def test_experiment_data(tmpdir, bioc_fetch):
bioconductor_skeleton.write_recipe('affydata', str(tmpdir), config, recursive=False, packages=bioc_fetch)
meta = utils.load_first_metadata(str(tmpdir.join('bioconductor-affydata'))).meta
assert any(dep.startswith('curl ') for dep in meta['requirements']['run'])
assert len(meta['source']['url']) == 3
assert not tmpdir.join('bioconductor-affydata', 'build.sh').exists()
assert tmpdir.join('bioconductor-affydata', 'post-link.sh').exists()
assert tmpdir.join('bioconductor-affydata', 'pre-unlink.sh').exists()
def test_nonexistent_pkg(tmpdir, bioc_fetch):
# no such package exists in the current bioconductor
with pytest.raises(bioconductor_skeleton.PackageNotFoundError):
bioconductor_skeleton.write_recipe(
'nonexistent', str(tmpdir), config, recursive=True, packages=bioc_fetch)
# package exists, but not this version
with pytest.raises(bioconductor_skeleton.PackageNotFoundError):
bioconductor_skeleton.write_recipe(
'DESeq', str(tmpdir), config, recursive=True, pkg_version='5000', packages=bioc_fetch)
def test_bioc_write_recipe_skip_in_condaforge(tmpdir, bioc_fetch):
bioconductor_skeleton.write_recipe(
'edgeR', recipe_dir=str(tmpdir), config=config, recursive=True,
packages=bioc_fetch,
skip_if_in_channels=['conda-forge'])
for pkg in [
'bioconductor-edger', 'bioconductor-limma',
]:
assert tmpdir.join(pkg).exists()
for pkg in ['r-cpp', 'r-lattice', 'r-locfit']:
assert not tmpdir.join(pkg).exists()
def test_bioc_write_recipe_no_skipping(tmpdir, bioc_fetch):
bioconductor_skeleton.write_recipe(
'edgeR', recipe_dir=str(tmpdir), config=config, recursive=True,
packages=bioc_fetch,
skip_if_in_channels=None)
for pkg in [
'bioconductor-edger', 'bioconductor-limma', 'r-rcpp'
# sometime locfit and lattice don't build correctly, but we should
# eventually ensure they are here as well.
# 'r-locfit',
# 'r-lattice',
]:
assert tmpdir.join(pkg).exists()
def test_meta_contents(tmpdir, bioc_fetch):
config = {
'channels': ['conda-forge', 'bioconda', 'defaults']
}
bioconductor_skeleton.write_recipe(
'edgeR', recipe_dir=str(tmpdir), config=config, recursive=False, packages=bioc_fetch)
edger_meta = utils.load_first_metadata(str(tmpdir.join('bioconductor-edger'))).meta
assert 'r-rcpp' in edger_meta['requirements']['run']
# The rendered meta has {{ compiler('c') }} filled in, so we need to check
# for one of those filled-in values.
names = [i.split()[0] for i in edger_meta['requirements']['build']]
assert 'libstdcxx-ng' in names or 'clang_osx-64' in names
# bioconductor, bioarchive, and cargoport
assert len(edger_meta['source']['url']) == 3
def test_meta_contents(tmpdir, bioc_fetch):
config = {'channels': ['conda-forge', 'bioconda', 'defaults']}
bioconductor_skeleton.write_recipe('edgeR',
recipe_dir=str(tmpdir),
config=config,
recursive=False,
packages=bioc_fetch)
edger_meta = utils.load_first_metadata(
str(tmpdir.join('bioconductor-edger'))).meta
assert 'r-rcpp' in edger_meta['requirements']['run']
# The rendered meta has {{ compiler('c') }} filled in, so we need to check
# for one of those filled-in values.
names = [i.split()[0] for i in edger_meta['requirements']['build']]
assert 'libstdcxx-ng' in names or 'clang_osx-64' in names
# bioconductor, bioarchive, and cargoport
assert len(edger_meta['source']['url']) == 3
def test_overwrite(tmpdir, bioc_fetch):
bioconductor_skeleton.write_recipe(
'edgeR', recipe_dir=str(tmpdir), config=config, recursive=False, packages=bioc_fetch)
# Same thing with force=False returns ValueError
with pytest.raises(ValueError):
bioconductor_skeleton.write_recipe(
'edgeR', recipe_dir=str(tmpdir), config=config, recursive=False, packages=bioc_fetch)
# But same thing with force=True is OK
bioconductor_skeleton.write_recipe(
'edgeR', recipe_dir=str(tmpdir), config=config, recursive=False, force=True, packages=bioc_fetch)
def test_overwrite(tmpdir, bioc_fetch):
bioconductor_skeleton.write_recipe(
'edgeR', recipe_dir=str(tmpdir), config=config, recursive=False, packages=bioc_fetch)
# Same thing with force=False returns ValueError
with pytest.raises(ValueError):
bioconductor_skeleton.write_recipe(
'edgeR', recipe_dir=str(tmpdir), config=config, recursive=False, packages=bioc_fetch)
# But same thing with force=True is OK
bioconductor_skeleton.write_recipe(
'edgeR', recipe_dir=str(tmpdir), config=config, recursive=False, force=True, packages=bioc_fetch)
recipe_folder = args[0]
config = args[1]
package_list = args[2]
assert os.path.exists(recipe_folder), "Recipe folder exists"
assert os.path.exists(config), "Config file exists"
assert os.path.exists(package_list), "Package list file exists"
handle = open(package_list, "r")
for line in handle:
pkg = line.strip()
metafile = recipe_folder + "/" + pkg + "/meta.yaml"
assert os.path.exists(metafile), "meta.yaml exists for %s" % (pkg)
metadata = MetaData(metafile)
# Get the package name (capitalized correctly), version, and Bioconductor
# release from the meta.yaml file. The purpose of this script is to fix
# existing recipes, not to update the package to the latest version.
name, version = metadata.get_value("source/fn").rstrip(".tar.gz").split(
"_")
bioc = metadata.get_value("source/url")[0].split("/")[4]
sys.stderr.write("Writing recipe for %s %s (%s)\n" % (name, version, bioc))
write_recipe(package=name,
recipe_dir=recipe_folder,
config=config,
force=True,
bioc_version=bioc,
pkg_version=version)
handle.close()