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https://github.com/ecell/kedro-bioimage
https://github.com/ecell/kedro-bioimage
Last synced: 12 days ago
JSON representation
- Host: GitHub
- URL: https://github.com/ecell/kedro-bioimage
- Owner: ecell
- Created: 2020-11-16T08:46:12.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2020-11-30T07:40:45.000Z (about 4 years ago)
- Last Synced: 2024-11-07T23:25:53.798Z (2 months ago)
- Language: Python
- Size: 58.6 KB
- Stars: 0
- Watchers: 6
- Forks: 0
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
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README
# kedro-bioimage
## Overview
This is a Kedro project for bioimage analysis, which was generated using `Kedro 0.16.6`.
## How to setup kedro-bioimage environment
1. install miniconda from https://docs.conda.io/en/latest/miniconda.html
2. Create a new Python virtual environment, called kedro-environment, using conda
```
conda create --name kedro-bioimage python=3.7 -y
```
3. This will create an isolated Python 3.7 environment. To activate it:
```
conda activate kedro-bioimage
```
4. Install dependencies with pip (and install numpy with conda for Windows)
```
pip install -r src/requirements.txt --user
conda install numpy
```
5. Remove scopyon example directory
```
rm -rf src/scopyon/examples
```
## Rules and guidelines
In order to get the best out of the template:
* Don't remove any lines from the `.gitignore` file we provide
* Make sure your results can be reproduced by following a [data engineering convention](https://kedro.readthedocs.io/en/stable/11_faq/01_faq.html#what-is-data-engineering-convention)
* Don't commit data to your repository
* Don't commit any credentials or your local configuration to your repository. Keep all your credentials and local configuration in `conf/local/`
## How to run your Kedro pipeline
You can run your Kedro project with:
```
kedro run
```
## How to test your Kedro project
Have a look at the file `src/tests/test_run.py` for instructions on how to write your tests. You can run your tests as follows:
```
kedro test
```
To configure the coverage threshold, go to the `.coveragerc` file.
## Project dependencies
If you'd like to update your project requirements, please update `src/requirements.in` and re-run `kedro build-reqs`.
*DO NOT UPDATE `src/requirements.txt` manually, if you do not understand what this will effect*
```
kedro build-reqs
```
To install new added packages,
```
kedro install
```
[Further information about project dependencies](https://kedro.readthedocs.io/en/stable/04_kedro_project_setup/01_dependencies.html#project-specific-dependencies)
## How to work with Kedro and notebooks
> Note: Using `kedro jupyter` or `kedro ipython` to run your notebook provides these variables in scope: `context`, `catalog`, and `startup_error`.
>
> Jupyter, JupyterLab, and IPython are already included in the project requirements by default, so once you have run `kedro install` you will not need to take any extra steps before you use them.
### Jupyter
You can start a local notebook server:
```
kedro jupyter notebook
```
### JupyterLab
You can also start JupyterLab:
```
kedro jupyter lab
```
### IPython
And if you want to run an IPython session:
```
kedro ipython
```
### How to convert notebook cells to nodes in a Kedro project
You can move notebook code over into a Kedro project structure using a mixture of [cell tagging](https://jupyter-notebook.readthedocs.io/en/stable/changelog.html#cell-tags) and Kedro CLI commands.
By adding the `node` tag to a cell and running the command below, the cell's source code will be copied over to a Python file within `src//nodes/`:
```
kedro jupyter convert
```
> *Note:* The name of the Python file matches the name of the original notebook.
Alternatively, you may want to transform all your notebooks in one go. Run the following command to convert all notebook files found in the project root directory and under any of its sub-folders:
```
kedro jupyter convert --all
```
### How to ignore notebook output cells in `git`
To automatically strip out all output cell contents before committing to `git`, you can run `kedro activate-nbstripout`. This will add a hook in `.git/config` which will run `nbstripout` before anything is committed to `git`.
> *Note:* Your output cells will be retained locally.
## Package your Kedro project
[Further information about building project documentation and packaging your project](https://kedro.readthedocs.io/en/stable/03_tutorial/05_package_a_project.html)