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Merge Kristo's work - #36

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eford wants to merge 732 commits into

RvSpectML:masterfrom

kment:master

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Merge Kristo's work#36
eford wants to merge 732 commits into
RvSpectML:masterfrom
kment:master

This pull request is big! We're only showing the most recent 250 commits

Commits on Jun 16, 2022
- adding score errors, and nicer plots
  christiangil
  committed
  22dc83f
- adding 22049 to gather
  christiangil
  committed
  6dedf86
- adding 22049 to reduce.jl and some script cleanup and removing SSOFU._scatter()
  christiangil
  committed
  3ab6152
- part of last one and adding an auto filter for χ²_orders
  christiangil
  committed
  63fca88
- adding nice print statements. ~100 orders are used for each analysis
  christiangil
  committed
  d5854fd
- adding dpca, better inits, and score errors to EXPRES/analysis.jl
  christiangil
  committed
  853ac0b
- simpified expres param
  christiangil
  committed
  902333a
Commits on Jun 17, 2022
- cleaning up EXPRES/gather.jl
  christiangil
  committed
  4d32391
- updating clean_dir.jl
  christiangil
  committed
  b0ded1b
- sigh
  christiangil
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  507be25
- ssiigghh
  christiangil
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  9e17bfd
- whoopsies
  christiangil
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  2950f71
- more nothing
  christiangil
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  e73b74a
- fixing standardizing reduce.jl
  christiangil
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  163758e
Commits on Jun 21, 2022
- adding remove_lm_score_means!() to cb() for Adam models
  christiangil
  committed
  7dd3c16
- whoops
  christiangil
  committed
  8afac86
Commits on Jun 23, 2022
- recording random activity indicators and tellurics from L2 files ;)
  christiangil
  committed
  68da1e5
Commits on Jun 27, 2022
- plotting neid activity indicators and dealing with lm_tel/lm_star error
  christiangil
  committed
  916109f
Commits on Jun 28, 2022
- only using best Hα
  christiangil
  committed
  2f7d0cb
- separating out neid_extras()
  christiangil
  committed
  af95a09
- making frozen tel models stay that way
  christiangil
  committed
  4639c06
- smol fix
  christiangil
  committed
  0110635
Commits on Jun 29, 2022
- SSOFUtliities -> SSOFUtilities
  christiangil
  committed
  b18fd5b
Commits on Jun 30, 2022
- adding neid lsf and only using lsfs on orders with good calibration.
  christiangil
  committed
  7d9c689
Commits on Jul 6, 2022
- adding flip_basis_vectors!().
  christiangil
  committed
  796906e
Commits on Jul 7, 2022
- using better fits for expres lsf
  christiangil
  committed
  3adfea5
- moving lsf functions to modules
  christiangil
  committed
  129aae9
Commits on Jul 14, 2022
- adding L2_μ back in, moving initializations to their own files, adding wvapor neid measurements to SSOFU.neid_extras, and separating out SSOFU.neid_extras
  christiangil
  committed
  2368343
- separating out initialize_model!(), adding neid_plots() and neid_activity_indicators(),
  christiangil
  committed
  3548df6
Commits on Jul 19, 2022
- smarter regularization finding strategy, adding compat entry for temporalgps, and taking out mean full model from plots
  christiangil
  committed
  0ced3a2
- sigh
  christiangil
  committed
  7830738
- getting EMPCA out
  christiangil
  committed
  3f61420
Commits on Jul 21, 2022
- supressing more plots
  christiangil
  committed
  a0d992d
- whoops
  christiangil
  committed
  50e08c5
- small things but mostly if !interactive; ENV["GKSwstype"] = "100" end
  christiangil
  committed
  b55e3db
- om.metadata[:todo][:initialized]
  christiangil
  committed
  f1db94d
- reverting to smarter starts and adding ability to not use the new regularization search strat lol
  christiangil
  committed
  061e43d
Commits on Jul 22, 2022
- sigh
  christiangil
  committed
  49c86d8
- dealing with edge effects and actually culling
  christiangil
  committed
  ebd0836
- dpca folder
  christiangil
  committed
  5cce675
- hmm
  christiangil
  committed
  fa844c5
- separate out empca
  christiangil
  committed
  060ccf2
Commits on Jul 25, 2022
- new reduce plots
  christiangil
  committed
  884d7dc
- new neid stars
  christiangil
  committed
  ea183f1
Commits on Jul 26, 2022
- better plots and automatic σ_floor choice and different testing_ratio
  christiangil
  committed
  90fd857
- our noreg rvs have been so wrong
  christiangil
  committed
  dd7708a
Commits on Jul 29, 2022
- experimental commit
  christiangil
  committed
  3676140
Commits on Aug 1, 2022
- more efficient memory usage in _solve_coeffs!(eigvec::AbstractVector, ...)
  christiangil
  committed
  a19c7c4
- whoops
  christiangil
  committed
  e90c3ec
Commits on Aug 4, 2022
- - better bad drift detection
  christiangil
  committed
  82d3dc1
- wobble-style error estimation
  christiangil
  committed
  288120b
Commits on Aug 5, 2022
- - adding est_∇()
  christiangil
  committed
  7242840
- - added update_interpolation_locations!()
  christiangil
  committed
  d80a6da
- adding update_interpolation_locations!() to _finish_downsizing
  christiangil
  committed
  06a3207
Commits on Aug 6, 2022
- - fix est_∇() (just use FiniteDifferences.jl)
  christiangil
  committed
  b7b62d4
- going to more model sampling
  christiangil
  committed
  8e10cb3
Commits on Aug 7, 2022
- whoops
  christiangil
  committed
  e717c22
- smol iter fix
  christiangil
  committed
  faeac83
- errors -> σ
  christiangil
  committed
  1335bbb
- part of last one
  christiangil
  committed
  c27d2be
- light_speed_nu -> SSOF.light_speed_nu
  christiangil
  committed
  cdff41b
Commits on Aug 8, 2022
- boop
  christiangil
  committed
  7a8f6f1
- σ_floor vs std_floor
  christiangil
  committed
  66bafdc
Commits on Aug 9, 2022
- smol bits
  christiangil
  committed
  e6cf648
- moar smol bits
  christiangil
  committed
  50553a0
Commits on Aug 12, 2022
- more small
  christiangil
  committed
  eec08f5
Commits on Aug 15, 2022
- hopefully fixing lsf
  christiangil
  committed
  5a56824
Commits on Aug 16, 2022
- you can use log linear models now this took forever
  christiangil
  committed
  b0dca4f
- rearranging script args
  christiangil
  committed
  c23c19b
- new folder structure
  christiangil
  committed
  be96b04
Commits on Aug 17, 2022
- fixing model init bug
  christiangil
  committed
  e4ac777
Commits on Aug 18, 2022
- improving estimate_σ_bootstrap
  christiangil
  committed
  9a583de
- whoops
  christiangil
  committed
  ef3273c
- whoops2
  christiangil
  committed
  810de75
- saving more error stuff
  christiangil
  committed
  17d4e6f
- smol buggy
  christiangil
  committed
  44b8b57
Commits on Aug 19, 2022
- update gather
  christiangil
  committed
  dd8d3fa
- looking in the right places
  christiangil
  committed
  1fcf1cc
- making EMPCA more robust to masked points
  christiangil
  committed
  e3b9f14
- simpler gather
  christiangil
  committed
  07a1631
Commits on Aug 20, 2022
- better clean dir and more lenient warning instead of assert in estimate_σ_curvature()
  christiangil
  committed
  2da7ff9
Commits on Aug 22, 2022
- new file strucutre in reduce
  christiangil
  committed
  1a91c37
- correct neid order rvs and generalized weighted_mean()
  christiangil
  committed
  14074b5
Commits on Aug 23, 2022
- fixed neid order RVs, going to linear continuum fits only in really red orders
  christiangil
  committed
  78ab943
Commits on Aug 24, 2022
- plotting lsf broadened model components
  christiangil
  committed
  52e06c9
- oop
  christiangil
  committed
  acea96a
Commits on Aug 25, 2022
- more continuum normalization I just cant decide
  christiangil
  committed
  bc31fdb
- no more intra_night_std warnings or useless plots
  christiangil
  committed
  f4113cd
- some easy multithreading support (~25% speedup)
  christiangil
  committed
  2d244ad
- smol
  christiangil
  committed
  a1d1a05
- more multithreading support that only works for the bootstrapping and not the curvature for some reason
  christiangil
  committed
  f8516d6
Commits on Aug 28, 2022
- adding telluric dominated model initialization
  christiangil
  committed
  e2cb088
Commits on Aug 29, 2022
- switching to ThreadsX
  christiangil
  committed
  e75535c
- fixed padding, more masking in initialization, taking out unnecesary plotting of μ_tel
  christiangil
  committed
  469489c
- oop
  christiangil
  committed
  35ee9b5
Commits on Aug 31, 2022
- high acceleration pixel masking
  christiangil
  committed
  c49cc64
- 122 -> 118
  christiangil
  committed
  7a725f3
- acceleration -> snap
  christiangil
  committed
  4bcc8f5
Commits on Sep 1, 2022
- consistent edge masking, some other continuum tweaks, new data usage plot
  christiangil
  committed
  08b52be
Commits on Sep 2, 2022
- adding gated_plot!() and adjusting nsigma
  christiangil
  committed
  63aae7e
- oop
  christiangil
  committed
  9730299
Commits on Sep 6, 2022
- replacing recognize_bad_normalization!() and recognize_bad_drift!()
  christiangil
  committed
  5ed3afc
- masking isolated pixels
  christiangil
  committed
  a70c00b
Commits on Sep 8, 2022
Commits on Sep 13, 2022
- adding use_custom_n_comp and edge masking
  christiangil
  committed
  c0aa3fe
- oops
  christiangil
  committed
  4f9a460
- oop2
  christiangil
  committed
  0e89b13
- should have committed this earlier
  christiangil
  committed
  1d29089
- better recalc
  christiangil
  committed
  acbc1e6
- fixing donwsize_model() bugs
  christiangil
  committed
  c07b396
- scaling scores in plot_model()
  christiangil
  committed
  af16f78
Commits on Sep 14, 2022
- fixing estimate_σ_curvature()
  christiangil
  committed
  595ae9f
Commits on Sep 16, 2022
- looked into mcmc and vi (not using either)
  christiangil
  committed
  69189a8
- adding by eye folder
  christiangil
  committed
  bab0ba5
- oop
  christiangil
  committed
  87d7c27
Commits on Sep 19, 2022
- better by-eye folder
  christiangil
  committed
  db7d1de
Commits on Sep 21, 2022
- adding 95735
  christiangil
  committed
  7a42523
Commits on Sep 23, 2022
- new lsf_gp analysis algorithm
  christiangil
  committed
  6fb5551
- oop
  christiangil
  committed
  9288372
Commits on Sep 28, 2022
- more better flipping
  christiangil
  committed
  78798e6
- traceable barycentric pixel masking
  christiangil
  committed
  91a94e0
- augment clean_dir
  christiangil
  committed
  e7b26cc
- verbose
  christiangil
  committed
  3deba75
- adding var_s, _mask -> mask!, more verbose
  christiangil
  committed
  5b887ff
- more consistent var_s behavior, always masking barycentric edges,
  christiangil
  committed
  0f94ec8
- oop
  christiangil
  committed
  8a0f7a5
Commits on Sep 29, 2022
- more verbose
  christiangil
  committed
  21750aa
Commits on Oct 3, 2022
- 7:118
  christiangil
  committed
  ac5b619
Commits on Oct 4, 2022
- better gather
  christiangil
  committed
  44e437e
Commits on Oct 5, 2022
- more flexible analysis (with better folders and input parsing)
  christiangil
  committed
  1674227
- oop
  christiangil
  committed
  e62c63a
- going back on parse_args
  christiangil
  committed
  14b45af
- can have - in parsed args
  christiangil
  committed
  ecbe5a4
- cant do parse(::String, ...)
  christiangil
  committed
  37ad66f
Commits on Oct 24, 2022
- starting to make reduce.jl better, fixed how_many_comps empty string parsing bug, .!isinf -> isfinite, add weighted project_doppler_comp!, adding reorthagonalize to empca_vec_by_vec, ability to spe…
  christiangil
  committed
  9d9c1ea
Commits on Oct 28, 2022
Commits on Oct 31, 2022
- diagnostic print statement
  christiangil
  committed
  23574ce
Commits on Nov 1, 2022
- making it easier to find the best constant models
  christiangil
  committed
  51b5b5c
- more robust calculate_initial_model()
  christiangil
  committed
  7399857
- oop
  christiangil
  committed
  71b0760
Commits on Nov 3, 2022
- mostly commented out useless changes
  christiangil
  committed
  35e6fe0
Commits on Nov 8, 2022
- ugh
  christiangil
  committed
  cee1bc8
Commits on Nov 15, 2022
- comparing 0,0 to -1,0 model before comparing to -1,1 model and μ_positive=true
  christiangil
  committed
  3725056
- more git ignore
  christiangil
  committed
  fcf5005
Commits on Nov 23, 2022
- adding the other metrics and metric plots
  christiangil
  committed
  b638f0e
Commits on Nov 30, 2022
- eachindex and some script deletion
  christiangil
  committed
  41236a2
- better gather.jl
  christiangil
  committed
  1e1253d
Commits on Dec 1, 2022
- reverting some axes bugs & better plot_model_rvs()
  christiangil
  committed
  65a2f84
Commits on Dec 5, 2022
- wavelength_range_star
  christiangil
  committed
  e24c919
Commits on Dec 6, 2022
- pls work
  christiangil
  committed
  aeae2c4
Commits on Dec 7, 2022
- fixing negative var issue
  christiangil
  committed
  f0c28a6
Commits on Dec 9, 2022
- 1d snap & various smol bugs
  christiangil
  committed
  f17ece9
- careful_first_step
  christiangil
  committed
  235cdbb
- replacing interp_helper (dumber but works better)
  christiangil
  committed
  7b0aa33
- save models after error estimation
  christiangil
  committed
  a9d7d69
- rm_doppler which works too well
  christiangil
  committed
  1bcaa0d
- speed_up_iterate!()
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  committed
  0aa7db2
- speed up is dangerous and killed CaHK
  christiangil
  committed
  6f6074c
Commits on Dec 12, 2022
- calc_doppler_component_RVSKL_log and order plots
  christiangil
  committed
  acb7f35
- Data Usage Plot
  christiangil
  committed
  098bf7a
- more of last one
  christiangil
  committed
  1af53c8
Commits on Dec 15, 2022
- std -> RMS, weights -> scores, fixing use_custom_n
  christiangil
  committed
  1378191
- undef reference bug, spectra_interp_gp bug swerve
  christiangil
  committed
  6452a79
Commits on Dec 20, 2022
- thing
  christiangil
  committed
  ada3c23
Commits on Dec 22, 2022
- adding barnard, star_str, more neid data filtering
  christiangil
  committed
  0aa2a11
- oop
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  committed
  82cf7db
Commits on Jan 3, 2023
- Update README.md
  christiangil
  authored
  787ebd3
- removing expres folder
  christiangil
  committed
  f238e30
- Merge branch 'master' of https://github.com/christiangil/StellarSpectraObservationFitting.jl
  christiangil
  committed
  c5cff8e
- removing periodogram folder
  christiangil
  committed
  99bee82
- Create LICENSE.md
  christiangil
  authored
  b03e207
Commits on Jan 6, 2023
- moving out EMPCA and some function renaming
  christiangil
  committed
  0989522
Commits on Jan 12, 2023
- adding docs folder
  christiangil
  committed
  144e8d7
- Add files via upload
  christiangil
  authored
  4f5f87e
- Update README.md
  christiangil
  authored
  ffd817c
- adding workflows and docs basics
  christiangil
  committed
  25d9167
Commits on Jan 13, 2023
- CompatHelper: add new compat entry for StatsBase at version 0.33, (keep existing compat)
  CompatHelper Julia
  committed
  cea6703
- CompatHelper: add new compat entry for DSP at version 0.7, (keep existing compat)
  CompatHelper Julia
  committed
  8995299
- CompatHelper: add new compat entry for SortFilters at version 0.1, (keep existing compat)
  CompatHelper Julia
  committed
  7a39b6f
- CompatHelper: add new compat entry for Unitful at version 1, (keep existing compat)
  CompatHelper Julia
  committed
  441c381
- CompatHelper: add new compat entry for ExpectationMaximizationPCA at version 0.2, (keep existing compat)
  CompatHelper Julia
  committed
  60179fc
- Merge pull request #28 from christiangil/compathelper/new_version/2023-01-13-01-14-25-255-01734543918
  christiangil
  authored
  6b08d2c
- Merge pull request #27 from christiangil/compathelper/new_version/2023-01-13-01-14-21-700-02185603131
  christiangil
  authored
  4e50643
- Merge pull request #21 from christiangil/compathelper/new_version/2023-01-13-01-13-59-480-00217928080
  christiangil
  authored
  2e55460
- Merge branch 'master' into compathelper/new_version/2023-01-13-01-13-56-116-00606789376
  christiangil
  authored
  d81e58c
- Merge pull request #20 from christiangil/compathelper/new_version/2023-01-13-01-13-56-116-00606789376
  christiangil
  authored
  1a976fc
- Merge branch 'master' into compathelper/new_version/2023-01-13-01-13-52-609-00211915814
  christiangil
  authored
  7af1a7d
- Merge pull request #19 from christiangil/compathelper/new_version/2023-01-13-01-13-52-609-00211915814
  christiangil
  authored
  5569618
Commits on Jan 20, 2023
- adding neid_lsf function with wavelengths, changing dpca, log_lm, and careful_first_step defaults, fixing _spectra_interp_gp!, renaming neid_temporal_gp_lsf_λ
  christiangil
  committed
  861244a
- Merge branch 'master' of https://github.com/christiangil/StellarSpectraObservationFitting.jl
  christiangil
  committed
  dc0de23
Commits on Jan 23, 2023
- simpler rv calc and variable spectra_interp_gp lengthscale
  christiangil
  committed
  bdaf96d
Commits on Jan 31, 2023
- Update README.md
  christiangil
  authored
  ff2533d
Commits on Mar 16, 2023
- adding example, DataInterpolations, moving stuff out of SSOFU
  christiangil
  committed
  e266d33
- adding the project file
  christiangil
  committed
  c5fa6ee
- adding instantiate
  christiangil
  committed
  c4012c8
- hacky github fix?
  christiangil
  committed
  c7b8456
- final hacky github fix
  christiangil
  committed
  5dcf9e3
- adding gettingstarted.md
  christiangil
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  a3ed75c
Commits on Mar 20, 2023
- example notebook
  christiangil
  committed
  c22d391
- continuum docs
  christiangil
  committed
  ac33e1e
Commits on Mar 21, 2023
- more documentation and a bugfix in trapz_small
  christiangil
  committed
  741803f
- Update README.md
  christiangil
  authored
  41f36ea
- picture in docs attempt
  christiangil
  authored
  07ae9e7
- pic attempt 2
  christiangil
  committed
  85094c1
Commits on Mar 29, 2023
- way more documentation
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  1092545
- docs yay
  christiangil
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  e46379e
Commits on Apr 3, 2023
- aicc
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  6b84755
Commits on Apr 4, 2023
- adding model_functions docstrings
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  committed
  4c977e6
- start to organize documentation and add logo
  christiangil
  committed
  ca489d7
- Update README.md
  christiangil
  authored
  d59951c
Commits on Apr 5, 2023
- larger logo
  christiangil
  committed
  14995b2
Commits on Apr 6, 2023
- rest of documentation
  christiangil
  committed
  c3e0e61
- oop
  christiangil
  committed
  52d191b
- fix attempt
  christiangil
  committed
  49289b2
- making example notebook nicer
  christiangil
  committed
  9b0bd02
- adding fits files for example
  christiangil
  committed
  4a140a0
Commits on Apr 7, 2023
- nb
  christiangil
  committed
  c2bc56f
- some doc fixes
  christiangil
  committed
  b2eed25
- sigh
  christiangil
  committed
  848025b
Commits on Apr 10, 2023
- making example independent. prep to sep utilities
  christiangil
  committed
  dec7afe
Commits on Apr 11, 2023
- removing folders from Git
  christiangil
  committed
  b1c7948
- and the corresponding git ignore
  christiangil
  committed
  5bb4242
- adding compat
  christiangil
  committed
  1b3bc89
Commits on Apr 12, 2023
- CompatHelper: bump compat for SpecialFunctions to 2, (keep existing compat)
  CompatHelper Julia
  committed
  8457a0c
- CompatHelper: bump compat for RollingFunctions to 0.7, (keep existing compat)
  CompatHelper Julia
  committed
  d52a8e0
- Merge pull request #31 from christiangil/compathelper/new_version/2023-04-12-01-05-59-310-01639046632
  christiangil
  authored
  8227848
- Merge pull request #30 from christiangil/compathelper/new_version/2023-04-12-01-05-51-772-03555233523
  christiangil
  authored
  8a90024
Commits on Apr 22, 2023
- lsf can be different at each time and star_str
  christiangil
  committed
  3fe3eea
- Merge branch 'master' of https://github.com/christiangil/StellarSpectraObservationFitting.jl
  christiangil
  committed
  858439a
Commits on Apr 28, 2023
- new version tag for bug fixes
  christiangil
  committed
  2b600fa
Commits on May 1, 2023
- oop
  christiangil
  committed
  d988f14
Commits on May 2, 2023
- CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat)
  CompatHelper Julia
  committed
  419b5da
- Merge pull request #34 from christiangil/compathelper/new_version/2023-05-02-01-08-14-530-02133843477
  christiangil
  authored
  36464e7
- Update README.md
  christiangil
  authored
  afe2635
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  eford
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  3b8f950
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- Restrict TemporalGPs version to avoid warnings while precompiling
  kment
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  christiangil
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  6d97f37
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  kment
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  0138dd8
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  kment
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  548d139
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- Telluric prior implementation
  kment
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  4256312
Commits on Aug 21, 2025
- Update optimization_functions.jl (quick fix)
  kment
  authored
  17fd8ca

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