Installation

Stable release

Installation of the latest stable release version.

With conda:

conda install -c conda-forge pyhdx

With pip:

pip install pyhdx

To install with web application:

pip install pyhdx[web]

To install with pdf output:

pip install pyhdx[pdf]

Installation via conda automatically installs all extras.

Running the web server

PyHDX web application can be launched from the command line using the pyhdx cli command with below options,

To run PyHDX server using default settings on your local server:

pyhdx serve

To run PyHDX server using the IP address and port number of your dask cluster:

pyhdx serve --scheduler_address <ip>:<port>

If no dask cluster is found at the specified address, a LocalCluster will be started (on localhost) using the specified port number.

To start a dask cluster separately, open another terminal tab and run:

python local_cluster.py

This will start a Dask cluster on the scheduler address as specified in the PyHDX config.

Downloading datasets

You can download public datasets from the HDX-MS database to directly load into PyHDX web.

To download up to 5 available datasets from the repository:

pyhdx datasets fetch 5

Install from source

Create a new conda environment in a local .venv folder:

conda create --prefix ./.venv python=3.9
conda activate ./.venv

Clone the GitHub repository:

git clone https://github.com/Jhsmit/PyHDX
cd PyHDX

You can install the dependencies from the pinned requirement files for your OS with pip:

$ pip install -r requirements/requirements-<operating-system>-3.9.txt

Then to editable install PyHDX:

$ pip install -e .

Running from source

To run the web application:

python pyhdx/web/serve.py

This runs the pyhx web application without a Dask cluster to submit jobs to, so submitting a fitting job will give an error.

To start a dask cluster separately, open another terminal tab and run:

python pyhdx/local_cluster.py

Configuration

A configuration file is located in the .pyhdx folder in the user home directory. This file is used by default and can be edited to change PyHDX default settings.

Alternatively, users can create additional .yaml configuration files in this directory, after which the scripts local_cluster.py and serve.py prompt the user for which file to use.

The section server configures the panel server settings. In this section the additional keys port and websocket_origin can be added, which are passed to panel.serve. See the panel Deploy and Export deploy section for more information.