pyratbay 2.0.0b2__tar.gz → 2.0.0b4__tar.gz

{pyratbay-2.0.0b2 → pyratbay-2.0.0b4}/CHANGELOG.txt

@@ -9514,3 +9514,119 @@ to allow renaming the post-process outputs.
 
 Updated version to 2.0.0b2
 
+
+*****  Di 22 Okt 2024 09:47:09 CEST  *****
+
+Corrected np.trapz() to np.trapezoid() to avoid deprecation warning.
+
+*****
+
+Removed numpy.core.numeric isscalar imports.
+
+*****
+
+Corrected np.in1d() to np.isin().
+
+
+*****  Di 05 Nov 2024 11:22:31 CET  *****
+
+Updated scipy requirement compatible with Numpy2.0.
+
+*****
+
+Updated docs theme, switched from read_the_docs to furo.
+
+Added docs/custom_style.py file.
+
+
+*****  Do 07 Nov 2024 11:47:50 CET  *****
+
+Added water isotopes for 228 and 227.
+
+*****
+
+Refactored tips() function to extend partition functions domain
+when some isotopes have higher temperature ranges.
+This is done with a cubic spline. Before the code was cutting off
+at the lowest maximum temperature.
+
+These are the affected molecules:
+H2O
+[5000 5000 5000 5000 5000 5000 6000 6000 6000]
+CO2 
+[5000 5000 3500 3500 3500 3500 5000 3500 5000 5000 3500 5000 5000]
+CH4
+[3500 3500 4500 3500]
+NO2
+[3500 1000]
+OH
+[9000 5000 5000]
+H2CO
+[3500 5000 5000]
+H2S
+[4000 5000 5000]
+
+****
+
+Refactored io.write_spectrum() to deal with the wavelength units
+always in microns. Removed wlunits argument.
+Added 'eclipse' type.
+
+Refactored io.read_spectrum() removing wlunits guessing.
+
+Refactored io.write_observations() to enable combining tophat
+and tabulated files as passband functions.
+
+*****
+
+Updated tests in test_io.py.
+test_read_write_spectrum
+test_read_write_spectrum_filter
+test_read_isotopes
+test_write_observations_mix_bandpass_tophats
+
+*****
+
+In spectrum.bin_spectrum() replaced ignore_gaps bool argument
+with gaps string argument.
+Allowed to keep the default behavior for gaps (raise Error),
+ignore them (keep nans), or patch with a linear interpolation.
+
+Updated docs and tests.
+
+*****
+
+Added wl variable to pyrat.spec, to return the wavelength array
+in microns.
+
+
+*****  Fr 22 Nov 2024 18:17:51 CET  *****
+
+Refactored PassBand() and Tophat() classes.
+Added counting_type argument and variable to specify whether the
+response function is per photon (default) or per energy.
+Re-named __call__() method to set_sampling().
+Added integrate() method to do the band_integration in-house.
+Now __call__() method points to intgrate().
+Added arguments to set the wn/wl sampling at initialization.
+Updated docstrings and tests.
+
+*****
+
+Added FILTERS constant, path pointing directly to the filters folder
+Added cheops and tess passbands filters.
+Renamed spitzer_irac?_sa.dat filters to spitzer_irac?.dat
+
+*****
+
+Updated tests on partition functions/isotopes according to latest
+changes.
+
+
+*****  Mo 25 Nov 2024 14:54:48 CET  *****
+
+Refactored PassBand() and Tophat() classes adding self.height
+and having self.response normalized to max(response)=1.
+Added passband docs to the cookbooks.
+Added kepler.dat passbands.
+

{pyratbay-2.0.0b2 → pyratbay-2.0.0b4}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pyratbay
-Version: 2.0.0b2
+Version: 2.0.0b4
 Summary: Python Radiative Transfer in a Bayesian Framework
 Author-email: Patricio Cubillos <patricio.cubillos@oeaw.ac.at>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -348,7 +348,7 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>=1.23.5
-Requires-Dist: scipy>=1.5.4
+Requires-Dist: scipy>=1.13.0
 Requires-Dist: matplotlib>=3.3.4
 Requires-Dist: mc3>=3.2.0
 Requires-Dist: chemcat>=0.3.8
@@ -356,6 +356,7 @@ Requires-Dist: h5py>=3.10.0
 Provides-Extra: test
 Requires-Dist: pytest>=3.9; extra == "test"
 Requires-Dist: mpi4py>=3.1.4; extra == "test"
+Dynamic: license-file
 
 # Pyrat Bay: Python Radiative Transfer in a Bayesian framework
 

{pyratbay-2.0.0b2 → pyratbay-2.0.0b4}/docs/atm_tutorial.rst

@@ -90,7 +90,7 @@ parameter (``tpars``): the temperature (:math:`T_0`) at all layers.
 Here is an example of an isothermal atmosphere configuration file:
 
 .. literalinclude:: ../examples/tutorial/pt_isothermal.cfg
-    :caption: pt_isothermal.cfg
+    :caption: File: pt_isothermal.cfg
 
 Guillot profile
 ^^^^^^^^^^^^^^^
@@ -126,6 +126,7 @@ Here is an example of a ``guillot`` atmosphere configuration file
 <https://github.com/pcubillos/pyratbay/blob/master/examples/tutorial/pt_guillot.cfg>`_):
 
 .. literalinclude:: ../examples/tutorial/pt_guillot.cfg
+    :caption: File: pt_guillot.cfg
 
 
 Madhu profile

{pyratbay-2.0.0b2 → pyratbay-2.0.0b4}/docs/conf.py

@@ -22,7 +22,7 @@ import re
 from datetime import date
 
 # Do not add path to the package (following example from astropy).
-#sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath('.'))
 import pyratbay as pb
 
 # -- General configuration ------------------------------------------------
@@ -58,7 +58,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'Pyrat Bay'
-copyright = u'2016-{:d}, Patricio Cubillos'.format(date.today().year)
+copyright = f'2016-{date.today().year:d}, Patricio Cubillos'
 author = u'Patricio Cubillos'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -103,7 +103,8 @@ exclude_patterns = ['_build', '.DS_Store']
 #show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+#pygments_style = 'sphinx'
+pygments_style = 'custom_style.CustomStyle'
 
 # A list of ignored prefixes for module index sorting.
 #modindex_common_prefix = []
@@ -119,12 +120,17 @@ pygments_style = 'sphinx'
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'furo'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+html_theme_options = {
+    "sidebar_hide_name": False,
+    "light_css_variables": {
+        "color-background-border": "#d0d0d0",
+    },
+}
 
 # Add any paths that contain custom themes here, relative to this directory.
 #html_theme_path = []
@@ -149,6 +155,7 @@ html_favicon = 'figures/favicon.ico'
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
+html_css_files = ["custom.css"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -164,7 +171,7 @@ html_static_path = ['_static']
 #html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {'*':['globaltoc.html', 'relations.html', 'searchbox.html']}
+#html_sidebars = {'*':['globaltoc.html', 'relations.html', 'searchbox.html']}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.

pyratbay-2.0.0b4/docs/custom_style.py

@@ -0,0 +1,19 @@
+from pygments.style import Style
+from pygments.styles.friendly import FriendlyStyle
+from pygments.token import Token
+
+
+class CustomStyle(Style):
+    styles = FriendlyStyle.styles.copy()
+
+    background_color = "#f0f8ff"
+    background_color = "#f0f2f6"
+    styles[Token.Background] = background_color
+
+    comment = "italic #bb3322"
+    styles[Token.Comment] = comment
+    styles[Token.Comment] = comment
+    styles[Token.Comment.Multiline] = comment
+    styles[Token.Comment.Preproc] = comment
+    styles[Token.Comment.Single] = comment
+    styles[Token.Comment.Special] = comment

{pyratbay-2.0.0b2 → pyratbay-2.0.0b4}/docs/docs_requirements.txt

@@ -1,4 +1,4 @@
-sphinx-rtd-theme>=2.0.0
+furo==2023.9.10
 nbsphinx
 sphinx_copybutton
 ipython>=8.17

{pyratbay-2.0.0b2 → pyratbay-2.0.0b4}/docs/getstarted.rst

@@ -36,7 +36,7 @@ The following table details what each of these steps do.
 | ``spectrum``   | Compute forward-modeling spectra (transmission or          |
 |                | emission)                                                  |
 +----------------+------------------------------------------------------------+
-| ``mcmc``       | Run an atmospheric retrieval                               |
+| ``retrieval``  | Run an atmospheric retrievals                              |
 +----------------+------------------------------------------------------------+
 
 Any of these steps can be run either interactively though the Python
@@ -71,19 +71,8 @@ through the ``Pyrat Bay`` sub modules (see :ref:`API`).
 System Requirements
 -------------------
 
-Pyrat-Bay (version 1.0+) has been extensively tested to work on
-Unix/Linux and OS X machines, with the following software
-requirements:
-
-* Python >= 3.6
-* Numpy >= 1.8.1
-* Scipy >= 0.13.3
-* Matplotlib >= 1.3.1
-* Sympy >= 0.7.6
-* mc3 >= 3.0.7
-
-``Pyrat Bay`` may work with previous software versions; however, we do
-not guarantee nor provide support for that.
+Pyrat-Bay (version 2.0+) has been extensively tested to work on
+Unix/Linux and OS X machines and is available for Python 3.9+.
 
 .. _install:
 
@@ -96,7 +85,7 @@ To install ``Pyrat Bay`` run the following command from the terminal:
 
 .. code-block:: shell
 
-    pip install pyratbay
+    pip install pyratbay>=2.0.0b3
 
 Or if you prefer conda:
 
@@ -145,16 +134,15 @@ Download the water line-transition database from the HITRAN server and unzip it:
 
 Copy the input and configuration files for the demo from the `examples
 folder
-<https://github.com/pcubillos/pyratbay/tree/master/examples/demo>`_ to
+<https://github.com/pcubillos/pyratbay/tree/ver2.0/examples/>`_ to
 your working directory.  For example, use the following shell commands:
 
 .. code-block:: shell
 
-    demo_path=https://raw.githubusercontent.com/pcubillos/pyratbay/master/examples/demo
-    wget $demo_path/demo_spectrum-emission.cfg
-    wget $demo_path/demo_spectrum-transmission.cfg
-    wget $demo_path/demo_tli-hitran.cfg
-    wget $demo_path/uniform.atm
+    demo=https://raw.githubusercontent.com/pcubillos/pyratbay/ver2.0/tutorials/
+    wget $demo/tutorial_tli_hitran_H2O.cfg
+    wget $demo/tutorial_spectrum_emission.cfg
+    wget $demo/tutorial_spectrum_transmission.cfg
 
 
 Execute these commands from the shell to create a
@@ -164,11 +152,11 @@ transmission and emission spectra:
 .. code-block:: shell
 
    # Format line-by-line opacity:
-   pbay -c demo_tli-hitran.cfg
+   pbay -c tutorial_tli_hitran_H2O.cfg
 
    # Compute transmission and emission spectra:
-   pbay -c demo_spectrum-transmission.cfg
-   pbay -c demo_spectrum-emission.cfg
+   pbay -c tutorial_spectrum_transmission.cfg
+   pbay -c tutorial_spectrum_emission.cfg
 
 .. Outputs
    ^^^^^^^
@@ -183,44 +171,51 @@ interactive mode, I suggest starting the session with ``ipython
 
 .. code-block:: python
 
+  import pyratbay as pb
+  import pyratbay.spectrum as ps
+  import pyratbay.io as io
   import matplotlib
-  from scipy.ndimage.filters import gaussian_filter1d as gaussf
   import matplotlib.pyplot as plt
   plt.ion()
 
-  import pyratbay as pb
-  import pyratbay.io as io
 
-  wl, transmission = io.read_spectrum("./transmission_spectrum_demo.dat", wn=False)
-  wl, emission     = io.read_spectrum("./emission_spectrum_demo.dat", wn=False)
+  wl, transmission = io.read_spectrum("./transmission_spectrum_tutorial.dat", wn=False)
+  wl, emission = io.read_spectrum("./emission_spectrum_tutorial.dat", wn=False)
+
+  bin_wl = ps.constant_resolution_spectrum(0.3, 8.0, resolution=200)
+  bin_transit = ps.bin_spectrum(bin_wl, wl, transmission)
+  bin_emission = ps.bin_spectrum(bin_wl, wl, emission)
 
-  plt.figure(0, figsize=(7,5))
+  fig = plt.figure(0)
   plt.clf()
-  plt.subplots_adjust(0.14, 0.1, 0.95, 0.95, hspace=0.15)
+  fig.set_size_inches(7,5)
+  plt.subplots_adjust(0.12, 0.1, 0.98, 0.95, hspace=0.15)
   ax = plt.subplot(211)
-  plt.plot(wl, 100*transmission, "b", label="pyrat transmission model", lw=1.0)
-  plt.plot(wl, gaussf(100*transmission, sigma=5.0), "orange", lw=1.25)
+  plt.plot(wl, 100*transmission, color="royalblue", label="transmission model", lw=1.0)
+  plt.plot(bin_wl, 100*bin_transit, "salmon", lw=1.5)
   plt.xscale('log')
-  plt.ylabel(r"$(R_{\rm p}/R_{\rm s})^2}$  (%)")
+  plt.ylabel('Transit depth (%)')
   ax.get_xaxis().set_major_formatter(matplotlib.ticker.ScalarFormatter())
-  ax.set_xticks([0.5, 0.7, 1.0, 2.0, 3.0, 4.0, 5.0])
-  plt.xlim(0.5, 5.5)
-  plt.ylim(1.88, 2.15)
+  ax.set_xticks([0.3, 0.5, 0.7, 1.0, 2.0, 3.0, 5.0, 7.0])
+  ax.tick_params(which='both', direction='in')
+  plt.xlim(0.3, 8.0)
+  plt.ylim(1.88, 2.17)
   plt.legend(loc="upper left")
 
   ax = plt.subplot(212)
-  plt.plot(wl, emission, "b", label="pyrat emission model", lw=1.0)
-  plt.plot(wl, gaussf(emission, sigma=5.0), "orange", lw=1.25)
+  plt.plot(wl, emission, "royalblue", label="emission model", lw=1.0)
+  plt.plot(bin_wl, bin_emission, "salmon", lw=1.5)
   plt.xscale('log')
   plt.xlabel(r"Wavelength  (um)")
-  plt.ylabel(r"$F_{\rm planet}$ (erg s$^{-1}$ cm$^{-2}$ cm)")
+  plt.ylabel(r"$F_{\rm p}$ (erg s$^{-1}$ cm$^{-2}$ cm)")
   ax.get_xaxis().set_major_formatter(matplotlib.ticker.ScalarFormatter())
-  ax.set_xticks([0.5, 0.7, 1.0, 2.0, 3.0, 4.0, 5.0])
-  plt.ylim(0, 60000)
-  plt.xlim(0.5, 5.5)
+  ax.set_xticks([0.3, 0.5, 0.7, 1.0, 2.0, 3.0, 5.0, 7.0])
+  ax.tick_params(which='both', direction='in')
+  plt.ylim(0, 52000)
+  plt.xlim(0.3, 8.0)
   plt.legend(loc="upper left")
   plt.draw()
-  plt.savefig("pyrat_spectrum_demo.pdf")
+  plt.savefig("pyrat_spectrum_demo.png", dpi=300)
 
 The output figure should look like this:
 
@@ -260,7 +255,7 @@ importing the ``Pyrat Bay`` package:
 .. code-block:: python
 
     import pyratbay as pb
-    pyrat = pb.run('demo_spectrum-transmission.cfg')
+    pyrat = pb.run('tutorial_spectrum_transmission.cfg')
     ax = pyrat.plot_spectrum()
 
 The output vary depending on the selected run mode.  Additional low-

{pyratbay-2.0.0b2 → pyratbay-2.0.0b4}/docs/index.rst

@@ -57,7 +57,7 @@ The radiative-transfer include opacity sources from:
 - Na and K alkali resonant lines
 - Gray and Mie (soon) aerosol opacities
 
-Bayesian (MCMC) posterior sampling of atmospheric parameters:
+Bayesian (MCMC and Nested sampling) posterior sampling of atmospheric parameters:
 
 - Molecular abundances
 - Temperature profile
@@ -81,10 +81,9 @@ Documentation
    :includehidden:
 
    getstarted
-   tli_tutorial
+   line_sampling
    atm_tutorial
    spec_tutorial
-   opac_tutorial
    retrieval_tutorial
    cookbooks/recipes
    api
@@ -103,7 +102,7 @@ If you found ``Pyrat Bay`` useful for your research, please cite this article:
 Please prefer to channel your feedback or inquiries through the Github issue tracker: `<https://github.com/pcubillos/pyratbay>`_, or alternatively through this email: `patricio.cubillos[at]oeaw.ac.at`_.
 
 ``Pyrat Bay`` is open-source software under the GNU GPL v2 license (see
-:ref:`license`) and is compatible with Python>=3.6.
+:ref:`license`) and is compatible with Python>=3.9.
 
 
 .. _Patricio Cubillos: https://github.com/pcubillos/

pyratbay-2.0.0b4/docs/line_sampling.rst

@@ -0,0 +1,222 @@
+.. |H2O| replace:: H\ :sub:`2`\ O
+.. |CO2| replace:: CO\ :sub:`2`
+.. |CH4| replace:: CH\ :sub:`4`
+.. |H2|  replace:: H\ :sub:`2`
+.. |N2O| replace:: N\ :sub:`2`\ O
+.. |NO2| replace:: NO\ :sub:`2`
+
+
+.. _line_sampling:
+
+Line Sampling
+=============
+
+
+`Pyrat Bay` enable users to generate their own line-sampled
+cross-section files out of line-by-line data.  In this process, users
+can make all the customization that they deem necessary (e.g.,
+line-wing cutoffs, sampling rates, wavelength ranges, temperature
+ranges, pressure ranges).
+
+There are two steps needed to compute cross sections:
+
+1. Convert line lists from their **original format** (e.g., HITRAN or
+   ExoMol) into transition-line information files (**TLI**).
+
+2. Conver **TLI** files into **cross-section tables** (saved as Numpy
+   ``.npz`` files).
+
+
+
+Available Databases
+-------------------
+
+``Pyrat Bay`` can process line-lists from the two main sources of
+line-transition data of interest for exoplanet atmospheres: HITRAN [Gordon2022]_ and
+Exomol [Tennyson2016]_.  Additionally, ``Pyrat Bay`` is also compatible with
+``repack`` [Cubillos2017b]_, a package extracting only the strong line
+transitions from large HITEMP, ExoMol, or AMES databases (reducing
+from billions to millions of lines).
+
+The tables below show the main species of interest to model exoplanet
+atmospheres from each database (non-exhaustive, there are move species
+available in each database).
+
+.. list-table:: Available linelists from HITRAN
+   :header-rows: 1
+   :widths: 7, 20, 25
+
+   * - Source
+     - Species (label)
+     - References
+   * - HITEMP
+     - `H2O <https://hitran.org/hitemp/>`__ (2010)
+     - [Rothman2010]_
+   * - 
+     - `CO2 <https://hitran.org/hitemp/>`__ (2024)
+     - [Hargreaves2025]_
+   * - 
+     - `CO <https://hitran.org/hitemp/>`__ (2019)
+     - [Li2015]_
+   * - 
+     - `CH4 <https://hitran.org/hitemp/>`__ (2020)
+     - [Hargreaves2020]_
+   * - 
+     - `N2O <https://hitran.org/hitemp/>`__ (2019)
+     - [Hargreaves2019]_
+   * - 
+     - `NO <https://hitran.org/hitemp/>`__ (2019)
+     - [Hargreaves2019]_
+   * - HITRAN
+     - `H2O, NH3, and many others <https://hitran.org/lbl/>`__
+     - [Gordon2022]_
+
+
+
+.. list-table:: Available linelists from ExoMol
+   :header-rows: 1
+   :widths: 7, 20, 25
+
+   * - Source
+     - Species (label)
+     - References
+   * - ExoMol
+     - `H2O <https://www.exomol.com/data/molecules/H2O/>`__ (pokazatel)
+     - [Polyansky2018]_
+   * - 
+     - `CO2 <https://www.exomol.com/data/molecules/CO2/12C-16O2/UCL-4000/>`__ (ucl4000)
+     - [Yurchenko2020]_
+   * - 
+     - `CH4 <https://www.exomol.com/data/molecules/CH4/12C-1H4/MM/>`__ (mm)
+     - [Yurchenko2024a]_
+   * - 
+     - `NH3 <https://www.exomol.com/data/molecules/NH3/>`__ (coyute)
+     - [Coles2019]_ [Yurchenko2024b]_
+   * - 
+     - `TiO <https://www.exomol.com/data/molecules/TiO/>`__ (toto)
+     - [McKemmish2019]_
+   * - 
+     - `VO <https://www.exomol.com/data/molecules/VO/51V-16O/HyVO/>`__ (hyvo)
+     - [Bowesman2024]_
+   * - 
+     - `HCN <https://www.exomol.com/data/molecules/HCN/>`__ (harris & larner)
+     - [Harris2008]_ [Barber2014]_
+   * - 
+     - `SO2 <https://www.exomol.com/data/molecules/SO2/32S-16O2/ExoAmes/>`__ (exoames)
+     - [Underwood2016]_
+   * - 
+     - `H2S <https://www.exomol.com/data/molecules/H2S/1H2-32S/AYT2/>`__ (ayt2)
+     - [Azzam2016]_ [Chubb2018]_
+   * - 
+     - `C2H2 <https://www.exomol.com/data/molecules/C2H2/12C2-1H2/aCeTY/>`__ (acety)
+     - [Chubb2020]_
+
+
+
+.. list-table:: Available linelists from repack
+   :header-rows: 1
+   :widths: 7, 20, 25
+
+   * - Source
+     - Species (label)
+     - References
+   * - repack
+     - `H2O <https://zenodo.org/api/records/14266247/draft/files/H2O_exomol_pokazatel_0.24-500.0um_100-3500K_threshold_0.01_lbl.dat>`__ (exomol, pokazatel)
+     -  [Cubillos2017b]_ [Polyansky2018]_
+   * - 
+     - `CO2 <https://zenodo.org/api/records/14266247/draft/files/CO2_exomol_ucl4000_0.5-500.0um_100-3500K_threshold_0.01_lbl.dat>`__ (exomol, ucl4000)
+     - [Cubillos2017b]_ [Yurchenko2020]_
+   * - 
+     - `CO2 <https://zenodo.org/api/records/14266247/draft/files/CO2_ames_ai3000k_0.5-50.0um_100-3500K_threshold_0.01_lbl.dat>`__ (ames, ai3000k) 
+     - [Cubillos2017b]_ 
+   * - 
+     - `CH4 <https://zenodo.org/api/records/14266247/draft/files/CH4_exomol_mm_0.83-50.0um_100-3000K_threshold_0.03_lbl.dat>`__ (exomol, mm)
+     - [Cubillos2017b]_ [Yurchenko2024a]_
+   * - 
+     - `NH3 <https://zenodo.org/api/records/14266247/draft/files/NH3_exomol_coyute_0.5-500.0um_100-3000K_threshold_0.01_lbl.dat>`__ (exomol, coyute)
+     - [Cubillos2017b]_ [Coles2019]_ [Yurchenko2024b]_
+   * - 
+     - `TiO <https://zenodo.org/api/records/14266247/draft/files/TiO_exomol_toto_0.33-500um_100-3500K_threshold_0.01_lbl.dat>`__ (exomol, toto)
+     - [Cubillos2017b]_ [McKemmish2019]_
+   * - 
+     - `VO <https://zenodo.org/api/records/14266247/draft/files/VO_exomol_hyvo_0.22-50um_100-3500K_threshold_0.01_lbl.dat>`__ (exomol, hyvo)
+     - [Cubillos2017b]_ [Bowesman2024]_
+   * - 
+     - `HCN <https://zenodo.org/api/records/14266247/draft/files/HCN_exomol_harris-larner_0.56-500um_100-3500K_threshold_0.01_lbl.dat>`__ (exomol, harris larner)
+     - [Cubillos2017b]_ [Harris2008]_ [Barber2014]_
+   * - 
+     - `SO2 <https://zenodo.org/api/records/14266247/draft/files/SO2_exomol_exoames_1.25-100.0um_100-3500K_threshold_0.03_lbl.dat>`__ (exomol, exoames)
+     - [Cubillos2017b]_ [Underwood2016]_
+   * - 
+     - `H2S <https://zenodo.org/api/records/14266247/draft/files/H2S_exomol_ayt2_0.28-500.0um_100-3500K_threshold_0.01_lbl.dat>`__ (exomol, ayt2) 
+     - [Cubillos2017b]_ [Azzam2016]_ [Chubb2018]_
+   * - 
+     - `C2H2 <https://zenodo.org/api/records/14266247/draft/files/C2H2_exomol_acety_1.0-500.0um_100-3500K_threshold_0.03_lbl.dat>`__ (exomol, acety)
+     - [Cubillos2017b]_ [Chubb2020]_
+   * - 
+     - `C2H4 <https://zenodo.org/api/records/14266247/draft/files/C2H4_exomol_mayty_1.4-500um_100-3500K_threshold_0.03_lbl.dat>`__ (exomol, mayty)
+     - [Cubillos2017b]_ [Mant2018]_
+
+
+
+.. _sample_tli_cfg:
+
+Line-sampling Tutorials
+-----------------------
+
+The following links show step-by-step tutorials to compute
+cross-section tables (i.e., line sampling) from each database:
+
+- :doc:`cookbooks/line_sampling/line_list_hitran`
+- :doc:`cookbooks/line_sampling/line_list_exomol`
+- :doc:`cookbooks/line_sampling/line_list_repack`
+
+
+Computing cross sections often require to sample millions-to-billions
+of line transitions. Thus, it can both become a computer-intensive
+calculation and require/produce large files. ``Pyrat Bay`` was
+designed with this two-step approach to optimize these calculations.
+
+Below there are a few useful notes to keep in mind when computing
+cross sections.
+
+
+Partition functions
+~~~~~~~~~~~~~~~~~~~
+
+While line-list databases do not change often with time, thus, TLI
+files containing the line transitions can typically be computed only
+once, and being used for many projects.  For this reason, it is
+recommended to compute TLI files with the widest possible available
+wavelength range.
+
+TLI calculations also requires the input of partition functions, which
+depend on the temperature.  Ideally, you also want to compute TLI
+files with the widest temperature range.  The tutorials above show how
+to obtain partition functions from each database.  In addition, this
+tutorial below shows more in general how to handle partition functions
+(e.g., how to compute PFs at high temperatures):
+
+- :doc:`cookbooks/partition_functions`
+
+
+Cross sections
+~~~~~~~~~~~~~~
+
+In contrast, cross sections might need to be more frequently
+re-computed for specific project to adjust, for example, to the
+sampling resolution or grid boundaries (in `T`, `p`, or
+:math:`\lambda`), or need to separate between different isotopes of a
+same species.  Use the tutorials above as a template, and modifies
+them to adjust to the scientific requirements/machine capabilities
+that each project requires.
+
+
+If in a hurry and want to immediately start computing spectra, ``Pyrat
+Bay`` is also compatible with the `petitRADTRANS
+<https://petitradtrans.readthedocs.io/en/latest/content/available_opacities.html#high-resolution-opacities-lbl-lambda-delta-lambda-10-6>`_
+cross section files [Molliere2019]_.  These files can be directly used
+as input in spectrum or retrieval calculations (and can be used in
+combination with the ``wn_thinning`` argument of the configuration
+files to reduce the sampling resolution).  More documentation on this
+is coming `soon`.