Merge pull request #147 from lephare-photoz/issue/115/test_suite

Port over test_suite.sh

examples/color.py → docs/historical_examples/color.py

@@ -1,8 +1,12 @@
-from sys import *
-from matplotlib.pyplot import *
+# ruff: noqa
+# These historical examples are not 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 *
 
 
 ############################

examples/figuresLPP.py → docs/historical_examples/figuresLPP.py

@@ -1,3 +1,6 @@
+# ruff: noqa
+# These historical examples are not maintained or covered by tests or linting!
+
 from sys import *
 
 from matplotlib.pyplot import *

examples/figuresLPZ.py → docs/historical_examples/figuresLPZ.py

@@ -1,3 +1,6 @@
+# ruff: noqa
+# These historical examples are not maintained or covered by tests or linting!
+
 from sys import *
 
 from matplotlib.pyplot import *

examples/spec.py → docs/historical_examples/spec.py

@@ -1,3 +1,6 @@
+# ruff: noqa
+# 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,
 # reading the info form .zsp and .pdz output

docs/historical_examples/test_suite.sh

@@ -0,0 +1,48 @@
+#!/usr/bin/env bash
+
+# Set the number of threads for OpenMP
+export OMP_NUM_THREADS='30'
+
+# 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
+
+# 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
+echo "Downloading to $CAT_IN..."
+curl -s -o $CAT_IN https://raw.githubusercontent.com/lephare-photoz/lephare-data/main/examples/COSMOS.in
+
+# Run commands
+echo "Running filter..."
+filter -c $CONFIG_FILE
+
+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
+
+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
+
+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
+
+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/
+
+echo "Generating figures and specs..."
+python $LEPHAREDIR/examples/figuresLPZ.py $CAT_OUT
+python $LEPHAREDIR/examples/spec.py *.spec -d pdf -o $LEPHAREWORK/zphota/spec
+
+echo "Moving output files..."
+mv $CAT_OUT Id*.spec figuresLPZ.pdf $LEPHAREWORK/zphota/

docs/notebooks/Command_line_demo.ipynb

@@ -0,0 +1,81 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "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.\n",
+    "\n",
+    "This is not the reccomended way to run lephare but provides access to the legacy running commands."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "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.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",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Run the script. This will take around ten minutes."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!bash ../historical_examples/test_suite.sh"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}