bloodhound/requirements.txt at main · fullscreen-triangle/bloodhound · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
# Bloodhound Virtual Machine - Python Dependencies
# Consciousness-Aware Scientific Computing Platform

# === Core Scientific Computing ===
numpy>=1.24.0
scipy>=1.10.0
pandas>=2.0.0
polars>=0.20.0
pyarrow>=14.0.0

# === Machine Learning and AI ===
scikit-learn>=1.3.0
torch>=2.1.0
transformers>=4.35.0
datasets>=2.14.0
accelerate>=0.24.0
peft>=0.6.0  # For LoRA adaptation in Purpose Framework
tokenizers>=0.15.0

# === Deep Learning Backends ===
onnxruntime>=1.16.0

# === Bioinformatics ===
biopython>=1.81
pysam>=0.22.0
pyvcf>=0.6.8
scanpy>=1.9.0  # Single-cell analysis
anndata>=0.10.0

# === Mass Spectrometry and Metabolomics ===
pyteomics>=4.6.0
pymzml>=2.5.0
matchms>=0.20.0

# === Networking and Async ===
aiohttp>=3.9.0
asyncio-mqtt>=0.16.0
websockets>=12.0
httpx>=0.25.0

# === Database and Storage ===
sqlalchemy>=2.0.0
alembic>=1.12.0
redis>=5.0.0
pymongo>=4.6.0

# === Data Validation and Serialization ===
pydantic>=2.5.0
msgpack>=1.0.0
orjson>=3.9.0

# === Configuration and CLI ===
typer>=0.9.0
rich>=13.7.0
click>=8.1.0
pyyaml>=6.0.0
toml>=0.10.0

# === Monitoring and Logging ===
loguru>=0.7.0
prometheus-client>=0.19.0
structlog>=23.2.0

# === Mathematical and Statistical ===
statsmodels>=0.14.0
sympy>=1.12
networkx>=3.2

# === Visualization ===
matplotlib>=3.8.0
seaborn>=0.13.0
plotly>=5.17.0
bokeh>=3.3.0

# === Jupyter Integration ===
jupyter>=1.0.0
ipywidgets>=8.1.0
ipykernel>=6.26.0

# === Development Dependencies ===
pytest>=7.4.0
pytest-asyncio>=0.21.0
pytest-cov>=4.1.0
pytest-mock>=3.12.0
hypothesis>=6.87.0
black>=23.11.0
isort>=5.12.0
flake8>=6.1.0
mypy>=1.7.0
pre-commit>=3.5.0
bandit>=1.7.0
safety>=2.3.0

# === Documentation ===
sphinx>=7.2.0
sphinx-rtd-theme>=1.3.0
myst-parser>=2.0.0
sphinx-autodoc-typehints>=1.25.0
nbsphinx>=0.9.0

# === Performance and Profiling ===
memory-profiler>=0.61.0
line-profiler>=4.1.0
py-spy>=0.3.0
scalene>=1.5.0

# === Advanced Scientific Computing ===
numba>=0.58.0
dask>=2023.11.0
xarray>=2023.11.0
zarr>=2.16.0
h5py>=3.10.0

# === Quantum Computing (Optional) ===
# qiskit>=0.45.0
# cirq>=1.3.0
# pennylane>=0.33.0