- :issue:`628`: FileType and FileCatalog clean up.
- :issue:`630`: Fix wrong shape (length of 6 instead of 3) of complex mesh stored in attrs.
- :issue:`640`: update for pmesh 0.1.56
- :issue:`641`: update for pandas 1.1.
- :issue:`622`: meshtools sets mu to zero instead of nan when appropriate.
- :issue:`618`: zhist fix
- :issue:`613`: gaussian filter fix (was not applied)
- :issue:`610`: odd multipole and wide angle fix in ConvFFTPower
- :issue:`604`: Allow any glob pattern.
- :issue:`000`: Update for new dask (csv)
- :issue:`597`: Update docrep.py
- :issue:`596`: Update documentation for NERSC usage. Python 3.5 is no longer supported on NERSC.
- :issue:`592`: Update for new dask (ndim)
- :issue:`587`: Reserve label == 0 for unconnected particles.
- :issue:`586`: Center the particles in fiber collision
- :issue:`582`: documentation infra update.
- :issue:`575,576`: Fix bug in painting particles to mesh in CatalogMesh
- :issue:`569`: Upgrade DistributedArray
- :issue:`570`: Add initial Query interface to FileCatalog.
- :issue:`571`: Typo in FKP
- :issue:`573`: Support Gadget variant binary format (with 4 byte header)
- :issue:`574`: DistributedArray.bincount fix
- :issue:`577`: Add doc examples for CVS and ArrayCatalog.
- :issue:`579`: compat-fix for mcfit-0.0.16
- :issue:`581`: compat-fix for sympy-1.4
- :issue:`555,556`: Impove dask interpolation in Catalog.save.
- :issue:`557`: Use dask's gufunc for sky transforms
- :issue:`558`: Note the unit of HaloRadius (proper, not comoving. bite me)
- :issue:`561`: Allow setting the position column in 2PCF.
- :issue:`563`: RedshiftHistogram extrapolates to zero rather than any number.
- :issue:`564`: Fix missing compensations with Multi-species meshes.
- :issue:`565`: add keyward header to HDFCatalog for reading additional meta data
- :issue:`566`: fix a bug sorting on float32, and add a persist method to Catalog.
- :issue:`567`: suppress redundant output in convpower.
- :issue:`544,549`: Use dask.store to save a catalog.
- :issue:`545`: Fix shotnoise estimation of weighted to_mesh() calls.
- :issue:`546`: Fix IndexError in painting during throttling.
- :issue:`547`: Update docrep
- :issue:`548`: Fix many deprecation warnings
- :issue:`550`: Documentation updates
- :issue:`553`: Fix error in TPCF module when there is only 1 bin.
- :issue:`543`: Further performance improvements on catalog slicing.
- :issue:`542`: The IO module shall make sure buffer is c-contiguous before reshaping
- :issue:`541`: Allow setting cartesian / sphericial transformation reference frame
- :issue:`540`: Allow not saving the header in Catalog.save
- :issue:`539`: Allow non-uniform redshifts in halo property transformations.
- :issue:`538`: Stop gathering catalog to a single rank in HaloCatalog
- :issue:`537`: Use numpy.sum for summing of integers.
- :issue:`536`: Fix boxsize mismatch comparision in pair counters.
- :issue:`535`: Improve working with a dask cluster.
- :issue:`532`: Improve speed of slicing of a catalog.
- :issue:`531`: Additional throttling during painting.
- :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=[]
- :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.
- :issue:`518`: Rework CurrentMPIComm
- :issue:`521`: Fix OOM errors with dask >= 0.19.0
- :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.
- :issue:`495`: Improve scaling of LogNormal catalog
- :issue:`497`: take method to BinnedStatistic
- :issue:`498`: add compute method to Catalog interface; CatalogMesh no longer a Catalog
- :issue:`500`: unique binning in FFTPower and FFTCorr
- :issue:`503`: redistributing a catalog spatially
- :issue:`504`: Catalog.copy hangs
- :issue:`505`: update docrep to 0.2.3
- :issue:`506`: compatible with dask 0.18.1.
- :issue:`491`: update compatibility with pandas 0.23.0 in cgm.
- :issue:`490`: write more useful weights and pairs in the paircount result.
- :issue:`493,494`: update for deprecation in pmesh
- :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.
- :issue:`468`: corrfunc and big-endian floating point numbers
- :issue:`470`: Add hankel tranforms for ell>0
- :issue:`469`: Fix a regression painting 'apply'ed meshes.
- :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
- :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.mplstylestyle file - :issue:`423`: support for Gadget 1 file format
- :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
- :issue:`384`: fix packaging bug causing
notebook.mplstyleto be missing from the conda build - rename test driver from
runtests.pytorun-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
- :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
- :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
Corrfunccode) - :issue:`370`: large addition of documentation for version 0.2.x; still partially completed
- DataSet has been renamed to BinnedStatistic
- calculation of
dkfixed in ProjectedFFTPower - paint() supports a Nmesh parameter, for easier re-sampling of mesh objects
- :issue:`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 - :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
- :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.
- use of
resamplerkeyword in thepaintfunction for compatibility with pmesh versions >= 0.1.24 - bug fixes and code cleanup
- package maintenance updates only
- 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 extended - galaxy type (central vs satellite) stored as integers in HODCatalog