pype.exceptions

Central exception handling for bio_pype.

Provides a hierarchy of custom exceptions for better error context and handling. Each exception type includes contextual information specific to its domain.

exception pype.exceptions.PypeError(message, context=None)

Bases: Exception

Base exception for all pype errors.

Parameters:

• message (str)

• context (Dict | None)

__init__(message, context=None)

Parameters:

• message (str)

• context (Dict | None)

exception pype.exceptions.PipelineError(message, pipeline_name=None, **kwargs)

Bases: PypeError

Base class for pipeline-related errors.

Parameters:

• message (str)

• pipeline_name (str | None)

__init__(message, pipeline_name=None, **kwargs)

Parameters:

• message (str)

• pipeline_name (str | None)

exception pype.exceptions.PipelineVersionError(current_version, required_version, pipeline_name)

Bases: PipelineError

Raised when pipeline version is incompatible.

Parameters:

• current_version (str)

• required_version (str)

• pipeline_name (str | None)

__init__(current_version, required_version, pipeline_name)

Parameters:

• current_version (str)

• required_version (str)

• pipeline_name (str | None)

exception pype.exceptions.PipelineItemError(message, item_name, item_type, pipeline_name=None)

Bases: PipelineError

Error in a specific pipeline item.

Parameters:

• message (str)

• item_name (str)

• item_type (str)

• pipeline_name (str | None)

__init__(message, item_name, item_type, pipeline_name=None)

Parameters:

• message (str)

• item_name (str)

• item_type (str)

• pipeline_name (str | None)

exception pype.exceptions.SnippetError(message, snippet_name=None, **kwargs)

Bases: PypeError

Base class for snippet-related errors.

Parameters:

• message (str)

• snippet_name (str | None)

__init__(message, snippet_name=None, **kwargs)

Parameters:

• message (str)

• snippet_name (str | None)

exception pype.exceptions.SnippetNotFoundError(snippet_name)

Bases: SnippetError

Raised when a snippet cannot be found.

Parameters:

snippet_name (str)

__init__(snippet_name)

Parameters:

snippet_name (str)

exception pype.exceptions.SnippetResultsTemplateSobstitutionError(snippet_name, chunk_id, missing_key, template_vars, available_keys, missing_keys)

Bases: SnippetError

Raised when a snippet results template sobstritution reports an error.

Parameters:

• snippet_name (str)

• chunk_id (str)

• missing_key (str)

• template_vars (set[str])

• available_keys (set[str])

• missing_keys (set[str])

__init__(snippet_name, chunk_id, missing_key, template_vars, available_keys, missing_keys)

Parameters:

• snippet_name (str)

• chunk_id (str)

• missing_key (str)

• template_vars (set[str])

• available_keys (set[str])

• missing_keys (set[str])

exception pype.exceptions.SnippetResultsArgumentError(snippet_name, missing_key, available_keys)

Bases: SnippetError

Raised when a snippet results from non-md snippet gives an error.

Parameters:

• snippet_name (str)

• missing_key (str)

• available_keys (set[str])

__init__(snippet_name, missing_key, available_keys)

Parameters:

• snippet_name (str)

• missing_key (str)

• available_keys (set[str])

exception pype.exceptions.SnippetExecutionError(message, snippet_name, exit_code=None)

Bases: SnippetError

Raised when snippet execution fails.

Parameters:

• message (str)

• snippet_name (str)

• exit_code (int | None)

__init__(message, snippet_name, exit_code=None)

Parameters:

• message (str)

• snippet_name (str)

• exit_code (int | None)

exception pype.exceptions.ArgumentError(message, argument=None, **kwargs)

Bases: PypeError

Base class for argument-related errors.

Parameters:

• message (str)

• argument (str | None)

__init__(message, argument=None, **kwargs)

Parameters:

• message (str)

• argument (str | None)

exception pype.exceptions.InvalidTemplateVariableMixError(message, argument_key=None, **kwargs)

Bases: ArgumentError

Raised when template variables are mixed with static text in pipeline arguments.

Parameters:

• message (str)

• argument_key (str | None)

__init__(message, argument_key=None, **kwargs)

Parameters:

• message (str)

• argument_key (str | None)

exception pype.exceptions.BatchArgumentError(message, batch_file)

Bases: ArgumentError

Error in batch argument processing.

Parameters:

• message (str)

• batch_file (str | None)

__init__(message, batch_file)

Parameters:

• message (str)

• batch_file (str | None)

exception pype.exceptions.ProfileError(message, profile_name=None, **kwargs)

Bases: PypeError

Base class for profile-related errors.

Parameters:

• message (str)

• profile_name (str | None)

__init__(message, profile_name=None, **kwargs)

Parameters:

• message (str)

• profile_name (str | None)

exception pype.exceptions.CommandError(message, command=None, exit_code=None)

Bases: PypeError

Base class for command execution errors.

Parameters:

• message (str)

• command (str | None)

• exit_code (int | None)

__init__(message, command=None, exit_code=None)

Parameters:

• message (str)

• command (str | None)

• exit_code (int | None)

exception pype.exceptions.CommandNamespaceError(message, command=None, exit_code=None)

Bases: CommandError

Error in command namespace.

Parameters:

• message (str)

• command (str | None)

• exit_code (int | None)

exception pype.exceptions.EnvModulesError(message, module_name=None)

Bases: PypeError

Error in environment modules.

Parameters:

• message (str)

• module_name (str | None)

__init__(message, module_name=None)

Parameters:

• message (str)

• module_name (str | None)