build: update packaging to use biocommons.example template

* replaces setup.cfg/setup.py with pyproject.toml
* fixes make devready
* adds .flake8 + tox.ini

.flake8

@@ -0,0 +1,12 @@
+[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/*

Makefile

@@ -5,7 +5,7 @@
 .PRECIOUS:
 .SUFFIXES:
 
-SHELL:=/bin/bash -e -o pipefail -O globstar
+SHELL:=bash -e -o pipefail -O globstar
 SELF:=$(firstword $(MAKEFILE_LIST))
 
 VE_DIR=venv
@@ -150,13 +150,13 @@ 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.

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "seqrepo-rest-service"
 authors = [
-  { name="biocommons contributors", email="biocommons-dev@googlegroups.com" },
+    { name = "biocommons contributors", email = "biocommons-dev@googlegroups.com" },
 ]
 description = "SeqRepo REST Service"
 readme = "README.md"
@@ -16,20 +16,57 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dynamic = ["version"]
+dependencies = [
+    "biocommons.seqrepo ~= 0.6",
+    "coloredlogs",
+    "connexion[swagger-ui] ~= 2.2",
+    "Flask ~= 2.2",
+]
+
+[project.optional-dependencies]
+dev = [
+	"bandit ~= 1.7",
+	"black ~= 22.3",
+	"build ~= 0.8",
+	"flake8 ~= 4.0",
+	"ipython ~= 8.4",
+	"isort ~= 5.10",
+	"mypy-extensions ~= 1.0",
+	"pre-commit ~= 3.4",
+	"pylint ~= 2.14",
+	"pytest-cov ~= 4.1",
+	"pytest-optional-tests",
+	"pytest ~= 7.1",
+	"pyright~=1.1",
+	"tox ~= 3.25",
+	"vcrpy",
+]
+docs = ["mkdocs"]
+
+[project.scripts]
+seqrepo-rest-service = "seqrepo_rest_service.cli:main"
 
 [project.urls]
 "Homepage" = "https://github.com/biocommons/seqrepo-rest-service"
 "Bug Tracker" = "https://github.com/biocommons/seqrepo-rest-service/issues"
 
-
 [build-system]
-requires = [
-	 "setuptools >= 65.3",
-   	 "setuptools_scm[toml] ~= 7.0"
-	 ]
+requires = ["setuptools ~= 69.0", "setuptools_scm[toml] ~= 8.0"]
 build-backend = "setuptools.build_meta"
 
 
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+exclude = ["__pycache__", "*.pyc"]
+namespaces = true
+
+[tool.setuptools.package-data]
+"*" = ["*.gz", "*.json", "*.yaml"]
+
+
 [tool.setuptools_scm]
 
 
@@ -44,8 +81,9 @@ doctest_optionflags = [
     "NORMALIZE_WHITESPACE",
 ]
 markers = [
-	"network: tests that require network connectivity",
-	"slow: slow tests that should be run infrequently",
+    "network: tests that require network connectivity",
+    "slow: slow tests that should be run infrequently",
+    "vcr: tests with cached data",
 ]
 
 
@@ -76,12 +114,19 @@ exclude_lines = [
 [tool.black]
 line-length = 100
 
+[tool.isort]
+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"]
+
+
 [tool.pylint.'MESSAGES CONTROL']
 disable = "R0913"
 

tox.ini

@@ -0,0 +1,8 @@
+[tox]
+envlist = py39,py310
+isolated_build = True
+
+[gh]
+python =
+    3.9 = py39, type
+    3.10 = py310