package

Allow to handles model package either on localhost or from a remote location. the model packages can be stored in github organization to be downloaded and installed locally. The classes below are used by msl_data, which is the entry point to manipulate models package.

package API reference

AbstractModelIndex

class macsylib.model_package.AbstractModelIndex(cache: str | None = None)[source]

This the base class for ModelIndex. This class cannot be implemented, it must be subclassed

__init__(cache: str | None = None) → None[source]

__weakref__: list of weak references to the object

unarchive_package(path: str) → str[source]

Unarchive and uncompress a package under <remote cache>/<organization name>/<package name>/<vers>/<package name>

Parameters:: path (str)
Returns:: The path to the package

LocalModelIndex

class macsylib.model_package.LocalModelIndex(cache: str | None = None)[source]

It allow to manage installation from a local package (tarball)

__init__(cache: str | None = None) → None[source]

RemoteModelIndex

class macsylib.model_package.RemoteModelIndex(org: str = 'macsy-models', cache: str | None = None)[source]

This class allow to interact with ModelIndex on github

__init__(org: str = 'macsy-models', cache: str | None = None) → None[source]

Parameters:: org – The name of the organization on github where are stored the models

_url_json(url: str) → dict[source]

Get the url, deserialize the data as json

Parameters:: url (str) – the url to download
Returns:: the json corresponding to the response url

download(pack_name: str, vers: str, dest: str | None = None) → str[source]

Download a package from a GitHub repos and save it as <remote cache>/<organization name>/<package name>/<vers>.tar.gz

Parameters:

pack_name (str) – the name of the package to download
vers (str) – the version of the package to download
dest (str) – The path to the directory where save the package This directory must exist If dest is None, the macsylib cache will be used

Returns:

The package archive path.

get_metadata(pack_name: str, vers: str = 'latest') → dict[source]

Fetch the metadata_path from a remote package

Parameters:

pack_name (str) – The package name
vers (str) – The package version

Returns:

the metadata_path corresponding to this package/version

Return type:

dictionary corresponding of the yaml parsing of the metadata_path file.

list_package_vers(pack_name: str) → list[str][source]

List all available versions from GitHub model repos for a given package

Parameters:: pack_name (str) – the name of the package
Returns:: the list of the versions

list_packages() → list[str][source]

list all model packages available on a model repos

Returns:: The list of package names.

remote_exists() → bool[source]

check if the remote exists and is an organization

Returns:: True if the Remote url point to a GitHub Organization, False otherwise

ModelPackage

class macsylib.model_package.ModelPackage(path: str)[source]

This class Modelize a package of Models a package is a directory with the name of the models family it must contain at least - a subdirectory definitions - a subdirectory profiles - a file metadata.yml it is also recommended to add a file for licensing and copyright and a README. for further explanation see documentation: modeler guide > package

__init__(path: str) → None[source]

Parameters:: path (str) – The of the package root directory

__weakref__: list of weak references to the object

_check_metadata() → tuple[list[str], list[str]][source]

Check the QA of package metadata_path

Returns:: errors and warnings
Return type:: tuple of 2 lists ([str error_1, …], [str warning_1, …])

_check_model_conf() → tuple[list[str], list[str]][source]

check if a model configuration file is present in the package (model_conf.xml) if the syntax of this file is good.

Returns:

_check_model_consistency() → tuple[list, list][source]

check if each xml seems well write, each genes have an associated profile, etc.

Returns:

_check_profiles(profile_suffix='.hmm')[source]

check if there is only one profile per hmm file

Returns:
Return type:

_check_structure() → tuple[list[str], list[str]][source]

Check the QA structure of the package

Returns:: errors and warnings
Return type:: tuple of 2 lists ([str error_1, …], [str warning_1, …])

_find_readme() → str | None[source]

find the README file

Returns:: The path to the README file or None if there is no file.

_load_metadata() → dict[slice(<class 'str'>, <class 'str'>, None)][source]: Open the metadata_path file and de-serialize it’s content :return:

check() → tuple[list[str], list[str]][source]: Check the QA of this package

help() → str[source]: return the content of the README file

info() → str[source]

Returns:: some information about the package

property metadata: dict[slice(<class 'str'>, <class 'str'>, None)]

Returns:: The parsed metadata as a dict