def ContactGroupL394(**kwargs):
with _TDir(suffix="_mdciao_example_CG") as t:
for fn in [
filenames.pdb_3SN6, filenames.traj_xtc, filenames.top_pdb,
filenames.adrb2_human_xlsx, filenames.CGN_3SN6
]:
_link(fn, _path.join(t, _path.basename(fn)))
with remember_cwd():
_chdir(t)
b = _io.StringIO()
try:
with _contextlib.redirect_stdout(b):
example_kwargs = {
"topology": _path.basename(filenames.top_pdb),
"n_smooth_hw": 1,
"figures": False,
"BW_uniprot":
_path.basename(filenames.adrb2_human_xlsx),
"CGN_PDB": _path.basename(filenames.CGN_3SN6),
"accept_guess": True
}
for key, val in kwargs.items():
example_kwargs[key] = val
return _residue_neighborhoods(
"L394",
_path.basename(filenames.traj_xtc),
**example_kwargs,
)["neighborhoods"][353]
except Exception as e:
print(b.getvalue())
b.close()
raise e
def startup():
'''Do basic setup for the program. This really should only be run once
but has some basic tests to prevent double-assignment'''
_chdir(sys.path[0])
_makedirs("logs", exist_ok=True)
global args, logger, loop
args = parseargs()
loop = asyncio.get_event_loop()
# Set up logging
open(settings.logfile, 'w').close()
logger = logging.getLogger(__name__)
rootLogger = logging.getLogger()
if len(rootLogger.handlers) is 0:
rootLogger.setLevel(logging.DEBUG)
conFmt = "[%(levelname)8s] %(name)s: %(message)s"
ch = logging.StreamHandler()
ch.setFormatter(logging.Formatter(conFmt))
rootLogger.addHandler(ch)
filFmt = "[%(levelname)8s] %(asctime)s %(name)s: %(message)s"
fh = logging.FileHandler(settings.logfile)
fh.setFormatter(logging.Formatter(filFmt, "%b-%d %H:%M:%S"))
rootLogger.addHandler(fh)
util.setLogLevel(args.verbose, True)
logger.debug('Logging set up.')
logger.debug('Args state: {}'.format(args))
logger.info('Badge check midlayer v{} starting on {} ({})'.format(
settings.version,
datetime.now().date(),
datetime.now().date().strftime("%A")))
# Set up API key
try:
with open(getSetting('apikey')) as f:
settings.magapi.headers['X-Auth-Token'] = str(
UUID(f.read().strip()))
except FileNotFoundError:
logger.fatal(
'Could not find API key file, refusing to run. ({})'.format(
path.abspath(getSetting('apikey'))))
raise SystemExit
except ValueError:
logger.fatal('API key not a valid UUID, refusing to run.')
raise SystemExit
global server
try:
server
except NameError:
server = loop.run_until_complete(
websockets.serve(
prcsConnection,
socket.gethostbyname_ex(socket.getfqdn())[-1] + ['127.0.0.1'],
getSetting('l_port')))
for s in server.sockets:
logger.info('Now listening for connections on {}:{}'.format(
*s.getsockname()))
import os
from os import chdir as _chdir
from unittest import TestCase
from mock import patch
import tut.sphinx
from tut.tests import util
from tut.tests.util import with_sphinx
@patch('os.chdir', new=lambda x: _chdir(x) if os.path.exists(x) else None)
@patch('tut.sphinx.git', return_value='original_branch')
class SphinxExtensionLifecycleTests(TestCase):
# the order of these decorators is *important*: cleanup needs to
# be replaced before the Sphinx Test Application is instantiated
@patch('tut.sphinx.cleanup')
@with_sphinx()
def test_cleanup_called(self, cleanup_mock, git_mock, sphinx_app=None):
sphinx_app.build(force_all=True)
self.assertEqual(cleanup_mock.call_count, 1)
@with_sphinx()
def test_cleanup_resets_paths(self, git_mock, sphinx_app=None):
start_dir = os.getcwd()
sphinx_app.build()
def exec(self, args: tuple = (), **kwargs):
"""Execute the command.
"""
app_path = _reg.get('paths.app')
config_path = _reg.get('paths.config')
stage = self.opt('stage')
stop_after = self.opt('stop-after')
_chdir(app_path)
_maintenance.enable()
d = self._get_update_data()
if not d['update_in_progress']:
d['pytsite_version_from'] = str(_package_info.version('pytsite'))
d['app_version_from'] = str(_package_info.version('app'))
d['update_in_progress'] = True
self._set_update_data(d)
# Stage 1: update pip and PytSite
if stage == 1:
_console.print_info(_lang.t('pytsite.update@updating_environment'))
# Update pip
_pip.install('pip', None, True, self.opt('debug'))
# Update PytSite
_pip.install('pytsite', _package_info.requires_pytsite('app'), True, self.opt('debug'))
d['pytsite_version_to'] = str(_package_info.version('pytsite', False))
self._set_update_data(d)
# Notify listeners
_events.fire('pytsite.update@stage_1')
if stop_after != 1:
_subprocess.call(['./console', 'update', '--stage=2'])
else:
_maintenance.disable()
# Stage 2: update application and configuration
elif stage == 2:
# Notify listeners about PytSite update
_events.fire('pytsite.update@pytsite', v_from=_semver.Version(d['pytsite_version_from']))
# Update configuration
if _path.exists(_path.join(config_path, '.git')):
_console.print_info(_lang.t('pytsite.update@updating_configuration'))
_subprocess_run(['git', '-C', config_path, 'pull'])
# Update application
if _path.exists(_path.join(app_path, '.git')):
_console.print_info(_lang.t('pytsite.update@updating_application'))
_subprocess_run(['git', '-C', app_path, 'pull'])
d['app_version_to'] = str(_package_info.version('app', False))
self._set_update_data(d)
# Notify listeners
_events.fire('pytsite.update@stage_2')
if stop_after != 2:
_subprocess.call(['./console', 'update', '--stage=3'])
else:
_maintenance.disable()
# Stage 3: finish update process
elif stage == 3:
_console.print_info(_lang.t('pytsite.update@applying_updates'))
# Notify listeners about application update
_events.fire('pytsite.update@app', v_from=_semver.Version(d['app_version_from']))
# Notify listeners
_events.fire('pytsite.update@update')
# Application's update hook
import app
if hasattr(app, 'app_update') and callable(app.app_update):
app.app_update(v_from=_semver.Version(d['app_version_from']))
# Mark that update was finished successfully
d['update_in_progress'] = False
self._set_update_data(d)
# Disable maintenance mode
_maintenance.disable()
# Reload the application
_reload.reload()
def os_chdir(path): return os._chdir(longpathify(uni(path)))
import os
from os import chdir as _chdir
from unittest import TestCase
from mock import patch
import tut.sphinx
from tut.tests import util
from tut.tests.util import with_sphinx
@patch('os.chdir', new=lambda x: _chdir(x) if os.path.exists(x) else None)
@patch('tut.sphinx.git', return_value='original_branch')
class SphinxExtensionLifecycleTests(TestCase):
# the order of these decorators is *important*: cleanup needs to
# be replaced before the Sphinx Test Application is instantiated
@patch('tut.sphinx.cleanup')
@with_sphinx()
def test_cleanup_called(self, cleanup_mock, git_mock, sphinx_app=None):
sphinx_app.build(force_all=True)
self.assertEqual(cleanup_mock.call_count, 1)
@with_sphinx()
def test_cleanup_resets_paths(self, git_mock, sphinx_app=None):
start_dir = os.getcwd()
sphinx_app.build()
def remember_cwd():
curdir = _getcwd()
try:
yield
finally:
_chdir(curdir)
def os_chdir(path):
return os._chdir(longpathify(uni(path)))
