Index

_

__call__() (ersilia.tools.bentoml.utils.dataclasses.json_serializer method)

A

activate() (ersilia.setup.requirements.git.GitLfsRequirement method), [1] activate_base() (ersilia.utils.conda.CondaUtils method) active_env() (ersilia.utils.conda.SimpleConda method) adapt() (ersilia.io.input.GenericInputAdapter method) (ersilia.io.output.GenericOutputAdapter method), [1] adapt_one_by_one() (ersilia.io.input.GenericInputAdapter method) add() (ersilia.db.disk.fetched.FetchedModelsManager method) add_info_api() (ersilia.hub.bundle.repo.ServiceFile method) add_model_install_commands() (ersilia.hub.bundle.bundle.BundleEnvironmentFile method) (ersilia.hub.bundle.bundle.BundleRequirementsFile method) airtable() (ersilia.hub.content.catalog.ModelCatalog method) ALL (ersilia.store.utils.OutputSource attribute) AnnotatedDataTyper (class in ersilia.io.annotated) Api (class in ersilia.serve.api) api() (ersilia.core.model.ErsiliaModel method) (ersilia.serve.autoservice.AutoService method) (ersilia.serve.services.CondaEnvironmentService method) (ersilia.serve.services.DockerImageService method) (ersilia.serve.services.DummyService method) (ersilia.serve.services.HostedService method) (ersilia.serve.services.PipInstalledService method) (ersilia.serve.services.PulledDockerImageService method) (ersilia.serve.services.SystemBundleService method) (ersilia.serve.services.VenvEnvironmentService method)

api_task() (ersilia.core.model.ErsiliaModel method) ApiClient (class in ersilia.store.utils) ApiErsiliaError ApiSchema (class in ersilia.serve.schema) ApiSpecifiedOutputError append_run_command() (ersilia.hub.bundle.repo.DockerfileFile method) ArbitraryIdentifier (class in ersilia.utils.identifiers.arbitrary) as_dict() (ersilia.hub.content.base_information.BaseInformation method) (ersilia.tools.bentoml.configuration.configparser.BentoMLConfigParser method) as_json() (ersilia.hub.content.catalog.CatalogTable method) as_list_of_dicts() (ersilia.hub.content.catalog.CatalogTable method) as_table() (ersilia.hub.content.catalog.CatalogTable method) async_pull() (ersilia.hub.pull.pull.ModelPuller method) async_serialize_to_json_one_column() (ersilia.serve.standard_api.StandardCSVRunApi method) Auth (class in ersilia.auth.auth) auth() (ersilia.cli.cmd.Command method) auth_cmd() (in module ersilia.cli.commands.auth) AutoService (class in ersilia.serve.autoservice) AwsConfig (class in ersilia.core.tracking)

B

BadGatewayError BASE (ersilia.publish.test.services.constants.Options attribute) base_conda() (ersilia.utils.installers.Installer method) (ersilia.utils.installers.Uninstaller method) base_conda_name() (ersilia.utils.versioning.Versioner method), [1] base_conda_slim() (ersilia.utils.installers.Installer method) base_installer() (in module ersilia.utils.installers) BASE_URL (ersilia.publish.test.services.setup.SetupService attribute) BaseAction (class in ersilia.hub.fetch.actions) BaseConda (class in ersilia.utils.conda) BaseInformation (class in ersilia.hub.content.base_information) BaseInformationError BaseInstaller (class in ersilia.utils.installers) BaseIOGetter (class in ersilia.io.input) BaseJsonFile (class in ersilia.io.readers.file) BasePack (class in ersilia.hub.fetch.pack.bentoml_pack) (class in ersilia.hub.fetch.pack.fastapi_pack) BaseServing (class in ersilia.serve.services) BaseTabularFile (class in ersilia.io.readers.file) bashrc_cli_snippet() (in module ersilia.default) bashrc_path() (in module ersilia.default) batch_iter() (ersilia.io.input.GenericInputAdapter method) BatchCacher (class in ersilia.io.readers.file) bentoml() (ersilia.hub.content.catalog.ModelCatalog method)

bentoml_common_params() (ersilia.cli.commands.ErsiliaCommandGroup static method) BENTOML_FILES (ersilia.publish.test.services.inspect.ModelInspector attribute) bentoml_version() (ersilia.utils.versioning.Versioner method), [1] BentoMLConfigException BentoMLConfigParser (class in ersilia.tools.bentoml.configuration.configparser) BentoMLException BentoMLRequirement (class in ersilia.setup.requirements.bentoml_requirement) biomedical_area (ersilia.hub.content.base_information.BaseInformation property) BiomedicalAreaBaseInformationError both_identifiers (ersilia.hub.content.base_information.BaseInformation property) BothIdentifiersBaseInformationError BOTTOM_LEFT (ersilia.default.TableConstants attribute) BOTTOM_MIDDLE (ersilia.default.TableConstants attribute) BOTTOM_RIGHT (ersilia.default.TableConstants attribute) build() (ersilia.db.environments.managers.DockerManager method) (ersilia.utils.docker.SimpleDocker method) build_image() (ersilia.publish.dockerhub.DockerHubUploader method) build_with_bentoml() (ersilia.db.environments.managers.DockerManager method) build_with_ersilia() (ersilia.db.environments.managers.DockerManager method) BuiltinExampleReader (class in ersilia.hub.fetch.actions.sniff_bentoml) (class in ersilia.hub.fetch.actions.sniff_fastapi) BundleDockerfileFile (class in ersilia.hub.bundle.bundle) BundleEnvironmentFile (class in ersilia.hub.bundle.bundle) BundleRequirementsFile (class in ersilia.hub.bundle.bundle)

C

cache_missing_results() (ersilia.store.dump.DumpLocalCache method) CACHE_ONLY (ersilia.store.utils.OutputSource attribute) calculate_directory_size() (ersilia.publish.test.services.io.IOService method) calculate_image_size() (ersilia.publish.test.services.io.IOService method) can_be_deleted() (ersilia.hub.delete.delete.ModelFullDeleter method) CardErsiliaError CardGetter (class in ersilia.hub.fetch.actions.content) catalog() (ersilia.cli.cmd.Command method) catalog_cmd() (in module ersilia.cli.commands.catalog) CatalogErsiliaError CatalogTable (class in ersilia.hub.content.catalog) CELL_PADDING (ersilia.default.TableConstants attribute) check() (ersilia.hub.bundle.bundle.BundleDockerfileFile method) (ersilia.hub.bundle.bundle.BundleEnvironmentFile method) (ersilia.hub.bundle.bundle.BundleRequirementsFile method) (ersilia.hub.bundle.repo.DockerfileFile method) (ersilia.hub.bundle.repo.PackFile method) (ersilia.hub.bundle.repo.ReadmeFile method) (ersilia.hub.bundle.repo.ServiceFile method) (ersilia.hub.fetch.actions.check.ModelChecker method) (ersilia.hub.fetch.actions.setup.SetupChecker method), [1] check_bentoml() (in module ersilia.setup.requirements) check_complete_folder_structure() (ersilia.publish.test.services.inspect.ModelInspector method) check_complete_metadata() (ersilia.publish.test.services.inspect.ModelInspector method) check_computational_performance() (ersilia.publish.test.services.inspect.ModelInspector method) check_consistent_output() (ersilia.publish.test.services.checks.CheckService method) check_dependencies_are_valid() (ersilia.publish.test.services.inspect.ModelInspector method) check_files() (ersilia.publish.test.services.checks.CheckService method) check_information() (ersilia.publish.test.services.checks.CheckService method) check_install_status() (in module ersilia) check_model_id() (ersilia.io.input.ExampleGenerator method) check_model_output_content() (ersilia.publish.test.services.checks.CheckService method) check_no_extra_files() (ersilia.publish.test.services.inspect.ModelInspector method) check_repo_exists() (ersilia.publish.test.services.inspect.ModelInspector method) check_simple_model_output() (ersilia.publish.test.services.checks.CheckService method) Checks (class in ersilia.publish.test.services.constants) CheckService (class in ersilia.publish.test.services.checks) CheckStrategy (class in ersilia.publish.test.services.inspect) checksum_from_conda_yml_file() (ersilia.utils.conda.CondaUtils static method) checksum_from_dockerfile() (ersilia.utils.conda.CondaUtils method) checksum_from_file() (ersilia.utils.conda.CondaUtils method) choice() (ersilia.utils.identifiers.model.ModelIdentifier method) clean() (ersilia.db.environments.localdb.EnvironmentDb method) (ersilia.db.hubdata.localslugs.SlugDb method) (ersilia.hub.delete.delete.ModelBentoDeleter method), [1] (ersilia.publish.rebase.TemplateRebaser method) clean_before_serving() (ersilia.serve.autoservice.AutoService method) clean_docker_containers() (ersilia.serve.autoservice.AutoService method) clean_temp() (ersilia.publish.test.test.ModelTester method) clean_temp_dir() (ersilia.serve.autoservice.AutoService method) cleanup_ersilia_images() (ersilia.utils.docker.SimpleDocker method) ClearErsiliaError ClickInterface (class in ersilia.store.utils) clone() (ersilia.setup.utils.clone.ErsiliaCloner method), [1] (ersilia.utils.conda.SimpleConda method) (ersilia.utils.download.GitHubDownloader method) clone_current_model() (ersilia.publish.rebase.TemplateRebaser method) clone_template() (ersilia.publish.rebase.TemplateRebaser method) close() (ersilia.cli.cmd.Command method) (ersilia.core.model.ErsiliaModel method) (ersilia.core.session.Session method) (ersilia.serve.autoservice.AutoService method) (ersilia.serve.services.CondaEnvironmentService method) (ersilia.serve.services.DockerImageService method) (ersilia.serve.services.DummyService method) (ersilia.serve.services.HostedService method) (ersilia.serve.services.PipInstalledService method) (ersilia.serve.services.PulledDockerImageService method) (ersilia.serve.services.SystemBundleService method) (ersilia.serve.services.VenvEnvironmentService method) close_cmd() (in module ersilia.cli.commands.close) CloseErsiliaError CLOUD (ersilia.store.utils.OutputSource attribute) CLOUD_ONLY (ersilia.store.utils.OutputSource attribute) collect_and_save_json() (ersilia.publish.test.services.io.IOService method) COLUMN_CHECK_FAILURE (ersilia.publish.test.services.constants.Checks attribute) COLUMN_CHECK_SUCCESS (ersilia.publish.test.services.constants.Checks attribute) column_delimiter() (ersilia.io.types.compound.IO method) (ersilia.io.types.text.IO method) COLUMN_NAME_VALIDITY (ersilia.publish.test.services.constants.Checks attribute)

COLUMN_SEPARATOR (ersilia.default.TableConstants attribute) columns (ersilia.io.output.DataFrame attribute) columns() (ersilia.hub.fetch.actions.sniff_fastapi.BuiltinExampleReader method), [1] ColumnsFileReader (class in ersilia.hub.fetch.actions.sniff_fastapi) ColumnsInformation (class in ersilia.hub.content.columns_information) Command (class in ersilia.cli.cmd) command() (ersilia.cli.commands.ErsiliaCommandGroup method) compare_csv_columns() (ersilia.publish.test.services.checks.CheckService method) CompoundIdentifier (class in ersilia.utils.identifiers.compound) COMPUTATIONAL_PERFORMANCE (ersilia.publish.test.services.constants.TableType attribute) computational_performance_fiftyeight (ersilia.hub.content.base_information.BaseInformation property) computational_performance_four (ersilia.hub.content.base_information.BaseInformation property) computational_performance_hundred (ersilia.hub.content.base_information.BaseInformation property) computational_performance_seven (ersilia.hub.content.base_information.BaseInformation property) computational_performance_thirtyfour (ersilia.hub.content.base_information.BaseInformation property) computational_performance_twelve (ersilia.hub.content.base_information.BaseInformation property) computational_performance_twenty (ersilia.hub.content.base_information.BaseInformation property) ComputationalPerformanceFiftyeightBaseInformationError ComputationalPerformanceFourBaseInformationError ComputationalPerformanceHundredBaseInformationError ComputationalPerformanceSevenBaseInformationError ComputationalPerformanceThirtyfourBaseInformationError ComputationalPerformanceTwelveBaseInformationError ComputationalPerformanceTwentyBaseInformationError conda() (ersilia.utils.installers.Installer method) conda_prefix() (ersilia.utils.conda.BaseConda method) (ersilia.utils.conda.BaseConda static method) CondaEnvironmentExistsError CondaEnvironmentService (class in ersilia.serve.services) CondaManager (class in ersilia.db.environments.managers) CondaPack (class in ersilia.hub.fetch.pack.bentoml_pack.runners) (class in ersilia.hub.fetch.pack.fastapi_pack.runners) CondaRequirement (class in ersilia.setup.requirements.conda) CondaSetupError CondaUtils (class in ersilia.utils.conda) Config (class in ersilia.utils.config) config() (ersilia.utils.installers.Installer method) (in module ersilia.tools.bentoml.configuration) config_json (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher attribute) (ersilia.hub.fetch.lazy_fetchers.hosted.ModelHostedFetcher attribute) (ersilia.hub.fetch.pack.bentoml_pack.mode.PackModeDecision attribute) (ersilia.io.output.DictlistDataframeConverter attribute) (ersilia.io.output.GenericOutputAdapter attribute) (ersilia.io.output.ResponseRefactor attribute) conn_redis() (ersilia.store.dump.DumpLocalCache method) CONSISTENCY (ersilia.publish.test.services.constants.Checks attribute) CONSISTENCY_BASH (ersilia.publish.test.services.constants.TableType attribute) container_exists() (ersilia.db.environments.managers.DockerManager method) container_peak() (ersilia.utils.docker.SimpleDocker method) ContainerMetricsSampler (class in ersilia.utils.docker) containers() (ersilia.db.environments.managers.DockerManager method) (ersilia.utils.docker.SimpleDocker method) containers_of_model() (ersilia.db.environments.managers.DockerManager method) contributor (ersilia.hub.content.base_information.BaseInformation property) Contributor (ersilia.utils.paths.Metadata attribute), [1] ContributorBaseInformationError convert_smiles_to_checksum() (ersilia.utils.identifiers.compound.CompoundIdentifier method) copy_example_if_available() (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher method), [1] copy_information() (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher method), [1] copy_metadata() (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher method), [1] copy_status() (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher method), [1] cp_from_container() (ersilia.utils.docker.SimpleDocker static method) cp_from_image() (ersilia.utils.docker.SimpleDocker method) create() (ersilia.utils.conda.SimpleConda method) (ersilia.utils.venv.SimpleVenv method), [1] create_ersilia_cli() (in module ersilia.cli.create_cli) create_event_data() (ersilia.core.tracking.RunTracker method) create_executable_bash_script() (ersilia.utils.conda.SimpleConda method) create_session_dir() (in module ersilia.utils.session) create_session_files() (in module ersilia.utils.session) create_table() (ersilia.db.environments.localdb.EnvironmentDb method) (ersilia.db.hubdata.localslugs.SlugDb method) create_temp_csv() (ersilia.store.utils.FileManager static method) Credentials (class in ersilia.utils.config) critical() (ersilia.utils.logging.Logger method), [1] CSV_CONTENT_CHECK (ersilia.publish.test.services.constants.Checks attribute) CsvDataLoader (class in ersilia.utils.csvfile) current_identifier() (ersilia.core.session.Session method) current_model_id() (ersilia.core.session.Session method) current_output_source() (ersilia.core.session.Session method) current_service_class() (ersilia.core.session.Session method)

D

data (ersilia.io.output.DataFrame attribute) DataclassJsonEncoder (class in ersilia.tools.bentoml.utils.dataclasses) Dataframe (class in ersilia.io.dataframe) DataFrame (class in ersilia.io.output) dataframe2dictlist() (ersilia.io.output.DictlistDataframeConverter method), [1] date (ersilia.hub.content.base_information.BaseInformation property) debug() (ersilia.utils.logging.Logger method), [1] decide() (ersilia.hub.fetch.pack.bentoml_pack.mode.PackModeDecision method), [1] (ersilia.hub.fetch.pack.fastapi_pack.mode.PackModeDecision method) decide_from_config_file_if_available() (ersilia.hub.fetch.pack.bentoml_pack.mode.PackModeDecision method), [1] (ersilia.hub.fetch.pack.fastapi_pack.mode.PackModeDecision method) decode() (ersilia.hub.content.slug.Slug method) decompose() (ersilia.io.output.DataFrame method), [1] DEEP_INPUT (ersilia.publish.test.services.constants.Options attribute) default() (ersilia.tools.bentoml.utils.dataclasses.DataclassJsonEncoder method), [1] default_env() (ersilia.utils.conda.BaseConda method) (ersilia.utils.conda.BaseConda static method) del_model() (in module ersilia.utils.cron) delete() (ersilia.cli.cmd.Command method) (ersilia.db.disk.fetched.FetchedModelsManager method) (ersilia.db.environments.localdb.EnvironmentDb method) (ersilia.db.hubdata.localslugs.SlugDb method) (ersilia.hub.delete.delete.ModelBentoDeleter method), [1] (ersilia.hub.delete.delete.ModelBundleDeleter method), [1] (ersilia.hub.delete.delete.ModelCondaDeleter method), [1] (ersilia.hub.delete.delete.ModelDockerDeleter method), [1] (ersilia.hub.delete.delete.ModelEosDeleter method), [1] (ersilia.hub.delete.delete.ModelFetchedEntryDeleter method), [1] (ersilia.hub.delete.delete.ModelFullDeleter method), [1] (ersilia.hub.delete.delete.ModelPipDeleter method), [1] (ersilia.hub.delete.delete.ModelSlugDeleter method), [1] (ersilia.hub.delete.delete.ModelTmpDeleter method), [1] (ersilia.hub.delete.delete.TmpCleaner method), [1] (ersilia.publish.test.services.runner.RunnerService method) (ersilia.setup.baseconda.SetupBaseConda method), [1] (ersilia.setup.basedocker.SetupBaseDocker method) (ersilia.utils.conda.SimpleConda method) (ersilia.utils.docker.SimpleDocker method) (ersilia.utils.venv.SimpleVenv method), [1] delete_by_model_id() (ersilia.db.hubdata.localslugs.SlugDb method) delete_by_slug() (ersilia.db.hubdata.localslugs.SlugDb method) delete_cmd() (in module ersilia.cli.commands.delete) delete_containers() (ersilia.db.environments.managers.DockerManager method) delete_file_upon_upload() (in module ersilia.store.utils)

delete_image() (ersilia.db.environments.managers.DockerManager method) delete_images() (ersilia.db.environments.managers.DockerManager method) delete_one() (ersilia.utils.conda.SimpleConda method) DEPENDECY_COLUMN_CHECK (ersilia.publish.test.services.constants.TableType attribute) DEPENDENCY_PINNED (ersilia.publish.test.services.constants.Checks attribute) deployment (ersilia.hub.content.base_information.BaseInformation property) DeploymentBaseInformationError deregister_model_session() (in module ersilia.utils.session) description (ersilia.hub.content.base_information.BaseInformation property) Description (ersilia.utils.paths.Metadata attribute), [1] DescriptionBaseInformationError details (ersilia.publish.test.services.inspect.Result attribute) determine_orphaned_session() (in module ersilia.utils.session) dictlist2dataframe() (ersilia.io.output.DictlistDataframeConverter method), [1] DictlistDataframeConverter (class in ersilia.io.output) DIR_SIZE (ersilia.publish.test.services.constants.Checks attribute) docker_architecture (ersilia.hub.content.base_information.BaseInformation property) DockerArchitecture (ersilia.utils.paths.Metadata attribute), [1] DockerArchitectureBaseInformationError DockerConventionalPullError DockerfileCreator (class in ersilia.hub.fetch.actions.get) DockerfileFile (class in ersilia.hub.bundle.repo) dockerhub (ersilia.hub.content.base_information.BaseInformation property) DockerHub (ersilia.utils.paths.Metadata attribute), [1] DockerhubBaseInformationError DockerHubUploader (class in ersilia.publish.dockerhub) DockerImageArchitectureNotAvailableError DockerImageNotAvailableError DockerImageService (class in ersilia.serve.services) dockerize() (ersilia.hub.fetch.actions.toolize.ModelToolizer method) DockerManager (class in ersilia.db.environments.managers) DockerNotActiveError, [1] DockerPack (class in ersilia.hub.fetch.pack.bentoml_pack.runners) DockerRequirement (class in ersilia.setup.requirements.docker) download_file_from_google_drive() (ersilia.utils.download.GoogleDriveDownloader method) download_from_s3() (ersilia.utils.download.S3Downloader method) download_single() (ersilia.utils.download.GitHubDownloader method) download_stream() (ersilia.store.utils.ApiClient method) DummyService (class in ersilia.serve.services) dump() (ersilia.cli.cmd.Command method) dump_cmd() (in module ersilia.cli.commands.dump) DumpLocalCache (class in ersilia.store.dump) dvc_part() (ersilia.publish.rebase.TemplateRebaser method) DynamoDbTable (class in ersilia.db.hubdata.tables)

E

echo() (ersilia.cli.messages.ModelNotFound method), [1] (ersilia.cli.messages.ModelNotInLocal method), [1] (ersilia.hub.content.information.InformationDisplayer method) (ersilia.store.utils.ClickInterface method) (ersilia.store.utils.ModelNotInStore method) (ersilia.store.utils.PrecalculationsInStore method) (ersilia.store.utils.PrecalculationsNotInStore method) (in module ersilia.cli) (in module ersilia.cli.echo) (in module ersilia.utils.exceptions_utils.handle_undecorated_exception) (in module ersilia.utils.exceptions_utils.throw_ersilia_exception) echo_found_shards() (in module ersilia.store.utils) echo_intro() (in module ersilia.store.utils) echo_job_submitted() (in module ersilia.store.utils) echo_job_succeeded() (in module ersilia.store.utils) echo_local_sample_warning() (in module ersilia.store.utils) echo_merged_saved() (in module ersilia.store.utils) echo_redis_fetched_missed() (in module ersilia.store.utils) echo_redis_job_submitted() (in module ersilia.store.utils) echo_redis_local_completed() (in module ersilia.store.utils) echo_small_sample_warning() (in module ersilia.store.utils) echo_status() (in module ersilia.store.utils) echo_submitting_job() (in module ersilia.store.utils) echo_upload_complete() (in module ersilia.store.utils) echo_uploading_inputs() (in module ersilia.store.utils) empty() (ersilia.serve.schema.ApiSchema method) empty_by_api() (ersilia.serve.schema.ApiSchema method) empty_by_field() (ersilia.serve.schema.ApiSchema method) empty_input_by_api() (ersilia.serve.schema.ApiSchema method) empty_output_by_api() (ersilia.serve.schema.ApiSchema method) EmptyField EmptyKey EmptyOutputError encode() (ersilia.hub.content.slug.Slug method) (ersilia.utils.identifiers.arbitrary.ArbitraryIdentifier method) (ersilia.utils.identifiers.compound.CompoundIdentifier method) (ersilia.utils.identifiers.file.FileIdentifier method) (ersilia.utils.identifiers.long.LongIdentifier method) (ersilia.utils.identifiers.long.LongIdentifier static method) (ersilia.utils.identifiers.model.ModelIdentifier method) (ersilia.utils.identifiers.short.ShortIdentifier method) (ersilia.utils.identifiers.text.TextIdentifier method) (ersilia.utils.identifiers.timestamp.TimeStampIdentifier method) encode_batch() (ersilia.utils.identifiers.compound.CompoundIdentifier method) ensure_redis_running() (ersilia.utils.cache.SetupRedis method) ENV_SIZE (ersilia.publish.test.services.constants.Checks attribute) Environment (class in ersilia.utils.environment) environment_size (ersilia.hub.content.base_information.BaseInformation property) EnvironmentDb (class in ersilia.db.environments.localdb) environments() (ersilia.db.environments.managers.CondaManager method) EnvironmentSizeMbBaseInformationError envs_of_model() (ersilia.db.environments.localdb.EnvironmentDb method) envs_with_same_model() (ersilia.db.environments.localdb.EnvironmentDb method) eos_home_path_exists() (ersilia.setup.requirements.eospath.EosHomePathRequirement method), [1] EosHomePathNotFoundError EosHomePathRequirement (class in ersilia.setup.requirements.eospath) error() (ersilia.utils.logging.Logger method), [1] ersilia module ersilia.app module ersilia.app.fastapi module ersilia.app.streamlit module ersilia.auth module ersilia.auth.auth module ersilia.cli module ersilia.cli.cmd module ersilia.cli.commands module ersilia.cli.commands.auth module ersilia.cli.commands.catalog module ersilia.cli.commands.close module ersilia.cli.commands.delete module ersilia.cli.commands.dump module ersilia.cli.commands.example module ersilia.cli.commands.fetch module ersilia.cli.commands.info module ersilia.cli.commands.run module ersilia.cli.commands.serve module ersilia.cli.commands.test module ersilia.cli.commands.uninstall module ersilia.cli.commands.utils module ersilia.cli.create_cli module ersilia.cli.echo module ersilia.cli.messages module ersilia.core module ersilia.core.base module ersilia.core.model module ersilia.core.modelbase module ersilia.core.session module ersilia.core.tracking module ersilia.db module ersilia.db.disk module ersilia.db.disk.fetched module ersilia.db.environments module ersilia.db.environments.localdb module ersilia.db.environments.managers module ersilia.db.hubdata module ersilia.db.hubdata.interfaces module ersilia.db.hubdata.localslugs module ersilia.db.hubdata.tables module ersilia.default module ersilia.hub module ersilia.hub.bundle module ersilia.hub.bundle.bundle module ersilia.hub.bundle.repo module ersilia.hub.bundle.status module ersilia.hub.content module ersilia.hub.content.base_information module ersilia.hub.content.card module ersilia.hub.content.catalog module ersilia.hub.content.columns_information module ersilia.hub.content.information module ersilia.hub.content.search module ersilia.hub.content.slug module ersilia.hub.delete module ersilia.hub.delete.delete module ersilia.hub.fetch module ersilia.hub.fetch.actions module ersilia.hub.fetch.actions.check module ersilia.hub.fetch.actions.content module ersilia.hub.fetch.actions.get module ersilia.hub.fetch.actions.inform module ersilia.hub.fetch.actions.modify module ersilia.hub.fetch.actions.pack_bentoml module ersilia.hub.fetch.actions.pack_fastapi module ersilia.hub.fetch.actions.prepare module ersilia.hub.fetch.actions.setup module ersilia.hub.fetch.actions.sniff_bentoml module ersilia.hub.fetch.actions.sniff_fastapi module ersilia.hub.fetch.actions.template_resolver module ersilia.hub.fetch.actions.toolize module ersilia.hub.fetch.fetch module ersilia.hub.fetch.fetch_bentoml module ersilia.hub.fetch.fetch_fastapi module ersilia.hub.fetch.lazy_fetchers module ersilia.hub.fetch.lazy_fetchers.dockerhub module ersilia.hub.fetch.lazy_fetchers.hosted module ersilia.hub.fetch.pack module ersilia.hub.fetch.pack.bentoml_pack module ersilia.hub.fetch.pack.bentoml_pack.mode module ersilia.hub.fetch.pack.bentoml_pack.runners module ersilia.hub.fetch.pack.fastapi_pack module ersilia.hub.fetch.pack.fastapi_pack.mode module ersilia.hub.fetch.pack.fastapi_pack.runners module ersilia.hub.fetch.register module ersilia.hub.fetch.register.register module ersilia.hub.fetch.register.standard_example module ersilia.hub.pull module ersilia.hub.pull.pull module ersilia.io module ersilia.io.annotated module ersilia.io.dataframe module ersilia.io.input module ersilia.io.output module ersilia.io.output_logger module ersilia.io.pure module ersilia.io.readers module ersilia.io.readers.file module ersilia.io.readers.pyinput module ersilia.io.shape module ersilia.io.types module

ersilia.io.types.compound module ersilia.io.types.examples module ersilia.io.types.examples.compound module ersilia.io.types.examples.text module ersilia.io.types.naive module ersilia.io.types.text module ersilia.publish module ersilia.publish.dockerhub module ersilia.publish.rebase module ersilia.publish.s3 module ersilia.publish.store module ersilia.publish.test module ersilia.publish.test.services module ersilia.publish.test.services.checks module ersilia.publish.test.services.constants module ersilia.publish.test.services.inspect module ersilia.publish.test.services.io module ersilia.publish.test.services.runner module ersilia.publish.test.services.setup module ersilia.publish.test.test module ersilia.serve module ersilia.serve.api module ersilia.serve.autoservice module ersilia.serve.environment module ersilia.serve.environment.environment_variables module ersilia.serve.schema module ersilia.serve.services module ersilia.serve.standard_api module ersilia.setup module ersilia.setup.baseconda module ersilia.setup.basedocker module ersilia.setup.conda module ersilia.setup.config module ersilia.setup.profile module ersilia.setup.requirements module ersilia.setup.requirements.bentoml_requirement module ersilia.setup.requirements.conda module ersilia.setup.requirements.docker module ersilia.setup.requirements.eospath module ersilia.setup.requirements.git module ersilia.setup.requirements.ping module ersilia.setup.requirements.setuptools_req module ersilia.setup.utils module ersilia.setup.utils.clone module ersilia.store module ersilia.store.api module ersilia.store.dump module ersilia.store.utils module ersilia.tools module ersilia.tools.bentoml module ersilia.tools.bentoml.configuration module ersilia.tools.bentoml.configuration.configparser module ersilia.tools.bentoml.exceptions module ersilia.tools.bentoml.utils module ersilia.tools.bentoml.utils.dataclasses module ersilia.utils module ersilia.utils.cache module ersilia.utils.cli_query module ersilia.utils.conda module ersilia.utils.config module ersilia.utils.cron module ersilia.utils.csvfile module ersilia.utils.docker module ersilia.utils.download module ersilia.utils.environment module ersilia.utils.exceptions_utils module ersilia.utils.exceptions_utils.api_exceptions module ersilia.utils.exceptions_utils.base_information_exceptions module ersilia.utils.exceptions_utils.card_exceptions module ersilia.utils.exceptions_utils.catalog_exceptions module ersilia.utils.exceptions_utils.clear_exceptions module ersilia.utils.exceptions_utils.close_exceptions module ersilia.utils.exceptions_utils.delete_exceptions module ersilia.utils.exceptions_utils.example_exceptions module ersilia.utils.exceptions_utils.exceptions module ersilia.utils.exceptions_utils.fetch_exceptions module ersilia.utils.exceptions_utils.handle_undecorated_exception module ersilia.utils.exceptions_utils.hubdata_exceptions module ersilia.utils.exceptions_utils.issue_reporting module ersilia.utils.exceptions_utils.pull_exceptions module ersilia.utils.exceptions_utils.serve_exceptions module ersilia.utils.exceptions_utils.setup_exceptions module ersilia.utils.exceptions_utils.test_exceptions module ersilia.utils.exceptions_utils.throw_ersilia_exception module ersilia.utils.exceptions_utils.tracking_exceptions module ersilia.utils.hdf5 module ersilia.utils.identifiers module ersilia.utils.identifiers.arbitrary module ersilia.utils.identifiers.compound module ersilia.utils.identifiers.file module ersilia.utils.identifiers.long module ersilia.utils.identifiers.model module ersilia.utils.identifiers.short module ersilia.utils.identifiers.text module ersilia.utils.identifiers.timestamp module ersilia.utils.import module ersilia.utils.installers module ersilia.utils.logging module ersilia.utils.paths module ersilia.utils.ports module ersilia.utils.remove module ersilia.utils.resolvers module ersilia.utils.session module ersilia.utils.spinner module ersilia.utils.supp module ersilia.utils.supp.conda_env_resolve module ersilia.utils.system module ersilia.utils.terminal module ersilia.utils.tracking module ersilia.utils.uninstall module ersilia.utils.upload module ersilia.utils.venv module ersilia.utils.versioning module ersilia.utils.zip module ersilia_development_path() (ersilia.utils.paths.Paths method), [1] ersilia_version() (ersilia.utils.versioning.Versioner method), [1] ersilia_version_from_path() (ersilia.utils.versioning.Versioner method), [1] ersilia_version_with_py() (ersilia.utils.versioning.Versioner method), [1] ErsiliaBase (class in ersilia.core.base) ErsiliaCloner (class in ersilia.setup.utils.clone) ErsiliaCommandGroup (class in ersilia.cli.commands) ErsiliaError ErsiliaMetadataLoader (class in ersilia.utils.paths) ErsiliaModel (class in ersilia.core.model) ERSILIAPACK_FILES (ersilia.publish.test.services.inspect.ModelInspector attribute) example() (ersilia.cli.cmd.Command method) (ersilia.core.model.ErsiliaModel method) (ersilia.hub.fetch.actions.sniff_bentoml.BuiltinExampleReader method), [1] (ersilia.io.input.ExampleGenerator method) (ersilia.io.types.compound.IO method) (ersilia.io.types.text.IO method) example_cmd() (in module ersilia.cli.commands.example) EXAMPLE_CSV (ersilia.publish.test.services.constants.Options attribute) ExampleErsiliaError ExampleGenerator (class in ersilia.io.input) exec() (ersilia.utils.docker.SimpleDocker method) exec_container() (ersilia.utils.docker.SimpleDocker static method) execute() (ersilia.publish.test.services.inspect.CheckStrategy method) exists() (ersilia.hub.fetch.fetch.ModelFetcher method) (ersilia.utils.conda.SimpleConda method) (ersilia.utils.conda.StandaloneConda method) (ersilia.utils.docker.SimpleDocker method) (ersilia.utils.identifiers.model.ModelIdentifier method) (ersilia.utils.paths.Paths method) (ersilia.utils.paths.Paths static method) (ersilia.utils.venv.SimpleVenv method) expand_env_var() (in module ersilia.tools.bentoml.configuration) export_env_yml() (ersilia.utils.conda.SimpleConda method)

F

FAILED (ersilia.publish.test.services.constants.STATUS_CONFIGS attribute) (ersilia.store.utils.JobStatus attribute) fetch() (ersilia.cli.cmd.Command method) (ersilia.core.model.ErsiliaModel method) (ersilia.hub.fetch.fetch.ModelFetcher method) (ersilia.hub.fetch.fetch_bentoml.ModelFetcherFromBentoML method) (ersilia.hub.fetch.fetch_fastapi.ModelFetcherFromFastAPI method) (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher method), [1] (ersilia.hub.fetch.lazy_fetchers.hosted.ModelHostedFetcher method), [1] (ersilia.publish.test.services.runner.RunnerService method) (ersilia.utils.download.OsfDownloader method) (ersilia.utils.download.PseudoDownloader method) fetch_all_cached() (ersilia.store.dump.DumpLocalCache method) fetch_cached_results() (ersilia.store.dump.DumpLocalCache method) fetch_cmd() (in module ersilia.cli.commands.fetch) fetch_or_cache_header() (ersilia.store.dump.DumpLocalCache method)

fetch_success (ersilia.hub.fetch.fetch.FetchResult attribute) fetch_zip() (ersilia.utils.download.GoogleDriveDownloader method) fetchall() (ersilia.db.environments.localdb.EnvironmentDb method) FetchedModelsManager (class in ersilia.db.disk.fetched) FetchErsiliaError FetchResult (class in ersilia.hub.fetch.fetch) file_names (ersilia.io.output.TabularOutputStacker attribute) FileIdentifier (class in ersilia.utils.identifiers.file) FileManager (class in ersilia.store.utils) FileTyper (class in ersilia.io.readers.file) FINAL_RUN_SUMMARY (ersilia.publish.test.services.constants.TableType attribute) find_closest_python_version() (ersilia.setup.baseconda.SetupBaseConda method), [1] find_free_port() (in module ersilia.utils.ports) FolderNotFoundError from_csv() (ersilia.io.dataframe.Dataframe method) from_dict() (ersilia.hub.content.base_information.BaseInformation method) full_installer() (in module ersilia.utils.installers)

G

generate() (ersilia.utils.identifiers.model.ModelIdentifier method) generate_redis_key() (ersilia.store.dump.DumpLocalCache method) generate_separator_line() (ersilia.hub.content.catalog.CatalogTable method) GenericInputAdapter (class in ersilia.io.input) GenericOutputAdapter (class in ersilia.io.output) get() (ersilia.core.session.Session method) (ersilia.core.tracking.AwsConfig method) (ersilia.hub.content.card.LocalCard method) (ersilia.hub.content.card.MetadataCard method) (ersilia.hub.content.card.ModelCard method) (ersilia.hub.content.card.ReadmeCard method) (ersilia.hub.content.card.S3JsonCard method) (ersilia.hub.content.information.Information method) (ersilia.hub.fetch.actions.content.CardGetter method) (ersilia.hub.fetch.actions.get.ModelGetter method) (ersilia.hub.fetch.actions.get.ModelParametersGetter method) (ersilia.hub.fetch.actions.get.ModelRepositoryGetter method) (ersilia.io.input.BaseIOGetter method) (ersilia.io.shape.InputShape method) (ersilia.serve.environment.environment_variables.GetEnvironmentVariable method) (ersilia.serve.schema.ApiSchema method) (ersilia.tools.bentoml.configuration.configparser.BentoMLConfigParser method) get_apis() (ersilia.core.model.ErsiliaModel method) (ersilia.serve.autoservice.AutoService method) (ersilia.serve.schema.ApiSchema method) get_average_metrics() (ersilia.utils.docker.ContainerMetricsSampler method) get_base_env() (ersilia.utils.conda.CondaUtils method) get_baseimage() (ersilia.utils.docker.SimpleDockerfileParser method) get_bentoml_deploy_version() (in module ersilia.tools.bentoml.configuration) get_bentoml_version() (ersilia.hub.bundle.bundle.BundleDockerfileFile method) (ersilia.hub.bundle.repo.DockerfileFile method) get_cached() (ersilia.store.dump.DumpLocalCache method) get_cached_files() (ersilia.io.readers.file.BatchCacher method) get_cached_input_files() (ersilia.io.readers.file.BatchCacher method) get_cached_output_files() (ersilia.io.readers.file.BatchCacher method) get_card_by_model_id() (ersilia.hub.content.card.S3JsonCard method) get_card_by_slug() (ersilia.hub.content.card.S3JsonCard method) get_conda_and_pip_install_commands_from_dockerfile_if_exclusive() (ersilia.utils.conda.CondaUtils method) get_conda_env_location() (ersilia.publish.test.services.setup.SetupService static method) get_conda_env_size() (ersilia.publish.test.services.io.IOService method) get_conda_env_yml_file() (ersilia.hub.bundle.repo.RepoUtils method) get_confirm_token() (ersilia.utils.download.GoogleDriveDownloader static method) get_current_pid() (in module ersilia.utils.session) get_debug_mode() (in module ersilia.tools.bentoml.configuration) get_delimiter() (ersilia.io.readers.file.BaseTabularFile method) (ersilia.io.readers.file.StandardTabularFileReader method) get_directories_sizes() (ersilia.publish.test.services.io.IOService method) get_docker_repo_image() (ersilia.hub.bundle.repo.RepoUtils method) get_env_sizes() (ersilia.publish.test.services.io.IOService method) get_expected_output_header() (ersilia.serve.standard_api.StandardCSVRunApi method) get_extension() (ersilia.io.readers.file.FileTyper method) get_file() (ersilia.hub.bundle.bundle.BundleDockerfileFile method) (ersilia.hub.bundle.bundle.BundleEnvironmentFile method) (ersilia.hub.bundle.repo.DockerfileFile method) (ersilia.hub.bundle.repo.PackFile method) (ersilia.hub.bundle.repo.ReadmeFile method) (ersilia.hub.bundle.repo.ServiceFile method)

get_file_requirements() (ersilia.publish.test.services.io.IOService method) get_file_sizes() (ersilia.core.tracking.RunTracker method) get_identifier_object_by_input_type() (ersilia.serve.standard_api.StandardCSVRunApi method) get_information() (ersilia.hub.fetch.lazy_fetchers.hosted.ModelHostedFetcher method), [1] get_inputs() (ersilia.publish.test.services.checks.CheckService method) get_install_commands() (ersilia.hub.bundle.repo.DockerfileFile method) get_install_commands_from_dockerfile() (ersilia.hub.bundle.repo.DockerfileFile method) get_json() (ersilia.store.utils.ApiClient method) get_json_or_yaml_file() (ersilia.hub.content.card.RepoMetadataFile method) get_list_from_csv() (ersilia.serve.standard_api.StandardCSVRunApi method) get_local_config_file() (in module ersilia.tools.bentoml.configuration) get_meta() (ersilia.serve.schema.ApiSchema method) get_meta_by_api() (ersilia.serve.schema.ApiSchema method) get_metadata() (ersilia.hub.fetch.lazy_fetchers.hosted.ModelHostedFetcher method), [1] get_metadata_from_base_dir() (in module ersilia.utils.paths) get_model() (ersilia.publish.test.services.setup.SetupService method) get_model_id() (ersilia.hub.bundle.repo.RepoUtils method) get_model_session() (in module ersilia.utils.session) get_model_type() (ersilia.publish.test.services.io.IOService static method) get_output_by_api() (ersilia.serve.schema.ApiSchema method) get_output_consistency() (ersilia.publish.test.services.io.IOService method) get_parent_pid() (in module ersilia.utils.session) get_precalculations() (ersilia.store.api.InferenceStoreApi method) get_python_path_env() (ersilia.utils.conda.SimpleConda method) get_python_version() (ersilia.hub.bundle.repo.DockerfileFile method) get_runner() (in module ersilia.hub.fetch.pack.bentoml_pack.runners) (in module ersilia.hub.fetch.pack.fastapi_pack.runners) get_runs() (ersilia.utils.docker.SimpleDockerfileParser method) get_schema_by_api() (ersilia.serve.schema.ApiSchema method) get_session_dir() (in module ersilia.utils.session) get_session_id() (in module ersilia.utils.session) get_session_uuid() (in module ersilia.utils.session) get_string_delimiter() (ersilia.io.readers.file.BaseTabularFile method) get_type() (ersilia.io.annotated.AnnotatedDataTyper method) (ersilia.io.pure.PureDataTyper method) get_type_from_metadata() (ersilia.io.pure.PureDataTyper method) GetEnvironmentVariable (class in ersilia.serve.environment.environment_variables) GetFetchErsiliaError git() (ersilia.utils.installers.Installer method) github (ersilia.hub.content.base_information.BaseInformation property) GithubBaseInformationError GithubCliRequirement (class in ersilia.setup.requirements.git) GithubCliSetupError GitHubDownloader (class in ersilia.utils.download) GitLfsRequirement (class in ersilia.setup.requirements.git) GitLfsSetupError GoogleDriveDownloader (class in ersilia.utils.download) guess_type() (ersilia.utils.identifiers.compound.CompoundIdentifier method)

H

handle_undecorated_exception() (in module ersilia.utils.exceptions_utils.handle_undecorated_exception) has_builtin_example() (ersilia.hub.fetch.actions.sniff_bentoml.BuiltinExampleReader method), [1] has_header() (ersilia.io.readers.file.BaseTabularFile method) has_module() (ersilia.utils.environment.Environment method) has_pack() (ersilia.hub.bundle.repo.Integrity method) has_profile_snippet() (in module ersilia.default) has_readme() (ersilia.hub.bundle.repo.Integrity method) has_runs() (ersilia.hub.bundle.repo.DockerfileFile method) has_service() (ersilia.hub.bundle.repo.Integrity method)

Hdf5Data (class in ersilia.utils.hdf5) Hdf5DataLoader (class in ersilia.utils.hdf5) Hdf5DataStacker (class in ersilia.utils.hdf5) head() (ersilia.store.utils.ApiClient method) headers (ersilia.publish.test.services.constants.TableConfig attribute) home() (ersilia.utils.paths.Paths static method) HORIZONTAL (ersilia.default.TableConstants attribute) HostedService (class in ersilia.serve.services) hub() (ersilia.hub.content.catalog.ModelCatalog method)

I

identifier (ersilia.hub.content.base_information.BaseInformation property) Identifier (ersilia.utils.paths.Metadata attribute), [1] (in module ersilia.utils.identifiers.arbitrary) (in module ersilia.utils.identifiers.compound) (in module ersilia.utils.identifiers.file) (in module ersilia.utils.identifiers.long) (in module ersilia.utils.identifiers.model) (in module ersilia.utils.identifiers.short) (in module ersilia.utils.identifiers.text) (in module ersilia.utils.identifiers.timestamp) identifier_exists() (ersilia.db.hubdata.interfaces.JsonModelsInterface method) IdentifierBaseInformationError image_exists() (ersilia.db.environments.managers.DockerManager method) image_size (ersilia.hub.content.base_information.BaseInformation property) IMAGE_SIZE (ersilia.publish.test.services.constants.Checks attribute) images() (ersilia.db.environments.managers.DockerManager method) (ersilia.utils.docker.SimpleDocker method) images_of_model() (ersilia.db.environments.managers.DockerManager method) ImageSizeMbBaseInformationError import_extra() (in module ersilia.utils.import) INCONSISTENCY (ersilia.publish.test.services.constants.Checks attribute) InconsistentOutputs InconsistentOutputTypes incorporation_date (ersilia.hub.content.base_information.BaseInformation property) IncorporationDateBaseInformationError InferenceStoreApi (class in ersilia.store.api) InferenceStoreMessage (class in ersilia.store.utils) info() (ersilia.cli.cmd.Command method) (ersilia.core.model.ErsiliaModel method) (ersilia.utils.logging.Logger method), [1] info_cmd() (in module ersilia.cli.commands.info) inform() (ersilia.hub.fetch.actions.inform.ModelInformer method) Information (class in ersilia.hub.content.information) InformationDisplayer (class in ersilia.hub.content.information) InformationFileNotExist init_redis() (ersilia.store.dump.DumpLocalCache method) input (ersilia.hub.content.base_information.BaseInformation property) Input (ersilia.utils.paths.Metadata attribute), [1] input() (ersilia.hub.fetch.actions.sniff_fastapi.BuiltinExampleReader method), [1] INPUT_CSV (ersilia.publish.test.services.constants.Options attribute) input_dimension (ersilia.hub.content.base_information.BaseInformation property) input_shape (ersilia.hub.content.base_information.BaseInformation property) input_type (ersilia.core.model.ErsiliaModel property) INPUT_TYPES (ersilia.publish.test.services.constants.Options attribute) InputBaseInformationError InputDimensionBaseInformationError InputFileNotFoundError InputShape (class in ersilia.io.shape) (ersilia.utils.paths.Metadata attribute), [1] InputShapeBaseInformationError InputShapeList (class in ersilia.io.shape) InputShapePairOfLists (class in ersilia.io.shape) InputShapeSingle (class in ersilia.io.shape) insert() (ersilia.db.environments.localdb.EnvironmentDb method) (ersilia.db.hubdata.localslugs.SlugDb method) INSPECT_SUMMARY (ersilia.publish.test.services.constants.TableType attribute) InspectService (class in ersilia.publish.test.services.inspect) install() (ersilia.setup.requirements.bentoml_requirement.BentoMLRequirement method) (ersilia.setup.requirements.conda.CondaRequirement method), [1] (ersilia.setup.requirements.git.GithubCliRequirement method), [1] (ersilia.setup.requirements.git.GitLfsRequirement method), [1] Installer (class in ersilia.utils.installers) Integrity (class in ersilia.hub.bundle.repo) interpretation (ersilia.hub.content.base_information.BaseInformation property) Interpretation (ersilia.utils.paths.Metadata attribute), [1] InterpretationBaseInformationError InvalidEntry InvalidModelIdentifierError InvalidUrlError InvalidUrlInAirtableError IO (class in ersilia.io.types.compound) (class in ersilia.io.types.naive) (class in ersilia.io.types.text) IOService (class in ersilia.publish.test.services.io) is_active() (ersilia.db.environments.managers.DockerManager method) (ersilia.setup.requirements.docker.DockerRequirement method), [1] is_amenable() (ersilia.serve.standard_api.StandardCSVRunApi method) is_arm64() (ersilia.utils.system.SystemChecker method), [1] is_available() (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher method), [1] (ersilia.hub.fetch.lazy_fetchers.hosted.ModelHostedFetcher method), [1] (ersilia.serve.autoservice.AutoService method) (ersilia.serve.services.CondaEnvironmentService method) (ersilia.serve.services.DockerImageService method) (ersilia.serve.services.DummyService method) (ersilia.serve.services.HostedService method) (ersilia.serve.services.PipInstalledService method) (ersilia.serve.services.PulledDockerImageService method) (ersilia.serve.services.SystemBundleService method) (ersilia.serve.services.VenvEnvironmentService method)

is_available_in_dockerhub() (ersilia.hub.pull.pull.ModelPuller method) is_available_locally() (ersilia.core.modelbase.ModelBase method) (ersilia.hub.pull.pull.ModelPuller method) is_base() (ersilia.utils.conda.BaseConda method), [1] is_bentoml() (ersilia.hub.bundle.status.ModelStatus method) (ersilia.hub.fetch.actions.template_resolver.TemplateResolver method), [1] is_bentoml_ersilia_version() (ersilia.setup.requirements.bentoml_requirement.BentoMLRequirement method) is_bundle() (ersilia.hub.bundle.status.ModelStatus method) is_cloud() (ersilia.store.utils.OutputSource class method) is_conda() (ersilia.hub.bundle.status.ModelStatus method) is_connected() (ersilia.setup.requirements.ping.PingRequirement method), [1] is_contributor() (ersilia.auth.auth.Auth method) is_csv() (ersilia.io.readers.file.FileTyper method) is_docker() (ersilia.hub.bundle.status.ModelStatus method) is_docker_active() (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher method), [1] is_docker_installed() (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher method), [1] (in module ersilia.utils.docker) is_downloaded() (ersilia.hub.bundle.status.ModelStatus method) is_fastapi() (ersilia.hub.fetch.actions.template_resolver.TemplateResolver method), [1] is_flattened() (ersilia.io.readers.file.BaseTabularFile method) is_github_action() (ersilia.utils.system.SystemChecker method), [1] is_h5_serializable() (ersilia.serve.schema.ApiSchema method) is_hdf5() (ersilia.io.readers.file.FileTyper method) is_input() (ersilia.io.readers.file.BaseTabularFile method) (ersilia.io.types.compound.IO method) (ersilia.io.types.text.IO method) is_input_header() (ersilia.utils.identifiers.compound.CompoundIdentifier method) is_input_type_standardizable() (ersilia.serve.standard_api.StandardCSVRunApi method) is_inside_docker() (ersilia.db.environments.managers.DockerManager method) (ersilia.setup.requirements.docker.DockerRequirement method), [1] (ersilia.utils.system.SystemChecker method), [1] (in module ersilia.utils.system) is_installed() (ersilia.db.environments.managers.DockerManager method) (ersilia.setup.requirements.bentoml_requirement.BentoMLRequirement method) (ersilia.setup.requirements.conda.CondaRequirement method), [1] (ersilia.setup.requirements.docker.DockerRequirement method), [1] (ersilia.setup.requirements.git.GithubCliRequirement method), [1] (ersilia.setup.requirements.git.GitLfsRequirement method), [1] is_json() (ersilia.io.readers.file.FileTyper method) is_key() (ersilia.io.readers.file.BaseTabularFile method) (ersilia.io.types.compound.IO method) (ersilia.io.types.text.IO method) is_key_header() (ersilia.utils.identifiers.compound.CompoundIdentifier method) is_local() (ersilia.store.utils.OutputSource class method) is_logged_in() (ersilia.db.environments.managers.DockerManager method) (ersilia.setup.requirements.docker.DockerRequirement method), [1] is_output_csv_file() (ersilia.serve.standard_api.StandardCSVRunApi method) is_output_type_standardizable() (ersilia.serve.standard_api.StandardCSVRunApi method) is_pip() (ersilia.hub.bundle.status.ModelStatus method) is_port_in_use() (in module ersilia.utils.ports) is_precalculation_enabled() (ersilia.store.utils.OutputSource class method) is_pulled_docker() (ersilia.hub.bundle.status.ModelStatus method) is_quiet() (in module ersilia.utils.terminal) is_served() (ersilia.serve.autoservice.AutoService method) is_silence() (ersilia.cli.echo.Silencer method), [1] is_single_input() (ersilia.io.readers.file.BaseJsonFile method) (ersilia.io.readers.file.BaseTabularFile method) (ersilia.io.readers.pyinput.PyInputReader method) is_single_model_without_conda() (ersilia.serve.services.CondaEnvironmentService static method) is_slug() (ersilia.hub.content.slug.Slug method) is_tabular() (ersilia.io.readers.file.FileTyper method) is_test() (ersilia.utils.identifiers.model.ModelIdentifier method) is_tsv() (ersilia.io.readers.file.FileTyper method) is_udocker_installed() (in module ersilia.utils.docker) is_url_available() (ersilia.serve.services.HostedService method) (ersilia.serve.services.PulledDockerImageService method) is_valid() (ersilia.core.model.ErsiliaModel method) (ersilia.core.modelbase.ModelBase method) (ersilia.core.tracking.AwsConfig method) (ersilia.utils.identifiers.model.ModelIdentifier method) is_valid_input_file() (ersilia.io.readers.file.FileTyper method) is_valid_output_file() (ersilia.io.readers.file.FileTyper method) is_working() (ersilia.setup.requirements.docker.DockerRequirement method), [1] is_worth_splitting() (ersilia.io.readers.file.StandardJsonFileReader method) (ersilia.io.readers.file.StandardTabularFileReader method) isfile() (ersilia.serve.schema.ApiSchema method) items() (ersilia.db.hubdata.interfaces.JsonModelsInterface method) items_all() (ersilia.db.hubdata.interfaces.JsonModelsInterface method) iterrows() (ersilia.io.dataframe.Dataframe method)

J

JobStatus (class in ersilia.store.utils) json_serializer (class in ersilia.tools.bentoml.utils.dataclasses)

JsonFileReader (class in ersilia.io.readers.file) JsonFileShapeStandardizer (class in ersilia.io.readers.file) JsonModelsInterface (class in ersilia.db.hubdata.interfaces)

K

keys() (ersilia.utils.config.Config method) (ersilia.utils.config.Credentials method)

kill() (ersilia.utils.docker.SimpleDocker static method)

L

LESS_FIELDS (ersilia.hub.content.catalog.ModelCatalog attribute), [1] levenshtein_ratio_and_distance() (ersilia.hub.content.search.ModelSearcher method) license (ersilia.hub.content.base_information.BaseInformation property) License (ersilia.utils.paths.Metadata attribute), [1] LicenseBaseInformationError list_cached_inputs() (ersilia.store.dump.DumpLocalCache method) load() (ersilia.hub.content.columns_information.ColumnsInformation method) (ersilia.utils.csvfile.CsvDataLoader method), [1] (ersilia.utils.hdf5.Hdf5DataLoader method), [1] load_config() (in module ersilia.tools.bentoml.configuration)

LOCAL (ersilia.store.utils.OutputSource attribute) local() (ersilia.hub.content.catalog.ModelCatalog method) LOCAL_ONLY (ersilia.store.utils.OutputSource attribute) LocalCard (class in ersilia.hub.content.card) log_files_metrics() (ersilia.core.tracking.RunTracker method) log_prefix() (in module ersilia.store.utils) Logger (class in ersilia.utils.logging) login() (ersilia.auth.auth.Auth method) logout() (ersilia.auth.auth.Auth method) LongIdentifier (class in ersilia.utils.identifiers.long)

M

make_hashable() (ersilia.store.dump.DumpLocalCache method) make_temp_dir() (in module ersilia.utils.logging) MemoryGbBaseInformationError merge() (ersilia.io.output.GenericOutputAdapter method) merge_csvs_stdlib() (in module ersilia.store.utils) merge_shards() (ersilia.store.utils.FileManager static method) meta (ersilia.core.model.ErsiliaModel property) meta() (ersilia.io.output.GenericOutputAdapter method) (ersilia.serve.api.Api method) Metadata (class in ersilia.utils.paths) metadata_constructor() (in module ersilia.utils.paths) MetadataCard (class in ersilia.hub.content.card) MIDDLE_LEFT (ersilia.default.TableConstants attribute) MIDDLE_MIDDLE (ersilia.default.TableConstants attribute) MIDDLE_RIGHT (ersilia.default.TableConstants attribute) MissingDependencyError MissingOutputs mode (ersilia.hub.content.base_information.BaseInformation property) Mode (ersilia.utils.paths.Metadata attribute), [1] ModeBaseInformationError model (ersilia.cli.messages.ModelNotFound attribute) model_cleanup() (in module ersilia.utils.cron) MODEL_CONSISTENCY (ersilia.publish.test.services.constants.Checks attribute) MODEL_DIRECTORY_SIZES (ersilia.publish.test.services.constants.TableType attribute) MODEL_FILE_CHECKS (ersilia.publish.test.services.constants.TableType attribute) model_id (ersilia.cli.messages.ModelNotInLocal attribute) (ersilia.hub.fetch.pack.bentoml_pack.mode.PackModeDecision attribute) (ersilia.io.output.GenericOutputAdapter attribute) model_id_from_path() (ersilia.utils.paths.Paths method), [1] model_image_version_reader() (in module ersilia.utils.docker) MODEL_INFORMATION_CHECKS (ersilia.publish.test.services.constants.TableType attribute) MODEL_OUTPUT (ersilia.publish.test.services.constants.TableType attribute) MODEL_RUN_CHECK (ersilia.publish.test.services.constants.TableType attribute) model_size (ersilia.hub.content.base_information.BaseInformation property) MODEL_SIZES (ersilia.publish.test.services.constants.TableType attribute) ModelBase (class in ersilia.core.modelbase) ModelBentoDeleter (class in ersilia.hub.delete.delete) ModelBundleDeleter (class in ersilia.hub.delete.delete) ModelCard (class in ersilia.hub.content.card) ModelCatalog (class in ersilia.hub.content.catalog) ModelChecker (class in ersilia.hub.fetch.actions.check) ModelCondaDeleter (class in ersilia.hub.delete.delete) ModelDeleteError ModelDockerDeleter (class in ersilia.hub.delete.delete) ModelDockerHubFetcher (class in ersilia.hub.fetch.lazy_fetchers.dockerhub) ModelEosDeleter (class in ersilia.hub.delete.delete) ModelFetchedEntryDeleter (class in ersilia.hub.delete.delete) ModelFetcher (class in ersilia.hub.fetch.fetch) ModelFetcherFromBentoML (class in ersilia.hub.fetch.fetch_bentoml) ModelFetcherFromFastAPI (class in ersilia.hub.fetch.fetch_fastapi) ModelFullDeleter (class in ersilia.hub.delete.delete) ModelGetter (class in ersilia.hub.fetch.actions.get) ModelHostedFetcher (class in ersilia.hub.fetch.lazy_fetchers.hosted) ModelIdentifier (class in ersilia.utils.identifiers.model) ModelInformer (class in ersilia.hub.fetch.actions.inform) ModelInspector (class in ersilia.publish.test.services.inspect) ModelModifier (class in ersilia.hub.fetch.actions.modify) ModelNotAvailableLocallyError ModelNotFound (class in ersilia.cli.messages) ModelNotInLocal (class in ersilia.cli.messages) ModelNotInStore (class in ersilia.store.utils) ModelPackageInstallError ModelPacker (class in ersilia.hub.fetch.actions.pack_bentoml) (class in ersilia.hub.fetch.actions.pack_fastapi) ModelParametersGetter (class in ersilia.hub.fetch.actions.get) ModelPipDeleter (class in ersilia.hub.delete.delete) ModelPreparer (class in ersilia.hub.fetch.actions.prepare) ModelPuller (class in ersilia.hub.pull.pull) ModelRegisterer (class in ersilia.hub.fetch.register.register) ModelRemover (class in ersilia.publish.store) ModelRepositoryGetter (class in ersilia.hub.fetch.actions.get) models_of_env() (ersilia.db.environments.localdb.EnvironmentDb method) models_of_slug() (ersilia.db.hubdata.localslugs.SlugDb method) models_with_same_env() (ersilia.db.environments.localdb.EnvironmentDb method) ModelSearcher (class in ersilia.hub.content.search) ModelSizeMbBaseInformationError ModelSlugDeleter (class in ersilia.hub.delete.delete) ModelSniffer (class in ersilia.hub.fetch.actions.sniff_bentoml) (class in ersilia.hub.fetch.actions.sniff_fastapi) ModelsTable (class in ersilia.db.hubdata.tables) ModelStandardExample (class in ersilia.hub.fetch.register.standard_example) ModelStatus (class in ersilia.hub.bundle.status) ModelStorager (class in ersilia.publish.store) ModelTester (class in ersilia.publish.test.test) ModelTmpDeleter (class in ersilia.hub.delete.delete) ModelToolizer (class in ersilia.hub.fetch.actions.toolize) ModelURLResolver (class in ersilia.hub.fetch) modify() (ersilia.hub.fetch.actions.modify.ModelModifier method), [1] modify_information() (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher method), [1] module ersilia ersilia.app ersilia.app.fastapi ersilia.app.streamlit ersilia.auth ersilia.auth.auth ersilia.cli ersilia.cli.cmd ersilia.cli.commands ersilia.cli.commands.auth ersilia.cli.commands.catalog ersilia.cli.commands.close ersilia.cli.commands.delete ersilia.cli.commands.dump ersilia.cli.commands.example ersilia.cli.commands.fetch ersilia.cli.commands.info ersilia.cli.commands.run ersilia.cli.commands.serve ersilia.cli.commands.test ersilia.cli.commands.uninstall ersilia.cli.commands.utils ersilia.cli.create_cli ersilia.cli.echo ersilia.cli.messages ersilia.core ersilia.core.base ersilia.core.model ersilia.core.modelbase ersilia.core.session ersilia.core.tracking ersilia.db ersilia.db.disk ersilia.db.disk.fetched ersilia.db.environments ersilia.db.environments.localdb ersilia.db.environments.managers ersilia.db.hubdata ersilia.db.hubdata.interfaces ersilia.db.hubdata.localslugs ersilia.db.hubdata.tables ersilia.default ersilia.hub ersilia.hub.bundle ersilia.hub.bundle.bundle ersilia.hub.bundle.repo ersilia.hub.bundle.status ersilia.hub.content ersilia.hub.content.base_information ersilia.hub.content.card ersilia.hub.content.catalog ersilia.hub.content.columns_information ersilia.hub.content.information ersilia.hub.content.search ersilia.hub.content.slug ersilia.hub.delete ersilia.hub.delete.delete ersilia.hub.fetch ersilia.hub.fetch.actions ersilia.hub.fetch.actions.check ersilia.hub.fetch.actions.content ersilia.hub.fetch.actions.get ersilia.hub.fetch.actions.inform ersilia.hub.fetch.actions.modify ersilia.hub.fetch.actions.pack_bentoml ersilia.hub.fetch.actions.pack_fastapi ersilia.hub.fetch.actions.prepare ersilia.hub.fetch.actions.setup ersilia.hub.fetch.actions.sniff_bentoml ersilia.hub.fetch.actions.sniff_fastapi ersilia.hub.fetch.actions.template_resolver ersilia.hub.fetch.actions.toolize ersilia.hub.fetch.fetch ersilia.hub.fetch.fetch_bentoml ersilia.hub.fetch.fetch_fastapi ersilia.hub.fetch.lazy_fetchers ersilia.hub.fetch.lazy_fetchers.dockerhub ersilia.hub.fetch.lazy_fetchers.hosted ersilia.hub.fetch.pack ersilia.hub.fetch.pack.bentoml_pack ersilia.hub.fetch.pack.bentoml_pack.mode ersilia.hub.fetch.pack.bentoml_pack.runners ersilia.hub.fetch.pack.fastapi_pack ersilia.hub.fetch.pack.fastapi_pack.mode ersilia.hub.fetch.pack.fastapi_pack.runners ersilia.hub.fetch.register ersilia.hub.fetch.register.register ersilia.hub.fetch.register.standard_example ersilia.hub.pull ersilia.hub.pull.pull ersilia.io ersilia.io.annotated ersilia.io.dataframe ersilia.io.input ersilia.io.output ersilia.io.output_logger ersilia.io.pure ersilia.io.readers ersilia.io.readers.file ersilia.io.readers.pyinput ersilia.io.shape ersilia.io.types ersilia.io.types.compound ersilia.io.types.examples ersilia.io.types.examples.compound ersilia.io.types.examples.text ersilia.io.types.naive ersilia.io.types.text ersilia.publish ersilia.publish.dockerhub ersilia.publish.rebase ersilia.publish.s3 ersilia.publish.store ersilia.publish.test ersilia.publish.test.services ersilia.publish.test.services.checks ersilia.publish.test.services.constants ersilia.publish.test.services.inspect ersilia.publish.test.services.io ersilia.publish.test.services.runner ersilia.publish.test.services.setup ersilia.publish.test.test ersilia.serve ersilia.serve.api ersilia.serve.autoservice ersilia.serve.environment ersilia.serve.environment.environment_variables ersilia.serve.schema ersilia.serve.services ersilia.serve.standard_api ersilia.setup ersilia.setup.baseconda ersilia.setup.basedocker ersilia.setup.conda ersilia.setup.config ersilia.setup.profile ersilia.setup.requirements ersilia.setup.requirements.bentoml_requirement ersilia.setup.requirements.conda ersilia.setup.requirements.docker ersilia.setup.requirements.eospath ersilia.setup.requirements.git ersilia.setup.requirements.ping ersilia.setup.requirements.setuptools_req ersilia.setup.utils ersilia.setup.utils.clone ersilia.store ersilia.store.api ersilia.store.dump ersilia.store.utils ersilia.tools ersilia.tools.bentoml ersilia.tools.bentoml.configuration ersilia.tools.bentoml.configuration.configparser ersilia.tools.bentoml.exceptions ersilia.tools.bentoml.utils ersilia.tools.bentoml.utils.dataclasses ersilia.utils ersilia.utils.cache ersilia.utils.cli_query ersilia.utils.conda ersilia.utils.config ersilia.utils.cron ersilia.utils.csvfile ersilia.utils.docker ersilia.utils.download ersilia.utils.environment ersilia.utils.exceptions_utils ersilia.utils.exceptions_utils.api_exceptions ersilia.utils.exceptions_utils.base_information_exceptions ersilia.utils.exceptions_utils.card_exceptions ersilia.utils.exceptions_utils.catalog_exceptions ersilia.utils.exceptions_utils.clear_exceptions ersilia.utils.exceptions_utils.close_exceptions ersilia.utils.exceptions_utils.delete_exceptions ersilia.utils.exceptions_utils.example_exceptions ersilia.utils.exceptions_utils.exceptions ersilia.utils.exceptions_utils.fetch_exceptions ersilia.utils.exceptions_utils.handle_undecorated_exception ersilia.utils.exceptions_utils.hubdata_exceptions ersilia.utils.exceptions_utils.issue_reporting ersilia.utils.exceptions_utils.pull_exceptions ersilia.utils.exceptions_utils.serve_exceptions ersilia.utils.exceptions_utils.setup_exceptions ersilia.utils.exceptions_utils.test_exceptions ersilia.utils.exceptions_utils.throw_ersilia_exception ersilia.utils.exceptions_utils.tracking_exceptions ersilia.utils.hdf5 ersilia.utils.identifiers ersilia.utils.identifiers.arbitrary ersilia.utils.identifiers.compound ersilia.utils.identifiers.file ersilia.utils.identifiers.long ersilia.utils.identifiers.model ersilia.utils.identifiers.short ersilia.utils.identifiers.text ersilia.utils.identifiers.timestamp ersilia.utils.import ersilia.utils.installers ersilia.utils.logging ersilia.utils.paths ersilia.utils.ports ersilia.utils.remove ersilia.utils.resolvers ersilia.utils.session ersilia.utils.spinner ersilia.utils.supp ersilia.utils.supp.conda_env_resolve ersilia.utils.system ersilia.utils.terminal ersilia.utils.tracking ersilia.utils.uninstall ersilia.utils.upload ersilia.utils.venv ersilia.utils.versioning ersilia.utils.zip

MORE_FIELDS (ersilia.hub.content.catalog.ModelCatalog attribute), [1]

N

NA (ersilia.publish.test.services.constants.STATUS_CONFIGS attribute) name_cached_output_files() (ersilia.io.readers.file.BatchCacher method) names() (ersilia.hub.fetch.actions.sniff_fastapi.ColumnsFileReader method), [1] needs_conda() (ersilia.hub.bundle.bundle.BundleEnvironmentFile method) (ersilia.hub.bundle.repo.DockerfileFile method) needs_delete() (ersilia.hub.delete.delete.ModelFullDeleter method) needs_model() (ersilia.hub.bundle.repo.PackFile method)

NoAWSCredentialsError NOT_PRESENT (ersilia.publish.test.services.constants.STATUS_CONFIGS attribute) NotInstallableError NotInstallableWithBentoML NotInstallableWithFastAPI NullModelIdentifierError NUM_SAMPLES (ersilia.publish.test.services.constants.Options attribute) NUMBER_OF_COMMON_PARAMS (ersilia.cli.commands.ErsiliaCommandGroup attribute)

O

oauth_token() (ersilia.auth.auth.Auth method) open() (ersilia.core.session.Session method) Options (class in ersilia.publish.test.services.constants) org_development_path() (ersilia.utils.paths.Paths method), [1] orient_to_json() (ersilia.store.dump.DumpLocalCache method) OsfDownloader (class in ersilia.utils.download) OsfRemover (class in ersilia.utils.remove) OsfUploader (class in ersilia.utils.upload) output (ersilia.hub.content.base_information.BaseInformation property) Output (ersilia.utils.paths.Metadata attribute), [1] output() (ersilia.hub.fetch.actions.sniff_fastapi.BuiltinExampleReader method), [1] OUTPUT1_CSV (ersilia.publish.test.services.constants.Options attribute) OUTPUT2_CSV (ersilia.publish.test.services.constants.Options attribute) output_consistency (ersilia.hub.content.base_information.BaseInformation property) OUTPUT_CSV (ersilia.publish.test.services.constants.Options attribute)

output_dimension (ersilia.hub.content.base_information.BaseInformation property) OUTPUT_FILES (ersilia.publish.test.services.constants.Options attribute) output_shape (ersilia.hub.content.base_information.BaseInformation property) output_type (ersilia.core.model.ErsiliaModel property) (ersilia.hub.content.base_information.BaseInformation property) OutputBaseInformationError OutputConsistencyBaseInformationError OutputDataTypesNotConsistentError OutputDimensionBaseInformationError OutputShape (ersilia.utils.paths.Metadata attribute), [1] OutputShapeBaseInformationError OutputSource (class in ersilia.store.utils) OutputType (ersilia.utils.paths.Metadata attribute), [1] OutputTypeBaseInformationError overwrite (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher attribute)

P

pack() (ersilia.hub.fetch.actions.pack_bentoml.ModelPacker method), [1] (ersilia.hub.fetch.actions.pack_fastapi.ModelPacker method), [1] pack_method (ersilia.hub.content.base_information.BaseInformation property) PackageInstaller (class in ersilia.publish.test.services.io) PackCreator (class in ersilia.hub.fetch.actions.get) PackFile (class in ersilia.hub.bundle.repo) PackMethodBaseInformationError PackMethodResolver (class in ersilia.utils.resolvers) PackModeDecision (class in ersilia.hub.fetch.pack.bentoml_pack.mode) (class in ersilia.hub.fetch.pack.fastapi_pack.mode) parameterized_config() (in module ersilia.tools.bentoml.configuration) parse() (ersilia.hub.content.card.ReadmeCard method) (ersilia.io.types.compound.IO method) (ersilia.io.types.naive.IO method) (ersilia.io.types.text.IO method) parse_smiles_list() (ersilia.serve.standard_api.StandardCSVRunApi method) parse_smiles_string() (ersilia.serve.standard_api.StandardCSVRunApi method) PASSED (ersilia.publish.test.services.constants.STATUS_CONFIGS attribute) Paths (class in ersilia.utils.paths) paths (ersilia.core.model.ErsiliaModel property) PENDING (ersilia.store.utils.JobStatus attribute) PingError PingRequirement (class in ersilia.setup.requirements.ping) pip_install() (ersilia.hub.fetch.actions.toolize.ModelToolizer method) pip_uninstall() (ersilia.hub.delete.delete.ModelPipDeleter method) PipInstalledService (class in ersilia.serve.services) post() (ersilia.serve.api.Api method) (ersilia.serve.standard_api.StandardCSVRunApi method) post_json() (ersilia.store.utils.ApiClient method) post_only_calculations() (ersilia.serve.api.Api method)

post_only_reads() (ersilia.serve.api.Api method) post_unique_input() (ersilia.serve.api.Api method) PrecalculationsInStore (class in ersilia.store.utils) PrecalculationsNotInStore (class in ersilia.store.utils) PREDEFINED_EXAMPLE (ersilia.publish.test.services.constants.Checks attribute) predefined_example() (ersilia.io.input.ExampleGenerator method) PredictionsTable (class in ersilia.db.hubdata.tables) prepare() (ersilia.hub.fetch.actions.get.TemplatePreparer method) (ersilia.hub.fetch.actions.prepare.ModelPreparer method), [1] print_result_table() (in module ersilia.utils.terminal) process_smiles() (ersilia.utils.identifiers.compound.CompoundIdentifier method) profile() (ersilia.utils.installers.Installer method) progress_bar() (ersilia.store.utils.ClickInterface method) prune() (ersilia.db.environments.managers.DockerManager method) PseudoDownloader (class in ersilia.utils.download) publication (ersilia.hub.content.base_information.BaseInformation property) Publication (ersilia.utils.paths.Metadata attribute), [1] publication_type (ersilia.hub.content.base_information.BaseInformation property) publication_year (ersilia.hub.content.base_information.BaseInformation property) PublicationBaseInformationError PublicationTypeBaseInformationError PublicationYearBaseInformationError publish() (ersilia.cli.cmd.Command method) pull() (ersilia.hub.pull.pull.ModelPuller method) PulledDockerImageService (class in ersilia.serve.services) PureDataTyper (class in ersilia.io.pure) push() (ersilia.utils.upload.OsfUploader method), [1] put() (ersilia.serve.environment.environment_variables.PutEnvironmentVariable method) PutEnvironmentVariable (class in ersilia.serve.environment.environment_variables) PyInputReader (class in ersilia.io.readers.pyinput) python_version() (ersilia.utils.versioning.Versioner method), [1]

Q

query_yes_no() (in module ersilia.utils.cli_query)

R

random_example() (ersilia.io.input.ExampleGenerator method) raw_input_with_timeout() (in module ersilia.utils.terminal) read() (ersilia.io.readers.file.JsonFileReader method) (ersilia.io.readers.file.StandardJsonFileReader method) (ersilia.io.readers.file.StandardTabularFileReader method) (ersilia.io.readers.file.TabularFileReader method) (ersilia.io.readers.pyinput.PyInputReader method) (ersilia.utils.csvfile.CsvDataLoader method), [1] read_checksum() (in module ersilia.utils.supp.conda_env_resolve) read_csv_values() (ersilia.publish.test.services.io.IOService static method) read_header() (ersilia.io.readers.file.StandardTabularFileReader method) read_information() (ersilia.hub.content.card.RepoMetadataFile method) read_input_columns() (ersilia.io.readers.file.BaseTabularFile method) read_input_json() (ersilia.io.readers.file.BaseJsonFile method) read_log() (ersilia.utils.installers.BaseInstaller method) ReadmeCard (class in ersilia.hub.content.card) ReadmeFile (class in ersilia.hub.bundle.repo) reason (ersilia.hub.fetch.fetch.FetchResult attribute) rebase() (ersilia.publish.rebase.TemplateRebaser method) refactor_response() (ersilia.io.output.ResponseRefactor method), [1] reformat_py() (ersilia.utils.versioning.Versioner method) (ersilia.utils.versioning.Versioner static method) register() (ersilia.hub.fetch.register.register.ModelRegisterer method) register_from_dockerhub() (ersilia.hub.fetch.register.register.ModelRegisterer method) register_from_hosted() (ersilia.hub.fetch.register.register.ModelRegisterer method) register_model_session() (in module ersilia.utils.session) register_not_from_dockerhub() (ersilia.hub.fetch.register.register.ModelRegisterer method) register_not_from_hosted() (ersilia.hub.fetch.register.register.ModelRegisterer method) register_output_source() (ersilia.core.session.Session method) register_service_class() (ersilia.core.session.Session method) remove() (ersilia.db.environments.managers.DockerManager method) (ersilia.publish.store.ModelRemover method) (ersilia.utils.docker.SimpleDocker static method) (ersilia.utils.remove.OsfRemover method) remove_from_log() (ersilia.utils.installers.BaseInstaller method) remove_log() (ersilia.utils.installers.BaseInstaller method) remove_orphaned_sessions() (in module ersilia.utils.session) remove_redis_image_if_exists() (ersilia.utils.cache.SetupRedis method) remove_session_dir() (in module ersilia.utils.session) remove_stopped_containers() (ersilia.db.environments.managers.DockerManager method) rename_service() (ersilia.hub.bundle.repo.RepoUtils static method) (ersilia.hub.bundle.repo.ServiceFile method) RepoMetadataFile (class in ersilia.hub.content.card) RepoUtils (class in ersilia.hub.bundle.repo)

REQUIRED_FIELDS (ersilia.publish.test.services.inspect.ModelInspector attribute) resolve_columns() (ersilia.io.readers.file.BaseTabularFile method) resolve_pack_method() (ersilia.utils.resolvers.PackMethodResolver method) resolve_pack_method_from_github_metadata() (ersilia.utils.resolvers.PackMethodResolver method) resolve_pack_method_source() (ersilia.utils.resolvers.PackMethodResolver method) resolve_pack_method_tracked_at_fetch() (ersilia.utils.resolvers.PackMethodResolver method) resolve_platform() (in module ersilia.utils.docker) resolve_valid_hosted_model_url() (ersilia.hub.fetch.ModelURLResolver method) ResponseRefactor (class in ersilia.io.output) restart() (ersilia.cli.cmd.Command method) Result (class in ersilia.publish.test.services.inspect) rmtree() (in module ersilia.hub.delete.delete) run() (ersilia.cli.cmd.Command method) (ersilia.core.model.ErsiliaModel method) (ersilia.db.environments.managers.DockerManager method) (ersilia.hub.fetch.actions.get.DockerfileCreator method) (ersilia.hub.fetch.actions.get.PackCreator method) (ersilia.hub.fetch.actions.get.ServiceCreator method) (ersilia.hub.fetch.pack.bentoml_pack.runners.CondaPack method), [1] (ersilia.hub.fetch.pack.bentoml_pack.runners.DockerPack method), [1] (ersilia.hub.fetch.pack.bentoml_pack.runners.SystemPack method), [1] (ersilia.hub.fetch.pack.bentoml_pack.runners.VenvPack method), [1] (ersilia.hub.fetch.pack.fastapi_pack.runners.CondaPack method) (ersilia.hub.fetch.pack.fastapi_pack.runners.SystemPack method) (ersilia.hub.fetch.register.standard_example.ModelStandardExample method) (ersilia.publish.test.services.inspect.InspectService method) (ersilia.publish.test.services.runner.RunnerService method) (ersilia.publish.test.test.ModelTester method) (ersilia.utils.docker.SimpleDocker method) RUN_BASH (ersilia.publish.test.services.constants.Checks attribute) run_bash() (ersilia.publish.test.services.runner.RunnerService method) run_cmd() (in module ersilia.cli.commands.run) run_command() (ersilia.publish.test.services.setup.SetupService static method) (in module ersilia.utils.terminal) run_command_check_output() (in module ersilia.utils.terminal) run_commandlines() (ersilia.utils.conda.SimpleConda method) (ersilia.utils.conda.StandaloneConda method) (ersilia.utils.venv.SimpleVenv method), [1] run_example() (ersilia.publish.test.services.runner.RunnerService method) run_from_terminal() (ersilia.utils.exceptions_utils.exceptions.EmptyOutputError method) run_model() (ersilia.publish.test.services.runner.RunnerService method) RUNNER_CHECKUP_STATUS (ersilia.publish.test.services.constants.TableType attribute) RunnerService (class in ersilia.publish.test.services.runner) RUNNING (ersilia.store.utils.JobStatus attribute) RunTracker (class in ersilia.core.tracking)

S

s3 (ersilia.hub.content.base_information.BaseInformation property) S3 (ersilia.utils.paths.Metadata attribute), [1] S3BaseInformationError S3BucketRepoUploader (class in ersilia.publish.s3) S3Downloader (class in ersilia.utils.download) S3DownloaderError S3JsonCard (class in ersilia.hub.content.card) save() (ersilia.utils.hdf5.Hdf5Data method) save_response_content() (ersilia.utils.download.GoogleDriveDownloader static method) schema (ersilia.core.model.ErsiliaModel property) (ersilia.serve.schema.ApiSchema property) search_mode() (ersilia.hub.content.search.ModelSearcher method) search_text() (ersilia.hub.content.search.ModelSearcher method) seconds_to_days() (in module ersilia.utils.cron) seems_installable() (ersilia.hub.fetch.fetch_bentoml.ModelFetcherFromBentoML method) (ersilia.hub.fetch.fetch_fastapi.ModelFetcherFromFastAPI method) send_exception_issue() (in module ersilia.utils.exceptions_utils.issue_reporting) serialize_to_csv() (ersilia.serve.standard_api.StandardCSVRunApi method) serialize_to_json() (ersilia.serve.standard_api.StandardCSVRunApi method) serialize_to_json_one_column() (ersilia.serve.standard_api.StandardCSVRunApi method) serialize_to_json_three_columns() (ersilia.serve.standard_api.StandardCSVRunApi method) serialize_to_json_two_columns() (ersilia.serve.standard_api.StandardCSVRunApi method) serve() (ersilia.cli.cmd.Command method) (ersilia.core.model.ErsiliaModel method) (ersilia.serve.autoservice.AutoService method) (ersilia.serve.services.CondaEnvironmentService method) (ersilia.serve.services.DockerImageService method) (ersilia.serve.services.DummyService method) (ersilia.serve.services.HostedService method) (ersilia.serve.services.PipInstalledService method) (ersilia.serve.services.PulledDockerImageService method) (ersilia.serve.services.SystemBundleService method) (ersilia.serve.services.VenvEnvironmentService method) serve_cmd() (in module ersilia.cli.commands.serve) ServeErsiliaError server_docker() (ersilia.utils.installers.Installer method) (ersilia.utils.installers.Uninstaller method) server_docker_name() (ersilia.utils.versioning.Versioner method), [1] server_docker_slim() (ersilia.utils.installers.Installer method) ServiceCreator (class in ersilia.hub.fetch.actions.get) ServiceFile (class in ersilia.hub.bundle.repo) Session (class in ersilia.core.session) set_credentials() (ersilia.publish.dockerhub.DockerHubUploader method) (ersilia.publish.s3.S3BucketRepoUploader method) set_debug_mode() (in module ersilia.tools.bentoml.configuration) set_docker_host() (in module ersilia.utils.docker) set_to_full() (ersilia.hub.bundle.bundle.BundleDockerfileFile method) set_to_slim() (ersilia.hub.bundle.bundle.BundleDockerfileFile method) set_verbosity() (ersilia.utils.logging.Logger method), [1] set_write_permissions() (in module ersilia.utils.session) setup() (ersilia.cli.cmd.Command method) (ersilia.core.model.ErsiliaModel method) (ersilia.io.types.compound.IO method) (ersilia.io.types.text.IO method) (ersilia.setup.baseconda.SetupBaseConda method), [1] (ersilia.setup.basedocker.SetupBaseDocker method) (ersilia.setup.conda.SetupConda method) (ersilia.setup.config.SetupConfig method) (ersilia.setup.profile.SetupProfile method) SetupBaseConda (class in ersilia.setup.baseconda) SetupBaseDocker (class in ersilia.setup.basedocker) SetupChecker (class in ersilia.hub.fetch.actions.setup) SetupConda (class in ersilia.setup.conda) SetupConfig (class in ersilia.setup.config) SetupProfile (class in ersilia.setup.profile) SetupRedis (class in ersilia.utils.cache) SetupService (class in ersilia.publish.test.services.setup) SHALLOW_CHECK_SUMMARY (ersilia.publish.test.services.constants.TableType attribute) shape() (ersilia.io.input.BaseIOGetter method) ShortIdentifier (class in ersilia.utils.identifiers.short) show_loader() (in module ersilia.utils.spinner) silence() (ersilia.cli.echo.Silencer method), [1] silence_file (ersilia.cli.echo.Silencer attribute)

Silencer (class in ersilia.cli.echo) simple_docker (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher attribute) SIMPLE_MODEL_RUN (ersilia.publish.test.services.constants.Checks attribute) SIMPLE_MODEL_RUN_COLUMNS (ersilia.publish.test.services.constants.Checks attribute) SimpleConda (class in ersilia.utils.conda) SimpleDocker (class in ersilia.utils.docker) SimpleDockerfileParser (class in ersilia.utils.docker) SimpleVenv (class in ersilia.utils.venv) size (ersilia.core.model.ErsiliaModel property) SIZE_CACL_FAILED (ersilia.publish.test.services.constants.Checks attribute) SIZE_CACL_SUCCESS (ersilia.publish.test.services.constants.Checks attribute) Slug (class in ersilia.hub.content.slug) slug (ersilia.hub.content.base_information.BaseInformation property) Slug (ersilia.utils.paths.Metadata attribute), [1] SlugBaseInformationError SlugDb (class in ersilia.db.hubdata.localslugs) slugs_of_model() (ersilia.db.hubdata.localslugs.SlugDb method) sniff() (ersilia.hub.fetch.actions.sniff_bentoml.ModelSniffer method), [1] (ersilia.hub.fetch.actions.sniff_fastapi.ModelSniffer method), [1] SniffFastApiColumnsDontMatch SniffFastApiColumnTypesIncompatibility source (ersilia.hub.content.base_information.BaseInformation property) source_code (ersilia.hub.content.base_information.BaseInformation property) source_type (ersilia.hub.content.base_information.BaseInformation property) SourceBaseInformationError SourceCode (ersilia.utils.paths.Metadata attribute), [1] SourceCodeBaseInformationError SourceTypeBaseInformationError speak() (ersilia.cli.echo.Silencer method), [1] specs_from_dockerfile() (ersilia.utils.conda.CondaUtils method) specs_from_dockerfile_as_json() (ersilia.utils.conda.CondaUtils method) Spinner (class in ersilia.utils.spinner) split_in_cache() (ersilia.io.readers.file.StandardJsonFileReader method) (ersilia.io.readers.file.StandardTabularFileReader method) stack() (ersilia.io.output.TabularOutputStacker method), [1] (ersilia.utils.hdf5.Hdf5DataStacker method) stack_hdf5() (ersilia.io.output.TabularOutputStacker method) stack_text() (ersilia.io.output.TabularOutputStacker method) StandaloneConda (class in ersilia.utils.conda) StandardCSVRunApi (class in ersilia.serve.standard_api) standardize() (ersilia.io.readers.file.JsonFileShapeStandardizer method) (ersilia.io.readers.file.TabularFileShapeStandardizer method) StandardJsonFileReader (class in ersilia.io.readers.file) StandardModelExampleError StandardTabularFileReader (class in ersilia.io.readers.file) start() (ersilia.db.environments.managers.DockerManager method) start_tracking() (ersilia.utils.docker.ContainerMetricsSampler method) startswith() (ersilia.utils.conda.SimpleConda method) status (ersilia.hub.content.base_information.BaseInformation property) Status (ersilia.utils.paths.Metadata attribute), [1] status() (ersilia.auth.auth.Auth method) (ersilia.hub.bundle.status.ModelStatus method) STATUS_CONFIGS (class in ersilia.publish.test.services.constants) StatusBaseInformationError stop() (ersilia.cli.cmd.Command method) (ersilia.db.environments.managers.DockerManager method) stop_containers() (ersilia.db.environments.managers.DockerManager method) stop_tracking() (ersilia.utils.docker.ContainerMetricsSampler method) store() (ersilia.publish.store.ModelStorager method) store_has_model() (in module ersilia.store.utils) string_delimiter() (ersilia.io.types.compound.IO method) (ersilia.io.types.text.IO method) subtask (ersilia.hub.content.base_information.BaseInformation property) SubtaskBaseInformationError SUCCEEDED (ersilia.store.utils.JobStatus attribute) SUCCESS (ersilia.publish.test.services.constants.STATUS_CONFIGS attribute) success (ersilia.publish.test.services.inspect.Result attribute) success() (ersilia.utils.logging.Logger method), [1] summarize_output() (ersilia.core.tracking.RunTracker method) summary() (ersilia.io.output_logger.TabularResultLogger method) SystemBundleService (class in ersilia.serve.services) SystemChecker (class in ersilia.utils.system) SystemPack (class in ersilia.hub.fetch.pack.bentoml_pack.runners) (class in ersilia.hub.fetch.pack.fastapi_pack.runners)

T

table (ersilia.db.environments.localdb.EnvironmentDb property) TableConfig (class in ersilia.publish.test.services.constants) TableConstants (class in ersilia.default) TableType (class in ersilia.publish.test.services.constants) TabularFileReader (class in ersilia.io.readers.file) TabularFileShapeStandardizer (class in ersilia.io.readers.file) TabularOutputStacker (class in ersilia.io.output) TabularResultLogger (class in ersilia.io.output_logger) tag (ersilia.hub.content.base_information.BaseInformation property) Tag (ersilia.utils.paths.Metadata attribute), [1] TagBaseInformationError target_organism (ersilia.hub.content.base_information.BaseInformation property) TargetOrganismBaseInformationError task (ersilia.hub.content.base_information.BaseInformation property) Task (ersilia.utils.paths.Metadata attribute), [1] TaskBaseInformationError TemplatePreparer (class in ersilia.hub.fetch.actions.get) TemplateRebaser (class in ersilia.publish.rebase) TemplateResolver (class in ersilia.hub.fetch.actions.template_resolver) test() (ersilia.cli.cmd.Command method) (ersilia.io.input.ExampleGenerator method) (ersilia.io.types.compound.IO method) (ersilia.io.types.text.IO method)

test_cmd() (in module ersilia.cli.commands.test) TextIdentifier (class in ersilia.utils.identifiers.text) throw_ersilia_exception() (in module ersilia.utils.exceptions_utils.throw_ersilia_exception) TimeStampIdentifier (class in ersilia.utils.identifiers.timestamp) title (ersilia.hub.content.base_information.BaseInformation property) (ersilia.publish.test.services.constants.TableConfig attribute) Title (ersilia.utils.paths.Metadata attribute), [1] TitleBaseInformationError tmp_pid_file() (in module ersilia.utils) TmpCleaner (class in ersilia.hub.delete.delete) toolize() (ersilia.hub.fetch.actions.toolize.ModelToolizer method), [1] TOP_LEFT (ersilia.default.TableConstants attribute) TOP_MIDDLE (ersilia.default.TableConstants attribute) TOP_RIGHT (ersilia.default.TableConstants attribute) TOTAL_DIR_SIZE (ersilia.publish.test.services.constants.Checks attribute) track() (ersilia.core.tracking.RunTracker method) tracking_status() (ersilia.core.session.Session method) TrackingNotSupportedError trim_string() (ersilia.publish.test.services.checks.CheckService method) types() (ersilia.hub.fetch.actions.sniff_fastapi.ColumnsFileReader method), [1]

U

uninstall() (ersilia.cli.cmd.Command method) (ersilia.utils.uninstall.Uninstaller method), [1] uninstall_cmd() (in module ersilia.cli.commands.uninstall) Uninstaller (class in ersilia.utils.installers) (class in ersilia.utils.uninstall) UnprocessableInputError unzip() (ersilia.utils.zip.Zipper method), [1] update_cpu_time() (ersilia.core.session.Session method) update_log() (ersilia.utils.installers.BaseInstaller method)

update_model_usage_time() (ersilia.core.model.ErsiliaModel method) update_peak_memory() (ersilia.core.session.Session method) update_total_memory() (ersilia.core.session.Session method) upload() (ersilia.publish.dockerhub.DockerHubUploader method) (ersilia.publish.s3.S3BucketRepoUploader method) upload_to_s3() (ersilia.core.tracking.RunTracker method) (ersilia.store.utils.FileManager static method) upload_zip() (ersilia.publish.s3.S3BucketRepoUploader method) url (ersilia.hub.fetch.lazy_fetchers.hosted.ModelHostedFetcher attribute) user() (ersilia.auth.auth.Auth method)

V

validate_aws_access() (ersilia.core.tracking.RunTracker method) validate_file_content() (ersilia.publish.test.services.checks.CheckService method) validate_repo_structure() (ersilia.publish.test.services.inspect.ModelInspector method) validate_smiles() (ersilia.utils.identifiers.compound.CompoundIdentifier method) VenvEnvironmentService (class in ersilia.serve.services)

VenvPack (class in ersilia.hub.fetch.pack.bentoml_pack.runners) verify_setuptools() (in module ersilia.setup.requirements.setuptools_req) Versioner (class in ersilia.utils.versioning) versioner (ersilia.hub.fetch.pack.bentoml_pack.mode.PackModeDecision attribute) VERTICAL (ersilia.default.TableConstants attribute) VirtualEnvironmentSetupError

W

WARNING (ersilia.publish.test.services.constants.STATUS_CONFIGS attribute) warning() (ersilia.utils.logging.Logger method), [1] was_fetched_from_dockerhub() (ersilia.core.modelbase.ModelBase method) WithToolFetchingNotWorking write() (ersilia.hub.content.catalog.CatalogTable method) (ersilia.io.output.DataFrame method), [1] write_apis() (ersilia.hub.fetch.lazy_fetchers.dockerhub.ModelDockerHubFetcher method), [1] (ersilia.hub.fetch.lazy_fetchers.hosted.ModelHostedFetcher method), [1]

write_hdf5() (ersilia.io.output.DataFrame method), [1] write_information() (ersilia.hub.content.card.RepoMetadataFile method) write_log() (ersilia.utils.installers.BaseInstaller method) write_status() (ersilia.hub.fetch.lazy_fetchers.hosted.ModelHostedFetcher method), [1] write_text() (ersilia.io.output.DataFrame method), [1] WrongCardIdentifierError

Y

yaml_constructors (ersilia.utils.paths.ErsiliaMetadataLoader attribute)

yes_no_input() (in module ersilia.utils.terminal)

Z

zip() (ersilia.utils.zip.Zipper method), [1]

Zipper (class in ersilia.utils.zip)