Command Line Interface

Command Line Interface to interact with the Ersilia Model Hub

The table details all the commands availabe in Ersilia's CLI.

Command	Flags	Description
auth		This command uses GitHub as an identity provider to log a user into Ersilia. Currently, Ersilia does not have user management and therefore this command is simply a wrapper around GitHub login. This is a developer command assumes that the user is an Ersilia developer or model contributor.
catalog	[?OPT]	List the catalog of Ersilia models. By default, this command only shows the catalog of models available locally on a user's system, in an ASCII table on the user's terminal.
catalog	-l/--local	This is equal to using the catalog command by itself. It only lists models present locally on the user's system.
catalog	-f/ --file_name	Write the requested catalog to a given file.
catalog	-h/--hub	List all the models present in the Ersilia Model Hub. This command utilities the information maintained in a JSON file on Ersilia's servers.
catalog	--more/--less	Print more or less information about the catalog. When less information is requested, only the identifier and slug are displayed. Otherwise, the following fields are displayed: identifier, slug, title, task, input shape, output, output shape, and model source. These flags work with both local and hub context.
catalog	--card [MODEL]	Displays the card for the specified model identifier. The requested model does not need to be available locally. Presently, only a single model can be requested.
catalog	-j, --as-json/ -t, --as-table	Displays the catalog in JSON format on the user's terminal. This may be helpful for downstream processing task. The default behavior to display the catalog in a tabular format. These flags can be used both in the local and hub context.
close		Closes the model running in the shell from which this command is executed. Does not close models running in other shells.
delete	[MODEL]	Deletes the model specified with its identifier.
delete	--all	Deletes all the models available on the user's system.
example	[?MODEL]	This command can sample inputs for a given model. By default, the command expects a model to be served in the current shell, otherwise a model needs to be explicitly specified. By default, five examples will be sampled for the model and displayed on the user's terminal. This behavior can be customized with relevant flags.
example	-n, --n_samples	Specify the number of example inputs to generate for the given model. Default value is five.
example	-f, --file_name	The file name to save the sampled example inputs. By default, this file is serialized with comma separated values (CSV), however, a file with tab separated values (TSV) can also be requested by providing a file name with a .tsv extension. If a file is not specified, the result is printed on the terminal.
example	-s, --simple / -c/--complete	Simple inputs only contain essential information such as input SMILES, while complete inputs contain the InChIKey and other fields such as the molecule's name.
example	-p, --predefined/-r, --random	If the model source contains an example input file, when the predefined flag is set, then inputs are sampled from that file. Only the number of samples present in the file are returned, especially if --n_samples is greater than that number. By default, Ersilia samples inputs randomly.
fetch	[MODEL]	Fetch a given Ersilia model. Ersilia is smart enough to decide how to fetch this model, ie either using its Docker image, or from source - in most cases, if your Docker engine is active, a model is fetched using its image. However, this behavior can be overridden. When a model is re-fetched, Ersilia deletes all artifacts related to it, but for the sake of efficiency, the user is prompted to override this behavior when running this command.
fetch	[MODEL] --from_dir	Fetch the given model, from source, using a local path provided on the user's system. The path can be relative or absolute.
fetch	[MODEL] --from_github	Fetch the given model, from source, by cloning the GitHub repository of the model on the user's system.
fetch	[MODEL] --from_dockerhub	Fetch the given model using its Docker image maintained in Ersilia's public DockerHub registry
fetch	[MODEL] --from_s3	Fetch the given model, from source, using the model's code archive maintained on Ersilia's S3 storage servers.
fetch	[MODEL] --from_hosted	Fetch the given model, using the URL where the model is hosted. This only creates a basic folder structure for the model, and the model is not actually downloaded.
fetch	[MODEL] [OPT] --overwrite/--reuse	This flag is useful from an efficiency perspective. When fetching a model from source or S3, a conda environment is created, which can be retained and reused, or overwritten, when re-fetching a model.
fetch	[MODEL] [OPT] --with_bentoml	This is a developer specific command and most users will not need to use it. This command fetches a model from source, and packs it using BentoML. For that to happen, the model source needs to follow a specific structure. During model contribution and troubleshooting, it is often useful to fetch a model again, however one may not want to rebuild the model's environment, in which case it can be useful to combine this flag with the --reuse flag.
fetch	[MODEL] [OPT] --with_fastapi	This is a developer specific command and most users will not need to use it. This command fetches a model from source, and packs it using Ersilia Pack, using FastAPI. For that to happen, the model source needs to follow a specific structure. During model contribution and troubleshooting, it is often useful to fetch a model again, however one may not want to rebuild the model's environment, in which case it can be useful to combine this flag with the --reuse flag.
info		Print the model card, ie its information on the terminal, for a currently running model.
run	[?OPT]	Run the model currently served in the shell where this command is executed.
run	-i, --input	Specify the input file, which must be a CSV. Alternatively a single SMILES input can be specified. The input file should ideally have a header. This is a required flag to run a model with an input.
run	-o, --output	Specify the file to save the model predictions. This can be a CSV, TSV, or JSON file. If flag is optional and if not specified, output is printed on the user's terminal in JSON format.
run	-b, --batch_size	Specify the batch size for generating model predictions. By default, Ersilia works with batch size of 100 inputs.
run	--as-table	Print the model predictions in an ASCII table on the terminal, optionally as required.
serve	[MODEL] [?OPT]	Serve the given model.
serve	[MODEL] --output_source	This flag is used to interact with the pre-calculations store maintained by Ersilia. Currently this is work in progress.
serve	[MODEL] --lake/--no-lake	Ersilia caches model predictions locally using a local lake, because this flag is True by default. However this functionality can be overridden.
serve	-p, --port	The port to use when creating a model server. If unspecified, Ersilia looks for empty ports to use on the user's system.
serve	-t, --track	Whether the model's runs should be tracked to monitor for model and system performance. This telemetry data can be uploaded to S3 if the appropriate credentials are provided. Currently only Ersilia developers and other Ersilia tools have that privilege
uninstall		Use this command to remove all Ersilia artifacts on the user's system.