pydantic errors on new install
I cleaned-up my environment, and then re-installed it. I see that lightning was upgraded to 2.0.6, pydantic is pinned to 1.10.x. I get the following error:
$ ptbench datamodule list
Traceback (most recent call last):
File "/Users/andre/mamba/envs/ptbench/bin/ptbench", line 5, in <module>
from ptbench.scripts.cli import cli
File "/Users/andre/work/biosignal/software/ptbench/src/ptbench/scripts/cli.py", line 9, in <module>
from . import (
File "/Users/andre/work/biosignal/software/ptbench/src/ptbench/scripts/evaluate.py", line 16, in <module>
from ..data.datamodule import CachingDataModule
File "/Users/andre/work/biosignal/software/ptbench/src/ptbench/data/datamodule.py", line 13, in <module>
import lightning
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/lightning/__init__.py", line 18, in <module>
from lightning.app import storage # noqa: E402
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/lightning/app/__init__.py", line 24, in <module>
from lightning.app import components # noqa: E402, F401
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/lightning/app/components/__init__.py", line 1, in <module>
from lightning.app.components.database.client import DatabaseClient
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/lightning/app/components/database/__init__.py", line 1, in <module>
from lightning.app.components.database.client import DatabaseClient
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/lightning/app/components/database/client.py", line 22, in <module>
from lightning.app.components.database.utilities import _GeneralModel
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/lightning/app/components/database/utilities.py", line 20, in <module>
from fastapi import Response, status
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/fastapi/__init__.py", line 7, in <module>
from .applications import FastAPI as FastAPI
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/fastapi/applications.py", line 16, in <module>
from fastapi import routing
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/fastapi/routing.py", line 32, in <module>
from fastapi.dependencies.models import Dependant
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/fastapi/dependencies/models.py", line 4, in <module>
from fastapi.security.base import SecurityBase
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/fastapi/security/__init__.py", line 1, in <module>
from .api_key import APIKeyCookie as APIKeyCookie
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/fastapi/security/api_key.py", line 3, in <module>
from fastapi.openapi.models import APIKey, APIKeyIn
File "/Users/andre/mamba/envs/ptbench/lib/python3.11/site-packages/fastapi/openapi/models.py", line 58, in <module>
class Contact(BaseModel):
File "pydantic/main.py", line 186, in pydantic.main.ModelMetaclass.__new__
TypeError: Argument 'bases' has incorrect type (expected list, got tuple)Shall we upgrade pydantic, or downgrade lightning?
Activity
assigned to @dcarron
@dcarron - I'm completely blocked until this is resolved. My environment is as such:
$ mamba list # packages in environment at /Users/andre/mamba/envs/ptbench: # # Name Version Build Channel absl-py 1.4.0 pyhd8ed1ab_0 conda-forge aiohttp 3.8.5 py311heffc1b2_0 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge alabaster 0.7.13 pyhd8ed1ab_0 conda-forge anyio 3.7.1 pyhd8ed1ab_0 conda-forge arrow 1.2.3 pyhd8ed1ab_0 conda-forge async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge auto-intersphinx 1.0.3 pyhd8ed1ab_0 conda-forge babel 2.12.1 pyhd8ed1ab_1 conda-forge backoff 2.2.1 pyhd8ed1ab_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.cached-property 1.0.2 pyhd8ed1ab_0 conda-forge backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.2 pyha770c72_0 conda-forge blessed 1.19.1 pyhe4f9e05_2 conda-forge blinker 1.6.2 pyhd8ed1ab_0 conda-forge brotli 1.0.9 h1a8c8d9_9 conda-forge brotli-bin 1.0.9 h1a8c8d9_9 conda-forge brotlipy 0.7.0 py311he2be06e_1005 conda-forge bzip2 1.0.8 h3422bc3_4 conda-forge c-ares 1.19.1 hb547adb_0 conda-forge ca-certificates 2023.7.22 hf0a4a13_0 conda-forge cachecontrol 0.12.14 pyhd8ed1ab_0 conda-forge cachecontrol-with-filecache 0.12.14 pyhd8ed1ab_0 conda-forge cachetools 5.3.1 pyhd8ed1ab_0 conda-forge certifi 2023.7.22 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py311hae827db_3 conda-forge cfgv 3.3.1 pyhd8ed1ab_0 conda-forge charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge clapper 1.0.1 pyhd8ed1ab_0 conda-forge cleo 2.0.1 pyhd8ed1ab_0 conda-forge click 8.1.3 unix_pyhd8ed1ab_2 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge contourpy 1.1.0 py311he4fd1f5_0 conda-forge coverage 7.2.7 py311heffc1b2_0 conda-forge crashtest 0.4.1 pyhd8ed1ab_0 conda-forge croniter 1.4.1 pyhd8ed1ab_0 conda-forge cryptography 41.0.2 py311h5fb2c35_0 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge dateutils 0.6.12 py_0 conda-forge deepdiff 6.3.1 pyhd8ed1ab_0 conda-forge distlib 0.3.7 pyhd8ed1ab_0 conda-forge docutils 0.19 py311h267d04e_1 conda-forge dulwich 0.21.5 py311heffc1b2_0 conda-forge exceptiongroup 1.1.2 pyhd8ed1ab_0 conda-forge fancycompleter 0.9.1 py311h267d04e_1005 conda-forge fastapi 0.100.0 pyhd8ed1ab_0 conda-forge filelock 3.12.2 pyhd8ed1ab_0 conda-forge fonttools 4.41.1 py311heffc1b2_0 conda-forge freetype 2.12.1 hd633e50_1 conda-forge frozenlist 1.4.0 py311heffc1b2_0 conda-forge fsspec 2023.6.0 pyh1a96a4e_0 conda-forge furo 2023.5.20 pyhd8ed1ab_1 conda-forge gmp 6.2.1 h9f76cd9_0 conda-forge gmpy2 2.1.2 py311h2ba9262_1 conda-forge google-auth 2.22.0 pyh1a96a4e_0 conda-forge google-auth-oauthlib 1.0.0 pyhd8ed1ab_1 conda-forge grpcio 1.54.2 py311ha891d26_2 conda-forge h11 0.14.0 pyhd8ed1ab_0 conda-forge html5lib 1.1 pyh9f0ad1d_0 conda-forge icu 72.1 he12128b_0 conda-forge identify 2.5.26 pyhd8ed1ab_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge imagesize 1.4.1 pyhd8ed1ab_0 conda-forge importlib-metadata 6.8.0 pyha770c72_0 conda-forge importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge importlib_resources 6.0.0 pyhd8ed1ab_1 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge inquirer 3.1.3 pyhd8ed1ab_0 conda-forge itsdangerous 2.1.2 pyhd8ed1ab_0 conda-forge jaraco.classes 3.3.0 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge joblib 1.3.0 pyhd8ed1ab_1 conda-forge jsonschema 4.18.4 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.7.1 pyhd8ed1ab_0 conda-forge keyring 23.13.1 py311h267d04e_0 conda-forge kiwisolver 1.4.4 py311hd6ee22a_1 conda-forge lcms2 2.15 hd835a16_1 conda-forge lerc 4.0.0 h9a09cb3_0 conda-forge libabseil 20230125.3 cxx17_h13dd4ca_0 conda-forge libblas 3.9.0 17_osxarm64_openblas conda-forge libbrotlicommon 1.0.9 h1a8c8d9_9 conda-forge libbrotlidec 1.0.9 h1a8c8d9_9 conda-forge libbrotlienc 1.0.9 h1a8c8d9_9 conda-forge libcblas 3.9.0 17_osxarm64_openblas conda-forge libcxx 16.0.6 h4653b0c_0 conda-forge libdeflate 1.18 h1a8c8d9_0 conda-forge libffi 3.4.2 h3422bc3_5 conda-forge libgfortran 5.0.0 12_3_0_hd922786_1 conda-forge libgfortran5 12.3.0 ha3a6a3e_1 conda-forge libgrpc 1.54.2 h0a338ca_2 conda-forge libiconv 1.17 he4db4b2_0 conda-forge libjpeg-turbo 2.1.5.1 h1a8c8d9_0 conda-forge liblapack 3.9.0 17_osxarm64_openblas conda-forge libopenblas 0.3.23 openmp_hc731615_0 conda-forge libpng 1.6.39 h76d750c_0 conda-forge libprotobuf 3.21.12 hb5ab8b9_0 conda-forge libsqlite 3.42.0 hb31c410_0 conda-forge libtiff 4.5.1 h23a1a89_0 conda-forge libwebp-base 1.3.1 hb547adb_0 conda-forge libxcb 1.15 hf346824_0 conda-forge libxml2 2.11.4 he3bdae6_0 conda-forge libxslt 1.1.37 h1728932_1 conda-forge libzlib 1.2.13 h53f4e23_5 conda-forge lightning 2.0.6 pyhd8ed1ab_0 conda-forge lightning-cloud 0.5.37 pyhd8ed1ab_0 conda-forge lightning-utilities 0.9.0 pyhd8ed1ab_0 conda-forge llvm-openmp 16.0.6 h1c12783_0 conda-forge lockfile 0.12.2 py_1 conda-forge lxml 4.9.3 py311hbafe683_0 conda-forge markdown 3.4.4 pyhd8ed1ab_0 conda-forge markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge markupsafe 2.1.3 py311heffc1b2_0 conda-forge matplotlib 3.7.1 py311ha1ab1f8_0 conda-forge matplotlib-base 3.7.1 py311h99a5f44_0 conda-forge mdurl 0.1.0 pyhd8ed1ab_0 conda-forge more-itertools 10.0.0 pyhd8ed1ab_0 conda-forge mpc 1.3.1 h91ba8db_0 conda-forge mpfr 4.2.0 he09a6ba_0 conda-forge mpmath 1.3.0 pyhd8ed1ab_0 conda-forge msgpack-python 1.0.5 py311hd6ee22a_0 conda-forge multidict 6.0.4 py311he2be06e_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge ncurses 6.4 h7ea286d_0 conda-forge networkx 3.1 pyhd8ed1ab_0 conda-forge nodeenv 1.8.0 pyhd8ed1ab_0 conda-forge numpy 1.24.4 py311hb8f3215_0 conda-forge oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge openjpeg 2.5.0 hbc2ba62_2 conda-forge openssl 3.1.1 h53f4e23_1 conda-forge ordered-set 4.1.0 pyhd8ed1ab_0 conda-forge orjson 3.9.2 py311he74e4cd_0 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge pandas 2.0.2 py311h9e438b8_0 conda-forge pdbpp 0.10.3 pyhd8ed1ab_0 conda-forge pexpect 4.8.0 pyh1a96a4e_2 conda-forge pillow 9.5.0 py311h095fde6_1 conda-forge pip 23.2.1 pyhd8ed1ab_0 conda-forge pkginfo 1.9.6 pyhd8ed1ab_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge platformdirs 3.9.1 pyhd8ed1ab_0 conda-forge pluggy 1.2.0 pyhd8ed1ab_0 conda-forge poetry 1.5.1 osx_pyhd8ed1ab_0 conda-forge poetry-core 1.6.1 pyhd8ed1ab_0 conda-forge poetry-plugin-export 1.4.0 pyhd8ed1ab_0 conda-forge pooch 1.7.0 pyha770c72_3 conda-forge pre-commit 3.3.3 pyha770c72_0 conda-forge protobuf 4.21.12 py311ha397e9f_0 conda-forge psutil 5.9.5 py311he2be06e_0 conda-forge ptbench 1.0.0b0 pypi_0 pypi pthread-stubs 0.4 h27ca646_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pyasn1 0.4.8 py_0 conda-forge pyasn1-modules 0.2.7 py_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pydantic 1.10.12 py311heffc1b2_0 conda-forge pygments 2.15.1 pyhd8ed1ab_0 conda-forge pyjwt 2.8.0 pyhd8ed1ab_0 conda-forge pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge pyparsing 3.1.0 pyhd8ed1ab_0 conda-forge pyproject_hooks 1.0.0 pyhd8ed1ab_0 conda-forge pyrepl 0.9.0 py311he2be06e_7 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytest 7.4.0 pyhd8ed1ab_0 conda-forge pytest-cov 4.1.0 pyhd8ed1ab_0 conda-forge python 3.11.0 h3ba56d0_1_cpython conda-forge python-build 0.10.0 pyhd8ed1ab_1 conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-editor 1.0.4 py_0 conda-forge python-installer 0.7.0 pyhd8ed1ab_0 conda-forge python-multipart 0.0.6 pyhd8ed1ab_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.11 3_cp311 conda-forge pytorch 2.0.0 cpu_py311hb4bb8ad_0 conda-forge pytorch-lightning 2.0.6 pyhd8ed1ab_0 conda-forge pytz 2023.3 pyhd8ed1ab_0 conda-forge pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge pyyaml 6.0 py311he2be06e_5 conda-forge rapidfuzz 2.15.1 py311ha397e9f_0 conda-forge re2 2023.03.02 hc5e2d97_0 conda-forge readchar 4.0.5 pyhd8ed1ab_0 conda-forge readline 8.2 h92ec313_1 conda-forge referencing 0.30.0 pyhd8ed1ab_0 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge requests-oauthlib 1.3.1 pyhd8ed1ab_0 conda-forge requests-toolbelt 1.0.0 pyhd8ed1ab_0 conda-forge rich 13.4.2 pyhd8ed1ab_0 conda-forge rpds-py 0.9.2 py311h0563b04_0 conda-forge rsa 4.9 pyhd8ed1ab_0 conda-forge scikit-learn 1.2.2 py311hf0b18b8_2 conda-forge scipy 1.11.0 py311h93d07a4_0 conda-forge setuptools 68.0.0 pyhd8ed1ab_0 conda-forge shellingham 1.5.1 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sleef 3.5.1 h156473d_2 conda-forge sniffio 1.3.0 pyhd8ed1ab_0 conda-forge snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge sphinx 6.2.1 pyhd8ed1ab_0 conda-forge sphinx-autodoc-typehints 1.21.8 pyhd8ed1ab_0 conda-forge sphinx-basic-ng 1.0.0b2 pyhd8ed1ab_0 conda-forge sphinx-click 4.4.0 pyhd8ed1ab_0 conda-forge sphinx-copybutton 0.5.2 pyhd8ed1ab_0 conda-forge sphinx-inline-tabs 2023.4.21 pyhd8ed1ab_0 conda-forge sphinxcontrib-applehelp 1.0.4 pyhd8ed1ab_0 conda-forge sphinxcontrib-devhelp 1.0.2 py_0 conda-forge sphinxcontrib-htmlhelp 2.0.1 pyhd8ed1ab_0 conda-forge sphinxcontrib-jsmath 1.0.1 py_0 conda-forge sphinxcontrib-qthelp 1.0.3 py_0 conda-forge sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge starlette 0.27.0 pyhd8ed1ab_0 conda-forge starsessions 1.3.0 pyhd8ed1ab_0 conda-forge sympy 1.12 pypyh9d50eac_103 conda-forge tabulate 0.9.0 pyhd8ed1ab_1 conda-forge tensorboard 2.13.0 pyhd8ed1ab_0 conda-forge tensorboard-data-server 0.7.0 py311h507f6e9_0 conda-forge threadpoolctl 3.2.0 pyha21a80b_0 conda-forge tk 8.6.12 he1e0b03_0 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tomli-w 1.0.0 pyhd8ed1ab_0 conda-forge tomlkit 0.11.8 pyha770c72_0 conda-forge torchmetrics 0.11.4 pyhd8ed1ab_0 conda-forge torchvision 0.15.2 cpu_py311h88737c0_1 conda-forge tornado 6.3.2 py311heffc1b2_0 conda-forge tqdm 4.65.0 pyhd8ed1ab_1 conda-forge traitlets 5.9.0 pyhd8ed1ab_0 conda-forge trove-classifiers 2023.7.6 pyhd8ed1ab_0 conda-forge typing 3.10.0.0 pyhd8ed1ab_0 conda-forge typing-extensions 4.7.1 hd8ed1ab_0 conda-forge typing_extensions 4.7.1 pyha770c72_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge ukkonen 1.0.1 py311hd6ee22a_3 conda-forge urllib3 1.26.15 pyhd8ed1ab_0 conda-forge uvicorn 0.23.1 py311h267d04e_0 conda-forge virtualenv 20.24.2 pyhd8ed1ab_0 conda-forge wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 py_1 conda-forge websocket-client 1.6.1 pyhd8ed1ab_0 conda-forge websockets 11.0.3 py311heffc1b2_0 conda-forge werkzeug 2.3.6 pyhd8ed1ab_0 conda-forge wheel 0.41.0 pyhd8ed1ab_0 conda-forge wmctrl 0.4 pyhd8ed1ab_0 conda-forge xattr 0.10.1 py311he2be06e_0 conda-forge xdg 6.0.0 pyhd8ed1ab_0 conda-forge xorg-libxau 1.0.11 hb547adb_0 conda-forge xorg-libxdmcp 1.1.3 h27ca646_0 conda-forge xz 5.2.6 h57fd34a_0 conda-forge yaml 0.2.5 h3422bc3_2 conda-forge yarl 1.9.2 py311heffc1b2_0 conda-forge zipp 3.16.2 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h53f4e23_5 conda-forge zstd 1.5.2 h4f39d0f_7 conda-forgeSuggestions?
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I think we are haunted by this again: https://gitlab.idiap.ch/biosignal/software/ptbench/-/jobs/349692
If anybody has ideas on how to solve this, @biosignal, I'd be glad to hear them ASAP.
Note that the above log is issued from a pip install and not from a mamba install as was before.
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A similar issue was closed on lightning's repo on July 8th: https://github.com/Lightning-AI/lightning/pull/18022, but that did not solve it completely.
Another fix was planned for 2.0.6: https://github.com/Lightning-AI/lightning/issues/18027, but looks like they missed it: https://github.com/Lightning-AI/lightning/pull/18030? (Says it was merged into
masteron July 10th, but there are further commits a couple of weeks ago, July 19th and 21st. - 2.0.6 is from July 24th., so it should be in...) -
In mamba/conda, packagers pinned
pydantic <2.0,>=1.7.4(https://github.com/conda-forge/lightning-feedstock/blob/main/recipe/meta.yaml). Because we are using pip, we don't get that "fix" during the test phase. The only solution I see for the time being is to bring this pin to the package declaration, and leave this issue opened until that is resolved on the lightning side. mentioned in commit e544d3cc
added Blocked on external input label
mentioned in commit d07d3970
mentioned in commit 6c09539b
mentioned in commit 05c24a29
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