Pynbody

What's Changed

Near complete re-implementation of the halo catalogue class hierarchy (https://github.com/pynbody/pynbody/pull/763)

This is a _breaking change_, and as such the major version number of pynbody has increased. Regular users probably _don't_ want to install a v2 release at this early stage, and as such it has been flagged as a beta.

* Halo classes are no longer imported directly into the `pynbody.halo` namespace.
* Users may now request a particular halo finder, or list of halo finders, by passing a `priority` kwarg to `SimSnap.halos()`
* `HaloCatalogue.precalculate()` has been renamed to `HaloCatalogue.load_all()`
* Halo classes supporting child/parent relationships now expose a `.subhalos` property, in which the child halos are enumerated
* Behind the scenes, the mapping from `iords` to file offsets has been improved and unified across all `HaloCatalogue` subclasses
* `GrpCatalogue` has been renamed to `HaloNumberCatalogue` to better reflect its meaning
* `AHFCatalogue` no longer renumbers the halos using a one-based scheme by default. If AHF has written out halo numbers, these are used by default; if it has not written out halo numbers, a zero-based indexing is used. Users can pass `halo_numbers='v1'` to `halos()` to obtain the old behaviour
* The ability to run halo finders has been removed (it anyway only ever worked for AHF, and even then was a bit flakey)


**Full Changelog**: https://github.com/pynbody/pynbody/compare/v1.6.0...v2.0.0-beta

What's Changed

Significant enhancements to the KDTree (https://github.com/pynbody/pynbody/pull/769):
* pynbody's sphere filters now make use of the KDTree to greatly enhance extracting spheres from large simulations.
* KDTrees will not automatically be built, so you should call `f.build_tree()` before `f[pynbody.filt.Sphere(...)]` to obtain the speed-up. Building the tree takes a while, so this is only worth doing if a large number of spheres will be extracted.
* KDTrees are now built in parallel, significantly speeding up operations that need them (such as SPH smoothing)
* KDTree data is now stored in numpy arrays, so it can be inspected from python and also can be stored in shared memory

**Full Changelog**: https://github.com/pynbody/pynbody/compare/v1.5.2...v1.6.0

This corrects an error in the minimum python version (should be 3.9, not 3.8).

Versions 1.5.0/1.5.1 are incompatible with 3.8, but will incorrectly attempt to install on 3.8. They will therefore be yanked from PyPI.

What's Changed
* Remove need for posix_ipc, making installation easier (and opening up path to one day supporting windows)
* Add tests to detect if shared memory is leaked
* Fix bug when accessing all_keys from CopyOnAccessSimSnap


**Full Changelog**: https://github.com/pynbody/pynbody/compare/v1.5.0...v1.5.1

New features
* Add support for 'galaxy' format for rockstar by cphyc in https://github.com/pynbody/pynbody/pull/709
* Refactors SubSnap into some smaller mixin classes that express different underlying concepts https://github.com/pynbody/pynbody/pull/749
* Introduces new "copy on access" concept, via `SimSnap.get_copy_on_access_simsnap()` which returns an initially empty simsnap that copies the parent simsnap lazily. (This is a facility introduced to make tangos able to use shared memory for efficiency: https://github.com/pynbody/tangos/pull/242)

Bug fixes
* Eliminates many warnings (745)
* Makes tests more reproducible (747)

Miscellaneous
* Move back to gcc for building macos wheels ([because clang's libomp introduces compatibility issues](https://github.com/pynbody/pynbody/pull/749/commits/42758300781a900a78ac096c8aeac7275cc9de49))

**Full Changelog**: https://github.com/pynbody/pynbody/compare/v1.4.2...v1.5.0

Enhancements
* Add default units to two-phase properties by bwkeller in https://github.com/pynbody/pynbody/pull/719

Bug fixes

* Fix tform conversion in Ramses snapshots by cphyc in https://github.com/pynbody/pynbody/pull/740
* Avoid bare excepts that can obscure KeyboardInterrupt by cphyc in https://github.com/pynbody/pynbody/pull/654

**Full Changelog**: https://github.com/pynbody/pynbody/compare/v1.4.1...v1.4.2