OGGM venv install script

install_oggm.sh

#!/bin/bash
set -xe

PIP="python3 -m pip"

export DEBIAN_FRONTEND=noninteractive
sudo apt-get -y update
sudo apt-get -y install --no-install-recommends \
        gfortran \
        fontconfig \
        fonts-dejavu \
        git \
        file \
        build-essential \
        cmake \
        ninja-build \
        liblapack-dev \
        libopenblas-dev \
        libfreetype6-dev \
        libagg-dev \
        liblapack-dev \
        netcdf-bin \
        libnetcdf-dev \
        libssl-dev \
        libffi-dev \
        libtiff-dev \
        libpng-dev \
        libgdal-dev \
        libproj-dev \
        libhdf4-alt-dev \
        libhdf5-dev \
        libqhull-dev \
        libxml2-dev \
        libgif-dev \
        libjpeg-dev \
        libopenjp2-7-dev \
        libwebp-dev \
        libjson-c-dev \
        libgeos-dev \
        blt-dev \
        libdb-dev \
        libreadline-dev \
        libncursesw5-dev \
        zlib1g-dev \
        libbz2-dev \
        liblzma-dev \
        libsqlite3-dev \
        libgdbm-dev \
        libmpdec-dev \
        libexpat1-dev \
        libblosc-dev \
        libbrotli-dev \
        liblcms2-dev \
        libjxr-dev \
        liblz4-dev \
        libsnappy-dev \
        libzopfli-dev \
        llvm-11 \
        llvm-11-dev \
        sqlite3 \
        curl \
        wget \
        ca-certificates \
        unzip \
        proj-bin \
        proj-data

$PIP install --no-cache-dir --upgrade pip setuptools wheel

# Work around https://github.com/pypa/setuptools_scm/issues/713 until pip releases a fix
$PIP install --no-cache-dir --upgrade git+https://github.com/pypa/pip.git

printf '[libs]\nsystem_freetype = True\n' > /tmp/mpl_setup.cfg
export MPLSETUPCFG=/tmp/mpl_setup.cfg
export LLVM_CONFIG=llvm-config-11
export NPY_NUM_BUILD_JOBS=$(nproc)

$PIP install --no-cache-dir --no-binary :all: numba
$PIP install --no-cache-dir --no-binary :all: numpy
$PIP install --no-cache-dir --no-binary :all: cython pybind11 six
$PIP install --no-cache-dir --no-binary :all: pythran
$PIP install --no-cache-dir --no-binary :all: cftime Bottleneck

$PIP install --no-cache-dir --no-binary :all: matplotlib
$PIP install --no-cache-dir --no-binary scipy scipy
$PIP install --no-cache-dir --no-binary :all: pandas shapely
$PIP install --no-cache-dir --no-binary cartopy cartopy

$PIP install --no-cache-dir "gdal<$(gdal-config --version | cut -d. -f1).$(( $(gdal-config --version | cut -d. -f2) + 1 ))" --install-option="build_ext" --install-option="$(gdal-config --cflags | sed 's/-I/--include-dirs=/')"
$PIP install --no-cache-dir fiona --install-option="build_ext" --install-option="$(gdal-config --cflags | sed 's/-I/--include-dirs=/')"

$PIP install --no-cache-dir --no-binary :all: pyproj

$PIP install --no-cache-dir --no-binary :all: \
    "git+https://github.com/rasterio/rasterio.git@1.3b1" \
    descartes \
    Pillow \
    geopandas \
    netCDF4 \
    "git+https://github.com/PyTables/PyTables.git" \
    configobj \
    joblib \
    dask \
    distributed \
    xarray \
    rioxarray \
    nose \
    filelock \
    pytest \
    pytest-cov \
    ilock \
    progressbar2 \
    motionless \
    versioneer \
    requests \
    tifffile \
    "git+https://github.com/OGGM/pytest-mpl.git" \
    "git+https://github.com/fmaussion/salem.git"

$PIP install --no-cache-dir --no-binary scikit-image,scikit-learn scikit-image scikit-learn

sed -i 's/^backend.*/backend : Agg/' "$(python3 -c "import matplotlib, os; print(os.path.dirname(matplotlib.__file__))")"/mpl-data/matplotlibrc

$PIP install --no-cache-dir --no-binary :all: git+https://github.com/OGGM/oggm.git