Source code for planemo.commands.cmd_clone

"""Module describing the planemo ``clone`` command."""

from typing import Callable

import click

from planemo import (
from planemo.cli import command_function
from planemo.config import planemo_option

    "tools-iuc": "galaxyproject/tools-iuc",
    "tools-devteam": "galaxyproject/tools-devteam",
    "galaxy": "galaxyproject/galaxy",
    "planemo": "galaxyproject/planemo",
    "tools-galaxyp": "galaxyproteomics/tools-galaxyp",
    "bioconda-recipes": "bioconda/bioconda-recipes",
    "homebrew-science": "Homebrew/homebrew-science",
    "workflows": "common-workflow-language/workflows",

[docs] def clone_target_arg() -> Callable: """Represent target to clone/branch.""" return click.argument( "target", metavar="TARGET", type=click.STRING, )
@click.command("clone") @planemo_option( "--fork/--skip_fork", default=True, is_flag=True, ) @planemo_option("--branch", type=click.STRING, default=None, help="Create a named branch on result.") @clone_target_arg() @options.optional_project_arg(exists=None, default="__NONE__") @command_function def cli(ctx, target, path, **kwds): """Short-cut to quickly clone, fork, and branch a relevant Github repo. For instance, the following will clone, fork, and branch the tools-iuc repository to allow a subsequent pull request to fix a problem with bwa. \b $ planemo clone --branch bwa-fix tools-iuc $ cd tools-iuc $ # Make changes. $ git add -p # Add desired changes. $ git commit -m "Fix bwa problem." $ planemo pull_request -m "Fix bwa problem." These changes do require that a github access token is specified in ~/.planemo.yml. An access token can be generated by going to """ if target in CLONE_GITHUB_TARGETS: target = "" % CLONE_GITHUB_TARGETS[target] # Pretty hacky that this path isn't treated as None. if path is None or path.endswith("__NONE__"): path = target.split("/")[-1] github_util.clone_fork_branch(ctx, target, path, **kwds)