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supreme-spoon's Introduction

supreme-SPOON

supreme-Steps to Process SOSS ObservatioNs

⭐⭐ Please note that supreme-SPOON has undergone a rebrand and future versions (>=1.4.0) will use a new name, exoTEDRF. ⭐⭐
This repository will remain in existence (though it will no longer be updated). All updates to this project will now be in the exoTEDRF repository.

supreme-SPOON is an end-to-end pipeline for NIRISS/SOSS time series observations (TSOs). The pipeline is divided into four stages:

  • Stage 1: Detector Level Processing
  • Stage 2: Spectroscopic Processing
  • Stage 3: 1D Spectral Extraction
  • Stage 4: Light Curve Fitting (optional)

Installation Instructions

The latest release of supreme-SPOON can be downloaded from PyPI by running:

pip install supreme_spoon

Depending on the operating system, the package jmespath may fail to install. In this case, run pip install jmespath, and then proceed with the supreme-SPOON installation.

The default pip installation only includes Stages 1 to 3. Stage 4 can be included via specifying the following option during installation:

pip install supreme_spoon[stage4]

Note that the radvel package may fail to build during the installation of Stage4. If so, simply run pip install cython, and then proceed with the supreme-SPOON installation as before.

The latest development version can be grabbed from GitHub (inlcludes all pipeline stages):

git clone https://github.com/radicamc/supreme-spoon
cd supreme_spoon
python setup.py install

Note that supreme-SPOON is currently compatible with python 3.10.4 and v1.12.5 of the jwst package maintained by STScI. If you wish to run a different version of jwst, certain functionalities of supreme-SPOON may not work.

Usage Instructions

The supreme-SPOON pipeline can be run in a similar fashion to jwst by individually calling each step. Alternatively, Stages 1 to 3 can be run at once via the run_DMS.py script.

  1. Copy the run_DMS.py script and the run_DMS.yaml config file into your working directory.
  2. Fill out the yaml file with the appropriate inputs.
  3. Once happy with the input parameters, enter python run_DMS.py run_DMS.yaml in the terminal.

To use the light curve fitting capabilities (if installed), simply follow the same procedure with the fit_lightcurves.py and .yaml files.

ATOCA Caveats

supreme-SPOON has the ability to run the ATOCA extraction algorithm to explicitly model the overlap of the first and second SOSS spectral orders on the detector. ATOCA is now the default extract1d method in the STScI jwst pipeline, however, since jwst v1.9.0 it is partially broken. In order to use ATOCA, you must install jwst v1.8.5. You may also need to specifically install astropy v5.3.4 and asdf v2.15.2. All other pipeline functionalities should work with this jwst version. With jwst v1.8.5 a pipeline error stpipe.config_parser.ValidationError: Extra value 'edge_size' in root may be encountered during the JumpStep, if specifying fit_up_ramp=True. This comes from a STScI update to the JumpStep parameter file which is not backwards compatible. To circumvent this error, one can download an older version of the parameter file from the CRDS. Navigate to the niriss downdown menu, and then to pars-jumpstep. Download the file jwst_niriss_pars-jumpstep_0020.asdf. Then rename it jwst_niriss_pars-jumpstep_0081.asdf (or whichever is the most recent version) and replace the automatically downloaded parameter file in your crds_cache directory.

Citations

If you make use of this code in your work, please cite Radica et al. (2023) and Feinstein et al. (2023).

Additional Citations

If you use the ATOCA extraction algorithm, please also cite Radica et al. (2022) and Darveau-Bernier et al. (2022).

If you make use of the light curve fitting routines, also include the following citations for juliet, batman, dynesty, and Kipping et al. (2013) for the limb-darkening sampling. If you use Gaussian Processes please cite celerite, and if you use ExoTiC-LD for limb darkening priors cite Grant & Wakeford (2022). Please also see the ExoTiC-LD documentation for information on the types of stellar grids available and ensure to correctly download and cite the desired models.

Lastly, you should cite the libraries upon which this code is built, namely: numpy, scipy, astropy, and of course jwst.

supreme-spoon's People

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witchblade101 lheinke

supreme-spoon's Issues

Incorporate pastasoss

Should incorporate pastasoss code to calculate trace positions/wavelength solution based on pupil wheel positions.

Pipeline crashes at `Extract1dStep`

I have been running the pipeline using the installation procedure described in issue #20 and the run_DMS.yaml setup. It crashes at the Extract1dStep:

2023-08-24 07:43:43,878 - stpipe.Extract1dStep - INFO - Extract1dStep instance created.
Traceback (most recent call last):
  File "/home/lheinke/Data/JWST/run_DMS.py", line 98, in <module>
    stage2_results = run_stage2(stage1_results,
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon/lib/python3.11/site-packages/supreme_spoon-1.1.1-py3.11.egg/supreme_spoon/stage2.py", line 1526, in run_stage2
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon/lib/python3.11/site-packages/supreme_spoon-1.1.1-py3.11.egg/supreme_spoon/stage2.py", line 336, in run
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon/lib/python3.11/site-packages/supreme_spoon-1.1.1-py3.11.egg/supreme_spoon/stage2.py", line 850, in tracingstep
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon/lib/python3.11/site-packages/supreme_spoon-1.1.1-py3.11.egg/supreme_spoon/utils.py", line 476, in get_trace_centroids
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon/lib/python3.11/site-packages/applesoss-2.0.0-py3.11.egg/applesoss/edgetrigger_centroids.py", line 1071, in get_soss_centroids
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon/lib/python3.11/site-packages/applesoss-2.0.0-py3.11.egg/applesoss/edgetrigger_centroids.py", line 295, in get_centroids_edgetrigger
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon/lib/python3.11/site-packages/applesoss-2.0.0-py3.11.egg/applesoss/edgetrigger_utils.py", line 146, in get_image_dim
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon/lib/python3.11/site-packages/numpy/__init__.py", line 319, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'int'.
`np.int` was a deprecated alias for the builtin `int`. To avoid this error in existing code, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'inf'?

I checked the APPLESOSS repository and found issue radicamc/applesoss#7 which seems to be exactly the problem I encountered. Looking at the day of the fix April 3 it becomes clear that it is not part of the most recent 2.0.0 release from March 13 that also gets installed via pip when installing supreme-SPOON.

Manually installing the package applesoss from GitHub fixes the issue as expected.

Update compatibility with jwst pipeline

Work on updating compatibility to more current versions of jwst pipeline. Namely to incorporate new charge migration mitigation step and improvements to jump detection.

Citations

I think you should probably add that one should really cite the JWST pipeline in your citation sections, supreme-spoon relies heavily on stage 1 and stage 2 pipeline steps.

i.e. at the least this needs to change to include the jwst pipeline

Lastly, you should cite the libraries upon which this code is built, namely: numpy, scipy, and astropy.

Incompatible asdf version on fresh install

Running the fit_lightcurves.py file with a fresh install of the new pipeline version (1.2.0) results in the following error:

Traceback (most recent call last):
  File "/home/lheinke/MIRI_Exo_GTO/JWST/1281 [HAT-P-12b]/Observation 3 [NIRISS-SOSS]/Reduction/supreme-SPOON/fit_lightcurves.py", line 25, in <module>
    from supreme_spoon import stage4
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon_new/lib/python3.10/site-packages/supreme_spoon/stage4.py", line 20, in <module>
    from jwst import datamodels
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon_new/lib/python3.10/site-packages/jwst/datamodels/__init__.py", line 1, in <module>
    from .model_base import JwstDataModel, DataModel
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon_new/lib/python3.10/site-packages/jwst/datamodels/model_base.py", line 2, in <module>
    from stdatamodels import DataModel as _DataModel
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon_new/lib/python3.10/site-packages/stdatamodels/__init__.py", line 1, in <module>
    from .model_base import DataModel
  File "/home/lheinke/.local/miniconda3/envs/supreme_spoon_new/lib/python3.10/site-packages/stdatamodels/model_base.py", line 21, in <module>
    from asdf.fits_embed import AsdfInFits
ModuleNotFoundError: No module named 'asdf.fits_embed'

I was able to fix it by manually installing asdf version 2.15.2. Perhaps this requirement should be added to the setup.py file. Given that this incompatibility originates from the dependency of the jwst package on asdf, this requirement will probably not be necessary anymore once supreme-SPOON migrates to a newer version of jwst.

Pip installing outdated version

I set up a conda environment with the Python version fixed to 3.10.4 as recommended in the README. When trying to install supreme-SPOON via pip it installs the outdated 1.0.0 version. This happens even when telling it to download it and not take it from cache and to upgrade it to the most recent version:

$ pip install --no-cache-dir --upgrade supreme_spoon

When fixing the version to the newest 1.1.6 release the following error occurs:

$ pip install supreme_spoon==1.1.6
ERROR: Ignored the following versions that require a different python version: 1.1.6 Requires-Python ==3.10
ERROR: Could not find a version that satisfies the requirement supreme_spoon==1.1.6 (from versions: 0.0.1, 0.1.0, 0.2.0, 1.0.0)
ERROR: No matching distribution found for supreme_spoon==1.1.6

This comes from is caused by the restriction added in commit 747c09e. I think the restriction should be removed/softened. Recommending a version as is done in the README makes sense, distributing an outdated version of the package to everyone with a slightly different Python version that contains #22 , a bug that breaks the pipeline will cause confusion. Perhaps the version should even be removed from PyPI?

Endless Loop at Jump Step

Michael,

I tried running Stage 1 as a test this afternoon. Everything looked OK until it tried the jump detection step, then it seemed to get into an endless loop. After an hour of no progress I killed the run.

My Run_DMS.yaml and the console output are attached.

run_DMS.yaml.txt

output.txt

Time axis not in spectrum files

It seems like the time axis is not being appended to the stage 3 output files.
Not sure if this is a global problem, or something funky with one or two datasets.

[Bug] Missing function in pip install

Trying to run the pipeline using run_DMS.py after installing via pip install supreme_spoon results in the following error:

$ python run_DMS.py run_DMS.yaml
WebbPSF not installed. Profile simulation not available.
Traceback (most recent call last):
  File "/home/lheinke/Data/JWST/1281/run_DMS.py", line 21, in <module>
    from supreme_spoon.utils import fancyprint, parse_config, unpack_input_dir, \
ImportError: cannot import name 'unpack_input_dir' from 'supreme_spoon.utils' (/home/lheinke/.virtualenvs/supreme_spoon/lib/python3.11/site-packages/supreme_spoon/utils.py)

This seems to be due to a very outdated version of the package on PyPI. The most recent available version is 1.0.0 while the latest release on this repository is already at 1.1.1.

Installation troubles (Linux)

I ran into an issue trying to install the package, which send me down a rabbit hole of fixing several new issues that popped up after each attempted fix. I tried to install the package using the GitHub repo like it is explained in the README.md file. These issues occurred on a Linux system, Ubuntu 23.04 to be precise, but I could exactly reproduce them on a Fedora 38 system.

I will briefly describe the problems that occurred, what I did to fix them, and then go to the resulting issue. I included more detailed excerpts of the log/traceback below.

  1. When trying to install the jwst package, there is an error that the numpy package is missing [1]
    • Attempted fix: Run pip install numpy before using the setup.py
  2. When trying to install the ultranest package, there is an error that the Cython package is missing [2]
    • Attempted fix: Run pip install numpy Cython before using the setup.py
  3. There is now another error during the ultranest installation process [3]](#issue-3)
    • Attempted fix: Run pip install numpy Cython ultranest before using the setup.py
  4. When trying to install the celerite package, there is an error that the pybind11 package is missing [4]
    • Attempted fix: Run pip install numpy Cython ultranest pybind11 before using the setup.py
  5. When trying to install the radvel package, there is an attribute error related to NumPy [5]
    • Attempted fix: Run pip install numpy Cython ultranest pybind11 radvel before using the setup.py
  6. This lead to a build error during the radvel package installation. Comments on the StackOverflow seemto suggest that this is again Cython related [6]
    • Attempted fix: Run pip install numpy Cython ultranest pybind11 first and then pip install radvel before using the setup.py

After this the installation using setup.py finishes without complaints. I am not confident that the resulting Python environment is in the correct state of packages. The final set of installed packages and their versions can be found below. The list provided by condais missing some packages that only show up when listing with pip. Very weirdly, there are also many duplicate listings. I think this is related to outdated installation methods that pip also constantly complained about during installation.

Question: Should a certain Python version be used? Perhaps the 3.11 version I installed is more recent than what supreme-SPOON has been developed for? The jwst pipeline requires at least Python 3.9.

Even if this environment should be functional, this complicated installation process should either be fixed or at least described within the README.md file.

Logs/tracebacks

Issue 1

Installed /home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/matplotlib-3.8.0rc1-py3.11-linux-x86_64.egg
Searching for jwst==1.8.5
Reading https://pypi.org/simple/jwst/
Downloading https://files.pythonhosted.org/packages/02/16/bfa4f888b7da338dfdf49bb758ff75ed5e6c8dadaa585b9184e50659b474/jwst-1.8.5.tar.gz#sha256=a8b09b4f90b425d2b132f1e1db1e4f20bc943cb1def76d9c5f811f371c47946f
Best match: jwst 1.8.5
Processing jwst-1.8.5.tar.gz
Writing /tmp/easy_install-jbw43e2t/jwst-1.8.5/setup.cfg
Running jwst-1.8.5/setup.py -q bdist_egg --dist-dir /tmp/easy_install-jbw43e2t/jwst-1.8.5/egg-dist-tmp-7lg189fo
Traceback (most recent call last):
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 156, in save_modules
    yield saved
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 198, in setup_context
    yield
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 259, in run_setup
    _execfile(setup_script, ns)
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 46, in _execfile
    exec(code, globals, locals)
  File "/tmp/easy_install-jbw43e2t/jwst-1.8.5/setup.py", line 4, in <module>
    from setuptools import setup
    ^^^^^^^^^^^^
ModuleNotFoundError: No module named 'numpy'

Issue 2

Installed /home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/asdf-2.15.1-py3.11.egg
Searching for ultranest
Reading https://pypi.org/simple/ultranest/
Downloading https://files.pythonhosted.org/packages/cb/0f/7b974d356e0242a0b2900dba9492ee13497766affcaaac4bcbadcd75a8c7/ultranest-3.6.2.tar.gz#sha256=57e7914604179c373c152a7fd50844c98038e1ac29a6f8e1119f2f0d8bd3544f
Best match: ultranest 3.6.2
Processing ultranest-3.6.2.tar.gz
Writing /tmp/easy_install-1lhmsnml/ultranest-3.6.2/setup.cfg
Running ultranest-3.6.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-1lhmsnml/ultranest-3.6.2/egg-dist-tmp-k6hozajc
Traceback (most recent call last):
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 156, in save_modules
    yield saved
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 198, in setup_context
    yield
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 259, in run_setup
    _execfile(setup_script, ns)
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 46, in _execfile
    exec(code, globals, locals)
  File "/tmp/easy_install-1lhmsnml/ultranest-3.6.2/setup.py", line 9, in <module>
    author='Michael Radica',
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'Cython'

Issue 3

Running ultranest-3.6.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-ssuwf55z/ultranest-3.6.2/egg-dist-tmp-m9jsigrn
/tmp/easy_install-ssuwf55z/ultranest-3.6.2/setup.py:15: UserWarning: The NumPy module was reloaded (imported a second time). This can in some cases result in small but subtle issues and is discouraged.
  import numpy
Compiling ultranest/mlfriends.pyx because it changed.
Compiling ultranest/stepfuncs.pyx because it changed.
[1/2] Cythonizing ultranest/mlfriends.pyx
Traceback (most recent call last):
  File "Cython/Compiler/Visitor.py", line 182, in Cython.Compiler.Visitor.TreeVisitor._visit
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/Cython/Compiler/ParseTreeTransforms.py", line 3110, in visit_StatListNode
    if not self.current_directives['remove_unreachable']:
           ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable

Issue 4

Installed /home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/emcee-3.1.4-py3.11.egg
Searching for celerite
Reading https://pypi.org/simple/celerite/
Downloading https://files.pythonhosted.org/packages/c2/62/aeb441bf9a59dc18f7eb1bb06b55459dd74f1516aa5751bf5650b9a3399d/celerite-0.4.2.tar.gz#sha256=65afd3f3e6f11421d1d8868da5fdca7318a892aea02b994b618e0ac8f3e4a92d
Best match: celerite 0.4.2
Processing celerite-0.4.2.tar.gz
Writing /tmp/easy_install-vdm6mqux/celerite-0.4.2/setup.cfg
Running celerite-0.4.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-vdm6mqux/celerite-0.4.2/egg-dist-tmp-2vtauifl
Traceback (most recent call last):
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 156, in save_modules
    yield saved
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 198, in setup_context
    yield
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 259, in run_setup
    _execfile(setup_script, ns)
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 46, in _execfile
    exec(code, globals, locals)
  File "/tmp/easy_install-vdm6mqux/celerite-0.4.2/setup.py", line 8, in <module>
    license='MIT',
^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'pybind11'

Issue 5

Searching for radvel
Reading https://pypi.org/simple/radvel/
Downloading https://files.pythonhosted.org/packages/f4/1a/b79c3f33e30ae8af8a7dd68fda734234f82a8cdd335160347759647258a0/radvel-1.4.9.tar.gz#sha256=fc02823028df29ac332073b98d945e0bf9bb251a99787da43c5a2f2177c6727c
Best match: radvel 1.4.9
Processing radvel-1.4.9.tar.gz
Writing /tmp/easy_install-5_jqo5a0/radvel-1.4.9/setup.cfg
Running radvel-1.4.9/setup.py -q bdist_egg --dist-dir /tmp/easy_install-5_jqo5a0/radvel-1.4.9/egg-dist-tmp-j1x3qtsh
/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

        ********************************************************************************
        Requirements should be satisfied by a PEP 517 installer.
        If you are using pip, you can try `pip install --use-pep517`.
        ********************************************************************************

!!
  dist.fetch_build_eggs(dist.setup_requires)
Traceback (most recent call last):
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 156, in save_modules
    yield saved
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 198, in setup_context
    yield
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 259, in run_setup
    _execfile(setup_script, ns)
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/sandbox.py", line 46, in _execfile
    exec(code, globals, locals)
  File "/tmp/easy_install-5_jqo5a0/radvel-1.4.9/setup.py", line 28, in <module>
    )
^^^^^
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/__init__.py", line 107, in setup
    return distutils.core.setup(**attrs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
    return run_commands(dist)
           ^^^^^^^^^^^^^^^^^^
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
    dist.run_commands()
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
    self.run_command(cmd)
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/dist.py", line 1233, in run_command
    super().run_command(command)
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
    cmd_obj.run()
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/command/bdist_egg.py", line 158, in run
    self.run_command("egg_info")
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
    self.distribution.run_command(command)
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/dist.py", line 1233, in run_command
    super().run_command(command)
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
    cmd_obj.run()
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/command/egg_info.py", line 319, in run
    self.find_sources()
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/command/egg_info.py", line 327, in find_sources
    mm.run()
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/command/egg_info.py", line 549, in run
    self.add_defaults()
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/command/egg_info.py", line 587, in add_defaults
    sdist.add_defaults(self)
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/command/sdist.py", line 113, in add_defaults
    super().add_defaults()
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/_distutils/command/sdist.py", line 251, in add_defaults
    self._add_defaults_ext()
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/_distutils/command/sdist.py", line 335, in _add_defaults_ext
    build_ext = self.get_finalized_command('build_ext')
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 305, in get_finalized_command
    cmd_obj.ensure_finalized()
  File "/home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 111, in ensure_finalized
    self.finalize_options()
  File "/tmp/easy_install-5_jqo5a0/radvel-1.4.9/setup.py", line 10, in finalize_options
    author_email='[email protected]',
      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'dict' object has no attribute '__NUMPY_SETUP__'

Issue 6

      writing manifest file 'radvel.egg-info/SOURCES.txt'
      /home/lheinke/.local/mambaforge/envs/supreme_spoon/lib/python3.11/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'radvel.templates' is absent from the `packages` configuration.
      !!
      
              ********************************************************************************
              ############################
              # Package would be ignored #
              ############################
              Python recognizes 'radvel.templates' as an importable package[^1],
              but it is absent from setuptools' `packages` configuration.
      
              This leads to an ambiguous overall configuration. If you want to distribute this
              package, please make sure that 'radvel.templates' is explicitly added
              to the `packages` configuration field.
      
              Alternatively, you can also rely on setuptools' discovery methods
              (for example by using `find_namespace_packages(...)`/`find_namespace:`
              instead of `find_packages(...)`/`find:`).
      
              You can read more about "package discovery" on setuptools documentation page:
      
              - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
      
              If you don't want 'radvel.templates' to be distributed and are
              already explicitly excluding 'radvel.templates' via
              `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
              you can try to use `exclude_package_data`, or `include-package-data=False` in
              combination with a more fine grained `package-data` configuration.
      
              You can read more about "package data files" on setuptools documentation page:
      
              - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
      
      
              [^1]: For Python, any directory (with suitable naming) can be imported,
                    even if it does not contain any `.py` files.
                    On the other hand, currently there is no concept of package data
                    directory, all directories are treated like packages.
              ********************************************************************************
      
      !!
        check.warn(importable)
      creating build/lib.linux-x86_64-cpython-311/radvel/templates
      copying radvel/templates/fig_corner.tex -> build/lib.linux-x86_64-cpython-311/radvel/templates
      copying radvel/templates/fig_corner_derived_pars.tex -> build/lib.linux-x86_64-cpython-311/radvel/templates
      copying radvel/templates/fig_rv_multipanel.tex -> build/lib.linux-x86_64-cpython-311/radvel/templates
      copying radvel/templates/report.tex -> build/lib.linux-x86_64-cpython-311/radvel/templates
      copying radvel/templates/tab_comparison.tex -> build/lib.linux-x86_64-cpython-311/radvel/templates
      copying radvel/templates/tab_crit.tex -> build/lib.linux-x86_64-cpython-311/radvel/templates
      copying radvel/templates/tab_derived.tex -> build/lib.linux-x86_64-cpython-311/radvel/templates
      copying radvel/templates/tab_params.tex -> build/lib.linux-x86_64-cpython-311/radvel/templates
      copying radvel/templates/tab_prior_summary.tex -> build/lib.linux-x86_64-cpython-311/radvel/templates
      copying radvel/templates/tab_rv.tex -> build/lib.linux-x86_64-cpython-311/radvel/templates
      running build_ext
      building 'radvel._kepler' extension
       (from 'src/_kepler.pyx')
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for radvel
  Running setup.py clean for radvel
Failed to build radvel
ERROR: Could not build wheels for radvel, which is required to install pyproject.toml-based projects

Package list

Using conda list

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
aiosignal                 1.3.1                    pypi_0    pypi
alabaster                 0.7.13                   pypi_0    pypi
asdf                      2.15.1                   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
astropy                   5.3.2                    pypi_0    pypi
astroquery                0.4.7.dev8738            pypi_0    pypi
asttokens                 2.2.1                    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
bleach                    6.0.0                    pypi_0    pypi
bottleneck                1.3.7                    pypi_0    pypi
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
certifi                   2023.7.22                pypi_0    pypi
cffi                      1.15.1                   pypi_0    pypi
charset-normalizer        3.2.0                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
comm                      0.1.4                    pypi_0    pypi
contourpy                 1.1.0                    pypi_0    pypi
corner                    2.2.2                    pypi_0    pypi
crds                      11.17.3                  pypi_0    pypi
cryptography              41.0.3                   pypi_0    pypi
cycler                    0.11.0                   pypi_0    pypi
cython                    3.0.0                    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
dill                      0.3.7                    pypi_0    pypi
docutils                  0.20.1                   pypi_0    pypi
drizzle                   1.13.7                   pypi_0    pypi
dynesty                   1.2.2                    pypi_0    pypi
emcee                     3.1.4                    pypi_0    pypi
executing                 1.2.0                    pypi_0    pypi
exofile                   0.0.0                    pypi_0    pypi
fastjsonschema            2.18.0                   pypi_0    pypi
filelock                  3.12.2                   pypi_0    pypi
fonttools                 4.42.1                   pypi_0    pypi
frozenlist                1.4.0                    pypi_0    pypi
future                    0.18.3                   pypi_0    pypi
grpcio                    1.57.0                   pypi_0    pypi
gwcs                      0.18.3                   pypi_0    pypi
html5lib                  1.1                      pypi_0    pypi
idna                      3.4                      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
ipykernel                 6.25.1                   pypi_0    pypi
ipython                   8.14.0                   pypi_0    pypi
jaraco-classes            3.3.0                    pypi_0    pypi
jedi                      0.19.0                   pypi_0    pypi
jeepney                   0.8.0                    pypi_0    pypi
jinja2                    3.1.2                    pypi_0    pypi
jmespath                  1.0.1                    pypi_0    pypi
joblib                    1.3.2                    pypi_0    pypi
jsonschema                4.19.0                   pypi_0    pypi
jsonschema-specifications 2023.7.1                 pypi_0    pypi
juliet                    2.2.1                    pypi_0    pypi
jupyter-client            8.3.0                    pypi_0    pypi
jupyter-core              5.3.1                    pypi_0    pypi
jupyterlab-pygments       0.2.2                    pypi_0    pypi
jwst                      1.8.5                    pypi_0    pypi
keyring                   24.2.0                   pypi_0    pypi
kiwisolver                1.4.4                    pypi_0    pypi
lazy-loader               0.3                      pypi_0    pypi
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.1.0               he5830b7_0    conda-forge
libgomp                   13.1.0               he5830b7_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libsqlite                 3.42.0               h2797004_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
markupsafe                2.1.3                    pypi_0    pypi
matplotlib                3.7.2                    pypi_0    pypi
matplotlib-inline         0.1.6                    pypi_0    pypi
mistune                   3.0.1                    pypi_0    pypi
more-itertools            10.1.0                   pypi_0    pypi
msgpack                   1.0.5                    pypi_0    pypi
nbclient                  0.8.0                    pypi_0    pypi
nbconvert                 7.7.4                    pypi_0    pypi
nbformat                  5.9.2                    pypi_0    pypi
nbsphinx                  0.9.2                    pypi_0    pypi
ncurses                   6.4                  hcb278e6_0    conda-forge
nest-asyncio              1.5.7                    pypi_0    pypi
networkx                  3.1                      pypi_0    pypi
numpy                     1.25.2                   pypi_0    pypi
opencv-python             4.8.0.76                 pypi_0    pypi
openssl                   3.1.2                hd590300_0    conda-forge
packaging                 23.1                     pypi_0    pypi
pandas                    2.0.3                    pypi_0    pypi
pandocfilters             1.5.0                    pypi_0    pypi
parsley                   1.3                      pypi_0    pypi
parso                     0.8.3                    pypi_0    pypi
pexpect                   4.8.0                    pypi_0    pypi
photutils                 1.9.0                    pypi_0    pypi
pickleshare               0.7.5                    pypi_0    pypi
pillow                    10.0.0                   pypi_0    pypi
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
platformdirs              3.10.0                   pypi_0    pypi
poppy                     1.1.1                    pypi_0    pypi
prompt-toolkit            3.0.39                   pypi_0    pypi
protobuf                  4.24.1                   pypi_0    pypi
psutil                    5.9.5                    pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.2                    pypi_0    pypi
pybind11                  2.11.1                   pypi_0    pypi
pycparser                 2.21                     pypi_0    pypi
pyerfa                    2.0.0.3                  pypi_0    pypi
pygments                  2.16.1                   pypi_0    pypi
pyparsing                 3.0.9                    pypi_0    pypi
python                    3.11.4          hab00c5b_0_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
pytz                      2023.3                   pypi_0    pypi
pyvo                      1.4.2                    pypi_0    pypi
pywavelets                1.4.1                    pypi_0    pypi
pyyaml                    6.0.1                    pypi_0    pypi
pyzmq                     25.1.1                   pypi_0    pypi
radvel                    1.4.9                    pypi_0    pypi
ray                       2.6.3                    pypi_0    pypi
readline                  8.2                  h8228510_1    conda-forge
referencing               0.30.2                   pypi_0    pypi
requests                  2.31.0                   pypi_0    pypi
rpds-py                   0.9.2                    pypi_0    pypi
scikit-image              0.21.0                   pypi_0    pypi
scikit-learn              1.3.0                    pypi_0    pypi
scipy                     1.11.2                   pypi_0    pypi
secretstorage             3.3.3                    pypi_0    pypi
semantic-version          2.10.0                   pypi_0    pypi
setuptools                68.1.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0                   pypi_0    pypi
snowballstemmer           2.2.0                    pypi_0    pypi
soupsieve                 2.4.1                    pypi_0    pypi
spherical-geometry        1.2.23                   pypi_0    pypi
sphinx                    7.2.2                    pypi_0    pypi
sphinxcontrib-applehelp   1.0.7                    pypi_0    pypi
sphinxcontrib-devhelp     1.0.5                    pypi_0    pypi
sphinxcontrib-htmlhelp    2.0.4                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-qthelp      1.0.6                    pypi_0    pypi
sphinxcontrib-serializinghtml 1.1.9                    pypi_0    pypi
stack-data                0.6.2                    pypi_0    pypi
stcal                     1.2.2                    pypi_0    pypi
stdatamodels              0.4.5                    pypi_0    pypi
stpipe                    0.5.0                    pypi_0    pypi
stsci-image               2.3.5                    pypi_0    pypi
stsci-imagestats          1.6.3                    pypi_0    pypi
stsci-stimage             0.2.6                    pypi_0    pypi
threadpoolctl             3.2.0                    pypi_0    pypi
tifffile                  2023.8.12                pypi_0    pypi
tinycss2                  1.2.1                    pypi_0    pypi
tk                        8.6.12               h27826a3_0    conda-forge
tornado                   6.3.3                    pypi_0    pypi
tqdm                      4.66.1                   pypi_0    pypi
traitlets                 5.9.0                    pypi_0    pypi
tweakwcs                  0.8.2                    pypi_0    pypi
tzdata                    2023.3                   pypi_0    pypi
ultranest                 3.6.2                    pypi_0    pypi
urllib3                   2.0.4                    pypi_0    pypi
wcwidth                   0.2.6                    pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
wiimatch                  0.3.1                    pypi_0    pypi
xz                        5.2.6                h166bdaf_0    conda-forge
zipp                      3.16.2                   pypi_0    pypi

Using pip list

Package                       Version
----------------------------- -------------
aiosignal                     1.3.1
aiosignal                     1.3.1
alabaster                     0.7.13
applesoss                     2.0.0
applesoss                     2.0.0
applesoss                     2.0.0
asdf                          2.15.1
asdf                          2.15.1
asdf-astropy                  0.4.0
asdf-astropy                  0.4.0
asdf-coordinates-schemas      0.2.0
asdf-coordinates-schemas      0.2.0
asdf-standard                 1.0.3
asdf-standard                 1.0.3
asdf-transform-schemas        0.3.0
asdf-transform-schemas        0.3.0
asdf-unit-schemas             0.1.0
asdf-unit-schemas             0.1.0
asdf-wcs-schemas              0.1.1
asdf-wcs-schemas              0.1.1
asdf-wcs-schemas              0.1.1
astropy                       5.3.2
astroquery                    0.4.7.dev8738
astroquery                    0.4.7.dev8738
asttokens                     2.2.1
attrs                         23.1.0
Babel                         2.12.1
backcall                      0.2.0
batman-package                2.4.9
batman-package                2.4.9
BayesicFitting                3.1.1
BayesicFitting                3.1.1
beautifulsoup4                4.12.2
bleach                        6.0.0
Bottleneck                    1.3.7
Bottleneck                    1.3.7
celerite                      0.0.0
celerite                      0.0.0
celerite                      0.0.0
certifi                       2023.7.22
certifi                       2022.5.18.1
cffi                          1.15.1
cffi                          1.15.1
charset-normalizer            3.2.0
click                         8.1.7
click                         8.1.7
comm                          0.1.4
contourpy                     1.1.0
corner                        2.2.2
crds                          11.17.3
crds                          11.17.3
cryptography                  41.0.3
cryptography                  41.0.3
cycler                        0.11.0
Cython                        3.0.0
debugpy                       1.6.7.post1
decorator                     5.1.1
defusedxml                    0.7.1
dill                          0.3.7
docutils                      0.20.1
drizzle                       1.13.7
drizzle                       1.13.7
dynesty                       1.2.2
dynesty                       1.2.2
emcee                         3.1.4
executing                     1.2.0
exofile                       0.0.0
exofile                       0.0.0
exotic-ld                     3.0.0
exotic-ld                     3.0.0
exotic-ld                     3.0.0
fastjsonschema                2.18.0
filelock                      3.12.2
filelock                      3.12.2
fonttools                     4.42.1
frozenlist                    1.4.0
frozenlist                    1.4.0
future                        0.18.3
future                        0.18.3
george                        0.0.0
george                        0.0.0
george                        0.0.0
grpcio                        1.57.0
grpcio                        1.57.0
gwcs                          0.18.3
gwcs                          0.18.3
html5lib                      1.1
html5lib                      1.1
idna                          3.4
imageio                       2.31.1
imageio                       2.31.1
imagesize                     1.4.1
importlib-metadata            6.8.0
importlib-metadata            6.8.0
ipykernel                     6.25.1
ipython                       8.14.0
jaraco.classes                3.3.0
jaraco.classes                3.3.0
jedi                          0.19.0
jeepney                       0.8.0
jeepney                       0.8.0
Jinja2                        3.1.2
jmespath                      1.0.1
jmespath                      1.0.1
joblib                        1.3.2
joblib                        1.3.2
jsonschema                    4.19.0
jsonschema-specifications     2023.7.1
juliet                        2.2.1
juliet                        2.2.1
jupyter_client                8.3.0
jupyter_core                  5.3.1
jupyterlab-pygments           0.2.2
jwst                          1.8.5
jwst                          1.8.5
keyring                       24.2.0
keyring                       24.2.0
kiwisolver                    1.4.4
lazy_loader                   0.3
lazy_loader                   0.3
MarkupSafe                    2.1.3
matplotlib                    3.7.2
matplotlib-inline             0.1.6
mistune                       3.0.1
more-itertools                10.1.0
more-itertools                10.1.0
msgpack                       1.0.5
msgpack                       1.0.5
nbclient                      0.8.0
nbconvert                     7.7.4
nbformat                      5.9.2
nbsphinx                      0.9.2
nest-asyncio                  1.5.7
networkx                      3.1
networkx                      3.1
numpy                         1.25.2
opencv-python                 4.8.0.76
opencv-python                 4.8.0.76
packaging                     23.1
pandas                        2.0.3
pandocfilters                 1.5.0
Parsley                       1.3
Parsley                       1.3
parso                         0.8.3
pexpect                       4.8.0
photutils                     1.9.0
photutils                     1.9.0
pickleshare                   0.7.5
Pillow                        10.0.0
pip                           23.2.1
platformdirs                  3.10.0
poppy                         1.1.1
poppy                         1.1.1
prompt-toolkit                3.0.39
protobuf                      4.24.1
protobuf                      4.24.1
psutil                        5.9.5
ptyprocess                    0.7.0
pure-eval                     0.2.2
pybind11                      2.11.1
pycparser                     2.21
pycparser                     2.21
pyerfa                        2.0.0.3
Pygments                      2.16.1
pyparsing                     3.0.9
python-dateutil               2.8.2
pytz                          2023.3
pyvo                          1.4.2
pyvo                          1.4.2
PyWavelets                    1.4.1
PyWavelets                    1.4.1
PyYAML                        6.0.1
pyzmq                         25.1.1
radvel                        1.4.9
ray                           2.6.3
ray                           2.6.3
referencing                   0.30.2
requests                      2.31.0
rpds-py                       0.9.2
scikit-image                  0.21.0
scikit-image                  0.21.0
scikit-learn                  1.3.0
scikit-learn                  1.3.0
scipy                         1.11.2
SecretStorage                 3.3.3
SecretStorage                 3.3.3
semantic-version              2.10.0
semantic-version              2.10.0
setuptools                    68.1.2
six                           1.16.0
snowballstemmer               2.2.0
soupsieve                     2.4.1
spherical-geometry            1.2.23
spherical-geometry            1.2.23
Sphinx                        7.2.3
sphinxcontrib-applehelp       1.0.7
sphinxcontrib-devhelp         1.0.5
sphinxcontrib-htmlhelp        2.0.4
sphinxcontrib-jsmath          1.0.1
sphinxcontrib-qthelp          1.0.6
sphinxcontrib-serializinghtml 1.1.9
stack-data                    0.6.2
stcal                         1.2.2
stcal                         1.2.2
stdatamodels                  0.4.5
stdatamodels                  0.4.5
stpipe                        0.5.0
stpipe                        0.5.0
stsci.image                   2.3.5
stsci.image                   2.3.5
stsci.imagestats              1.6.3
stsci.imagestats              1.6.3
stsci.stimage                 0.2.6
stsci.stimage                 0.2.6
supreme-spoon                 1.1.1
supreme-spoon                 1.1.1
supreme-spoon                 1.1.1
threadpoolctl                 3.2.0
threadpoolctl                 3.2.0
tifffile                      2023.8.12
tifffile                      2023.8.12
tinycss2                      1.2.1
tornado                       6.3.3
tqdm                          4.66.1
tqdm                          4.66.1
traitlets                     5.9.0
tweakwcs                      0.8.2
tweakwcs                      0.8.2
tzdata                        2023.3
ultranest                     3.6.2
urllib3                       2.0.4
wcwidth                       0.2.6
webencodings                  0.5.1
wheel                         0.41.2
wiimatch                      0.3.1
wiimatch                      0.3.1
zipp                          3.16.2
zipp                          3.16.2

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