SeqTrainer/pyproject.toml at main · SynBioDex/SeqTrainer · GitHub

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[build-system]
requires = ["setuptools>=68", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "seqtrainer"
version = "0.1.0"
description = "Synthetic biology domain toolkit for SBOL/SynBioHub ML workflows"
readme = "README.md"
requires-python = ">=3.9"
license = { file = "LICENSE" }
keywords = ["synthetic biology", "sbol", "synbiohub", "machine learning", "dna"]
authors = [
  { name = "Gonzalo Vidal", email = "Gonzalo.VidalPena@colorado.edu" },
  { name = "Sai Wong", email = "sai.wong@sjsu.edu" }
]
classifiers = [
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",
  "License :: OSI Approved :: MIT License",
  "Operating System :: OS Independent",
]

dependencies = [
  "pandas>=1.5",
  "numpy>=1.24",
  "rdflib>=6.3.2",
  "scikit-learn>=1.3",
  "requests>=2.31",
  "sbol2>=1.4",
]

[project.optional-dependencies]
keras = [
  "tensorflow>=2.12",
]
torch = [
  # PyTorch 2.3+ no longer publishes Intel macOS wheels.
  "torch>=2.2,<2.3; sys_platform == 'darwin' and platform_machine == 'x86_64'",
  "torch>=2.2; sys_platform != 'darwin' or platform_machine != 'x86_64'",
  "transformers>=4.30",
  "numpy<2",
]
bacteria-titan = [
  "pyarrow>=12",
  "matplotlib>=3.7",
]
evo2-tokenizer = [
  # Evo 2 constructs vortex.model.tokenizer.CharLevelTokenizer(512).
  "vtx>=1.1.0; python_version >= '3.10'",
]
gnn = [
  "torch>=2.2",
  "torch-geometric>=2.4",
]
dev = [
  "pytest>=8.0",
  "pytest-cov>=5.0",
  "ruff>=0.4",
  "mypy>=1.9",
]

[project.scripts]
seqtrainer = "seqtrainer.cli.main:main"
seqtrainer-titans-stage-a-benchmark = "seqtrainer.torch.titans_paper_mac.benchmark:main"
seqtrainer-titans-stage-b-benchmark = "seqtrainer.torch.titans_paper_mac_stage_b.benchmark:main"
seqtrainer-titans-stage-b-long-context = "seqtrainer.torch.titans_paper_mac_stage_b.long_context_benchmark:main"
seqtrainer-titans-stage-b-audit = "seqtrainer.torch.titans_paper_mac_stage_b.audit:main"
seqtrainer-titans-stage-b-a100-pilot = "seqtrainer.torch.titans_paper_mac_stage_b.a100_pilot:main"
seqtrainer-titans-stage-c-tokenizers = "seqtrainer.torch.titans_paper_mac_stage_c.cli:tokenizer_study_main"
seqtrainer-titans-stage-c-cpu-pilot = "seqtrainer.torch.titans_paper_mac_stage_c.cli:cpu_pilot_main"
seqtrainer-titans-stage-c-hardware-preflight = "seqtrainer.torch.titans_paper_mac_stage_c.cli:hardware_preflight_main"
seqtrainer-titans-stage-c-train = "seqtrainer.torch.titans_paper_mac_stage_c.train_cli:main"
seqtrainer-titans-stage-c-capacity = "seqtrainer.torch.titans_paper_mac_stage_c.capacity_cli:main"
seqtrainer-titans-stage-c-gpu-smoke = "seqtrainer.torch.titans_paper_mac_stage_c.smoke_cli:main"
seqtrainer-titans-stage-c-t4-evidence = "seqtrainer.torch.titans_paper_mac_stage_c.t4_evidence_cli:main"
seqtrainer-titans-stage-c-evaluate = "seqtrainer.torch.titans_paper_mac_stage_c.evaluate_cli:main"
seqtrainer-titans-stage-c-colab-run = "seqtrainer.torch.titans_paper_mac_stage_c.colab_cli:main"
seqtrainer-titans-stage-c-study = "seqtrainer.torch.titans_paper_mac_stage_c.study:main"
seqtrainer-titans-stage-c-resume-verify = "seqtrainer.torch.titans_paper_mac_stage_c.resume_verify_cli:main"
seqtrainer-titans-stage-c-memory-trace = "seqtrainer.torch.titans_paper_mac_stage_c.memory_trace_cli:main"
seqtrainer-titans-stage-c-memory-behavior = "seqtrainer.torch.titans_paper_mac_stage_c.memory_behavior_cli:main"
seqtrainer-titans-stage-c-architecture = "seqtrainer.torch.titans_paper_mac_stage_c.architecture_cli:main"
seqtrainer-titans-stage-c-generate = "seqtrainer.torch.titans_paper_mac_stage_c.generation_cli:main"
seqtrainer-titans-stage-c-panel = "seqtrainer.torch.titans_paper_mac_stage_c.panel_cli:main"
seqtrainer-titans-stage-c-scale-gate = "seqtrainer.torch.titans_paper_mac_stage_c.scale_gate_cli:main"

[project.urls]
Homepage = "https://github.com/SynBioDex/SeqTrainer"
"Bug Tracker" = "https://github.com/SynBioDex/SeqTrainer/issues"

[tool.setuptools]
package-dir = {"" = "src"}

[tool.setuptools.packages.find]
where = ["src"]
include = ["seqtrainer*"]