Unmerged updates for stacking and auto spectrum analyses - #16

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sjforeman wants to merge 102 commits into

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Commits on Sep 29, 2021

fix: correct M_10 definition and change defaults to use new templates
jrs65
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9be4509
feat(models): add ability for sampler to run in a transformed basis
jrs65
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f5036a1
refactor: tidy up class constructors to avoid repetition
jrs65
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61799cf
fix: switch default params for new templates
jrs65
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5af9cfa
feat: option to explicitly symmetrize templates
jrs65
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640d9c9
feat(signal): option to reverse templates
jrs65
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aa03d86
feat(models): add option to effectively reverse the data
jrs65
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c2148eb
feat(signal,models): add some useful debug logging
jrs65
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08662c7
fix(mcmc): broken slicing with single polarisation fits
jrs65
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45fcfcf
feat(mcmc): add `flag_ind` option to manually exclude data points
jrs65
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ab54a0e
feat(models): transform to FoG+/FoG- basis when sampling
jrs65
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37ae7eb

Commits on Dec 20, 2024

style: black
sjforeman
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649017b
refactor: fix ruff warnings
sjforeman
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36aaf0a
feat: add code for power spectrum containers and fits
sjforeman
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eab14af
fix(SignalTemplate): fix to work with updated utils routines
sjforeman
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c4e72f4
feat: add ability to have models starting from 2d power spectra
sjforeman
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1698d7e
feat(models, signal): add FoG-kernel power spectrum model
sjforeman
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a59fe07
fix(SignalTemplateFoG): fix typo in weights for FoG scale calulation
sjforeman
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5b57235
fix(AutoSignalTemplate2DFoG): fix error in variances for scale calculation
sjforeman
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8be758e
docs(SignalTemplateFoG): add comments about effective FoG scale
sjforeman
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764addb

Commits on Jun 18, 2025

feat(RunMCMC): add config property for data_2d

albin
authored and
sjforeman
committed
7c20776
fix(AutoSignalTemplate2D): set default nbins = 7

albin
authored and
sjforeman
committed
e99181d
feat(load_from_ps2Dfiles): modify to load templates based on new filename

albin
authored and
sjforeman
committed
240ebc8
fix(multiply_pre_noncomp): calculate the conversion factor connecting tau and k_parallel

albin
authored and
sjforeman
committed
15b737d
feat(average_data): modify the variance calculation when we have single mock

albin
authored and
sjforeman
committed
e60578f
refactor(AutoSignalTemplate2D): change print to logger.debug
sjforeman
committed
c4a706d
refactor(AutoSignalTemplate2DFoG): use cora definitions of nu21, c
sjforeman
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1a3609b
refactor(average_data): remove commented line
sjforeman
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d848c4a
fix: update power spectrum container/dataset/axis names
sjforeman
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7bd5f25
fix(containers): redefine datasets in Mock containers
sjforeman
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14efcd1
fix(mcmc, utils): update for PowerSpectrum pol labels
sjforeman
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03625d3
fix(average_data): set axes and k datasets correctly
sjforeman
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10190e5
feat: add force_real option
sjforeman
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97bfeeb
fix(average_data): propagate mask and neff for 2d power spectrum
sjforeman
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81f7c3d
fix(models, signal): fix docstring escape sequence errors
sjforeman
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157748a
feat(Model): add negative_log_likelihood method
sjforeman
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c9c75e6
feat(models): add null model
sjforeman
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f2f0caa
fix(AutoSimulationTemplate2Dto1D): remove unused k1D check
sjforeman
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c2008ca
fix(containers, mcmc, utils): correctly handle datasets without mock axis
sjforeman
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663595a
feat(mcmc, utils): handle inputs with Stokes parameters
sjforeman
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21eb14e
feat(run_mcmc): add warning if thinned chain has length zero
sjforeman
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4aaf13b
fix(AutoSignalTemplate2D): switch to more general regex for templates
sjforeman
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1f08f21
feat(models, signal): add ability to specify filename glob for templates
sjforeman
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9e511dc
fix(AutoSignalTemplate2D): fix template directory regex
sjforeman
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5963516
fix(run_mcmc): save PowerSpectrum1D k1D to output container
sjforeman
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a1b1350
feat(run_mcmc): save model/param info in output container
sjforeman
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c17dc7c
feat(models, signal): add 2d models that sample in omega^2
sjforeman
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bb8520a
feat(chisq, containers): add code for detection significance computation via Monte Carlo
sjforeman
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92af6f8
fix(mcmc), style: fix bug in saving pol_fit, and blacken
sjforeman
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b9982ff
(feat): add MockPowerSpectrum1D container support from fitstack

albin
authored and
sjforeman
committed
6dafbea
(feat): add cached binning scheme for 1D power spectrum template

albin
authored and
sjforeman
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5188a90
feat(models): allow user to toggle slow 2d-to-1d binning
sjforeman
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7e61bf4
style: blacken
sjforeman
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0a5d758
refactor(initialize_pol): remove unused variables
sjforeman
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e517a26

Commits on Aug 14, 2025

Commits on Oct 3, 2025

fix(get_bounds): correctly handle PowerLaw prior
sjforeman
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1b02afd
fix(powerspectrum1d_min_chisq_fit): fix bug when loading chain from file
sjforeman
committed
48c2db8
fix(powerspectrum1d_min_chisq_fit): fix issue accessing input spectrum)
sjforeman
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b410d52
fix(powerspectrum1d_min_chisq_fit): fix bug in previous commit
sjforeman
committed
aa37c85
fix(powerspectrum1d_min_chisq_fit): fix reference to input container
sjforeman
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2f04511
fix(powerspectrum1d_min_chisq_fit): switch to more stable computation of p-value and nsigmas
sjforeman
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f12e89d
feat(powerspectrum1d_min_chisq_fit): save param0 to output container
sjforeman
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205a406
feat(models): add 1d power spectrum classes that sample in Omega^2
sjforeman
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4bbc5c5
fix(AutoSimulationTemplate2Dto1D_Omega2): fix bug in complexifying omega^2
sjforeman
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32a7db0
feat(powerspectrum1d_min_chisq_fit): add option to use mocks from second input container
sjforeman
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213ea97
refactor(mcmc): factor out code that prepares inputs to MCMC
sjforeman
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cb5daa4
feat(mcmc): add option to apply Hartlap factor to inverse covariance
sjforeman
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0d364db
feat(chisq, containers): add option to start optimizer from several points
sjforeman
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86d56f6
feat(chisq): add ability to use leave-one-out covariance for each mock
sjforeman
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4ab6b10
feat(chisq): save each optimizer starting point to output container
sjforeman
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f87d224
feat(chisq): add ability to split mocks for cov estimation and fitting
sjforeman
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17a41b8
feat(chisq): add ability to specify seed for extra starts
sjforeman
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dfcf12d
fix(AutoSignalTemplate1DFoG): evaluate model at abs value of alphaFoG
sjforeman
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b621862
refactor, fix(chisq): refactor code for setting up minimizer
sjforeman
committed
a87b70b
fix(AutoSimulationTemplate1D_Omega2): select polarizations correctly in model evaluation
sjforeman
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39c33cf
feat(initialize_mcmc_ingredients): save useful quantities as container attributes
sjforeman
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1c0b7a5
feat(chisq): allow starting points for optimizer to be chosen in log(parameter)
sjforeman
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4907829
fix(get_powerspectrum1d_LOO_invcovariance): handle single-pol option correctly
sjforeman
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3ae3f7d
fix(AutoSignalTemplate1D): fix typo in shot noise template parsing
sjforeman
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8817a0d
fix(signal): allow for FoGh=1 template to have 1.0 in filename
sjforeman
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20de49e
feat(chisq): add routine to combine Delta chi^2 results from multiple containers
sjforeman
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421637b
fix(get_powerspectrum1d_LOO_invcovariance): remove pol selection
sjforeman
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d1548d7
feat(Model): add amplitude parameter to likelihood evaluation
sjforeman
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a4f679b
feat(stats): add routines for fitting to distributions
sjforeman
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1cc48e4
feat(chisq): add more detection significance calculations
sjforeman
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0100517
fix(signal): fix shot noise template bugs
sjforeman
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3021017
fix(chisq): align task properties with routine arguments
sjforeman
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46d88f1
feat(chisq): add option to center mocks on data
sjforeman
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d25d6e7
docs(compute_MC_calibrated_distribution_test): add details to docstring
sjforeman
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130ab9e
fix bool

Arnab Chakraborty
authored and
sjforeman
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3c2b1ab
add chaintools

Arnab Chakraborty
authored and
sjforeman
committed
e2fd2e0
example notebooks

Arnab Chakraborty
authored and
sjforeman
committed
1cf715f
Create README

Arnab-half-blood-prince
authored and
sjforeman
committed
f76d74d
fix(mcmc): set seed for the sampler

albin
authored and
sjforeman
committed
3f7972b

Commits on Oct 4, 2025

feat(chisq_test): code that was used for stacking analysis

Seth Siegel
authored and
sjforeman
committed
14ca63f
feat(mcmc): add ability to toggle emcee progress bar
sjforeman
committed
a4e86a5

Commits on Nov 17, 2025