ersilia package

Subpackages

• ersilia.app package
  • Subpackages
    • ersilia.app.fastapi package
      • Module contents
    • ersilia.app.streamlit package
      • Module contents
  • Module contents
• ersilia.auth package
  • Submodules
  • ersilia.auth.auth module
    • Auth
      • Auth.is_contributor()
      • Auth.login()
      • Auth.logout()
      • Auth.oauth_token()
      • Auth.status()
      • Auth.user()
  • Module contents
• ersilia.cli package
  • Subpackages
    • ersilia.cli.commands package
      • Subpackages
      • Submodules
      • ersilia.cli.commands.auth module
      • ersilia.cli.commands.catalog module
      • ersilia.cli.commands.close module
      • ersilia.cli.commands.delete module
      • ersilia.cli.commands.example module
      • ersilia.cli.commands.fetch module
      • ersilia.cli.commands.info module
      • ersilia.cli.commands.publish module
      • ersilia.cli.commands.run module
      • ersilia.cli.commands.serve module
      • ersilia.cli.commands.setup module
      • ersilia.cli.commands.test module
      • ersilia.cli.commands.uninstall module
      • Module contents
  • Submodules
  • ersilia.cli.cmd module
    • Command
      • Command.auth()
      • Command.catalog()
      • Command.close()
      • Command.delete()
      • Command.example()
      • Command.fetch()
      • Command.info()
      • Command.publish()
      • Command.restart()
      • Command.run()
      • Command.serve()
      • Command.setup()
      • Command.stop()
      • Command.test()
      • Command.uninstall()
  • ersilia.cli.create_cli module
    • create_ersilia_cli()
  • ersilia.cli.echo module
    • Silencer
      • Silencer.silence_file
      • Silencer.is_silence()
      • Silencer.speak()
      • Silencer.silence()
      • Silencer.is_silence()
      • Silencer.silence()
      • Silencer.speak()
    • echo()
  • ersilia.cli.messages module
    • ModelNotFound
      • ModelNotFound.model
      • ModelNotFound.echo()
      • ModelNotFound.echo()
    • ModelNotInLocal
      • ModelNotInLocal.model_id
      • ModelNotInLocal.echo()
      • ModelNotInLocal.echo()
  • Module contents
    • echo()
• ersilia.core package
  • Submodules
  • ersilia.core.base module
    • ErsiliaBase
  • ersilia.core.model module
    • ErsiliaModel
      • ErsiliaModel.api()
      • ErsiliaModel.api_task()
      • ErsiliaModel.close()
      • ErsiliaModel.example()
      • ErsiliaModel.fetch()
      • ErsiliaModel.get_apis()
      • ErsiliaModel.info()
      • ErsiliaModel.input_type
      • ErsiliaModel.is_valid()
      • ErsiliaModel.meta
      • ErsiliaModel.output_type
      • ErsiliaModel.paths
      • ErsiliaModel.run()
      • ErsiliaModel.schema
      • ErsiliaModel.serve()
      • ErsiliaModel.setup()
      • ErsiliaModel.size
      • ErsiliaModel.update_model_usage_time()
  • ersilia.core.modelbase module
    • ModelBase
      • ModelBase.is_available_locally()
      • ModelBase.is_valid()
      • ModelBase.was_fetched_from_dockerhub()
  • ersilia.core.session module
    • Session
      • Session.close()
      • Session.current_identifier()
      • Session.current_model_id()
      • Session.current_output_source()
      • Session.current_service_class()
      • Session.get()
      • Session.open()
      • Session.register_output_source()
      • Session.register_service_class()
      • Session.tracking_status()
      • Session.update_cpu_time()
      • Session.update_peak_memory()
      • Session.update_total_memory()
  • ersilia.core.tracking module
    • RunTracker
      • RunTracker.check_types()
      • RunTracker.get_file_sizes()
      • RunTracker.get_memory_info()
      • RunTracker.get_peak_memory()
      • RunTracker.log_result()
      • RunTracker.track()
    • flatten_dict()
    • get_nan_counts()
    • log_files_metrics()
    • serialize_session_json_to_csv()
    • serialize_tracking_json_to_csv()
    • upload_to_cddvault()
    • upload_to_s3()
  • Module contents
• ersilia.db package
  • Subpackages
    • ersilia.db.disk package
      • Submodules
      • ersilia.db.disk.fetched module
      • Module contents
    • ersilia.db.environments package
      • Submodules
      • ersilia.db.environments.localdb module
      • ersilia.db.environments.managers module
      • Module contents
    • ersilia.db.hubdata package
      • Submodules
      • ersilia.db.hubdata.interfaces module
      • ersilia.db.hubdata.localslugs module
      • ersilia.db.hubdata.sanitize module
      • ersilia.db.hubdata.tables module
      • Module contents
  • Module contents
• ersilia.hub package
  • Subpackages
    • ersilia.hub.bundle package
      • Submodules
      • ersilia.hub.bundle.bundle module
      • ersilia.hub.bundle.repo module
      • ersilia.hub.bundle.status module
      • Module contents
    • ersilia.hub.content package
      • Submodules
      • 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
      • Module contents
    • ersilia.hub.delete package
      • Submodules
      • ersilia.hub.delete.delete module
      • Module contents
    • ersilia.hub.fetch package
      • Subpackages
      • Submodules
      • ersilia.hub.fetch.fetch module
      • ersilia.hub.fetch.fetch_bentoml module
      • ersilia.hub.fetch.fetch_fastapi module
      • Module contents
    • ersilia.hub.pull package
      • Submodules
      • ersilia.hub.pull.pull module
      • Module contents
  • Module contents
• ersilia.io package
  • Subpackages
    • ersilia.io.readers package
      • Submodules
      • ersilia.io.readers.file module
      • ersilia.io.readers.pyinput module
      • Module contents
    • ersilia.io.types package
      • Subpackages
      • Submodules
      • ersilia.io.types.compound module
      • ersilia.io.types.naive module
      • ersilia.io.types.protein module
      • ersilia.io.types.text module
      • Module contents
  • Submodules
  • ersilia.io.annotated module
    • AnnotatedDataTyper
      • AnnotatedDataTyper.get_type()
  • ersilia.io.dataframe module
    • Dataframe
      • Dataframe.from_csv()
      • Dataframe.iterrows()
  • ersilia.io.input module
    • BaseIOGetter
      • BaseIOGetter.get()
      • BaseIOGetter.shape()
    • ExampleGenerator
      • ExampleGenerator.check_model_id()
      • ExampleGenerator.example()
      • ExampleGenerator.predefined_example()
      • ExampleGenerator.random_example()
      • ExampleGenerator.test()
    • GenericInputAdapter
      • GenericInputAdapter.adapt()
      • GenericInputAdapter.adapt_one_by_one()
      • GenericInputAdapter.batch_iter()
  • ersilia.io.output module
    • DataFrame
      • DataFrame.data
      • DataFrame.columns
      • DataFrame.decompose()
      • DataFrame.write_hdf5()
      • DataFrame.write_text()
      • DataFrame.write()
      • DataFrame.decompose()
      • DataFrame.write()
      • DataFrame.write_hdf5()
      • DataFrame.write_text()
    • DictlistDataframeConverter
      • DictlistDataframeConverter.config_json
      • DictlistDataframeConverter.dictlist2dataframe()
      • DictlistDataframeConverter.dataframe2dictlist()
      • DictlistDataframeConverter.dataframe2dictlist()
      • DictlistDataframeConverter.dictlist2dataframe()
    • GenericOutputAdapter
      • GenericOutputAdapter.model_id
      • GenericOutputAdapter.config_json
      • GenericOutputAdapter.adapt()
      • GenericOutputAdapter.adapt()
      • GenericOutputAdapter.merge()
      • GenericOutputAdapter.meta()
    • ResponseRefactor
      • ResponseRefactor.config_json
      • ResponseRefactor.refactor_response()
      • ResponseRefactor.refactor_response()
    • TabularOutputStacker
      • TabularOutputStacker.file_names
      • TabularOutputStacker.stack()
      • TabularOutputStacker.stack()
      • TabularOutputStacker.stack_hdf5()
      • TabularOutputStacker.stack_text()
  • ersilia.io.output_logger module
    • TabularResultLogger
      • TabularResultLogger.tabulate()
  • ersilia.io.pure module
    • PureDataTyper
      • PureDataTyper.get_type()
      • PureDataTyper.get_type_from_metadata()
  • ersilia.io.shape module
    • InputShape
      • InputShape.get()
    • InputShapeList
    • InputShapePairOfLists
    • InputShapeSingle
  • Module contents
• ersilia.lake package
  • Submodules
  • ersilia.lake.base module
    • LakeBase
      • LakeBase.lake_dir
      • LakeBase.is_installed()
  • ersilia.lake.interface module
    • IsauraInterface
      • IsauraInterface.model_id
      • IsauraInterface.api_name
      • IsauraInterface.hdf5
      • IsauraInterface.converter
      • IsauraInterface.is_available
      • IsauraInterface.done_todo()
      • IsauraInterface.read()
      • IsauraInterface.write()
  • ersilia.lake.manager module
    • IsauraManager
      • IsauraManager.model_id
      • IsauraManager.hdf5
      • IsauraManager.append_local_to_public()
      • IsauraManager.pull()
      • IsauraManager.push()
      • IsauraManager.remove_local_duplicates()
  • ersilia.lake.s3_logger module
  • Module contents
• ersilia.publish package
  • Submodules
  • ersilia.publish.deploy module
  • ersilia.publish.dockerhub module
    • DockerHubUploader
      • DockerHubUploader.build_image()
      • DockerHubUploader.set_credentials()
      • DockerHubUploader.upload()
  • ersilia.publish.inspect module
    • ModelInspector
      • ModelInspector.BENTOML_FILES
      • ModelInspector.BENTOML_FOLDERS
      • ModelInspector.COMMON_FILES
      • ModelInspector.ERSILIAPACK_FILES
      • ModelInspector.ERSILIAPACK_FOLDERS
      • ModelInspector.REQUIRED_FIELDS
      • ModelInspector.RUN_FILE
      • ModelInspector.check_complete_folder_structure()
      • ModelInspector.check_complete_metadata()
      • ModelInspector.check_computational_performance()
      • ModelInspector.check_dependencies_are_valid()
      • ModelInspector.check_no_extra_files()
      • ModelInspector.check_repo_exists()
      • ModelInspector.get_pack_type()
      • ModelInspector.validate_repo_structure()
    • Result
      • Result.details
      • Result.success
  • ersilia.publish.lake module
    • LakeStorer
      • LakeStorer.store()
  • ersilia.publish.publish module
    • ModelPublisher
      • ModelPublisher.create()
      • ModelPublisher.docker()
      • ModelPublisher.dvc()
      • ModelPublisher.git_push()
      • ModelPublisher.push()
      • ModelPublisher.rebase()
      • ModelPublisher.test()
  • ersilia.publish.rebase module
    • TemplateRebaser
      • TemplateRebaser.clean()
      • TemplateRebaser.clone_current_model()
      • TemplateRebaser.clone_template()
      • TemplateRebaser.dvc_part()
      • TemplateRebaser.rebase()
  • ersilia.publish.s3 module
    • S3BucketRepoUploader
      • S3BucketRepoUploader.set_credentials()
      • S3BucketRepoUploader.upload()
      • S3BucketRepoUploader.upload_zip()
  • ersilia.publish.store module
    • ModelRemover
      • ModelRemover.remove()
    • ModelStorager
      • ModelStorager.store()
  • ersilia.publish.test module
    • CheckService
      • CheckService.INPUT_SHAPE
      • CheckService.MODEL_OUTPUT
      • CheckService.MODEL_TASKS
      • CheckService.OUTPUT_SHAPE
      • CheckService.check_consistent_output()
      • CheckService.check_example_input()
      • CheckService.check_files()
      • CheckService.check_information()
      • CheckService.check_model_output_content()
      • CheckService.get_inputs()
      • CheckService.validate_file_content()
    • CheckStrategy
      • CheckStrategy.execute()
    • Checks
      • Checks.CONSISTENCY
      • Checks.DIR_SIZE
      • Checks.ENV_SIZE
      • Checks.IMAGE_SIZE
      • Checks.INCONSISTENCY
      • Checks.MODEL_CONSISTENCY
      • Checks.PREDEFINED_EXAMPLE
      • Checks.RUN_BASH
      • Checks.SIZE_CACL_FAILED
      • Checks.SIZE_CACL_SUCCESS
    • IOService
      • IOService.BENTOML_FILES
      • IOService.ERSILIAPACK_FILES
      • IOService.RUN_FILE
      • IOService.calculate_directory_size()
      • IOService.calculate_image_size()
      • IOService.collect_and_save_json()
      • IOService.get_conda_env_size()
      • IOService.get_directories_sizes()
      • IOService.get_env_sizes()
      • IOService.get_file_requirements()
      • IOService.get_model_type()
      • IOService.read_information()
      • IOService.update_metadata()
    • InspectService
      • InspectService.run()
    • ModelTester
      • ModelTester.run()
    • Options
      • Options.BASE
      • Options.INPUT_CSV
      • Options.INPUT_TYPES
      • Options.NUM_SAMPLES
      • Options.OUTPUT1_CSV
      • Options.OUTPUT2_CSV
      • Options.OUTPUT_CSV
      • Options.OUTPUT_FILES
    • RunnerService
      • RunnerService.fetch()
      • RunnerService.run()
      • RunnerService.run_bash()
      • RunnerService.run_example()
      • RunnerService.run_model()
    • STATUS_CONFIGS
      • STATUS_CONFIGS.FAILED
      • STATUS_CONFIGS.NA
      • STATUS_CONFIGS.PASSED
      • STATUS_CONFIGS.SUCCESS
      • STATUS_CONFIGS.WARNING
    • SetupService
      • SetupService.BASE_URL
      • SetupService.get_conda_env_location()
      • SetupService.get_model()
      • SetupService.run_command()
    • TableConfig
      • TableConfig.headers
      • TableConfig.title
    • TableType
      • TableType.COMPUTATIONAL_PERFORMANCE
      • TableType.CONSISTENCY_BASH
      • TableType.DEPENDECY_CHECK
      • TableType.FINAL_RUN_SUMMARY
      • TableType.INSPECT_SUMMARY
      • TableType.MODEL_DIRECTORY_SIZES
      • TableType.MODEL_ENV_SIZES
      • TableType.MODEL_FILE_CHECKS
      • TableType.MODEL_INFORMATION_CHECKS
      • TableType.MODEL_OUTPUT
      • TableType.RUNNER_CHECKUP_STATUS
      • TableType.SHALLOW_CHECK_SUMMARY
  • Module contents
• ersilia.serve package
  • Subpackages
    • ersilia.serve.environment package
      • Submodules
      • ersilia.serve.environment.environment_variables module
      • Module contents
  • Submodules
  • ersilia.serve.api module
    • Api
      • Api.meta()
      • Api.post()
      • Api.post_amenable_to_h5()
      • Api.post_only_calculations()
      • Api.post_only_reads()
      • Api.post_unique_input()
  • ersilia.serve.autoservice module
    • AutoService
      • AutoService.api()
      • AutoService.clean_before_serving()
      • AutoService.clean_docker_containers()
      • AutoService.clean_temp_dir()
      • AutoService.close()
      • AutoService.get_apis()
      • AutoService.is_available()
      • AutoService.is_served()
      • AutoService.serve()
  • ersilia.serve.schema module
    • ApiSchema
      • ApiSchema.empty()
      • ApiSchema.empty_by_api()
      • ApiSchema.empty_by_field()
      • ApiSchema.empty_input_by_api()
      • ApiSchema.empty_output_by_api()
      • ApiSchema.get()
      • ApiSchema.get_apis()
      • ApiSchema.get_meta()
      • ApiSchema.get_meta_by_api()
      • ApiSchema.get_output_by_api()
      • ApiSchema.get_schema_by_api()
      • ApiSchema.is_h5_serializable()
      • ApiSchema.isfile()
      • ApiSchema.schema
  • ersilia.serve.services module
    • BaseServing
    • CondaEnvironmentService
      • CondaEnvironmentService.api()
      • CondaEnvironmentService.close()
      • CondaEnvironmentService.is_available()
      • CondaEnvironmentService.is_single_model_without_conda()
      • CondaEnvironmentService.serve()
    • DockerImageService
      • DockerImageService.api()
      • DockerImageService.close()
      • DockerImageService.is_available()
      • DockerImageService.serve()
    • DummyService
      • DummyService.api()
      • DummyService.close()
      • DummyService.is_available()
      • DummyService.serve()
    • HostedService
      • HostedService.api()
      • HostedService.close()
      • HostedService.is_available()
      • HostedService.is_url_available()
      • HostedService.serve()
    • PipInstalledService
      • PipInstalledService.api()
      • PipInstalledService.close()
      • PipInstalledService.is_available()
      • PipInstalledService.serve()
    • PulledDockerImageService
      • PulledDockerImageService.api()
      • PulledDockerImageService.close()
      • PulledDockerImageService.is_available()
      • PulledDockerImageService.is_url_available()
      • PulledDockerImageService.serve()
    • SystemBundleService
      • SystemBundleService.api()
      • SystemBundleService.close()
      • SystemBundleService.is_available()
      • SystemBundleService.serve()
    • VenvEnvironmentService
      • VenvEnvironmentService.api()
      • VenvEnvironmentService.close()
      • VenvEnvironmentService.is_available()
      • VenvEnvironmentService.serve()
  • ersilia.serve.standard_api module
    • StandardCSVRunApi
      • StandardCSVRunApi.async_serialize_to_json_one_column()
      • StandardCSVRunApi.get_expected_output_header()
      • StandardCSVRunApi.get_identifier_object_by_input_type()
      • StandardCSVRunApi.get_list_from_csv()
      • StandardCSVRunApi.is_amenable()
      • StandardCSVRunApi.is_input_type_standardizable()
      • StandardCSVRunApi.is_output_csv_file()
      • StandardCSVRunApi.is_output_type_standardizable()
      • StandardCSVRunApi.parse_smiles_list()
      • StandardCSVRunApi.parse_smiles_string()
      • StandardCSVRunApi.post()
      • StandardCSVRunApi.serialize_to_csv()
      • StandardCSVRunApi.serialize_to_json()
      • StandardCSVRunApi.serialize_to_json_one_column()
      • StandardCSVRunApi.serialize_to_json_three_columns()
      • StandardCSVRunApi.serialize_to_json_two_columns()
  • Module contents
• ersilia.setup package
  • Subpackages
    • ersilia.setup.requirements package
      • Submodules
      • ersilia.setup.requirements.bentoml module
      • ersilia.setup.requirements.compound module
      • ersilia.setup.requirements.conda module
      • ersilia.setup.requirements.docker module
      • ersilia.setup.requirements.eospath module
      • ersilia.setup.requirements.git module
      • ersilia.setup.requirements.isaura module
      • ersilia.setup.requirements.ping module
      • Module contents
    • ersilia.setup.utils package
      • Submodules
      • ersilia.setup.utils.clone module
      • Module contents
  • Submodules
  • ersilia.setup.baseconda module
    • SetupBaseConda
      • SetupBaseConda.find_closest_python_version()
      • SetupBaseConda.setup()
      • SetupBaseConda.delete()
      • SetupBaseConda.delete()
      • SetupBaseConda.find_closest_python_version()
      • SetupBaseConda.setup()
  • ersilia.setup.basedocker module
    • SetupBaseDocker
      • SetupBaseDocker.delete()
      • SetupBaseDocker.setup()
  • ersilia.setup.conda module
    • SetupConda
      • SetupConda.setup()
  • ersilia.setup.config module
    • SetupConfig
      • SetupConfig.setup()
  • ersilia.setup.profile module
    • SetupProfile
      • SetupProfile.setup()
  • Module contents
• ersilia.store package
  • Submodules
  • ersilia.store.api module
    • InferenceStoreApi
      • InferenceStoreApi.get_precalculations()
  • ersilia.store.utils module
    • InferenceStoreMessage
    • ModelNotInStore
      • ModelNotInStore.echo()
    • OutputSource
      • OutputSource.ALL
      • OutputSource.CLOUD_ONLY
      • OutputSource.LOCAL_ONLY
      • OutputSource.is_cloud()
      • OutputSource.is_local()
    • PrecalculationsInStore
      • PrecalculationsInStore.echo()
    • PrecalculationsNotInStore
      • PrecalculationsNotInStore.echo()
    • delete_file_upon_upload()
    • store_has_model()
  • Module contents
• ersilia.tools package
  • Subpackages
    • ersilia.tools.bentoml package
      • Subpackages
      • Submodules
      • ersilia.tools.bentoml.exceptions module
      • ersilia.tools.bentoml.types module
      • Module contents
  • Module contents
• ersilia.utils package
  • Subpackages
    • ersilia.utils.exceptions_utils package
      • Submodules
      • 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
      • Module contents
    • ersilia.utils.identifiers package
      • Submodules
      • 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.protein module
      • ersilia.utils.identifiers.short module
      • ersilia.utils.identifiers.text module
      • ersilia.utils.identifiers.timestamp module
      • Module contents
    • ersilia.utils.supp package
      • Submodules
      • ersilia.utils.supp.conda_env_resolve module
      • Module contents
  • Submodules
  • ersilia.utils.cli_query module
    • query_yes_no()
  • ersilia.utils.conda module
    • BaseConda
      • BaseConda.default_env()
      • BaseConda.is_base()
      • BaseConda.conda_prefix()
      • BaseConda.conda_prefix()
      • BaseConda.default_env()
      • BaseConda.is_base()
    • CondaUtils
      • CondaUtils.activate_base()
      • CondaUtils.checksum_from_conda_yml_file()
      • CondaUtils.checksum_from_dockerfile()
      • CondaUtils.checksum_from_file()
      • CondaUtils.get_base_env()
      • CondaUtils.get_conda_and_pip_install_commands_from_dockerfile_if_exclusive()
      • CondaUtils.specs_from_dockerfile()
      • CondaUtils.specs_from_dockerfile_as_json()
    • SimpleConda
      • SimpleConda.active_env()
      • SimpleConda.clone()
      • SimpleConda.create()
      • SimpleConda.create_executable_bash_script()
      • SimpleConda.delete()
      • SimpleConda.delete_one()
      • SimpleConda.exists()
      • SimpleConda.export_env_yml()
      • SimpleConda.get_python_path_env()
      • SimpleConda.run_commandlines()
      • SimpleConda.startswith()
    • StandaloneConda
      • StandaloneConda.exists()
      • StandaloneConda.run_commandlines()
  • ersilia.utils.config module
    • Config
      • Config.keys()
    • Credentials
      • Credentials.keys()
  • ersilia.utils.cron module
    • del_model()
    • model_cleanup()
    • seconds_to_days()
  • ersilia.utils.csvfile module
    • CsvDataLoader
      • CsvDataLoader.load()
      • CsvDataLoader.read()
      • CsvDataLoader.load()
      • CsvDataLoader.read()
  • ersilia.utils.docker module
    • ContainerMetricsSampler
      • ContainerMetricsSampler.get_average_metrics()
      • ContainerMetricsSampler.start_tracking()
      • ContainerMetricsSampler.stop_tracking()
    • SimpleDocker
      • SimpleDocker.build()
      • SimpleDocker.cleanup_ersilia_images()
      • SimpleDocker.container_peak()
      • SimpleDocker.containers()
      • SimpleDocker.cp_from_container()
      • SimpleDocker.cp_from_image()
      • SimpleDocker.delete()
      • SimpleDocker.exec()
      • SimpleDocker.exec_container()
      • SimpleDocker.exists()
      • SimpleDocker.images()
      • SimpleDocker.kill()
      • SimpleDocker.remove()
      • SimpleDocker.run()
    • SimpleDockerfileParser
      • SimpleDockerfileParser.get_baseimage()
      • SimpleDockerfileParser.get_runs()
    • is_docker_installed()
    • is_udocker_installed()
    • model_image_version_reader()
    • resolve_pack_method_docker()
    • resolve_platform()
  • ersilia.utils.download module
    • GitHubDownloader
      • GitHubDownloader.clone()
      • GitHubDownloader.download_single()
    • GoogleDriveDownloader
      • GoogleDriveDownloader.download_file_from_google_drive()
      • GoogleDriveDownloader.fetch_zip()
      • GoogleDriveDownloader.get_confirm_token()
      • GoogleDriveDownloader.save_response_content()
    • OsfDownloader
      • OsfDownloader.fetch()
    • PseudoDownloader
      • PseudoDownloader.fetch()
    • S3Downloader
      • S3Downloader.download_from_s3()
  • ersilia.utils.dvc module
    • DVCBrancher
    • DVCFetcher
      • DVCFetcher.check_dvc_exists()
      • DVCFetcher.check_h5_exists()
      • DVCFetcher.get_data()
      • DVCFetcher.has_data()
    • DVCSetup
      • DVCSetup.gdrive_folder_id()
      • DVCSetup.gdrive_setup()
      • DVCSetup.git_add_and_commit()
      • DVCSetup.set_dvc_gdrive()
    • set_secrets_file()
  • ersilia.utils.environment module
    • Environment
      • Environment.has_module()
  • ersilia.utils.hdf5 module
    • Hdf5Data
      • Hdf5Data.save()
    • Hdf5DataLoader
      • Hdf5DataLoader.load()
      • Hdf5DataLoader.load()
    • Hdf5DataStacker
      • Hdf5DataStacker.stack()
  • ersilia.utils.import module
    • import_extra()
  • ersilia.utils.installers module
    • BaseInstaller
      • BaseInstaller.read_log()
      • BaseInstaller.remove_from_log()
      • BaseInstaller.remove_log()
      • BaseInstaller.update_log()
      • BaseInstaller.write_log()
    • Installer
      • Installer.base_conda()
      • Installer.base_conda_slim()
      • Installer.conda()
      • Installer.config()
      • Installer.git()
      • Installer.profile()
      • Installer.rdkit()
      • Installer.server_docker()
      • Installer.server_docker_slim()
    • Uninstaller
      • Uninstaller.base_conda()
      • Uninstaller.rdkit()
      • Uninstaller.server_docker()
    • base_installer()
    • full_installer()
  • ersilia.utils.logging module
    • Logger
      • Logger.set_verbosity()
      • Logger.debug()
      • Logger.info()
      • Logger.warning()
      • Logger.error()
      • Logger.critical()
      • Logger.success()
      • Logger.critical()
      • Logger.debug()
      • Logger.error()
      • Logger.info()
      • Logger.set_verbosity()
      • Logger.success()
      • Logger.warning()
    • make_temp_dir()
  • ersilia.utils.paths module
    • ErsiliaMetadataLoader
      • ErsiliaMetadataLoader.yaml_constructors
    • Metadata
      • Metadata.Identifier
      • Metadata.Slug
      • Metadata.Title
      • Metadata.Description
      • Metadata.Mode
      • Metadata.Input
      • Metadata.InputShape
      • Metadata.Task
      • Metadata.Output
      • Metadata.OutputType
      • Metadata.OutputShape
      • Metadata.Interpretation
      • Metadata.Tag
      • Metadata.Publication
      • Metadata.SourceCode
      • Metadata.License
      • Metadata.DockerHub
      • Metadata.DockerArchitecture
      • Metadata.S3
      • Metadata.Status
      • Metadata.Contributor
      • Metadata.Contributor
      • Metadata.Description
      • Metadata.DockerArchitecture
      • Metadata.DockerHub
      • Metadata.Identifier
      • Metadata.Input
      • Metadata.InputShape
      • Metadata.Interpretation
      • Metadata.License
      • Metadata.Mode
      • Metadata.Output
      • Metadata.OutputShape
      • Metadata.OutputType
      • Metadata.Publication
      • Metadata.S3
      • Metadata.Slug
      • Metadata.SourceCode
      • Metadata.Status
      • Metadata.Tag
      • Metadata.Task
      • Metadata.Title
    • Paths
      • Paths.model_id_from_path()
      • Paths.org_development_path()
      • Paths.ersilia_development_path()
      • Paths.exists()
      • Paths.ersilia_development_path()
      • Paths.exists()
      • Paths.home()
      • Paths.model_id_from_path()
      • Paths.org_development_path()
    • get_metadata_from_base_dir()
    • metadata_constructor()
    • resolve_pack_method()
    • resolve_pack_method_source()
  • ersilia.utils.ports module
    • find_free_port()
    • is_port_in_use()
  • ersilia.utils.remove module
    • OsfRemover
      • OsfRemover.remove()
  • ersilia.utils.session module
    • create_session_dir()
    • create_session_files()
    • deregister_model_session()
    • determine_orphaned_session()
    • get_current_pid()
    • get_model_session()
    • get_parent_pid()
    • get_session_dir()
    • get_session_id()
    • get_session_uuid()
    • register_model_session()
    • remove_orphaned_sessions()
    • remove_session_dir()
  • ersilia.utils.spinner module
    • Spinner
    • show_loader()
  • ersilia.utils.system module
    • SystemChecker
      • SystemChecker.is_arm64()
      • SystemChecker.is_github_action()
      • SystemChecker.is_inside_docker()
      • SystemChecker.is_arm64()
      • SystemChecker.is_github_action()
      • SystemChecker.is_inside_docker()
    • is_inside_docker()
  • ersilia.utils.terminal module
    • is_quiet()
    • print_result_table()
    • raw_input_with_timeout()
    • run_command()
    • run_command_check_output()
    • yes_no_input()
  • ersilia.utils.tracking module
  • ersilia.utils.uninstall module
    • Uninstaller
      • Uninstaller.uninstall()
      • Uninstaller.uninstall()
  • ersilia.utils.upload module
    • OsfUploader
      • OsfUploader.push()
      • OsfUploader.push()
  • ersilia.utils.venv module
    • SimpleVenv
      • SimpleVenv.create()
      • SimpleVenv.delete()
      • SimpleVenv.run_commandlines()
      • SimpleVenv.create()
      • SimpleVenv.delete()
      • SimpleVenv.exists()
      • SimpleVenv.run_commandlines()
  • ersilia.utils.versioning module
    • Versioner
      • Versioner.python_version()
      • Versioner.ersilia_version()
      • Versioner.ersilia_version_with_py()
      • Versioner.ersilia_version_from_path()
      • Versioner.bentoml_version()
      • Versioner.server_docker_name()
      • Versioner.base_conda_name()
      • Versioner.reformat_py()
      • Versioner.base_conda_name()
      • Versioner.bentoml_version()
      • Versioner.ersilia_version()
      • Versioner.ersilia_version_from_path()
      • Versioner.ersilia_version_with_py()
      • Versioner.python_version()
      • Versioner.reformat_py()
      • Versioner.server_docker_name()
  • ersilia.utils.zip module
    • Zipper
      • Zipper.unzip()
      • Zipper.zip()
      • Zipper.unzip()
      • Zipper.zip()
  • Module contents
    • tmp_pid_file()

Submodules

ersilia.default module

class ersilia.default.TableConstants(value)

Bases: str, Enum

An enumeration.

BOTTOM_LEFT = '└'

BOTTOM_MIDDLE = '┴'

BOTTOM_RIGHT = '┘'

CELL_PADDING = ' '

COLUMN_SEPARATOR = ' | '

HORIZONTAL = '─'

MIDDLE_LEFT = '├'

MIDDLE_MIDDLE = '┼'

MIDDLE_RIGHT = '┤'

TOP_LEFT = '┌'

TOP_MIDDLE = '┬'

TOP_RIGHT = '┐'

VERTICAL = '│'

ersilia.default.bashrc_cli_snippet(overwrite=True)

Write a conda snippet in the user profile.

This function writes on the user profile to create an executable to work with conda environments based on model identifiers.

Motivation behind this function is to define an ersilia CLI.

Parameters:

overwrite (-) – Overwrite the current bash profile file if the eosconda string is found.

ersilia.default.bashrc_path()

ersilia.default.has_profile_snippet()

Module contents

ersilia.check_install_status()