From b0cff3e6540980d61c209bf7a1fd4b45e2246e87 Mon Sep 17 00:00:00 2001
From: Nicholas Minor <nrminor@wisc.edu>
Date: Mon, 30 Sep 2024 08:30:48 -0500
Subject: [PATCH] bringing pyright configuration into the pyproject.toml

---
 pyproject.toml | 94 ++++++++++++++++++++++++++------------------------
 1 file changed, 49 insertions(+), 45 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index fb39ff3..cd54085 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,47 +3,47 @@ name = "oneroof"
 version = "0.1.0"
 description = "Base-, Variant-, and Consensus-calling under One Proverbial Roof. Work in progress!"
 authors = [
-  { name = "Nicholas R. Minor", email = "nrminor@wisc.edu" },
-  { name = "Andrew J. Lail", email = "ajlail@wisc.edu" },
-  { name = "Annabelle Kalweit", email = "akalweit@wisc.edu" },
+    { name = "Nicholas R. Minor", email = "nrminor@wisc.edu" },
+    { name = "Andrew J. Lail", email = "ajlail@wisc.edu" },
+    { name = "Annabelle Kalweit", email = "akalweit@wisc.edu" },
 ]
 requires-python = ">= 3.10"
 keywords = [
-  "science",
-  "biology",
-  "research",
-  "bioinformatics",
-  "sequencing",
-  "genomics",
-  "virus",
-  "SARS-CoV-2",
-  "H5N1",
-  "influenze",
-  "haplotyping",
+    "science",
+    "biology",
+    "research",
+    "bioinformatics",
+    "sequencing",
+    "genomics",
+    "virus",
+    "SARS-CoV-2",
+    "H5N1",
+    "influenze",
+    "haplotyping",
 ]
 classifiers = [
-  "Development Status :: 3 - Alpha",
+    "Development Status :: 3 - Alpha",
 
-  "Intended Audience :: Science/Research",
-  "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
 
-  "License :: OSI Approved :: MIT License",
+    "License :: OSI Approved :: MIT License",
 
-  "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
-  "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 dependencies = [
-  "polars-lts-cpu",
-  "xlsxwriter",
-  "xlsx2csv",
-  "biopython",
-  "pysam",
-  "marimo",
-  "numpy",
-  "scipy",
-  "paramiko",
+    "polars-lts-cpu",
+    "xlsxwriter",
+    "xlsx2csv",
+    "biopython",
+    "pysam",
+    "marimo",
+    "numpy",
+    "scipy",
+    "paramiko",
 ]
 
 [build-system]
@@ -53,6 +53,9 @@ build-backend = "setuptools.build_meta:__legacy__"
 [tool.setuptools]
 py-modules = ["bin"]
 
+[project.scripts]
+"oneroof" = "bin.__main__:main"
+
 [tool.pixi.project]
 channels = ["conda-forge", "bioconda", "anaconda"]
 platforms = ["osx-64", "linux-64"]
@@ -90,20 +93,21 @@ cffi = ">=1.15.0,<1.17.0"
 
 [tool.uv]
 dev-dependencies = [
-  "ipykernel>=6.29.5",
-  "ipython>=8.12.3",
-  "jupyter>=0.6.4",
-  "just>=0.8.162",
-  "mamba>=0.11.3",
-  "marimo[sql]>=0.8.14",
-  "pip>=24.2",
-  "pre-commit>=3.8.0",
-  "pytest>=8.3.3",
-  "quarto>=0.1.0",
-  "ruff>=0.6.4",
-  "tox>=4.18.1",
+    "ipykernel>=6.29.5",
+    "ipython>=8.12.3",
+    "jupyter>=0.6.4",
+    "just>=0.8.162",
+    "mamba>=0.11.3",
+    "marimo[sql]>=0.8.14",
+    "pip>=24.2",
+    "pre-commit>=3.8.0",
+    "pytest>=8.3.3",
+    "quarto>=0.1.0",
+    "ruff>=0.6.4",
+    "tox>=4.18.1",
 ]
 compile-bytecode = true
 
-[project.scripts]
-"oneroof" = "bin.__main__:main"
+[tool.pyright]
+venvPath = "."
+venv = ".venv"