adamjbea/libtest

Prime Analysis Tools

• Quick Start - Running Application
  • Requirements
  • OPTIONAL - Git Bash
  • Clone The Repository
  • Virtual Environment
  • Running Tests, and Running the App
• Developer Section
  • Directory
    • Directory Structure
    • Directory Summary:
  • Primary Tool Development

Quick Start - Running Application

Requirements

All that is needed to start the Quick Start Guide is Python v=3.9.1

OPTIONAL - Git Bash

• Using Git Bash is helpful when it comes to navigating directories and running scripts from the command line
• Download here:
  • https://git-scm.com
• Should already have it if Git is on your system

Clone The Repository

• Navigate to where your project directory is, or create a new one.
• Using preferred method, clone the repsoitory
  • git clone https://[email protected]/missionbio/prime.git

Virtual Environment

1. Download and install Anconda from
   • https://www.anaconda.com/products/individual
2. Navigate to the /build folder in the repository, open your choice of command prompt.
3. Enter the following command:
   • conda env create --file environment.yml
4. Navigate back to the root directory
5. Activate your new virtual environment with the following code
   • conda activate prime_env

Running Tests, and Running the App

1. Verify installation by running the tests from the root directory with
   • pythom -m pytest
2. Run the application with
   • streamlit run app.py

Developer Section

Directory

Directory Structure

• The directory for the application is set up as follows
  • |_build
    • |_requirements.txt
    • |_build_env.yml
  • |_helper
    • |_init.py
    • |_Analyze.py
    • |_Beadcounting.py
    • |_Detection.py
    • |_Tools.py
    • |_Visualization.py
  • |_prime
    • |_init.py
    • |_Brightfield.py
    • |_Fluoresence.py
    • |_TubeVolume.py
  • |_tests
    • |_helper_tests
    • |_imgs
    • |_prime_tests
    • |_test_example.py
  • |_.gitignore
  • |_README.MD
  • |_app.py

Directory Summary:

• Build: Contains files to help build the application
  • Contains .yml file for venv creation
  • Contains requirements.txt for future build needs
• Helper: Contains files with helper functions
• Prime: Contains all the primary analysis functions: Brightfield, Fluorescence, and Tube Volume.
• Tests: Contains tests for each type of function and images needed for those tests
  • helper_Tests: Tests for helper functions
  • prime_Tests: Tests for prime functions
  • imgs: Images for prime_tests
  • test_example.py: File showing how to write a pytest
• app.py: application entry point

Primary Tool Development