Storing and loading transport to hdf5 is not functional

[mrcromulent]

Describe the bug When calling the store_transport_to_hdf function in tardis.io.model_reader, TARDIS attempts to access a non-existent attribute

  File "/home/149/ub0692/miniconda3/envs/tardis/lib/python3.11/site-packages/tardis/io/model_reader.py", line 554, in transport_to_dict
    "Edotlu_estimator": transport.Edotlu_estimator,
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'MonteCarloTransportSolver' object has no attribute 'Edotlu_estimator'

To Reproduce

• Run tardis, then call store_transport_to_hdf on the returned simulation.transport object

def main():

    from tardis.io.model_reader import transport_from_hdf, store_transport_to_hdf
    from tardis import run_tardis

    sim_core = run_tardis("./example_config.yml",
                          virtual_packet_logging=True,
                          show_convergence_plots=False,
                          export_convergence_plots=False,
                          log_level="INFO")

    hdf_filename = "my_file.hdf5"
    store_transport_to_hdf(sim_core.transport, hdf_filename)
    loaded_transport = transport_from_hdf(hdf_filename)
    print(loaded_transport)

if __name__ == "__main__":
    main()

System

• OS:

  • [x] GNU/Linux
  • [ ] macOS

• Environment (conda list):

# Name                    Version                   Build  Channel
_ipython_minor_entry_point 8.7.0                h3b92ee0_0    conda-forge
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
alabaster                 0.7.13             pyhd8ed1ab_0    conda-forge
anyio                     4.0.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py311h459d7ec_4    conda-forge
arrow                     1.2.3              pyhd8ed1ab_0    conda-forge
astropy                   5.3.3           py311h1f0f07a_0    conda-forge
astropy-sphinx-theme      1.1                pyhd8ed1ab_0    conda-forge
asttokens                 2.4.0              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
atk-1.0                   2.38.0               hd4edc92_1    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
babel                     2.12.1             pyhd8ed1ab_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.5              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
black                     22.3.0             pyhd8ed1ab_0    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.5               h0f2a231_0    conda-forge
brotli                    1.1.0                hd590300_0    conda-forge
brotli-bin                1.1.0                hd590300_0    conda-forge
brotli-python             1.1.0           py311hb755f60_0    conda-forge
brotlipy                  0.7.0           py38h0a891b7_1005    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.19.1               hd590300_0    conda-forge
c-blosc2                  2.10.2               hb4ffafa_0    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.16.0            h0c91306_1017    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py311hb3a22ac_5    conda-forge
charset-normalizer        3.2.0              pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
colored                   1.4.4              pyhd8ed1ab_0    conda-forge
comm                      0.1.4              pyhd8ed1ab_0    conda-forge
commonmark                0.9.1                      py_0    conda-forge
contourpy                 1.1.1           py311h9547e67_1    conda-forge
coverage                  7.3.1           py311h459d7ec_1    conda-forge
cryptography              40.0.2           py38h3d167d9_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
debugpy                   1.8.0           py311hb755f60_1    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.17.1          py311h38be061_4    conda-forge
dot2tex                   2.11.3             pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.1.3              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
flit-core                 3.9.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.42.1          py311h459d7ec_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
gdk-pixbuf                2.42.10              h6c15284_3    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
giflib                    5.2.1                h0b41bf4_3    conda-forge
git-lfs                   3.4.0                ha770c72_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmpy2                     2.1.2           py311h6a5fa03_1    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
graphviz                  8.1.0                h28d9a01_0    conda-forge
gtk2                      2.24.33              h90689f9_2    conda-forge
gts                       0.7.6                h977cf35_4    conda-forge
h5py                      3.9.0           nompi_py311h3839ddf_103    conda-forge
harfbuzz                  8.2.1                h3d44ed6_0    conda-forge
hdf5                      1.14.2          nompi_h4f84152_100    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
importlib_metadata        6.8.0                hd8ed1ab_0    conda-forge
importlib_resources       6.1.0              pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.25.2             pyh2140261_0    conda-forge
ipython                   8.15.0             pyh0d859eb_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.8.0              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.0             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
json5                     0.9.14             pyhd8ed1ab_0    conda-forge
jsonpointer               2.4             py311h38be061_3    conda-forge
jsonschema                4.19.1             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.7.1           pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.19.1             pyhd8ed1ab_0    conda-forge
jupyter-lsp               2.2.0              pyhd8ed1ab_0    conda-forge
jupyter_client            8.3.1              pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.2           py311h38be061_0    conda-forge
jupyter_events            0.7.0              pyhd8ed1ab_2    conda-forge
jupyter_server            2.7.3              pyhd8ed1ab_1    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab                4.0.6              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.25.0             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.1.7              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5           py311h9547e67_1    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
latexcodec                2.0.1              pyh9f0ad1d_0    conda-forge
lcms2                     2.15                 h7f713cb_2    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libaec                    1.0.6                hcb278e6_1    conda-forge
libblas                   3.9.0           18_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hd590300_0    conda-forge
libbrotlidec              1.1.0                hd590300_0    conda-forge
libbrotlienc              1.1.0                hd590300_0    conda-forge
libcblas                  3.9.0           18_linux64_openblas    conda-forge
libcurl                   8.3.0                hca28451_0    conda-forge
libdeflate                1.19                 hd590300_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_2    conda-forge
libgd                     2.3.3                he9388d3_8    conda-forge
libgfortran-ng            13.2.0               h69a702a_2    conda-forge
libgfortran5              13.2.0               ha4646dd_2    conda-forge
libglib                   2.78.0               hebfc3b9_0    conda-forge
libgomp                   13.2.0               h807b86a_2    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libjpeg-turbo             2.1.5.1              hd590300_1    conda-forge
liblapack                 3.9.0           18_linux64_openblas    conda-forge
libllvm10                 10.0.1               he513fc3_3    conda-forge
libllvm14                 14.0.6               hcd5def8_4    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                hd590300_1    conda-forge
libopenblas               0.3.24          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
librsvg                   2.56.3               h98fae49_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.43.0               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_2    conda-forge
libtiff                   4.6.0                h29866fb_1    conda-forge
libtool                   2.4.7                h27087fc_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp                   1.3.2                hdffd6e0_0    conda-forge
libwebp-base              1.3.2                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxml2                   2.11.5               h232c23b_1    conda-forge
libxslt                   1.1.37               h0054252_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
llvmlite                  0.40.1          py311ha6695c7_0    conda-forge
lxml                      4.9.3           py311h1a07684_1    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
markupsafe                2.1.3           py311h459d7ec_1    conda-forge
matplotlib-base           3.8.0           py311h54ef318_1    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   3.0.1              pyhd8ed1ab_0    conda-forge
mock                      5.0.2              pyhd8ed1ab_0    conda-forge
mpc                       1.3.1                hfe3b2da_0    conda-forge
mpfr                      4.2.0                hb012696_0    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mypy_extensions           1.0.0              pyha770c72_0    conda-forge
nbclassic                 1.0.0              pyhb4ecaf3_1    conda-forge
nbclient                  0.8.0              pyhd8ed1ab_0    conda-forge
nbconvert                 7.8.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.8.0              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.8.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.9.2              pyhd8ed1ab_0    conda-forge
nbsphinx                  0.9.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
networkx                  3.1                pyhd8ed1ab_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
notebook                  7.0.4              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge
numba                     0.57.1          py311h96b013e_0    conda-forge
numexpr                   2.8.7           py311h320fe9a_100    conda-forge
numpy                     1.24.4          py311h64a7726_0    conda-forge
numpydoc                  1.5.0              pyhd8ed1ab_0    conda-forge
openjpeg                  2.5.0                h488ebb8_3    conda-forge
openssl                   3.1.3                hd590300_0    conda-forge
overrides                 7.4.0              pyhd8ed1ab_0    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
pandas                    2.1.1           py311h320fe9a_0    conda-forge
pandoc                    3.1.3                h32600fe_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.50.14              ha41ecd1_2    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pathspec                  0.11.2             pyhd8ed1ab_0    conda-forge
pbr                       5.11.1             pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.0.1          py311h8aef010_1    conda-forge
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pixman                    0.42.2               h59595ed_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              3.10.0             pyhd8ed1ab_0    conda-forge
plotly                    5.17.0             pyhd8ed1ab_0    conda-forge
pluggy                    1.3.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.17.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.39             pyha770c72_0    conda-forge
prompt_toolkit            3.0.39               hd8ed1ab_0    conda-forge
psutil                    5.9.5           py311h459d7ec_1    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py                        1.11.0             pyh6c4a22f_0    conda-forge
py-cpuinfo                9.0.0              pyhd8ed1ab_0    conda-forge
pybtex                    0.24.0             pyhd8ed1ab_2    conda-forge
pybtex-docutils           1.0.3           py311h38be061_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyerfa                    2.0.0.3         py311h1f0f07a_1    conda-forge
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
pygraphviz                1.11            py311h72a77b7_1    conda-forge
pyopenssl                 23.1.1             pyhd8ed1ab_0    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3           py38h1de0b5d_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytables                  3.8.0           py311h10c7f7f_3    conda-forge
pytest                    7.4.2              pyhd8ed1ab_0    conda-forge
pytest-cov                4.1.0              pyhd8ed1ab_0    conda-forge
pytest-doctestplus        1.0.0              pyhd8ed1ab_0    conda-forge
pytest-html               3.2.0              pyhd8ed1ab_1    conda-forge
pytest-metadata           3.0.0              pyhd8ed1ab_1    conda-forge
python                    3.11.5          hab00c5b_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-dokuwiki           1.3.3              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.18.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.11                    4_cp311    conda-forge
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py311h459d7ec_1    conda-forge
pyzmq                     25.1.1          py311h75c88c4_1    conda-forge
qgrid                     1.3.1              pyhd8ed1ab_4    conda-forge
radioactivedecay          0.4.21             pyhd8ed1ab_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
recommonmark              0.7.1              pyhd8ed1ab_0    conda-forge
referencing               0.30.2             pyhd8ed1ab_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.10.3          py311h46250e7_0    conda-forge
scipy                     1.11.3          py311h64a7726_0    conda-forge
send2trash                1.8.2              pyh41d4057_0    conda-forge
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
setuptools-scm            8.0.3              pyhd8ed1ab_0    conda-forge
setuptools_scm            8.0.3                hd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snakeviz                  2.2.0              pyhd8ed1ab_0    conda-forge
snappy                    1.1.10               h9fff704_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sphinx                    5.3.0              pyhd8ed1ab_0    conda-forge
sphinx-astropy            1.9.1              pyhd8ed1ab_0    conda-forge
sphinx-automodapi         0.16.0             pyh6ff6d48_0    conda-forge
sphinx-gallery            0.14.0             pyhd8ed1ab_0    conda-forge
sphinx-jsonschema         1.19.1             pyhd8ed1ab_0    conda-forge
sphinx_bootstrap_theme    0.8.1              pyhd8ed1ab_0    conda-forge
sphinx_rtd_theme          1.3.0              pyha770c72_0    conda-forge
sphinxcontrib-apidoc      0.3.0                      py_1    conda-forge
sphinxcontrib-applehelp   1.0.7              pyhd8ed1ab_0    conda-forge
sphinxcontrib-bibtex      2.6.1              pyhd8ed1ab_1    conda-forge
sphinxcontrib-devhelp     1.0.5              pyhd8ed1ab_0    conda-forge
sphinxcontrib-htmlhelp    2.0.4              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jquery      4.1                pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-qthelp      1.0.6              pyhd8ed1ab_0    conda-forge
sphinxcontrib-serializinghtml 1.1.9              pyhd8ed1ab_0    conda-forge
sqlite                    3.40.0               h4ff8645_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
sympy                     1.12            pypyh9d50eac_103    conda-forge
syrupy                    4.5.0              pyhd8ed1ab_0    conda-forge
tardis                    2024.4.16.0.dev2+g13612976          pypi_0    pypi
tenacity                  8.2.3              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h2797004_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.3.3           py311h459d7ec_1    conda-forge
tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.10.1             pyhd8ed1ab_0    conda-forge
typed-ast                 1.5.5           py311h459d7ec_1    conda-forge
typing-extensions         4.8.0                hd8ed1ab_0    conda-forge
typing_extensions         4.8.0              pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
unicodedata2              15.0.0           py38h0a891b7_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.0.5              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webcolors                 1.13               pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.6.3              pyhd8ed1ab_0    conda-forge
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.6.6              pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.6                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zlib-ng                   2.0.7                h0b41bf4_0    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Additional context

• I have been trying to save simulations or parts of simulations (e.g. transport objects) to disk so that I don't need to re-run tardis. The .to_hdf method also does not seem to work for me
• If anyone has a workaround for saving simulations to disk this would be helpful

[mrcromulent]

Github wouldn't let me attach the auxillary files, sorry

File example_config.yml

# Example YAML configuration for TARDIS
tardis_config_version: v1.0

supernova:
  luminosity_requested: 9.44 log_lsun
  time_explosion: 13 day

atom_data: kurucz_cd23_chianti_H_He.h5

csvy_model: example_csvy.csvy

plasma:
  disable_electron_scattering: no
  ionization: lte
  excitation: lte
  radiative_rates_type: dilute-blackbody
  line_interaction_type: macroatom

montecarlo:
  seed: 23111963
  no_of_packets: 4.0e+4
  iterations: 20
  nthreads: 1

  last_no_of_packets: 1.e+5
  no_of_virtual_packets: 10

  convergence_strategy:
    type: damped
    damping_constant: 1.0
    threshold: 0.05
    fraction: 0.8
    hold_iterations: 3
    t_inner:
      damping_constant: 0.5

spectrum:
  start: 500 angstrom
  stop: 20000 angstrom
  num: 10000

File example_csvy.csvy

---
name: csvy_full
model_density_time_0: 4.62963e-05 day
model_isotope_time_0: 0.0266667 day
description: Example
tardis_model_config_version: v1.0
datatype:
  fields:
    -  name: velocity
       unit: cm/s
       desc: velocities of shell outer bounderies.
    -  name: density
       unit: g/cm^3
       desc: density of shell.
    -  name: C12
       desc: fractional C12 abundance.
    -  name: O16
       desc: fractional O16 abundance.

---
velocity,density,C12,O16
1.37331e+09,76.4061,6.36293e-06,0.438889
1.43156e+09,65.1115,4.00259e-06,0.630709
1.4914e+09,41.5399,1.16434e-05,0.662441
1.55411e+09,25.1586,9.12116e-05,0.646794
1.62089e+09,15.2277,0.000414912,0.620527
1.69108e+09,10.136,0.00124593,0.588458
1.76214e+09,6.72036,0.00277819,0.542888
1.83348e+09,4.90628,0.00546722,0.483187
1.90602e+09,3.42798,0.00871367,0.410087
1.974e+09,2.58831,0.0119094,0.343264
2.05064e+09,2.29487,0.0136243,0.277051
2.11975e+09,1.41053,0.0146015,0.22898
2.19132e+09,1.39823,0.0143288,0.178491
2.26874e+09,0.926097,0.0159026,0.142512
2.33824e+09,0.903295,0.01617,0.122333
2.41396e+09,0.654972,0.0134753,0.0852562
2.48099e+09,0.474333,0.0130918,0.0640767
2.55252e+09,0.440394,0.0172914,0.0614422
2.62229e+09,0.366044,0.0136179,0.039855
2.6953e+09,0.284077,0.0134391,0.0292639