Set up data science tools

basic-ds-setup.sh

python -m pip install --upgrade pip
pip install cython pybind11 pythran numpy
OPENBLAS=$(brew --prefix openblas) CFLAGS="-falign-functions=8 ${CFLAGS}" pip install --no-use-pep517 scipy==1.7.0
pip install pandas matplotlib jupyter jupyterlab
OPENBLAS=$(brew --prefix openblas) CFLAGS="-falign-functions=8 ${CFLAGS}" pip install --no-use-pep517 scikit-learn==1.0.1
jupyter nbextension enable --py widgetsnbextension

deep-learning-env.sh

# --- activate env and pip install:
python -m pip install --upgrade pip
pip install cython pybind11 pythran numpy
OPENBLAS=$(brew --prefix openblas) CFLAGS="-falign-functions=8 ${CFLAGS}" pip install --no-use-pep517 scipy
OPENBLAS=$(brew --prefix openblas) CFLAGS="-falign-functions=8 ${CFLAGS}" pip install --no-use-pep517 scikit-learn
pip install jax jaxlib==0.1.70 -f "https://dfm.io/custom-wheels/jaxlib/index.html"
pip install numpyro
pip install -Uq "tfp-nightly[jax]" > /dev/null
pip install torch torchvision

# -- install node for tqdm progress bar in notebooks
jupyter nbextension enable --py widgetsnbextension

ds_setup.txt

# --- install brew and then:
# brew install pyenv
# brew install pyenv-virtualenv
# brew install openblas          # required by scipy, scikit-learn and others
# brew install bazel             # required for tensorflow-probability on jax
# brew install node              # for nicer tqdm progress bars in notebooks
# brew install imagemagick       # for sphinx-gallery, which makes jupyter notebooks to rst

### Required for the transformers library
# brew install cmake


# --- install python version
# pyenv install 3.8.10
# pyenv virtualenv 3.8.10 myenv
# --- if CPython framework is needed use:
# PYTHON_CONFIGURE_OPTS="--enable-framework" pyenv install 3.8.10

# --- activate env and pip install:
# python -m pip install --upgrade pip

# -- note install scipy and scikit-learn requires openblas:
# pip install cython pybind11 pythran numpy pandas matplotlib
# OPENBLAS=$(brew --prefix openblas) CFLAGS="-falign-functions=8 ${CFLAGS}" pip install --no-use-pep517 scipy
# OPENBLAS=$(brew --prefix openblas) CFLAGS="-falign-functions=8 ${CFLAGS}" pip install --no-use-pep517 scikit-learn

# -- install jax from wheel file, at least until they fix it:
# python -m pip install jax jaxlib==0.1.70 -f "https://dfm.io/custom-wheels/jaxlib/index.html"

# -- install numpyro:
# pip install numpyro

# -- installing tensorflow-probablity on jax requires bazel
# pip install -Uq "tfp-nightly[jax]" > /dev/null

# -- install node for tqdm progress bar in notebooks
# jupyter nbextension enable --py widgetsnbextension

# -- install arviz:
# brew install hdf5
# export HDF5_DIR=/opt/homebrew/Cellar/hdf5/1.12.1 # Check folder and version. Might be different
# pip install --no-binary=h5py h5py
# brew install netcdf
# pip install netCDF4
# pip install arviz

# Might need to upgrade numpy:
# pip install -U numpy # needs versios 1.22 to avoid ufunc size error on import