pyproject.toml.bak

[tool.poetry]
name = "mixs-envo-struct-knowl-extraction"
version = "0.1.0"
description = ""
authors = ["Mark Andrew Miller <MAM@lbl.gov>", "Genoic 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]
exhaustion-check = "^0.1.4"
#schemasheets = { path = "/home/mark/gitrepos/schemasheets", develop = true }
#schemasheets = { git = "https://github.com/linkml/schemasheets.git", branch = "exporting-without-tsv-templ" }
schemasheets = "^0.1.23"
linkml = "^1.5.3"
nltk = "^3.8.1"
openpyxl = "^3.1.2"
pandas = "^2.0"
python = "^3.9"
scikit-learn = "^1.2.2" # for text mining. possibly heavyweight

#linkml-runtime = { path = "/home/mark/gitrepos/linkml-runtime", develop = true }
# # for presentation
#geopy = "^2.3.0"
#requests-cache = "^1.1.0"
#geopandas = "^0.13.2"
#matplotlib = "^3.7.2"
#matplotlib-venn = "^0.11.9"
oaklib = "^0.5.12"

[tool.poetry.group.dev.dependencies]
pytest = "^7.1.3"
pytest-sugar = "^0.9.5"
pytest-clarity = "^1.0.1"
pytest-random-order = "^1.0.4"
coverage = { extras = ["toml"], version = "^6.4.4" }
pytest-cov = "^3.0.0"
black = "^22.8.0"
isort = "^5.10.1"
flake8 = "^4"
flakeheaven = "^3.0.0"
darglint = "^1.8.1"
flake8-bandit = "^3.0"
flake8-pytest-style = "^1.6.0"
flake8-bugbear = "^22.8.23"
flake8-docstrings = "^1.6.0"
flake8-comprehensions = "^3.10.0"
flake8-isort = "^4.2.0"
flake8-mutable = "^1.2.0"
flake8-simplify = "^0.19.3"
pep8-naming = "^0.13.2"
safety = "^2.1.1"
mypy = "^0.971"
Faker = "^14.2.0"

mkdocs = "^1.4.2"
mkdocs-material = "^9.0.12"
mkdocs-mermaid2-plugin = "^0.6.0"

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

[tool.coverage.paths]
source = ["src"]

[tool.coverage.run]
branch = true
source = ["mixs-envo-struct-knowl-extraction"]

[tool.coverage.report]
fail_under = 100
show_missing = true

[tool.pytest.ini_options]
pythonpath = ["src"]
testpaths = [
    "tests",
]
addopts = ["--random-order", "-vv"]

[tool.flakeheaven]
exclude = ["*.md", ".env", ".git", ".gitignore"]
format = "grouped"
max_line_length = 88
show_source = true

[tool.flakeheaven.plugins]
darglint = ["+*"]
flake8-bandit = ["+*", "-S322"]
flake8-bugbear = ["+*", "-B950"]
flake8-builtins = ["+*"]
flake8-comprehensions = ["+*"]
flake8-docstrings = ["+*", "-D400"]
flake8-isort = ["+*"]
flake8-mutable = ["+*"]
flake8-pytest-style = ["+*"]
flake8-simplify = ["+*"]
mccabe = ["+*"]
pep8-naming = ["+*"]
pycodestyle = ["+*", "-W503"]
pyflake = ["+*"]
pyflakes = ["+*"]

[tool.flakeheaven.exceptions."tests/"]
flake8-bandit = ["-S101"]
flake8-docstrings = ["-D100"]

[tool.mypy]
warn_return_any = true
warn_unused_configs = true
exclude = "tests"

[tool.isort]
profile = "black"
atomic = true
line_length = 88
use_parentheses = true

[tool.black]
line_length = 88
include = '\.pyi?$'

[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"