Model Package for Bluesky Instrument Minimal Installation

Model of a Bluesky Data Acquisition Instrument in console, notebook, & queueserver.

Installation

Clone the repository.

git clone [email protected]:BCDA-APS/tomo-bits.git
cd tomo-bits

Set up the development environment.

export ENV_NAME=tomo_bits
conda create -y -n $ENV_NAME python=3.11 pyepics
conda activate $ENV_NAME
pip install -e ."[all]"

IPython console

To start the bluesky instrument session in a ipython execute the next command in a terminal:

ipython

Inside the ipython console execute:

from instrument.startup import *

Jupyter notebook

Start JupyterLab, a Jupyter notebook server, or a notebook, VSCode.

Start the data acquisition:

from instrument.startup import *

Sim Plan Demo

To run some simulated plans that ensure the installation worked as expected please run the next commands inside an ipython session or a jupyter notebook after starting the data acquisition:

RE(sim_print_plan())
RE(sim_count_plan())
RE(sim_rel_scan_plan())

See this example.

Configuration files

The files that can be configured to adhere to your preferences are:

• configs/iconfig.yml - configuration for data collection
• configs/logging.yml - configuration for session logging to console and/or files
• qserver/qs-config.yml - contains all configuration of the QS host process. See the documentation for more details of the configuration.

queueserver

The queueserver has a host process that manages a RunEngine. Client sessions will interact with that host process.

Run a queueserver host process

Use the queueserver host management script to start the QS host process. The restart option stops the server (if it is running) and then starts it. This is the usual way to (re)start the QS host process. Using restart, the process runs in the background.

./qserver/qs_host.sh restart

Run a queueserver client GUI

To run the gui client for the queueserver you can use the next command inside the terminal:

queue-monitor &

Shell script explained

A shell script is used to start the QS host process. Below are all the command options, and what they do.

(bstest) $ ./qserver/qs_host.sh help
Usage: qs_host.sh {start|stop|restart|status|checkup|console|run} [NAME]

    COMMANDS
        console   attach to process console if process is running in screen
        checkup   check that process is running, restart if not
        restart   restart process
        run       run process in console (not screen)
        start     start process
        status    report if process is running
        stop      stop process

    OPTIONAL TERMS
        NAME      name of process (default: bluesky_queueserver-)

Alternatively, run the QS host's startup command directly within the ./qserver/ subdirectory.

cd ./qserver
start-re-manager --config=./qs-config.yml

Testing

Use this command to run the test suite locally:

pytest -vvv --lf ./src

Documentation

prerequisite

To build the documentation locally, install pandoc in your conda environment:

conda install conda-forge::pandoc

Use this command to build the documentation locally:

make -C docs clean html

Once the documentation builds, view the HTML pages using your web browser:

BROWSER ./docs/build/html/index.html &

Adding to the documentation source

The documentation source is located in files and directories under ./docs/source. Various examples are provided.

Documentation can be added in these formats: .rst (reStructured text), .md (markdown), and .ipynb (Jupyter notebook). For more information, see the Sphinx documentation.

Warnings

Bluesky Queueserver

The QS host process writes files into the qserver/ directory. This directory can be relocated. However, it should not be moved into the instrument package since that might be installed into a read-only directory.

How-To Guides

• APS Data Management Plans