Merge branch 'main' into 301-test-pyapp-action

.github/workflows/python-app.yml

@@ -39,4 +39,4 @@ jobs:
     - name: Test with pytest
       run: |
         make up-test
-        make test
+        make test-run

demo/metadata_migration/notebooks/migrate_9_3_2_to_10_0_0.ipynb

@@ -93,7 +93,7 @@
     "       # Run in the same directory as this notebook:\n",
     "       $ cp .notebook.env.example .notebook.env\n",
     "       ```\n",
-    "3. Create and populate **MongoDB configuration files** for connecting to the origin (typically, local) and transformer (typically, remote) MongoDB servers.\n",
+    "3. Create and populate **MongoDB configuration files** for connecting to the origin (typically, remote) and transformer (typically, local) MongoDB servers.\n",
     "    1. You can use the `.mongo.yaml.example` file as a template:\n",
     "       ```shell\n",
     "       # Run in the same directory as this notebook:\n",

docker-compose.test.yml

@@ -95,8 +95,6 @@ services:
     container_name: test
     env_file:
       - .env.test
-    profiles:
-      - donotstart
     depends_on:
       - mongo
       - fastapi

nmdc_runtime/test.Dockerfile

@@ -34,6 +34,7 @@ RUN chmod +x wait-for-it.sh
 # Best practices: Prepare for C crashes.
 ENV PYTHONFAULTHANDLER=1
 
+
 # uncomment line below to run all tests
 # ENTRYPOINT [ "./wait-for-it.sh", "fastapi:8000" , "--strict" , "--timeout=300" , "--" , "pytest"]