Bug Report: Exomol, hdf5 tests failing on travis (buffer error)

[anandxkumar]

🐛 Describe the bug

Travis failing: https://app.travis-ci.com/github/radis/radis/jobs/571532389

Steps to reproduce:

• create a new virtual environment using conda create -n radis_env python=3.8 and fetch latest develop branch locally
• pip install -e . (pip install -e .[dev] -v didn't work)
• delete radis.json and .radisdb
• pytest

Following is the version of dependencies in the environment:

• anyio==3.6.1
• aplus==0.11.0
• argon2-cffi==21.3.0
• argon2-cffi-bindings==21.2.0
• asgiref==3.5.2
• astropy==5.1
• astroquery==0.4.6
• asttokens==2.0.5
• attrs==21.4.0
• backcall==0.2.0
• beautifulsoup4==4.11.1
• blake3==0.3.1
• bleach==5.0.0
• bqplot==0.12.33
• cachetools==5.2.0
• certifi==2022.5.18.1
• cffi==1.15.0
• charset-normalizer==2.0.12
• click==8.1.3
• cloudpickle==2.1.0
• commonmark==0.9.1
• configparser==5.2.0
• cryptography==37.0.2
• cycler==0.11.0
• Cython==0.29.30
• dask==2022.5.2
• debugpy==1.6.0
• decorator==5.1.1
• defusedxml==0.7.1
• entrypoints==0.4
• executing==0.8.3
• fastapi==0.78.0
• fastjsonschema==2.15.3
• filelock==3.7.0
• fonttools==4.33.3
• frozendict==2.3.2
• fsspec==2022.5.0
• future==0.18.2
• h11==0.13.0
• h5py==3.7.0
• habanero==1.2.2
• hitran-api==1.2.2.0
• hjson==3.0.2
• html5lib==1.1
• httptools==0.4.0
• idna==3.3
• importlib-metadata==4.11.4
• importlib-resources==5.7.1
• iniconfig==1.1.1
• ipydatawidgets==4.3.1.post1
• ipykernel==6.13.0
• ipyleaflet==0.16.0
• ipympl==0.9.1
• ipython==8.4.0
• ipython-genutils==0.2.0
• ipyvolume==0.5.2
• ipyvue==1.7.0
• ipyvuetify==1.8.2
• ipywebrtc==0.6.0
• ipywidgets==7.7.0
• jedi==0.18.1
• jeepney==0.8.0
• Jinja2==3.1.2
• joblib==1.1.0
• json-tricks==3.15.5
• jsonschema==4.5.1
• jupyter-client==7.3.1
• jupyter-core==4.10.0
• jupyterlab-pygments==0.2.2
• jupyterlab-widgets==1.1.0
• keyring==23.5.1
• kiwisolver==1.4.2
• llvmlite==0.38.1
• locket==1.0.0
• lxml==4.8.0
• MarkupSafe==2.1.1
• matplotlib==3.5.2
• matplotlib-inline==0.1.3
• mistune==0.8.4
• mpldatacursor==0.7.1
• nbclient==0.6.3
• nbconvert==6.5.0
• nbformat==5.4.0
• nest-asyncio==1.5.5
• notebook==6.4.11
• numba==0.55.2
• numexpr==2.8.1
• numpy==1.22.4
• packaging==21.3
• pandas==1.4.2
• pandocfilters==1.5.0
• parso==0.8.3
• partd==1.2.0
• PeakUtils==1.3.3
• pexpect==4.8.0
• pickleshare==0.7.5
• Pillow==9.1.1
• plotly==5.8.0
• pluggy==1.0.0
• progressbar2==4.0.0
• prometheus-client==0.14.1
• prompt-toolkit==3.0.29
• psutil==5.9.1
• ptyprocess==0.7.0
• publib==0.3.3
• pure-eval==0.2.2
• py==1.11.0
• pyarrow==8.0.0
• pycparser==2.21
• pydantic==1.9.1
• pyerfa==2.0.0.1
• Pygments==2.12.0
• pyparsing==3.0.9
• pyrsistent==0.18.1
• pytest==7.1.2
• python-dateutil==2.8.2
• python-dotenv==0.20.0
• python-utils==3.3.2
• pythreejs==2.3.0
• pytz==2022.1
• pyvo==1.3
• PyYAML==6.0
• pyzmq==23.0.0
• -e git+https://github.com/anandxkumar/radis.git@1136890cc2b84734fe037373a48969b3444ce190#egg=radis
• requests==2.27.1
• rich==12.4.4
• scipy==1.8.1
• seaborn==0.11.2
• SecretStorage==3.3.2
• Send2Trash==1.8.0
• six==1.16.0
• sniffio==1.2.0
• soupsieve==2.3.2.post1
• stack-data==0.2.0
• starlette==0.19.1
• tables==3.7.0
• tabulate==0.8.9
• tenacity==8.0.1
• termcolor==1.1.0
• terminado==0.15.0
• tinycss2==1.1.1
• tomli==2.0.1
• toolz==0.11.2
• tornado==6.1
• tqdm==4.64.0
• traitlets==5.2.1.post0
• traittypes==0.2.1
• tuna==0.5.11
• typing_extensions==4.2.0
• urllib3==1.26.9
• uvicorn==0.17.6
• uvloop==0.16.0
• vaex==4.9.1
• vaex-astro==0.9.1
• vaex-core==4.9.1
• vaex-hdf5==0.12.1
• vaex-jupyter==0.7.0
• vaex-ml==0.17.0
• vaex-server==0.8.1
• vaex-viz==0.5.1
• watchgod==0.8.2
• wcwidth==0.2.5
• webencodings==0.5.1
• websockets==10.3
• widgetsnbextension==3.6.0
• xarray==2022.3.0
• xyzservices==2022.4.0
• zipp==3.8.0

Error

platform linux -- Python 3.8.13, pytest-7.1.2, pluggy-1.0.0
rootdir: /home/travis/build/radis/radis, configfile: setup.cfg
plugins: cov-3.0.0, asdf-2.11.1, anyio-3.6.1
collected 227 items / 16 deselected / 211 selected
radis/test/test_misc.py ...... [ 2%]
radis/test/test_phys.py .. [ 3%]
radis/test/db/test_molecule_lists.py .. [ 4%]
radis/test/db/test_molecules.py ... [ 6%]
radis/test/db/test_molparams.py . [ 6%]
radis/test/io/test_exomol.py .FF [ 8%]
radis/test/io/test_geisa.py ... [ 9%]
radis/test/io/test_hdf5.py FF [ 10%]
radis/test/io/test_hitemp.py Warning : 1 files were written but not combined. Deleting them.
['/home/travis/.radisdb/hitemp/OH-13_HITEMP2020_temp00000.hdf5']
F..Warning : 1 files were written but not combined. Deleting them.
['/home/travis/.radisdb/hitemp/OH-13_HITEMP2020_temp00000.hdf5']
Exception ignored in: <function DataFileManager.del at 0x7fcecc2eec10>
Traceback (most recent call last):
File "/home/travis/build/radis/radis/radis/api/hdf5.py", line 238, in del
self._close_temp_batch_files()
File "/home/travis/build/radis/radis/radis/api/hdf5.py", line 225, in _close_temp_batch_files
os.remove(self._temp_batch_files[i])
FileNotFoundError: [Errno 2] No such file or directory: '/home/travis/.radisdb/hitemp/OH-13_HITEMP2020_temp00000.hdf5'
FFWarning : 1 files were written but not combined. Deleting them.
['/home/travis/.radisdb/hitemp/CO2-02_02500-03000_HITEMP2010_temp00000.hdf5']
FFF [ 14%]
radis/test/io/test_hitran_cdsd.py ....... [ 17%]
radis/test/io/test_query.py ....Warning : 1 files were written but not combined. Deleting them.
['/home/travis/.radisdb/hitemp/CO-05_HITEMP2019_temp00000.hdf5']
FWarning : 1 files were written but not combined. Deleting them.
['/home/travis/build/radis/radis/radis/test/files/hitran/CO_temp00000.hdf5']
FWarning : 1 files were written but not combined. Deleting them.
['/home/travis/.radisdb/hitran/CO_temp00000.hdf5']
F [ 20%]
radis/test/lbl/test_bands.py . [ 21%]
radis/test/lbl/test_base.py .......F [ 25%]
radis/test/lbl/test_broadening.py ........FF [ 29%]
radis/test/lbl/test_calc.py .FF.FWarning : 1 files were written but not combined. Deleting them.
['/home/travis/.radisdb/hitran/CO2_temp00000.hdf5']
FWarning : 1 files were written but not combined. Deleting them.
['/home/travis/.radisdb/hitran/CO_temp00000.hdf5']
F.F. [ 34%]
radis/test/lbl/test_database.py .. [ 35%]
radis/test/lbl/test_factory.py ................ [ 43%]
radis/test/lbl/test_labels.py . [ 43%]
radis/test/lbl/test_loader.py .... [ 45%]
radis/test/lbl/test_overp.py . [ 45%]
radis/test/lbl/test_spectrum.py .... [ 47%]
radis/test/levels/test_partfunc.py ............. [ 54%]
radis/test/los/test_slabs.py .... [ 55%]
radis/test/misc/test_arrays.py ............. [ 62%]
radis/test/misc/test_basics.py ... [ 63%]
radis/test/misc/test_config.py .. [ 64%]
radis/test/misc/test_utils.py .. [ 65%]
radis/test/phys/test_blackbody.py ... [ 66%]
radis/test/phys/test_dunham.py .. [ 67%]
radis/test/phys/test_units.py . [ 68%]
radis/test/spectrum/test_compare.py .FF [ 69%]
radis/test/spectrum/test_operations.py ............ [ 75%]
radis/test/spectrum/test_rescale.py ........ [ 79%]
radis/test/spectrum/test_spectrum.py ............... [ 86%]
radis/test/spectrum/test_utils.py .. [ 87%]
radis/test/tools/test_database.py ....F [ 89%]
radis/test/tools/test_gascomp.py . [ 90%]
radis/test/tools/test_line_survey.py .. [ 90%]
radis/test/tools/test_slit.py ........... [ 96%]
radis/test/tools/test_track_ref.py .FWarning : 1 files were written but not combined. Deleting them.
['/home/travis/.radisdb/hitran/CO_temp00000.hdf5']
FWarning : 1 files were written but not combined. Deleting them.
['/home/travis/.radisdb/hitran/CO_temp00000.hdf5']
FF [ 98%]
radis/test/validation/test_CO2_3Tvib_vs_klarenaar.py . [ 99%]
radis/test/validation/test_RADIS_vs_HAPI_line_broadening.py F [ 99%]
radis/test/validation/test_validation_vs_specair_noneqCO.py . [100%]Warning : 1 files were written but not combined. Deleting them.
['/home/travis/.radisdb/hitran/CO2_temp00000.hdf5']
=================================== FAILURES ===================================
__________________________ test_calc_exomol_spectrum ___________________________
verbose = True, plot = True, args = (), kwargs = {}
calc_spectrum = <function calc_spectrum at 0x7fcec4b66b80>
@pytest.mark.needs_connection
def test_calc_exomol_spectrum(verbose=True, plot=True, *args, **kwargs):
"""Auto-fetch and calculate a SiO spectrum from the ExoMol database

    https://github.com/radis/radis/pull/320#issuecomment-884508206
    """
    from radis import calc_spectrum

  s = calc_spectrum(

        1080,
        1320,  # cm-1
        molecule="SiO",
        isotope="1",
        pressure=1.01325,  # bar
        Tgas=1000,  # K
        mole_fraction=0.1,
        path_length=1,  # cm
        broadening_method="fft",  # @ dev: Doesn't work with 'voigt'
        databank=("exomol", "EBJT"),
        verbose=verbose,
    )

radis/test/io/test_exomol.py:55:

---

radis/lbl/calc.py:514: in calc_spectrum
generated_spectrum = _calc_spectrum_one_molecule(
radis/lbl/calc.py:753: in _calc_spectrum_one_molecule
sf.fetch_databank(**conditions)
radis/lbl/loader.py:1302: in fetch_databank
df, local_path, Z_exomol = fetch_exomol(
radis/io/exomol.py:202: in fetch_exomol
mdb = MdbExomol(
radis/api/exomolapi.py:1104: in init
mgr.write(mgr.cache_file(self.states_file), states)
radis/api/hdf5.py:192: in write
df.export_hdf5(file, group=key, mode="w")
../../../micromamba/envs/radis-env/lib/python3.8/site-packages/vaex/dataframe.py:6912: in export_hdf5
writer.write(
../../../micromamba/envs/radis-env/lib/python3.8/site-packages/vaex/hdf5/writer.py:42: in exit
self.close()

---

self = <vaex.hdf5.writer.Writer object at 0x7fcec09fcc40>
def close(self):
if self.mmap is not None:

      self.mmap.close()

E BufferError: cannot close exported pointers exist
../../../micromamba/envs/radis-env/lib/python3.8/site-packages/vaex/hdf5/writer.py:34: BufferError
----------------------------- Captured stdout call -----------------------------
Background atmosphere: Air
Downloading http://www.exomol.com/db/SiO/28Si-16O/EBJT/28Si-16O__EBJT.def
Downloading http://www.exomol.com/db/SiO/28Si-16O/EBJT/28Si-16O__EBJT.pf
Downloading http://www.exomol.com/db/SiO/28Si-16O/EBJT/28Si-16O__EBJT.states.bz2
Downloading http://www.exomol.com/db/SiO/28Si-16O/28Si-16O__H2.broad
Error: Couldn't download .broad file at http://www.exomol.com/db/SiO/28Si-16O/28Si-16O__H2.broad and save.
Downloading http://www.exomol.com/db/SiO/28Si-16O/28Si-16O__He.broad
Error: Couldn't download .broad file at http://www.exomol.com/db/SiO/28Si-16O/28Si-16O__He.broad and save.
Downloading http://www.exomol.com/db/SiO/28Si-16O/28Si-16O__air.broad
Error: Couldn't download .broad file at http://www.exomol.com/db/SiO/28Si-16O/28Si-16O__air.broad and save.
Note: Caching states data to the vaex format. After the second time, it will become much faster.

💡 Possible solutions

Error is possibly occurring when fetching data from hitran, hitemp, and merging the temporary data files causing buffer issues. The issue might lie in the hdf5.py file which is responsible for downloading and merging the data lines.

Also, a thing to note is that the issue is not reproducible on radis-lab so it may be a dependency version specific issue, some compatibility issue between vaex or other packages.

🎲 Radis version

'0.13.0'

💻 Operating system

Linux

[erwanp]

BTW do you confirm that you tested with the latest develop version?

[anandxkumar]

Yes!
The radis/radis/test/files/hitemp and hitran gets updated upon pytest which didn't occur earlier.
Also, I had a python=3.6 environment for radis, and pytest is passing for the same.

Only 1 test in test_query failed

Error

radis/test/io/test_query.py:113:

---

radis/io/hitran.py:1424: in fetch_hitran
ldb.register()

---

self = <radis.io.hitran.HITRANDatabaseManager object at 0x7f43cc0c7208>

def register(self):
    """register in ~/radis.json"""

    from radis.db import MOLECULES_LIST_NONEQUILIBRIUM

    local_files = self.get_filenames()

    if self.wmin is None or self.wmax is None:
        print(
            "Somehow wmin and wmax was not given for this database. Reading from the files"
        )
        ##  fix:
        # (can happen if database was downloaded & parsed, but registration failed a first time)
        df_full = self.load(
            local_files,
            columns=["wav"],
            isotope=None,
            load_wavenum_min=None,

          load_wavenum_max=None,

        )

E TypeError: load() got an unexpected keyword argument 'isotope'

radis/io/hitran.py:1252: TypeError

Dependencies version

absl-py==1.0.0
alabaster==0.7.12
aplus==0.11.0
appdirs==1.4.4
argh==0.26.2
argon2-cffi==21.1.0
arrow==0.13.1
asdf==2.8.3
asdf-astropy==0.1.0
asdf-transform-schemas==0.2.0
asdf-wcs-schemas==0.1.1
asgiref==3.4.1
astroid @ file:///tmp/build/80754af9/astroid_1628055155277/work
astropy==4.1
astroquery==0.4.3
async-generator==1.10
atomicwrites==1.4.0
attrs @ file:///tmp/build/80754af9/attrs_1620827162558/work
autopep8 @ file:///tmp/build/80754af9/autopep8_1615918855173/work
Babel @ file:///tmp/build/80754af9/babel_1620871417480/work
backcall @ file:///home/ktietz/src/ci/backcall_1611930011877/work
backports.entry-points-selectable==1.1.0
beautifulsoup4==4.10.0
binaryornot @ file:///tmp/build/80754af9/binaryornot_1617751525010/work
black==21.9b0
blake3==0.2.0
bleach==4.1.0
bokeh==2.3.3
bqplot==0.12.31
brotlipy==0.7.0
bs4==0.0.1
cached-property==1.5.2
cachetools==4.2.4
certifi==2021.5.30
cffi @ file:///tmp/build/80754af9/cffi_1625814693874/work
cfgv==3.3.1
chardet @ file:///tmp/build/80754af9/chardet_1607706739153/work
charset-normalizer==2.0.6
click @ file:///tmp/build/80754af9/click_1621604852318/work
cloudpickle @ file:///tmp/build/80754af9/cloudpickle_1632508026186/work
commonmark==0.9.1
configparser==5.0.2
contextvars==2.4
cookiecutter @ file:///tmp/build/80754af9/cookiecutter_1617748928239/work
cryptography==35.0.0
cssselect==1.1.0
cycler==0.10.0
Cython==0.29.24
dask==2021.3.0
dataclasses==0.8
decorator @ file:///tmp/build/80754af9/decorator_1632776554403/work
defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work
diff-match-patch @ file:///Users/ktietz/demo/mc3/conda-bld/diff-match-patch_1630511840874/work
distlib==0.3.3
distributed==2021.3.0
docutils @ file:///tmp/build/80754af9/docutils_1620827982266/work
entrypoints==0.3
fake-useragent==0.1.11
fastapi==0.68.2
filelock==3.3.0
flake8 @ file:///tmp/build/80754af9/flake8_1620776156532/work
frozendict==2.0.6
fsspec==2021.10.1
future==0.18.2
gwcs==0.18.0
h11==0.12.0
h5py==3.1.0
habanero==0.7.4
HeapDict==1.0.1
hitran-api==1.2.2.0
hjson==3.0.2
html5lib==1.1
httptools==0.2.0
identify==2.3.0
idna @ file:///tmp/build/80754af9/idna_1622654382723/work
imagesize @ file:///Users/ktietz/demo/mc3/conda-bld/imagesize_1628863108022/work
immutables==0.16
importlib-metadata @ file:///tmp/build/80754af9/importlib-metadata_1631916693255/work
importlib-resources==5.2.2
inflection==0.5.1
iniconfig==1.1.1
intervaltree @ file:///Users/ktietz/demo/mc3/conda-bld/intervaltree_1630511889664/work
ipydatawidgets==4.2.0
ipykernel==5.5.5
ipyleaflet==0.14.0
ipympl==0.8.0
ipython @ file:///tmp/build/80754af9/ipython_1593447367857/work
ipython-genutils @ file:///tmp/build/80754af9/ipython_genutils_1606773439826/work
ipyvolume==0.5.2
ipyvue==1.6.0
ipyvuetify==1.8.1
ipywebrtc==0.6.0
ipywidgets==7.6.5
isort @ file:///tmp/build/80754af9/isort_1628603791788/work
jedi==0.18.0
jeepney @ file:///tmp/build/80754af9/jeepney_1627537048313/work
Jinja2==3.0.2
jinja2-time @ file:///tmp/build/80754af9/jinja2-time_1617751524098/work
jmespath==0.10.0
joblib==1.0.1
json-tricks==3.15.5
jsonschema @ file:///Users/ktietz/demo/mc3/conda-bld/jsonschema_1630511932244/work
jupyter-client==7.0.6
jupyter-core==4.8.1
jupyterlab-pygments @ file:///tmp/build/80754af9/jupyterlab_pygments_1601490720602/work
jupyterlab-widgets==1.0.2
k-means-constrained==0.5.2
keyring==23.2.1
kiwisolver==1.3.1
lazy-object-proxy @ file:///tmp/build/80754af9/lazy-object-proxy_1616526919073/work
llvmlite==0.36.0
locket==0.2.1
lxml==4.6.3
MarkupSafe==2.0.1
matplotlib==3.3.4
mccabe==0.6.1
mimeparse==0.1.3
mistune==0.8.4
MouseInfo==0.1.3
mpldatacursor==0.7.1
msgpack==1.0.2
mypy-extensions==0.4.3
nbclient==0.5.4
nbconvert @ file:///tmp/build/80754af9/nbconvert_1601914804165/work
nbformat @ file:///tmp/build/80754af9/nbformat_1617383369282/work
nest-asyncio @ file:///tmp/build/80754af9/nest-asyncio_1613680548246/work
nodeenv==1.6.0
notebook==6.4.4
numba==0.53.1
numexpr==2.7.3
numpy==1.19.5
numpydoc @ file:///tmp/build/80754af9/numpydoc_1605117425582/work
opencv-contrib-python==4.5.5.62
ortools==9.3.10497
packaging @ file:///tmp/build/80754af9/packaging_1625611678980/work
pandas==1.1.5
pandocfilters==1.5.0
parse==1.19.0
parso==0.8.2
partd==1.2.0
pathspec==0.9.0
PeakUtils==1.3.3
pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work
pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work
Pillow==8.3.2
platformdirs==2.4.0
plotly==5.3.1
pluggy==1.0.0
plumbum==1.7.2
poyo @ file:///tmp/build/80754af9/poyo_1617751526755/work
pre-commit==2.15.0
progressbar2==3.53.3
prometheus-client==0.11.0
prompt-toolkit @ file:///tmp/build/80754af9/prompt-toolkit_1633440160888/work
protobuf==3.19.4
psutil @ file:///tmp/build/80754af9/psutil_1612297621795/work
ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
publib==0.3.3
py==1.10.0
pyarrow==5.0.0
PyAutoGUI==0.9.53
pycodestyle @ file:///tmp/build/80754af9/pycodestyle_1615748559966/work
pycparser @ file:///tmp/build/80754af9/pycparser_1594388511720/work
pydantic==1.8.2
pydocstyle @ file:///tmp/build/80754af9/pydocstyle_1621600989141/work
pyee==8.2.2
pyflakes @ file:///tmp/build/80754af9/pyflakes_1617200973297/work
PyGetWindow==0.0.9
Pygments @ file:///tmp/build/80754af9/pygments_1629234116488/work
pylint @ file:///tmp/build/80754af9/pylint_1627536508692/work
pyls-spyder==0.4.0
PyMsgBox==1.0.9
pyOpenSSL @ file:///tmp/build/80754af9/pyopenssl_1608057966937/work
pyparsing @ file:///home/linux1/recipes/ci/pyparsing_1610983426697/work
pyperclip==1.8.2
pyppeteer==0.2.6
pyquery==1.4.3
PyRect==0.1.4
pyrsistent==0.18.0
PyScreeze==0.1.28
PySocks @ file:///tmp/build/80754af9/pysocks_1605305763431/work
pytest==6.2.5
python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work
python-dotenv==0.19.0
python-jsonrpc-server @ file:///tmp/build/80754af9/python-jsonrpc-server_1600278539111/work
python-lsp-black @ file:///tmp/build/80754af9/python-lsp-black_1634232156041/work
python-lsp-jsonrpc==1.0.0
python-lsp-server==1.2.4
python-slugify @ file:///tmp/build/80754af9/python-slugify_1620405669636/work
python-utils==2.5.6
python-xlib==0.31
python3-xlib==0.15
pythreejs==2.3.0
pytweening==1.0.4
pytz==2021.3
pyvo==1.1
pyxdg @ file:///tmp/build/80754af9/pyxdg_1603822279816/work
PyYAML==5.4.1
pyzmq==22.3.0
QDarkStyle @ file:///tmp/build/80754af9/qdarkstyle_1617386714626/work
qstylizer @ file:///tmp/build/80754af9/qstylizer_1617713584600/work/dist/qstylizer-0.1.10-py2.py3-none-any.whl
QtAwesome @ file:///tmp/build/80754af9/qtawesome_1615991616277/work
qtconsole @ file:///tmp/build/80754af9/qtconsole_1632739723211/work
QtPy @ file:///tmp/build/80754af9/qtpy_1629397026935/work
-e git+https://github.com/anandxkumar/radis.git@1136890cc2b84734fe037373a48969b3444ce190#egg=radis
regex==2021.9.30
requests @ file:///tmp/build/80754af9/requests_1629994808627/work
requests-html==0.10.0
rich==12.0.0
rope @ file:///tmp/build/80754af9/rope_1623703006312/work
rpyc==5.0.1
Rtree @ file:///tmp/build/80754af9/rtree_1618420379819/work
scikit-learn==0.24.2
scipy==1.5.4
seaborn==0.11.2
SecretStorage @ file:///tmp/build/80754af9/secretstorage_1614022884787/work
semantic-version==2.9.0
Send2Trash==1.8.0
simplestRPC==1.4.13
six @ file:///tmp/build/80754af9/six_1623709665295/work
sklearn==0.0
snowballstemmer @ file:///tmp/build/80754af9/snowballstemmer_1611258885636/work
sortedcontainers @ file:///tmp/build/80754af9/sortedcontainers_1623949099177/work
soupsieve==2.2.1
specutils==1.3.1
Sphinx @ file:///tmp/build/80754af9/sphinx_1632506123190/work
sphinxcontrib-applehelp @ file:///home/ktietz/src/ci/sphinxcontrib-applehelp_1611920841464/work
sphinxcontrib-devhelp @ file:///home/ktietz/src/ci/sphinxcontrib-devhelp_1611920923094/work
sphinxcontrib-htmlhelp @ file:///tmp/build/80754af9/sphinxcontrib-htmlhelp_1623945626792/work
sphinxcontrib-jsmath @ file:///home/ktietz/src/ci/sphinxcontrib-jsmath_1611920942228/work
sphinxcontrib-qthelp @ file:///home/ktietz/src/ci/sphinxcontrib-qthelp_1611921055322/work
sphinxcontrib-serializinghtml @ file:///tmp/build/80754af9/sphinxcontrib-serializinghtml_1624451540180/work
spyder @ file:///home/conda/feedstock_root/build_artifacts/spyder_1631797899126/work
spyder-kernels @ file:///home/conda/feedstock_root/build_artifacts/spyder-kernels_1633270854915/work
starlette==0.14.2
tables==3.6.1
tabulate==0.8.9
tblib==1.7.0
tenacity==8.0.1
termcolor==1.1.0
terminado==0.12.1
terminal==0.4.0
testpath @ file:///tmp/build/80754af9/testpath_1624638946665/work
text-unidecode @ file:///Users/ktietz/demo/mc3/conda-bld/text-unidecode_1629401354553/work
textdistance @ file:///tmp/build/80754af9/textdistance_1612461398012/work
threadpoolctl==3.1.0
three-merge @ file:///tmp/build/80754af9/three-merge_1607553261110/work
tinycss @ file:///tmp/build/80754af9/tinycss_1617713798712/work
toml @ file:///tmp/build/80754af9/toml_1616166611790/work
tomli==1.2.1
toolz==0.11.1
tornado @ file:///tmp/build/80754af9/tornado_1606942266872/work
tqdm==4.62.3
traitlets @ file:///tmp/build/80754af9/traitlets_1632746497744/work
traittypes==0.2.1
tuna==0.5.8
typed-ast @ file:///tmp/build/80754af9/typed-ast_1624953671446/work
typing-extensions @ file:///tmp/build/80754af9/typing_extensions_1631814937681/work
ujson @ file:///tmp/build/80754af9/ujson_1611259495878/work
Unidecode @ file:///tmp/build/80754af9/unidecode_1614712377438/work
urllib3==1.26.7
uvicorn==0.15.0
uvloop==0.14.0
vaex==4.8.0
vaex-astro==0.9.0
vaex-core==4.8.0
vaex-hdf5==0.12.0
vaex-jupyter==0.7.0
vaex-ml==0.17.0
vaex-server==0.8.1
vaex-viz==0.5.1
varenv==1.0.7
virtualenv==20.8.1
w3lib==1.22.0
watchdog @ file:///tmp/build/80754af9/watchdog_1624955002849/work
watchgod==0.7
wcwidth @ file:///Users/ktietz/demo/mc3/conda-bld/wcwidth_1629357192024/work
webencodings==0.5.1
websockets==9.1
whichcraft @ file:///tmp/build/80754af9/whichcraft_1617751293875/work
widgetsnbextension==3.5.1
wrapt==1.12.1
wurlitzer @ file:///tmp/build/80754af9/wurlitzer_1626947800350/work
xarray==0.16.2
xexplorer @ git+https://github.com/spark-cleantech/xexplorer.git@059616c9dc667b1702d7abe77c32da51e7864f60
yapf @ file:///tmp/build/80754af9/yapf_1615749224965/work
zict==2.0.0
zipp==3.6.0

This indicates that the issue is definitely due to some package's version incompatibility, which can be the ones used in hdf5.py, hitran.py or hitemp.py, like astroquery or vaex (update_pytables_to_vaex to be specific)

[erwanp]

I think at least one error

ipdb> df.close()
*** BufferError: cannot close exported pointers exist

is related to vaexio/vaex#2062 ; will be fixed in Vaex 4.9.2

[erwanp]

@anandxkumar : still not fixed despite Vaex recent Vaex update on Travis-CI.
Apparently we're not the only ones : vaexio/vaex#2062 (comment)
It seems this issue will take some time to resolve.
In the meantime, what we could do is restrict numpy<=1.22.3 in setup.py and environment.yml
Do you wanna give it a try?

[anandxkumar]

Sure! I will give it a try and let you know.