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Source code for galaxy.tool_util.deps.mulled.mulled_build_channel

#!/usr/bin/env python
"""Build a mulled images for all recent conda recipe updates that don't have existing images.


Build mulled images for recent bioconda changes with:

    mulled-build-channel build

Build, test, and publish images with the follow command:

    mulled-build-channel all

See recent changes that would be built with:

    mulled-build-channel list


import os
import subprocess
import sys
import time

import requests

from ._cli import arg_parser
from .mulled_build import (
from .util import quay_versions, version_sorted

def _fetch_repo_data(args):
    repo_data = args.repo_data
    channel = args.channel
    if not os.path.exists(repo_data):
        platform_tag = 'osx-64' if sys.platform == 'darwin' else 'linux-64'
            'wget', '--quiet', 'https://conda.anaconda.org/{}/{}/repodata.json.bz2'.format(channel, platform_tag),
            '-O', '%s.bz2' % repo_data
            'bzip2', '-d', '%s.bz2' % repo_data
    return repo_data

def _new_versions(quay, conda):
    """Calculate the versions that are in conda but not on quay.io."""
    sconda = set(conda)
    squay = set(quay) if quay else set()
    return sconda - squay  # sconda.symmetric_difference(squay)

def run_channel(args, build_last_n_versions=1):
    """Build list of involucro commands (as shell snippet) to run."""
    session = requests.session()
    for pkg_name, pkg_tests in get_affected_packages(args):
        repo_data = _fetch_repo_data(args)
        c = conda_versions(pkg_name, repo_data)
        # only package the most recent N versions
        c = version_sorted(c)[:build_last_n_versions]

        if not args.force_rebuild:
            q = quay_versions(args.namespace, pkg_name, session)
            versions = _new_versions(q, c)
            versions = c

        for tag in versions:
            target = build_target(pkg_name, tag=tag)
            targets = [target]
            mull_targets(targets, test=pkg_tests, **args_to_mull_targets_kwds(args))

def get_pkg_names(args):
    """Print package names that would be affected."""
    print('\n'.join(pkg_name for pkg_name, pkg_tests in get_affected_packages(args)))

def add_channel_arguments(parser):
    """Add arguments only used if running mulled over a whole conda channel."""
    parser.add_argument('--repo-data', dest='repo_data', required=True,
                        help='Published repository data. If you want to build all containers for bioconda, this parameter needs to be set to "bioconda"')
    parser.add_argument('--diff-hours', dest='diff_hours', default="25",
                        help='If finding all recently changed recipes, use this number of hours.')
    parser.add_argument('--recipes-dir', dest="recipes_dir", default="./bioconda-recipes")
    parser.add_argument('--force-rebuild', dest="force_rebuild", action="store_true",
                        help="Rebuild package even if already published.")

[docs]def main(argv=None): """Main entry-point for the CLI tool.""" parser = arg_parser(argv, globals()) add_channel_arguments(parser) add_build_arguments(parser) parser.add_argument('command', metavar='COMMAND', help='Command (list, build-and-test, build, all)') parser.add_argument('--targets', dest="targets", default=None, help="Build a single container with specific package(s).") parser.add_argument('--repository-name', dest="repository_name", default=None, help="Name of a single container (leave blank to auto-generate based on packages).") args = parser.parse_args() if args.command == "list": get_pkg_names(args) else: run_channel(args)
__all__ = ("main", ) if __name__ == '__main__': main()