snakedeploy package

Submodules

snakedeploy.client module

snakedeploy.client.get_parser()

snakedeploy.client.main()

main entrypoint for snakedeploy

snakedeploy.providers module

class snakedeploy.providers.Github(source_url)

Bases: Provider

checkout(path: str, ref: str)

clone(path: str)

Clone the known source URL to a temporary directory

get_raw_file(path: str, tag: str)

get_source_file_declaration(path: str, tag: str, branch: str)

classmethod matches(source_url: str)

property name

class snakedeploy.providers.Gitlab(source_url)

Bases: Github

get_raw_file(path: str, tag: str)

class snakedeploy.providers.Local(source_url)

Bases: Provider

checkout(path: str, ref: str)

clone(tmpdir: str)

A local “clone” means moving files.

get_raw_file(path: str, tag: str)

get_source_file_declaration(path: str, tag: str, branch: str)

classmethod matches(source_url: str)

class snakedeploy.providers.Provider(source_url)

Bases: ABC

abstract checkout(path: str, ref: str)

abstract clone(path: str)

abstract get_raw_file(path: str, tag: str)

get_repo_name()

abstract classmethod matches(source_url: str)

snakedeploy.providers.get_provider(source_url)

snakedeploy.logging module

class snakedeploy.logger.ColorizingStreamHandler(nocolor=False, stream=<_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>)

Bases: StreamHandler

BLACK = 0

BLUE = 4

BOLD_SEQ = '\x1b[1m'

COLOR_SEQ = '\x1b[%dm'

CYAN = 6

GREEN = 2

MAGENTA = 5

RED = 1

RESET_SEQ = '\x1b[0m'

WHITE = 7

YELLOW = 3

can_color_tty()

colors = {'CRITICAL': 1, 'DEBUG': 4, 'ERROR': 1, 'INFO': 2, 'WARNING': 3}

decorate(record)

emit(record)

Emit a record.

If a formatter is specified, it is used to format the record. The record is then written to the stream with a trailing newline. If exception information is present, it is formatted using traceback.print_exception and appended to the stream. If the stream has an ‘encoding’ attribute, it is used to determine how to do the output to the stream.

property is_tty

class snakedeploy.logger.Logger

Bases: object

cleanup()

debug(msg)

error(msg)

exit(msg, return_code=1)

handler(msg)

info(msg)

location(msg)

progress(done=None, total=None)

set_level(level)

set_stream_handler(stream_handler)

shellcmd(msg)

text_handler(msg)

The default snakemake log handler. Prints the output to the console. Args:

msg (dict): the log message dictionary

warning(msg)

snakedeploy.logger.setup_logger(quiet=False, nocolor=False, stdout=False, debug=False)