merge stage into main

[aditya-arcot]

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[Copilot]

Pull request overview

This PR merges changes from stage into main, primarily refactoring the server to use dependency-injected Settings (instead of a global settings singleton), adding coverage/type-check tooling, expanding test coverage, and adding client-side theming support.

Changes:

• Server: introduce get_settings() + DI throughout services/dependencies; add app factory (create_app) and update logging/health endpoints.
• Tooling/CI: add Pyright + pytest-cov + coverage config; update Makefile targets and CI workflows to run coverage.
• Client: add theme toggling (next-themes) and migrate several UI primitive imports to radix-ui; regenerate API client for new endpoints.

Reviewed changes

Copilot reviewed 88 out of 100 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
server/uv.lock	Updates Python dependency lock (adds pyright/coverage/pytest-cov, bumps packages).
server/pyproject.toml	Adds deps + pyright/coverage tool config.
server/makefile	Adds cov/open-cov, switches check to pyright, renames migrate target.
server/conftest.py	Registers new pytest fixtures (logging/settings).
server/app/tests/test_main.py	Adds test verifying app.main import behavior.
server/app/tests/services/test_email.py	Updates email tests for new service signatures/settings fixture.
server/app/tests/services/auth/test_request_access.py	Updates tests for settings injection + background task args.
server/app/tests/services/auth/test_login.py	Updates login tests for settings injection.
server/app/tests/fixtures/settings.py	Adds centralized test Settings fixture and disables env file loading.
server/app/tests/fixtures/overrides.py	Refactors settings/email override fixtures (no global mutation).
server/app/tests/fixtures/logging.py	Adds root logger restoration fixture for logging tests.
server/app/tests/fixtures/database.py	Improves test DB setup; flags migrations as testing; safer rollback.
server/app/tests/fixtures/client.py	Builds test app via factory + overrides get_settings/get_db.
server/app/tests/core/test_logging.py	Adds tests for setup_logging behavior and file output.
server/app/tests/core/test_handlers.py	Adds tests for exception handler prod vs non-prod behavior.
server/app/tests/core/test_config.py	Adds tests for settings validation/caching and env-specific behavior.
server/app/tests/core/security/test_verify_jwt.py	Adds verify_jwt tests with settings-driven secrets.
server/app/tests/core/security/test_get_token.py	Adds token retrieval tests for registration/reset tokens.
server/app/tests/core/security/test_expire_tokens.py	Adds tests for expiring existing tokens.
server/app/tests/core/security/test_create_token.py	Adds tests for token creation helpers/wrappers.
server/app/tests/core/security/test_create_jwt.py	Adds tests for JWT creation helpers/wrappers.
server/app/tests/core/security/test_create_access_token.py	Removes old access token test (superseded by new suite).
server/app/tests/core/security/test_authenticate_user.py	Updates auth tests; renames one test case.
server/app/tests/core/dependencies/test_get_sessionmaker.py	Adds tests for cached sessionmaker behavior.
server/app/tests/core/dependencies/test_get_db.py	Adds tests for get_db(settings) yielding configured session.
server/app/tests/core/dependencies/test_get_current_user.py	Updates dependency tests for settings injection + JWT helpers.
server/app/tests/core/dependencies/test_get_current_admin.py	Updates admin dependency tests to use settings fixture.
server/app/tests/api/utilities.py	Refactors test request helper and admin login helper (settings-aware).
server/app/tests/api/test_user_get_current_user.py	Updates API tests to use login_admin(..., settings).
server/app/tests/api/test_feedback_create_feedback.py	Adds API tests for feedback creation endpoint.
server/app/tests/api/health/test_get_health.py	Adds status-code comment; no logic change.
server/app/tests/api/health/test_get_db_health.py	Adds API test for new /api/health/db endpoint.
server/app/tests/api/auth/test_reset_password.py	Updates tests for settings fixture + status code constant.
server/app/tests/api/auth/test_request_access.py	Updates expected 422 status constant.
server/app/tests/api/auth/test_register.py	Updates tests for settings fixture + status code constant.
server/app/tests/api/auth/test_refresh_token.py	Updates test to use settings-aware login helper.
server/app/tests/api/auth/test_logout.py	Updates test to use settings-aware login helper.
server/app/tests/api/auth/test_login.py	Updates tests for settings fixture + status code constant.
server/app/tests/api/auth/test_forgot_password.py	Updates test signature to use settings fixture.
server/app/tests/api/admin/test_update_access_request_status.py	Updates admin API tests for settings injection.
server/app/tests/api/admin/test_get_users.py	Updates admin API tests for settings injection + typing ignores.
server/app/tests/api/admin/test_get_access_requests.py	Updates admin API tests for settings injection + typing ignores.
server/app/services/github.py	Makes GitHub service settings-driven via DI and call-time settings arg.
server/app/services/feedback.py	Passes settings into feedback storage + GitHub issue creation.
server/app/services/email.py	Makes email service settings-driven via DI; updates send signatures.
server/app/services/auth.py	Threads settings through auth flows (JWT/email/background tasks).
server/app/services/admin.py	Threads settings through admin flow for email background tasks.
server/app/migrations/versions/2025_12_22_1054-b38ada12f56b_seed_admin_user.py	Adds test-mode branch to avoid reading .env during test migrations.
server/app/migrations/env.py	Switches migrations config to get_settings() instead of global settings.
server/app/main.py	Simplifies to app factory usage (fastapi_app, app = create_app()).
server/app/core/security.py	Refactors security helpers to require settings; improves typing.
server/app/core/logging.py	Refactors logging setup to accept params instead of global settings.
server/app/core/handlers.py	Makes prod/non-prod error detail behavior app-state driven.
server/app/core/dependencies.py	Makes DB/session/JWT dependencies settings-driven; adds cached sessionmaker.
server/app/core/config.py	Introduces cached get_settings() and is_prod_like; adjusts settings model.
server/app/api/endpoints/health.py	Adds /api/health/db endpoint that validates DB connectivity.
server/app/api/endpoints/feedback.py	Passes settings into background task for feedback creation.
server/app/api/endpoints/auth.py	Threads settings into auth endpoints and cookie behavior.
server/app/api/endpoints/admin.py	Threads settings into admin endpoint to support email flows.
server/app/init.py	Adds create_app() factory; installs swagger dark in non-prod-like envs.
server/.gitignore	Ignores .coverage output.
scripts/generate_api.sh	Suppresses logging while importing app for OpenAPI generation.
package.json	Adds check:py and runs pyright in lint/lint-staged.
package-lock.json	Updates dev tooling deps (lint-staged/npm-check-updates/etc.).
client/src/main.tsx	Wraps app with ThemeProvider.
client/src/layout/AppLayout.tsx	Adds theme mode toggle control to layout.
client/src/components/ui/separator.tsx	Switches separator primitive import to radix-ui.
client/src/components/ui/select.tsx	Switches select primitive import to radix-ui.
client/src/components/ui/popover.tsx	Switches popover primitive import to radix-ui.
client/src/components/ui/label.tsx	Switches label primitive import to radix-ui.
client/src/components/ui/dropdown-menu.tsx	Switches dropdown menu primitive import to radix-ui.
client/src/components/ui/dialog.tsx	Switches dialog primitive import to radix-ui.
client/src/components/ui/checkbox.tsx	Switches checkbox primitive import to radix-ui.
client/src/components/ui/button.tsx	Switches Slot usage to radix-ui API (Slot.Root).
client/src/components/ui/badge.tsx	Switches Slot usage to radix-ui API (Slot.Root).
client/src/components/ModeToggle.tsx	Adds theme mode dropdown UI using next-themes.
client/src/api/generated/zod.gen.ts	Regenerates Zod schemas (includes new db health endpoint + minor schema changes).
client/src/api/generated/types.gen.ts	Regenerates TS API types (adds GetDbHealth*).
client/src/api/generated/sdk.gen.ts	Regenerates SDK (adds HealthService.getDbHealth).
client/src/api/generated/index.ts	Re-exports newly generated endpoint types.
client/src/api/generated/core/params.gen.ts	Fixes empty-slot stripping logic for array params.
client/src/api/generated/client/types.gen.ts	Allows async CreateClientConfig and exposes onRequest.
client/src/api/generated/client.gen.ts	Aligns CreateClientConfig type with async support.
client/src/App.tsx	Removes hard-coded toaster theme (to follow app theme).
client/package.json	Adds radix-ui, bumps assorted deps.
.vscode/settings.json	Enables nearest Python analysis configuration.
.prettierignore	Ignores server/htmlcov/ and server/logs/.
.github/workflows/test-server.yml	Renames workflow and runs tests via make cov.
.github/workflows/merge-main-into-stage.yml	Renames workflow/job for clarity.
.github/workflows/generate-api.yml	Renames workflow/job, adds macOS keychain unlock, adjusts env creation.
.github/workflows/format-and-lint.yml	Renames workflow/job and updates trigger workflow name.
.github/workflows/deploy.yml	Renames workflow/jobs for clarity and updates reusable workflow wiring.
.github/workflows/deploy-server.yml	Renames reusable workflow and job.
.github/workflows/deploy-infra.yml	Renames reusable workflow and job.
.github/workflows/deploy-client.yml	Renames reusable workflow and job.
.github/workflows/codeql.yml	Renames workflow/job for clarity.
.github/workflows/build.yml	Renames workflow/jobs for clarity.