From 79268304e0f4978ca1bdcd402a192ad1b6832258 Mon Sep 17 00:00:00 2001
From: Camilla Pacifici <cpacifici@stsci.edu>
Date: Wed, 13 Sep 2023 16:14:40 -0400
Subject: [PATCH] Fix requirement file and notebook to run again

---
 .../isha_nayak_ysos_in_the_lmc.ipynb              | 14 +++++++++++---
 notebooks/MIRI_IFU_YSOs_in_the_LMC/pre-install.sh |  6 ------
 .../MIRI_IFU_YSOs_in_the_LMC/pre-requirements.txt |  1 -
 .../MIRI_IFU_YSOs_in_the_LMC/requirements.txt     | 15 ++++++---------
 4 files changed, 17 insertions(+), 19 deletions(-)
 delete mode 100644 notebooks/MIRI_IFU_YSOs_in_the_LMC/pre-install.sh
 delete mode 100644 notebooks/MIRI_IFU_YSOs_in_the_LMC/pre-requirements.txt

diff --git a/notebooks/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb b/notebooks/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb
index cf0d48937..c8371118b 100644
--- a/notebooks/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb
+++ b/notebooks/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb
@@ -62,7 +62,8 @@
     "\n",
     "from scipy.optimize import curve_fit\n",
     "from spectral_cube import SpectralCube\n",
-    "from photutils import DAOStarFinder, CircularAperture\n",
+    "from photutils.detection import DAOStarFinder\n",
+    "from photutils.aperture import CircularAperture\n",
     "\n",
     "from specutils import Spectrum1D, SpectralRegion\n",
     "from specutils.analysis import snr, line_flux, centroid, equivalent_width\n",
@@ -199,7 +200,7 @@
    "source": [
     "Using ALMA 13CO from a known star formation region in the LMC host to nearly 150 massive YSOs.\n",
     "\n",
-    "#### Note that the data file is ~2 GB, so download will take a while depending on your intenet speed. You can also download directly using the link below."
+    "#### Note that the data file is ~2 GB, so download will take a while depending on your internet speed. You can also download directly using the link below."
    ]
   },
   {
@@ -1156,6 +1157,13 @@
     "plt.show()\n",
     "plt.close()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -1174,7 +1182,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.11.5"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/MIRI_IFU_YSOs_in_the_LMC/pre-install.sh b/notebooks/MIRI_IFU_YSOs_in_the_LMC/pre-install.sh
deleted file mode 100644
index 10760c24b..000000000
--- a/notebooks/MIRI_IFU_YSOs_in_the_LMC/pre-install.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-source bin/activate
-pip install astropy-helpers==1.1.2
-pip install spectral-cube==0.4.5
diff --git a/notebooks/MIRI_IFU_YSOs_in_the_LMC/pre-requirements.txt b/notebooks/MIRI_IFU_YSOs_in_the_LMC/pre-requirements.txt
deleted file mode 100644
index 18a126d45..000000000
--- a/notebooks/MIRI_IFU_YSOs_in_the_LMC/pre-requirements.txt
+++ /dev/null
@@ -1 +0,0 @@
-numpy==1.19.0
\ No newline at end of file
diff --git a/notebooks/MIRI_IFU_YSOs_in_the_LMC/requirements.txt b/notebooks/MIRI_IFU_YSOs_in_the_LMC/requirements.txt
index 837839e6f..904d7f0ed 100644
--- a/notebooks/MIRI_IFU_YSOs_in_the_LMC/requirements.txt
+++ b/notebooks/MIRI_IFU_YSOs_in_the_LMC/requirements.txt
@@ -1,10 +1,7 @@
-jupyter
-aplpy
-astrodendro==0.2.0
-astropy==4.0.1.post1
 jwst
-matplotlib==3.3.0rc1
-pandas==1.0.5
-photutils==0.7.2
-scipy>=1.5.0
-specutils==1.0
+matplotlib
+pandas
+spectral-cube
+specutils
+aplpy
+git+https://github.com/dendrograms/astrodendro.git