Moved vlm-plx-all.fits since the website was taken offline

tomasstolker · Mar 18, 2024 · 6f5fa16 · 6f5fa16
1 parent fec520b
commit 6f5fa16
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Showing 2 changed files with 20 additions and 19 deletions.
diff --git a/docs/tutorials/running_species.ipynb b/docs/tutorials/running_species.ipynb
@@ -57,18 +57,19 @@
      "output_type": "stream",
      "text": [
       "==============\n",
-      "species v0.7.4\n",
+      "species v0.8.0\n",
       "==============\n",
       "\n",
       "Working folder: /Users/tomasstolker/applications/species/docs/tutorials\n",
+      "\n",
       "Creating species_config.ini... [DONE]\n",
+      "Creating species_database.hdf5... [DONE]\n",
+      "Creating data folder... [DONE]\n",
       "\n",
       "Configuration settings:\n",
       "   - Database: /Users/tomasstolker/applications/species/docs/tutorials/species_database.hdf5\n",
       "   - Data folder: /Users/tomasstolker/applications/species/docs/tutorials/data\n",
       "   - Magnitude of Vega: 0.03\n",
-      "Creating species_database.hdf5... [DONE]\n",
-      "Creating data folder... [DONE]\n",
       "\n",
       "Multiprocessing: mpi4py installed\n",
       "Process number 1 out of 1...\n"
@@ -77,7 +78,7 @@
     {
      "data": {
       "text/plain": [
-       "<species.core.species_init.SpeciesInit at 0x152ada3d0>"
+       "<species.core.species_init.SpeciesInit at 0x15695d510>"
       ]
      },
      "execution_count": 2,
@@ -128,7 +129,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Downloading data from 'http://www.as.utexas.edu/~tdupuy/plx/Database_of_Ultracool_Parallaxes_files/vlm-plx-all.fits' to file '/Users/tomasstolker/applications/species/docs/tutorials/data/vlm-plx-all.fits'.\n"
+      "Downloading data from 'https://home.strw.leidenuniv.nl/~stolker/species/vlm-plx-all.fits' to file '/Users/tomasstolker/applications/species/docs/tutorials/data/vlm-plx-all.fits'.\n"
      ]
     },
     {
@@ -148,7 +149,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|████████████████████████████████████████| 314k/314k [00:00<00:00, 136MB/s]\n"
+      "100%|████████████████████████████████████████| 314k/314k [00:00<00:00, 448MB/s]\n"
      ]
     }
    ],
@@ -179,15 +180,15 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Adding companion: 51 Eri b\n"
+      "Add companion: ['51 Eri b']\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
       "Downloading data from 'https://archive.stsci.edu/hlsps/reference-atlases/cdbs/current_calspec/alpha_lyr_stis_011.fits' to file '/Users/tomasstolker/applications/species/docs/tutorials/data/alpha_lyr_stis_011.fits'.\n",
-      "100%|████████████████████████████████████████| 288k/288k [00:00<00:00, 183MB/s]"
+      "100%|████████████████████████████████████████| 288k/288k [00:00<00:00, 121MB/s]"
      ]
     },
     {
@@ -210,22 +211,22 @@
      "text": [
       "Reference: Bohlin et al. 2014, PASP, 126\n",
       "URL: https://ui.adsabs.harvard.edu/abs/2014PASP..126..711B/abstract\n",
-      "Adding companion: beta Pic b\n"
+      "Add companion: ['beta Pic b']\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/tomasstolker/applications/species/species/data/database.py:1356: UserWarning: Found 33 fluxes with NaN in the data of GPI_YJHK. Removing the spectral fluxes that contain a NaN.\n",
+      "/Users/tomasstolker/applications/species/species/data/database.py:1373: UserWarning: Found 33 fluxes with NaN in the data of GPI_YJHK. Removing the spectral fluxes that contain a NaN.\n",
       "  warnings.warn(\n"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Adding companion: PZ Tel B\n"
+      "Add companion: ['PZ Tel B']\n"
      ]
     }
    ],

diff --git a/species/data/phot_data/phot_vlm_plx.py b/species/data/phot_data/phot_vlm_plx.py
@@ -1,6 +1,6 @@
 """
-Module for the photometric data and parallaxes
-from the Database of Ultracool Parallaxes.
+Module for the photometric data and parallaxes from the
+Database of Ultracool Parallaxes.
 """
 
 import os
@@ -17,8 +17,11 @@
 
 def add_vlm_plx(input_path, database):
     """
-    Function for adding the Database of Ultracool
-    Parallaxes to the database.
+    Function for adding the Database of Ultracool Parallaxes to the
+    database. The FITS file with data was originally downloaded from
+    http://www.as.utexas.edu/~tdupuy/plx/Database_of_Ultracool_Parallaxes_files/vlm-plx-all.fits
+    but that website has been taken offline, probably because of the
+    new table at http://bit.ly/UltracoolSheet.
 
     Parameters
     ----------
@@ -35,10 +38,7 @@ def add_vlm_plx(input_path, database):
 
     data_file = os.path.join(input_path, "vlm-plx-all.fits")
 
-    url = (
-        "http://www.as.utexas.edu/~tdupuy/plx/"
-        "Database_of_Ultracool_Parallaxes_files/vlm-plx-all.fits"
-    )
+    url = "https://home.strw.leidenuniv.nl/~stolker/species/vlm-plx-all.fits"
 
     if not os.path.isfile(data_file):
         pooch.retrieve(