chore: Move to use make targets in CI

.github/workflows/ci.yaml

@@ -13,19 +13,27 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
-      - name: Install uv
-        uses: astral-sh/setup-uv@v3
+      - uses: ./.github/actions/setup
       - name: mypy
-        run: MYPYPATH=stubs uv run mypy src
+        run: make mypy
+
+  pre-commit:
+    if: ${{ !github.event.pull_request.draft }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - uses: ./.github/actions/setup
+      - name: pre-commit
+        run: make pre-commit
 
   docs:
     if: ${{ !github.event.pull_request.draft }}
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
-      - name: Install uv
-        uses: astral-sh/setup-uv@v3
+      - uses: ./.github/actions/setup
       - name: docs
         run: uv run mkdocs build
 

Makefile

@@ -22,17 +22,18 @@ export PRINT_HELP_PYSCRIPT
 help:  ## print short description of each target
 	@python3 -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
-.PHONY: checks
-checks:  ## run all the linting checks of the codebase
-	@echo "=== pre-commit ==="; uv run pre-commit run --all-files || echo "--- pre-commit failed ---" >&2; \
-		echo "=== mypy ==="; MYPYPATH=stubs uv run mypy packages || echo "--- mypy failed ---" >&2; \
-		echo "======"
+.PHONY: pre-commit
+pre-commit:  ## run all the linting checks of the codebase
+	uv run pre-commit run --all-files
+
+
+.PHONY: mypy
+mypy:  ## run mypy on the codebase
+	MYPYPATH=stubs uv run --package ref-core mypy packages/ref-core
+	MYPYPATH=stubs uv run --package ref-metrics-example mypy packages/ref-metrics-example
 
 .PHONY: ruff-fixes
 ruff-fixes:  ## fix the code using ruff
-    # format before and after checking so that the formatted stuff is checked and
-    # the fixed stuff is formatted
-	uv run ruff format
 	uv run ruff check --fix
 	uv run ruff format
 
@@ -52,14 +53,10 @@ test-metrics-example:  ## run the tests
 test: test-core test-metrics-example ## run the tests
 
 # Note on code coverage and testing:
-# You must specify cov=src as otherwise funny things happen when doctests are
-# involved.
 # If you want to debug what is going on with coverage, we have found
 # that adding COVERAGE_DEBUG=trace to the front of the below command
 # can be very helpful as it shows you if coverage is tracking the coverage
 # of all of the expected files or not.
-# We are sure that the coverage maintainers would appreciate a PR that improves
-# the coverage handling when there are doctests and a `src` layout like ours.
 
 .PHONY: docs
 docs:  ## build the docs