Releases¶
dev-version¶
v3.3.4 [08 Jan 2021]¶
Bugfixes
Added
validate()
method that is automatically called after__init__()
andupdate()
and also (optionally) on everyparameter
update. This can cross-validate different inputs. NOTE: if you currently have code that sets parameters directly, egmf.z=2.0
, you should update to using theupdate()
method, as this allows multiple parameters to be set, and then a call tovalidate()
.
v3.3.2 [11th Dec 2020]¶
Changes
camb
is no longer installed by default. If you want to install it along withhmf
(as well as other useful utilities) install withpip install hmf[all]
.
v3.3.0 [24th Nov 2020]¶
Features
Option to extrapolate high-k for CAMB transfer using EH. This gives a fast and reasonably consistent high-k transfer function. If not extrapolating with EH (which is still the default) you can now set
transfer_params={'kmax':1e3}
to get better low-mass/small-scale accuracy. By default, kmax is the same as the default from CAMB, which is about 1.4 h/Mpc. Above this value, the transfer function is by default linearly extrapolated in log-log space.Components now automatically keep track of models, and the base component class tracks Component types. This also means that user-defined models can be input via strings into a framework (useful for running from CLI).
3.2.0¶
Features
Updated (working) CLI: use
hmf run
to produce mass functions on the command-line!
Internals
Deprecated astropy_to_colossus function.
3.1.0¶
Notes
New versions of CAMB (1.0.0+) seem to run significantly slower by default than previous versions. This could just be a setting in CAMB that has changed its default. Be aware of this.
Features
Added new
CambGrowth
growth factor model, which computes the growth using CAMB. This is useful especially when using w > -1, for which the other growth factor models are inadequate. Solves issue #19 raised by @tijmen.Added new module
mass_definitions
which more robustly deals with various halo mass definitions, and also includes ability to convert mass functions between different definitions.New set of tutorials: quickstart/first plot and a broad overview.
Added shortcuts to
halo_overdensity_mean
andhalo_overdensity_crit
Added
normalized_filter
toMassFunction
class to make it easier to use a filter with a pre-normalized power spectrum.Added
.clone()
method to allFramework
classes, which gives ability to clone the current instance (while also changing some parameters).
Bugfixes
When using camb for the transfer function, some cosmologies would lead to a segfault (i.e. when Ob0 or Tcmb0 are not set explicitly). This now raises a helpful error.
Fixed bug in ordering of iterator in
get_hmf
.
Internals
Removed logging, which was redundant.
Moved from nose to pytest
Significant overhaul of package structure to more modularised form.
Added flake8 checks and black formatting
Moved away from git-flow as it is not easy to use with GitHub.
v3.0.8 [26th March 2020]¶
Bugfixes
Some documentation and CI fixes.
Enhancement
Added
get_dependencies
method to _Framework, to enable finding all parameters that a quantity depends on.Growth factor speed-up (thanks to @jlashner)
Added use_splined_growth argument (thanks to @jlashner)
v3.0.7 [29th April 2019]¶
Bugfixes
Fixed bugs in WDM models that remained from previous versions.
Fixed bug in SharpK Ellipsoid filter following previous API change.
v3.0.5 [23rd April 2019]¶
Bugfixes
Fixed naming of WDM
alter_dndm
toalter_model
to be consistent.Fixed bug which made CAMB transfer function not pickleable or copyable. NOTE: the fix is not perfect – if you provide a custom CAMBparams class
to
transfer_params
, it is not certain that results will be consistent, as a few of the attributes of this object are not pickleable, and thus are ignored.
v3.0.3 [1st Dec 2017]¶
Bugfixes
Fixed usage of deprecated MsolMass in wdm
Fixed Bhattachrya fitting function (thanks to Benedikt Diemer!)
Fixed typo in Watson fitting function (thanks to Benedikt Diemer!)
Update cosmo test to use new Astropy constants.
Fixed issue with sampling function where zeros in ngtm would yield an error.
v3.0.1 [31st Oct 2017]¶
Enhancement
Normalised all <>_model properties to be actual classes, rather than either class or string.
Added consistent checking of dictionaries for <>_params parameters.
v3.0.0 [7th June 2017]¶
Features
Now provides compatibility with Python 3.x. Support for 2.x will be removed in hmf v3.1 (whenever that comes).
Complete overhaul of the caching system. Should be invisible to the user, but streamlines writing of framework code considerably. Removes required manual specification of dependencies between quantities, and adds ability to specify parameter kinds (model, param, res, option, switch).
Bugfixes
Fixed bug in Caroll1992 GrowthFactor class which affected high-redshift growth factors (thanks to Olmo Piana).
Fixed astropy dependency to be >= 1.1
Fixed bug where Takahashi parameters were always passed through regardess of
takahashi
setting.Fixed small bug where the functional.get_label method returned differently ordered parameters because of dicts.
Note that the fitting subpackage is temporarily unsupported and I discourage its use for the time being.
Enhancement
Completely removes dependence on archaic pycamb package. Now supports natively supplied python interface to CAMB. Install camb with
pip install --egg camb
. This means that much more modern versions of CAMB can be used.Many new tests, to bring total coverage up to >80%, and continuous testing on Python 2.7, 3.5 and 3.6
v2.0.5 [12th January 2017]¶
Bugfixes
Fixed bug in GrowthFactor which gave ripples in functions of z when a coarse grid was used. Thanks to @mirochaj and @thomasguillet!
Enhancments
Streamlined the caching framework a bit (removing cruft)
Totally removed dependency on the Cache (super)class – caching indexes now inherent to the called class.
More robust parameter information based on introspection.
v2.0.4 [11th November, 2016]¶
Bugfixes
IMPORTANT: Fixed a bug in which updating the cosmology after creation did not update the transfer function.
v2.0.3 [22nd September, 2016]¶
Bugfixes
SharpK filter integrated over incorrect range of k, now fixed.
Enhancments
WDM models now more consistent with MassFunction API.
Better warning in HALOFIT module when derivatives don’t work first time.
v2.0.2 [2nd August, 2016]¶
Features
Added a bunch of information to each hmf_model, indicating simulation parameters from which the fit was derived.
Added
FromArray
transfer model, allowing an array to be passed programmatically for k and T.Added
Carroll1992
growth factor approximation model.
Enhancments
how_big now gives the boxsize required to expect at least one halo above m in 95% of boxes.
Bugfixes
Removed unnecessary multiplication by 1e6 in cosmo.py (thanks @iw381)
IMPORTANT: normalisation now calculated using convergent limits on k, rather than user-supplied values.
IMPORTANT: fixed bug in Bhattacharya fit, which was multiplying by an extra delta_c/sigma.
fixed issue with
nonlinear_mass
raising exception when mass outside given mass range.
v2.0.1 [2nd May, 2016]¶
Bugfixes
Corrects the default sigma_8 and n (spectral index) parameters to be from Planck15 (previously from Planck13), which corresponds to the default cosmology. NOTE: this will change user-code output silently unless sigma_8 and n are explicitly set.
v2.0.0¶
v2.0.0 is a (long overdue) major release with several backward-incompatible changes. There are several major features still to come in v2.1.0, which may again be backward incompatible. Though this is not ideal (ideally backwards-incompatible changes will be restricted to increase in the major version number), this has been driven by time constraints.
Known issues with this version, to be addressed by the next, are that both scripts (hmf and hmf-fit) are buggy and untested. Don’t use these until the next version unless you’re crazy.
Features
New methods on all frameworks to list all parameters, defaults and current values.
New general structure for Frameworks and Components makes for simpler delineation and extensibility
New growth_factor module which adds extensibility to the growth factor calculation
New transfer_models module which separates the transfer models from the general framework
New Component which can alter dn/dm in WDM via ad-hoc adjustment
Added a Prior() abstract base class to the fitting routines
Added a guess() method to fitting routines
Added ll() method to Prior classes for future extendibility
New fit from Ishiyama+2015, Manera+2010 and Pillepich+2009
Enhancments
Removed nz and z2 from MassFunction. They will return in a later version but better.
Improved structure for FittingFunction Component, with
cutmask
property defining valid mass range. NOTE: the default MassFunction is no longer to mask values outside the valid range. In fact, the parametercut_fit
no longer exists. One can achieve the effect by accessing a relevant array as dndm[MassFunction.hmf.cutmask]Renamed some parameters/quantities for more consistency (esp. M –> m)
No longer dependent on cosmolopy, but rather uses Astropy (v1.0+)
mean_dens
nowmean_density0
, as per AstropyAdded exception to catch when dndm has many NaN values in it.
Many more tests
Made the
cosmo
class pickleable by cutting out a method and using it as a function instead.Added normalise() to Transfer class.
Updated fit.py extensively, and provided new example config files
Send arbitrary kwargs to downhill solver
New internal _utils module provides inheritable docstrings
Bugfixes
fixed problem with _gtm method returning nans.
fixed simple bugs in BBKS and BondEfs transfer models.
fixes in _cache module
simple bug when updating sigma_8 fixed.
Made the EnsembleSampler object pickleable by setting
__getstate__
Major bug fix for EH transfer function without BAO wiggles
@parameter properties now return docstrings
v1.8.0 [February 2, 2015]¶
Features
Better WDM models
Added SharpK and SharpKEllipsoid filters and overhauled filter system.
Enhancments
Separated WDM models from main class for extendibility
Enhanced caching to deal with subclassing
Bugfixes
Minor bugfixes
1.7.1 [January 28, 2015]¶
Enhancments
Added warning to docstring of _dlnsdlnm and n_eff for non-physical oscillations.
1.7.0 [October 28, 2014]¶
Features
Very much updated fitting routines, in class structure
Made fitting_functions more flexible and model-like.
Enhancments
Modified get_hmf to be more general
Moved get_hmf and related functions to “functional.py”
1.6.2 [September 16, 2014]¶
Features
New HALOFIT option for original co-oefficients from Smith+03
Enhancments
Better Singleton labelling in get_hmf
Much cleaning of mass function integrations. New separate module for it.
IMPORTANT: Removal of nltm routine altogether, as it is inconsistent.
IMPORTANT: mltm now called rho_ltm, and mgtm called rho_gtm
IMPORTANT: Definition of rho_ltm now assumes all mass is in halos.
Behroozi-specific modifications moved to Behroozi class
New property hmf which is the actual class for mf_fit
Bugfixes
Fixed bug in Behroozi fit which caused an infinite recursion
Tests fixed for new cumulants.
1.6.1 [September 8, 2014]¶
Enhancments
Better get_hmf function
Bugfixes
Fixed “transfer” property
Updates fixed for transfer_fit
Updates fixed for nu
Fixed cache bug where unexecuted branches caused some properties to be misinterpreted
Fixed bug in CAMB transfer options, where defaults would overwrite user-given values (introduced in 1.6.0)
Fixed dependence on transfer_options
Fixed typo in Tinker10 fit at z = 0
1.6.0 [August 19, 2014]¶
Features
New Tinker10 fit (Tinker renamed Tinker08, but Tinker still available)
Enhancments
Completely re-worked caching module to be easier to code and faster.
Better Cosmology class – more input combinations available.
Bugfixes
Fixed all tests.
1.5.0 [May 08, 2014]¶
Features
Introduced _cache module: Extracts all caching logic to a separate module which defines decorators – much simpler coding!
1.4.5 [January 24, 2014]¶
Features
Added get_hmf function to tools.py – easy iteration over models!
Added hmf script which provides cmd-line access to most functionality.
Enhancments
Added Behroozi alias to fits
Changed kmax and k_per_logint back to have
transfer__
prefix.
Bugfixes
Fixed a bug on updating delta_c
Changed default kmax and k_per_logint values a little higher for accuracy.
1.4.4 [January 23, 2014]¶
Features
Added ability to change the default cosmology parameters
Enhancments
Made updating Cosmology simpler.
Bugfixes
Fixed a bug in the Tinker function (log was meant to be log10): - thanks to Sebastian Bocquet for pointing this out!
Fixed a bug in updating n and sigma_8 on their own (introduced in 1.4.0)
Fixed a bug when using a file for the transfer function.
1.4.2 [January 10, 2014]¶
Enhancments
Mocked imports of cosmolopy for setup
Cleaner imports of cosmolopy
1.4.0 [January 10, 2014]¶
Enhancments
Upgraded API once more: - Now Perturbations –> MassFunction
Added transfer.py which handles all k-based quantities
Upgraded docs significantly.
1.3.0 [January 03, 2014]¶
Enhancments
A few more documentation updates (especially tools.py)
Removed new_k_bounds function from tools.py
Added
w
parameter to cosmolopy dictionary incosmo.py
Changed cosmography significantly to use cosmolopy in general
Generally tidied up some of the update mechanisms.
API CHANGE: cosmography.py no longer exists – I’ve chosen to utilise cosmolopy more heavily here.
Added Travis CI usage
Bugfixes
Fixed a pretty bad bug where updating h/H0 would crash the program if only one of omegab/omegac was updated alongside it
Fixed a compatibility issue with older versions of numpy in cumulative functions
1.2.0 [December 5, 2013]¶
Features
Addition of cosmo module, which deals with the cosmological parameters in a cleaner way
Enhancments
Major documentation overhaul – most docstrings are now in Sphinx/numpydoc format
Some tidying up of several functions.
1.1.10 [October 29, 2013]¶
Enhancements - Better updating – checks if update value is actually different. - Now performs a check to see if mass range is inside fit range.
Bugfixes
Fixed bug in mltm property
1.1.85 [October 2, 2013]¶
Enhancments
The normalization of the power spectrum now saved as an attribute
1.1.7 [September 19, 2013]¶
Enhancments
Updated “ST” fit to “SMT” fit to avoid confusion. “ST” is still available for now.
Now uses trapezoid rule for integration as it is faster.
1.1.6 [September 05, 2013]¶
Enhancments
Included an option to use delta_halo as compared to critical rather than mean density (thanks to A. Vikhlinin and anonymous referree)
Bugfixes
Couple of bugfixes for fitting_functions.py
Fixed mass range of Tinker (thanks to J. Tinker and anonymous referee for this)
1.1.5 [September 03, 2013]¶
Enhancments
-Added a whole suite of tests against genmf that actually work
Bugfixes
Fixed bug in mgtm (thanks to J. Mirocha)
Fixed an embarrassing error in Reed07 fitting function
Fixed a bug in which dndlnm and its dependents (ngtm, etc..) were calculated wrong if dndlog10m was called first.
Fixed error in which for some choices of M, the whole extension in ngtm would be NAN and give error
1.1.4 [August 27, 2013]¶
Features
Added ability to change resolution in CAMB from hmf interface (This requires a re-install of pycamb to the newest version on the fork)
1.1.2 [July 02, 2013]¶
Features
Ability to calculate fitting functions to whatever mass you want (BEWARE!!)
1.1.1 [July 02, 2013]¶
Features
Added Eisenstein-Hu fit to the transfer function
Enhancments
Improved docstring for Perturbations class
Bugfixes
Corrections to Watson fitting function from latest update on arXiv (thanks to W. Watson)
IMPORTANT: Fixed units for k and transfer function (Thanks to A. Knebe)
1.1.0 [June 27, 2013]¶
Enhancments
Massive overhaul of structure: Now dependencies are tracked throughout the program, making updates even faster
1.0.9 [June 19, 2013]¶
Bugfixes
Fixed an error with an extra ln(10) in the mass function (quoted as dn/dlnM but actually outputting dn/dlog10M)
1.0.8 [June 19, 2013]¶
Enhancments
Took out log10 from cumulative mass functions
Better cumulative mass function logic
1.0.4 [June 6, 2013]¶
Features
Added Bhattacharya fitting function
Bugfixes
Fixed concatenation of list and dict issue
1.0.1 [May 20, 2013]¶
Enhancments
Added better warnings for non-updated variables passed to update()
Made default cosmology WMAP7
0.9.99 [May 10, 2013]¶
Enhancments
Added warning for k*R limits
Bugfixes
Couple of minor bugfixes
Important Angulo fitting function corrected (arXiv version had a typo).
0.9.95 [April 09, 2013]¶
Features
Added cascading variable changes for optimization
Added the README
Added update() function to simply change parameters using cascading approach
0.9.9 [April 08, 2013]¶
Features
First version in its own package
Added pycamb integration
Enhancments
Removed fitting function from being a class variable
Removed overdensity form being a class variable
0.9.7 [March 18, 2013]¶
Enhancments
Modified set_z() so it only does calculations necessary when z changes
Made calculation of dlnsdlnM in init since it is same for all z
Removed mean density redshift dependence
0.9.5 [March 10, 2013]¶
Features
The class has been in the works for almost a year now, but it currently will calculate a mass function based on any of several fitting functions.