Merge branch 'main' into python-312

.git-blame-ignore-revs

@@ -0,0 +1,3 @@
+# .git-blame-ignore-revs
+# Initial formatting with Ruff
+2b56cd434a129fe0ab1311f7fe9a65767ed88b9e

.github/workflows/python-package.yml

@@ -4,42 +4,27 @@ on:
   push:
 
 jobs:
-  # cqa:
-  #   runs-on: ubuntu-latest
-
-  #   steps:
-  #   - uses: actions/checkout@v3
-
-  #   - name: Set up Python
-  #     uses: actions/setup-python@v4
-  #     with:
-  #       python-version: "3.10"
-  #       cache: pip
-  #       cache-dependency-path: '**/setup.cfg'
-
-  #   - name: Install test dependencies
-  #     run: |
-  #       python -m pip install --upgrade pip
-  #       pip install --use-deprecated=legacy-resolver -e .[dev]
-
-  #   - name: Lint with flake8
-  #     run: |
-  #       # stop the build if there are Python syntax errors or undefined names
-  #       flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-  #       # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-  #       flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-  #   - name: Format check with isort
-  #     run: |
-  #       isort --check src
-
-  #   - name: Format check with black
-  #     run: |
-  #       black --check src
-
-  #   - name: Security check with bandit
-  #     run: |
-  #       bandit -ll -r src
+  cqa:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+        cache: pip
+        cache-dependency-path: '**/setup.cfg'
+
+    - name: Install test dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install --use-deprecated=legacy-resolver -e .[dev]
+
+    - name: Format check with ruff
+      run: |
+        ruff format --check src
 
   test:
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -0,0 +1,6 @@
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.4
+  hooks:
+    - id: ruff-format
+      args: [ --check ]
+

Makefile

@@ -65,7 +65,7 @@ build: %:
 cqa:
 	flake8 src --count --select=E9,F63,F7,F82 --show-source --statistics
 	isort --profile black --check src
-	black --check src
+	ruff format --check src
 	bandit -ll -r src
 
 #=> test: execute tests
@@ -93,13 +93,13 @@ tox:
 ############################################################################
 #= UTILITY TARGETS
 
-#=> reformat: reformat code with yapf and commit
+#=> reformat: reformat code with ruff/isort and commit
 .PHONY: reformat
 reformat:
 	@if ! git diff --cached --exit-code >/dev/null; then echo "Repository not clean" 1>&2; exit 1; fi
-	black src tests
+	ruff format src tests
 	isort src tests
-	git commit -a -m "reformatted with black and isort"
+	git commit -a -m "reformatted with ruff and isort"
 
 #=> rename: rename files and substitute content for new repo name
 .PHONY: rename

pyproject.toml

@@ -12,7 +12,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
-    "License :: OSI Approved :: MIT License",
+    "License :: OSI Approved :: Apache Software License",
     "Operating System :: OS Independent",
 ]
 dynamic = ["version"]
@@ -26,7 +26,6 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
     "bandit ~= 1.7",
-    "black ~= 22.3",
     "build ~= 0.8",
     "flake8 ~= 4.0",
     "ipython ~= 8.4",
@@ -38,6 +37,7 @@ dev = [
     "pytest-optional-tests",
     "pytest ~= 7.1",
     "pyright~=1.1",
+    "ruff == 0.4.4",
     "tox ~= 3.25",
     "vcrpy",
 ]
@@ -111,9 +111,6 @@ exclude_lines = [
     "if __name__ == .__main__.:",
 ]
 
-[tool.black]
-line-length = 100
-
 [tool.isort]
 profile = "black"
 src_paths = ["src", "tests"]
@@ -128,3 +125,8 @@ disable = "R0913"
 
 [tool.pylint.format]
 max-line-length = 100
+
+[tool.ruff]
+src = ["src", "tests"]
+line-length = 100
+

src/seqrepo_rest_service/cli.py

@@ -1,6 +1,4 @@
-"""start seqrepo rest service
-
-"""
+"""start seqrepo rest service"""
 
 import argparse
 import importlib.resources

src/seqrepo_rest_service/refget/routes/metadata.py

@@ -3,8 +3,7 @@
 from connexion import NoContent, request
 
 from ...threadglobals import get_seqrepo
-from ...utils import (base64url_to_hex, get_sequence_id, problem,
-                      valid_content_types)
+from ...utils import base64url_to_hex, get_sequence_id, problem, valid_content_types
 
 _logger = logging.getLogger(__name__)
 

src/seqrepo_rest_service/seqrepo/routes/ping.py

@@ -1,6 +1,6 @@
 import biocommons.seqrepo
 import bioutils
-from pkg_resources import get_distribution
+from importlib import metadata
 
 from ...threadglobals import get_seqrepo
 
@@ -9,7 +9,7 @@ def get():
     sr = get_seqrepo()
 
     return {
-        "version": get_distribution("seqrepo-rest-service").version,
+        "version": metadata.version("seqrepo-rest-service"),
         "url": "https://github.com/biocommons/seqrepo-rest-service/",
         "dependencies": {
             "seqrepo": {

src/seqrepo_rest_service/threadglobals.py

@@ -1,6 +1,4 @@
-"""per-thread globals for seqrepo REST APIs
-
-"""
+"""per-thread globals for seqrepo REST APIs"""
 
 import logging