Update setup and testing config

.flake8

@@ -0,0 +1,30 @@
+#########################
+# Flake8 Configuration  #
+# (.flake8)             #
+#########################
+[flake8]
+# flake8
+exclude =
+    *.egg-info,
+    *.pyc,
+    .cache,
+    .eggs
+    .git,
+    .tox,
+    __pycache__,
+    build,
+    dist,
+    docs/source/conf.py,
+format = ${cyan}%(path)s${reset}:${yellow_bold}%(row)d${reset}:${green_bold}%(col)d${reset}: ${red_bold}%(code)s${reset} %(text)s
+ignore = S101
+max-line-length = 120
+
+# flake8-import-order
+application-import-names =
+    bio2bel_phosphosite
+    bio2bel
+    tests
+import-order-style = pycharm
+
+# mccabe
+max-complexity = 10

.readthedocs.yml

@@ -0,0 +1,6 @@
+# See: https://docs.readthedocs.io/en/latest/yaml-config.html
+python:
+  version: 3
+  pip_install: true
+  extra_requirements:
+  - docs

.travis.yml

@@ -1,28 +1,42 @@
 sudo: false
 cache: pip
-services:
-- mysql
 language: python
-python: 3.6
-env:
-  global:
-  - BIO2BEL_CONNECTION=mysql+pymysql://travis@localhost/bio2bel?charset=utf8'
-  matrix:
-  - TOXENV=py
-  - TOXENV=docs
-  - TOXENV=manifest
-  - TOXENV=readme
-before_install:
-- pip install codecov
-- pip install pymysql
-- mysql -e 'CREATE DATABASE bio2bel CHARACTER SET utf8 COLLATE utf8_general_ci;'
-- mysql -e "GRANT ALL PRIVILEGES ON bio2bel.* to 'travis'@'%' WITH GRANT OPTION;"
+python:
+- 3.6
+stages:
+  - lint
+  - docs
+  - test
+jobs:
+  include:
+    # lint stage
+    - stage: lint
+      env: TOXENV=manifest
+    - env: TOXENV=flake8
+    - env: TOXENV=vulture
+    - env: TOXENV=mypy
+    - env: TOXENV=pyroma
+    # docs stage
+    - stage: docs
+      env: TOXENV=doc8
+    - env: TOXENV=readme
+    - env: TOXENV=docs
+    # test stage
+    - stage: test
+      env: TOXENV=py
+matrix:
+  allow_failures:
+      - env: TOXENV=doc8
+      - env: TOXENV=docs
+      - env: TOXENV=flake8
+      - env: TOXENV=vulture
+      - env: TOXENV=mypy
+      - env: TOXENV=pyroma
 install:
-- pip install tox
+    - sh -c 'if [ "$TOXENV" = "py" ]; then pip install tox codecov; else pip install tox; fi'
 script:
 - tox
 after_success:
-- tox -e coverage-report
-- codecov
+    - sh -c 'if [ "$TOXENV" = "py" ]; then tox -e coverage-report; codecov; fi'
 notifications:
   slack: pybel:n2KbWKBum3musnBg3L76gGwq

MANIFEST.in

@@ -8,4 +8,4 @@ include docs/Makefile
 global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
 
 exclude .bumpversion.cfg
-include *.rst *.txt *.yml LICENSE tox.ini .coveragerc
+include *.rst *.txt *.yml *.ini LICENSE .coveragerc

tox.ini

@@ -2,55 +2,142 @@
 envlist =
     coverage-clean
     manifest
+    flake8
     readme
+    doc8
     docs
     py
     coverage-report
 
 [testenv]
 commands = coverage run -p -m pytest tests {posargs}
-passenv = TRAVIS CI
+passenv = CI TRAVIS TRAVIS_*
 deps =
     coverage
     pytest
+    pybel
+    flask
+    flask-admin
 whitelist_externals =
     /bin/cat
     /bin/cp
     /bin/mkdir
+    /usr/bin/git
+    /usr/local/bin/hub
 
 [testenv:coverage-clean]
 deps = coverage
 skip_install = true
 commands = coverage erase
 
-[testenv:manifest]
-deps = check-manifest
-skip_install = true
-commands = check-manifest
-
 [testenv:coverage-report]
 deps = coverage
 skip_install = true
 commands =
     coverage combine
     coverage report
 
-[testenv:readme]
-commands = rst-lint README.rst
+[testenv:manifest]
+deps = check-manifest
+commands = check-manifest
+skip_install = true
+
+[testenv:vulture]
+deps = vulture
 skip_install = true
+commands = vulture src/bio2bel_phosphosite/
+description = Run the vulture tool to look for dead code.
+
+[testenv:xenon]
+deps = xenon
+skip_install = true
+commands = xenon --max-average A --max-modules A --max-absolute B .
+description = Run the xenon tool to monitor code complexity.
+
+[testenv:mypy]
+deps = mypy
+skip_install = true
+commands = mypy --ignore-missing-imports src/bio2bel_phosphosite/
+description = Run the mypy tool to check static typing on the project.
+
+[testenv:pyroma]
 deps =
-    restructuredtext_lint
     pygments
+    pyroma
+skip_install = true
+commands = pyroma --min=10 .
+description = Run the pyroma tool to check the project's package friendliness.
 
 [testenv:docs]
 changedir = docs
 deps =
     sphinx
-    sphinx_rtd_theme
+    sphinx-rtd-theme
+    sphinx-autodoc-typehints
 commands =
     mkdir -p {envtmpdir}
     cp -r source {envtmpdir}/source
     sphinx-build -W -b html -d {envtmpdir}/build/doctrees {envtmpdir}/source {envtmpdir}/build/html
     sphinx-build -W -b coverage -d {envtmpdir}/build/doctrees {envtmpdir}/source {envtmpdir}/build/coverage
     cat {envtmpdir}/build/coverage/c.txt
     cat {envtmpdir}/build/coverage/python.txt
+
+[testenv:readme]
+commands = rst-lint README.rst
+skip_install = true
+deps =
+    restructuredtext_lint
+    pygments
+
+[testenv:flake8]
+basepython = python3
+skip_install = true
+deps =
+    flake8
+    flake8-docstrings>=0.2.7
+    flake8-import-order>=0.9
+    pep8-naming
+    flake8-colors
+commands =
+    flake8 src/bio2bel_phosphosite/ tests/ setup.py
+
+[testenv:doc8]
+basepython = python3
+skip_install = true
+deps =
+    sphinx
+    doc8
+commands =
+    doc8 docs/source/ README.rst
+
+[testenv:build]
+basepython = python3
+skip_install = true
+deps =
+    wheel
+    setuptools
+commands =
+    python setup.py -q sdist bdist_wheel
+
+[testenv:release]
+basepython = python3
+skip_install = true
+deps =
+    {[testenv:build]deps}
+    twine >= 1.5.0
+commands =
+    {[testenv:build]commands}
+    twine upload --skip-existing dist/*
+
+[testenv:finish]
+basepython = python3
+skip_install = true
+deps =
+    {[testenv:build]deps}
+    {[testenv:release]deps}
+    bumpversion
+commands =
+    bumpversion release
+    {[testenv:release]commands}
+    git push
+    bumpversion patch