Untrack other local files and update .gitignore

*.swo

*~

.pre-commit-config.yaml

.ruff_cache/

# Testing

.pytest_cache/

localDocs/

oldCode/

scripts/

test_smoke_report_components.pckl

mock.pckl

PyAETNA/TOI5572.code-workspace

builds/3c-Rr9_if/0/gitlab/gaetano.scandariato/detached-head-20260426T145445Z-8e72ba51450c.bundle

- Test files in `tests/`

- Inline documentation in source code

## Repository Structure

This needs to be updated #TODO

```

PyAETNA/

├── runPyAETNA.py              # CLI entrypoint

├── pyproject.toml             # Packaging metadata and dependencies

├── requirements.txt           # Dependency pins (fallback)

├── README.md                  # This file

├── LICENSE                    # MIT licence

│

├── PyAETNA/                   # Core library package

│   ├── __init__.py            #   Package exports and __version__

│   ├── run.py                 #   Pipeline orchestrator (sampling → reports → physics)

│   ├── planet_phys.py         #   Derived physics (eclipse depths, albedo, Cowan & Agol)

│   ├── body_models.py         #   JAX planetary models (transit, eclipse, RV via jaxoplanet)

│   ├── gp.py                  #   GP kernel utilities (tinygp quasisep + dense)

│   ├── model_utils.py         #   Shared model assembly and detrending helpers

│   ├── _device_config.py      #   JAX device/platform auto-detection

│   ├── sampling/              #   Modular sampling engine and model assembly

│   │   ├── __init__.py        #     Public sampling API

│   │   ├── data.py            #     Input data structures and validation

│   │   ├── precision.py       #     JAX precision/casting helpers

│   │   ├── utils.py           #     Shared sampling math utilities

│   │   ├── model/             #     PlModel core + detrending + GP builders

│   │   ├── config/            #     Config parsing and prior handling

│   │   │   ├── priors.py      #       Prior string parsing and dist mapping

│   │   │   └── parser/        #       Scoped parser modules (star/planet/gp/...)

│   │   └── engine/            #     Sampling loop and NumPyro integration

│   │       ├── runner.py      #       runSampler_NumPyro main runner

│   │       ├── numpyro_model.py #     Model closure and log-joint helpers

│   │       ├── logging.py     #       Sampling log/summary formatters

│   │       ├── data_loader.py #       Resume-safe data loading utilities

│   │       ├── checkpoint.py  #       Checkpoint save/restore logic

│   │       ├── sampler_utils.py #     Shared runner helpers

│   │       └── utils/         #       Engine utility modules

│   ├── reporting/             #   Modular report-generation package

│   │   ├── __init__.py        #     Reporting package exports

│   │   ├── plot_models.py     #     Main plotting/report orchestration

│   │   ├── confidence_bands.py #    Posterior confidence band computations

│   │   ├── grid_builder.py    #     Grids for phase/time-domain plotting

│   │   ├── lightcurve_plots.py #    Light-curve plotting routines

│   │   ├── periodogram_plots.py #   Periodogram and PSD diagnostics

│   │   ├── phase_plots.py     #     Phase-folded visualization helpers

│   │   ├── residual_plotting.py #   Residual panels and KDE inset helpers

│   │   ├── corner_plot.py     #     Posterior corner plot generation

│   │   ├── diagnostics.py     #     MCMC and model diagnostics

│   │   ├── pdf_report.py      #     Multi-page PDF report assembly

│   │   └── ...                #     Additional plotting/support modules

│   └── scripts/               #   Auxiliary CLI scripts

│

├── docs/                      # Documentation

│   ├── configuration.md       #   Full YAML config reference

│   ├── configuration_keys.md  #   Quick-reference key table

│   ├── dependencies.md        #   Installation guide (CPU & GPU)

│   ├── programmatic_usage.md  #   Calling PyAETNA from Python

│   ├── phase_curve_physics.md #   Phase-curve theory, derivations, references

│   ├── ARCH_DECISIONS.md      #   Architecture rationale (vectorisation, precision)

│   ├── CITATIONS.md           #   Full reference list with BibTeX entries

│   └── gp_per_visit_analysis/ #   GP per-visit block-diagonal documentation

│

├── examples/                  # Example configurations and data

│   ├── reference_config.yaml  #   Annotated reference with EVERY supported key

│   ├── 501.yaml               #   CHEOPS dayside emission example

│   ├── transits.yaml          #   TESS transit-only example

│   ├── example_lc_rv_joint.yaml # Joint LC + RV example

│   └── *.dat                  #   Accompanying data files

│

├── tests/                     # Test suite

│   ├── generate_test_datasets.py # Synthetic data generator

│   ├── test_lc_only.yaml      #   LC-only test config

│   ├── test_rv_only.yaml      #   RV-only test config

│   ├── test_lc_rv_joint.yaml  #   Joint LC + RV test config

│   ├── test_lc_gp_rv.yaml    #   LC (GP) + RV test config

│   ├── test_gp_per_visit.yaml #   GP per-visit block-diagonal test

│   ├── test_phase_curve.yaml  #   Phase curve + RV test config

│   ├── test_exptime_integration.py # Exposure-time supersampling tests

│   └── *.dat                  #   Synthetic test data

│

└── localDocs/                 # Internal development notes (not shipped)

```

## Citation

If you use PyAETNA in your research, please add the following citation in your publication: