use tox for running tests

.gitignore

@@ -24,3 +24,4 @@ sourmash/_minhash.cpp
 .pytest_cache
 .python-version
 sourmash/version.py
+.tox/

.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+repos:
+-   repo: https://github.com/python/black
+    rev: 19.3b0
+    hooks:
+    -   id: black
+        args: [--safe]
+        language_version: python3.7
+-   repo: https://github.com/asottile/blacken-docs
+    rev: v0.5.0
+    hooks:
+    -   id: blacken-docs
+        additional_dependencies: [black==19.3b0]
+        language_version: python3.7
+-   repo: https://github.com/asottile/seed-isort-config
+    rev: v1.7.0
+    hooks:
+    -   id: seed-isort-config
+        args: [--application-directories, "sourmash:."]
+-   repo: https://github.com/pre-commit/mirrors-isort
+    rev: v4.3.15
+    hooks:
+    -   id: isort
+        additional_dependencies: [toml]
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.1.0
+    hooks:
+    -   id: trailing-whitespace
+        exclude: 'tests/test-data'
+    -   id: end-of-file-fixer
+        exclude: 'tests/test-data'
+    -   id: check-yaml
+    -   id: debug-statements
+    -   id: flake8
+        additional_dependencies: ["flake8-bugbear == 18.8.0"]
+        language_version: python3.7
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v1.12.0
+    hooks:
+    -   id: pyupgrade

.travis.yml

@@ -1,6 +1,9 @@
 language: python
 os: linux
 dist: xenial
+addons:
+  apt_packages:
+    - pandoc
 
 cache:
   directories:
@@ -56,7 +59,7 @@ jobs:
         - CIBW_SKIP='*-manylinux1_i686'
       install: skip
       script:
-        - sudo $PIP install cibuildwheel==0.10.2
+        - $PIP install cibuildwheel==0.11.1
         - cibuildwheel --output-dir wheelhouse
       deploy:
         provider: releases
@@ -71,8 +74,6 @@ jobs:
       os: osx
       osx_image: xcode10.1
       language: generic
-      before_script:
-        - sudo $PIP install -U pip setuptools
       env:
         - PIP=pip2
         - CIBW_ENVIRONMENT_MACOS='MACOSX_DEPLOYMENT_TARGET=10.11'

Makefile

@@ -15,17 +15,14 @@ install: all
 dist: FORCE
 	$(PYTHON) setup.py sdist
 
-test: all
-	pip install -e '.[test]'
-	$(PYTHON) -m pytest
+test:
+	tox -e py37
 
 doc: .PHONY
-	cd doc && make html
+	tox -e docs
 
 coverage: all
-	$(PYTHON) setup.py clean --all
-	SOURMASH_COVERAGE=1 $(PYTHON) setup.py build_ext -i
-	$(PYTHON) -m pytest --cov=.
+	tox -e coverage
 
 benchmark: all
 	asv continuous master

pyproject.toml

@@ -0,0 +1,9 @@
+[build-system]
+requires = [
+    "setuptools >= 40.0.4",
+    "setuptools_scm >= 2.0.0, <4",
+    "setuptools_scm_git_archive",
+    "wheel >= 0.29.0",
+    "Cython >= 0.25.2",
+]
+build-backend = 'setuptools.build_meta'

setup.py

@@ -69,9 +69,9 @@
                        'setuptools_scm', 'setuptools_scm_git_archive'],
     "use_scm_version": {"write_to": "sourmash/version.py"},
     "extras_require": {
-        'test' : ['pytest', 'pytest-cov', 'numpy', 'matplotlib', 'scipy','recommonmark'],
+        'test' : ['pytest', 'pytest-cov', 'numpy', 'matplotlib', 'scipy'],
         'demo' : ['jupyter', 'jupyter_client', 'ipython'],
-        'doc' : ['sphinx'],
+        'doc' : ['sphinx', 'recommonmark', "sphinxcontrib-napoleon", "nbsphinx"],
         '10x': ['pathos', 'bamnostic>=0.9.2'],
         },
     "include_package_data": True,

tox.ini

@@ -1,18 +1,111 @@
 [tox]
-envlist=py27,py35,py36,py37
+envlist =
+  py35,
+  py36,
+  py37,
+  coverage,
+  docs,
+  package_description
+#  fix_lint,
+isolated_build = true
+skip_missing_interpreters = true
 
 [testenv]
-passenv = CI TRAVIS TRAVIS_*
-whitelist_externals=
-    make
-deps=
-    codecov
-    ipfshttpclient
-    redis
-    bamnostic
-    pathos
-commands=
-    pip install -r requirements.txt
-    pip install -e .[test]
-    make coverage
-    codecov --gcov-glob third-party
+description = run the tests with pytest under {basepython}
+setenv = PIP_DISABLE_VERSION_CHECK = 1
+         COVERAGE_FILE = {env:COVERAGE_FILE:{toxworkdir}/.coverage.{envname}}
+         VIRTUALENV_NO_DOWNLOAD = 1
+passenv = http_proxy https_proxy no_proxy SSL_CERT_FILE PYTEST_*
+deps =
+  pip >= 19.1
+extras = test
+changedir = tests
+commands = pytest \
+           --cov "{envsitepackagesdir}/sourmash" \
+           --cov-config "{toxinidir}/tox.ini" \
+           --junitxml {toxworkdir}/junit.{envname}.xml \
+           {posargs:.}
+
+[tox:.package]
+basepython = python3
+
+[testenv:docs]
+description = invoke sphinx-build to build the HTML docs
+basepython = python3.7
+extras = doc
+whitelist_externals = pandoc
+passenv = HOME
+changedir = {toxinidir}
+#commands = sphinx-build -d "{toxworkdir}/docs_doctree" doc "{toxworkdir}/docs_out" --color -W -bhtml {posargs}
+commands = sphinx-build -d "{toxworkdir}/docs_doctree" doc "{toxworkdir}/docs_out" --color -bhtml {posargs}
+           python -c 'import pathlib; print("documentation available under file://\{0\}".format(pathlib.Path(r"{toxworkdir}") / "docs_out" / "index.html"))'
+
+[testenv:package_description]
+description = check that the long description is valid
+basepython = python3.7
+deps = twine >= 1.12.1
+       # TODO installing readme-renderer[md] should not be necessary
+       readme-renderer[md] >= 24.0
+       pip >= 19.1
+skip_install = true
+changedir = {toxinidir}
+extras =
+commands = pip wheel -w {envtmpdir}/build --no-deps .
+           twine check {envtmpdir}/build/*
+
+[testenv:fix_lint]
+description = format the code base to adhere to our styles, and complain about what we cannot do automatically
+basepython = python3.7
+passenv = {[testenv]passenv}
+          # without PROGRAMDATA cloning using git for Windows will fail with an
+          # `error setting certificate verify locations` error
+          PROGRAMDATA
+extras = lint
+deps = pre-commit >= 1.14.4, < 2
+skip_install = True
+commands = pre-commit run --all-files --show-diff-on-failure
+           python -c 'import pathlib; print("hint: run \{\} install to add checks as pre-commit hook".format(pathlib.Path(r"{envdir}") / "bin" / "pre-commit"))'
+
+[testenv:coverage]
+description = [run locally after tests]: combine coverage data and create report;
+              generates a diff coverage against origin/master (can be changed by setting DIFF_AGAINST env var)
+deps = {[testenv]deps}
+       coverage >= 4.4.1, < 5
+       diff_cover
+skip_install = True
+passenv = {[testenv]passenv}
+          DIFF_AGAINST
+setenv = COVERAGE_FILE={toxworkdir}/.coverage
+commands = coverage combine
+           coverage report -m
+           coverage xml -o {toxworkdir}/coverage.xml
+           coverage html -d {toxworkdir}/htmlcov
+           diff-cover --compare-branch {env:DIFF_AGAINST:origin/master} {toxworkdir}/coverage.xml
+depends = py27, py34, py35, py36, py37, pypy, pypy3
+parallel_show_output = True
+
+[testenv:codecov]
+description = [only run on CI]: upload coverage data to codecov (depends on coverage running first)
+passenv = {[testenv]passenv}
+          CODECOV_TOKEN
+deps = codecov
+skip_install = True
+changedir = {toxinidir}
+depends = coverage
+commands = codecov --file "{toxworkdir}/coverage.xml" {posargs}
+
+[coverage:run]
+branch = true
+parallel = true
+
+[travis]
+python =
+  3.7: py37, docs, package_description
+
+[flake8]
+max-complexity = 22
+max-line-length = 99
+ignore = E203, W503, C901, E402
+
+[pep8]
+max-line-length = 99