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Manuel
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Update CI/CD
- run tests with tox - build docu with tox - run example scripts using tox - run codecoverage using tox - configure travis to use tox envs - configure appveyor to use tox envs - configure travis to deploy package to pypi on tag - update .gitignore - update requirements, docs/requirements and add requirements_dev - codecov will post change in coverage under pull requests - add pre-commit config to run common style fixes and black
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‎.appveyor.yml

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

‎.gitignore

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*.html
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dist
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*.log
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.coverage
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.scannerwork
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.tox
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pymzml.egg-info
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docs/source/code_inc/

‎.pre-commit-config.yaml

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v2.1.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: debug-statements
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- repo: https://github.com/ambv/black
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rev: 18.9b0
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hooks:
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- id: black
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language_version: python
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exclude: ^docs/, ^tests/

‎.travis.yml

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language: python
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python:
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- "3.4"
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- "3.5"
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- "3.6"
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- '3.6'
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sudo: false
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before_install: pip install codecov
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after_success: codecov
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install:
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- pip install -r requirements.txt
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script: nosetests --with-coverage
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branches:
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only:
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- master
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matrix:
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include:
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- python: 3.5
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env: TOXENV=py35
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- python: 3.6
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env: TOXENV=py36
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- python: 3.7
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env: TOXENV=py37
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dist: xenial
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- python: 3.6
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env: TOXENV=docu
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- python: 3.6
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env: TOXENV=coverage
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- python: 3.6
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env: TOXENV=example_scripts
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script:
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echo
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deploy:
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provider: pypi
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user: pyratez
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password:
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secure: HKI1+vjzjYohYeLFC9BmlZGmpG5Y0zbBiwHjTvTI4Uy6g3KrmP+Lkj2Ean+r9LVrzghcLWu7ze4mN+33jR4ke2DLpryFSQCP3+V1GLBuNk4SYfFmE9VKcGhSmPrHWEgClj1BK6jV5Fiun2dqGcj3oCFXMXiqPLuqlzmYh1MtSG3OefRMUAb1jFz2griQYDVa+qmU7LSHj9oCzJqo6NID1pt/V9vXXl2J+F1zY7Ag7dWbcKFbiPT30rIo2BLvPCQl9XjEvOudixbsvaOPAvD9Cdl5xU9BtieHhBJEBhV+oUiT0fuee0hbEW1mVLg/N8vSpbWxbXoSosZoVCVRzYzl1o+33y85zCjdTECPkiTyEVjhJ8HlWWQie5CKFT04jLypA3RgR9ms+SEmx4v49tvuorVZCosJrF5J0JCD29PBu1gKOL0Mpy3ysUf4veytaYhgJMqBldJTk0LHwfR/hCHX+kFQbZPY/Ge5TyA3NXdfSYeJA5tBqVcXAQprKvGJmKcjyEPUhO5JgX/A0kMussyNyvguTE4oW7CSoErSEQcOgwPkej7DhurqLaYI/C6unFpGBT/YBbR6Isv4YOD8KSzyxpJqmTsRgZohn/Wnn5IfeoxqVoVTSdEW/qQ3LJMRMpUvwcDLQGtW/2X3eaXZI54BNO5zdXWniSuxaPHUBBiv2DE=
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distributions: sdist bdist_wheel bdist_egg
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on:
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tags: true

‎codecov.yml

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codecov:
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notify:
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require_ci_to_pass: yes
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coverage:
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precision: 2
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round: down
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range: "70...100"
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status:
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project: yes
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patch: yes
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changes: no
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parsers:
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gcov:
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branch_detection:
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conditional: True
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loop: True
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method: False
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changes: False
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macro: False
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comment:
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layout: "head, diff"
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behaviour: default
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require_change: no
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‎docs/requirements.txt

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sphinx >= 1.3.0
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sphinx_rtd_theme >= 0.1.9
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regex

‎requirements.txt

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# Installation
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numpy >= 1.8.0
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plotly < 2.0
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numpy
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plotly
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pynumpress >= 0.0.4
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regex
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# Testing and dev
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cython
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coverage >= 4.2
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nose >= 1.3.7
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sphinx
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sphinx_rtd_theme
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tox

‎requirements_dev.txt

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# install requirements
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-r requirements.txt
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# Testing and Development
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cython
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coverage >= 4.2
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codecov
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pytest
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tox
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regex

‎tox.ini

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[tox]
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envlist = py35,py36,py37,coverage,example_scripts,docu
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[testenv]
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deps =
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numpy
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pytest
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whitelist_externals = pytest
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commands =
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pip install -r {toxinidir}/requirements_dev.txt
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pytest tests/
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[testenv:docu]
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whitelist_externals =
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make
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/bin/bash
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/usr/bin/bash
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deps =
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-Ur{toxinidir}/docs/requirements.txt
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changedir = {toxinidir}/docs
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commands =
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sphinx-build source build
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sphinx-build -b latex source build
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#[testenv:format]
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#deps =
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# black
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#commands =
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# #pycodestyle -qq --statistics --count --ignore=E221,E203,E402 --max-line-length=90 pymzml
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# black --check pymzml
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[testenv:coverage]
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passenv =
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CI TRAVIS TRAVIS_*
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deps =
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numpy
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commands =
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pip install -e .
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pip install -q -r {toxinidir}/requirements_dev.txt
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coverage erase
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coverage run {envbindir}/pytest
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coverage report --omit=".tox/*","tests/*"
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codecov
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[testenv:example_scripts]
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deps =
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numpy
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commands =
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pip install -Ur{toxinidir}/requirements.txt
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python example_scripts/access_run_info.py
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python example_scripts/compare_spectra.py
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python example_scripts/extract_ion_chromatogram.py
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python example_scripts/extreme_values.py
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python example_scripts/get_precursors.py
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python example_scripts/has_peak.py
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python example_scripts/highest_peaks.py

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