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kevin218 / Eureka

Eureka! is a data reduction and analysis pipeline intended for time-series observations with JWST.
https://eurekadocs.readthedocs.io/
MIT License
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[Bug]: AttributeError: No attribute 'wcs' #569

Closed taylorbell57 closed 9 months ago

taylorbell57 commented 10 months ago

FAQ check

Instrument

NIRCam (Stages 1-3)

What happened?

I'm currently unable to get Stage 2 to run for some new NIRCam data that I'm trying to work on, getting an error message that I've copied below. I've tried running Stage 2 on newer Stage 1 files (where I encountered this issue) and old Stage 1 files (where I know Stage 2 previously worked) from different datasets, and the result is the same either way, so the issue isn't with the particular dataset I'm using. I've also tried different choices of tsgrism_extract_height (128, 64, None, or removed from the ECF) and slit_y_low and slit_y_high (removed from the ECF, or both set to None), and had no success either.

I don't have all the information about my old environment (got corrupted), but I do know that I was using jwst=1.8.3; CRDS=11.16.16; and pmap=1019 when Stage 2 previously worked for me on one specific dataset. Currently, I'm using jwst=1.10.2; CRDS=11.17.2; and pmap=1137 which is giving me this current issue. I've tried

I'm a bit at a loss as to what is causing this issue with the assign_wcs step (which then cascades down to the later steps), but I'm logging these details here and will circle back to try fixing this when I get the chance. If anyone else has encountered and overcode this issue, please let me know.

Error traceback output

2023-10-16 17:49:27,794 - stpipe.EurekaSpec2Pipeline.assign_wcs - INFO - Step assign_wcs running with args (<CubeModel(190, 256, 2048) from jw01185002001_04103_00001-seg001_nrcalong_rateints.fits>,).
2023-10-16 17:49:27,796 - stpipe.EurekaSpec2Pipeline.assign_wcs - INFO - Step assign_wcs parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/Volumes/DataDrive/WASP-80b_Transit_F322W2/Stage1/S1_2022-12-14_WASP80b_transit_F322W2_run1', 'sip_approx': True, 'sip_max_pix_error': 0.1, 'sip_degree': None, 'sip_max_inv_pix_error': 0.1, 'sip_inv_degree': None, 'sip_npoints': 12, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2023-10-16 17:49:28,176 - stpipe.EurekaSpec2Pipeline.assign_wcs - INFO - Added Barycentric velocity correction: 0.9999031902262419
2023-10-16 17:49:29,317 - stpipe.EurekaSpec2Pipeline.assign_wcs - WARNING - /Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/stdatamodels/validate.py:38: ValidationWarning: While validating wcs the following error occurred:
[<Polynomial2D(3, c0_0=-40.95308741, c1_0=0.03452866, c2_0=-0.00001798, c3_0=0., c0_1=0.00613772, c0_2=0.0000072, c0_3=-0., c1_1=-0.00001475, c1_2=0., c2_1=0.)>, <Polynomial2D(3, c0_0=36.1952759, c1_0=-0.06538841, c2_0=0.00003367, c3_0=-0.00000001, c0_1=-0.00570083, c0_2=-0.00001767, c0_3=0., c1_1=0.00002132, c1_2=0., c2_1=-0.00000001)>, <Polynomial2D(3, c0_0=-20.02206904, c1_0=0.03284551, c2_0=-0.0000166, c3_0=0., c0_1=-0.00243588, c0_2=0.00001326, c0_3=-0., c1_1=-0.00000786, c1_2=-0., c2_1=0.)>] is not of type 'object'

Failed validating 'type' in schema['allOf'][1]['properties']['ymodels']['items']:
    {'$schema': 'http://stsci.edu/schemas/yaml-schema/draft-01',
     'additionalProperties': True,
     'definitions': {'bound': {'anyOf': [{'type': 'number'},
                                         {'type': 'null'}]}},
     'description': 'These objects are designed to be nested in arbitrary '
                    'ways to build up transformation pipelines out of a '
                    'number of low-level pieces.\n',
     'examples': [['A transform with no bounding_box or '
                   'compound_bounding_box',
                   '!transform/transform-1.2.0\n'
                   '  name: test\n'
                   "  inputs: ['x', 'y']\n"
                   "  outputs: ['z']\n"
                   '  fixed:\n'
                   '    a: True\n'
                   '    b: False\n'
                   '  bounds:\n'
                   '    c: [-1, 2]\n'
                   '    d: [-3, null]\n'],
                  ['A transform with old-style 1D bounding_box',
                   '!transform/transform-1.2.0\n'
                   '  name: test\n'
                   "  inputs: ['x']\n"
                   "  outputs: ['y']\n"
                   '  bounding_box: [1.0, 2.0]\n'],
                  ['A transform with new-style 1D bounding_box',
                   '!transform/constant-1.4.0\n'
                   '  name: test\n'
                   '  value: 1\n'
      ...
  warnings.warn(errmsg, ValidationWarning)

2023-10-16 17:49:29,319 - stpipe.EurekaSpec2Pipeline.assign_wcs - INFO - COMPLETED assign_wcs
2023-10-16 17:49:29,341 - stpipe.EurekaSpec2Pipeline.assign_wcs - INFO - Step assign_wcs done
2023-10-16 17:49:29,453 - stpipe.EurekaSpec2Pipeline.imprint_subtract - INFO - Step imprint_subtract running with args (<CubeModel(190, 256, 2048) from jw01185002001_04103_00001-seg001_nrcalong_rateints.fits>, []).
2023-10-16 17:49:29,454 - stpipe.EurekaSpec2Pipeline.imprint_subtract - INFO - Step imprint_subtract parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/Volumes/DataDrive/WASP-80b_Transit_F322W2/Stage1/S1_2022-12-14_WASP80b_transit_F322W2_run1'}
2023-10-16 17:49:29,454 - stpipe.EurekaSpec2Pipeline.imprint_subtract - INFO - Step skipped.
2023-10-16 17:49:29,458 - stpipe.EurekaSpec2Pipeline.imprint_subtract - INFO - Step imprint_subtract done
2023-10-16 17:49:29,560 - stpipe.EurekaSpec2Pipeline.bkg_subtract - INFO - Step bkg_subtract running with args (<CubeModel(190, 256, 2048) from jw01185002001_04103_00001-seg001_nrcalong_rateints.fits>, []).
2023-10-16 17:49:29,561 - stpipe.EurekaSpec2Pipeline.bkg_subtract - INFO - Step bkg_subtract parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/Volumes/DataDrive/WASP-80b_Transit_F322W2/Stage1/S1_2022-12-14_WASP80b_transit_F322W2_run1', 'save_combined_background': False, 'sigma': 3.0, 'maxiters': None, 'wfss_mmag_extract': None}
2023-10-16 17:49:29,561 - stpipe.EurekaSpec2Pipeline.bkg_subtract - INFO - Step skipped.
2023-10-16 17:49:29,566 - stpipe.EurekaSpec2Pipeline.bkg_subtract - INFO - Step bkg_subtract done
2023-10-16 17:49:29,683 - stpipe.EurekaSpec2Pipeline.msa_flagging - INFO - Step msa_flagging running with args (<CubeModel(190, 256, 2048) from jw01185002001_04103_00001-seg001_nrcalong_rateints.fits>,).
2023-10-16 17:49:29,684 - stpipe.EurekaSpec2Pipeline.msa_flagging - INFO - Step msa_flagging parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/Volumes/DataDrive/WASP-80b_Transit_F322W2/Stage1/S1_2022-12-14_WASP80b_transit_F322W2_run1'}
2023-10-16 17:49:29,685 - stpipe.EurekaSpec2Pipeline.msa_flagging - INFO - Step skipped.
2023-10-16 17:49:29,691 - stpipe.EurekaSpec2Pipeline.msa_flagging - INFO - Step msa_flagging done
2023-10-16 17:49:29,810 - stpipe.EurekaSpec2Pipeline.flat_field - INFO - Step flat_field running with args (<CubeModel(190, 256, 2048) from jw01185002001_04103_00001-seg001_nrcalong_rateints.fits>,).
2023-10-16 17:49:29,811 - stpipe.EurekaSpec2Pipeline.flat_field - INFO - Step flat_field parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/Volumes/DataDrive/WASP-80b_Transit_F322W2/Stage1/S1_2022-12-14_WASP80b_transit_F322W2_run1', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2023-10-16 17:49:31,013 - stpipe.EurekaSpec2Pipeline.flat_field - INFO - Extracting matching subarray from flat
2023-10-16 17:49:32,558 - stpipe.EurekaSpec2Pipeline.flat_field - INFO - Step flat_field done
2023-10-16 17:49:32,672 - stpipe.EurekaSpec2Pipeline.extract_2d - INFO - Step extract_2d running with args (<CubeModel(190, 256, 2048) from jw01185002001_04103_00001-seg001_nrcalong_rateints.fits>,).
2023-10-16 17:49:32,673 - stpipe.EurekaSpec2Pipeline.extract_2d - INFO - Step extract_2d parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/Volumes/DataDrive/WASP-80b_Transit_F322W2/Stage1/S1_2022-12-14_WASP80b_transit_F322W2_run1', 'slit_name': None, 'extract_orders': None, 'grism_objects': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'wfss_mmag_extract': None, 'wfss_nbright': 1000}
2023-10-16 17:49:32,708 - stpipe.EurekaSpec2Pipeline.extract_2d - INFO - EXP_TYPE is NRC_TSGRISM
2023-10-16 17:49:32,708 - stpipe.EurekaSpec2Pipeline.extract_2d - INFO - Setting extraction height to 64
2023-10-16 17:49:32,732 - stpipe.EurekaSpec2Pipeline.extract_2d - INFO - Using default order extraction from reference file
2023-10-16 17:49:32,732 - stpipe.EurekaSpec2Pipeline.extract_2d - INFO - Extracting order: [1]
Traceback (most recent call last):
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/stdatamodels/properties.py", line 327, in __getattr__
    val = self._instance[attr]
KeyError: 'wcs'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/pipeline/calwebb_spec2.py", line 120, in process
    result = self.process_exposure_product(
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/pipeline/calwebb_spec2.py", line 264, in process_exposure_product
    calibrated = self._process_grism(calibrated)
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/pipeline/calwebb_spec2.py", line 470, in _process_grism
    calibrated = self.extract_2d(calibrated)
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/stpipe/step.py", line 454, in run
    step_result = self.process(*args)
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/extract_2d/extract_2d_step.py", line 37, in process
    output_model = extract_2d.extract2d(dm, self.slit_name,
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/extract_2d/extract_2d.py", line 74, in extract2d
    output_model = extract_tso_object(input_model,
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/extract_2d/grisms.py", line 125, in extract_tso_object
    subwcs = copy.deepcopy(input_model.meta.wcs)
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/stdatamodels/properties.py", line 330, in __getattr__
    raise AttributeError("No attribute '{0}'".format(attr))
AttributeError: No attribute 'wcs'
Traceback (most recent call last):
  File "/Users/tjbell1/Research/JWST/ERS/Eureka/ecfs/WASP80b_transit_F444W/run_eureka.ecf", line 21, in <module>
    s2_meta = s2.calibrateJWST(eventlabel)
  File "/Users/tjbell1/Research/JWST/ERS/Eureka/ecfs/WASP80b_transit_F444W/../../src/eureka/S2_calibrations/s2_calibrate.py", line 177, in calibrateJWST
    pipeline.run_eurekaS2(filename, meta, log)
  File "/Users/tjbell1/Research/JWST/ERS/Eureka/ecfs/WASP80b_transit_F444W/../../src/eureka/S2_calibrations/s2_calibrate.py", line 279, in run_eurekaS2
    self(filename)
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/stpipe/step.py", line 454, in run
    step_result = self.process(*args)
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/pipeline/calwebb_spec2.py", line 138, in process
    raise RuntimeError('\n'.join(failures))
RuntimeError: Traceback (most recent call last):
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/stdatamodels/properties.py", line 327, in __getattr__
    val = self._instance[attr]
KeyError: 'wcs'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/pipeline/calwebb_spec2.py", line 120, in process
    result = self.process_exposure_product(
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/pipeline/calwebb_spec2.py", line 264, in process_exposure_product
    calibrated = self._process_grism(calibrated)
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/pipeline/calwebb_spec2.py", line 470, in _process_grism
    calibrated = self.extract_2d(calibrated)
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/stpipe/step.py", line 454, in run
    step_result = self.process(*args)
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/extract_2d/extract_2d_step.py", line 37, in process
    output_model = extract_2d.extract2d(dm, self.slit_name,
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/extract_2d/extract_2d.py", line 74, in extract2d
    output_model = extract_tso_object(input_model,
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/jwst/extract_2d/grisms.py", line 125, in extract_tso_object
    subwcs = copy.deepcopy(input_model.meta.wcs)
  File "/Users/tjbell1/miniconda3/envs/eureka_starry/lib/python3.9/site-packages/stdatamodels/properties.py", line 330, in __getattr__
    raise AttributeError("No attribute '{0}'".format(attr))
AttributeError: No attribute 'wcs'

What operating system are you using?

macOS Ventura 13.6

What version of Python are you running?

Python 3.9.7

What Python packages do you have installed?

# Name                    Version                   Build  Channel
aesara-theano-fallback    0.1.0                    pypi_0    pypi
alabaster                 0.7.13                   pypi_0    pypi
anyio                     3.7.1                    pypi_0    pypi
appnope                   0.1.3                    pypi_0    pypi
argon2-cffi               21.3.0                   pypi_0    pypi
argon2-cffi-bindings      21.2.0                   pypi_0    pypi
arrow                     1.2.3                    pypi_0    pypi
arviz                     0.12.1                   pypi_0    pypi
asciitree                 0.3.3                    pypi_0    pypi
asdf                      2.15.0                   pypi_0    pypi
asdf-astropy              0.4.0                    pypi_0    pypi
asdf-coordinates-schemas  0.2.0                    pypi_0    pypi
asdf-standard             1.0.3                    pypi_0    pypi
asdf-transform-schemas    0.3.0                    pypi_0    pypi
asdf-unit-schemas         0.1.0                    pypi_0    pypi
asdf-wcs-schemas          0.1.1                    pypi_0    pypi
asteval                   0.9.31                   pypi_0    pypi
astraeus                  0.3                      pypi_0    pypi
astropy                   5.3.1                    pypi_0    pypi
astropy-healpix           0.7                      pypi_0    pypi
astroquery                0.4.6                    pypi_0    pypi
astroscrappy              1.1.0                    pypi_0    pypi
asttokens                 2.2.1                    pypi_0    pypi
async-lru                 2.0.4                    pypi_0    pypi
attrs                     23.1.0                   pypi_0    pypi
babel                     2.12.1                   pypi_0    pypi
backcall                  0.2.0                    pypi_0    pypi
batman-package            2.4.9                    pypi_0    pypi
bayesicfitting            3.1.1                    pypi_0    pypi
beautifulsoup4            4.12.2                   pypi_0    pypi
bidict                    0.22.1                   pypi_0    pypi
bleach                    6.0.0                    pypi_0    pypi
bokeh                     2.4.3                    pypi_0    pypi
bottleneck                1.3.7                    pypi_0    pypi
ca-certificates           2023.7.22            h8857fd0_0    conda-forge
cachetools                5.3.1                    pypi_0    pypi
ccdproc                   2.4.1                    pypi_0    pypi
celerite                  0.4.2                    pypi_0    pypi
celerite2                 0.3.0rc2.dev11+g74b0705.d20230915          pypi_0    pypi
certifi                   2023.7.22                pypi_0    pypi
cffi                      1.15.1                   pypi_0    pypi
cftime                    1.6.2                    pypi_0    pypi
charset-normalizer        3.2.0                    pypi_0    pypi
click                     8.1.6                    pypi_0    pypi
cloudpickle               2.2.1                    pypi_0    pypi
comm                      0.1.4                    pypi_0    pypi
contourpy                 1.1.0                    pypi_0    pypi
corner                    2.2.2                    pypi_0    pypi
coverage                  7.3.0                    pypi_0    pypi
crds                      11.17.2                  pypi_0    pypi
cycler                    0.11.0                   pypi_0    pypi
cython                    3.0.0                    pypi_0    pypi
dask                      2023.8.0                 pypi_0    pypi
debugpy                   1.6.7.post1              pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
defusedxml                0.7.1                    pypi_0    pypi
deprecat                  2.1.1                    pypi_0    pypi
dill                      0.3.7                    pypi_0    pypi
docutils                  0.18.1                   pypi_0    pypi
drizzle                   1.13.7                   pypi_0    pypi
dynesty                   2.1.2                    pypi_0    pypi
emcee                     3.1.4                    pypi_0    pypi
entrypoints               0.4                      pypi_0    pypi
eureka                    0.10.dev72+g819c00ba.d20230814          pypi_0    pypi
exceptiongroup            1.1.3                    pypi_0    pypi
executing                 1.2.0                    pypi_0    pypi
exoplanet                 0.5.3                    pypi_0    pypi
exoplanet-core            0.1.2                    pypi_0    pypi
exotic-ld                 3.0.0                    pypi_0    pypi
fasteners                 0.18                     pypi_0    pypi
fastjsonschema            2.18.0                   pypi_0    pypi
fastprogress              1.0.3                    pypi_0    pypi
filelock                  3.12.2                   pypi_0    pypi
flake8                    6.1.0                    pypi_0    pypi
fonttools                 4.42.0                   pypi_0    pypi
fqdn                      1.5.1                    pypi_0    pypi
fsspec                    2023.6.0                 pypi_0    pypi
future                    0.18.3                   pypi_0    pypi
george                    0.4.0                    pypi_0    pypi
gwcs                      0.18.3                   pypi_0    pypi
h5netcdf                  1.2.0                    pypi_0    pypi
h5py                      3.9.0                    pypi_0    pypi
html5lib                  1.1                      pypi_0    pypi
idna                      3.4                      pypi_0    pypi
image-registration        0.2.7.dev20+gb42a1af          pypi_0    pypi
imageio                   2.31.1                   pypi_0    pypi
imagesize                 1.4.1                    pypi_0    pypi
importlib-metadata        6.8.0                    pypi_0    pypi
importlib-resources       6.0.1                    pypi_0    pypi
iniconfig                 2.0.0                    pypi_0    pypi
ipykernel                 6.25.1                   pypi_0    pypi
ipython                   8.14.0                   pypi_0    pypi
ipython-genutils          0.2.0                    pypi_0    pypi
ipywidgets                8.1.0                    pypi_0    pypi
isoduration               20.11.0                  pypi_0    pypi
jaraco-classes            3.3.0                    pypi_0    pypi
jedi                      0.19.0                   pypi_0    pypi
jinja2                    3.1.2                    pypi_0    pypi
jmespath                  1.0.1                    pypi_0    pypi
json5                     0.9.14                   pypi_0    pypi
jsonpointer               2.4                      pypi_0    pypi
jsonschema                4.17.3                   pypi_0    pypi
jupyter                   1.0.0                    pypi_0    pypi
jupyter-client            8.3.0                    pypi_0    pypi
jupyter-console           6.6.3                    pypi_0    pypi
jupyter-core              5.3.1                    pypi_0    pypi
jupyter-events            0.6.3                    pypi_0    pypi
jupyter-lsp               2.2.0                    pypi_0    pypi
jupyter-server            2.7.0                    pypi_0    pypi
jupyter-server-terminals  0.4.4                    pypi_0    pypi
jupyterlab                4.0.5                    pypi_0    pypi
jupyterlab-pygments       0.2.2                    pypi_0    pypi
jupyterlab-server         2.24.0                   pypi_0    pypi
jupyterlab-widgets        3.0.8                    pypi_0    pypi
jwst                      1.10.2                   pypi_0    pypi
keyring                   24.2.0                   pypi_0    pypi
kiwisolver                1.4.4                    pypi_0    pypi
libcxx                    16.0.6               hd57cbcb_0    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libsqlite                 3.42.0               h58db7d2_0    conda-forge
libzlib                   1.2.13               h8a1eda9_5    conda-forge
llvm-openmp               16.0.6               hff08bdf_0    conda-forge
lmfit                     1.2.2                    pypi_0    pypi
locket                    1.0.0                    pypi_0    pypi
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                2.1.3                    pypi_0    pypi
matplotlib                3.7.1                    pypi_0    pypi
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Code of Conduct

taylorbell57 commented 10 months ago

Huh, well I don't know whether or not this is resolvable with jwst==1.10.2, but upgrading to jwst==1.11.4 (which updates stcal, stdatamodels, and stpipe, one of which is likely what is causing my bug, and none of which can be updated with jwst==1.10.2) and setting a new upper limit of xarray<2023.10.0 (to avoid issues with pymc3) did the job for me. Any reservations against applying those changes, @kevin218?

One headache that we have coming is that jwst>=1.12 requires numpy>1.22 while all the pymc3 code requires numpy<1.22... No idea how we're going to overcome that one in the future without (1) abandoning the pymc3 code which would be such an enormous pain (so many hours spent on that code) and wouldn't allow for eclipse mapping, or (2) not allowing jwst and pymc3 to be installed in the same environment...

kevin218 commented 10 months ago

As long as it works for all instruments, I support applying these changes. We should then move to v0.10.

Neither of these options is desirable. Is there any hope of submitting a PR that updates pymc3 to be compatible with newer versions of numpy?

taylorbell57 commented 10 months ago

I re-ran the tests and they all worked fine, but I haven't had the time yet to re-run some old datasets to make sure they're processed reasonably; I'll do so in a few days when I get the chance.

As for updating pymc3, I'm pretty sure that version of the code (which is now called just pymc) is officially deprecated since theano is officially deprecated and not accepting edits, but I did find https://github.com/exoplanet-dev/theano-exoplanet which might help us get part of the way. I also know Dan and some other students/postdocs are working on revamping starry to eventually use jax or something else (potentially it is this under-development repo: https://github.com/exoplanet-dev/jaxoplanet).