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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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TypeError: bad operand type for unary ~: 'NoneType' #466

Closed mbess8 closed 4 weeks ago

mbess8 commented 1 year ago

Instrument

Light curve fitting (Stages 4-6)

What happened?

Getting this error once I get to the stage 6 in the quickstart demos. I was also curious if there is a way to start directly at stage 6 with the S5 data from a previous run.

Error traceback output

Starting Stage 6: Light Curve Fitting

Input directory: /Users/michael/Eureka_test/DataAnalysis/JWST/MyFirstEureka/Stage5/S5_2022-09-28_wasp39b_run2/ap6_bg7/
Output directory: /Users/michael/Eureka_test/DataAnalysis/JWST/MyFirstEureka/Stage6/S6_2022-09-28_wasp39b_run2/ap6_bg7/
Copying S6 control file
Calculated g=55.25 m/s^2 with Rp=0.95 R_jup and Mp=2 M_jup
Calculated H=91.6 km with g=55.25 m/s^2, Teq=1400 K, and mu=2.3 u

Total time (min): 0.02
Saving results as astropy table
Saving results
Exception ignored in: <function CachingFileManager.__del__ at 0x7f7eef4e81f0>
Traceback (most recent call last):
  File "/Users/michael/opt/anaconda3/lib/python3.9/site-packages/xarray/backends/file_manager.py", line 244, in __del__
  File "/Users/michael/opt/anaconda3/lib/python3.9/site-packages/xarray/backends/file_manager.py", line 222, in close
  File "/Users/michael/opt/anaconda3/lib/python3.9/site-packages/h5netcdf/core.py", line 1130, in close
  File "/Users/michael/opt/anaconda3/lib/python3.9/site-packages/h5py/_hl/files.py", line 445, in close
TypeError: bad operand type for unary ~: 'NoneType'
Exception ignored in: <function File.close at 0x7f7eef53e040>
Traceback (most recent call last):
  File "/Users/michael/opt/anaconda3/lib/python3.9/site-packages/h5netcdf/core.py", line 1130, in close
  File "/Users/michael/opt/anaconda3/lib/python3.9/site-packages/h5py/_hl/files.py", line 445, in close
TypeError: bad operand type for unary ~: 'NoneType'

What operating system are you using?

macOS 12.5.1 Monterey

What version of Python are you running?

Python 3.9.12

What Python packages do you have installed?

# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0            py39hecd8cb5_1  
aiohttp                   3.8.1            py39hca72f7f_1  
aiosignal                 1.2.0              pyhd3eb1b0_0  
alabaster                 0.7.12             pyhd3eb1b0_0  
altair                    4.2.0                    pypi_0    pypi
anaconda                  2022.05                  py39_0  
anaconda-client           1.9.0            py39hecd8cb5_0  
anaconda-navigator        2.3.0            py39hecd8cb5_0  
anaconda-project          0.10.2             pyhd3eb1b0_0  
anyio                     3.5.0            py39hecd8cb5_0  
appdirs                   1.4.4              pyhd3eb1b0_0  
applaunchservices         0.2.1              pyhd3eb1b0_0  
appnope                   0.1.2           py39hecd8cb5_1001  
appscript                 1.1.2            py39h9ed2024_0  
argon2-cffi               21.3.0             pyhd3eb1b0_0  
argon2-cffi-bindings      21.2.0           py39hca72f7f_0  
arrow                     1.2.2              pyhd3eb1b0_0  
asdf                      2.13.0                   pypi_0    pypi
asdf-astropy              0.2.2                    pypi_0    pypi
asdf-coordinates-schemas  0.1.0                    pypi_0    pypi
asdf-standard             1.0.3                    pypi_0    pypi
asdf-transform-schemas    0.3.0                    pypi_0    pypi
asdf-wcs-schemas          0.1.1                    pypi_0    pypi
asteval                   0.9.27                   pypi_0    pypi
astraeus                  0.2                      pypi_0    pypi
astroid                   2.6.6            py39hecd8cb5_0  
astropy                   5.1                      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                 2.0.5              pyhd3eb1b0_0  
async-timeout             4.0.1              pyhd3eb1b0_0  
atomicwrites              1.4.0                      py_0  
attrs                     21.4.0             pyhd3eb1b0_0  
automat                   20.2.0                     py_0  
autopep8                  1.6.0              pyhd3eb1b0_0  
babel                     2.9.1              pyhd3eb1b0_0  
backcall                  0.2.0              pyhd3eb1b0_0  
backports                 1.1                pyhd3eb1b0_0  
backports.functools_lru_cache 1.6.4              pyhd3eb1b0_0  
backports.tempfile        1.0                pyhd3eb1b0_1  
backports.weakref         1.0.post1                  py_1  
batman-package            2.4.9                    pypi_0    pypi
bayesicfitting            3.0.1                    pypi_0    pypi
bcrypt                    3.2.0            py39h9ed2024_0  
beautifulsoup4            4.11.1           py39hecd8cb5_0  
binaryornot               0.4.4              pyhd3eb1b0_1  
bitarray                  2.4.1            py39hca72f7f_0  
bkcharts                  0.2              py39hecd8cb5_0  
black                     19.10b0                    py_0  
blas                      1.0                         mkl  
bleach                    4.1.0              pyhd3eb1b0_0  
blosc                     1.21.0               h2842e9f_0  
bokeh                     2.4.2            py39hecd8cb5_0  
boto3                     1.21.32            pyhd3eb1b0_0  
botocore                  1.24.32            pyhd3eb1b0_0  
bottleneck                1.3.4            py39h67323c0_0  
brotli                    1.0.9                hb1e8313_2  
brotlipy                  0.7.0           py39h9ed2024_1003  
brunsli                   0.1                  h23ab428_0  
bzip2                     1.0.8                h1de35cc_0  
c-ares                    1.18.1               hca72f7f_0  
ca-certificates           2022.3.29            hecd8cb5_1  
cachetools                4.2.2              pyhd3eb1b0_0  
ccdproc                   2.3.1                    pypi_0    pypi
celerite                  0.4.2                    pypi_0    pypi
certifi                   2021.10.8        py39hecd8cb5_2  
cffi                      1.15.0           py39hc55c11b_1  
cfitsio                   3.470                hee0f690_6  
cftime                    1.6.2                    pypi_0    pypi
chardet                   4.0.0           py39hecd8cb5_1003  
charls                    2.2.0                h23ab428_0  
charset-normalizer        2.0.4              pyhd3eb1b0_0  
chromatic-lightcurves     0.3.9                    pypi_0    pypi
click                     8.0.4            py39hecd8cb5_0  
cloudpickle               2.0.0              pyhd3eb1b0_0  
clyent                    1.2.2            py39hecd8cb5_1  
colorama                  0.4.4              pyhd3eb1b0_0  
colorcet                  2.0.6              pyhd3eb1b0_0  
conda                     4.14.0           py39hecd8cb5_0  
conda-build               3.21.8           py39hecd8cb5_2  
conda-content-trust       0.1.1              pyhd3eb1b0_0  
conda-env                 2.6.0                         1  
conda-pack                0.6.0              pyhd3eb1b0_0  
conda-package-handling    1.8.1            py39hca72f7f_0  
conda-repo-cli            1.0.4              pyhd3eb1b0_0  
conda-token               0.3.0              pyhd3eb1b0_0  
conda-verify              3.4.2                      py_1  
constantly                15.1.0             pyh2b92418_0  
cookiecutter              1.7.3              pyhd3eb1b0_0  
corner                    2.2.1                    pypi_0    pypi
crds                      11.16.12                 pypi_0    pypi
cryptography              3.4.8            py39h2fd3fbb_0  
cssselect                 1.1.0              pyhd3eb1b0_0  
curl                      7.82.0               hca72f7f_0  
cycler                    0.11.0             pyhd3eb1b0_0  
cython                    0.29.28          py39he9d5cce_0  
cytoolz                   0.11.0           py39h9ed2024_0  
daal4py                   2021.5.0         py39h24a4e90_0  
dal                       2021.5.0           hecd8cb5_782  
dask                      2022.2.1           pyhd3eb1b0_0  
dask-core                 2022.2.1           pyhd3eb1b0_0  
dataclasses               0.8                pyh6d0b6a4_7  
datashader                0.13.0             pyhd3eb1b0_1  
datashape                 0.5.4            py39hecd8cb5_1  
debugpy                   1.5.1            py39he9d5cce_0  
decorator                 5.1.1              pyhd3eb1b0_0  
defusedxml                0.7.1              pyhd3eb1b0_0  
diff-match-patch          20200713           pyhd3eb1b0_0  
distributed               2022.2.1           pyhd3eb1b0_0  
docutils                  0.17.1           py39hecd8cb5_1  
drizzle                   1.13.6                   pypi_0    pypi
dynesty                   1.2.3                    pypi_0    pypi
emcee                     3.1.2                    pypi_0    pypi
entrypoints               0.4              py39hecd8cb5_0  
ers-transit-tutorial-requirements 0.0.2                    pypi_0    pypi
et_xmlfile                1.1.0            py39hecd8cb5_0  
eureka                    0.4                      pypi_0    pypi
executing                 0.8.3              pyhd3eb1b0_0  
exotic-ld                 2.0.0                    pypi_0    pypi
filelock                  3.6.0              pyhd3eb1b0_0  
flake8                    3.9.2              pyhd3eb1b0_0  
flask                     1.1.2              pyhd3eb1b0_0  
fonttools                 4.25.0             pyhd3eb1b0_0  
freetype                  2.11.0               hd8bbffd_0  
frozenlist                1.2.0            py39hca72f7f_0  
fsspec                    2022.2.0           pyhd3eb1b0_0  
future                    0.18.2           py39hecd8cb5_1  
gensim                    4.1.2            py39he9d5cce_0  
george                    0.4.0                    pypi_0    pypi
giflib                    5.2.1                haf1e3a3_0  
glob2                     0.7                pyhd3eb1b0_0  
gmp                       6.2.1                h23ab428_2  
gmpy2                     2.1.2            py39hd5de756_0  
google-api-core           1.25.1             pyhd3eb1b0_0  
google-auth               1.33.0             pyhd3eb1b0_0  
google-cloud-core         1.7.1              pyhd3eb1b0_0  
google-cloud-storage      1.31.0                     py_0  
google-crc32c             1.1.2            py39h9ed2024_0  
google-resumable-media    1.3.1              pyhd3eb1b0_1  
googleapis-common-protos  1.53.0           py39hecd8cb5_0  
greenlet                  1.1.1            py39h23ab428_0  
grpcio                    1.42.0           py39ha29bfda_0  
gwcs                      0.18.2                   pypi_0    pypi
h5netcdf                  1.0.2                    pypi_0    pypi
h5py                      3.1.0                    pypi_0    pypi
hdf5                      1.10.6               hdbbcd12_0  
heapdict                  1.0.1              pyhd3eb1b0_0  
holoviews                 1.14.8             pyhd3eb1b0_0  
html5lib                  1.1                      pypi_0    pypi
hvplot                    0.7.3              pyhd3eb1b0_1  
hyperlink                 21.0.0             pyhd3eb1b0_0  
icu                       58.2                 h0a44026_3  
idna                      3.3                pyhd3eb1b0_0  
imagecodecs               2021.8.26        py39ha952a84_0  
imageio                   2.9.0              pyhd3eb1b0_0  
imagesize                 1.3.0              pyhd3eb1b0_0  
importlib-metadata        4.11.3           py39hecd8cb5_0  
importlib_metadata        4.11.3               hd3eb1b0_0  
incremental               21.3.0             pyhd3eb1b0_0  
inflection                0.5.1            py39hecd8cb5_0  
iniconfig                 1.1.1              pyhd3eb1b0_0  
intake                    0.6.5              pyhd3eb1b0_0  
intel-openmp              2021.4.0          hecd8cb5_3538  
intervaltree              3.1.0              pyhd3eb1b0_0  
ipykernel                 6.9.1            py39hecd8cb5_0  
ipython                   8.2.0            py39hecd8cb5_0  
ipython_genutils          0.2.0              pyhd3eb1b0_1  
ipywidgets                7.6.5              pyhd3eb1b0_1  
isort                     5.9.3              pyhd3eb1b0_0  
itemadapter               0.3.0              pyhd3eb1b0_0  
itemloaders               1.0.4              pyhd3eb1b0_1  
itsdangerous              2.0.1              pyhd3eb1b0_0  
jdcal                     1.4.1              pyhd3eb1b0_0  
jedi                      0.18.1           py39hecd8cb5_1  
jinja2                    2.11.3             pyhd3eb1b0_0  
jinja2-time               0.2.0              pyhd3eb1b0_3  
jmespath                  0.10.0             pyhd3eb1b0_0  
joblib                    1.1.0              pyhd3eb1b0_0  
jpeg                      9e                   hca72f7f_0  
jq                        1.6               h9ed2024_1000  
json5                     0.9.6              pyhd3eb1b0_0  
jsonschema                4.4.0            py39hecd8cb5_0  
jupyter                   1.0.0            py39hecd8cb5_7  
jupyter_client            6.1.12             pyhd3eb1b0_0  
jupyter_console           6.4.0              pyhd3eb1b0_0  
jupyter_core              4.9.2            py39hecd8cb5_0  
jupyter_server            1.13.5             pyhd3eb1b0_0  
jupyterlab                3.3.2              pyhd3eb1b0_0  
jupyterlab_pygments       0.1.2                      py_0  
jupyterlab_server         2.10.3             pyhd3eb1b0_1  
jupyterlab_widgets        1.0.0              pyhd3eb1b0_1  
jwst                      1.6.0                    pypi_0    pypi
jxrlib                    1.1                  haf1e3a3_2  
keyring                   23.4.0           py39hecd8cb5_0  
kiwisolver                1.3.2            py39he9d5cce_0  
krb5                      1.19.2               hcd88c3b_0  
lazy-object-proxy         1.6.0            py39h9ed2024_0  
lcms2                     2.12                 hf1fd2bf_0  
lerc                      3.0                  he9d5cce_0  
libaec                    1.0.4                hb1e8313_1  
libarchive                3.4.2                haa3ed63_0  
libcrc32c                 1.1.1                hb1e8313_2  
libcurl                   7.82.0               h6dfd666_0  
libcxx                    12.0.0               h2f01273_0  
libdeflate                1.8                  h9ed2024_5  
libedit                   3.1.20210910         hca72f7f_0  
libev                     4.33                 h9ed2024_1  
libffi                    3.3                  hb1e8313_2  
libgfortran               3.0.1                h93005f0_2  
libiconv                  1.16                 hca72f7f_2  
libidn2                   2.3.2                h9ed2024_0  
liblief                   0.11.5               he9d5cce_1  
libllvm11                 11.1.0               h46f1229_1  
libnghttp2                1.46.0               ha29bfda_0  
libpng                    1.6.37               ha441bb4_0  
libprotobuf               3.19.1               h8346a28_0  
libsodium                 1.0.18               h1de35cc_0  
libspatialindex           1.9.3                h23ab428_0  
libssh2                   1.10.0               h0a4fc7d_0  
libtiff                   4.2.0                h87d7836_0  
libunistring              0.9.10               h9ed2024_0  
libwebp                   1.2.2                h56c3ce4_0  
libwebp-base              1.2.2                hca72f7f_0  
libxml2                   2.9.12               hcdb78fc_0  
libxslt                   1.1.34               h83b36ba_0  
libzopfli                 1.0.3                hb1e8313_0  
llvm-openmp               12.0.0               h0dcd299_1  
llvmlite                  0.38.0           py39h8346a28_0  
lmfit                     1.0.3                    pypi_0    pypi
locket                    0.2.1            py39hecd8cb5_2  
lxml                      4.8.0            py39h65b224f_0  
lz4-c                     1.9.3                h23ab428_1  
lzo                       2.10                 haf1e3a3_2  
markdown                  3.3.4            py39hecd8cb5_0  
markupsafe                2.0.1            py39h9ed2024_0  
matplotlib                3.5.1            py39hecd8cb5_1  
matplotlib-base           3.5.1            py39hfb0c5b7_1  
matplotlib-inline         0.1.2              pyhd3eb1b0_2  
mccabe                    0.6.1            py39hecd8cb5_1  
mistune                   0.8.4           py39h9ed2024_1000  
mkl                       2021.4.0           hecd8cb5_637  
mkl-service               2.4.0            py39h9ed2024_0  
mkl_fft                   1.3.1            py39h4ab4a9b_0  
mkl_random                1.2.2            py39hb2f4e1b_0  
mock                      4.0.3              pyhd3eb1b0_0  
mpc                       1.1.0                h6ef4df4_1  
mpfr                      4.0.2                h9066e36_1  
mpi                       1.0                       mpich  
mpich                     3.3.2                hc856adb_0  
mpmath                    1.2.1            py39hecd8cb5_0  
msgpack-python            1.0.2            py39hf7b0b51_1  
multidict                 5.2.0            py39hca72f7f_2  
multipledispatch          0.6.0            py39hecd8cb5_0  
munkres                   1.1.4                      py_0  
mypy_extensions           0.4.3            py39hecd8cb5_1  
navigator-updater         0.2.1                    py39_1  
nbclassic                 0.3.5              pyhd3eb1b0_0  
nbclient                  0.5.13           py39hecd8cb5_0  
nbconvert                 6.4.4            py39hecd8cb5_0  
nbformat                  5.3.0            py39hecd8cb5_0  
nbsphinx                  0.8.9                    pypi_0    pypi
ncurses                   6.3                  hca72f7f_2  
nest-asyncio              1.5.5            py39hecd8cb5_0  
netcdf4                   1.6.1                    pypi_0    pypi
networkx                  2.7.1              pyhd3eb1b0_0  
nltk                      3.7                pyhd3eb1b0_0  
nose                      1.3.7           pyhd3eb1b0_1008  
notebook                  6.4.8            py39hecd8cb5_0  
numba                     0.55.1           py39hae1ba45_0  
numexpr                   2.8.1            py39h2e5f0a9_0  
numpy                     1.21.5           py39h2e5f0a9_1  
numpy-base                1.21.5           py39h3b1a694_1  
numpydoc                  1.2                pyhd3eb1b0_0  
olefile                   0.46               pyhd3eb1b0_0  
oniguruma                 6.9.7.1              h9ed2024_0  
openjpeg                  2.4.0                h66ea3da_0  
openpyxl                  3.0.9              pyhd3eb1b0_0  
openssl                   1.1.1n               hca72f7f_0  
packaging                 21.3               pyhd3eb1b0_0  
pandas                    1.4.2            py39he9d5cce_0  
pandocfilters             1.5.0              pyhd3eb1b0_0  
panel                     0.13.0           py39hecd8cb5_0  
param                     1.12.0             pyhd3eb1b0_0  
parsel                    1.6.0            py39hecd8cb5_0  
parsley                   1.3                      pypi_0    pypi
parso                     0.8.3              pyhd3eb1b0_0  
partd                     1.2.0              pyhd3eb1b0_1  
pathspec                  0.7.0                      py_0  
patsy                     0.5.2            py39hecd8cb5_1  
pep8                      1.7.1            py39hecd8cb5_0  
pexpect                   4.8.0              pyhd3eb1b0_3  
photutils                 1.5.0                    pypi_0    pypi
pickleshare               0.7.5           pyhd3eb1b0_1003  
pillow                    9.0.1            py39hde71d04_0  
pip                       22.2.2                   pypi_0    pypi
pkginfo                   1.8.2              pyhd3eb1b0_0  
plotly                    5.6.0              pyhd3eb1b0_0  
pluggy                    1.0.0            py39hecd8cb5_1  
poppy                     1.0.3                    pypi_0    pypi
poyo                      0.5.0              pyhd3eb1b0_0  
prometheus_client         0.13.1             pyhd3eb1b0_0  
prompt-toolkit            3.0.20             pyhd3eb1b0_0  
prompt_toolkit            3.0.20               hd3eb1b0_0  
protego                   0.1.16                     py_0  
protobuf                  3.19.1           py39he9d5cce_0  
psutil                    5.8.0            py39h9ed2024_1  
ptyprocess                0.7.0              pyhd3eb1b0_2  
pure_eval                 0.2.2              pyhd3eb1b0_0  
py                        1.11.0             pyhd3eb1b0_0  
py-lief                   0.11.5           py39he9d5cce_1  
pyasn1                    0.4.8              pyhd3eb1b0_0  
pyasn1-modules            0.2.8                      py_0  
pycodestyle               2.7.0              pyhd3eb1b0_0  
pycosat                   0.6.3            py39h9ed2024_0  
pycparser                 2.21               pyhd3eb1b0_0  
pyct                      0.4.6            py39hecd8cb5_0  
pycurl                    7.44.1           py39hbcfaee0_1  
pydispatcher              2.0.5            py39hecd8cb5_2  
pydocstyle                6.1.1              pyhd3eb1b0_0  
pyerfa                    2.0.0            py39h9ed2024_0  
pyflakes                  2.3.1              pyhd3eb1b0_0  
pygments                  2.11.2             pyhd3eb1b0_0  
pyhamcrest                2.0.2              pyhd3eb1b0_2  
pyjwt                     2.1.0            py39hecd8cb5_0  
pylint                    2.9.6            py39hecd8cb5_1  
pyls-spyder               0.4.0              pyhd3eb1b0_0  
pyodbc                    4.0.32           py39he9d5cce_1  
pyopenssl                 21.0.0             pyhd3eb1b0_1  
pyparsing                 3.0.4              pyhd3eb1b0_0  
pyqt                      5.9.2            py39h23ab428_6  
pyrsistent                0.18.0           py39hca72f7f_0  
pysocks                   1.7.1            py39hecd8cb5_0  
pysynphot                 2.0.0                    pypi_0    pypi
pytables                  3.6.1            py39h648f197_1  
pytest                    7.1.1            py39hecd8cb5_0  
python                    3.9.12               hdfd78df_0  
python-dateutil           2.8.2              pyhd3eb1b0_0  
python-fastjsonschema     2.15.1             pyhd3eb1b0_0  
python-libarchive-c       2.9                pyhd3eb1b0_1  
python-lsp-black          1.0.0              pyhd3eb1b0_0  
python-lsp-jsonrpc        1.0.0              pyhd3eb1b0_0  
python-lsp-server         1.2.4              pyhd3eb1b0_0  
python-slugify            5.0.2              pyhd3eb1b0_0  
python-snappy             0.6.0            py39h23ab428_3  
python.app                3                py39hca72f7f_0  
pytz                      2021.3             pyhd3eb1b0_0  
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pyzmq                     22.3.0           py39he9d5cce_2  
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qt                        5.9.7                h468cd18_1  
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zope.interface            5.4.0            py39h9ed2024_0  
zstd                      1.4.9                h322a384_0

Code of Conduct

taylorbell57 commented 1 year ago

I have gotten that Stage 6 error before, but I'm pretty sure I fixed that with a patch to Eureka a little while ago. I do see that you're using v0.4 of Eureka, so updating to the latest v0.5 might help resolve that issue. As for your question about running just Stage 6 alone, if you edit your run_eureka.py file you can just comment out any stages that you don't want to run (and you'll need to remove the s5_meta argument to the Stage 6 function if it is there in your run_eureka.py file).

mbess8 commented 1 year ago

I updated to v0.5 but still got that error. However, when I ran stage 6 alone that error does not come up

taylorbell57 commented 1 year ago

Oh right, so that isn't actually an error (Stage 6 should've run to completion successfully), but somehow an xarray save file gets closed and then something else tries to close the already closed file. I wouldn't be too worried about it if the code does run successfully when that message is displayed, but I'll keep this open for now until we figure out what's causing this (it may well not be our code, but one of our dependencies' code)

mbess8 commented 1 year ago

Alright sounds good. Thanks for your help!