Update conda env to use ~/.conda

Switch from using a conda environment specified by a path to a conda
environment specified by a name assumed to be in `~/.conda`. Might work
with an absolute path still, but requires testing.

batch/hpc_init.sh

@@ -45,12 +45,11 @@ fi
 
 # Conda init
 if [ -z "${FLEPI_CONDA}" ]; then
-    echo -n "An explicit \$FLEPI_CONDA was not provided, please set one (or press enter to use '$USERDIR/flepimop-env'): "
+    echo -n "An explicit \$FLEPI_CONDA was not provided, please set one (or press enter to use 'flepimop-env'): "
     read FLEPI_CONDA
     if [ -z "${FLEPI_CONDA}" ]; then
-        export FLEPI_CONDA="$USERDIR/flepimop-env"
+        export FLEPI_CONDA="flepimop-env"
     fi
-    export FLEPI_CONDA=$( realpath "$FLEPI_CONDA" )
     echo "Using '$FLEPI_CONDA' for \$FLEPI_CONDA."
 fi
 conda activate $FLEPI_CONDA
@@ -116,6 +115,7 @@ Otherwise make sure this diagnostic info looks correct before continuing:
 * Cluster:         $1
 * User directory:  $USERDIR
 * Work directory:  $WORKDIR
+* Flepi conda:     $FLEPI_CONDA
 * Flepi path:      $FLEPI_PATH
 * Project path:    $PROJECT_PATH
 * Python:          $WHICH_PYTHON

build/hpc_install_or_update.sh

@@ -68,24 +68,25 @@ fi
 
 # Setup the conda environment
 if [ -z "${FLEPI_CONDA}" ]; then
-    echo -n "An explicit \$FLEPI_CONDA was not provided, please set one (or press enter to use '$USERDIR/flepimop-env'): "
+    echo -n "An explicit \$FLEPI_CONDA was not provided, please set one (or press enter to use 'flepimop-env'): "
     read FLEPI_CONDA
     if [ -z "${FLEPI_CONDA}" ]; then
-        export FLEPI_CONDA="$USERDIR/flepimop-env"
+        export FLEPI_CONDA="flepimop-env"
     fi
-    export FLEPI_CONDA=$( realpath "$FLEPI_CONDA" )
     echo "Using '$FLEPI_CONDA' for \$FLEPI_CONDA."
 fi
-if [ ! -d $FLEPI_CONDA ]; then
+FLEPI_CONDA_ENV_MATCHES=$( conda info --envs | awk '{print $1}' | grep -x "$FLEPI_CONDA" | wc -l )
+if [ "$FLEPI_CONDA_ENV_MATCHES" -eq 0 ]; then
 conda env create --prefix $FLEPI_CONDA --file $FLEPI_PATH/environment.yml
-cat << EOF > $FLEPI_CONDA/conda-meta/pinned
-r-arrow==17.0.0
-arrow==17.0.0
-EOF
 fi
 
 # Load the conda environment
 conda activate $FLEPI_CONDA
+[ -e "$CONDA_PREFIX/conda-meta/pinned" ] && rm $CONDA_PREFIX/conda-meta/pinned
+cat << EOF > $CONDA_PREFIX/conda-meta/pinned
+r-arrow==17.0.0
+arrow==17.0.0
+EOF
 
 # Install the gempyor package from local
 pip install --editable --force-reinstall $FLEPI_PATH/flepimop/gempyor_pkg