Additional halos features by nikfilippas · Pull Request #1068 · LSSTDESC/CCL

nikfilippas · 2023-04-17T15:46:30Z

This is a rebased copy of 1065.

I brought the extra stuff from 1064 to here, so that we keep the other PR as clean as possible, and this PR also defines a library-level control to turn on/off the custom __eq__ methods, just as we had with the __repr__ methods.

Old Description

The main change this PR introduces, is to make mass_def an optional argument in HMCalculator because if mass_function and halo_bias are passed as instances (rather than str) we can just use their own mass_def. We can do that because some lines below we enforce that all mass_defs are equal.
So an HMCalculator can be instantiated in one of the following ways:

## From strings
# hmc way 1
hmc = ccl.halos.HMCalculator(mass_function="Tinker10", halo_bias="Tinker10", mass_def="200c")


## From instances
# Initialize instances
# instances way 1
mdef = ccl.halos.MassDef200c()
hmf = ccl.halos.MassFunctionTinker10(mass_def=mdef)  # mass_def can also be a string
hbf = ccl.halos.HaloBiasTinker10(mass_def=mdef)      # mass_def can also be a string

# instances way 2
hmf = ccl.halos.MassFunc.from_name("Tinker10")(mass_def="200c")  # mass_def can also be an instance
hbf = ccl.halos.HaloBias.from_name("Tinker10")(mass_def="200c")  # mass_def can also be an instance

# instances way 3
hmf = ccl.halos.MassFunc.create_instance("Tinker10", mass_def="200c")  # mass_def can also be an instance
hbf = ccl.halos.HaloBias.create_instance("Tinker10", mass_def="200c")  # mass_def can also be an instance

# hmc way 2
hmc = ccl.halos.HMCalculator(mass_function=hmf, halo_bias=hbf, mass_def=mdef)

# hmc way 3
hmc = ccl.halos.HMCalculator(mass_function=hmf, halo_bias=hbf)

damonge

Small things

damonge · 2023-04-17T16:57:11Z

pyccl/halos/massdef.py

-            raise ValueError(f"Unknown Delta type {Delta}.")
+        if isinstance(Delta, str):
+            if Delta.isdigit():
+                Delta = int(Delta)


Why are you allowing for people to pass numbers as strings?

It's mainly for our convenience, so that a mass definition can be insantiated using MassDef.from_name("300c").
It takes less lines of code to convert a string to digit than splitting up the string, checking if it can be converted to digit, and then converting it to one.
Internally "300c" becomes 2 strings: "300" and "c". So doesn't hurt to make this feature public.

Unfortunately there is no string method that checks for floats, only for integers.
So MassDef.from_name("350.4c") won't work. I can make it work but it will be a couple more lines for very little benefit I reckon.

damonge · 2023-04-17T16:59:22Z

pyccl/halos/halo_model.py

+            if isinstance(mass_function, str) or isinstance(halo_bias, str):
+                raise ValueError("Need to provide mass_def if mass_function "
+                                 "or halo_bias are str.")
+            self.mass_def = mass_function.mass_def


I haven't seen a test for this, right?

added tests

damonge

merge if tests pass

* ported changes in halos/profiles * changes from star in halos/ (no tests) * refactor concentration, mass_function, halo_bias; improvements in HMCalculator * HaloProfile subclasses & HaloProfile.normprof attribute * simplify imports * remove HaloProfile.name * cleaned up pk_Npt * add extrap_pk argument * FFTLogParams class instead of dictionary in HaloProfile * simplified code * removed mass_def from HMIngredients; comprehensive code review 1 * re-implementation, bugfixes, tests * c_m_relation >> concentration; code improvements; A_SPLINE_MAX in Python * HMIngredients initializers - no repeated code * rogue file * patch for new changes * updated Build Status badge website * fix websites * added a DOI badge & links * added nonbreaking space * removed extra space * FancyRepr out of CCLObject to simplify * update tests to match changes * coverage * simple test for tkkssc * more tests for tkkssc * addressed comments 1 * addressed comments 2: mass_def defaults are name strings etc. * deprecate Gaussian & PowerLaw profiles * bugfix in master: sometimes mass_def_strict=False fails unexpectedly * typo * addressed comments * New feature: Arbitrary function for profile normalization * gain efficiency * comments + deprecate k_min from HMCalculator * renamed initialize_from_input --> create_instance * brought in CCLNamedClass from docs_v3 * brought in from docs_v3: directly callable HMIngredients * prep for Davids input * renamed HMCalculator --> HaloModel * fix typo * brought in from docs_v3: initialize mass_def from any string (e.g. 400c) * Revert "renamed HMCalculator --> HaloModel" This reverts commit 43591ce. * counterterms func inside of 4pt func * replace deprecated abstractproperty * abstract linked methods for HaloProfile, MassFunc, HaloBias, Concentration * fully working implementation * renamed lM --> log10M etc. * minor cosmetic fix * alternative way to include linked abstract methods and declare the template methods * reorder * even simpler * bring back eq_attrs * r -> r_t * Additional halos features (#1068) * first commit * enclose classmethods in the class * brought in minor improvements to halos * coverage

* ported changes in halos/profiles * changes from star in halos/ (no tests) * refactor concentration, mass_function, halo_bias; improvements in HMCalculator * HaloProfile subclasses & HaloProfile.normprof attribute * simplify imports * remove HaloProfile.name * cleaned up pk_Npt * add extrap_pk argument * FFTLogParams class instead of dictionary in HaloProfile * simplified code * removed mass_def from HMIngredients; comprehensive code review 1 * re-implementation, bugfixes, tests * c_m_relation >> concentration; code improvements; A_SPLINE_MAX in Python * HMIngredients initializers - no repeated code * rogue file * patch for new changes * updated Build Status badge website * fix websites * added a DOI badge & links * added nonbreaking space * removed extra space * FancyRepr out of CCLObject to simplify * update tests to match changes * coverage * simple test for tkkssc * more tests for tkkssc * addressed comments 1 * addressed comments 2: mass_def defaults are name strings etc. * deprecate Gaussian & PowerLaw profiles * bugfix in master: sometimes mass_def_strict=False fails unexpectedly * typo * addressed comments * New feature: Arbitrary function for profile normalization * gain efficiency * comments + deprecate k_min from HMCalculator * renamed initialize_from_input --> create_instance * brought in CCLNamedClass from docs_v3 * brought in from docs_v3: directly callable HMIngredients * prep for Davids input * renamed HMCalculator --> HaloModel * fix typo * brought in from docs_v3: initialize mass_def from any string (e.g. 400c) * Revert "renamed HMCalculator --> HaloModel" This reverts commit 43591ce. * counterterms func inside of 4pt func * replace deprecated abstractproperty * abstract linked methods for HaloProfile, MassFunc, HaloBias, Concentration * fully working implementation * renamed lM --> log10M etc. * minor cosmetic fix * first commit * alternative way to include linked abstract methods and declare the template methods * reorder * even simpler * enclose classmethods in the class * brought in minor improvements to halos * clone of 1064 * bring back eq_attrs * r -> r_t * Additional halos features (#1068) * first commit * enclose classmethods in the class * brought in minor improvements to halos * coverage * removed MassConcentration * full implementation (v3 only) * comments * single-liner * coverage

* halo profiles in their own directory * concentrations in their own directory * mass functions & halo biases in their own directory * moved CIB stuff to profiles & 2pts * split halo model into 1/2/4-pt * fix imports * remove empty module * fix typo * Baryons in v3 (#1039) * Added new baryons module that will deprecate old BCM * Tracers v3 (#1040) * Tracers in V3 * Background, boltzmann, and cls in v3 (#1041) * Background, boltzmann and cls in v3 * Covariances in v3 (#1046) * Covariances in V3 * Correlations v3 (#1042) * Correlations in v3 * split base.py and restructured into its own dir to simplify * Neutrinos, parameters, power in v3 (#1047) * done * Make `T_ncdm` a cosmological parameter + (v3) (#1049) * first commit * rename TNCDM to T_ncdm but preserve API * T_CMB directly into cosmo struct * Omega_g in ccl_parameters_create; no split between C/Python * physical_constants.T_CMB doesn't mutate anymore! * force mutate T_CMB in benchmarks * define defaults on instantiation just in case constants mutate * A_s & sigma8: don't play with numbers * simplify * remove leftover mallocs * temporarily preserve API for CCLv3 * Unfreeze option for `physical_constants` (#1050) * first commit * update rtd * addressed comments 1 * Remove `T_CMB` and `T_ncdm` as constants (reloaded) (#1058) * first commit * OmNuh2 fix * addressed comments * keep only massive * first step * temp commit * debug neutrinos & deprecate Omnuh2 * ccl_omega_x & ccl_Omeganuh2 consistency --------- Co-authored-by: David Alonso <dam.phys@gmail.com> * RTD: Removed The Docs --------- Co-authored-by: David Alonso <dam.phys@gmail.com> * flaked --------- Co-authored-by: Nick Koukoufilippas <nikfilippas@gmail.com> * Pk2D and Tk3D in v3 (#1048) * tk3d and pk2d in v3 --------- Co-authored-by: Nick Koukoufilippas <nikfilippas@gmail.com> * PT biases in v3 (#1056) * New PT bias framework * Halos v3 (#1043) * ported changes in halos/profiles * changes from star in halos/ (no tests) * refactor concentration, mass_function, halo_bias; improvements in HMCalculator * HaloProfile subclasses & HaloProfile.normprof attribute * simplify imports * remove HaloProfile.name * cleaned up pk_Npt * add extrap_pk argument * FFTLogParams class instead of dictionary in HaloProfile * simplified code * removed mass_def from HMIngredients; comprehensive code review 1 * re-implementation, bugfixes, tests * c_m_relation >> concentration; code improvements; A_SPLINE_MAX in Python * HMIngredients initializers - no repeated code * rogue file * patch for new changes * updated Build Status badge website * fix websites * added a DOI badge & links * added nonbreaking space * removed extra space * FancyRepr out of CCLObject to simplify * update tests to match changes * coverage * simple test for tkkssc * more tests for tkkssc * addressed comments 1 * addressed comments 2: mass_def defaults are name strings etc. * deprecate Gaussian & PowerLaw profiles * bugfix in master: sometimes mass_def_strict=False fails unexpectedly * typo * addressed comments * New feature: Arbitrary function for profile normalization * gain efficiency * comments + deprecate k_min from HMCalculator * renamed initialize_from_input --> create_instance * brought in CCLNamedClass from docs_v3 * brought in from docs_v3: directly callable HMIngredients * prep for Davids input * renamed HMCalculator --> HaloModel * fix typo * brought in from docs_v3: initialize mass_def from any string (e.g. 400c) * Revert "renamed HMCalculator --> HaloModel" This reverts commit 43591ce. * counterterms func inside of 4pt func * replace deprecated abstractproperty * abstract linked methods for HaloProfile, MassFunc, HaloBias, Concentration * fully working implementation * renamed lM --> log10M etc. * minor cosmetic fix * alternative way to include linked abstract methods and declare the template methods * reorder * even simpler * bring back eq_attrs * r -> r_t * Additional halos features (#1068) * first commit * enclose classmethods in the class * brought in minor improvements to halos * coverage * Tests v3 (#1059) * ported changes in halos/profiles * changes from star in halos/ (no tests) * refactor concentration, mass_function, halo_bias; improvements in HMCalculator * HaloProfile subclasses & HaloProfile.normprof attribute * simplify imports * remove HaloProfile.name * cleaned up pk_Npt * add extrap_pk argument * FFTLogParams class instead of dictionary in HaloProfile * simplified code * removed mass_def from HMIngredients; comprehensive code review 1 * re-implementation, bugfixes, tests * c_m_relation >> concentration; code improvements; A_SPLINE_MAX in Python * HMIngredients initializers - no repeated code * rogue file * patch for new changes * updated Build Status badge website * fix websites * added a DOI badge & links * added nonbreaking space * removed extra space * FancyRepr out of CCLObject to simplify * update tests to match changes * coverage * simple test for tkkssc * more tests for tkkssc * addressed comments 1 * addressed comments 2: mass_def defaults are name strings etc. * deprecate Gaussian & PowerLaw profiles * remove all warnings in testing * use pytest as per docs instead of numpy.testing and pyutils.assert_warns * bugfix in master: sometimes mass_def_strict=False fails unexpectedly * typo * addressed comments * New feature: Arbitrary function for profile normalization * gain efficiency * comments + deprecate k_min from HMCalculator * renamed initialize_from_input --> create_instance * brought in CCLNamedClass from docs_v3 * brought in from docs_v3: directly callable HMIngredients * prep for Davids input * renamed HMCalculator --> HaloModel * fix typo * brought in from docs_v3: initialize mass_def from any string (e.g. 400c) * Revert "renamed HMCalculator --> HaloModel" This reverts commit 43591ce. * comments * comments * shortcut for __eq__ methods * Eq. for EulerianPT calculator (#1073) * __eq_attrs__ for nl_pt * No normprof (#1072) * extricated normprof * Cosmology v3 (#1071) * rename core --> Cosmology * renamed core --> cosmology in docs/imports except docstrings * cosmology v2 * first pass * neutrinosneutrinosneutrinos * simplified * yamlyamlyaml * fully fix neutrino mayhem * new arg names in tests * comments * comments on comments on comments * removed tests * no warn --------- Co-authored-by: David Alonso <dam.phys@gmail.com> * avoid warning due to zeros (#1076) * Fix halo inconsistencies v3 (#1069) * ported changes in halos/profiles * changes from star in halos/ (no tests) * refactor concentration, mass_function, halo_bias; improvements in HMCalculator * HaloProfile subclasses & HaloProfile.normprof attribute * simplify imports * remove HaloProfile.name * cleaned up pk_Npt * add extrap_pk argument * FFTLogParams class instead of dictionary in HaloProfile * simplified code * removed mass_def from HMIngredients; comprehensive code review 1 * re-implementation, bugfixes, tests * c_m_relation >> concentration; code improvements; A_SPLINE_MAX in Python * HMIngredients initializers - no repeated code * rogue file * patch for new changes * updated Build Status badge website * fix websites * added a DOI badge & links * added nonbreaking space * removed extra space * FancyRepr out of CCLObject to simplify * update tests to match changes * coverage * simple test for tkkssc * more tests for tkkssc * addressed comments 1 * addressed comments 2: mass_def defaults are name strings etc. * deprecate Gaussian & PowerLaw profiles * bugfix in master: sometimes mass_def_strict=False fails unexpectedly * typo * addressed comments * New feature: Arbitrary function for profile normalization * gain efficiency * comments + deprecate k_min from HMCalculator * renamed initialize_from_input --> create_instance * brought in CCLNamedClass from docs_v3 * brought in from docs_v3: directly callable HMIngredients * prep for Davids input * renamed HMCalculator --> HaloModel * fix typo * brought in from docs_v3: initialize mass_def from any string (e.g. 400c) * Revert "renamed HMCalculator --> HaloModel" This reverts commit 43591ce. * counterterms func inside of 4pt func * replace deprecated abstractproperty * abstract linked methods for HaloProfile, MassFunc, HaloBias, Concentration * fully working implementation * renamed lM --> log10M etc. * minor cosmetic fix * first commit * alternative way to include linked abstract methods and declare the template methods * reorder * even simpler * enclose classmethods in the class * brought in minor improvements to halos * clone of 1064 * bring back eq_attrs * r -> r_t * Additional halos features (#1068) * first commit * enclose classmethods in the class * brought in minor improvements to halos * coverage * removed MassConcentration * full implementation (v3 only) * comments * single-liner * coverage * Final checklist v3 (#1075) * imports * homogenize all imports as per PEP8 and the Python Import System * homogenize all imports as per PEP8 and the Python Import System * instance checks * all exceptions raised correctly * comments * add aliases * reverted changes and introduced proper enums * Preserve API in v2.final (#1077) * first commit * Einasto mass translator + MassDef concentration API * universal api no-break * comments * MassDef vars * Coverage v3 (#1078) * coverage * comments --------- Co-authored-by: David Alonso <dam.phys@gmail.com>

nikfilippas added 4 commits April 17, 2023 17:05

first commit

1387f02

Merge branch 'halos_v3' into eq_control

55d2991

enclose classmethods in the class

b98dc40

brought in minor improvements to halos

d4c2815

damonge requested changes Apr 17, 2023

View reviewed changes

nikfilippas added 2 commits April 17, 2023 20:16

Merge branch 'halos_v3' into additional_halos_features

e8a7368

coverage

adfced3

damonge approved these changes Apr 17, 2023

View reviewed changes

nikfilippas merged commit 3fad2e1 into halos_v3 Apr 17, 2023

nikfilippas deleted the additional_halos_features branch April 17, 2023 17:46

nikfilippas mentioned this pull request Apr 20, 2023

v2.final #1038

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Additional halos features#1068

Additional halos features#1068
nikfilippas merged 6 commits intohalos_v3from
additional_halos_features

nikfilippas commented Apr 17, 2023

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nikfilippas Apr 17, 2023 •

edited

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nikfilippas commented Apr 17, 2023

Old Description

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