Implemented chi create functionality for command line

chi_pet/chi.py

@@ -32,8 +32,9 @@ def read_opts(self):
             self.opts.workdir = Path.cwd()
 
         if not self.opts.states and self.opts.args_file:
-            yd = clib.create_dict_from_yaml_file(self.opts.args_file)
-            self.opts.states = list(yd.keys())
+            with self.opts.args_file.open('r') as af:
+                yd = clib.load_yaml_in_order(af)
+                self.opts.states = list(yd.keys())
 
     def execute(self):
         if self.opts.command == "launch":
@@ -58,24 +59,8 @@ def execute(self):
 
         elif self.opts.command == 'create':
             # TODO NEXT implement this functionality
-            pass
-            # run_not_path.touch()
-            # # touch(os.path.join(wd, "run.not"))
-            # chi_root_node = ChiNode(self.opts)
-            # chi_root_node.Grow()
-
-            # c = ChiCreate(self.opts, self.opts.workdir)
-            # c.Create(self.opts.create)
-
-        # elif self.opts.particleswarmcreate:
-        #     pass
-        #     # c = ChiParticleSwarm(self.opts, self.opts.workdir, 0)
-        #     # c.Create(self.opts.particleswarmcreate)
-
-        # elif self.opts.geneticalgorithmcreate:
-        #     pass
-        #     # c = ChiGeneticAlgorithm(self.opts, self.opts.workdir, 0)
-        #     # c.Create(self.opts.geneticalgorithmcreate)
+            chi_root_node = ChiNode(self.opts.workdir, opts=self.opts)
+            chi_root_node.make_subnodes()
 
         elif self.opts.command == 'run':
             pass

chi_pet/chi_node.py

@@ -56,11 +56,11 @@ def __init__(self, node_path: Path,
         if chi_dict:
             self._chi_dict = chi_dict
         else:
-            if not self._opts.param_file_paths:
+            if not self._opts.param_files:
                 raise RuntimeError(
                     "If a ChiDict is not supplied, a params_file_path list must be supplied instead.")
             self._chi_dict = ChiDict(
-                file_path_list=self._opts.param_file_paths)
+                file_path_list=self._opts.param_files)
 
         self._chi_params = self._chi_dict.search_dict_for_chi_params()
         self._level = level if len(self._chi_params) == 0 else min(

chi_pet/chi_parse.py

@@ -11,8 +11,6 @@
 
 from pathlib import Path
 
-# TODO NTEST add parser test
-
 
 def parse_chi_options():
     parent_parser = argparse.ArgumentParser(add_help=False)

chi_pet/chi_run.py

@@ -55,12 +55,16 @@ def run(self, opts):
                 args_dict = load_yaml_in_order(f)
 
         print(dump_yaml_in_order(args_dict, default_flow_style=False))
-        for k, vals in args_dict.items():
+
+        # Loop through all states in args.yaml.
+        # TODO Add option to see if sim_action file exists and only run those states.
+        for run_state, vals in args_dict.items():
             args = [str(a) for a in vals]
-            sim_action = Path('sim.{}'.format(k))
+            sim_action = Path('sim.{}'.format(run_state))
 
-            if k in opts.states:
-                if self.run_args(opts.workdir, k, args):
+            # If sim action file exists then run the state
+            if run_state in opts.states:
+                if self.run_args(opts.workdir, run_state, args):
                     (opts.workdir / '.error').touch()
                 elif sim_action.exists():
                     sim_action.unlink()
@@ -86,8 +90,7 @@ def run_args(workdir, state, args):
 
 
 if __name__ == '__main__':
-
-    opts = chi_parse()
+    opts = parse_chi_options()
 
     c = ChiRun(opts)
-    c.Run(opts)
+    c.execute(opts)

tests/node_tree_example/args.yaml

@@ -0,0 +1,14 @@
+setup:
+  - init_test_prog.py
+  - --argA
+  - argA_value
+  - --argB
+  - 1
+
+run:
+  - test_prog.py
+  - --arg1
+  - arg1_value
+
+analyze:
+  - test_analyze.py

tests/test_chi_parse.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 """Tests for `chi_pet` package."""
 
-import argparse
 from pathlib import Path
 import pytest
 import sys

tests/test_chi_run.py

@@ -0,0 +1,7 @@
+# -*- coding: utf-8 -*-
+"""Tests for `chi_run` module of `chi_pet` package."""
+
+from pathlib import Path
+import pytest
+
+# TODO NTEST add tests for chi_run.py