BUG: cannot use pymc using official installation method

[Dr-yangyangzhang]

Describe the issue:

I used the official installation method for pymc installation and afterwards, a simple import pymc as pm raises the errors:

Reproduceable code example:

import pymc as pm

Error message:

/opt/anaconda3/envs/3dby/bin/python /Users/yangyangzhang/Library/Application Support/JetBrains/PyCharm2025.2/scratches/scratch_7.py 
Traceback (most recent call last):
  File "/Users/yangyangzhang/Library/Application Support/JetBrains/PyCharm2025.2/scratches/scratch_7.py", line 1, in <module>
    import pymc as pm
  File "/opt/anaconda3/envs/3dby/lib/python3.13/site-packages/pymc/__init__.py", line 50, in <module>
    from pymc import _version, gp, ode, sampling
  File "/opt/anaconda3/envs/3dby/lib/python3.13/site-packages/pymc/gp/__init__.py", line 17, in <module>
    from pymc.gp import cov, mean, util
  File "/opt/anaconda3/envs/3dby/lib/python3.13/site-packages/pymc/gp/util.py", line 25, in <module>
    from pymc.model.core import modelcontext
  File "/opt/anaconda3/envs/3dby/lib/python3.13/site-packages/pymc/model/__init__.py", line 17, in <module>
    from pymc.model.core import *
  File "/opt/anaconda3/envs/3dby/lib/python3.13/site-packages/pymc/model/core.py", line 54, in <module>
    from pymc.initial_point import PointType, make_initial_point_fn
  File "/opt/anaconda3/envs/3dby/lib/python3.13/site-packages/pymc/initial_point.py", line 31, in <module>
    from pymc.logprob.transforms import Transform
  File "/opt/anaconda3/envs/3dby/lib/python3.13/site-packages/pymc/logprob/__init__.py", line 52, in <module>
    import pymc.logprob.linalg
  File "/opt/anaconda3/envs/3dby/lib/python3.13/site-packages/pymc/logprob/linalg.py", line 17, in <module>
    from pytensor.tensor.math import _matmul
ImportError: cannot import name '_matmul' from 'pytensor.tensor.math' (/opt/anaconda3/envs/3dby/lib/python3.13/site-packages/pytensor/tensor/math.py)

PyMC version information:

pymc: 5.26.1
python: 3.13.9
pytensor: 2.31.7
MacOS 26.0.1
I use official installation method: conda

Context for the issue:

No response

[ricardoV94]

The version of PyTensor you have installed is not compatible with PyMC 5.26.1. It should be:

pymc/requirements.txt

Line 6 in c7222f0

pytensor>=2.35.0,<2.36

Did you make sure to use conda-forge channel? Are you sure you are activating the correct conda environment?

For the latter you can do import sys; print(sys.executable) to check which python is being picked up

[Dr-yangyangzhang]

The version of PyTensor you have installed is not compatible with PyMC 5.26.1. It should be:

pymc/requirements.txt

Line 6 in c7222f0

pytensor>=2.35.0,<2.36
Did you make sure to use conda-forge channel? Are you sure you are activating the correct conda environment?

For the latter you can do import sys; print(sys.executable) to check which python is being picked up

I use the official installation method:

conda create -c conda-forge -n pymc_env "pymc>=5"
conda activate pymc_env

Does this mean I have to manually install the 'correct' version of pytensor? I thought by using the official instruction, everything should be fine.

Also I tried the same installation on Windows 11 and everything works fine.

[ricardoV94]

No that should be enough. That's why I asked if you're sure you're activating the right environment. What the output of conda list, and sys.executable?

[Dr-yangyangzhang]

No that should be enough. That's why I asked if you're sure you're activating the right environment. What the output of conda list, and sys.executable?

I checked the 'conda list' and 'sys.executable' in the env created by the official instruction and these are the results. The pytensor by default is 2.31.7.

conda list:

(3dby) ➜  ~ git:(master) ✗ conda list
# packages in environment at /opt/anaconda3/envs/3dby:
#
# Name                       Version          Build                    Channel
adwaita-icon-theme           49.0             unix_0                   conda-forge
arviz                        0.22.0           pyhd8ed1ab_0             conda-forge
atk-1.0                      2.38.0           hd03087b_2               conda-forge
brotli                       1.2.0            hca488c2_0               conda-forge
brotli-bin                   1.2.0            hce9b42c_0               conda-forge
bzip2                        1.0.8            hd037594_8               conda-forge
c-ares                       1.34.5           h5505292_0               conda-forge
ca-certificates              2025.10.5        hbd8a1cb_0               conda-forge
cached-property              1.5.2            hd8ed1ab_1               conda-forge
cached_property              1.5.2            pyha770c72_1             conda-forge
cachetools                   6.2.1            pyhd8ed1ab_0             conda-forge
cairo                        1.18.4           h6a3b0d2_0               conda-forge
cctools_osx-arm64            973.0.1          hef52d2f_13              conda-forge
clang                        14.0.6           hce30654_1               conda-forge
clang-14                     14.0.6           default_h5dc8d65_1       conda-forge
clang_osx-arm64              14.0.6           h15773ab_6               conda-forge
clangxx                      14.0.6           default_h610c423_1       conda-forge
clangxx_osx-arm64            14.0.6           he29aa18_6               conda-forge
cloudpickle                  3.1.2            pyhd8ed1ab_0             conda-forge
compiler-rt                  14.0.6           h30b49de_0               conda-forge
compiler-rt_osx-arm64        14.0.6           h48302dc_0               conda-forge
cons                         0.4.7            pyhd8ed1ab_2             conda-forge
contourpy                    1.3.3            py313hc50a443_2          conda-forge
cycler                       0.12.1           pyhd8ed1ab_1             conda-forge
epoxy                        1.5.10           hc919400_2               conda-forge
etuples                      0.3.10           pyhd8ed1ab_1             conda-forge
filelock                     3.20.0           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             h77eed37_3               conda-forge
fontconfig                   2.15.0           h1383a14_1               conda-forge
fonts-conda-ecosystem        1                0                        conda-forge
fonts-conda-forge            1                0                        conda-forge
fonttools                    4.60.1           py313h7d74516_0          conda-forge
freetype                     2.14.1           hce30654_0               conda-forge
fribidi                      1.0.16           hc919400_0               conda-forge
gdk-pixbuf                   2.44.4           h7542897_0               conda-forge
glib-tools                   2.86.1           hb9d6e3a_1               conda-forge
graphite2                    1.3.14           hec049ff_2               conda-forge
graphviz                     13.1.2           hcd33d8b_0               conda-forge
gtk3                         3.24.43          h5febe37_6               conda-forge
gts                          0.7.6            he42f4ea_4               conda-forge
h5netcdf                     1.7.3            pyhd8ed1ab_0             conda-forge
h5py                         3.15.1           nompi_py313h7aa1c8b_100  conda-forge
harfbuzz                     12.1.0           haf38c7b_0               conda-forge
hdf5                         1.14.6           nompi_he65715a_103       conda-forge
hicolor-icon-theme           0.17             hce30654_2               conda-forge
icu                          75.1             hfee45f7_0               conda-forge
kiwisolver                   1.4.9            py313hf88c9ab_1          conda-forge
krb5                         1.21.3           h237132a_0               conda-forge
lcms2                        2.17             h7eeda09_0               conda-forge
ld64_osx-arm64               609              h7167370_13              conda-forge
lerc                         4.0.0            hd64df32_1               conda-forge
libaec                       1.1.4            h51d1e36_0               conda-forge
libblas                      3.9.0            38_h51639a9_openblas     conda-forge
libbrotlicommon              1.2.0            h87ba0bc_0               conda-forge
libbrotlidec                 1.2.0            h95a88de_0               conda-forge
libbrotlienc                 1.2.0            hb1b9735_0               conda-forge
libcblas                     3.9.0            38_hb0561ab_openblas     conda-forge
libclang-cpp14               14.0.6           default_h5dc8d65_1       conda-forge
libcurl                      8.16.0           hdece5d2_0               conda-forge
libcxx                       21.1.4           hf598326_2               conda-forge
libdeflate                   1.25             hc11a715_0               conda-forge
libedit                      3.1.20250104     pl5321hafb1f1b_0         conda-forge
libev                        4.33             h93a5062_2               conda-forge
libexpat                     2.7.1            hec049ff_0               conda-forge
libffi                       3.5.2            he5f378a_0               conda-forge
libfreetype                  2.14.1           hce30654_0               conda-forge
libfreetype6                 2.14.1           h6da58f4_0               conda-forge
libgd                        2.3.3            hb2c3a21_11              conda-forge
libgfortran                  15.2.0           hfcf01ff_1               conda-forge
libgfortran5                 15.2.0           h742603c_1               conda-forge
libglib                      2.86.1           he69a767_1               conda-forge
libiconv                     1.18             h23cfdf5_2               conda-forge
libintl                      0.25.1           h493aca8_0               conda-forge
libjpeg-turbo                3.1.2            hc919400_0               conda-forge
liblapack                    3.9.0            38_hd9741b5_openblas     conda-forge
libllvm14                    14.0.6           hd1a9a77_4               conda-forge
liblzma                      5.8.1            h39f12f2_2               conda-forge
libmpdec                     4.0.0            h5505292_0               conda-forge
libnghttp2                   1.67.0           hc438710_0               conda-forge
libopenblas                  0.3.30           openmp_ha158390_3        conda-forge
libpng                       1.6.50           h280e0eb_1               conda-forge
librsvg                      2.60.0           h5c55ec3_0               conda-forge
libsqlite                    3.50.4           h4237e3c_0               conda-forge
libssh2                      1.11.1           h1590b86_0               conda-forge
libtiff                      4.7.1            h4030677_1               conda-forge
libwebp-base                 1.6.0            h07db88b_0               conda-forge
libxcb                       1.17.0           hdb1d25a_0               conda-forge
libxml2-16                   2.15.1           h0ff4647_0               conda-forge
libzlib                      1.3.1            h8359307_2               conda-forge
llvm-openmp                  21.1.4           h4a912ad_0               conda-forge
llvm-tools                   14.0.6           hd1a9a77_4               conda-forge
logical-unification          0.4.7            pyhd8ed1ab_0             conda-forge
markdown-it-py               4.0.0            pyhd8ed1ab_0             conda-forge
matplotlib-base              3.10.7           py313h58042b9_0          conda-forge
mdurl                        0.1.2            pyhd8ed1ab_1             conda-forge
minikanren                   1.0.5            pyhd8ed1ab_1             conda-forge
multipledispatch             0.6.0            pyhd8ed1ab_1             conda-forge
munkres                      1.1.4            pyhd8ed1ab_1             conda-forge
ncurses                      6.5              h5e97a16_3               conda-forge
numpy                        2.3.4            py313h9771d21_0          conda-forge
openjpeg                     2.5.4            hbfb3c88_0               conda-forge
openssl                      3.5.4            h5503f6c_0               conda-forge
packaging                    25.0             pyh29332c3_1             conda-forge
pandas                       2.3.3            py313h7d16b84_1          conda-forge
pango                        1.56.4           h875632e_0               conda-forge
pcre2                        10.46            h7125dd6_0               conda-forge
pillow                       12.0.0           py313h54da0cd_0          conda-forge
pip                          25.2             pyh145f28c_0             conda-forge
pixman                       0.46.4           h81086ad_1               conda-forge
pthread-stubs                0.4              hd74edd7_1002            conda-forge
pygments                     2.19.2           pyhd8ed1ab_0             conda-forge
pymc                         5.26.1           hd8ed1ab_0               conda-forge
pymc-base                    5.26.1           pyhd8ed1ab_0             conda-forge
pyparsing                    3.2.5            pyhcf101f3_0             conda-forge
pytensor                     2.31.7           py313h778ac1f_0
pytensor-base                2.35.1           np2py313h9ce8dcc_0       conda-forge
python                       3.13.9           hfc2f54d_101_cp313       conda-forge
python-dateutil              2.9.0.post0      pyhe01879c_2             conda-forge
python-graphviz              0.21             pyhbacfb6d_0             conda-forge
python-tzdata                2025.2           pyhd8ed1ab_0             conda-forge
python_abi                   3.13             8_cp313                  conda-forge
pytz                         2025.2           pyhd8ed1ab_0             conda-forge
qhull                        2020.2           h420ef59_5               conda-forge
readline                     8.2              h1d1bf99_2               conda-forge
rich                         14.2.0           pyhcf101f3_0             conda-forge
scipy                        1.16.3           py313h0d10b07_0          conda-forge
setuptools                   80.9.0           pyhff2d567_0             conda-forge
sigtool                      0.1.3            h44b9a77_0               conda-forge
six                          1.17.0           pyhe01879c_1             conda-forge
tapi                         1100.0.11        he4954df_0               conda-forge
threadpoolctl                3.6.0            pyhecae5ae_0             conda-forge
tk                           8.6.13           h892fb3f_2               conda-forge
toolz                        1.1.0            pyhd8ed1ab_1             conda-forge
typing_extensions            4.15.0           pyhcf101f3_0             conda-forge
tzdata                       2025b            h78e105d_0               conda-forge
xarray                       2025.10.1        pyhd8ed1ab_0             conda-forge
xarray-einstats              0.9.1            pyhd8ed1ab_0             conda-forge
xorg-libxau                  1.0.12           h5505292_0               conda-forge
xorg-libxdmcp                1.1.5            hd74edd7_0               conda-forge
zlib-ng                      2.2.5            h3470cca_0               conda-forge
zstd                         1.5.7            h6491c7d_2               conda-forge

and

>>> print(sys.executable)
/opt/anaconda3/envs/3dby/bin/python

[ricardoV94]

Seems like you are in an env called 3dby not pymc_env if you followed the specific official instructions.

Name doesn't matter but just checking you are in the environment you expected to be? In either case try to update PyTensor manually

[Dr-yangyangzhang]

Seems like you are in an env called 3dby not pymc_env if you followed the specific official instructions.

Name doesn't matter but just checking you are in the environment you expected to be? In either case try to update PyTensor manually

Yes I use the official installation instruction but I changed the name into 3dby. So I confirm I am in the correct evn.
I tried to update pytensor manually but it seems conda doesn't know there is a newer version:

(3dby) ➜  ~ git:(master) ✗ conda install pytensor
Channels:
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: done

# All requested packages already installed.

and if I specify the version I get:

(3dby) ➜  ~ git:(master) ✗ conda install pytensor==2.35.0
Channels:
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - pytensor==2.35.0

Current channels:

  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

[ricardoV94]

You need conda-forge channel. conda install -c conda-forge pytensor==2.35.0

Regular anaconda channels lag a lot behind. I see in your list above that pytensor was the only package not installed from conda-forge.

CC @maresb why would that happen?

[Dr-yangyangzhang]

You need conda-forge channel. conda install -c conda-forge pytensor==2.35.0

Regular anaconda channels lag a lot behind. I see in your list above that pytensor was the only package not installed from conda-forge.

CC @maresb why would that happen?

Ok I upgrade pytensor to 2.35.1 now. But it seems there is still some issue:

/opt/anaconda3/envs/3dby/bin/python /Users/yangyangzhang/Library/CloudStorage/OneDrive-Personal/Documents/Documents/Postdoc/exercises/Bayesian_3D/3dprior_pymc.py 
Traceback (most recent call last):
  File "/Users/yangyangzhang/Library/CloudStorage/OneDrive-Personal/Documents/Documents/Postdoc/exercises/Bayesian_3D/3dprior_pymc.py", line 2, in <module>
    import pymc as pm
  File "/opt/anaconda3/envs/3dby/lib/python3.13/site-packages/pymc/__init__.py", line 48, in <module>
    __set_compiler_flags()
    ~~~~~~~~~~~~~~~~~~~~^^
  File "/opt/anaconda3/envs/3dby/lib/python3.13/site-packages/pymc/__init__.py", line 33, in __set_compiler_flags
    current = pytensor.config.gcc__cxxflags
              ^^^^^^^^^^^^^^^
AttributeError: module 'pytensor' has no attribute 'config'

Process finished with exit code 1

[ricardoV94]

I suspect PyTensor isn't really installed. If you just import pytensor and type dir(pytensor) what do you get?

[Dr-yangyangzhang]

I suspect PyTensor isn't really installed. If you just import pytensor and type dir(pytensor) what do you get?

the output is:

>>> import pytensor
>>> dir(pytensor)
['__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__']
>>>

[maresb]

Are you in a directory containing a subdirectory named pytensor/ or a file named pytensor.py?

Could you please show the output of

conda config --show-sources

I agree with @ricardoV94 that there is a channel-mixing problem.

[ricardoV94]

I've seen that fake package issue often with conda, when it fails to actually remove a previous package. Usually I just manually delete the folder (location would be that shown in pytensor.__path__) and then install again

[Dr-yangyangzhang]

Are you in a directory containing a subdirectory named pytensor/ or a file named pytensor.py?

Could you please show the output of

conda config --show-sources
I agree with @ricardoV94 that there is a channel-mixing problem.

Well I don't know the file structure. I only use conda to create an env named 3dby with pycm installed (and later manually install pytensor 2.35.1).
The output is:

(3dby) ➜  ~ git:(master) ✗ conda config --show-sources
==> /opt/anaconda3/.condarc <==
channels:
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r

==> envvars <==
allow_softlinks: False