From 8a97e926fd7bf4917c4e20cc0a2a38818b75322f Mon Sep 17 00:00:00 2001
From: Tomas Stolker <stolker@strw.leidenuniv.nl>
Date: Mon, 25 Sep 2023 12:39:10 +0200
Subject: [PATCH] Added support for the SPHINX model spectra

---
 docs/overview.rst             |  3 ++-
 species/data/database.py      |  2 +-
 species/data/model_data.json  | 10 ++++++++++
 species/data/model_spectra.py | 17 +++++++++--------
 species/read/read_model.py    |  4 ++--
 species/util/plot_util.py     |  3 +++
 6 files changed, 27 insertions(+), 12 deletions(-)

diff --git a/docs/overview.rst b/docs/overview.rst
index 24c3a97f..104e0e0c 100644
--- a/docs/overview.rst
+++ b/docs/overview.rst
@@ -30,9 +30,10 @@ The following data and models are currently supported:
 - `Morley et al. (2012) T/Y dwarf spectra <https://ui.adsabs.harvard.edu/abs/2012ApJ...756..172M/abstract>`_
 - `petitCODE <http://www.mpia.de/~molliere/#petitcode>`_
 - `petitRADTRANS <https://petitradtrans.readthedocs.io>`_
+- `Saumon & Marley (2008) <https://ui.adsabs.harvard.edu/abs/2008ApJ...689.1327S/abstract>`_
 - `Sonora Bobcat <https://zenodo.org/record/5063476>`_
 - `Sonora Cholla <https://zenodo.org/record/4450269>`_
-- `Saumon & Marley (2008) <https://ui.adsabs.harvard.edu/abs/2008ApJ...689.1327S/abstract>`_
+- `SPHINX <https://zenodo.org/record/7416042>`_
 
 .. tip::
   It is also possible to add your own custom grid of model spectra with :func:`~species.data.database.Database.add_custom_model()`. Have a look at the documentation for details on the required file format.
diff --git a/species/data/database.py b/species/data/database.py
index 447e6741..3196d1ca 100644
--- a/species/data/database.py
+++ b/species/data/database.py
@@ -708,7 +708,7 @@ def add_model(
             'blackbody', bt-cond', 'bt-cond-feh, 'morley-2012',
             'sonora-cholla', 'sonora-bobcat', 'sonora-bobcat-co',
             'koester-wd', 'saumon2008-clear', 'saumon2008-cloudy',
-            'petrus2023').
+            'petrus2023', 'sphinx').
         wavel_range : tuple(float, float), None
             Wavelength range (um) for adding a subset of the spectra.
             The full wavelength range is used if the argument is set
diff --git a/species/data/model_data.json b/species/data/model_data.json
index db16544f..555280fc 100644
--- a/species/data/model_data.json
+++ b/species/data/model_data.json
@@ -259,5 +259,15 @@
         "information": "[Fe/H] = 0.0, log(g) = 5.0",
         "reference": "Marley et al. (2021)",
         "url": "https://zenodo.org/record/5063476"
+    },
+    "sphinx": {
+        "parameters": ["teff", "logg", "feh", "c_o_ratio"],
+        "name": "SPHINX",
+        "file size": "143 Mb",
+        "wavelength range": [0.1, 20],
+        "resolution": 250,
+        "teff range": [2000, 4000],
+        "reference": "Aishwarya et al. (2022)",
+        "url": "https://zenodo.org/record/7416042"
     }
 }
diff --git a/species/data/model_spectra.py b/species/data/model_spectra.py
index 251b4288..5991d043 100644
--- a/species/data/model_spectra.py
+++ b/species/data/model_spectra.py
@@ -72,14 +72,15 @@ def add_model_grid(
     else:
         raise ValueError(
             f"The {model_name} atmospheric model is not available. "
-            f"Please choose one of the following models: "
-            f"'ames-cond', 'ames-dusty', 'atmo', 'bt-settl', "
-            f"'bt-nextgen', 'drift-phoexnix', 'petitcode-cool-clear', "
-            f"'petitcode-cool-cloudy', 'petitcode-hot-clear', "
-            f"'petitcode-hot-cloudy', 'exo-rem', 'bt-settl-cifist', "
-            f"'bt-cond', 'bt-cond-feh', 'blackbody', 'sonora-cholla', "
-            f"'sonora-bobcat', 'sonora-bobcat-co', 'koester-wd', "
-            f"'saumon2008-clear', 'saumon2008-cloudy', 'petrus2023' "
+            "Please choose one of the following models: "
+            "'ames-cond', 'ames-dusty', 'atmo', 'bt-settl', "
+            "'bt-nextgen', 'drift-phoexnix', 'petitcode-cool-clear', "
+            "'petitcode-cool-cloudy', 'petitcode-hot-clear', "
+            "'petitcode-hot-cloudy', 'exo-rem', 'bt-settl-cifist', "
+            "'bt-cond', 'bt-cond-feh', 'blackbody', 'sonora-cholla', "
+            "'sonora-bobcat', 'sonora-bobcat-co', 'koester-wd', "
+            "'saumon2008-clear', 'saumon2008-cloudy', 'petrus2023', "
+            "'sphinx'"
         )
 
     if model_name == "bt-settl":
diff --git a/species/read/read_model.py b/species/read/read_model.py
index ba80a2fa..73d917e2 100644
--- a/species/read/read_model.py
+++ b/species/read/read_model.py
@@ -1121,8 +1121,8 @@ def get_model(
         if np.isnan(np.sum(model_box.flux)):
             warnings.warn(
                 f"The resampled spectrum contains {np.sum(np.isnan(model_box.flux))} "
-                f"NaNs, probably because the original wavelength range does not fully "
-                f"encompass the new wavelength range. The happened with the "
+                "NaNs, probably because the original wavelength range does not fully "
+                "encompass the new wavelength range. The happened with the "
                 f"following parameters: {model_param}."
             )
 
diff --git a/species/util/plot_util.py b/species/util/plot_util.py
index 207c9609..7c51c8e2 100644
--- a/species/util/plot_util.py
+++ b/species/util/plot_util.py
@@ -929,6 +929,9 @@ def convert_model_name(in_name: str) -> str:
     elif in_name == "sonora-bobcat-co":
         out_name = "Sonora Bobcat C/O"
 
+    elif in_name == "sphinx":
+        out_name = "SPHINX"
+
     elif in_name == "petitradtrans":
         out_name = "petitRADTRANS"