misc review cleanup

Author: dwhswenson

paths_cli/parsing/tools.py

@@ -1,8 +1,17 @@
 import numpy as np
 
 def custom_eval(obj, named_objs=None):
+    """Parse user input to allow simple math.
+
+    This allows certain user input to be treated as a simplified subset of
+    Python. In particular, this is intended to allow simple arithmetic. It
+    allows use of the modules numpy (as ``np``) and math, which provide
+    potentially useful functions (e.g., ``cos``) as well as constants (e.g.,
+    ``pi``).
+    """
     string = str(obj)
     # TODO: check that the only attribute access comes from a whitelist
+    # (parse the AST for that)
     namespace = {
         'np': __import__('numpy'),
         'math': __import__('math'),

paths_cli/tests/parsing/test_tools.py

@@ -1,10 +1,14 @@
 import pytest
 import numpy.testing as npt
+import numpy as np
+import math
 
 from paths_cli.parsing.tools import *
 
 @pytest.mark.parametrize('expr,expected', [
-    ('1+1', 2)
+    ('1+1', 2),
+    ('np.pi / 2', np.pi / 2),
+    ('math.cos(1.5)', math.cos(1.5)),
 ])
 def test_custom_eval(expr, expected):
     npt.assert_allclose(custom_eval(expr), expected)

paths_cli/tests/utils.py

@@ -0,0 +1,18 @@
+import urllib.request
+
+try:
+    urllib.request.urlopen('https://www.google.com')
+except:
+    HAS_INTERNET = False
+else:
+    HAS_INTERNET = True
+
+def assert_url(url):
+    if not HAS_INTERNET:
+        pytest.skip("Internet connection seems faulty")
+
+    # TODO: On a 404 this will raise a urllib.error.HTTPError. It would be
+    # nice to give some better output to the user here.
+    resp = urllib.request.urlopen(url)
+    assert resp.status == 200
+

paths_cli/tests/wizard/test_core.py

@@ -10,26 +10,6 @@
     make_mock_wizard, make_mock_retry_wizard
 )
 
-# def test_name():
-    # wizard = make_mock_wizard('foo')
-    # cv = CoordinateFunctionCV(lambda s: s.xyz[0][0])
-    # assert not cv.is_named
-    # result = name(wizard, cv, obj_type="CV", store_name="cvs")
-    # assert result is cv
-    # assert result.is_named
-    # assert result.name == 'foo'
-
-# def test_name_exists():
-    # wizard = make_mock_retry_wizard(['foo', 'bar'])
-    # wizard.cvs['foo'] = 'placeholder'
-    # cv = CoordinateFunctionCV(lambda s: s.xyz[0][0])
-    # assert not cv.is_named
-    # result = name(wizard, cv, obj_type="CV", store_name="cvs")
-    # assert result is cv
-    # assert result.is_named
-    # assert result.name == 'bar'
-    # assert wizard.console.input.call_count == 2
-
 @pytest.mark.parametrize('req,expected', [
     (('foo', 2, 2), '2'), (('foo', 2, float('inf')), 'at least 2'),
     (('foo', 0, 2), 'at most 2'),

paths_cli/tests/wizard/test_openmm.py

@@ -2,11 +2,14 @@
 from unittest import mock
 
 from paths_cli.tests.wizard.mock_wizard import mock_wizard
+from paths_cli.tests.utils import assert_url
 
 from paths_cli.wizard.openmm import (
-    _load_openmm_xml, _load_topology, openmm
+    _load_openmm_xml, _load_topology, openmm, OPENMM_SERIALIZATION_URL
 )
 
+def test_helper_url():
+    assert_url(OPENMM_SERIALIZATION_URL)
 
 @pytest.mark.parametrize('obj_type', ['system', 'integrator', 'foo'])
 def test_load_openmm_xml(ad_openmm, obj_type):

paths_cli/tests/wizard/test_tools.py

@@ -12,7 +12,7 @@ def test_a_an(word, expected):
 
 @pytest.mark.parametrize('user_inp,expected', [
     ('y', True), ('n', False),
-    # ('Y', True), ('N', False), ('yes', True), ('no', False)
+    ('Y', True), ('N', False), ('yes', True), ('no', False)
 ])
 def test_yes_no(user_inp, expected):
     assert yes_no(user_inp) == expected

paths_cli/wizard/cvs.py

@@ -78,12 +78,12 @@ def _mdtraj_function_cv(wizard, cv_does_str, cv_user_prompt, func,
     indices = _get_atom_indices(wizard, topology, n_atoms=n_atoms,
                                 cv_user_str=cv_user_prompt)
     kwargs = {kwarg_name: indices}
+    atoms_str = " ".join([str(topology.mdtraj.atom(i)) for i in indices[0]])
 
     summary = ("Here's what we'll create:\n"
                f"  Function: {func.__name__}\n"
-               f"     Atoms: {" ".join([str(topology.mdtraj.atom(i))
-                                        for i in indices[0]])} \n"
-               f"  Topology: {repr(topology.mdtraj))}"
+               f"     Atoms: {atoms_str}\n"
+               f"  Topology: {repr(topology.mdtraj)}")
     wizard.say(summary)
 
     return MDTrajFunctionCV(func, topology, period_min=period_min,

paths_cli/wizard/load_from_ops.py

@@ -9,7 +9,7 @@ def list_items(wizard, user_input):
         store = getattr(storage, store_name)
         names = [obj for obj in store if obj.is_named]
         outstr = "\n".join(['* ' + obj.name for obj in names])
-        wizard.say(f"Here's what I found:\n\n{outstr})
+        wizard.say(f"Here's what I found:\n\n{outstr}")
 
     return list_items
 

paths_cli/wizard/openmm.py

@@ -8,13 +8,15 @@
 else:
     HAS_OPENMM = True
 
+OPENMM_SERIALIZATION_URL=(
+    "http://docs.openmm.org/latest/api-python/generated/"
+    "simtk.openmm.openmm.XmlSerializer.html"
+)
 
 def _openmm_serialization_helper(wizard, user_input):  # no-cov
     wizard.say("You can write OpenMM objects like systems and integrators "
                "to XML files using the XMLSerializer class. Learn more "
-               "here: \n"
-               "http://docs.openmm.org/latest/api-python/generated/"
-               "simtk.openmm.openmm.XmlSerializer.html")
+               f"here: \n{OPENMM_SERIALIZATION_URL}")
 
 
 @get_object

paths_cli/wizard/tools.py

@@ -2,4 +2,4 @@ def a_an(obj):
     return "an" if obj[0].lower() in "aeiou" else "a"
 
 def yes_no(char):
-    return {'y': True, 'n': False}[char]
+    return {'yes': True, 'no': False, 'y': True, 'n': False}[char.lower()]