Fix stochastic test failures

moldesign/__main__.py

@@ -68,6 +68,11 @@
                               'end if')
 CONFIG_PATH = os.path.join(CONFIG_DIR, 'moldesign.yml')
 
+NO_NBMOLVIZ_ERR = 10
+JUPYTER_ERR = 128
+NO_EXAMPLE_OVERWRITE_ERR = 200
+OUTDATED_EXAMPLES_ERR = 201
+
 
 def main():
     print('Molecular Design Toolkit v%s Launcher' % MDTVERSION)
@@ -96,11 +101,13 @@ def main():
         CONFIG_PATH = args.config_file
 
     if args.command == 'intro':
+        nbmolviz_check()
         copy_example_dir(use_existing=True)
         launch(cwd=EXAMPLE_DIR_TARGET,
                path='notebooks/Getting%20Started.ipynb')
 
     elif args.command == 'launch':
+        nbmolviz_check()
         launch()
 
     elif args.command == 'copyexamples':
@@ -124,6 +131,15 @@ def main():
         raise ValueError("Unhandled CLI command '%s'" % args.command)
 
 
+def nbmolviz_check():
+    # Checks for the existence of nbmolviz before attempting to launch a notebook
+    from . import widgets
+    if not widgets.nbmolviz_installed:
+        print('ERROR: nbmolviz not found - notebooks not available. Install it by running\n'
+              ' $ pip install nbmolviz`')
+        sys.exit(NO_NBMOLVIZ_ERR)
+
+
 def launch(cwd=None, path=''):
     server, portnum = launch_jupyter_server(cwd=cwd)
     wait_net_service('localhost', portnum, server)
@@ -154,7 +170,7 @@ def check_existing_examples(use_existing):
               '%s, but you are using version %s'%(version, MDTVERSION))
         print('To update your examples, please rename or remove "%s"'
               % EXAMPLE_DIR_TARGET)
-        sys.exit(201)
+        sys.exit(OUTDATED_EXAMPLES_ERR)
 
     if use_existing:
         return
@@ -164,7 +180,7 @@ def check_existing_examples(use_existing):
                  ' 1) Rename or remove the existing directory at %s,'%EXAMPLE_DIR_TARGET,
                  ' 2) Run this command in a different location, or'
                  ' 3) Run `python -m moldesign intro` to launch the example gallery.']))
-        sys.exit(200)
+        sys.exit(NO_EXAMPLE_OVERWRITE_ERR)
 
 
 def launch_jupyter_server(cwd=None):  # pragma: no cover
@@ -238,7 +254,7 @@ def wait_net_service(server, port, process, timeout=None):  # pragma: no cover
     while True:
         if process.poll() is not None:
             print('ERROR: Jupyter process exited prematurely')
-            sys.exit(128)
+            sys.exit(JUPYTER_ERR)
 
         s = socket.socket()
         s.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)

moldesign/_tests/test_wfn.py

@@ -60,7 +60,7 @@ def test_basis_function_3d_grids_same_in_pyscf_and_mdt(molkey, request):
     pyscf_vals = basis_values(mol, mol.wfn.aobasis, randocoords)
     with np.errstate(under='ignore'):
         mdt_vals = mol.wfn.aobasis(randocoords)
-    helpers.assert_almost_equal(mdt_vals, pyscf_vals, decimal=6)
+    helpers.assert_almost_equal(mdt_vals, pyscf_vals, decimal=5)
 
 
 @pytest.mark.parametrize('molkey', ['h2_rhf_augccpvdz', 'h2_rhf_sto3g'])

moldesign/fileio.py

@@ -116,7 +116,8 @@ def read(f, format=None):
     if filename is not None and mol.name not in (None, 'untitled'):
         mol.name = filename
 
-    mdt.helpers.atom_name_check(mol)
+    if isinstance(mol, mdt.Molecule):
+        mdt.helpers.atom_name_check(mol)
     return mol