file setup for TestINIT_TRAJ

Author: dwhswenson

paths_cli/commands/contents.py

@@ -65,3 +65,4 @@ def get_section_string_nameable(section, store, get_named):
 
 CLI = nclist
 SECTION = "Miscellaneous"
+REQUIRES_OPS = (1, 0)

paths_cli/commands/strip_snapshots.py

@@ -73,3 +73,4 @@ def strip_snapshots_main(input_storage, output_storage, cvs, blocksize):
 
 CLI = strip_snapshots
 SECTION = "Miscellaneous"
+REQUIRES_OPS = (1, 0)

paths_cli/parameters.py

@@ -64,7 +64,8 @@ def get(self, storage, name):
         result = None
         # if the we can get by name/number, do it
         if name is not None:
-            result =  store[name]
+            # note: new storage may do a try/except here
+            result = store[name]
 
             if result is None:
                 try:
@@ -95,6 +96,24 @@ def get(self, storage, name):
 
         return result
 
+def init_traj_fallback(parameter, storage, name):
+    result = None
+    if name and os.path.isfile(name):
+        # TODO: read from file
+        pass
+
+    if name is None:
+        # fallback to final_conditions, initial_conditions, only trajectory
+        # the "get" here may need to be changed for new storage
+        for tag in ['final_conditions', 'initial_conditions']:
+            result = storage.tags[tag]
+            if result:
+                return [result]
+
+        if len(storage.samplesets) == 1:
+            return [s.trajectory for s in storage.samplesets[0]]
+
+
 ENGINE = OPSStorageLoadSingle(
     param=Option('-e', '--engine', help="identifer for the engine"),
     store='engines',
@@ -112,7 +131,7 @@ def get(self, storage, name):
                  help="identifier for initial trajectory"),
     store='tags',
     num_store='trajectories',
-    fallback=None  # for now
+    fallback=init_traj_fallback
 )
 
 CVS = OPSStorageLoadNames(

paths_cli/tests/test_parameters.py

@@ -3,6 +3,7 @@
 import os
 
 import openpathsampling as paths
+from openpathsampling.tests.test_helpers import make_1d_traj
 
 from paths_cli.parameters import *
 
@@ -98,6 +99,7 @@ def teardown(self):
             os.remove(os.path.join(self.tempdir, temp_f))
         os.rmdir(self.tempdir)
 
+
 class TestENGINE(ParamInstanceTest):
     PARAMETER = ENGINE
     def setup(self):
@@ -126,16 +128,72 @@ def test_get(self, getter):
         self._getter_test(getter)
 
 
-class TestINIT_TRAJ(object):
+class TestINIT_TRAJ(ParamInstanceTest):
+    PARAMETER = INIT_TRAJ
     def setup(self):
-        pytest.skip()
-        pass
+        super(TestINIT_TRAJ, self).setup()
+        self.traj = make_1d_traj([-0.1, 1.0, 4.4, 7.7, 10.01])
+        ensemble = self.scheme.network.sampling_ensembles[0]
+        self.sample_set = paths.SampleSet([
+            paths.Sample(trajectory=self.traj,
+                         replica=0,
+                         ensemble=ensemble)
+        ])
+        self.other_traj = make_1d_traj([-1.0, 1.0, 100.0])
+        self.other_sample_set = paths.SampleSet([
+            paths.Sample(trajectory=self.other_traj,
+                         replica=0,
+                         ensemble=ensemble)
+        ])
+
+    @staticmethod
+    def _parse_getter(getter):
+        split_up = getter.split('-')
+        get_type = split_up[-1]
+        getter_style = "-".join(split_up[:-1])
+        return get_type, getter_style
 
-    @pytest.mark.parametrize("getter", ['name', 'number', 'tag-final',
-                                        'tag-initial', 'file'])
+    def create_file(self, getter):
+        filename = self._filename(getter)
+        storage = paths.Storage(filename, 'w')
+        storage.save(self.traj)
+        storage.save(self.other_traj)
+        get_type, getter_style = self._parse_getter(getter)
+        main, other = {
+            'traj': (self.traj, self.other_traj),
+            'sset': (self.sample_set, self.other_sample_set)
+        }[get_type]
+        if get_type == 'sset':
+            storage.save(self.sample_set)
+            storage.save(self.other_sample_set)
+
+        tag, other_tag = {
+            'name': ('traj', None),
+            'number': (None, None),
+            'tag-final': ('final_conditions', 'initial_conditions'),
+            'tag-initial': ('initial_conditions', None)
+        }[getter_style]
+        if tag:
+            storage.tags[tag] = main
+
+        if other_tag:
+            storage.tags[other_tag] = other
+        storage.close()
+        return filename
+
+    @pytest.mark.parametrize("getter", [
+        'name-traj', 'number-traj', 'tag-final-traj', 'tag-initial-traj',
+        'name-sset', 'number-sset', 'tag-final-sset', 'tag-initial-sset'
+    ])
     def test_get(self, getter):
+        filename = self.create_file(getter)
+        pytest.skip()
         pass
 
+    def test_get_file(self):
+        pytest.skip()
+
+
 class TestCVS(ParamInstanceTest):
     PARAMETER = CVS
     def setup(self):
@@ -147,12 +205,20 @@ def setup(self):
     def test_get(self, getter):
         self._getter_test(getter)
 
-class TestSTATES(object):
+
+class TestSTATES(ParamInstanceTest):
     PARAMETER = STATES
     def setup(self):
-        pytest.skip()
-        pass
+        super(TestSTATES, self).setup()
+        self.get_arg = {'name': "A", 'number': 0}
+        self.obj = self.state_A
 
     @pytest.mark.parametrize("getter", ['name', 'number'])
     def test_get(self, getter):
-        pass
+        self._getter_test(getter)
+
+    @pytest.mark.parametrize("getter", ['name', 'number'])
+    def test_get_other(self, getter):
+        self.get_arg = {'name': 'B', 'number': 1}
+        self.obj = self.state_B
+        self._getter_test(getter)