PyTransit 2.9.1__tar.gz → 2.9.3__tar.gz

pytransit-2.9.3/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

pytransit-2.9.3/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

pytransit-2.9.3/.github/workflows/python-package.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "main", "dev" ]
+  pull_request:
+    branches: [ "main", "dev" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest pytest-cov
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Install package
+      run: |
+        python -m pip install .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest --cov tests
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

pytransit-2.9.3/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      url: https://pypi.org/p/PyTransit
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

pytransit-2.9.3/.gitignore

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+*.o
+*.so
+*.mod
+*.log
+*.pyc
+*~
+*pkl
+*pdf
+.DS_Store
+
+.coverage
+
+.ipynb_checkpoints
+PyTransit.egg-info
+build
+venv
+dist
+
+.idea/*
+notebooks
+
+htmlcov
+
+pytransit/_version.py

pytransit-2.9.3/.readthedocs.yaml

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+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  apt_packages:
+    - pandoc  # nbsphinx converts the notebooks' Markdown cells with pandoc
+  jobs:
+    # Read the Docs clones shallowly, but setuptools-scm needs the tags to work out the version.
+    post_checkout:
+      - git fetch --unshallow --tags || true
+
+python:
+  install:
+    - method: pip
+      path: .
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/source/conf.py

pytransit-2.9.3/.travis.yml

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+language: python
+python:
+  - "3.6"
+  - "3.7"
+  - "3.8"
+
+os:
+  - linux
+
+dist: bionic
+
+cache: pip
+
+install:
+#  - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install libpocl-dev pocl-opencl-icd; fi
+  - pip install -r requirements.txt
+  - pip install codecov coverage
+  - python setup.py install
+
+script: nosetests -w tests --with-coverage
+
+after_success:
+  - codecov

pytransit-2.9.3/CHANGELOG.md

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+# Changelog
+
+## [2.9.3] - 2026-10-15
+
+### Changed
+
+- The package version is now derived from Git tags with `setuptools-scm` instead of being hard-coded.
+- Updated the RoadRunner documentation for the quadrature-based model, with new figures of the quadrature nodes and
+  the mean intensity table.
+
+### Fixed
+
+- The Read the Docs build, which pointed at the old `doc/` directory and lacked some Sphinx extensions.
+- A `SyntaxWarning` from an invalid escape sequence in the `BaseLPF.add_as_prior` docstring.
+
+## [2.9.2] - 2026-09-08
+
+### Added
+
+- `LCDataGroup.plot` for plotting light curves in a filterable, annotated grid.
+- Robust running-median outlier removal: `LCData.outlier_mask`, `LCData.remove_outliers`, and
+  `LCDataGroup.remove_outliers`.
+- Interactive marking and removal of bad light curves in `LCDataGroup` (`mark_for_removal`, `remove_marked`, etc.).
+- `add_time_covariates` for `LCData` and `LCDataGroup` to model polynomial time trends via the covariates.
+- `LCData.linear_model` and `LCDataGroup.lcslices`.
+- `ncores` and `start_method` arguments to `optimize_global` and `sample_mcmc` for automatic, fork-safe process pools.
+
+### Changed
+
+- The RoadRunner models now use Gauss quadrature instead of stellar disk annuli. The new accuracy parameter is `nq`;
+  `nz`, `nzin`, `nzlimb`, `zcut`, `precompute_weights`, `klims`, and `nk` are deprecated and ignored.
+- `RoadRunnerModelCL` uses the same quadrature and the MeepMeep orbit as the Numba model, and accepts a `precision`
+  argument (`'single'` or `'double'`).
+- 1D radius ratio arrays are interpreted consistently by the Numba and OpenCL RoadRunner models.
+- `optimize_global` and `sample_mcmc` raise a `ValueError` when a pool is combined with `vectorize=True`, and attach
+  the pool only for the duration of the call.
+
+### Fixed
+
+- RoadRunner models now return NaN instead of raising for invalid radius ratios.
+- RoadRunner population evaluation with 1D radius ratio arrays, scalar `e` and `w`, and 1D `t0` vectors.
+- RoadRunner radius ratio weight table indexing and small-planet profile lookup.
+- Single sample counts and exposure times are now broadcast to all light curves.
+- The OpenCL models defaulted the exposure times to one day instead of zero.
+- Importing an OpenCL model no longer silences PyOpenCL compiler warnings process-wide.
+- NumPy 2 incompatibilities in `pytransit.lpf`.
+- `ParameterSet` and `LogPosteriorFunction` pickling, which made pool-based runs hang.
+
+## [2.9.1] - 2026-08-24
+
+### Added
+
+- `LCData` and `LCDataGroup` light curve containers in `pytransit.utils.io`.
+- `RVData` and `RVDataGroup` radial velocity containers in `pytransit.utils.io`.
+
+## [2.9.0] - 2026-08-18
+
+### Added
+
+- `LSTSQBaseline`, a parameterless baseline fitted by linear least squares at every evaluation.
+- Analytic disk-integrated intensity functions for all limb darkening models.
+- `exact_areas`, `exact_ld`, and `nannuli` options to `OblatePlanetModel`.
+- Exact and θ-sampled ellipse-circle intersection area routines.
+- Support for non-transiting planets in `RVLPF`.
+
+### Changed
+
+- **Breaking**: `RVLPF` and `RVModel` require `rvis` and `is_transiting` arguments, `tc_{i}` is renamed `t0_{i}`,
+  and the reference time is now `floor(min(times))`.
+- The limb darkening models moved from `pytransit.models.numba.ldmodels` to `pytransit.models.limb_darkening`.
+- The `RoadRunnerModel` `small_planet_limit` default changed from 0.05 to 0.01.
+- Improved the RoadRunner model parallelization and thread count handling.
+- Improved the `OblatePlanetModel` weight calculations and bounding box handling.
+
+### Fixed
+
+- Incorrect scanline ellipse-circle intersection areas for some geometries.
+- `BaseLPF.remove_outliers` left the covariates inconsistent with the clipped data.
+- `BaseLPF` covariate standardisation.
+
+### Deprecated
+
+- `pytransit.models.numba.ldmodels`, in favour of `pytransit.models.limb_darkening`.
+
+## [2.8.1] - 2026-06-21
+
+### Fixed
+
+- Broken tests.
+
+## [2.8.0] - 2026-06-19
+
+### Changed
+
+- **Breaking**: The Numba `QuadraticModel`, `UniformModel`, `QPower2Model`, `ChromosphereModel`, and `EclipseModel`
+  no longer have an `evaluate_pv` method; use `evaluate` instead.
+- All the models use the MeepMeep 1.0 API.
+- The RoadRunner-family models use transit bounding boxes.
+
+### Fixed
+
+- Eclipse model bounding box calculations.
+
+## [2.7.1] - 2026-05-07
+
+### Added
+
+- `pytransit.models.new_eclipse_model.EclipseModel`, a multiplicative secondary eclipse model.
+
+## [2.7.0] - 2026-04-27
+
+### Added
+
+- `EclipseSpectroscopyModel` for modelling eclipse spectroscopy.
+
+## [2.6.19] - 2026-03-18
+
+### Changed
+
+- NumPy >= 2.0 is now required.
+
+## [2.6.18] - 2026-01-28
+
+### Changed
+
+- Package data is accessed with `importlib.resources` instead of the deprecated `pkg_resources`.
+
+### Fixed
+
+- `RoadRunnerModel` flux array indexing and bounding box handling, broken in 2.6.17.
+
+## [2.6.17] - 2025-11-27
+
+### Changed
+
+- Improved the `RoadRunnerModel` transit bounding box calculation for eccentric orbits.
+
+## [2.6.16] - 2025-10-29
+
+### Fixed
+
+- NumPy 2.0 incompatibilities.
+
+## [2.6.9] - 2025-07-22
+
+### Changed
+
+- Improved `TSModel` accuracy by using a first-order Taylor series expansion of the planet-star intersection area. The
+  error in transit depth estimates should now be ~1 ppm for Jupiter-sized planets and below this for smaller planets.
+- Fixed issues with Numpy 2.0.
+
+## [2.6.0] - 2024-02-01
+
+### Added
+
+- *TSModel:* An extremely fast transit model for transmission spectroscopy. The model is based on the RoadRunnerModel and can use any 
+  rotationally symmetric function to model stellar limb darkening.
+- *LDTkLDM:* A RoadRunnerModel limb darkening model that uses directly stellar intensity profiles created by the LDTk. The model is
+  parameterised by the effective stellar temperature, surface gravity, and metallicity. This should be quite valuable for transmission
+  spectroscopy since the number of limb darkening parameters is independent of the number of passbands.
+
+## [2.4.0] - 2020-10-14
+
+### Added
+
+- *EclipseModel:* an easy-to-use secondary eclipse model.
+
+## [2.3.0] - 2020-09-16
+
+### Added
+
+ - *OblateStarModel:* transit model to model transits over rapidly rotating gravity-darkened stars by Barnes (2009).
+   This is an initial release of the model (only a CPU version works at the moment) but I expect to 
+   have it on-par with the rest of the models by v2.4.
+ 
+### Changed
+
+ - Renamed the *Swift* transit model introduced in v2.1 to *RoadRunner* transit model.
+ - Fixed several *RoadRunner* model issues caused by the transition to calculating the
+   projected distances using Taylor series expansion.
+ - Changed several of the OpenCL models use the Taylor series expansion approach to calculate
+   the projected distances.
+ - Lots of minor bug fixes.
+
+## [2.2.0] - 2020-09-13
+
+PyTransit version 2.2 now calculates the normalized planet-star distances using a Taylor series expansion
+of the x, and y positions in the sky plane (Parviainen and Korth, 2020, submitted to MNRAS). This gives a 
+significant speed boost in transit model evaluation that is especially noticeable for eccentric orbits. 
+
+## [2.1.0] - 2020-07-07
+
+PyTransit version 2.1 adds a new transit model named *swift* that can use any Python callable to model the stellar
+limb darkening while still giving equal or better performance than the analytical quadratic transit
+model.
+
+### Added
+
+- *Swift* transit model (Parviainen, submitted) to allow fast and flexible transit modelling with
+  any radially symmetric limb darkening model.
+
+## [2.0.0] - 2020-07-07
+
+PyTransit Version 2 removes the Fortran dependencies in v1 by implementing all the transit models
+in *numba*-accelerated Python. Version 2 also adds a number of new transit models, and implements
+most models both in CPU and GPU versions.
+
+### Added
+- New API that is consistent across all transit models.
+
+### Changed
+- Nearly everything.
+
+## [1.0.0 beta] - 2014-09-02
+
+PyTransit 1.0 implements the quadratic model by Mandel & Agol and the general model by 
+Giménez with special optimisation that significantly improve the model evaluation speed.
+
+## Early history - 2010
+
+The first version of PyTransit saw light in 2010. It implemented the transit model for general
+limb darkening law by Giménez and was used in 20-30 papers before the public release of v1.0.

pytransit-2.9.3/CITATIONS.bib

@@ -0,0 +1,38 @@
+
+@article{Parviainen2015,
+	title = {{PYTRANSIT}: {Fast} and easy exoplanet transit modelling in {PYTHON}},
+	volume = {450},
+	url = {https://academic.oup.com/mnras/article/450/3/3233/1074637},
+	doi = {10.1093/mnras/stv894},
+	number = {3},
+	journal = {Monthly Notices of the Royal Astronomical Society},
+	author = {Parviainen, Hannu},
+	month = jul,
+	year = {2015},
+	pages = {3233--3238}
+}
+
+@article{Parviainen2020a,
+	title = {Going back to basics: accelerating exoplanet transit modelling using {Taylor}-series expansion of the orbital motion},
+	volume = {499},
+	number = {3},
+	url = {https://academic.oup.com/mnras/article/499/3/3356/5911608},
+	doi = {10.1093/mnras/staa2953},
+	journal = {Monthly Notices of the Royal Astronomical Society},
+	author = {Parviainen, Hannu and Korth, Judith},
+	month = sep,
+	year = {2020},
+}
+
+@article{Parviainen2020b,
+	title = {{RoadRunner}: a fast and flexible exoplanet transit model},
+	volume = {499},
+	url = {https://academic.oup.com/mnras/article/499/2/1633/5911588},
+	doi = {10.1093/mnras/staa2901},
+	number = {2},
+	journal = {Monthly Notices of the Royal Astronomical Society},
+	author = {Parviainen, Hannu},
+	month = oct,
+	year = {2020},
+	pages = {1633--1639}
+}

pytransit-2.9.3/CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+hannu@iac.es.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

{pytransit-2.9.1 → pytransit-2.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyTransit
-Version: 2.9.1
+Version: 2.9.3
 Summary: Fast and painless exoplanet transit light curve modelling.
 Author-email: Hannu Parviainen <hpparvi@gmail.com>
 License: GPLv2
@@ -32,15 +32,17 @@ Requires-Dist: deprecated
 Requires-Dist: seaborn
 Requires-Dist: emcee
 Requires-Dist: pyopencl
+Requires-Dist: mako
 Requires-Dist: corner
 Requires-Dist: celerite
-Requires-Dist: meepmeep>=1.0.0
+Requires-Dist: meepmeep>=1.1.0
 Dynamic: license-file
 
 PyTransit
 =========
 
 [![Licence](http://img.shields.io/badge/license-GPLv2-blue.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html)
+[![Documentation Status](https://readthedocs.org/projects/pytransit/badge/?version=stable)](https://pytransit.readthedocs.io/en/stable/)
 [![MNRAS](https://img.shields.io/badge/MNRAS-10.1093%2Fmnras%2Fstv894-blue.svg)](http://mnras.oxfordjournals.org/content/450/3/3233)
 [![arXiv](http://img.shields.io/badge/arXiv-1504.07433-blue.svg?style=flat)](http://arxiv.org/abs/1504.07433)
 [![ASCL](https://img.shields.io/badge/ASCL-A1505.024-blue.svg?style=flat)](http://ascl.net/1505.024)