Mercurial > repos > shellac > sam_consensus_v3
diff env/lib/python3.9/site-packages/planemo/commands/cmd_clone.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/planemo/commands/cmd_clone.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,70 @@ +"""Module describing the planemo ``recipe_init`` command.""" +import click + +from planemo import github_util +from planemo import options +from planemo.cli import command_function +from planemo.config import planemo_option + + +CLONE_GITHUB_TARGETS = { + "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", +} + + +def clone_target_arg(): + """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 https://github.com/settings/tokens. + """ + if target in CLONE_GITHUB_TARGETS: + target = "https://github.com/%s" % 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)