Fix Python dependency management in CI workflows

- Add comprehensive requirements.txt with all necessary packages including pytest
- Remove redundant package installations from CI workflows
- Add package verification steps in CI for better debugging
- Include testing, linting, and build dependencies in requirements.txt
- Ensure consistent dependency management across all workflows

Fixes CI failure: No module named pytest

Author: WenyinWei

.github/workflows/ci.yml

@@ -30,8 +30,12 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
-        # Install additional testing dependencies
-        pip install pytest pytest-cov flake8
+        echo "Python dependencies installed successfully"
+        
+        # Verify key packages are installed
+        python -c "import pytest; print('pytest version:', pytest.__version__)"
+        python -c "import numpy; print('numpy version:', numpy.__version__)"
+        python -c "import flake8; print('flake8 installed successfully')"
 
     - name: Lint with flake8
       run: |
@@ -60,7 +64,6 @@ jobs:
 
     - name: Generate coverage report
       run: |
-        pip install coverage
         coverage run -m pytest tests/
         coverage xml
 
@@ -87,7 +90,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install build twine
+        pip install -r requirements.txt
 
     - name: Build package
       run: |

.github/workflows/docs.yml

@@ -34,9 +34,16 @@ jobs:
 
     - name: Install Python dependencies
       run: |
+        Write-Host "Installing Python dependencies..."
         python -m pip install --upgrade pip
         pip install -r requirements.txt
-        pip install matplotlib seaborn pandas
+        Write-Host "Python dependencies installed successfully"
+        
+        # Verify key packages are installed
+        python -c "import pytest; print('pytest version:', pytest.__version__)"
+        python -c "import numpy; print('numpy version:', numpy.__version__)"
+        python -c "import matplotlib; print('matplotlib version:', matplotlib.__version__)"
+        Write-Host "Package verification completed"
     
     - name: Install Doxygen and Graphviz
       run: |

requirements.txt

@@ -1,2 +1,22 @@
+# Core dependencies
 numpy>=1.20.0
-matplotlib>=3.3.0
+matplotlib>=3.3.0
+
+# Testing dependencies
+pytest>=6.0.0
+pytest-cov>=2.10.0
+unittest-xml-reporting>=3.0.0
+coverage>=5.0.0
+
+# Data analysis and visualization
+seaborn>=0.11.0
+pandas>=1.3.0
+
+# Code quality and linting
+flake8>=3.8.0
+
+# Development and CI dependencies
+setuptools>=40.0.0
+wheel>=0.34.0
+build>=0.7.0
+twine>=3.4.0