Yt-astro-analysis

What's Changed
* MNT: bump dev version by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/173
* MNT: bump github action versions by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/174
* TST: upgrade all Python versions in tests by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/176
* BLD: migrate metadata to pyproject.toml, and drop setup.cfg by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/175
* STY: upgrade pre-commit hooks, bump minimal version for pyupgrade and reduce auto-upgrade frequency by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/177
* BLD: drop dependency on more_itertools by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/178
* STY: upgrade black to 23.1.0 by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/179
* TST: ensure test dependencies are correctly installed in CI by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/184
* MNT: enable dependabot autoupdates for GitHub workflows by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/181
* STY: migrate linting to ruff, add basic pre-commit hooks, cleanup .pre-commit-config.yaml by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/180
* Bump pypa/cibuildwheel from 2.11.4 to 2.12.0 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/185
* BUG: handle deprecation warning from numpy 1.25 (np.product is deprecated in favour of np.prod) by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/186
* MNT: upgrade pre-commit hooks, simplify ruff config, update blacken-docs url by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/188
* Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.4 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/189
* Bump pypa/cibuildwheel from 2.12.0 to 2.12.1 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/190
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/yt-project/yt_astro_analysis/pull/191
* Bump pypa/cibuildwheel from 2.12.1 to 2.12.3 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/192
* Bump pypa/gh-action-pypi-publish from 1.8.4 to 1.8.5 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/193
* DOC: migrate away from configuration key format deprecated in Sphinx 7.0 by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/195
* STY: activate flake8-comprehensions (ruff) by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/196
* Bump pypa/gh-action-pypi-publish from 1.8.5 to 1.8.6 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/197
* Bump pypa/cibuildwheel from 2.12.3 to 2.13.0 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/198
* TST: treat warnings as errors by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/201
* Bump pypa/cibuildwheel from 2.13.0 to 2.13.1 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/202
* Bump pypa/gh-action-pypi-publish from 1.8.6 to 1.8.7 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/203
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/yt-project/yt_astro_analysis/pull/204
* DEP: set upper limit to runtime numpy by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/205
* MNT: avoid usage of deprecated unyt API by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/207
* DOC: fix RadMC3DWriter's docstring (compat with modern yt) by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/206
* MNT: cleanup unused variables by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/212
* MNT: cleanup free of uninitialized variable by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/213
* Bump pypa/gh-action-pypi-publish from 1.8.7 to 1.8.8 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/214
* Bump pypa/cibuildwheel from 2.13.1 to 2.14.1 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/215
* BLD: stop building wheels for Windows 32 by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/217
* BLD: switch to Cython 3.0, forbid deprecated Numpy C API in generated code by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/211
* BLD: add wheels for CPython 3.12 by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/216
* BLD: migrate from oldest-supported-numpy to NPY_TARGET_VERSION (Python >= 3.9) by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/218
* Bump pypa/gh-action-pypi-publish from 1.8.8 to 1.8.10 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/220
* Support installation of rockstar through conda by cphyc in https://github.com/yt-project/yt_astro_analysis/pull/219
* DEP: drop support for CPython 3.8 by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/222
* Bump actions/checkout from 3 to 4 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/223
* BUG: fix usage of deprecated (and removed) clobber argument from astropy by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/226
* Updated ppv_cube.py to avoid deprecated function 'update_all_headers' by spectram in https://github.com/yt-project/yt_astro_analysis/pull/225
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/yt-project/yt_astro_analysis/pull/230
* Bump pypa/cibuildwheel from 2.15.0 to 2.16.2 in /.github/workflows by dependabot in https://github.com/yt-project/yt_astro_analysis/pull/231
* BUG: fix a couple bugs in PPVCube notebook by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/228
* DOC: pin doc requirements by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/235
* DOC: upgrade sphinx to latest version and enable automated upgrades for doc dependencies by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/237
* REL: prep release 1.1.3 by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/239

New Contributors
* dependabot made their first contribution in https://github.com/yt-project/yt_astro_analysis/pull/185
* spectram made their first contribution in https://github.com/yt-project/yt_astro_analysis/pull/225

**Full Changelog**: https://github.com/yt-project/yt_astro_analysis/compare/yt_astro_analysis-1.1.2...yt_astro_analysis-1.1.3

This is a bugfix release with no new features. We fixed compatibility with numpy 1.24 and Python 3.11
This release supports CPython 3.8 to 3.11

What's Changed
* Update version and citation. by brittonsmith in https://github.com/yt-project/yt_astro_analysis/pull/136
* Update package name for conda/pip installation. by brittonsmith in https://github.com/yt-project/yt_astro_analysis/pull/138
* TST: hotfix CI (workaround upstream change of behaviour) by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/145
* Increase timeout on data download. by brittonsmith in https://github.com/yt-project/yt_astro_analysis/pull/147
* BLD: drop support for CPython 3.7 by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/157
* MNT: cleanup unused and outdated requirements file by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/164
* BUG: fix compatibility with numpy 1.24 (numpy.float was removed) by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/169
* BLD: switch ubuntu image to 20.04 (18.04 image is deprecated) by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/167
* BLD: build wheels for Python 3.11 by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/170
* TST: test on Python 3.11 by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/163
* REL: prep release 1.1.2 by neutrinoceros in https://github.com/yt-project/yt_astro_analysis/pull/172


**Full Changelog**: https://github.com/yt-project/yt_astro_analysis/compare/yt_astro_analysis-1.1.1...yt_astro_analysis-1.1.2

yt_astro_analysis is a yt extension package for astrophysical analysis. This package contains functionality for:
* Halo finding and analysis
* Lightcones
* Planning cosmological simulations for making lightcones and lightrays
* Exporting to the RADMC-3D radiation transport code
* Creating PPV FITS cubes

This is a bugfix release; no new features have been added.

Bugfixes
* Make sure to initialize index before checking particle types https://github.com/yt-project/yt_astro_analysis/pull/127
* Fix broken example with halo plotting https://github.com/yt-project/yt_astro_analysis/pull/132
* Make total particles a 64 bit integer https://github.com/yt-project/yt_astro_analysis/pull/133
* Set output directory properly for rockstar halo finder https://github.com/yt-project/yt_astro_analysis/pull/134

**Full Changelog**: https://github.com/yt-project/yt_astro_analysis/compare/yt_astro_analysis-1.1.0...yt_astro_analysis-1.1.1

**yt_astro_analysis version 1.1 is released!**

yt_astro_analysis is an extension of yt for astrophysical analysis. This is the first stable release of yt_astro_analysis to be compatible with yt version 4.0 and later.

New Features
* The HaloCatalog has been significantly refactored (https://github.com/yt-project/yt_astro_analysis/pull/58, https://github.com/yt-project/yt_astro_analysis/pull/62) with the following additional improvements:
* the interface to the Rockstar halo finder is now compatible with the latest version of Rockstar Galaxies https://github.com/yt-project/yt_astro_analysis/pull/55
* all halo finders now support being run with time-series of datasets
* halo particle ids now savable with FoF and HOP halo finders https://github.com/yt-project/yt_astro_analysis/pull/52
* looping over halos is done with io chunks instead of ds.all_data for a significant speedup and reduction in memory
* Allow more flexibility for specifying rockstar particle mass https://github.com/yt-project/yt_astro_analysis/pull/84
* Add restart option for rockstar https://github.com/yt-project/yt_astro_analysis/pull/82
* Adding an outer_radius parameter to the iterative COM callback https://github.com/yt-project/yt_astro_analysis/pull/34
* Remove the sunyaev_zeldovich analysis module. This is now [ytsz](https://github.com/jzuhone/ytsz). https://github.com/yt-project/yt_astro_analysis/pull/79
* Drop support for python 3.6 https://github.com/yt-project/yt_astro_analysis/pull/100, https://github.com/yt-project/yt_astro_analysis/pull/101

Minor Enhancements and Bugfixes
* significant project management and ci improvements https://github.com/yt-project/yt_astro_analysis/pull/89, https://github.com/yt-project/yt_astro_analysis/pull/90, https://github.com/yt-project/yt_astro_analysis/pull/91, https://github.com/yt-project/yt_astro_analysis/pull/92, https://github.com/yt-project/yt_astro_analysis/pull/96, https://github.com/yt-project/yt_astro_analysis/pull/95, https://github.com/yt-project/yt_astro_analysis/pull/97, https://github.com/yt-project/yt_astro_analysis/pull/108, https://github.com/yt-project/yt_astro_analysis/pull/109
* Add annotate_halos function https://github.com/yt-project/yt_astro_analysis/pull/98
* only access particle_type field in rockstar if it exists and is needed https://github.com/yt-project/yt_astro_analysis/pull/111
* fix light cone projections with weight fields https://github.com/yt-project/yt_astro_analysis/pull/37
* Fix HaloCatalog progress bar https://github.com/yt-project/yt_astro_analysis/pull/40
* clarify rockstar error message about using the wrong number of MPI processes https://github.com/yt-project/yt_astro_analysis/pull/42, https://github.com/yt-project/yt_astro_analysis/pull/113
* check derived_field_list for base fields https://github.com/yt-project/yt_astro_analysis/pull/43
* allow cosmology splice from a single dataset https://github.com/yt-project/yt_astro_analysis/pull/49
* Fix iterator https://github.com/yt-project/yt_astro_analysis/pull/68
* Support new config file format https://github.com/yt-project/yt_astro_analysis/pull/65
* Enable circleci testing https://github.com/yt-project/yt_astro_analysis/pull/44
* Add max_box_fraction to plan_cosmology_splice https://github.com/yt-project/yt_astro_analysis/pull/76
* Fix HaloCatalog output_dir https://github.com/yt-project/yt_astro_analysis/pull/81
* remove deprecated dm_only keyword from halo finder https://github.com/yt-project/yt_astro_analysis/pull/57
* update amr_grid.inp https://github.com/yt-project/yt_astro_analysis/pull/77

New Contributors
* Corentin Cadiou (cphyc)
* Nathan Goldbaum (ngoldbaum)
* Meng Yuan Ho (willsonho2000)
* Cameron Hummels (chummels)
* Clément Robert (neutrinoceros)

**Full Changelog**: https://github.com/yt-project/yt_astro_analysis/compare/yt_astro_analysis-1.0.0...yt_astro_analysis-1.1.0

yt_astro_analysis version 1.0 is released!

yt_astro_analysis is an extension of [yt](https://github.com/yt-project/yt) for astrophysical analysis. yt_astro_analysis is the new home of yt's `analysis_modules`. The 1.0 release of yt_astro_analysis is functionally identical to the code in `analysis_modules` in yt version 3.5.0. After the 3.5 release of yt, `analysis_modules` was removed and all development transitioned to yt_astro_analysis.

yt_astro_analysis version 1.0 includes:

- Halo finding
- Halo analysis (the HaloCatalog)
- LightCones and CosmologySplices
- RADMC-3D exporting