jnkepler 0.2.0__tar.gz

jnkepler-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2022 Kento Masuda
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

jnkepler-0.2.0/MANIFEST.in

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+include src/jnkepler/data/kep51_ttv.txt
+include src/jnkepler/data/kep51_dt1.0_start155.00_end2950.00_de.csv
+include src/jnkepler/data/kep51_dt1.0_start155.00_end2950.00_params.txt
+include src/jnkepler/data/kep51_dt1.0_start155.00_end2950.00_pdict_ttvfast.csv
+include src/jnkepler/data/kep51_dt1.0_start155.00_end2950.00_pdict.csv
+include src/jnkepler/data/kep51_dt1.0_start155.00_end2950.00_tc.csv
+include src/jnkepler/data/kep51_dt1.0_start155.00_end2950.00_grad.txt
+include src/jnkepler/data/tcbug_elements.txt
+include src/jnkepler/data/tcbug_masses.txt
+include src/jnkepler/data/kep51_lc_model.txt
+include src/jnkepler/data/kep51_lc_photodtest.csv
+include src/jnkepler/data/kep51_ttv_photodtest.txt
+include src/jnkepler/data/info.txt
+include src/jnkepler/data/hessian.txt
+include src/jnkepler/data/JaxTTVobject.pkl
+include src/jnkepler/data/kep51_nbodytransit_optim.npy
+include src/jnkepler/data/kep51_4planet.csv
+include src/jnkepler/data/kep51_4planet_sol.csv
+include src/jnkepler/data/kep51_4planet_sol-2.csv
+include src/jnkepler/data/tcs_ttvfast_for_test-all.txt
+include src/jnkepler/data/tcs_ttvfast_for_test-nontransiting.txt
+include src/jnkepler/data/tcs_ttvfast_for_test-obs-nontransiting.txt
+include src/jnkepler/data/tcs_ttvfast_for_test-obs-nontransiting2.txt
+include src/jnkepler/data/tcs_ttvfast_for_test-ttandrv.txt
+include src/jnkepler/data/rvs_ttvfast_for_test-ttandrv.txt
+
+global-exclude *.py[co]

jnkepler-0.2.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: jnkepler
+Version: 0.2.0
+Summary: JAX code for modeling nearly-Keplerian orbits
+Home-page: https://github.com/kemasuda/jnkepler
+Author: Kento Masuda
+Author-email: kmasuda@ess.sci.osaka-u.ac.jp
+Maintainer: Kento Masuda
+Maintainer-email: kmasuda@ess.sci.osaka-u.ac.jp
+License: MIT
+Classifier: Programming Language :: Python
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: jax
+Requires-Dist: numpyro
+Requires-Dist: pandas
+Requires-Dist: numpy<2.0
+Requires-Dist: matplotlib
+Requires-Dist: importlib_resources
+
+# jnkepler
+
+*A differentiable N-body model for multi-planet systems.*
+
+`jnkepler` is a Python package for modeling photometric and radial velocity data of multi-planet systems via N-body integration. Built with [JAX](https://jax.readthedocs.io/en/latest/index.html), it leverages automatic differentiation for efficient computation of model gradients. This enables seamless integration with gradient-based optimizers and Hamiltonian Monte Carlo methods, including the No-U-Turn Sampler (NUTS) in [NumPyro](https://num.pyro.ai). The package is particularly suited for efficiently sampling from multi-planet posteriors involving a larger number of parameters and strong degeneracy.
+
+## Subpackages
+
+- **jnkepler.jaxttv**: A differentialble N-body model for analyzing transit timing variations (TTVs) and radial velocities (RVs) of multi-planet systems.
+- **jnkepler.nbodytransit**: A differentialble photodynamical model. [`jaxoplanet`](https://jax.exoplanet.codes/en/latest/) needs to be installed for using this package.
+- **jnkepler.nbodyrv**: A differentiable RV model taking into account mutual interactions between planets.
+
+See [readthedocs](https://jnkepler.readthedocs.io/en/latest/index.html) for more details.
+
+## Installation
+
+```python setup.py install```
+
+
+## Examples
+
+Explore example notebooks in the `examples/` directory to see `jnkepler` in action:
+
+- **minimal example for computing transit times**: `examples/minimal_example.ipynb`
+
+- **TTV modeling**: `examples/kep51_ttv_iidnormal.ipynb` 
+  - posterior sampling with NUTS
+  - reproducing the result in [Libby-Roberts et al. 2020](https://ui.adsabs.harvard.edu/abs/2020AJ....159...57L/abstract)
+- **Photodynamical modeling**: `examples/kep51_photodynamics_gp.ipynb`
+  - SVI optimization & posterior sampling with NUTS
+  - noise modeling using Gaussian Process with [`celerite2.jax`](https://celerite2.readthedocs.io/en/latest/api/jax/)
+
+
+
+## Applications
+
+- TOI-1136: TTV modeling of 6-planets in a resonance chain [[paper]](https://ui.adsabs.harvard.edu/abs/2022arXiv221009283D/abstract)
+- TOI-2015: joint TTV & RV modeling of a two-planet system [[paper]](https://arxiv.org/abs/2310.11775)
+- Kepler-51: four-planet modeling including JWST data [[paper]](https://arxiv.org/abs/2410.01625) [[repository]](https://github.com/kemasuda/kep51_jwst)
+
+## References
+
+- Masuda et al. (2024), [A Fourth Planet in the Kepler-51 System Revealed by Transit Timing Variations](https://arxiv.org/abs/2410.01625), AJ in press.
+

jnkepler-0.2.0/README.md

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+# jnkepler
+
+*A differentiable N-body model for multi-planet systems.*
+
+`jnkepler` is a Python package for modeling photometric and radial velocity data of multi-planet systems via N-body integration. Built with [JAX](https://jax.readthedocs.io/en/latest/index.html), it leverages automatic differentiation for efficient computation of model gradients. This enables seamless integration with gradient-based optimizers and Hamiltonian Monte Carlo methods, including the No-U-Turn Sampler (NUTS) in [NumPyro](https://num.pyro.ai). The package is particularly suited for efficiently sampling from multi-planet posteriors involving a larger number of parameters and strong degeneracy.
+
+## Subpackages
+
+- **jnkepler.jaxttv**: A differentialble N-body model for analyzing transit timing variations (TTVs) and radial velocities (RVs) of multi-planet systems.
+- **jnkepler.nbodytransit**: A differentialble photodynamical model. [`jaxoplanet`](https://jax.exoplanet.codes/en/latest/) needs to be installed for using this package.
+- **jnkepler.nbodyrv**: A differentiable RV model taking into account mutual interactions between planets.
+
+See [readthedocs](https://jnkepler.readthedocs.io/en/latest/index.html) for more details.
+
+## Installation
+
+```python setup.py install```
+
+
+## Examples
+
+Explore example notebooks in the `examples/` directory to see `jnkepler` in action:
+
+- **minimal example for computing transit times**: `examples/minimal_example.ipynb`
+
+- **TTV modeling**: `examples/kep51_ttv_iidnormal.ipynb` 
+  - posterior sampling with NUTS
+  - reproducing the result in [Libby-Roberts et al. 2020](https://ui.adsabs.harvard.edu/abs/2020AJ....159...57L/abstract)
+- **Photodynamical modeling**: `examples/kep51_photodynamics_gp.ipynb`
+  - SVI optimization & posterior sampling with NUTS
+  - noise modeling using Gaussian Process with [`celerite2.jax`](https://celerite2.readthedocs.io/en/latest/api/jax/)
+
+
+
+## Applications
+
+- TOI-1136: TTV modeling of 6-planets in a resonance chain [[paper]](https://ui.adsabs.harvard.edu/abs/2022arXiv221009283D/abstract)
+- TOI-2015: joint TTV & RV modeling of a two-planet system [[paper]](https://arxiv.org/abs/2310.11775)
+- Kepler-51: four-planet modeling including JWST data [[paper]](https://arxiv.org/abs/2410.01625) [[repository]](https://github.com/kemasuda/kep51_jwst)
+
+## References
+
+- Masuda et al. (2024), [A Fourth Planet in the Kepler-51 System Revealed by Transit Timing Variations](https://arxiv.org/abs/2410.01625), AJ in press.
+