### Install Build Dependencies

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/installation.rst

Install essential packages if third-party installation fails.

```bash
pip install -U setuptools cython
```

--------------------------------

### Verify Installation

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/installation.rst

Test the installation by initializing a Radtrans object, which triggers the automatic download of required opacity data.

```python
from petitRADTRANS.radtrans import Radtrans
radtrans = Radtrans(line_species=['CH4'])
```

--------------------------------

### Install Pre-installation Dependencies

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/installation.rst

Install required Python packages before proceeding with the main installation.

```bash
pip install numpy meson-python ninja
```

--------------------------------

### Initialize Retrieval Model

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/retrieval_models.ipynb

Example of setting up a retrieval model instance.

```python
from petitRADTRANS import Retrieval

retrieval = Retrieval(line_species=['H2O', 'CH4'],
                      cloud_species=['Mg2SiO4(c)'],
                      rayleigh_species=['H2', 'He'])

```

--------------------------------

### Example Utility Function

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/utility_functions.ipynb

A placeholder example demonstrating the structure of utility functions in the project.

```python
def example_utility(data):
    """Example utility function."""
    return data * 2
```

--------------------------------

### Example Utility Function

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/utility_functions.ipynb

A placeholder example demonstrating the structure of utility functions.

```python
def example_utility(x):
    return x * 2
```

--------------------------------

### Generate High Resolution Spectra

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/high_resolution_spectra.ipynb

Example demonstrating the setup and generation of a high-resolution spectrum.

```python
import numpy as np
from petitRADTRANS import Radtrans

# Setup the atmosphere
atmosphere = Radtrans(line_species=['CO2', 'H2O'], rayleigh_species=['H2', 'He'])
atmosphere.setup_opa_structure(pressures=np.logspace(-6, 2, 100))

# Calculate spectrum
atmosphere.calc_flux(temperature=1500, mass_fractions={'CO2': 1e-4, 'H2O': 1e-4}, gravity=1e3)

# Access the high resolution spectrum
wavelengths = atmosphere.wavelength
flux = atmosphere.flux
```

--------------------------------

### Setup Atmosphere Parameters

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/rebinning_opacities.ipynb

Initializes temperature and mass fraction arrays for atmospheric modeling.

```python
from petitRADTRANS import physical_constants as cst
temperatures = 1200.0 * np.ones_like(atmosphere.pressures) # note that pressures is in cgs units now, multiply by 1e-6 to get bars.

mass_fractions = {
    'H2': 0.74 * np.ones_like(temperatures), 
    'He': 0.24 * np.ones_like(temperatures),
    'H2O': 1e-3 * np.ones_like(temperatures), 
    'CO-NatAbund': 1e-2 * np.ones_like(temperatures),
```

--------------------------------

### Install dependencies on Linux

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/installation.rst

Use apt-get to install the necessary Python, pip, Fortran compiler, and Chromium packages.

```bash
sudo apt-get install python python-pip gfortran chromium
```

--------------------------------

### Install Fortran compiler on Mac OS

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/installation.rst

Install the GCC compiler suite using Homebrew.

```bash
brew install gcc
```

--------------------------------

### Install development dependencies

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/contributing.rst

Install the package in editable mode with test dependencies.

```bash
pip install -e .[test] --no-build-isolation
```

--------------------------------

### Setup Temperature Profile and Atmospheric Parameters

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/rebinning_opacities.ipynb

Initializes the temperature profile and atmospheric parameters required for rebinning opacities.

```python
from petitRADTRANS.physics import temperature_profile_function_guillot_global

planet_radius = 1.0*cst.r_jup_mean
reference_gravity = 10**3.5
reference_pressure = 0.01

pressures_bar = atmosphere_high_res.pressures*1e-6 # cgs to bar
kappa_IR = 0.01
gamma = 0.4
T_int = 200.
```

--------------------------------

### Initialize Retrieval Model

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/retrieval_models.ipynb

Example of initializing a retrieval model instance.

```python
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
```

--------------------------------

### Run Retrieval

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/retrieval_models.ipynb

Example of executing the retrieval process.

```python
retrieval.run(n_live_points=500,
              output_dir='output_dir',
              resume=False)

```

--------------------------------

### Initialize High Resolution Spectra

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/high_resolution_spectra.ipynb

Basic setup for high-resolution spectral calculations.

```python
from petitRADTRANS import Radtrans
import numpy as np

# Define the atmosphere
atmosphere = Radtrans(line_species=['H2O', 'CO2'], 
                     rayleigh_species=['H2', 'He'], 
                     continuum_opacities=['H2-H2', 'H2-He'], 
                     wlen_bords_micron=[0.3, 15.0])
```

--------------------------------

### Compile petitRADTRANS from Source

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/installation.rst

Clone the repository and install from the local directory.

```bash
git clone https://gitlab.com/mauricemolli/petitRADTRANS.git
```

```bash
pip install . --no-build-isolation
```

```bash
pip install ".[retrieval]" --no-build-isolation
```

--------------------------------

### Handle opacity file selection prompt

Source: https://petitradtrans.readthedocs.io/en/latest/content/installation.html

Example of the prompt displayed when multiple opacity files are detected and user input is required.

```text
More than one file detected in <long/path> and no default file set for this path in petitRADTRANS' configuration
Please select one of the files in the list below by typing the corresponding integer:
```

--------------------------------

### Initialize High Resolution Spectra

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/high_resolution_spectra.ipynb

Setup the necessary environment and imports to begin working with high-resolution spectra.

```python
from petitRADTRANS import Radtrans
import numpy as np
import matplotlib.pyplot as plt
```

--------------------------------

### Rebinning Opacities

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/rebinning_opacities.ipynb

Example demonstrating how to rebin opacity data to a lower resolution.

```python
import numpy as np
from petitRADTRANS import Radtrans

# Define the atmosphere and rebin the opacities
rt = Radtrans(line_species=['H2O'], rayleigh_species=['H2'], continuum_species=['H2-H2', 'H2-He'])
rt.rebin_opacities(1000)
```

--------------------------------

### Run tests with tox and conda

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/contributing.rst

Example commands to set up a conda environment and execute specific tox test environments.

```bash
conda create --name toxfun python=3.11
conda activate toxfun
pip install tox
pip install tox-conda
conda install numba
tox -e flake8
tox -e py311
```

--------------------------------

### Example Output Keys

Source: https://petitradtrans.readthedocs.io/en/latest/content/notebooks/retrieval_multiple_data.html

Displays the keys returned by the model generating function after enabling the output parameters.

```text
opacities
continuum_opacities_scattering
transmission_contribution
```

--------------------------------

### Initial Radtrans opacity loading output

Source: https://petitradtrans.readthedocs.io/en/latest/content/notebooks/rebinning_opacities.html

Example console output showing the loading process for line and CIA opacities.

```text
Loading Radtrans opacities...
 Loading line opacities of species 'H2O.R100' from file '/home/dblain/petitRADTRANS/input_data/opacities/lines/correlated_k/H2O/1H2-16O/1H2-16O__HITEMP.R100_0.1-250mu.ktable.petitRADTRANS.h5'... Done.
 Done.ng line opacities of species 'CO-NatAbund.R100' from file '/home/dblain/petitRADTRANS/input_data/opacities/lines/correlated_k/CO/C-O-NatAbund/C-O-NatAbund__HITEMP.R100_0.1-250mu.ktable.petitRADTRANS.h5'...
 Done.ng line opacities of species 'CH4.R100' from file '/home/dblain/petitRADTRANS/input_data/opacities/lines/correlated_k/CH4/12C-1H4/12C-1H4__YT34to10.R100_0.3-50mu.ktable.petitRADTRANS.h5'...
 Done.ng line opacities of species 'CO2.R100' from file '/home/dblain/petitRADTRANS/input_data/opacities/lines/correlated_k/CO2/12C-16O2/12C-16O2__UCL-4000.R100_0.3-50mu.ktable.petitRADTRANS.h5'...
 Loading line opacities of species 'Na.R100' from file '/home/dblain/petitRADTRANS/input_data/opacities/lines/correlated_k/Na/23Na/23Na__Allard.R100_0.1-250mu.ktable.petitRADTRANS.h5'... Done.
 Loading line opacities of species 'K.R100' from file '/home/dblain/petitRADTRANS/input_data/opacities/lines/correlated_k/K/39K/39K__Allard.R100_0.1-250mu.ktable.petitRADTRANS.h5'... Done.
 Successfully loaded all line opacities
 Loading CIA opacities for H2--H2 from file '/home/dblain/petitRADTRANS/input_data/opacities/continuum/collision_induced_absorptions/H2--H2/H2--H2-NatAbund/H2--H2-NatAbund__BoRi.R831_0.6-250mu.ciatable.petitRADTRANS.h5'... Done.
 Loading CIA opacities for H2--He from file '/home/dblain/petitRADTRANS/input_data/opacities/continuum/collision_induced_absorptions/H2--He/H2--He-NatAbund/H2--He-NatAbund__BoRi.DeltaWavenumber2_0.5-500mu.ciatable.petitRADTRANS.h5'... Done.
 Successfully loaded all CIA opacities
Successfully loaded all opacities
```

--------------------------------

### Prepare Homebrew on Mac OS

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/installation.rst

Update and check the Homebrew environment before installing dependencies.

```bash
brew update
brew upgrade
brew doctor
```

--------------------------------

### Load Opacities for Emission Spectra

Source: https://petitradtrans.readthedocs.io/en/latest/content/notebooks/including_clouds.html

Example output showing the successful loading of line, CIA, and cloud opacities for a petitRADTRANS simulation.

```text
Loading Radtrans opacities...
 Loading line opacities of species 'H2O' from file '/home/dblain/petitRADTRANS/input_data/opacities/lines/correlated_k/H2O/1H2-16O/1H2-16O__HITEMP.R1000_0.1-250mu.ktable.petitRADTRANS.h5'... Done.
 Done.ng line opacities of species 'CO-NatAbund' from file '/home/dblain/petitRADTRANS/input_data/opacities/lines/correlated_k/CO/C-O-NatAbund/C-O-NatAbund__HITEMP.R1000_0.1-250mu.ktable.petitRADTRANS.h5'...
 Done.ng line opacities of species 'CH4' from file '/home/dblain/petitRADTRANS/input_data/opacities/lines/correlated_k/CH4/12C-1H4/12C-1H4__YT34to10.R1000_0.3-50mu.ktable.petitRADTRANS.h5'...
 Loading line opacities of species 'CO2' from file '/home/dblain/petitRADTRANS/input_data/opacities/lines/correlated_k/CO2/12C-16O2/12C-16O2__UCL-4000.R1000_0.3-50mu.ktable.petitRADTRANS.h5'... Done.
 Loading line opacities of species 'Na' from file '/home/dblain/petitRADTRANS/input_data/opacities/lines/correlated_k/Na/23Na/23Na__Allard.R1000_0.1-250mu.ktable.petitRADTRANS.h5'... Done.
 Done.ng line opacities of species 'K' from file '/home/dblain/petitRADTRANS/input_data/opacities/lines/correlated_k/K/39K/39K__Allard.R1000_0.1-250mu.ktable.petitRADTRANS.h5'...
 Successfully loaded all line opacities
 Loading CIA opacities for H2--H2 from file '/home/dblain/petitRADTRANS/input_data/opacities/continuum/collision_induced_absorptions/H2--H2/H2--H2-NatAbund/H2--H2-NatAbund__BoRi.R831_0.6-250mu.ciatable.petitRADTRANS.h5'... Done.
 Loading CIA opacities for H2--He from file '/home/dblain/petitRADTRANS/input_data/opacities/continuum/collision_induced_absorptions/H2--He/H2--He-NatAbund/H2--He-NatAbund__BoRi.DeltaWavenumber2_0.5-500mu.ciatable.petitRADTRANS.h5'... Done.
 Successfully loaded all CIA opacities
 Loading opacities of cloud species 'Mg2SiO4(s)_crystalline__DHS' from file '/home/dblain/petitRADTRANS/input_data/opacities/continuum/clouds/Mg2SiO4(s)_crystalline_000/Mg2-Si-O4-NatAbund(s)_crystalline_000/Mg2-Si-O4-NatAbund(s)_crystalline_000__DHS.R39_0.1-250mu.cotable.petitRADTRANS.h5' (crystalline_000, using DHS scattering)... Done.
 Loading opacities of cloud species 'Fe(s)_amorphous__Mie' from file '/home/dblain/petitRADTRANS/input_data/opacities/continuum/clouds/Fe(s)_amorphous/Fe-NatAbund(s)_amorphous/Fe-NatAbund(s)_amorphous__Mie.R39_0.1-250mu.cotable.petitRADTRANS.h5' (amorphous, using Mie scattering)... Done.
 Successfully loaded all clouds opacities
Successfully loaded all opacities
```

--------------------------------

### Configure Species Pressure Broadening

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/adding_opacities.rst

Example configuration for species pressure broadening using specific broadening files for H2 and He.

```bash
species
  0 gamma 0.06 n 0.5 t0 296 file path_toH2_broadening_information_file model J ratio 0.860000
  1 gamma 0.06 n 0.5 t0 296 file path_toHe_broadening_information_file model J ratio 0.140000
end
```

--------------------------------

### setup_exoatmos

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/autoapi/petitRADTRANS/chemistry/prt_easychem/index.rst

Initializes the exoatmos environment.

```APIDOC
## setup_exoatmos()

### Description
Performs the necessary setup operations for exoatmos calculations.
```

--------------------------------

### setup_data(scaling=10, width=3)

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/autoapi/petitRADTRANS/retrieval/retrieval/index.rst

Creates a pRT object for each data set and prepares low resolution c-k models if necessary.

```APIDOC
## setup_data(scaling=10, width=3)

### Description
Initializes pRT objects for data sets and ensures low-resolution c-k models are available. The scaling and width parameters configure the AMR grid.

### Parameters
- **scaling** (int) - Optional - Multiplicative factor for the high-resolution pressure grid size.
- **width** (int) - Optional - Number of cells in the low-pressure grid to replace with the high-resolution grid.
```

--------------------------------

### setup_data(scaling=10, width=3)

Source: https://petitradtrans.readthedocs.io/en/latest/autoapi/petitRADTRANS/retrieval/index.html

Creates pRT objects for data sets and prepares AMR grids.

```APIDOC
## setup_data(scaling=10, width=3)

### Description
Creates a pRT object for each data set and checks for low resolution c-k models, creating them if necessary. The scaling and width parameters adjust the AMR grid.

### Parameters
- **scaling** (int) - Optional - Multiplicative factor for the high resolution pressure grid size.
- **width** (int) - Optional - Number of cells in the low pressure grid to replace with the high resolution grid.
```

--------------------------------

### Initialize Planet Atmosphere

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/planet.ipynb

Sets up the atmospheric structure for a planet, including pressure levels and atmospheric composition.

```python
import numpy as np
from petitRADTRANS import Radtrans

# Define pressure levels
pressures = np.logspace(-6, 2, 100)

# Initialize Radtrans object
atmosphere = Radtrans(line_species=['H2O', 'CH4'], rayleigh_species=['H2', 'He'], continuum_opacities=['H2-H2', 'H2-He'], pressure_grid=pressures, r_pl=1.0, p_n_range=[1e-6, 1e2])
```

--------------------------------

### Install mpi4py via Conda

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/installation.rst

Install the conda-specific version of mpi4py to resolve library linking issues.

```bash
conda install mpi4py
```

--------------------------------

### Install petitRADTRANS via pip

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/installation.rst

Install the package using pip with the required build isolation flag.

```bash
pip install petitRADTRANS --no-build-isolation
```

```bash
pip install "petitRADTRANS[retrieval]" --no-build-isolation
```

--------------------------------

### setup_clouds(pressures, parameters, cloud_species)

Source: https://petitradtrans.readthedocs.io/en/latest/autoapi/petitRADTRANS/chemistry/clouds/index.html

Provides the set of cloud parameters used in the model.

```APIDOC
## setup_clouds(pressures, parameters, cloud_species)

### Description
This function provides the set of cloud parameters used in the model.

### Parameters
- **pressures** - The pressure array for the model.
- **parameters** - The dictionary of model parameters.
- **cloud_species** - A list of cloud species to include.
```

--------------------------------

### Identify Installation Errors

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/installation.rst

Common error messages encountered when Fortran extensions are incorrectly installed in temporary directories.

```python
# For a pip install
ModuleNotFoundError: No module named 'petitRADTRANS.<fortran_extension>'

# For an editable pip install
FileNotFoundError: [Errno 2] No such file or directory: '/a/temporary/directory/overlay/bin/ninja'
```

--------------------------------

### Initialize Environment and Imports

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/retrieval_models.ipynb

Sets up the necessary environment by importing required libraries and configuring the plotting style.

```python
# Let's start by importing everything we need
import os

import matplotlib.pyplot as plt
import numpy as np

import petitRADTRANS as prt
from petitRADTRANS import physical_constants as cst
from petitRADTRANS.retrieval.parameter import Parameter
from petitRADTRANS.plotlib.style import set_petitradtrans_plot_style

set_petitradtrans_plot_style()
```

--------------------------------

### setup_simple_clouds_hazes(parameters)

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/autoapi/petitRADTRANS/chemistry/clouds/index.rst

Sets up clouds for transmission spectrum calculations.

```APIDOC
### Function: setup_simple_clouds_hazes(parameters)

#### Description
Setup clouds for transmission spectrum.

#### Parameters
- **parameters** (dict) - Dictionary of atmospheric parameters.
```

--------------------------------

### Instantiate SpectralModel with SysRem

Source: https://petitradtrans.readthedocs.io/en/latest/content/notebooks/spectral_model.html

Configure the SpectralModel by mapping the preparation step to the custom wrapper and providing SysRem-specific parameters.

```python
spectral_model = SpectralModel(
    # Preparation parameters
    spectral_modification_functions_map={
        'prepare': sysrem_wrapper  # modify the preparation step
    },
    n_passes=10,
    n_iterations_max=300,
    convergence_criterion=1e-15,
    tellurics_mask_threshold=0.8,  # mask the fitted transmittances if it is below this value
    polynomial_fit_degree=2,  # degree of the polynomial fit
    uncertainties=data_uncertainties,
    # Radtrans parameters
    pressures=np.logspace(-6, 2, 100),
    line_species=[
        'CO-NatAbund',
        'H2O'
    ],
    rayleigh_species=['H2', 'He'],
    gas_continuum_contributors=['H2--H2', 'H2--He'],
    line_opacity_mode='lbl',
    line_by_line_opacity_sampling=4,
    # SpectralModel parameters
    # Planet parameters
    planet_radius=planet.radius,
    reference_gravity=planet.reference_gravity,
    reference_pressure=1e-2,
    star_radius=planet.star_radius,
    transit_duration=planet.transit_duration,
    orbital_period=planet.orbital_period,
    # Velocity paramters
    star_mass=planet.star_mass,
    orbit_semi_major_axis=planet.orbit_semi_major_axis,
    orbital_inclination=planet.orbital_inclination,
    rest_frame_velocity_shift=-5e5,  # (cm.s-1) V_rest
    system_observer_radial_velocities=star_radial_velocity - barycentric_velocities,
    # Temperature profile parameters
    temperature_profile_mode='isothermal',
    temperature=planet.equilibrium_temperature,
    # Cloud parameters
    opaque_cloud_top_pressure=1e-2,  # added opaque cloud
    # Mass fractions
    use_equilibrium_chemistry=False,
    imposed_mass_fractions={
        'CO-NatAbund': 1e-2,
        'H2O': 1e-3,
    },
    filling_species={
        'H2': 37,
        'He': 12
    },
    # Observation parameters
    rebinned_wavelengths=data_wavelengths,  # (cm) used for the rebinning, and also to set the wavelengths boundaries
    rebin_range_margin_power=4,  # used to set the wavelengths boundaries, adding a margin of ~1 Angstrom (1e-4 * ~1 µm)
    convolve_resolving_power=8e4,  # used for the convolution
    mid_transit_time=mid_transit_time,
    times=times
)
```

--------------------------------

### Install Python via Deadsnakes on Linux

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/installation.rst

Commands to add the deadsnakes PPA and install a specific Python version and its development headers.

```bash
sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt-get update
sudo apt-get install pkg-config
sudo apt-get install python3.x
sudo apt-get install python3.x-dev
```

--------------------------------

### Initialize SpectralModel with Cloud Parameters

Source: https://petitradtrans.readthedocs.io/en/latest/content/notebooks/including_clouds.html

Configure a SpectralModel instance with physical cloud parameters, gas species, and planet properties.

```python
spectral_model = SpectralModel(
    # Cloud parameters
    eddy_diffusion_coefficients=eddy_diffusion_coefficients,
    cloud_f_sed=cloud_f_sed,
    cloud_particle_radius_distribution_std=cloud_particle_radius_distribution_std,
    complete_coverage_clouds=['Fe(s)_amorphous__Mie'],
    cloud_fraction=1.0,
    # Other cloud parameters
    #opaque_cloud_top_pressure=1e-2,
    #haze_factor=10,
    #power_law_opacity_350nm=power_law_opacity_350nm,
    #power_law_opacity_coefficient=power_law_opacity_coefficient,
    #additional_absorption_opacities_function=cloud_opas,
    # Radtrans parameters
    pressures=np.logspace(-6, 2, 100),
    line_species=[
        'H2O',
        'CO-NatAbund',
        'CH4',
        'CO2',
        'Na',
        'K'
    ],
    rayleigh_species=['H2', 'He'],
    gas_continuum_contributors=['H2--H2', 'H2--He'],
    cloud_species = [
        'Mg2SiO4(s)_crystalline__DHS',
        'Fe(s)_amorphous__Mie'
    ],
    wavelength_boundaries=[0.3, 15],
    # Model parameters
    # Planet parameters
    planet_radius=planet_radius,
    reference_gravity=reference_gravity,
    reference_pressure=reference_pressure,
    # Temperature profile parameters
    temperature_profile_mode='guillot',
    temperature=equilibrium_temperature,
    intrinsic_temperature=intrinsic_temperature,
    guillot_temperature_profile_infrared_mean_opacity_solar_metallicity=infrared_mean_opacity,
    guillot_temperature_profile_gamma=gamma,
    # Mass fractions
    imposed_mass_fractions={
        'H2O': 1e-3,
        'CO-NatAbund': 1e-2,
        'CH4': 1e-6,
        'CO2': 1e-5,
        'Na': 1e-5,
        'K': 1e-6,
        'Mg2SiO4(s)_crystalline__DHS': 5e-7,
        'Fe(s)_amorphous__Mie': 5e-7
    },
    filling_species={
        'H2': 37,
        'He': 12
    }
)
```

--------------------------------

### petitRADTRANS.retrieval.preparing.__sysrem_iteration_orders_a

Source: https://petitradtrans.readthedocs.io/en/latest/autoapi/petitRADTRANS/retrieval/preparing/index.html

Performs a SYSREM iteration for all orders starting with the 'a' parameter.

```APIDOC
## petitRADTRANS.retrieval.preparing.__sysrem_iteration_orders_a(spectrum_uncertainties_squared, uncertainties_squared_inverted, a)

### Description
Performs a SYSREM iteration for all orders at once, starting with 'a'. For the first iteration, 'a' should be 1. The inputs are chosen to maximize speed.

### Parameters
- **spectrum_uncertainties_squared** (array) - Spectral data to correct over the uncertainties squared (..., exposure, wavelength).
- **uncertainties_squared_inverted** (array) - Inverse of the squared uncertainties on the data (..., exposure, wavelength).
- **a** (array) - 2-D matrix (..., exposures, wavelengths) containing the a-priori 'airmass'.

### Returns
- **tuple** - The lower-rank estimation of the spectrum (systematics) and the estimated 'extinction coefficients'.
```

--------------------------------

### Check petitRADTRANS Version

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/content/notebooks/getting_started.ipynb

Verify the installed version of the petitRADTRANS package.

```python
import petitRADTRANS
print(f"petitRADTRANS version: {petitRADTRANS.__version__}")
```

--------------------------------

### Initialize SpectralModel

Source: https://petitradtrans.readthedocs.io/en/latest/content/notebooks/analysis_tools.html

Imports and configures a SpectralModel instance with atmospheric parameters, species, and physical properties.

```python
from petitRADTRANS.spectral_model import SpectralModel
```

```python
spectral_model = SpectralModel(
    # Radtrans parameters
    pressures=np.logspace(-6, 3, 100),
    line_species=[
        'H2O',
        'CO-NatAbund',
        'CH4',
        'CO2',
        'Na__Burrows',
        'K__Burrows'
    ],
    rayleigh_species=['H2', 'He'],
    gas_continuum_contributors=['H2--H2', 'H2--He'],
    cloud_species=['MgSiO3(s)_crystalline__DHS'],
    wavelength_boundaries=[0.3, 15],
    # Model parameters
    temperature=temperatures,
    imposed_mass_fractions={  # using constant mass fractions with pressure
        'H2O': 1e-3,
        'CO-NatAbund': 1e-2,
        'CO2': 1e-4,
        'CH4': 1e-5,
        'Na__Burrows': 1e-4,
        'K__Burrows': 1e-6,
        'MgSiO3(s)_crystalline__DHS': 1e-6
    },
    filling_species={'H2': 37, 'He': 12},
    cloud_particles_mean_radii={'MgSiO3(s)_crystalline__DHS': 1e-4},  # (cm)
    cloud_particle_radius_distribution_std=2,  # 1 for a delta function
    reference_gravity=reference_gravity,
    planet_radius=planet_radius,
    reference_pressure=reference_pressure
)
```

--------------------------------

### Data Class Placeholder

Source: https://petitradtrans.readthedocs.io/en/latest/content/notebooks/retrieval_basic.html

Placeholder for Data class configuration examples.

```python
[5]:
```

--------------------------------

### petitRADTRANS.retrieval.preparing.__sysrem_iteration_orders_c

Source: https://petitradtrans.readthedocs.io/en/latest/autoapi/petitRADTRANS/retrieval/preparing/index.html

Performs a SYSREM iteration for all orders starting with the 'c' parameter.

```APIDOC
## petitRADTRANS.retrieval.preparing.__sysrem_iteration_orders_c(spectrum_uncertainties_squared, uncertainties_squared_inverted, c)

### Description
Performs a SYSREM iteration for all orders at once, starting with 'c'. For the first iteration, 'c' should be 1. The inputs are chosen to maximize speed.

### Parameters
- **spectrum_uncertainties_squared** (array) - Spectral data to correct over the uncertainties squared (..., exposure, wavelength).
- **uncertainties_squared_inverted** (array) - Inverse of the squared uncertainties on the data (..., exposure, wavelength).
- **c** (array) - 2-D matrix (..., exposures, wavelengths) containing the a-priori 'extinction coefficients'.

### Returns
- **tuple** - The lower-rank estimation of the spectrum (systematics) and the estimated 'extinction coefficients'.
```

--------------------------------

### list_available_cia_species()

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/autoapi/petitRADTRANS/retrieval/index.rst

Lists the currently installed opacity tables available for CIA species.

```APIDOC
### Method
`list_available_cia_species()`

### Description
Returns a list of currently installed opacity tables available for CIA species.
```

--------------------------------

### list_available_cloud_species()

Source: https://petitradtrans.readthedocs.io/en/latest/_sources/autoapi/petitRADTRANS/retrieval/index.rst

Lists the currently installed opacity tables available for cloud species.

```APIDOC
### Method
`list_available_cloud_species()`

### Description
Returns a list of currently installed opacity tables available for cloud species.
```