install_miniforge.bash

#!/bin/bash

set -Eeuo pipefail
trap cleanup SIGINT SIGTERM ERR EXIT

# Save user's .mambarc and .condarc for safety using mktemp
# ---------------------------------------------------------

ORIG_MAMBARC=$(mktemp)
MAMBARC_FOUND=FALSE
if [[ -f ~/.mambarc ]]
then
   MAMBARC_FOUND=TRUE
   echo "Found existing .mambarc. Saving to $ORIG_MAMBARC"
   cp -v ~/.mambarc "$ORIG_MAMBARC"
fi

ORIG_CONDARC=$(mktemp)
CONDARC_FOUND=FALSE
if [[ -f ~/.condarc ]]
then
   CONDARC_FOUND=TRUE
   echo "Found existing .condarc. Saving to $ORIG_CONDARC"
   cp -v ~/.condarc "$ORIG_CONDARC"
fi

# The cleanup function will restore the user's .mambarc and .condarc
# ------------------------------------------------------------------
cleanup() {
   trap - SIGINT SIGTERM ERR EXIT
   local ret=$?
   echo "Cleaning up..."
   if [[ $MAMBARC_FOUND == TRUE ]]
   then
      echo "Restoring original .mambarc"
      cp -v "$ORIG_MAMBARC" ~/.mambarc
   fi
   if [[ $CONDARC_FOUND == TRUE ]]
   then
      echo "Restoring original .condarc"
      cp -v "$ORIG_CONDARC" ~/.condarc
   fi
   exit $ret
}

# -----------------
# Detect usual bits
# -----------------

ARCH=$(uname -s)
MACH=$(uname -m)
NODE=$(uname -n)

# -----------------------------------
# Set the Default BLAS implementation
# -----------------------------------

if [[ $ARCH == Darwin ]]
then
   if [[ $MACH == arm64 ]]
   then
      BLAS_IMPL=accelerate
      # Note: accelerate might have issues with scipy
      #       See https://github.com/conda-forge/numpy-feedstock/issues/253
   else
      BLAS_IMPL=mkl
   fi
else
   BLAS_IMPL=mkl
fi
# -----
# Usage
# -----

EXAMPLE_PY_VERSION="3.12"
EXAMPLE_MINI_VERSION="24.9.2-0"
EXAMPLE_INSTALLDIR="/opt/GEOSpyD"
EXAMPLE_DATE=$(date +%F)
usage() {
   echo "Usage: $0 --python_version <python version> --miniforge_version <miniforge> --prefix <prefix> [--micromamba | --mamba] [--blas <blas>] [--ffnet-hack]"
   echo ""
   echo "   Required arguments:"
   echo "      --python_version <python version> (e.g., ${EXAMPLE_PY_VERSION})"
   echo "      --miniforge_version <miniforge_version version> (e.g., ${EXAMPLE_MINI_VERSION})"
   echo "      --prefix <full path to installation directory> (e.g, ${EXAMPLE_INSTALLDIR})"
   echo ""
   echo "   Optional arguments:"
   echo "      --blas <blas> (default: ${BLAS_IMPL}, options: mkl, openblas, accelerate, blis)"
   echo "      --micromamba: Use micromamba installer (default)"
   echo "      --mamba: Use mamba installer"
   echo "      --ffnet-hack: Install ffnet from fork (used on Bucy due to odd issue not finding gfortran)"
   echo "      --help: Print this message"
   echo ""
   echo "   By default we use the micromamba installer on both Linux and macOS"
   echo "   For BLAS, we use accelerate on macOS and MKL on Linux"
   echo ""
   echo "   NOTE 1: This script installs within ${EXAMPLE_INSTALLDIR} with a path based on:"
   echo ""
   echo "        1. The Miniforge version"
   echo "        2. The Python version"
   echo "        3. The date of the installation"
   echo ""
   echo "   For example: $0 --python_version ${EXAMPLE_PY_VERSION} --miniforge_version ${EXAMPLE_MINI_VERSION} --prefix ${EXAMPLE_INSTALLDIR}"
   echo ""
   echo "   will create an install at:"
   echo "       ${EXAMPLE_INSTALLDIR}/${EXAMPLE_MINI_VERSION}_py${EXAMPLE_PY_VERSION}/${EXAMPLE_DATE}"
   echo ""
   echo "  NOTE 2: This script will create or substitute a .mambarc    "
   echo "  and .condarc file in the user's home directory.  If you     "
   echo "  have an existing .mambarc and/or .condarc file, it will be  "
   echo "  restored after installation.  We do this to ensure that the "
   echo "  installation uses conda-forge as the default channel.       "
}

if [[ $# -lt 4 ]]
then
   usage
   exit 1
fi

# From http://stackoverflow.com/a/246128/1876449
# ----------------------------------------------
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
  DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
  SOURCE="$(readlink "$SOURCE")"
  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
SCRIPTDIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"

# ------------------------------
# Define an in-place sed command
# Because Mac sed is stupid old,
# use gsed if found.
# ------------------------------

if [[ $ARCH == Darwin ]]
then
   if [[ $(command -v gsed) ]]
   then
      #echo "Found gsed on macOS. Good job! You are smart!"
      SED="$(command -v gsed) -i "
   else
      #echo "It is recommended to use GNU sed since macOS default"
      #echo "sed is a useless BSD variant. Consider installing"
      #echo "GNU sed from a packager like Homebrew:"
      #echo "  brew install gnu-sed"
      SED="$(command -v sed) -i.macbak "
   fi
else
   SED="$(command -v sed) -i "
fi

# ----------------------
# Command line arguments
# ----------------------

USE_MAMBA=FALSE
USE_MICROMAMBA=TRUE
FFNET_HACK=FALSE

while [[ $# -gt 0 ]]
do
   case "$1" in
      --python_version)
         PYTHON_VER=$2
         shift
         ;;
      --miniforge_version)
         MINIFORGE_VER=$2
         shift
         ;;
      --mamba)
         USE_MAMBA=TRUE
         USE_MICROMAMBA=FALSE
         ;;
      --micromamba)
         USE_MAMBA=FALSE
         USE_MICROMAMBA=TRUE
         ;;
      --ffnet-hack)
         FFNET_HACK=TRUE
         ;;
      --prefix)
         MINIFORGE_DIR=$2
         shift
         ;;
      --blas)
         BLAS_IMPL=$2
         shift
         ;;
      --help | -h)
         usage
         exit 1
         ;;
      *)
         echo "Option $1 not recognized"
         usage
         exit 1
         ;;
   esac
   shift
done

if [[ -z $PYTHON_VER ]]
then
   echo "ERROR: Python version not sent in"
   usage
   exit 1
fi

if [[ -z $MINIFORGE_VER ]]
then
   echo "ERROR: Miniforge version not sent in"
   usage
   exit 1
fi

if [[ -z $MINIFORGE_DIR ]]
then
   echo "ERROR: Miniforge installation directory not sent in"
   usage
   exit 1
fi

# We will only allow BLAS_IMPL to be: mkl, openblas, accelerate, or blis
if [[ $BLAS_IMPL != mkl && $BLAS_IMPL != openblas && $BLAS_IMPL != accelerate && $BLAS_IMPL != blis ]]
then
   echo "ERROR: BLAS implementation $BLAS_IMPL not recognized"
   usage
   exit 1
fi


# To install ffnet we require a Fortran
# compiler and for portability's sake we require gfortran. Moreover, we
# require that gfortran be at least version 8.3.0.
#
# We'll do the test now as to not waste time if the user has a
# too-old gfortran.
#
# We have two situations. On Linux we *require* gfortran to be
# installed. We assume that it's called gfortran as it is on most Linux
# distros. On macOS, we check for gfortran, gfortran-11, -12, or -13 (as
# those are available via brew).

# First look if gfortran is available
# -----------------------------------

FORTRAN_AVAILABLE=FALSE

if [[ $ARCH == Darwin ]]
then
   if [[ $(command -v gfortran) ]]
   then
      echo "Found gfortran on macOS. Will be used for ffnet"
      FORTRAN_AVAILABLE=TRUE
   elif [[ $(command -v gfortran-11) ]]
   then
      echo "Found gfortran-11 on macOS. Will be used for ffnet"
      FORTRAN_AVAILABLE=TRUE
   elif [[ $(command -v gfortran-12) ]]
   then
      echo "Found gfortran-12 on macOS. Will be used for ffnet"
      FORTRAN_AVAILABLE=TRUE
   elif [[ $(command -v gfortran-13) ]]
   then
      echo "Found gfortran-13 on macOS. Will be used for ffnet"
      FORTRAN_AVAILABLE=TRUE
   else
      echo "WARNING: gfortran is not available. If you wish to install ffnet, please install it or load an appropriate module."
      echo "         For now we will skip the installation of ffnet"
   fi
else
   if [[ $(command -v gfortran) ]]
   then
      echo "Found gfortran on Linux. Will be used for ffnet"
      FORTRAN_AVAILABLE=TRUE
   else
      echo "ERROR: gfortran is not available. Please install it or load an appropriate module."
      echo "       We require at least version 8.3.0 to install ffnet"
      exit 9
   fi
fi

# Now check the version
# ---------------------

if [[ $FORTRAN_AVAILABLE == TRUE ]]
then

   # First get the version string as the last field of the first
   # line of the output of gfortran --version
   GFORTRAN_VERSION=$(gfortran --version | head -n 1 | awk '{print $NF}')

   # Now split the version string into its components
   # and capture the major, minor, and patch versions
   GFORTRAN_MAJOR=$(echo $GFORTRAN_VERSION | awk -F. '{print $1}')
   GFORTRAN_MINOR=$(echo $GFORTRAN_VERSION | awk -F. '{print $2}')
   GFORTRAN_PATCH=$(echo $GFORTRAN_VERSION | awk -F. '{print $3}')

   # Now, we want to know if gfortran is 8.3 or higher.

   # First check if the major version is less than 8
   if [[ $GFORTRAN_MAJOR -lt 8 ]]
   then
      echo "ERROR: gfortran is too old. Please install at least version 8.3.0 or load an appropriate module."
      exit 9
   fi

   # Now check if the major version is 8 and the minor version is less
   # than 3
   if [[ $GFORTRAN_MAJOR -eq 8 && $GFORTRAN_MINOR -lt 3 ]]
   then
      echo "ERROR: gfortran is too old. Please install at least version 8.3.0 or load an appropriate module."
      exit 9
   fi

   # At this point we know that gfortran is available and that it is
   # at least version 8.3.0. So we can install ffnet.
fi

# ---------------------------
# Miniforge version variables
# ---------------------------

PYTHON_MAJOR_VERSION=${PYTHON_VER:0:1}
if [[ "$PYTHON_MAJOR_VERSION" != "3" ]]
then
   echo "Python version $PYTHON_VER implies Python major version $PYTHON_MAJOR_VERSION"
   echo "This script only supports Python 3"
   exit 2
fi
PYTHON_EXEC=python${PYTHON_MAJOR_VERSION}
PYTHON_VER_WITHOUT_DOT="${PYTHON_VER//./}"

MINIFORGE_DISTVER=Miniforge${PYTHON_MAJOR_VERSION}

MINIFORGE_SRCDIR=${SCRIPTDIR}/$MINIFORGE_DISTVER

# ------------------------------
# Set the Miniforge Architecture
# ------------------------------

if [[ $ARCH == Darwin ]]
then
   MINIFORGE_ARCH=MacOSX
   if [[ $MACH == arm64 ]]
   then
      MICROMAMBA_ARCH=osx-arm64
      # Note: accelerate might have issues with scipy
      #       See https://github.com/conda-forge/numpy-feedstock/issues/253
   else
      MICROMAMBA_ARCH=osx-64
   fi
else
   MINIFORGE_ARCH=Linux
   MICROMAMBA_ARCH=linux-64
fi

# -----------------------------------------------------
# Create the installtion directory if it does not exist
# -----------------------------------------------------

if [ ! -d "$MINIFORGE_DIR" ]
then
   mkdir -p $MINIFORGE_DIR
fi

DATE=$(date +%F)
MINIFORGE_INSTALLDIR=$MINIFORGE_DIR/${MINIFORGE_VER}/$DATE
MINIFORGE_ENVDIR=$MINIFORGE_INSTALLDIR/envs/py${PYTHON_VER}

CANONICAL_INSTALLER=${MINIFORGE_DISTVER}-${MINIFORGE_VER}-${MINIFORGE_ARCH}-${MACH}.sh
if [[ "$MINIFORGE_VER" == "latest" ]]
then
   DATED_INSTALLER=${MINIFORGE_DISTVER}-${MINIFORGE_VER}-${MINIFORGE_ARCH}-${MACH}.${DATE}.sh
fi

echo "MINIFORGE_SRCDIR     = $MINIFORGE_SRCDIR"
echo "CANONICAL_INSTALLER  = $MINIFORGE_SRCDIR/$CANONICAL_INSTALLER"
if [[ "$MINIFORGE_VER" == "latest" ]]
then
   echo "DATED_INSTALLER      = $MINIFORGE_SRCDIR/$DATED_INSTALLER"
fi
echo "Miniforge $MINIFORGE_VER for Python $PYTHON_VER will be installed in $MINIFORGE_ENVDIR"

if [[ -d $MINIFORGE_ENVDIR ]]
then
   echo "ERROR: $MINIFORGE_ENVDIR already exists! Exiting!"
   exit 9
fi

if [[ ! -f $MINIFORGE_SRCDIR/$CANONICAL_INSTALLER ]]
then
   REPO=https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VER}
   echo "Downloading $CANONICAL_INSTALLER from $REPO"
   echo "Running curl -OL $REPO/$CANONICAL_INSTALLER"
   (cd $MINIFORGE_SRCDIR; curl -OL $REPO/$CANONICAL_INSTALLER)
fi

if [[ "$MINIFORGE_VER" == "latest" ]]
then
   mv -v $MINIFORGE_SRCDIR/$CANONICAL_INSTALLER $MINIFORGE_SRCDIR/$DATED_INSTALLER
   INSTALLER=$DATED_INSTALLER
else
   INSTALLER=$CANONICAL_INSTALLER
fi

# NOTE: We have to use strict conda-forge channel
# -----------------------------------------------

# Now create the good one (we restore the old one at the end)
cat << EOF > ~/.mambarc
# Temporary mambarc from install_miniforge.bash
channels:
  - conda-forge
  - nodefaults
channel_priority: strict
show_channel_urls: True
use_lockfiles: False
EOF

cat << EOF > ~/.condarc
# Temporary condarc from install_miniforge.bash
channels:
  - conda-forge
  - nodefaults
channel_priority: strict
show_channel_urls: True
use_lockfiles: False
EOF

# ----------------------
# Install Miniforge Base
# ----------------------

if [[ ! -d $MINIFORGE_INSTALLDIR ]]
then
   bash $MINIFORGE_SRCDIR/$INSTALLER -b -p $MINIFORGE_INSTALLDIR
fi

export MAMBA_ROOT_PREFIX=$MINIFORGE_INSTALLDIR

MINIFORGE_BINDIR=$MINIFORGE_INSTALLDIR/bin

# --------------------------------
# Create the Miniforge environment
# --------------------------------

$MINIFORGE_BINDIR/mamba create -y -p $MINIFORGE_ENVDIR python=${PYTHON_VER}

# Now install regular mamba packages
# ----------------------------------

function mamba_install {
   MAMBA_INSTALL_COMMAND="$MINIFORGE_BINDIR/mamba install -p $MINIFORGE_ENVDIR -y"

   echo
   echo "(mamba) Now installing $*"
   $MAMBA_INSTALL_COMMAND $*
   echo
}

function micromamba_install {
   MICROMAMBA_INSTALL_COMMAND="$MINIFORGE_BINDIR/micromamba install -p $MINIFORGE_ENVDIR -y"

   echo
   echo "(micromamba) Now installing $*"
   $MICROMAMBA_INSTALL_COMMAND $*
   echo
}

if [[ "$USE_MICROMAMBA" == "TRUE" ]]
then
   echo "=== Using micromamba as package manager ==="

   PACKAGE_INSTALL=micromamba_install

   # We also need to fetch micromamba
   # --------------------------------

   echo "=== Installing micromamba ==="
   MICROMAMBA_URL="https://micro.mamba.pm/api/micromamba/${MICROMAMBA_ARCH}/latest"
   curl -Ls ${MICROMAMBA_URL} | tar -C $MINIFORGE_INSTALLDIR -xvj bin/micromamba

elif [[ "$USE_MAMBA" == "TRUE" ]]
then
   echo "=== Using mamba as package manager ==="
   PACKAGE_INSTALL=mamba_install

else
   echo "ERROR: No package manager selected! We should not get here. Exiting!"
   exit 9
fi

# --------------
# MAMBA PACKAGES
# --------------

$PACKAGE_INSTALL mamba

echo "BLAS_IMPL: $BLAS_IMPL"
$PACKAGE_INSTALL "libblas=*=*${BLAS_IMPL}"

# in libcxx 14.0.6 (from miniforge), __string is a file, but in 16.0.6
# it is a directory so, in order for libcxx to be updated, we have to
# remove it because the updater will fail
#
# This seems to only happen on macOS

if [[ $ARCH == Darwin ]]
then
   # First let's check the version of libcxx installed by asking mamba

   LIBCXX_VERSION=$($MINIFORGE_ENVDIR/bin/mamba list libcxx | grep libcxx | awk '{print $2}')

   # This is the version X.Y.Z and we want to do things only if X is 14 as it's a directory in 15+
   # Let's use bash to extract the first number
   LIBCXX_MAJOR_VERSION=${LIBCXX_VERSION%%.*}
   MINIFORGE_MAJOR_VERSION=${MINIFORGE_VER%%.*}

   if [[ $LIBCXX_MAJOR_VERSION -lt 15 && $MINIFORGE_MAJOR_VERSION -ge 23 ]]
   then
      if [[ -f $MINIFORGE_ENVDIR/include/c++/v1/__string ]]
      then
         echo "Removing $MINIFORGE_ENVDIR/include/c++/v1/__string"
         rm $MINIFORGE_ENVDIR/include/c++/v1/__string
      fi
      if [[ -f $MINIFORGE_ENVDIR/include/c++/v1/__tuple ]]
      then
         echo "Removing $MINIFORGE_ENVDIR/include/c++/v1/__tuple"
         rm $MINIFORGE_ENVDIR/include/c++/v1/__tuple
      fi
   fi
fi

$PACKAGE_INSTALL esmpy
$PACKAGE_INSTALL xesmf
$PACKAGE_INSTALL pytest
$PACKAGE_INSTALL xgcm
$PACKAGE_INSTALL s3fs boto3

$PACKAGE_INSTALL numpy scipy numba
$PACKAGE_INSTALL netcdf4 cartopy proj matplotlib
$PACKAGE_INSTALL virtualenv pipenv configargparse
$PACKAGE_INSTALL psycopg2 gdal xarray geotiff plotly
$PACKAGE_INSTALL iris pyhdf pip biggus hpccm cdsapi
$PACKAGE_INSTALL babel beautifulsoup4 colorama gmp jupyter jupyterlab
$PACKAGE_INSTALL movingpandas geoviews hvplot">=0.11.0" geopandas bokeh
$PACKAGE_INSTALL intake intake-parquet intake-xarray

# Looks like mo_pack, libmo_pack, pyspharm, windspharm are not available on arm64
if [[ $MACH == arm64 ]]
then
   $PACKAGE_INSTALL pygrib f90nml seawater
   $PACKAGE_INSTALL cmocean eofs
else
   $PACKAGE_INSTALL pygrib f90nml seawater mo_pack libmo_unpack
   # Next it looks like pyspharm and windspharm are not available for Python 3.11
   if [[ $PYTHON_VER_WITHOUT_DOT -lt 311 ]]
   then
      $PACKAGE_INSTALL cmocean eofs pyspharm windspharm
   else
      $PACKAGE_INSTALL cmocean eofs
   fi
fi

$PACKAGE_INSTALL pyasn1 ujson configobj argcomplete biopython
# mdp only exists from 3.10 and older
if [[ $PYTHON_VER_WITHOUT_DOT -le 310 ]]
then
   $PACKAGE_INSTALL mdp
fi
$PACKAGE_INSTALL requests-toolbelt twine wxpython
$PACKAGE_INSTALL sockjs-tornado sphinx_rtd_theme django
$PACKAGE_INSTALL pypng seaborn astropy
$PACKAGE_INSTALL fastcache greenlet imageio jbig lzo
$PACKAGE_INSTALL mock pytables
$PACKAGE_INSTALL pydap
$PACKAGE_INSTALL gsw

$PACKAGE_INSTALL timezonefinder
$PACKAGE_INSTALL cython
$PACKAGE_INSTALL zarr

$PACKAGE_INSTALL scikit-learn

$PACKAGE_INSTALL yamllint
$PACKAGE_INSTALL verboselogs

$PACKAGE_INSTALL pykdtree pyogrio contourpy sunpy
$PACKAGE_INSTALL haversine
$PACKAGE_INSTALL ford
$PACKAGE_INSTALL autopep8
$PACKAGE_INSTALL mdutils
$PACKAGE_INSTALL earthaccess

$PACKAGE_INSTALL uxarray

# Only install pythran on linux. On mac it brings in an old clang
if [[ $MINIFORGE_ARCH == Linux ]]
then
   $PACKAGE_INSTALL f90wrap
   $PACKAGE_INSTALL pythran
fi

# esmpy installs mpi. We don't want any of those in the bin dir
# so we rename and relink. First we rename the files:

cd $MINIFORGE_ENVDIR/bin

/bin/mv -v mpicc         esmf-mpicc
/bin/mv -v mpicxx        esmf-mpicxx
/bin/mv -v mpiexec.hydra esmf-mpiexec.hydra
/bin/mv -v mpifort       esmf-mpifort
/bin/mv -v mpichversion  esmf-mpichversion
/bin/mv -v mpivars       esmf-mpivars

# Now we have to handle the symlinks
/bin/rm -v mpic++  && /bin/ln -sv esmf-mpicxx        esmf-mpic++
/bin/rm -v mpiexec && /bin/ln -sv esmf-mpiexec.hydra esmf-mpiexec
/bin/rm -v mpirun  && /bin/ln -sv esmf-mpiexec.hydra esmf-mpirun
/bin/rm -v mpif77  && /bin/ln -sv esmf-mpifort       esmf-mpif77
/bin/rm -v mpif90  && /bin/ln -sv esmf-mpifort       esmf-mpif90

# We also want to link f2py to f2py3 for Python 3
/bin/ln -sv f2py f2py3

cd $SCRIPTDIR

# Install weird nc_time_axis package
# ----------------------------------
$PACKAGE_INSTALL -c conda-forge/label/renamed nc_time_axis

# ------------
# PIP PACKAGES
# ------------

PIP_INSTALL="$MINIFORGE_ENVDIR/bin/$PYTHON_EXEC -m pip install"
PIP_UNINSTALL="$MINIFORGE_ENVDIR/bin/$PYTHON_EXEC -m pip uninstall -y"

$PIP_INSTALL PyRTF3 pipenv pymp-pypi rasterio h5py
$PIP_INSTALL pycircleci metpy siphon questionary xgrads
$PIP_INSTALL ruamel.yaml
$PIP_INSTALL xgboost
$PIP_INSTALL tensorflow evidential-deep-learning silence_tensorflow
$PIP_INSTALL yaplon
$PIP_INSTALL lxml
$PIP_INSTALL juliandate
$PIP_INSTALL pybufrkit
$PIP_INSTALL pyephem
$PIP_INSTALL basemap
$PIP_INSTALL redis
$PIP_INSTALL Flask

# some packages require a Fortran compiler. This sometimes isn't available
# on macs (though usually is)
if [[ $FORTRAN_AVAILABLE == TRUE ]]
then
   # we need to install ffnet from https://github.com/mrkwjc/ffnet.git
   # This is because the version in PyPI is not compatible with Python 3
   # and latest scipy
   #
   # 1. This package now requires meson to build (for Python 3.12)
   $PIP_INSTALL meson
   # 2. We also need f2py but that is in our install directory bin
   #    so we need to add that to the PATH
   export PATH=$MINIFORGE_ENVDIR/bin:$PATH
   # 3. We also should redefine TMPDIR as on some systems (discover)
   #    it seems to not work as hoped. So, we create a new directory
   #    relative to the install script called tmp, and use that.
   #    It appears meson uses TMPDIR to store its build files.
   mkdir -p $SCRIPTDIR/tmp-for-ffnet
   export TMPDIR=$SCRIPTDIR/tmp-for-ffnet
   # 4. Now we can install ffnet
   if [[ $FFNET_HACK == TRUE ]]
   then
      $PIP_INSTALL git+https://github.com/mathomp4/ffnet@force-env-gfortran
   else
      $PIP_INSTALL git+https://github.com/mrkwjc/ffnet
   fi
   # 5. We can now remove the tmp directory
   rm -rf $SCRIPTDIR/tmp-for-ffnet
fi

# Finally pygrads is not in pip
# -----------------------------

PYGRADS_VERSION="pygrads-3.0.b1"
if [[ -d $MINIFORGE_SRCDIR/$PYGRADS_VERSION ]]
then
   rm -rf $MINIFORGE_SRCDIR/$PYGRADS_VERSION
fi

tar xf $MINIFORGE_SRCDIR/$PYGRADS_VERSION.tar.gz -C $MINIFORGE_SRCDIR

cd $MINIFORGE_SRCDIR/$PYGRADS_VERSION

$MINIFORGE_ENVDIR/bin/$PYTHON_EXEC setup.py install

# Inject code fix for spectral
# ----------------------------
find $MINIFORGE_ENVDIR/lib -name 'gacm.py' -print0 | xargs -0 $SED -i -e '/cm.spectral,/ s/spectral/nipy_spectral/'

cd $SCRIPTDIR

# Edit matplotlibrc to use TkAgg as the default backend for matplotlib
# on Linux, but MacOSX on macOS
# --------------------------------------------------------------------
#
# What we need to do is look for the string "backend:" in matplotlibrc
# and change line (which might have one or more comment characters at
# the beginning) to be "backend: MacOSX" on macOS and "backend: TkAgg"
# on Linux.
#
if [[ $ARCH == Darwin ]]
then
   find $MINIFORGE_ENVDIR/lib -name 'matplotlibrc' -print0 | xargs -0 $SED -e '/.*backend:/ s/^.*backend:.*/backend: MacOSX/'
else
   find $MINIFORGE_ENVDIR/lib -name 'matplotlibrc' -print0 | xargs -0 $SED -e '/.*backend:/ s/^.*backend:.*/backend: TkAgg/'
fi

# There currently seems to be a bug with ipython3
# (see https://github.com/ipython/ipython/issues/14260)
# the solution seems to be to pip uninstall prompt_toolkit
# and then reinstall it. This is a temporary fix until
# the issue is resolved.
$PIP_UNINSTALL prompt_toolkit
$PIP_INSTALL prompt_toolkit

# Use mamba to output list of packages installed
# ----------------------------------------------
cd $MINIFORGE_ENVDIR
./bin/mamba list --show-channel-urls --explicit > distribution_spec_file.txt
./bin/mamba list --show-channel-urls > mamba_list_packages.txt
./bin/pip freeze > pip_freeze_packages.txt

# Restore User's .mambarc and .condarc using cleanup function
# -----------------------------------------------------------
cleanup

# As a final check to make sure the defaults channel has not
# infected the environment, we will check the mamba_list_packages.txt
# and make sure 'defaults' does not appear in the channel list (fourth
# field)
# -------------------------------------------------------------------

if grep -q defaults mamba_list_packages.txt
then
   echo "ERROR: The defaults channel is in the mamba_list_packages.txt file"
   echo "       This is not allowed. The offending package(s) are:"
   grep defaults mamba_list_packages.txt
   echo "       Please fix this and try again."
   exit 9
fi

cd $SCRIPTDIR