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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "nmdc_submission_schema"
version = "0.0.0"
description = "The home of the NMDC submission schema. *Not* the home of sheets_and_friends. *Not* a GH pages host of NMDC DataHarmonizer interfaces."
authors = ["Mark Andrew Miller <[email protected]>"]
license = "MIT"
readme = "README.md"
include = [
# These files are copied from the top-level project folder at build time. Without
# the copy step they end up in a weird location when installed via wheel.
# See: https://github.com/python-poetry/poetry/issues/7153
{ path = "src/nmdc_submission_schema/project/**/*", format = ["sdist", "wheel"] }
]
# note that the nmdc-schema is not imported as a module,
# but one file from the nmdc-schema is accessed via sheets_and_friends/tsv_in/import_slots_regardless.tsv
# and project.Makefile
# look for strings like
# https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v7.7.2/nmdc_schema/nmdc_materialized_patterns.yaml
[tool.poetry.dependencies]
python = "^3.9"
linkml-runtime = "^1.6.2"
[tool.poetry.group.dev.dependencies]
exhaustion-check = "^0.1.3"
linkml = "^1.7.10"
mkdocs-material = "^9.1.2"
mkdocs-mermaid2-plugin = "^0.6.0"
oaklib = "^0.5.28" # https://pypi.org/project/oaklib/0.5.6/
rdflib = "^6.2.0"
sheets-and-friends = "^0.5.4"
jupyter = "^1.1.1"
matplotlib = "^3.9.2"
textdistance = "^4.6.3"
jupyter-datatables = "^0.3.9"
[tool.poetry-dynamic-versioning]
# We need poetry-dynamic-versioning to update the version in the src schema file,
# then generate project artifacts from that schema with the real version populated,
# and then perform any build or publish actions. Since this requires running
# `poetry dynamic-versioning` manually before `poetry build`, we set enable = false.
# similar dynamic versioning doesn't seem to be working for nmdc-schema right now
enable = false
vcs = "git"
style = "pep440"
[tool.poetry-dynamic-versioning.substitution]
files = [
"*.py",
"src/**/__init__.py",
"src/**/__version__.py",
"src/**/_version.py",
"src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml"
]
patterns = [
"(^\\s*__version__\\s*(?::.*?)?=\\s*['\\\"])[^'\\\"]*(['\\\"])",
"(^version:\\s*['\\\"]?)[^'\\\"]*?(['\\\"]?)$"
]
## /Users/MAM/Documents/gitrepos/sheets_and_friends
## /home/mark/gitrepos/sheets_and_friends
#sheets-and-friends = { path = "/home/mark/gitrepos/sheets_and_friends", develop = true }
[build-system]
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
build-backend = "poetry_dynamic_versioning.backend"
[tool.poetry.extras]
docs = ["linkml", "mkdocs-material"]
[tool.poetry.scripts]
oak-tree-to-pv-list = "nmdc_submission_schema.scripts.oak_tree_to_pv_list:main"
dh-json2linkml = 'nmdc_submission_schema.scripts.dh_json2linkml:update_json'
linkml-json2dh = 'nmdc_submission_schema.scripts.linkml_json2dh:extract_lists'
inject-gold-pathway-terms = 'nmdc_submission_schema.scripts.gold:main'
inject-env-triad-terms = 'nmdc_submission_schema.scripts.generate_env_triad_enums:main'