Migrate to uv and other 2026-03 devops conventions

Why these changes are being introduced:

This repository required an updated from pipenv to uv and/or a handful of python project
updated conventions.

How this addresses that need:
* Migrate dependencies from Pipfile/Pipfile.lock to pyproject.toml with uv
* Delete Pipfile and Pipfile.lock
* Remove black, replace with ruff format
* Update Makefile: pipenv run to uv run, consolidated lint/lint-fix/security targets, pre-push hooks
* Replace .pre-commit-config.yaml: default_stages pre-push, ruff-format with --diff, ruff-check without --fix, mypy with broader exclude
* Update CI workflow: on push to on pull_request with paths-ignore, add permissions read-all, use python-uv-shared-* workflows
* Update README: pipenv references replaced with uv
* Use importlib.metadata for dynamic __version__ instead of hardcoded string
* Bump project version to 4.0.0

Side effects of this change:
* Pre-commit hooks now fire on push instead of commit
* Linting hooks no longer auto-fix code; run make lint-fix manually

Relevant ticket(s):
* https://mitlibraries.atlassian.net/browse/TIMX-600

Author: ghukill

.github/workflows/ci.yml

@@ -1,7 +1,11 @@
 name: CI
-on: push
+permissions: read-all
+on:
+  pull_request:
+    paths-ignore:
+      - '.github/**'
 jobs:
   test:
-    uses: mitlibraries/.github/.github/workflows/python-shared-test.yml@main
+    uses: mitlibraries/.github/.github/workflows/python-uv-shared-test.yml@main
   lint:
-    uses: mitlibraries/.github/.github/workflows/python-shared-lint.yml@main
+    uses: mitlibraries/.github/.github/workflows/python-uv-shared-lint.yml@main

.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: pipenv 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: pipenv run mypy
+        entry: uv run mypy
         language: system
         pass_filenames: true
-        types: ["python"]
-        exclude: "tests/"
-      - id: ruff-apply
-        name: ruff-apply
-        entry: pipenv 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: pipenv run pip-audit
-        language: system
-        pass_filenames: false
+        types: [ "python" ]

Makefile

@@ -7,56 +7,60 @@ help: # Preview Makefile commands
 	@awk 'BEGIN { FS = ":.*#"; print "Usage:  make <target>\n\nTargets:" } \
 /^[-_[:alpha:]]+:.?*#/ { printf "  %-15s%s\n", $$1, $$2 }' $(MAKEFILE_LIST)
 
-#######################
-# Dependency commands
-#######################
+# ensure OS binaries aren't called if naming conflict with Make recipes
+.PHONY: help install venv update test coveralls lint lint-fix security minio-start
 
-install: # Install Python dependencies
-	pipenv install --dev
-	pipenv run pre-commit install
+##############################################
+# Python Environment and Dependency commands
+##############################################
 
-update: install # Update Python dependencies
-	pipenv clean
-	pipenv update --dev
+install: .venv .git/hooks/pre-commit .git/hooks/pre-push # Install Python dependencies and create virtual environment if not exists
+	uv sync --dev
+
+.venv: # Creates virtual environment if not found
+	@echo "Creating virtual environment at .venv..."
+	uv venv .venv
+
+.git/hooks/pre-commit: # Sets up pre-commit commit hooks if not setup
+	@echo "Installing pre-commit commit hooks..."
+	uv run pre-commit install --hook-type pre-commit
+
+.git/hooks/pre-push: # Sets up pre-commit push hooks if not setup
+	@echo "Installing pre-commit push hooks..."
+	uv run pre-commit install --hook-type pre-push
+
+venv: .venv # Create the Python virtual environment
+
+update: # Update Python dependencies
+	uv lock --upgrade
+	uv sync --dev
 
 ######################
 # Unit test commands
 ######################
 
 test: # Run tests and print a coverage report
-	pipenv run coverage run --source=timdex_dataset_api -m pytest -vv
-	pipenv run coverage report -m
+	uv run coverage run --source=timdex_dataset_api -m pytest -vv
+	uv run coverage report -m
 
 coveralls: test # Write coverage data to an LCOV report
-	pipenv run coverage lcov -o ./coverage/lcov.info
+	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
-	pipenv run black --check --diff .
-
-mypy: # Run 'mypy' linter
-	pipenv run mypy .
-
-ruff: # Run 'ruff' linter and print a preview of errors
-	pipenv run ruff check .
-
-safety: # Check for security vulnerabilities and verify Pipfile.lock is up-to-date
-	pipenv run pip-audit
-	pipenv verify
-
-lint-apply: black-apply ruff-apply # Apply changes with 'black' and resolve 'fixable errors' with 'ruff'
-
-black-apply: # Apply changes with 'black'
-	pipenv run black .
+lint: # Run linting, alerts only, no code changes
+	uv run ruff format --diff
+	uv run mypy .
+	uv run ruff check .
 
-ruff-apply: # Resolve 'fixable errors' with 'ruff'
-	pipenv run ruff check --fix .
+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
 
 ######################
 # Minio S3 Instance
@@ -69,4 +73,4 @@ minio-start:
 	-v $(MINIO_DATA):/data \
 	-e "MINIO_ROOT_USER=$(MINIO_USERNAME)" \
 	-e "MINIO_ROOT_PASSWORD=$(MINIO_PASSWORD)" \
-	quay.io/minio/minio server /data --console-address ":9001"
+	quay.io/minio/minio server /data --console-address ":9001"