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ERIC VLIC & QCDIS team at University of Amsterdam","email":"gabriel.pelouze@lifewatch.eu"},"license":"Apache-2.0","homepage":"https://github.com/NaaVRE/NaaVRE-workflow-jupyterlab","keywords":["jupyter","jupyterlab","jupyterlab-extension"],"repository":{"type":"git","url":"git+https://github.com/NaaVRE/NaaVRE-workflow-jupyterlab.git"},"description":"NaaVRE workflow editor frontend on Jupyter Lab","maintainers":[{"name":"gpelouze","email":"gabriel@pelouze.net"},{"name":"koen_greuell","email":"koen.greuell@lifewatch.eu"}],"readme":"# NaaVRE_workflow_jupyterlab\n\n[![Github Actions Status](https://github.com/NaaVRE/NaaVRE-workflow-jupyterlab/workflows/Build/badge.svg)](https://github.com/NaaVRE/NaaVRE-workflow-jupyterlab/actions/workflows/build.yml)\n\nNaaVRE workflow editor frontend on Jupyter Lab\n\n## Requirements\n\n- JupyterLab >= 4.0.0\n\n## Install\n\nTo install the extension, execute:\n\n```bash\npip install NaaVRE_workflow_jupyterlab\n```\n\n## Uninstall\n\nTo remove the extension, execute:\n\n```bash\npip uninstall NaaVRE_workflow_jupyterlab\n```\n\n## Contributing\n\n### Development install\n\nNote: You will need NodeJS to build the extension package.\n\nThe `jlpm` command is JupyterLab's pinned version of\n[yarn](https://yarnpkg.com/) that is installed with JupyterLab. You may use\n`yarn` or `npm` in lieu of `jlpm` below.\n\n```bash\n# Clone the repo to your local environment\n# Change directory to the NaaVRE_workflow_jupyterlab directory\n# Create a virtual environment and activate it\nvirtualenv venv\n. venv/bin/activate\n# Install jupyterlab and refresh the virtual lab\npip install 'jupyterlab>=4.0.0,<5'\n. venv/bin/activate\n# Install package in development mode\npip install -e \".\"\n# Link your development version of the extension with JupyterLab\njupyter labextension develop . --overwrite\n# Rebuild extension Typescript source after making changes\njlpm build\n```\n\nThis extension communicates with external NaaVRE services. During development, you can run a local version of those services with Docker compose. Initial setup:\n\n1. Create a file `./dev/workflow-config.json` by copying `./dev/workflow-config-example.json` and fill-in values for `api_endpoint` and `access_token`. To obtain these values, either use an existing argo instance, or run [NaaVRE/NaaVRE-dev-integration](https://github.com/NaaVRE/NaaVRE-dev-integration), and run `echo \"Bearer $(kubectl get secret vre-api.service-account-token -o=jsonpath='{.data.token}' | base64 --decode)\"` to get the access token. (TODO: this should be simplified in the future, after addressing NaaVRE/NaaVRE-workflow-service#1.)\n2. Copy the Jupyter Lab configuration\n   ```bash\n   mkdir venv/share/jupyter/lab/settings/\n   cp dev/overrides.json venv/share/jupyter/lab/settings/\n   ```\n3. Start docker compose\n   ```bash\n   docker compose -f dev/docker-compose.yaml up\n   ```\n\nYou can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.\n\n```bash\n# Watch the source directory in one terminal, automatically rebuilding when needed\njlpm watch\n# Run JupyterLab in another terminal\nwhile read env; do export $env; done < ./dev/jupyterlab.env\njupyter lab --notebook-dir ./notebook-dir\n```\n\nWith the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).\n\nBy default, the `jlpm build` command generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:\n\n```bash\njupyter lab build --minimize=False\n```\n\n### Development uninstall\n\n```bash\npip uninstall NaaVRE_workflow_jupyterlab\n```\n\nIn development mode, you will also need to remove the symlink created by `jupyter labextension develop`\ncommand. To find its location, you can run `jupyter labextension list` to figure out where the `labextensions`\nfolder is located. Then you can remove the symlink named `@naavre/workflow-jupyterlab` within that folder.\n\n### Isolated component development\n\nRebuilding the extension and refreshing JupyterLab to see changes in the browser takes several seconds. This makes it hard to quickly iterate on presentation aspects such as layout.\n\nTo get a quick preview of some components, we use [Storybook](https://storybook.js.org/):\n\n```shell\njlpm run storybook\n```\n\nNote that in Storybook, components don’t get the full context from Jupyter Lab and rely on some mocking. 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