build: modernize build configs (#279)

* Use the "src" layout instead of a "flat" layout. It is argued that this is better: https://packaging.python.org/en/latest/discussions/src-layout-vs-flat-layout/ * Move build settings into `pyproject.toml`. People seem to think this is more "modern". At the very least, it means fewer files for us to manage. Removed some deprecated settings while in here. * Add a few additional PyPI classifiers. * Update default test command options (they were showing their age)
cancervariants · Oct 4, 2023 · 6e7ae63 · 6e7ae63
1 parent 23d477d
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Showing 34 changed files with 92 additions and 105 deletions.
diff --git a/.gitignore b/.gitignore
@@ -149,7 +149,7 @@ pytest.ini
 
 # ignore data dir
 data/*
-gene/data/
+src/gene/data/
 
 # IDE materials
 .idea/

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,12 +1,94 @@
-[build-system]
-requires = ["setuptools", "wheel"]
-build-backend = "setuptools.build_meta:__legacy__"
+[project]
+name = "gene-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 genes"
+license = {file = "LICENSE"}
+dependencies = [
+    "pydantic",
+    "fastapi",
+    "uvicorn",
+    "click",
+    "boto3",
+    "ga4gh.vrsatile.pydantic~=0.0.12",
+    "ga4gh.vrs~=0.8.1"
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+pg = ["psycopg[binary]"]
+
+etl = ["gffutils", "biocommons.seqrepo"]
+
+test = ["pytest>=6.0", "pytest-cov", "mock", "httpx"]
+
+dev = ["pre-commit", "black", "ruff"]
+
+docs = [
+    "sphinx==6.1.3",
+    "sphinx-autodoc-typehints==1.22.0",
+    "sphinx-autobuild==2021.3.14",
+    "sphinx-copybutton==0.5.2",
+    "sphinxext-opengraph==0.8.2",
+    "furo==2023.3.27",
+    "gravis==0.1.0"
+]
+
+[project.urls]
+Homepage = "https://github.com/cancervariants/gene-normalization"
+Documentation = "https://gene-normalizer.readthedocs.io/en/latest/"
+Changelog = "https://github.com/cancervariants/gene-normalization/releases"
+Source = "https://github.com/cancervariants/gene-normalization"
+"Bug Tracker" = "https://github.com/cancervariants/gene-normalization/issues"
+
+[project.scripts]
+gene_norm_update = "gene.cli:update_normalizer_db"
+gene_norm_update_remote = "gene.cli:update_from_remote"
+gene_norm_dump = "gene.cli:dump_database"
+gene_norm_check_db = "gene.cli:check_db"
+
+[tool.setuptools.dynamic]
+version = {attr = "gene.version.__version__"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"gene.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
 extend-exclude = "^/docs/source/conf.py"
 
 [tool.ruff]
+src = ["src"]
 # pycodestyle (E, W)
 # Pyflakes (F)
 # flake8-annotations (ANN)
@@ -40,7 +122,6 @@ docstring-quotes = "double"
 # I001 - Import block unsorted or unformatted
 # N805 - invalid-first-argument-name-for-method
 "tests/*" = ["ANN001", "ANN102", "ANN2"]
-"setup.py" = ["F821"]
 "*__init__.py" = ["F401"]
 "gene/schemas.py" = ["ANN001", "ANN201", "N805"]
 "docs/source/conf.py" = ["D100", "I001", "D103", "ANN201", "ANN001"]
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/gene/__init__.py → src/gene/__init__.py b/gene/__init__.py → src/gene/__init__.py
@@ -5,7 +5,7 @@
 
 from .version import __version__  # noqa: F401
 
-APP_ROOT = Path(__file__).resolve().parents[0]
+APP_ROOT = Path(__file__).resolve().parent
 
 logging.basicConfig(
     filename="gene.log", format="[%(asctime)s] - %(name)s - %(levelname)s : %(message)s"

diff --git a/gene/cli.py → src/gene/cli.py b/gene/cli.py → src/gene/cli.py
diff --git a/gene/database/__init__.py → src/gene/database/__init__.py b/gene/database/__init__.py → src/gene/database/__init__.py
diff --git a/gene/database/database.py → src/gene/database/database.py b/gene/database/database.py → src/gene/database/database.py
diff --git a/gene/database/dynamodb.py → src/gene/database/dynamodb.py b/gene/database/dynamodb.py → src/gene/database/dynamodb.py
diff --git a/gene/database/postgresql.py → src/gene/database/postgresql.py b/gene/database/postgresql.py → src/gene/database/postgresql.py
diff --git a/gene/database/postgresql/add_fkeys.sql → src/gene/database/postgresql/add_fkeys.sql b/gene/database/postgresql/add_fkeys.sql → src/gene/database/postgresql/add_fkeys.sql
diff --git a/gene/database/postgresql/add_indexes.sql → src/gene/database/postgresql/add_indexes.sql b/gene/database/postgresql/add_indexes.sql → src/gene/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/gene/database/postgresql/create_tables.sql → ...ene/database/postgresql/create_tables.sql b/gene/database/postgresql/create_tables.sql → ...ene/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/gene/database/postgresql/drop_fkeys.sql → src/gene/database/postgresql/drop_fkeys.sql b/gene/database/postgresql/drop_fkeys.sql → src/gene/database/postgresql/drop_fkeys.sql
diff --git a/gene/database/postgresql/drop_indexes.sql → ...gene/database/postgresql/drop_indexes.sql b/gene/database/postgresql/drop_indexes.sql → ...gene/database/postgresql/drop_indexes.sql
diff --git a/gene/etl/__init__.py → src/gene/etl/__init__.py b/gene/etl/__init__.py → src/gene/etl/__init__.py
diff --git a/gene/etl/base.py → src/gene/etl/base.py b/gene/etl/base.py → src/gene/etl/base.py
diff --git a/gene/etl/ensembl.py → src/gene/etl/ensembl.py b/gene/etl/ensembl.py → src/gene/etl/ensembl.py
diff --git a/gene/etl/exceptions.py → src/gene/etl/exceptions.py b/gene/etl/exceptions.py → src/gene/etl/exceptions.py
diff --git a/gene/etl/hgnc.py → src/gene/etl/hgnc.py b/gene/etl/hgnc.py → src/gene/etl/hgnc.py
diff --git a/gene/etl/merge.py → src/gene/etl/merge.py b/gene/etl/merge.py → src/gene/etl/merge.py
diff --git a/gene/etl/ncbi.py → src/gene/etl/ncbi.py b/gene/etl/ncbi.py → src/gene/etl/ncbi.py
diff --git a/gene/etl/vrs_locations/__init__.py → src/gene/etl/vrs_locations/__init__.py b/gene/etl/vrs_locations/__init__.py → src/gene/etl/vrs_locations/__init__.py
diff --git a/.../etl/vrs_locations/chromosome_location.py → .../etl/vrs_locations/chromosome_location.py b/.../etl/vrs_locations/chromosome_location.py → .../etl/vrs_locations/chromosome_location.py
diff --git a/gene/etl/vrs_locations/sequence_location.py → ...ne/etl/vrs_locations/sequence_location.py b/gene/etl/vrs_locations/sequence_location.py → ...ne/etl/vrs_locations/sequence_location.py
diff --git a/gene/main.py → src/gene/main.py b/gene/main.py → src/gene/main.py
diff --git a/gene/query.py → src/gene/query.py b/gene/query.py → src/gene/query.py
diff --git a/gene/schemas.py → src/gene/schemas.py b/gene/schemas.py → src/gene/schemas.py
diff --git a/gene/version.py → src/gene/version.py b/gene/version.py → src/gene/version.py
diff --git a/tests/unit/test_ensembl_source.py b/tests/unit/test_ensembl_source.py
@@ -1,9 +1,9 @@
 """Test that the gene normalizer works as intended for the Ensembl source."""
 import pytest
+from tests.conftest import check_resp_single_record
 
 from gene.query import QueryHandler
 from gene.schemas import Gene, MatchType, SourceName
-from tests.conftest import check_resp_single_record
 
 
 @pytest.fixture(scope="module")

diff --git a/tests/unit/test_hgnc_source.py b/tests/unit/test_hgnc_source.py
@@ -2,10 +2,10 @@
 from datetime import datetime
 
 import pytest
+from tests.conftest import check_resp_single_record
 
 from gene.query import QueryHandler
 from gene.schemas import Gene, MatchType, SourceName
-from tests.conftest import check_resp_single_record
 
 
 @pytest.fixture(scope="module")

diff --git a/tests/unit/test_ncbi_source.py b/tests/unit/test_ncbi_source.py
@@ -2,15 +2,15 @@
 from datetime import datetime
 
 import pytest
-
-from gene.query import QueryHandler
-from gene.schemas import Gene, MatchType, SourceName
 from tests.conftest import (
     assertion_checks,
     check_ncbi_discontinued_gene,
     check_resp_single_record,
 )
 
+from gene.query import QueryHandler
+from gene.schemas import Gene, MatchType, SourceName
+
 
 @pytest.fixture(scope="module")
 def ncbi(database):