updating example

README.md

@@ -17,10 +17,9 @@ pip install continuation-jax
 
 ```python
 import cjax
-help(cjax)
 ```
 
-#### Simple Math on Pytrees
+#### Math operations on Pytrees
 ```python
 >>> import cjax
 >>> from cjax.utils import math_trees
@@ -35,52 +34,78 @@ help(cjax)
 
 #### Examples:
 - Examples: https://github.com/harsh306/continuation-jax/tree/main/examples
-- Sample Runner: https://github.com/harsh306/continuation-jax/blob/main/run.py
+- Sample Runner: https://github.com/harsh306/continuation-jax/blob/main/model_simple_classifier/run.py
 
 ```python
+"""
+Main file to run contination on the user defined problem. Examples can be found in the examples/ directory.
+
+
+Continuation is topological procedure to train a neural network. This module tracks all
+the critical points or fixed points and dumps them to  output file provided in hparams.json file.
+
+  Typical usage example:
+
+  continuation = ContinuationCreator(
+            problem=problem, hparams=hparams
+        ).get_continuation_method()
+        continuation.run()
+
+
+"""
 from cjax.continuation.creator.continuation_creator import ContinuationCreator
-from examples.toy.vectror_pitchfork import SigmoidFold
+from examples.model_simple_classifier.model_classifier import ModelContClassifier
 from cjax.utils.abstract_problem import ProblemWraper
 import json
 from jax.config import config
 from datetime import datetime
-from cjax.utils.visualizer import bif_plot, pick_array
+import mlflow
+from cjax.utils.visualizer import pick_array, bif_plot
 
 config.update("jax_debug_nans", True)
 
 # TODO: use **kwargs to reduce params
 
 if __name__ == "__main__":
-    problem = SigmoidFold()
+    problem = ModelContClassifier()
     problem = ProblemWraper(problem)
 
     with open(problem.HPARAMS_PATH, "r") as hfile:
         hparams = json.load(hfile)
-    start_time = datetime.now()
-
-    if hparams["n_perturbs"] > 1:
-        for perturb in range(hparams["n_perturbs"]):
-            print(f"Running perturb {perturb}")
+    mlflow.set_tracking_uri(hparams['meta']["mlflow_uri"])
+    mlflow.set_experiment(hparams['meta']["name"])
+
+    with mlflow.start_run(run_name=hparams['meta']["method"]+"-"+hparams["meta"]["optimizer"]) as run:
+        mlflow.log_dict(hparams, artifact_file="hparams/hparams.json")
+        mlflow.log_text("", artifact_file="output/_touch.txt")
+        artifact_uri = mlflow.get_artifact_uri("output/")
+        hparams["meta"]["output_dir"] = artifact_uri
+        print(f"URI: {artifact_uri}")
+        start_time = datetime.now()
+
+        if hparams["n_perturbs"] > 1:
+            for perturb in range(hparams["n_perturbs"]):
+                print(f"Running perturb {perturb}")
+                continuation = ContinuationCreator(
+                    problem=problem, hparams=hparams, key=perturb
+                ).get_continuation_method()
+                continuation.run()
+        else:
             continuation = ContinuationCreator(
-                problem=problem, hparams=hparams, key=perturb
+                problem=problem, hparams=hparams
             ).get_continuation_method()
             continuation.run()
-    else:
-        continuation = ContinuationCreator(
-            problem=problem, hparams=hparams
-        ).get_continuation_method()
-        continuation.run()
 
-    end_time = datetime.now()
-    print(f"Duration: {end_time-start_time}")
-
-    bif_plot(hparams['output_dir'], pick_array, hparams['n_perturbs'])
+        end_time = datetime.now()
+        print(f"Duration: {end_time-start_time}")
+
+        figure = bif_plot(hparams["meta"]["output_dir"], pick_array)
+        mlflow.log_figure(figure, artifact_file="plots/fig.png")
 ```
 
 #### Note on Hyperparameters   
 
 #### Papers:
 
-
 #### Contact: 
 `[email protected]`

examples/toy/run.py

@@ -15,7 +15,7 @@
 
 """
 from cjax.continuation.creator.continuation_creator import ContinuationCreator
-from examples.toy.vectror_pitchfork import SigmoidFold, PitchForkProblem
+from examples.toy.vectror_pitchfork import PitchForkProblem
 from cjax.utils.abstract_problem import ProblemWraper
 import json
 from jax.config import config