Aspire

This is a small patch release to update several dependent packages with recent versions.

It includes commits for the following:

* Enforcing the latest version of `gemmi` and the associated code change
* Very minor doc updates
* Symmetry Boosting in `MeanEstimator`
* `finufft` version updates
* `cufinufft` version updates
* Ability to load `RelionSource`s as double precision
* `MeanEstimator` volume coef checkpointing
* Minor flake/black style updates

ASPIRE v0.12.1 is bugfix release, adding a mix of new features and cleanup.

This release provides the following features:

* Interoperable 2D basis (covar2d, class averaging)
* Improved Relion interoperability
* Common Line SDP method
* Shared 2D Basis tests
* Common Lines optional fuzzy mask
* Add `Coef` class
* Nearest rotation (SVD) util method
* FRC and FSC plotting option (disable cutoff)


Bug fixes:

* Enforce grid conventions
* FLE expand unit test convergence
* Sync voting unit test patch
* Whitening extremal value patch
* Adds improved image projection tests
* Adds improved volume rotation tests
* FBBasis3D NaN values for large resolution
* {F}PSWF basis float32 patch
* Extend `eval_coords` to many volumes
* Enforce block dtypes on assignment
* Reduce package import resource util


Systems/CI Updates:

* Flake8 Style Updates
* Add public Issue template
* Docstring cleanup
* Adds docstring linting util to CI
* Additional `pytest` conversions
* Removes `parameterized_class`
* Workaround Ray/pydantic dependency conflict


Documentation:

* Adds Relion interoperability gallery
* Adds Weighted spectral volume gallery
* Update public facing Code of Conduct
* Add K2 camera note to CTF estimator module
* Removes deprecated legacy example scripts

ASPIRE v0.12.0 is minor release, adding new scientific features, components, and several improvements.

This release provides the following features:

* `MicrographSimulation` component
* `MicrographSource`s with `CoordinateSource` integration
* Data Downloader utility (via `pooch`)
* `WeightedVolumesEstimator` for heterogeneous 3D reconstruction
* TIFF `Image` loading support
* Common Lines method for C2 symmetry
* `DiagMatrix` operator

Bug fixes:

* `clean_image` caching
* Apple unit test patch (following `numpy` updates)
* Rename `PolarBasis2D` to `PolarFT` and consistently use compact (real symmetric) representation

Systems/CI Updates:

* Add Python 3.11, drop Python 3.7
* Modernize Python packaging via `pyproject.toml`
* Warnings cleanup
* Migrate several tests towards `pytest.fixture`
* Modular and `pytest.fixture` based tests for Common Lines methods
* Reduce APPLE unit test time
* Apple M1/M2 arm-64 install documentation
* `cufinufft` v1.3 final adoption
* GRPC dependency updates

ASPIRE v0.11.1 is patch release, mainly for minor demo updates.

This release provides the following features:

* `FourierRingCorrelation` and `FourierShellCorrelation`

Bug fixes:

* Tutorial MRC file download path
* Reorders FLE indices to aid in compatibility with FB
* Exposes class indices attributes in more places (after `Source` slicing)
* Improved CL logging messages

Systems/CI Updates:

* Simplifies install instructions

ASPIRE v0.11.0 is minor release, adding several scientific and API changes.

This release provides the following features:

* Extensible `ClassAvgSource` framework
* Ab-initio modeling for Cn symmetry (`CLSymmetryCn`)
* FLE Basis (`FLEBasis2d`)
* `IndexedSource` for source slicing and remapping
* Immutable source API migration
* `Image` and `Volume` API cleanup (return types)
* `asnumpy` as immutable views
* Additional RELION 3.1 STAR file support
* SNR Estimation and Simulation utilities
* Improved `whiten` syntax
* Immutable Source API

Documentation and Logging:

* Tutorial Gallery restructuring
* Lecture Feature Demo updates
* Class Averaging API documentation and UML
* Introductory API documentation and UML (gallery)
* Continued filtering of log messages
* CTF forward model validation and tutorial

Bug fixes:

* Redundant `Image` conversion bug in `denoised_src`
* Fixed `eval_coords` clustering (adjusted Rand score)
* Negative `Image` index slicing (wraparound bug)
* Polar Fourier Row Major cleanup

Systems/CI Updates:

* `conda` BLAS accelerated numerical backends (`mkl`, `openblas`, `accelerate`)
* Relaxed `pip` version requirements
* Long running test suite on `review-ready`
* CI documentation and gallery build on `push`
* Windows CI patches
* Resolve deprecation warnings (`pandas`, `scipy`)
* Partial removal of `parameterized_class`
* `black` 23.1.0 updates

ASPIRE v0.10.1 is a patch release focused on adding several API improvements, bug fixes, and CI updates.

This release provides the following features:

* Synthetic volume generators (Legacy and compact Asymmetric, Cn, Dn, T, O)
* `confuse` based ASPIRE config
* Multi dimensional stack axis for `Image` and `Volume`
* Parallel and batched BFR and BFSR alignment
* Scale `colorbar` for `Image.show` utilities
* Implement and check top level imports (`import aspire`)
* Restores ability to use `cufinufft` via config
* `NoiseAdder` framework and updates

Documentation and Logging:

* User configuration tutorial
* Dramatically reduced console log spam
* Replaced some logging with `tqdm` progress bars
* Support user/runtime logger and `tqdm` configuration
* Updated simulation docstring
* Docstring formatting
* Pipeline demo gallery

Bug Fixes and Cleanup:

* Updates rotation convention to be counter-clockwise
* Real coefficient rotations
* Normalize background dtype
* Fourier Bessel zero finding cleanup
* `im_translate` and preprocessing cleanup/deprecation
* `CTFEstimator` and `voltage_to_wavelength` unit fixes
* CTF starfile output column name
* Unit test fixes for averagers
* Pytest parallel processing limits
* Added missing `paramatrized` test cases
* Gaussian 2D and 3D util cleanup
* Unified `transpose` and `flip` for Volume and Image
* `covar2d` ells mask bug fix
* Consistently use recent `about_axis()` and `Volume.load()`
* ImageSource.save() dict return
* Remove `Micrograph` and `MrcStack` in favor of `ImageSource`
* Consistent use of `fft` module
* Dtype updates (`Basis`, `Simulation`, `Volume`, `CLOrient3D`, `nufft`)
* Filter indices bug fix
* Migration to `Image.Resolution` from `Image.res` (via DeprecationWarning)
* Workaround for `scipy==v0.10.0` 2D interpolation
* `importlib` resources updates

Systems/CI Updates:

* GPU CI
* Daily documentation build testing (`develop`)
* CI config and additional logging
* Disable `ray` on Azure for OSX and Windows
* Adds `pytest-xdist` plugin for developers
* Support building docs without running gallery
* Updates for latest `scikit-learn` release
* Began migration towards pure `pytest`s
* `tox` v4 support
* Azure OSX 12 updates
* Github actions v3/v4 updates