ersilia.utils package¶

Subpackages¶

Submodules¶

ersilia.utils.cli_query module¶

ersilia.utils.cli_query.query_yes_no(question)[source]¶

ersilia.utils.conda module¶

class ersilia.utils.conda.BaseConda[source]¶

Bases: object

Base class for managing conda environments.

default_env()[source]¶: Get the default conda environment.

is_base()[source]¶: Check if the current environment is the base environment.

conda_prefix(is_base)[source]¶: Get the conda prefix path.

static conda_prefix(is_base)[source]¶

Get the conda prefix path.

Parameters:: is_base (bool) – Whether the current environment is the base environment.
Returns:: The conda prefix path.
Return type:: str

static default_env()[source]¶

Get the default conda environment.

Returns:: The name of the default conda environment.
Return type:: str

is_base()[source]¶

Check if the current environment is the base environment.

Returns:: True if the current environment is the base environment, False otherwise.
Return type:: bool

class ersilia.utils.conda.CondaUtils(config_json=None)[source]¶

Bases: BaseConda

Utility class for managing conda environments and packages.

Parameters:: config_json (dict, optional) – Configuration settings in JSON format. Default is None.

Examples

conda_utils = CondaUtils()
conda_utils.create("myenv", "3.8")

activate_base()[source]¶

Generate a script to activate the base conda environment.

Returns:: The script to activate the base conda environment.
Return type:: str

static checksum_from_conda_yml_file(self, env_yml, overwrite)[source]¶

Generate a checksum for a conda environment YAML file.

Parameters:

env_yml (str) – The path to the conda environment YAML file.
overwrite (bool) – Whether to overwrite the name and prefix in the YAML file with the checksum.

Returns:

The checksum of the YAML file contents.

Return type:

str

checksum_from_dockerfile(dockerfile_dir, dest=None)[source]¶

Generate a checksum for a Dockerfile.

Parameters:

dockerfile_dir (str) – The directory containing the Dockerfile.
dest (str, optional) – The destination directory for the checksum file. Default is None.

Returns:

The checksum of the Dockerfile.

Return type:

str

checksum_from_file(filename)[source]¶

Generate a checksum for the contents of a file.

Parameters:: filename (str) – The path to the file.
Returns:: The checksum of the file contents.
Return type:: str

get_base_env(path)[source]¶

Get the base environment from a JSON file.

Parameters:: path (str) – The path to the JSON file.
Returns:: The base environment.
Return type:: str

get_conda_and_pip_install_commands_from_dockerfile_if_exclusive(path, force_exclusive=True)[source]¶

Identify install commands from a Dockerfile.

Parameters:

path (str) – The path to the Dockerfile.
force_exclusive (bool, optional) – Whether to force exclusive conda and pip commands. Default is True.

Returns:

A list of install commands.

Return type:

list

specs_from_dockerfile(dockerfile_dir, dest=None, use_checksum=False, name=None)[source]¶

Generate specs from a Dockerfile.

Parameters:

dockerfile_dir (str) – The directory containing the Dockerfile.
dest (str, optional) – The destination directory for the specs file. Default is None.
use_checksum (bool, optional) – Whether to use a checksum for the specs. Default is False.
name (str, optional) – The name to use for the specs. Default is None.

Returns:

The name or checksum of the specs.

Return type:

str

specs_from_dockerfile_as_json(dockerfile_dir, dest)[source]¶

Write a JSON file with the install requirements inferred from the Dockerfile.

Parameters:

dockerfile_dir (str) – The directory containing the Dockerfile.
dest (str) – The destination directory for the JSON file.

Returns:

The path to the JSON file.

Return type:

str

class ersilia.utils.conda.SimpleConda(config_json=None)[source]¶

Bases: CondaUtils

A class to manage conda environments using simple commands.

Parameters:: config_json (dict, optional) – Configuration settings in JSON format. Default is None.

Examples

simple_conda = SimpleConda()
simple_conda.create("myenv", "3.8")

active_env()[source]¶

Get the currently active conda environment.

Returns:: The name of the currently active conda environment.
Return type:: str

clone(src_env, dst_env)[source]¶

Make an exact copy of a conda environment.

Parameters:

src_env (str) – The name of the source environment.
dst_env (str) – The name of the destination environment.

Raises:

Exception – If the source environment does not exist or the destination environment already exists.

create(environment, python_version)[source]¶

Create a new conda environment.

Parameters:

environment (str) – The name of the new environment.
python_version (str) – The Python version to use in the new environment.

Return type:

None

create_executable_bash_script(environment, commandlines, file_name)[source]¶

Create an executable bash script to run commands in a conda environment.

Parameters:

environment (str) – The name of the environment.
commandlines (str or list) – The commands to run.
file_name (str) – The name of the bash script file.

Returns:

The path to the bash script file.

Return type:

str

delete(environment)[source]¶

Delete a conda environment.

Parameters:: environment (str) – The name of the environment to delete.

delete_one(environment)[source]¶

Delete a conda environment.

Parameters:: environment (str) – The name of the environment to delete.

exists(environment)[source]¶

Check if a conda environment exists.

Parameters:: environment (str) – The name of the environment to check.
Returns:: True if the environment exists, False otherwise.
Return type:: bool

export_env_yml(environment, dest)[source]¶

Export a conda environment as an environment YAML file.

Parameters:

environment (str) – The name of the environment to export.
dest (str) – The destination directory for the YAML file.

get_python_path_env(environment)[source]¶

Get the Python path for a conda environment.

Parameters:: environment (str) – The name of the environment.
Returns:: The Python path for the environment.
Return type:: str

run_commandlines(**kwargs)¶

startswith(environment)[source]¶

Get a list of conda environments that start with the given prefix.

Parameters:: environment (str) – The prefix to check.
Returns:: A list of conda environments that start with the given prefix.
Return type:: list

class ersilia.utils.conda.StandaloneConda[source]¶

Bases: object

A class to manage standalone conda environments.

exists(environment)[source]¶

Check if a standalone conda environment exists.

Parameters:: environment (str) – The name of the environment to check.
Returns:: True if the environment exists, False otherwise.
Return type:: bool

run_commandlines(environment, commandlines)[source]¶

Run commands in a given standalone conda environment.

Parameters:

environment (str) – The name of the environment.
commandlines (str or list) – The commands to run.

ersilia.utils.config module¶

class ersilia.utils.config.Config(json_file=None)[source]¶

Bases: object

Config class.

An instance of this object holds config file section as attributes.

Parameters:: json_file (str, optional) – The path to the JSON configuration file. Default is None.

keys()[source]¶

Get the keys of the configuration.

Returns:: The keys of the configuration.
Return type:: dict_keys

class ersilia.utils.config.Credentials(json_file=None)[source]¶

Bases: object

A class to manage credentials.

Parameters:: json_file (str, optional) – The path to the JSON credentials file. Default is None.

keys()[source]¶

Get the keys of the credentials.

Returns:: The keys of the credentials.
Return type:: dict_keys

ersilia.utils.cron module¶

ersilia.utils.cron.del_model(model_id)[source]¶

ersilia.utils.cron.model_cleanup()[source]¶

ersilia.utils.cron.seconds_to_days(s)[source]¶

ersilia.utils.csvfile module¶

class ersilia.utils.csvfile.CsvDataLoader[source]¶

Bases: object

A class to load and process data from CSV and JSON files.

load(csv_file)[source]¶: Load data from a CSV file.

read(file_path)[source]¶: Read data from a CSV, TSV, or JSON file.

load(csv_file)[source]¶

Load data from a CSV file.

Parameters:: csv_file (str) – The path to the CSV file.

read(file_path)[source]¶

Read data from a CSV, TSV, or JSON file.

Parameters:: file_path (str) – The path to the file.
Returns:: The data read from the file.
Return type:: list or dict
Raises:: ValueError – If the file format is unsupported.

ersilia.utils.docker module¶

class ersilia.utils.docker.ContainerMetricsSampler(model_id, sampling_interval=0.01)[source]¶

Bases: object

A class to sample metrics from Docker containers.

Parameters:

model_id (str) – The model identifier.
sampling_interval (float, optional) – The interval between samples in seconds. Default is 0.01.

get_average_metrics()[source]¶

Get the average metrics from the tracked samples.

Returns:: A dictionary containing the average CPU and memory usage, and the peak CPU and memory usage.
Return type:: dict

start_tracking()[source]¶: Start tracking metrics from the Docker container.

stop_tracking()[source]¶: Stop tracking metrics from the Docker container.

class ersilia.utils.docker.SimpleDocker(use_udocker=None)[source]¶

Bases: object

A class to manage Docker containers and images.

Parameters:: use_udocker (bool, optional) – Whether to use udocker instead of Docker. Default is None.

build(path, org, img, tag)[source]¶

Build a Docker image.

Parameters:

path (str) – The path to the Dockerfile.
org (str) – The organization name.
img (str) – The image name.
tag (str) – The image tag.

cleanup_ersilia_images()[source]¶: Remove all Ersilia-related Docker images.

container_peak(model_id)[source]¶

Get the peak memory usage of a Docker container running an Ersilia model.

Parameters:: model_id (str) – The model identifier.
Returns:: The peak memory usage in MB, or None if the container is not found or an error occurs.
Return type:: float or None

containers(only_run)[source]¶

Get a dictionary of Docker containers.

Parameters:: only_run (bool) – Whether to include only running containers.
Returns:: A dictionary of Docker containers with container names as keys and image names as values.
Return type:: dict

static cp_from_container(name, img_path, local_path, org=None, img=None, tag=None)[source]¶

Copy files from a Docker container to the local filesystem.

Parameters:

name (str) – The container name.
img_path (str) – The path inside the container.
local_path (str) – The local path to copy files to.
org (str, optional) – The organization name. Default is None.
img (str, optional) – The image name. Default is None.
tag (str, optional) – The image tag. Default is None.
None

async cp_from_image(img_path, local_path, org, img, tag)[source]¶

Copy files from a Docker image to the local filesystem.

Parameters:

img_path (str) – The path inside the image.
local_path (str) – The local path to copy files to.
org (str) – The organization name.
img (str) – The image name.
tag (str) – The image tag.

delete(org, img, tag)[source]¶

Delete a Docker image.

Parameters:

org (str) – The organization name.
img (str) – The image name.
tag (str) – The image tag.

exec(cmd, org, img, tag, name)[source]¶

Execute a command in a Docker container and then kill the container.

Parameters:

cmd (str) – The command to execute.
org (str) – The organization name.
img (str) – The image name.
tag (str) – The image tag.
name (str) – The container name.

static exec_container(name, cmd)[source]¶

Execute a command in a Docker container.

Parameters:

name (str) – The container name.
cmd (str) – The command to execute.

exists(org, img, tag)[source]¶

Check if a Docker image exists.

Parameters:

org (str) – The organization name.
img (str) – The image name.
tag (str) – The image tag.

Returns:

True if the image exists, False otherwise.

Return type:

bool

images()[source]¶

Get a dictionary of Docker images.

Returns:: A dictionary of Docker images with image names as keys and image IDs as values.
Return type:: dict

static kill(name)[source]¶

Kill a Docker container.

Parameters:: name (str) – The container name.

static remove(name)[source]¶

Remove a Docker container.

Parameters:: name (str) – The container name.

run(org, img, tag, name, memory=None)[source]¶

Run a Docker container.

Parameters:

org (str) – The organization name.
img (str) – The image name.
tag (str) – The image tag.
name (str) – The container name.
memory (int, optional) – The memory limit for the container in GB. Default is None.

Returns:

The name of the running container.

Return type:

str

class ersilia.utils.docker.SimpleDockerfileParser(path)[source]¶

Bases: DockerfileParser

A class to parse Dockerfiles.

Parameters:: path (str) – The path to the Dockerfile or the directory containing the Dockerfile.

get_baseimage()[source]¶

Get the base image from the Dockerfile.

Returns:: The base image.
Return type:: str

get_runs()[source]¶

Get the RUN commands from the Dockerfile.

Returns:: A list of RUN commands.
Return type:: list

ersilia.utils.docker.is_docker_installed()[source]¶

ersilia.utils.docker.is_udocker_installed()[source]¶

ersilia.utils.docker.model_image_version_reader(dir)[source]¶: Read the requested model image version from a file.

ersilia.utils.docker.resolve_pack_method_docker(model_id)[source]¶

ersilia.utils.docker.resolve_platform()[source]¶

ersilia.utils.download module¶

Download utilities

class ersilia.utils.download.GitHubDownloader(overwrite, token=None)[source]¶

Bases: object

A class to download files and repositories from GitHub.

Parameters:

overwrite (bool) – Whether to overwrite existing files.
token (str, optional) – The GitHub token for authentication. Default is None.

clone(org, repo, destination, ungit=False)[source]¶

Clone a GitHub repository.

Parameters:

org (str) – The GitHub organization name.
repo (str) – The GitHub repository name.
destination (str) – The destination directory.
ungit (bool, optional) – Whether to remove Git-related files. Default is False.

download_single(org, repo, repo_path, destination)[source]¶

Download a single file from a GitHub repository.

Parameters:

org (str) – The GitHub organization name.
repo (str) – The GitHub repository name.
repo_path (str) – The path to the file in the repository.
destination (str) – The destination path.

Returns:

True if the file was downloaded successfully, False otherwise.

Return type:

bool

class ersilia.utils.download.GoogleDriveDownloader[source]¶

Bases: object

A class to download files from Google Drive.

download_file_from_google_drive(file_id, destination)[source]¶

Download a file from Google Drive.

Parameters:

file_id (str) – The Google Drive file ID.
destination (str) – The destination path.

fetch_zip(file_id, destination)[source]¶

Download a ZIP file from Google Drive and extract it.

Parameters:

file_id (str) – The Google Drive file ID.
destination (str) – The destination directory.

static get_confirm_token(response)[source]¶

Get the confirmation token from the response.

Parameters:: response (object) – The response object.
Returns:: The confirmation token, if available.
Return type:: str

static save_response_content(response, destination)[source]¶

Save the response content to a file.

Parameters:

response (object) – The response object.
destination (str) – The destination file path.

class ersilia.utils.download.OsfDownloader(overwrite)[source]¶

Bases: object

A class to download files from the Open Science Framework (OSF).

Parameters:: overwrite (bool) – Whether to overwrite existing files.

fetch(project_id, filename, destination, tmp_folder)[source]¶

Fetch a file from OSF.

Parameters:

project_id (str) – The OSF project ID.
filename (str) – The name of the file to fetch.
destination (str) – The destination directory.
tmp_folder (str) – The temporary folder to use.

class ersilia.utils.download.PseudoDownloader(overwrite)[source]¶

Bases: object

A class to simulate downloading by copying local directories.

Parameters:: overwrite (bool) – Whether to overwrite existing files.

fetch(src, dst)[source]¶

Copy entire directory.

Parameters:

src (str) – The source directory.
dst (str) – The destination directory.

class ersilia.utils.download.S3Downloader[source]¶

Bases: object

A class to download files from an S3 bucket.

download_from_s3(bucket_url, file_name, destination)[source]¶

Download a file from an S3 bucket.

Parameters:

bucket_url (str) – The URL of the S3 bucket.
file_name (str) – The name of the file to download.
destination (str) – The destination path.

ersilia.utils.dvc module¶

class ersilia.utils.dvc.DVCBrancher[source]¶

Bases: object

A class to manage DVC branches.

class ersilia.utils.dvc.DVCFetcher(local_repo_path)[source]¶

Bases: object

A class to fetch data using DVC (Data Version Control).

Parameters:: local_repo_path (str) – The local repository path.

check_dvc_exists()[source]¶

Check if DVC file exists.

Returns:: True if DVC file exists, False otherwise.
Return type:: bool

check_h5_exists()[source]¶

Check if H5 file exists.

Returns:: True if H5 file exists, False otherwise.
Return type:: bool

get_data()[source]¶: Fetch data using DVC.

has_data()[source]¶

Check if H5 file contains data.

Returns:: True if H5 file contains data, False otherwise.
Return type:: bool

class ersilia.utils.dvc.DVCSetup(local_repo_path, model_id)[source]¶

Bases: object

A class to set up DVC with Google Drive.

Parameters:

local_repo_path (str) – The local repository path.
model_id (str) – The model identifier.

gdrive_folder_id()[source]¶

Get the Google Drive folder ID for the model.

Returns:: The Google Drive folder ID.
Return type:: str

gdrive_setup()[source]¶: Set up Google Drive folder for DVC.

git_add_and_commit(message='Set to public data repo')[source]¶

Add and commit changes to Git.

Parameters:: message (str, optional) – The commit message. Default is “Set to public data repo”.

set_dvc_gdrive()[source]¶: Set up DVC remote storage on Google Drive.

ersilia.utils.dvc.set_secrets_file()[source]¶

ersilia.utils.environment module¶

Utility functions to get information about the working environment.

class ersilia.utils.environment.Environment[source]¶

Bases: object

Class to handle environment settings.

has_module(module_name)[source]¶: Check if Python module is installed.

ersilia.utils.hdf5 module¶

class ersilia.utils.hdf5.Hdf5Data(values, keys, inputs, features)[source]¶

Bases: object

A class to handle HDF5 data storage.

Parameters:

values (array-like) – The data values.
keys (array-like) – The keys associated with the data.
inputs (array-like) – The inputs associated with the data.
features (array-like) – The features associated with the data.

save(filename)[source]¶

Save the data to an HDF5 file.

Parameters:: filename (str) – The path to the HDF5 file.

class ersilia.utils.hdf5.Hdf5DataLoader[source]¶

Bases: object

A class to load data from HDF5 files.

load(h5_file)[source]¶: Load data from an HDF5 file.

load(h5_file)[source]¶

Load data from an HDF5 file.

Parameters:: h5_file (str) – The path to the HDF5 file.

class ersilia.utils.hdf5.Hdf5DataStacker(h5_files)[source]¶

Bases: object

A class to stack multiple HDF5 files into one.

Parameters:: h5_files (list) – A list of paths to the HDF5 files to stack.

stack(h5_file)[source]¶

Stack the HDF5 files into one.

Parameters:: h5_file (str) – The path to the output HDF5 file.

ersilia.utils.import module¶

ersilia.utils.import.import_extra(mod)[source]¶: Try to import a module, if not found return None

ersilia.utils.installers module¶

class ersilia.utils.installers.BaseInstaller(check_install_log, config_json, credentials_json)[source]¶

Bases: ErsiliaBase

Base class for managing installations in Ersilia.

Parameters:

check_install_log (bool) – Whether to check the installation log.
config_json (dict, optional) – Configuration settings in JSON format. Default is None.
credentials_json (dict, optional) – Credentials settings in JSON format. Default is None.

read_log()[source]¶: Read the installation log from a file.

remove_from_log(task)[source]¶

Remove a task from the installation log.

Parameters:: task (str) – The task to remove from the log.

remove_log()[source]¶: Remove the installation log file.

update_log(task)[source]¶

Update the installation log with a new task.

Parameters:: task (str) – The task to add to the log.

write_log()[source]¶: Write the installation log to a file.

class ersilia.utils.installers.Installer(check_install_log=True, config_json=None, credentials_json=None)[source]¶

Bases: BaseInstaller

A class to manage the installation of dependencies for Ersilia.

Parameters:

check_install_log (bool, optional) – Whether to check the installation log. Default is True.
config_json (dict, optional) – Configuration settings in JSON format. Default is None.
credentials_json (dict, optional) – Credentials settings in JSON format. Default is None.

base_conda()[source]¶: Create a base Conda environment.

base_conda_slim()[source]¶: Create a slim base Conda environment.

conda()[source]¶: Check if Conda is installed.

config()[source]¶: Set up the configuration file.

git()[source]¶: Check if Git is installed.

profile()[source]¶: Set up the ‘ersilia’ CLI in the user profile.

rdkit()[source]¶: Install RDKit from Conda if not already installed.

server_docker()[source]¶: Build the Docker server image.

server_docker_slim()[source]¶: Build the slim Docker server image.

class ersilia.utils.installers.Uninstaller(check_install_log=True, config_json=None, credentials_json=None)[source]¶

Bases: BaseInstaller

A class to manage the uninstallation of dependencies for Ersilia.

Parameters:

check_install_log (bool, optional) – Whether to check the installation log. Default is True.
config_json (dict, optional) – Configuration settings in JSON format. Default is None.
credentials_json (dict, optional) – Credentials settings in JSON format. Default is None.

base_conda()[source]¶: Delete the base Conda environment.

rdkit()[source]¶: Uninstall RDKit.

server_docker()[source]¶: Delete the Docker server image.

ersilia.utils.installers.base_installer(ignore_status=False)[source]¶

Perform a bare minimum installation of dependencies.

This function is mainly used to create a base environment for the models.

Parameters:: ignore_status (bool, optional) – Whether to ignore the current installation status. Default is False.
Return type:: None

ersilia.utils.installers.full_installer(ignore_status=False)[source]¶

Perform a full installation of dependencies for Ersilia.

Parameters:: ignore_status (bool, optional) – Whether to ignore the current installation status. Default is False.

ersilia.utils.logging module¶

class ersilia.utils.logging.Logger(*args, **kwargs)[source]¶

Bases: object

A singleton class to manage logging in Ersilia.

set_verbosity(verbose)[source]¶: Set the verbosity of the logger.

debug(text)[source]¶: Log a debug message.

info(text)[source]¶: Log an info message.

warning(text)[source]¶: Log a warning message.

error(text)[source]¶: Log an error message.

critical(text)[source]¶: Log a critical message.

success(text)[source]¶: Log a success message.

critical(text)[source]¶

Log a critical message.

Parameters:: text (str) – The message to log.

debug(text)[source]¶

Log a debug message.

Parameters:: text (str) – The message to log.

error(text)[source]¶

Log an error message.

Parameters:: text (str) – The message to log.

info(text)[source]¶

Log an info message.

Parameters:: text (str) – The message to log.

set_verbosity(verbose)[source]¶

Set the verbosity of the logger.

Parameters:: verbose (bool) – Whether to enable verbose logging.

success(text)[source]¶

Log a success message.

Parameters:: text (str) – The message to log.

warning(text)[source]¶

Log a warning message.

Parameters:: text (str) – The message to log.

ersilia.utils.logging.make_temp_dir(prefix)[source]¶

Create a temporary directory with a symbolic link in the session logs directory.

Parameters:: prefix (str) – The prefix for the temporary directory name.
Returns:: The path to the temporary directory.
Return type:: str

ersilia.utils.paths module¶

class ersilia.utils.paths.ErsiliaMetadataLoader(stream)[source]¶

Bases: SafeLoader

Custom YAML loader for Ersilia metadata.

yaml_constructors = {'tag:yaml.org,2002:binary': <function SafeConstructor.construct_yaml_binary>, 'tag:yaml.org,2002:bool': <function SafeConstructor.construct_yaml_bool>, 'tag:yaml.org,2002:float': <function SafeConstructor.construct_yaml_float>, 'tag:yaml.org,2002:int': <function SafeConstructor.construct_yaml_int>, 'tag:yaml.org,2002:map': <function metadata_constructor>, 'tag:yaml.org,2002:null': <function SafeConstructor.construct_yaml_null>, 'tag:yaml.org,2002:omap': <function SafeConstructor.construct_yaml_omap>, 'tag:yaml.org,2002:pairs': <function SafeConstructor.construct_yaml_pairs>, 'tag:yaml.org,2002:seq': <function SafeConstructor.construct_yaml_seq>, 'tag:yaml.org,2002:set': <function SafeConstructor.construct_yaml_set>, 'tag:yaml.org,2002:str': <function SafeConstructor.construct_yaml_str>, 'tag:yaml.org,2002:timestamp': <function SafeConstructor.construct_yaml_timestamp>, None: <function SafeConstructor.construct_undefined>}¶

class ersilia.utils.paths.Metadata(Identifier: str, Slug: str, Title: str, Description: str, Mode: str, Input: List[str], InputShape: str, Task: List[str], Output: List[str], OutputType: List[str], OutputShape: str, Interpretation: str, Tag: List[str], Publication: str, SourceCode: str, License: str, DockerHub: str | None = None, DockerArchitecture: List[str] | None = None, S3: str | None = None, Status: str | None = None, Contributor: str | None = None)[source]¶

Bases: object

A dataclass to represent metadata for Ersilia models.

Identifier¶

The model identifier.

Type:: str

Slug¶

The model slug.

Type:: str

Title¶

The model title.

Type:: str

Description¶

The model description.

Type:: str

Mode¶

The model mode.

Type:: str

Input¶

The model input types.

Type:: List[str]

InputShape¶

The shape of the model input.

Type:: str

Task¶

The tasks the model performs.

Type:: List[str]

Output¶

The model output types.

Type:: List[str]

OutputType¶

The types of the model output.

Type:: List[str]

OutputShape¶

The shape of the model output.

Type:: str

Interpretation¶

The interpretation of the model output.

Type:: str

Tag¶

The tags associated with the model.

Type:: List[str]

Publication¶

The publication associated with the model.

Type:: str

SourceCode¶

The source code repository for the model.

Type:: str

License¶

The license for the model.

Type:: str

DockerHub¶

The DockerHub repository for the model. Default is None.

Type:: Optional[str], optional

DockerArchitecture¶

The Docker architectures supported by the model. Default is None.

Type:: Optional[List[str]], optional

S3¶

The S3 bucket for the model. Default is None.

Type:: Optional[str], optional

Status¶

The status of the model. Default is None.

Type:: Optional[str], optional

Contributor¶

The contributor of the model. Default is None.

Type:: Optional[str], optional

Contributor: str | None = None¶

Description: str¶

DockerArchitecture: List[str] | None = None¶

DockerHub: str | None = None¶

Identifier: str¶

Input: List[str]¶

InputShape: str¶

Interpretation: str¶

License: str¶

Mode: str¶

Output: List[str]¶

OutputShape: str¶

OutputType: List[str]¶

Publication: str¶

S3: str | None = None¶

Slug: str¶

SourceCode: str¶

Status: str | None = None¶

Tag: List[str]¶

Task: List[str]¶

Title: str¶

class ersilia.utils.paths.Paths[source]¶

Bases: object

A class to handle various path-related operations in Ersilia.

model_id_from_path(path)[source]¶: Guess model identifier based on the path.

org_development_path()[source]¶: Guess generic development path.

ersilia_development_path()[source]¶: Try to guess the package development path in the local computer.

exists(path)[source]¶: Check if a path exists.

ersilia_development_path()[source]¶

Try to guess the package development path in the local computer.

Returns:: The package development path if found, otherwise None.
Return type:: str or None

static exists(path)[source]¶

Check if a path exists.

Parameters:: path (str) – The path to check.
Returns:: True if the path exists, False otherwise.
Return type:: bool

static home()[source]¶

Get home directory.

Returns:: The home directory path.
Return type:: str

model_id_from_path(path)[source]¶

Guess model identifier based on the path.

Parameters:: path (str) – The path to guess the model identifier from.
Returns:: The model identifier if found, otherwise None.
Return type:: str or None

org_development_path()[source]¶

Guess generic development path.

Returns:: The generic development path if found, otherwise None.
Return type:: str or None

ersilia.utils.paths.get_metadata_from_base_dir(path)[source]¶

Get metadata from the base directory of a model.

Parameters:: path (str) – The path to the base directory.
Returns:: The metadata dictionary.
Return type:: dict
Raises:: FileNotFoundError – If the metadata file is not found.

ersilia.utils.paths.metadata_constructor(loader, node)[source]¶

ersilia.utils.paths.resolve_pack_method(model_path)[source]¶

Resolve the packaging method for a model.

Parameters:: model_path (str) – The path to the model directory.
Returns:: The packaging method.
Return type:: str

ersilia.utils.paths.resolve_pack_method_source(model_path)[source]¶

Resolve the packaging method for a model based on its source files.

Parameters:: model_path (str) – The path to the model directory.
Returns:: The packaging method if found, otherwise None.
Return type:: str or None

ersilia.utils.ports module¶

ersilia.utils.ports.find_free_port(preferred_port=None)[source]¶

Find a free port.

Parameters:: preferred_port (int, optional) – The preferred port number to check first. Default is None.
Returns:: A free port number.
Return type:: int

ersilia.utils.ports.is_port_in_use(port)[source]¶

Check if a port is in use.

Parameters:: port (int) – The port number to check.
Returns:: True if the port is in use, False otherwise.
Return type:: bool

ersilia.utils.remove module¶

class ersilia.utils.remove.OsfRemover(username, password)[source]¶

Bases: object

A class to remove files from the Open Science Framework (OSF).

Parameters:

username (str) – The OSF username.
password (str) – The OSF password.

remove(project_id, filename)[source]¶

Remove a file from OSF.

Parameters:

project_id (str) – The OSF project ID.
filename (str) – The name of the file to remove.

ersilia.utils.session module¶

ersilia.utils.session.create_session_dir()[source]¶: Create a session directory.

ersilia.utils.session.create_session_files(session_name)[source]¶

Create session directory and necessary files.

Parameters:: session_name (str) – The name of the session.

ersilia.utils.session.deregister_model_session(model_id)[source]¶

Remove a model from a session.

Parameters:: model_id (str) – The model ID.

ersilia.utils.session.determine_orphaned_session()[source]¶

Determine orphaned sessions.

Returns:: A list of orphaned session names.
Return type:: list

ersilia.utils.session.get_current_pid()[source]¶

Get the current process ID.

Returns:: The current process ID.
Return type:: int

ersilia.utils.session.get_model_session(model_id)[source]¶

Get the model session.

Parameters:: model_id (str) – The model ID.
Returns:: The session ID.
Return type:: str

ersilia.utils.session.get_parent_pid()[source]¶

Get the parent process ID.

Returns:: The parent process ID.
Return type:: int

ersilia.utils.session.get_session_dir()[source]¶

Get the session directory.

Returns:: The session directory path.
Return type:: str

ersilia.utils.session.get_session_id()[source]¶

Get the session ID.

Returns:: The session ID.
Return type:: str

ersilia.utils.session.get_session_uuid()[source]¶

Get the session UUID.

Returns:: The session UUID.
Return type:: str

ersilia.utils.session.register_model_session(model_id, session_dir)[source]¶

Parameters:

model_id (str) – The model ID.
session_dir (str) – The session directory.

ersilia.utils.session.remove_orphaned_sessions()[source]¶: Remove orphaned sessions.

ersilia.utils.session.remove_session_dir(session_name)[source]¶

Remove a session directory.

Parameters:: session_name (str) – The name of the session.

ersilia.utils.spinner module¶

class ersilia.utils.spinner.Spinner(text='Loading...', spinner=None, color='cyan')[source]¶

Bases: object

A colorful and animated loader for terminal applications.

ersilia.utils.spinner.show_loader(text='Loading...', color='cyan')[source]¶

ersilia.utils.system module¶

class ersilia.utils.system.SystemChecker[source]¶

Bases: object

A class to check various system properties.

is_arm64()[source]¶: Check if the system architecture is ARM64.

is_github_action()[source]¶: Check if the code is running inside a GitHub Action.

is_inside_docker()[source]¶: Check if the code is running inside a Docker container.

is_arm64()[source]¶

Check if the system architecture is ARM64.

Returns:: True if the system architecture is ARM64, False otherwise.
Return type:: bool

is_github_action()[source]¶

Check if the code is running inside a GitHub Action.

Returns:: True if running inside a GitHub Action, False otherwise.
Return type:: bool

is_inside_docker()[source]¶

Check if the code is running inside a Docker container.

Returns:: True if running inside a Docker container, False otherwise.
Return type:: bool

ersilia.utils.system.is_inside_docker()[source]¶

Check if the current environment is inside a Docker container.

Returns:: True if inside a Docker container, False otherwise.
Return type:: bool

ersilia.utils.terminal module¶

ersilia.utils.terminal.is_quiet()[source]¶

Check if the current session is in quiet mode.

Returns:: True if the session is in quiet mode, False otherwise.
Return type:: bool

ersilia.utils.terminal.print_result_table(data)[source]¶: Print a result table with solid borders from JSON, CSV, or HDF5-like data. Supports formatted JSON strings.

ersilia.utils.terminal.raw_input_with_timeout(prompt, default_answer, timeout=5)[source]¶

Prompt the user for input with a timeout.

Parameters:

prompt (str) – The prompt message.
default_answer (str) – The default answer if the user does not respond within the timeout.
timeout (int, optional) – The timeout in seconds. Default is 5.

Returns:

The user’s input or the default answer if the timeout is reached.

Return type:

str

ersilia.utils.terminal.run_command(cmd, quiet=None)[source]¶

Run a shell command.

Parameters:

cmd (str or list) – The command to run.
quiet (bool, optional) – Whether to run the command in quiet mode. Default is None.

ersilia.utils.terminal.run_command_check_output(cmd)[source]¶

Run a shell command and capture its output.

Parameters:: cmd (str or list) – The command to run.
Returns:: The output of the command.
Return type:: str

ersilia.utils.terminal.yes_no_input(prompt, default_answer, timeout=5)[source]¶

Prompt the user for a yes/no input with a timeout.

Parameters:

prompt (str) – The prompt message.
default_answer (str) – The default answer if the user does not respond within the timeout.
timeout (int, optional) – The timeout in seconds. Default is 5.

Returns:

True if the user’s input is ‘yes’, False otherwise.

Return type:

bool

ersilia.utils.tracking module¶

ersilia.utils.uninstall module¶

class ersilia.utils.uninstall.Uninstaller[source]¶

Bases: object

A class to manage the uninstallation of Ersilia and its dependencies.

uninstall()[source]¶: Main uninstallation method.

uninstall()[source]¶: Main uninstallation method.

ersilia.utils.upload module¶

class ersilia.utils.upload.OsfUploader(overwrite, username, password)[source]¶

Bases: object

A class to upload files to the Open Science Framework (OSF).

Parameters:

overwrite (bool) – Whether to overwrite existing files.
username (str) – The OSF username.
password (str) – The OSF password.

push(project_id, filename, destination)[source]¶: Upload a file to OSF.

push(project_id, filename, destination)[source]¶

Upload a file to OSF.

Parameters:

project_id (str) – The OSF project ID.
filename (str) – The path to the file to upload.
destination (str) – The destination path on OSF.

ersilia.utils.venv module¶

class ersilia.utils.venv.SimpleVenv(root)[source]¶

Bases: ErsiliaBase

A class to manage virtual environments for Ersilia.

Parameters:: root (str) – The root directory for the virtual environments.

create(environment)¶: Create a new virtual environment.

delete(environment)[source]¶: Delete a virtual environment.

run_commandlines(environment, commandlines)¶: Run command lines in a virtual environment.

create(**kwargs)¶

delete(environment)[source]¶

Delete a virtual environment.

Parameters:: environment (str) – The name of the virtual environment.
Return type:: None

exists(environment)[source]¶

Check if a virtual environment exists.

Parameters:: environment (str) – The name of the virtual environment.
Returns:: True if the virtual environment exists, False otherwise.
Return type:: bool

run_commandlines(**kwargs)¶

ersilia.utils.versioning module¶

class ersilia.utils.versioning.Versioner(config_json=None)[source]¶

Bases: ErsiliaBase

A class to manage versioning information for Ersilia.

python_version(py_format=False)[source]¶: Get the current Python version.

ersilia_version()[source]¶: Get the current Ersilia version.

ersilia_version_with_py()[source]¶: Get the current Ersilia version with Python version.

ersilia_version_from_path(path)[source]¶: Get the Ersilia version from a given path.

bentoml_version()[source]¶: Get the current BentoML version.

server_docker_name(tag=None, as_tuple=False)[source]¶: Get the server Docker image name.

base_conda_name(org, tag)[source]¶: Get the base Conda environment name.

reformat_py(v)[source]¶: Reformat a Python version string.

base_conda_name(org, tag)[source]¶

Get the base Conda environment name.

Parameters:

org (str) – The organization name.
tag (str) – The tag for the Conda environment.

Returns:

The base Conda environment name.

Return type:

str

bentoml_version()[source]¶

Get the current BentoML version.

Returns:: The current BentoML version if available, otherwise None.
Return type:: str or None

ersilia_version()[source]¶

Get the current Ersilia version.

Returns:: The current Ersilia version.
Return type:: str

ersilia_version_from_path(path)[source]¶

Get the Ersilia version from a given path.

Parameters:: path (str) – The path to the Ersilia installation.
Returns:: The Ersilia version if found, otherwise None.
Return type:: str or None

ersilia_version_with_py()[source]¶

Get the current Ersilia version with Python version.

Returns:: The current Ersilia version with Python version.
Return type:: str

python_version(py_format=False)[source]¶

Get the current Python version.

Parameters:: py_format (bool, optional) – Whether to return the version in Python format (e.g., ‘py38’). Default is False.
Returns:: The current Python version.
Return type:: str

static reformat_py(v)[source]¶

Reformat a Python version string.

Parameters:: v (str) – The Python version string.
Returns:: The reformatted Python version string.
Return type:: str
Raises:: Exception – If the version string is too short.

server_docker_name(tag=None, as_tuple=False)[source]¶

Get the server Docker image name.

Parameters:

tag (str, optional) – The tag for the Docker image. Default is None.
as_tuple (bool, optional) – Whether to return the name as a tuple. Default is False.

Returns:

The server Docker image name, or a tuple of (org, img, tag) if as_tuple is True.

Return type:

str or tuple

ersilia.utils.zip module¶

class ersilia.utils.zip.Zipper(remove)[source]¶

Bases: object

A class to handle zipping and unzipping files.

Parameters:: remove (bool) – Whether to remove the original files after zipping/unzipping.

unzip(file, destination)[source]¶: Unzip a file to the specified destination.

zip(dir_name, file)[source]¶: Zip a directory into a file.

unzip(file, destination)[source]¶

Unzip a file to the specified destination.

Parameters:

file (str) – The path to the zip file.
destination (str) – The destination directory.

Return type:

None

zip(dir_name, file)[source]¶

Zip a directory into a file.

Parameters:

dir_name (str) – The path to the directory to zip.
file (str) – The path to the output zip file.

Return type:

None

Module contents¶

ersilia.utils.tmp_pid_file(model_id)[source]¶: Gets filename to store process ID