Update Makefile, pre-commit, linting, and dependency conventions

Why these changes are being introduced:

These changes encapsulate some discussions to update some devops conventions
that operate at the intersection of the Makefile, pre-commit hooks, linting,
and dependency handling.  These changes were prompted by a critical mass of
some structure creep over time, and some feedback of unhelpful friction
in some areas.

How this addresses that need:
* linting section reworked in Makefile
* pre-commit fires only on git push
* pre-commit no longer runs commands that modify code
* `ruff format` is used in place of `black`
* vulernability scanning moved to `make security`
* security scanning removed from linting and pre-commit hooks

Side effects of this change:
* Vulnerability scanning is an ad-hoc decision by developers in the short-term,
with notifications in Github via dependabot.  Longer term, we will rely on
renovate for rolling dependency updates.
* Local commits are no longer constrained by pre-commit hooks, but hooks
are enforced when pushing to Github.
* We move further into the ecosystem of astral's ruff library, using the
built-in formatter instead of black.

Relevant ticket(s):
* https://mitlibraries.atlassian.net/browse/IN-1676

Author: ghukill

.pre-commit-config.yaml

@@ -1,29 +1,28 @@
 default_language_version:
   python: python3.12
+default_stages:
+  - pre-push
 repos:
   - repo: local
     hooks:
-      - id: black-apply
-        name: black-apply
-        entry: uv run black
+      - id: ruff-format
+        name: ruff-format
+        entry: uv run ruff format --diff
         language: system
         pass_filenames: true
-        types: ["python"]
+        types: [ "python" ]
+
       - id: mypy
         name: mypy
         entry: uv run mypy
         language: system
         pass_filenames: true
-        types: ["python"]
-        exclude: "tests/"
-      - id: ruff-apply
-        name: ruff-apply
-        entry: uv run ruff check --fix
+        types: [ "python" ]
+        exclude: "(tests/|output/|migrations/)"
+
+      - id: ruff-check
+        name: ruff-check
+        entry: uv run ruff check
         language: system
         pass_filenames: true
-        types: ["python"]
-      - id: pip-audit
-        name: pip-audit
-        entry: uv run pip-audit
-        language: system
-        pass_filenames: false
+        types: [ "python" ]

Makefile

@@ -21,7 +21,7 @@ install: .venv .git/hooks/pre-commit # Install Python dependencies and create vi
 
 .git/hooks/pre-commit: # Sets up pre-commit hook if not setup
 	@echo "Installing pre-commit hooks..."
-	uv run pre-commit install
+	pre-commit install --hook-type pre-push --hook-type pre-commit
 
 venv: .venv # Create the Python virtual environment
 
@@ -41,31 +41,21 @@ coveralls: test # Write coverage data to an LCOV report
 	uv run coverage lcov -o ./coverage/lcov.info
 
 ####################################
-# Code quality and safety commands
+# Code linting and formatting
 ####################################
 
-lint: black mypy ruff safety # Run linters
-
-black: # Run 'black' linter and print a preview of suggested changes
-	uv run black --check --diff .
-
-mypy: # Run 'mypy' linter
+lint: # Run linting, alerts only, no code changes
+	uv run ruff format --diff
 	uv run mypy .
-
-ruff: # Run 'ruff' linter and print a preview of errors
 	uv run ruff check .
 
-safety: # Check for security vulnerabilities
-	uv run pip-audit
-
-lint-apply: black-apply ruff-apply # Apply changes with 'black' and resolve 'fixable errors' with 'ruff'
-
-black-apply: # Apply changes with 'black'
-	uv run black .
-
-ruff-apply: # Resolve 'fixable errors' with 'ruff'
+lint-fix: # Run linting, auto fix behaviors where supported
+	uv run ruff format .
 	uv run ruff check --fix .
 
+security: # Run security / vulnerability checks
+	uv run pip-audit
+
 ##############################
 # CLI convenience commands
 ##############################

pyproject.toml

@@ -14,7 +14,6 @@ dependencies = [
 
 [dependency-groups]
 dev = [
-    "black>=25.1.0",
     "coveralls>=4.0.1",
     "mypy>=1.17.1",
     "pip-audit>=2.9.0",