MicroGrowth and AutoGrowth

Repository for Streamlit apps based on growthcurves package.

The MicroGrowth app is designed for analysis of optical density (OD) measurements.

The AutoGrowth app is designed for analysis of optical density (OD) measurements produced mainly with a mini reactors, such as PioReactor or Chi.Bio.

The code translated to Python was based on the original R code from the Shiny apps.

MicroGrowth: Install and start app

In a new environment you can install the app using the app's requirements.txt

pip install -r MicroGrowth/requirements.txt

Start the app from the root of the repository (as it's done on Streamlit Cloud):

streamlit run MicroGrowth/app.py

AutoGrowth: Install and start app

In a new environment you can install the app using

pip install .

Start the app from the root of the repository (as it's done on Streamlit Cloud):

streamlit run AutoGrowth/main.py

Development environment for shared ui code

Install package so that new code is picked up in a restared python interpreter:

pip install -e ".[dev]"

Versioning

This repository uses a hybrid strategy:

• The shared package growthcurve-app uses git-tag based versioning via setuptools_scm.
• Each app keeps its own version in a local VERSION file.

Current app version files:

• AutoGrowth/VERSION
• MicroGrowth/VERSION

Bump app version (choose):

bump-my-version bump patch --config-file .bumpversion-autogrowth.toml
bump-my-version bump patch --config-file .bumpversion-microgrowth.toml

History

Growthcurves, AutoGrowth and the MicroGrowth app were developed in parallel. The growthcurves package severes as the backend for both apps, and the apps were developed and aligned to feature a similar design.

The joint app combining three Shiny apps for PioReactor tools was started as the three individual apps mentioned above using shiny, but never completed. You can find the last development version in the original repository of this fork (see: milnus/PioGrowth).

It was created on the basis of three individual apps

• milnus/pioreactor_turbidostat_shiny
• milnus/Batch_analysis
• milnus/OD_calibration_bioreactor

Then it was moved from biosustain/PioGrowth to this repository, to start sharing functionality with similarly designed MicroGrowth app.

The original code for the MicroGrowth app was developed in the repository sambra95/TheGrowthAnalysisApp