SwiftSeal / resistify

Resistify is a program which rapidly identifies and classifies plant resistance genes from protein sequences. It is designed to be lightweight and easy to use.
GNU General Public License v3.0
26 stars 2 forks source link

Relax dependencies? #26

Closed SwiftSeal closed 2 days ago

SwiftSeal commented 3 days ago

scikit-learn dependency initially set as strict due to InconsistentVersionWarning warnings. Tests indicate not an issue - removing this restriction would greatly reduce "strictness". Also need to check transformers dependency for similar.

SwiftSeal commented 3 days ago

Following env works fine? apart from scikit-learn crying

  Name                              Version       Build                      Channel    
──────────────────────────────────────────────────────────────────────────────────────────
  _libgcc_mutex                     0.1           conda_forge                conda-forge
  _openmp_mutex                     4.5           2_kmp_llvm                 conda-forge
  aiohappyeyeballs                  2.4.3         pyhd8ed1ab_0               conda-forge
  aiohttp                           3.11.8        py312h178313f_0            conda-forge
  aiosignal                         1.3.1         pyhd8ed1ab_0               conda-forge
  antlr-python-runtime              4.9.3         pyhd8ed1ab_1               conda-forge
  attrs                             24.2.0        pyh71513ae_0               conda-forge
  aws-c-auth                        0.8.0         hb88c0a9_10                conda-forge
  aws-c-cal                         0.8.0         hecf86a2_2                 conda-forge
  aws-c-common                      0.10.3        hb9d3cd8_0                 conda-forge
  aws-c-compression                 0.3.0         hf42f96a_2                 conda-forge
  aws-c-event-stream                0.5.0         h1ffe551_7                 conda-forge
  aws-c-http                        0.9.1         hab05fe4_2                 conda-forge
  aws-c-io                          0.15.2        hdeadb07_2                 conda-forge
  aws-c-mqtt                        0.11.0        h7bd072d_8                 conda-forge
  aws-c-s3                          0.7.2         h3a84f74_0                 conda-forge
  aws-c-sdkutils                    0.2.1         hf42f96a_1                 conda-forge
  aws-checksums                     0.2.2         hf42f96a_1                 conda-forge
  aws-crt-cpp                       0.29.5        h0e61686_1                 conda-forge
  aws-sdk-cpp                       1.11.449      hdaa582e_3                 conda-forge
  azure-core-cpp                    1.14.0        h5cfcd09_0                 conda-forge
  azure-identity-cpp                1.10.0        h113e628_0                 conda-forge
  azure-storage-blobs-cpp           12.13.0       h3cf044e_1                 conda-forge
  azure-storage-common-cpp          12.8.0        h736e048_1                 conda-forge
  azure-storage-files-datalake-cpp  12.12.0       ha633028_1                 conda-forge
  biopython                         1.84          py312h9a8786e_0            conda-forge
  biotite                           1.0.1         py312hca68cad_0            conda-forge
  biotraj                           1.2.2         py312h2ec8cdc_0            conda-forge
  brotli-python                     1.1.0         py312h2ec8cdc_2            conda-forge
  bzip2                             1.0.8         h4bc722e_7                 conda-forge
  c-ares                            1.34.3        hb9d3cd8_1                 conda-forge
  ca-certificates                   2024.8.30     hbcca054_0                 conda-forge
  certifi                           2024.8.30     pyhd8ed1ab_0               conda-forge
  cffi                              1.17.1        py312h06ac9bb_0            conda-forge
  charset-normalizer                3.4.0         pyhd8ed1ab_0               conda-forge
  colorama                          0.4.6         pyhd8ed1ab_0               conda-forge
  coverage                          7.6.8         py312h178313f_0            conda-forge
  cpython                           3.12.7        py312hd8ed1ab_0            conda-forge
  datasets                          3.1.0         pyhff2d567_0               conda-forge
  dill                              0.3.8         pyhd8ed1ab_0               conda-forge
  exceptiongroup                    1.2.2         pyhd8ed1ab_0               conda-forge
  fair-esm                          2.0.0         pyhd8ed1ab_0               conda-forge
  filelock                          3.16.1        pyhd8ed1ab_0               conda-forge
  frozenlist                        1.5.0         py312h66e93f0_0            conda-forge
  fsspec                            2024.9.0      pyhff2d567_0               conda-forge
  gflags                            2.2.2         h5888daf_1005              conda-forge
  glog                              0.7.1         hbabe93e_0                 conda-forge
  gmp                               6.3.0         hac33072_2                 conda-forge
  gmpy2                             2.1.5         py312h7201bc8_2            conda-forge
  googledrivedownloader             0.4           pyhd3deb0d_1               conda-forge
  h2                                4.1.0         pyhd8ed1ab_0               conda-forge
  hmmer                             3.4           hdbdd923_2                 bioconda   
  hpack                             4.0.0         pyh9f0ad1d_0               conda-forge
  huggingface_hub                   0.26.2        pyh0610db2_0               conda-forge
  hyperframe                        6.0.1         pyhd8ed1ab_0               conda-forge
  idna                              3.10          pyhd8ed1ab_0               conda-forge
  iniconfig                         2.0.0         pyhd8ed1ab_0               conda-forge
  isodate                           0.7.2         pyhd8ed1ab_0               conda-forge
  jinja2                            3.1.4         pyhd8ed1ab_0               conda-forge
  joblib                            1.4.2         pyhd8ed1ab_0               conda-forge
  keyutils                          1.6.1         h166bdaf_0                 conda-forge
  krb5                              1.21.3        h659f571_0                 conda-forge
  ld_impl_linux-64                  2.43          h712a8e2_2                 conda-forge
  libabseil                         20240722.0    cxx17_h5888daf_1           conda-forge
  libarrow                          18.1.0        h94eee4b_0_cpu             conda-forge
  libarrow-acero                    18.1.0        h5888daf_0_cpu             conda-forge
  libarrow-dataset                  18.1.0        h5888daf_0_cpu             conda-forge
  libarrow-substrait                18.1.0        h5c8f2c3_0_cpu             conda-forge
  libblas                           3.9.0         25_linux64_openblas        conda-forge
  libbrotlicommon                   1.1.0         hb9d3cd8_2                 conda-forge
  libbrotlidec                      1.1.0         hb9d3cd8_2                 conda-forge
  libbrotlienc                      1.1.0         hb9d3cd8_2                 conda-forge
  libcblas                          3.9.0         25_linux64_openblas        conda-forge
  libcrc32c                         1.1.2         h9c3ff4c_0                 conda-forge
  libcurl                           8.10.1        hbbe4b11_0                 conda-forge
  libedit                           3.1.20191231  he28a2e2_2                 conda-forge
  libev                             4.33          hd590300_2                 conda-forge
  libevent                          2.1.12        hf998b51_1                 conda-forge
  libexpat                          2.6.4         h5888daf_0                 conda-forge
  libffi                            3.4.2         h7f98852_5                 conda-forge
  libgcc                            14.2.0        h77fa898_1                 conda-forge
  libgcc-ng                         14.2.0        h69a702a_1                 conda-forge
  libgfortran                       14.2.0        h69a702a_1                 conda-forge
  libgfortran5                      14.2.0        hd5240d6_1                 conda-forge
  libgoogle-cloud                   2.31.0        h804f50b_0                 conda-forge
  libgoogle-cloud-storage           2.31.0        h0121fbd_0                 conda-forge
  libgrpc                           1.67.1        hc2c308b_0                 conda-forge
  libhwloc                          2.11.1        default_hecaa2ac_1000      conda-forge
  libiconv                          1.17          hd590300_2                 conda-forge
  liblapack                         3.9.0         25_linux64_openblas        conda-forge
  libnghttp2                        1.64.0        h161d5f1_0                 conda-forge
  libnsl                            2.0.1         hd590300_0                 conda-forge
  libopenblas                       0.3.28        pthreads_h94d23a6_1        conda-forge
  libparquet                        18.1.0        h6bd9018_0_cpu             conda-forge
  libprotobuf                       5.28.2        h5b01275_0                 conda-forge
  libre2-11                         2024.07.02    hbbce691_1                 conda-forge
  libsentencepiece                  0.2.0         h413892a_9                 conda-forge
  libsqlite                         3.47.0        hadc24fc_1                 conda-forge
  libssh2                           1.11.1        hf672d98_0                 conda-forge
  libstdcxx                         14.2.0        hc0a3c3a_1                 conda-forge
  libstdcxx-ng                      14.2.0        h4852527_1                 conda-forge
  libthrift                         0.21.0        h0e7cc3e_0                 conda-forge
  libtorch                          2.5.1         cpu_mkl_hb9d73ce_103       conda-forge
  libutf8proc                       2.8.0         h166bdaf_0                 conda-forge
  libuuid                           2.38.1        h0b41bf4_0                 conda-forge
  libuv                             1.49.2        hb9d3cd8_0                 conda-forge
  libxcrypt                         4.4.36        hd590300_1                 conda-forge
  libxml2                           2.13.5        h064dc61_0                 conda-forge
  libzlib                           1.3.1         hb9d3cd8_2                 conda-forge
  llvm-openmp                       19.1.4        h024ca30_0                 conda-forge
  lz4-c                             1.9.4         hcb278e6_0                 conda-forge
  markdown-it-py                    3.0.0         pyhd8ed1ab_0               conda-forge
  markupsafe                        3.0.2         py312h178313f_0            conda-forge
  mdurl                             0.1.2         pyhd8ed1ab_0               conda-forge
  mkl                               2024.2.2      ha957f24_16                conda-forge
  mpc                               1.3.1         h24ddda3_1                 conda-forge
  mpfr                              4.2.1         h90cbb55_3                 conda-forge
  mpmath                            1.3.0         pyhd8ed1ab_0               conda-forge
  msgpack-python                    1.1.0         py312h68727a3_0            conda-forge
  multidict                         6.1.0         py312h178313f_1            conda-forge
  multiprocess                      0.70.16       py312h66e93f0_1            conda-forge
  ncurses                           6.5           he02047a_1                 conda-forge
  networkx                          3.4.2         pyh267e887_2               conda-forge
  numpy                             2.1.3         py312h58c1407_0            conda-forge
  omegaconf                         2.3.0         pyhd8ed1ab_0               conda-forge
  openssl                           3.4.0         hb9d3cd8_0                 conda-forge
  orc                               2.0.3         he039a57_0                 conda-forge
  packaging                         24.2          pyhff2d567_1               conda-forge
  pandas                            2.2.3         py312hf9745cd_1            conda-forge
  pip                               24.3.1        pyh8b19718_0               conda-forge
  pluggy                            1.5.0         pyhd8ed1ab_0               conda-forge
  propcache                         0.2.0         py312h66e93f0_2            conda-forge
  pyarrow                           18.1.0        py312h7900ff3_0            conda-forge
  pyarrow-core                      18.1.0        py312h01725c0_0_cpu        conda-forge
  pycparser                         2.22          pyhd8ed1ab_0               conda-forge
  pygments                          2.18.0        pyhd8ed1ab_0               conda-forge
  pyparsing                         3.2.0         pyhd8ed1ab_1               conda-forge
  pysocks                           1.7.1         pyha2e5f31_6               conda-forge
  pytest                            8.3.3         pyhd8ed1ab_0               conda-forge
  pytest-cov                        6.0.0         pyhd8ed1ab_0               conda-forge
  python                            3.12.7        hc5c86c4_0_cpython         conda-forge
  python-dateutil                   2.9.0.post0   pyhff2d567_0               conda-forge
  python-tzdata                     2024.2        pyhd8ed1ab_0               conda-forge
  python-wget                       3.2           py_0                       conda-forge
  python-xxhash                     3.5.0         py312h66e93f0_1            conda-forge
  python_abi                        3.12          5_cp312                    conda-forge
  pytorch                           2.5.1         cpu_mkl_py312h01fbe9c_103  conda-forge
  pytorch_geometric                 2.1.0.post1   pyhd8ed1ab_0               conda-forge
  pytorch_scatter                   2.1.2         cpu_py312hb813311_9        conda-forge
  pytorch_sparse                    0.6.18        py312hb813311_5            conda-forge
  pytz                              2024.1        pyhd8ed1ab_0               conda-forge
  pyyaml                            6.0.2         py312h66e93f0_1            conda-forge
  rdflib                            7.1.1         pyh0610db2_0               conda-forge
  re2                               2024.07.02    h77b4e00_1                 conda-forge
  readline                          8.2           h8228510_1                 conda-forge
  regex                             2024.11.6     py312h66e93f0_0            conda-forge
  requests                          2.32.3        pyhd8ed1ab_0               conda-forge
  rich                              13.9.4        pyhd8ed1ab_0               conda-forge
  rich-argparse                     1.6.0         pyhd8ed1ab_0               conda-forge
  s2n                               1.5.9         h0fd0ee4_0                 conda-forge
  safetensors                       0.4.5         py312h12e396e_0            conda-forge
  scikit-learn                      1.5.2         py312h7a48858_1            conda-forge
  scipy                             1.14.1        py312h62794b6_1            conda-forge
  sentencepiece                     0.2.0         h7900ff3_9                 conda-forge
  sentencepiece-python              0.2.0         py312he5bdc40_9            conda-forge
  sentencepiece-spm                 0.2.0         h413892a_9                 conda-forge
  setuptools                        75.6.0        pyhff2d567_1               conda-forge
  six                               1.16.0        pyh6c4a22f_0               conda-forge
  sleef                             3.7           h1b44611_2                 conda-forge
  snappy                            1.2.1         ha2e4443_0                 conda-forge
  sympy                             1.13.3        pyh2585a3b_104             conda-forge
  tbb                               2021.13.0     h84d6215_0                 conda-forge
  threadpoolctl                     3.5.0         pyhc1e730c_0               conda-forge
  tk                                8.6.13        noxft_h4845f30_101         conda-forge
  tokenizers                        0.20.4        py312h8360d73_0            conda-forge
  toml                              0.10.2        pyhd8ed1ab_0               conda-forge
  tomli                             2.1.0         pyhff2d567_0               conda-forge
  torch-scatter                     2.1.1         py312hbc0f9b7_10           conda-forge
  tqdm                              4.67.1        pyhd8ed1ab_0               conda-forge
  transformers                      4.46.3        pyhd8ed1ab_0               conda-forge
  typing-extensions                 4.12.2        hd8ed1ab_0                 conda-forge
  typing_extensions                 4.12.2        pyha770c72_0               conda-forge
  tzdata                            2024b         hc8b5060_0                 conda-forge
  urllib3                           2.2.3         pyhd8ed1ab_0               conda-forge
  wheel                             0.45.1        pyhd8ed1ab_0               conda-forge
  xxhash                            0.8.2         hd590300_0                 conda-forge
  xz                                5.2.6         h166bdaf_0                 conda-forge
  yaml                              0.2.5         h7f98852_2                 conda-forge
  yarl                              1.18.0        py312h66e93f0_0            conda-forge
  zstandard                         0.23.0        py312hef9b889_1            conda-forge
  zstd                              1.5.6         ha6fb4c9_0                 conda-forge
SwiftSeal commented 2 days ago

yeah lets fix this - what's the WORST that could happen