Update CI/CD

- adapt appveyor and make travis deploy to pypi
- add codecov bot to comment on pull requests

Author: Manuel

.appveyor.yml

@@ -1,17 +1,82 @@
-version: 1.0.{build}
-
 environment:
+  # SDK v7.0 MSVC Express 2008's SetEnv.cmd script will fail if the
+  # /E:ON and /V:ON options are not enabled in the batch script intepreter
+  # See: http://stackoverflow.com/a/13751649/163740
+  CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\appveyor\\run_with_env.cmd"
+  # TOX_ENV: "pywin"
+
   matrix:
-    - PYTHON: "C:\\Python36-x64"
+    # - PYTHON: "C:\\Python35-x64"
+    #   PYTHON_VERSION: '3.5'
+    #   PYTHON_ARCH: '64'
+    #   TOXENV: "py35"
+    #   # PYTHON_HOME: C:\Python35
+    #   # TOXPYTHON: C:\Python35-x64\python.exe
+
+    # - PYTHON: "C:\\Python36-x64"
+    #   PYTHON_VERSION: '3.6'
+    #   PYTHON_ARCH: '64'
+    #   TOXENV: "py36"
+    #   # PYTHON_HOME: C:\Python36
+    #   # TOXPYTHON: C:\Python36-x64\python.exe
+
+    - PYTHON: "C:\\Python37-x64"
+      PYTHON_VERSION: '3.7'
+      PYTHON_ARCH: '64'
+      TOXENV: "py37"
+      # PYTHON_HOME: C:\Python37
+      # TOXPYTHON: C:\Python37-x64\python.exe
+
+    - PYTHON: "C:\\Python37-x64"
+      PYTHON_VERSION: '3.7'
+      PYTHON_ARCH: '64'
+      TOXENV: "docu"
+
+    # - PYTHON: "C:\\Python37-x64"
+    #   PYTHON_VERSION: '3.7'
+    #   PYTHON_ARCH: '64'
+    #   TOXENV: "example_scripts"
+      # PYTHON_HOME: C:\Python37
+      # TOXPYTHON: C:\Python37-x64\python.exe
+
+
+init:
+  - ps: echo $env:TOXENV
+  - ps: echo $env:PYTHON_HOME
+  - ps: ls C:\Python*
 
 install:
-  - cmd: "%PYTHON%\\python.exe setup.py install"
-  - cmd: "%PYTHON%/Scripts/pip.exe install numpy"
-  - cmd: "%PYTHON%/Scripts/pip.exe install -r requirements.txt"
-  - cmd: "%PYTHON%\\python.exe install_resources.py omssa_2_1_9"
-  - cmd: "%PYTHON%/Scripts/nosetests.exe"
+  # - python -u ci\appveyor-bootstrap.py
+  # Download setup scripts and unzip
+  - ps: "wget https://github.com/cloudify-cosmo/appveyor-utils/archive/master.zip -OutFile ./master.zip"
+  - "7z e master.zip */appveyor/* -oappveyor"
+
+  # Install Python (from the official .msi of http://python.org) and pip when
+  # not already installed.
+  - "powershell ./appveyor/install.ps1"
+
+  # Prepend newly installed Python to the PATH of this build (this cannot be
+  # done from inside the powershell script as it would require to restart
+  # the parent CMD process).
+  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
+
+  # Check that we have the expected version and architecture for Python
+  - "python --version"
+  - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
+
+
+build: false  # Not a C# project, build stuff at the test step instead.
+
+before_test:
+  - "%CMD_IN_ENV% pip install tox"
+  - ps: 'ls C:\Python35\Scripts'
+
+test_script:
+  - "%CMD_IN_ENV% tox -e %TOXENV%"
 
-# test_script:
-#   - nosetests
+# on_failure:
+#   - ps: dir "env:"
+#   - ps: get-content .tox\*\log\*
 
-build: off
+artifacts:
+  - path: dist\*

.travis.yml

@@ -1,36 +1,31 @@
 language: python
 python:
-  - "3.6"
+- '3.6'
 sudo: false
-
-branches:
-  only:
-    - master
-
 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:
-  - 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
+  - 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=coverage
+  - python: 3.6
+    env: TOXENV=example_scripts
+script: tox
+deploy:
+  provider: pypi
+  user: pyratez
+  password:
+    secure: "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"
+  distributions: sdist bdist_wheel bdist_egg
+  on:
+    tags: true
+    all_branches: true
+    skip_existing: true
+    skip_cleanup: true

codecov.yml

@@ -0,0 +1,26 @@
+codecov:
+  notify:
+    require_ci_to_pass: yes
+coverage:
+  precision: 2
+  round: down
+  range: "70...100"
+
+  status:
+    project: yes
+    patch: yes
+    changes: no
+
+parsers:
+  gcov:
+    branch_detection:
+      conditional: True
+      loop: True
+      method: False
+      changes: False
+      macro: False
+
+  comment:
+    layout: "head, diff"
+    behaviour: default
+    require_change: no

requirements.txt

@@ -1,6 +1,9 @@
-pymzml>=2.0
-nose>=1.3
+pymzml >= 2.0
+nose >=1.3
 regex
-pyahocorasick>=1.1.4; sys_platform != 'win32'
-pyqms
+pyahocorasick >= 1.1.4; sys_platform != 'win32'
+pyqms==0.6.2
+coverage
+codecov
 tox
+pre-commit

requirements_dev.txt

@@ -1,14 +1,11 @@
 [tox]
-envlist=py35,py36,py37,docu,example_scripts
-requires= tox
+envlist=py35,py36,py37,coverage,docu
+
 [testenv]
 deps = 
-  -Ur{toxinidir}/requirements_dev.txt
+  -Ur{toxinidir}/requirements.txt
 commands = 
-  coverage erase
-  coverage run {envbindir}/nosetests
-  coverage report --include=ursgal/* --omit=test/
-  codecov
+    nosetests
 
 [testenv:docu]
 deps = 
@@ -18,15 +15,15 @@ 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
+[testenv:coverage]
+passenv = 
+  CI TRAVIS TRAVIS_*
+deps =
+  numpy
+commands =
+  pip install -e .
+  pip install -q -r {toxinidir}/requirements.txt
+  coverage erase
+  coverage run {envbindir}/nosetests
+  coverage report --include=ursgal/* --omit=test/
+  codecov