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Changelog

0.3.8 (Unreleased)

  • :issue:`530`: Use setuptools (need to change conda-build-bccp recipe)
  • :issue:`529`: Add kmax(rmax) to FFTPower, FFTCorr, ConvPower.
  • :issue:`528`: Add dataset= to Catalog.save, deprecate datasets=[]

0.3.7 (2018-10-17)

  • :issue:`519`: Rework the class hierarchy of Catalogmesh.
  • :issue:`526`: Reduce the paint size for systems with lower mem per core
  • :issue:`527`: Aggregate attrs of header and the main datasets.

0.3.6 (2018-09-26)

0.3.5 (2018-08-23)

  • :issue:`509`: Fix auto detection of f8 type in Gadget1 file reader
  • :issue:`513`: Ignore divide errors.
  • :issue:`516`: Fix several bugs in three point function
  • :issue:`517`: Improve compatibility with numpy 1.15.x's new indexing convention.

0.3.4 (2018-06-29)

0.3.3 (2018-05-30)

0.3.2 (2018-05-14)

  • :issue:`475`: proper normalization of the Landy-Szalay estimator, included R1R2 option and to_xil function
  • :issue:`487`: Linear theory correspondant of nbody simulation. (three fluid model)
  • :issue:`486`: overdecomposition in FOF
  • :issue:`483`: switching to a new type in BinnedStatistics.copy()
  • :issue:`482`: Fix a crash when two datasets passed into corrfunc are of different dtypes.
  • :issue:`480`: BigFileCatalog shall look for header relative to the root of file.
  • :issue:`479`: GatherArray allows root=Ellipsis (for allbather)
  • :issue:`476`: Fix MeshSource.apply if MeshSource.action is overriden
  • :issue:`471`: Decompose of surveydata to the correct bounds.

0.3.1 (2018-04-10)

0.3.0 (2017-12-18)

  • :issue:`439`: added updated pair counter algorithms, SurveyDataPairCount and SimulationBoxPairCount.
  • :issue:`439`: added correlation function algorithms, SurveyData2PCF and SimulationBox2PCF
  • :issue:`441`: add a DemoHaloCatalog for tutorials that downloads small halo catalogs using Halotools
  • :issue:`441`: add hod module with wrapper classes for Halotools models and create HOD catalog by calling the populate() method of a HaloCatalog
  • :issue:`445`: add a global cache with fixed size for dask calculations
  • :issue:`446`: fixes future warning generated by pandas
  • :issue:`447`: adds PCS sampling windows

0.2.9 (2017-11-15)

  • :issue:`442`: bug fix: fixes MemoryError when data is larger than memory in paint(); adds paint_chunk_size default option
  • :issue:`440`: Selection, Value, Weight specified as "default" columns; default columns are not saved to disk
  • :issue:`437`: bug fix: make sure to copy attributes of catalog when copy() is called
  • :issue:`436`: FFT-based correlation function algorithm, FFTCorr addded
  • :issue:`435`: binder badge added to README and documentation for cookbook recipes
  • :issue:`433`: by default, the header file will be found automatically in Bigfile
  • :issue:`429,432`: updates to documentation
  • :issue:`430`: fix bug in FOF due to stricter numpy casting rules in numpy 1.13.3
  • :issue:`428`: fixes bug in painting normalization when using interlacing is used
  • :issue:`422`: proper list of attributes/methods added to documentation of Cosmology class
  • :issue:`425`: latex requirement removed from notebook.mplstyle style file
  • :issue:`423`: support for Gadget 1 file format

0.2.8 (2017-10-06)

  • :issue:`398`: AngularPairCount algorithm added to compute pair counts for survey data as a function of angular separation
  • :issue:`364`: fix load balancing for survey pair counting algorithms
  • :issue:`415`: fix sympy pickling issue
  • :issue:`409`: fix periodic boundary condition issues with FOF for low number of ranks
  • :issue:`420`: fix bug introduced in 0.2.7 causing selection of CatalogSources to sometimes hang
  • :issue:`420`: remove dask selection optimizations, which can cause the code to crash in uncontrollable ways
  • :issue:`421`: better error messaging when using deprecated __init__ syntax for Cosmology class
  • :issue:`406`: add global sort and slice operations to CatalogSource objects

0.2.7 (2017-09-25)

  • :issue:`384`: fix packaging bug causing notebook.mplstyle to be missing from the conda build
  • rename test driver from runtests.py to run-tests.py
  • set_options context manager add to set global configuration variables
  • :issue:`392,403`: add optimized slicing via dask when applying a boolean selection index to a CatalogSource
  • :issue:`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
  • :issue:`386`: bug fixes related to behavior of Cosmology.clone

0.2.6 (2017-08-29)

  • :issue:`379`: updated Cosmology class built on classylss, a Python binding of the CLASS Boltzmann code
  • :issue:`379`: LinearPower object added with CLASS or Eisenstein-Hu transfer
  • :issue:`379`: ZeldovichPower object added to compute Zel'dovich power spectrum
  • :issue:`379`:HalofitPower object added to compute nonlinear power
  • :issue:`379`: CorrelationFunction object added to FFT power spectra to compute theoretical correlation functions
  • :issue:`379`: EHPower and NoWiggleEHPower deprecated in favor of LinearPower object

0.2.5 (2017-08-25)

  • :issue:`359`: CSVFile and CSVCatalog no longer fail to read the last line of data when the file does not end in a newline
  • :issue:`361`: add CylindricalGroups algorithm for computing groups of objects using the cylindrical grouping method of arXiv:1611.04165
  • :issue:`355`: SimulationBoxPairCount and SurveyDataPairCount classes added to perform pair counting of objects in either simulation boxes or from survey data catalogs (using Corrfunc code)
  • :issue:`370`: large addition of documentation for version 0.2.x; still partially completed
  • DataSet has been renamed to BinnedStatistic
  • calculation of dk fixed in ProjectedFFTPower
  • paint() supports a Nmesh parameter, for easier re-sampling of mesh objects
  • :issue:`368`: addition of Value column 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 position keyword
  • :issue:`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
  • :issue:`373`: fix bug in ConstantArray when length is 1

0.2.4 (2017-06-18)

  • :issue:`339`: transform.StackColumns renamed to vstack
  • :issue:`339`: transform.concatenate function added, which takes a list of source objects, and returns a new Source that has the concatenation of all data
  • :issue:`345`: fix compatibility with halotools version 0.5
  • :issue:`346`: ability to resample a MemoryMesh object
  • :issue:`344`: bug fixes related to calculation of growth rate in cosmology module
  • :issue:`347`: ArrayCatalog can now be initialized from a dictionary or structured array
  • :issue:`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
  • :issue:`353`: FITSCatalog added to the io module, for reading FITS files
  • :issue:`352`: KDDensity to quickly estimate local density in density region.
  • :issue:`352`: FOF also identifies Peak position and velocity.

0.2.3 (2017-05-19)

  • use of resampler keyword in the paint function for compatibility with pmesh versions >= 0.1.24
  • bug 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 .apply operation is no longer in place for sources; it returns a view with the list of actions extended
  • galaxy type (central vs satellite) stored as integers in HODCatalog