Changelog¶
0.3.16 (UNRELEASED)¶
0.3.15 (2020-09-08)¶
0.3.14 (2020-07-08)¶
0.3.13 (2019-08-01)¶
0.3.12 (2019-07-06)¶
0.3.11 (2019-04-28)¶
#575, #576: Fix bug in painting particles to mesh in CatalogMesh
#569: Upgrade DistributedArray
#570: Add initial Query interface to FileCatalog.
#571: Typo in FKP
#573: Support Gadget variant binary format (with 4 byte header)
#574: DistributedArray.bincount fix
#577: Add doc examples for CVS and ArrayCatalog.
#579: compat-fix for mcfit-0.0.16
#581: compat-fix for sympy-1.4
0.3.10 (2019-02-07)¶
#557: Use dask’s gufunc for sky transforms
#558: Note the unit of HaloRadius (proper, not comoving. bite me)
#561: Allow setting the position column in 2PCF.
#563: RedshiftHistogram extrapolates to zero rather than any number.
#564: Fix missing compensations with Multi-species meshes.
#565: add keyward header to HDFCatalog for reading additional meta data
#566: fix a bug sorting on float32, and add a persist method to Catalog.
#567: suppress redundant output in convpower.
0.3.9 (2019-01-07)¶
0.3.8 (2018-12-29)¶
#543: Further performance improvements on catalog slicing.
#542: The IO module shall make sure buffer is c-contiguous before reshaping
#541: Allow setting cartesian / sphericial transformation reference frame
#540: Allow not saving the header in Catalog.save
#539: Allow non-uniform redshifts in halo property transformations.
#538: Stop gathering catalog to a single rank in HaloCatalog
#537: Use numpy.sum for summing of integers.
#536: Fix boxsize mismatch comparision in pair counters.
#535: Improve working with a dask cluster.
#532: Improve speed of slicing of a catalog.
#531: Additional throttling during painting.
#530: Use setuptools (need to change conda-build-bccp recipe)
#529: Add kmax(rmax) to FFTPower, FFTCorr, ConvPower.
#528: Add dataset= to Catalog.save, deprecate datasets=[]
0.3.7 (2018-10-17)¶
0.3.6 (2018-09-26)¶
0.3.5 (2018-08-23)¶
0.3.4 (2018-06-29)¶
#495: Improve scaling of LogNormal catalog
#497: take method to BinnedStatistic
#498: add compute method to Catalog interface; CatalogMesh no longer a Catalog
#500: unique binning in FFTPower and FFTCorr
#503: redistributing a catalog spatially
#504: Catalog.copy hangs
#505: update docrep to 0.2.3
#506: compatible with dask 0.18.1.
0.3.3 (2018-05-30)¶
0.3.2 (2018-05-14)¶
#475: proper normalization of the Landy-Szalay estimator, included R1R2 option and to_xil function
#487: Linear theory correspondant of nbody simulation. (three fluid model)
#486: overdecomposition in FOF
#483: switching to a new type in BinnedStatistics.copy()
#482: Fix a crash when two datasets passed into corrfunc are of different dtypes.
#480: BigFileCatalog shall look for header relative to the root of file.
#479: GatherArray allows root=Ellipsis (for allbather)
#476: Fix MeshSource.apply if MeshSource.action is overriden
#471: Decompose of surveydata to the correct bounds.
0.3.1 (2018-04-10)¶
0.3.0 (2017-12-18)¶
#439: added updated pair counter algorithms, SurveyDataPairCount and SimulationBoxPairCount.
#439: added correlation function algorithms, SurveyData2PCF and SimulationBox2PCF
#441: add a DemoHaloCatalog for tutorials that downloads small halo catalogs using Halotools
#441: add hod module with wrapper classes for Halotools models and create HOD catalog by calling the populate() method of a HaloCatalog
#445: add a global cache with fixed size for dask calculations
#446: fixes future warning generated by pandas
#447: adds PCS sampling windows
0.2.9 (2017-11-15)¶
#442: bug fix: fixes MemoryError when data is larger than memory in paint(); adds paint_chunk_size default option
#440: Selection, Value, Weight specified as “default” columns; default columns are not saved to disk
#437: bug fix: make sure to copy attributes of catalog when copy() is called
#436: FFT-based correlation function algorithm, FFTCorr addded
#435: binder badge added to README and documentation for cookbook recipes
#433: by default, the header file will be found automatically in Bigfile
#430: fix bug in FOF due to stricter numpy casting rules in numpy 1.13.3
#428: fixes bug in painting normalization when using interlacing is used
#422: proper list of attributes/methods added to documentation of Cosmology class
#425: latex requirement removed from
notebook.mplstylestyle file#423: support for Gadget 1 file format
0.2.8 (2017-10-06)¶
#398: AngularPairCount algorithm added to compute pair counts for survey data as a function of angular separation
#364: fix load balancing for survey pair counting algorithms
#415: fix sympy pickling issue
#409: fix periodic boundary condition issues with FOF for low number of ranks
#420: fix bug introduced in 0.2.7 causing selection of CatalogSources to sometimes hang
#420: remove dask selection optimizations, which can cause the code to crash in uncontrollable ways
#421: better error messaging when using deprecated __init__ syntax for Cosmology class
#406: add global sort and slice operations to CatalogSource objects
0.2.7 (2017-09-25)¶
#384: fix packaging bug causing
notebook.mplstyleto be missing from the conda buildrename test driver from
runtests.pytorun-tests.pyset_options context manager add to set global configuration variables
#392, #403: add optimized slicing via dask when applying a boolean selection index to a CatalogSource
#393: CatalogMesh is implemented as a view of a CatalogSource – column set/gets operate on the underlying CatalogSource
ConvolvedFFTPower supports cross-correlations of 2 mesh objects originating from the same data/randoms, allowing users to apply different weighting schemes to the two meshes
transform.SkyToCartesion deprecated in favor of transform.SkyToCartesian
#386: bug fixes related to behavior of Cosmology.clone
0.2.6 (2017-08-29)¶
#379: updated Cosmology class built on classylss, a Python binding of the CLASS Boltzmann code
#379: LinearPower object added with CLASS or Eisenstein-Hu transfer
#379: ZeldovichPower object added to compute Zel’dovich power spectrum
#379:HalofitPower object added to compute nonlinear power
#379: CorrelationFunction object added to FFT power spectra to compute theoretical correlation functions
#379: EHPower and NoWiggleEHPower deprecated in favor of LinearPower object
0.2.5 (2017-08-25)¶
#359: CSVFile and CSVCatalog no longer fail to read the last line of data when the file does not end in a newline
#361: add CylindricalGroups algorithm for computing groups of objects using the cylindrical grouping method of arXiv:1611.04165
#355: SimulationBoxPairCount and SurveyDataPairCount classes added to perform pair counting of objects in either simulation boxes or from survey data catalogs (using
Corrfunccode)#370: large addition of documentation for version 0.2.x; still partially completed
DataSet has been renamed to BinnedStatistic
calculation of
dkfixed in ProjectedFFTPowerpaint() supports a Nmesh parameter, for easier re-sampling of mesh objects
#368: addition of
Valuecolumn for painting mesh objects; this represents the value of the field painted, i.e., unity to paint density, or velocity to paint momentum (number-weighted velocity)addition of style module with matplotlib style sheet to make nice plots in our doc tutorials; this makes the docs reproducible by users
transform.vstack deprecated in favor of transform.StackColumns
transform.concatenate deprecated in favor of transform.ConcatenateSources
when painting catalogs to a mesh, users can specify the position column to use via the
positionkeyword#142: MultipleSpeciesCatalog object added to support painting multiple species of particles to the same mesh, i.e, baryons and dark matter particles in hydro simulations
CatalogMeshSource renamed to CatalogMesh internally
can now delete a column from a CatalogSource
can now slice a CatalogSource using a list of column names
#373: fix bug in ConstantArray when length is 1
0.2.4 (2017-06-18)¶
#339: transform.StackColumns renamed to
vstack#339: transform.concatenate function added, which takes a list of source objects, and returns a new Source that has the concatenation of all data
#345: fix compatibility with halotools version 0.5
#346: ability to resample a MemoryMesh object
#344: bug fixes related to calculation of growth rate in cosmology module
#347: ArrayCatalog can now be initialized from a dictionary or structured array
#348: add a ProjectedFFTPower algorithm, that computes the FFT Power, but can project over certain axes, i.e., projected axes have their power averaged over
#353: FITSCatalog added to the io module, for reading FITS files
#352: KDDensity to quickly estimate local density in density region.
#352: FOF also identifies Peak position and velocity.
0.2.3 (2017-05-19)¶
use of
resamplerkeyword in thepaintfunction for compatibility with pmesh versions >= 0.1.24bug fixes and code cleanup
0.2.2 (2017-04-27)¶
package maintenance updates only
0.2.1 (2017-04-26)¶
base dependencies + extras (halotools, h5py); install all dependencies via pip nbodykit[extras]
meta-data calculations in FKPCatalog now account for Source selection properly
support for numpy int/float meta-data in JSON output files
Cosmology instances no longer return attributes as Quantity instances, assuming a default set of units
renaming of various classes/module related to the nbodykit.Source syntax
no more nbodykit.Source in nbodykit.lab
nbodykit.source.particle has been renamed to nbodykit.source.catalog
source objects are now catalogs – there class names have “Catalog” appended to their names
added individual catalogs for different file types in nbodykit.io, i.e., CSVCatalog, HDFCatalog, etc
the
.applyoperation is no longer in place for sources; it returns a view with the list of actions extendedgalaxy type (central vs satellite) stored as integers in HODCatalog