build: use pyproject.toml for build configuration

cancervariants · Oct 26, 2023 · 16e94c7 · 16e94c7
1 parent 074dd51
commit 16e94c7
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Showing 29 changed files with 73 additions and 76 deletions.
diff --git a/.gitignore b/.gitignore
@@ -149,7 +149,7 @@ pytest.ini
 
 # ignore data dir
 data/*
-disease/data/*
+src/disease/data/*
 
 # IDE materials
 .idea/

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,7 +1,78 @@
+[project]
+name = "disease-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 diseases"
+license = {file = "LICENSE"}
+dependencies = [
+    "pydantic==2.*",
+    "fastapi",
+    "uvicorn",
+    "click",
+    "boto3",
+    "ga4gh.vrs~=2.0.0a1",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+pg = ["psycopg[binary]"]
+etl = ["owlready2==0.40", "rdflib", "requests", "typing-extensions", "bioversions"]
+test = ["pytest>=6.0", "pytest-cov"]
+dev = ["pre-commit", "black", "ruff", "lxml", "xmlformatter"]
+
+[project.urls]
+Homepage = "https://github.com/cancervariants/disease-normalization"
+Documentation = "https://github.com/cancervariants/disease-normalization"
+Changelog = "https://github.com/cancervariants/disease-normalization/releases"
+Source = "https://github.com/cancervariants/disease-normalization"
+"Bug Tracker" = "https://github.com/cancervariants/disease-normalization/issues"
+
+[project.scripts]
+disease_norm_update = "disease.cli:update_normalizer_db"
+disease_norm_update_remote = "disease.cli:update_from_remote"
+disease_norm_dump = "disease.cli:dump_database"
+disease_norm_check_db = "disease.cli:check_db"
+
 [build-system]
-requires = ["setuptools", "wheel"]
+requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 
+[tool.setuptools.dynamic]
+version = {attr = "disease.version.__version__"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"disease.database.postgresql" = ["*.sql"]
+
+[tool.pytest.ini_options]
+addopts = "--cov=src --cov-report term-missing"
+testpaths = ["tests"]
+
+[tool.coverage.run]
+branch = true
+
 [tool.black]
 line-length = 88
 

diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/disease/__init__.py → src/disease/__init__.py b/disease/__init__.py → src/disease/__init__.py
diff --git a/disease/cli.py → src/disease/cli.py b/disease/cli.py → src/disease/cli.py
diff --git a/disease/database/__init__.py → src/disease/database/__init__.py b/disease/database/__init__.py → src/disease/database/__init__.py
diff --git a/disease/database/database.py → src/disease/database/database.py b/disease/database/database.py → src/disease/database/database.py
diff --git a/disease/database/dynamodb.py → src/disease/database/dynamodb.py b/disease/database/dynamodb.py → src/disease/database/dynamodb.py
diff --git a/disease/database/postgresql.py → src/disease/database/postgresql.py b/disease/database/postgresql.py → src/disease/database/postgresql.py
diff --git a/disease/database/postgresql/add_fkeys.sql → ...disease/database/postgresql/add_fkeys.sql b/disease/database/postgresql/add_fkeys.sql → ...disease/database/postgresql/add_fkeys.sql
diff --git a/disease/database/postgresql/add_indexes.sql → ...sease/database/postgresql/add_indexes.sql b/disease/database/postgresql/add_indexes.sql → ...sease/database/postgresql/add_indexes.sql
diff --git a/.../postgresql/create_record_lookup_view.sql → .../postgresql/create_record_lookup_view.sql b/.../postgresql/create_record_lookup_view.sql → .../postgresql/create_record_lookup_view.sql
diff --git a/...ase/database/postgresql/create_tables.sql → ...ase/database/postgresql/create_tables.sql b/...ase/database/postgresql/create_tables.sql → ...ase/database/postgresql/create_tables.sql
diff --git a/...postgresql/delete_normalized_concepts.sql → ...postgresql/delete_normalized_concepts.sql b/...postgresql/delete_normalized_concepts.sql → ...postgresql/delete_normalized_concepts.sql
diff --git a/disease/database/postgresql/drop_fkeys.sql → ...isease/database/postgresql/drop_fkeys.sql b/disease/database/postgresql/drop_fkeys.sql → ...isease/database/postgresql/drop_fkeys.sql
diff --git a/disease/database/postgresql/drop_indexes.sql → ...ease/database/postgresql/drop_indexes.sql b/disease/database/postgresql/drop_indexes.sql → ...ease/database/postgresql/drop_indexes.sql
diff --git a/disease/etl/__init__.py → src/disease/etl/__init__.py b/disease/etl/__init__.py → src/disease/etl/__init__.py
diff --git a/disease/etl/base.py → src/disease/etl/base.py b/disease/etl/base.py → src/disease/etl/base.py
diff --git a/disease/etl/do.py → src/disease/etl/do.py b/disease/etl/do.py → src/disease/etl/do.py
diff --git a/disease/etl/merge.py → src/disease/etl/merge.py b/disease/etl/merge.py → src/disease/etl/merge.py
diff --git a/disease/etl/mondo.py → src/disease/etl/mondo.py b/disease/etl/mondo.py → src/disease/etl/mondo.py
diff --git a/disease/etl/ncit.py → src/disease/etl/ncit.py b/disease/etl/ncit.py → src/disease/etl/ncit.py
diff --git a/disease/etl/omim.py → src/disease/etl/omim.py b/disease/etl/omim.py → src/disease/etl/omim.py
diff --git a/disease/etl/oncotree.py → src/disease/etl/oncotree.py b/disease/etl/oncotree.py → src/disease/etl/oncotree.py
diff --git a/disease/main.py → src/disease/main.py b/disease/main.py → src/disease/main.py
diff --git a/disease/query.py → src/disease/query.py b/disease/query.py → src/disease/query.py
diff --git a/disease/schemas.py → src/disease/schemas.py b/disease/schemas.py → src/disease/schemas.py
diff --git a/disease/version.py → src/disease/version.py b/disease/version.py → src/disease/version.py