add bwa as a submodule

fulcrumgenomics · Jan 14, 2025 · 2f5e17c · 2f5e17c
1 parent 8154424
commit 2f5e17c
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Showing 4 changed files with 7 additions and 4 deletions.
diff --git 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
@@ -0,0 +1,3 @@
+[submodule "bwa"]
+	path = bwa
+	url = [email protected]:lh3/bwa.git
diff --git 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