Source code for bioconda_utils.pkg_test

Mulled Tests

import subprocess as sp
import tempfile
import tarfile
import os
import shlex
from shutil import which
import logging

from . import utils

import conda_build.api
from conda_build.metadata import MetaData

logger = logging.getLogger(__name__)

# TODO: Make this configurable in and bioconda_utils.cli.

[docs]def get_tests(path): "Extract tests from a built package" tmp = tempfile.mkdtemp() t = t.extractall(tmp) input_dir = os.path.join(tmp, 'info', 'recipe') tests = [ '/usr/local/env-execute true', '. /usr/local/', ] recipe_meta = MetaData(input_dir) tests_commands = recipe_meta.get_value('test/commands') tests_imports = recipe_meta.get_value('test/imports') requirements = recipe_meta.get_value('requirements/run') if tests_imports or tests_commands: if tests_commands: tests.append(' && '.join(tests_commands)) if tests_imports and 'python' in requirements: tests.append( ' && '.join('python -c "import %s"' % imp for imp in tests_imports) ) elif tests_imports and ( 'perl' in requirements or 'perl-threaded' in requirements ): tests.append( ' && '.join('''perl -e "use %s;"''' % imp for imp in tests_imports) ) tests = ' && '.join(tests) tests = tests.replace('$R ', 'Rscript ') # this is specific to involucro, the way how we build our containers tests = tests.replace('$PREFIX', '/usr/local') tests = tests.replace('${PREFIX}', '/usr/local') return f"bash -c {shlex.quote(tests)}"
[docs]def get_image_name(path): """ Returns name of generated docker image. Parameters ---------- path : str Path to .tar.by2 package build by conda-build """ assert path.endswith('.tar.bz2') pkg = os.path.basename(path).replace('.tar.bz2', '') toks = pkg.split('-') build_string = toks[-1] version = toks[-2] name = '-'.join(toks[:-2]) spec = '%s=%s--%s' % (name, version, build_string) return spec
[docs]def test_package( path, name_override=None, channels=("conda-forge", "local", "bioconda", "defaults"), mulled_args="", base_image=None, conda_image=MULLED_CONDA_IMAGE, ): """ Tests a built package in a minimal docker container. Parameters ---------- path : str Path to a .tar.bz2 package built by conda-build name_override : str Passed as the --name-override argument to mulled-build channels : list List of Conda channels to use. Must include an entry "local" for the local build channel. mulled_args : str Mechanism for passing arguments to the mulled-build command. They will be split with shlex.split and passed to the mulled-build command. E.g., mulled_args="--dry-run --involucro-path /opt/involucro" base_image : None | str Specify custom base image. Busybox is used in the default case. conda_image : None | str Conda Docker image to install the package with during the mulled based tests. """ assert path.endswith('.tar.bz2'), "Unrecognized path {0}".format(path) # assert os.path.exists(path), '{0} does not exist'.format(path) conda_bld_dir = os.path.abspath(os.path.dirname(os.path.dirname(path))) conda_build.api.update_index([conda_bld_dir]) spec = get_image_name(path) if "local" not in channels: raise ValueError('"local" must be in channel list') channels = [ 'file://{0}'.format(conda_bld_dir) if channel == 'local' else channel for channel in channels ] channel_args = ['--channels', ','.join(channels)] tests = get_tests(path) logger.debug('Tests to run: %s', tests) cmd = [ 'mulled-build', 'build-and-test', spec, '-n', 'biocontainers', '--test', tests ] if name_override: cmd += ['--name-override', name_override] cmd += channel_args cmd += shlex.split(mulled_args) # galaxy-lib always downloads involucro, unless it's in cwd or its path is explicitly given. # We inject a POSTINSTALL to the involucro command with a small wrapper to # create activation / entrypoint scripts for the container. # We also inject a PREINSTALL to alias conda to mamba so `mamba install` is # used instead of `conda install` in the container builds. involucro_path = os.path.join(os.path.dirname(__file__), 'involucro') if not os.path.exists(involucro_path): raise RuntimeError('internal involucro wrapper missing') cmd += ['--involucro-path', involucro_path] logger.debug('mulled-build command: %s' % cmd) env = os.environ.copy() if base_image is not None: env["DEST_BASE_IMAGE"] = base_image env["CONDA_IMAGE"] = conda_image with tempfile.TemporaryDirectory() as d: with utils.Progress(): p =, env=env, cwd=d, mask=False) return p