Change CI/CD settings

 - start tests with tox
   * test python 3.5 to 3.7
   * test building docs
   * run example_scripts
   * optionally check coding style

 - add setup.cfg to build docs using setup.py
 - add development requirements
 - setup.py reads requirements and installs them with setup.py install/develop
 - make  development compatible with tox
 - make travis autodeploy when new tag is set

Author: Manuel

.travis.yml

@@ -1,15 +1,36 @@
 language: python
 python:
-  - "3.5"
   - "3.6"
 sudo: false
 
-before_install: pip install codecov
-after_success:  codecov
+branches:
+  only:
+    - master
 
-install:
-  - pip install numpy
-  - pip install -r requirements.txt
-  - python install_resources.py omssa_2_1_9
+matrix:
+  include:
+    - python: 3.5
+      env: TOXENV=py35
+    - python: 3.6
+      env: TOXENV=py36
+    - python: 3.7
+      env: TOXENV=py37
+      dist: xenial
+    - python: 3.6
+      env: TOXENV=docu
+    - python: 3.6
+      env: TOXENV=example_scripts
 
-script: nosetests --with-coverage
+
+script:
+  - tox
+  - |
+    if [[ $TRAVIS_TAG ]]; then
+      # upload package to pypi
+      python setup.py sdist
+      python setup.py bdist_wheel --universal
+      pip install twine
+      twine upload --repository-url https://test.pypi.org/legacy/ -u $TWINE_USERNAMEE -p $TWINE_TEST_PASSWORD dist/*
+      twine upload -u $TWINE_USERNAME -p $TWINE_PASSWORD dist/*
+      # upload docu
+    fi

requirements.txt

@@ -1,6 +1,5 @@
-pymzml >= 2.0
-nose >=1.3
+pymzml>=2.0
+nose>=1.3
 regex
-pyahocorasick >= 1.1.4; sys_platform != 'win32'
-https://github.com/pygcluster/pyGCluster/archive/master.zip
-https://github.com/pyQms/pyqms/archive/master.zip
+pyahocorasick>=1.1.4; sys_platform != 'win32'
+pyqms

requirements_dev.txt

@@ -0,0 +1,4 @@
+-r requirements.txt
+coverage
+codecov
+tox

setup.cfg

@@ -0,0 +1,4 @@
+[build_sphinx]
+source-dir = docs/source
+build-dir = docs/build
+all_files = 1

setup.py

@@ -47,6 +47,8 @@ def run(self):
 with open(version_path, 'r') as version_file:
     ursgal_version = version_file.read().strip()
 
+with open('requirements.txt') as req:
+    requirements = req.readlines()
 
 setup(
     name='ursgal',
@@ -66,12 +68,7 @@ def run(self):
     build_requires=[
         'numpy',
     ],
-    install_requires=[
-        'pymzml',
-        'regex',
-        'pyqms',
-        "pyahocorasick >= 1.1.4;sys_platform!='win32'",
-    ],
+    install_requires=requirements,
     long_description='Universal Python module combining common bottom-up proteomics tools for large-scale analysis',
     author='Lukas P. M. Kremer, Purevdulam Oyunchimeg, Johannes Barth, Stefan Schulze and Christian Fufezan',
     author_email='[email protected]',
@@ -97,4 +94,4 @@ def run(self):
         'Topic :: Software Development :: Libraries :: Python Modules'
     ],
     cmdclass={'install_lib': my_install_lib}
-)
+)

tox.ini

@@ -0,0 +1,31 @@
+[tox]
+envlist=py35,py36,py37,docu,example_scripts
+[testenv]
+deps = 
+  -Ur{toxinidir}/requirements_dev.txt
+commands = 
+  coverage erase
+  coverage run {envbindir}/nosetests
+  coverage report --include=ursgal/* --omit=test/
+  codecov
+
+[testenv:docu]
+deps = 
+  -Ur{toxinidir}/docs/requirements.txt
+changedir = {toxinidir}/docs
+commands = 
+    make latex
+    make html
+
+[testenv:example_scripts]
+deps = 
+  -Ur{toxinidir}/requirements.txt
+changedir = {toxinidir}/example_scripts
+commands = 
+    # selected example_scripts here
+    python filter_csv_validation_example.py
+    python filter_csv_for_mods_example.py
+
+[testenv:pycodestyle]
+commands = 
+    pycodestyle ursgal