Particle Accelerator MIddle LAyer (PAMILA) - Python middle layer package for control of particle accelerators, compatible with bluesky / ophyd / tiled

How to set up (TL;DR version)

Assuming you have the git and conda (or mamba) commands, run the installation bash script:

$ git clone https://github.com/python-accelerator-middle-layer/pamila.git
$ cd pamila
$ bash install.sh

This will perform the steps "Environment setup", "How to install pamila with poetry", and "Generate and run example Jupyter notebooks" below.

You will be prompted to enter the new conda environment name, your facility name (e.g., nsls2), and whether to use conda or mamba.

If no error occurs, you are ready to start using PAMIAL once you activate the newly created envirnoment.

Environment setup

$ conda create -n pamila python=3.11 poetry numpy=1 scipy pint pyepics caproto h5py matplotlib=3.8 ipython jupyter ipympl jupytext pytest black pre-commit pydantic=2.9 -c conda-forge

(Note that pydantic=2.10 causes an error when the ge arg of Field() is a non-jsonable object like pint.Quantity() as of 11/27/2024. v2.9 works.)

Then activate the created environment:

$ conda activate pamila

Now you need to specify some environment variables for this environment. Run the following two commands:

(pamila) $ echo 'export PAMILA_FACILITY="nsls2"' > $(dirname $(dirname $(which python)))/etc/conda/activate.d/pamila_activate.sh

(pamila) $ echo 'unset PAMILA_FACILITY' > $(dirname $(dirname $(which python)))/etc/conda/deactivate.d/pamila_deactivate.sh

"nsls2" in pamila_activate.sh should be replaced with your facility name.

Deactivate and re-activate the environment for this environment variable setup to take effect, and confirm it:

(pamila) $ conda deactivate
$ conda activate pamila
(pamila) $ echo $PAMILA_FACILITY
nsls2

Install other dependent packages with pip:

(pamila) $ pip install ophyd
(pamila) $ pip install bluesky==1.13
(pamila) $ pip install tiled[all]
(pamila) $ pip install accelerator-toolbox

How to install pamila with poetry

(pamila) $ git clone https://github.com/python-accelerator-middle-layer/pamila.git
(pamila) $ cd pamila
(pamila) $ poetry build
(pamila) $ pip install dist/pamila-0.1.0-py3-none-any.whl

If the actual wheel file name generated by the poetry build command is different from pamila-0.1.0-py3-none-any.whl, use the actual file name.

If you modify the source for pamila and re-install it, you can run the following commands instead:

(pamila) $ poetry build
(pamila) $ pip install dist/pamila-0.1.0-py3-none-any.whl --force-reinstall --no-deps

Generate and run example Jupyter notebooks

Run the following commands to generate example notebooks:

(pamila) $ cd pamila/examples/nb_gen
(pamila) $ python auto_gen_notebooks.py

Try running the notebooks in the order of the file names, starting with "00".

pre-commit setup

Before pre-commit starts automatically formats all the files included in the git repository, it needs to be set up as follows:

(pamila) $ cd pamila
(pamila) $ pre-commit install
pre-commit installed at .git/hooks/pre-commit