Light-curve-python

Added

- **Breaking change in experimental features**: Multiband support is introduced for features implemented in Python. It
changes class inheritance interface in a backward-incompatible way
- `light-curve[full]` extras which installs all optional Python dependencies required by experimental features
- New `LinexpFit` feature for parametric model fit comes with `light-curve-feature` v0.6.0
- Experimental `RainbowFit` feature for fitting multiband light curves with a single model, Russeil+23 in prep. It
requires Python 3.8 or later because of `iminuit` dependency
- Optional `iminuit>=2,<3` Python dependency (included into `[full]`) for `RainbowFit` feature
- Add `once_cell` v1 dependency

Changed

- **Breaking change in experimental features** `scipy` dependency is now optional for experimental features implemented
in Python
- **Breaking change in experimental features**: All experimental features implemented in Python require keyword-only
arguments in their constructors. Also, all names of the arguments are changed to be the same as for Rust features
- **Build breaking**: "abi3-py310" Cargo feature is replaced with "abi3-py311". "abi3" feature is now linked to "
abi3-py311" feature. This is because our aim with ABI is to support future versions of Python
- **Build breaking**: minimum supported Rust version (MSRV) is changed from 1.62 to 1.67 (released 2023-01-26)
- Update `*Fit` fatures doc-strings to list names of the features they output
- Bump `light-curve-feature` 0.5.5 -> 0.6.0
- Bump `pyO3` 0.18.3 -> 0.19.1, it simplified signature generations for
classes https://github.com/light-curve/light-curve-python/pull/230
- Bump `rust-numpy` 0.18.0 -> 0.19.0 https://github.com/light-curve/light-curve-python/pull/230
- Bump `enum-iterator` 1.2.0 -> 1.4.1 https://github.com/light-curve/light-curve-python/pull/233
- Bump `thiserror` 1.0.41 -> 1.0.48 https://github.com/light-curve/light-curve-python/pull/242

Added

- All Rust features got `.to_json()` method to serialize their state to JSON
string. https://github.com/light-curve/light-curve-python/pull/226
- New special Rust feature `JSONDeserializedFeature` and a helper function `feature_from_json()` to deserialize features
from JSON string. https://github.com/light-curve/light-curve-python/pull/226
- Build: "abi3" and "abi3-py310" Cargo features (the least one is enabled by the first one) to build a wheel for CPython
3.10+. This stable ABI wheel is less performant than the regular one, but it is compatible with all future Python
versions. See [PEP 384](https://www.python.org/dev/peps/pep-0384/) for
details. https://github.com/light-curve/light-curve-python/issues/79

Changed

- **Build breaking**: the only Python build requirement `maturin` updated from v0.14.x to
v1.0 https://github.com/light-curve/light-curve-python/pull/216 https://github.com/light-curve/light-curve-python/pull/215
- CI: bump cibuildwheel to 2.13.1 https://github.com/light-curve/light-curve-python/pull/225
- Bump `itertools` 0.10.5 -> 0.11.0 https://github.com/light-curve/light-curve-python/pull/224
- Bump `pyO3` 0.18.2 -> 0.18.3 https://github.com/light-curve/light-curve-python/pull/207

Fixed

- Building from sdist on x86-64 macOS required manual setting of `$MACOSX_DEPLOYMENT_TARGET` to 10.9 or higher.
Recent `maturin` update allowed us to specify it via `pyproject.toml`

Added

- Feature transformations via `transform` constructor keyword. For most of the features it could accept string with a
transformation name such as 'arcsinh' or 'clipped_lg', `True` or 'default' for the default transformation, `None`
or `False` for no
transformation https://github.com/light-curve/light-curve-python/issues/184 https://github.com/light-curve/light-curve-python/pull/188
- Binary wheels for x86_64 Windows built with no Ceres nor GSL
features https://github.com/light-curve/light-curve-python/issues/12 https://github.com/light-curve/light-curve-python/pull/185
- `enum-iterator` crate dependency https://github.com/light-curve/light-curve-python/pull/188
- CI: code coverage with `codecov` https://github.com/light-curve/light-curve-python/pull/197
- Development: now project has extras for testing (`test`) and
development (`dev`) https://github.com/light-curve/light-curve-python/pull/197

Changed

- **Build breaking**: minimum supported Rust version (MSRV) is bump from 1.60 to 1.62
- Bump `light-curve-feature` 0.5.4 -> 0.5.5
- Bump `pyO3` 0.18.1 -> 0.18.2
- Most of the parametric features have default values for their parameters now, which, due to `pyO3` limitations, are
not presented in the signatures, but documented in the docstrings. It also makes Python and Rust implementations more
consistent https://github.com/light-curve/light-curve-python/issues/194 https://github.com/light-curve/light-curve-python/pull/195
- Development: switch from `pytest-markdown` to `markdown-pytest` which allowed us to use up-to-date
pytest https://github.com/light-curve/light-curve-python/pull/198

Deprecated

- `BazinFit` and `VillarFit` constructors will not accept `None` for `mcmc_niter`, `ceres_niter`, and `lmsder_niter`
arguments in the future, just do not specify them to use defaults
instead. https://github.com/light-curve/light-curve-python/pull/195
- `Periodogram` constructor will not accept `None` for `peaks`, `resolution`, `max_freq_factor`, `nyquist` and `fast` in
the future, just do not specify them to use defaults
instead. https://github.com/light-curve/light-curve-python/pull/195

Fixed

- `Bins` feature had non-optimal lower boundary check for time series length: it checked if it is at least unity for any
underlying features. Now it takes underlying feature requirements into account. It was fixed by
updating `light-curve-feature` to v0.5.5.

Fixed

- Bug introduced in v0.6.5: `*Fit.model(t, params)` wrongly checked `t` and `params` arrays to have the same length

Added

- `BazinFit` and `VillarFit` have got `ceres` and `mcmc-ceres` algorithms using [Ceres Solver](http://ceres-solver.org)
as a non-linear least squares optimizer. `ceres` is found to be more robust than `lmsder` algorithm (available
via `gsl` Cargo feature) but working roughly twice slower. Ceres can be built from source (`ceres-source` Cargo
feature, enabled by default in `Cargo.toml`) or linked to system library (`ceres-system` Cargo feature, enabled for
cibuildwheel in `pyproject.toml`)

Changed

- **API breaking:** Features' `__call__()` signature changed to make `sorted=None`, `check=True` and `fill_value=None`
arguments to be keyword-only
- **API breaking:** Features' `many()` signature changed to make all arguments but the first `lcs` to be keyword-only
- **API breaking:** `Bins` constructor signature changed to make `offset` and `window` arguments to be keyword-only. For
Rust implementation `__getnewargs__` is replaced with `__getnewargs_ex__`. Please note that for the specific case of
Python implementation and Python version < 3.10, `Bins` still accepts positional arguments
- **API breaking:** `BazinFit` and `VillarFit` constructor signatures changed to make everything but the first `lcs`
argument to be keyword-only
- **API breaking:** `Periodogram` constructor signature changed to make all arguments to be keyword-only
- **API breaking:** `DmDt` constructor signature changed to make all arguments but `dt` and `dm` to be
keyword-only, `__getnewargs__` is replaced with `__getnewargs_ex__`. `DmDt.from_borders` class-method constructor has
all arguments to be keyword-only
- **API breaking:** `DmDt` methods' signatures changed to make all arguments but data (like `t`, `t, m` or `lcs`) to be
keyword-only
- **Build breaking:** building with Ceres Solver (`ceres-source` Cargo feature) is now a default, and potentially could
break a building pipeline in some cases. If you want to build without Ceres Solver, you need to explicitly disable
default features with `--no-default-features` maturin flag
- CI: switch from `macos-11` to `macos-latest` for testing
- Bump `pyo3` 0.17.3 -> 0.18.1
- Bump `rust-numpy` 0.17.2 -> 0.18.0

Removed

- **Build breaking:** `fftw-static`, `fftw-dynamic`, `mkl` Cargo features are removed after deprecation in v0.6.2 and
replaced with `fftw-source`, `fftw-system` and `fftw-mkl`.

Fixed

- Bug introduced in v0.6.5: `*Fit.model(t, params)` wrongly checked `t` and `params` arrays to have the same length