Added run testing

chi_pet/chi_run.py

@@ -12,51 +12,57 @@
 '''
 
 
+def run_args(workdir, state, args):
+    current_dir = Path.cwd()
+    try:
+        action = state + '-ing'
+        action_file = Path('.' + action)
+        print("Started {} sim using args {}".format(action, args))
+        sys.stdout.flush()
+        if workdir.exists():
+            os.chdir(workdir)
+            action_file.touch()  # Keeps track of current pipeline state
+            status = run(args)
+            if status.returncode:
+                print(f"Run failed: State {state} did not succeed.")
+            action_file.unlink()  # Remove once completed successfully
+            return status.returncode
+        else:
+            print(
+                f"Run failed: could not find work directory {workdir} to do action {state}.")
+            return 1
+    except:
+        print(f"Run failed: State {state} did not succeed.")
+        return 1
+    finally:
+        os.chdir(current_dir)
+
+
 class ChiRun(object):
     def __init__(self, opts):
         self._opts = opts
-        self._arg_dict = opts.args_dict
+        self._args_dict = opts.args_dict
         self._states = opts.states
 
     def run(self):
         """Run simulation pipeline defined in the the args.yaml file defined as self._opts.args_file.
 
         """
 
-        # TODO Add option to see if sim_action file exists and only run those states.
         for run_state, vals in self._args_dict.items():
             args = [str(a) for a in vals]
             sim_state = Path('sim.{}'.format(run_state))
 
             # If sim action file exists then run the state
             if run_state in self._states:
-                if self.run_args(self._workdir, run_state, args):
+                if run_args(self._opts.workdir, run_state, args):
                     (self._opts.workdir / '.error').touch()
                 elif sim_state.exists():
                     sim_state.unlink()
 
     def get_run_states(self):
         return self._states
 
-    @classmethod
-    def run_args(workdir, state, args):
-        action = state + '-ing'
-        action_file = Path('.' + action)
-        print("Started {} sim using args {}".format(action, args))
-        sys.stdout.flush()
-        if workdir.exists():
-            os.chdir(workdir)
-            action_file.touch()  # Keeps track of current pipeline state
-            status = run(args)
-            if status.returncode:
-                print(f"Run failed: State {state} did not succeed.")
-            action_file.unlink()  # Remove once completed successfully
-            return status.returncode
-        else:
-            print(
-                f"Run failed: could not find work directory {workdir} to do action {state}.")
-            return 1
-
 
 if __name__ == '__main__':
     opts = parse_chi_options()

tests/mhelpers.py

@@ -23,7 +23,8 @@
 MOCK_ARGS_FILE_DICT = {'stage1': ['arg1', 'arg2', 'arg3'],
                        'stage2': ['arg4', 'arg5', 'arg6']}
 
-MOCK_SHELL_ARGS_FILE_DICT = {'touch': ['touch', 'mock_command.txt']}
+MOCK_SHELL_ARGS_FILE_DICT = {'touch1': ['touch', 'mock_output1.txt'],
+                             'touch2': ['touch', 'mock_output2.txt'], }
 
 MOCK_PARAM_DICT_PATH = 'mock_param.yaml'
 MOCK_CHI_PARAM_DICT_PATH = 'mock_param_chi_param.yaml'
@@ -33,7 +34,7 @@ def clean_mocks():
     """Clean up mock directories and files before testing to make sure we are
     working from a clean slate.
     """
-    for mpath in Path('.').glob('tests/mock*'):
+    for mpath in Path.cwd().glob('tests/mock*'):
         if mpath.is_file():
             mpath.unlink()
         elif mpath.is_dir():
@@ -90,11 +91,6 @@ def mock_leaf_dir():
     with yaml_param_path.open('w') as ypp:
         yaml.dump(MOCK_PARAM_DICT, ypp)
 
-    args_file_path = chi_leaf_path / 'mock_args.yaml'
-    with args_file_path.open('w') as aff:
-        yaml.dump(MOCK_ARGS_FILE_DICT, aff)
-    yield args_file_path
-
     yield chi_leaf_path
 
 
@@ -134,8 +130,6 @@ def mock_run_opts():
     def opts(x): return None
     opts.command = 'run'
     opts.use_sim_states = 'False'
-    opts.replace = 'False'
-    opts.non_yaml = []
     opts.args_dict = MOCK_ARGS_FILE_DICT
     opts.states = list(opts.args_dict.keys())
     yield opts

tests/test_chi_run.py

@@ -15,14 +15,39 @@ def test_chi_run_states(mock_run_opts):
     assert crun.get_run_states() == mock_run_opts.states
 
 
-def test_chi_run_with_touch(mock_run_opts):
+def test_chi_run_touch(mock_leaf_dir, mock_run_opts):
     """Test chi_run."""
+    mock_leaf_path = mock_leaf_dir
+    # Create and modify run optoins
+    mock_run_opts.args_dict = MOCK_SHELL_ARGS_FILE_DICT
+    mock_run_opts.states = mock_run_opts.args_dict.keys()
+    mock_run_opts.workdir = mock_leaf_path
+
     # Make a ChiRun object
     crun = ChiRun(mock_run_opts)
+    # Run the pipeline
+    crun.run()
+
+    # Make sure action is carried out
+    assert (mock_leaf_path / 'mock_output1.txt').exists()
+    assert (mock_leaf_path / 'mock_output2.txt').exists()
 
-    assert crun.get_run_states() == mock_run_opts.states
 
+def test_chi_run_only_one_touch(mock_leaf_dir, mock_run_opts):
+    """Test chi_run."""
+    mock_leaf_path = mock_leaf_dir
+    # Create and modify run optoins
+    mock_run_opts.args_dict = MOCK_SHELL_ARGS_FILE_DICT
+    mock_run_opts.states = ['touch1']
+    mock_run_opts.workdir = mock_leaf_path
+
+    # Make a ChiRun object
+    crun = ChiRun(mock_run_opts)
     # Run the pipeline
+    crun.run()
+
     # Make sure action is carried out
+    assert (mock_leaf_path / 'mock_output1.txt').exists()
+    assert not (mock_leaf_path / 'mock_output2.txt').exists()
 
-# TODO NEXT TEST add tests for chi_run.py
+# TODO NEXT TEST test run args to make sure it always returns you to the right directory