From 2f5e17c2b21bbbaab0e9b781f70aa90c8a827ffa Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Tue, 14 Jan 2025 15:01:39 -0700
Subject: [PATCH] add bwa as a submodule

---
 .github/workflows/ci.yml | 4 +---
 .gitmodules              | 3 +++
 .readthedocs.yml         | 3 ++-
 bwa                      | 1 +
 4 files changed, 7 insertions(+), 4 deletions(-)
 create mode 100644 .gitmodules
 create mode 160000 bwa

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index dbc7767..69918a8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -11,11 +11,9 @@ jobs:
       matrix:
         PYTHON_VERSION: ["3.9", "3.10", "3.11", "3.12"]
     steps:
-    - uses: actions/checkout@v4
     - uses: actions/checkout@v4
       with:
-        repository: "lh3/bwa"
-        path: "bwa"
+        submodules: 'true'
     - name: Set up Python ${{matrix.PYTHON_VERSION}}
       uses: actions/setup-python@v1
       with:
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..294fcff
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "bwa"]
+	path = bwa
+	url = git@github.com:lh3/bwa.git
diff --git a/.readthedocs.yml b/.readthedocs.yml
index 33c42f0..72effb3 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -5,10 +5,11 @@ build:
     python: "3.9"
   jobs:
     pre_install:
-      - git clone https://github.com/lh3/bwa.git
       - pip install poetry==1.8.3
       - poetry config virtualenvs.create false
       - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install
+submodules:
+  include: all
 sphinx:
   configuration: docs/conf.py
 python:
diff --git a/bwa b/bwa
new file mode 160000
index 0000000..79b230d
--- /dev/null
+++ b/bwa
@@ -0,0 +1 @@
+Subproject commit 79b230de48c74156f9d3c26795a360fc5a2d5d3b