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2d4f9ea
checking to see if a no telluric model is preffered
christiangil Jun 7, 2022
6a6f0f0
masking out bad component plot points
christiangil Jun 7, 2022
a5104a5
removing metadata[:todo][:optimized]
christiangil Jun 7, 2022
0a7b07b
adding star_prior() to FrozenTelWorkspace and taking out remove_lm_sc…
christiangil Jun 8, 2022
5b87ec1
updatde clean_dir
christiangil Jun 8, 2022
5e4a55c
use_aic and iter=300
christiangil Jun 8, 2022
a298948
fixing _spectra_interp_gp!() bug
christiangil Jun 9, 2022
1621af1
adding eps eri
christiangil Jun 9, 2022
de9a603
undoing plot mask thing
christiangil Jun 13, 2022
caa36a5
fixing _spectra_interp_gp_div_gp!() bug
christiangil Jun 14, 2022
68ad1dc
sigh
christiangil Jun 15, 2022
91de866
more sensible stopping criteria that is barely used
christiangil Jun 15, 2022
c1cb0b7
adding more copying for safer behaviour, preventing accidental double…
christiangil Jun 15, 2022
43eff45
part of last one and also passing kwargs... in test_ℓ_for_n_comps()
christiangil Jun 15, 2022
e4b872b
whoops
christiangil Jun 16, 2022
e5f9b7e
better airmass visibility in plots
christiangil Jun 16, 2022
22dc83f
adding score errors, and nicer plots
christiangil Jun 16, 2022
6dedf86
adding 22049 to gather
christiangil Jun 16, 2022
3ab6152
adding 22049 to reduce.jl and some script cleanup and removing SSOFU.…
christiangil Jun 16, 2022
63fca88
part of last one and adding an auto filter for χ²_orders
christiangil Jun 16, 2022
d5854fd
adding nice print statements. ~100 orders are used for each analysis
christiangil Jun 16, 2022
853ac0b
adding dpca, better inits, and score errors to EXPRES/analysis.jl
christiangil Jun 16, 2022
902333a
simpified expres param
christiangil Jun 16, 2022
4d32391
cleaning up EXPRES/gather.jl
christiangil Jun 17, 2022
b0ded1b
updating clean_dir.jl
christiangil Jun 17, 2022
507be25
sigh
christiangil Jun 17, 2022
9e17bfd
ssiigghh
christiangil Jun 17, 2022
2950f71
whoopsies
christiangil Jun 17, 2022
e73b74a
more nothing
christiangil Jun 17, 2022
163758e
fixing standardizing reduce.jl
christiangil Jun 17, 2022
7dd3c16
adding remove_lm_score_means!() to cb() for Adam models
christiangil Jun 21, 2022
8afac86
whoops
christiangil Jun 21, 2022
68da1e5
recording random activity indicators and tellurics from L2 files ;)
christiangil Jun 23, 2022
916109f
plotting neid activity indicators and dealing with lm_tel/lm_star error
christiangil Jun 27, 2022
2f7d0cb
only using best Hα
christiangil Jun 28, 2022
af95a09
separating out neid_extras()
christiangil Jun 28, 2022
4639c06
making frozen tel models stay that way
christiangil Jun 28, 2022
0110635
smol fix
christiangil Jun 28, 2022
b18fd5b
SSOFUtliities -> SSOFUtilities
christiangil Jun 29, 2022
7d9c689
adding neid lsf and only using lsfs on orders with good calibration.
christiangil Jun 30, 2022
796906e
adding flip_basis_vectors!().
christiangil Jul 6, 2022
3adfea5
using better fits for expres lsf
christiangil Jul 7, 2022
129aae9
moving lsf functions to modules
christiangil Jul 7, 2022
2368343
adding L2_μ back in, moving initializations to their own files, addin…
christiangil Jul 14, 2022
3548df6
separating out initialize_model!(), adding neid_plots() and neid_acti…
christiangil Jul 14, 2022
0ced3a2
smarter regularization finding strategy, adding compat entry for temp…
christiangil Jul 19, 2022
7830738
sigh
christiangil Jul 19, 2022
3f61420
getting EMPCA out
christiangil Jul 19, 2022
a0d992d
supressing more plots
christiangil Jul 21, 2022
50e08c5
whoops
christiangil Jul 21, 2022
b55e3db
small things but mostly if !interactive; ENV["GKSwstype"] = "100" end
christiangil Jul 21, 2022
f1db94d
om.metadata[:todo][:initialized]
christiangil Jul 21, 2022
061e43d
reverting to smarter starts and adding ability to not use the new reg…
christiangil Jul 21, 2022
49c86d8
sigh
christiangil Jul 22, 2022
ebd0836
dealing with edge effects and actually culling
christiangil Jul 22, 2022
5cce675
dpca folder
christiangil Jul 22, 2022
fa844c5
hmm
christiangil Jul 22, 2022
060ccf2
separate out empca
christiangil Jul 22, 2022
884d7dc
new reduce plots
christiangil Jul 25, 2022
ea183f1
new neid stars
christiangil Jul 25, 2022
90fd857
better plots and automatic σ_floor choice and different testing_ratio
christiangil Jul 26, 2022
dd7708a
our noreg rvs have been so wrong
christiangil Jul 26, 2022
3676140
experimental commit
christiangil Jul 29, 2022
a19c7c4
more efficient memory usage in _solve_coeffs!(eigvec::AbstractVector,…
christiangil Aug 1, 2022
e90c3ec
whoops
christiangil Aug 1, 2022
82d3dc1
- better bad drift detection
christiangil Aug 4, 2022
288120b
wobble-style error estimation
christiangil Aug 4, 2022
7242840
- adding est_∇()
christiangil Aug 5, 2022
d80a6da
- added update_interpolation_locations!()
christiangil Aug 5, 2022
06a3207
adding update_interpolation_locations!() to _finish_downsizing
christiangil Aug 5, 2022
b7b62d4
- fix est_∇() (just use FiniteDifferences.jl)
christiangil Aug 6, 2022
8e10cb3
going to more model sampling
christiangil Aug 6, 2022
e717c22
whoops
christiangil Aug 7, 2022
faeac83
smol iter fix
christiangil Aug 7, 2022
1335bbb
errors -> σ
christiangil Aug 7, 2022
c27d2be
part of last one
christiangil Aug 7, 2022
cdff41b
light_speed_nu -> SSOF.light_speed_nu
christiangil Aug 7, 2022
7a8f6f1
boop
christiangil Aug 8, 2022
66bafdc
σ_floor vs std_floor
christiangil Aug 8, 2022
e6cf648
smol bits
christiangil Aug 9, 2022
50553a0
moar smol bits
christiangil Aug 9, 2022
eec08f5
more small
christiangil Aug 12, 2022
5a56824
hopefully fixing lsf
christiangil Aug 15, 2022
b0dca4f
you can use log linear models now this took forever
christiangil Aug 16, 2022
c23c19b
rearranging script args
christiangil Aug 16, 2022
be96b04
new folder structure
christiangil Aug 16, 2022
e4ac777
fixing model init bug
christiangil Aug 17, 2022
9a583de
improving estimate_σ_bootstrap
christiangil Aug 18, 2022
ef3273c
whoops
christiangil Aug 18, 2022
810de75
whoops2
christiangil Aug 18, 2022
17d4e6f
saving more error stuff
christiangil Aug 18, 2022
44b8b57
smol buggy
christiangil Aug 18, 2022
dd8d3fa
update gather
christiangil Aug 19, 2022
1fcf1cc
looking in the right places
christiangil Aug 19, 2022
e3b9f14
making EMPCA more robust to masked points
christiangil Aug 19, 2022
07a1631
simpler gather
christiangil Aug 19, 2022
2da7ff9
better clean dir and more lenient warning instead of assert in estima…
christiangil Aug 20, 2022
1a91c37
new file strucutre in reduce
christiangil Aug 22, 2022
14074b5
correct neid order rvs and generalized weighted_mean()
christiangil Aug 22, 2022
78ab943
fixed neid order RVs, going to linear continuum fits only in really r…
christiangil Aug 23, 2022
52e06c9
plotting lsf broadened model components
christiangil Aug 24, 2022
acea96a
oop
christiangil Aug 24, 2022
bc31fdb
more continuum normalization I just cant decide
christiangil Aug 25, 2022
f4113cd
no more intra_night_std warnings or useless plots
christiangil Aug 25, 2022
2d244ad
some easy multithreading support (~25% speedup)
christiangil Aug 25, 2022
a1d1a05
smol
christiangil Aug 25, 2022
f8516d6
more multithreading support that only works for the bootstrapping and…
christiangil Aug 25, 2022
e2cb088
adding telluric dominated model initialization
christiangil Aug 28, 2022
e75535c
switching to ThreadsX
christiangil Aug 29, 2022
469489c
fixed padding, more masking in initialization, taking out unnecesary …
christiangil Aug 29, 2022
35ee9b5
oop
christiangil Aug 29, 2022
c49cc64
high acceleration pixel masking
christiangil Aug 31, 2022
7a725f3
122 -> 118
christiangil Aug 31, 2022
4bcc8f5
acceleration -> snap
christiangil Aug 31, 2022
08b52be
consistent edge masking, some other continuum tweaks, new data usage …
christiangil Sep 1, 2022
63aae7e
adding gated_plot!() and adjusting nsigma
christiangil Sep 2, 2022
9730299
oop
christiangil Sep 2, 2022
5ed3afc
replacing recognize_bad_normalization!() and recognize_bad_drift!()
christiangil Sep 6, 2022
a70c00b
masking isolated pixels
christiangil Sep 6, 2022
1621490
fixing status plot, now able to start with no components, vander -> _…
christiangil Sep 8, 2022
b7f615f
no print statements for parallel bootstrap
christiangil Sep 8, 2022
23692a5
adding rassine and new continuum rebalancing that I probably wont use
christiangil Sep 8, 2022
c0aa3fe
adding use_custom_n_comp and edge masking
christiangil Sep 13, 2022
4f9a460
oops
christiangil Sep 13, 2022
0e89b13
oop2
christiangil Sep 13, 2022
1d29089
should have committed this earlier
christiangil Sep 13, 2022
acbc1e6
better recalc
christiangil Sep 13, 2022
c07b396
fixing donwsize_model() bugs
christiangil Sep 13, 2022
af16f78
scaling scores in plot_model()
christiangil Sep 13, 2022
595ae9f
fixing estimate_σ_curvature()
christiangil Sep 14, 2022
69189a8
looked into mcmc and vi (not using either)
christiangil Sep 16, 2022
bab0ba5
adding by eye folder
christiangil Sep 16, 2022
87d7c27
oop
christiangil Sep 16, 2022
db7d1de
better by-eye folder
christiangil Sep 19, 2022
7a42523
adding 95735
christiangil Sep 21, 2022
6fb5551
new lsf_gp analysis algorithm
christiangil Sep 23, 2022
9288372
oop
christiangil Sep 23, 2022
78798e6
more better flipping
christiangil Sep 28, 2022
91a94e0
traceable barycentric pixel masking
christiangil Sep 28, 2022
e7b26cc
augment clean_dir
christiangil Sep 28, 2022
3deba75
verbose
christiangil Sep 28, 2022
5b887ff
adding var_s, _mask -> mask!, more verbose
christiangil Sep 28, 2022
0f94ec8
more consistent var_s behavior, always masking barycentric edges,
christiangil Sep 28, 2022
8a0f7a5
oop
christiangil Sep 28, 2022
21750aa
more verbose
christiangil Sep 29, 2022
ac5b619
7:118
christiangil Oct 3, 2022
44e437e
better gather
christiangil Oct 4, 2022
1674227
more flexible analysis (with better folders and input parsing)
christiangil Oct 5, 2022
e62c63a
oop
christiangil Oct 5, 2022
14b45af
going back on parse_args
christiangil Oct 5, 2022
ecbe5a4
can have - in parsed args
christiangil Oct 5, 2022
37ad66f
cant do parse(::String, ...)
christiangil Oct 5, 2022
9d9c1ea
starting to make reduce.jl better, fixed how_many_comps empty string …
christiangil Oct 24, 2022
484f900
reusing code in project_doppler_comp!() and _reorthogonalize!(), can …
christiangil Oct 28, 2022
2a73f8d
adding calculate_initial_model() and get_data()
christiangil Oct 28, 2022
41759a5
oop
christiangil Oct 28, 2022
d9f7a6d
actually filling the early template models
christiangil Oct 28, 2022
6303adf
nothing really
christiangil Oct 28, 2022
23574ce
diagnostic print statement
christiangil Oct 31, 2022
51b5b5c
making it easier to find the best constant models
christiangil Nov 1, 2022
7399857
more robust calculate_initial_model()
christiangil Nov 1, 2022
71b0760
oop
christiangil Nov 1, 2022
35e6fe0
mostly commented out useless changes
christiangil Nov 3, 2022
cee1bc8
ugh
christiangil Nov 8, 2022
3725056
comparing 0,0 to -1,0 model before comparing to -1,1 model and μ_posi…
christiangil Nov 15, 2022
fcf5005
more git ignore
christiangil Nov 15, 2022
b638f0e
adding the other metrics and metric plots
christiangil Nov 23, 2022
41236a2
eachindex and some script deletion
christiangil Nov 30, 2022
1e1253d
better gather.jl
christiangil Nov 30, 2022
65a2f84
reverting some axes bugs & better plot_model_rvs()
christiangil Dec 1, 2022
e24c919
wavelength_range_star
christiangil Dec 5, 2022
aeae2c4
pls work
christiangil Dec 6, 2022
f0c28a6
fixing negative var issue
christiangil Dec 7, 2022
f17ece9
1d snap & various smol bugs
christiangil Dec 9, 2022
235cdbb
careful_first_step
christiangil Dec 9, 2022
7b0aa33
replacing interp_helper (dumber but works better)
christiangil Dec 9, 2022
a9d7d69
save models after error estimation
christiangil Dec 9, 2022
1bcaa0d
rm_doppler which works too well
christiangil Dec 9, 2022
0aa7db2
speed_up_iterate!()
christiangil Dec 9, 2022
6f6074c
speed up is dangerous and killed CaHK
christiangil Dec 9, 2022
acb7f35
calc_doppler_component_RVSKL_log and order plots
christiangil Dec 12, 2022
098bf7a
Data Usage Plot
christiangil Dec 12, 2022
1af53c8
more of last one
christiangil Dec 12, 2022
1378191
std -> RMS, weights -> scores, fixing use_custom_n
christiangil Dec 15, 2022
6452a79
undef reference bug, spectra_interp_gp bug swerve
christiangil Dec 15, 2022
ada3c23
thing
christiangil Dec 20, 2022
0aa2a11
adding barnard, star_str, more neid data filtering
christiangil Dec 22, 2022
82cf7db
oop
christiangil Dec 22, 2022
787ebd3
Update README.md
christiangil Jan 3, 2023
f238e30
removing expres folder
christiangil Jan 3, 2023
c5cff8e
Merge branch 'master' of https://github.com/christiangil/StellarSpect…
christiangil Jan 3, 2023
99bee82
removing periodogram folder
christiangil Jan 3, 2023
b03e207
Create LICENSE.md
christiangil Jan 3, 2023
0989522
moving out EMPCA and some function renaming
christiangil Jan 6, 2023
144e8d7
adding docs folder
christiangil Jan 12, 2023
4f5f87e
Add files via upload
christiangil Jan 12, 2023
ffd817c
Update README.md
christiangil Jan 12, 2023
25d9167
adding workflows and docs basics
christiangil Jan 12, 2023
cea6703
CompatHelper: add new compat entry for StatsBase at version 0.33, (ke…
Jan 13, 2023
8995299
CompatHelper: add new compat entry for DSP at version 0.7, (keep exis…
Jan 13, 2023
7a39b6f
CompatHelper: add new compat entry for SortFilters at version 0.1, (k…
Jan 13, 2023
441c381
CompatHelper: add new compat entry for Unitful at version 1, (keep ex…
Jan 13, 2023
60179fc
CompatHelper: add new compat entry for ExpectationMaximizationPCA at …
Jan 13, 2023
6b08d2c
Merge pull request #28 from christiangil/compathelper/new_version/202…
christiangil Jan 13, 2023
4e50643
Merge pull request #27 from christiangil/compathelper/new_version/202…
christiangil Jan 13, 2023
2e55460
Merge pull request #21 from christiangil/compathelper/new_version/202…
christiangil Jan 13, 2023
d81e58c
Merge branch 'master' into compathelper/new_version/2023-01-13-01-13-…
christiangil Jan 13, 2023
1a976fc
Merge pull request #20 from christiangil/compathelper/new_version/202…
christiangil Jan 13, 2023
7af1a7d
Merge branch 'master' into compathelper/new_version/2023-01-13-01-13-…
christiangil Jan 13, 2023
5569618
Merge pull request #19 from christiangil/compathelper/new_version/202…
christiangil Jan 13, 2023
861244a
adding neid_lsf function with wavelengths, changing dpca, log_lm, and…
christiangil Jan 20, 2023
dc0de23
Merge branch 'master' of https://github.com/christiangil/StellarSpect…
christiangil Jan 20, 2023
bdaf96d
simpler rv calc and variable spectra_interp_gp lengthscale
christiangil Jan 23, 2023
ff2533d
Update README.md
christiangil Jan 31, 2023
e266d33
adding example, DataInterpolations, moving stuff out of SSOFU
christiangil Mar 16, 2023
c5fa6ee
adding the project file
christiangil Mar 16, 2023
c4012c8
adding instantiate
christiangil Mar 16, 2023
c7b8456
hacky github fix?
christiangil Mar 16, 2023
5dcf9e3
final hacky github fix
christiangil Mar 16, 2023
a3ed75c
adding gettingstarted.md
christiangil Mar 16, 2023
c22d391
example notebook
christiangil Mar 20, 2023
ac33e1e
continuum docs
christiangil Mar 20, 2023
741803f
more documentation and a bugfix in trapz_small
christiangil Mar 21, 2023
41f36ea
Update README.md
christiangil Mar 21, 2023
07ae9e7
picture in docs attempt
christiangil Mar 21, 2023
85094c1
pic attempt 2
christiangil Mar 21, 2023
1092545
way more documentation
christiangil Mar 29, 2023
e46379e
docs yay
christiangil Mar 29, 2023
6b84755
aicc
christiangil Apr 3, 2023
4c977e6
adding model_functions docstrings
christiangil Apr 4, 2023
ca489d7
start to organize documentation and add logo
christiangil Apr 4, 2023
d59951c
Update README.md
christiangil Apr 4, 2023
14995b2
larger logo
christiangil Apr 5, 2023
c3e0e61
rest of documentation
christiangil Apr 6, 2023
52d191b
oop
christiangil Apr 6, 2023
49289b2
fix attempt
christiangil Apr 6, 2023
9b0bd02
making example notebook nicer
christiangil Apr 6, 2023
4a140a0
adding fits files for example
christiangil Apr 6, 2023
c2bc56f
nb
christiangil Apr 7, 2023
b2eed25
some doc fixes
christiangil Apr 7, 2023
848025b
sigh
christiangil Apr 7, 2023
dec7afe
making example independent. prep to sep utilities
christiangil Apr 10, 2023
b1c7948
removing folders from Git
christiangil Apr 11, 2023
5bb4242
and the corresponding git ignore
christiangil Apr 11, 2023
1b3bc89
adding compat
christiangil Apr 11, 2023
8457a0c
CompatHelper: bump compat for SpecialFunctions to 2, (keep existing c…
Apr 12, 2023
d52a8e0
CompatHelper: bump compat for RollingFunctions to 0.7, (keep existing…
Apr 12, 2023
8227848
Merge pull request #31 from christiangil/compathelper/new_version/202…
christiangil Apr 12, 2023
8a90024
Merge pull request #30 from christiangil/compathelper/new_version/202…
christiangil Apr 12, 2023
0ee7d2a
CompatHelper: bump compat for Nabla to 0.13, (keep existing compat)
Apr 13, 2023
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44 changes: 44 additions & 0 deletions .github/workflows/CompatHelper.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
name: CompatHelper
on:
schedule:
- cron: 0 0 * * *
workflow_dispatch:
permissions:
contents: write
pull-requests: write
jobs:
CompatHelper:
runs-on: ubuntu-latest
steps:
- name: Check if Julia is already available in the PATH
id: julia_in_path
run: which julia
continue-on-error: true
- name: Install Julia, but only if it is not already available in the PATH
uses: julia-actions/setup-julia@v1
with:
version: '1'
arch: ${{ runner.arch }}
if: steps.julia_in_path.outcome != 'success'
- name: "Add the General registry via Git"
run: |
import Pkg
ENV["JULIA_PKG_SERVER"] = ""
Pkg.Registry.add("General")
shell: julia --color=yes {0}
- name: "Install CompatHelper"
run: |
import Pkg
name = "CompatHelper"
uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
version = "3"
Pkg.add(; name, uuid, version)
shell: julia --color=yes {0}
- name: "Run CompatHelper"
run: |
import CompatHelper
CompatHelper.main()
shell: julia --color=yes {0}
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
33 changes: 33 additions & 0 deletions .github/workflows/TagBot.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
name: TagBot
on:
issue_comment:
types:
- created
workflow_dispatch:
inputs:
lookback:
default: 3
permissions:
actions: read
checks: read
contents: write
deployments: read
issues: read
discussions: read
packages: read
pages: read
pull-requests: read
repository-projects: read
security-events: read
statuses: read
jobs:
TagBot:
if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
runs-on: ubuntu-latest
steps:
- uses: JuliaRegistries/TagBot@v1
with:
token: ${{ secrets.GITHUB_TOKEN }}
# Edit the following line to reflect the actual name of the GitHub Secret containing your private key
ssh: ${{ secrets.DOCUMENTER_KEY }}
# ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}
26 changes: 26 additions & 0 deletions .github/workflows/documentation.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
name: Documentation

on:
push:
branches:
- master # update to match your development branch (master, main, dev, trunk, ...)
tags: '*'
pull_request:

jobs:
build:
permissions:
contents: write
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: julia-actions/setup-julia@v1
with:
version: '1.6'
- name: Install dependencies
run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
- name: Build and deploy
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
run: julia --project=docs/ docs/make.jl
25 changes: 25 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,28 @@ lines
old
examples/generate_example_data.jl
*.png
*.gif
*data_locs.jl
Manifest.toml
*.csv
test.jl
*.pbs
outputs/
*.jld2
*.txt
alex_stuff/
*scrap.jl
NEID/testing.jl
*.fits
*.par
*analysis_wobble.jl
*test_linearsolve.jl
*init_testing.jl
*model_functions0.jl
*.pptx
*.xlsx
EXPRES/
*_backup.jl
periodogram/
NEID/
SSOFUtilities/
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