Covalent API#

The following API documentation describes how to use Covalent.

Electrons and Lattice are used for constructing workflows
Local Executor is used to execute electrons locally
File and Data Transfer is used to queue remote or local file transfer operations prior or post electron execution.
File transfer strategies are used to perform download/upload/copy operations over various protocols.
🔌 Dask Executor is used to execute electrons in a Dask cluster
Dependencies are used to specify any kind of electron dependency
Pip Dependencies are used to specify PyPI packages that are required to run an electron
Bash Dependencies are used to specify optional pre-execution shell commands for an electron
Call Dependencies are used to specify functions or dependencies that are called in an electron’s execution environment
Results is used for collecting and manipulating results
Dispatcher is used for dispatching workflows
The Covalent CLI Tool is used for interfacing with the Covalent server

Electron#

class covalent._workflow.electron.Electron(function, node_id=None, metadata=None)[source]#

An electron (or task) object that is a modular component of a work flow and is returned by electron.

function#: Function to be executed.

node_id#: Node id of the electron.

metadata#: Metadata to be used for the function execution.

kwargs#: Keyword arguments if any.

Methods:

`add_collection_node_to_graph`(graph, prefix)	Adds the node to lattice’s transport graph in the case where a collection of electrons is passed as an argument to another electron.
`connect_node_with_others`(node_id, …)	Adds a node along with connecting edges for all the arguments to the electron.
`get_metadata`(name)	Get value of the metadata of given name.
`get_op_function`(operand_1, operand_2, op)	Function to handle binary operations with electrons as operands.
`set_metadata`(name, value)	Function to add/edit metadata of given name and value to electron’s metadata.
`wait_for`(electrons)	Waits for the given electrons to complete before executing this one.

add_collection_node_to_graph(graph, prefix)[source]#

Adds the node to lattice’s transport graph in the case where a collection of electrons is passed as an argument to another electron.

Parameters

graph (_TransportGraph) – Transport graph of the lattice
prefix (str) – Prefix of the node

Returns

Node id of the added node

Return type

node_id

connect_node_with_others(node_id, param_name, param_value, param_type, arg_index, transport_graph)[source]#

Adds a node along with connecting edges for all the arguments to the electron.

Parameters

node_id (int) – Node number of the electron
param_name (str) – Name of the parameter
param_value (Union[Any, ForwardRef]) – Value of the parameter
param_type (str) – Type of parameter, positional or keyword
transport_graph (_TransportGraph) – Transport graph of the lattice

Returns

None

get_metadata(name)[source]#

Get value of the metadata of given name.

Parameters: name (str) – Name of the metadata whose value is needed.
Returns: Value of the metadata of given name.
Return type: value
Raises: KeyError – If metadata of given name is not present.

get_op_function(operand_1, operand_2, op)[source]#

Function to handle binary operations with electrons as operands. This will not execute the operation but rather create another electron which will be postponed to be executed according to the default electron configuration/metadata.

This also makes sure that if these operations are being performed outside of a lattice, then they are performed as is.

Parameters

operand_1 (Union[Any, Electron]) – First operand of the binary operation.
operand_2 (Union[Any, Electron]) – Second operand of the binary operation.
op (str) – Operator to be used in the binary operation.

Returns

Electron object corresponding to the operation execution.: Behaves as a normal function call if outside a lattice.

Return type

electron

set_metadata(name, value)[source]#

Function to add/edit metadata of given name and value to electron’s metadata.

Parameters

name (str) – Name of the metadata to be added/edited.
value (Any) – Value of the metadata to be added/edited.

Return type

None

Returns

None

wait_for(electrons)[source]#

Waits for the given electrons to complete before executing this one. Adds the necessary edges between this and those electrons without explicitly connecting their inputs/outputs.

Useful when execution of this electron relies on a side-effect from the another one.

Parameters: electrons (Union[Electron, Iterable[Electron]]) – Electron(s) which will be waited for to complete execution before starting execution for this one
Returns: Electron

Lattice#

class covalent._workflow.lattice.Lattice(workflow_function, transport_graph=None)[source]#

A lattice workflow object that holds the work flow graph and is returned by lattice decorator.

workflow_function#: The workflow function that is decorated by lattice decorator.

transport_graph#: The transport graph which will be the basis on how the workflow is executed.

metadata#: Dictionary of metadata of the lattice.

post_processing#: Boolean to indicate if the lattice is in post processing mode or not.

kwargs#: Keyword arguments passed to the workflow function.

electron_outputs#: Dictionary of electron outputs received after workflow execution.

Methods:

`build_graph`(args, *kwargs)	Builds the transport graph for the lattice by executing the workflow function which will trigger the call of all underlying electrons and they will get added to the transport graph for later execution.
`dispatch`(args, *kwargs)	DEPRECATED: Function to dispatch workflows.
`dispatch_sync`(args, *kwargs)	DEPRECATED: Function to dispatch workflows synchronously by waiting for the result too.
`draw`(args, *kwargs)	Generate lattice graph and display in UI taking into account passed in arguments.
`get_metadata`(name)	Get value of the metadata of given name.
`set_metadata`(name, value)	Function to add/edit metadata of given name and value to lattice’s metadata.

build_graph(*args, **kwargs)[source]#

Builds the transport graph for the lattice by executing the workflow function which will trigger the call of all underlying electrons and they will get added to the transport graph for later execution.

Also redirects any print statements inside the lattice function to null and ignores any exceptions caused while executing the function.

GRAPH WILL NOT BE BUILT AFTER AN EXCEPTION HAS OCCURRED.

Parameters

*args – Positional arguments to be passed to the workflow function.
**kwargs – Keyword arguments to be passed to the workflow function.

Return type

None

Returns

None

dispatch(*args, **kwargs)[source]#

DEPRECATED: Function to dispatch workflows.

Parameters

*args – Positional arguments for the workflow
**kwargs – Keyword arguments for the workflow

Return type

str

Returns

Dispatch id assigned to job

dispatch_sync(*args, **kwargs)[source]#

DEPRECATED: Function to dispatch workflows synchronously by waiting for the result too.

Parameters

*args – Positional arguments for the workflow
**kwargs – Keyword arguments for the workflow

Return type

Result

Returns

Result of workflow execution

draw(*args, **kwargs)[source]#

Generate lattice graph and display in UI taking into account passed in arguments.

Parameters

*args – Positional arguments to be passed to build the graph.
**kwargs – Keyword arguments to be passed to build the graph.

Return type

None

Returns

None

get_metadata(name)[source]#

Get value of the metadata of given name.

Parameters: name (str) – Name of the metadata whose value is needed.
Returns: Value of the metadata of given name.
Return type: value
Raises: KeyError – If metadata of given name is not present.

set_metadata(name, value)[source]#

Function to add/edit metadata of given name and value to lattice’s metadata.

Parameters

name (str) – Name of the metadata to be added/edited.
value (Any) – Value of the metadata to be added/edited.

Return type

None

Returns

None

Local Executor#

Executing tasks (electrons) directly on the local machine

File Transfer#

File Transfer from (source) and to (destination) local or remote files prior/post electron execution. Instances are are provided to files keyword argument in an electron decorator.

class covalent._file_transfer.file.File(filepath=None, is_remote=False, is_dir=False, include_folder=False)[source]#

File class to store components of provided URI including scheme (s3://, file://, ect.) determine if the file is remote, and acts a facade to facilitate filesystem operations.

filepath#: File path corresponding to the file.

is_remote#: Flag determining if file is remote (override). Default is resolved automatically from file scheme.

is_dir#: Flag determining if file is a directory (override). Default is determined if file uri contains trailing slash.

include_folder#: Flag that determines if the folder should be included in the file transfer, if False only contents of folder are transfered.

class covalent._file_transfer.folder.Folder(filepath=None, is_remote=False, is_dir=True, include_folder=False)[source]#

Folder class to store components of provided URI including scheme (s3://, file://, ect.), determine if the file is remote, and act as facade to facilitate filesystem operations. Folder is a child of the File class which sets is_dir flag to True.

include_folder#: Flag that determines if the folder should be included in the file transfer, if False only contents of folder are transfered.

class covalent._file_transfer.file_transfer.FileTransfer(from_file=None, to_file=None, order=<Order.BEFORE: 'before'>, strategy=None)[source]#

FileTransfer object class that takes two File objects or filepaths (from, to) and a File Transfer Strategy to perform remote or local file transfer operations.

from_file#: Filepath or File object corresponding to the source file.

to_file#: Filepath or File object corresponding to the destination file.

order#: Order (enum) to execute the file transfer before (Order.BEFORE) or after (Order.AFTER) electron execution.

strategy#: Optional File Transfer Strategy to perform file operations - default will be resolved from provided file schemes.

covalent._file_transfer.file_transfer.TransferFromRemote(from_filepath, to_filepath=None, strategy=None, order=<Order.BEFORE: 'before'>)[source]#

Factory for creating a FileTransfer instance where from_filepath is implicitly created as a remote File Object, and the order (Order.BEFORE) is set so that this file transfer will occur prior to electron execution.

Parameters

from_filepath (str) – File path corresponding to remote file (source).
to_filepath (Optional[str]) – File path corresponding to local file (destination)
strategy (Optional[FileTransferStrategy]) – Optional File Transfer Strategy to perform file operations - default will be resolved from provided file schemes.
order (Order) – Order (enum) to execute the file transfer before (Order.BEFORE) or after (Order.AFTER) electron execution - default is BEFORE

Return type

FileTransfer

Returns

FileTransfer instance with implicit Order.BEFORE enum set and from (source) file marked as remote

covalent._file_transfer.file_transfer.TransferToRemote(to_filepath, from_filepath=None, strategy=None, order=<Order.AFTER: 'after'>)[source]#

Factory for creating a FileTransfer instance where to_filepath is implicitly created as a remote File Object, and the order (Order.AFTER) is set so that this file transfer will occur post electron execution.

Parameters

to_filepath (str) – File path corresponding to remote file (destination)
from_filepath (Optional[str]) – File path corresponding to local file (source).
strategy (Optional[FileTransferStrategy]) – Optional File Transfer Strategy to perform file operations - default will be resolved from provided file schemes.
order (Order) – Order (enum) to execute the file transfer before (Order.BEFORE) or after (Order.AFTER) electron execution - default is AFTER

Return type

FileTransfer

Returns

FileTransfer instance with implicit Order.AFTER enum set and to (destination) file marked as remote

File Transfer Strategies#

A set of classes with a shared interface to perform copy, download, and upload operations given two (source & destination) File objects that support various protocols.

class covalent._file_transfer.strategies.transfer_strategy_base.FileTransferStrategy[source]#: Base FileTransferStrategy class that defines the interface for file transfer strategies exposing common methods for performing copy, download, and upload operations.

class covalent._file_transfer.strategies.rsync_strategy.Rsync(user='', host='', private_key_path=None)[source]#

Implements Base FileTransferStrategy class to use rsync to move files to and from remote or local filesystems. Rsync via ssh is used if one of the provided files is marked as remote.

user#: (optional) Determine user to specify for remote host if using rsync with ssh

host#: (optional) Determine what host to connect to if using rsync with ssh

private_key_path#: (optional) Filepath for ssh private key to use if using rsync with ssh

Dask Executor#

Executing tasks (electrons) in a Dask cluster

Dependencies#

Generic dependencies for an electron

class covalent._workflow.deps.Deps(apply_fn=None, apply_args=[], apply_kwargs={}, *, retval_keyword='')[source]#

Generic dependency class used in specifying any kind of dependency for an electron.

apply_fn#: function to be executed in the backend environment

apply_args#: list of arguments to be applied in the backend environment

apply_kwargs#: dictionary of keyword arguments to be applied in the backend environment

Methods:

apply()

Encapsulates the exact function and args/kwargs to be executed in the backend environment.

apply()[source]#

Encapsulates the exact function and args/kwargs to be executed in the backend environment.

Parameters: None –
Return type: Tuple[TransportableObject, TransportableObject, TransportableObject, str]
Returns: A tuple of transportable objects containing the function and optional args/kwargs

Pip Dependencies#

PyPI packages to be installed before executing an electron

class covalent._workflow.depspip.DepsPip(packages=[], reqs_path='')[source]#

PyPI packages to be installed before executing an electron

A specification of Pip packages to be installed

packages#: A list of PyPI packages to install

reqs_path#: Path to requirements.txt (overrides packages)

These packages are installed in an electron’s execution environment just before the electron is run.

Methods:

`from_dict`(object_dict)	Rehydrate a dictionary representation
`to_dict`()	Return a JSON-serializable dictionary representation of self

from_dict(object_dict)[source]#

Rehydrate a dictionary representation

Parameters: object_dict – a dictionary representation returned by to_dict
Return type: DepsPip
Returns: self

Instance attributes will be overwritten.

to_dict()[source]#

Return a JSON-serializable dictionary representation of self

Return type: dict

Bash Dependencies#

Shell commands to run before an electron

class covalent._workflow.depsbash.DepsBash(commands=[])[source]#

Shell commands to run before an electron

Deps class to encapsulate Bash dependencies for an electron.

The specified commands will be executed as subprocesses in the same environment as the electron.

commands#: A list of bash commands to execute before the electron runs.

Methods:

`from_dict`(object_dict)	Rehydrate a dictionary representation
`to_dict`()	Return a JSON-serializable dictionary representation of self

from_dict(object_dict)[source]#

Rehydrate a dictionary representation

Parameters: object_dict – a dictionary representation returned by to_dict
Return type: DepsBash
Returns: self

Instance attributes will be overwritten.

to_dict()[source]#

Return a JSON-serializable dictionary representation of self

Return type: dict

Call Dependencies#

Functions, shell commands, PyPI packages, and other types of dependencies to be called in an electron’s execution environment

class covalent._workflow.depscall.DepsCall(func=None, args=[], kwargs={}, *, retval_keyword='', override_reserved_retval_keys=False)[source]#

Functions, shell commands, PyPI packages, and other types of dependencies to be called in an electron’s execution environment

Deps class to encapsulate python functions to be called in the same execution environment as the electron.

func#: A callable

args#: args list

kwargs#: kwargs dict

retval_keyword#: An optional string referencing the return value of func.

If retval_keyword is specified, the return value of func will be passed during workflow execution as an argument to the electron corresponding to the parameter of the same name.

Notes

Electron parameters to be injected during execution must have default parameter values.

It is the user’s responsibility to ensure that retval_keyword is actually a parameter of the electron. Unexpected behavior may occur otherwise.

Methods:

`from_dict`(object_dict)	Rehydrate a dictionary representation
`to_dict`()	Return a JSON-serializable dictionary representation of self

from_dict(object_dict)[source]#

Rehydrate a dictionary representation

Parameters: object_dict – a dictionary representation returned by to_dict
Return type: DepsCall
Returns: self

Instance attributes will be overwritten.

to_dict()[source]#

Return a JSON-serializable dictionary representation of self

Return type: dict

Dispatcher#

Dispatching jobs to the server

Results#

Collecting and managing results

Covalent CLI Tool#

This Command Line Interface (CLI) tool is used to manage Covalent server.