add pgscatalog.calc

pgscatalog.calc/noxfile.py

@@ -0,0 +1,58 @@
+import nox
+
+nox.options.error_on_external_run = True
+nox.options.default_venv_backend = "uv"
+
+
+# test every version of python we support!
+@nox.session
+@nox.parametrize("python", ["3.12", "3.11", "3.10"])
+def tests(session):
+    """Run pytest for all supported python versions"""
+    session.run_install(
+        "uv",
+        "sync",
+        env={"UV_PROJECT_ENVIRONMENT": session.virtualenv.location},
+    )
+    session.run("pytest", "--ignore", "noxfile.py")
+
+
+@nox.session
+@nox.parametrize("python", ["3.10"])
+def lint(session):
+    """Run linting checks"""
+    # https://nox.thea.codes/en/stable/cookbook.html#using-a-lockfile
+    # note: uv is set up to install the test and lint dependency groups
+    session.run_install(
+        "uv",
+        "sync",
+        env={"UV_PROJECT_ENVIRONMENT": session.virtualenv.location},
+    )
+    session.run("ruff", "check")
+    session.run("mypy", ".")
+
+
+@nox.session(default=False)
+def coverage(session):
+    """Run pytest and output a coverage report.
+
+    Not default for codecov.io integration with GitHub actions
+    """
+    session.run_install(
+        "uv",
+        "sync",
+        env={"UV_PROJECT_ENVIRONMENT": session.virtualenv.location},
+    )
+    session.run("pytest", "--ignore", "noxfile.py", "--cov", "--cov-report", "xml")
+
+
+# nox cookbook: https://nox.thea.codes/en/stable/cookbook.html
+# It's a good idea to keep your dev session out of the default list
+# so it's not run twice accidentally
+@nox.session(default=False)
+def dev(session: nox.Session) -> None:
+    """
+    Set up a python development environment for the project at ".venv".
+    """
+    session.run("uv", "venv")
+    session.run("uv", "sync")

pgscatalog.calc/pyproject.toml

@@ -1,38 +1,85 @@
-[tool.poetry]
+[project]
 name = "pgscatalog.calc"
 version = "0.3.0"
 description = "Libraries and applications for working with calculated polygenic scores"
-authors = ["Benjamin Wingfield <[email protected]>", "Samuel Lambert <[email protected]>", "Laurent Gil <[email protected]>"]
+license = {text = "Apache License (2.0)"}
+authors = [
+    {name = "Benjamin Wingfield", email = "[email protected]"},
+    {name = "Samuel Lambert", email = "[email protected]"},
+    {name = "Laurent Gil", email = "[email protected]"},
+    {name = "Florent Yvon", email = "[email protected]"}
+]
 readme = "README.md"
-packages = [
-    { include = "pgscatalog", from = "src" },
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 
-[tool.poetry.dependencies]
-python = ">=3.10"
-"pgscatalog.core" = "^0.3.1"
-numpy = "^1.26.4"
-pandas = "^2.2.0"
-pyarrow = "^15.0.0"
-scikit-learn = "^1.4.0"
-scipy = "^1.12.0"
+requires-python = ">=3.10"
+dependencies = [
+    "numpy~=1.26",
+    "pandas~=2.2.0",
+    "pgscatalog-core>=0.3.3",
+    "pyarrow~=15.0.0",
+    "scikit-learn~=1.4",
+    "scipy~=1.12",
+]
 
-[tool.poetry.scripts]
+# https://peps.python.org/pep-0621/
+[project.scripts]
 pgscatalog-aggregate = 'pgscatalog.calc.cli.aggregate_cli:run_aggregate'
 pgscatalog-ancestry-adjust = 'pgscatalog.calc.cli.ancestry_cli:run_ancestry'
 
-[tool.poetry.group.dev.dependencies]
-pytest = "^8.0.0"
-pytest-cov = "^4.1.0"
+# https://peps.python.org/pep-0735/
+[dependency-groups]
+lint = [
+    "ruff>=0.9.4",
+    "mypy>=1.14.1"
+    ]
+test = [
+    "pytest>=8.3.4",
+    "pytest-coverage>=0.0",
+]
 
 [build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src"]
 
 [tool.pytest.ini_options]
-minversion = "6.0"
-addopts = "-ra -q --doctest-modules"
+minversion = "8.0"
+addopts = "--doctest-modules"
 filterwarnings = ["error"]
+pythonpath = [
+  "src"
+]
+consider_namespace_packages = true
 
 [tool.coverage.run]
-source = ['src/pgscatalog/calc', "tests"]
+source = ["src/pgscatalog/core", "tests"]
+concurrency = ["multiprocessing"]
+parallel = true
+sigterm = true
+
+[tool.uv]
+default-groups = ["test", "lint"]
+
+[tool.mypy]
+files = ["src/**/*.py"]
+warn_unused_configs = true
+ignore_missing_imports = true
+follow_imports = "silent"
+disallow_untyped_calls = false
+disallow_incomplete_defs = true
+
+[tool.setuptools.packages.find]
+where = ["src"]

pgscatalog.calc/src/pgscatalog/calc/cli/__init__.py

@@ -1 +0,0 @@
-__all__ = []

pgscatalog.calc/src/pgscatalog/calc/lib/_ancestry/read.py

@@ -1,3 +1,5 @@
+# mypy: ignore-errors
+
 import logging
 import pandas as pd
 

pgscatalog.calc/src/pgscatalog/calc/lib/_ancestry/tools.py

@@ -1,3 +1,5 @@
+# mypy: ignore-errors
+
 import logging
 import pandas as pd
 import numpy as np
@@ -342,7 +344,9 @@ def pgs_adjust(
         if np.var(results_ref[sum_col]) == 0:
             scorecols_drop.add(c_pgs)
             logger.warning(
-                "Skipping adjustment: {} has 0 variance in PGS SUM [REFERENCE]".format(c_pgs)
+                "Skipping adjustment: {} has 0 variance in PGS SUM [REFERENCE]".format(
+                    c_pgs
+                )
             )
 
     # Report PGS values with respect to distribution of PGS in the most similar reference population