Skip test_map_only if MDTraj is not present

Remove unimplemented prewhile condition in Progress

pycgtool/interface.py

@@ -210,23 +210,18 @@ class Progress:
     Display a progress bar during the main loop of a program.
     """
 
-    def __init__(self, maxits, length=20, prewhile=None, postwhile=None, quiet=False):
+    def __init__(self, maxits, length=20, dowhile=None, quiet=False):
         """
         Return progress bar instance to handle printing of a progress bar within loops.
 
         :param maxits: Expected number of iterations
         :param length: Length of progress bar in characters
-        :param prewhile: Function to check before each iteration, stops if False
-        :param postwhile: Function to check after each iteration, stops if False
+        :param dowhile: Function to call after each iteration, stops if False
         :param quiet: Skip printing of progress bar - for testing
         """
-        if prewhile is not None:
-            raise NotImplementedError("Prewhile conditions are not yet implemented")
-
         self._maxits = maxits
         self._length = length
-        self._prewhile = prewhile
-        self._postwhile = postwhile
+        self._dowhile = dowhile
         self._quiet = quiet
         self._its = 0
         self._start_time = time.clock()
@@ -236,14 +231,14 @@ class Progress:
 
     def __next__(self):
         """
-        Allow iteration over Progress while testing prewhile and postwhile conditions.
+        Allow iteration over Progress while testing dowhile condition.
 
         Will catch Ctrl-C and return control as if the iterator has been fully consumed.
 
         :return: Iteration number
         """
         try:
-            if self._postwhile is not None and self._its > 0 and not self._postwhile():
+            if self._dowhile is not None and self._its > 0 and not self._dowhile():
                 self._stop()
 
         except KeyboardInterrupt:
@@ -263,9 +258,7 @@ class Progress:
         """
         Iterate through self until stopped by maximum iterations or False condition.
         """
-        # collections.deque(self, maxlen=0)
-        for _ in self:
-            pass
+        collections.deque(self, maxlen=0)
         return self._its
 
     @property

pycgtool/pycgtool.py

@@ -51,7 +51,7 @@ def main(args, config):
 
     numframes = frame.numframes - args.begin if args.end == -1 else args.end - args.begin
     logger.info("Beginning analysis of {0} frames".format(numframes))
-    Progress(numframes, postwhile=main_loop, quiet=args.quiet).run()
+    Progress(numframes, dowhile=main_loop, quiet=args.quiet).run()
 
     if args.bnd:
         if args.map:
@@ -94,5 +94,5 @@ def map_only(args, config):
 
         numframes = frame.numframes - args.begin if args.end == -1 else args.end - args.begin
         logger.info("Beginning analysis of {0} frames".format(numframes))
-        Progress(numframes, postwhile=main_loop, quiet=args.quiet).run()
+        Progress(numframes, dowhile=main_loop, quiet=args.quiet).run()
 

test/test_interface.py

@@ -10,16 +10,9 @@ class UtilTest(unittest.TestCase):
             sum += i
         self.assertEqual(45, sum)
 
-    @unittest.expectedFailure
-    def test_progress_prewhile(self):
-        sum = 0
-        for i in Progress(20, prewhile=lambda: sum < 20, quiet=True):
-           sum += i
-        self.assertEqual(15, sum)
-
     def test_progress_postwhile(self):
         sum = 0
-        for i in Progress(20, postwhile=lambda: sum < 20, quiet=True):
+        for i in Progress(20, dowhile=lambda: sum < 20, quiet=True):
             sum += i
         self.assertEqual(21, sum)
 

test/test_pycgtool.py

@@ -6,6 +6,12 @@ import numpy as np
 
 from simpletraj.trajectory import XtcTrajectory
 
+try:
+    import mdtraj
+    mdtraj_present = True
+except ImportError:
+    mdtraj_present = False
+
 from pycgtool.interface import Options
 from pycgtool.pycgtool import main, map_only
 
@@ -40,6 +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")
     def test_map_only(self):
         map_only(Args("sugar"), self.config)