def printRootNodes(config_path, recipe_folder, sinceNDays, missing, rootNodes):
config = utils.load_config(config_path)
blacklist = utils.get_blacklist(config, recipe_folder)
recipes = utils.get_recipes(recipe_folder)
if sinceNDays:
timeStamp = datetime.timestamp(datetime.now() - timedelta(sinceNDays))
linux, noarch, osx = getRepoData(timeStamp)
arch = linux.intersection(osx)
ready = noarch.union(arch)
print(
"{} built in noarch and both archs combined: {} noarch, {} linux-64, {} osx-64"
.format(len(ready), len(noarch), len(linux), len(osx)))
dag, name2recipes = graph.build(recipes,
config=config_path,
blacklist=blacklist)
if not rootNodes:
root_nodes = sorted([
(len(nx.algorithms.descendants(dag, k)), k)
for k, v in dag.in_degree().items()
if (k.startswith('bioconductor') or k.startswith('r-'))
])
else:
root_nodes = sorted([
(len(nx.algorithms.descendants(dag, k)), k)
for k, v in dag.in_degree().items()
if v == 0 and (k.startswith('bioconductor') or k.startswith('r-'))
])
print("Package\tNumber of dependant packages")
for n in root_nodes:
# blacklisted packages also show up as root nodes with out degree 0
if n[1] in blacklist:
continue
if sinceNDays:
if n[1] in ready:
if not missing:
print("recipes/{}\t{}".format(n[1], n[0]))
elif missing:
print("recipes/{}\t{}".format(n[1], n[0]))
else:
print("recipes/{}\t{}".format(n[1], n[0]))
def printMissingCRAN(config_path, recipe_folder):
config = utils.load_config(config_path)
recipes = utils.get_recipes(recipe_folder)
repo = getRepoData()
# Construct a set of all dependencies (ignoring versions)
dependencies = set()
for r in recipes:
if "bioconductor" not in r:
continue
d = utils.load_meta_fast(r)[
0] # a dictionary with keys requirements, build, etc.
for dep in d['requirements']['run']:
if dep.startswith('r-'):
dependencies.add(dep.split(' ')[0])
missing = dependencies - repo
print("Missing {} packages!".format(len(missing)))
for m in missing:
print(m)
def test_nested_recipes(config_fixture):
"""
Test get_recipes ability to identify different nesting depths of recipes
"""
r = Recipes(
"""
shallow:
meta.yaml: |
package:
name: shallow
version: "0.1"
build.sh: |
#!/bin/bash
echo "Shallow Created"
pwd
normal/normal:
meta.yaml: |
package:
name: normal
version: "0.1"
build:
skip: true
requirements:
build:
- python 3.6
build.sh: |
#!/bin/bash
echo "Testing build.sh through python"
python -h
deep/deep/deep:
meta.yaml: |
package:
name: deep
version: "0.1"
requirements:
build:
- python
run:
- python
build.sh: |
#!/bin/bash
## Empty script
F/I/V/E/deep:
meta.yaml: |
package:
name: fivedeep
version: "0.1"
requirements:
build:
- python 3.6
run:
- python 3.6
""", from_string=True)
r.write_recipes()
build_results = build.build_recipes(
r.basedir,
config=config_fixture,
packages="*",
testonly=False,
force=False,
mulled_test=False,
)
assert build_results
assert len(list(utils.get_recipes(r.basedir))) == 4
for k, v in r.recipe_dirs.items():
for i in utils.built_package_paths(v):
assert os.path.exists(i)
ensure_missing(i)
def bioc_name(recipe):
"""
Returns the Bioconductor name (rather than the sanitized lowercase bioconda
name) that can be provided to bioconda-scraper.py
"""
return MetaData(recipe).meta['source']['fn'].split('_')[0]
if __name__ == "__main__":
import argparse
ap = argparse.ArgumentParser()
ap.add_argument('--repository', default='recipes', help='Recipes directory')
args = ap.parse_args()
recipes = list(utils.get_recipes(args.repository, 'bioconductor-*'))
deps = itertools.chain(
itertools.chain(*(utils.get_deps(i, build=True) for i in recipes)),
itertools.chain(*(utils.get_deps(i, build=False) for i in recipes))
)
deps = list(filter(lambda x: x.startswith(('r-', 'bioconductor-')), deps))
bioconda_deps = list(
filter(
lambda x: os.path.isdir(x),
itertools.chain(*(utils.get_recipes(args.repository, i) for i in deps))
)
)
dag, name2recipe = utils.get_dag(bioconda_deps)
def bioc_name(recipe):
"""
Returns the Bioconductor name (rather than the sanitized lowercase bioconda
name) that can be provided to bioconda-scraper.py
"""
return MetaData(recipe).meta['source']['fn'].split('_')[0]
if __name__ == "__main__":
import argparse
ap = argparse.ArgumentParser()
ap.add_argument('--recipes', default='recipes', help='Recipes directory')
ap.add_argument('--config', default='recipes', help='Config YAML')
args = ap.parse_args()
recipes = list(utils.get_recipes(args.recipes, 'bioconductor-*'))
deps = itertools.chain(
itertools.chain(*(utils.get_deps(i, build=True, config=args.config)
for i in recipes)),
itertools.chain(*(utils.get_deps(i, build=False, config=args.config)
for i in recipes)))
deps = list(filter(lambda x: x.startswith(('r-', 'bioconductor-')), deps))
bioconda_deps = list(
filter(
lambda x: os.path.isdir(x),
itertools.chain(*(utils.get_recipes(args.recipes, i)
for i in deps))))
dag, name2recipe = utils.get_dag(bioconda_deps, config=args.config)
def test_nested_recipes(config_fixture):
"""
Test get_recipes ability to identify different nesting depths of recipes
"""
r = Recipes(
"""
shallow:
meta.yaml: |
package:
name: shallow
version: "0.1"
build.sh: |
#!/bin/bash
echo "Shallow Created"
pwd
normal/normal:
meta.yaml: |
package:
name: normal
version: "0.1"
build:
skip: true
requirements:
build:
- python 3.6
build.sh: |
#!/bin/bash
echo "Testing build.sh through python"
python -h
deep/deep/deep:
meta.yaml: |
package:
name: deep
version: "0.1"
requirements:
build:
- python
run:
- python
build.sh: |
#!/bin/bash
## Empty script
F/I/V/E/deep:
meta.yaml: |
package:
name: fivedeep
version: "0.1"
requirements:
build:
- python 3.6
run:
- python 3.6
""", from_string=True)
r.write_recipes()
build_results = build.build_recipes(
r.basedir,
config=config_fixture,
packages="*",
testonly=False,
force=False,
mulled_test=False,
)
assert build_results
assert len(list(utils.get_recipes(r.basedir))) == 4
for k, v in r.recipe_dirs.items():
for i in utils.built_package_paths(v):
assert os.path.exists(i)
ensure_missing(i)
