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from __future__ import print_function
import sys
import pytest
import pymol
import __main__
from pymol import cmd, testing, stored
from typing import List
class TestCommanding(testing.PyMOLTestCase):
def testAlias(self):
stored.v = None
cmd.alias('foo', '/stored.v = 123')
cmd.do('_ foo', echo=0)
self.assertEqual(stored.v, 123)
@testing.requires('gui', 'no_run_all')
def testCls(self):
cmd.set('internal_prompt', 0)
cmd.set('text', 1)
cmd.cls()
# check on black screen
img = self.get_imagearray()
self.assertFalse(img[...,:3].any())
def testDelete(self):
cmd.pseudoatom('m1')
cmd.pseudoatom('m2')
cmd.pseudoatom('m3')
cmd.delete('m1 m2')
self.assertEqual(cmd.get_names(), ['m3'])
def testDeleteStates(self):
cmd.pseudoatom('m1', state=10)
self.assertEqual(cmd.count_states('m1'), 10)
cmd.delete_states('m1', '4-8')
self.assertEqual(cmd.count_states('m1'), 5)
def testDo(self):
# tested with other methods
pass
def testExtend(self):
def check(v):
stored.v = None
cmd.do('foo', echo=0)
self.assertEqual(stored.v, v)
cmd.extend('foo', lambda: setattr(stored, 'v', 123))
check(123)
@cmd.extend
def foo():
stored.v = 456
check(456)
def testLog(self):
with testing.mktemp('.pml') as logfile:
cmd.log_open(logfile)
cmd.do('_ color blue')
cmd.log('hello world')
cmd.log_close()
lines = [_f for _f in map(str.strip, open(logfile)) if _f]
self.assertEqual(lines, ['color blue', 'hello world'])
@testing.requires_version('1.8.1.0')
def testLog2(self):
"""
Tests robustness of different logging methods:
1) Python implementation (cmd.log) vs. C implementation (PLog, via cmd.do)
2) pml vs. py syntax
3) handling of quoted input (''' broken in 1.8.2)
"""
self.ambientOnly()
cmd.viewport(100, 100)
cmd.fragment('gly')
cmd.orient()
cmd.show_as('spheres')
for ext in ['.pml', '.py']:
with testing.mktemp(ext) as logfile:
cmd.log_open(logfile)
cmd.do('_ color blue')
cmd.do('/cmd.color("yellow", "elem O")')
cmd.do('cmd.color("""green""",' " '''elem N''')")
cmd.log('bg red\n')
cmd.log('', 'cmd.color(\'magenta\', "hydro")\n')
cmd.log_close()
cmd.color('white')
cmd.bg_color('white')
if ext == '.pml':
cmd.do('@' + logfile)
else:
cmd.do('run ' + logfile)
img = self.get_imagearray()
self.assertImageHasColor('blue', img)
self.assertImageHasColor('yellow', img)
self.assertImageHasColor('green', img)
self.assertImageHasColor('red', img)
self.assertImageHasColor('magenta', img)
self.assertImageHasNotColor('white', img)
def testLogClose(self):
# see testLog
pass
def testLogOpen(self):
# see testLog
pass
def testQuit(self):
cmd.quit
self.skipTest("cannot test quit")
def testReinitialize(self):
def check(v, names):
self.assertEqual(v, cmd.get('pdb_conect_all'))
self.assertEqual(cmd.get_names(), names)
cmd.pseudoatom('m1')
v = cmd.set('pdb_conect_all')
cmd.reinitialize('store_defaults')
cmd.reinitialize('original_settings')
check('off', ['m1'])
cmd.reinitialize('settings')
check('on', ['m1'])
cmd.reinitialize('purge_defaults')
cmd.reinitialize('settings')
check('off', ['m1'])
cmd.reinitialize('everything')
check('off', [])
def testResume(self):
with testing.mktemp('.pml') as logfile:
with open(logfile, 'w') as f:
print('bg yellow', file=f)
cmd.resume(logfile)
self.assertEqual('yellow', cmd.get('bg_rgb'))
cmd.log('hello world')
cmd.log_close()
lines = [_f for _f in map(str.strip, open(logfile)) if _f]
self.assertEqual(lines, ['bg yellow', 'hello world'])
def testSplash(self):
cmd.feedback('disable', 'all', 'output')
cmd.splash()
def testSync(self):
cmd.sync()
@testing.foreach(
('local', 'pymol', False),
('global', 'pymol', True),
('module', '', False),
('main', '__main__', True),
('private', '__main__', False),
)
def testRun(self, namespace, mod, rw):
stored.tmp = False
with testing.mktemp('.py') as filename:
varname = '_tmp_' + namespace
with open(filename, 'w') as handle:
print('from pymol import stored', file=handle)
if mod:
print('stored.tmp = (__name__ == "%s")' % (mod), file=handle)
else:
print('stored.tmp = True', file=handle)
print(varname + ' = True', file=handle)
cmd.do('run %s, %s' % (filename, namespace), 0, 0)
self.assertTrue(stored.tmp)
if mod:
self.assertEqual(rw, hasattr(sys.modules[mod], varname))
def test_declare_command_casting():
from pathlib import Path
@cmd.declare_command
def func(a: int, b: Path):
assert isinstance(a, int) and a == 1
assert isinstance(b, (Path, str)) and "/tmp" == str(b)
func(1, "/tmp")
cmd.do('func 1, /tmp')
def test_declare_command_default(capsys):
from pymol.commanding import Selection
@cmd.declare_command
def func(a: Selection = "sele"):
assert a == "sele"
func()
cmd.do("func")
out, err = capsys.readouterr()
assert out == ''
def test_declare_command_docstring():
@cmd.declare_command
def func():
"""docstring"""
assert func.__doc__ == "docstring"
@cmd.declare_command
def func():
"""
docstring
Test:
--foo
"""
assert func.__doc__ == "docstring\nTest:\n --foo"
def test_declare_command_type_return(capsys):
@cmd.declare_command
def func() -> int:
return 1
assert func() == 1
out, err = capsys.readouterr()
assert out == ''
@cmd.declare_command
def func():
return 1
assert func() == 1
def test_declare_command_list_str(capsys):
@cmd.declare_command
def func(a: List[str]):
print(a[-1])
func(["a", "b", "c"])
cmd.do('func a b c')
out, err = capsys.readouterr()
assert out == 'c\nc\n'
def test_declare_command_list_int(capsys):
@cmd.declare_command
def func(a: List[int]):
print(a[-1] ** 2)
return a[-1] ** 2
assert func([1, 2, 3]) == 9
cmd.do('func 1 2 3')
out, err = capsys.readouterr()
assert out == '9\n9\n'
def test_declare_command_list_float(capsys):
@cmd.declare_command
def func(a: List[float]):
print(a[-1]**2)
return a[-1]**2
assert func([1.1, 2.0, 3.0]) == 9.0
cmd.do('func 1 2 3')
out, err = capsys.readouterr()
assert out == '9.0\n9.0\n'
def test_declare_command_bool(capsys):
@cmd.declare_command
def func(a: bool, b: bool):
assert a
assert not b
func(True, False)
cmd.do("func yes, no")
out, err = capsys.readouterr()
assert out == '' and err == ''
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