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.