def __call__(self, match):
name, suffix, rest = match.groups()
if rest is None:
rest = ''
if not any(name.startswith(p) for p in ('$', '#')):
if self.working_dir is None:
log.warning(
'no working directory found, you will have broken links'
)
rel = Path(name + suffix)
else:
try:
rel = ((self.current_file.parent /
(name + suffix)).resolve().relative_to(
self.working_dir))
except ValueError as e:
log.error('path went outside current repo')
return name + suffix + rest
if suffix in ('.md', '.org', '.ipynb'):
rel = rel.with_suffix('.html')
rel_path = rel.as_posix() + rest
#print('aaaaaaaaaaa', suffix, rel, rel_path)
return self.base + rel_path
elif name.startswith('$'):
raise self.MakeMeAnInlineSrcBlock(match.group())
else:
#print('bbbbbbbbbbb', match.group())
return match.group() # rel_path = name + ext + rest
def _ontology_data_files():
resources = 'resources'
relpaths = [
'ttl/phenotype-core.ttl',
'ttl/phenotype-indicators.ttl',
'ttl/phenotypes.ttl',
'ttl/generated/part-of-self.ttl',
]
if RELEASE:
from augpathlib import RepoPath as Path
### KILL IT WITH FIRE
try:
from neurondm.core import auth ### this is NOT ok
except Exception:
# can't catch an error that you can never import because
# it will be raised before you can import it ... SIGH
import orthauth as oa
from pyontutils.config import auth as pauth
auth = oa.configure(Path('neurondm/auth-config.py').resolve(),
include=pauth)
###
olr = Path(auth.get_path('ontology-local-repo'))
### KILL IT WITH FIRE
if not olr.exists():
original = auth.get('ontology-local-repo')
raise FileNotFoundError(
f'ontology local repo does not exist: {olr}'
f'path expanded from {original}')
elif olr.repo.active_branch.name != auth.get('neurons-branch'):
# FIXME yes indeed having to call Config in a way that is
# invoked at import time is REALLY REALLY BAD :/
raise ValueError('git is on the wrong branch! '
f'{olr.repo.active_branch}')
###
resources = Path(resources)
resources.mkdir(
) # if we add resources to git, this will error before we delete by accident
paths = [olr / rp for rp in relpaths]
for p in paths:
p.copy_to(resources / p.name)
else:
from pathlib import Path
resources = Path(resources)
paths = [Path(rp) for rp in relpaths]
return resources.absolute(), [(resources / p.name).as_posix()
for p in paths]
def test_init_from_local_repo(self):
rp = testing_base / 'test-repo'
this_repo_path = RepoPath(__file__).working_dir
if rp.working_dir is not None:
pytest.skip('not testing inside another git repo')
if this_repo_path is None:
pytest.skip(
'this test file is not under version control, so there is no local repo'
)
else:
this_repo = this_repo_path.repo
repo = rp.init(this_repo_path, depth=1)
assert repo, f'{rp!r} {repo}'
return rp
def test_stale_repo_cache(self):
rp = self.test_init()
rp.repo
aug.AugmentedPath(
rp).rmtree() # have to call rmtree that won't invoke repo.close()
try:
rp.repo
assert False, 'should have failed'
except exc.NotInRepoError:
pass
rp2 = RepoPath(rp)
try:
rp2.repo
assert False, 'should have failed'
except exc.NotInRepoError:
pass
def tearDown(self):
RepoPath(testing_base).rmtree(onerror=onerror)
def test_working_dir(self):
[RepoPath._repos.pop(k) for k in list(RepoPath._repos)]
rp = RepoPath(str(self.test_file))
assert rp.working_dir is not None, f'wat {rp}'
assert rp.repo is not None, f'wat {rp} {rp.working_dir}'
import os
import pathlib
import unittest
import pytest
import augpathlib as aug
from augpathlib import RepoPath, LocalPath, exceptions as exc
from .common import onerror, skipif_no_net, temp_path
testing_base = RepoPath(temp_path)
class HybridPath(RepoPath, LocalPath):
""" Combined functionality """
HybridPath._bind_flavours()
class TestRepoPath(unittest.TestCase):
def setUp(self):
if not testing_base.exists():
testing_base.mkdir()
def tearDown(self):
RepoPath(testing_base).rmtree(onerror=onerror)
def test_init(self):
rp = testing_base / 'test-repo'
repo = rp.init()
assert repo, f'hrm {rp!r} {repo}'
return rp