Halos v3 #1043

nikfilippas · 2023-03-21T23:44:01Z

This PR modifies the halos/ sub-package in line with the v3 mind map.

Also fixes the badges on README.md from this

to this

Other changes:

Deprecate attribute normprof (only implemented above) in favor of arbitrary profile normalization functions.
~~@templatemethod decorator for template methods in HaloProfile which do not pass the implementation checks.~~
~~@abstractlinkedmethod decorator for linked abstract methods in HaloProfile, MassFunc, HaloBias, Concentration.~~
Directly callable HMIngredients: MassFunc, HaloBias, Concentration & deprecate getter methods.
Introduce CCLNamedClass for particular subclasses implementing models with names.
Extend from_name functionality for CCLNamedClasses with create_instance so that the object is directly constructed.
Option to initialize MassDef from any string, and pass strings to all HMIngredients: MassFunc, HaloBias, Concentration.
Option for developers to disable relaxing of mass_def_strict if no universal model implementation exists (e.g. MassFuncBocquet16 which so far raised with an unhelpful msg).
Unlock all CCLObjects until v3 because it was a breaking change we originally made.

…alculator

nikfilippas · 2023-04-05T19:00:24Z

To update the thread, if a number is returned from _normalization(), the current implementation does not integrate over mass; it just returns that number. David now to add a shortcut in the normalization of the HOD profile.

benchmarks/test_cib.py

This reverts commit 43591ce.

damonge

OK, for now just one comment on the new stuff you've introduced. I'll get back to normprof now

pyccl/base/schema.py

damonge

OK, one last push

pyccl/halos/halo_model_base.py

pyccl/halos/profiles/profile_base.py

pyccl/halos/halo_model.py

pyccl/halos/pk_2pt.py

pyccl/halos/pk_4pt.py

…ation

nikfilippas · 2023-04-11T21:44:25Z

@damonge unless there are more comments, work towards this PR is complete, but for the tests to pass we #1033 merged to master.

damonge · 2023-04-17T13:24:39Z

I think we are close, but I am strongly against the changes implemented in commits 4da0f8f to 1f923a7. Revert those changes and simply do not enforce mass functions and bias functions to be parametrised in terms of sigma. At that point we're basically done.

…mplate methods

nikfilippas · 2023-04-17T14:37:19Z

Just to update the thread, we took a part of this discussion to Slack and agreed that the proposed code would introduce a lot of complexity for little benefit. However, I stand by the argument that all template methods in HaloProfile have to be declared in the base class, to assist developers in understanding what can and cannot be implemented.

@damonge I did a great deal of simplification, removing all of the added lines (there are no net extra lines of code now).

damonge

Something must have gone wrong when porting the __eq_attrs__. One other comment too. Then we're done.

pyccl/halos/massdef.py

pyccl/halos/profiles/einasto.py

pyccl/halos/profiles/cib_shang12.py

pyccl/halos/profiles/gaussian.py

pyccl/halos/profiles/hernquist.py

pyccl/halos/profiles/nfw.py

pyccl/halos/profiles/powerlaw.py

pyccl/halos/profiles/pressure_gnfw.py

pyccl/halos/profiles/profile_base.py

damonge

Happy to merge if tests pass.

* first commit * enclose classmethods in the class * brought in minor improvements to halos * 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 13 commits March 21, 2023 04:30

ported changes in halos/profiles

c510aca

Merge branch 'v3_wip' into halos_v3

5b84d70

Merge branch 'v3_wip' into halos_v3

ad286d8

changes from star in halos/ (no tests)

2bb015c

Merge branch 'v3_wip' into halos_v3

af2dcb0

refactor concentration, mass_function, halo_bias; improvements in HMC…

13c1206

…alculator

HaloProfile subclasses & HaloProfile.normprof attribute

5d67de8

simplify imports

d8b0d85

remove HaloProfile.name

9f4dde5

cleaned up pk_Npt

6408590

add extrap_pk argument

5896fa4

FFTLogParams class instead of dictionary in HaloProfile

99dc8eb

simplified code

fe3a6a3

This was linked to issues Mar 27, 2023

Why do we use normprof? #985

Closed

Inconsistent use of cosmo in HMCalculator, MassFunc, HaloBias #884

Closed

nikfilippas added 14 commits March 29, 2023 22:54

removed mass_def from HMIngredients; comprehensive code review 1

1205e95

re-implementation, bugfixes, tests

1b7f385

c_m_relation >> concentration; code improvements; A_SPLINE_MAX in Python

fdefd88

HMIngredients initializers - no repeated code

6a45e72

rogue file

f59089d

Merge branch 'v3_wip' into halos_v3

551c173

patch for new changes

55817de

updated Build Status badge website

043bfaa

fix websites

f96aab2

added a DOI badge & links

4d27c79

added nonbreaking space

a1b41ac

removed extra space

a668101

FancyRepr out of CCLObject to simplify

c6a30c5

Merge branch 'v3_wip' into halos_v3

b71a210

nikfilippas marked this pull request as ready for review March 30, 2023 18:07

fix typo

598c253

damonge requested changes Apr 5, 2023

View reviewed changes

benchmarks/test_cib.py Outdated Show resolved Hide resolved

nikfilippas added 3 commits April 6, 2023 06:22

brought in from docs_v3: initialize mass_def from any string (e.g. 400c)

4eb9a18

Merge branch 'halos_v3' of https://github.com/LSSTDESC/CCL into halos_v3

db75d30

Revert "renamed HMCalculator --> HaloModel"

590cc0e

This reverts commit 43591ce.

damonge reviewed Apr 6, 2023

View reviewed changes

pyccl/base/schema.py Outdated Show resolved Hide resolved

damonge requested changes Apr 6, 2023

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nikfilippas added 7 commits April 6, 2023 22:11

counterterms func inside of 4pt func

208f8c1

replace deprecated abstractproperty

096cfbd

abstract linked methods for HaloProfile, MassFunc, HaloBias, Concentr…

4da0f8f

…ation

fully working implementation

1f923a7

renamed lM --> log10M etc.

8e77d88

minor cosmetic fix

b471c24

Merge branch 'v3_wip' into halos_v3

adddaeb

Merge branch 'v3_wip' into halos_v3

666134a

nikfilippas added 2 commits April 17, 2023 17:30

alternative way to include linked abstract methods and declare the te…

a7da728

…mplate methods

reorder

02d3630

even simpler

d43b2f3

damonge requested changes Apr 17, 2023

View reviewed changes

nikfilippas added 2 commits April 17, 2023 20:09

bring back eq_attrs

b79f658

r -> r_t

f8f2a66

damonge approved these changes Apr 17, 2023

View reviewed changes

Additional halos features (#1068)

3fad2e1

* first commit * enclose classmethods in the class * brought in minor improvements to halos * coverage

nikfilippas merged commit e93b317 into v3_wip Apr 17, 2023

nikfilippas deleted the halos_v3 branch April 17, 2023 18:09

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Halos v3 #1043

Halos v3 #1043

nikfilippas commented Mar 21, 2023 •

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Halos v3 #1043

Halos v3 #1043

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