[License & Tests]: Updating the license to Apache-2 and reworking the tests slightly

.github/workflows/tests.yml

@@ -1,4 +1,4 @@
-name: Fast Tests
+name: Tests
 
 on:
   push:
@@ -7,14 +7,15 @@ on:
       - ".github/badges/coverage.svg"
   pull_request:
     branches: [main, master]
+  workflow_dispatch:
 
 permissions:
   contents: read
 
 jobs:
-  fast-test:
+  test:
     runs-on: ubuntu-latest
-    timeout-minutes: 15
+    timeout-minutes: 75
 
     steps:
       - uses: actions/checkout@v4
@@ -31,10 +32,49 @@ jobs:
       - name: Install dependencies
         run: uv sync --python 3.11 --all-extras
 
-      - name: Run fast test gate
+      - name: Run test suite
         run: >
-          uv run --python 3.11 pytest tests/
-          -m "(unit or component or optimization) and not slow and not characterization and not pdk"
+          uv run --no-active --python 3.11 python -m pytest tests/
           -v
           --tb=short
-          --durations=25
+          --durations=50
+          --cov=beamz
+          --cov-report=term-missing
+          --cov-report=xml
+          --cov-fail-under=75
+
+      - name: Upload coverage report
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-xml
+          path: coverage.xml
+
+  coverage-badge:
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    needs: test
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download coverage report
+        uses: actions/download-artifact@v4
+        with:
+          name: coverage-xml
+
+      - name: Generate coverage badge
+        run: python scripts/update_coverage_badge.py coverage.xml .github/badges/coverage.svg
+
+      - name: Commit coverage badge
+        run: |
+          if git diff --quiet -- .github/badges/coverage.svg; then
+            exit 0
+          fi
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add .github/badges/coverage.svg
+          git commit -m "ci: update coverage badge"
+          git push

AGENTS.md

@@ -0,0 +1,27 @@
+# Codex refactoring rules
+
+Goal: make this repository smaller, clearer, and easier to maintain without changing public behavior.
+
+Hard constraints:
+- Do not change public APIs unless explicitly requested.
+- Do not change numerical results except within documented tolerances.
+- Do not rewrite large subsystems in one PR.
+- Prefer deleting dead code, merging duplicated logic, simplifying files, and removing unused abstractions.
+- Keep every PR small and reviewable.
+- Every change must pass tests, linting, and type checks.
+- If behavior changes are necessary, stop and explain before editing.
+
+Definition of done:
+- Tests pass.
+- New or updated tests cover the refactored behavior.
+- Public imports still work.
+- Numerical regression tests pass.
+- LOC, complexity, or duplication improves.
+- PR description explains what was removed, what was preserved, and how correctness was checked.
+
+For JAX code:
+- Do not accidentally move dynamic values into static arguments.
+- Do not introduce recompilation loops.
+- Do not change dtype behavior without tests.
+- Do not change array shapes, pytree structure, or JIT boundaries unless explicitly asked.
+- Do not optimize for elegance at the cost of compile time or memory use.

DEVELOPMENT.md

@@ -51,17 +51,16 @@ All development commands use the Makefile:
 ```bash
 make help          # Show all available commands
 make test          # Run tests with coverage
-make test-fast     # Run quick tests
 make format        # Format code and fix package lint issues
 make lint          # Check code quality
 make dead-code     # Check for high-confidence dead code
-make audit         # Run lint, dead-code checks, and fast tests
+make audit         # Run lint, dead-code checks, and tests
 make build         # Build distribution
 ```
 
 Or use uv directly:
 ```bash
-uv run pytest tests/
+uv run python -m pytest tests/
 uv run --extra lint ruff check beamz/
 uv run --extra lint ruff format beamz/
 ```
@@ -90,18 +89,15 @@ uv remove <package-name>
 # All tests with coverage
 make test
 
-# Fast tests (skip @pytest.mark.slow)
-make test-fast
-
 # Single test file
 make test-single FILE=test_physics_energy.py
 
 # Specific test function
-uv run pytest tests/test_physics_energy.py::test_energy_conservation -v
+uv run python -m pytest tests/test_physics_energy.py::test_energy_conservation -v
 
 # Tests by marker
-uv run pytest -m design
-uv run pytest -m simulation
+uv run python -m pytest -m design
+uv run python -m pytest -m simulation
 ```
 
 ### Writing Tests
@@ -267,14 +263,15 @@ uv sync
 
 GitHub Actions workflows use uv:
 - `.github/workflows/tests.yml` - Run tests on push/PR
-- Configured for Python 3.10 and 3.11
+- Configured for Python 3.11
 - Uses `astral-sh/setup-uv@v5` action
+- Runs the full suite with coverage and enforces the current coverage baseline
 
 ## Best Practices
 
 1. **Always use `uv add/remove`** for dependencies (keeps lockfile in sync)
 2. **Run `make format`** before committing
-3. **Run `make test-fast`** during development
+3. **Run focused `uv run python -m pytest ...` commands** while iterating
 4. **Run `make test`** before pushing
 5. **Keep lockfile committed** (ensures reproducibility)
 6. **Use `make` commands** for consistency