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
-----------------

1. create python environment. Here use ``conda`` as example. ::

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

2. clone repository. ::

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

3. update pip. ::

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

4. build. ::

    python -m build

5. install. ::

        pip install dist/neurocarto-0.0.0-py3-none-any.whl

   Or installing in the develop mode, ::

        pip install -e .

   change version ``0.0.0`` to latest when needed.

Build Document
--------------

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

1. install extra dependencies. ::

    pip install -r requirements-doc.txt

2. build. ::

    cd doc
    make html

3. open generated html at ``doc/build/html/index.html``.

build github wiki
~~~~~~~~~~~~~~~~~

For contributors only.

1. (first time) initialize submodule and update it. ::

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

2. under ``doc`` directory. run make. ::

    make markdown

3. 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