Refactor project structure (#19)

* format core.py

* update README.rst

* update setup.py

* Revert "update setup.py"

This reverts commit 1b49acc.

* update setup.py and README.rst

* Refactor project structure

README.rst

@@ -1,5 +1,5 @@
 CFXplorer
-==========================================================================
+=========
 
 **Deployment & Documentation & Stats & License**
 
@@ -15,23 +15,23 @@ CFXplorer
    :target: https://pepy.tech/project/focus-cfe
    :alt: Downloads
 
-.. image:: https://codecov.io/gh/kyosek/focus/branch/master/graph/badge.svg?token=G5I7TJR0JQ
-    :target: https://codecov.io/gh/kyosek/focus
+.. image:: https://codecov.io/gh/kyosek/CFXplorer/branch/master/graph/badge.svg?token=G5I7TJR0JQ
+    :target: https://codecov.io/gh/kyosek/CFXplorer
 
-.. image:: https://dl.circleci.com/status-badge/img/gh/kyosek/focus/tree/master.svg?style=svg
-    :target: https://dl.circleci.com/status-badge/redirect/gh/kyosek/focus/tree/master
+.. image:: https://dl.circleci.com/status-badge/img/gh/kyosek/CFXplorer/tree/master.svg?style=svg
+    :target: https://dl.circleci.com/status-badge/redirect/gh/kyosek/CFXplorer/tree/master
     :alt: Circle CI
 
 .. image:: https://api.codeclimate.com/v1/badges/93840d29606abb212051/maintainability
    :target: https://codeclimate.com/github/kyosek/focus-cfe/maintainability
    :alt: Maintainability
 
 .. image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit
-   :target: https://github.com/kyosek/focus-cfe
+   :target: https://github.com/kyosek/CFXplorer
    :alt: pre-commit
 
-.. image:: https://img.shields.io/github/license/kyosek/focus.svg
-   :target: https://github.com/kyosek/focus/blob/master/LICENSE
+.. image:: https://img.shields.io/github/license/kyosek/CFXplorer.svg
+   :target: https://github.com/kyosek/CFXplorer/blob/master/LICENSE
    :alt: License
 
 ---------
@@ -53,7 +53,7 @@ It is recommended to use **pip** or **conda** for installation. Please make sure
 
 .. code-block:: bash
 
-   conda install -c conda-forge focus-cfe
+   conda install -c conda-forge CFXplorer
 
 Requirements
 ------------
@@ -80,9 +80,9 @@ Usage
 Examples
 --------
 
-- Comprehensive examples can be found in the `examples folder <https://github.com/kyosek/focus/blob/master/examples/focus_example.py>`_.
-- Kaggle notebook example can be found `here <https://www.kaggle.com/code/kyosukemorita/focus-cfe-example>`_.
-- Below is demonstrated a comparison of before and after Focus-cfe is applied to feature set from the example given above.
+- Comprehensive examples can be found in the `examples folder <https://github.com/kyosek/CFXplorer/blob/master/examples/focus_example.py>`_.
+- Kaggle notebook example can be found `here <https://www.kaggle.com/code/kyosukemorita/focus-example>`__.
+- Below is demonstrated a comparison of before and after Focus is applied to feature set from the example given above.
 
 .. image:: https://raw.githubusercontent.com/kyosek/focus/master/docs/plot.png
     :width: 800px
@@ -100,16 +100,16 @@ Limitations of Focus class
 Documentation
 -------------
 
-The documentation can be found `here <https://cfxplorer.readthedocs.io/en/latest/>`_.
+The documentation can be found `here <https://cfxplorer.readthedocs.io/en/latest/>`__.
 
 Contributing
 ------------
 
 If you would like to contribute to the project, please refer to;
 
-- `ISSUE_TEMPLATE <https://github.com/kyosek/focus/tree/master/.github/ISSUE_TEMPLATE>`_ for raising an issue
-- `PULL_REQUEST_TEMPLATE.md <https://github.com/kyosek/focus/blob/master/.github/PULL_REQUEST_TEMPLATE.md>`_ for raising a PR
+- `ISSUE_TEMPLATE <https://github.com/kyosek/CFXplorer/tree/master/.github/ISSUE_TEMPLATE>`_ for raising an issue
+- `PULL_REQUEST_TEMPLATE.md <https://github.com/kyosek/CFXplorer/blob/master/.github/PULL_REQUEST_TEMPLATE.md>`_ for raising a PR
 
 License
 -------
-This package is using the `Apache License 2.0 <https://github.com/kyosek/focus/blob/master/LICENSE>`_ license.
+This package is using the `Apache License 2.0 <https://github.com/kyosek/CFXplorer/blob/master/LICENSE>`_ license.

cfxplorer/__init__.py

@@ -1,4 +1,4 @@
-from cfxplorer.focus.core import Focus
+from cfxplorer.focus import Focus
 
 # Let users know if they're missing any of our hard dependencies
 _hard_dependencies = ("tensorflow", "numpy")

cfxplorer/focus/core.py → cfxplorer/focus.py

@@ -10,7 +10,7 @@
 from sklearn.ensemble import AdaBoostClassifier, RandomForestClassifier
 from sklearn.tree import DecisionTreeClassifier
 
-from .utils import calculate_distance
+from cfxplorer.utils import calculate_distance
 
 os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"
 
@@ -67,12 +67,12 @@ class Focus:
 
     Examples
     --------
-    - Initialize FOCUS with default parameters
+    - Initialize FOCUS on default parameters
     - Generate counterfactual explanations
 
-    cfxplorer = Focus()
+    focus = Focus()
 
-    cfe_features = cfxplorer.generate(model, X)
+    cfe_features = focus.generate(model, X)
     """
 
     def __init__(
@@ -475,16 +475,16 @@ def filter_hinge_loss(
         Calculates the filtered probabilities of each data point for the given model.
 
         Args:
-        - n_class (int): Number of classes.
-        - mask_vector (np.ndarray): A boolean mask indicating which data points should be considered.
-        - X (tf.Tensor): The feature input for the model.
-        - sigma (float): The value of sigma for computing the probabilities.
-        - temperature (float): The temperature to be used for the softmax function.
-        - model: The machine learning model;
+        n_class (int): Number of classes.
+        mask_vector (np.ndarray): A boolean mask indicating which data points should be considered.
+        X (tf.Tensor): The feature input for the model.
+        sigma (float): The value of sigma for computing the probabilities.
+        temperature (float): The temperature to be used for the softmax function.
+        model: The machine learning model;
             e.g., DecisionTreeClassifier, RandomForestClassifier, AdaBoostClassifier.
 
         Returns:
-        - hinge_loss (tf.Tensor): The filtered probabilities of each data point.
+        hinge_loss (tf.Tensor): The filtered probabilities of each data point.
         """
         n_input = X.shape[0]
 

cfxplorer/tests/test_utils.py

@@ -4,7 +4,7 @@
 import pytest
 import tensorflow as tf
 
-from cfxplorer.focus.utils import (
+from cfxplorer.utils import (
     calculate_distance,
     safe_cosine,
     safe_euclidean,

cfxplorer/version.py

@@ -1,6 +1,6 @@
 """
-``cfxplorer`` is a python package for
-generating counterfactual explanations for a tree-based model
+``CFXplorer`` is a python package for
+generating counterfactual explanations for a given model and feature set.
 """
 # PEP0440 compatible formatted version, see:
 # https://www.python.org/dev/peps/pep-0440/
@@ -18,4 +18,4 @@
 # Dev branch marker is: 'X.Y.dev' or 'X.Y.devN' where N is an integer.
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
-__version__ = "0.0.dev4"  # pragma: no cover
+__version__ = "0.0.dev7"  # pragma: no cover

setup.py

@@ -3,10 +3,7 @@
 
 from setuptools import find_packages, setup
 
-DESCRIPTION = (
-    "CFXplorer is a python package for " "generating counterfactual explanations"
-)
-
+DESCRIPTION = "CFXplorer is a python package for generating counterfactual explanations for given model and feature set"
 
 # get __version__ from _version.py
 ver_file = path.join("cfxplorer", "version.py")
@@ -22,10 +19,6 @@ def readme():
         return f.read()
 
 
-# read the contents of requirements.txt
-with open(path.join(this_directory, "requirements.txt"), encoding="utf-8") as f:
-    requirements = f.read().splitlines()
-
 setup(
     name="CFXplorer",
     version=__version__,