solidipes.utils.utils module

exception solidipes.utils.utils.DataRepositoryException

Bases: ValueError

exception solidipes.utils.utils.ExecError

Bases: RuntimeError

solidipes.utils.utils._get_config_path(current_working_dir, filename_var, initial_path='', check_existence=False, user=False)

solidipes.utils.utils.add_completed_stage(stage) → None

class solidipes.utils.utils.bcolors

Bases: object

BLACK = '\x1b[30m'

BLINK = '\x1b[5m'

BLUE = '\x1b[34m'

BOLD = '\x1b[1m'

BRIGHT_BLACK = '\x1b[90m'

BRIGHT_BLUE = '\x1b[94m'

BRIGHT_CYAN = '\x1b[96m'

BRIGHT_GREEN = '\x1b[92m'

BRIGHT_MAGENTA = '\x1b[95m'

BRIGHT_RED = '\x1b[91m'

BRIGHT_WHITE = '\x1b[97m'

BRIGHT_YELLOW = '\x1b[93m'

CYAN = '\x1b[36m'

GREEN = '\x1b[32m'

MAGENTA = '\x1b[35m'

RED = '\x1b[31m'

RESET = '\x1b[0m'

UNDERLINE = '\x1b[4m'

WHITE = '\x1b[37m'

YELLOW = '\x1b[33m'

solidipes.utils.utils.check_process_return(process, fail_message) → None

class solidipes.utils.utils.classproperty(func: Callable)

Bases: object

solidipes.utils.utils.compute_checksum(filepath: str) → str

solidipes.utils.utils.dict_to_pretty_str(d: dict, indent=0, indent_size=4)

solidipes.utils.utils.find_config_directory(initial_path='', dir_name='.solidipes')

Find a directory in the current path or any of its parents.

solidipes.utils.utils.generate_readme(*args, with_title=True, **kwargs) → None

solidipes.utils.utils.get_completed_stages()

solidipes.utils.utils.get_config(filename_var, *args, **kwargs)

solidipes.utils.utils.get_config_path(filename_var, initial_path='', check_existence=False, user=False)

solidipes.utils.utils.get_git_repository(initial_path='')

solidipes.utils.utils.get_git_root(initial_path='')

solidipes.utils.utils.get_ignore(*args, **kwargs) → set[str]

solidipes.utils.utils.get_mimes(*args, **kwargs)

solidipes.utils.utils.get_mimes_path(*args, **kwargs)

solidipes.utils.utils.get_path_relative_to_root(path)

Express path relative to study root.

solidipes.utils.utils.get_path_relative_to_workdir(path)

Convert path expressed relative to study root to path expressed relative to current working directory.

solidipes.utils.utils.get_readme_path(*args, **kwargs)

solidipes.utils.utils.get_solidipes_directory(initial_path='')

Get the path to the .solidipes directory.

solidipes.utils.utils.get_study_description_path(*args, **kwargs)

solidipes.utils.utils.get_study_log_path()

solidipes.utils.utils.get_study_metadata(*args, md_to_html=False, **kwargs)

solidipes.utils.utils.get_study_metadata_path(*args, **kwargs)

solidipes.utils.utils.get_study_root_path(initial_path='', **kwargs)

solidipes.utils.utils.get_user_solidipes_directory()

solidipes.utils.utils.get_zenodo_infos(*args, **kwargs)

solidipes.utils.utils.include_metadata_description(metadata, generate_readme=False, use_readme=False, md_to_html=False, **kwargs)

Update metadata description field with DESCRIPTION.md file.

solidipes.utils.utils.init_git_repository(initial_path='')

solidipes.utils.utils.is_readonly(*args, **kwargs) → bool

returns true if the study is readonly

solidipes.utils.utils.is_stage_completed(stage)

solidipes.utils.utils.load_yaml(filename)

solidipes.utils.utils.make_tree(*args, only_dirs=False, **kwargs) → str

solidipes.utils.utils.populate_metadata_mandatory_fields(metadata) → None

solidipes.utils.utils.remove_completed_stage(stage) → None

solidipes.utils.utils.rename_file(old_name, new_name) → None

solidipes.utils.utils.run_and_check_return(command, headless=False, fail_message='Error', timeout=15, cwd=None) → None

solidipes.utils.utils.save_yaml(filename, config)

solidipes.utils.utils.separate_metadata_description(metadata, html_to_md=False, **kwargs) → None

Remove description from saved yml and put it in a separate file.

solidipes.utils.utils.set_config(filename_var, config, *args, **kwargs) → None

solidipes.utils.utils.set_ignore(config: set[str], *args, **kwargs) → None

solidipes.utils.utils.set_mimes(config, *args, **kwargs) → None

solidipes.utils.utils.set_study_metadata(config, *args, html_to_md=False, **kwargs) → None

solidipes.utils.utils.set_zenodo_infos(config, *args, **kwargs) → None

solidipes.utils.utils.string_to_regex_pattern(pattern: str) → str

Convert a string into a pattern that matches exactly.

solidipes.utils.utils.transform_data_containers_to_dict(data)

solidipes.utils.utils.transform_dict_to_data_containers(data)