pyproject.toml

[tool.poetry]
name = "mixs-envo-struct-knowl-extraction"
version = "0.1.0"
description = ""
authors = ["Mark Andrew Miller <MAM@lbl.gov>", "Genomic Standards Consortium"]
readme = "README.md"
license = "MIT"
homepage = "https://microbiomedata.github.io/mixs-6-2-release-candidate/"
repository = "https://github.com/microbiomedata/mixs-6-2-release-candidate"

[tool.poetry.dependencies]
python = ">=3.9,<3.13"
exhaustion-check = "^0.1.4"
linkml-runtime = "^1.5"
mkdocs = "^1.4.2"
mkdocs-material = "^9.0.12"
mkdocs-mermaid2-plugin = "^0.6.0"
pandas = "^2.1.1"
pydantic = "^1.10.13"
rdflib = "^6.3.2"
schemasheets = "^0.1.24"
scikit-learn = "^1.3.1"

[tool.poetry.group.dev.dependencies]
python = ">=3.9,<3.13"

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

[tool.poetry.extras]
docs = ["linkml", "mkdocs-material"]

[tool.poetry.scripts]
write-mixs-linkml = "mixs_envo_struct_knowl_extraction.mixs_linkml_from_xlsx:create_schema"
add-notes-from-text-mining = "mixs_envo_struct_knowl_extraction.slot_text_mining:cli"
find-Xs-with-multiple-Ys = "mixs_envo_struct_knowl_extraction.find_Xs_with_multiple_Ys:main"
mixs-scns-vs-ncbi-harmonized-attributes = "mixs_envo_struct_knowl_extraction.mixs_scns_vs_ncbi_harmonized_attributes:cli"
remove-elements-by-deprecation-val = "mixs_envo_struct_knowl_extraction.remove_elements_by_deprecation_val:main"
usage-detector = "mixs_envo_struct_knowl_extraction.usage_detector:main"
rdflib-validation = "mixs_envo_struct_knowl_extraction.rdflib_validate:main"
regenerate-data-harmonizer-menu = "mixs_envo_struct_knowl_extraction.regenerate_data_harmonizer_menu:cli"
find-ontology-mentions = "mixs_envo_struct_knowl_extraction.find_ontology_mentions:cli"