install

Installation

Require

Require Python 3.10, and (recommended) a Python virtual environment.

Install

pip install neurocarto

Run

neurocarto

Optional dependency packages

bg-atlasapi Atlas Brain background image supporting.
Pillow, tifffile other background image format supporting.
probeinterface probe/channelmap format import/export
pandas, polars channelmap data export.

Build from source

create python environment. Here use conda as example.

conda create -n neurocarto python~=3.10.0
conda activate neurocarto

clone repository.

git clone https://github.com/AntonioST/NeuroCarto.git
cd neura_carto

update pip.

python -m pip install --upgrade pip
python -m pip install --upgrade build

build.
```
python -m build
```
install.
```
pip install dist/neurocarto-0.0.0-py3-none-any.whl
```
change version 0.0.0 to latest when needed.

Or installing in the develope mode,
```
pip install -e .
```

Build Document

Make sure the package has been installed or added in PYTHONPATH.

install extra dependencies.
```
pip install -r requirements-doc.txt
```
build.
```
cd doc
make html
```
open generated html at doc/build/html/index.html.

build github wiki

For contributors only.

(first time) initialize submodule and update it.

git submodule init doc/wiki
git submodule update doc/wiki

under doc directory. run make.
```
make markdown
```
check the output at doc/wiki. Note that the rst output may be not suitable for md. Check the git difference and modify the contents are necessary.

testing library versions

# environment
pip                            23.3.1                        pypi_0     pypi
python                         3.10.13                   h955ad1f_0
# required
bokeh                          3.3.2                         pypi_0     pypi
matplotlib                     3.7.1                py310h06a4308_1
numpy                          1.22.3               py310h4f1e569_0
scipy                          1.7.3                py310hac523dd_2
typing_extensions              4.6.3                py310h06a4308_0
# optional
bg-atlasapi                    1.0.2                         pypi_0     pypi
pillow                         9.4.0                py310h6a678d5_0
pandas                         1.5.3                py310h1128e8f_0
polars                         0.18.2                        pypi_0     pypi
probeinterface                 0.2.21                        pypi_0     pypi
tifffile                       2023.12.9                     pypi_0     pypi
# document
jupyter                        1.0.0                         pypi_0     pypi
jupyter-contrib-nbextensions   0.7.0                         pypi_0     pypi
nbsphinx                       0.9.3                         pypi_0     pypi
sphinx                         7.2.6                         pypi_0     pypi
sphinx-markdown-builder        0.6.6                         pypi_0     pypi
sphinx-rtd-theme               2.0.0                         pypi_0     pypi