Rtichoke 014

docs/conf.py

@@ -1,3 +1,4 @@
+"""docs file"""
 # Configuration file for the Sphinx documentation builder.
 #
 # This file only contains a selection of the most common options. For a full
@@ -7,7 +8,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "rtichoke"
-copyright = "2023, Uriah Finkel"
+copyrights = "2023, Uriah Finkel"
 author = "Uriah Finkel"
 
 # -- General configuration ---------------------------------------------------

requirements.txt

@@ -0,0 +1,6 @@
+numpy==1.25.2
+bokeh==3.2.2
+scikit-learn==1.3.0
+pandas==2.1.0
+IPython==8.14.0
+tqdm==4.66.1

rtichoke/__init__.py

@@ -0,0 +1,7 @@
+"""rtichoke is a package for interactive vizualization of performance metrics
+"""
+from importlib.metadata import version
+
+# __version__ = version("rtichoke")
+
+from .rtichoke import Rtichoke

src/rtichoke/helpers/validations.py → rtichoke/helpers/validations.py

@@ -52,7 +52,7 @@ def check_probs_vs_reals(probs, reals):
         raise ValueError(
             f"Probs and reals shapes are inconsistent ({probs.shape} and {reals.shape})"
         )
-    elif len(probs) < 2:
+    if len(probs) < 2:
         raise ValueError("At least two entries should be included reals and probs")
 
 

src/rtichoke/plot/bokeh/plot_bokeh.py → rtichoke/plot/bokeh/plot_bokeh.py

@@ -109,9 +109,7 @@ def plot_bokeh(self, generic_plot_dict, filename=None):
     )
 
     # add scatter
-    filtered_scatter = [
-        True if th == slider.value else False for th in df[stratification]
-    ]
+    filtered_scatter = [th == slider.value for th in df[stratification]]
     scatter_source = ColumnDataSource(data=df.loc[filtered_scatter])
 
     for j, pop in enumerate(pops):
@@ -132,7 +130,7 @@ def plot_bokeh(self, generic_plot_dict, filename=None):
     # Adding callback code
     source = ColumnDataSource(data=df.set_index("Population"))
     callback = CustomJS(
-        args=dict(source=source, scatter_source=scatter_source, val=slider),
+        args={"source": source, "scatter_source": scatter_source, "val": slider},
         code=create_JS_code(x=x, y=y, stratification=stratification),
     )
 

src/rtichoke/__init__.py → rtichoke/rtichoke.py

@@ -1,16 +1,9 @@
 """rtichoke is a package for interactive vizualization of performance metrics
 """
-
-from importlib.metadata import version
-
-# __version__ = version("rtichoke")
-
-from .helpers.helper_functions import *
-
+from .helpers.helper_functions import tprint
 
 class Rtichoke:
     """Main Rtichoke class"""
-
     # import methods
     from .performance_data.prepare_performance_data import (
         prepare_performance_data,
@@ -20,7 +13,6 @@ class Rtichoke:
         prepare_calibration_data,
         prepare_calibration_table,
     )
-
     from .helpers.validations import validate_inputs, validate_plot_inputs, check_by
     from .helpers.helper_functions import (
         select_data_table,

src/tests/__init__.py → rtichoke/tests/__init__.py

@@ -1,3 +1,4 @@
 """
 testing module
+
 """

src/tests/test_calculate_performance_data.py → rtichoke/tests/test_calculate_performance_data.py

@@ -3,19 +3,19 @@
 import numpy as np
 import pandas as pd
 from numpy.testing import assert_allclose
-from rtichoke import Rtichoke
-
-# UnitTests created with ChatGPT! :-)
+import rtichoke
 
 
 class TestPreparePerformanceTable(unittest.TestCase):
-    """UnitTest class to test performance tables"""
+    """UnitTest class to test performance tables
+       Tests were created with ChatGPT :-)
+    """
 
     def setUp(self):
         """Simulate an Rtichoke object"""
         probs = {"pop1": np.array([0.7, 0.8, 0.9, 0.4, 0.2, 0.6, 0.5])}
         reals = {"pop1": np.array([1, 1, 1, 0, 0, 1, 0])}
-        self.r = Rtichoke(probs=probs, reals=reals, by=0.1)
+        self.r = rtichoke.Rtichoke(probs=probs, reals=reals, by=0.1)
 
     def test_performance_table_type_and_size(self):
         """Test performance table type and size"""
@@ -78,17 +78,17 @@ def test_performance_data_with_two_populations(self):
             "pop1": np.array([1, 1, 1, 0, 0, 1, 0]),
             "pop2": np.array([1, 1, 1, 0, 0, 1, 0]),
         }
-        r = Rtichoke(probs=probs, reals=reals, by=0.1)
+        r = rtichoke.Rtichoke(probs=probs, reals=reals, by=0.1)
 
-        expected_pop_name = ["pop1", "pop2"]
-        pt_table_pop_name = r.performance_table_pt["Population"].unique()
-        ppcr_table_pop_name = r.performance_table_ppcr["Population"].unique()
+        expected_pop_name = {"pop1", "pop2"}
+        pt_table_pop_name = set(r.performance_table_pt["Population"].unique())
+        ppcr_table_pop_name = set(r.performance_table_ppcr["Population"].unique())
 
         self.assertEqual(expected_pop_name, pt_table_pop_name)
         self.assertEqual(expected_pop_name, ppcr_table_pop_name)
 
-        self.assertEqual(r.performance_table_pt.shape, (15, 22))
-        self.assertEqual(r.performance_table_ppcr.shape, (15, 22))
+        self.assertEqual(r.performance_table_pt.shape, (22, 15))
+        self.assertEqual(r.performance_table_ppcr.shape, (22, 15))
 
 
 if __name__ == "__main__":

src/tests/test_vericiation_tests.py → rtichoke/tests/test_vericiation_tests.py

@@ -2,7 +2,7 @@
 import unittest
 import numpy as np
 from rtichoke.helpers.validations import check_probs, check_probs_vs_reals, check_reals
-from rtichoke import Rtichoke
+from rtichoke import rtichoke
 
 
 class TestCheckProbs(unittest.TestCase):
@@ -95,13 +95,13 @@ class TestCheckBy(unittest.TestCase):
 
     def test_valid_by_value(self):
         """Test check_by: valid value"""
-        Rtichoke(probs=np.array([0.1, 0.5, 0.9]), reals=np.array([0, 1, 0]), by=0.25)
+        rtichoke.Rtichoke(probs=np.array([0.1, 0.5, 0.9]), reals=np.array([0, 1, 0]), by=0.25)
 
     def test_by_not_a_float(self):
         """Test check_by: `by` argument not a float"""
         # Test that an exception is raised when the input is not a float
         with self.assertRaises(ValueError) as e:
-            Rtichoke(
+            rtichoke.Rtichoke(
                 probs=np.array([0.1, 0.5, 0.9]), reals=np.array([0, 1, 0]), by="0.25"
             )
         self.assertEqual(
@@ -112,7 +112,7 @@ def test_by_out_of_range(self):
         """Test check_by: `by` argument out of range"""
         # Test that an exception is raised when the input is out of range
         with self.assertRaises(ValueError) as e:
-            Rtichoke(
+            rtichoke.Rtichoke(
                 probs=np.array([0.1, 0.5, 0.9]), reals=np.array([0, 1, 0]), by="0.6"
             )
         self.assertEqual(
@@ -125,7 +125,7 @@ class TestValidateInputs(unittest.TestCase):
 
     def test_validate_inputs(self):
         """End-to-end test with valid inputs"""
-        r = Rtichoke(probs=np.array([0.1, 0.5, 0.9]), reals=np.array([0, 1, 0]), by=0.2)
+        r = rtichoke.Rtichoke(probs=np.array([0.1, 0.5, 0.9]), reals=np.array([0, 1, 0]), by=0.2)
 
         # test for valid input
         probs = np.array([0.1, 0.5, 0.9])