ExoIris 0.19.2__tar.gz → 0.21.0__tar.gz

{exoiris-0.19.2 → exoiris-0.21.0}/CHANGELOG.md

@@ -5,7 +5,27 @@ All notable changes to ExoIris will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [0.21.0] - 2025-11-24
+
+### Added
+- Added a `loglikelihood.LogLikelihood` class for reduced-rank Gaussian log-likelihood calculation.
+- Added `ExoIris.create_loglikelihood_function` method to generate log-likelihood instances for atmospheric retrieval.
+- Added `ExoIris.radius_ratio_spectrum` and `ExoIris.area_ratio_spectrum` methods to compute posterior transmission 
+  spectrum distributions for given wavelengths.
+- Added `exoiris.util.create_mock_model` utility function for generating mock transmission spectra.
+
+## [0.20.0] - 2025-11-19
+
+### Added
+- Added the ability to model star spot crossings. The spots are modeled as generalized Gaussians parameterized by their 
+  center time, amplitude in a given reference wavelength, full width at half maximum (FWHM), spot temperature in Kelvin,
+  and spot shape. The spot amplitude along the wavelength is modeled using the theoretical BT-Settl spectra, the stellar
+  effective temperature, the spot temperature, and the reference wavelength in which the spot amplitude is measured.
+- Added the ability to model the contamination from unocculted spots and faculae (**the transit light source effect**,
+  or TLSE). This is modeled also using BT-Settl spectra following the formalism described by Rackham et al. (2018).
+- Included two new radius ratio interpolation options: "nearest" and "linear".
+
+## [0.19.2] - 2025-09-12
 
 ### Added
 
@@ -38,7 +58,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-- Added support for masked data support with GP noise model.
+- Added support for masked data with GP noise model.
 - Added an option to set the GP hyperparameters for an individual data set.
 - Added  `white_times`, `white_fluxes`, `white_models`, and `white_errors` properties to `ExoIris` to access white ligth curve data.
 

exoiris-0.21.0/ExoIris.egg-info/PKG-INFO

@@ -0,0 +1,118 @@
+Metadata-Version: 2.4
+Name: ExoIris
+Version: 0.21.0
+Summary: Easy and robust exoplanet transmission spectroscopy.
+Author-email: Hannu Parviainen <hannu@iac.es>
+License: GPLv3
+Project-URL: homepage, https://github.com/hpparvi/ExoIris
+Keywords: astronomy,astrophysics,exoplanets
+Classifier: Topic :: Scientific/Engineering
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pytransit>=2.6.15
+Requires-Dist: ldtk>=1.8.5
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: numba
+Requires-Dist: emcee
+Requires-Dist: matplotlib
+Requires-Dist: celerite2
+Requires-Dist: pandas
+Requires-Dist: xarray
+Requires-Dist: seaborn
+Requires-Dist: astropy
+Requires-Dist: uncertainties
+Dynamic: license-file
+
+# ExoIris: Fast and Flexible Transmission Spectroscopy in Python
+
+[![Docs](https://readthedocs.org/projects/exoiris/badge/)](https://exoiris.readthedocs.io)
+![Python package](https://github.com/hpparvi/ExoIris/actions/workflows/python-package.yml/badge.svg)
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.0-4baaaa.svg)](CODE_OF_CONDUCT.md)
+[![Licence](http://img.shields.io/badge/license-GPLv3-blue.svg?style=flat)](http://www.gnu.org/licenses/gpl-3.0.html)
+[![PyPI version](https://badge.fury.io/py/exoiris.svg)](https://pypi.org/project/ExoIris/)
+
+**ExoIris** is a Python package for modeling exoplanet transmission spectroscopy. ExoIris removes the typical 
+limitations of the two-step workflow by modeling the full two-dimensional spectroscopic transit time series *directly*.
+It supports combining transmission spectroscopy datasets from multiple instruments observed in different epochs, yielding 
+self-consistent wavelength-independent and wavelength-dependent parameters, simplifying joint analyses, and delivering 
+results quickly.
+
+![](doc/source/examples/e01/example1.png)
+
+## Why ExoIris?
+
+Transmission spectroscopy is often done following a **two-step workflow**: (1) fit a white light curve to infer 
+wavelength-independent parameters; (2) fit each spectroscopic light curve independently, constrained by the white-light 
+solution. This split can introduce approximations and inconsistencies.
+
+**ExoIris takes a different approach.** It models spectrophotometric time series *end-to-end*, enabling:
+
+- Self-consistent inference of shared (wavelength-independent) and spectral (wavelength-dependent) parameters.
+- **Joint** modeling of multiple datasets from different instruments and epochs.
+- Accounting for **transit timing variations** and dataset-dependent offsets within a unified framework.
+
+This design is a natural fit for **JWST-class** data, where correlated noise, multi-epoch observations, and 
+cross-instrument combinations are the norm.
+
+## Documentation
+
+Full documentation and tutorials: <https://exoiris.readthedocs.io>
+
+## Installation
+
+Install from PyPI:
+
+```bash
+pip install exoiris
+```
+
+Latest development version:
+
+```bash
+git clone https://github.com/hpparvi/ExoIris.git
+cd ExoIris
+pip install -e .
+```
+
+ExoIris supports Python 3.9+. See the docs for dependency details and optional extras.
+
+## Key Features
+
+- **Direct modelling of spectroscopic transit time series**  
+  Built on PyTransit’s `TSModel`, optimised for transmission spectroscopy; scales to hundreds–thousands of light curves simultaneously.
+
+- **Flexible limb darkening**  
+  Use standard analytical laws (quadratic, power-2, non-linear), numerical intensity profiles from stellar atmosphere models, or user-defined radially symmetric functions.
+
+- **Robust noise treatment**  
+  Choose white noise or **time-correlated** noise via a Gaussian Process likelihood, without changing the overall workflow.
+
+- **Full control of spectral resolution**  
+  The transmission spectrum is represented as a cubic spline with user-defined knots, allowing variable resolution across wavelength.
+
+- **Reproducible, incremental workflows**  
+  Save and reload models to refine a low-resolution run into a high-resolution analysis seamlessly.
+
+- **Joint multi-dataset analyses**  
+  Combine instruments and epochs in one fit, with support for transit timing variations and dataset-specific systematics and offsets.
+
+## Performance
+
+ExoIris is designed for speed and stability:
+
+- A transmission spectroscopy analysis of a single JWST/NIRISS dataset at **R ≈ 100** typically runs in **3–5 minutes** 
+  assuming white noise, or **5–15 minutes** with a GP noise model, on a standard desktop CPU.
+- A high-resolution analysis of the JWST/NIRISS **WASP-39 b** dataset (~3800 spectroscopic light curves; see Feinstein 
+  et al. 2023) can be optimised and sampled in about **1.5 hours** on an AMD Ryzen 7 5800X (8 cores, ~3-year-old desktop).
+
+---
+
+© 2025 Hannu Parviainen

{exoiris-0.19.2 → exoiris-0.21.0}/ExoIris.egg-info/SOURCES.txt

@@ -45,6 +45,8 @@ exoiris/binning.py
 exoiris/ephemeris.py
 exoiris/exoiris.py
 exoiris/ldtkld.py
+exoiris/loglikelihood.py
+exoiris/spotmodel.py
 exoiris/tsdata.py
 exoiris/tslpf.py
 exoiris/tsmodel.py

exoiris-0.21.0/PKG-INFO

@@ -0,0 +1,118 @@
+Metadata-Version: 2.4
+Name: ExoIris
+Version: 0.21.0
+Summary: Easy and robust exoplanet transmission spectroscopy.
+Author-email: Hannu Parviainen <hannu@iac.es>
+License: GPLv3
+Project-URL: homepage, https://github.com/hpparvi/ExoIris
+Keywords: astronomy,astrophysics,exoplanets
+Classifier: Topic :: Scientific/Engineering
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pytransit>=2.6.15
+Requires-Dist: ldtk>=1.8.5
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: numba
+Requires-Dist: emcee
+Requires-Dist: matplotlib
+Requires-Dist: celerite2
+Requires-Dist: pandas
+Requires-Dist: xarray
+Requires-Dist: seaborn
+Requires-Dist: astropy
+Requires-Dist: uncertainties
+Dynamic: license-file
+
+# ExoIris: Fast and Flexible Transmission Spectroscopy in Python
+
+[![Docs](https://readthedocs.org/projects/exoiris/badge/)](https://exoiris.readthedocs.io)
+![Python package](https://github.com/hpparvi/ExoIris/actions/workflows/python-package.yml/badge.svg)
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.0-4baaaa.svg)](CODE_OF_CONDUCT.md)
+[![Licence](http://img.shields.io/badge/license-GPLv3-blue.svg?style=flat)](http://www.gnu.org/licenses/gpl-3.0.html)
+[![PyPI version](https://badge.fury.io/py/exoiris.svg)](https://pypi.org/project/ExoIris/)
+
+**ExoIris** is a Python package for modeling exoplanet transmission spectroscopy. ExoIris removes the typical 
+limitations of the two-step workflow by modeling the full two-dimensional spectroscopic transit time series *directly*.
+It supports combining transmission spectroscopy datasets from multiple instruments observed in different epochs, yielding 
+self-consistent wavelength-independent and wavelength-dependent parameters, simplifying joint analyses, and delivering 
+results quickly.
+
+![](doc/source/examples/e01/example1.png)
+
+## Why ExoIris?
+
+Transmission spectroscopy is often done following a **two-step workflow**: (1) fit a white light curve to infer 
+wavelength-independent parameters; (2) fit each spectroscopic light curve independently, constrained by the white-light 
+solution. This split can introduce approximations and inconsistencies.
+
+**ExoIris takes a different approach.** It models spectrophotometric time series *end-to-end*, enabling:
+
+- Self-consistent inference of shared (wavelength-independent) and spectral (wavelength-dependent) parameters.
+- **Joint** modeling of multiple datasets from different instruments and epochs.
+- Accounting for **transit timing variations** and dataset-dependent offsets within a unified framework.
+
+This design is a natural fit for **JWST-class** data, where correlated noise, multi-epoch observations, and 
+cross-instrument combinations are the norm.
+
+## Documentation
+
+Full documentation and tutorials: <https://exoiris.readthedocs.io>
+
+## Installation
+
+Install from PyPI:
+
+```bash
+pip install exoiris
+```
+
+Latest development version:
+
+```bash
+git clone https://github.com/hpparvi/ExoIris.git
+cd ExoIris
+pip install -e .
+```
+
+ExoIris supports Python 3.9+. See the docs for dependency details and optional extras.
+
+## Key Features
+
+- **Direct modelling of spectroscopic transit time series**  
+  Built on PyTransit’s `TSModel`, optimised for transmission spectroscopy; scales to hundreds–thousands of light curves simultaneously.
+
+- **Flexible limb darkening**  
+  Use standard analytical laws (quadratic, power-2, non-linear), numerical intensity profiles from stellar atmosphere models, or user-defined radially symmetric functions.
+
+- **Robust noise treatment**  
+  Choose white noise or **time-correlated** noise via a Gaussian Process likelihood, without changing the overall workflow.
+
+- **Full control of spectral resolution**  
+  The transmission spectrum is represented as a cubic spline with user-defined knots, allowing variable resolution across wavelength.
+
+- **Reproducible, incremental workflows**  
+  Save and reload models to refine a low-resolution run into a high-resolution analysis seamlessly.
+
+- **Joint multi-dataset analyses**  
+  Combine instruments and epochs in one fit, with support for transit timing variations and dataset-specific systematics and offsets.
+
+## Performance
+
+ExoIris is designed for speed and stability:
+
+- A transmission spectroscopy analysis of a single JWST/NIRISS dataset at **R ≈ 100** typically runs in **3–5 minutes** 
+  assuming white noise, or **5–15 minutes** with a GP noise model, on a standard desktop CPU.
+- A high-resolution analysis of the JWST/NIRISS **WASP-39 b** dataset (~3800 spectroscopic light curves; see Feinstein 
+  et al. 2023) can be optimised and sampled in about **1.5 hours** on an AMD Ryzen 7 5800X (8 cores, ~3-year-old desktop).
+
+---
+
+© 2025 Hannu Parviainen

exoiris-0.21.0/README.md

@@ -0,0 +1,85 @@
+# ExoIris: Fast and Flexible Transmission Spectroscopy in Python
+
+[![Docs](https://readthedocs.org/projects/exoiris/badge/)](https://exoiris.readthedocs.io)
+![Python package](https://github.com/hpparvi/ExoIris/actions/workflows/python-package.yml/badge.svg)
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.0-4baaaa.svg)](CODE_OF_CONDUCT.md)
+[![Licence](http://img.shields.io/badge/license-GPLv3-blue.svg?style=flat)](http://www.gnu.org/licenses/gpl-3.0.html)
+[![PyPI version](https://badge.fury.io/py/exoiris.svg)](https://pypi.org/project/ExoIris/)
+
+**ExoIris** is a Python package for modeling exoplanet transmission spectroscopy. ExoIris removes the typical 
+limitations of the two-step workflow by modeling the full two-dimensional spectroscopic transit time series *directly*.
+It supports combining transmission spectroscopy datasets from multiple instruments observed in different epochs, yielding 
+self-consistent wavelength-independent and wavelength-dependent parameters, simplifying joint analyses, and delivering 
+results quickly.
+
+![](doc/source/examples/e01/example1.png)
+
+## Why ExoIris?
+
+Transmission spectroscopy is often done following a **two-step workflow**: (1) fit a white light curve to infer 
+wavelength-independent parameters; (2) fit each spectroscopic light curve independently, constrained by the white-light 
+solution. This split can introduce approximations and inconsistencies.
+
+**ExoIris takes a different approach.** It models spectrophotometric time series *end-to-end*, enabling:
+
+- Self-consistent inference of shared (wavelength-independent) and spectral (wavelength-dependent) parameters.
+- **Joint** modeling of multiple datasets from different instruments and epochs.
+- Accounting for **transit timing variations** and dataset-dependent offsets within a unified framework.
+
+This design is a natural fit for **JWST-class** data, where correlated noise, multi-epoch observations, and 
+cross-instrument combinations are the norm.
+
+## Documentation
+
+Full documentation and tutorials: <https://exoiris.readthedocs.io>
+
+## Installation
+
+Install from PyPI:
+
+```bash
+pip install exoiris
+```
+
+Latest development version:
+
+```bash
+git clone https://github.com/hpparvi/ExoIris.git
+cd ExoIris
+pip install -e .
+```
+
+ExoIris supports Python 3.9+. See the docs for dependency details and optional extras.
+
+## Key Features
+
+- **Direct modelling of spectroscopic transit time series**  
+  Built on PyTransit’s `TSModel`, optimised for transmission spectroscopy; scales to hundreds–thousands of light curves simultaneously.
+
+- **Flexible limb darkening**  
+  Use standard analytical laws (quadratic, power-2, non-linear), numerical intensity profiles from stellar atmosphere models, or user-defined radially symmetric functions.
+
+- **Robust noise treatment**  
+  Choose white noise or **time-correlated** noise via a Gaussian Process likelihood, without changing the overall workflow.
+
+- **Full control of spectral resolution**  
+  The transmission spectrum is represented as a cubic spline with user-defined knots, allowing variable resolution across wavelength.
+
+- **Reproducible, incremental workflows**  
+  Save and reload models to refine a low-resolution run into a high-resolution analysis seamlessly.
+
+- **Joint multi-dataset analyses**  
+  Combine instruments and epochs in one fit, with support for transit timing variations and dataset-specific systematics and offsets.
+
+## Performance
+
+ExoIris is designed for speed and stability:
+
+- A transmission spectroscopy analysis of a single JWST/NIRISS dataset at **R ≈ 100** typically runs in **3–5 minutes** 
+  assuming white noise, or **5–15 minutes** with a GP noise model, on a standard desktop CPU.
+- A high-resolution analysis of the JWST/NIRISS **WASP-39 b** dataset (~3800 spectroscopic light curves; see Feinstein 
+  et al. 2023) can be optimised and sampled in about **1.5 hours** on an AMD Ryzen 7 5800X (8 cores, ~3-year-old desktop).
+
+---
+
+© 2025 Hannu Parviainen