Release 1.0.0b2

.github/workflows/ci.yml

@@ -0,0 +1,59 @@
+name: Python CI
+
+on:
+  push:
+    branches: [ master, main, dev-master, dev-refactored, refactor-phylo ]
+  pull_request:
+    branches: [ master, main, dev-master, dev-refactored, refactor-phylo ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache pip
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get install -qq phyml
+        python -m pip install --upgrade pip setuptools wheel
+        pip install --only-binary=numpy,scipy numpy scipy
+        pip install matplotlib ipython jupyter sympy pytest codecov pytest-cov
+        pip install -r requirements.txt
+        pip install -e .
+
+    - name: Run tests
+      run: pytest --cov=OrthoEvol --cov-report=xml --junitxml=junit.xml tests/
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: false
+
+    - name: Upload test results to Codecov
+      if: ${{ !cancelled() }}
+      uses: codecov/test-results-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Notify failure
+      if: failure()
+      run: echo "Build failed"

.github/workflows/docs.yml

@@ -0,0 +1,73 @@
+name: Documentation
+
+on:
+  push:
+    branches: [ master, main, dev-master, dev-refactored ]
+    paths:
+      - 'docs/**'
+      - 'OrthoEvol/**'
+      - 'setup.py'
+      - '.readthedocs.yml'
+  pull_request:
+    branches: [ master, main, dev-master, dev-refactored ]
+    paths:
+      - 'docs/**'
+      - 'OrthoEvol/**'
+      - 'setup.py'
+      - '.readthedocs.yml'
+  workflow_dispatch:
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+
+    - name: Cache pip
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-docs-${{ hashFiles('**/requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-docs-
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install sphinx pypandoc
+        pip install -r requirements.txt
+        pip install -e .
+
+    - name: Update and build documentation
+      run: |
+        python docs/update_docs.py
+
+    - name: Check for documentation errors
+      run: |
+        if [ -d "docs/docs/_build" ] && [ -f "docs/docs/_build/index.html" ]; then
+          echo "✓ Documentation built successfully"
+          echo "Found HTML files:"
+          find docs/docs/_build -maxdepth 1 -name "*.html" | head -5
+          echo "Build directory structure:"
+          ls -la docs/docs/_build/ | head -10
+        else
+          echo "✗ Documentation build failed"
+          echo "Checking build directory:"
+          ls -la docs/docs/_build/ 2>&1 || echo "Build directory does not exist"
+          exit 1
+        fi
+
+    - name: Upload documentation artifacts
+      if: success()
+      uses: actions/upload-artifact@v4
+      with:
+        name: documentation
+        path: docs/docs/_build
+        retention-days: 7

.readthedocs.yml

@@ -1,6 +1,25 @@
+# Read the Docs configuration for OrthoEvolution
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+
+version: 2
+
 build:
   image: latest
+  os: ubuntu-22.04
+  # Pre-build job: Run update_docs.py to regenerate API docs and convert READMEs
+  # This runs before Sphinx builds the documentation
+  commands:
+    - python docs/update_docs.py --skip-build
 
 python:
-  version: 3.6
-  setup_py_install: true
+  version: 3.9
+  install:
+    - method: pip
+      path: .
+    - method: pip
+      # Install documentation dependencies
+      pip_install:
+        - sphinx
+        - pypandoc
+
+# Sphinx will be auto-detected from docs/docs/source/conf.py

CHANGELOG.md

@@ -0,0 +1,70 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [1.0.0b2] - 2025-12-02
+
+### Added
+- Comprehensive test suites for `utilities`, `Manager`, and `Tools` modules
+  - Added 20+ test methods for `BlastUtils`, `GenbankUtils`, `OrthologUtils`, `ManagerUtils`, `PackageVersion`, and `FullUtilities` classes
+  - Added 16 test methods for `Management`, `RepoManagement`, `UserManagement`, `WebsiteManagement`, `ProjectManagement`, and `BaseDatabaseManagement` classes
+  - Added 5 test methods for `LogIt`, `PyBasher`, `NcbiFTPClient`, and `Multiprocess` classes
+  - Total of ~705 lines of new test code across three test files
+- Docstrings added to Orthologs module
+
+### Fixed
+- Fixed typo in `FullUtilities.__init__()`: `Ortho0logUtils` → `OrthologUtils` (resolves `AttributeError`)
+- Fixed missing docstrings across codebase
+- Fixed various test issues and code coverage gaps
+
+### Changed
+- Updated Python version requirements and examples
+- Refactored code structure (#177)
+- Moved templates to `.github` directory
+- Updated Python tasks configuration
+
+## [1.0.0b1] - Development
+
+### Added
+- Test infrastructure improvements and codecov integration
+- GitHub Actions CI/CD pipeline replacing Travis CI
+- pytest configuration and test suite expansion
+- Test GPCR dataset for testing
+- PyBasher commands for bash operations
+- Tarfile member sanitization for security (#173)
+
+### Changed
+- Removed Travis CI in favor of GitHub Actions
+- Updated Python version support (3.9, 3.10, 3.11)
+- Upgraded Biopython version
+- Bumped dependencies: tqdm (4.25.0 → 4.66.3), jinja2, werkzeug, sqlalchemy
+
+### Fixed
+- Fixed tarfile member sanitization in extractall() (#173)
+- Fixed various test failures and code coverage issues
+- Fixed requirements.txt security vulnerabilities (#179, #175, #176, #170, #169, #168)
+- Fixed Cookies tests and Oven/CookBook text issues
+- Fixed log level color formatting
+- Fixed Flask version requirements and psutil requirement
+
+## [0.9.0a2] - Previous Release
+
+### Added
+- Initial test suite
+- Basic CI/CD setup
+
+### Changed
+- Package structure and organization
+
+---
+
+## Version History Notes
+
+- **1.0.0b2**: Latest release (2025-12-02) - Test coverage improvements and bug fixes
+- **1.0.0b1**: Previous beta release - Test infrastructure and CI/CD improvements
+- **0.9.0a2**: Previous tagged release (alpha)

OrthoEvol/Cookies/README.md

@@ -7,20 +7,105 @@ to set up your directory if you intend to create a web app/interface for your pr
 
 Learn more about the [cookiecutter](https://github.com/audreyr/cookiecutter) package.
 
-## Examples
+## Overview
+
+The Cookies module provides two main classes:
+
+- **CookBook**: Manages cookiecutter template paths and configurations
+- **Oven**: Deploys cookiecutter templates to create directory structures
 
 The [Manager module](https://github.com/datasnakes/OrthoEvolution/tree/master/OrthoEvol/Manager)
 uses the _CookBook_ and _Oven_ classes as a primary means of functioning.
 
-### A Simple Implementation
+## Available Templates
+
+* Templates used when creating a full repository:
+  * `new_repository` - Creates a full repository structure
+  * `new_user` - Creates a user directory structure
+  * `new_project` - Creates a project directory structure
+  * `new_research` - Creates a research directory structure
+  * `new_database_repo` - Creates database repository structure
+  * `new_app` - Creates R-Shiny application structure
+  * `new_website` - Creates Flask website structure
+
+* Template for standalone projects:
+  * `new_basic_project` - Creates a basic standalone project structure
+
+## Examples
+
+### Simple Implementation
 
 ```python
 from OrthoEvol.Cookies import Oven
 
+# Create an Oven instance
 Kitchen = Oven(repo="repo", user="username", project="project-name",
                output_dir="path/to/project")
+
+# Access ingredients (parameters)
 Pantry = Kitchen.Ingredients
 
-# To create a user directory
-Kitchen.bake_the_user()
+# Create different directory structures
+Kitchen.bake_the_repo()      # Create repository
+Kitchen.bake_the_user()      # Create user directory
+Kitchen.bake_the_project()   # Create project directory
+```
+
+### Full Repository Setup
+
+```python
+from OrthoEvol.Cookies import Oven
+from pathlib import Path
+import os
+
+# Set up paths and names
+home = os.getcwd()
+repo = "Development"
+user = "username"
+project = "MyProject"
+research = "GPCR"
+research_type = "comparative_genetics"
+
+# Create paths
+repo_path = Path(home) / Path(repo)
+user_path = repo_path / Path('users')
+project_path = user_path / Path(user) / Path('projects')
+research_path = project_path / Path(project)
+
+# Initialize Oven for full repository
+Full_Kitchen = Oven(repo=repo, user=user, project=project, 
+                    basic_project=False, output_dir=home)
+
+# Create the full structure
+Full_Kitchen.bake_the_repo()
+Full_Kitchen.bake_the_user(cookie_jar=user_path)
+Full_Kitchen.bake_the_project(cookie_jar=project_path)
+Full_Kitchen.bake_the_research(research=research, 
+                               research_type=research_type, 
+                               cookie_jar=research_path)
+```
+
+### Basic Standalone Project
+
+```python
+from OrthoEvol.Cookies import Oven
+
+# Initialize Oven for basic project
+Basic_Kitchen = Oven(project="MyProject", basic_project=True, 
+                     output_dir=os.getcwd())
+
+# Create the basic project
+Basic_Kitchen.bake_the_project()
 ```
+
+### Available Methods
+
+The `Oven` class provides the following methods:
+
+- `bake_the_repo(cookie_jar=None)` - Create a repository structure
+- `bake_the_user(cookie_jar=None)` - Create a user directory structure
+- `bake_the_project(cookie_jar=None)` - Create a project directory structure
+- `bake_the_research(research_type, research, cookie_jar=None)` - Create a research directory
+- `bake_the_db_repo(db_config_file, db_path, cookie_jar=None, archive_flag=False, delete=False)` - Create database repository
+- `bake_the_website(host, port, website_path, cookie_jar=None)` - Create a Flask website
+- `bake_the_app(app, cookie_jar=None)` - Create an R-Shiny app structure