Implemented DPMON, cleaned up old files, updated documentation.

.github/workflows/docs.yml

@@ -1,48 +1,39 @@
-import os
-import sys
-import pkg_resources
-
-# -- Path setup --------------------------------------------------------------
-
-sys.path.insert(0, os.path.abspath('../../'))
-
-# -- Project information -----------------------------------------------------
-
-project = 'BioNeuralNet'
-author = 'Vicente Ramos'
-release = pkg_resources.get_distribution("bioneuralnet").version
-
-extensions = [
-    'sphinx.ext.autodoc',      
-    'sphinx.ext.napoleon',     
-    'sphinx.ext.viewcode',     
-    'sphinx.ext.autosummary',  
-    'sphinx.ext.intersphinx', 
-]
-
-napoleon_google_docstring = True
-napoleon_numpy_docstring = False
-templates_path = ['_templates']
-
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-
-# -- Options for HTML output -------------------------------------------------
-
-html_theme = 'sphinx_rtd_theme'  
-html_static_path = ['_static']
-
-# -- Autosummary configuration -----------------------------------------------
-
-autosummary_generate = True
-
-# -- Intersphinx configuration ------------------------------------------------
-
-intersphinx_mapping = {
-    'python': ('https://docs.python.org/3', None),
-    'pandas': ('https://pandas.pydata.org/docs/', None),
-    'numpy': ('https://numpy.org/doc/stable/', None),
-    'torch': ('https://pytorch.org/docs/stable/', None),
-    'scikit-learn': ('https://scikit-learn.org/stable/', None),
-    'matplotlib': ('https://matplotlib.org/stable/', None),
-    'networkx': ('https://networkx.org/documentation/stable/', None),
-}
+name: Build Documentation for Read the Docs
+
+on:
+  push:
+    branches:
+      - main  
+  pull_request:
+    branches:
+      - main  
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0  
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.8'
+
+      - name: Install Documentation Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements-dev.txt
+          pip install sphinx sphinx_rtd_theme
+
+      - name: Build Documentation
+        run: |
+          sphinx-build -b html source/ build/html/
+
+      - name: Validate Documentation Build
+        run: |
+          echo "Documentation build completed successfully. Files are located in build/html/"
+          ls -R build/html/

.github/workflows/python-app.yml

@@ -8,36 +8,47 @@ on:
 
 jobs:
   build:
-
-    runs-on: ubuntu-latest
-
     strategy:
       matrix:
-        python-version: [3.8, 3.9, 3.10]
+        os: [ubuntu-latest] 
+        python-version: ['3.8']                  
+
+    runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v3
+    - name: Checkout repository
+      uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
         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: Install dependencies
+    - name: Install R and its dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install -r requirements-dev.txt
-        # Install CPU-specific dependencies
-        pip install -r requirements-cpu.txt
+        chmod +x scripts/setup-R.sh
+        ./scripts/setup-R.sh
 
-    - name: Lint with flake8
+    - name: Run setup-env.sh (Non-Interactive)
+      env:
+        INSTALL_TYPE: 1   #use cpu
+        INSTALL_DEV: y    #install dev dependencies
       run: |
-        flake8 bioneuralnet tests docs
+        chmod +x scripts/setup-env.sh
+        ./scripts/setup-env.sh
 
-    - name: Format with black
+    - name: Verify R installation and WGCNA
+      shell: bash
       run: |
-        black --check bioneuralnet tests docs
+        R --version
+        Rscript -e "library(WGCNA); cat('WGCNA loaded successfully')"
 
     - name: Run tests with pytest
       run: |
@@ -49,4 +60,4 @@ jobs:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml
         flags: unittests
-        name: codecov-umbrella
+        name: codecov-umbrella

.pre-commit-config.yml

@@ -11,18 +11,27 @@ repos:
     rev: 23.3.0
     hooks:
       - id: black
+        name: Format Python code with Black
         language_version: python3
 
   - repo: https://github.com/PyCQA/flake8
     rev: 6.0.0
     hooks:
       - id: flake8
+        name: Lint Python code with Flake8
         additional_dependencies: [flake8>=6.0.0]
 
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.6.1
+    hooks:
+      - id: mypy
+        name: Static type checking with MyPy
+        args: [--ignore-missing-imports]
+
   - repo: local
     hooks:
       - id: run-tests
-        name: Run Tests
-        entry: pytest
+        name: Run Tests with Pytest
+        entry: pytest --cov=bioneuralnet --cov-report=term-missing
         language: system
         types: [python]

MANIFEST.in

@@ -2,22 +2,21 @@
 include README.md
 include LICENSE
 
-# Include all .yml files in the utils directory
-recursive-include bioneuralnet/utils *.yml
+# Include assets and images 
+recursive-include assets *.png *.jpg *.svg
 
-# Include shell scripts in the scripts directory
-recursive-include bioneuralnet/scripts *.sh
+# Include documentation source files
+recursive-include docs *
 
-# Include all requirements files
-include requirements.txt
-include requirements-cpu.txt
-include requirements-cuda.txt
-include requirements-dev.txt
+# Include example scripts
+recursive-include examples *.py
 
-# Include documentation source files
-recursive-include docs/source *.rst
-recursive-include docs *.md
+# Include scripts installation files
+recursive-include scripts *
+
+# Exclude __pycache__ and compiled Python files
+global-exclude __pycache__ *.pyc *.pyo *.pyd
 
-# Include examples
-recursive-include examples *
+# Exclude editor backup and temporary files
+global-exclude *~ *.bak *.swp