From e69da757258c088ff55b7bedd26206dfb667339c Mon Sep 17 00:00:00 2001
From: Charlie <ctbushman@gmail.com>
Date: Wed, 20 Aug 2025 14:17:17 -0400
Subject: [PATCH] Use pyproject and drop scripts

---
 pyproject.toml             | 24 ++++++++++++++++++++++++
 scripts/backup_illumina.py |  4 ----
 seqBackupLib/backup.py     | 10 ++++------
 setup.py                   | 18 ------------------
 4 files changed, 28 insertions(+), 28 deletions(-)
 create mode 100644 pyproject.toml
 delete mode 100644 scripts/backup_illumina.py
 delete mode 100644 setup.py

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..16c687a
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,24 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "seqBackup"
+description = "Set of rules to organize our fastq storage on the server."
+authors = [{name = "Ceylan Tanes", email = "ctanes@gmail.com"}]
+readme = "README.md"
+requires-python = ">=3.9"
+dynamic = ["version"]
+
+[project.urls]
+homepage = "https://github.com/PennChopMicrobiomeProgram"
+
+[project.scripts]
+backup_illumina = "seqBackupLib.backup:main"
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["seqBackupLib"]
+
+[tool.setuptools.dynamic]
+version = {attr = "seqBackupLib.version.__version__"}
diff --git a/scripts/backup_illumina.py b/scripts/backup_illumina.py
deleted file mode 100644
index 7fcb1c7..0000000
--- a/scripts/backup_illumina.py
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/usr/bin/env python
-from seqBackupLib.backup import main
-
-main()
diff --git a/seqBackupLib/backup.py b/seqBackupLib/backup.py
index 920f206..db16847 100644
--- a/seqBackupLib/backup.py
+++ b/seqBackupLib/backup.py
@@ -121,11 +121,9 @@ def main(argv=None):
         help="The sample sheet associated with the run.",
     )
     parser.add_argument(
-        "--has-index",
-        required=False,
-        type=bool,
-        default=True,
-        help="Are index reads generated",
+        "--no-index",
+        action="store_true",
+        help="Skip index reads (I1/I2) during backup",
     )
     parser.add_argument(
         "--min-file-size",
@@ -140,7 +138,7 @@ def main(argv=None):
         args.forward_reads,
         args.destination_dir,
         args.sample_sheet,
-        args.has_index,
+        not args.no_index,
         args.min_file_size,
     )
 
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 00df46d..0000000
--- a/setup.py
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env python
-
-from distutils.core import setup
-
-# Get version number from package
-exec(open("seqBackupLib/version.py").read())
-
-setup(
-    name="seqBackup",
-    version=__version__,
-    description="Set of rules to organize our fastq storage on the server.",
-    author="Ceylan Tanes",
-    author_email="ctanes@gmail.com",
-    url="https://github.com/PennChopMicrobiomeProgram",
-    packages=["seqBackupLib"],
-    scripts=["scripts/backup_illumina.py"],
-    python_requires=">=3.9",
-)