Adding transit fitting tutorial (#48)

* Removing `quad` submodule and simplifying some jaxprs (#46)

* remove quad, simplify jaxprs

* adding zero-safe sqrt function

* Adding tutorials (#35)

* adding initial autodiff tutorial

* updating tutorial dependencies

* fixing autodiff tutorial

* updating gitignore file to ignore __pycache__ directories

* [pre-commit.ci] pre-commit autoupdate (#47)

updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.270 → v0.0.272](astral-sh/ruff-pre-commit@v0.0.270...v0.0.272)

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* adding transit tutorial notebook

* additional minor changes to transit tutorial notebook

* updating transit fitting tutorial notebook

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* [pre-commit.ci] pre-commit autoupdate (#50)

updates:
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.272 → v0.0.276](astral-sh/ruff-pre-commit@v0.0.272...v0.0.276)

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* Bump pypa/gh-action-pypi-publish from 1.8.6 to 1.8.7 (#51)

Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.6 to 1.8.7.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](pypa/gh-action-pypi-publish@v1.8.6...v1.8.7)

---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
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* [pre-commit.ci] pre-commit autoupdate (#52)

updates:
- [github.com/psf/black: 23.3.0 → 23.7.0](psf/black@23.3.0...23.7.0)
- [github.com/astral-sh/ruff-pre-commit: v0.0.276 → v0.0.277](astral-sh/ruff-pre-commit@v0.0.276...v0.0.277)

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* [pre-commit.ci] pre-commit autoupdate (#53)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.277 → v0.0.278](astral-sh/ruff-pre-commit@v0.0.277...v0.0.278)

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* [pre-commit.ci] pre-commit autoupdate (#54)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.278 → v0.0.281](astral-sh/ruff-pre-commit@v0.0.278...v0.0.281)

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* update transit tutorial

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* changing number of steps in chain

* change mcmc steps

* [pre-commit.ci] pre-commit autoupdate (#56)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.281 → v0.0.282](astral-sh/ruff-pre-commit@v0.0.281...v0.0.282)

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* [pre-commit.ci] pre-commit autoupdate (#58)

updates:
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* [pre-commit.ci] pre-commit autoupdate (#59)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.284 → v0.0.285](astral-sh/ruff-pre-commit@v0.0.284...v0.0.285)

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* Migrating to hatch instead of poetry for build backend (#60)

* migrating to hatch for infra

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* lint

* fewer tests

* only one macos test

* not hashable

* nothing really

* fixing deprecation warning

* faster tests

---------

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* [pre-commit.ci] pre-commit autoupdate (#62)

updates:
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* [pre-commit.ci] pre-commit autoupdate (#64)

updates:
- [github.com/psf/black: 23.7.0 → 23.9.1](psf/black@23.7.0...23.9.1)
- [github.com/astral-sh/ruff-pre-commit: v0.0.286 → v0.0.288](astral-sh/ruff-pre-commit@v0.0.286...v0.0.288)

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* [pre-commit.ci] pre-commit autoupdate (#66)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.288 → v0.0.291](astral-sh/ruff-pre-commit@v0.0.288...v0.0.291)

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* Implement exposure time integration (#57)

* adding initial autodiff tutorial

* updating tutorial dependencies

* fixing autodiff tutorial

* updating gitignore file to ignore __pycache__ directories

* adding transit tutorial notebook

* additional minor changes to transit tutorial notebook

* updating transit fitting tutorial notebook

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update transit tutorial

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* changing number of steps in chain

* change mcmc steps

* Doesn't work yet but adding changes for implementing exposure time integration

* adding stencil_order variable to separate from order variable

* storing cchanges (doesn't work yet)

* changes made for implementing a working version of exposure time integration

* adding documentation text for order keyword argument

* changing order keyword to limbdark_order for clarity and updating docs

* removing tutorial notebooks from this branch

---------

Co-authored-by: Dan F-M <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Bump actions/checkout from 3 to 4 (#67)

Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v3...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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* [pre-commit.ci] pre-commit autoupdate (#68)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.291 → v0.0.292](astral-sh/ruff-pre-commit@v0.0.291...v0.0.292)

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* [pre-commit.ci] pre-commit autoupdate (#69)

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0)

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* Alternative implementation for rotation matrices (#63)

* adding initial port of starry wigner code

* fixing bug in rotation.dotR

* fixing implementation for u2

* removing one condition

* adding some TODOs to me

* slight refactor

* one more todo

* don't test with square matrices

* adding simple implementation of cel integral at tests

* skip some tests that are hard for x64

* adding closed form implementaion of low order solution vector

* removing closed form solution vector... moved to new branch

* handling normalization; moving symbolic test

* better tolerance handling

* handling edge cases

* removing cel

* push before checking out main branch

* always ensure kite area is non-negative

* Update .gitignore

* Ensuring the square of the kite area calculation is non-negative (#73)

* updating gitignore file to ignore __pycache__ directories

* always ensure kite area is non-negative

* Update .gitignore

---------

Co-authored-by: Dan Foreman-Mackey <[email protected]>

* Update the basis computations to use sparse linear algebra (#72)

* using sparse linear algebra for the basis computations

* rename A -> basis

* Adding initial flux implementation

* adding special case of rotation for just z axis

* removing tensordot function

* removing flux function from this PR

* Introducing units and refactoring Keplerian orbit models (#61)

* adding units

* adding example of how we might use units

* adding tests for quantity_input decorator

* adding docstring to decorator

* adding doctring and tests for field

* adding tests for keplerian

* fixing edge cases test

* updating keplerian tests

* adding units to TransitOrbit

* fixing python 3.9 errors

* remove pyright from pre-commit

* less stringent test comparisons

* test tol for soln

* sketching OO interface

* default central

* improving interface for keplerian system

* Implementing polynomial basis (#76)

* [pre-commit.ci] pre-commit autoupdate (#78)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 23.9.1 → 23.10.1](psf/black@23.9.1...23.10.1)
- [github.com/astral-sh/ruff-pre-commit: v0.0.292 → v0.1.3](astral-sh/ruff-pre-commit@v0.0.292...v0.1.3)

* Upper limit on xarray version

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Dan Foreman-Mackey <[email protected]>

* [pre-commit.ci] pre-commit autoupdate (#79)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.3 → v0.1.4](astral-sh/ruff-pre-commit@v0.1.3...v0.1.4)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* fixing jpu bug

* adding light curve test

* use jnpu.outer function in light_curve function since it's now implemented

* [pre-commit.ci] pre-commit autoupdate (#85)

updates:
- [github.com/psf/black: 23.10.1 → 23.11.0](psf/black@23.10.1...23.11.0)
- [github.com/astral-sh/ruff-pre-commit: v0.1.4 → v0.1.5](astral-sh/ruff-pre-commit@v0.1.4...v0.1.5)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Fixing issue where light curve computation fails because of incorporating JPU units (#86)

* updating gitignore file to ignore __pycache__ directories

* always ensure kite area is non-negative

* Update .gitignore

* fixing jpu bug

* adding light curve test

* use jnpu.outer function in light_curve function since it's now implemented

---------

Co-authored-by: Dan Foreman-Mackey <[email protected]>

* [pre-commit.ci] pre-commit autoupdate (#88)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.5 → v0.1.6](astral-sh/ruff-pre-commit@v0.1.5...v0.1.6)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 (#90)

Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.10 to 1.8.11.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](pypa/gh-action-pypi-publish@v1.8.10...v1.8.11)

---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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* [pre-commit.ci] pre-commit autoupdate (#93)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.6 → v0.1.7](astral-sh/ruff-pre-commit@v0.1.6...v0.1.7)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#94)

updates:
- [github.com/psf/black: 23.11.0 → 23.12.0](psf/black@23.11.0...23.12.0)
- [github.com/astral-sh/ruff-pre-commit: v0.1.7 → v0.1.8](astral-sh/ruff-pre-commit@v0.1.7...v0.1.8)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Bump actions/download-artifact from 3 to 4 (#98)

Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](actions/download-artifact@v3...v4)

---
updated-dependencies:
- dependency-name: actions/download-artifact
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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* [pre-commit.ci] pre-commit autoupdate (#95)

updates:
- [github.com/psf/black: 23.12.0 → 23.12.1](psf/black@23.12.0...23.12.1)
- [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](astral-sh/ruff-pre-commit@v0.1.8...v0.1.9)

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* Bump actions/setup-python from 4 to 5 (#96)

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4...v5)

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  update-type: version-update:semver-major
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* Bump actions/upload-artifact from 3 to 4 (#97)

Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](actions/upload-artifact@v3...v4)

---
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  update-type: version-update:semver-major
...

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* [pre-commit.ci] pre-commit autoupdate (#99)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](astral-sh/ruff-pre-commit@v0.1.9...v0.1.11)

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* [pre-commit.ci] pre-commit autoupdate (#100)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](astral-sh/ruff-pre-commit@v0.1.11...v0.1.13)

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* [pre-commit.ci] pre-commit autoupdate (#101)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 23.12.1 → 24.1.1](psf/black@23.12.1...24.1.1)
- [github.com/astral-sh/ruff-pre-commit: v0.1.13 → v0.1.14](astral-sh/ruff-pre-commit@v0.1.13...v0.1.14)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

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* [pre-commit.ci] pre-commit autoupdate (#103)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.0](astral-sh/ruff-pre-commit@v0.1.14...v0.2.0)
- [github.com/kynan/nbstripout: 0.6.1 → 0.7.1](kynan/nbstripout@0.6.1...0.7.1)

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* adding light_curves to init file so that LimbDarkLightCurve can be called

* Adding Zenodo info for releases (#92)

* Create .zenodo.json

* Adding Lionel

* Adding light_curves.py file to __init__ file (#104)

* updating gitignore file to ignore __pycache__ directories

* always ensure kite area is non-negative

* Update .gitignore

* fixing jpu bug

* adding light curve test

* use jnpu.outer function in light_curve function since it's now implemented

* adding light_curves to init file so that LimbDarkLightCurve can be called

---------

Co-authored-by: Dan Foreman-Mackey <[email protected]>

* update transit-fitting tutorial

* update notebook

* updating index toctree

* update .gitignore file

* adding ipywidgets to pyproject.toml

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Dan Foreman-Mackey <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Dan Foreman-Mackey <[email protected]>

.gitignore

@@ -14,3 +14,4 @@ build
 dist
 poetry.lock
 .*_cache
+.jupyter/

.pre-commit-config.yaml

@@ -19,3 +19,13 @@ repos:
     rev: "0.7.1"
     hooks:
       - id: nbstripout
+  # - repo: https://github.com/RobertCraigie/pyright-python
+  #   rev: v1.1.324
+  #   hooks:
+  #     - id: pyright
+  #       additional_dependencies:
+  #         - nox
+  #         - pytest
+  #         - jax
+  #         - equinox
+  #         - jpu>=0.0.2

docs/index.md

@@ -79,4 +79,5 @@ maxdepth: 2
 start
 api
 tutorials/autodiff.ipynb
+tutorials/transit.ipynb
 ```