Fixed issues with new package structure

Makefile

@@ -19,6 +19,7 @@ pypi-test:
 docs:
 	rm -f docs/species.core.rst
 	rm -f docs/species.data.rst
+	rm -f docs/species.data.*.rst
 	rm -f docs/species.fit.rst
 	rm -f docs/species.phot.rst
 	rm -f docs/species.plot.rst
@@ -28,6 +29,8 @@ docs:
 	cd docs/
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html
+	rm -f docs/species_config.ini
+	rm -f docs/species_database.hdf5
 
 coverage:
 	coverage run --source=species -m pytest

README.rst

@@ -28,7 +28,7 @@
 
 There are tools available for grid and free retrievals using Bayesian inference, synthetic photometry, interpolating a variety atmospheric and evolutionary model grids (including the possibility to add a custom grid), color-magnitude and color-color diagrams, empirical spectral analysis, spectral and photometric calibration, and analysis of emission lines. The package has been released on `PyPI <https://pypi.org/project/species/>`_ and is actively developed and maintained on Github.
 
-**Important:** Importing the *species* package had become slow because of the many classes and functions that were implicitly imported. The initialization of the package has therefore been adjusted. In the latest version, any functionalities should be explicitly imported from the modules that they are part of.
+**Important:** Importing the *species* package had become slow because of the many classes and functions that were implicitly imported. The initialization of the package has therefore been adjusted. Any functionalities should now be explicitly imported from the modules that they are part of.
 
 Documentation
 -------------

docs/index.rst

@@ -6,7 +6,7 @@ Documentation for *species*
 *species* is a toolkit for atmospheric characterization of directly imaged exoplanets.
 
 .. important::
-   Importing the ``species`` package had become slow because of the many classes and functions that were implicitly imported. The initialization of the package has therefore been adjusted. In the latest version, any functionalities should be explicitly imported from the modules that they are part of.
+   Importing the ``species`` package had become slow because of the many classes and functions that were implicitly imported. The initialization of the package has therefore been adjusted. Any functionalities should now be explicitly imported from the modules that they are part of.
 
 .. toctree::
    :maxdepth: 2

docs/species.data.companion_data.rst

@@ -0,0 +1,21 @@
+species.data.companion\_data package
+====================================
+
+Submodules
+----------
+
+species.data.companion\_data.companion\_spectra module
+------------------------------------------------------
+
+.. automodule:: species.data.companion_data.companion_spectra
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: species.data.companion_data
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/species.data.filter_data.rst

@@ -0,0 +1,21 @@
+species.data.filter\_data package
+=================================
+
+Submodules
+----------
+
+species.data.filter\_data.filter\_data module
+---------------------------------------------
+
+.. automodule:: species.data.filter_data.filter_data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: species.data.filter_data
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/species.data.isochrone_data.rst

@@ -0,0 +1,21 @@
+species.data.isochrone\_data package
+====================================
+
+Submodules
+----------
+
+species.data.isochrone\_data.add\_isochrone module
+--------------------------------------------------
+
+.. automodule:: species.data.isochrone_data.add_isochrone
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: species.data.isochrone_data
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/species.data.misc_data.rst

@@ -0,0 +1,29 @@
+species.data.misc\_data package
+===============================
+
+Submodules
+----------
+
+species.data.misc\_data.accretion\_data module
+----------------------------------------------
+
+.. automodule:: species.data.misc_data.accretion_data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+species.data.misc\_data.dust\_data module
+-----------------------------------------
+
+.. automodule:: species.data.misc_data.dust_data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: species.data.misc_data
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/species.data.model_data.rst

@@ -0,0 +1,29 @@
+species.data.model\_data package
+================================
+
+Submodules
+----------
+
+species.data.model\_data.custom\_model module
+---------------------------------------------
+
+.. automodule:: species.data.model_data.custom_model
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+species.data.model\_data.model\_spectra module
+----------------------------------------------
+
+.. automodule:: species.data.model_data.model_spectra
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: species.data.model_data
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/species.data.phot_data.rst

@@ -0,0 +1,29 @@
+species.data.phot\_data package
+===============================
+
+Submodules
+----------
+
+species.data.phot\_data.phot\_leggett module
+--------------------------------------------
+
+.. automodule:: species.data.phot_data.phot_leggett
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+species.data.phot\_data.phot\_vlm\_plx module
+---------------------------------------------
+
+.. automodule:: species.data.phot_data.phot_vlm_plx
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: species.data.phot_data
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/species.data.rst

@@ -1,48 +1,22 @@
 species.data package
 ====================
 
-Submodules
-----------
-
-species.data.accretion module
------------------------------
-
-.. automodule:: species.data.accretion
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-species.data.allers2013 module
-------------------------------
-
-.. automodule:: species.data.allers2013
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-species.data.bonnefoy2014 module
---------------------------------
-
-.. automodule:: species.data.bonnefoy2014
-   :members:
-   :undoc-members:
-   :show-inheritance:
+Subpackages
+-----------
 
-species.data.companion\_spectra module
---------------------------------------
+.. toctree::
+   :maxdepth: 4
 
-.. automodule:: species.data.companion_spectra
-   :members:
-   :undoc-members:
-   :show-inheritance:
+   species.data.companion_data
+   species.data.filter_data
+   species.data.isochrone_data
+   species.data.misc_data
+   species.data.model_data
+   species.data.phot_data
+   species.data.spec_data
 
-species.data.custom\_model module
----------------------------------
-
-.. automodule:: species.data.custom_model
-   :members:
-   :undoc-members:
-   :show-inheritance:
+Submodules
+----------
 
 species.data.database module
 ----------------------------
@@ -52,86 +26,6 @@ species.data.database module
    :undoc-members:
    :show-inheritance:
 
-species.data.dust module
-------------------------
-
-.. automodule:: species.data.dust
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-species.data.filters module
----------------------------
-
-.. automodule:: species.data.filters
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-species.data.irtf module
-------------------------
-
-.. automodule:: species.data.irtf
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-species.data.isochrones module
-------------------------------
-
-.. automodule:: species.data.isochrones
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-species.data.kesseli2017 module
--------------------------------
-
-.. automodule:: species.data.kesseli2017
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-species.data.leggett module
----------------------------
-
-.. automodule:: species.data.leggett
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-species.data.model\_spectra module
-----------------------------------
-
-.. automodule:: species.data.model_spectra
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-species.data.spex module
-------------------------
-
-.. automodule:: species.data.spex
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-species.data.vega module
-------------------------
-
-.. automodule:: species.data.vega
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-species.data.vlm\_plx module
-----------------------------
-
-.. automodule:: species.data.vlm_plx
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 Module contents
 ---------------