{"id":18810797,"url":"https://github.com/ecell/kedro-bioimage","last_synced_at":"2026-01-11T00:30:14.194Z","repository":{"id":56030489,"uuid":"313240314","full_name":"ecell/kedro-bioimage","owner":"ecell","description":null,"archived":false,"fork":false,"pushed_at":"2020-11-30T07:40:45.000Z","size":60,"stargazers_count":0,"open_issues_count":5,"forks_count":0,"subscribers_count":6,"default_branch":"main","last_synced_at":"2024-12-29T23:44:15.663Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ecell.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-11-16T08:46:12.000Z","updated_at":"2020-11-30T07:40:48.000Z","dependencies_parsed_at":"2022-08-15T11:50:17.079Z","dependency_job_id":null,"html_url":"https://github.com/ecell/kedro-bioimage","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fkedro-bioimage","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fkedro-bioimage/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fkedro-bioimage/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecell%2Fkedro-bioimage/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ecell","download_url":"https://codeload.github.com/ecell/kedro-bioimage/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239748254,"owners_count":19690232,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-07T23:22:28.768Z","updated_at":"2026-01-11T00:30:14.126Z","avatar_url":"https://github.com/ecell.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# kedro-bioimage\n\n## Overview\n\nThis is a Kedro project for bioimage analysis, which was generated using `Kedro 0.16.6`.\n\n## How to setup kedro-bioimage environment\n\n1. install miniconda from https://docs.conda.io/en/latest/miniconda.html\n2. Create a new Python virtual environment, called kedro-environment, using conda\n    ```\n    conda create --name kedro-bioimage python=3.7 -y\n    ```\n3. This will create an isolated Python 3.7 environment. To activate it:\n    ```\n    conda activate kedro-bioimage\n    ```\n4. Install dependencies with pip (and install numpy with conda for Windows)\n    ```\n    pip install -r src/requirements.txt --user\n    conda install numpy\n    ```\n5. Remove scopyon example directory\n    ```\n    rm -rf src/scopyon/examples\n    ```\n\n## Rules and guidelines\n\nIn order to get the best out of the template:\n\n* Don't remove any lines from the `.gitignore` file we provide\n* 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)\n* Don't commit data to your repository\n* Don't commit any credentials or your local configuration to your repository. Keep all your credentials and local configuration in `conf/local/`\n\n## How to run your Kedro pipeline\n\nYou can run your Kedro project with:\n\n```\nkedro run\n```\n\n## How to test your Kedro project\n\nHave 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:\n\n```\nkedro test\n```\n\nTo configure the coverage threshold, go to the `.coveragerc` file.\n\n## Project dependencies\n\nIf you'd like to update your project requirements, please update `src/requirements.in` and re-run `kedro build-reqs`.\n\n*DO NOT UPDATE `src/requirements.txt` manually, if you do not understand what this will effect*\n\n```\nkedro build-reqs\n```\n\nTo install new added packages,\n\n```\nkedro install\n```\n\n[Further information about project dependencies](https://kedro.readthedocs.io/en/stable/04_kedro_project_setup/01_dependencies.html#project-specific-dependencies)\n\n## How to work with Kedro and notebooks\n\n\u003e Note: Using `kedro jupyter` or `kedro ipython` to run your notebook provides these variables in scope: `context`, `catalog`, and `startup_error`.\n\u003e\n\u003e 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.\n\n### Jupyter\n\nYou can start a local notebook server:\n\n```\nkedro jupyter notebook\n```\n\n### JupyterLab\n\nYou can also start JupyterLab:\n\n```\nkedro jupyter lab\n```\n\n### IPython\nAnd if you want to run an IPython session:\n\n```\nkedro ipython\n```\n\n### How to convert notebook cells to nodes in a Kedro project\nYou 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.\n\nBy 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/\u003cpackage_name\u003e/nodes/`:\n\n```\nkedro jupyter convert \u003cfilepath_to_my_notebook\u003e\n```\n\u003e *Note:* The name of the Python file matches the name of the original notebook.\n\nAlternatively, 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:\n\n```\nkedro jupyter convert --all\n```\n\n### How to ignore notebook output cells in `git`\nTo 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`.\n\n\u003e *Note:* Your output cells will be retained locally.\n\n## Package your Kedro project\n\n[Further information about building project documentation and packaging your project](https://kedro.readthedocs.io/en/stable/03_tutorial/05_package_a_project.html)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fecell%2Fkedro-bioimage","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fecell%2Fkedro-bioimage","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fecell%2Fkedro-bioimage/lists"}