style: add flake8/other style configs from template

.flake8

@@ -0,0 +1,13 @@
+[flake8]
+ignore = E129,E133,E203,E221,E241,E251,E303,E266,H106,H904,W291
+max-line-length = 100
+max-complexity = 15
+hang-closing = true
+exclude =
+    .eggs
+    .tox
+    build
+    dist
+    docs/conf.py
+    tests/*
+    **/_data/migrations/*

.github/workflows/python-package.yml

@@ -4,42 +4,42 @@ 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: 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
 
   test:
     runs-on: ubuntu-latest
@@ -71,7 +71,7 @@ jobs:
     - name: Test with pytest
       run: |
         make test
-        
+
   deploy:
     needs:
     # - cqa

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+- repo: local
+  hooks:
+    -  id: flake8
+       name: flake8
+       entry: flake8
+       language: system
+       types: [python]
+    -  id: pyright
+       name: pyright
+       entry: pyright
+       language: system
+       types: [python]
+    -  id: isort
+       name: isort
+       entry: isort
+       language: system
+       types: [python]
+    -  id: black
+       name: black
+       entry: black
+       language: system
+       types: [python]

Makefile

@@ -6,7 +6,7 @@
 .SUFFIXES:
 
 
-SHELL:=bash -e -o pipefail -O globstar
+SHELL:=bash -e -o pipefail # -O globstar
 
 SELF:=$(firstword $(MAKEFILE_LIST))
 
@@ -47,6 +47,7 @@ ${VE_DIR}:
 .PHONY: develop
 develop:
 	pip install -e .[dev]
+	pre-commit install
 
 #=> install: install package
 .PHONY: install
@@ -91,6 +92,18 @@ test-%:
 tox:
 	tox
 
+#=> cqa: execute code quality tests
+cqa:
+	flake8 src --show-source --statistics
+	pyright
+	isort --check src --profile black
+	black --check src
+	bandit -ll -r src
+
+#=> reformat: reformat code
+.PHONY: reformat
+reformat:
+	pre-commit
 
 ############################################################################
 #= UTILITY TARGETS
@@ -144,13 +157,13 @@ distclean: cleanest
 
 ## <LICENSE>
 ## Copyright 2023 Source Code Committers
-## 
+##
 ## Licensed under the Apache License, Version 2.0 (the "License");
 ## you may not use this file except in compliance with the License.
 ## You may obtain a copy of the License at
-## 
+##
 ##     http://www.apache.org/licenses/LICENSE-2.0
-## 
+##
 ## Unless required by applicable law or agreed to in writing, software
 ## distributed under the License is distributed on an "AS IS" BASIS,
 ## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

README.md

@@ -124,11 +124,11 @@ tested. Patches to get other systems working would be welcomed.
     $ pip install seqrepo
     $ sudo mkdir -p /usr/local/share/seqrepo
     $ sudo chown $USER /usr/local/share/seqrepo
-    $ seqrepo pull -i 2018-11-26 
-    $ seqrepo show-status -i 2018-11-26 
+    $ seqrepo pull -i 2018-11-26
+    $ seqrepo show-status -i 2018-11-26
     seqrepo 0.2.3.post3.dev8+nb8298bd62283
     root directory: /usr/local/share/seqrepo/2018-11-26, 7.9 GB
-    backends: fastadir (schema 1), seqaliasdb (schema 1) 
+    backends: fastadir (schema 1), seqaliasdb (schema 1)
     sequences: 773587 sequences, 93051609959 residues, 192 files
     aliases: 5579572 aliases, 5480085 current, 26 namespaces, 773587 sequences
 
@@ -187,6 +187,15 @@ Here's how to get started developing:
     source venv/bin/activate
     seqrepo --version
 
+Code reformatting:
+
+    make reformat
+
+Install pre-commit hook:
+
+    # included in `make devready`, not necessary for new installations
+    pre-commit install
+
 ## Building a docker image
 
 Docker images are available at https://hub.docker.com/r/biocommons/seqrepo.

pyproject.toml

@@ -124,11 +124,6 @@ line-length = 100
 profile = "black"
 src_paths = ["src", "tests"]
 
-# [tool.flake8]
-# flake8 does not support configuration in pyproject.toml
-# https://github.com/PyCQA/flake8/issues/234#issuecomment-812800832
-# The config in setup.cfg
-
 [tool.pyright]
 include = ["src", "tests"]