I've just started going through Statistical Rethinking v2, so I cloned the repo and tried to run the notebooks from chapter 2 to 6. I've encountered the following errors, for which I've identified the root causes and some possible solutions. However since I don't know how these would affect future chapters I didn't issue a pull request.
Installation info
I'm on Ubuntu 20.04 and I installed using the recommended command: conda env create -f environment_v4.yml then added the kernel with python -m ipykernel install --user --name stat-rethink2-pymc4 --display-name "Python 3.10 (stat-rethink2-pymc4)" (even though this doesn't exist in the README, I assume it should be as in pymc3 version).
Issue 01: Failure to import scipy.stats as stats
Already from chapter 02 when I tried to run the notebook I got the following error
---------------------------------------------------------------------------
NoSectionError Traceback (most recent call last)
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/aesara/configparser.py:237, in AesaraConfigParser.fetch_val_for_key(self, key, delete_key)
236 try:
--> 237 return self._aesara_cfg.get(section, option)
238 except InterpolationError:
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/configparser.py:782, in RawConfigParser.get(self, section, option, raw, vars, fallback)
781 try:
--> 782 d = self._unify_values(section, vars)
783 except NoSectionError:
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/configparser.py:1153, in RawConfigParser._unify_values(self, section, vars)
1152 if section != self.default_section:
-> 1153 raise NoSectionError(section) from None
1154 # Update with the entry specific variables
NoSectionError: No section: 'blas'
During handling of the above exception, another exception occurred:
KeyError Traceback (most recent call last)
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/aesara/configparser.py:353, in ConfigParam.__get__(self, cls, type_, delete_key)
352 try:
--> 353 val_str = cls.fetch_val_for_key(self.name, delete_key=delete_key)
354 self.is_default = False
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/aesara/configparser.py:241, in AesaraConfigParser.fetch_val_for_key(self, key, delete_key)
240 except (NoOptionError, NoSectionError):
--> 241 raise KeyError(key)
KeyError: 'blas__ldflags'
During handling of the above exception, another exception occurred:
ModuleNotFoundError Traceback (most recent call last)
Input In [1], in <cell line: 4>()
2 import matplotlib.pyplot as plt
3 import numpy as np
----> 4 import pymc as pm
5 import scipy.stats as stats
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/pymc/__init__.py:50, in <module>
45 augmented = f"{augmented} -fno-unwind-tables -fno-asynchronous-unwind-tables"
47 aesara.config.gcc__cxxflags = augmented
---> 50 __set_compiler_flags()
52 from pymc import gp, ode, sampling
53 from pymc.aesaraf import *
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/pymc/__init__.py:33, in __set_compiler_flags()
31 def __set_compiler_flags():
32 # Workarounds for Aesara compiler problems on various platforms
---> 33 import aesara
35 current = aesara.config.gcc__cxxflags
36 augmented = f"{current} -Wno-c++11-narrowing"
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/aesara/__init__.py:126, in <module>
122 return as_tensor_variable(x, **kwargs)
125 # isort: off
--> 126 from aesara import scalar, tensor
127 from aesara.compile import (
128 In,
129 Mode,
(...)
135 shared,
136 )
137 from aesara.compile.function import function, function_dump
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/aesara/tensor/__init__.py:98, in <module>
96 # adds shared-variable constructors
97 from aesara.tensor import sharedvar # noqa
---> 98 from aesara.tensor import ( # noqa
99 basic_opt,
100 blas,
101 blas_c,
102 blas_scipy,
103 nnet,
104 opt_uncanonicalize,
105 subtensor_opt,
106 xlogx,
107 )
110 # isort: off
111 from aesara.tensor import linalg # noqa
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/aesara/tensor/blas.py:165, in <module>
163 from aesara.tensor import basic as at
164 from aesara.tensor.basic_opt import local_dimshuffle_lift
--> 165 from aesara.tensor.blas_headers import blas_header_text, blas_header_version
166 from aesara.tensor.elemwise import DimShuffle, Elemwise
167 from aesara.tensor.exceptions import NotScalarConstantError
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/aesara/tensor/blas_headers.py:1015, in <module>
997 header += textwrap.dedent(
998 """\
999 static float sdot_(int* Nx, float* x, int* Sx, float* y, int* Sy)
(...)
1009 """
1010 )
1012 return header + blas_code
-> 1015 if not config.blas__ldflags:
1016 _logger.warning("Using NumPy C-API based implementation for BLAS functions.")
1019 def mkl_threads_text():
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/aesara/configparser.py:357, in ConfigParam.__get__(self, cls, type_, delete_key)
355 except KeyError:
356 if callable(self.default):
--> 357 val_str = self.default()
358 else:
359 val_str = self.default
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/aesara/link/c/cmodule.py:2710, in default_blas_ldflags()
2699 warn_record = []
2700 try:
2701 # We do this import only here, as in some setup, if we
2702 # just import aesara and exit, with the import at global
(...)
2708 # This happen with Python 2.7.3 |EPD 7.3-1 and numpy 1.8.1
2709 # isort: off
-> 2710 import numpy.distutils.system_info # noqa
2712 # We need to catch warnings as in some cases NumPy print
2713 # stuff that we don't want the user to see.
2714 # I'm not able to remove all printed stuff
2715 with warnings.catch_warnings(record=True):
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/numpy/distutils/system_info.py:196, in <module>
191 from numpy.distutils.exec_command import (
192 find_executable, filepath_from_subprocess_output,
193 )
194 from numpy.distutils.misc_util import (is_sequence, is_string,
195 get_shared_lib_extension)
--> 196 from numpy.distutils.command.config import config as cmd_config
197 from numpy.distutils import customized_ccompiler as _customized_ccompiler
198 from numpy.distutils import _shell_utils
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/numpy/distutils/command/config.py:19, in <module>
17 import distutils
18 from numpy.distutils.exec_command import filepath_from_subprocess_output
---> 19 from numpy.distutils.mingw32ccompiler import generate_manifest
20 from numpy.distutils.command.autodist import (check_gcc_function_attribute,
21 check_gcc_function_attribute_with_intrinsics,
22 check_gcc_variable_attribute,
(...)
25 check_restrict,
26 check_compiler_gcc)
28 LANG_EXT['f77'] = '.f'
File ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/numpy/distutils/mingw32ccompiler.py:28, in <module>
26 import distutils.cygwinccompiler
27 from distutils.unixccompiler import UnixCCompiler
---> 28 from distutils.msvccompiler import get_build_version as get_build_msvc_version
29 from distutils.errors import UnknownFileError
30 from numpy.distutils.misc_util import (msvc_runtime_library,
31 msvc_runtime_version,
32 msvc_runtime_major,
33 get_build_architecture)
ModuleNotFoundError: No module named 'distutils.msvccompiler'
Issue 01: Possible Solution.
I assume this is because Python 3.10 deprecated distutils. This has been fixed on later versions of the aesara library, but version 2.6.6 which is fixed at the env, still doesn't have the change. After removing the fixed package number of the environment file on all packages except PyMC, and recreating the environment the issue disappeared.. However, I don't know if this would break anything else on the other chapters, due to dependencies.
Issue 02: Failure when importing causalgraphicalmodels
In chapter 05, we have from causalgraphicalmodels import CausalGraphicalModel. When I try to execute this I'm getting ImportError: cannot import name 'Iterable' from 'collections'. As shown on the link the solution is to modify the import statement for the causalgraphicalmodels package.
In my case the file was ~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/causalgraphicalmodels/cgm.py and I had to change:
from collections import Iterable
to
try:
# Python <= 3.9
from collections import Iterable
except ImportError:
# Python > 3.9
from collections.abc import Iterable
I know that this is another packages issue, but I'm putting it as a ref in case anyone else has the same issues.
Hello,
I've just started going through Statistical Rethinking v2, so I cloned the repo and tried to run the notebooks from chapter 2 to 6. I've encountered the following errors, for which I've identified the root causes and some possible solutions. However since I don't know how these would affect future chapters I didn't issue a pull request.
Installation info
I'm on Ubuntu 20.04 and I installed using the recommended command:
conda env create -f environment_v4.ymlthen added the kernel withpython -m ipykernel install --user --name stat-rethink2-pymc4 --display-name "Python 3.10 (stat-rethink2-pymc4)"(even though this doesn't exist in the README, I assume it should be as in pymc3 version).Issue 01: Failure to import scipy.stats as stats
Already from chapter 02 when I tried to run the notebook I got the following error
Issue 01: Possible Solution.
I assume this is because Python 3.10 deprecated distutils. This has been fixed on later versions of the aesara library, but version 2.6.6 which is fixed at the env, still doesn't have the change. After removing the fixed package number of the environment file on all packages except PyMC, and recreating the environment the issue disappeared.. However, I don't know if this would break anything else on the other chapters, due to dependencies.
Issue 02: Failure when importing causalgraphicalmodels
In chapter 05, we have
from causalgraphicalmodels import CausalGraphicalModel. When I try to execute this I'm getting ImportError: cannot import name 'Iterable' from 'collections'. As shown on the link the solution is to modify the import statement for the causalgraphicalmodels package.In my case the file was
~/anaconda3/envs/stat-rethink2-pymc_v4/lib/python3.10/site-packages/causalgraphicalmodels/cgm.pyand I had to change:to
I know that this is another packages issue, but I'm putting it as a ref in case anyone else has the same issues.