wipt

.github/workflows/testing.yaml

@@ -21,12 +21,23 @@ jobs:
           - "3.10"
     runs-on: ${{ matrix.os }}
     steps:
-      - name: Checkout
-        uses: actions/checkout@v3
+      - name: Get token from Github App
+      uses: actions/create-github-app-token@v1
+      id: app_token
+      with:
+        app-id: ${{ secrets.APP_ID }}
+        private-key: ${{ secrets.APP_PEM }}
+        # owner is required, otherwise the creds will fail the checkout step
+        owner: ${{ github.repository_owner }}
+
+      - name: Checkout from GitHub
+        uses: actions/checkout@v4
         with:
           lfs: 'false'
-          submodules: 'recursive'
+          submodules: true
           ssh-key: ${{ secrets.git_ssh_key  }}
+          token: ${{ steps.app_token.outputs.token }}
+
       - name: Get changed files
         uses: dorny/paths-filter@v2
         id: filter

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "zetta_utils/alignment"]
+	path = zetta_utils/alignment
+	url = [email protected]:ZettaAI/alignment.git

zetta_utils/__init__.py

@@ -30,10 +30,14 @@ def try_load_train_inference():  # pragma: no cover
     except ImportError:
         ...
 
+def try_load_submodules():
+    try:
+        from . import alignment
+    except ImportError:
+        ...
 
 def load_inference_modules():
     from . import (
-        alignment,
         augmentations,
         convnet,
         mazepa,
@@ -46,11 +50,11 @@ def load_inference_modules():
     from .layer import volumetric
     from .layer.volumetric import cloudvol
     from .message_queues import sqs
+    try_load_submodules()
 
 
 def load_training_modules():
     from . import (
-        alignment,
         augmentations,
         convnet,
         mazepa,
@@ -61,6 +65,7 @@ def load_training_modules():
     )
     from .layer import volumetric
     from .layer.volumetric import cloudvol
+    try_load_submodules()
 
 
 try_load_train_inference()