sync with current biocommons conventions: use setup.cfg, use src/, Ma…

…kefile updates, drop req files

Makefile

@@ -10,8 +10,9 @@ SELF:=$(firstword $(MAKEFILE_LIST))
 
 PKG=eutils
 PKGD=$(subst .,/,${PKG})
+PYV:=3.7
+VEDIR=venv/${PYV}
 
-VEDIR=venv/3.6
 
 
 ############################################################################
@@ -27,48 +28,35 @@ help:
 #= SETUP, INSTALLATION, PACKAGING
 
 #=> venv: make a Python 3 virtual environment
-.PHONY: venv/2.7
-venv/2.7:
-	virtualenv -p $$(type -p python2.7) $@; \
-	source $@/bin/activate; \
-	pip install --upgrade pip setuptools
-
-#=> venv: make a Python 3 virtual environment
-.PHONY: ${VEDIR}
-${VEDIR}:
-	pyvenv $@; \
+.PHONY: venv/%
+venv/%:
+	python$* -m venv $@; \
 	source $@/bin/activate; \
 	python -m ensurepip --upgrade; \
 	pip install --upgrade pip setuptools
 
-#=> setup: setup/upgrade packages *in current environment*
-.PHONY: setup
-setup: etc/develop.reqs etc/test.reqs etc/install.reqs
-	if [ -s $(word 1,$^) ]; then pip install --upgrade -r $(word 1,$^); fi
-	if [ -s $(word 2,$^) ]; then pip install --upgrade -r $(word 2,$^); fi
-	if [ -s $(word 3,$^) ]; then pip install --upgrade -r $(word 3,$^); fi
+#=> develop: install package in develop mode
+.PHONY: develop
+develop:
+	pip install -e .[dev,extras,notebooks]
 
 #=> devready: create venv, install prerequisites, install pkg in develop mode
 .PHONY: devready
 devready:
-	make ${VEDIR} && source ${VEDIR}/bin/activate && make setup develop
+	make ${VEDIR} && source ${VEDIR}/bin/activate && make develop
 	@echo '#################################################################################'
 	@echo '###  Do not forget to `source ${VEDIR}/bin/activate` to use this environment  ###'
 	@echo '#################################################################################'
 
-#=> develop: install package in develop mode
 #=> install: install package
 #=> bdist bdist_egg bdist_wheel build sdist: distribution options
-.PHONY: bdist bdist_egg bdist_wheel build build_sphinx sdist install develop
-bdist bdist_egg bdist_wheel build sdist install develop: %:
+.PHONY: bdist bdist_egg bdist_wheel build build_sphinx sdist install
+bdist bdist_egg bdist_wheel build sdist install: %:
 	python setup.py $@
 
-#=> upload: upload to pypi
-#=> upload_*: upload to named pypi service (requires config in ~/.pypirc)
-.PHONY: upload upload_%
-upload: upload_pypi
-upload_%:
-	python setup.py bdist_egg bdist_wheel sdist upload -r $*
+.PHONY: install-extras
+install-extras:
+	pip install -e .[extras]
 
 
 ############################################################################
@@ -78,7 +66,7 @@ upload_%:
 #=> test: execute tests
 .PHONY: test
 test:
-	pytest --cov=${PKG}
+	python setup.py pytest
 
 #=> tox: execute tests via tox
 .PHONY: tox
@@ -93,10 +81,9 @@ tox:
 #=> reformat: reformat code with yapf and commit
 .PHONY: reformat
 reformat:
-	@if hg sum | grep -qL '^commit:.*modified'; then echo "Repository not clean" 1>&2; exit 1; fi
-	@if hg sum | grep -qL ' applied'; then echo "Repository has applied patches" 1>&2; exit 1; fi
+	@if ! git diff --cached --exit-code; then echo "Repository not clean" 1>&2; exit 1; fi
 	yapf -i -r "${PKGD}" tests
-	hg commit -m "reformatted with yapf"
+	git commit -a -m "reformatted with yapf"
 
 #=> docs -- make sphinx docs
 .PHONY: docs
@@ -115,7 +102,7 @@ clean:
 #=> cleaner: remove files and directories that are easily rebuilt
 .PHONY: cleaner
 cleaner: clean
-	rm -fr .cache *.egg-info build dist doc/_build htmlcov
+	rm -fr .cache *.egg-info .pytest_cache build dist doc/_build htmlcov
 	find . \( -name \*.pyc -o -name \*.orig -o -name \*.rej \) -print0 | xargs -0r rm
 	find . -name __pycache__ -print0 | xargs -0r rm -fr
 

README.rst

@@ -1,4 +1,3 @@
-====================================================
 eutils -- a simplified interface to NCBI E-Utilities
 ====================================================
 

setup.cfg

@@ -1,3 +1,81 @@
+[metadata]
+name = eutils
+author = Source Code Contributors
+author-email = biocommons-dev@googlegroups.com
+home-page = https://github.com/biocommons/eutils
+long-description = file:README.rst
+long-description-content-type = text/x-rst; charset=UTF-8
+description = "Python interface to NCBI's eutilities API"
+license-file = LICENSE
+platform = any
+
+classifiers =
+    Development Status :: 3 - Alpha
+    Intended Audience :: Developers
+    Intended Audience :: Healthcare Industry
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: Apache Software License
+    Operating System :: OS Independent
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Topic :: Scientific/Engineering :: Bio-Informatics
+    Topic :: Scientific/Engineering :: Medical Science Apps.
+keywords =
+    bioinformatics
+    eutilities
+    ncbi
+
+
+[options]
+packages = find:
+python_requires = >= 3.6
+zip_safe = true
+package_dir =
+    = src
+install_requires =
+    lxml
+    pytz
+    requests
+    six
+setup_requires =
+    pytest-runner
+    setuptools_scm
+    wheel
+tests_require =
+    mock
+    pytest
+    pytest-cov
+    pyyaml
+    tox
+    vcrpy
+
+# TODO: Needed?
+[options.packages.find]
+where = src
+exclude =
+    __pycache__
+    *.pyc
+
+
+[options.extras_require]
+dev =
+    flake8
+    ipython
+    mock
+    pytest
+    pytest-cov
+    restview
+    setuptools
+    sphinx
+    sphinx_rtd_theme
+    tox
+    vcrpy
+    yapf
+
+
 [aliases]
 test = pytest
 
@@ -13,3 +91,11 @@ max-line-length = 120
 exclude = tests/*
 max-complexity = 10
 ignore = E129,E221,E241,E251,E303,W291
+
+[tool:pytest]
+# TODO: add src to testpaths to trigger doctests. However, this
+# requires injecting fixtures, which requires conftest.py in src/,
+# which requires packaging changes. Deferred.
+testpaths = src tests
+doctest_optionflags = ALLOW_UNICODE ALLOW_BYTES ELLIPSIS IGNORE_EXCEPTION_DETAIL NORMALIZE_WHITESPACE
+addopts = --doctest-modules --cov-config=setup.cfg --cov-report=term-missing --cov=ga4gh

setup.py

@@ -1,81 +1,3 @@
-# -*- coding: utf-8 -*-
+from setuptools import setup
 
-from setuptools import setup, find_packages
-
-package_name = "eutils"
-
-with open("doc/short-description.txt") as short_desc:
-    short_description = short_desc.read()
-
-with open("README.rst") as long_desc:
-    long_description = long_desc.read()
-
-
-setup(
-    author = package_name + " Committers",
-    description = short_description.replace("\n", " "),
-    license = "Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)",
-    long_description = long_description,
-    name = package_name,
-    packages = find_packages(),
-    use_scm_version = True,
-    zip_safe = True,
-
-    author_email = "biocommons-dev@googlegroups.com",
-    url = "https://github.com/biocommons/" + package_name,
-
-    classifiers = [
-        "Development Status :: 3 - Alpha",
-        "Intended Audience :: Developers",
-        "Intended Audience :: Healthcare Industry",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: Apache Software License",
-        "Operating System :: OS Independent",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3",
-        "Topic :: Database :: Front-Ends",
-        "Topic :: Scientific/Engineering :: Bio-Informatics",
-        "Topic :: Scientific/Engineering :: Medical Science Apps.",
-    ],
-
-    keywords = [
-        'bioinformatics',
-    ],
-
-    install_requires = [
-        'lxml',
-        'pytz',
-        'requests',
-        'six',
-        ],
-
-    setup_requires = [
-        "pytest-runner",
-        "setuptools_scm",
-        "wheel",
-    ],
-
-    tests_require = [
-        "mock",
-        "pytest",
-        "pytest-cov",
-        "tox",
-        "vcrpy",
-    ],
-)
-
-# <LICENSE>
-# Copyright 2016 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.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-# </LICENSE>
+setup(use_scm_version=True)