Update environment.yml

environment.yml

@@ -1,175 +1,23 @@
 name: FusionDTI
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
   - defaults
 dependencies:
+  - python=3.8
   - flask
-  - appnope=0.1.2=py38hca03da5_1001
-  - aria2=1.37.0=hfa5e12f_2
-  - asttokens=2.0.5=pyhd3eb1b0_0
-  - backcall=0.2.0=pyhd3eb1b0_0
-  - biopython=1.79=py38hb991d35_3
-  - bzip2=1.0.8=h99b78c6_7
-  - c-ares=1.34.5=h5505292_0
-  - ca-certificates=2025.4.26=hbd8a1cb_0
-  - decorator=5.1.1=pyhd3eb1b0_0
-  - executing=0.8.3=pyhd3eb1b0_0
-  - foldseek=10.941cd33=h45d0289_1
-  - gawk=5.3.1=h8a92848_0
-  - gmp=6.3.0=h7bae524_2
-  - icu=75.1=hfee45f7_0
-  - ipython=8.12.2=py38hca03da5_0
-  - jedi=0.18.1=py38hca03da5_1
-  - libasprintf=0.24.1=h493aca8_0
-  - libblas=3.9.0=31_h10e41b3_openblas
-  - libcblas=3.9.0=31_hb3479ef_openblas
-  - libcxx=20.1.5=ha82da77_0
-  - libffi=3.4.4=hca03da5_1
-  - libgettextpo=0.24.1=h493aca8_0
-  - libgfortran=14.2.0=heb5dd2a_105
-  - libgfortran5=14.2.0=h2c44a93_105
-  - libiconv=1.18=hfe07756_1
-  - libintl=0.24.1=h493aca8_0
-  - liblapack=3.9.0=31_hc9a63f6_openblas
-  - libopenblas=0.3.29=openmp_hf332438_0
-  - libsqlite=3.49.2=h3f77e49_0
-  - libssh2=1.11.1=h1590b86_0
-  - libxml2=2.12.7=h01dff8b_4
-  - libzlib=1.3.1=h8359307_2
-  - llvm-openmp=20.1.5=hdb05f8b_0
-  - matplotlib-inline=0.1.6=py38hca03da5_0
-  - mpfr=4.2.1=hb693164_3
-  - ncurses=6.5=h5e97a16_3
-  - openssl=3.5.0=h81ee809_1
-  - parso=0.8.3=pyhd3eb1b0_0
-  - pexpect=4.8.0=pyhd3eb1b0_3
-  - pickleshare=0.7.5=pyhd3eb1b0_1003
-  - pip=24.0=py38hca03da5_0
-  - prompt-toolkit=3.0.43=py38hca03da5_0
-  - ptyprocess=0.7.0=pyhd3eb1b0_2
-  - pure_eval=0.2.2=pyhd3eb1b0_0
-  - python=3.8.20=h7d35d02_2_cpython
-  - python_abi=3.8=6_cp38
-  - readline=8.2=h1a28f6b_0
-  - setuptools=69.5.1=py38hca03da5_0
-  - six=1.16.0=pyhd3eb1b0_1
-  - stack_data=0.2.0=pyhd3eb1b0_0
-  - tk=8.6.13=h5083fa2_1
-  - traitlets=5.14.3=py38hca03da5_0
-  - typing_extensions=4.11.0=py38hca03da5_0
-  - wcwidth=0.2.5=pyhd3eb1b0_0
-  - wheel=0.43.0=py38hca03da5_0
-  - xz=5.4.6=h80987f9_1
-  - zlib=1.3.1=h8359307_2
+  - torch
+  - transformers
+  - matplotlib
+  - biopython
+  - pandas
+  - numpy
+  - scikit-learn
+  - rdkit
+  - selfies
+  - pip
   - pip:
-      - aiofiles==23.2.1
-      - altair==5.3.0
-      - annotated-types==0.7.0
-      - anyio==4.4.0
-      - attrs==23.2.0
-      - bertviz==1.4.0
-      - blinker==1.8.2
-      - boto3==1.34.126
-      - botocore==1.34.126
-      - certifi==2024.6.2
-      - charset-normalizer==3.3.2
-      - click==8.1.7
-      - contourpy==1.1.1
-      - cycler==0.12.1
-      - dill==0.4.0
-      - dnspython==2.6.1
-      - docker-pycreds==0.4.0
-      - email-validator==2.1.1
-      - exceptiongroup==1.2.1
-      - fastapi==0.111.0
-      - fastapi-cli==0.0.4
-      - ffmpy==0.3.2
-      - filelock==3.15.1
-      - flask==3.0.3
-      - fonttools==4.53.0
-      - fsspec==2024.6.0
-      - gitdb==4.0.11
-      - gitpython==3.1.43
-      - gradio==4.36.1
-      - gradio-client==1.0.1
-      - h11==0.14.0
-      - httpcore==1.0.5
-      - httptools==0.6.1
-      - httpx==0.27.0
-      - huggingface-hub==0.23.4
-      - idna==3.7
-      - importlib-metadata==7.1.0
-      - importlib-resources==6.4.0
-      - itsdangerous==2.2.0
-      - jinja2==3.1.4
-      - jmespath==1.0.1
-      - jsonschema==4.22.0
-      - jsonschema-specifications==2023.12.1
-      - kiwisolver==1.4.5
-      - markdown-it-py==3.0.0
-      - markupsafe==2.1.5
-      - matplotlib==3.7.5
-      - mdurl==0.1.2
-      - mpmath==1.3.0
-      - networkx==3.1
-      - numpy==1.24.4
-      - orjson==3.10.5
-      - packaging==24.1
-      - pandarallel==1.6.5
-      - pandas==2.0.3
-      - pillow==10.3.0
-      - pkgutil-resolve-name==1.3.10
-      - platformdirs==4.2.2
-      - protobuf==5.27.1
-      - psutil==5.9.8
-      - pydantic==2.7.4
-      - pydantic-core==2.18.4
-      - pydub==0.25.1
-      - pygments==2.18.0
-      - pyparsing==3.1.2
-      - python-dateutil==2.9.0.post0
-      - python-dotenv==1.0.1
-      - python-multipart==0.0.9
-      - pytz==2024.1
-      - pyyaml==6.0.1
-      - rdkit-pypi==2022.9.5
-      - referencing==0.35.1
-      - regex==2024.5.15
-      - requests==2.32.3
-      - rich==13.7.1
-      - rpds-py==0.18.1
-      - ruff==0.4.9
-      - s3transfer==0.10.1
-      - safetensors==0.4.3
-      - selfies==2.2.0
-      - semantic-version==2.10.0
-      - sentencepiece==0.2.0
-      - sentry-sdk==2.5.1
-      - setproctitle==1.3.3
-      - shellingham==1.5.4
-      - smmap==5.0.1
-      - sniffio==1.3.1
-      - starlette==0.37.2
-      - sympy==1.12.1
-      - tokenizers==0.19.1
-      - tomlkit==0.12.0
-      - toolz==0.12.1
-      - torch==2.3.1
-      - tqdm==4.66.4
-      - transformers==4.41.2
-      - typer==0.12.3
-      - typing-extensions==4.12.2
-      - tzdata==2024.1
-      - ujson==5.10.0
-      - urllib3==2.2.1
-      - uvicorn==0.30.1
-      - uvloop==0.19.0
-      - wandb==0.17.1
-      - watchfiles==0.22.0
-      - websockets==11.0.3
-      - werkzeug==3.0.3
-      - zipp==3.19.2
-prefix: /Applications/anaconda3/envs/FusionDTI
+      - ipython
+