Error installing dedalus
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George Aristides
Sep 12, 2023, 2:16:02 PM9/12/23
to Dedalus Users
I am attempting to install dedalus on a 2023 MacBook Pro with the Apple M2 Pro chip.
After completing step 5 on the installing dedalus guide page I received an error message. Here is everything printed after running the command, the command is included for reference.
# Upgrade to Dedalus v3
conda uninstall --force dedalus
CC=mpicc pip3 install --no-cache --no-build-isolation http://github.com/dedalusproject/dedalus/zipball/master/
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.3.1
latest version: 23.7.3
Please update conda by running
$ conda update -n base -c conda-forge conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.7.3
## Package Plan ##
environment location: /Users/georgearistides/miniforge3/envs/dedalus3
added / updated specs:
- c-compiler
- cython[version='<3.0']
- dedalus
- h5py[build=mpi*]
The following packages will be downloaded:
package | build
---------------------------|-----------------
brotli-1.1.0 | h0dc2134_0 19 KB conda-forge
brotli-bin-1.1.0 | h0dc2134_0 16 KB conda-forge
brotli-python-1.1.0 | py311hdf8f085_0 358 KB conda-forge
bzip2-1.0.8 | h0d85af4_4 155 KB conda-forge
c-ares-1.19.1 | h0dc2134_0 101 KB conda-forge
c-compiler-1.6.0 | h63c33a9_0 6 KB conda-forge
ca-certificates-2023.7.22 | h8857fd0_0 146 KB conda-forge
cached-property-1.5.2 | hd8ed1ab_1 4 KB conda-forge
cached_property-1.5.2 | pyha770c72_1 11 KB conda-forge
cctools-973.0.1 | hd9ad811_14 21 KB conda-forge
cctools_osx-64-973.0.1 | habff3f6_14 1.1 MB conda-forge
clang-15.0.7 | h694c41f_3 130 KB conda-forge
clang-15-15.0.7 |default_hdb78580_3 776 KB conda-forge
clang_osx-64-15.0.7 | h03d6864_3 20 KB conda-forge
clangxx-15.0.7 |default_hdb78580_3 130 KB conda-forge
compiler-rt-15.0.7 | he1888fc_1 90 KB conda-forge
compiler-rt_osx-64-15.0.7 | he1888fc_1 10.7 MB conda-forge
contourpy-1.1.0 | py311h5fe6e05_0 220 KB conda-forge
coverage-7.3.1 | py311h2725bcf_0 348 KB conda-forge
cycler-0.11.0 | pyhd8ed1ab_0 10 KB conda-forge
cython-0.29.36 | py311hdf8f085_0 2.3 MB conda-forge
dedalus-2.2207.3 | py311h5b20a79_0 458 KB conda-forge
docopt-0.6.2 | py_1 14 KB conda-forge
exceptiongroup-1.1.3 | pyhd8ed1ab_0 19 KB conda-forge
fftw-3.3.10 |mpi_mpich_h4a8b384_8 1.8 MB conda-forge
fonttools-4.42.1 | py311h2725bcf_0 2.5 MB conda-forge
freetype-2.12.1 | h3f81eb7_1 586 KB conda-forge
h5py-3.9.0 |mpi_mpich_py311h69d8d04_2 1.0 MB conda-forge
hdf5-1.14.2 |mpi_mpich_h3618df7_0 3.6 MB conda-forge
icu-73.2 | hf5e326d_0 11.2 MB conda-forge
iniconfig-2.0.0 | pyhd8ed1ab_0 11 KB conda-forge
kiwisolver-1.4.5 | py311h5fe6e05_0 59 KB conda-forge
krb5-1.21.2 | hb884880_0 1.1 MB conda-forge
lcms2-2.15 | h2dcdeff_1 222 KB conda-forge
ld64-609 | ha91a046_14 19 KB conda-forge
ld64_osx-64-609 | h0fd476b_14 1.0 MB conda-forge
lerc-4.0.0 | hb486fe8_0 284 KB conda-forge
libaec-1.0.6 | hf0c8a7f_1 29 KB conda-forge
libblas-3.9.0 |18_osx64_openblas 14 KB conda-forge
libbrotlicommon-1.1.0 | h0dc2134_0 66 KB conda-forge
libbrotlidec-1.1.0 | h0dc2134_0 29 KB conda-forge
libbrotlienc-1.1.0 | h0dc2134_0 292 KB conda-forge
libcblas-3.9.0 |18_osx64_openblas 14 KB conda-forge
libclang-cpp15-15.0.7 |default_hdb78580_3 11.9 MB conda-forge
libcurl-8.2.1 | h5f667d7_0 346 KB conda-forge
libcxx-16.0.6 | hd57cbcb_0 1.1 MB conda-forge
libdeflate-1.18 | hac1461d_0 65 KB conda-forge
libedit-3.1.20191231 | h0678c8f_2 103 KB conda-forge
libev-4.33 | haf1e3a3_1 99 KB conda-forge
libexpat-2.5.0 | hf0c8a7f_1 68 KB conda-forge
libffi-3.4.2 | h0d85af4_5 50 KB conda-forge
libgfortran-5.0.0 |13_2_0_h97931a8_1 107 KB conda-forge
libgfortran5-13.2.0 | h2873a65_1 1.5 MB conda-forge
libiconv-1.17 | hac89ed1_0 1.3 MB conda-forge
libjpeg-turbo-2.1.5.1 | hb7f2c08_0 448 KB conda-forge
liblapack-3.9.0 |18_osx64_openblas 14 KB conda-forge
libllvm15-15.0.7 | he4b1e75_3 22.8 MB conda-forge
libnghttp2-1.52.0 | he2ab024_0 599 KB conda-forge
libopenblas-0.3.24 |openmp_h48a4ad5_0 5.9 MB conda-forge
libpng-1.6.39 | ha978bb4_0 265 KB conda-forge
libsqlite-3.43.0 | h58db7d2_0 870 KB conda-forge
libssh2-1.11.0 | hd019ec5_0 253 KB conda-forge
libtiff-4.5.1 | hf955e92_1 384 KB conda-forge
libwebp-base-1.3.1 | h0dc2134_0 338 KB conda-forge
libxcb-1.15 | hb7f2c08_0 306 KB conda-forge
libxml2-2.11.5 | h3346baf_1 609 KB conda-forge
libzlib-1.2.13 | h8a1eda9_5 58 KB conda-forge
llvm-openmp-16.0.6 | hff08bdf_0 289 KB conda-forge
llvm-tools-15.0.7 | he4b1e75_3 10.9 MB conda-forge
matplotlib-base-3.7.1 | py311h2bf763f_0 7.2 MB conda-forge
mpi-1.0 | mpich 4 KB conda-forge
mpi4py-3.1.4 | py311hbdc7f45_0 535 KB conda-forge
mpich-4.1.2 | hd33e60e_100 19.9 MB conda-forge
munkres-1.1.4 | pyh9f0ad1d_0 12 KB conda-forge
ncurses-6.4 | hf0c8a7f_0 809 KB conda-forge
numpy-1.25.2 | py311hc44ba51_0 7.3 MB conda-forge
openjpeg-2.5.0 | h13ac156_2 322 KB conda-forge
openssl-3.1.2 | h8a1eda9_0 2.2 MB conda-forge
pillow-10.0.0 | py311h7cb0e2d_0 43.5 MB conda-forge
platformdirs-3.10.0 | pyhd8ed1ab_0 19 KB conda-forge
pooch-1.7.0 | pyha770c72_3 50 KB conda-forge
pthread-stubs-0.4 | hc929b4f_1001 6 KB conda-forge
py-1.11.0 | pyh6c4a22f_0 74 KB conda-forge
py-cpuinfo-9.0.0 | pyhd8ed1ab_0 24 KB conda-forge
pyparsing-3.1.1 | pyhd8ed1ab_0 87 KB conda-forge
pytest-7.4.2 | pyhd8ed1ab_0 239 KB conda-forge
pytest-benchmark-4.0.0 | pyhd8ed1ab_0 39 KB conda-forge
pytest-cov-4.1.0 | pyhd8ed1ab_0 25 KB conda-forge
pytest-parallel-0.1.1 | pyhd8ed1ab_0 10 KB conda-forge
python-3.11.5 |h30d4d87_0_cpython 14.8 MB conda-forge
python-dateutil-2.8.2 | pyhd8ed1ab_0 240 KB conda-forge
python_abi-3.11 | 3_cp311 6 KB conda-forge
readline-8.2 | h9e318b2_1 250 KB conda-forge
scipy-1.11.2 | py311h16c3c4d_0 15.7 MB conda-forge
sigtool-0.1.3 | h88f4db0_0 209 KB conda-forge
six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge
tapi-1100.0.11 | h9ce4665_0 196 KB conda-forge
tblib-1.7.0 | pyhd8ed1ab_0 15 KB conda-forge
tk-8.6.12 | h5dbffcc_0 3.4 MB conda-forge
toml-0.10.2 | pyhd8ed1ab_0 18 KB conda-forge
tomli-2.0.1 | pyhd8ed1ab_0 16 KB conda-forge
typing-extensions-4.7.1 | hd8ed1ab_0 10 KB conda-forge
typing_extensions-4.7.1 | pyha770c72_0 35 KB conda-forge
xorg-libxau-1.0.11 | h0dc2134_0 13 KB conda-forge
xorg-libxdmcp-1.1.3 | h35c211d_0 17 KB conda-forge
xz-5.2.6 | h775f41a_0 233 KB conda-forge
zstd-1.5.5 | h829000d_0 488 KB conda-forge
------------------------------------------------------------
Total: 219.2 MB
The following NEW packages will be INSTALLED:
brotli conda-forge/osx-64::brotli-1.1.0-h0dc2134_0
brotli-bin conda-forge/osx-64::brotli-bin-1.1.0-h0dc2134_0
brotli-python conda-forge/osx-64::brotli-python-1.1.0-py311hdf8f085_0
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
c-ares conda-forge/osx-64::c-ares-1.19.1-h0dc2134_0
c-compiler conda-forge/osx-64::c-compiler-1.6.0-h63c33a9_0
ca-certificates conda-forge/osx-64::ca-certificates-2023.7.22-h8857fd0_0
cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1
cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1
cctools conda-forge/osx-64::cctools-973.0.1-hd9ad811_14
cctools_osx-64 conda-forge/osx-64::cctools_osx-64-973.0.1-habff3f6_14
certifi conda-forge/noarch::certifi-2023.7.22-pyhd8ed1ab_0
charset-normalizer conda-forge/noarch::charset-normalizer-3.2.0-pyhd8ed1ab_0
clang conda-forge/osx-64::clang-15.0.7-h694c41f_3
clang-15 conda-forge/osx-64::clang-15-15.0.7-default_hdb78580_3
clang_osx-64 conda-forge/osx-64::clang_osx-64-15.0.7-h03d6864_3
clangxx conda-forge/osx-64::clangxx-15.0.7-default_hdb78580_3
colorama conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0
compiler-rt conda-forge/osx-64::compiler-rt-15.0.7-he1888fc_1
compiler-rt_osx-64 conda-forge/noarch::compiler-rt_osx-64-15.0.7-he1888fc_1
contourpy conda-forge/osx-64::contourpy-1.1.0-py311h5fe6e05_0
coverage conda-forge/osx-64::coverage-7.3.1-py311h2725bcf_0
cycler conda-forge/noarch::cycler-0.11.0-pyhd8ed1ab_0
cython conda-forge/osx-64::cython-0.29.36-py311hdf8f085_0
dedalus conda-forge/osx-64::dedalus-2.2207.3-py311h5b20a79_0
docopt conda-forge/noarch::docopt-0.6.2-py_1
exceptiongroup conda-forge/noarch::exceptiongroup-1.1.3-pyhd8ed1ab_0
fftw conda-forge/osx-64::fftw-3.3.10-mpi_mpich_h4a8b384_8
fonttools conda-forge/osx-64::fonttools-4.42.1-py311h2725bcf_0
freetype conda-forge/osx-64::freetype-2.12.1-h3f81eb7_1
h5py conda-forge/osx-64::h5py-3.9.0-mpi_mpich_py311h69d8d04_2
hdf5 conda-forge/osx-64::hdf5-1.14.2-mpi_mpich_h3618df7_0
icu conda-forge/osx-64::icu-73.2-hf5e326d_0
idna conda-forge/noarch::idna-3.4-pyhd8ed1ab_0
iniconfig conda-forge/noarch::iniconfig-2.0.0-pyhd8ed1ab_0
kiwisolver conda-forge/osx-64::kiwisolver-1.4.5-py311h5fe6e05_0
krb5 conda-forge/osx-64::krb5-1.21.2-hb884880_0
lcms2 conda-forge/osx-64::lcms2-2.15-h2dcdeff_1
ld64 conda-forge/osx-64::ld64-609-ha91a046_14
ld64_osx-64 conda-forge/osx-64::ld64_osx-64-609-h0fd476b_14
lerc conda-forge/osx-64::lerc-4.0.0-hb486fe8_0
libaec conda-forge/osx-64::libaec-1.0.6-hf0c8a7f_1
libblas conda-forge/osx-64::libblas-3.9.0-18_osx64_openblas
libbrotlicommon conda-forge/osx-64::libbrotlicommon-1.1.0-h0dc2134_0
libbrotlidec conda-forge/osx-64::libbrotlidec-1.1.0-h0dc2134_0
libbrotlienc conda-forge/osx-64::libbrotlienc-1.1.0-h0dc2134_0
libcblas conda-forge/osx-64::libcblas-3.9.0-18_osx64_openblas
libclang-cpp15 conda-forge/osx-64::libclang-cpp15-15.0.7-default_hdb78580_3
libcurl conda-forge/osx-64::libcurl-8.2.1-h5f667d7_0
libcxx conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0
libdeflate conda-forge/osx-64::libdeflate-1.18-hac1461d_0
libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2
libev conda-forge/osx-64::libev-4.33-haf1e3a3_1
libexpat conda-forge/osx-64::libexpat-2.5.0-hf0c8a7f_1
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_1
libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_1
libiconv conda-forge/osx-64::libiconv-1.17-hac89ed1_0
libjpeg-turbo conda-forge/osx-64::libjpeg-turbo-2.1.5.1-hb7f2c08_0
liblapack conda-forge/osx-64::liblapack-3.9.0-18_osx64_openblas
libllvm15 conda-forge/osx-64::libllvm15-15.0.7-he4b1e75_3
libnghttp2 conda-forge/osx-64::libnghttp2-1.52.0-he2ab024_0
libopenblas conda-forge/osx-64::libopenblas-0.3.24-openmp_h48a4ad5_0
libpng conda-forge/osx-64::libpng-1.6.39-ha978bb4_0
libsqlite conda-forge/osx-64::libsqlite-3.43.0-h58db7d2_0
libssh2 conda-forge/osx-64::libssh2-1.11.0-hd019ec5_0
libtiff conda-forge/osx-64::libtiff-4.5.1-hf955e92_1
libwebp-base conda-forge/osx-64::libwebp-base-1.3.1-h0dc2134_0
libxcb conda-forge/osx-64::libxcb-1.15-hb7f2c08_0
libxml2 conda-forge/osx-64::libxml2-2.11.5-h3346baf_1
libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5
llvm-openmp conda-forge/osx-64::llvm-openmp-16.0.6-hff08bdf_0
llvm-tools conda-forge/osx-64::llvm-tools-15.0.7-he4b1e75_3
matplotlib-base conda-forge/osx-64::matplotlib-base-3.7.1-py311h2bf763f_0
mpi conda-forge/osx-64::mpi-1.0-mpich
mpi4py conda-forge/osx-64::mpi4py-3.1.4-py311hbdc7f45_0
mpich conda-forge/osx-64::mpich-4.1.2-hd33e60e_100
munkres conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0
ncurses conda-forge/osx-64::ncurses-6.4-hf0c8a7f_0
numpy conda-forge/osx-64::numpy-1.25.2-py311hc44ba51_0
openjpeg conda-forge/osx-64::openjpeg-2.5.0-h13ac156_2
openssl conda-forge/osx-64::openssl-3.1.2-h8a1eda9_0
packaging conda-forge/noarch::packaging-23.1-pyhd8ed1ab_0
pillow conda-forge/osx-64::pillow-10.0.0-py311h7cb0e2d_0
pip conda-forge/noarch::pip-23.2.1-pyhd8ed1ab_0
platformdirs conda-forge/noarch::platformdirs-3.10.0-pyhd8ed1ab_0
pluggy conda-forge/noarch::pluggy-1.3.0-pyhd8ed1ab_0
pooch conda-forge/noarch::pooch-1.7.0-pyha770c72_3
pthread-stubs conda-forge/osx-64::pthread-stubs-0.4-hc929b4f_1001
py conda-forge/noarch::py-1.11.0-pyh6c4a22f_0
py-cpuinfo conda-forge/noarch::py-cpuinfo-9.0.0-pyhd8ed1ab_0
pyparsing conda-forge/noarch::pyparsing-3.1.1-pyhd8ed1ab_0
pysocks conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6
pytest conda-forge/noarch::pytest-7.4.2-pyhd8ed1ab_0
pytest-benchmark conda-forge/noarch::pytest-benchmark-4.0.0-pyhd8ed1ab_0
pytest-cov conda-forge/noarch::pytest-cov-4.1.0-pyhd8ed1ab_0
pytest-parallel conda-forge/noarch::pytest-parallel-0.1.1-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.11.5-h30d4d87_0_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/osx-64::python_abi-3.11-3_cp311
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
requests conda-forge/noarch::requests-2.31.0-pyhd8ed1ab_0
scipy conda-forge/osx-64::scipy-1.11.2-py311h16c3c4d_0
setuptools conda-forge/noarch::setuptools-68.1.2-pyhd8ed1ab_0
sigtool conda-forge/osx-64::sigtool-0.1.3-h88f4db0_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
tapi conda-forge/osx-64::tapi-1100.0.11-h9ce4665_0
tblib conda-forge/noarch::tblib-1.7.0-pyhd8ed1ab_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
toml conda-forge/noarch::toml-0.10.2-pyhd8ed1ab_0
tomli conda-forge/noarch::tomli-2.0.1-pyhd8ed1ab_0
typing-extensions conda-forge/noarch::typing-extensions-4.7.1-hd8ed1ab_0
typing_extensions conda-forge/noarch::typing_extensions-4.7.1-pyha770c72_0
tzdata conda-forge/noarch::tzdata-2023c-h71feb2d_0
urllib3 conda-forge/noarch::urllib3-2.0.4-pyhd8ed1ab_0
wheel conda-forge/noarch::wheel-0.41.2-pyhd8ed1ab_0
xorg-libxau conda-forge/osx-64::xorg-libxau-1.0.11-h0dc2134_0
xorg-libxdmcp conda-forge/osx-64::xorg-libxdmcp-1.1.3-h35c211d_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
zstd conda-forge/osx-64::zstd-1.5.5-h829000d_0
Proceed ([y]/n)?
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
zsh: command not found: #
==> WARNING: A newer version of conda exists. <==
current version: 23.3.1
latest version: 23.7.3
Please update conda by running
$ conda update -n base -c conda-forge conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.7.3
## Package Plan ##
environment location: /Users/georgearistides/miniforge3/envs/dedalus3
removed specs:
- dedalus
The following packages will be REMOVED:
dedalus-2.2207.3-py311h5b20a79_0
Proceed ([y]/n)?
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Collecting http://github.com/dedalusproject/dedalus/zipball/master/
Downloading http://github.com/dedalusproject/dedalus/zipball/master/
/ 25.7MB 40.1MB/s
Preparing wheel metadata ... error
ERROR: Command errored out with exit status 1:
command: /Library/Developer/CommandLineTools/usr/bin/python3 /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /var/folders/f4/s6c8f1h51x1fc0fp219d7qzm0000gn/T/tmp_bb8_cnr
cwd: /private/var/folders/f4/s6c8f1h51x1fc0fp219d7qzm0000gn/T/pip-req-build-7coacldd
Complete output (16 lines):
Traceback (most recent call last):
File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 207, in <module>
main()
File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 197, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 69, in prepare_metadata_for_build_wheel
return hook(metadata_directory, config_settings)
File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/site-packages/setuptools/build_meta.py", line 156, in prepare_metadata_for_build_wheel
self.run_setup()
File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/site-packages/setuptools/build_meta.py", line 236, in run_setup
super(_BuildMetaLegacyBackend,
File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/site-packages/setuptools/build_meta.py", line 142, in run_setup
exec(compile(code, __file__, 'exec'), locals())
File "setup.py", line 17, in <module>
from Cython.Build import cythonize
ModuleNotFoundError: No module named 'Cython'
----------------------------------------
ERROR: Command errored out with exit status 1: /Library/Developer/CommandLineTools/usr/bin/python3 /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /var/folders/f4/s6c8f1h51x1fc0fp219d7qzm0000gn/T/tmp_bb8_cnr Check the logs for full command output.
WARNING: You are using pip version 19.2.3, however version 23.2.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
(dedalus3) georgearistides@ ~ %
Keaton Burns
Sep 19, 2023, 1:37:05 PM9/19/23
to dedalu...@googlegroups.com
Hi George,
It looks like the issue is that the final pip3 command is hitting the system python (3.8), not the version from the conda environment. This might be a problem with some shell settings, i.e. using zsh instead bash, which may be the new default on macs. Can you try reactivating the environment and rerunning the final pip command, making sure you’re using pip/python from conda?
Thanks,
-Keaton
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