Merge pull request #219 from prabhuramachandran/fix-misc-bugs

Fix many miscellaneous bugs

pysph/solver/application.py

@@ -173,13 +173,15 @@ def create_scheme(self):
 
     """
 
-    def __init__(self, fname=None, domain=None):
+    def __init__(self, fname=None, output_dir=None, domain=None):
         """ Constructor
 
         Parameters
         ----------
         fname : str
             file name to use for the output files.
+        output_dir : str
+            output directory name.
         domain : pysph.base.nnps_base.DomainManager
             A domain manager to use. This is used for periodic domains etc.
         """
@@ -218,11 +220,14 @@ def __init__(self, fname=None, domain=None):
             'none': None
         }
 
-        self.output_dir = abspath(self._get_output_dir_from_fname())
+        if output_dir is None:
+            self.output_dir = abspath(self._get_output_dir_from_fname())
+        else:
+            self.output_dir = output_dir
         self.particles = []
         self.inlet_outlet = []
         # The default value that is overridden by the command line
-        # options passed or in initializee.
+        # options passed or in initialize.
         self.cache_nnps = False
         self.iom = None
 
@@ -419,7 +424,7 @@ def _setup_argparse(self):
             "--directory",
             action="store",
             dest="output_dir",
-            default=self._get_output_dir_from_fname(),
+            default=self.output_dir,
             help="Dump output in the specified directory.")
 
         # --openmp
@@ -791,11 +796,20 @@ def _parse_command_line(self, force=False):
 
         self.options = options
 
+    def _process_command_line(self):
+        """Process the parsed command line arguments.
+
+        This method calls the scheme's ``consume_user_options`` and
+        :py:meth:`consume_user_options` as well as the
+        :py:meth:`configure_scheme`.
+
+        """
+        options = self.options
         # save the path where we want to dump output
         self.output_dir = abspath(options.output_dir)
         mkdir(self.output_dir)
         if self.scheme is not None:
-            self.scheme.consume_user_options(self.options)
+            self.scheme.consume_user_options(options)
         self.consume_user_options()
         if self.scheme is not None:
             self.configure_scheme()
@@ -824,6 +838,7 @@ def _setup_logging(self):
             for handler in logging.root.handlers[:]:
                 logging.root.removeHandler(handler)
             lfn = os.path.join(self.output_dir, filename)
+            mkdir(self.output_dir)
             format = '%(levelname)s|%(asctime)s|%(name)s|%(message)s'
             logging.basicConfig(
                 level=level, format=format, filename=lfn, filemode='a')
@@ -1451,7 +1466,12 @@ def read_info(self, fname_or_dir):
         info_dir = dirname(fname_or_dir)
         with open(fname_or_dir, 'r') as f:
             info = json.load(f)
+
+        self.args = info.get('args', self.args)
+        self._parse_command_line(force=True)
+
         self.fname = info.get('fname', self.fname)
+
         output_dir = info.get('output_dir', self.output_dir)
         if realpath(info_dir) != realpath(output_dir):
             # Happens if someone moved the directory!
@@ -1460,8 +1480,11 @@ def read_info(self, fname_or_dir):
         else:
             self.output_dir = output_dir
 
-        self.args = info.get('args', self.args)
-        self._parse_command_line(force=True)
+        # Set the output directory of the options so it is corrected as per the
+        # info file.
+        self.options.output_dir = self.output_dir
+        self._process_command_line()
+
         return info
 
     def run(self, argv=None):
@@ -1474,6 +1497,7 @@ def run(self, argv=None):
             start_time = time.time()
 
             self._parse_command_line(force=argv is not None)
+            self._process_command_line()
             self._setup_logging()
             self._configure_global_config()
 
@@ -1574,6 +1598,7 @@ def setup(self, solver, equations, nnps=None, inlet_outlet_factory=None,
         self.equations = equations
         solver.get_options(self.arg_parse)
         self._parse_command_line()
+        self._process_command_line()
         self._setup_logging()
         self._configure_global_config()
 

pysph/solver/tests/test_application.py

@@ -11,6 +11,11 @@
 except ImportError:
     import mock
 
+import os
+import shutil
+import sys
+from tempfile import mkdtemp
+
 from pysph.solver.application import Application
 from pysph.solver.solver import Solver
 
@@ -54,10 +59,22 @@ def create_nnps(self):
 
 class TestApplication(TestCase):
 
-    # Test When testarg is  notpassed
-    def test_user_options_false(self):
+    def setUp(self):
+        self.output_dir = mkdtemp()
+        self.app = MockApp(output_dir=self.output_dir)
+
+    def tearDown(self):
+        if sys.platform.startswith('win'):
+            try:
+                shutil.rmtree(self.output_dir)
+            except WindowsError:
+                pass
+        else:
+            shutil.rmtree(self.output_dir)
+
+    def test_user_options_when_args_are_not_passed(self):
         # Given
-        app = MockApp()
+        app = self.app
 
         # When
         args = []
@@ -69,10 +86,9 @@ def test_user_options_false(self):
         error_message = "Expected %f, got %f" % (expected, app.testarg)
         self.assertEqual(expected, app.testarg, error_message)
 
-    # Test When testarg is passed
-    def test_user_options_true(self):
+    def test_user_options_when_args_are_passed(self):
         # Given
-        app = MockApp()
+        app = self.app
 
         # When
         args = ['--testarg', '20']
@@ -82,3 +98,26 @@ def test_user_options_true(self):
         expected = 20.0
         error_message = "Expected %f, got %f" % (expected, app.testarg)
         self.assertEqual(expected, app.testarg, error_message)
+
+    def test_output_dir_when_moved_and_read_info_called(self):
+        # Given
+        app = self.app
+
+        args = ['-d', app.output_dir]
+        app.run(args)
+
+        copy_root = mkdtemp()
+        copy_dir = os.path.join(copy_root, 'new')
+        shutil.copytree(app.output_dir, copy_dir)
+        self.addCleanup(shutil.rmtree, copy_root)
+        orig_fname = app.fname
+
+        # When
+        app = MockApp()
+        app.read_info(copy_dir)
+
+        # Then
+        realpath = os.path.realpath
+        assert realpath(app.output_dir) != realpath(self.output_dir)
+        assert realpath(app.output_dir) == realpath(copy_dir)
+        assert app.fname == orig_fname

pysph/tools/mayavi_viewer.py

@@ -229,9 +229,9 @@ def _update_plot(self):
                     plot = mlab.pipeline.surface(src, colormap='viridis')
                 self.plot = plot
                 scm = plot.module_manager.scalar_lut_manager
-                scm.set(show_legend=self.show_legend,
-                        use_default_name=False,
-                        data_name=self.scalar)
+                scm.trait_set(show_legend=self.show_legend,
+                              use_default_name=False,
+                              data_name=self.scalar)
                 self.sync_trait('show_legend', scm, mutual=True)
             else:
                 self.plot.visible = True
@@ -467,9 +467,9 @@ def _particle_array_changed(self, old, pa):
             )
             p.actor.property.point_size = 6
             scm = p.module_manager.scalar_lut_manager
-            scm.set(show_legend=self.show_legend,
-                    use_default_name=False,
-                    data_name=self.scalar)
+            scm.trait_set(show_legend=self.show_legend,
+                          use_default_name=False,
+                          data_name=self.scalar)
             self.sync_trait('visible', p, mutual=True)
             self.sync_trait('show_legend', scm, mutual=True)
             self.sync_trait('point_size', p.actor.property, mutual=True)
@@ -508,6 +508,7 @@ def _range_changed(self, value):
         scm = self.plot.module_manager.scalar_lut_manager
         try:
             rng = eval(value)
+            len(rng)
         except Exception:
             rng = None
 
@@ -566,36 +567,37 @@ def _show_time_changed(self, value):
                 txt.visible = False
 
     def _get_vectors_for_plot(self, vectors):
-        comps = [x.strip() for x in vectors.split(',')]
+        comps = vectors.split(',')
         namespace = self._eval_ns
         if len(comps) == 3:
             try:
-                vec = [eval(c, namespace) for c in comps]
+                vec = eval(vectors, namespace)
             except Exception:
                 return None
             else:
                 return vec
 
+    def _set_vector_plot_data(self, vectors):
+        vec = self._get_vectors_for_plot(vectors)
+        if vec is not None:
+            self.plot.mlab_source.vectors = numpy.column_stack(vec)
+
     def _vectors_changed(self, value):
         if self.plot_vectors is None:
             return
-        vec = self._get_vectors_for_plot(value)
-        if vec is not None:
-            self.plot.mlab_source.set(
-                vectors=numpy.c_[vec[0], vec[1], vec[2]]
-            )
+        self._set_vector_plot_data(value)
 
     def _show_vectors_changed(self, value):
         pv = self.plot_vectors
         if pv is not None:
             pv.visible = value
         elif self.plot is not None and value:
-            self._vectors_changed(self.vectors)
+            self._set_vector_plot_data(self.vectors)
             pv = self.scene.mlab.pipeline.vectors(
                 self.plot.mlab_source.m_data,
                 mask_points=self.mask_on_ratio,
                 scale_factor=self.scale_factor,
-                colormap='viridis'
+                colormap='viridis', reset_zoom=False
             )
             self.plot_vectors = pv
 
@@ -851,7 +853,7 @@ def update_plot(self):
                 pa = controller.get_named_particle_array(name)
                 arrays.append(pa)
                 pah = self.particle_arrays[idx]
-                pah.set(particle_array=pa, time=t)
+                pah.trait_set(particle_array=pa, time=t)
 
             self.interpolator.particle_arrays = arrays
 
@@ -984,7 +986,9 @@ def _client_changed(self, old, new):
         else:
             # Turn on the legend for the first particle array.
             if len(self.particle_arrays) > 0:
-                self.particle_arrays[0].set(show_legend=True, show_time=True)
+                self.particle_arrays[0].trait_set(
+                    show_legend=True, show_time=True
+                )
 
     def _timer_event(self):
         # catch all Exceptions else timer will stop
@@ -1021,11 +1025,12 @@ def _record_changed(self, value):
 
     def _files_changed(self, value):
         if len(value) == 0:
+            self._n_files = 0
             return
         else:
             d = os.path.dirname(os.path.abspath(value[0]))
             self.movie_directory = os.path.join(d, 'movie')
-            self.set(directory=d, trait_change_notify=False)
+            self.trait_set(directory=d, trait_change_notify=False)
         self._n_files = len(value) - 1
         self._frame_count = 0
         self._count = 0
@@ -1047,8 +1052,14 @@ def _files_changed(self, value):
     def _file_count_changed(self, value):
         # Save out any updates for the previous file if needed.
         self._handle_particle_array_updates()
+        if not self.files:
+            return
         # Load the new file.
+        value = min(value, len(self.files))
         fname = self.files[value]
+        if not os.path.exists(fname):
+            print("File %s is missing, ignoring!" % fname)
+            return
         self._file_name = fname
         self.current_file = os.path.basename(fname)
         # Code to read the file, create particle array and setup the helper.
@@ -1070,14 +1081,14 @@ def _file_count_changed(self, value):
                 pa = arrays[name]
                 pah = self._make_particle_array_helper(self.scene, name)
                 # Must set this after setting the scene.
-                pah.set(particle_array=pa, time=t)
+                pah.trait_set(particle_array=pa, time=t)
                 pas.append(pah)
             self.particle_arrays = pas
         else:
             for idx, name in enumerate(pa_names):
                 pa = arrays[name]
                 pah = self.particle_arrays[idx]
-                pah.set(particle_array=pa, time=t)
+                pah.trait_set(particle_array=pa, time=t)
 
         self.interpolator.particle_arrays = list(arrays.values())
 
@@ -1125,12 +1136,17 @@ def _scalar_changed(self, value):
 
     def _update_files_fired(self):
         fc = self.file_count
-        files = glob_files(self.files[fc])
+        if len(self.files) == 0:
+            files = get_files_in_dir(self.directory)
+        else:
+            files = glob_files(self.files[fc])
         sort_file_list(files)
         self.files = files
-        self.file_count = fc
-        if self.play:
-            self._play_changed(self.play)
+        if len(files) > 0:
+            fc = min(len(files), fc)
+            self.file_count = fc
+            if self.play:
+                self._play_changed(self.play)
 
     def _shell_fired(self):
         ns = self._get_shell_namespace()
@@ -1282,6 +1298,7 @@ def main(args=None):
     kw = {}
     files = []
     scripts = []
+    directory = None
     for arg in args:
         if '=' not in arg:
             if arg.endswith('.py'):
@@ -1298,6 +1315,7 @@ def main(args=None):
                 files.extend(glob.glob(arg))
                 continue
             elif os.path.isdir(arg):
+                directory = arg
                 _files = get_files_in_dir(arg)
                 files.extend(_files)
                 config_file = os.path.join(arg, 'mayavi_config.py')
@@ -1321,7 +1339,10 @@ def main(args=None):
     # If we set the particle arrays before the scene is activated, the arrays
     # are not displayed on screen so we use do_later to set the  files.
     m = MayaviViewer(live_mode=live_mode)
-    do_later(m.set, files=files, **kw)
+    if not directory and len(files) > 0:
+        directory = os.path.dirname(files[0])
+    m.trait_set(directory=directory, trait_change_notify=False)
+    do_later(m.trait_set, files=files, **kw)
     for script in scripts:
         do_later(m.run_script, script)
     m.configure_traits()