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Update the basis computations to use sparse linear algebra #72

Merged
merged 6 commits into from
Oct 12, 2023
Merged

Update the basis computations to use sparse linear algebra #72

merged 6 commits into from
Oct 12, 2023

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dfm
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@dfm dfm commented Oct 10, 2023

The basis matrices are all sparse so we can take advantage of that. This PR updates the A computation to use scipy.sparse (it's all precomputed so it doesn't depend on JAX) and it now produces a jax.experimental.sparse.BCOO object. The performance doesn't really matter too much since it is computed at compile time, but this will help with memory usage for higher order models.

dfm
dfm commented Oct 11, 2023
View reviewed changes
src/jaxoplanet/experimental/starry/flux.py Outdated
Comment on lines 9 to 30
def flux(deg, theta, xo, yo, zo, ro, inc, obl, y, u, f):
b = jnp.sqrt(jnp.square(xo) + jnp.square(yo))
b_rot = jnp.logical_or(jnp.greater_equal(b, 1.0 + ro), jnp.less_equal(zo, 0.0))
b_occ = jnp.logical_not(b_rot)

# Occultation
theta_z = jnp.arctan2(xo, yo)
sT = solution_vector(deg)(b, ro)
sTA = sT @ basis(deg)
sTAR = dot_rotation_matrix(deg, None, None, 1.0, theta_z)(sTA)

x = jnp.where(b_occ, sTAR, rTA1(deg))

x = dot_rotation_matrix(
deg, -jnp.cos(obl), -jnp.sin(obl), 0.0, -(0.5 * jnp.pi - inc)
)(x)
x = dot_rotation_matrix(deg, None, None, 1.0, obl)(x)
x = dot_rotation_matrix(deg, 1.0, 0.0, 0.0, -0.5 * jnp.pi)(x)
x = dot_rotation_matrix(deg, None, None, 1.0, theta)(x)
x = dot_rotation_matrix(deg, 1.0, 0.0, 0.0, 0.5 * jnp.pi)(x)

return x @ y
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@lgrcia — I've added this function to compute the flux which I think you've also looked into. I've found that in some initial benchmarks that this is about and order of magnitude faster than starry on my computer! Let's chat.

@dfm dfm enabled auto-merge October 12, 2023 14:36
@dfm dfm added this pull request to the merge queue Oct 12, 2023
Merged via the queue into main with commit b9f3cc2 Oct 12, 2023
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dfm added a commit that referenced this pull request Feb 10, 2024
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Adding transit fitting tutorial (#48)
7691073 
* 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

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

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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

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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

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* 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

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* Implementing polynomial basis (#76)

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* Upper limit on xarray version

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* 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

---------

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

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dfm added a commit that referenced this pull request Feb 10, 2024
@soichiro-hattori @dfm
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Adding transit fitting tutorial (#48)
e7ed2a3 
* 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

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

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

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

* [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)

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

* 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:
- [github.com/astral-sh/ruff-pre-commit: v0.0.282 → v0.0.284](astral-sh/ruff-pre-commit@v0.0.282...v0.0.284)

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

* [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)

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

* 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

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

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---------

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

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

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.285 → v0.0.286](astral-sh/ruff-pre-commit@v0.0.285...v0.0.286)

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

* [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)

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

* [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)

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

* 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
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* [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)

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

* [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)

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

* 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

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* adding units to TransitOrbit

* fixing python 3.9 errors

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* 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)

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* 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
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* [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
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* [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)

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

* 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)

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

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* 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)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-type: direct:production
  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)

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

* [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)

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

* [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

---------

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

* [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)

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

* 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

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* 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>
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Co-authored-by: Dan Foreman-Mackey <[email protected]>
github-merge-queue bot pushed a commit that referenced this pull request Feb 11, 2024
@dfm @soichiro-hattori
@pre-commit-ci @dependabot
Merge tutorials updates from tutorials branch into main (#118)
c8f588d 
* adding initial autodiff tutorial

* updating tutorial dependencies

* fixing autodiff tutorial

* 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)

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

* 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)

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

* Bump pypa/gh-action-pypi-publish from 1.8.6 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
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* [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)

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

* [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)

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

* [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)

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

* 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

* [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)

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

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

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.282 → v0.0.284](astral-sh/ruff-pre-commit@v0.0.282...v0.0.284)

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

* [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)

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

* 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

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

* lint

* fewer tests

* only one macos test

* not hashable

* nothing really

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---------

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

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

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.285 → v0.0.286](astral-sh/ruff-pre-commit@v0.0.285...v0.0.286)

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

* [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)

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

* [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)

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

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

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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

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* [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)

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* 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)

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* 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

---------

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

updates:
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* 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
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  update-type: version-update:semver-patch
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* [pre-commit.ci] pre-commit autoupdate (#93)

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

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* [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)

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* 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)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  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)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-type: direct:production
  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]>
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Co-authored-by: Dan Foreman-Mackey <[email protected]>

* fixing blank line in pyproject.toml

* Drafting faster transit fitting tutorial (#119)

* drafting faster transit fitting tutorial

* removing text and section on divergences

---------

Co-authored-by: Soichiro Hattori <[email protected]>

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: soichiro-hattori <[email protected]>
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@lgrcia lgrcia deleted the sparse-basis branch October 18, 2024 17:41
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