From 84c8ec48dc7098fdc6cc3e6497e118ce97db1c73 Mon Sep 17 00:00:00 2001
From: Erin McAuley <erin@fulcrumgenomics.com>
Date: Fri, 2 Aug 2024 18:12:31 -0400
Subject: [PATCH] fix:  RTD needs an  `__init__.py` in `fgpyo/platform/` (#174)

* refactor: add init, docs: add docstring to illumina.py

* style: mkdocs docstring formatting
---
 fgpyo/platform/__init__.py            |  0
 fgpyo/platform/illumina.py            | 20 ++++++++++++++++----
 tests/fgpyo/platform/test_illumina.py |  2 ++
 3 files changed, 18 insertions(+), 4 deletions(-)
 create mode 100644 fgpyo/platform/__init__.py

diff --git a/fgpyo/platform/__init__.py b/fgpyo/platform/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/fgpyo/platform/illumina.py b/fgpyo/platform/illumina.py
index 161382c2..c3c0305e 100644
--- a/fgpyo/platform/illumina.py
+++ b/fgpyo/platform/illumina.py
@@ -1,3 +1,15 @@
+"""
+Methods for working with Illumina-specific UMIs in SAM files
+------------------------------------
+
+The functions in this module make it easy to:
+
+* check whether a UMI is valid
+* extract UMI(s) from an Illumina-style read name
+* copy a UMI from an alignment's read name to its `RX` SAM tag
+
+"""
+
 from typing import Optional
 from typing import Set
 
@@ -35,10 +47,10 @@ def extract_umis_from_read_name(
         read_name_delimiter: The delimiter separating the components of the read name.
         umi_delimiter: The delimiter separating multiple UMIs.
         strict: If `strict` is `True`, the read name must contain either 7 or 8 colon-separated
-          segments. The UMI is assumed to be the last one in the case of 8 segments and `None`
-          in the case of 7 segments. `strict` requires the UMI to be valid and consistent with
-          Illumina's allowed UMI characters. If `strict` is `False`, the last segment is returned
-          so long as it appears to be a valid UMI.
+            segments. The UMI is assumed to be the last one in the case of 8 segments and `None`
+            in the case of 7 segments. `strict` requires the UMI to be valid and consistent with
+            Illumina's allowed UMI characters. If `strict` is `False`, the last segment is returned
+            so long as it appears to be a valid UMI.
 
     Returns:
         The UMI extracted from the read name, or None if no UMI was found. Multiple UMIs are
diff --git a/tests/fgpyo/platform/test_illumina.py b/tests/fgpyo/platform/test_illumina.py
index c68df023..43d05324 100644
--- a/tests/fgpyo/platform/test_illumina.py
+++ b/tests/fgpyo/platform/test_illumina.py
@@ -1,3 +1,5 @@
+"""Basic tests for Illumina-specific UMI Methods"""
+
 from typing import Optional
 
 import pytest