def have_variant_but_for_python(meta: MetaData) -> bool:
"""Checks if we have an exact or ``py[23]_`` prefixed match to
name/version/buildstring
Ignores osx.
Args:
meta: Variant MetaData object
Returns:
True if FIXME
"""
def strip_py(build):
if build.startswith("py"):
return build[4:]
return build
builds = RepoData().get_package_data('build',
name=meta.name(),
version=meta.version(),
platform=['linux', 'noarch'])
res = [
build for build in builds
if strip_py(build) == strip_py(meta.build_id())
]
if res:
logger.debug("Package %s=%s has %s (want %s)", meta.name(),
meta.version(), res, meta.build_id())
return bool(res)
def setup(*args):
"""
Go through every folder in the `bioconda-recipes/recipes` dir
and generate a README.rst file.
"""
print('Generating package READMEs...')
summaries = []
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
try:
metadata = MetaData(op.join(RECIPE_DIR, folder))
if metadata.version() not in versions:
versions.insert(0, metadata.version())
except SystemExit:
if versions:
metadata = MetaData(op.join(RECIPE_DIR, folder, versions[0]))
else:
# ignore non-recipe folders
continue
# Format the README
notes = metadata.get_section('extra').get('notes', '')
if 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),
'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
}
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')
with open(output_file, 'wb') as ofh:
ofh.write(readme.encode('utf-8'))
def setup(*args):
"""
Go through every folder in the `bioconda-recipes/recipes` dir
and generate a README.rst file.
"""
print('Generating package READMEs...')
summaries = []
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
try:
metadata = MetaData(op.join(RECIPE_DIR, folder))
if metadata.version() not in versions:
versions.insert(0, metadata.version())
except SystemExit:
if versions:
metadata = MetaData(op.join(RECIPE_DIR, folder, versions[0]))
else:
# ignore non-recipe folders
continue
# Format the README
notes = metadata.get_section('extra').get('notes', '')
if 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),
'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
}
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')
with open(output_file, 'wb') as ofh:
ofh.write(readme.encode('utf-8'))
def version_compare(package, versions):
if not versions:
# PyPI is case sensitive, this will pass control
# to a method in main() to take care of that.
return
nv = normalized_version
norm_versions = [nv(ver) for ver in versions]
recipe_dir = abspath(package.lower())
if not isdir(recipe_dir):
sys.exit("Error: no such directory: %s" % recipe_dir)
m = MetaData(recipe_dir)
local_version = nv(m.version())
print("Local recipe for %s has version %s" % (package, local_version))
if local_version not in versions:
sys.exit("Error: %s %s is not available on PyPI." %
(package, local_version))
else:
# Comparing normalized versions, displaying non normalized ones
new_versions = versions[:norm_versions.index(local_version)]
if len(new_versions) > 0:
print("Following new versions of %s are avaliable" % (package))
for ver in new_versions:
print(ver)
else:
print("No new version for %s is available" % (package))
sys.exit()
def version_compare(package, versions):
if not versions:
# PyPI is case sensitive, this will pass control
# to a method in main() to take care of that.
return
nv = normalized_version
norm_versions = [nv(ver) for ver in versions]
recipe_dir = abspath(package.lower())
if not isdir(recipe_dir):
sys.exit("Error: no such directory: %s" % recipe_dir)
m = MetaData(recipe_dir)
local_version = nv(m.version())
print("Local recipe for %s has version %s" % (package, local_version))
if local_version not in versions:
sys.exit("Error: %s %s is not available on PyPI."
% (package, local_version))
else:
# Comparing normalized versions, displaying non normalized ones
new_versions = versions[:norm_versions.index(local_version)]
if len(new_versions) > 0:
print("Following new versions of %s are avaliable" % (package))
for ver in new_versions:
print(ver)
else:
print("No new version for %s is available" % (package))
sys.exit()
def read_recipe_name_version_build(meta_yaml_path):
"""
Read the given metadata file and return (package_name, version, build_number)
meta_yaml_path: May be a path to a meta.yaml file or it's parent recipe directory.
"""
# Provide these default values, otherwise conda-build will
# choke on jinja templates that reference them.
# This will be fixed when they finally merge conda-build PR#662 and PR#666
if "CONDA_NPY" not in os.environ:
os.environ["CONDA_NPY"] = '19'
if "CONDA_PY" not in os.environ:
os.environ["CONDA_PY"] = '27'
os.environ["GIT_FULL_HASH"] = "9999999"
if os.path.isdir(meta_yaml_path):
recipe_dir = meta_yaml_path
else:
recipe_dir = os.path.split(meta_yaml_path)[0]
try:
metadata = MetaData(recipe_dir)
return (metadata.name(), metadata.version(), metadata.build_number())
except SystemExit as ex:
raise Exception(*ex.args)
def read_recipe_name_version_build(meta_yaml_path):
"""
Read the given metadata file and return (package_name, version, build_number)
meta_yaml_path: May be a path to a meta.yaml file or it's parent recipe directory.
"""
# Provide these default values, otherwise conda-build will
# choke on jinja templates that reference them.
# This will be fixed when they finally merge conda-build PR#662 and PR#666
if "CONDA_NPY" not in os.environ:
os.environ["CONDA_NPY"] = '19'
if "CONDA_PY" not in os.environ:
os.environ["CONDA_PY"] = '27'
os.environ["GIT_FULL_HASH"] = "9999999"
if os.path.isdir(meta_yaml_path):
recipe_dir = meta_yaml_path
else:
recipe_dir = os.path.split(meta_yaml_path)[0]
try:
metadata = MetaData(recipe_dir)
return (metadata.name(), metadata.version(), metadata.build_number())
except SystemExit as ex:
raise Exception(*ex.args)
def have_variant(meta: MetaData) -> bool:
"""Checks if we have an exact match to name/version/buildstring
Args:
meta: Variant MetaData object
Returns:
True if the variant's build string exists already in the repodata
"""
res = RepoData().get_package_data(name=meta.name(),
version=meta.version(),
build=meta.build_id(),
platform=['linux', 'noarch'])
if res:
logger.debug("Package %s=%s=%s exists", meta.name(), meta.version(),
meta.build_id())
return res
def have_noarch_python_build_number(meta: MetaData) -> bool:
"""Checks if we have a noarch:python build with same version+build_number
Args:
meta: Variant MetaData object
Returns:
True if noarch:python and version+build_number exists already in repodata
"""
if meta.get_value('build/noarch') != 'python':
return False
res = RepoData().get_package_data(
name=meta.name(), version=meta.version(),
build_number=meta.build_number(),
platform=['noarch'],
)
if res:
logger.debug("Package %s=%s[build_number=%s, subdir=noarch] exists",
meta.name(), meta.version(), meta.build_number())
return res
def will_build_variant(meta: MetaData) -> bool:
"""Check if the recipe variant will be built as currently rendered
Args:
meta: Variant MetaData object
Returns:
True if all extant build numbers are smaller than the one indicated
by the variant MetaData.
"""
build_numbers = RepoData().get_package_data(
'build_number',
name=meta.name(), version=meta.version(),
platform=['linux', 'noarch'],
)
current_num = int(meta.build_number())
res = all(num < current_num for num in build_numbers)
if res:
logger.debug("Package %s=%s will be built already because %s < %s)",
meta.name(), meta.version(),
max(build_numbers) if build_numbers else "N/A",
meta.build_number())
return res
def __add_metadata(self, recipe_file: str, metadata: MetaData):
pkg_name = metadata.name()
pkg_version = metadata.version()
effective_pkg_name = pkg_name
if metadata.is_output: # i.e. it's a sub-package
toplevel = metadata.get_top_level_recipe_without_outputs()
parent_pkg_name = toplevel[PACKAGE][NAME]
# Map sub-package to parent
self.__add_sub_package((parent_pkg_name, pkg_version), pkg_name)
# We want to record subsequent details as if they apply to
# the parent package because that's the package we'll actually
# build. Sub-packages are built as a consequence of that. The
# MetaData.ms_depends() method doesn't return a complete set of
# requirements (that I can see).
effective_pkg_name = parent_pkg_name
# The MetaData objects for some recipes don't appear to include
# toplevel requirements (needed to build the sub-package),
# so we manually dig into the parsed Dict here.
if REQUIREMENTS in toplevel:
# We could also look at requirements[BUILD]
if HOST in toplevel[REQUIREMENTS]:
nv = (effective_pkg_name, pkg_version)
for spec in toplevel[REQUIREMENTS][HOST]:
m = MatchSpec(spec)
self.__add_package_requirement(nv, (m.name, m.version))
nv = (effective_pkg_name, pkg_version)
self.__add_package_recipe(nv, recipe_file)
self.__add_package_version(nv)
for dep in metadata.ms_depends(HOST):
self.__add_package_requirement(nv, (dep.name, dep.version))
return
def render_recipe(recipe_path,
config,
no_download_source=False,
variants=None,
permit_unsatisfiable_variants=True,
reset_build_id=True,
bypass_env_check=False):
"""Returns a list of tuples, each consisting of
(metadata-object, needs_download, needs_render_in_env)
You get one tuple per variant. Outputs are not factored in here (subpackages won't affect these
results returned here.)
"""
arg = recipe_path
# Don't use byte literals for paths in Python 2
if not PY3:
arg = arg.decode(getpreferredencoding() or 'utf-8')
if isfile(arg):
if arg.endswith(('.tar', '.tar.gz', '.tgz', '.tar.bz2')):
recipe_dir = tempfile.mkdtemp()
t = tarfile.open(arg, 'r:*')
t.extractall(path=recipe_dir)
t.close()
need_cleanup = True
elif arg.endswith('.yaml'):
recipe_dir = os.path.dirname(arg)
need_cleanup = False
else:
print("Ignoring non-recipe: %s" % arg)
return None, None
else:
recipe_dir = abspath(arg)
need_cleanup = False
if not isdir(recipe_dir):
sys.exit("Error: no such directory: %s" % recipe_dir)
try:
m = MetaData(recipe_dir, config=config)
except exceptions.YamlParsingError as e:
sys.stderr.write(e.error_msg())
sys.exit(1)
rendered_metadata = {}
# important: set build id *before* downloading source. Otherwise source goes into a different
# build folder.
if config.set_build_id:
m.config.compute_build_id(m.name(), m.version(), reset=reset_build_id)
# this source may go into a folder that doesn't match the eventual build folder.
# There's no way around it AFAICT. We must download the source to be able to render
# the recipe (from anything like GIT_FULL_HASH), but we can't know the final build
# folder until rendering is complete, because package names can have variant jinja2 in them.
if m.needs_source_for_render and not m.source_provided:
try_download(m, no_download_source=no_download_source)
if m.final:
if not hasattr(m.config, 'variants') or not m.config.variant:
m.config.ignore_system_variants = True
if os.path.isfile(os.path.join(m.path, 'conda_build_config.yaml')):
m.config.variant_config_files = [
os.path.join(m.path, 'conda_build_config.yaml')
]
m.config.variants = get_package_variants(m, variants=variants)
m.config.variant = m.config.variants[0]
rendered_metadata = [
(m, False, False),
]
else:
# merge any passed-in variants with any files found
variants = get_package_variants(m, variants=variants)
# when building, we don't want to fully expand all outputs into metadata, only expand
# whatever variants we have (i.e. expand top-level variants, not output-only variants)
rendered_metadata = distribute_variants(
m,
variants,
permit_unsatisfiable_variants=permit_unsatisfiable_variants,
allow_no_other_outputs=True,
bypass_env_check=bypass_env_check)
if need_cleanup:
utils.rm_rf(recipe_dir)
return rendered_metadata
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
name = metadata.name()
versions_in_channel = repodata.get_versions(name)
# Format the README
template_options = {
'name': name,
'about': (metadata.get_section('about') or {}),
'extra': (metadata.get_section('extra') or {}),
'versions': versions_in_channel,
'gh_recipes':
'https://github.com/bioconda/bioconda-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, folder, 'README.rst'),
'readme.rst_t', template_options)
recipes = []
for version, version_info in sorted(versions_in_channel.items()):
t = template_options.copy()
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 '',
'Version':
version
})
recipes.append(t)
return recipes
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)
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
def setup(*args):
"""
Go through every folder in the `bioconda-recipes/recipes` dir
and generate a README.rst file.
"""
print("Generating package READMEs...")
# TODO obtain information from repodata.json.
summaries = []
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
# Format the README
notes = metadata.get_section("extra").get("notes", "")
if 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),
"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,
}
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")
with open(output_file, "wb") as ofh:
ofh.write(readme.encode("utf-8"))