Testing example 3

.github/workflows/docs.yml

@@ -1,4 +1,4 @@
-name: Build Documentation for Read the Docs
+name: Build and Deploy Documentation
 
 on:
   push:
@@ -7,47 +7,36 @@ on:
     branches: [ main ]
 
 jobs:
-  build-docs:
+  build-deploy-docs:
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v3
         with:
-          fetch-depth: 0  
+          fetch-depth: 0
 
-      - name: Set up Python
+      - name: Set up Python 3.10
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.10'
           check-latest: true
 
-      - name: List repository contents
-        run: ls -la
-
-      - name: List docs directory contents
-        run: ls -la docs/
-
-      - name: Run setup-env.sh (Non-Interactive)
-        env:
-          INSTALL_TYPE: 1   # cpu only
-          INSTALL_DEV: y    # dev dependencies
-        run: |
-          chmod +x scripts/setup-env.sh
-          ./scripts/setup-env.sh
-
-      # Build and install the package
-      - name: Build and install package
+      - name: Install Dependencies and Set Up Environment
         run: |
-          source .venv/bin/activate
-          pip install -e .
+          python -m pip install --upgrade pip
+          python fast-install.py --cuda --cuda-version 12.1 --dev
+        shell: bash
 
       - name: Build Documentation
         run: |
-          source .venv/bin/activate
+          source ./bioneuralnet-env/bin/activate
+          mkdir -p docs/build/html
           sphinx-build -b html docs/source/ docs/build/html/
-
-      - name: Validate Documentation Build
-        run: |
-          echo "Documentation build completed successfully. Files are located in docs/build/html/"
-          ls -R docs/build/html/
+        shell: bash
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/build/html

.github/workflows/python-app.yml

@@ -10,8 +10,8 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [ubuntu-latest] 
-        python-version: ['3.8']                  
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.10', '3.11']
 
     runs-on: ${{ matrix.os }}
 
@@ -25,41 +25,55 @@ jobs:
         python-version: ${{ matrix.python-version }}
         check-latest: true
 
-    - name: Install R
-      uses: r-lib/actions/setup-r@v2
-
-    - name: List scripts directory contents
-      run: ls -la scripts/
+    - name: Cache pip dependencies
+      uses: actions/cache@v3
+      with:
+        path: |
+          ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt', '**/scripts/requirements-dev.txt', 'fast-install.py') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
 
-    - name: Install R and its dependencies
+    - name: Install dependencies using fast-install.py (Unix)
+      if: matrix.os != 'windows-latest'
       run: |
-        chmod +x scripts/setup-R.sh
-        ./scripts/setup-R.sh
+        chmod +x fast-install.py
+        ./fast-install.py --cuda --cuda-version 12.1 --dev
+      shell: bash
 
-    - name: Run setup-env.sh (Non-Interactive)
-      env:
-        INSTALL_TYPE: 1   #use cpu
-        INSTALL_DEV: y    #install dev dependencies
+    - name: Install dependencies using fast-install.py (Windows)
+      if: matrix.os == 'windows-latest'
       run: |
-        chmod +x scripts/setup-env.sh
-        ./scripts/setup-env.sh
-
-    - name: Verify installed Python packages
+        python fast-install.py --cuda --cuda-version 12.1 --dev
+      shell: powershell
+
+    - name: Verify installed Python packages (Unix)
+      if: matrix.os != 'windows-latest'
       run: |
-        source .venv/bin/activate
+        source ./bioneuralnet-env/bin/activate
         pip list
+      shell: bash
 
+    - name: Verify installed Python packages (Windows)
+      if: matrix.os == 'windows-latest'
+      run: |
+        .\bioneuralnet-env\Scripts\Activate.ps1
+        pip list
+      shell: powershell
 
-    - name: Verify R installation and WGCNA
-      shell: bash
+    - name: Run tests with pytest (Unix)
+      if: matrix.os != 'windows-latest'
       run: |
-        R --version
-        Rscript -e "library(WGCNA); cat('WGCNA loaded successfully')"
+        source ./bioneuralnet-env/bin/activate
+        pytest --cov=bioneuralnet --cov-report=xml tests/
+      shell: bash
 
-    - name: Run tests with pytest
+    - name: Run tests with pytest (Windows)
+      if: matrix.os == 'windows-latest'
       run: |
-        source .venv/bin/activate
+        .\bioneuralnet-env\Scripts\Activate.ps1
         pytest --cov=bioneuralnet --cov-report=xml tests/
+      shell: powershell
 
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3

.github/workflows/readthedocs.yml

@@ -0,0 +1,18 @@
+version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
+
+python:
+  install:
+    - method: pip
+      path: .
+    - requirements: requirements.txt
+    - requirements: scripts/requirements-dev.txt
+    - path: .
+      command: python fast-install.py --dev
+
+sphinx:
+  configuration: docs/source/conf.py

.gitignore

@@ -9,6 +9,8 @@ ENV/
 env.bak/
 venv.bak/
 .pytest_cache
+release.md
+bioneuralnet.egg-info
 
 # Sphinx documentation build
 docs/build/
@@ -20,6 +22,7 @@ env/
 env.bak/
 venv.bak/
 .venv/
+bioneuralnet-env/
 
 # IDE and editor directories
 .vscode/
@@ -51,3 +54,7 @@ test_report/
 # Other
 *.bak
 *.tmp
+test_output/
+dpmon_output_*
+lib/
+.DS_Store

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2024 Big Data Management and Mining Laboratory
+Copyright (c) [2024] [Big Data Management and Mining Laboratory]
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal