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Open Source Science

https://github.com/computationalphysiology/mps_automation

Scripts for automating the mps analysis

https://github.com/computationalphysiology/mps_automation

Science Score: 13.0%

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Repository

Scripts for automating the mps analysis

Basic Info
  • Host: GitHub
  • Owner: ComputationalPhysiology
  • Language: Python
  • Default Branch: main
  • Size: 91.8 KB
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  • Watchers: 3
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Created over 5 years ago · Last pushed almost 4 years ago
Metadata Files
Readme Changelog Contributing Authors

README.md

MPS Automation Scripts

CI

Scripts for automating the mps analysis

  • Source code: https://github.com/ComputationalPhysiology/mps_automation

Install

Create a virtual environment python -m virtualenv venv Activate virtual environment (Unix) source venv/bin/activate (Windows) .\venv\Scripts\activate

Install private dependencies

Install package with its dependencies python -m pip install .

Usage

Command line interface

Once installed you should be able to run the command python -m mps_automation --help and this should display some information about how to run the script. In brief, if you have a folder. Put the config file (see info below) in the root folder of the folder you want to analyze. For example if you want to analyze /Users/finsberg/data/experiment1 then you should also have a file at /Users/finsberg/data/experiment1/config.yaml. If is also possible to specify a path to this file

To analyze the the folder you execute the command

python -m mps_automation <folder> for example python -m mps_automation /Users/finsberg/data/experiment1 (note that you can also use relative paths).

Once this is done you should see the following files and folder appearing in your experiment folder

  • database.db
    • This is file containing all the information about all the files in the experiment. This is basically a huge table (or SQLite database) where each row is one recording that contains information about chips, media, doses, drugs, pacing, trace type, as well as the full analysis. You can open and inspect this file with to tool like DB Browser for SQLite
  • data.xlsx
    • This is an excel file with a few sheets summarizing the analysis of the folder
  • plots
    • TBW

Credits

This package was created with Cookiecutter and the finsberg/cookiecutter-pypackage project template.

Owner

  • Name: Computational Physiology at Simula Research Laboratory
  • Login: ComputationalPhysiology
  • Kind: organization
  • Location: Fornebu, Norway

GitHub organization for the computational physiology department at Simula Research Laboratory

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Dependencies

.github/workflows/main.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
  • webfactory/ssh-agent v0.4.1 composite
  • webfactory/ssh-agent master composite
.github/workflows/pre-commit.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
  • pre-commit/action v3.0.0 composite
requirements_dev.txt pypi
  • Click ==7.0 development
  • SQLAlchemy * development
  • Sphinx * development
  • black * development
  • bump2version * development
  • flake8 * development
  • ipython * development
  • isort * development
  • mypy * development
  • numpy * development
  • openpyxl * development
  • pandas * development
  • pandoc * development
  • pdbpp * development
  • pip * development
  • pre-commit * development
  • pytest * development
  • pytest-cov * development
  • pyyaml * development
  • sphinx_rtd_theme * development
  • sqlalchemy-stubs * development
  • twine * development
  • typer * development
  • watchdog * development
  • wheel * development