IA profile v3 #1074

damonge · 2023-04-19T17:38:23Z

Ports #922 (by @chrgeorgiou) directly to v3 API

* Added new baryons module that will deprecate old BCM

* Tracers in V3

* Background, boltzmann and cls in v3

* Covariances in V3

* Correlations in v3

* 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 <[email protected]> * RTD: Removed The Docs --------- Co-authored-by: David Alonso <[email protected]> * flaked --------- Co-authored-by: Nick Koukoufilippas <[email protected]>

* tk3d and pk2d in v3 --------- Co-authored-by: Nick Koukoufilippas <[email protected]>

* New PT bias framework

* 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 * 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

* __eq_attrs__ for nl_pt

* extricated normprof

* first commit * Einasto mass translator + MassDef concentration API * universal api no-break * comments * MassDef vars

* coverage * comments

coveralls · 2023-05-04T07:16:23Z

Pull Request Test Coverage Report for Build 4927972783

155 of 163 (95.09%) changed or added relevant lines in 4 files are covered.
2 unchanged lines in 1 file lost coverage.
Overall coverage decreased (-0.03%) to 97.133%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyccl/halos/profiles/ia.py	148	156	94.87%

Files with Coverage Reduction	New Missed Lines	%
pyccl/base/deprecations.py	2	83.84%

Totals
Change from base Build 4927900328:	-0.03%
Covered Lines:	5996
Relevant Lines:	6173

💛 - Coveralls

carlosggarcia

As discussed with @damonge, I have checked all the non-IA changes and they look good to me.

nikfilippas · 2023-05-04T10:26:01Z

I'll chime in before this gets merged just to point out that having flags indicating the NC profiles is probably a bad idea. OOP works with inheritance, so it would be best to define an HOD superclass and then use composition, instead of reinstating flags for everything.
Having flags like that clutters the code, and makes it error prone.
https://stackoverflow.com/questions/41001932/oo-design-inheritance-vs-type-enum-variable
For our needs, composition is a simpler and better solution to the issue we have (allowing an HOD subclass to either represent NC or not represent NC).

It also makes no physical sense to define a NC HOD profile, and then be able to change it to non-NC. A profile is, or is not, NC.

Also, all module names in Python are lowercase by convention.
https://peps.python.org/pep-0008/#package-and-module-names

chrgeorgiou · 2023-05-08T09:49:09Z

Going through the code now, will post my comments here. To start, I see in the tests that the halo model is now called by
cM = ccl.halos.ConcentrationDuffy08(mass_def="200m") and ccl.halos.SatelliteShearHOD(concentration=cM) but ccl.halos.SatelliteShearHOD(cM) throws an error. Is there no way to initialize the class now without keyword arguments?

benchmarks/test_ia_profile.py

chrgeorgiou · 2023-05-08T12:09:31Z

pyccl/halos/profiles/IA.py

+
+    def get_normalization(self, cosmo, a, hmc):
+        """Returns the normalization of this profile, which is the
+        mean galaxy number density.


Currently testing this normalization but this seems to not be doing the right thing. Also, in the _get_prefactor method in my PR the normalization is 1/n_gal.

Here it's n_gal (the galaxy number density).

Okay, I have run some more tests and this does what it should do, but now the user has to explicitly request the normalization of the profiles (which is the correct thing to do). I also noticed this will be the default option in v3, correct?

damonge · 2023-05-08T22:00:36Z

@chrgeorgiou yep, indeed. In v3 we introduced a star operator to force users to pass some keyword-only arguments (this is to prevent some functions doing the wrong thing silently only because users passed arguments in the wrong order - we realised there were many instances where this could happen).

Your IA profile is the first fully v3 piece of code!

nikfilippas and others added 30 commits March 20, 2023 16:43

halo profiles in their own directory

87c8639

Merge branch 'master' into v3_wip

9474b15

concentrations in their own directory

b8bb8e9

mass functions & halo biases in their own directory

c40cf0c

moved CIB stuff to profiles & 2pts

4da043f

split halo model into 1/2/4-pt

ee5e535

fix imports

8c20b40

Merge branch 'v3_wip' of https://github.com/LSSTDESC/CCL into v3_wip

fa9e215

remove empty module

8f29fa2

fix typo

8df3d79

Baryons in v3 (#1039)

388629a

* Added new baryons module that will deprecate old BCM

Tracers v3 (#1040)

ef815c4

* Tracers in V3

Merge branch 'master' into v3_wip

4162fed

Background, boltzmann, and cls in v3 (#1041)

909695d

* Background, boltzmann and cls in v3

Covariances in v3 (#1046)

7772dd6

* Covariances in V3

Correlations v3 (#1042)

f1c1546

* Correlations in v3

split base.py and restructured into its own dir to simplify

41b92dd

Pk2D and Tk3D in v3 (#1048)

2c9039a

* tk3d and pk2d in v3 --------- Co-authored-by: Nick Koukoufilippas <[email protected]>

PT biases in v3 (#1056)

d5ed640

* New PT bias framework

Merge branch 'master' into v3_wip

26fc035

shortcut for __eq__ methods

931101a

Eq. for EulerianPT calculator (#1073)

fa4b977

* __eq_attrs__ for nl_pt

No normprof (#1072)

27c6cc9

* extricated normprof

porting

0c3f998

implemented but tests aren't passing

193d69f

tested

ac58f3c

fixed test

50730f6

nikfilippas added 2 commits April 22, 2023 13:05

Preserve API in v2.final (#1077)

26c2bd5

* first commit * Einasto mass translator + MassDef concentration API * universal api no-break * comments * MassDef vars

Coverage v3 (#1078)

9d92f94

* coverage * comments

Base automatically changed from v3_wip to master May 3, 2023 08:01

damonge changed the base branch from master to v3_wip May 3, 2023 10:30

merged v3_wip

4d03d04

damonge changed the base branch from v3_wip to master May 3, 2023 10:39

damonge added 4 commits May 3, 2023 11:43

merged master

78e97dc

is_number_counts back

7983d51

fixed tests

cf6d5e6

fixed benchmark

9e3475e

damonge added 2 commits May 4, 2023 08:24

removed a few warnings in tests

8303a1b

increased coverage

1bbe156

carlosggarcia approved these changes May 4, 2023

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chrgeorgiou reviewed May 8, 2023

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chrgeorgiou reviewed May 8, 2023

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damonge and others added 4 commits May 8, 2023 23:01

lowercase

48e1064

lowercase

2fe53ba

Updated benchmark code to v3.

91f7d04

Merge remote-tracking branch 'origin/ia_profile' into ia_profile

f48b65b

chrgeorgiou approved these changes May 9, 2023

View reviewed changes

Merge branch 'master' into ia_profile

4529cea

damonge merged commit 0264d66 into master May 9, 2023

damonge deleted the ia_profile branch May 9, 2023 16:31

damonge mentioned this pull request May 9, 2023

IA halo model #922

Closed

nikfilippas restored the ia_profile branch May 10, 2023 11:43

nikfilippas deleted the ia_profile branch May 10, 2023 11:44

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IA profile v3 #1074

IA profile v3 #1074

damonge commented Apr 19, 2023

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damonge commented May 8, 2023

IA profile v3 #1074

IA profile v3 #1074

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damonge commented Apr 19, 2023

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