pyproject.toml

[tool.poetry]
name = "gempipe"
version = "1.37.5"
description = ""
authors = ["Gioele Lazzari"]
license = "GNU General Public License v3.0"
readme = "README.md"

[tool.poetry.dependencies]
python = ">=3.9"
cobra = ">=0.29"
pandas = ">=2.0.0"
openpyxl = ">=3.1.0"
ncbi-genome-download = ">=0.3.3"
biopython = ">=1.80"
ipython = ">=8.7.0"
matplotlib = ">=3.7.0"
seaborn = ">=0.13.0"
scipy = ">=1.10.0"
scikit-learn = ">=1.3.0"

# non-pip dependencies:
# pigz >= 2.5
# prokka >= 1.14.6
# prodigal >= 2.6.3
# busco >= 5.4.0
# seqkit >= 2.2.0
# cd-hit >= 4.8.1
# blast >= 2.12.0
# eggnog-mapper >= 2.1.7
# diamond >= 2.0.15 

# for validation (just pip)
# memote >= 0.17.0 (requires git)

# suspect fixes:
# htslib==1.16

# test alternative solvers
# osqp >= 0.6.3
# libosqp >= 0.6.3
# highs >= 1.6.0

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.poetry.scripts]
gempipe = "gempipe:main"