AttributeError: module 'pydantic' has no attribute 'ConfigDict'

Question

AttributeError: module 'pydantic' has no attribute 'ConfigDict'

Closed this issue 9 months ago · 11 comments

Describe the bug
Python error when running varfish-cli
AttributeError: module 'pydantic' has no attribute 'ConfigDict'

To Reproduce
Steps to reproduce the behavior:

Install varfish-cli as described in the readme
execute conda activate varfish-cli
execute varfish-cli --help

Expected behavior
showing help info.

Additional context

Traceback (most recent call last):
File "/home/humgen/miniconda3/envs/varfish-cli-ex/bin/varfish-cli", line 6, in
from varfish_cli.main import main
File "/home/humgen/miniconda3/envs/varfish-cli-ex/lib/python3.6/site-packages/varfish_cli/main.py", line 3, in
from varfish_cli import cli
File "/home/humgen/miniconda3/envs/varfish-cli-ex/lib/python3.6/site-packages/varfish_cli/cli/init.py", line 10, in
from varfish_cli.cli import cases, importer, projects, tools, varannos
File "/home/humgen/miniconda3/envs/varfish-cli-ex/lib/python3.6/site-packages/varfish_cli/cli/cases.py", line 8, in
from varfish_cli import api, common
File "/home/humgen/miniconda3/envs/varfish-cli-ex/lib/python3.6/site-packages/varfish_cli/api/init.py", line 3, in
from varfish_cli.api.case import * # noqa: F403, F401
File "/home/humgen/miniconda3/envs/varfish-cli-ex/lib/python3.6/site-packages/varfish_cli/api/case.py", line 12, in
from varfish_cli.api import models
File "/home/humgen/miniconda3/envs/varfish-cli-ex/lib/python3.6/site-packages/varfish_cli/api/models.py", line 20, in
class Project(pydantic.BaseModel):
File "/home/humgen/miniconda3/envs/varfish-cli-ex/lib/python3.6/site-packages/varfish_cli/api/models.py", line 21, in Project
model_config = pydantic.ConfigDict(frozen=True)
AttributeError: module 'pydantic' has no attribute 'ConfigDict'

Answer 1 · 2024-02-08T09:29:20.000Z

@flokraft85 thank you for the report. Can you provide us with the output of pip freeze in the conda env?

Answer 2 · 2024-02-08T09:36:23.000Z

Hi,
yes, of cause. Please find the requested information below.

attrs @ file:///opt/conda/conda-bld/attrs_1642510447205/work
brotlipy==0.7.0
cattrs @ file:///tmp/build/80754af9/cattrs_1616441511098/work
certifi==2021.5.30
cffi @ file:///tmp/build/80754af9/cffi_1625814693874/work
charset-normalizer @ file:///tmp/build/80754af9/charset-normalizer_1630003229654/work
cheroot==8.6.0
CherryPy==18.6.1
click==8.0.3
colorama @ file:///tmp/build/80754af9/colorama_1607707115595/work
cryptography @ file:///tmp/build/80754af9/cryptography_1635366128178/work
glob2==0.7
idna @ file:///tmp/build/80754af9/idna_1637925883363/work
importlib-metadata @ file:///tmp/build/80754af9/importlib-metadata_1631916693255/work
importlib-resources==5.4.0
jaraco.classes==3.2.1
jaraco.collections==3.4.0
jaraco.context==4.1.1
jaraco.functools==3.4.0
jaraco.text==3.7.0
jasmine==3.99.0
jasmine-core==3.99.0
Jinja2==2.11.3
jsonschema @ file:///Users/ktietz/demo/mc3/conda-bld/jsonschema_1630511932244/work
logzero @ file:///home/conda/feedstock_root/build_artifacts/logzero_1615999420643/work
MarkupSafe==2.0.1
more-itertools==8.12.0
ordereddict==1.1
polyleven @ file:///home/conda/feedstock_root/build_artifacts/polyleven_1614058563248/work
portend==3.0.0
pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work
pydantic @ file:///tmp/build/80754af9/pydantic_1621546914171/work
pyOpenSSL @ file:///opt/conda/conda-bld/pyopenssl_1643788558760/work
pyrsistent @ file:///tmp/build/80754af9/pyrsistent_1600141725711/work
PySocks @ file:///tmp/build/80754af9/pysocks_1605305763431/work
python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work
pytz==2021.3
PyYAML==6.0
requests @ file:///opt/conda/conda-bld/requests_1641824580448/work
selenium==3.141.0
shellingham @ file:///Users/ktietz/demo/mc3/conda-bld/shellingham_1629144685686/work
simplejson==3.8.1
six==1.16.0
tabulate==0.8.9
tempora==4.1.2
toml @ file:///tmp/build/80754af9/toml_1616166611790/work
tqdm==4.7.2
typeguard @ file:///home/conda/feedstock_root/build_artifacts/typeguard_1658932097418/work
typer @ file:///tmp/build/80754af9/typer_1637667998014/work
typing_extensions @ file:///opt/conda/conda-bld/typing_extensions_1647553014482/work
urllib3==1.26.8
varfish_cli @ file:///opt/conda/conda-bld/varfish-cli_1706102364935/work
zc.lockfile==2.0
zipp==3.6.0

Answer 3 · 2024-02-08T09:37:38.000Z

That turns out to not be helpful. Could you show conda list?

Answer 4 · 2024-02-08T09:39:24.000Z

sure, your welcome.

Answer 5 · 2024-02-08T09:40:34.000Z

Could you try conda install pydantic=2?

Answer 6 · 2024-02-08T10:01:01.000Z

done. However, still the same error.

conda install pydantic=2
Your installed version is: 2.35

Traceback (most recent call last):
File "/home/humgen/miniconda3/envs/varfish-cli2/bin/varfish-cli", line 6, in
from varfish_cli.main import main
File "/home/humgen/miniconda3/envs/varfish-cli2/lib/python3.6/site-packages/varfish_cli/main.py", line 3, in
from varfish_cli import cli
File "/home/humgen/miniconda3/envs/varfish-cli2/lib/python3.6/site-packages/varfish_cli/cli/init.py", line 10, in
from varfish_cli.cli import cases, importer, projects, tools, varannos
File "/home/humgen/miniconda3/envs/varfish-cli2/lib/python3.6/site-packages/varfish_cli/cli/cases.py", line 8, in
from varfish_cli import api, common
File "/home/humgen/miniconda3/envs/varfish-cli2/lib/python3.6/site-packages/varfish_cli/api/init.py", line 3, in
from varfish_cli.api.case import * # noqa: F403, F401
File "/home/humgen/miniconda3/envs/varfish-cli2/lib/python3.6/site-packages/varfish_cli/api/case.py", line 12, in
from varfish_cli.api import models
File "/home/humgen/miniconda3/envs/varfish-cli2/lib/python3.6/site-packages/varfish_cli/api/models.py", line 20, in
class Project(pydantic.BaseModel):
File "/home/humgen/miniconda3/envs/varfish-cli2/lib/python3.6/site-packages/varfish_cli/api/models.py", line 21, in Project
model_config = pydantic.ConfigDict(frozen=True)
AttributeError: module 'pydantic' has no attribute 'ConfigDict'

_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
attrs 21.4.0 pyhd3eb1b0_0
brotlipy 0.7.0 py36h27cfd23_1003
ca-certificates 2023.12.12 h06a4308_0
cattrs 1.4.0 pyhd3eb1b0_0
certifi 2021.5.30 py36h06a4308_0
cffi 1.14.6 py36h400218f_0
charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.0.3 pyhd3eb1b0_0
colorama 0.4.4 pyhd3eb1b0_0
cryptography 35.0.0 py36hd23ed53_0
idna 3.3 pyhd3eb1b0_0
importlib-metadata 4.8.1 py36h06a4308_0
importlib_metadata 4.8.1 hd3eb1b0_0
jsonschema 3.2.0 pyhd3eb1b0_2
ld_impl_linux-64 2.38 h1181459_1
libffi 3.3 he6710b0_2
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libstdcxx-ng 11.2.0 h1234567_1
logzero 1.7.0 py36h5fab9bb_0 conda-forge
ncurses 6.4 h6a678d5_0
openssl 1.1.1w h7f8727e_0
pip 21.2.2 py36h06a4308_0
polyleven 0.7 py36h8f6f2f9_0 conda-forge
pycparser 2.21 pyhd3eb1b0_0
pydantic 1.8.2 py36h27cfd23_0
pyopenssl 22.0.0 pyhd3eb1b0_0
pyrsistent 0.17.3 py36h7b6447c_0
pysocks 1.7.1 py36h06a4308_0
python 3.6.13 h12debd9_1
python-dateutil 2.8.2 pyhd3eb1b0_0
python_abi 3.6 2_cp36m conda-forge
readline 8.2 h5eee18b_0
requests 2.27.1 pyhd3eb1b0_0
setuptools 58.0.4 py36h06a4308_0
shellingham 1.3.1 pyhd3eb1b0_0
simplejson 3.8.1 py36_0 bioconda
six 1.16.0 pyhd3eb1b0_1
sqlite 3.41.2 h5eee18b_0
tabulate 0.8.9 py36h06a4308_0
tk 8.6.12 h1ccaba5_0
toml 0.10.2 pyhd3eb1b0_0
tqdm 4.7.2 py36_0 bioconda
typeguard 2.13.3 pyhd8ed1ab_0 conda-forge
typer 0.4.0 pyhd3eb1b0_0
typing-extensions 4.1.1 hd3eb1b0_0
typing_extensions 4.1.1 pyh06a4308_0
urllib3 1.26.8 pyhd3eb1b0_0
varfish-cli 0.6.3 pyhdfd78af_0 bioconda
wheel 0.37.1 pyhd3eb1b0_0
xz 5.4.5 h5eee18b_0
zipp 3.6.0 pyhd3eb1b0_0
zlib 1.2.13 h5eee18b_0

Answer 7 · 2024-02-08T10:02:28.000Z

Ah ok, it is still pydantic 1.8.2 py36h27cfd23_0, altough conda updated it successfully.

Answer 8 · 2024-02-08T10:17:02.000Z

You should be able to get a working environment with this:

mamba create -y -n varfish-cli -c bioconda varfish-cli pydantic=2

I will see to the bioconda recipe.

Answer 9 · 2024-02-08T12:33:27.000Z

Yes this works! Thanks :)!

Answer 10 · 2024-02-08T13:10:31.000Z

OK, once someone from the bioconda core team reviews this, the original instructions should work again.

Answer 11 · 2024-02-09T08:51:10.000Z

Updated recipe to require Python>=3.9. Then it should work.

Name Version Build Channel