# env/requirements.txt
# scientific computing stack
numpy== 1.26.0
pandas==2.1.1
#polars
openpyxl==3.1.2
# xlrd with pandas
xlrd== 2.0.1
# pyreader use with RDS
pyreadr==0.4.9
scipy==1.11.4
networkx==3.2.1
#dask
umap-learn==0.5.3

# configuration
hydra-core==1.3.2

# torch stack
torch==2.1.0
torch_geometric==2.4.0
torchmetrics==1.2.1
lightning==2.1.2
# torch-scatter==2.1.2

# visualization stack and logging
wandb==0.15.8
matplotlib==3.7.2
# adjustTest used with with matplotlib
adjustText== 0.8
#pydot Don't think I am using this... outdate
pydot== 1.4.2
# pygraphviz don't think I am using this
 # graphviz don't think I am using this.
# graphviz
plotly==5.18.0
seaborn==0.12.2

# ML stack
scikit-learn==1.2.2

# Transformer / Huggingface Stack
transformers==4.31.0
## used with protT5 model
sentencepiece==0.1.99

# Bio stack
biopython==1.81
goatools== 1.3.1
intermine== 1.13.0
gffutils== 0.12

# stubs and types
pandas-stubs==2.0.3.230814
types-tqdm==  4.65.0.2
types-requests== 2.31.0.2

# data stack
sortedcontainers==2.4.0
attrs== 23.1.0
pydantic==2.5.2
h5py== 3.9.0

# database stack
lmdb== 1.4.1


# web stack
aiohttp==3.8.5

# ontology stack
pronto==2.5.4
nxontology==0.5.0
owlready2==0.45


# Workspace
python-dotenv==1.0.0

# dev-tools
bumpver== 2023.1129
pre-commit==  3.3.3
# ptpython==3.0.23
pip-tools==7.1.0
snakeviz== 2.2.0
twine==4.0.2

# biocypher
biocypher>=0.5.34 
