Release v0.1 (#35)

Author: sdhutchins

PULL_REQUEST_TEMPLATE.md .github/PULL_REQUEST_TEMPLATE.mdPULL_REQUEST_TEMPLATE.md renamed to .github/PULL_REQUEST_TEMPLATE.md

@@ -1,13 +1,15 @@
 ### This pull request addresses issue #
 
 ### Features Added
+
 - Feature added - *details*
 
 ### Bugs Fixed
+
 - Bug fixed - *details*
 
 ### Features Deprecated
+
 - Feature deprecated - *details*
-<br>
 
 :warning: Delete this line! Please request a review from @sdhutchins! Delete any unused heading or line.

.github/workflows/test-build.yml

@@ -0,0 +1,49 @@
+name: Test Package Build
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build-and-test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build pytest pytest-cov
+
+      - name: Install package dependencies
+        run: |
+          pip install -r requirements.txt
+
+      - name: Build package
+        run: |
+          python -m build
+
+      - name: Install built package
+        run: |
+          pip install dist/*.whl
+
+      - name: Run tests with coverage
+        run: |
+          pytest tests/ -v --cov=labrat --cov-report=xml --cov-report=term
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: sdhutchins/labrat

.readthedocs.yaml

@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: "ubuntu-24.04"
+  tools:
+    python: "3.11"
+  jobs:
+    pre_install:
+      - pip install mkdocs
+      - pip install mkdocs-material
+
+mkdocs:
+  configuration: mkdocs.yml

CHANGELOG.md

@@ -0,0 +1,38 @@
+# 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).
+
+## [0.1.0] - 2025-11-21
+
+### Added
+- Command-line interface (CLI) with comprehensive testing infrastructure
+- Protein analysis functionality with test coverage
+- Project management system with `.labrat` folder support for project metadata
+- Documentation structure including API, CLI, installation, and index pages
+- Test documentation for contributors
+- Comprehensive test suite covering:
+  - CLI functionality
+  - Math functions
+  - Protein analysis
+  - Archiver
+  - File organizer
+  - Project manager
+- `jinja2-time` dependency for template functionality
+
+### Changed
+- PyPI package name changed from `labrat` to `pylabrat` to avoid naming conflicts
+- Moved pull request template to `.github` folder for better organization
+
+### Fixed
+- Logic error in `dilute_stock` function
+- Math function test failures
+- Protein analysis implementation issues
+- Various errors throughout the codebase
+- Missing dependency declarations
+
+### Improved
+- Code comments and documentation throughout
+- Test coverage and reliability

MANIFEST.IN

@@ -1 +1,3 @@
-include tests/
+include tests/
+include labrat/genetics/codons.json
+recursive-include labrat *.json

README.md

@@ -1,6 +1,7 @@
 # labrat
 
 [![Build Status](https://app.travis-ci.com/sdhutchins/labrat.svg?token=xfnbNTQhjNbir5xACn8R&branch=master)](https://app.travis-ci.com/sdhutchins/labrat)
+[![codecov](https://codecov.io/gh/sdhutchins/labrat/graph/badge.svg?token=LqA1Lqf0uu)](https://codecov.io/gh/sdhutchins/labrat)
 
 A basic science lab framework aimed at reproducibility and lab management. This package is in the very early stages of development.
 
@@ -75,6 +76,40 @@ archive_base_dir = "/Users/shutchens/Archive"
 archived_path = project_manager.delete_project(project_path, archive_base_dir)
 ```
 
+## Tests
+
+Before running tests, ensure all dependencies are installed:
+
+```bash
+pip install -r requirements.txt
+```
+
+Or if installing the package:
+
+```bash
+pip install .
+```
+
+Run all tests using unittest:
+
+```bash
+python -m unittest discover -s tests
+```
+
+Or run tests with pytest (if installed):
+
+```bash
+pytest tests/
+```
+
+To run a specific test file:
+
+```bash
+python -m unittest tests.test_archiver
+python -m unittest tests.test_file_organizer
+python -m unittest tests.test_project_manager
+```
+
 ## ToDo
 
 - [ ] Add a lab inventory app

docs/api.md

@@ -0,0 +1,39 @@
+# API Reference
+
+## Math Functions
+
+::: labrat.math.functions
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Genetics
+
+::: labrat.genetics.dna_analysis
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: labrat.genetics.protein_analysis
+    options:
+      show_root_heading: true
+      show_source: false
+
+## Project Management
+
+::: labrat.project.projectmanager
+    options:
+      show_root_heading: true
+      show_source: false
+
+## File Management
+
+::: labrat.filemanager.archive
+    options:
+      show_root_heading: true
+      show_source: false
+
+::: labrat.filemanager.organize
+    options:
+      show_root_heading: true
+      show_source: false

docs/cli.md

@@ -0,0 +1,44 @@
+# CLI Reference
+
+labrat provides a command-line interface for common tasks.
+
+## Commands
+
+### Project Management
+
+```bash
+# Create a new project
+labrat project new --type <type> --name <name> --path <path>
+
+# List all projects
+labrat project list
+
+# Delete a project
+labrat project delete --path <path>
+```
+
+### Archiving
+
+```bash
+labrat archive --source <source_dir> --destination <dest_dir> --name <name>
+```
+
+### File Organization
+
+```bash
+# Organize scientific files
+labrat organize --science
+
+# Organize by keyword
+labrat organize --keyword <keyword>
+
+# Organize all file types
+labrat organize --all
+```
+
+For detailed help on any command:
+
+```bash
+labrat --help
+labrat <command> --help
+```

docs/index.md

@@ -0,0 +1,57 @@
+# labrat
+
+A basic science lab framework aimed at reproducibility and lab management.
+
+## Features
+
+- Math functions for dilutions, molarity calculations, and more
+- Command-line tools for archiving and organizing files
+- Project management for computational biology workflows
+- DNA and protein analysis utilities
+
+## Quick Start
+
+Install labrat:
+
+```bash
+pip install .
+```
+
+Or for development:
+
+```bash
+pip install -e .
+```
+
+## Usage
+
+### Command Line
+
+```bash
+# Create a new project
+labrat project new --type computational-biology --name "My Project"
+
+# List projects
+labrat project list
+
+# Archive a directory
+labrat archive --source /path/to/source --destination /path/to/archive --name project_name
+
+# Organize files
+labrat organize --science --all
+```
+
+### Python API
+
+```python
+from labrat.math import dilute_stock
+
+# Calculate final concentration
+final_conc = dilute_stock(100, 2, vF=4)
+```
+
+## Documentation
+
+- [Installation Guide](installation.md)
+- [CLI Reference](cli.md)
+- [API Reference](api.md)

docs/installation.md

@@ -0,0 +1,57 @@
+# Installation
+
+## Requirements
+
+- Python 3.8 or higher
+- pip
+
+## Install from Source
+
+1. Clone the repository:
+
+```bash
+git clone https://github.com/sdhutchins/labrat.git
+cd labrat
+```
+
+2. Install the package:
+
+```bash
+pip install .
+```
+
+For development mode:
+
+```bash
+pip install -e .
+```
+
+## Install Dependencies
+
+Install all required dependencies:
+
+```bash
+pip install -r requirements.txt
+```
+
+## Install Documentation Dependencies
+
+To build and serve the documentation locally:
+
+```bash
+pip install -e ".[docs]"
+```
+
+Or install manually:
+
+```bash
+pip install mkdocs-material mkdocs-click mkdocstrings[python] pymdown-extensions
+```
+
+## Verify Installation
+
+Run the tests to verify everything is working:
+
+```bash
+pytest tests/
+```