Merge pull request #7 from ZviBaratz/suggestions

Suggestions

Author: poldrack

.github/workflows/python-app.yml

@@ -5,32 +5,30 @@ name: Python application
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.8
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest numpy pandas scipy
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        python -m pytest 
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          python -m pytest

.gitignore

@@ -1,2 +1,18 @@
-__pycache__
+# Virtual environment directory
+venv
+.venv
+
+# Cache directories and byte-code files
+*.py[cod]
+__pycache__/
+.pytest_cache/
+.ipynb_checkpoints
 .coverage
+
+# Editor directories and files
+.idea
+.vscode
+.vs
+
+# Local solutions directory
+solutions

README.md

@@ -0,0 +1,7 @@
+coverage
+flake8
+numpy
+pandas
+pytest
+pytest-cov
+scipy

requirements.txt

@@ -19,8 +19,9 @@ def generate_test_df(meanRT, sdRT, meanAcc, n=100):
     # get random accuracy values and threshold for intended proportion
     accuracy_continuous = np.random.rand(n)
     accuracy = pd.Series(
-        accuracy_continuous < scipy.stats.scoreatpercentile(
-            accuracy_continuous, 100 * meanAcc))
+        accuracy_continuous
+        < scipy.stats.scoreatpercentile(accuracy_continuous, 100 * meanAcc)
+    )
 
     # scale the correct RTs only
     rt_correct = rt.mask(~accuracy)
@@ -29,8 +30,7 @@ def generate_test_df(meanRT, sdRT, meanAcc, n=100):
     # NB: .where() replaces values where the condition is False
     rt_scaled_with_inaccurate_rts = rt_scaled.where(accuracy, rt)
 
-    return(pd.DataFrame({'rt': rt_scaled_with_inaccurate_rts,
-                         'accuracy': accuracy}))
+    return pd.DataFrame({"rt": rt_scaled_with_inaccurate_rts, "accuracy": accuracy})
 
 
 def scale_values(values, mean, sd):
@@ -44,4 +44,4 @@ def scale_values(values, mean, sd):
     values = values * (sd / np.std(values))
     values = (values - np.mean(values)) + mean
 
-    return(values)
+    return values

rtanalysis/generate_testdata.py

@@ -8,8 +8,8 @@
 
 # %%
 class RTAnalysis:
-    """[summary]
-    """
+    """[summary]"""
+
     def __init__(self, outlier_cutoff_sd=None):
         """
         RT analysis
@@ -35,30 +35,30 @@ def fit(self, rt, accuracy, verbose=True):
 
         try:
             assert rt.shape[0] == accuracy.shape[0]
-        except AssertionError:
-            raise ValueError('rt and accuracy must be the same length!')
+        except AssertionError as e:
+            raise ValueError("rt and accuracy must be the same length!") from e
 
         # ensure that accuracy values are boolean
-        assert len(set(accuracy.unique()).difference([True, False])) == 0
+        assert not set(accuracy.unique()).difference([True, False])
 
         if self.outlier_cutoff_sd is not None:
             cutoff = rt.std() * self.outlier_cutoff_sd
             if verbose:
-                print(f'outlier rejection excluded {(rt > cutoff).sum()} trials')
+                print(f"outlier rejection excluded {(rt > cutoff).sum()} trials")
             rt = rt.mask(rt > cutoff)
 
         self.meanacc_ = accuracy.mean()
         try:
             assert self.meanacc_ > 0
-        except:
-            raise ValueError('accuracy is zero')
+        except AssertionError as e:
+            raise ValueError("accuracy is zero") from e
 
         rt = rt.mask(~accuracy)
         self.meanrt_ = rt.mean()
 
         if verbose:
-            print(f'mean RT: {self.meanrt_}')
-            print(f'mean accuracy: {self.meanacc_}')
+            print(f"mean RT: {self.meanrt_}")
+            print(f"mean accuracy: {self.meanacc_}")
 
     @staticmethod
     def _ensure_series_type(var):
@@ -74,4 +74,4 @@ def _ensure_series_type(var):
 
         if type(var) is not pd.core.series.Series:
             var = pd.Series(var)
-        return(var)
+        return var

rtanalysis/rtanalysis.py

@@ -1,10 +1,9 @@
 """test suite for rtanalysis
 """
-
 import pytest
 from rtanalysis.rtanalysis import RTAnalysis
 
+
 def test_rtanalysis_smoke():
     rta = RTAnalysis()
     assert rta is not None
-

tests/test_1_smoketest.py

@@ -3,10 +3,9 @@
 - in this test, we will create a simulated dataset and fit
 it, ensuring that the answers are correct
 """
-
 import numpy as np
-from rtanalysis.rtanalysis import RTAnalysis
 from rtanalysis.generate_testdata import generate_test_df
+from rtanalysis.rtanalysis import RTAnalysis
 
 
 def test_rtanalysis_fit():

tests/test_2_fit.py

@@ -2,10 +2,9 @@
 test for rtanalysis
 - in this test, we will ensure that the function raises a ValueError
 """
-
 import pytest
-from rtanalysis.rtanalysis import RTAnalysis
 from rtanalysis.generate_testdata import generate_test_df
+from rtanalysis.rtanalysis import RTAnalysis
 
 
 # This xfail decorator tells pytest to run the test

tests/test_3_type_fail.py

@@ -2,10 +2,9 @@
 test for rtanalysis
 - in this test, we will ensure that the function raises a ValueError
 """
-
 import pytest
-from rtanalysis.rtanalysis import RTAnalysis
 from rtanalysis.generate_testdata import generate_test_df
+from rtanalysis.rtanalysis import RTAnalysis
 
 
 def test_dataframe_error_with_raises():