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Source code for galaxy.tools.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.
Examples:
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
"""
from __future__ import print_function
import os
import subprocess
import sys
import time
from ._cli import arg_parser
from .mulled_build import (
add_build_arguments,
args_to_mull_targets_kwds,
build_target,
conda_versions,
get_affected_packages,
mull_targets,
)
from .util import quay_versions, version_sorted
def _fetch_repo_data(args):
repo_data = args.repo_data
channel = args.channel
if repo_data is None:
repo_data = "%s-repodata.json" % channel
if not os.path.exists(repo_data):
platform_tag = 'osx-64' if sys.platform == 'darwin' else 'linux-64'
subprocess.check_call([
'wget', '--quiet', 'https://conda.anaconda.org/%s/%s/repodata.json.bz2' % (channel, platform_tag),
'-O', '%s.bz2' % repo_data
])
subprocess.check_call([
'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."""
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:
time.sleep(1)
q = quay_versions(args.namespace, pkg_name)
versions = _new_versions(q, c)
else:
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', default=None,
help='Published repository data (will be fetched from --channel if not available and written). Defaults to [channel_name]-repodata.json.')
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()