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Decapretated Documentation

Examples

example

Server Deployment

Currently out of date for pipenv
Requires environment with all files

UNT servers

  1. poetry run python combined.py -server on compute node
  2. ssh -L 5006:cX-X-X:5006 [email protected] on local
  3. open localhost:5006 on local browser

Generally

  1. poetry run python combined.py -server on server
  2. port forwarding depending on network configuration
  3. open address:5006 on local browser

File formats

.3nc: Raman data, unsuported
.5nc: old RASHG data, netCDF4, uses fiveD.py
.zarr: new RASHG, zarr, uses sixD.py

Submodule

Using a git submodule to reference files from the https://github.com/UNTNeogiLab/RASHG project RASHG is developed in parellel with the project
When cloning use --recurse-submodules or run
git submodule init
git submodule update

Using setup.py (requires python and anaconda)

python setup.py (older script, depends upon mamba/conda, slower, harder to maintain)

Using bare pip

pip install -r config/requirements.txt

Jupyter Lab:

Jupyter lab is decapretated in favor of python scripts

Server Deployment

Requires environment with all files

UNT servers

  1. panel serve combined.py --address 0.0.0.0 on compute node
  2. ssh -L 5006:cX-X-X:5006 [email protected] on local
  3. open localhost:5006 on local browser

Generally

  1. panel serve parameterized.ipynb --address 0.0.0.0 on server
  2. port forwarding depending on network configuration
  3. open address:5006 on local browser

Troubleshooting information

Hangs on creating Virtual environment
virtualenv pyenv --read-only-app-data
then activate it (source pyenv/bin/activate) and run
pipenv sync
followed by pipenv run whatever