Merge pull request #26 from bioio-devs/admin/use-git-lfs

BrianWhitneyAI · web-flow · commit 5f4021bb5627 · 2025-07-09T10:11:00.000-07:00
admin/use-git-lfs
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+bioio_sldy/tests/resources/** filter=lfs diff=lfs merge=lfs -text
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -39,20 +39,14 @@ jobs:
       matrix:
         python-version: ["3.10", 3.11, 3.12, 3.13]
         os: [ubuntu-latest, macOS-latest, windows-latest]
-    env:
-      BUCKET_NAME : "bioio-dev-test-resources"
-      AWS_REGION : "us-west-2"
     permissions:
       id-token: write   # This is required for requesting the JWT
       contents: read    # This is required for actions/checkout
 
     steps:
     - uses: actions/checkout@v4
-    - uses: aws-actions/configure-aws-credentials@v4
       with:
-        role-to-assume: arn:aws:iam::978220035532:role/bioio_github
-        role-session-name: bioio-sldy-${{ github.sha }}
-        aws-region: ${{ env.AWS_REGION }}
+        lfs: true # For test files
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
@@ -64,15 +58,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install .[test]
-    - uses: actions/cache@v4
-      id: cache
-      with:
-        path: bioio_sldy/tests/resources
-        key: ${{ hashFiles('scripts/TEST_RESOURCES_HASH.txt') }}
-    - name: Download Test Resources
-      if: steps.cache.outputs.cache-hit != 'true'
-      run: |
-        python scripts/download_test_resources.py --debug
     - name: Run Tests
       shell: bash
       run: just test
diff --git a/.gitignore b/.gitignore
@@ -6,9 +6,6 @@ __pycache__/
 # C extensions
 *.so
 
-# Test file resources
-bioio_sldy/tests/resources
-
 # Distribution / packaging
 .Python
 env/
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -9,6 +9,27 @@ If something goes wrong at any point during installing the library please see ho
 [our CI/CD on GitHub Actions](.github/workflows/build-main.yml) installs and builds the
 project as it will always be the most up-to-date.
 
+## Test Resources and Git LFS
+
+   This project uses Git Large File Storage (LFS) to store large test resources under /tests/resources/.
+   Before cloning, make sure you have Git LFS installed:
+
+   ### macOS
+   ```
+   brew install git-lfs
+   git lfs install
+   ```
+
+   ### Debian/Ubuntu
+   ```
+   sudo apt-get install git-lfs
+   git lfs install
+   ```
+
+   ### Or install manually: https://git-lfs.github.com/
+
+   ⚠️ If you skip git lfs install, large files will appear as plain-text pointers and your tests may fail.
+   
 ## Get Started!
 
 Ready to contribute? Here's how to set up `bioio-sldy` for local development.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1 @@
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diff --git a/pyproject.toml b/pyproject.toml
@@ -50,7 +50,6 @@ lint = [
 test = [
   "coverage>=5.1",
   "dask[array,distributed]>=2021.4.1",
-  "quilt3",  # no pin to avoid pip cycling (boto is really hard to manage)
   "pytest>=5.4.3",
   "pytest-cov>=2.9.0",
   "pytest-raises>=0.11",
diff --git a/scripts/TEST_RESOURCES_HASH.txt b/scripts/TEST_RESOURCES_HASH.txt
diff --git a/scripts/download_test_resources.py b/scripts/download_test_resources.py
diff --git a/scripts/upload_test_resources.py b/scripts/upload_test_resources.py

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