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Installation

Brian Kim edited this page Oct 23, 2023 · 1 revision

Installing NeuroPy

Minimum Requirements

  • Python 3.9 or higher
  • NumPy 1.20.2 or higher
  • SciPy 1.6.2. or higher

Step-by-step Installation

1. Install Mamba

  • Mamba is a fast, flexible, and multi-platform package manager. It helps manage Python environments and dependencies.
  • Visit Mamba Installation Guide for detailed installation instructions.

2. Fork the Repository

  • We recommend forking the repository rather than cloning, because this allows you to freely experiment with changes without affecting the source,
  • Navigate to NeuroPy's GitHub page and click on the "Fork" button at the top right.

3. Clone Your Forked Repository

  • On your forked GitHub repository page, click the "Code" button and copy the URL.
  • In your local machine's terminal or command prompt, navigate to the directory where you want to place the code.
  • Run:
git clone [insert github link here]

4. Navigate to the "NeuroPy" Directory

  • You can use the terminal or command prompt to change into the cloned directory:
cd NeuroPy

5. Set up the Virtual Environment

It's essential to set up a proper Python environment for your projects. This ensures that all the required dependencies and packages are correctly installed. Depending on your preference, choose either the stable version or the latest beta version:

  • For a stable environment, run:
mamba env create -f environment.yml
  • For the most up-to-date beta version, run:
mamba env create -f environment_beta.yml

6. Set up Python Path

  • This is to setup your Python environment so that it knows where to find the NeuroPy code.
  • Add the NeuroPy directory to your Python path. The exact method can vary based on your preferred Python interactive environment (e.g., Jupyter, IPython). Generally, this involves appending the path of your NeuroPy directory to the PYTHONPATH environment variable.

Analyses

  • artifact.py
  • brainstates.py
  • decoders.py
  • laps.py
  • ms_connectivity.py
  • neurons_correlation.py
  • neurons_stability.py
  • oscillations.py
  • placefields.py
  • reactivation.py
  • spkepochs.py
  • time_dependent_placefields.py
  • trace_fc.py
  • animal.py
  • ca_neurons.py
  • datawriter.py
  • epoch.py
  • event.py
  • neurons.py
  • position.py
  • probe.py
  • ratemap.py
  • signal.py

IO

  • binarysignalio.py
  • dlcio.py
  • minianio.py
  • miniscopeio.py
  • movie.py
  • neuroscopeio.py
  • openyphysio.py
  • optitrackio.py
  • phyio.py
  • spykingcircusio.py
  • usvio.py

Plotting

  • ca_events.py
  • dataviz.py
  • epochs.py
  • figure.py
  • placemaps.py
  • position.py
  • probe.py
  • ratemaps.py
  • signals.py
  • spikes.py

Utilities

  • align_util.py
  • ccg.py
  • ccg_gpu.py
  • chunkingData.py
  • colors_util.py
  • debug_helpers.py
  • decoding.py
  • dynamic_container.py
  • efficient_interval_search.py
  • eventCorr.py
  • load_exported.py
  • manipulate_files.py
  • mathuil.py
  • matplotlib_helpers.py
  • minian_util.py
  • miniscope_denoise.py
  • misc.py
  • neurons_util.py
  • plot_util.py
  • position_util.py
  • probe_util.py
  • result_context.py
  • signal_process.py

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