docs: update instructions for FastAPI, pytest, alembic, and Copilot

Generated-by: aiautocommit

Author: iloveitaly

.cursor/rules/alembic-migrations.mdc

@@ -3,7 +3,6 @@ description:
 globs: migrations/versions/*.py
 alwaysApply: false
 ---
-
 ## Alembic Migrations
 
 ### Data Migrations

.github/copilot-instructions.md

@@ -34,5 +34,5 @@ session_id = client_secret_id.split("_secret")[0]
 
 ### Agent instructions
 
-- Run python tests with `pytest` only. If tests fail because of a configuration or system error, do not attempt to fix and let me know. I will fix it.
+- Run python tests with `pytest` only. Do not `cat` the output and do not use `-q`. If tests fail because of a configuration or system error, do not attempt to fix and let me know. I will fix it.
 - If you added models, generate a migration with `just migration {add,delete,update}_model_other_description`

.github/instructions/alembic-migrations.instructions.md

@@ -0,0 +1,29 @@
+---
+applyTo: "migrations/versions/*.py"
+---
+## Alembic Migrations
+
+### Data Migrations
+
+For migrations that include data mutation, and not only schema modifications, use this pattern to setup a session:
+
+```python
+from alembic import op
+from sqlmodel import Session
+from activemodel.session_manager import global_session
+from app import log
+
+def run_migration_helper():
+  pass
+
+def upgrade() -> None:
+  session = Session(bind=op.get_bind())
+
+  with global_session(session):
+      run_migration_helper()
+      flip_point_coordinates()
+      backfill_screening_host_data()
+
+  # flush before running any other operations, otherwise not all changes will persist to the transaction
+  session.flush()
+```

.github/instructions/fastapi.instructions.md

@@ -5,3 +5,4 @@ applyTo: "app/routes/**/*.py"
 
 - When throwing a `HTTPException`, do not add a `detail=` and use a named status code (`status.HTTP_400_BAD_REQUEST`)
 - Do not return a `dict`, instead create a `class RouteNameResponse`
+  - Locate these classes right above the `def route_name():` function which uses them.

.github/instructions/pytest-tests.instructions.md

@@ -0,0 +1,9 @@
+---
+applyTo: "tests/**/*.py"
+---
+## Pytest Tests
+
+- Look to tests/factories.py to generate any required database state
+  - Here's an example of how to create + persist a factory `DistributionFactory.save()`
+- Use the `faker` factory to generate emails, etc.
+- Do not mock or patch unless I instruct you to. Test as much of the application stack as possible in each test.

constants.py

@@ -9,10 +9,12 @@
     "Python": "**/*.py",
     "Python App": "**/*.py",
     "Pytest Integration Tests": "tests/integration/**/*.py",
+    "Pytest Tests": "tests/**/*.py",
     "Python Route Tests": "tests/routes/**/*.py",
+    "Alembic Migrations": "migrations/versions/*.py",
     "FastAPI": "app/routes/**/*.py",
 
-    "React": "**/*.tsx", 
+    "React": "**/*.tsx",
     "React Router": "web/app/routes/**/*.tsx",
     "React Router Client Loader": None,