Follow desidatamodel's env vars

run.sh

@@ -27,14 +27,17 @@ if [ -z "$DESI_RELEASE" ]; then
     export DESI_RELEASE=edr
 fi
 DESI_RELEASE=${DESI_RELEASE,,}
+
+# Set environment variables as per
+# https://desidatamodel.readthedocs.io/en/latest/
 echo "+ Set \$DESI_ROOT to the $DESI_RELEASE release."
 export DESI_ROOT=$DESI_DATA/$DESI_RELEASE
-export DESI_RAW=$DESI_DATA/raw_spectro_data
-export DESI_TARGET=$DESI_DATA/target
-
-# used by the desispec library
+export DESI_SPECTRO_DATA=$DESI_DATA/raw_spectro_data
 export DESI_SPECTRO_REDUX=$DESI_ROOT/spectro/redux
+export DESI_SPECTRO_CALIB=$DESI_ROOT/spectro/desi_spectro_calib
+export DESI_TARGET=$DESI_DATA/target
 
+# Symlink to NERSC-like directories
 ln -s $DESI_ROOT/spectro $DESI_NERSC/spectro
 ln -s $DESI_ROOT/survey $DESI_NERSC/survey
 ln -s $DESI_TARGET $DESI_NERSC/target

welcome.ipynb

@@ -13,7 +13,7 @@
     "  * `$DESI_ROOT` points to **~/desidata/edr** unless you specified another `$DESI_RELEASE` when running this container.\n",
     "* Unlike at NERSC, raw spectrographic and targeting data that are shared across data releases\n",
     "  have been moved their own directories, outside the releases themselves.\n",
-    "  * `$DESI_RAW` points to **~/desidata/raw_spectro_data**, corresponding to `$DESI_ROOT/spectro/data` at NERSC.\n",
+    "  * `$DESI_SPECTRO_DATA` points to **~/desidata/raw_spectro_data**, corresponding to `$DESI_ROOT/spectro/data` at NERSC.\n",
     "  * `$DESI_TARGET` points to **~/desidata/target**, corresponding to `$DESI_ROOT/target` at NERSC.\n",
     "* Example code for analyzing the data can be found at **~/tutorials**.\n",
     "* Pipeline code for processing the data are installed at **~/desihub**.\n",
@@ -471,7 +471,7 @@
    "source": [
     "### Relocated raw spectroscopic and targeting data\n",
     "\n",
-    "Because they have significant duplicates across data releases, raw spectroscopic data have been relocated from `$DESI_ROOT/spectro/data` to **~/desihub/raw_spectro_data** (`$DESI_RAW`), and targeting data have been removed from `$DESI_ROOT/target` to **~/desihub/target** (`$DESI_TARGET`). They can be accessed like so:"
+    "Because they have significant duplicates across data releases, raw spectroscopic data have been relocated from `$DESI_ROOT/spectro/data` to **~/desihub/raw_spectro_data** (`$DESI_SPECTRO_DATA`), and targeting data have been removed from `$DESI_ROOT/target` to **~/desihub/target** (`$DESI_TARGET`). They can be accessed like so:"
    ]
   },
   {
@@ -502,7 +502,7 @@
     }
    ],
    "source": [
-    "fits_path = os.path.expandvars(\"$DESI_RAW/20200201/00045677/gfa-00045677.fits.fz\")\n",
+    "fits_path = os.path.expandvars(\"$DESI_SPECTRO_DATA/20200201/00045677/gfa-00045677.fits.fz\")\n",
     "hdul = fits.open(fits_path)\n",
     "hdul.info()"
    ]