Skip to content

Commit

Permalink
Add conda-forge install/release info (#107)
Browse files Browse the repository at this point in the history
* add some conda-forge info etc.

* added url
  • Loading branch information
espenhgn authored Nov 27, 2020
1 parent a2e089a commit ca7aeb6
Showing 1 changed file with 40 additions and 22 deletions.
62 changes: 40 additions & 22 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,8 +1,7 @@
LFPykit
=======
# LFPykit

This Python module contain freestanding implementations of electrostatic
forward models presently incorporated in LFPy
forward models incorporated in LFPy
(https://github.com/LFPy/LFPy, https://LFPy.readthedocs.io).

The aim of the `LFPykit` module is to provide electrostatic models
Expand Down Expand Up @@ -50,20 +49,23 @@ as described in various papers and books:
Neurosci. 11:490. doi: 10.3389/fnhum.2017.00490


Build Status
------------
## Build Status

[![DOI](https://zenodo.org/badge/288660131.svg)](https://zenodo.org/badge/latestdoi/288660131)
[![Coverage Status](https://coveralls.io/repos/github/LFPy/LFPykit/badge.svg?branch=master)](https://coveralls.io/github/LFPy/LFPykit?branch=master)
[![Documentation Status](https://readthedocs.org/projects/lfpykit/badge/?version=latest)](https://lfpykit.readthedocs.io/en/latest/?badge=latest)
[![Lintly flake8 checks](https://github.com/LFPy/lfpykit/workflows/Lintly%20flake8%20checks/badge.svg)](https://github.com/LFPy/LFPykit/actions?query=workflow%3A%22Lintly+flake8+checks%22)
[![Python application](https://github.com/LFPy/LFPykit/workflows/Python%20application/badge.svg)](https://github.com/LFPy/LFPykit/actions?query=workflow%3A%22Python+application%22)
[![Upload Python Package](https://github.com/LFPy/LFPykit/workflows/Upload%20Python%20Package/badge.svg)](https://pypi.org/project/LFPykit)
[![Conda Recipe](https://img.shields.io/badge/recipe-lfpykit-green.svg)](https://anaconda.org/conda-forge/lfpykit)
[![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/lfpykit.svg)](https://anaconda.org/conda-forge/lfpykit)
[![Conda Version](https://img.shields.io/conda/vn/conda-forge/lfpykit.svg)](https://anaconda.org/conda-forge/lfpykit)
[![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/lfpykit.svg)](https://anaconda.org/conda-forge/lfpykit)
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/LFPy/LFPykit.git/master)
[![License](http://img.shields.io/:license-GPLv3+-green.svg)](http://www.gnu.org/licenses/gpl-3.0.html)

Features
--------

## Features

`LFPykit` presently incorporates different electrostatic forward models for extracellular potentials
and magnetic signals that has been derived using volume conductor theory.
Expand Down Expand Up @@ -102,7 +104,9 @@ to different measurement modalities:
* `LaminarCurrentSourceDensity`:
For computing the 'ground truth' current source density across
cylindrical volumes aligned with the z-axis

* `VolumetricCurrentSourceDensity`:
For computing the 'ground truth' current source density on regularly
spaced 3D grid

Different classes built to map current dipole moments (i.e., computed using `CurrentDipoleMoment`)
to extracellular measurements:
Expand All @@ -125,8 +129,7 @@ that returns the linear map between the transmembrane currents or current dipole
and corresponding measurements (see Usage below)


Usage
-----
## Usage

A basic usage example using a mock 3-segment stick-like neuron,
treating each segment as a point source in a linear, isotropic and homogeneous volume conductor,
Expand Down Expand Up @@ -216,8 +219,7 @@ remote locations away from the cell geometry:
[ 1.96075587e-06, -1.96075587e-06]])


Physical units
--------------
## Physical units

Notes on physical units used in `LFPykit`:

Expand All @@ -236,8 +238,7 @@ Notes on physical units used in `LFPykit`:
- Magnetic fields are assumed to be in units of (nA/µm)


Dimensionality
--------------
## Dimensionality

- Transmembrane currents are represented by arrays with shape `(n_seg, n_timesteps)`
where `n_seg` is the number of segments of the neuron model.
Expand All @@ -253,15 +254,13 @@ Dimensionality
`(n_points, n_timesteps)`


Documentation
-------------
## Documentation

The online Documentation of `LFPykit` can be found here:
https://lfpykit.readthedocs.io/en/latest


Dependencies
------------
## Dependencies

`LFPykit` is implemented in Python and is written (and continuously tested) for `Python >= 3.7`.
The main `LFPykit` module depends on `numpy`, `scipy` and `MEAutility` (https://github.com/alejoe91/MEAutility, https://meautility.readthedocs.io/en/latest/).
Expand All @@ -272,10 +271,9 @@ Running all unit tests and example files may in addition require `py.test`, `mat
`LFPy` (https://github.com/LFPy/LFPy, https://LFPy.readthedocs.io).


Installation
------------
## Installation

First, make sure that the above dependencies are installed in the current Python environment.
### From development sources (https://github.com/LFPy/LFPykit)

Install the current development version on https://GitHub.com using `git` (https://git-scm.com):

Expand All @@ -291,6 +289,26 @@ For active development, link the repository location

$ python setup.py develop # --user optional

Installing from the Python Package Index (pypi.org):
### Installation of stable releases on PyPI.org (https://www.pypi.org)

Installing from the Python Package Index (https://www.pypi.org/project/lfpykit):

$ pip install lfpykit # --user optional

To upgrade the installation using pip:

$ pip install --upgrade --no-deps lfpykit

### Installation of stable releases on conda-forge (https://conda-forge.org)

Installing `lfpykit` from the `conda-forge` channel can be achieved by adding `conda-forge` to your channels with:

$ conda config --add channels conda-forge

Once the `conda-forge` channel has been enabled, `lfpykit` can be installed with:

$ conda install lfpykit

It is possible to list all of the versions of `lfpykit` available on your platform with:

$ conda search lfpykit --channel conda-forge

0 comments on commit ca7aeb6

Please sign in to comment.