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Error when running run_hackett_inference.py #13

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augeorge opened this issue Apr 17, 2024 · 6 comments · Fixed by #14
Closed

Error when running run_hackett_inference.py #13

augeorge opened this issue Apr 17, 2024 · 6 comments · Fixed by #14
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@mcnaughtonadm
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@augeorge
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augeorge commented Apr 17, 2024 •
edited
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I created a new environment and installed packages using python -m pip install -e . after cloning the repo.

When I run try to run run_hackett_inference.py I get the following error (showing the full output):

(emll_env) (base) geor228@WE49311 notebooks % /Users/geor228/miniconda3/envs/emll_env/bin/python /Users/geor228/Github/emll/notebooks/run_hackett_inference.py
WARNING (pytensor.tensor.blas): Using NumPy C-API based implementation for BLAS functions.
Traceback (most recent call last):
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/tensor/elemwise.py", line 438, in get_output_info
    [
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/tensor/elemwise.py", line 439, in <listcomp>
    broadcast_static_dim_lengths(shape)
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/tensor/utils.py", line 162, in broadcast_static_dim_lengths
    raise ValueError
ValueError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/geor228/Github/emll/notebooks/run_hackett_inference.py", line 142, in <module>
    hist = approx.fit(
           ^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pymc/variational/inference.py", line 149, in fit
    step_func = self.objective.step_function(score=score, **kwargs)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/configparser.py", line 47, in res
    return f(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pymc/variational/opvi.py", line 379, in step_function
    updates = self.updates(
              ^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pymc/variational/opvi.py", line 268, in updates
    self.add_obj_updates(
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pymc/variational/opvi.py", line 316, in add_obj_updates
    grads = pm.updates.get_or_compute_grads(obj_target, self.obj_params + more_obj_params)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pymc/variational/updates.py", line 177, in get_or_compute_grads
    return pytensor.grad(loss_or_grads, params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 607, in grad
    _rval: Sequence[Variable] = _populate_grad_dict(
                                ^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1407, in _populate_grad_dict
    rval = [access_grad_cache(elem) for elem in wrt]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1407, in <listcomp>
    rval = [access_grad_cache(elem) for elem in wrt]
            ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in access_term_cache
    output_grads = [access_grad_cache(var) for var in node.outputs]
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1037, in <listcomp>
    output_grads = [access_grad_cache(var) for var in node.outputs]
                    ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1192, in access_term_cache
    input_grads = node.op.L_op(inputs, node.outputs, new_output_grads)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/scan/op.py", line 2569, in L_op
    dC_dinps_t = compute_all_gradients(known_grads)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/scan/op.py", line 2483, in compute_all_gradients
    grads = grad(
            ^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 607, in grad
    _rval: Sequence[Variable] = _populate_grad_dict(
                                ^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1407, in _populate_grad_dict
    rval = [access_grad_cache(elem) for elem in wrt]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1407, in <listcomp>
    rval = [access_grad_cache(elem) for elem in wrt]
            ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1362, in access_grad_cache
    term = access_term_cache(node)[idx]
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/gradient.py", line 1192, in access_term_cache
    input_grads = node.op.L_op(inputs, node.outputs, new_output_grads)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/Github/emll/src/emll/pytensor_utils.py", line 105, in L_op
    A_bar = force_outer(b - A.dot(c), x) - force_outer(b_bar, c)
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/tensor/variable.py", line 125, in __sub__
    return pt.math.sub(self, other)
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/graph/op.py", line 292, in __call__
    node = self.make_node(*inputs, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/tensor/elemwise.py", line 482, in make_node
    out_dtypes, out_shapes, inputs = self.get_output_info(DimShuffle, *inputs)
                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/geor228/miniconda3/envs/emll_env/lib/python3.11/site-packages/pytensor/tensor/elemwise.py", line 444, in get_output_info
    raise ValueError(
ValueError: Incompatible Elemwise input shapes [(192, 203), (192, 192)]

I'm using python 3.11.8 on a M2 pro macbook running macOS sonoma 14.4.2.

For reference here's my current conda environment:

(emll_env) (base) geor228@WE49311 notebooks % conda list
# packages in environment at /Users/geor228/miniconda3/envs/emll_env:
#
# Name                    Version                   Build  Channel
annotated-types           0.6.0                    pypi_0    pypi
anyio                     4.3.0                    pypi_0    pypi
appdirs                   1.4.4                    pypi_0    pypi
arviz                     0.18.0                   pypi_0    pypi
bzip2                     1.0.8                h80987f9_5  
ca-certificates           2024.3.11            hca03da5_0  
cachetools                5.3.3                    pypi_0    pypi
certifi                   2024.2.2                 pypi_0    pypi
cloudpickle               3.0.0                    pypi_0    pypi
cobra                     0.29.0                   pypi_0    pypi
cons                      0.4.6                    pypi_0    pypi
contourpy                 1.2.1                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
cython                    3.0.10                   pypi_0    pypi
depinfo                   2.2.0                    pypi_0    pypi
diskcache                 5.6.3                    pypi_0    pypi
dm-tree                   0.1.8                    pypi_0    pypi
emll                      0.1.1.dev0               pypi_0    pypi
etuples                   0.3.9                    pypi_0    pypi
filelock                  3.13.4                   pypi_0    pypi
fonttools                 4.51.0                   pypi_0    pypi
future                    1.0.0                    pypi_0    pypi
h11                       0.14.0                   pypi_0    pypi
h5netcdf                  1.3.0                    pypi_0    pypi
h5py                      3.11.0                   pypi_0    pypi
httpcore                  1.0.5                    pypi_0    pypi
httpx                     0.27.0                   pypi_0    pypi
idna                      3.7                      pypi_0    pypi
importlib-resources       6.4.0                    pypi_0    pypi
kiwisolver                1.4.5                    pypi_0    pypi
libffi                    3.4.4                hca03da5_0  
logical-unification       0.4.6                    pypi_0    pypi
markdown-it-py            3.0.0                    pypi_0    pypi
matplotlib                3.8.4                    pypi_0    pypi
mdurl                     0.1.2                    pypi_0    pypi
minikanren                1.0.3                    pypi_0    pypi
mpmath                    1.3.0                    pypi_0    pypi
multipledispatch          1.0.0                    pypi_0    pypi
ncurses                   6.4                  h313beb8_0  
numpy                     1.26.4                   pypi_0    pypi
openssl                   3.0.13               h1a28f6b_0  
optlang                   1.8.1                    pypi_0    pypi
packaging                 24.0                     pypi_0    pypi
pandas                    2.2.2                    pypi_0    pypi
patsy                     0.5.6                    pypi_0    pypi
pillow                    10.3.0                   pypi_0    pypi
pip                       23.3.1          py311hca03da5_0  
pydantic                  2.7.0                    pypi_0    pypi
pydantic-core             2.18.1                   pypi_0    pypi
pygments                  2.17.2                   pypi_0    pypi
pymc                      5.13.1                   pypi_0    pypi
pyparsing                 3.1.2                    pypi_0    pypi
pytensor                  2.20.0                   pypi_0    pypi
python                    3.11.8               hb885b13_0  
python-dateutil           2.9.0.post0              pypi_0    pypi
python-libsbml            5.20.2                   pypi_0    pypi
pytz                      2024.1                   pypi_0    pypi
readline                  8.2                  h1a28f6b_0  
rich                      13.7.1                   pypi_0    pypi
ruamel-yaml               0.18.6                   pypi_0    pypi
ruamel-yaml-clib          0.2.8                    pypi_0    pypi
scipy                     1.13.0                   pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
setuptools                68.2.2          py311hca03da5_0  
six                       1.16.0                   pypi_0    pypi
sniffio                   1.3.1                    pypi_0    pypi
sqlite                    3.41.2               h80987f9_0  
swiglpk                   5.0.10                   pypi_0    pypi
sympy                     1.12                     pypi_0    pypi
tk                        8.6.12               hb8d0fd4_0  
toolz                     0.12.1                   pypi_0    pypi
tqdm                      4.66.2                   pypi_0    pypi
typing-extensions         4.11.0                   pypi_0    pypi
tzdata                    2024.1                   pypi_0    pypi
wheel                     0.41.2          py311hca03da5_0  
xarray                    2024.3.0                 pypi_0    pypi
xarray-einstats           0.7.0                    pypi_0    pypi
xz                        5.4.6                h80987f9_0  
zlib                      1.2.13               h5a0b063_0
@augeorge
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@djinnome @mcnaughtonadm any ideas?

@mcnaughtonadm
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This seems like a PyTensor issue, so it could be the version. My current build is at:

# packages in environment at /Users/mcna892/mambaforge/envs/emll_dev:
#
# Name                    Version                   Build  Channel
pytensor                  2.17.4                   pypi_0    pypi

which is able to run the scripts and tests in the package.

I will update to your version 2.20.0 and see if we need to enforce a lower version of PyTensor until we can update the code to reflect the newer versions.

@augeorge
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it looks like the pytensor version was bumped for more recent pyMC versions. https://github.com/pymc-devs/pymc/releases

I will try pyMC version 5.9.11 which supports pytensor 2.17

@mcnaughtonadm
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I am able to replicate your error with the following versions of PyMC and PyTensor

# packages in environment at /Users/mcna892/mambaforge/envs/test_emll:
#
# Name                    Version                   Build  Channel
pymc                      5.13.1                   pypi_0    pypi
pytensor                  2.20.0                   pypi_0    pypi

We can use this issue to narrow down either a code-fix or set a constraint on the setup.cfg file to restrict PyTensor and PyMC to working versions.

@mcnaughtonadm mcnaughtonadm self-assigned this Apr 17, 2024
@mcnaughtonadm mcnaughtonadm added the bug Something isn't working label Apr 17, 2024
@augeorge
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ok it now runs when I use

pymc                      5.9.2                    pypi_0    pypi
pytensor                  2.17.4                   pypi_0    pypi
python                    3.11.8               hb885b13_0

@augeorge
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augeorge commented Apr 17, 2024 •
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if we fix pymc to version 5.9.2 in the setup file then it should fix the problem (for now)

@mcnaughtonadm mcnaughtonadm linked a pull request Apr 17, 2024 that will close this issue
Pin pytensor version #14
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@mcnaughtonadm mcnaughtonadm mentioned this issue Apr 17, 2024
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@augeorge augeorge mentioned this issue May 6, 2024
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Pin pytensor version pnnl-predictive-phenomics/emll
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