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Merge v1.2.5 into master #577

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merged 1,915 commits into from
Sep 28, 2023
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ba90d48
Merge pull request #519 from nespinoza/fix-field-sim-crash
bourque Sep 27, 2021
683b514
Trying to resolve contam tool trace orientation
hover2pi Dec 29, 2021
246d765
Trying to resolve contam tool trace orientation
hover2pi Dec 29, 2021
053a457
Merge conflicts
hover2pi Dec 29, 2021
e22ea43
Update astropy from 4.0.2 to 5.0
pyup-bot Jan 1, 2022
42f78bd
Update bandit from 1.7.0 to 1.7.1
pyup-bot Jan 1, 2022
134137d
Update bokeh from 2.3.3 to 2.4.2
pyup-bot Jan 1, 2022
59a0c72
Update boto3 from 1.18.33 to 1.20.26
pyup-bot Jan 1, 2022
7905d5d
Update cython from 0.29.24 to 0.29.26
pyup-bot Jan 1, 2022
1b36b89
Update ddtrace from 0.52.1 to 0.57.0
pyup-bot Jan 1, 2022
1de9656
Update docutils from 0.17.1 to 0.18.1
pyup-bot Jan 1, 2022
fa7329a
Update flake8 from 3.9.2 to 4.0.1
pyup-bot Jan 1, 2022
d50a8da
Update flask from 2.0.1 to 2.0.2
pyup-bot Jan 1, 2022
72870b4
Update flask_wtf from 0.15.1 to 1.0.0
pyup-bot Jan 1, 2022
283cd23
Update h5py from 3.4.0 to 3.6.0
pyup-bot Jan 1, 2022
753c6af
Update ipython from 7.27.0 to 7.30.1
pyup-bot Jan 1, 2022
0a2ea74
Update matplotlib from 3.4.3 to 3.5.1
pyup-bot Jan 1, 2022
5660cee
Update numpy from 1.21.2 to 1.22.0
pyup-bot Jan 1, 2022
e929d3a
Update pandas from 1.3.2 to 1.3.5
pyup-bot Jan 1, 2022
734216d
Update paramiko from 2.7.2 to 2.9.1
pyup-bot Jan 1, 2022
e43d0e9
Update platon from 4.0 to 5.3
pyup-bot Jan 1, 2022
8050671
Update pysynphot from 1.0.1 to 2.0.0
pyup-bot Jan 1, 2022
f541799
Update pyyaml from 5.4.1 to 6.0
pyup-bot Jan 1, 2022
f53e24d
Update scipy from 1.7.1 to 1.7.3
pyup-bot Jan 1, 2022
92f5a8d
Update scp from 0.13.6 to 0.14.2
pyup-bot Jan 1, 2022
57edf9f
Update sphinx from 4.1.2 to 4.3.2
pyup-bot Jan 1, 2022
8dd584b
Update sphinx_astropy from 1.5 to 1.6.0
pyup-bot Jan 1, 2022
9478a5c
Update sphinx-automodapi from 0.13 to 0.14.0
pyup-bot Jan 1, 2022
53bdb84
Update sqlalchemy from 1.4.23 to 1.4.29
pyup-bot Jan 1, 2022
b7f77db
Update twine from 3.4.2 to 3.7.1
pyup-bot Jan 1, 2022
4a53b1f
Update wtforms from 2.3.3 to 3.0.1
pyup-bot Jan 1, 2022
5424076
Pyup jan 2022 updates
bourque Jan 7, 2022
89625ea
Small change to retrigger rtd build
bourque Jan 7, 2022
ac3a272
Revert numpy
bourque Jan 7, 2022
a2a90a0
Revert docutils
bourque Jan 7, 2022
5d59c45
Revert paramiko
bourque Jan 7, 2022
498dff9
move around import of get_config to avoid CI failures
bourque Jan 7, 2022
00f00be
move around import of _apply_factors and PlatonWrapper to avoid CI fa…
bourque Jan 7, 2022
dc0a4dd
Skipping atmospheric retrievals tests on Actions
bourque Jan 7, 2022
5c9e0f7
Merge pull request #523 from ExoCTK/pyup/scheduled-update-2022-01-01
bourque Jan 7, 2022
3cedad5
Fixed trace generator to work with pandeia v1.6.1
hover2pi Jan 18, 2022
f90991f
Fixed trace generator to work with pandeia v1.6.1
hover2pi Jan 18, 2022
a16d311
Fixing date format on hover tool. Removing TOOLTIPS and making hover …
mfixstsci Jan 18, 2022
b24f7c6
Merge pull request #524 from mfixstsci/fix-contam-bokeh-dates
nespinoza Jan 18, 2022
12766f0
Updated version number and changelog for v1.2.3
bourque Jan 19, 2022
cf095d9
Merge branch 'develop' into low_hanging_fruit
bourque Feb 1, 2022
4af7b05
Revert ipython and numpy dependencies to avoid security vulnerabilities
bourque Feb 1, 2022
da589b2
Update numpy and ipython to avoid security vulnerabilities
bourque Feb 1, 2022
3a8789b
Using consistent ipython and numpy versions across environments
bourque Feb 1, 2022
8c5689d
Merge pull request #515 from ExoCTK/low_hanging_fruit
bourque Feb 1, 2022
5dcc6c1
Merge branch 'develop' of github.com:ExoCTK/exoctk into v1.2.3
bourque Feb 1, 2022
de9dbce
Updated version numnber
bourque Feb 1, 2022
48a798d
Update CHANGELOG.md
nespinoza Feb 1, 2022
89a5b9b
Update CHANGELOG.md
nespinoza Feb 1, 2022
259f6f9
Merge pull request #525 from ExoCTK/v1.2.3
bourque Feb 2, 2022
fc19f66
Hacking away at an optmial solution here.
hover2pi Feb 10, 2022
17fd573
Hacking away at an optmial solution here.
hover2pi Feb 10, 2022
ddf7ce4
Merge
hover2pi Feb 10, 2022
84d25e0
The contam slog continues
hover2pi Feb 14, 2022
c551acb
The contam slog continues
hover2pi Feb 14, 2022
d3919da
Ugh
hover2pi Feb 17, 2022
37b3419
Ugh
hover2pi Feb 17, 2022
97761da
shakespeare
hover2pi Apr 5, 2022
8896b01
shakespeare
hover2pi Apr 5, 2022
36f5bc9
Updated contam notebook to debug the field_simulator
hover2pi May 12, 2022
367860d
Added model caching for LDC to speed up calculations
hover2pi May 31, 2022
5ed1ec3
Bump version to 1.2.5
hover2pi May 31, 2022
9bac63e
Starting to add order 0 support
hover2pi Jul 29, 2022
ccdfe0b
more improvements
hover2pi Aug 9, 2022
37ab7d2
Major updates to contam tool. Everything works. Just adding finishing…
hover2pi Nov 2, 2022
c1cadeb
Incorporated old contam plot back into the web app
hover2pi Nov 30, 2022
2ed1fff
Merge conflicts
hover2pi Dec 1, 2022
971e40a
Merge conflicts again
hover2pi Dec 2, 2022
839441b
Downgrade batman because of install error in current
hover2pi Dec 2, 2022
09b0eea
i am the batman
hover2pi Dec 2, 2022
82c8a7d
Me code pretty one day
hover2pi Dec 2, 2022
a207a18
Dinna dinna dinna dinnna dinna dinna dinna dinna BATMAM
hover2pi Dec 2, 2022
6c3b829
more conflicts
hover2pi Dec 2, 2022
a09666d
Merge pull request #539 from ExoCTK/cache_ldc_model
hover2pi Dec 2, 2022
0cbc223
merging with develop
hover2pi Jan 23, 2023
652b234
update version in base.html
jaymedina Oct 30, 2020
49132af
pep8 compliance
jaymedina Oct 30, 2020
004d7d9
add condition w/ badPAs
falkben Nov 9, 2020
6e5087d
make binComp a list of floats
jaymedina Oct 20, 2020
a7aabff
removed print statement
jaymedina Oct 20, 2020
975079d
Added CHANGELOG.md to repo
hover2pi Nov 9, 2020
92281ff
Minor edit
hover2pi Nov 9, 2020
824efab
Removed deprecated astropy.extern.six.StringIO dependency, replaced w…
bourque Nov 4, 2020
55bd438
updated asteval dependency
bourque Nov 10, 2020
3ffc816
Attempting to kick-start GitHub which for some reason is not respondi…
bourque Nov 10, 2020
6e09718
Repaired logging code and added logging to all Web tools
hover2pi Dec 4, 2020
e420c3e
Added throughputs from pandeia and helpers function to fetch them
hover2pi Dec 23, 2020
9e5a289
Converted fits files to txt so svo_filters can read them and updated …
hover2pi Dec 23, 2020
56a4675
Updated LDC code to work with svo_filters 0.3.0
hover2pi Dec 31, 2020
8601c28
Checking if PyYAML install is case sensitive
hover2pi Dec 31, 2020
e28f92e
Trying to resolve scipy1.6.0 requires PyYAML5.1.0 but bandit requires…
hover2pi Dec 31, 2020
0364820
Removed bandit temporarily to see if builds pass
hover2pi Jan 4, 2021
1fb4810
Bump svo_filters to v0.3.0 in py3.7 env
hover2pi Jan 4, 2021
81a52fd
Setting scipy bandit and pyyaml versions
hover2pi Jan 4, 2021
565b7ed
PEP compliance for utils.py
hover2pi Jan 4, 2021
0840c56
Removed pinned pyyaml version in setup.py that was breking the conda …
hover2pi Jan 5, 2021
7e0b9fd
werkzug version pin
hover2pi Jan 5, 2021
6146064
Added code to generate JWST throughputs and populated the throughputs…
hover2pi Feb 17, 2021
ca510e1
Upgraded PyYAML>=5.4 as per pyup recommendation
hover2pi Feb 17, 2021
46b64d3
Added try except for pandeia install which is only needed to generate…
hover2pi Feb 18, 2021
b77cf1b
Update cython from 0.29.21 to 0.29.22
pyup-bot Mar 1, 2021
8a4f0a1
Update pandas from 1.2.0 to 1.2.2
pyup-bot Mar 1, 2021
75fe8a6
Update pytest from 6.2.1 to 6.2.2
pyup-bot Mar 1, 2021
723f160
Update pyyaml from 5.3.1 to 5.4.1
pyup-bot Mar 1, 2021
e09bbbf
Update scipy from 1.6.0 to 1.6.1
pyup-bot Mar 1, 2021
73f0927
Update sphinx from 3.4.1 to 3.5.1
pyup-bot Mar 1, 2021
5308f76
Update sqlalchemy from 1.3.22 to 1.3.23
pyup-bot Mar 1, 2021
7ae8db1
Update boto3 from 1.16.47 to 1.16.63
pyup-bot Feb 1, 2021
ba02d90
Update matplotlib from 3.3.3 to 3.3.4
pyup-bot Feb 1, 2021
952b259
Update numpy from 1.19.4 to 1.20.0
pyup-bot Feb 1, 2021
7f42161
Update pandas from 1.2.0 to 1.2.1
pyup-bot Feb 1, 2021
ba7a656
Update pytest from 6.2.1 to 6.2.2
pyup-bot Feb 1, 2021
1db8686
Update pyyaml from 5.3.1 to 5.4.1
pyup-bot Feb 1, 2021
ff33c63
Update sphinx from 3.4.1 to 3.4.3
pyup-bot Feb 1, 2021
04c0d1d
pyup updates 02/21
bourque Feb 2, 2021
87a59ca
Moving flask-wtf back to pip since the latest version doesnt appear t…
bourque Feb 2, 2021
9bbd681
Reverting svo_filters as I dont think updating this may break some th…
bourque Feb 2, 2021
0f863c8
Reverting astropy after some failed tests
bourque Feb 2, 2021
b5a22b1
Added explicity pip dependency
bourque Feb 16, 2021
ec85713
Added python3.8 travis build
bourque Feb 16, 2021
ccb4539
Added dependencies
bourque Feb 16, 2021
8f8bdaa
Initial commit of conda 3.9 env
bourque Feb 16, 2021
e1cae03
Added 3.9 build
bourque Feb 16, 2021
4825865
Skipping jwst_gtvt test when using python3.9
bourque Feb 19, 2021
d9e4b55
Remove support for python 3.6
bourque Feb 19, 2021
2151d0f
March 2021 pyup updates
bourque Mar 2, 2021
56cfadb
Added citation information
bourque Feb 22, 2021
7ca31c4
Fixed and added some badges
bourque Feb 22, 2021
5363c85
The README logo is a bit unecissarily large
bourque Feb 22, 2021
86e209e
Fixed typo
bourque Feb 22, 2021
db2ac5e
Added pysiaf to NIRISS fieldsim
hover2pi Mar 30, 2021
2125f87
optimizing contam tool but need to fix data sources.
hover2pi Apr 27, 2021
b829c35
Undoing previous mess
hover2pi Jan 23, 2023
a16ba26
Merging LDC updates into develop
hover2pi Jan 26, 2023
575fde8
Bump to v1.2.5
hover2pi Jan 26, 2023
922e79b
REsolving rest of LDC merge conflicts
hover2pi Jan 26, 2023
c4e64bb
Merge conflicts
hover2pi Jan 26, 2023
f35a9a0
pinning docutils version
hover2pi Jan 26, 2023
38b85e8
regions and docutils versions
hover2pi Jan 26, 2023
db77b58
Removing docutils pin in setup.py
hover2pi Jan 26, 2023
116adef
Updating test to reflect new value in exomast
hover2pi Jan 26, 2023
4a92d44
Play nice, packages
hover2pi Jan 26, 2023
0142e0e
Messing with sphinx version
hover2pi Jan 26, 2023
7c2b48b
This package stuff is the absolute worst part of programming. I hate it.
hover2pi Jan 26, 2023
72ba5e8
Messing with packages to get build passing
hover2pi Jan 26, 2023
051c7ca
docutils is killing me
hover2pi Jan 26, 2023
a98b794
I hate you sphinx
hover2pi Jan 26, 2023
2e9984c
upgrade astropy
hover2pi Jan 26, 2023
a1a3307
typo
hover2pi Jan 26, 2023
5fffb3d
numpy upgrade so astropy 4.2 works
hover2pi Jan 26, 2023
9bd9f42
astropy bump
hover2pi Jan 30, 2023
fba6531
astropy bump
hover2pi Jan 30, 2023
0c0a736
Starting over with dependencies
hover2pi Feb 14, 2023
965c144
Updated tests
hover2pi Feb 14, 2023
e57ae33
Removed Python 3.7 support
hover2pi Feb 14, 2023
3182119
Removed Python 3.7 support
hover2pi Feb 14, 2023
b30477c
Added python 3.10 support
hover2pi Feb 14, 2023
42b56f1
Upgraded hotsoss to v0.1.8 and fixed broken tests
hover2pi Feb 22, 2023
3036dd7
Why isnt conda installing the astropy version I specify
hover2pi Feb 22, 2023
6acd7d3
Astro-why
hover2pi Feb 22, 2023
3c54f1a
Rolling back dependencies to see what tests fail with old installs
hover2pi Feb 22, 2023
961bf44
I am the batman
hover2pi Feb 22, 2023
1233568
Pinning pyvo
hover2pi Feb 23, 2023
578893f
Perhaps pip installing numpy instead of conda will preserve the versi…
hover2pi Feb 23, 2023
ac6cdd2
Removing old Travis env build.
hover2pi Feb 23, 2023
92ea4e7
Removing reinstall of numpy from ci.yml file
hover2pi Feb 23, 2023
59ff48f
Adding --no-deps flag to exoctk install because everything else is al…
hover2pi Feb 23, 2023
1442195
Adding regions to deps
hover2pi Feb 23, 2023
87b8d57
Adding erfa to deps
hover2pi Feb 23, 2023
1a229c8
Adding pyerfa to deps
hover2pi Feb 23, 2023
656ab61
Reconfigure github actions to only run tests on pull_request
hover2pi Feb 23, 2023
d22b4a1
Use conda, not pip, to install numpy with python3.9 apparently
hover2pi Feb 23, 2023
54b5c6a
Merge pull request #492 from ExoCTK/optimize_contam
hover2pi Feb 23, 2023
8e374aa
Fixed contam_visibility form that got messed up in the merge
hover2pi Mar 1, 2023
3f8c942
Switch pyup ownership from bourque to hover2pi
bourque Mar 1, 2023
e17c310
Merge branch 'develop' into switch-pyup-ownership
hover2pi Mar 1, 2023
819e5bf
Merge pull request #557 from ExoCTK/switch-pyup-ownership
hover2pi Mar 2, 2023
1dc5ffd
Bug fixes
hover2pi Mar 2, 2023
89c2a8b
Updated deps
hover2pi Mar 2, 2023
721ae88
astropy looser pin
hover2pi Mar 2, 2023
0f5821a
Dependencies
hover2pi Mar 2, 2023
907c7f9
Et tu pip?
hover2pi Mar 2, 2023
b33a699
Numpy update
hover2pi Mar 2, 2023
c214c97
Numpy you scaliwag
hover2pi Mar 2, 2023
fc7ab89
numpy you fool
hover2pi Mar 2, 2023
9878072
gtvt commit pin since 0.3.1 not available
hover2pi Mar 2, 2023
990041e
gtvt business
hover2pi Mar 2, 2023
0f5de1e
gtvt business
hover2pi Mar 2, 2023
038d5b1
Updating deprecated readthedocs build info
hover2pi Mar 3, 2023
834f997
Setting python version maybe?
hover2pi Mar 3, 2023
db038a6
Readthedocs... or dont... see if I care
hover2pi Mar 3, 2023
6a38e13
Renamed requirements file
hover2pi Mar 3, 2023
c4fe089
Fixed broken filepath for contam tool plot
hover2pi Mar 3, 2023
7074c89
Merge pull request #559 from ExoCTK/web_patch
hover2pi Mar 7, 2023
030d511
Updated LDC header text written before JWST launched
hover2pi Mar 8, 2023
a68f3f2
Still messing with numpy version
hover2pi Mar 8, 2023
f8186fb
Still messing with numpy version
hover2pi Mar 8, 2023
263517b
Merge pull request #560 from ExoCTK/batbugs
hover2pi Mar 8, 2023
18b3677
Update environment-3.8.yml
hover2pi Mar 8, 2023
3c610e7
Update environment-3.9.yml
hover2pi Mar 8, 2023
61c3d87
Fixed indexing bug in ModelGrid and bumped h5py and numpy
hover2pi Mar 9, 2023
2d939d1
Fixed visPA bug and updated pysiaf and scipy to get tests passing
hover2pi Mar 10, 2023
4988cb3
Package not found errors in build
hover2pi Mar 10, 2023
c27eefc
Merge pull request #561 from ExoCTK/brucewayneisbatman
hover2pi Mar 10, 2023
537ea89
Fixed pa_val bug in contam tool
hover2pi Mar 29, 2023
38155bd
Merge pull request #562 from ExoCTK/pa_val
hover2pi Mar 29, 2023
b5f3bd1
Removing old envs adding new updates ones
mfixstsci Jul 19, 2023
6a7d267
Removing astroconda as install source
mfixstsci Jul 19, 2023
5643b6f
Updating python versions we support in GHA pipeline
mfixstsci Jul 19, 2023
a9ca52d
Added alternate model grid function that just selects the model with …
hover2pi Jul 19, 2023
c78a90f
Changed arg names
hover2pi Jul 19, 2023
6d03187
Added print statement
hover2pi Jul 19, 2023
bdc48ea
Adding conda forge to source
mfixstsci Jul 19, 2023
57ec4a4
Updated LDC and ModelGrid to skip interpolation and just get closest …
hover2pi Jul 19, 2023
9a02df5
Updated hotsoss to v0.1.9 for python 3.9+ support
hover2pi Jul 21, 2023
b434630
Bumping hotsoss version
mfixstsci Jul 21, 2023
f4c42fc
Downgrading hotsoss, hasnt been released to pip yet
mfixstsci Jul 21, 2023
9ab9c33
Upgraded svo_filters to v0.5.0 for py10 support
hover2pi Jul 21, 2023
fd5b704
Bumped hotsoss version to v0.1.9
hover2pi Aug 16, 2023
92430e0
Merge pull request #574 from mfixstsci/update-dependencies-july-18-2023
hover2pi Aug 28, 2023
fd8babc
Merge conflicts
hover2pi Aug 28, 2023
2d0820d
Bumper hotsoss to v0.1.9
hover2pi Aug 28, 2023
fc4492f
Loosened up dependencies
hover2pi Aug 28, 2023
1302925
Updated Panel to TabPanel for bokeh
hover2pi Aug 28, 2023
04800de
Updated LDC tests for bokeh 3.0
hover2pi Aug 28, 2023
979a8c7
Merging develop into ldc_fix
hover2pi Aug 29, 2023
946cd05
Adding new_vis_plot.py module
hover2pi Aug 29, 2023
82f9d19
Added tests for new_vis_plot.py
hover2pi Aug 29, 2023
bae34a3
Fixed plotting stuff
hover2pi Aug 29, 2023
24e940e
Fixed bokeh plot_width issue in LDC and added wavelength ranges to mo…
hover2pi Aug 29, 2023
0ab536d
bohel plot keyword fix
hover2pi Aug 30, 2023
2f2cf7a
pinning werkzeug
hover2pi Aug 30, 2023
2f0795a
Trying to fix visibility table download button
hover2pi Aug 30, 2023
d2517fd
Trying download button
hover2pi Aug 30, 2023
ea1844f
Trying by passing DF to form
hover2pi Aug 30, 2023
d391c89
Save as dat
hover2pi Aug 30, 2023
505d5d8
typo
hover2pi Aug 30, 2023
c40a343
Fixing visib download
hover2pi Aug 30, 2023
e85ffe2
Spruced up contam plot reeeeal nice
hover2pi Sep 1, 2023
f890313
Hovertool kwarg update
hover2pi Sep 1, 2023
0621b0f
Reduced max cores to 8
hover2pi Sep 1, 2023
0b190ac
Superfluous line
hover2pi Sep 1, 2023
efcc196
Fixed the tap tool for contam plots
hover2pi Sep 5, 2023
8382b56
Fixed requirements so RTD build passes
hover2pi Sep 26, 2023
4270614
Merge pull request #575 from ExoCTK/ldc_fix
hover2pi Sep 26, 2023
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Update pytest from 6.2.1 to 6.2.2
  • Loading branch information
pyup-bot authored and hover2pi committed Jan 23, 2023
commit 75fe8a6928f92b975e70010b5b5fa9f51364611d
2 changes: 1 addition & 1 deletion pip_requirements.txt
Original file line number Diff line number Diff line change
@@ -25,7 +25,7 @@ paramiko==2.7.2
platon==5.1.2
pysiaf==0.10.0
pysynphot==1.0.0
pytest==6.2.1
pytest==6.2.2
pyyaml==5.3.1
scipy==1.6.0
scp==0.13.3