ersilia.publish.test package

Subpackages

• ersilia.publish.test.services package
  • Submodules
  • ersilia.publish.test.services.checks module
    • CheckService
      • CheckService.check_consistent_output()
      • CheckService.check_files()
      • CheckService.check_information()
      • CheckService.check_model_output_content()
      • CheckService.check_simple_model_async_output()
      • CheckService.check_simple_model_output()
      • CheckService.compare_csv_columns()
      • CheckService.find_missing_first_output_col()
      • CheckService.get_inputs()
      • CheckService.trim_string()
      • CheckService.validate_file_content()
  • ersilia.publish.test.services.constants module
    • Checks
      • Checks.COLUMN_CHECK_FAILURE
      • Checks.COLUMN_CHECK_SUCCESS
      • Checks.COLUMN_MISMATCH
      • Checks.COLUMN_NAME_VALIDITY
      • Checks.CONSISTENCY
      • Checks.CSV_CONTENT_CHECK
      • Checks.DEPENDENCY_PINNED
      • Checks.DIR_SIZE
      • Checks.EMPTY_COLUMNS
      • Checks.ENV_SIZE
      • Checks.FETCH_FAILS
      • Checks.IMAGE_SIZE
      • Checks.INCONSISTENCY
      • Checks.MODEL_CONSISTENCY
      • Checks.PREDEFINED_EXAMPLE
      • Checks.RUN_BASH
      • Checks.SIMPLE_MODEL_RUN
      • Checks.SIMPLE_MODEL_RUN_ASYNC
      • Checks.SIMPLE_MODEL_RUN_COLUMNS
      • Checks.SIZE_CACL_FAILED
      • Checks.SIZE_CACL_SUCCESS
      • Checks.TOTAL_DIR_SIZE
    • Options
      • Options.ASYNC_OUTPUT_CSV
      • Options.BASE
      • Options.DEEP_INPUT
      • Options.DEEP_OUTPUT
      • Options.EXAMPLE_CSV
      • Options.INPUT_CSV
      • Options.INPUT_TYPES
      • Options.INPUT_TYPES_TEST
      • Options.NUM_SAMPLES
      • Options.OUTPUT1_CSV
      • Options.OUTPUT2_CSV
      • Options.OUTPUT_CSV
      • Options.OUTPUT_FILES
      • Options.OUTPUT_FILES_TEST
    • STATUS_CONFIGS
      • STATUS_CONFIGS.FAILED
      • STATUS_CONFIGS.NA
      • STATUS_CONFIGS.NOT_PRESENT
      • STATUS_CONFIGS.PASSED
      • STATUS_CONFIGS.SKIPPED
      • STATUS_CONFIGS.SUCCESS
      • STATUS_CONFIGS.WARNING
    • TableConfig
      • TableConfig.headers
      • TableConfig.title
    • TableType
      • TableType.ASNC_MODEL_RUN_CHECK
      • TableType.COMPUTATIONAL_PERFORMANCE
      • TableType.CONSISTENCY_BASH
      • TableType.DEPENDECY_COLUMN_CHECK
      • TableType.FETCH_STATUS_SURFACE
      • TableType.FINAL_RUN_SUMMARY
      • TableType.INSPECT_SUMMARY
      • TableType.MODEL_DIRECTORY_SIZES
      • TableType.MODEL_FILE_CHECKS
      • TableType.MODEL_INFORMATION_CHECKS
      • TableType.MODEL_OUTPUT
      • TableType.MODEL_RUN_CHECK
      • TableType.MODEL_SIZES
      • TableType.RUNNER_CHECKUP_STATUS
      • TableType.SHALLOW_CHECK_SUMMARY
  • ersilia.publish.test.services.inspect module
    • CheckStrategy
      • CheckStrategy.execute()
    • InspectService
      • InspectService.run()
    • ModelInspector
      • ModelInspector.BENTOML_FILES
      • ModelInspector.ERSILIAPACK_FILES
      • ModelInspector.REQUIRED_FIELDS
      • 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.validate_repo_structure()
    • Result
      • Result.details
      • Result.success
  • ersilia.publish.test.services.io module
    • IOService
      • 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.get_output_consistency()
      • IOService.read_csv_values()
      • IOService.submit_smiles_and_get_results()
    • PackageInstaller
      • PackageInstaller.install_packages_from_dir()
  • ersilia.publish.test.services.parser module
    • DockerfileInstallParser
    • InstallParser
      • InstallParser.check_file_exists()
      • InstallParser.get_python_exe()
      • InstallParser.write_bash_script()
    • YAMLInstallParser
    • eval_conda_prefix()
  • ersilia.publish.test.services.runner module
    • RunnerService
      • RunnerService.delete()
      • RunnerService.fetch()
      • RunnerService.run()
      • RunnerService.run_bash()
      • RunnerService.run_example()
      • RunnerService.run_model()
      • RunnerService.serve_model()
  • ersilia.publish.test.services.setup module
    • SetupService
      • SetupService.BASE_URL
      • SetupService.get_conda_env_location()
      • SetupService.get_model()
      • SetupService.run_command()
  • Module contents

Submodules

ersilia.publish.test.noxfile module

ersilia.publish.test.test module

class ersilia.publish.test.test.ModelTester(model, from_dir, from_github, from_dockerhub, from_s3, version, shallow, deep, surface, inspect, report_path, clean)

Bases: ErsiliaBase

Class to handle model testing. Initializes the model tester services and runs the tests.

Parameters:

• model (str) – The ID of the model.

• from_dir (str) – The directory for the model.

• from_github (bool) – Flag indicating whether to fetch the repository from GitHub.

• from_dockerhub (bool) – Flag indicating whether to fetch the repository from DockerHub.

• from_s3 (bool) – Flag indicating whether to fetch the repository from S3.

• version (str) – Version of the model.

• shallow (bool) – Flag indicating whether to perform shallow checks.

• deep (bool) – Flag indicating whether to perform deep checks.

• surface (bool) – Flag indicating whether to perform surface checks.

• inspect (bool) – Flag indicating whether to perform inspect checks.

• report_path (str) – Flag to specify the path for output as json.

• clean (bool) – Flag indicating whether to clean temp folder.

clean_temp()

Clean up the temp model directory.

run()

Run the model tester.

Module contents