Pyunicorn

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Package:

- Improved `test coverage <https://app.codecov.io/gh/pik-copan/pyunicorn?search=&trend=all%20time>`_.
- Improved style and linting by revising and reducing global message disables
(`224 <https://github.com/pik-copan/pyunicorn/pull/224>`_,
`231 <https://github.com/pik-copan/pyunicorn/pull/231>`_,
`233 <https://github.com/pik-copan/pyunicorn/pull/233>`_).
- Ensured ``numpy=2.0`` support
(`234 <https://github.com/pik-copan/pyunicorn/pull/234>`_).
- Removed experimental and untested code
(`40 <https://github.com/pik-copan/pyunicorn/issues/40>`_,
`239 <https://github.com/pik-copan/pyunicorn/pull/239>`_).

New/Updated functionality:

- Extended Caching to ``RecurrenceNetwork`` and child classes as well as ``Surrogates``.
(`236 <https://github.com/pik-copan/pyunicorn/pull/236>`_).
- Revised API of ``Surrogates`` to conform to OO structure assumed by ``Cached``.
(`236 <https://github.com/pik-copan/pyunicorn/pull/236>`_).

Documentation:

- Removed malfunctioning links from Introduction
(`369b086 <https://github.com/pik-copan/pyunicorn/commit/369b086a8535dbfad6651caa62bee5a5488a0bfd>`_).
- Moved tutorial notebooks into ``docs``, dropped ``nbsphinx-link`` dependency
(`c54102e <https://github.com/pik-copan/pyunicorn/commit/c54102e42b767271be6299f8bf8170b27bda28e6>`_).
- Added ``EventSeriesClimateNetwork`` to API documentation
(`232 <https://github.com/pik-copan/pyunicorn/pull/232>`_).
- Removed outdated MathJax path for correct math display
(`0dd133c <https://github.com/pik-copan/pyunicorn/commit/0dd133c59da252b8c0e0e17f82290881508d0274>`_).

Bug fixes:

- Fixed unnoticed bug in ``SpatialNetwork.{in|out}average_link_distance()``
(`6b40587 <https://github.com/pik-copan/pyunicorn/commit/6b405873bede4ec18cd72164c734ed47964d2930>`_).
- Substituted deprecated shorthand ``scipy.sparse.*_matrix.A`` for ``scipy>=1.14`` compatibility
(`1d96e58 <https://github.com/pik-copan/pyunicorn/commit/1d96e58040c831afdcd7f7bf97be3ebd6ae6815a>`_).
- Substituted variable name ``I`` in C code, which might interfere with C's own macro for complex numbers
(`225 <https://github.com/pik-copan/pyunicorn/issues/225>`_,
`226 <https://github.com/pik-copan/pyunicorn/pull/232>`_).
- Fixed setup of Travis-CI on Windows builds
(`237 <https://github.com/pik-copan/pyunicorn/pull/237>`_).

-----

Package:

- Migrated to PEP 517/518 package format
(`a6c4c83 <https://github.com/pik-copan/pyunicorn/commit/a6c4c83905fcc4b73f46643fbe2f160917755e0e>`_).
- Added full Windows support
(`159 <https://github.com/pik-copan/pyunicorn/issues/159>`_,
`160 <https://github.com/pik-copan/pyunicorn/issues/160>`_).
- Reestablished `CI <https://app.travis-ci.com/github/pik-copan/pyunicorn>`_ on Linux
(`191 <https://github.com/pik-copan/pyunicorn/issues/191>`_,
`192 <https://github.com/pik-copan/pyunicorn/pull/192>`_)
and added macOS and Windows
(`214 <https://github.com/pik-copan/pyunicorn/pull/214>`_).
- Improved `test coverage <https://app.codecov.io/gh/pik-copan/pyunicorn?search=&trend=all%20time>`_.
- Discontinued Python 3.7 support
(`4cf6969 <https://github.com/pik-copan/pyunicorn/commit/4cf6969c40de39f01f31ea141767ec67cc3d6d31>`_).
- Replaced optional dependecy ``netcdf4`` with ``h5netcdf``
(`cd8ee00 <https://github.com/pik-copan/pyunicorn/commit/cd8ee00a534c0eae9440414d38a0eaaa5100aaec>`_,
`12 <https://github.com/pik-copan/pyunicorn/issues/12>`_,
`210 <https://github.com/pik-copan/pyunicorn/issues/210>`_).
- Replaced outdated ``progressbar`` with ``tqdm``
(`202 <https://github.com/pik-copan/pyunicorn/pull/202>`_).

Documentation:

- Added new tutorials
(`175 <https://github.com/pik-copan/pyunicorn/pull/175>`_,
`180 <https://github.com/pik-copan/pyunicorn/pull/180>`_,
`190 <https://github.com/pik-copan/pyunicorn/pull/190>`_).
- Edited tutorials and included notebooks in documentation
(`179 <https://github.com/pik-copan/pyunicorn/pull/179>`_,
`185 <https://github.com/pik-copan/pyunicorn/issues/185>`_,
`213 <https://github.com/pik-copan/pyunicorn/pull/213>`_).

New/Updated functionality:

- Generalized spatial and interacting network analysis
(`131 <https://github.com/pik-copan/pyunicorn/pull/131>`_):
added ``SpatialNetwork`` class, added Watts-Strogatz model to ``Network``,
added new metrics to ``RecurrencePlot``, ``CoupledClimateNetwork`` and
``InteractingNetworks``.
- Added ``EventSeries`` and ``EventSeriesClimateNetwork`` classes
(`156 <https://github.com/pik-copan/pyunicorn/pull/156>`_).
- Extended n.s.i. measures in ``Network`` with directed and weighted versions
(`153 <https://github.com/pik-copan/pyunicorn/pull/153>`_).
- Replaced ``MapPlots`` class with simplified ``MapPlot`` based on ``Cartopy``
(`174 <https://github.com/pik-copan/pyunicorn/pull/174>`_,
`203 <https://github.com/pik-copan/pyunicorn/issues/203>`_).

Extensions:

- Overhauled the Python/Cython interface
(`3dab5bf <https://github.com/pik-copan/pyunicorn/commit/3dab5bf89d2e224fc319ddd64aeeecc480f27fba>`_,
`402197f <https://github.com/pik-copan/pyunicorn/commit/402197fedff6dc4ce9796b5d2c32bb63ef6ecba8>`_).
- Made Cython/C extensions compatible with MSVC
(`160 <https://github.com/pik-copan/pyunicorn/issues/160>`_,
`165 <https://github.com/pik-copan/pyunicorn/issues/165>`_).
- Ported most of the remaining C extensions to Cython
(`128 <https://github.com/pik-copan/pyunicorn/issues/128>`_,
`142 <https://github.com/pik-copan/pyunicorn/issues/142>`_,
`145 <https://github.com/pik-copan/pyunicorn/issues/145>`_,
`187 <https://github.com/pik-copan/pyunicorn/issues/187>`_,
`195 <https://github.com/pik-copan/pyunicorn/pull/195>`_).

Bug fixes:

- Resolved indexing and typing problems in extensions
(`126 <https://github.com/pik-copan/pyunicorn/issues/126>`_,
`141 <https://github.com/pik-copan/pyunicorn/issues/141>`_,
`145 <https://github.com/pik-copan/pyunicorn/issues/145>`_,
`162 <https://github.com/pik-copan/pyunicorn/issues/162>`_,
`163 <https://github.com/pik-copan/pyunicorn/issues/163>`_).
- Overhauled the memoization/caching system
(`124 <https://github.com/pik-copan/pyunicorn/issues/124>`_,
`148 <https://github.com/pik-copan/pyunicorn/issues/148>`_,
`219 <https://github.com/pik-copan/pyunicorn/pull/219>`_).
- Shifted the histogram index in ``RecurrencePlot`` line distributions
(`166 <https://github.com/pik-copan/pyunicorn/issues/166>`_,
`209 <https://github.com/pik-copan/pyunicorn/pull/209>`_).
- Resolved numerous other issues related to inheritance and method overloading,
deprecated APIs, etc. For a full list, see the `release milestone
<https://github.com/pik-copan/pyunicorn/milestone/1?closed=1>`_.

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- Fixed some bugs and compatibility issues.
- Improved test framework.
- Added ``pyunicorn`` description paper reference to all code files.

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- Migrated from Python 2.7 to Python 3.7.
- Completed transition from ``Weave`` to ``Cython``.
- Added Event Coincidence Analysis.

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- Updated test suite and CI.

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- Added reference to ``pyunicorn`` description paper published in the
journal *Chaos*.