Merge pull request #4 from alistairewj/gh_actions

Add GH actions, improve usage

.github/workflows/main.yml

@@ -0,0 +1,35 @@
+name: Run tests on Python
+
+on:
+  release:
+    types: [published]
+    branches: ["main"]
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    name: Test pyroc
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    steps:
+      - name: Checkout pyroc repo
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          pip install .
+      - name: Test with pytest
+        run: |
+          pytest tests

README.rst

@@ -29,6 +29,8 @@ Use:
     print(auroc)
     print(ci)
 
+A usage.ipynb notebook is provided demonstrating common usage of the package (requires Jupyter: `pip install jupyter`).
+
 Documentation
 -------------
 

environment.yml

@@ -4,5 +4,6 @@ channels:
 dependencies:
   - matplotlib>=3.0.0
   - numpy>=1.15.2
-  - pandas>=0.22.0
-  - python>=3.5.6
+  - pandas>=1.0.0
+  - scipy>=1.8.1
+  - python>=3.7.0

pyroc.py

@@ -212,12 +212,20 @@ def ci(self, alpha=0.05):
 
         return ci
 
-    def compare(self, contrast, alpha=0.05):
+    def compare(self, contrast=None, alpha=0.05):
         """Compare predictions given a contrast
 
+        If no contrast is provided, and N classifiers are provided (C[0,N-1]),
+            all classifiers in C[1,N-1] is compared to C[0]
+
         If there are two predictions, you can compare as:
             roc.compare(contrast=[1, -1], alpha=0.05)
         """
+        # If no contrast is provided, and N classifiers are provided (C[0,N-1])
+        # compare classifiers C[1,N-1] to C[0]
+        if contrast is None:
+            contrast = -np.identity(self.K - 1)
+            contrast = np.insert(contrast, 0, np.ones(self.K - 1), axis=1)
 
         # Validate alpha
         if (alpha <= 0) | (alpha >= 1):
@@ -290,7 +298,7 @@ def _roc(self, pred):
         (fpr, tpr)
             np.ndarrays containing the false positive rate and the true
             positive rate, respectively.
-        
+
         """
         # Transform to matrices
         y_prob = np.array([pred])

requirements.txt

@@ -0,0 +1,4 @@
+matplotlib==3.5.2
+numpy==1.23.0
+pandas==1.4.3
+scipy==1.8.1

setup.py

@@ -25,7 +25,7 @@
     url='https://github.com/alistairewj/pyroc',
 
     # Author details
-    author='Alistair Johnson, Lucas Bulgarelli',
+    author='Alistair Johnson, Lucas Bulgarelli, Tom Pollard',
     author_email='[email protected]',
 
     # Choose your license
@@ -46,5 +46,5 @@
     # your project is installed. For an analysis of "install_requires" vs pip's
     # requirements files see:
     # https://packaging.python.org/en/latest/requirements.html
-    install_requires=['pandas>=0.22.0', 'numpy>=1.12.1', 'scipy>=0.18.1']
+    install_requires=['pandas>=1.0.0', 'numpy>=1.15.2', 'scipy>=1.8.1']
 )