def test_meta_contents(tmpdir):
env_matrix = helpers.tmp_env_matrix()
config = {
'env_matrix': env_matrix,
'channels': ['bioconda', 'conda-forge', 'defaults']
}
bioconductor_skeleton.write_recipe('edgeR',
recipe_dir=str(tmpdir),
config=config,
recursive=False)
edger_meta = utils.load_meta(str(tmpdir.join('bioconductor-edger')), {})
assert 'r-rcpp' in edger_meta['requirements']['build']
# note that the preprocessing selector is stripped off by yaml parsing, so
# just check for gcc
if sys.platform == 'linux':
assert 'gcc' in edger_meta['requirements']['build']
elif sys.platform == 'darwin':
assert 'llvm' in edger_meta['requirements']['build']
else:
raise ValueError('Unhandled platform: {}'.format(sys.platform))
# bioconductor, bioarchive, and cargoport
assert len(edger_meta['source']['url']) == 3
def _build_pkg(recipe):
r = Recipes(recipe, from_string=True)
r.write_recipes()
env_matrix = list(utils.EnvMatrix(tmp_env_matrix()))[0]
recipe = r.recipe_dirs['one']
built_package = utils.built_package_path(recipe)
ensure_missing(built_package)
build.build(recipe=r.recipe_dirs['one'], recipe_folder='.', env=env_matrix)
return built_package
def single_build(request, recipes_fixture):
"""
Builds the "one" recipe.
"""
env_matrix = list(utils.EnvMatrix(tmp_env_matrix()))[0]
if request.param:
docker_builder = docker_utils.RecipeBuilder(use_host_conda_bld=True)
else:
docker_builder = None
build.build(
recipe=recipes_fixture.recipe_dirs['one'],
recipe_folder='.',
docker_builder=docker_builder,
env=env_matrix,
)
built_package = recipes_fixture.pkgs['one']
yield built_package
ensure_missing(built_package)
def single_upload():
"""
Creates a randomly-named recipe and uploads it using a label so that it
doesn't affect the main bioconda channel. Tests that depend on this fixture
get a tuple of name, pakage, recipe dir. Cleans up when it's done.
"""
name = 'upload-test-' + str(uuid.uuid4()).split('-')[0]
r = Recipes('''
{0}:
meta.yaml: |
package:
name: {0}
version: "0.1"
'''.format(name),
from_string=True)
r.write_recipes()
env_matrix = list(utils.EnvMatrix(tmp_env_matrix()))[0]
build.build(
recipe=r.recipe_dirs[name],
recipe_folder='.',
docker_builder=None,
mulled_test=False,
env=env_matrix,
)
pkg = utils.built_package_path(r.recipe_dirs[name])
with utils.temp_env(
dict(TRAVIS_BRANCH='master', TRAVIS_PULL_REQUEST='false')):
upload.anaconda_upload(pkg, label=TEST_LABEL)
yield (name, pkg, r.recipe_dirs[name])
p = sp.run([
'anaconda', '-t',
os.environ.get('ANACONDA_TOKEN'), 'remove',
'bioconda/{0}'.format(name), '--force'
],
stdout=sp.PIPE,
stderr=sp.STDOUT,
check=True,
universal_newlines=True)
def _build_pkg():
r = Recipes(dedent("""
one:
meta.yaml: |
package:
name: one
version: 0.1
test:
commands:
- "ls -la"
"""),
from_string=True)
r.write_recipes()
env_matrix = list(utils.EnvMatrix(tmp_env_matrix()))[0]
recipe = r.recipe_dirs['one']
built_package = utils.built_package_path(recipe)
ensure_missing(built_package)
build.build(recipe=r.recipe_dirs['one'], recipe_folder='.', env=env_matrix)
return built_package
import sys
import pytest
from bioconda_utils import bioconductor_skeleton
from bioconda_utils import cran_skeleton
from bioconda_utils import utils
import helpers
env_matrix = helpers.tmp_env_matrix()
config = {
'env_matrix': env_matrix,
'channels': ['bioconda', 'conda-forge', 'defaults']
}
def test_cran_write_recipe(tmpdir):
cran_skeleton.write_recipe('locfit',
recipe_dir=str(tmpdir),
recursive=False)
assert tmpdir.join('r-locfit', 'meta.yaml').exists()
assert tmpdir.join('r-locfit', 'build.sh').exists()
assert tmpdir.join('r-locfit', 'bld.bat').exists()
def test_cran_write_recipe_no_windows(tmpdir):
cran_skeleton.write_recipe('locfit',
recipe_dir=str(tmpdir),
recursive=False,
no_windows=True)
