`ovo.core.configuration`¶

Module Contents¶

Classes¶

`BaseConfigModel`
`DBConfig`
`AWSConfig`
`StorageConfig`
`SchedulerConfig`
`AuthConfig`
`ConfigProps`
`TemplatesConfig`
`OVOConfig`

Functions¶

`save_global_home_dir`
`get_shell_config_path`	Get path to .bashrc or .zshrc based on the current shell.
`get_source_command`	Print the command for the user to source the shell config file.
`load_config`	Load OVOConfig from config dir config.yml
`save_default_config`

Data¶

`DEFAULT_OVO_HOME`
`GLOBAL_OVO_HOME`
`site_packages_dir`
`global_config_flag`
`default_data`

API¶

class ovo.core.configuration.BaseConfigModel(_case_sensitive: bool | None = None, _nested_model_default_partial_update: bool | None = None, _env_prefix: str | None = None, _env_file: pydantic_settings.sources.DotenvType | None = ENV_FILE_SENTINEL, _env_file_encoding: str | None = None, _env_ignore_empty: bool | None = None, _env_nested_delimiter: str | None = None, _env_nested_max_split: int | None = None, _env_parse_none_str: str | None = None, _env_parse_enums: bool | None = None, _cli_prog_name: str | None = None, _cli_parse_args: bool | list[str] | tuple[str, ...] | None = None, _cli_settings_source: pydantic_settings.sources.CliSettingsSource[Any] | None = None, _cli_parse_none_str: str | None = None, _cli_hide_none_type: bool | None = None, _cli_avoid_json: bool | None = None, _cli_enforce_required: bool | None = None, _cli_use_class_docs_for_groups: bool | None = None, _cli_exit_on_error: bool | None = None, _cli_prefix: str | None = None, _cli_flag_prefix_char: str | None = None, _cli_implicit_flags: bool | None = None, _cli_ignore_unknown_args: bool | None = None, _cli_kebab_case: bool | None = None, _cli_shortcuts: collections.abc.Mapping[str, str | list[str]] | None = None, _secrets_dir: pydantic_settings.sources.PathType | None = None, **values: Any)¶

Bases: pydantic_settings.BaseSettings

model_config¶: ‘SettingsConfigDict(…)’

class ovo.core.configuration.DBConfig¶

url: str | None¶: None

verbose: bool¶: False

class ovo.core.configuration.AWSConfig¶

region: str¶: None

assume_role_arn: str¶: None

class ovo.core.configuration.StorageConfig¶

path: str | None¶: None

verbose: bool¶: False

aws: ovo.core.configuration.AWSConfig | None¶: ‘field(…)’

class ovo.core.configuration.SchedulerConfig¶

type: str¶: None

name: str¶: None

workdir: str¶: None

aws: ovo.core.configuration.AWSConfig | None¶: ‘field(…)’

submission_args: dict¶: ‘field(…)’

class ovo.core.configuration.AuthConfig¶

admin_users: list[str]¶: ‘field(…)’

streamlit_auth: bool¶: ‘field(…)’

allow_private_project_link_access: bool¶: ‘field(…)’

hide_admin_warning: bool¶: ‘field(…)’

always_require_token: bool¶: ‘field(…)’

class ovo.core.configuration.ConfigProps¶

pyrosetta_license: bool¶: False

read_only: bool¶: False

rfdiffusion_backbones_limit: int¶: 1000

rfdiffusion_backbones_limit_admin: int¶: 5000

mpnn_sequences_limit: int¶: 100

class ovo.core.configuration.TemplatesConfig¶

welcome: str | None¶: None

welcome_appendix: str | None¶: None

class ovo.core.configuration.OVOConfig(_case_sensitive: bool | None = None, _nested_model_default_partial_update: bool | None = None, _env_prefix: str | None = None, _env_file: pydantic_settings.sources.DotenvType | None = ENV_FILE_SENTINEL, _env_file_encoding: str | None = None, _env_ignore_empty: bool | None = None, _env_nested_delimiter: str | None = None, _env_nested_max_split: int | None = None, _env_parse_none_str: str | None = None, _env_parse_enums: bool | None = None, _cli_prog_name: str | None = None, _cli_parse_args: bool | list[str] | tuple[str, ...] | None = None, _cli_settings_source: pydantic_settings.sources.CliSettingsSource[Any] | None = None, _cli_parse_none_str: str | None = None, _cli_hide_none_type: bool | None = None, _cli_avoid_json: bool | None = None, _cli_enforce_required: bool | None = None, _cli_use_class_docs_for_groups: bool | None = None, _cli_exit_on_error: bool | None = None, _cli_prefix: str | None = None, _cli_flag_prefix_char: str | None = None, _cli_implicit_flags: bool | None = None, _cli_ignore_unknown_args: bool | None = None, _cli_kebab_case: bool | None = None, _cli_shortcuts: collections.abc.Mapping[str, str | list[str]] | None = None, _secrets_dir: pydantic_settings.sources.PathType | None = None, **values: Any)¶

Bases: ovo.core.configuration.BaseConfigModel

dir: str¶: ‘field(…)’

reference_files_dir: str¶: ‘field(…)’

db: ovo.core.configuration.DBConfig¶: ‘field(…)’

auth: ovo.core.configuration.AuthConfig¶: ‘field(…)’

storage: ovo.core.configuration.StorageConfig¶: ‘field(…)’

default_scheduler: str | None¶: None

local_scheduler: str | None¶: None

schedulers: dict[str, ovo.core.configuration.SchedulerConfig]¶: ‘field(…)’

nextflow_home: str¶: ‘field(…)’

templates: ovo.core.configuration.TemplatesConfig¶: ‘field(…)’

props: ovo.core.configuration.ConfigProps¶: ‘field(…)’

resolve_relative_paths()¶

Resolve relative paths to absolute paths based on config directory

Config paths are stored as relative to config directory, but in the config object instance they are resolved to full absolute paths.

classmethod default(props: ovo.core.configuration.ConfigProps, default_profile=None, admin_users: list[str] = None) → str¶

static default_nextflow_config()¶

ovo.core.configuration.DEFAULT_OVO_HOME¶: ‘abspath(…)’

ovo.core.configuration.GLOBAL_OVO_HOME¶: None

ovo.core.configuration.site_packages_dir¶: ‘dirname(…)’

ovo.core.configuration.global_config_flag¶: ‘join(…)’

ovo.core.configuration.default_data¶: ‘safe_load(…)’

ovo.core.configuration.save_global_home_dir(home_dir: str)¶

ovo.core.configuration.get_shell_config_path()¶: Get path to .bashrc or .zshrc based on the current shell.

ovo.core.configuration.get_source_command()¶: Print the command for the user to source the shell config file.

ovo.core.configuration.load_config(home_dir: str) → ovo.core.configuration.OVOConfig¶: Load OVOConfig from config dir config.yml

ovo.core.configuration.save_default_config(home_dir, config_props: ovo.core.configuration.ConfigProps, default_profile: str = None, admin_users: list[str] = None) → str¶

ovo.core.configuration¶