build: use pyproject.toml for build configuration

cancervariants · Oct 27, 2023 · 13bd23b · 13bd23b
1 parent a1d10d4
commit 13bd23b
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Showing 25 changed files with 69 additions and 72 deletions.
diff --git a/.gitignore b/.gitignore
@@ -149,6 +149,7 @@ pytest.ini
 # data directories
 data/*
 therapy/data/
+src/therapy/data/*
 
 # dynamodb
 dynamodb_local_latest/*

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,8 +1,74 @@
+[project]
+name = "therapy-normalizer"
+authors = [
+    {name = "Alex Wagner"},
+    {name = "Kori Kuzma"},
+    {name = "James Stevenson"}
+]
+readme = "README.md"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Framework :: FastAPI",
+    "Framework :: Pydantic",
+    "Framework :: Pydantic :: 2",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+]
+requires-python = ">=3.8"
+description = "VICC normalization routines for therapeutics"
+license = {file = "LICENSE"}
+dependencies = [
+    "pydantic==2.*",
+    "fastapi",
+    "uvicorn",
+    "click",
+    "boto3",
+    "ga4gh.vrs~=2.0.0a1",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+etl = ["disease-normalizer~=0.4.0.dev0", "owlready2", "rdflib", "wikibaseintegrator>=0.12.0", "chembl-downloader", "bioversions>=0.4.3"]
+test = ["pytest", "pytest-cov"]
+dev = ["pre-commit", "ruff>=0.1.2", "lxml", "xmlformatter", "mypy", "types-requests", "types-pyyaml"]
+
+[project.urls]
+Homepage = "https://github.com/cancervariants/therapy-normalization"
+Documentation = "https://github.com/cancervariants/therapy-normalization"
+Changelog = "https://github.com/cancervariants/therapy-normalization/releases"
+Source = "https://github.com/cancervariants/therapy-normalization"
+"Bug Tracker" = "https://github.com/cancervariants/therapy-normalization/issues"
+
 [build-system]
-requires = ["setuptools", "wheel"]
-build-backend = "setuptools.build_meta:__legacy__"
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+version = {attr = "therapy.version.__version__"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+addopts = "--cov=src --cov-report term-missing"
+testpaths = ["tests"]
+
+[tool.coverage.run]
+branch = true
+
+[tool.mypy]
+plugins = "pydantic.mypy"
+ignore_missing_imports = true
 
 [tool.ruff]
+src = ["src"]
 # pycodestyle (E, W)
 # Pyflakes (F)
 # flake8-annotations (ANN)

diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/therapy/__init__.py → src/therapy/__init__.py b/therapy/__init__.py → src/therapy/__init__.py
diff --git a/therapy/cli.py → src/therapy/cli.py b/therapy/cli.py → src/therapy/cli.py
diff --git a/therapy/database.py → src/therapy/database.py b/therapy/database.py → src/therapy/database.py
diff --git a/therapy/etl/__init__.py → src/therapy/etl/__init__.py b/therapy/etl/__init__.py → src/therapy/etl/__init__.py
diff --git a/therapy/etl/base.py → src/therapy/etl/base.py b/therapy/etl/base.py → src/therapy/etl/base.py
diff --git a/therapy/etl/chembl.py → src/therapy/etl/chembl.py b/therapy/etl/chembl.py → src/therapy/etl/chembl.py
diff --git a/therapy/etl/chemidplus.py → src/therapy/etl/chemidplus.py b/therapy/etl/chemidplus.py → src/therapy/etl/chemidplus.py
diff --git a/therapy/etl/drugbank.py → src/therapy/etl/drugbank.py b/therapy/etl/drugbank.py → src/therapy/etl/drugbank.py
diff --git a/therapy/etl/drugsatfda.py → src/therapy/etl/drugsatfda.py b/therapy/etl/drugsatfda.py → src/therapy/etl/drugsatfda.py
diff --git a/therapy/etl/guidetopharmacology.py → src/therapy/etl/guidetopharmacology.py b/therapy/etl/guidetopharmacology.py → src/therapy/etl/guidetopharmacology.py
diff --git a/therapy/etl/hemonc.py → src/therapy/etl/hemonc.py b/therapy/etl/hemonc.py → src/therapy/etl/hemonc.py
diff --git a/therapy/etl/merge.py → src/therapy/etl/merge.py b/therapy/etl/merge.py → src/therapy/etl/merge.py
diff --git a/therapy/etl/ncit.py → src/therapy/etl/ncit.py b/therapy/etl/ncit.py → src/therapy/etl/ncit.py
diff --git a/therapy/etl/rules.csv → src/therapy/etl/rules.csv b/therapy/etl/rules.csv → src/therapy/etl/rules.csv
diff --git a/therapy/etl/rules.py → src/therapy/etl/rules.py b/therapy/etl/rules.py → src/therapy/etl/rules.py
diff --git a/therapy/etl/rxnorm.py → src/therapy/etl/rxnorm.py b/therapy/etl/rxnorm.py → src/therapy/etl/rxnorm.py
diff --git a/therapy/etl/wikidata.py → src/therapy/etl/wikidata.py b/therapy/etl/wikidata.py → src/therapy/etl/wikidata.py
diff --git a/therapy/main.py → src/therapy/main.py b/therapy/main.py → src/therapy/main.py
diff --git a/therapy/query.py → src/therapy/query.py b/therapy/query.py → src/therapy/query.py
diff --git a/therapy/schemas.py → src/therapy/schemas.py b/therapy/schemas.py → src/therapy/schemas.py
diff --git a/therapy/version.py → src/therapy/version.py b/therapy/version.py → src/therapy/version.py