Pull 1.3 into Release branch

[AstroPatty]

• Implement some index operations
• Some take operations
• some more implementation
• Implement chunked_from_chunked
• Fixes for unsorted chunks
• Add changelog, fix type-check
• Make index typing more consistent
• Add index stubs
• Update tree handling
• Fix index exclusion
• Updates to contributing documentation
• Update building CI pipeline
• Update healsparse map logic to build from scratch
• Move healsparse map creation logic out of get_data
• Process all columns in healpixmap at once when making healsparse map.
• Add changelog
• Small test fix
• Implement masked numpy arrays for healpix output
• Update documentation
• Update changelog
• added animate_halo function
• debugging animate_halo function + other things
• can call either visualize_halo or alo
• documenting animate_halos
• changelog
• rendering animate_halo docs
• type checker
• type check
• type check
• type check
• type check
• Move everything to column producers
• Basic writes working with producers
• Correct raw data caching behavior with column conversions
• Add new instantiate file, remove derived file
• All serial tests working
• Move rest of dataset instantiation logic to new file
• Move make_schema to its own file
• Changelog
• type check
• addressing failing tests
• Move with_new_columns out of state
• Add correct file
• Significant rewrite to ensure column producer uniqueness with UUIDs
• bugfix + updated docs
• type check again...
• docs
• docs
• Add no_cache option to derived columns
• Add reindexing logic for diffsky
• Add allow_overwrite to with_new_columns and evalute apis
• Offset plugin for diffsky lightcones
• Add basic plugin specification
• Move top_host_idx reindexing into plugin system
• Add new test and changelog
• Add fixes for writing with stacking
• Fix docs for renaming
• Skip setting up AWS cli if cache already exists
• Add some MPI logic, which will be wired up in a later PR
• Add support for index plugins
• Reorganization for lightcone
• More plugin work
• Small reworks to guarantee plugin consistency
• Unify 'take' operations on DatasetState to ensure consistent plugin application
• Diffsky plugins now work with sorting
• Changelog
• Small bugfixes
• Small bugfixes
• Fixes for healpixmap tests
• Whatever you do, do not look at this commit
• Add diffsky partition plugin
• Add tests for diffsky partition plugin
• Update diffsky partitioning algorithm.
• Write tests for mpi write partitioning
• Add changelog, fix tests
• Add context and hook implementation
• Move plugin registration and calls to new system
• Move lightcone radec generation into plugin
• Fix keep_top_host logic to only fire on single datasets
• Move verification code out of the dataset
• Break DatasetState apart for future changes
• Update tests and fix changelog
• One more test fix
• Global random take implementation
• Global take_range implementation
• no longer throw, fix take with
• Fix unbound local error, fix test for new behavior
• Implement in structurecollection, implement helper index routine for Lightcone
• Takes working for chunked index as well
• Updates for lightcone, significant testing
• Fixes for a few tests
• Small updates, add changelog
• Fix for zero-length lightcones
• Fix sorted lightcones, disable tests that will be updated in different PR
• Unify column and metadata column handling in hdf5 handler
• Unify column and metadata column in state and instantiation
• Add test for metadata column arithmetic
• Revert accidental changelog overwrite
• Initial working implementation of the lightcone structure collection
• Generate ra, theta, chi, redshift, from raw coordinates
• Linking to galaxies in a lightcone structure collection is working
• Add rebuilding for nested galaxy structure collections
• Updates to fix galaxy linking
• Implement filtering with derived columns
• Implement additional testing
• Changelog, additional test
• Remove unneeded force_binary flag
• Implement writing and re-reading for lightcone structure collections
• Make updates for sorted lightcone structure collection
• Writes with galaxy linking
• Implement fixes for parallel output
• Implement lightcone convinience methods on structure collection
• Add changelog
• Fixed a bug that could cause failures when one rank had no data to write for a multi-dimension column
• Fix a bug that may be causing some MPI tests to fail periodically
• Remove debugginc code
• Fix a test that was incorrectly failing
• One more test fix
• More robust setup for lightcone test
• Implement get_pixels and pixel_search on lightcone
• Add docstrings and implement on structure collection
• Add changelog
• Fix type errors
• Some fixes and new tests
• Implement projection in rust
• Updated healpix containment algorithm to improve spatial query speed
• Remove debugging code
• Update release pipeline for pre-releases
• Update bumpmyversion
• Update version locations
• Update bumpversion config
• Allow release to run on main for pre-release versions
• Correctly serialize hyphenated pre-release
• Add jax output, allow evaluate to use other formats
• Add updated evaluate formats tests
• Add support for other formats to StructureCollection.evaluate
• Update docstrings to better reflect behavior
• Add changelog
• Delete a bunch of dead code