Merge pull request #139 from biocommons/138-seqrepo-cli-not-installed…

…-in-066-and-067

fix: finish migrating from setup.cfg to pyproject.toml in order to install seqrepo cli

Makefile

@@ -5,7 +5,9 @@
 .PRECIOUS:
 .SUFFIXES:
 
-SHELL:=/bin/bash -e -o pipefail -O globstar
+
+SHELL:=bash -e -o pipefail -O globstar
+
 SELF:=$(firstword $(MAKEFILE_LIST))
 
 VE_DIR=venv

README.md

@@ -105,10 +105,18 @@ answer](https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-inv
 
 ## Quick Start
 
-On Ubuntu 16.04:
+### OSX
+
+    $ brew install python libpq
+
+### On Ubuntu 16.04
 
     $ sudo apt install -y python3-dev gcc zlib1g-dev tabix
-    (OSX: $ brew install python libpq)
+
+### All platforms
+
+    $ python -m venv venv
+    $ source venv/bin/activate
     $ pip install seqrepo
     $ sudo mkdir -p /usr/local/share/seqrepo
     $ sudo chown $USER /usr/local/share/seqrepo
@@ -157,6 +165,14 @@ a moderate value (>10) will greatly increase performance of sequence retrieval.
 
 ## Developing
 
+### OSX
+
+    brew install python libpq bash
+
+### Ubuntu
+
+    sudo apt install -y python3-dev gcc zlib1g-dev tabix
+
 Here's how to get started developing:
 
     make devready

pyproject.toml

@@ -1,11 +1,11 @@
 [project]
 name = "biocommons.seqrepo"
 authors = [
-  { name="biocommons contributors", email="[email protected]" },
+    { name = "biocommons contributors", email = "[email protected]" },
 ]
 description = "Non-redundant, compressed, journalled, file-based storage for biological sequences"
 readme = "README.md"
-license = { file="LICENSE.txt" }
+license = { file = "LICENSE.txt" }
 requires-python = ">=3.9"
 classifiers = [
     "Programming Language :: Python :: 3",
@@ -15,31 +15,64 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
 ]
-dynamic = ["version", "optional-dependencies"]
+dynamic = ["version"]
 dependencies = [
     "bioutils > 0.4",
-    "coloredlogs",
-    "ipython",
-    "pysam",
-    "requests",
-    "requests_html",
-    "six",
-    "tqdm",
-    "yoyo-migrations"
+    "coloredlogs ~= 15.0",
+    "ipython ~= 8.4",
+    "pysam ~= 0.22",
+    "requests ~= 2.31",
+    "six ~= 1.16",
+    "yoyo-migrations ~= 8.2",
 ]
 
+[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",
+    "requests_html ~= 0.10",
+    "tqdm ~= 4.66",
+    "tox ~= 3.25",
+    "vcrpy",
+]
+docs = ["mkdocs"]
+
+[project.scripts]
+seqrepo = "biocommons.seqrepo.cli:main"
+
 [project.urls]
 "Homepage" = "https://github.com/biocommons/biocommons.seqrepo"
 "Bug Tracker" = "https://github.com/biocommons/biocommons.seqrepo/issues"
 
 [build-system]
-requires = [
-    "setuptools >= 69.0.2",
-    "setuptools_scm[toml] >= 8.0"
-]
+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]
+"biocommons.seqrepo.fastadir" = ["_data/migrations/*"]
+"biocommons.seqrepo.seqaliasdb" = ["_data/migrations/*"]
+
+
 [tool.setuptools_scm]
 
 
@@ -54,9 +87,9 @@ doctest_optionflags = [
     "NORMALIZE_WHITESPACE",
 ]
 markers = [
-	"network: tests that require network connectivity",
-	"slow: slow tests that should be run infrequently",
-	"vcr: tests with cached data",
+    "network: tests that require network connectivity",
+    "slow: slow tests that should be run infrequently",
+    "vcr: tests with cached data",
 ]
 
 
@@ -87,12 +120,19 @@ 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"