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aareproc (0.1.2)

Published 2025-07-02 16:16:38 +02:00 by leonarski_f

Installation

pip install --index-url  aareproc

About this package

HPC data processing pipeline (AareProc) for Swiss Light Source (SLS) 2.0 PXI, PXII, PXIII

AareProc

Description

Data processing pipeline that interacts with AareDB and process data for MX beamlines at SLS 2.0.

Current Features

  • db_slurm_handler: communicate with AareDB on SLURM job submission status (to be tested), now can be used on both ra and mx-x06da-queue-01. The script figures out what machine it is on and submits jobs accordingly. For db communication to be working, only ra-c-094 is working so need to run the db_slurm_handler here. It runs currently (since 2025-06-18) in a tmux session on mx-x06da-queue-01.
  • On mx-x06da-queue-01, activate the virtual env in AareProc folder by source sourceme
  • Default pipeline (when run python db_slurm_handler.py):
    1. inp_writer write XDS.INP according to the AareDB parameters. Default path is in sls/mx/data/<pgroup>/work/pytest/<job_id>_<sample_id>
    2. run xds
    3. download/find .pdb [Currently only with lyso pdb ]
    4. phenix.xtriage & pointless
    5. [Disabled] reindex with pointless output (optional)
    6. dimple
    7. extract_results and feedback to database (to be determined)
  • Manual test and processing (used interactive python):
    1. in src/aareproc start a python session by typing python
    2. in the interactive python session:
      1. import db_slurm_handler
      2. db_slurm_handler.path_test()
      3. You can edit the function in get_mock_param_for_filepath() in inp_writer.py if needed. Then restart the python session and repeat step 1 and 2.
  • log with customized log_config (with options print and loguru)
  • cloud_handler: upload raw data to DECTRIS Cloud, potentially set up experiment

Installation

To install the package using pip, run the following command:

pip install --index-url https://gitea.psi.ch/api/packages/mx/pypi/simple/ aareproc

Usage

Activate environment at the folder with uv.lock with source .venv/bin/activate For the database communication to work, need to export the shared password in the current shell.

Contributing

Jiaxin (Dawn) Duan

Authors and acknowledgment

  • Filip Leonarski (Advisor)
  • Guillaume Gotthard (AareDB)

License

To be determined

Project status

In initial development

Requirements

Requires Python: >=3.10
Details
PyPI
2025-07-02 16:16:38 +02:00
0
78 KiB
Assets (2)
aareproc-0.1.2-py3-none-any.whl 41 KiB
aareproc-0.1.2.tar.gz 36 KiB
Versions (8) View all
0.1.2 2025-07-02
0.1.1a11 2025-06-26
0.1.1a9 2025-06-18
0.1.1a6 2025-06-16
0.1.1 2025-05-22