v2.1.2

This is a patch release, primarily to fix the units of sigman_{com,L2com} in CompaSOHaloCatalog.

sigman_com and sigman_L2com were having their values inappropriately multiplied by the box size in CompaSOHaloCatalog. These fields are the square roots of the eigenvalues of the second moment tensor formed from the unit vectors of the halo particle positions, so they should be dimensionless.

Also, sigmav{Min,Mid,Maj,rad,tan}_{L2com,com} were all being unpacked as redshift-space displacements (units of comoving Mpc/h). We unpack all other velocity fields as proper km/s, so we now do the same for these.

sigmav3d_{L2com,com} are unaffected, as are the eigenvectors.

What's Changed [autogenerated, minus bots]

• AbacusHOD: Moving mock dir creation to run_hod by @SBouchard01 in #187
• compaso: fix sigman units, change sigmav units (sigmav3d unaffected) by @lgarrison in #191
• v2.1.2 fixups by @lgarrison in #192

New Contributors

• @SBouchard01 made their first contribution in #187

Full Changelog: v2.1.1...v2.1.2

v2.1.1

This is a patch release, primarily to publish the reduction in memory usage in the HOD module.

There is a small change to tsc_parallel() that may be breaking: when passing in a pre-allocated ndarray, that ndarray is no longer returned to make it clear that the array is being modified in-place.

Breaking Changes

• tsc: return None from tsc_parallel when the user passes a pre-allocated ndarray [#180]

Fixes

• hod: reduce menv memory usage in prepare_sim [#172]
• halo light cones: reduce memory usage in prepare_sim [#173]

Documentation

• Added a subsample particle tracking tutorial
• Other documentation tweaks and improvements

---

What's Changed [autogenerated]

• hod: reduce menv memory usage in prepare_sim by @lgarrison in #172
• halo light cones: reduce memory usage in prepare_sim by @boryanah in #173
• tsc: return None from tsc_parallel when the user passes a pre-allocated ndarray by @lgarrison in #180

Full Changelog: v2.1.0...v2.1.1

v2.1.0

This is a small release with a few quality-of-life changes, notably to reduce memory usage in the CompaSO module and improve error reporting in the HOD module. It also adds asdf 4 support, which is important because 2.0.1 does not include an asdf version upper bound.

Thanks to @epaillas, @pburger112, and @zacharyburnett for their contributions!

Supported Python versions are 3.9-3.13.

Enhancements

• hod.prepare_sim: detect and report when a prepare_slab subprocess fails [#151]
• ci: add python 3.12 and enhance NUMBA_DISABLE_JIT support [#153]
• Improve CompaSO subsample loading [#154]
• deprecate asdf.open(copy_arrays=True) in favor of asdf.open(memmap=False) [#157]
• compaso: add passthrough support [#162]
• compaso: more flexible search for cleaning info [#167]
• ci: add python 3.13 [#168]
• Add prepare_sim.Nthread_per_load parameter [#145]
• Implement logger for AbacusHOD [#134]
• power spectrum: don't assume normalized weights [#146]

Fixes

• Fixes to halo light cone randoms [#142]
• Fix read_asdf on rv data [#165]

New Contributors

• @epaillas made their first contribution in #134
• @pburger112 made their first contribution in #142
• @zacharyburnett made their first contribution in #157

Full Changelog: v2.0.1...v2.1.0

v2.0.1

This is a bugfix release primarily to add support for ASDF 3.1.0. Several other bugs in the ZCV and HOD modules are also fixed.

Fixes

• Fix ASDF error in ZCV module, add ASDF 3.1.0 support [#130]
• bug fix keys() [#126]
• Sandydev: fixed reseeding bug [#127]
• fix reseed bug [#128]
• backward compatible fix for velocity bias [#121]

What's Changed [autogenerated]

• backward compatible fix for velocity bias by @SandyYuan in #121
• build(deps): bump actions/download-artifact from 3 to 4 by @dependabot in #124
• build(deps): bump actions/setup-python from 4 to 5 by @dependabot in #122
• build(deps): bump actions/upload-artifact from 3 to 4 by @dependabot in #123
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #125
• bug fix keys() by @SandyYuan in #126
• Sandydev: fixed reseeding bug by @SandyYuan in #127
• fix reseed bug by @SandyYuan in #128
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #129
• Fix ASDF error in ZCV module, add ASDF 3.1.0 support by @lgarrison in #130

Full Changelog: v2.0.0...v2.0.1

v2.0.0

abacusutils 2.0 introduces a power spectrum module based on fast, parallelized TSC
and FFT, including grid interlacing and window compensation, that can output bandpowers,
Legendre multipoles, (k,mu) wedges, and more.

Furthermore, there's a new Zel'dovich Control Variates (ZCV) module, and the HOD module
has many additions, performance improvements, and bug fixes.

The set of default installed dependencies has also been reduced to avoid trouble with
source-only distributions. Use pip install abacusutils[all] if you need functionality
provided by a non-default dependency.

This is a relatively large release, so the version number has been bumped to 2.0.0, since
there may be associated backwards incompatibilities.

Supported Python versions are 3.8-3.11. Python 3.7 continues to work, although we'll
drop support if/when this is no longer the case.

New Features

• HOD now supports a new ELG conformity model
• Add a power spectrum module, and a zeldovich control variates (ZCV) module that uses it [#68]
• New parallel TSC module [#79]

Fixes

• Bump Numba requirement to fixed version and enable parallelism in env calc [#60]
• Many small bug fixes

Enhancements

• Add power spectrum to metadata module [#69]
• Upgrade docs and CI [#71]
• Power spectrum optimization and parallelization [#102]
• Compute Xi(rp,pi) from P(k) [#115]
• Update CI test and build infrastructure [#118]

Installation

• Refactor optional dependencies; Corrfunc now optional. Migrate build to pyproject.toml. [#89]

What's Changed [autogenerated]

• Sandydev by @SandyYuan in #57
• Re-enable Numba parallelism in environment calculation by @lgarrison in #60
• Sandydev by @SandyYuan in #62
• Fix lc pos interp by @boryanah in #63
• updating calculate_ngal by @boryanah in #64
• impemented P(k, mu) and checked against nbodykit by @boryanah in #65
• implemented kernel deconvolution and interlacing; fixed k_hMpc_max choice by @boryanah in #67
• Update metadata module with power spectrum by @lgarrison in #69
• Add a power spectrum module, and a zeldovich control variates (ZCV) module that uses it by @boryanah in #68
• Fix docs and zcv imports; upgrade docs and CI by @lgarrison in #71
• Bump actions/setup-python from 2 to 4 by @dependabot in #72
• Bump pypa/gh-action-pypi-publish from 1.4.2 to 1.6.4 by @dependabot in #73
• Bump actions/checkout from 2 to 3 by @dependabot in #74
• Initial run of pre-commit by @lgarrison in #75
• More installation instructions; test pre-commit.ci by @lgarrison in #76
• Add tutorial notebook on CompaSO subsample particles by @lgarrison in #77
• Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.4 by @dependabot in #80
• Add parallel TSC module by @lgarrison in #79
• Bump pypa/gh-action-pypi-publish from 1.8.4 to 1.8.5 by @dependabot in #82
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #83
• Bump pypa/gh-action-pypi-publish from 1.8.5 to 1.8.6 by @dependabot in #86
• Power spec by @lgarrison in #85
• Sandydev by @SandyYuan in #78
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #87
• added NFW profile, improved multipoles, consolidated shear calculation by @SandyYuan in #88
• fixed savedir bug for shear by @SandyYuan in #91
• fix rvir bug in nfw sats by @SandyYuan in #92
• Bump pypa/gh-action-pypi-publish from 1.8.6 to 1.8.7 by @dependabot in #96
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #97
• Refactor optional dependencies; Corrfunc now optional. Migrate build to pyproject.toml. by @lgarrison in #89
• ci: add python 3.11 by @lgarrison in #99
• Add missing analysis docs to Sphinx doc tree by @lgarrison in #98
• Sandydev by @SandyYuan in #100
• added fix for secondary z by @SandyYuan in #101
• fixes for py3.10 by @SandyYuan in #103
• power spectrum module optimization and parallelization by @lgarrison in #102
• Bump pypa/gh-action-pypi-publish from 1.8.7 to 1.8.8 by @dependabot in #106
• Preparing for v1.4 by @lgarrison in #104
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #107
• Power spec by @boryanah in #108
• Bump pypa/gh-action-pypi-publish from 1.8.8 to 1.8.10 by @dependabot in #110
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #111
• Sandydev nfw by @SandyYuan in #112
• Bump actions/checkout from 3 to 4 by @dependabot in #113
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #114
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #117
• Functionality for Xi_rppi from Pk by @boryanah in #115
• Update CI test and build infrastructure by @lgarrison in #118
• Sandydev: fixing velocity bias along x and y direction by @SandyYuan in #119
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #120

New Contributors

• @dependabot made their first contribution in #72
• @pre-commit-ci made their first contribution in #83

Full Changelog: v1.3.0...v2.0.0

v1.3.0

This release adds the metadata module and drops support for Python 3.6. It also contains several features, bugfixes, and optimizations for the HOD and light cone modules.

What's Changed

• Fix read lc rv by @boryanah in #37
• fixed dtype mismatch in tpcf calculator by @SandyYuan in #40
• Fix origin by @boryanah in #41
• some nice numba accelerations for fenv calculation by @SandyYuan in #45
• Factorize dependencies by @lgarrison in #46
• allows user to output code in chunks when simulation input (or output… by @boryanah in #48
• Ftr chunk by @boryanah in #50
• new particle subsampling by @SandyYuan in #49
• Reduce memory usage in Menv tree queries by @lgarrison in #51
• Try to fix tests and remove temporary files by @lgarrison in #52
• added two conformity parameters for ELGs by @SandyYuan in #54
• Add metadata module containing simulation headers by @lgarrison in #56

Full Changelog: v1.2.0...v1.3.0

v1.2.0

This release adds the capability to generate HOD mocks from the halo light cone catalogs, as well as a few other small improvements/fixes.

What's Changed

• Add Python 3.10 to CI config by @lgarrison in #19
• Halo lc hod by @boryanah in #28
• fixed random number by @SandyYuan in #26

Full Changelog: v1.1.0...v1.2.0

v1.1.0

This is a feature release of abacusutils, containing new functionality in the data and hod modules, as well as several bug fixes and performance improvements. This is also the first version that can read the light cone halo catalogs [#11].

What's Changed

• fixed ic issue for QSOs by @SandyYuan in #15
• Add superslab filtering functionality by @lgarrison in #16
• Start migration to GitHub CI by @lgarrison in #17
• Fix cleandir and propagate cleaning info in header by @lgarrison in #18
• remove halotools from setup.py by @SandyYuan in #21
• Added altsimname argument to prepare_sim by @SandyYuan in #22
• added reseeding option to abacushod.run_hod() by @SandyYuan in #23
• Add pack9 reader by @lgarrison in #25
• sped up the reseeding process by @SandyYuan in #24
• Automatic versioning and releasing by @lgarrison in #27
• working version for reading light cone files; by @boryanah in #11

New Contributors

• @boryanah made their first contribution in #11

Full Changelog: v1.0.4...v1.1.0

v1.0.4

This is a bugfix release, fixing the ELG HOD generation and the ic parameter in the example config file

v1.0.3

This is a bug fix release, fixing a bug in the prepare_sim script in the HOD module (#14).