Better error messages if MDTraj can't find Scipy

.gitignore

@@ -5,6 +5,7 @@
 /*.itp
 /fftest.ff
 /env
+/minenv
 .coverage
 /cover
 /tmp

pycgtool/frame.py

@@ -11,10 +11,23 @@ import numpy as np
 
 from simpletraj import trajectory
 
+
+class MDTrajState:
+    # __slots__ = ["found", "missing_scipy", "not_found"]
+    _default = "XTC output requires both MDTraj and Scipy - "
+    found = _default + "both are present"
+    missing_scipy = _default + "Scipy is missing"
+    not_found = _default + "both are missing"
+
 try:
     import mdtraj
-except ImportError:
-    pass
+except ImportError as e:
+    if "no module named 'scipy'" in repr(e).lower():
+        mdtraj_state = MDTrajState.missing_scipy
+    else:
+        mdtraj_state = MDTrajState.not_found
+else:
+    mdtraj_state = MDTrajState.found
 
 
 from .util import backup_file
@@ -179,7 +192,7 @@ class Frame:
             e.args = ("Error opening file '{0}'".format(xtc),)
             raise
         except NameError as e:
-            raise ImportError("No module named 'mdtraj'") from e
+            raise ImportError(mdtraj_state) from e
 
         if self.xtc.n_atoms != self.natoms:
             raise AssertionError("Number of atoms does not match between gro and xtc files.")
@@ -281,7 +294,7 @@ class Frame:
             try:
                 self._xtc_buffer = mdtraj.formats.XTCTrajectoryFile(filename, mode="w")
             except NameError as e:
-                raise ImportError("No module named 'mdtraj'") from e
+                raise ImportError(mdtraj_state) from e
 
         xyz = np.ndarray((1, self.natoms, 3), dtype=np.float32)
         i = 0

pycgtool/interface.py

@@ -226,6 +226,16 @@ class Progress:
         self._its = 0
         self._start_time = time.clock()
 
+    def __len__(self):
+        """
+        Maximum iterator length.
+
+        This length will be reached if the iterator is not stopped by a False dowhile condition or KeyboardInterrupt.
+
+        :return: Maximum length of iterator
+        """
+        return self._maxits - self._its
+
     def __iter__(self):
         return self
 

test/test_frame.py

@@ -96,13 +96,13 @@ class FrameTest(unittest.TestCase):
         np.testing.assert_allclose(np.array([1.90325272, 1.90325272, 1.90325272]),
                                    frame.box)
 
-    @unittest.skipIf(not mdtraj_present, "MDTRAJ not present")
+    @unittest.skipIf(not mdtraj_present, "MDTRAJ or Scipy not present")
     def test_frame_read_xtc_mdtraj_numframes(self):
         frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc",
                       xtc_reader="mdtraj")
         self.assertEqual(12, frame.numframes)
 
-    @unittest.skipIf(not mdtraj_present, "MDTRAJ not present")
+    @unittest.skipIf(not mdtraj_present, "MDTRAJ or Scipy not present")
     def test_frame_read_xtc_mdtraj(self):
         frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc",
                       xtc_reader="mdtraj")
@@ -124,7 +124,7 @@ class FrameTest(unittest.TestCase):
         np.testing.assert_allclose(np.array([1.90325272, 1.90325272, 1.90325272]),
                                    frame.box)
 
-    @unittest.skipIf(not mdtraj_present, "MDTRAJ not present")
+    @unittest.skipIf(not mdtraj_present, "MDTRAJ or Scipy not present")
     def test_frame_write_xtc_mdtraj(self):
         try:
             os.remove("water_test2.xtc")

test/test_pycgtool.py

@@ -46,7 +46,7 @@ class PycgtoolTest(unittest.TestCase):
         path = os.path.dirname(os.path.dirname(__file__))
         self.assertEqual(0, subprocess.check_call([os.path.join(path, "pycgtool.py"), "-h"], stdout=subprocess.PIPE))
 
-    @unittest.skipIf(not mdtraj_present, "MDTRAJ not present")
+    @unittest.skipIf(not mdtraj_present, "MDTRAJ or Scipy not present")
     def test_map_only(self):
         map_only(Args("sugar"), self.config)