Updated setup.py, only add zorder to kwargs in plot_spectrum if not a…

…lready provided, fixed issue with the autocorrelation for multiple dimensions in FitModel, bug fix with the distance prior in run_ultranest, allow to show intead of write plots in EmissionLine, style maintenance, updated tutorials
tomasstolker · Apr 11, 2022 · d3a9edc · d3a9edc
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diff --git a/docs/tutorials.rst b/docs/tutorials.rst
@@ -46,9 +46,9 @@ This page contains a list of tutorials which highlight some of the functionaliti
 .. toctree::
    :maxdepth: 1
 
-   tutorials/spectral_library.ipynb
    tutorials/flux_calibration.ipynb
    tutorials/emission_line.ipynb
+   tutorials/spectral_library.ipynb
 
 .. important::
    A flux calibrated spectrum of Vega is used for the conversion between a flux density and magnitude. The magnitude of Vega is set to 0.03 for all filters. If needed, the magnitude of Vega can be changed with the ``vega_mag`` attribute of a ``SyntheticPhotometry`` object:

diff --git a/docs/tutorials/color_magnitude_broadband.ipynb b/docs/tutorials/color_magnitude_broadband.ipynb
diff --git a/docs/tutorials/companion_data.ipynb b/docs/tutorials/companion_data.ipynb
@@ -60,7 +60,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Initiating species v0.4.0... [DONE]\n",
+      "Initiating species v0.5.0... [DONE]\n",
       "Creating species_config.ini... [DONE]\n",
       "Database: /Users/tomasstolker/applications/species/docs/tutorials/species_database.hdf5\n",
       "Data folder: /Users/tomasstolker/applications/species/docs/tutorials/data\n",
@@ -72,7 +72,7 @@
     {
      "data": {
       "text/plain": [
-       "<species.core.init.SpeciesInit at 0x14abebaf0>"
+       "<species.core.init.SpeciesInit at 0x14e6ea4c0>"
       ]
      },
      "execution_count": 2,
@@ -131,7 +131,26 @@
      "output_type": "stream",
      "text": [
       "Downloading Vega spectrum (270 kB)... [DONE]\n",
-      "Adding Vega spectrum... [DONE]\n"
+      "Adding Vega spectrum... [DONE]\n",
+      "Adding object: beta Pic b"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/tomasstolker/applications/species/species/data/database.py:958: 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": [
+      " [DONE]\n",
+      "Adding object: beta Pic c [DONE]\n",
+      "Adding object: HIP 65426 b [DONE]\n",
+      "Adding object: 51 Eri b [DONE]\n"
      ]
     },
     {
@@ -141,6 +160,48 @@
       "/Users/tomasstolker/applications/species/species/data/filters.py:210: UserWarning: The minimum transmission value of Subaru/CIAO.z is smaller than zero (-1.80e-03). Wavelengths with negative transmission values will be removed.\n",
       "  warnings.warn(\n"
      ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Adding object: HR 8799 b [DONE]\n",
+      "Adding object: HR 8799 c [DONE]\n",
+      "Adding object: HR 8799 d [DONE]\n",
+      "Adding object: HR 8799 e [DONE]\n",
+      "Adding object: HD 95086 b [DONE]\n",
+      "Adding object: PDS 70 b [DONE]\n",
+      "Adding object: PDS 70 c [DONE]\n",
+      "Adding object: 2M 1207 B [DONE]\n",
+      "Adding object: AB Pic B [DONE]\n",
+      "Adding object: HD 206893 B [DONE]\n",
+      "Adding object: RZ Psc B [DONE]\n",
+      "Adding object: GQ Lup B [DONE]\n",
+      "Adding object: PZ Tel B [DONE]\n",
+      "Adding object: kappa And b [DONE]\n",
+      "Adding object: HD 1160 B [DONE]\n",
+      "Adding object: ROXs 12 B [DONE]\n",
+      "Adding object: ROXs 42 Bb [DONE]\n",
+      "Adding object: GJ 504 b [DONE]\n",
+      "Adding object: GU Psc b [DONE]\n",
+      "Adding object: 2M0103 ABb [DONE]\n",
+      "Adding object: 1RXS 1609 B [DONE]\n",
+      "Adding object: GSC 06214 B [DONE]\n",
+      "Adding object: HD 72946 B [DONE]\n",
+      "Adding object: HIP 64892 B [DONE]\n",
+      "Adding object: HD 13724 B [DONE]\n",
+      "Adding object: TYC 8988 B [DONE]\n",
+      "Adding object: TYC 8988 C [DONE]\n",
+      "Adding object: HD 142527 B [DONE]\n",
+      "Adding object: CS Cha B [DONE]\n",
+      "Adding object: CT Cha B [DONE]\n",
+      "Adding object: SR 12 C [DONE]\n",
+      "Adding object: DH Tau B [DONE]\n",
+      "Adding object: HD 4747 B [DONE]\n",
+      "Adding object: HR 3549 B [DONE]\n",
+      "Adding object: CHXR 73 B [DONE]\n",
+      "Adding object: HD 19467 B [DONE]\n"
+     ]
     }
    ],
    "source": [
@@ -382,9 +443,9 @@
       "Opening ObjectBox...\n",
       "name = beta Pic b\n",
       "filters = ['Gemini/NICI.ED286', 'Magellan/VisAO.Ys', 'Paranal/NACO.H', 'Paranal/NACO.J', 'Paranal/NACO.Ks', 'Paranal/NACO.Lp', 'Paranal/NACO.Mp', 'Paranal/NACO.NB374', 'Paranal/NACO.NB405']\n",
-      "mean_wavel = {'Gemini/NICI.ED286': 1.5841804, 'Magellan/VisAO.Ys': 0.9826820974261752, 'Paranal/NACO.H': 1.6588092, 'Paranal/NACO.J': 1.2650998, 'Paranal/NACO.Ks': 2.1449544, 'Paranal/NACO.Lp': 3.8050284, 'Paranal/NACO.Mp': 4.780971, 'Paranal/NACO.NB374': 3.744805, 'Paranal/NACO.NB405': 4.0558634}\n",
+      "mean_wavel = {'Gemini/NICI.ED286': 1.5841803431418238, 'Magellan/VisAO.Ys': 0.9826820974261752, 'Paranal/NACO.H': 1.6588090664617747, 'Paranal/NACO.J': 1.265099894847529, 'Paranal/NACO.Ks': 2.144954491491888, 'Paranal/NACO.Lp': 3.8050282724280526, 'Paranal/NACO.Mp': 4.780970919324577, 'Paranal/NACO.NB374': 3.744805012092439, 'Paranal/NACO.NB405': 4.055862923806052}\n",
       "magnitude = {'Gemini/NICI.ED286': array([13.18,  0.15]), 'Magellan/VisAO.Ys': array([15.53,  0.34]), 'Paranal/NACO.H': array([13.32,  0.14]), 'Paranal/NACO.J': array([14.11,  0.21]), 'Paranal/NACO.Ks': array([12.64,  0.11]), 'Paranal/NACO.Lp': array([11.3 ,  0.06]), 'Paranal/NACO.Mp': array([11.1 ,  0.12]), 'Paranal/NACO.NB374': array([11.25,  0.23]), 'Paranal/NACO.NB405': array([10.98,  0.05])}\n",
-      "flux = {'Gemini/NICI.ED286': array([6.98948226e-15, 9.68707404e-16]), 'Magellan/VisAO.Ys': array([4.24517648e-15, 1.35121790e-15]), 'Paranal/NACO.H': array([5.47258430e-15, 7.07618199e-16]), 'Paranal/NACO.J': array([6.86840623e-15, 1.33676609e-15]), 'Paranal/NACO.Ks': array([4.04416805e-15, 4.10431111e-16]), 'Paranal/NACO.Lp': array([1.58988155e-15, 8.79048273e-17]), 'Paranal/NACO.Mp': array([7.85616914e-16, 8.70064771e-17]), 'Paranal/NACO.NB374': array([1.69319029e-15, 3.61370437e-16]), 'Paranal/NACO.NB405': array([1.61004054e-15, 7.41713169e-17])}\n",
+      "flux = {'Gemini/NICI.ED286': array([6.98948256e-15, 9.68707446e-16]), 'Magellan/VisAO.Ys': array([4.24517648e-15, 1.35121790e-15]), 'Paranal/NACO.H': array([5.47258456e-15, 7.07618234e-16]), 'Paranal/NACO.J': array([6.86840606e-15, 1.33676606e-15]), 'Paranal/NACO.Ks': array([4.04416794e-15, 4.10431099e-16]), 'Paranal/NACO.Lp': array([1.58988159e-15, 8.79048294e-17]), 'Paranal/NACO.Mp': array([7.85616937e-16, 8.70064796e-17]), 'Paranal/NACO.NB374': array([1.69319021e-15, 3.61370420e-16]), 'Paranal/NACO.NB405': array([1.61004056e-15, 7.41713178e-17])}\n",
       "distance = [19.75  0.13]\n",
       "spectrum = None\n"
      ]