############################
# Core ML & Scientific Stack
############################
torch~=2.8.0
torchvision
torchaudio
torch-cluster
torch-geometric
torch-scatter
numpy~=2.2.5
scipy>=1.12.0
pandas>=1.3.0
scikit-learn>=0.24.0
numexpr
bottleneck
numba
llvmlite
einops>=0.4.0
performer-pytorch
axial-positional-embedding
local-attention
fair-esm
rna-fm
pytorch-lightning
pytorch-ignite>=0.4.6
torchmetrics
torchsummary
qmllib

############################
# Bioinformatics / Sequence Models
############################
biopython~=1.85
biotite
mygene>=3.2.0
biothings-client>=0.2.0
tape-proteins

############################
# NLP / Transformer Ecosystem
############################
transformers
tokenizers
huggingface-hub
sacremoses
regex
protobuf
filelock
dm-tree

############################
# Configuration / Structured Config
############################
hydra-core>=1.0.0
omegaconf>=2.0.0
pydantic>=2.5.0
pydantic-settings>=2.1.0
python-box>=6.0.0
ml-collections>=0.1.0

############################
# Visualization & Plotting
############################
matplotlib>=3.5.0
seaborn
pillow>=9.0.0
contourpy>=1.0.0
cycler>=0.11.0
fonttools>=4.30.0

############################
# Jupyter / Notebook Environment
############################
ipykernel
ipython
jupyter
jupyter-client
jupyter-console
jupyter-core
jupyterlab-widgets
widgetsnbextension
ipywidgets
nbclient
nbconvert
nbformat
nest-asyncio
prometheus-client
pygments
jupyterlab
jupytext
ipympl

############################
# Web / Network / Auth
############################
requests>=2.26.0
aiohttp>=3.8.0
yarl
frozenlist
aiosignal
async-timeout
charset-normalizer>=2.0.0
idna>=3.0
urllib3>=1.26.0
google-auth>=1.34.0
google-auth-oauthlib
oauthlib
requests-oauthlib
s3transfer
boto3
botocore
rsa
pyopenssl
cryptography
pysocks

############################
# Data / I-O / Extended
############################
lxml
pandas-datareader
opencv-python
pyyaml>=6.0.0

############################
# Utilities / Core Helpers
############################
packaging>=21.0
pyparsing>=3.0.0
python-dateutil>=2.8.0
six>=1.15.0
joblib>=1.0.0
tabulate>=0.8.9
colorama>=0.4.4
contextlib2>=21.0.0
psutil
typing-extensions
future
attrs
more-itertools
pluggy
py
cachetools
importlib-metadata
importlib-resources
setuptools
wheel
openmm
huggingface_hub
hf_xet
requests>=2.25.0
beautifulsoup4>=4.9.0
tqdm>=4.60.0

############################
# Jupyter Security / Sanitization
############################
bleach
defusedxml
webencodings
markdown
mistune
jsonschema
pyrsistent
pandocfilters
send2trash
terminado
testpath

############################
# Dev / QA / Tooling
############################
tqdm>=4.62.0
absl-py>=1.0.0
tensorboard>=2.6.0
tensorboard-data-server>=0.6.0
tensorboard-plugin-wit>=1.8.0
tensorboardx
mypy
mypy-extensions
typed-ast
flake8
pycodestyle
pyflakes
autopep8
pytest
ipython-genutils
jedi
parso
jmespath
decorator
entrypoints
prompt-toolkit
traitlets
wcwidth
monkeytype
pre-commit
pylint
pytest-cov
build
twine

############################
# Low-level / C Extensions
############################
cffi
pycparser
cython
