Merge pull request #57 from DynamicsAndNeuralSystems/jmoo2880-add-new-spi-testing

New benchmarking dataset and dependency updates

Author: joshuabmoore

.github/workflows/run_unit_tests.yaml

@@ -25,7 +25,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install -r requirements.txt
           pip install .
-          pip install pandas==1.3.3 numpy==1.22.0
       - name: Run pyspi calculator unit tests
         run: |
           pytest -v ./tests/test_calc.py

README.md

@@ -1,6 +1,6 @@
 <p align="center">
   <picture>
-    <source srcset="img/pyspi_logo_dark.png" media="(prefers-color-scheme: dark)">
+    <source srcset="img/pyspi_logo_darkmode.png" media="(prefers-color-scheme: dark)">
     <img src="img/pyspi_logo.png" alt="pyspi logo" height="200"/>
   </picture>
 </p>

img/pyspi_logo_dark.png

@@ -1,8 +1,8 @@
 pytest
-scikit-learn==0.24.1
+scikit-learn==1.0.1
 scipy==1.7.3
 numpy>=1.21.1
-pandas>=1.3.3
+pandas==1.5.0
 statsmodels==0.12.1
 pyyaml==5.4
 tqdm==4.50.2

img/pyspi_logo_darkmode.png

@@ -3,15 +3,15 @@
 # http://www.diveintopython3.net/packaging.html
 # https://pypi.python.org/pypi?:action=list_classifiers
 
-with open('README.md') as file:
+with open('README.md', 'r', encoding='utf-8') as file:
     long_description = file.read()
 
 
 install_requires = [
-        'scikit-learn==0.24.1',
+        'scikit-learn==1.0.1',
         'scipy==1.7.3',
         'numpy>=1.21.1',
-        'pandas>=1.3.3',
+        'pandas==1.5.0',
         'statsmodels==0.12.1',
         'pyyaml==5.4',
         'tqdm==4.50.2',
@@ -59,9 +59,10 @@
                         'lib/PhiToolbox/utility/Gauss/logdet.m',
                         'data/cml.npy',
                         'data/forex.npy',
-                        'data/standard_normal.npy']},
+                        'data/standard_normal.npy',
+                        'data/cml7.npy']},
     include_package_data=True,
-    version='0.4.1',
+    version='0.4.2',
     description='Library for pairwise analysis of time series data.',
     author='Oliver M. Cliff',
     author_email='[email protected]',

pyspi/data/cml7.npy

@@ -0,0 +1,50 @@
+import pytest
+
+@pytest.fixture(scope="session")
+def spi_warning_logger(request):
+    warnings_log = list()
+
+    def add_warning(spi, module_name, max_z, num_exceed, num_iteractions):
+        warnings_log.append((spi, module_name, max_z, num_exceed, num_iteractions))
+    
+    request.session.spi_warnings = warnings_log
+    return add_warning
+
+def pytest_sessionfinish(session, exitstatus):
+    # retrieve the spi warnings from the session object
+    spi_warnings = getattr(session, 'spi_warnings', [])
+
+    # styling
+    header_line = "=" * 80
+    content_line = "-" * 80
+    footer_line = "=" * 80
+    header = " SPI BENCHMARKING SUMMARY"
+    footer = f" Session completed with exit status: {exitstatus} "
+    padded_header = f"{header:^80}"
+    padded_footer = f"{footer:^80}"
+
+    print("\n")
+    print(header_line)
+    print(padded_header)
+    print(header_line)
+
+    # print problematic SPIs in table format
+    if spi_warnings:
+        print(f"\nDetected {len(spi_warnings)} SPI(s) with outputs exceeding the specified 2 sigma threshold.\n")
+
+        # table header
+        print(f"{'SPI':<25}{'Cat':<10}{'Max ZSc.':>10}{'# Exceed. Pairs':>20}{'Unq. Pairs':>15}")
+        print(content_line)
+
+        # table content
+        for est, module_name, max_z, num_exceed, num_iteractions in spi_warnings:
+            # add special character for v.large zscores
+            error = ""
+            if max_z > 10:
+                error = " **"
+            print(f"{est+error:<25}{module_name:<10}{max_z:>10.4g}{num_exceed:>15}{num_iteractions:>20}")
+    else:
+        print("\n\nNo SPIs exceeded the sigma threshold.\n")
+
+    print(footer_line)
+    print(padded_footer)