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 main():
recipe_dir = os.environ["RECIPE_DIR"]
conda_platform = 'win-32' if os.environ["ARCH"] == '32' else 'win-64'
prefix = os.environ['PREFIX']
metadata = MetaData(recipe_dir)
msys2_tar_xz_url = metadata.get_section(
'extra')['msys2-binaries'][conda_platform]['url']
msys2_md5 = metadata.get_section(
'extra')['msys2-binaries'][conda_platform]['md5']
mv_srcs_list = metadata.get_section(
'extra')['msys2-binaries'][conda_platform]['mv-srcs']
mv_dsts_list = metadata.get_section(
'extra')['msys2-binaries'][conda_platform]['mv-dsts']
msys2_tar_xz = get_tar_xz(msys2_tar_xz_url, msys2_md5)
tar = tarfile.open(msys2_tar_xz, 'r|xz')
tar.extractall(path=prefix)
try:
patches = metadata.get_section(
'extra')['msys2-binaries'][conda_platform]['patches']
except:
patches = []
if len(patches):
for patchname in patches:
patchset = patch.fromfile(join(getenv('RECIPE_DIR'), patchname))
patchset.apply(1, root=prefix)
# shutil is a bit funny (like mv) with regards to how it treats
# the destination depending on whether it is an existing directory or not
# (i.e. moving into that versus moving as that).
# Therefore, the rules employed are:
# 1. If mv_dst ends with a '/' it is a directory that you want mv_src
# moved into.
# 2. If mv_src has a wildcard, mv_dst is a directory that you want mv_src
# moved into.
# In these cases we makedirs(mv_dst) and then call move(mv_src, mv_dst)
# .. otherwise we makedirs(dirname(mv_dst)) and call move(mv_src, mv_dst)
# .. however, if no mv_srcs exist we don't makedirs at all.
for mv_src, mv_dst in zip(mv_srcs_list, mv_dsts_list):
mv_dst_definitely_dir = False
mv_srcs = glob(join(prefix, normpath(mv_src)))
if '*' in mv_src or mv_dst.endswith('/') or len(mv_srcs) > 1:
mv_dst_definitely_dir = True
if len(mv_srcs):
mv_dst = join(prefix, normpath(mv_dst))
mv_dst_mkdir = mv_dst
if not mv_dst_definitely_dir:
mv_dst_mkdir = dirname(mv_dst_mkdir)
try:
makedirs(mv_dst_mkdir)
except:
pass
for mv_src in mv_srcs:
move(mv_src, mv_dst)
tar.close()
def main():
recipe_dir = os.environ["RECIPE_DIR"]
conda_platform = 'win-32' if os.environ["ARCH"] == '32' else 'win-64'
prefix = os.environ['PREFIX']
metadata = MetaData(recipe_dir)
msys2_tar_xz_url = metadata.get_section(
'extra')['msys2-binaries'][conda_platform]['url']
msys2_md5 = metadata.get_section(
'extra')['msys2-binaries'][conda_platform]['md5']
mv_srcs_list = metadata.get_section(
'extra')['msys2-binaries'][conda_platform]['mv-srcs']
mv_dsts_list = metadata.get_section(
'extra')['msys2-binaries'][conda_platform]['mv-dsts']
msys2_tar_xz = get_tar_xz(msys2_tar_xz_url, msys2_md5)
tar = tarfile.open(msys2_tar_xz, 'r|xz')
tar.extractall(path=prefix)
try:
patches = metadata.get_section(
'extra')['msys2-binaries'][conda_platform]['patches']
except:
patches = []
if len(patches):
for patchname in patches:
patchset = patch.fromfile(join(getenv('RECIPE_DIR'), patchname))
patchset.apply(1, root=prefix)
# shutil is a bit funny (like mv) with regards to how it treats
# the destination depending on whether it is an existing directory or not
# (i.e. moving into that versus moving as that).
# Therefore, the rules employed are:
# 1. If mv_dst ends with a '/' it is a directory that you want mv_src
# moved into.
# 2. If mv_src has a wildcard, mv_dst is a directory that you want mv_src
# moved into.
# In these cases we makedirs(mv_dst) and then call move(mv_src, mv_dst)
# .. otherwise we makedirs(dirname(mv_dst)) and call move(mv_src, mv_dst)
# .. however, if no mv_srcs exist we don't makedirs at all.
for mv_src, mv_dst in zip(mv_srcs_list, mv_dsts_list):
mv_dst_definitely_dir = False
mv_srcs = glob(join(prefix, normpath(mv_src)))
if '*' in mv_src or mv_dst.endswith('/') or len(mv_srcs) > 1:
mv_dst_definitely_dir = True
if len(mv_srcs):
mv_dst = join(prefix, normpath(mv_dst))
mv_dst_mkdir = mv_dst
if not mv_dst_definitely_dir:
mv_dst_mkdir = dirname(mv_dst_mkdir)
try:
makedirs(mv_dst_mkdir)
except:
pass
for mv_src in mv_srcs:
move(mv_src, mv_dst)
tar.close()
def execute(args, parser):
import sys
import shutil
import tarfile
import tempfile
from os.path import abspath, isdir, isfile, join
from conda.lock import Locked
import conda_build.build as build
import conda_build.source as source
from conda_build.config import croot
from conda_build.metadata import MetaData
check_external()
with Locked(croot):
for arg in args.recipe:
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
else:
print("Ignoring non-recipe: %s" % arg)
continue
else:
recipe_dir = abspath(arg)
need_cleanup = False
if not isdir(recipe_dir):
sys.exit("Error: no such directory: %s" % recipe_dir)
m = MetaData(recipe_dir)
binstar_upload = False
if args.check and len(args.recipe) > 1:
print(m.path)
m.check_fields()
if args.check:
continue
if args.output:
print(build.bldpkg_path(m))
continue
elif args.test:
build.test(m)
elif args.source:
source.provide(m.path, m.get_section('source'))
print('Source tree in:', source.get_dir())
else:
build.build(m)
if not args.notest:
build.test(m)
binstar_upload = True
if need_cleanup:
shutil.rmtree(recipe_dir)
if binstar_upload:
handle_binstar_upload(build.bldpkg_path(m), args)
def main():
metadata = MetaData(os.environ["RECIPE_DIR"])
build_id = os.getcwd().split(os.path.sep)[-3]
print "build_id:", build_id
for name, section in metadata.get_section("extra").items():
source.provide(
Source(section),
config.Config(build_id=build_id))
def main():
recipe_dir = os.environ["RECIPE_DIR"]
src_dir = os.environ["SRC_DIR"]
main_work_dir = source.WORK_DIR
metadata = MetaData(recipe_dir)
extra_sources_sections = metadata.get_section('extra')['sources']
for name, source_section in extra_sources_sections.items():
# Override the location to clone into
source.WORK_DIR = main_work_dir + '/' + name
os.makedirs(source.WORK_DIR)
# Download source
source.provide(recipe_dir, source_section)
def main():
recipe_dir = os.environ["RECIPE_DIR"]
src_dir = os.environ["SRC_DIR"]
main_work_dir = source.WORK_DIR
metadata = MetaData(recipe_dir)
extra_sources_sections = metadata.get_section('extra')['sources']
for name, source_section in extra_sources_sections.items():
# Override the location to clone into
source.WORK_DIR = main_work_dir + '/' + name
os.makedirs(source.WORK_DIR)
# Download source
source.provide(recipe_dir, source_section)
def execute(args, parser):
import sys
import shutil
import tarfile
import tempfile
from os.path import abspath, isdir, isfile
from conda.lock import Locked
import conda_build.build as build
import conda_build.source as source
from conda_build.config import config
from conda_build.metadata import MetaData
check_external()
if args.python:
if args.python == ['all']:
for py in [26, 27, 33, 34]:
args.python = [str(py)]
execute(args, parser)
return
if len(args.python) > 1:
for py in args.python[:]:
args.python = [py]
execute(args, parser)
else:
config.CONDA_PY = int(args.python[0].replace('.', ''))
if args.perl:
config.CONDA_PERL = args.perl
if args.numpy:
if args.numpy == ['all']:
for npy in [16, 17, 18, 19]:
args.numpy = [str(npy)]
execute(args, parser)
return
if len(args.numpy) > 1:
for npy in args.numpy[:]:
args.numpy = [npy]
execute(args, parser)
else:
config.CONDA_NPY = int(args.numpy[0].replace('.', ''))
with Locked(config.croot):
recipes = deque(args.recipe)
while recipes:
arg = recipes.popleft()
try_again = False
# Don't use byte literals for paths in Python 2
if not PY3:
arg = arg.decode(getpreferredencoding())
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
else:
print("Ignoring non-recipe: %s" % arg)
continue
else:
recipe_dir = abspath(arg)
need_cleanup = False
if not isdir(recipe_dir):
sys.exit("Error: no such directory: %s" % recipe_dir)
m = MetaData(recipe_dir)
binstar_upload = False
if args.check and len(args.recipe) > 1:
print(m.path)
m.check_fields()
if args.check:
continue
if args.output:
print(build.bldpkg_path(m))
continue
elif args.test:
build.test(m, verbose=not args.quiet)
elif args.source:
source.provide(m.path, m.get_section('source'))
print('Source tree in:', source.get_dir())
else:
# This loop recursively builds dependencies if recipes exist
if args.build_only:
post = False
args.notest = True
args.binstar_upload = False
elif args.post:
post = True
args.notest = True
args.binstar_upload = False
else:
post = None
try:
build.build(m, verbose=not args.quiet, post=post)
except RuntimeError as e:
error_str = str(e)
if error_str.startswith('No packages found'):
# Build dependency if recipe exists
dep_pkg = error_str.split(': ')[1]
# Handle package names that contain version deps.
if ' ' in dep_pkg:
dep_pkg = dep_pkg.split(' ')[0]
recipe_glob = glob(dep_pkg + '-[v0-9][0-9.]*')
if exists(dep_pkg):
recipe_glob.append(dep_pkg)
if recipe_glob:
recipes.appendleft(arg)
try_again = True
for recipe_dir in recipe_glob:
print(("Missing dependency {0}, but found" +
" recipe directory, so building " +
"{0} first").format(dep_pkg))
recipes.appendleft(recipe_dir)
else:
raise
else:
raise
if try_again:
continue
if not args.notest:
build.test(m, verbose=not args.quiet)
binstar_upload = True
if need_cleanup:
shutil.rmtree(recipe_dir)
if binstar_upload:
handle_binstar_upload(build.bldpkg_path(m), args)
def execute(args, parser):
import sys
import shutil
import tarfile
import tempfile
from os.path import abspath, isdir, isfile
from conda.lock import Locked
import conda_build.build as build
import conda_build.source as source
from conda_build.config import croot
from conda_build.metadata import MetaData
check_external()
with Locked(croot):
recipes = deque(args.recipe)
while recipes:
arg = recipes.popleft()
try_again = False
# Don't use byte literals for paths in Python 2
if not PY3:
arg = arg.decode(getpreferredencoding())
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
else:
print("Ignoring non-recipe: %s" % arg)
continue
else:
recipe_dir = abspath(arg)
need_cleanup = False
if not isdir(recipe_dir):
sys.exit("Error: no such directory: %s" % recipe_dir)
m = MetaData(recipe_dir)
binstar_upload = False
if args.check and len(args.recipe) > 1:
print(m.path)
m.check_fields()
if args.check:
continue
if args.output:
print(build.bldpkg_path(m))
continue
elif args.test:
build.test(m)
elif args.source:
source.provide(m.path, m.get_section('source'))
print('Source tree in:', source.get_dir())
else:
# This loop recursively builds dependencies if recipes exist
try:
build.build(m)
except RuntimeError as e:
error_str = str(e)
if error_str.startswith('No packages found matching:'):
# Build dependency if recipe exists
dep_pkg = error_str.split(': ')[1].replace(' ', '-')
recipe_glob = glob(dep_pkg + '-[v0-9][0-9.]*')
if exists(dep_pkg):
recipe_glob.append(dep_pkg)
if recipe_glob:
recipes.appendleft(arg)
try_again = True
for recipe_dir in recipe_glob:
print(("Missing dependency {0}, but found" +
" recipe directory, so building " +
"{0} first").format(dep_pkg))
recipes.appendleft(recipe_dir)
else:
raise
else:
raise
if try_again:
continue
if not args.notest:
build.test(m)
binstar_upload = True
if need_cleanup:
shutil.rmtree(recipe_dir)
if binstar_upload:
handle_binstar_upload(build.bldpkg_path(m), args)
def execute(args, parser):
import sys
import shutil
import tarfile
import tempfile
from os.path import abspath, isdir, isfile
from conda.lock import Locked
import conda_build.build as build
import conda_build.source as source
from conda_build.config import config
from conda_build.metadata import MetaData
check_external()
all_versions = {
'python': [26, 27, 33, 34],
'numpy': [16, 17, 18, 19],
'perl': None,
'R': None,
}
conda_version = {
'python': 'CONDA_PY',
'numpy': 'CONDA_NPY',
'perl': 'CONDA_PERL',
'R': 'CONDA_R',
}
for lang in ['python', 'numpy', 'perl', 'R']:
versions = getattr(args, lang)
if not versions:
continue
if versions == ['all']:
if all_versions[lang]:
versions = all_versions[lang]
else:
parser.error("'all' is not supported for --%s" % lang)
if len(versions) > 1:
for ver in versions[:]:
setattr(args, lang, [str(ver)])
execute(args, parser)
# This is necessary to make all combinations build.
setattr(args, lang, versions)
return
else:
version = int(versions[0].replace('.', ''))
setattr(config, conda_version[lang], version)
if not len(str(version)) == 2:
if all_versions[lang]:
raise RuntimeError("%s must be major.minor, like %s, not %s" %
(conda_version[lang], all_versions[lang][-1]/10, version))
else:
raise RuntimeError("%s must be major.minor, not %s" %
(conda_version[lang], version))
with Locked(config.croot):
recipes = deque(args.recipe)
while recipes:
arg = recipes.popleft()
try_again = False
# 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
else:
print("Ignoring non-recipe: %s" % arg)
continue
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)
except exceptions.YamlParsingError as e:
sys.stderr.write(e.error_msg())
sys.exit(1)
binstar_upload = False
if args.check and len(args.recipe) > 1:
print(m.path)
m.check_fields()
if args.check:
continue
if args.output:
print(build.bldpkg_path(m))
continue
elif args.test:
build.test(m, verbose=not args.quiet)
elif args.source:
source.provide(m.path, m.get_section('source'))
print('Source tree in:', source.get_dir())
else:
# This loop recursively builds dependencies if recipes exist
if args.build_only:
post = False
args.notest = True
args.binstar_upload = False
elif args.post:
post = True
args.notest = True
args.binstar_upload = False
else:
post = None
channel_urls = args.channel or ()
try:
build.build(m, verbose=not args.quiet, post=post,
channel_urls=channel_urls, override_channels=args.override_channels)
except RuntimeError as e:
error_str = str(e)
if error_str.startswith('No packages found') or error_str.startswith('Could not find some'):
# Build dependency if recipe exists
dep_pkg = error_str.split(': ')[1]
# Handle package names that contain version deps.
if ' ' in dep_pkg:
dep_pkg = dep_pkg.split(' ')[0]
recipe_glob = glob(dep_pkg + '-[v0-9][0-9.]*')
if exists(dep_pkg):
recipe_glob.append(dep_pkg)
if recipe_glob:
recipes.appendleft(arg)
try_again = True
for recipe_dir in recipe_glob:
print(("Missing dependency {0}, but found" +
" recipe directory, so building " +
"{0} first").format(dep_pkg))
recipes.appendleft(recipe_dir)
else:
raise
else:
raise
if try_again:
continue
if not args.notest:
build.test(m, verbose=not args.quiet,
channel_urls=channel_urls, override_channels=args.override_channels)
binstar_upload = True
if need_cleanup:
shutil.rmtree(recipe_dir)
if binstar_upload:
handle_binstar_upload(build.bldpkg_path(m), args)
def execute(args, parser):
import sys
import shutil
import tarfile
import tempfile
from os import makedirs
from os.path import abspath, isdir, isfile
from conda.lock import Locked
import conda_build.build as build
import conda_build.source as source
from conda_build.config import config
from conda_build.metadata import MetaData
check_external()
# change globals in build module, see comment there as well
build.channel_urls = args.channel or ()
build.override_channels = args.override_channels
build.verbose = not args.quiet
if on_win:
try:
# needs to happen before any c extensions are imported that might be
# hard-linked by files in the trash. one of those is markupsafe,
# used by jinja2. see https://github.com/conda/conda-build/pull/520
delete_trash(None)
except:
# when we can't delete the trash, don't crash on AssertionError,
# instead inform the user and try again next time.
# see https://github.com/conda/conda-build/pull/744
warnings.warn("Cannot delete trash; some c extension has been "
"imported that is hard-linked by files in the trash. "
"Will try again on next run.")
conda_version = {
'python': 'CONDA_PY',
'numpy': 'CONDA_NPY',
'perl': 'CONDA_PERL',
'R': 'CONDA_R',
}
for lang in ['python', 'numpy', 'perl', 'R']:
versions = getattr(args, lang)
if not versions:
continue
if versions == ['all']:
if all_versions[lang]:
versions = all_versions[lang]
else:
parser.error("'all' is not supported for --%s" % lang)
if len(versions) > 1:
for ver in versions[:]:
setattr(args, lang, [str(ver)])
execute(args, parser)
# This is necessary to make all combinations build.
setattr(args, lang, versions)
return
else:
version = versions[0]
if lang in ('python', 'numpy'):
version = int(version.replace('.', ''))
setattr(config, conda_version[lang], version)
if not len(str(version)) in (2, 3) and lang in ['python', 'numpy']:
if all_versions[lang]:
raise RuntimeError("%s must be major.minor, like %s, not %s" %
(conda_version[lang], all_versions[lang][-1]/10, version))
else:
raise RuntimeError("%s must be major.minor, not %s" %
(conda_version[lang], version))
# Using --python, --numpy etc. is equivalent to using CONDA_PY, CONDA_NPY, etc.
# Auto-set those env variables
for var in conda_version.values():
if getattr(config, var):
# Set the env variable.
os_environ[var] = str(getattr(config, var))
if args.skip_existing:
if not isdir(config.bldpkgs_dir):
makedirs(config.bldpkgs_dir)
update_index(config.bldpkgs_dir)
index = build.get_build_index(clear_cache=True)
already_built = []
to_build_recursive = []
with Locked(config.croot):
recipes = deque(args.recipe)
while recipes:
arg = recipes.popleft()
try_again = False
# 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
else:
print("Ignoring non-recipe: %s" % arg)
continue
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)
if m.get_value('build/noarch_python'):
config.noarch = True
except exceptions.YamlParsingError as e:
sys.stderr.write(e.error_msg())
sys.exit(1)
binstar_upload = False
if args.check and len(args.recipe) > 1:
print(m.path)
m.check_fields()
if args.check:
continue
if args.skip_existing:
if m.pkg_fn() in index or m.pkg_fn() in already_built:
print("%s is already built, skipping." % m.dist())
continue
if m.skip():
print("Skipped: The %s recipe defines build/skip for this "
"configuration." % m.dist())
continue
if args.output:
try:
m.parse_again(permit_undefined_jinja=False)
except SystemExit:
# Something went wrong; possibly due to undefined GIT_ jinja variables.
# Maybe we need to actually download the source in order to resolve the build_id.
source.provide(m.path, m.get_section('source'))
# Parse our metadata again because we did not initialize the source
# information before.
m.parse_again(permit_undefined_jinja=False)
print(build.bldpkg_path(m))
continue
elif args.test:
build.test(m, move_broken=False)
elif args.source:
source.provide(m.path, m.get_section('source'))
print('Source tree in:', source.get_dir())
else:
# This loop recursively builds dependencies if recipes exist
if args.build_only:
post = False
args.notest = True
args.binstar_upload = False
elif args.post:
post = True
args.notest = True
args.binstar_upload = False
else:
post = None
try:
build.build(m, post=post,
include_recipe=args.include_recipe)
except (RuntimeError, SystemExit) as e:
error_str = str(e)
if error_str.startswith('No packages found') or error_str.startswith('Could not find some'):
# Build dependency if recipe exists
dep_pkg = error_str.split(': ')[1]
# Handle package names that contain version deps.
if ' ' in dep_pkg:
dep_pkg = dep_pkg.split(' ')[0]
recipe_glob = glob(dep_pkg + '-[v0-9][0-9.]*')
if exists(dep_pkg):
recipe_glob.append(dep_pkg)
if recipe_glob:
recipes.appendleft(arg)
try_again = True
for recipe_dir in recipe_glob:
if dep_pkg in to_build_recursive:
sys.exit(str(e))
print(("Missing dependency {0}, but found" +
" recipe directory, so building " +
"{0} first").format(dep_pkg))
recipes.appendleft(recipe_dir)
to_build_recursive.append(dep_pkg)
else:
raise
elif error_str.strip().startswith("Hint:"):
lines = [line for line in error_str.splitlines() if line.strip().startswith('- ')]
pkgs = [line.lstrip('- ') for line in lines]
# Typically if a conflict is with one of these
# packages, the other package needs to be rebuilt
# (e.g., a conflict with 'python 3.5*' and 'x' means
# 'x' isn't build for Python 3.5 and needs to be
# rebuilt).
skip_names = ['python', 'r']
pkgs = [pkg for pkg in pkgs if pkg.split(' ')[0] not
in skip_names]
for pkg in pkgs:
# Handle package names that contain version deps.
if ' ' in pkg:
pkg = pkg.split(' ')[0]
recipe_glob = glob(pkg + '-[v0-9][0-9.]*')
if exists(pkg):
recipe_glob.append(pkg)
if recipe_glob:
recipes.appendleft(arg)
try_again = True
for recipe_dir in recipe_glob:
if pkg in to_build_recursive:
sys.exit(str(e))
print(error_str)
print(("Missing dependency {0}, but found" +
" recipe directory, so building " +
"{0} first").format(pkg))
recipes.appendleft(recipe_dir)
to_build_recursive.append(pkg)
else:
raise
else:
raise
if try_again:
continue
if not args.notest:
build.test(m)
binstar_upload = True
if need_cleanup:
shutil.rmtree(recipe_dir)
if binstar_upload:
handle_binstar_upload(build.bldpkg_path(m), args)
already_built.append(m.pkg_fn())
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"))
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 execute(args, parser):
import sys
import shutil
import tarfile
import tempfile
from os.path import abspath, isdir, isfile
from conda.lock import Locked
import conda_build.build as build
import conda_build.source as source
from conda_build.config import config
from conda_build.metadata import MetaData
check_external()
if args.python:
if args.python == ['all']:
for py in [26, 27, 33, 34]:
args.python = [str(py)]
execute(args, parser)
return
if len(args.python) > 1:
for py in args.python[:]:
args.python = [py]
execute(args, parser)
else:
config.CONDA_PY = int(args.python[0].replace('.', ''))
if args.perl:
config.CONDA_PERL = args.perl
if args.numpy:
if args.numpy == ['all']:
for npy in [16, 17, 18]:
args.numpy = [str(npy)]
execute(args, parser)
return
if len(args.numpy) > 1:
for npy in args.numpy[:]:
args.numpy = [npy]
execute(args, parser)
else:
config.CONDA_NPY = int(args.numpy[0].replace('.', ''))
with Locked(config.croot):
recipes = deque(args.recipe)
while recipes:
arg = recipes.popleft()
try_again = False
# Don't use byte literals for paths in Python 2
if not PY3:
arg = arg.decode(getpreferredencoding())
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
else:
print("Ignoring non-recipe: %s" % arg)
continue
else:
recipe_dir = abspath(arg)
need_cleanup = False
if not isdir(recipe_dir):
sys.exit("Error: no such directory: %s" % recipe_dir)
m = MetaData(recipe_dir)
binstar_upload = False
if args.check and len(args.recipe) > 1:
print(m.path)
m.check_fields()
if args.check:
continue
if args.output:
print(build.bldpkg_path(m))
continue
elif args.test:
build.test(m, verbose=not args.quiet)
elif args.source:
source.provide(m.path, m.get_section('source'))
print('Source tree in:', source.get_dir())
else:
# This loop recursively builds dependencies if recipes exist
if args.build_only:
post = False
args.notest = True
args.binstar_upload = False
elif args.post:
post = True
args.notest = True
args.binstar_upload = False
else:
post = None
try:
build.build(m, verbose=not args.quiet, post=post)
except RuntimeError as e:
error_str = str(e)
if error_str.startswith('No packages found matching:'):
# Build dependency if recipe exists
dep_pkg = error_str.split(': ')[1]
# Handle package names that contain version deps.
if ' ' in dep_pkg:
dep_pkg = dep_pkg.split(' ')[0]
recipe_glob = glob(dep_pkg + '-[v0-9][0-9.]*')
if exists(dep_pkg):
recipe_glob.append(dep_pkg)
if recipe_glob:
recipes.appendleft(arg)
try_again = True
for recipe_dir in recipe_glob:
print(("Missing dependency {0}, but found" +
" recipe directory, so building " +
"{0} first").format(dep_pkg))
recipes.appendleft(recipe_dir)
else:
raise
else:
raise
if try_again:
continue
if not args.notest:
build.test(m, verbose=not args.quiet)
binstar_upload = True
if need_cleanup:
shutil.rmtree(recipe_dir)
if binstar_upload:
handle_binstar_upload(build.bldpkg_path(m), args)
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
"""
output_file = op.join(OUTPUT_DIR, folder, 'README.rst')
# 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 []
# Read the meta.yaml file(s)
try:
metadata = MetaData(meta_fname)
except UnableToParse:
logger.error("Failed to parse recipe %s", meta_fname)
return []
name = metadata.name()
versions_in_channel = repodata.get_versions(name)
sorted_versions = sorted(versions_in_channel.keys(), key=VersionOrder, reverse=True)
# Format the README
template_options = {
'name': name,
'about': (metadata.get_section('about') or {}),
'extra': (metadata.get_section('extra') or {}),
'versions': sorted_versions,
'gh_recipes': 'https://github.com/bioconda/bioconda-recipes/tree/master/recipes/',
'recipe_path': meta_fname,
'Package': '<a href="recipes/{0}/README.html">{0}</a>'.format(folder)
}
renderer.render_to_file(output_file, 'readme.rst_t', template_options)
versions = []
for version in sorted_versions:
version_info = versions_in_channel[version]
version = template_options.copy()
version.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
})
versions.append(version)
return versions
def execute(args, parser):
import sys
import shutil
import tarfile
import tempfile
from os import makedirs
from os.path import abspath, isdir, isfile
from conda.lock import Locked
import conda_build.build as build
import conda_build.source as source
from conda_build.config import config
from conda_build.metadata import MetaData
check_external()
channel_urls = args.channel or ()
if on_win:
# needs to happen before any c extensions are imported that might be
# hard-linked by files in the trash. one of those is markupsafe, used
# by jinja2. see https://github.com/conda/conda-build/pull/520
assert "markupsafe" not in sys.modules
delete_trash(None)
conda_version = {"python": "CONDA_PY", "numpy": "CONDA_NPY", "perl": "CONDA_PERL", "R": "CONDA_R"}
for lang in ["python", "numpy", "perl", "R"]:
versions = getattr(args, lang)
if not versions:
continue
if versions == ["all"]:
if all_versions[lang]:
versions = all_versions[lang]
else:
parser.error("'all' is not supported for --%s" % lang)
if len(versions) > 1:
for ver in versions[:]:
setattr(args, lang, [str(ver)])
execute(args, parser)
# This is necessary to make all combinations build.
setattr(args, lang, versions)
return
else:
version = versions[0]
if lang in ("python", "numpy"):
version = int(version.replace(".", ""))
setattr(config, conda_version[lang], version)
if not len(str(version)) in (2, 3) and lang in ["python", "numpy"]:
if all_versions[lang]:
raise RuntimeError(
"%s must be major.minor, like %s, not %s"
% (conda_version[lang], all_versions[lang][-1] / 10, version)
)
else:
raise RuntimeError("%s must be major.minor, not %s" % (conda_version[lang], version))
# Using --python, --numpy etc. is equivalent to using CONDA_PY, CONDA_NPY, etc.
# Auto-set those env variables
for var in conda_version.values():
if getattr(config, var):
# Set the env variable.
os_environ[var] = str(getattr(config, var))
if args.skip_existing:
if not isdir(config.bldpkgs_dir):
makedirs(config.bldpkgs_dir)
update_index(config.bldpkgs_dir)
index = build.get_build_index(
clear_cache=True, channel_urls=channel_urls, override_channels=args.override_channels
)
already_built = []
to_build_recursive = []
with Locked(config.croot):
recipes = deque(args.recipe)
while recipes:
arg = recipes.popleft()
try_again = False
# 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
else:
print("Ignoring non-recipe: %s" % arg)
continue
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)
if m.get_value("build/noarch_python"):
config.noarch = True
except exceptions.YamlParsingError as e:
sys.stderr.write(e.error_msg())
sys.exit(1)
binstar_upload = False
if args.check and len(args.recipe) > 1:
print(m.path)
m.check_fields()
if args.check:
continue
if args.skip_existing:
if m.pkg_fn() in index or m.pkg_fn() in already_built:
print("%s is already built, skipping." % m.dist())
continue
if args.output:
print(build.bldpkg_path(m))
continue
elif args.test:
build.test(
m, verbose=not args.quiet, channel_urls=channel_urls, override_channels=args.override_channels
)
elif args.source:
source.provide(m.path, m.get_section("source"))
print("Source tree in:", source.get_dir())
else:
# This loop recursively builds dependencies if recipes exist
if args.build_only:
post = False
args.notest = True
args.binstar_upload = False
elif args.post:
post = True
args.notest = True
args.binstar_upload = False
else:
post = None
try:
if m.skip():
print("Skipped: The %s recipe defines build/skip for this " "configuration." % m.dist())
continue
build.build(
m,
verbose=not args.quiet,
post=post,
channel_urls=channel_urls,
override_channels=args.override_channels,
include_recipe=args.include_recipe,
)
except (RuntimeError, SystemExit) as e:
error_str = str(e)
if error_str.startswith("No packages found") or error_str.startswith("Could not find some"):
# Build dependency if recipe exists
dep_pkg = error_str.split(": ")[1]
# Handle package names that contain version deps.
if " " in dep_pkg:
dep_pkg = dep_pkg.split(" ")[0]
recipe_glob = glob(dep_pkg + "-[v0-9][0-9.]*")
if exists(dep_pkg):
recipe_glob.append(dep_pkg)
if recipe_glob:
recipes.appendleft(arg)
try_again = True
for recipe_dir in recipe_glob:
if dep_pkg in to_build_recursive:
sys.exit(str(e))
print(
(
"Missing dependency {0}, but found"
+ " recipe directory, so building "
+ "{0} first"
).format(dep_pkg)
)
recipes.appendleft(recipe_dir)
to_build_recursive.append(dep_pkg)
else:
raise
elif error_str.strip().startswith("Hint:"):
lines = [line for line in error_str.splitlines() if line.strip().startswith("- ")]
pkgs = [line.lstrip("- ") for line in lines]
# Typically if a conflict is with one of these
# packages, the other package needs to be rebuilt
# (e.g., a conflict with 'python 3.5*' and 'x' means
# 'x' isn't build for Python 3.5 and needs to be
# rebuilt).
skip_names = ["python", "r"]
pkgs = [pkg for pkg in pkgs if pkg.split(" ")[0] not in skip_names]
for pkg in pkgs:
# Handle package names that contain version deps.
if " " in pkg:
pkg = pkg.split(" ")[0]
recipe_glob = glob(pkg + "-[v0-9][0-9.]*")
if exists(pkg):
recipe_glob.append(pkg)
if recipe_glob:
recipes.appendleft(arg)
try_again = True
for recipe_dir in recipe_glob:
if pkg in to_build_recursive:
sys.exit(str(e))
print(error_str)
print(
(
"Missing dependency {0}, but found"
+ " recipe directory, so building "
+ "{0} first"
).format(pkg)
)
recipes.appendleft(recipe_dir)
to_build_recursive.append(pkg)
else:
raise
else:
raise
if try_again:
continue
if not args.notest:
build.test(
m, verbose=not args.quiet, channel_urls=channel_urls, override_channels=args.override_channels
)
binstar_upload = True
if need_cleanup:
shutil.rmtree(recipe_dir)
if binstar_upload:
handle_binstar_upload(build.bldpkg_path(m), args)
already_built.append(m.pkg_fn())
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 execute(args, parser):
import sys
import shutil
import tarfile
import tempfile
from os.path import abspath, isdir, isfile
from conda.lock import Locked
import conda_build.build as build
import conda_build.source as source
from conda_build.config import config
from conda_build.metadata import MetaData
check_external()
channel_urls = args.channel or ()
if on_win:
# needs to happen before any c extensions are imported that might be
# hard-linked by files in the trash. one of those is markupsafe, used
# by jinja2. see https://github.com/conda/conda-build/pull/520
assert 'markupsafe' not in sys.modules
delete_trash(None)
conda_version = {
'python': 'CONDA_PY',
'numpy': 'CONDA_NPY',
'perl': 'CONDA_PERL',
'R': 'CONDA_R',
}
for lang in ['python', 'numpy', 'perl', 'R']:
versions = getattr(args, lang)
if not versions:
continue
if versions == ['all']:
if all_versions[lang]:
versions = all_versions[lang]
else:
parser.error("'all' is not supported for --%s" % lang)
if len(versions) > 1:
for ver in versions[:]:
setattr(args, lang, [str(ver)])
execute(args, parser)
# This is necessary to make all combinations build.
setattr(args, lang, versions)
return
else:
version = int(versions[0].replace('.', ''))
setattr(config, conda_version[lang], version)
if not len(str(version)) == 2 and lang in ['python', 'numpy']:
if all_versions[lang]:
raise RuntimeError("%s must be major.minor, like %s, not %s" %
(conda_version[lang], all_versions[lang][-1]/10, version))
else:
raise RuntimeError("%s must be major.minor, not %s" %
(conda_version[lang], version))
if args.skip_existing:
update_index(config.bldpkgs_dir)
index = build.get_build_index(clear_cache=True,
channel_urls=channel_urls,
override_channels=args.override_channels)
already_built = []
to_build = args.recipe[:]
with Locked(config.croot):
recipes = deque(args.recipe)
while recipes:
arg = recipes.popleft()
try_again = False
# 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
else:
print("Ignoring non-recipe: %s" % arg)
continue
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)
if m.get_value('build/noarch_python'):
config.noarch = True
except exceptions.YamlParsingError as e:
sys.stderr.write(e.error_msg())
sys.exit(1)
binstar_upload = False
if args.check and len(args.recipe) > 1:
print(m.path)
m.check_fields()
if args.check:
continue
if args.skip_existing:
if m.pkg_fn() in index or m.pkg_fn() in already_built:
print("%s is already built, skipping." % m.dist())
continue
if args.output:
print(build.bldpkg_path(m))
continue
elif args.test:
build.test(m, verbose=not args.quiet,
channel_urls=channel_urls, override_channels=args.override_channels)
elif args.source:
source.provide(m.path, m.get_section('source'))
print('Source tree in:', source.get_dir())
else:
# This loop recursively builds dependencies if recipes exist
if args.build_only:
post = False
args.notest = True
args.binstar_upload = False
elif args.post:
post = True
args.notest = True
args.binstar_upload = False
else:
post = None
try:
build.build(m, verbose=not args.quiet, post=post,
channel_urls=channel_urls,
override_channels=args.override_channels, include_recipe=args.include_recipe)
except RuntimeError as e:
error_str = str(e)
if error_str.startswith('No packages found') or error_str.startswith('Could not find some'):
# Build dependency if recipe exists
dep_pkg = error_str.split(': ')[1]
# Handle package names that contain version deps.
if ' ' in dep_pkg:
dep_pkg = dep_pkg.split(' ')[0]
recipe_glob = glob(dep_pkg + '-[v0-9][0-9.]*')
if exists(dep_pkg):
recipe_glob.append(dep_pkg)
if recipe_glob:
recipes.appendleft(arg)
try_again = True
for recipe_dir in recipe_glob:
if dep_pkg in to_build:
sys.exit(str(e))
print(("Missing dependency {0}, but found" +
" recipe directory, so building " +
"{0} first").format(dep_pkg))
recipes.appendleft(recipe_dir)
to_build.append(dep_pkg)
else:
raise
else:
raise
if try_again:
continue
if not args.notest:
build.test(m, verbose=not args.quiet,
channel_urls=channel_urls, override_channels=args.override_channels)
binstar_upload = True
if need_cleanup:
shutil.rmtree(recipe_dir)
if binstar_upload:
handle_binstar_upload(build.bldpkg_path(m), args)
already_built.append(m.pkg_fn())
def execute(args, parser):
import sys
import shutil
import tarfile
import tempfile
from os import makedirs
from os.path import abspath, isdir, isfile
from conda.lock import Locked
import conda_build.build as build
import conda_build.source as source
from conda_build.config import config
from conda_build.metadata import MetaData
check_external()
# change globals in build module, see comment there as well
build.channel_urls = args.channel or ()
build.override_channels = args.override_channels
build.verbose = not args.quiet
if on_win:
try:
# needs to happen before any c extensions are imported that might be
# hard-linked by files in the trash. one of those is markupsafe,
# used by jinja2. see https://github.com/conda/conda-build/pull/520
delete_trash(None)
except:
# when we can't delete the trash, don't crash on AssertionError,
# instead inform the user and try again next time.
# see https://github.com/conda/conda-build/pull/744
warnings.warn(
"Cannot delete trash; some c extension has been "
"imported that is hard-linked by files in the trash. "
"Will try again on next run.")
conda_version = {
'python': 'CONDA_PY',
'numpy': 'CONDA_NPY',
'perl': 'CONDA_PERL',
'R': 'CONDA_R',
}
for lang in ['python', 'numpy', 'perl', 'R']:
versions = getattr(args, lang)
if not versions:
continue
if versions == ['all']:
if all_versions[lang]:
versions = all_versions[lang]
else:
parser.error("'all' is not supported for --%s" % lang)
if len(versions) > 1:
for ver in versions[:]:
setattr(args, lang, [str(ver)])
execute(args, parser)
# This is necessary to make all combinations build.
setattr(args, lang, versions)
return
else:
version = versions[0]
if lang in ('python', 'numpy'):
version = int(version.replace('.', ''))
setattr(config, conda_version[lang], version)
if not len(str(version)) in (2, 3) and lang in ['python', 'numpy']:
if all_versions[lang]:
raise RuntimeError("%s must be major.minor, like %s, not %s" %
(conda_version[lang],
all_versions[lang][-1] / 10, version))
else:
raise RuntimeError("%s must be major.minor, not %s" %
(conda_version[lang], version))
# Using --python, --numpy etc. is equivalent to using CONDA_PY, CONDA_NPY, etc.
# Auto-set those env variables
for var in conda_version.values():
if getattr(config, var):
# Set the env variable.
os_environ[var] = str(getattr(config, var))
if args.skip_existing:
if not isdir(config.bldpkgs_dir):
makedirs(config.bldpkgs_dir)
update_index(config.bldpkgs_dir)
index = build.get_build_index(clear_cache=True)
already_built = []
to_build_recursive = []
with Locked(config.croot):
recipes = deque(args.recipe)
while recipes:
arg = recipes.popleft()
try_again = False
# 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
else:
print("Ignoring non-recipe: %s" % arg)
continue
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)
if m.get_value('build/noarch_python'):
config.noarch = True
except exceptions.YamlParsingError as e:
sys.stderr.write(e.error_msg())
sys.exit(1)
binstar_upload = False
if args.check and len(args.recipe) > 1:
print(m.path)
m.check_fields()
if args.check:
continue
if args.skip_existing:
if m.pkg_fn() in index or m.pkg_fn() in already_built:
print("%s is already built, skipping." % m.dist())
continue
if m.skip():
print("Skipped: The %s recipe defines build/skip for this "
"configuration." % m.dist())
continue
if args.output:
try:
m.parse_again(permit_undefined_jinja=False)
except SystemExit:
# Something went wrong; possibly due to undefined GIT_ jinja variables.
# Maybe we need to actually download the source in order to resolve the build_id.
source.provide(m.path, m.get_section('source'))
# Parse our metadata again because we did not initialize the source
# information before.
m.parse_again(permit_undefined_jinja=False)
print(build.bldpkg_path(m))
continue
elif args.test:
build.test(m, move_broken=False)
elif args.source:
source.provide(m.path, m.get_section('source'))
print('Source tree in:', source.get_dir())
else:
# This loop recursively builds dependencies if recipes exist
if args.build_only:
post = False
args.notest = True
args.binstar_upload = False
elif args.post:
post = True
args.notest = True
args.binstar_upload = False
else:
post = None
try:
build.build(m,
post=post,
include_recipe=args.include_recipe)
except (RuntimeError, SystemExit) as e:
error_str = str(e)
if error_str.startswith(
'No packages found') or error_str.startswith(
'Could not find some'):
# Build dependency if recipe exists
dep_pkg = error_str.split(': ')[1]
# Handle package names that contain version deps.
if ' ' in dep_pkg:
dep_pkg = dep_pkg.split(' ')[0]
recipe_glob = glob(dep_pkg + '-[v0-9][0-9.]*')
if exists(dep_pkg):
recipe_glob.append(dep_pkg)
if recipe_glob:
recipes.appendleft(arg)
try_again = True
for recipe_dir in recipe_glob:
if dep_pkg in to_build_recursive:
sys.exit(str(e))
print(("Missing dependency {0}, but found" +
" recipe directory, so building " +
"{0} first").format(dep_pkg))
recipes.appendleft(recipe_dir)
to_build_recursive.append(dep_pkg)
else:
raise
elif error_str.strip().startswith("Hint:"):
lines = [
line for line in error_str.splitlines()
if line.strip().startswith('- ')
]
pkgs = [line.lstrip('- ') for line in lines]
# Typically if a conflict is with one of these
# packages, the other package needs to be rebuilt
# (e.g., a conflict with 'python 3.5*' and 'x' means
# 'x' isn't build for Python 3.5 and needs to be
# rebuilt).
skip_names = ['python', 'r']
pkgs = [
pkg for pkg in pkgs
if pkg.split(' ')[0] not in skip_names
]
for pkg in pkgs:
# Handle package names that contain version deps.
if ' ' in pkg:
pkg = pkg.split(' ')[0]
recipe_glob = glob(pkg + '-[v0-9][0-9.]*')
if exists(pkg):
recipe_glob.append(pkg)
if recipe_glob:
recipes.appendleft(arg)
try_again = True
for recipe_dir in recipe_glob:
if pkg in to_build_recursive:
sys.exit(str(e))
print(error_str)
print(
("Missing dependency {0}, but found" +
" recipe directory, so building " +
"{0} first").format(pkg))
recipes.appendleft(recipe_dir)
to_build_recursive.append(pkg)
else:
raise
else:
raise
if try_again:
continue
if not args.notest:
build.test(m)
binstar_upload = True
if need_cleanup:
shutil.rmtree(recipe_dir)
if binstar_upload:
handle_binstar_upload(build.bldpkg_path(m), args)
already_built.append(m.pkg_fn())
def execute(args, parser):
import sys
import shutil
import tarfile
import tempfile
from os.path import abspath, isdir, isfile
from conda.lock import Locked
import conda_build.build as build
import conda_build.source as source
from conda_build.config import config
from conda_build.metadata import MetaData
check_external()
channel_urls = args.channel or ()
all_versions = {
'python': [26, 27, 33, 34],
'numpy': [16, 17, 18, 19],
'perl': None,
'R': None,
}
conda_version = {
'python': 'CONDA_PY',
'numpy': 'CONDA_NPY',
'perl': 'CONDA_PERL',
'R': 'CONDA_R',
}
for lang in ['python', 'numpy', 'perl', 'R']:
versions = getattr(args, lang)
if not versions:
continue
if versions == ['all']:
if all_versions[lang]:
versions = all_versions[lang]
else:
parser.error("'all' is not supported for --%s" % lang)
if len(versions) > 1:
for ver in versions[:]:
setattr(args, lang, [str(ver)])
execute(args, parser)
# This is necessary to make all combinations build.
setattr(args, lang, versions)
return
else:
version = int(versions[0].replace('.', ''))
setattr(config, conda_version[lang], version)
if not len(str(version)) == 2:
if all_versions[lang]:
raise RuntimeError("%s must be major.minor, like %s, not %s" %
(conda_version[lang], all_versions[lang][-1]/10, version))
else:
raise RuntimeError("%s must be major.minor, not %s" %
(conda_version[lang], version))
if args.skip_existing:
update_index(config.bldpkgs_dir)
index = build.get_build_index(clear_cache=True,
channel_urls=channel_urls,
override_channels=args.override_channels)
with Locked(config.croot):
recipes = deque(args.recipe)
while recipes:
arg = recipes.popleft()
try_again = False
# 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
else:
print("Ignoring non-recipe: %s" % arg)
continue
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)
if m.get_value('build/noarch_python'):
config.noarch = True
except exceptions.YamlParsingError as e:
sys.stderr.write(e.error_msg())
sys.exit(1)
binstar_upload = False
if args.check and len(args.recipe) > 1:
print(m.path)
m.check_fields()
if args.check:
continue
if args.skip_existing:
if m.pkg_fn() in index:
print("%s is already built, skipping." % m.dist())
continue
if args.output:
print(build.bldpkg_path(m))
continue
elif args.test:
build.test(m, verbose=not args.quiet,
channel_urls=channel_urls, override_channels=args.override_channels)
elif args.source:
source.provide(m.path, m.get_section('source'))
print('Source tree in:', source.get_dir())
else:
# This loop recursively builds dependencies if recipes exist
if args.build_only:
post = False
args.notest = True
args.binstar_upload = False
elif args.post:
post = True
args.notest = True
args.binstar_upload = False
else:
post = None
try:
build.build(m, verbose=not args.quiet, post=post,
channel_urls=channel_urls, override_channels=args.override_channels)
except RuntimeError as e:
error_str = str(e)
if error_str.startswith('No packages found') or error_str.startswith('Could not find some'):
# Build dependency if recipe exists
dep_pkg = error_str.split(': ')[1]
# Handle package names that contain version deps.
if ' ' in dep_pkg:
dep_pkg = dep_pkg.split(' ')[0]
recipe_glob = glob(dep_pkg + '-[v0-9][0-9.]*')
if exists(dep_pkg):
recipe_glob.append(dep_pkg)
if recipe_glob:
recipes.appendleft(arg)
try_again = True
for recipe_dir in recipe_glob:
print(("Missing dependency {0}, but found" +
" recipe directory, so building " +
"{0} first").format(dep_pkg))
recipes.appendleft(recipe_dir)
else:
raise
else:
raise
if try_again:
continue
if not args.notest:
build.test(m, verbose=not args.quiet,
channel_urls=channel_urls, override_channels=args.override_channels)
binstar_upload = True
if need_cleanup:
shutil.rmtree(recipe_dir)
if binstar_upload:
handle_binstar_upload(build.bldpkg_path(m), args)
def main():
print()
print("Getting extra source packages.")
# Force verbose mode
config.verbose = True
cwd = os.getcwd()
# Get the metadata for the recipe
recipe_dir = os.environ["RECIPE_DIR"]
metadata = MetaData(recipe_dir)
print(metadata.name())
print("-" * 75)
print(' cwd:', cwd)
# Figure out the work_dir
# Look upwards for a directory with the name 'work'.
# FIXME: Why does metadata.config.work_dir not return the correct
# directory?
bits = split_path(cwd)
dirname = []
while bits and bits[-1] != 'work':
dirname.insert(0, bits.pop(-1))
dirname = os.path.join(*dirname, '')
work_dir = bits.pop(-1)
assert work_dir == 'work'
build_id = bits.pop(-1)
croot = os.path.join(*bits)
work_dir = os.path.join(croot, build_id, 'work')
if has_only_one_dir(work_dir):
real_work_dir = work_dir
else:
real_work_dir = os.path.join(croot, build_id)
print(' work dir:', real_work_dir)
print('conda root:', croot)
print(' build id:', build_id)
print(' src dir:', dirname)
extra_sources_sections = metadata.get_section('extra')['sources']
for name, source_section in extra_sources_sections.items():
print()
print("Extra source: %s" % name)
print("-" * 75)
# Create a fake metadata which contains the extra source_section.
newmetadata = metadata.copy()
newmetadata.meta['source'] = source_section
if has_only_one_dir(work_dir):
extra_work_dir = real_work_dir
else:
extra_work_dir = os.path.join(real_work_dir, name)
newmetadata.config.__class__ = SpecialConfig
newmetadata.config._work_dir = extra_work_dir
print("Work Directory:", newmetadata.config.work_dir)
# Download+extract source.
source.provide(newmetadata, newmetadata.config)
print("-" * 75)
print()
print("Extra source packages download and extracted!")
print()
print("Work Directory contents (%s)" % real_work_dir)
print("-" * 75)
print(os.listdir(real_work_dir))
print()
