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Created: | May 30, 2025 at 1:58 p.m. (UTC) | |
Last updated: | Jun 03, 2025 at 5:55 p.m. (UTC) | |
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Abstract
This resource contains the following bash scripts which can be used by the user in any of the JupterHub instances accessible via the "Open with" functionality of HydroShare to create conda environment to run AORC related notebooks. In order to run any of the listed bash script files in JupyterHub, first make the file executable using the JupyterHub terminal. Here is an example:
chmod +x setup_aorc_conda_env_cuahsi_jh.sh
Then the above script can be executed from the command line as follows:
./setup_aorc_conda_env_cuahsi_jh.sh
After executing the script as above, it will create a new conda environment called 'aorc'. It will also register this new conda environment as a new Jupyter kernel with name 'Python [conda env:.conda-aorc]'. In order for any of the AORC related notebooks to use this kernel you have to first shut down all kernels and then use the option 'Change Kernel" to select this new kernel.
- setup_aorc_conda_env_cuahsi_jh.sh (This script should be used in CUAHSI JupyterHub to create a new conda environment called 'aorc')
- setup_aorc_conda_env_cybergis_jh.sh (This script should be used in CyberGIS Jupyter for Water) to create a new conda environment called 'aorc')
- environment.yml (This file contains the python modules needed to run the AORC notebooks - similar to requirements.txt file used with pip install). The above script files use this file to install the python modules specified in this yml file.
- delete_aorc_conda_env_cuahsi_jh,sh (This script can be run to delete the conda env 'aorc' in CUAHSI JupyterHub)
- delete_aorc_conda_env_cybergis_jh,sh (This script can be run to delete the conda env 'aorc' in CyberGIS Jupyter for Water)
- setup_aorc_conda_env_2i2c_jh_uv.sh (This script should be used in 2i2c JupyterHub to create a new conda environment called 'aorc')
- environment-2i2c.yml (This file is used in the above script that creates the aorc conda env in 2i2c. This environment file has few python modules for conda installation)
- requirements-2i2c.txt (This file is used in the above script that creates the aorc conda env in 2i2c to pip install most of the python modules needed for AORC notebooks.
- delete_aorc_conda_env_2i2c_jh,sh (This script can be run to delete the conda env 'aorc' in 2i2c JupyterHub)
- sample_commands_to_create_conda_env_jh.md (This file contains example commands to create a new conda environment - without using a bash script)
How to update the aorc conda environment after it has been created?
Update here means installing additional python modules or upgrading to a newer version of any modules that is already installed in the aorc conda environment. The following commands are applicable to CUAHSI and CyberGIS JH instances.
- Update the environment.yml file by adding new modules or updating the version of any modules in that file.
- In the JupyterHub instance, use a terminal and run the following 2 commands:
- conda activate aorc
- mamba env update -f environment.yml
Update aorc environment in 2i2c:
If you have updated the environments-2i2c.yml, run
- conda env update -f environment-2i2c.yml
If you have updated the requirements-2i2c.txt file, run
- pip install -r requirements-2i2c.txt
If you just want to install fe new modules or upgrade existing modules without updating environment or requirements file, then run
conda install <module-1-name> <module-2-name>
OR
pip install <module-1-name> <module-2-name>
NOTE: It is better to update environment or requirements file when there is a need to update the environment as it helps reproducibility.
Subject Keywords
Content
README.md
AORC Conda Environment Setup Scripts
This repository contains bash scripts for setting up conda environments to run AORC-related notebooks in various JupyterHub instances accessible via HydroShare's "Open with" functionality.
Usage Instructions
To use any of the bash scripts, first make them executable using the JupyterHub terminal:
bash
chmod +x setup_aorc_conda_env_cuahsi_jh.sh
Then execute the script:
bash
./setup_aorc_conda_env_cuahsi_jh.sh
Available Scripts
Environment Setup Scripts
setup_aorc_conda_env_cuahsi_jh.sh
- Creates a new conda environment 'aorc' in CUAHSI JupyterHubsetup_aorc_conda_env_cybergis_jh.sh
- Creates a new conda environment 'aorc' in CyberGIS Jupyter for Watersetup_aorc_conda_env_2i2c_jh_uv.sh
- Creates a new conda environment 'aorc' in 2i2c JupyterHub
Environment Cleanup Scripts
delete_aorc_conda_env_cuahsi_jh.sh
- Deletes the 'aorc' conda environment in CUAHSI JupyterHubdelete_aorc_conda_env_cybergis_jh.sh
- Deletes the 'aorc' conda environment in CyberGIS Jupyter for Waterdelete_aorc_conda_env_2i2c_jh.sh
- Deletes the 'aorc' conda environment in 2i2c JupyterHub
Configuration Files
environment.yml
- Contains python modules for AORC notebooks (used by CUAHSI and CyberGIS scripts)environment-2i2c.yml
- Contains python modules for conda installation in 2i2c environment (used by 2i2c script)requirements-2i2c.txt
- Contains python modules for pip installation in 2i2c environment (used by 2i2c script)
Updating the Environment
For CUAHSI and CyberGIS JupyterHub
- Update the
environment.yml
file with new modules or version changes - Run the following commands in the JupyterHub terminal:
bash conda activate aorc mamba env update -f environment.yml
For 2i2c JupyterHub
For conda-managed packages:
bash
conda env update -f environment-2i2c.yml
For pip-managed packages:
bash
pip install -r requirements-2i2c.txt
Quick Updates Without File Modifications
You can directly install or upgrade modules using:
```bash
conda install
or
pip install
Sample Commands for Manual Conda Environment Creation
sample_commands_to_create_conda_env_jh.md
- Example commands for manual conda environment creation
Note: For better reproducibility, it's recommended to update the environment or requirements files when making changes to the environment.
How to Cite
This resource is shared under the Creative Commons Attribution CC BY.
http://creativecommons.org/licenses/by/4.0/
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