def test_filter_recipes_force_existing_package():
"same as above but force the recipe"
# same as above, but this time force the recipe
# TODO: refactor as py.test fixture
r = Recipes("""
one:
meta.yaml: |
package:
name: gffutils
version: "0.8.7.1"
requirements:
run:
- python
""",
from_string=True)
r.write_recipes()
recipes = list(r.recipe_dirs.values())
env_matrix = {
'CONDA_PY': [27, 35],
}
pkgs = utils.get_channel_packages('bioconda')
pth = utils.built_package_path(recipes[0])
filtered = list(
utils.filter_recipes(recipes,
env_matrix,
channels=['bioconda'],
force=True))
assert len(filtered) == 1
def test_filter_recipes_existing_package():
"use a known-to-exist package in bioconda"
# note that we need python as a run requirement in order to get the "pyXY"
# in the build string that matches the existing bioconda built package.
r = Recipes("""
one:
meta.yaml: |
package:
name: gffutils
version: "0.8.7.1"
requirements:
run:
- python
""",
from_string=True)
r.write_recipes()
recipes = list(r.recipe_dirs.values())
env_matrix = {
'CONDA_PY': [27, 35],
}
pkgs = utils.get_channel_packages('bioconda')
pth = utils.built_package_path(recipes[0])
filtered = list(
utils.filter_recipes(recipes, env_matrix, channels=['bioconda']))
assert len(filtered) == 0
def __init__(self):
logger.info('Loading packages...')
repodata = defaultdict(lambda: defaultdict(list))
for platform in ['linux', 'osx']:
channel_packages = utils.get_channel_packages(channel='bioconda',
platform=platform)
for pkg_key in channel_packages.keys():
repodata[pkg_key.name][pkg_key.version].append(platform)
self.repodata = repodata
def __init__(self):
logger.info('Loading packages...')
repodata = defaultdict(lambda: defaultdict(list))
for platform in ['linux', 'osx']:
for pkg in utils.get_channel_packages(channel='bioconda',
platform=platform):
name, version, _ = self._parse_pkgname(pkg)
repodata[name][version].append(platform)
self.repodata = repodata
def test_get_channel_packages():
with pytest.raises(requests.HTTPError):
utils.get_channel_packages('bioconda_xyz_nonexistent_channel')
utils.get_channel_packages('bioconda')
def setup(*args):
"""
Go through every folder in the `bioconda-recipes/recipes` dir
and generate a README.rst file.
"""
print('Generating package READMEs...')
repodata = defaultdict(lambda: defaultdict(list))
for platform in ['linux', 'osx']:
for pkg in utils.get_channel_packages(channel='bioconda',
platform=platform):
d = parse_pkgname(pkg)
repodata[d['name']][d['version']].append(platform)
# e.g., repodata = {
# 'package1': {
# '0.1': ['linux'],
# '0.2': ['linux', 'osx'],
# },
#}
summaries = []
recipes = []
for folder in os.listdir(RECIPE_DIR):
# 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:
print("'{}' does not look like a proper version!".format(sf))
continue
versions.append(sf)
#versions.sort(key=LooseVersion, reverse=True)
# Read the meta.yaml file
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
continue
name = metadata.name()
versions_in_channel = sorted(repodata[name].keys())
# Format the README
notes = metadata.get_section('extra').get('notes', '')
if notes:
if isinstance(notes, list): notes = "\n".join(notes)
notes = 'Notes\n-----\n\n' + notes
summary = metadata.get_section('about').get('summary', '')
summaries.append(summary)
template_options = {
'title':
metadata.name(),
'title_underline':
'=' * len(metadata.name()),
'summary':
summary,
'home':
metadata.get_section('about').get('home', ''),
'versions':
', '.join(versions_in_channel),
'license':
metadata.get_section('about').get('license', ''),
'recipe':
('https://github.com/bioconda/bioconda-recipes/tree/master/recipes/'
+ op.dirname(op.relpath(metadata.meta_path, RECIPE_DIR))),
'notes':
notes
}
# Add additional keys to template_options for use in the recipes
# datatable.
template_options['Package'] = (
'<a href="recipes/{0}/README.html">{0}</a>'.format(name))
for version in versions_in_channel:
t = template_options.copy()
if 'linux' in repodata[name][version]:
t['Linux'] = '<i class="fa fa-linux"></i>'
if 'osx' in repodata[name][version]:
t['OSX'] = '<i class="fa fa-apple"></i>'
t['Version'] = version
recipes.append(t)
readme = README_TEMPLATE.format(**template_options)
# Write to file
try:
os.makedirs(op.join(OUTPUT_DIR,
folder)) # exist_ok=True on Python 3
except OSError:
pass
output_file = op.join(OUTPUT_DIR, folder, 'README.rst')
# avoid re-writing the same contents, which invalidates the
# sphinx-build cache
if os.path.exists(output_file):
if open(output_file, encoding='utf-8').read() == readme:
continue
with open(output_file, 'wb') as ofh:
ofh.write(readme.encode('utf-8'))
# render the recipes datatable page
t = Template(RECIPES_TEMPLATE)
recipes_contents = t.render(
recipes=recipes,
# order of columns in the table; must be keys in template_options
keys=['Package', 'Version', 'License', 'Linux', 'OSX'])
recipes_rst = 'source/recipes.rst'
if not (os.path.exists(recipes_rst) and
(open(recipes_rst).read() == recipes_contents)):
with open(recipes_rst, 'w') as fout:
fout.write(recipes_contents)
