PT biases in v3 #1056

damonge · 2023-04-02T17:55:01Z

The usage of the new PT module would be as follows:

cosmo = ccl.CosmologyVanillaLCDM()

# Initialize a perturbation theory calculator
ptc = ccl.nl_pt.EulerianPTCalculator(with_NC=True, cosmo=cosmo)

# If you need to update the PT P(k) kernels to a new cosmology:
ptc.update_ingredients(cosmo)

# Now you can calculate biased power spectra, e.g.:
tg = ccl.nl_pt.PTNumberCountsTracer(b1=1.0, b2=0.5)
tm = ccl.nl_pt.PTMatterTracer()
pk_gg = ptc.get_pk2d_biased(tg, tracer2=tg)
pk_gm = ptc.get_pk2d_biased(tg, tracer2=tm)

# You can also ask for specific P(k) templates.
# E.g. this will get you the <delta * s^2> template
pk_d1_s2 = ptc.get_pk2d_template('b1:bs')

coveralls · 2023-04-02T18:09:41Z

Pull Request Test Coverage Report for Build 4595207464

2909 of 2948 (98.68%) changed or added relevant lines in 70 files are covered.
2 unchanged lines in 2 files lost coverage.
Overall coverage increased (+0.03%) to 97.894%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyccl/halos/concentration/concentration_base.py	42	43	97.67%
pyccl/halos/concentration/constant.py	18	19	94.74%
pyccl/halos/concentration/diemer15.py	42	43	97.67%
pyccl/halos/concentration/ishiyama21.py	131	132	99.24%
pyccl/halos/hbias/bhattacharya11.py	24	25	96.0%
pyccl/halos/hbias/sheth01.py	25	26	96.15%
pyccl/halos/hmfunc/angulo12.py	21	22	95.45%
pyccl/halos/hmfunc/jenkins01.py	20	21	95.24%
pyccl/halos/hmfunc/press74.py	20	21	95.24%
pyccl/base/caching.py	161	163	98.77%

Files with Coverage Reduction	New Missed Lines	%
pyccl/core.py	1	95.74%
pyccl/covariances.py	1	98.59%

Totals
Change from base Build 4577061095:	0.03%
Covered Lines:	6042
Relevant Lines:	6172

💛 - Coveralls

anicola · 2023-04-03T11:53:18Z

Thanks a lot @damonge! I haven't looked much at the IAs as I am not so familiar with it, but pgg ang pgm look good to me! Just to check - this assumes that stochasticity will be handled outside CCL, right?

pyccl/nl_pt/ept.py

pyccl/nl_pt/__init__.py

nikfilippas

A quick comment.

pyccl/nl_pt/power_deprecated.py

damonge · 2023-04-03T15:17:35Z

@anicola Good point. Yes, indeed, I've added a note about stochastic bias in the docstring.

nikfilippas

'Some' comments mainly regarding naming, efficiency, and consistency.

pyccl/nl_pt/ept.py

pyccl/tests/test_ept_power.py

pyccl/nl_pt/tracers.py

pyccl/nl_pt/ept.py

damonge · 2023-04-06T14:19:39Z

Back to you @nikfilippas

nikfilippas

A final comment, and we have the unresolved ones remaining.

pyccl/nl_pt/ept.py

pyccl/tests/test_ept_power.py

damonge · 2023-04-16T10:21:11Z

All done, back to you @nikfilippas

nikfilippas

There are 4 uncovered lines. Do you think we can cover the last 3 of them? I'm approving either way.

damonge · 2023-04-16T14:08:25Z

All should be covered now.

nikfilippas · 2023-04-16T14:46:38Z

@damonge you do the honours

* 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 <[email protected]> * RTD: Removed The Docs --------- Co-authored-by: David Alonso <[email protected]> * flaked --------- Co-authored-by: Nick Koukoufilippas <[email protected]> * Pk2D and Tk3D in v3 (#1048) * tk3d and pk2d in v3 --------- Co-authored-by: Nick Koukoufilippas <[email protected]> * 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 <[email protected]> * 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 <[email protected]>

damonge added 5 commits April 2, 2023 16:53

refactored, not tested

54265a4

documented, 1/2 factors included

5852687

deprecation warnings

fca6bcb

benchmarks migrated

f71318c

deprecated tests

169bd9f

damonge added 5 commits April 2, 2023 23:03

mostly tested

5818524

fully tested

0cee9d1

rearanged tests

40643f2

objectify

e4a4c50

typo in benchmarks

857f942

damonge marked this pull request as ready for review April 3, 2023 10:01

damonge requested review from tilmantroester and anicola April 3, 2023 10:01

damonge changed the base branch from master to v3_wip April 3, 2023 10:02

tilmantroester reviewed Apr 3, 2023

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v2.final #1038

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nikfilippas linked an issue Apr 9, 2023 that may be closed by this pull request

sub_lowk option for P_II #831

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damonge added 2 commits April 16, 2023 11:11

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damonge merged commit d5ed640 into v3_wip Apr 16, 2023

damonge deleted the nl_pt_v3 branch April 16, 2023 15:32

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PT biases in v3 #1056

PT biases in v3 #1056

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PT biases in v3 #1056

PT biases in v3 #1056

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