HydroShare on Jupyter

HydroShare on Jupyter brings HydroShare resource management to JupyterLab's development environment. Download, edit, upload, and synchronize your HydroShare resources without leaving Jupyter! Collaborate, iterate, and stay up to date with HydroShare on Jupyter.

Installation

In accordance with the python community, we support and advise the usage of virtual environments in any workflow using python. In the following installation guide, we use python's built-in venv module to create a virtual environment in which the tools will be installed. Note this is just personal preference, any python virtual environment manager should work just fine (conda, pipenv, etc. ).

# Create and activate python environment, requires python >= 3.7

python3 -m venv venv
source venv/bin/activate
python3 -m pip install --upgrade pip

# Install
python3 -m pip install hydroshare_on_jupyter

# Link extension to JupyterLab
python3 -m hydroshare_on_jupyter configure

# Launch JupyterLab and start collaborating!
python3 -m jupyter lab

Configuration

HydroShare on Jupyter looks for configuration information in environment variables first, then at the following path locations:

1. ~/.config/hydroshare_on_jupyter/config
2. ~/.hydroshare_on_jupyter_config

The first configuration file found is used if it exists. However, environment variables take precedence, meaning they override configuration file values if they are set.

HydroShare on Jupyter configuration files use KEY=VALUE semantics (example below). Only one configuration variable should be specified per line. Line comments can be created by starting a line with #.

Configuration Variables

• DATA : directory where HydroShare resources are saved, default ~/hydroshare.
• OAUTH : canonical HydroShare OAuth2 pickle file, default None. Allows bypassing login by using OAuth2 via HydroShare.

Example configuration file

# file: ~/.config/hydroshare_on_jupyter/config
DATA=~/Downloads

Note

By default, HydroShare on Jupyter saves HydroShare resources to ~/hydroshare. This means, if JupyterLab is started from a directory where ~/hydroshare is not a descendent (e.g. ~/Downloads), you will not be able to open the HydroShare resource files you download using HydroShare on Jupyter. To resolve this, either open JupyterLab from ~ or change the directory HydroShare on Jupyter saves resources to using the data DATA configuration variable.

Development

HydroShare on Jupyter is open source and is available on GitHub. For contributing, please follow the following steps:

1. Clone the repository: git clone https://github.com/hydroshare/hydroshare_on_jupyter.git

2. Create a branch: git checkout -b my-branch

3. Create and activate a virtual environment (python >= 3.7): python3 -m venv venv

4. Activate the virtual environment: source venv/bin/activate

5. Build the frontend: Refer to webapp/README.md for instructions.

6. Build the backend:

   6.1. Navigate to the root of the project: hydroshare_on_jupyter

   6.2. Run: python3 pip install -e .

7. Link extension to JupyterLab: python3 -m hydroshare_on_jupyter configure

8. Check the list of configured extensions: jupyter labextension list --verbose

   8.1. Make sure the HydroShare on Jupyter extension is listed

9. Check the list of server extensions: jupyter server extension list

   9.1. Make sure the HydroShare on Jupyter server extension is listed

10. Set up the DATA environment variable: export DATA=~/hydroshare/Downloads

11. Launch JupyterLab: python3 -m jupyter lab --debug --notebook-dir=~/hydroshare

12. You should see the HydroShare on Jupyter extension in the JupyterLab launcher. Double click to open HydroShare on Jupyter.

13. Commit and push your changes.

14. Create a pull request GitHub.