requirements.lock

# generated by rye
# use `rye lock` or `rye sync` to update this lockfile
#
# last locked with the following flags:
#   pre: false
#   features: []
#   all-features: false
#   with-sources: false
#   generate-hashes: false
#   universal: false

-e file:.
absl-py==2.3.0
    # via tensorboard
aiohappyeyeballs==2.6.1
    # via aiohttp
aiohttp==3.12.2
    # via fsspec
aiosignal==1.3.2
    # via aiohttp
alembic==1.16.1
    # via optuna
altgraph==0.17.4
    # via macholib
    # via pyinstaller
annoy==1.17.3
    # via trimap
arrow==1.3.0
    # via rq-dashboard
astrochem-embedding @ git+https://github.com/aravindhnivas/astrochem_embedding.git@a7208ce3afb39eb0331e6164ab2ba6fa2487167c
    # via cxml-lib
asttokens==3.0.0
    # via stack-data
attrs==25.3.0
    # via aiohttp
    # via jsonschema
    # via referencing
bidict==0.23.1
    # via python-socketio
blinker==1.9.0
    # via flask
blosc2==3.3.4
    # via tables
bottle==0.13.3
    # via optuna-dashboard
catboost==1.2.8
    # via cxml-lib
certifi==2025.4.26
    # via requests
cfgv==3.4.0
    # via pre-commit
charset-normalizer==3.4.2
    # via requests
cleanlab==2.7.1
    # via cxml-lib
click==8.2.1
    # via astrochem-embedding
    # via dask
    # via distributed
    # via flask
    # via rq
cloudpickle==3.1.1
    # via dask
    # via dask-glm
    # via distributed
    # via shap
colorlog==6.9.0
    # via optuna
contourpy==1.3.2
    # via matplotlib
cycler==0.12.1
    # via matplotlib
dask==2025.5.1
    # via cxml-lib
    # via dask-glm
    # via dask-ml
    # via distributed
dask-glm==0.3.2
    # via dask-ml
dask-ml==2025.1.0
    # via cxml-lib
dbcv @ git+https://github.com/FelSiq/DBCV.git@13c3896ef78d12f1e3e1cbd394f2db9a09637ffd
    # via cxml-lib
decorator==5.2.1
    # via ipython
    # via scprep
deprecated==1.2.18
    # via graphtools
    # via phate
    # via tasklogger
dill==0.4.0
    # via multiprocess
    # via pathos
distlib==0.3.9
    # via virtualenv
distributed==2025.5.1
    # via dask-glm
    # via dask-ml
dnspython==2.7.0
    # via eventlet
eventlet==0.40.0
    # via cxml-lib
executing==2.2.0
    # via stack-data
fastjsonschema==2.21.1
    # via nbformat
filelock==3.18.0
    # via huggingface-hub
    # via torch
    # via transformers
    # via virtualenv
flask==3.1.1
    # via cxml-lib
    # via flask-cors
    # via flask-socketio
    # via rq-dashboard
flask-cors==6.0.0
    # via cxml-lib
flask-socketio==5.5.1
    # via cxml-lib
fonttools==4.58.1
    # via matplotlib
frozenlist==1.6.0
    # via aiohttp
    # via aiosignal
fsspec==2025.5.1
    # via dask
    # via huggingface-hub
    # via lightning
    # via pytorch-lightning
    # via torch
future==1.0.0
    # via graphtools
    # via phate
gensim==4.3.3
    # via cxml-lib
    # via mol2vec
graphtools==1.5.3
    # via phate
graphviz==0.20.3
    # via catboost
greenlet==3.2.2
    # via eventlet
grpcio==1.71.0
    # via tensorboard
h11==0.16.0
    # via wsproto
h5py==3.13.0
    # via cxml-lib
hf-xet==1.1.2
    # via huggingface-hub
huggingface-hub==0.32.2
    # via tokenizers
    # via transformers
identify==2.6.12
    # via pre-commit
idna==3.10
    # via requests
    # via yarl
ipython==9.2.0
    # via mol2vec
ipython-pygments-lexers==1.1.1
    # via ipython
itsdangerous==2.2.0
    # via flask
jedi==0.19.2
    # via ipython
jinja2==3.1.6
    # via distributed
    # via flask
    # via torch
joblib==1.5.1
    # via astrochem-embedding
    # via cxml-lib
    # via mol2vec
    # via pynndescent
    # via scikit-learn
jsonschema==4.24.0
    # via nbformat
jsonschema-specifications==2025.4.1
    # via jsonschema
jupyter-core==5.8.1
    # via nbformat
kaleido==0.2.1
    # via cxml-lib
kiwisolver==1.4.8
    # via matplotlib
lightgbm==4.6.0
    # via cxml-lib
lightning==2.5.1.post0
    # via astrochem-embedding
    # via cxml-lib
lightning-utilities==0.14.3
    # via lightning
    # via pytorch-lightning
    # via torchmetrics
llvmlite==0.44.0
    # via numba
    # via pynndescent
locket==1.0.0
    # via distributed
    # via partd
loguru==0.7.3
    # via cxml-lib
macholib==1.16.3
    # via pyinstaller
mako==1.3.10
    # via alembic
mapply==0.1.28
    # via cxml-lib
markdown==3.8
    # via tensorboard
markupsafe==3.0.2
    # via flask
    # via jinja2
    # via mako
    # via werkzeug
matplotlib==3.10.3
    # via catboost
    # via cxml-lib
    # via mol2vec
    # via phate
    # via seaborn
matplotlib-inline==0.1.7
    # via ipython
mol2vec @ git+https://github.com/aravindhnivas/mol2vec.git@6e8924c3a3512e4ceb83419515948d925b225d90
    # via cxml-lib
mpmath==1.3.0
    # via dbcv
    # via sympy
msgpack==1.1.0
    # via blosc2
    # via distributed
multidict==6.4.4
    # via aiohttp
    # via yarl
multipledispatch==1.0.0
    # via dask-glm
    # via dask-ml
multiprocess==0.70.18
    # via mapply
    # via pathos
narwhals==1.41.0
    # via plotly
nbformat==5.10.4
    # via cxml-lib
ndindex==1.10.0
    # via blosc2
networkx==3.4.2
    # via torch
nodeenv==1.9.1
    # via pre-commit
numba==0.61.2
    # via cxml-lib
    # via dask-ml
    # via pynndescent
    # via shap
    # via sparse
    # via trimap
    # via umap-learn
numexpr==2.10.2
    # via blosc2
    # via tables
numpy==1.26.4
    # via astrochem-embedding
    # via blosc2
    # via catboost
    # via cleanlab
    # via contourpy
    # via cxml-lib
    # via dask
    # via dask-ml
    # via dbcv
    # via gensim
    # via graphtools
    # via h5py
    # via lightgbm
    # via matplotlib
    # via mol2vec
    # via numba
    # via numexpr
    # via optuna
    # via pandas
    # via patsy
    # via phate
    # via pygsp
    # via rdkit
    # via s-gd2
    # via scikit-learn
    # via scipy
    # via scprep
    # via seaborn
    # via shap
    # via sparse
    # via statsmodels
    # via tables
    # via tensorboard
    # via torchmetrics
    # via transformers
    # via umap-learn
    # via xgboost
optuna==4.3.0
    # via cxml-lib
    # via optuna-dashboard
    # via optuna-integration
optuna-dashboard==0.18.0
    # via cxml-lib
optuna-integration==4.3.0
    # via cxml-lib
packaging==24.2
    # via dask
    # via dask-ml
    # via distributed
    # via huggingface-hub
    # via lightning
    # via lightning-utilities
    # via matplotlib
    # via optuna
    # via optuna-dashboard
    # via plotly
    # via pyinstaller
    # via pyinstaller-hooks-contrib
    # via pytorch-lightning
    # via scprep
    # via shap
    # via statsmodels
    # via tables
    # via tensorboard
    # via torchmetrics
    # via transformers
pandas==2.2.3
    # via astrochem-embedding
    # via catboost
    # via cleanlab
    # via cxml-lib
    # via dask
    # via dask-ml
    # via mapply
    # via mol2vec
    # via scprep
    # via seaborn
    # via shap
    # via statsmodels
parso==0.8.4
    # via jedi
partd==1.4.2
    # via dask
pathos==0.3.4
    # via mapply
patsy==1.0.1
    # via statsmodels
pexpect==4.9.0
    # via ipython
phate==1.0.11
    # via cxml-lib
pillow==11.2.1
    # via matplotlib
    # via rdkit
platformdirs==4.3.8
    # via blosc2
    # via jupyter-core
    # via virtualenv
plotly==6.1.2
    # via catboost
pox==0.3.6
    # via pathos
ppft==1.7.7
    # via pathos
pre-commit==4.2.0
    # via cxml-lib
prompt-toolkit==3.0.51
    # via ipython
propcache==0.3.1
    # via aiohttp
    # via yarl
protobuf==6.31.0
    # via tensorboard
psutil==7.0.0
    # via distributed
    # via mapply
ptyprocess==0.7.0
    # via pexpect
pure-eval==0.2.3
    # via stack-data
py-cpuinfo==9.0.0
    # via blosc2
    # via tables
pyarrow==20.0.0
    # via dask
pygments==2.19.1
    # via ipython
    # via ipython-pygments-lexers
pygsp==0.5.1
    # via graphtools
pyinstaller==6.14.1
    # via cxml-lib
pyinstaller-hooks-contrib==2025.4
    # via cxml-lib
    # via pyinstaller
pynndescent==0.5.13
    # via umap-learn
pyparsing==3.2.3
    # via matplotlib
python-dateutil==2.9.0.post0
    # via arrow
    # via matplotlib
    # via pandas
python-engineio==4.12.1
    # via python-socketio
python-socketio==5.13.0
    # via flask-socketio
pytorch-lightning==2.5.1.post0
    # via lightning
pytz==2025.2
    # via pandas
pyyaml==6.0.2
    # via dask
    # via distributed
    # via huggingface-hub
    # via lightning
    # via optuna
    # via pre-commit
    # via pytorch-lightning
    # via transformers
rdkit==2025.3.2
    # via cxml-lib
redis==6.2.0
    # via cxml-lib
    # via redis-sentinel-url
    # via rq
    # via rq-dashboard
redis-sentinel-url==1.0.1
    # via rq-dashboard
referencing==0.36.2
    # via jsonschema
    # via jsonschema-specifications
regex==2024.11.6
    # via transformers
requests==2.32.3
    # via blosc2
    # via huggingface-hub
    # via transformers
rpds-py==0.25.1
    # via jsonschema
    # via referencing
rq==2.3.3
    # via cxml-lib
    # via rq-dashboard
rq-dashboard==0.8.2.2
    # via cxml-lib
ruamel-yaml==0.18.11
    # via astrochem-embedding
ruamel-yaml-clib==0.2.12
    # via ruamel-yaml
s-gd2==1.8.1
    # via phate
safetensors==0.5.3
    # via transformers
scikit-learn==1.6.1
    # via astrochem-embedding
    # via cleanlab
    # via cxml-lib
    # via dask-glm
    # via dask-ml
    # via dbcv
    # via graphtools
    # via optuna-dashboard
    # via phate
    # via pynndescent
    # via scprep
    # via shap
    # via trimap
    # via umap-learn
scipy==1.13.1
    # via catboost
    # via cxml-lib
    # via dask-glm
    # via dask-ml
    # via dbcv
    # via gensim
    # via graphtools
    # via lightgbm
    # via phate
    # via pygsp
    # via pynndescent
    # via scikit-learn
    # via scprep
    # via shap
    # via statsmodels
    # via umap-learn
    # via xgboost
scprep==1.1.0
    # via phate
seaborn==0.13.2
    # via cxml-lib
    # via mol2vec
selfies==2.2.0
    # via astrochem-embedding
    # via cxml-lib
setuptools==80.9.0
    # via lightning-utilities
    # via pyinstaller
    # via pyinstaller-hooks-contrib
    # via tensorboard
    # via torch
shap==0.47.2
    # via cxml-lib
sigfig==1.3.19
    # via cxml-lib
simple-websocket==1.1.0
    # via python-engineio
six==1.17.0
    # via catboost
    # via python-dateutil
    # via tensorboard
slicer==0.0.8
    # via shap
smart-open==7.1.0
    # via gensim
sortedcontainers==2.4.0
    # via distributed
    # via sigfig
sparse==0.17.0
    # via dask-glm
sqlalchemy==2.0.41
    # via alembic
    # via optuna
stack-data==0.6.3
    # via ipython
statsmodels==0.14.4
    # via cxml-lib
sympy==1.14.0
    # via torch
tables==3.10.2
    # via cxml-lib
tasklogger==1.2.0
    # via graphtools
    # via phate
tblib==3.1.0
    # via distributed
tensorboard==2.19.0
    # via astrochem-embedding
tensorboard-data-server==0.7.2
    # via tensorboard
termcolor==3.1.0
    # via cleanlab
threadpoolctl==3.6.0
    # via scikit-learn
tokenizers==0.21.1
    # via transformers
toolz==1.0.0
    # via dask
    # via distributed
    # via partd
torch==2.7.0
    # via astrochem-embedding
    # via lightning
    # via pytorch-lightning
    # via torchmetrics
torchinfo==1.8.0
    # via astrochem-embedding
torchmetrics==1.7.1
    # via lightning
    # via pytorch-lightning
tornado==6.5.1
    # via distributed
tqdm==4.67.1
    # via cleanlab
    # via huggingface-hub
    # via lightning
    # via mapply
    # via mol2vec
    # via optuna
    # via pytorch-lightning
    # via shap
    # via transformers
    # via umap-learn
traitlets==5.14.3
    # via ipython
    # via jupyter-core
    # via matplotlib-inline
    # via nbformat
transformers==4.52.3
    # via cxml-lib
trimap==1.1.4
    # via cxml-lib
types-python-dateutil==2.9.0.20250516
    # via arrow
typing-extensions==4.13.2
    # via alembic
    # via huggingface-hub
    # via lightning
    # via lightning-utilities
    # via pytorch-lightning
    # via referencing
    # via shap
    # via sqlalchemy
    # via tables
    # via torch
tzdata==2025.2
    # via pandas
umap-learn==0.5.7
    # via cxml-lib
uncertainties==3.2.3
    # via cxml-lib
urllib3==2.4.0
    # via distributed
    # via requests
virtualenv==20.31.2
    # via pre-commit
waitress==3.0.2
    # via cxml-lib
wcwidth==0.2.13
    # via prompt-toolkit
werkzeug==3.1.3
    # via flask
    # via flask-cors
    # via tensorboard
wrapt==1.17.2
    # via deprecated
    # via smart-open
wsproto==1.2.0
    # via simple-websocket
xgboost==3.0.2
    # via cxml-lib
yarl==1.20.0
    # via aiohttp
zict==3.0.0
    # via distributed