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Kernel crashing with certain plotting elements #246

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@mdtanker

Description

@mdtanker

Describe the bug
I've been experiencing lots of crashing of kernel with certain aspects of maps.plot_grd, mostly with hist=True or even with show_region. It appears to be an issue with some dependency. I can reliably recreate the crash with the below code:

from polartoolkit import fetch, maps, profiles, regions
import os
os.environ["POLARTOOLKIT_HEMISPHERE"] = "south"

ibcso = fetch.ibcso(
    layer="bed",
    region=(-40e3, 110e3, -1600e3, -1400e3),
)
fig = maps.plot_grd(
    ibcso,
    show_region=(-40e3, 110e3, -1600e3, -1400e3),
    fig_height=10,
    title="Bathymetry",
    hist=True,
    cmap="rain",
    reverse_cpt=True,
    cbar_label="elevation (m)",
    robust=True,
)
fig.savefig("ibcso_bed.png", dpi=300)
double free or corruption (out)
Aborted (core dumped)

The main differences between the environment that works and the one that doesn't seems to be:

  • good env has cartopy 0.24, bad env doesn't have cartopy
  • good env has geopandas 1.0.1, bad env has 0.14.4
  • good env has zarr 2.18.7, bad env has 3.0.7
Fails with this environment:
     _openmp_mutex                     4.5             3_kmp_llvm                      conda-forge
  adjusttext                        1.3.0           pyhd8ed1ab_0                    conda-forge
  affine                            2.4.0           pyhd8ed1ab_1                    conda-forge
  aiobotocore                       2.21.1          pyhd8ed1ab_0                    conda-forge
  aiohappyeyeballs                  2.6.1           pyhd8ed1ab_0                    conda-forge
  aiohttp                           3.11.18         py312h178313f_0                 conda-forge
  aioitertools                      0.12.0          pyhd8ed1ab_1                    conda-forge
  aiosignal                         1.3.2           pyhd8ed1ab_0                    conda-forge
  alembic                           1.15.2          pyhd8ed1ab_0                    conda-forge
  alsa-lib                          1.2.14          hb9d3cd8_0                      conda-forge
  anyio                             4.9.0           pyh29332c3_0                    conda-forge
  aom                               3.9.1           hac33072_0                      conda-forge
  argon2-cffi                       23.1.0          pyhd8ed1ab_1                    conda-forge
  argon2-cffi-bindings              21.2.0          py312h66e93f0_5                 conda-forge
  arrow                             1.3.0           pyhd8ed1ab_1                    conda-forge
  astroid                           3.3.9           py312h7900ff3_0                 conda-forge
  asttokens                         3.0.0           pyhd8ed1ab_1                    conda-forge
  async-lru                         2.0.5           pyh29332c3_0                    conda-forge
  attr                              2.5.1           h166bdaf_1                      conda-forge
  attrs                             25.3.0          pyh71513ae_0                    conda-forge
  aws-c-auth                        0.9.0           h094d708_2                      conda-forge
  aws-c-cal                         0.8.9           hada3f3f_0                      conda-forge
  aws-c-common                      0.12.2          hb9d3cd8_0                      conda-forge
  aws-c-compression                 0.3.1           hc2d532b_4                      conda-forge
  aws-c-event-stream                0.5.4           h8170a11_5                      conda-forge
  aws-c-http                        0.9.5           hca9d837_2                      conda-forge
  aws-c-io                          0.18.0          h7b13e6b_1                      conda-forge
  aws-c-mqtt                        0.12.3          h773eac8_2                      conda-forge
  aws-c-s3                          0.7.15          h46af1f8_1                      conda-forge
  aws-c-sdkutils                    0.2.3           hc2d532b_4                      conda-forge
  aws-checksums                     0.2.5           hc2d532b_1                      conda-forge
  aws-crt-cpp                       0.32.4          h7d42c6f_0                      conda-forge
  aws-sdk-cpp                       1.11.510        h5b777a2_5                      conda-forge
  azure-core-cpp                    1.14.0          h5cfcd09_0                      conda-forge
  azure-identity-cpp                1.10.0          h113e628_0                      conda-forge
  azure-storage-blobs-cpp           12.13.0         h3cf044e_1                      conda-forge
  azure-storage-common-cpp          12.8.0          h736e048_1                      conda-forge
  azure-storage-files-datalake-cpp  12.12.0         ha633028_1                      conda-forge
  babel                             2.17.0          pyhd8ed1ab_0                    conda-forge
  beautifulsoup4                    4.13.4          pyha770c72_0                    conda-forge
  bleach                            6.2.0           pyh29332c3_4                    conda-forge
  bleach-with-css                   6.2.0           h82add2a_4                      conda-forge
  blosc                             1.21.6          he440d0b_1                      conda-forge
  bokeh                             3.7.2           pyhd8ed1ab_1                    conda-forge
  botocore                          1.37.1          pyge310_1234567_0               conda-forge
  boule                             0.5.0           pyhd8ed1ab_1                    conda-forge
  bounded-pool-executor             0.0.3           pyhd8ed1ab_0                    conda-forge
  branca                            0.8.1           pyhd8ed1ab_0                    conda-forge
  brotli                            1.1.0           hb9d3cd8_2                      conda-forge
  brotli-bin                        1.1.0           hb9d3cd8_2                      conda-forge
  brotli-python                     1.1.0           py312h2ec8cdc_2                 conda-forge
  bzip2                             1.0.8           h4bc722e_7                      conda-forge
  c-ares                            1.34.5          hb9d3cd8_0                      conda-forge
  ca-certificates                   2025.1.31       hbd8a1cb_1                      conda-forge
  cached-property                   1.5.2           hd8ed1ab_1                      conda-forge
  cached_property                   1.5.2           pyha770c72_1                    conda-forge
  cairo                             1.18.4          h3394656_0                      conda-forge
  certifi                           2025.1.31       pyhd8ed1ab_0                    conda-forge
  cf_xarray                         0.10.5          pyhd8ed1ab_0                    conda-forge
  cffi                              1.17.1          py312h06ac9bb_0                 conda-forge
  cfgv                              3.3.1           pyhd8ed1ab_1                    conda-forge
  cftime                            1.6.4           py312hc0a28a1_1                 conda-forge
  charset-normalizer                3.4.1           pyhd8ed1ab_0                    conda-forge
  choclo                            0.3.2           pyhd8ed1ab_0                    conda-forge
  click                             8.1.8           pyh707e725_0                    conda-forge
  click-plugins                     1.1.1           pyhd8ed1ab_1                    conda-forge
  cligj                             0.7.2           pyhd8ed1ab_2                    conda-forge
  cloudpickle                       3.1.1           pyhd8ed1ab_0                    conda-forge
  cmocean                           4.0.3           pyhd8ed1ab_1                    conda-forge
  colorama                          0.4.6           pyhd8ed1ab_1                    conda-forge
  colorlog                          6.9.0           pyh707e725_1                    conda-forge
  colorspacious                     1.1.2           pyhecae5ae_1                    conda-forge
  comm                              0.2.2           pyhd8ed1ab_1                    conda-forge
  contourpy                         1.3.2           py312h68727a3_0                 conda-forge
  cpython                           3.12.10         py312hd8ed1ab_0                 conda-forge
  crc32c                            2.7.1           py312h66e93f0_1                 conda-forge
  cuda-crt-tools                    12.8.93         ha770c72_3                      conda-forge
  cuda-cudart                       12.8.90         h5888daf_1                      conda-forge
  cuda-cudart_linux-64              12.8.90         h3f2d84a_1                      conda-forge
  cuda-cuobjdump                    12.8.90         hbd13f7d_1                      conda-forge
  cuda-cupti                        12.8.90         h5888daf_1                      conda-forge
  cuda-nvcc-tools                   12.8.93         he02047a_3                      conda-forge
  cuda-nvdisasm                     12.8.90         hbd13f7d_1                      conda-forge
  cuda-nvrtc                        12.8.93         h5888daf_1                      conda-forge
  cuda-nvtx                         12.8.90         h5888daf_1                      conda-forge
  cuda-nvvm-tools                   12.8.93         he02047a_3                      conda-forge
  cuda-version                      12.8            h5d125a7_3                      conda-forge
  cudnn                             9.8.0.87        h81d5506_1                      conda-forge
  curl                              8.13.0          h332b0f4_0                      conda-forge
  cycler                            0.12.1          pyhd8ed1ab_1                    conda-forge
  cyrus-sasl                        2.1.27          h54b06d7_7                      conda-forge
  cytoolz                           1.0.1           py312h66e93f0_0                 conda-forge
  dask                              2025.4.0        pyhd8ed1ab_0                    conda-forge
  dask-core                         2025.4.0        pyhd8ed1ab_0                    conda-forge
  dav1d                             1.2.1           hd590300_0                      conda-forge
  dbus                              1.13.6          h5008d03_3                      conda-forge
  dcw-gmt                           2.2.0           ha770c72_0                      conda-forge
  debugpy                           1.8.14          py312h2ec8cdc_0                 conda-forge
  decorator                         5.2.1           pyhd8ed1ab_0                    conda-forge
  defusedxml                        0.7.1           pyhd8ed1ab_0                    conda-forge
  deprecated                        1.2.18          pyhd8ed1ab_0                    conda-forge
  deprecation                       2.1.0           pyh9f0ad1d_0                    conda-forge
  dill                              0.4.0           pyhd8ed1ab_0                    conda-forge
  distlib                           0.3.9           pyhd8ed1ab_1                    conda-forge
  distributed                       2025.4.0        pyhd8ed1ab_0                    conda-forge
  docrep                            0.3.2           pyh44b312d_0                    conda-forge
  donfig                            0.8.1.post1     pyhd8ed1ab_1                    conda-forge
  double-conversion                 3.3.1           h5888daf_0                      conda-forge
  earthaccess                       0.12.0          pyhd8ed1ab_1                    conda-forge
  esmf                              8.8.1           nompi_h4441c20_0                conda-forge
  esmpy                             8.8.1           pyhecae5ae_0                    conda-forge
  et_xmlfile                        2.0.0           pyhd8ed1ab_1                    conda-forge
  exceptiongroup                    1.2.2           pyhd8ed1ab_1                    conda-forge
  executing                         2.1.0           pyhd8ed1ab_1                    conda-forge
  expat                             2.7.0           h5888daf_0                      conda-forge
  fftw                              3.3.10          nompi_hf1063bd_110              conda-forge
  filelock                          3.18.0          pyhd8ed1ab_0                    conda-forge
  fiona                             1.10.1          py312h02b19dd_3                 conda-forge
  folium                            0.19.5          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            h77eed37_3                      conda-forge
  fontconfig                        2.15.0          h7e30c49_1                      conda-forge
  fonts-conda-ecosystem             1               0                               conda-forge
  fonts-conda-forge                 1               0                               conda-forge
  fonttools                         4.57.0          py312h178313f_0                 conda-forge
  fqdn                              1.5.1           pyhd8ed1ab_1                    conda-forge
  freetype                          2.13.3          ha770c72_1                      conda-forge
  freexl                            2.0.0           h9dce30a_2                      conda-forge
  frozenlist                        1.5.0           py312h178313f_1                 conda-forge
  fsspec                            2025.3.2        pyhd8ed1ab_0                    conda-forge
  future                            1.0.0           pyhd8ed1ab_2                    conda-forge
  geopandas                         0.14.4          pyhd8ed1ab_0                    conda-forge
  geopandas-base                    0.14.4          pyha770c72_0                    conda-forge
  geos                              3.13.1          h97f6797_0                      conda-forge
  geotiff                           1.7.4           h3551947_0                      conda-forge
  gflags                            2.2.2           h5888daf_1005                   conda-forge
  ghostscript                       10.04.0         h5888daf_0                      conda-forge
  giflib                            5.2.2           hd590300_0                      conda-forge
  gl2ps                             1.4.2           hae5d5c5_1                      conda-forge
  glew                              2.1.0           h9c3ff4c_2                      conda-forge
  glog                              0.7.1           hbabe93e_0                      conda-forge
  gmp                               6.3.0           hac33072_2                      conda-forge
  gmpy2                             2.1.5           py312h7201bc8_3                 conda-forge
  gmt                               6.5.0           h8300b2c_8                      conda-forge
  graphite2                         1.3.13          h59595ed_1003                   conda-forge
  greenlet                          3.2.0           py312h2ec8cdc_0                 conda-forge
  gshhg-gmt                         2.3.7           ha770c72_1003                   conda-forge
  h11                               0.14.0          pyhd8ed1ab_1                    conda-forge
  h2                                4.2.0           pyhd8ed1ab_0                    conda-forge
  harfbuzz                          11.1.0          h3beb420_0                      conda-forge
  harmonica                         0.7.0           pyhd8ed1ab_1                    conda-forge
  hdf4                              4.2.15          h2a13503_7                      conda-forge
  hdf5                              1.14.3          nompi_h2d575fe_109              conda-forge
  hpack                             4.1.0           pyhd8ed1ab_0                    conda-forge
  httpcore                          1.0.7           pyh29332c3_1                    conda-forge
  httpx                             0.28.1          pyhd8ed1ab_0                    conda-forge
  hyperframe                        6.1.0           pyhd8ed1ab_0                    conda-forge
  icu                               75.1            he02047a_0                      conda-forge
  identify                          2.6.10          pyhd8ed1ab_0                    conda-forge
  idna                              3.10            pyhd8ed1ab_1                    conda-forge
  importlib-metadata                8.6.1           pyha770c72_0                    conda-forge
  importlib-resources               6.5.2           pyhd8ed1ab_0                    conda-forge
  importlib_resources               6.5.2           pyhd8ed1ab_0                    conda-forge
  iniconfig                         2.0.0           pyhd8ed1ab_1                    conda-forge
  invert4geom                       0.13.0          pyhd8ed1ab_0                    conda-forge
  ipykernel                         6.29.5          pyh3099207_0                    conda-forge
  ipython                           9.1.0           pyhfb0248b_0                    conda-forge
  ipython_pygments_lexers           1.1.1           pyhd8ed1ab_0                    conda-forge
  ipywidgets                        8.1.6           pyhd8ed1ab_0                    conda-forge
  isoduration                       20.11.0         pyhd8ed1ab_1                    conda-forge
  isort                             6.0.1           pyhd8ed1ab_0                    conda-forge
  jedi                              0.19.2          pyhd8ed1ab_1                    conda-forge
  jinja2                            3.1.6           pyhd8ed1ab_0                    conda-forge
  jmespath                          1.0.1           pyhd8ed1ab_1                    conda-forge
  joblib                            1.4.2           pyhd8ed1ab_1                    conda-forge
  json-c                            0.18            h6688a6e_0                      conda-forge
  json5                             0.12.0          pyhd8ed1ab_0                    conda-forge
  jsoncpp                           1.9.6           hf42df4d_1                      conda-forge
  jsonpointer                       3.0.0           py312h7900ff3_1                 conda-forge
  jsonschema                        4.23.0          pyhd8ed1ab_1                    conda-forge
  jsonschema-specifications         2024.10.1       pyhd8ed1ab_1                    conda-forge
  jsonschema-with-format-nongpl     4.23.0          hd8ed1ab_1                      conda-forge
  jupyter-lsp                       2.2.5           pyhd8ed1ab_1                    conda-forge
  jupyter_client                    8.6.3           pyhd8ed1ab_1                    conda-forge
  jupyter_core                      5.7.2           pyh31011fe_1                    conda-forge
  jupyter_events                    0.12.0          pyh29332c3_0                    conda-forge
  jupyter_server                    2.15.0          pyhd8ed1ab_0                    conda-forge
  jupyter_server_terminals          0.5.3           pyhd8ed1ab_1                    conda-forge
  jupyterlab                        4.4.1           pyhd8ed1ab_0                    conda-forge
  jupyterlab_execute_time           3.2.0           pyhd8ed1ab_1                    conda-forge
  jupyterlab_pygments               0.3.0           pyhd8ed1ab_2                    conda-forge
  jupyterlab_server                 2.27.3          pyhd8ed1ab_1                    conda-forge
  jupyterlab_widgets                3.0.14          pyhd8ed1ab_0                    conda-forge
  keyutils                          1.6.1           h166bdaf_0                      conda-forge
  kiwisolver                        1.4.8           py312h84d6215_0                 conda-forge
  kneebow                           1.0.2           pypi_0                          pypi       
  krb5                              1.21.3          h659f571_0                      conda-forge
  lcms2                             2.17            h717163a_0                      conda-forge
  ld_impl_linux-64                  2.43            h712a8e2_4                      conda-forge
  lerc                              4.0.0           h0aef613_1                      conda-forge
  libabseil                         20250127.1      cxx17_hbbce691_0                conda-forge
  libaec                            1.1.3           h59595ed_0                      conda-forge
  libarchive                        3.7.7           h75ea233_4                      conda-forge
  libarrow                          19.0.1          h27f8bab_8_cpu                  conda-forge
  libarrow-acero                    19.0.1          hcb10f89_8_cpu                  conda-forge
  libarrow-dataset                  19.0.1          hcb10f89_8_cpu                  conda-forge
  libarrow-substrait                19.0.1          h1bed206_8_cpu                  conda-forge
  libavif16                         1.2.1           hbb36593_2                      conda-forge
  libblas                           3.9.0           31_hfdb39a5_mkl                 conda-forge
  libbrotlicommon                   1.1.0           hb9d3cd8_2                      conda-forge
  libbrotlidec                      1.1.0           hb9d3cd8_2                      conda-forge
  libbrotlienc                      1.1.0           hb9d3cd8_2                      conda-forge
  libcap                            2.75            h39aace5_0                      conda-forge
  libcblas                          3.9.0           31_h372d94f_mkl                 conda-forge
  libclang-cpp20.1                  20.1.3          default_h1df26ce_0              conda-forge
  libclang13                        20.1.3          default_he06ed0a_0              conda-forge
  libcrc32c                         1.1.2           h9c3ff4c_0                      conda-forge
  libcublas                         12.8.4.1        h9ab20c4_1                      conda-forge
  libcudss                          0.5.0.16        h14340ca_1                      conda-forge
  libcufft                          11.3.3.83       h5888daf_1                      conda-forge
  libcufile                         1.13.1.3        h628e99a_1                      conda-forge
  libcups                           2.3.3           h4637d8d_4                      conda-forge
  libcurand                         10.3.9.90       h9ab20c4_1                      conda-forge
  libcurl                           8.13.0          h332b0f4_0                      conda-forge
  libcusolver                       11.7.3.90       h9ab20c4_1                      conda-forge
  libcusparse                       12.5.8.93       h5888daf_1                      conda-forge
  libde265                          1.0.15          h00ab1b0_0                      conda-forge
  libdeflate                        1.23            h86f0d12_0                      conda-forge
  libdrm                            2.4.124         hb9d3cd8_0                      conda-forge
  libedit                           3.1.20250104    pl5321h7949ede_0                conda-forge
  libegl                            1.7.0           ha4b6fd6_2                      conda-forge
  libev                             4.33            hd590300_2                      conda-forge
  libevent                          2.1.12          hf998b51_1                      conda-forge
  libexpat                          2.7.0           h5888daf_0                      conda-forge
  libffi                            3.4.6           h2dba641_1                      conda-forge
  libfreetype                       2.13.3          ha770c72_1                      conda-forge
  libfreetype6                      2.13.3          h48d6fc4_1                      conda-forge
  libgcc                            14.2.0          h767d61c_2                      conda-forge
  libgcc-ng                         14.2.0          h69a702a_2                      conda-forge
  libgcrypt-lib                     1.11.0          hb9d3cd8_2                      conda-forge
  libgdal-core                      3.10.2          h05269f4_1                      conda-forge
  libgdal-jp2openjpeg               3.10.2          ha1d2769_1                      conda-forge
  libgfortran                       14.2.0          h69a702a_2                      conda-forge
  libgfortran-ng                    14.2.0          h69a702a_2                      conda-forge
  libgfortran5                      14.2.0          hf1ad2bd_2                      conda-forge
  libgl                             1.7.0           ha4b6fd6_2                      conda-forge
  libglib                           2.84.1          h2ff4ddf_0                      conda-forge
  libglu                            9.0.3           h03adeef_0                      conda-forge
  libglvnd                          1.7.0           ha4b6fd6_2                      conda-forge
  libglx                            1.7.0           ha4b6fd6_2                      conda-forge
  libgoogle-cloud                   2.36.0          hc4361e1_1                      conda-forge
  libgoogle-cloud-storage           2.36.0          h0121fbd_1                      conda-forge
  libgpg-error                      1.54            hbd13f7d_0                      conda-forge
  libgrpc                           1.71.0          h8e591d7_1                      conda-forge
  libheif                           1.19.7          gpl_hc18d805_100                conda-forge
  libhwloc                          2.11.2          default_h0d58e46_1001           conda-forge
  libiconv                          1.18            h4ce23a2_1                      conda-forge
  libjpeg-turbo                     3.1.0           hb9d3cd8_0                      conda-forge
  libkml                            1.3.0           hf539b9f_1021                   conda-forge
  liblapack                         3.9.0           31_hc41d3b0_mkl                 conda-forge
  libllvm20                         20.1.3          he9d0ab4_0                      conda-forge
  liblzma                           5.8.1           hb9d3cd8_0                      conda-forge
  libmagma                          2.8.0           h566cb83_2                      conda-forge
  libnetcdf                         4.9.2           nompi_h00e09a9_116              conda-forge
  libnghttp2                        1.64.0          h161d5f1_0                      conda-forge
  libnl                             3.11.0          hb9d3cd8_0                      conda-forge
  libnsl                            2.0.1           hd590300_0                      conda-forge
  libntlm                           1.8             hb9d3cd8_0                      conda-forge
  libnvjitlink                      12.8.93         h5888daf_1                      conda-forge
  libogg                            1.3.5           h4ab18f5_0                      conda-forge
  libopentelemetry-cpp              1.20.0          hd1b1c89_0                      conda-forge
  libopentelemetry-cpp-headers      1.20.0          ha770c72_0                      conda-forge
  libparquet                        19.0.1          h081d1f1_8_cpu                  conda-forge
  libpciaccess                      0.18            hd590300_0                      conda-forge
  libpng                            1.6.47          h943b412_0                      conda-forge
  libpq                             17.4            h27ae623_1                      conda-forge
  libprotobuf                       5.29.3          h501fc15_1                      conda-forge
  libre2-11                         2024.07.02      hba17884_3                      conda-forge
  librttopo                         1.1.0           hd718a1a_18                     conda-forge
  libsodium                         1.0.20          h4ab18f5_0                      conda-forge
  libspatialindex                   2.1.0           he57a185_0                      conda-forge
  libspatialite                     5.1.0           h366e088_13                     conda-forge
  libsqlite                         3.49.1          hee588c1_2                      conda-forge
  libssh2                           1.11.1          hf672d98_0                      conda-forge
  libstdcxx                         14.2.0          h8f9b012_2                      conda-forge
  libstdcxx-ng                      14.2.0          h4852527_2                      conda-forge
  libsystemd0                       257.4           h4e0b6ca_1                      conda-forge
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  mkl                               2024.2.2        ha957f24_16                     conda-forge
  more-itertools                    10.7.0          pyhd8ed1ab_0                    conda-forge
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  python-cmr                        0.13.0          pyhff2d567_1                    conda-forge
  python-dateutil                   2.9.0.post0     pyhff2d567_1                    conda-forge
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  python-tzdata                     2025.2          pyhd8ed1ab_0                    conda-forge
  python_abi                        3.12            7_cp312                         conda-forge
  pytorch                           2.6.0           cuda126_mkl_py312_h9a1f04f_302  conda-forge
  pytz                              2025.2          pyhd8ed1ab_0                    conda-forge
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  qhull                             2020.2          h434a139_5                      conda-forge
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  tbb                               2021.13.0       hceb3a55_1                      conda-forge
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  zlib                              1.3.1           hb9d3cd8_2                      conda-forge
  zstandard                         0.23.0          py312h66e93f0_1                 conda-forge
  zstd                              1.5.7           hb8e6e7a_2                      conda-forge

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