refactor: migrate to src layout

- Move code_annotations/ to src/code_annotations/
- Add where = ["src"] to [tool.setuptools.packages.find]
- Update tox.ini quality commands to src/code_annotations paths
- Update docs/conf.py sphinx-apidoc path to src/code_annotations
- Update coverage omit path in pyproject.toml
- Rewrite Makefile to use direct uv run --group commands (no tox)
- Regenerate uv.lock

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: salman2013

Makefile

@@ -34,27 +34,32 @@ coverage: clean ## generate and view HTML coverage report
 	$(BROWSER) htmlcov/index.html
 
 docs: ## generate Sphinx HTML documentation, including API docs
-	uv run tox -e docs
+	uv run --group doc doc8 --ignore-path docs/_build README.rst docs
+	uv run --group doc sphinx-build -b html docs docs/_build/html
 	$(BROWSER) docs/_build/html/index.html
 
 upgrade: ## update uv.lock and regenerate uv constraint-dependencies
-	uv run --with edx-lint edx_lint write_uv_constraints pyproject.toml
+	uv run --group quality edx_lint write_uv_constraints pyproject.toml
 	uv lock --upgrade
 
 quality: ## check coding style with pycodestyle and pylint
-	uv run tox -e quality
+	uv run --group quality pylint src/code_annotations tests test_utils
+	uv run --group quality pycodestyle src/code_annotations tests
+	uv run --group quality pydocstyle src/code_annotations tests
+	uv run --group quality isort --check-only --diff tests test_utils src/code_annotations
 
 requirements: ## install development environment requirements
 	uv sync --group dev
 
 test: clean ## run tests in the current virtualenv
-	uv run pytest
+	uv run --group test python -Wd -m pytest
 
 diff_cover: test ## find diff lines that need test coverage
 	diff-cover coverage.xml
 
-test-all: ## run tests on every supported Python
-	uv run tox
+test-all: ## run tests on every supported Django version
+	uv run --group django42 python -Wd -m pytest
+	uv run --group test python -Wd -m pytest
 
 validate: quality test ## run tests and quality checks
 

docs/conf.py

@@ -502,8 +502,8 @@ def on_init(app):  # pylint: disable=unused-argument
         # If we are, assemble the path manually
         bin_path = os.path.abspath(os.path.join(sys.prefix, 'bin'))
         apidoc_path = os.path.join(bin_path, apidoc_path)
-    check_call([apidoc_path, '-o', docs_path, os.path.join(root_path, 'code_annotations'),
-                os.path.join(root_path, 'code_annotations/migrations')])
+    check_call([apidoc_path, '-o', docs_path, os.path.join(root_path, 'src', 'code_annotations'),
+                os.path.join(root_path, 'src', 'code_annotations', 'migrations')])
 
 
 def setup(app):

pyproject.toml

@@ -48,6 +48,7 @@ local_scheme = "no-local-version"
 fallback_version = "0.0.0.dev0"
 
 [tool.setuptools.packages.find]
+where = ["src"]
 include = ["code_annotations*"]
 
 [tool.setuptools.package-data]
@@ -78,10 +79,11 @@ test = [{include-group = "test-base"}, "Django>=5.2,<5.3"]
 django42 = [{include-group = "test-base"}, "Django>=4.2,<4.3"]
 quality = [
     {include-group = "test"},
-    "edx-lint",
+    "edx-lint<6",
     "isort",
     "pycodestyle",
     "pydocstyle",
+    "setuptools<81",
 ]
 doc = [
     {include-group = "test"},
@@ -122,7 +124,7 @@ branch = true
 source = ["code_annotations"]
 omit = [
     "test_settings",
-    "code_annotations/extensions/tests/python_test_files/*",
+    "src/code_annotations/extensions/tests/python_test_files/*",
 ]
 
 [tool.coverage.report]