Included interp_method parameter in config file, fixed issues with so…

…me mathtext

docs/overview.rst

@@ -32,6 +32,17 @@ The following data and models are currently supported:
 - `Sonora Bobcat <https://zenodo.org/record/5063476>`_
 - `Sonora Cholla <https://zenodo.org/record/4450269>`_
 
+The :func:`~species.data.database.Database.available_models()` method of the :class:`~species.data.database.Database` class can be used for getting a complete overview of all model grids, including details on the input parameters, wavelength range, :math:`T_\mathrm{eff}` range, and spectral resolution:
+
+.. code-block:: python
+
+   import species
+
+   species.SpeciesInit()
+
+   database = species.Database()
+   database.available_models()
+
 **Spectral libraries**
 
 - `IRTF Spectral Library <http://irtfweb.ifa.hawaii.edu/~spex/IRTF_Spectral_Library/>`_

species/core/box.py

@@ -135,8 +135,10 @@ def create_box(boxtype, **kwargs):
         box.spectrum = kwargs["spectrum"]
         box.wavelength = kwargs["wavelength"]
         box.flux = kwargs["flux"]
-        box.error = kwargs["error"]
-        box.name = kwargs["name"]
+        if "error" in kwargs:
+            box.error = kwargs["error"]
+        if "name" in kwargs:
+            box.name = kwargs["name"]
         if "simbad" in kwargs:
             box.simbad = kwargs["simbad"]
         if "sptype" in kwargs:

species/core/init.py

@@ -57,9 +57,18 @@ def __init__(self):
             print("Creating species_config.ini...", end="", flush=True)
 
             with open(config_file, "w") as file_obj:
-                file_obj.write("[species]\n")
-                file_obj.write("database = species_database.hdf5\n")
-                file_obj.write("data_folder = ./data/\n")
+                file_obj.write("[species]\n\n")
+
+                file_obj.write("; File with the HDF5 database\n")
+                file_obj.write("database = species_database.hdf5\n\n")
+
+                file_obj.write("; Folder where data will be downloaded\n")
+                file_obj.write("data_folder = ./data/\n\n")
+
+                file_obj.write("; Method for the grid interpolation\n")
+                file_obj.write("; Options: linear, nearest, slinear, "
+                               "cubic, quintic, pchip\n")
+                file_obj.write("interp_method = linear\n")
 
             print(" [DONE]")
 

species/read/read_model.py

@@ -86,6 +86,7 @@ def __init__(
         config.read(config_file)
 
         self.database = config["species"]["database"]
+        self.interp_method = config["species"]["interp_method"]
 
         self.extra_param = [
             "radius",
@@ -209,7 +210,11 @@ def interpolate_model(self) -> None:
         flux = flux[..., self.wl_index]
 
         self.spectrum_interp = RegularGridInterpolator(
-            points, flux, method="linear", bounds_error=False, fill_value=np.nan
+            points,
+            flux,
+            method=self.interp_method,
+            bounds_error=False,
+            fill_value=np.nan,
         )
 
     @typechecked
@@ -382,7 +387,11 @@ def interpolate_grid(
             self.wl_points = wavel_resample
 
         self.spectrum_interp = RegularGridInterpolator(
-            points, flux_new, method="linear", bounds_error=False, fill_value=np.nan
+            points,
+            flux_new,
+            method=self.interp_method,
+            bounds_error=False,
+            fill_value=np.nan,
         )
 
     @staticmethod

species/util/plot_util.py

@@ -268,7 +268,7 @@ def update_labels(param: List[str]) -> List[str]:
 
     if "parallax" in param:
         index = param.index("parallax")
-        param[index] = r"$\pi$ (mas)"
+        param[index] = r"$\varpi$ (mas)"
 
     if "mass" in param:
         index = param.index("mass")
@@ -320,11 +320,11 @@ def update_labels(param: List[str]) -> List[str]:
 
     if "mcore_1" in param:
         index = param.index("mcore_1")
-        param[index] = r"$M_\mathrm{core, b}$"
+        param[index] = r"$M_\mathrm{core,b}$ ($M_\mathrm{E}$)"
 
     if "mcore_2" in param:
         index = param.index("mcore_2")
-        param[index] = r"$M_\mathrm{core, c}$"
+        param[index] = r"$M_\mathrm{core,c}$ ($M_\mathrm{E}$)"
 
     if "luminosity" in param:
         index = param.index("luminosity")
@@ -809,7 +809,7 @@ def quantity_unit(
             unit.append(r"$R_\mathrm{J}$")
 
         elif object_type == "star":
-            unit.append(r"$R_\mathrm{\odot}$$")
+            unit.append(r"$R_\mathrm{\odot}$")
 
         label.append(r"$R$")
 
@@ -830,7 +830,7 @@ def quantity_unit(
                 unit.append(r"$R_\mathrm{J}$")
 
             elif object_type == "star":
-                unit.append(r"$R_\mathrm{\odot}$$")
+                unit.append(r"$R_\mathrm{\odot}$")
 
             label.append(rf"$R_\mathrm{{{i+1}}}$")
 
@@ -849,14 +849,14 @@ def quantity_unit(
             unit.append(r"$M_\mathrm{J}$")
 
         elif object_type == "star":
-            unit.append(r"$M_\mathrm{\odot}$$")
+            unit.append(r"$M_\mathrm{\odot}$")
 
         label.append("M")
 
     if "luminosity" in param:
         quantity.append("luminosity")
         unit.append(None)
-        label.append(r"$\log\,L/L_\mathrm{\odot}$$")
+        label.append(r"$\log\,L/L_\mathrm{\odot}$")
 
     if "ism_ext" in param:
         quantity.append("ism_ext")

species/util/test_util.py

@@ -25,7 +25,7 @@ def create_config(test_path):
     data_folder = os.path.join(test_path, "data/")
 
     with open(config_file, "w", encoding="utf-8") as config:
-        print(dir(config))
         config.write("[species]\n")
-        config.write("database = " + database_file + "\n")
-        config.write("data_folder = " + data_folder)
+        config.write(f"database = {database_file}\n")
+        config.write(f"data_folder = {data_folder}\n")
+        config.write("interp_method = linear")