From feb8207ffc3e7582f80ba35de5a375f6c5f1f39a Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Thu, 7 Jul 2016 15:36:51 +0100
Subject: [PATCH] Better error messages if MDTraj can't find Scipy
---
.gitignore | 1 +
pycgtool/frame.py | 21 +++++++++++++++++----
pycgtool/interface.py | 10 ++++++++++
test/test_frame.py | 6 +++---
test/test_pycgtool.py | 2 +-
5 files changed, 32 insertions(+), 8 deletions(-)
diff --git a/.gitignore b/.gitignore
index 49b0a71..a721a33 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@
/*.itp
/fftest.ff
/env
+/minenv
.coverage
/cover
/tmp
diff --git a/pycgtool/frame.py b/pycgtool/frame.py
index ab2742b..a7f7c97 100644
--- a/pycgtool/frame.py
+++ b/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
diff --git a/pycgtool/interface.py b/pycgtool/interface.py
index 6e3ccaa..e878d02 100644
--- a/pycgtool/interface.py
+++ b/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
diff --git a/test/test_frame.py b/test/test_frame.py
index 604e88f..59942f1 100644
--- a/test/test_frame.py
+++ b/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")
diff --git a/test/test_pycgtool.py b/test/test_pycgtool.py
index 42c36c7..f71f8ac 100644
--- a/test/test_pycgtool.py
+++ b/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)
--
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