Day1-Experiment Database

An exercise in adding Dependency-Documented Reproducibility to a Napari App

This contains an image editor application that opens a picture of coins and makes it so that whenever the user adds a point to the Points Layer, it tries to find an area near that point where there is a coin.

Setup

(Instructions Here)

Running the App

Run the app directly with a

streamlit run label_coins

Exercise

Step 1: Fork this Project to Get your Own Copy

In GitHub, click the "Fork" Button in the upper-right corner of the GitHub Window:

Step 2: Clone Your Fork Into a VSCode Project

Command	Description
git clone <url> label_coins	Clone the project into a folder called "label_coins"
cd label_coins	Change the working directory to the label_coins folder.
code .	Launch VSCode in the Current Folder

Step 3: Get the Application to Run

Choose a Package Manager: Either Conda or Pixi.

If Using Conda:

Command	Description
conda create -p ./venv	Setup Environment
conda activate ./venv	Activate Environment
conda install python=3.12	Install Conda Dep
pip install numpy	Install Python Dep with Pip (note: Python must be installed first)

If Using Pixi:

Command	Description
pixi init	Setup Environment
pixi shell	Activate Environment
pixi add python=3.12	Install Conda Dep
pixi add --pypi numpy	Install Python Dep with Pip (note: Python must be installed first)

Step 4: Add the needed dependencies to a file in the root directory of this project

If using Conda:

Command	Description
conda env export -f environment.yaml	Make environment file

If using Pixi, the pixi.toml should already be made--nothing to do!

Step 5: Check that your dependency file is working, by deleting the environment and starting again.

If using Conda:

Command	Description
conda env remove -p ./venv	Delete the environment.
conda env create -p ./venv -f environment.yaml	Create a new environment from the environment.yaml file.

If using Pixi:

Command	Description
rmdir ./venv	Delete the environment directory (doens't use Pixi, just deletes the folder)
pixi install	Create a new environment from the pixi.toml file.

Step 6: Commit the dependencies to the git repo

If using Git for the first time, you'll need to add your name and email first for signing your commits:

Command	Description
git config --global user.name "My Name"	Add your name to commits. Usually this is your real name, not a GitHub username, but it doesn't matter what you use.
git config --global user.email "[email protected]"	Add your email to commits. Note: doesn't have to be the same email you used with GitHub, but it is helpful if it is a real email address (because it helps your portfolio throuhg GitHub)

Only add the environment.yaml or pixi.toml file, not any of the files in the venv/ folder.

Command	Description
git status	See what Git is noticing as changes.
git add myfile	Start tracking "myfile"
git commit -am "message"	Commit all changes to the tracked files with the note "message"
git log	See what the recent commits were. May need to press the q key to exit the log.

Step 7: Document the Installation in the Readme

Write the required steps for installing the dependencies for this code in the "Setup" section of this Readme file, then commit the updated Readme file.

Step 8: Push the latest commits to your GitHub Fork

Command	Description
git remote -v	See the name and urls of all remote repositories
git remote add <name> <url>	Add a new git remote, if needed. Name can be anything, URL should be a github repo.
git remote remove <name>	Remove a git remote, if needed.
git branch	See the names or all branches. The one with a star next to it is the active branch.
git push origin main	Push the branch called "main" to the remote called "origin"

Step 9: On the GitHub website Make a Pull Request to the main repository, requesting that your changes be added!

1. Click on the Pull Request Tab:

2. Click New Pull Request:

3. Fill out the form and send the request!

Done!

Now a more-reproducible application has been made, and contributed to the original author--a collaboration on open-source software!