From 08349f015d8c41c4f63f99d8f2ecfdcb68b46c3d Mon Sep 17 00:00:00 2001
From: Olivia Lynn <olynn@andrew.cmu.edu>
Date: Fri, 17 May 2024 06:56:39 -0700
Subject: [PATCH 1/6] Read in proper env vars; curl data; run first command
 successfully

---
 tests/test_suite.sh | 50 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 tests/test_suite.sh

diff --git a/tests/test_suite.sh b/tests/test_suite.sh
new file mode 100644
index 00000000..a8e88879
--- /dev/null
+++ b/tests/test_suite.sh
@@ -0,0 +1,50 @@
+#!/usr/bin/env bash
+
+export OMP_NUM_THREADS='30'
+tmpdir=$(python -c "import lephare as lp; print(f'{lp.LEPHAREDIR}')" | tail -n 1) # use tail to ignore the on-import print statement
+tmpwork=$(python -c "import lephare as lp; print(f'{lp.dm.LEPHAREWORK}')" | tail -n 1)
+export LEPHAREDIR=$tmpdir
+export LEPHAREWORK=$tmpwork
+
+echo "LEPHAREDIR:" $LEPHAREDIR # TODO remove these at the end
+echo "LEPHAREWORK:" $LEPHAREWORK
+
+# TODO check the paths in the files themselves - as in, the list files and such
+
+# Get the data
+#curl -s -o ${LEPHAREDIR}/COSMOS.in https://raw.githubusercontent.com/lephare-photoz/lephare-data/main/examples/COSMOS.in
+echo "STARTING DOWNLOAD"
+if [ -d "$LEPHAREDIR" ]; then
+    curl -o ${LEPHAREDIR}/examples/COSMOS.in https://raw.githubusercontent.com/lephare-photoz/lephare-data/main/examples/COSMOS.in
+    if [ $? -eq 0 ]; then
+        echo "Download successful."
+    else
+        echo "Download failed."
+    fi
+else
+    echo "Directory $LEPHAREDIR does not exist."
+fi
+
+# Variables
+export CONFIG_FILE="$LEPHAREDIR/examples/COSMOS.para"
+
+# Test suite commands
+filter -c $CONFIG_FILE
+
+# sedtolib -c ./COSMOS.para -t S --STAR_SED $LEPHAREDIR/examples/STAR_MOD_ALL.list --LIB_ASCII YES
+# mag_gal -c ./COSMOS.para -t S --LIB_ASCII YES --STAR_LIB_OUT ALLSTAR_COSMOS
+
+# sedtolib -c $LEPHAREDIR/examples/COSMOS.para -t Q --QSO_SED  $LEPHAREDIR/sed/QSO/SALVATO09/AGN_MOD.list
+# mag_gal -c $LEPHAREDIR/examples/COSMOS.para -t Q --MOD_EXTINC 0,1000  --EB_V 0.,0.1,0.2,0.3 --EXTINC_LAW SB_calzetti.dat --LIB_ASCII NO  --Z_STEP 0.04,0,6 --LIB_ASCII YES
+
+# sedtolib -c $LEPHAREDIR/examples/COSMOS.para -t G --GAL_SED $LEPHAREDIR/examples/COSMOS_MOD.list  --GAL_LIB LIB_VISTA
+# mag_gal  -c $LEPHAREDIR/examples/COSMOS.para -t G --GAL_LIB_IN LIB_VISTA --GAL_LIB_OUT VISTA_COSMOS_FREE --MOD_EXTINC 18,26,26,33,26,33,26,33  --EXTINC_LAW SMC_prevot.dat,SB_calzetti.dat,SB_calzetti_bump1.dat,SB_calzetti_bump2.dat  --EM_LINES EMP_UV  --EM_DISPERSION 0.5,0.75,1.,1.5,2. --Z_STEP 0.04,0,6 --LIB_ASCII YES
+
+# cat_out=zphot_short.out
+
+# zphota -c $LEPHAREDIR/examples/COSMOS.para --CAT_IN $LEPHAREDIR/examples/COSMOS.in --CAT_OUT $cat_out --ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS  --ADD_EMLINES 0,100 --AUTO_ADAPT YES   --Z_STEP 0.04,0,6 --CAT_LINES 1,100 --SPEC_OUT YES --PARA_OUT $LEPHAREDIR/examples/output.para --VERBOSE NO --ZFIX NO --PDZ_OUT $LEPHAREWORK/zphota/
+
+# python $LEPHAREDIR/examples/figuresLPZ.py $cat_out
+# python $LEPHAREDIR/examples/spec.py *.spec -d pdf -o $LEPHAREWORK/zphota/spec
+
+# mv $cat_out Id*.spec figuresLPZ.pdf $LEPHAREWORK/zphota/
\ No newline at end of file

From 8e0ad675892ec4b7a9dd727d1428ae39f1129ad5 Mon Sep 17 00:00:00 2001
From: Olivia Lynn <olynn@andrew.cmu.edu>
Date: Fri, 17 May 2024 07:41:47 -0700
Subject: [PATCH 2/6] All commands run; add some extra organization

---
 tests/test_suite.sh | 70 ++++++++++++++++++++++-----------------------
 1 file changed, 34 insertions(+), 36 deletions(-)

diff --git a/tests/test_suite.sh b/tests/test_suite.sh
index a8e88879..879b2a92 100644
--- a/tests/test_suite.sh
+++ b/tests/test_suite.sh
@@ -1,50 +1,48 @@
 #!/usr/bin/env bash
 
+# Set the number of threads for OpenMP
 export OMP_NUM_THREADS='30'
-tmpdir=$(python -c "import lephare as lp; print(f'{lp.LEPHAREDIR}')" | tail -n 1) # use tail to ignore the on-import print statement
-tmpwork=$(python -c "import lephare as lp; print(f'{lp.dm.LEPHAREWORK}')" | tail -n 1)
-export LEPHAREDIR=$tmpdir
-export LEPHAREWORK=$tmpwork
 
-echo "LEPHAREDIR:" $LEPHAREDIR # TODO remove these at the end
-echo "LEPHAREWORK:" $LEPHAREWORK
+# Set the LEPHAREDIR and LEPHAREWORK variables
+export LEPHAREDIR=$(python -c "import lephare as lp; print(f'{lp.LEPHAREDIR}')" | tail -n 1) # use tail to ignore the on-import print statement
+export LEPHAREWORK=$(python -c "import lephare as lp; print(f'{lp.dm.LEPHAREWORK}')" | tail -n 1) # use tail to ignore the on-import print statement
 
-# TODO check the paths in the files themselves - as in, the list files and such
+# Set catalog and config file names
+CAT_IN="$LEPHAREDIR/examples/COSMOS.in"
+CAT_OUT="zphot_short.out"
+CONFIG_FILE="$LEPHAREDIR/examples/COSMOS.para"
+
+# For debugging:
+# echo "LEPHAREDIR:" $LEPHAREDIR 
+# echo "LEPHAREWORK:" $LEPHAREWORK
+# echo "CONFIG_FILE:" $CONFIG_FILE
 
 # Get the data
-#curl -s -o ${LEPHAREDIR}/COSMOS.in https://raw.githubusercontent.com/lephare-photoz/lephare-data/main/examples/COSMOS.in
-echo "STARTING DOWNLOAD"
-if [ -d "$LEPHAREDIR" ]; then
-    curl -o ${LEPHAREDIR}/examples/COSMOS.in https://raw.githubusercontent.com/lephare-photoz/lephare-data/main/examples/COSMOS.in
-    if [ $? -eq 0 ]; then
-        echo "Download successful."
-    else
-        echo "Download failed."
-    fi
-else
-    echo "Directory $LEPHAREDIR does not exist."
-fi
-
-# Variables
-export CONFIG_FILE="$LEPHAREDIR/examples/COSMOS.para"
-
-# Test suite commands
-filter -c $CONFIG_FILE
+echo "Downloading to $CAT_IN..."
+curl -s -o $CAT_IN https://raw.githubusercontent.com/lephare-photoz/lephare-data/main/examples/COSMOS.in
 
-# sedtolib -c ./COSMOS.para -t S --STAR_SED $LEPHAREDIR/examples/STAR_MOD_ALL.list --LIB_ASCII YES
-# mag_gal -c ./COSMOS.para -t S --LIB_ASCII YES --STAR_LIB_OUT ALLSTAR_COSMOS
+# Run commands
+echo "Running filter..."
+filter -c $CONFIG_FILE
 
-# sedtolib -c $LEPHAREDIR/examples/COSMOS.para -t Q --QSO_SED  $LEPHAREDIR/sed/QSO/SALVATO09/AGN_MOD.list
-# mag_gal -c $LEPHAREDIR/examples/COSMOS.para -t Q --MOD_EXTINC 0,1000  --EB_V 0.,0.1,0.2,0.3 --EXTINC_LAW SB_calzetti.dat --LIB_ASCII NO  --Z_STEP 0.04,0,6 --LIB_ASCII YES
+echo "Running sedtolib and mag_gal for stars..."
+sedtolib -c $CONFIG_FILE -t S --STAR_SED $LEPHAREDIR/examples/STAR_MOD_ALL.list --LIB_ASCII YES
+mag_gal  -c $CONFIG_FILE -t S --LIB_ASCII YES --STAR_LIB_OUT ALLSTAR_COSMOS
 
-# sedtolib -c $LEPHAREDIR/examples/COSMOS.para -t G --GAL_SED $LEPHAREDIR/examples/COSMOS_MOD.list  --GAL_LIB LIB_VISTA
-# mag_gal  -c $LEPHAREDIR/examples/COSMOS.para -t G --GAL_LIB_IN LIB_VISTA --GAL_LIB_OUT VISTA_COSMOS_FREE --MOD_EXTINC 18,26,26,33,26,33,26,33  --EXTINC_LAW SMC_prevot.dat,SB_calzetti.dat,SB_calzetti_bump1.dat,SB_calzetti_bump2.dat  --EM_LINES EMP_UV  --EM_DISPERSION 0.5,0.75,1.,1.5,2. --Z_STEP 0.04,0,6 --LIB_ASCII YES
+echo "Running sedtolib and mag_gal for QSOs..."
+sedtolib -c $CONFIG_FILE -t Q --QSO_SED  $LEPHAREDIR/sed/QSO/SALVATO09/AGN_MOD.list
+mag_gal  -c $CONFIG_FILE -t Q --MOD_EXTINC 0,1000  --EB_V 0.,0.1,0.2,0.3 --EXTINC_LAW SB_calzetti.dat --LIB_ASCII NO  --Z_STEP 0.04,0,6 --LIB_ASCII YES
 
-# cat_out=zphot_short.out
+echo "Running sedtolib and mag_gal for galaxies..."
+sedtolib -c $CONFIG_FILE -t G --GAL_SED $LEPHAREDIR/examples/COSMOS_MOD.list  --GAL_LIB LIB_VISTA
+mag_gal  -c $CONFIG_FILE -t G --GAL_LIB_IN LIB_VISTA --GAL_LIB_OUT VISTA_COSMOS_FREE --MOD_EXTINC 18,26,26,33,26,33,26,33  --EXTINC_LAW SMC_prevot.dat,SB_calzetti.dat,SB_calzetti_bump1.dat,SB_calzetti_bump2.dat  --EM_LINES EMP_UV  --EM_DISPERSION 0.5,0.75,1.,1.5,2. --Z_STEP 0.04,0,6 --LIB_ASCII YES
 
-# zphota -c $LEPHAREDIR/examples/COSMOS.para --CAT_IN $LEPHAREDIR/examples/COSMOS.in --CAT_OUT $cat_out --ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS  --ADD_EMLINES 0,100 --AUTO_ADAPT YES   --Z_STEP 0.04,0,6 --CAT_LINES 1,100 --SPEC_OUT YES --PARA_OUT $LEPHAREDIR/examples/output.para --VERBOSE NO --ZFIX NO --PDZ_OUT $LEPHAREWORK/zphota/
+echo "Running zphota..."
+zphota -c $CONFIG_FILE --CAT_IN $CAT_IN --CAT_OUT $CAT_OUT --ZPHOTLIB VISTA_COSMOS_FREE,ALLSTAR_COSMOS,QSO_COSMOS  --ADD_EMLINES 0,100 --AUTO_ADAPT YES   --Z_STEP 0.04,0,6 --CAT_LINES 1,100 --SPEC_OUT YES --PARA_OUT $LEPHAREDIR/examples/output.para --VERBOSE NO --ZFIX NO --PDZ_OUT $LEPHAREWORK/zphota/
 
-# python $LEPHAREDIR/examples/figuresLPZ.py $cat_out
-# python $LEPHAREDIR/examples/spec.py *.spec -d pdf -o $LEPHAREWORK/zphota/spec
+echo "Generating figures and specs..."
+python $LEPHAREDIR/examples/figuresLPZ.py $CAT_OUT
+python $LEPHAREDIR/examples/spec.py *.spec -d pdf -o $LEPHAREWORK/zphota/spec
 
-# mv $cat_out Id*.spec figuresLPZ.pdf $LEPHAREWORK/zphota/
\ No newline at end of file
+echo "Moving output files..."
+mv $CAT_OUT Id*.spec figuresLPZ.pdf $LEPHAREWORK/zphota/

From 8c69e69928e966f091c842d313b386ff33f0222b Mon Sep 17 00:00:00 2001
From: Olivia Lynn <olynn@andrew.cmu.edu>
Date: Fri, 17 May 2024 08:08:35 -0700
Subject: [PATCH 3/6] Add initial demo notebook for running test_suite.sh

---
 docs/notebooks/Command_line_demo.ipynb | 57 ++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 docs/notebooks/Command_line_demo.ipynb

diff --git a/docs/notebooks/Command_line_demo.ipynb b/docs/notebooks/Command_line_demo.ipynb
new file mode 100644
index 00000000..3267eab6
--- /dev/null
+++ b/docs/notebooks/Command_line_demo.ipynb
@@ -0,0 +1,57 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Command line demo\n",
+    "\n",
+    "For the time being, we assume you have \"test_suite.sh\" at the top level of your LEPHAREDIR dir.\n",
+    "\n",
+    "To discuss where we want to store this in the long term."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import lephare as lp\n",
+    "\n",
+    "test_suite_file = os.path.join(os.environ[\"LEPHAREDIR\"], \"test_suite.sh\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!bash $test_suite_file"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python (lph)",
+   "language": "python",
+   "name": "lph"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.14"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

From febf74a0799283ac0c80024b63a38f7ec99485d1 Mon Sep 17 00:00:00 2001
From: Raphael Shirley <rshirley@mpe.mpg.de>
Date: Fri, 17 May 2024 21:09:49 +0200
Subject: [PATCH 4/6] Renamed folders and updated example notebook to download
 data first

---
 .../historical_examples}/color.py             |  8 +++-
 .../historical_examples}/figuresLPP.py        |  3 ++
 .../historical_examples}/figuresLPZ.py        |  3 ++
 .../historical_examples}/spec.py              |  3 ++
 .../historical_examples}/test_suite.sh        |  0
 docs/notebooks/Command_line_demo.ipynb        | 44 ++++++++++++++-----
 6 files changed, 48 insertions(+), 13 deletions(-)
 rename {examples => docs/historical_examples}/color.py (99%)
 rename {examples => docs/historical_examples}/figuresLPP.py (99%)
 rename {examples => docs/historical_examples}/figuresLPZ.py (99%)
 rename {examples => docs/historical_examples}/spec.py (99%)
 rename {tests => docs/historical_examples}/test_suite.sh (100%)

diff --git a/examples/color.py b/docs/historical_examples/color.py
similarity index 99%
rename from examples/color.py
rename to docs/historical_examples/color.py
index 1b4b4b07..3b5165cf 100644
--- a/examples/color.py
+++ b/docs/historical_examples/color.py
@@ -1,8 +1,12 @@
-from sys import *
-from matplotlib.pyplot import *
+# ruff: noqa
+# These historical examples are note maintained or covered by tests or linting!
+
 from math import *
+from sys import *
+
 import numpy as np
 from matplotlib.backends.backend_pdf import PdfPages
+from matplotlib.pyplot import *
 
 
 ############################
diff --git a/examples/figuresLPP.py b/docs/historical_examples/figuresLPP.py
similarity index 99%
rename from examples/figuresLPP.py
rename to docs/historical_examples/figuresLPP.py
index f6674411..167dd06b 100644
--- a/examples/figuresLPP.py
+++ b/docs/historical_examples/figuresLPP.py
@@ -1,3 +1,6 @@
+# ruff: noqa
+# These historical examples are note maintained or covered by tests or linting!
+
 from sys import *
 
 from matplotlib.pyplot import *
diff --git a/examples/figuresLPZ.py b/docs/historical_examples/figuresLPZ.py
similarity index 99%
rename from examples/figuresLPZ.py
rename to docs/historical_examples/figuresLPZ.py
index 051a6f96..b04b9639 100644
--- a/examples/figuresLPZ.py
+++ b/docs/historical_examples/figuresLPZ.py
@@ -1,3 +1,6 @@
+# ruff: noqa
+# These historical examples are note maintained or covered by tests or linting!
+
 from sys import *
 
 from matplotlib.pyplot import *
diff --git a/examples/spec.py b/docs/historical_examples/spec.py
similarity index 99%
rename from examples/spec.py
rename to docs/historical_examples/spec.py
index bc1634b2..8720bd86 100644
--- a/examples/spec.py
+++ b/docs/historical_examples/spec.py
@@ -1,3 +1,6 @@
+# ruff: noqa
+# These historical examples are note maintained or covered by tests or linting!
+
 # Plot (file or window) the observed magnitudes
 # of the objects, along with best-fit templates,
 # reading the info form .zsp and .pdz output
diff --git a/tests/test_suite.sh b/docs/historical_examples/test_suite.sh
similarity index 100%
rename from tests/test_suite.sh
rename to docs/historical_examples/test_suite.sh
diff --git a/docs/notebooks/Command_line_demo.ipynb b/docs/notebooks/Command_line_demo.ipynb
index 3267eab6..f0c6e7da 100644
--- a/docs/notebooks/Command_line_demo.ipynb
+++ b/docs/notebooks/Command_line_demo.ipynb
@@ -6,9 +6,7 @@
    "source": [
     "# Command line demo\n",
     "\n",
-    "For the time being, we assume you have \"test_suite.sh\" at the top level of your LEPHAREDIR dir.\n",
-    "\n",
-    "To discuss where we want to store this in the long term."
+    "In this very simple notebook we download the files required to run lephare and demonstrate the command line example script."
    ]
   },
   {
@@ -18,9 +16,33 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "import lephare as lp\n",
-    "\n",
-    "test_suite_file = os.path.join(os.environ[\"LEPHAREDIR\"], \"test_suite.sh\")"
+    "import lephare as lp"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Download the data required in the example config file."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "config = lp.read_config(\"./data/COSMOS.para\")\n",
+    "lp.data_retrieval.get_auxiliary_data(\n",
+    "    keymap=config, additional_files=[\"examples/COSMOS.in\", \"examples/output.para\", \"examples/COSMOS.para\"]\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Run the script. This will take around ten minutes."
    ]
   },
   {
@@ -29,15 +51,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!bash $test_suite_file"
+    "!bash ../historical_examples/test_suite.sh"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python (lph)",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "lph"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -49,9 +71,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

From 258e6d0413afb5666c5d299056cf0dbabd7b9e52 Mon Sep 17 00:00:00 2001
From: Raphael Shirley <rshirley@mpe.mpg.de>
Date: Fri, 17 May 2024 21:11:44 +0200
Subject: [PATCH 5/6] Typo fix

---
 docs/historical_examples/color.py      | 2 +-
 docs/historical_examples/figuresLPP.py | 2 +-
 docs/historical_examples/figuresLPZ.py | 2 +-
 docs/historical_examples/spec.py       | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/historical_examples/color.py b/docs/historical_examples/color.py
index 3b5165cf..3eeea802 100644
--- a/docs/historical_examples/color.py
+++ b/docs/historical_examples/color.py
@@ -1,5 +1,5 @@
 # ruff: noqa
-# These historical examples are note maintained or covered by tests or linting!
+# These historical examples are not maintained or covered by tests or linting!
 
 from math import *
 from sys import *
diff --git a/docs/historical_examples/figuresLPP.py b/docs/historical_examples/figuresLPP.py
index 167dd06b..58a3dccb 100644
--- a/docs/historical_examples/figuresLPP.py
+++ b/docs/historical_examples/figuresLPP.py
@@ -1,5 +1,5 @@
 # ruff: noqa
-# These historical examples are note maintained or covered by tests or linting!
+# These historical examples are not maintained or covered by tests or linting!
 
 from sys import *
 
diff --git a/docs/historical_examples/figuresLPZ.py b/docs/historical_examples/figuresLPZ.py
index b04b9639..1ff970dd 100644
--- a/docs/historical_examples/figuresLPZ.py
+++ b/docs/historical_examples/figuresLPZ.py
@@ -1,5 +1,5 @@
 # ruff: noqa
-# These historical examples are note maintained or covered by tests or linting!
+# These historical examples are not maintained or covered by tests or linting!
 
 from sys import *
 
diff --git a/docs/historical_examples/spec.py b/docs/historical_examples/spec.py
index 8720bd86..7029b56f 100644
--- a/docs/historical_examples/spec.py
+++ b/docs/historical_examples/spec.py
@@ -1,5 +1,5 @@
 # ruff: noqa
-# These historical examples are note maintained or covered by tests or linting!
+# These historical examples are not maintained or covered by tests or linting!
 
 # Plot (file or window) the observed magnitudes
 # of the objects, along with best-fit templates,

From ac00039d3727af0b3a2df0289c8f73afd5e2dc00 Mon Sep 17 00:00:00 2001
From: Raphael Shirley <rshirley@mpe.mpg.de>
Date: Sat, 18 May 2024 00:04:35 +0200
Subject: [PATCH 6/6] Updated to work with the default config

---
 docs/notebooks/Command_line_demo.ipynb | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/docs/notebooks/Command_line_demo.ipynb b/docs/notebooks/Command_line_demo.ipynb
index f0c6e7da..c7df69b2 100644
--- a/docs/notebooks/Command_line_demo.ipynb
+++ b/docs/notebooks/Command_line_demo.ipynb
@@ -6,7 +6,9 @@
    "source": [
     "# Command line demo\n",
     "\n",
-    "In this very simple notebook we download the files required to run lephare and demonstrate the command line example script."
+    "In this very simple notebook we download the files required to run lephare and demonstrate the command line example script.\n",
+    "\n",
+    "This is not the reccomended way to run lephare but provides access to the legacy running commands."
    ]
   },
   {
@@ -32,7 +34,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "config = lp.read_config(\"./data/COSMOS.para\")\n",
+    "config = lp.string_dict_to_keymap(lp.default_cosmos_config)\n",
     "lp.data_retrieval.get_auxiliary_data(\n",
     "    keymap=config, additional_files=[\"examples/COSMOS.in\", \"examples/output.para\", \"examples/COSMOS.para\"]\n",
     ")"