Provide user the possibility to pip install the ClearMap project (graph-tool is installed separately)

[edoumazane]

To test this feature:

Method 1: install ClearMap in a fresh environment

conda env create -f https://raw.githubusercontent.com/ClearAnatomics/ClearMap/refs/heads/v3.0.0-pyproject/ClearMap3pip.yml
conda activate ClearMap3pip

## !!! At this step, please double-check the ClearMap3pip is activated!!!

pip install git+https://github.com/ClearAnatomics/ClearMap.git@v3.0.0-pyproject

Method 2: install ClearMap in an existing environment (this will override an existing ClearMap install)

pip install git+https://github.com/ClearAnatomics/ClearMap.git@v3.0.0-pyproject

Method 3: developer (editable mode)

mkdir -p ~/code/ClearAnatomics
cd $_
git clone git@github.com:ClearAnatomics/ClearMap.git
cd ClearMap
git checkout v3.0.0-pyproject
conda env create -f ClearMap3pip.yml
pip install -e .

If you are using a Mac (>=M1), you need to remove mkl from the dependencies listed in the yaml file, or use this method:

conda create -n ClearMap3pip "python=3.11" pip "graph-tool<=2.45"  
conda activate ClearMap3pip
conda env config vars set PYTHONNOUSERSITE=1
conda env config vars set TMPDIR="/data/tmp" # change if different

# then proceed to:
pip install git+https://github.com/ClearAnatomics/ClearMap.git@v3.0.0-pyproject

This is a draft PR

• test on 2 Linux workstation
• check code for regressions
• check compiled modules for performance loss
• compare package versions between the conventional conda install of ClearMap and the fresh pip install
• support elastix path patch
• handle mkl for MacOS darwin
• test on Windows