polaris-hub / polaris

Foster the development of impactful AI models in drug discovery.
https://polaris-hub.github.io/polaris/
Apache License 2.0
82 stars 4 forks source link

PolarisHubSettings does not play well with other .env files #201

Open ThomasRochefortB opened 1 week ago

ThomasRochefortB commented 1 week ago

Polaris version

0.7.9

Python Version

3.12.5

Operating System

MacOS

Installation

Micromamba

Description

Hello!

I am running polaris from a directory that has a .env file to store other API keys. When I try to do so, the PolarisHubSettings class is trying to read from the .env file and throws the error:

ValidationError: 3 validation errors for PolarisHubSettings
is_local
  Extra inputs are not permitted [type=extra_forbidden, input_value='true', input_type=str]
    For further information visit https://errors.pydantic.dev/2.9/v/extra_forbidden
wandb_api_key
  Extra inputs are not permitted [type=extra_forbidden, input_value='wandb_api_key_obfuscated', input_type=str]
    For further information visit https://errors.pydantic.dev/2.9/v/extra_forbidden
model_name
  Extra inputs are not permitted [type=extra_forbidden, input_value='model-v0', input_type=str]
    For further information visit https://errors.pydantic.dev/2.9/v/extra_forbidden

This is caused by pydantic which by default does not allow extra argument.

I am going around this problem by moving directory or moving the .env file before using Polaris.

Thank you for the help!

Steps to reproduce

Write a .env file with some random stuff/ fake API keys. Run polaris login from this folder.

Additional output

  Name                              Version       Build                 Channel    
─────────────────────────────────────────────────────────────────────────────────────
  annotated-types                   0.7.0         pyhd8ed1ab_0          conda-forge
  anyio                             4.4.0         pyhd8ed1ab_0          conda-forge
  asciitree                         0.3.3         py_2                  conda-forge
  authlib                           1.3.0         pyhd8ed1ab_0          conda-forge
  aws-c-auth                        0.7.31        hc27b277_0            conda-forge
  aws-c-cal                         0.7.4         h41dd001_1            conda-forge
  aws-c-common                      0.9.28        hd74edd7_0            conda-forge
  aws-c-compression                 0.2.19        h41dd001_1            conda-forge
  aws-c-event-stream                0.4.3         h40a8fc1_2            conda-forge
  aws-c-http                        0.8.10        hf5a2c8c_0            conda-forge
  aws-c-io                          0.14.18       hc3cb426_9            conda-forge
  aws-c-mqtt                        0.10.5        h3acc7b9_1            conda-forge
  aws-c-s3                          0.6.5         hd16c091_7            conda-forge
  aws-c-sdkutils                    0.1.19        h41dd001_3            conda-forge
  aws-checksums                     0.1.20        h41dd001_0            conda-forge
  aws-crt-cpp                       0.28.3        hfd2b498_3            conda-forge
  aws-sdk-cpp                       1.11.379      h0455a66_11           conda-forge
  azure-core-cpp                    1.13.0        hd01fc5c_0            conda-forge
  azure-identity-cpp                1.8.0         h13ea094_2            conda-forge
  azure-storage-blobs-cpp           12.12.0       hfde595f_0            conda-forge
  azure-storage-common-cpp          12.7.0        hcf3b6fd_1            conda-forge
  azure-storage-files-datalake-cpp  12.11.0       h082e32e_1            conda-forge
  brotli                            1.1.0         hd74edd7_2            conda-forge
  brotli-bin                        1.1.0         hd74edd7_2            conda-forge
  brotli-python                     1.1.0         py312hde4cb15_2       conda-forge
  bzip2                             1.0.8         h99b78c6_7            conda-forge
  c-ares                            1.33.1        hd74edd7_0            conda-forge
  ca-certificates                   2024.8.30     hf0a4a13_0            conda-forge
  cairo                             1.18.0        hb4a6bf7_3            conda-forge
  certifi                           2024.8.30     pyhd8ed1ab_0          conda-forge
  cffi                              1.17.1        py312h0fad829_0       conda-forge
  chardet                           5.2.0         py312h81bd7bf_2       conda-forge
  charset-normalizer                3.3.2         pyhd8ed1ab_0          conda-forge
  click                             8.1.7         unix_pyh707e725_0     conda-forge
  colorama                          0.4.6         pyhd8ed1ab_0          conda-forge
  contourpy                         1.3.0         py312h6142ec9_1       conda-forge
  cryptography                      43.0.1        py312h3ddc590_0       conda-forge
  cycler                            0.12.1        pyhd8ed1ab_0          conda-forge
  datamol                           0.12.5        pyhd8ed1ab_0          conda-forge
  exceptiongroup                    1.2.2         pyhd8ed1ab_0          conda-forge
  expat                             2.6.3         hf9b8971_0            conda-forge
  fasteners                         0.17.3        pyhd8ed1ab_0          conda-forge
  filelock                          3.16.0        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_2            conda-forge
  fontconfig                        2.14.2        h82840c6_0            conda-forge
  fonts-conda-ecosystem             1             0                     conda-forge
  fonts-conda-forge                 1             0                     conda-forge
  fonttools                         4.53.1        py312h024a12e_1       conda-forge
  freetype                          2.12.1        hadb7bae_2            conda-forge
  freetype-py                       2.3.0         pyhd8ed1ab_0          conda-forge
  fsspec                            2024.9.0      pyhff2d567_0          conda-forge
  gflags                            2.2.2         hf9b8971_1005         conda-forge
  glog                              0.7.1         heb240a5_0            conda-forge
  greenlet                          3.1.0         py312hde4cb15_2       conda-forge
  h11                               0.14.0        pyhd8ed1ab_0          conda-forge
  h2                                4.1.0         pyhd8ed1ab_0          conda-forge
  hpack                             4.0.0         pyh9f0ad1d_0          conda-forge
  httpcore                          1.0.5         pyhd8ed1ab_0          conda-forge
  httpx                             0.27.2        pyhd8ed1ab_0          conda-forge
  hyperframe                        6.0.1         pyhd8ed1ab_0          conda-forge
  icu                               75.1          hfee45f7_0            conda-forge
  idna                              3.10          pyhd8ed1ab_0          conda-forge
  importlib_resources               6.4.5         pyhd8ed1ab_0          conda-forge
  joblib                            1.4.2         pyhd8ed1ab_0          conda-forge
  kiwisolver                        1.4.7         py312h6142ec9_0       conda-forge
  krb5                              1.21.3        h237132a_0            conda-forge
  lcms2                             2.16          ha0e7c42_0            conda-forge
  lerc                              4.0.0         h9a09cb3_0            conda-forge
  libabseil                         20240116.2    cxx17_h00cdb27_1      conda-forge
  libarrow                          17.0.0        h3ba790a_15_cpu       conda-forge
  libarrow-acero                    17.0.0        hf9b8971_15_cpu       conda-forge
  libarrow-dataset                  17.0.0        hf9b8971_15_cpu       conda-forge
  libarrow-substrait                17.0.0        hbf8b706_15_cpu       conda-forge
  libblas                           3.9.0         23_osxarm64_openblas  conda-forge
  libboost                          1.84.0        h29978a0_6            conda-forge
  libboost-python                   1.84.0        py312h707656b_6       conda-forge
  libbrotlicommon                   1.1.0         hd74edd7_2            conda-forge
  libbrotlidec                      1.1.0         hd74edd7_2            conda-forge
  libbrotlienc                      1.1.0         hd74edd7_2            conda-forge
  libcblas                          3.9.0         23_osxarm64_openblas  conda-forge
  libcrc32c                         1.1.2         hbdafb3b_0            conda-forge
  libcurl                           8.10.0        h13a7ad3_0            conda-forge
  libcxx                            18.1.8        h3ed4263_7            conda-forge
  libdeflate                        1.21          h99b78c6_0            conda-forge
  libedit                           3.1.20191231  hc8eb9b7_2            conda-forge
  libev                             4.33          h93a5062_2            conda-forge
  libevent                          2.1.12        h2757513_1            conda-forge
  libexpat                          2.6.3         hf9b8971_0            conda-forge
  libffi                            3.4.2         h3422bc3_5            conda-forge
  libgfortran                       5.0.0         13_2_0_hd922786_3     conda-forge
  libgfortran5                      13.2.0        hf226fd6_3            conda-forge
  libglib                           2.80.3        h59d46d9_2            conda-forge
  libgoogle-cloud                   2.29.0        hfa33a2f_0            conda-forge
  libgoogle-cloud-storage           2.29.0        h90fd6fa_0            conda-forge
  libgrpc                           1.62.2        h9c18a4f_0            conda-forge
  libiconv                          1.17          h0d3ecfb_2            conda-forge
  libintl                           0.22.5        h8414b35_3            conda-forge
  libjpeg-turbo                     3.0.0         hb547adb_1            conda-forge
  liblapack                         3.9.0         23_osxarm64_openblas  conda-forge
  libnghttp2                        1.58.0        ha4dd798_1            conda-forge
  libopenblas                       0.3.27        openmp_h517c56d_1     conda-forge
  libparquet                        17.0.0        hf0ba9ef_15_cpu       conda-forge
  libpng                            1.6.44        hc14010f_0            conda-forge
  libpq                             16.4          h671472c_1            conda-forge
  libprotobuf                       4.25.3        hbfab5d5_0            conda-forge
  librdkit                          2024.03.5     h54a62e4_3            conda-forge
  libre2-11                         2023.09.01    h7b2c953_2            conda-forge
  libsqlite                         3.46.1        hc14010f_0            conda-forge
  libssh2                           1.11.0        h7a5bd25_0            conda-forge
  libthrift                         0.20.0        h64651cc_1            conda-forge
  libtiff                           4.6.0         hf8409c0_4            conda-forge
  libutf8proc                       2.8.0         h1a8c8d9_0            conda-forge
  libwebp-base                      1.4.0         h93a5062_0            conda-forge
  libxcb                            1.16          hc9fafa5_1            conda-forge
  libxml2                           2.12.7        h01dff8b_4            conda-forge
  libzlib                           1.3.1         hfb2fe0b_1            conda-forge
  llvm-openmp                       18.1.8        hde57baf_1            conda-forge
  loguru                            0.7.2         py312h81bd7bf_2       conda-forge
  lz4-c                             1.9.4         hb7217d7_0            conda-forge
  markdown-it-py                    3.0.0         pyhd8ed1ab_0          conda-forge
  matplotlib-base                   3.9.2         py312h9bd0bc6_1       conda-forge
  mdurl                             0.1.2         pyhd8ed1ab_0          conda-forge
  msgpack-python                    1.1.0         py312h6142ec9_0       conda-forge
  munkres                           1.1.4         pyh9f0ad1d_0          conda-forge
  ncurses                           6.5           h7bae524_1            conda-forge
  numcodecs                         0.13.0        py312h8ae5369_0       conda-forge
  numpy                             1.26.4        py312h8442bc7_0       conda-forge
  openjpeg                          2.5.2         h9f1df11_0            conda-forge
  openssl                           3.3.2         h8359307_0            conda-forge
  orc                               2.0.2         h75dedd0_0            conda-forge
  packaging                         24.1          pyhd8ed1ab_0          conda-forge
  pandas                            2.1.4         py312h9e53831_0       conda-forge
  patsy                             0.5.6         pyhd8ed1ab_0          conda-forge
  pcre2                             10.44         h297a79d_2            conda-forge
  pillow                            10.4.0        py312h8609ca0_1       conda-forge
  pip                               24.2          pyh8b19718_1          conda-forge
  pixman                            0.43.4        hebf3989_0            conda-forge
  platformdirs                      4.3.3         pyhd8ed1ab_0          conda-forge
  polaris                           0.7.9         pyhecae5ae_0          conda-forge
  pthread-stubs                     0.4           h27ca646_1001         conda-forge
  pyarrow                           17.0.0        py312ha814d7c_1       conda-forge
  pyarrow-core                      17.0.0        py312he20ac61_1_cpu   conda-forge
  pycairo                           1.27.0        py312h798cee4_0       conda-forge
  pycparser                         2.22          pyhd8ed1ab_0          conda-forge
  pydantic                          2.9.2         pyhd8ed1ab_0          conda-forge
  pydantic-core                     2.23.4        py312he431725_0       conda-forge
  pydantic-settings                 2.5.2         pyhd8ed1ab_0          conda-forge
  pygments                          2.18.0        pyhd8ed1ab_0          conda-forge
  pyparsing                         3.1.4         pyhd8ed1ab_0          conda-forge
  pysocks                           1.7.1         pyha2e5f31_6          conda-forge
  python                            3.12.6        h739c21a_0_cpython    conda-forge
  python-dateutil                   2.9.0         pyhd8ed1ab_0          conda-forge
  python-dotenv                     1.0.1         pyhd8ed1ab_0          conda-forge
  python-tzdata                     2024.1        pyhd8ed1ab_0          conda-forge
  python_abi                        3.12          5_cp312               conda-forge
  pytz                              2024.2        pyhd8ed1ab_0          conda-forge
  pyyaml                            6.0.2         py312h024a12e_1       conda-forge
  qhull                             2020.2        h420ef59_5            conda-forge
  rdkit                             2024.03.5     py312h619ea94_3       conda-forge
  re2                               2023.09.01    h4cba328_2            conda-forge
  readline                          8.2           h92ec313_1            conda-forge
  reportlab                         4.2.2         py312h024a12e_1       conda-forge
  requests                          2.32.3        pyhd8ed1ab_0          conda-forge
  rich                              13.8.1        pyhd8ed1ab_0          conda-forge
  rlpycairo                         0.2.0         pyhd8ed1ab_0          conda-forge
  scikit-learn                      1.5.2         py312h387f99c_1       conda-forge
  scipy                             1.14.1        py312heb3a901_0       conda-forge
  seaborn                           0.13.2        hd8ed1ab_2            conda-forge
  seaborn-base                      0.13.2        pyhd8ed1ab_2          conda-forge
  selfies                           2.1.1         pyhd8ed1ab_0          conda-forge
  setuptools                        73.0.1        pyhd8ed1ab_0          conda-forge
  shellingham                       1.5.4         pyhd8ed1ab_0          conda-forge
  six                               1.16.0        pyh6c4a22f_0          conda-forge
  snappy                            1.2.1         hd02b534_0            conda-forge
  sniffio                           1.3.1         pyhd8ed1ab_0          conda-forge
  sqlalchemy                        2.0.35        py312h024a12e_0       conda-forge
  statsmodels                       0.14.3        py312h755e627_0       conda-forge
  tenacity                          9.0.0         pyhd8ed1ab_0          conda-forge
  termcolor                         2.4.0         pyhd8ed1ab_0          conda-forge
  threadpoolctl                     3.5.0         pyhc1e730c_0          conda-forge
  tk                                8.6.13        h5083fa2_1            conda-forge
  tqdm                              4.66.5        pyhd8ed1ab_0          conda-forge
  typer                             0.12.5        pyhd8ed1ab_0          conda-forge
  typer-slim                        0.12.5        pyhd8ed1ab_0          conda-forge
  typer-slim-standard               0.12.5        hd8ed1ab_0            conda-forge
  typing-extensions                 4.12.2        hd8ed1ab_0            conda-forge
  typing_extensions                 4.12.2        pyha770c72_0          conda-forge
  tzdata                            2024a         h8827d51_1            conda-forge
  urllib3                           2.2.3         pyhd8ed1ab_0          conda-forge
  wheel                             0.44.0        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
  yaspin                            2.2.0         pyhd8ed1ab_0          conda-forge
  zarr                              2.18.3        pyhd8ed1ab_0          conda-forge
  zipp                              3.20.2        pyhd8ed1ab_0          conda-forge
  zlib                              1.3.1         hfb2fe0b_1            conda-forge
  zstandard                         0.23.0        py312h15fbf35_1       conda-forge
  zstd                              1.5.6         hb46c0d2_0            conda-forge