def test_empty_recipe(tmpdir):
r = Recipe('recipes/sina', 'recipes/')
with pytest.raises(EmptyRecipe):
r.load_from_string("")
with open(op.join(tmpdir, 'meta.yaml'), "w"):
pass
with pytest.raises(EmptyRecipe):
Recipe.from_file(str(tmpdir), str(tmpdir))
res = Recipe.from_file(str(tmpdir), str(tmpdir), return_exceptions=True)
assert isinstance(res, EmptyRecipe)
def _run(contents, expect_pass=True):
"""
Build the recipe and run the lint function on the rendered recipe
"""
r = Recipes(contents, from_string=True)
r.write_recipes()
assert len(r.recipe_dirs) == 1
name = list(r.recipe_dirs.keys())[0]
recipe = Recipe.from_file(r.basedir, r.recipe_dirs[name])
metas = []
for platform in ["linux", "osx"]:
config = utils.load_conda_build_config(platform=platform, trim_skip=False)
metas.extend(utils.load_all_meta(r.recipe_dirs[name], config=config, finalize=False))
if expect_pass:
assert func(recipe, metas) is None, "lint did not pass"
else:
assert func(recipe, metas) is not None, "lint did not fail"
def _run(contents, expect_pass=True):
"""
Build the recipe and run the lint function on the rendered recipe
"""
r = Recipes(contents, from_string=True)
r.write_recipes()
assert len(r.recipe_dirs) == 1
name = list(r.recipe_dirs.keys())[0]
recipe = Recipe.from_file(r.basedir, r.recipe_dirs[name])
metas = []
for platform in ["linux", "osx"]:
config = utils.load_conda_build_config(platform=platform,
trim_skip=False)
metas.extend(
utils.load_all_meta(r.recipe_dirs[name],
config=config,
finalize=False))
if expect_pass:
assert func(recipe, metas) is None, "lint did not pass"
else:
assert func(recipe, metas) is not None, "lint did not fail"
def generate_readme(recipe_basedir, output_dir, folder, repodata, renderer):
"""Generates README.rst for the recipe in folder
Args:
folder: Toplevel folder name in recipes directory
repodata: RepoData object
renderer: Renderer object
Returns:
List of template_options for each concurrent version for
which meta.yaml files exist in the recipe folder and its
subfolders
"""
output_file = op.join(output_dir, folder, 'README.rst')
# Select meta yaml
meta_fname = op.join(recipe_basedir, folder, 'meta.yaml')
if not op.exists(meta_fname):
for item in os.listdir(op.join(recipe_basedir, folder)):
dname = op.join(recipe_basedir, folder, item)
if op.isdir(dname):
fname = op.join(dname, 'meta.yaml')
if op.exists(fname):
meta_fname = fname
break
else:
logger.error("No 'meta.yaml' found in %s", folder)
return []
meta_relpath = meta_fname[len(recipe_basedir) + 1:]
# Read the meta.yaml file(s)
try:
recipe = Recipe.from_file(recipe_basedir, meta_fname)
except RecipeError as e:
logger.error("Unable to process %s: %s", meta_fname, e)
return []
# Format the README
packages = []
for package in sorted(list(set(recipe.package_names))):
versions_in_channel = set(
repodata.get_package_data(['version', 'build_number'],
channels='bioconda',
name=package))
sorted_versions = sorted(versions_in_channel,
key=lambda x: (VersionOrder(x[0]), x[1]),
reverse=True)
if sorted_versions:
depends = [
depstring.split(' ', 1) if ' ' in depstring else
(depstring, '') for depstring in repodata.get_package_data(
'depends',
name=package,
version=sorted_versions[0][0],
build_number=sorted_versions[0][1],
)[0]
]
else:
depends = []
packages.append({
'name':
package,
'versions': ['-'.join(str(w) for w in v) for v in sorted_versions],
'depends':
depends,
})
template_options = {
'name': recipe.name,
'about': recipe.get('about', None),
'extra': recipe.get('extra', None),
'recipe': recipe,
'packages': packages,
}
renderer.render_to_file(output_file, 'readme.rst_t', template_options)
return [output_file]
def generate_readme(recipe_basedir, output_dir, folder, repodata, renderer):
"""Generates README.rst for the recipe in folder
Args:
folder: Toplevel folder name in recipes directory
repodata: RepoData object
renderer: Renderer object
Returns:
List of template_options for each concurrent version for
which meta.yaml files exist in the recipe folder and its
subfolders
"""
output_file = op.join(output_dir, folder, 'README.rst')
# Select meta yaml
meta_fname = op.join(recipe_basedir, folder, 'meta.yaml')
if not op.exists(meta_fname):
for item in os.listdir(op.join(recipe_basedir, folder)):
dname = op.join(recipe_basedir, folder, item)
if op.isdir(dname):
fname = op.join(dname, 'meta.yaml')
if op.exists(fname):
meta_fname = fname
break
else:
logger.error("No 'meta.yaml' found in %s", folder)
return []
meta_relpath = meta_fname[len(recipe_basedir)+1:]
# Read the meta.yaml file(s)
try:
recipe = Recipe.from_file(recipe_basedir, meta_fname)
except RecipeError as e:
logger.error("Unable to process %s: %s", meta_fname, e)
return []
# Format the README
packages = []
for package in sorted(list(set(recipe.package_names))):
versions_in_channel = set(repodata.get_package_data(['version', 'build_number'],
channels='bioconda', name=package))
sorted_versions = sorted(versions_in_channel,
key=lambda x: (VersionOrder(x[0]), x[1]),
reverse=True)
if sorted_versions:
depends = [
depstring.split(' ', 1) if ' ' in depstring else (depstring, '')
for depstring in
repodata.get_package_data('depends', name=package,
version=sorted_versions[0][0],
build_number=sorted_versions[0][1],
)[0]
]
else:
depends = []
packages.append({
'name': package,
'versions': ['-'.join(str(w) for w in v) for v in sorted_versions],
'depends' : depends,
})
template_options = {
'name': recipe.name,
'about': recipe.get('about'),
'extra': recipe.get('extra'),
'recipe': recipe,
'packages': packages,
}
renderer.render_to_file(output_file, 'readme.rst_t', template_options)
return [output_file]
def create_recipe(bioconda_recipe_path, recipe_path, strategy):
# Load meta.yaml file and instantiate Recipe object
temp_folder_name = hashlib.md5(recipe_path.encode("utf-8")).hexdigest()
recipes_pkg_path = os.path.join(bioconda_recipe_path, "recipes",
temp_folder_name)
try:
os.mkdir(recipes_pkg_path)
copytree(recipe_path, recipes_pkg_path)
bioconda_recipe = bioconda_utils_Recipe.from_file(
bioconda_recipe_path, recipes_pkg_path)
finally:
rmtree(recipes_pkg_path)
name = bioconda_recipe.get("package/name")
version = bioconda_recipe.get("package/version")
recipe = Recipe(name, version, recipe_path, strategy)
# Parse values from file to Recipe object
try:
recipe.add_source_url(bioconda_recipe.get("source/url"))
except KeyError:
sys.exit(
"No source url was found in the given meta.yaml file, please add a source url"
)
recipe.add_build_number(bioconda_recipe.get("build/number", "0"))
try:
recipe.add_checksum_sha256(bioconda_recipe.get("source/sha256"))
except KeyError:
recipe.add_checksum_md5(
bioconda_recipe.get(
"source/md5",
calculate_md5_checksum(bioconda_recipe.get("source/url"))))
build_requirements = bioconda_recipe.get("requirements/build", [])
for requirement in build_requirements:
recipe.add_requirement(requirement, "build")
host_requirements = bioconda_recipe.get("requirements/host", [])
for requirement in host_requirements:
recipe.add_requirement(requirement, "host", host_only=True)
run_requirements = bioconda_recipe.get("requirements/run", [])
for requirement in run_requirements:
recipe.add_requirement(requirement, "run")
try:
recipe.add_test_commands(bioconda_recipe.get("test/commands"))
except KeyError:
pass
try:
recipe.add_test_files_with_list(bioconda_recipe.get("test/files"))
except KeyError:
pass
try:
recipe.add_patches_with_list(bioconda_recipe.get("source/patches"),
recipe_path)
except KeyError:
pass
# Conda will not accept the compiler dependency given by bioconda
try:
build_requirements = recipe.recipe_dict["requirements"]["build"]
if "compiler_c" in build_requirements:
recipe.recipe_dict["requirements"]["build"].remove("compiler_c")
recipe.recipe_dict["requirements"]["build"].append(
"{{compiler('c')}}")
if "compiler_cxx" in build_requirements:
recipe.recipe_dict["requirements"]["build"].remove("compiler_cxx")
recipe.recipe_dict["requirements"]["build"].append(
"{{compiler('cxx')}}")
except KeyError:
if strategy == "cmake":
recipe.add_requirement("{{ compiler('c') }}", "build")
recipe.add_requirement("cmake", "build")
recipe.add_requirement("make", "build")
elif strategy == "autoconf":
recipe.add_requirement("make", "build")
recipe.add_requirement("autoconf", "build")
recipe.add_requirement("automake", "build")
recipe.add_requirement("{{ compiler('c') }}", "build")
if strategy.startswith("python"):
try:
host_environment = recipe.recipe_dict["requirements"]["host"]
if not any(
map(lambda req: req.startswith("python"),
host_environment)):
if strategy == "python2":
recipe.add_requirement("python =2.7", "host")
else:
recipe.add_requirement("python >=3", "host")
except KeyError:
if strategy == "python2":
recipe.add_requirement("python =2.7", "host")
else:
recipe.add_requirement("python >=3", "host")
try:
recipe.script = bioconda_recipe.get("build/script")
except KeyError:
pass
try:
recipe.add_command_imports(bioconda_recipe.get("test/imports"))
except KeyError:
pass
try:
recipe.add_entry_point(bioconda_recipe.get("build/entry_points"))
except KeyError:
pass
try:
recipe.add_noarch(bioconda_recipe.get("build/noarch"))
except KeyError:
pass
try:
recipe.add_test_requires(bioconda_recipe.get("test/requires"))
except KeyError:
pass
recipe.increment_build_number()
return recipe
def test_file_not_found():
with pytest.raises(MissingMetaYaml):
Recipe.from_file('/', '/doesnotexist')
res = Recipe.from_file('/', '/doesnotexist', return_exceptions=True)
assert isinstance(res, MissingMetaYaml)
def test_stub():
r = Recipe('recipes/sina', 'recipes/')
assert r.path == 'recipes/sina/meta.yaml'
assert r.relpath == 'sina/meta.yaml'
assert r.reldir == 'sina'
assert str(r) == 'sina'
def recipe(recipe_dir, recipes_folder):
yield Recipe.from_file(recipes_folder, recipe_dir)
def generate_readme(folder, repodata, renderer):
"""Generates README.rst for the recipe in folder
Args:
folder: Toplevel folder name in recipes directory
repodata: RepoData object
renderer: Renderer object
Returns:
List of template_options for each concurrent version for
which meta.yaml files exist in the recipe folder and its
subfolders
"""
# Subfolders correspond to different versions
versions = []
for sf in os.listdir(op.join(RECIPE_DIR, folder)):
if not op.isdir(op.join(RECIPE_DIR, folder, sf)):
# Not a folder
continue
try:
LooseVersion(sf)
except ValueError:
logger.error("'{}' does not look like a proper version!"
"".format(sf))
continue
versions.append(sf)
# Read the meta.yaml file(s)
try:
recipe = op.join(RECIPE_DIR, folder, "meta.yaml")
if op.exists(recipe):
metadata = MetaData(recipe)
if metadata.version() not in versions:
versions.insert(0, metadata.version())
else:
if versions:
recipe = op.join(RECIPE_DIR, folder, versions[0], "meta.yaml")
metadata = MetaData(recipe)
else:
# ignore non-recipe folders
return []
except UnableToParse as e:
logger.error("Failed to parse recipe {}".format(recipe))
raise e
## Get all versions and build numbers for data package
# Select meta yaml
meta_fname = op.join(RECIPE_DIR, folder, 'meta.yaml')
if not op.exists(meta_fname):
for item in os.listdir(op.join(RECIPE_DIR, folder)):
dname = op.join(RECIPE_DIR, folder, item)
if op.isdir(dname):
fname = op.join(dname, 'meta.yaml')
if op.exists(fname):
meta_fname = fname
break
else:
logger.error("No 'meta.yaml' found in %s", folder)
return []
meta_relpath = meta_fname[len(RECIPE_DIR)+1:]
# Read the meta.yaml file(s)
try:
recipe_object = Recipe.from_file(RECIPE_DIR, meta_fname)
except RecipeError as e:
logger.error("Unable to process %s: %s", meta_fname, e)
return []
# Format the README
for package in sorted(list(set(recipe_object.package_names))):
versions_in_channel = set(repodata.get_package_data(['version', 'build_number'],
channels='ggd-genomics', name=package))
sorted_versions = sorted(versions_in_channel,
key=lambda x: (VersionOrder(x[0]), x[1]),
reverse=False)
if sorted_versions:
depends = [
depstring.split(' ', 1) if ' ' in depstring else (depstring, '')
for depstring in
repodata.get_package_data('depends', name=package,
version=sorted_versions[0][0],
build_number=sorted_versions[0][1],
)[0]
]
else:
depends = []
# Format the README
name = metadata.name()
versions_in_channel = repodata.get_versions(name)
template_options = {
'name': name,
'about': (metadata.get_section('about') or {}),
'species': (metadata.get_section('about')["identifiers"]["species"] if "species" in metadata.get_section('about')["identifiers"] else {}),
'genome_build': (metadata.get_section('about')["identifiers"]["genome-build"] if "genome-build" in metadata.get_section('about')["identifiers"] else {}),
'ggd_channel': (metadata.get_section('about')["tags"]["ggd-channel"] if "ggd-channel" in metadata.get_section('about')["tags"] else "genomics"),
'extra': (metadata.get_section('extra') or {}),
'versions': ["-".join(str(w) for w in v) for v in sorted_versions],
'gh_recipes': 'https://github.com/gogetdata/ggd-recipes/tree/master/recipes/',
'recipe_path': op.dirname(op.relpath(metadata.meta_path, RECIPE_DIR)),
'Package': '<a href="recipes/{0}/README.html">{0}</a>'.format(name)
}
renderer.render_to_file(
op.join(OUTPUT_DIR, name, 'README.rst'),
'readme.rst_t',
template_options)
recipes = []
latest_version = "-".join(str(w) for w in sorted_versions[-1])
for version, version_info in sorted(versions_in_channel.items()):
t = template_options.copy()
if 'noarch' in version_info:
t.update({
'Linux': '<i class="fa fa-linux"></i>' if 'linux' in version_info else '<i class="fa fa-dot-circle-o"></i>',
'OSX': '<i class="fa fa-apple"></i>' if 'osx' in version_info else '<i class="fa fa-dot-circle-o"></i>',
'NOARCH': '<i class="fa fa-desktop"></i>' if 'noarch' in version_info else '',
'Version': latest_version ## The latest version
#'Version': version
})
else:
t.update({
'Linux': '<i class="fa fa-linux"></i>' if 'linux' in version_info else '',
'OSX': '<i class="fa fa-apple"></i>' if 'osx' in version_info else '',
'NOARCH': '<i class="fa fa-desktop"></i>' if 'noarch' in version_info else '',
'Version': latest_version ## The latest version
#'Version': version
})
recipes.append(t)
return recipes