTeX formatted string of citations for this app and all composed input apps.

`check_data_type` `property` `writable`

toggle whether the type of input data matches the defined compatible types

Notes

If False, and an invalid data type is passed, the error will still be caught, but in a potentially less informative way. For instance "'NoneType' object has no attribute 'blah'"

`citations` `property`

Citations for this app and all composed input apps.

`as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)`

invokes self composable function on the provided data store

Parameters:

Name	Type	Description	Default
`dstore`	`DataStoreABC \| Iterable[Any] \| str`	a path, list of paths, or DataStore to which the process will be applied.	required
`parallel`	`bool`	run in parallel, according to arguments in par_kwargs. If True, the last step of the composable function serves as the master process, with earlier steps being executed in parallel for each member of dstore.	`False`
`par_kw`	`dict[str, Any] \| None`	dict of values for configuring parallel execution.	`None`
`id_from_source`	`GetIdFuncType \| None`	extracts a unique identifier from each input. If not provided, defaults to the function registered via `scinexus.data_store.set_id_from_source`, falling back to `scinexus.data_store.get_unique_id`.	`None`
`show_progress`	`bool \| Progress`	controls progress bar display. Pass `True` for the default progress bar, `False` to disable, or a `Progress` instance for a custom backend.	`False`

Notes

If run in parallel, this instance serves as the master object and aggregates results. If run in serial, results are returned in the same order as provided.

`disconnect()`

Deprecated. No longer required since composition uses copies.

`scinexus.composable.LoaderApp`

Bases: ComposableApp[T, R]

Intermediate base class for LOADER apps.

Subclasses of LoaderApp are automatically assigned app_type=LOADER. Loaders sit at the start of a composed pipeline and have no input attribute.

Raises:

Type	Description
`TypeError`	If a subclass defines any method name reserved by the app framework: `__call__`, `__repr__`, `__str__`, `__new__`, `__copy__`, `__eq__`, `_validate_data_type`, `as_completed`, `check_data_type`, `_get_citations`, `citations`, `bib`, `__add__`, `disconnect`, `input`.

Examples:

Define a loader by inheritance::

class my_loader(LoaderApp):
    def main(self, path):
        return path

`bib` `property`

BibTeX formatted string of citations for this app and all composed input apps.

`check_data_type` `property` `writable`

toggle whether the type of input data matches the defined compatible types

Notes

If False, and an invalid data type is passed, the error will still be caught, but in a potentially less informative way. For instance "'NoneType' object has no attribute 'blah'"

`citations` `property`

Citations for this app and all composed input apps.

`as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)`

invokes self composable function on the provided data store

Parameters:

Name	Type	Description	Default
`dstore`	`DataStoreABC \| Iterable[Any] \| str`	a path, list of paths, or DataStore to which the process will be applied.	required
`parallel`	`bool`	run in parallel, according to arguments in par_kwargs. If True, the last step of the composable function serves as the master process, with earlier steps being executed in parallel for each member of dstore.	`False`
`par_kw`	`dict[str, Any] \| None`	dict of values for configuring parallel execution.	`None`
`id_from_source`	`GetIdFuncType \| None`	extracts a unique identifier from each input. If not provided, defaults to the function registered via `scinexus.data_store.set_id_from_source`, falling back to `scinexus.data_store.get_unique_id`.	`None`
`show_progress`	`bool \| Progress`	controls progress bar display. Pass `True` for the default progress bar, `False` to disable, or a `Progress` instance for a custom backend.	`False`

Notes

If run in parallel, this instance serves as the master object and aggregates results. If run in serial, results are returned in the same order as provided.

`disconnect()`

Deprecated. No longer required since composition uses copies.

`scinexus.composable.WriterApp`

Bases: ComposableApp[T, R]

Adds apply_to and set_logger for WRITER.

Raises:

Type	Description
`TypeError`	If a subclass defines any method name reserved by the app framework: `__call__`, `__repr__`, `__str__`, `__new__`, `__copy__`, `__eq__`, `_validate_data_type`, `as_completed`, `check_data_type`, `_get_citations`, `citations`, `bib`, `__add__`, `disconnect`, `input`, `apply_to`, `set_logger`.

`bib` `property`

BibTeX formatted string of citations for this app and all composed input apps.

`check_data_type` `property` `writable`

toggle whether the type of input data matches the defined compatible types

Notes

If False, and an invalid data type is passed, the error will still be caught, but in a potentially less informative way. For instance "'NoneType' object has no attribute 'blah'"

`citations` `property`

Citations for this app and all composed input apps.

`apply_to(dstore, id_from_source=None, parallel=False, par_kw=None, logger=True, cleanup=True, show_progress=False)`

invokes self composable function on the provided data store

Parameters:

Name	Type	Description	Default
`dstore`	`DataStoreABC \| Iterable[Any] \| str \| Path`	a path, list of paths, or DataStore to which the process will be applied.	required
`id_from_source`	`GetIdFuncType \| None`	makes the unique identifier from elements of dstore that will be used for writing results. If not provided, defaults to the function registered via `scinexus.data_store.set_id_from_source`, falling back to `scinexus.data_store.get_unique_id`.	`None`
`parallel`	`bool`	run in parallel, according to arguments in par_kwargs. If True, the last step of the composable function serves as the master process, with earlier steps being executed in parallel for each member of dstore.	`False`
`par_kw`	`dict[str, Any] \| None`	dict of values for configuring parallel execution.	`None`
`logger`	`bool \| CachingLogger`	Controls logging. If True (default), a CachingLogger is created automatically. If False, logging is disabled. A CachingLogger instance can be passed directly.	`True`
`cleanup`	`bool`	after copying of log files into the data store, it is deleted from the original location	`True`
`show_progress`	`bool \| Progress`	controls progress bar display	`False`

Returns:

Type	Description
`The output data store instance`

Notes

This is an append only function, meaning that if a member already exists in self.data_store for an input, it is skipped.

If run in parallel, this instance spawns workers and aggregates results.

`as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)`

invokes self composable function on the provided data store

Parameters:

Name	Type	Description	Default
`dstore`	`DataStoreABC \| Iterable[Any] \| str`	a path, list of paths, or DataStore to which the process will be applied.	required
`parallel`	`bool`	run in parallel, according to arguments in par_kwargs. If True, the last step of the composable function serves as the master process, with earlier steps being executed in parallel for each member of dstore.	`False`
`par_kw`	`dict[str, Any] \| None`	dict of values for configuring parallel execution.	`None`
`id_from_source`	`GetIdFuncType \| None`	extracts a unique identifier from each input. If not provided, defaults to the function registered via `scinexus.data_store.set_id_from_source`, falling back to `scinexus.data_store.get_unique_id`.	`None`
`show_progress`	`bool \| Progress`	controls progress bar display. Pass `True` for the default progress bar, `False` to disable, or a `Progress` instance for a custom backend.	`False`

Notes

If run in parallel, this instance serves as the master object and aggregates results. If run in serial, results are returned in the same order as provided.

`disconnect()`

Deprecated. No longer required since composition uses copies.

`scinexus.composable.NonComposableApp`

Bases: AppBase[T, R]

Intermediate base class for NON_COMPOSABLE apps.

Subclasses of NonComposableApp are automatically assigned app_type=NON_COMPOSABLE. Non-composable apps cannot participate in pipeline composition via +.

Raises:

Type	Description
`TypeError`	If a subclass defines any method name reserved by the app framework: `__call__`, `__repr__`, `__str__`, `__new__`, `__copy__`, `__eq__`, `_validate_data_type`, `as_completed`, `check_data_type`, `_get_citations`, `citations`, `bib`.

Examples:

Define a non-composable app by inheritance::

class my_app(NonComposableApp):
    def main(self, val):
        return val

`bib` `property`

BibTeX formatted string of citations for this app and all composed input apps.

`check_data_type` `property` `writable`

toggle whether the type of input data matches the defined compatible types

Notes

If False, and an invalid data type is passed, the error will still be caught, but in a potentially less informative way. For instance "'NoneType' object has no attribute 'blah'"

`citations` `property`

Citations for this app and all composed input apps.

`as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)`

invokes self composable function on the provided data store

Parameters:

Name	Type	Description	Default
`dstore`	`DataStoreABC \| Iterable[Any] \| str`	a path, list of paths, or DataStore to which the process will be applied.	required
`parallel`	`bool`	run in parallel, according to arguments in par_kwargs. If True, the last step of the composable function serves as the master process, with earlier steps being executed in parallel for each member of dstore.	`False`
`par_kw`	`dict[str, Any] \| None`	dict of values for configuring parallel execution.	`None`
`id_from_source`	`GetIdFuncType \| None`	extracts a unique identifier from each input. If not provided, defaults to the function registered via `scinexus.data_store.set_id_from_source`, falling back to `scinexus.data_store.get_unique_id`.	`None`
`show_progress`	`bool \| Progress`	controls progress bar display. Pass `True` for the default progress bar, `False` to disable, or a `Progress` instance for a custom backend.	`False`

Notes

If run in parallel, this instance serves as the master object and aggregates results. If run in serial, results are returned in the same order as provided.

App classes

scinexus.composable.AppBase

bib property

check_data_type property writable

citations property

as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)

scinexus.composable.ComposableApp

bib property

check_data_type property writable

citations property

as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)

disconnect()

scinexus.composable.LoaderApp

bib property

check_data_type property writable

citations property

as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)

disconnect()

scinexus.composable.WriterApp

bib property

check_data_type property writable

citations property

apply_to(dstore, id_from_source=None, parallel=False, par_kw=None, logger=True, cleanup=True, show_progress=False)

as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)

disconnect()

scinexus.composable.NonComposableApp

bib property

check_data_type property writable

citations property

as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)

`scinexus.composable.AppBase`

`bib` `property`

`check_data_type` `property` `writable`

`citations` `property`

`as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)`

`scinexus.composable.ComposableApp`

`bib` `property`

`check_data_type` `property` `writable`

`citations` `property`

`as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)`

`disconnect()`

`scinexus.composable.LoaderApp`

`bib` `property`

`check_data_type` `property` `writable`

`citations` `property`

`as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)`

`disconnect()`

`scinexus.composable.WriterApp`

`bib` `property`

`check_data_type` `property` `writable`

`citations` `property`

`apply_to(dstore, id_from_source=None, parallel=False, par_kw=None, logger=True, cleanup=True, show_progress=False)`

`as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)`

`disconnect()`

`scinexus.composable.NonComposableApp`

`bib` `property`

`check_data_type` `property` `writable`

`citations` `property`

`as_completed(dstore, parallel=False, par_kw=None, id_from_source=None, show_progress=False)`