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Diff for: .gitignore

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*.dmg
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*.egg
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*.egg-info/
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*.gem
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*.log
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*.manifest
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*.mo
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*.pot
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*.py[cod]
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*.rbc
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*.sage.py
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*.so
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*.spec
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*.swp
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.cache
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.coverage
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.coverage.*
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.dat*
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.DS_Store
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.eggs/
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.env
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.mypy_cache/
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.Python
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.python-version
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.repl_history
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.ropeproject
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.ruby-gemset
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.ruby-version
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.rvmrc
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.scrapy
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.spyderproject
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.spyproject
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.tox/
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.vagrant/
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.venv
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.webassets-cache
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/.bundle/
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/.config
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/.yardoc/
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/_yardoc/
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/coverage/
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/doc/
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/InstalledFiles
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/lib/bundler/man/
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/pkg/
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/rdoc/
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/site
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/spec/reports/
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/test/tmp/
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/test/version_tmp/
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/tmp/
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/vendor/bundle
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__pycache__/
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build/
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build/
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celerybeat-schedule
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coverage.xml
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develop-eggs/
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eggs/
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env/
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ENV/
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Gemfile.lock
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htmlcov/
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instance/
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lib/

Diff for: vagrant/README.rst

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# metabolism
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## Getting started
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1. Download and install [Vagrant](https://www.vagrantup.com/downloads.html).
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1. Download and install [VirtualBox](https://www.virtualbox.org/wiki/Downloads).
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1. Clone this repository:
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```sh
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git clone [email protected]:CellProfiler/metabolism.git
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```
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## Usage
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Install Virtualbox (https://www.virtualbox.org/wiki/Downloads)
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Then:
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```sh
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cd metabolism
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vagrant up
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```
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Clone CP and CPA:
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```sh
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git clone https://github.com/CellProfiler/CellProfiler
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git clone https://github.com/CellProfiler/CellProfiler-Analyst
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```
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SSH into virtual machine
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```sh
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vagrant ssh
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```
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Start CellProfiler Analyst
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```sh
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python /vagrant/CellProfiler-Analyst/CellProfiler-Analyst.py
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```

Diff for: vagrant/Vagrantfile

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# -*- mode: ruby -*-
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# vi: set ft=ruby :
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# All Vagrant configuration is done below. The "2" in Vagrant.configure
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# configures the configuration version (we support older styles for
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# backwards compatibility). Please don't change it unless you know what
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# you're doing.
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Vagrant.configure(2) do |config|
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# The most common configuration options are documented and commented below.
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# For a complete reference, please see the online documentation at
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# https://docs.vagrantup.com.
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# Every Vagrant development environment requires a box. You can search for
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# boxes at https://atlas.hashicorp.com/search.
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config.vm.box = "bento/ubuntu-16.04"
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# Disable automatic box update checking. If you disable this, then
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# boxes will only be checked for updates when the user runs
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# `vagrant box outdated`. This is not recommended.
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# config.vm.box_check_update = false
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# Create a forwarded port mapping which allows access to a specific port
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# within the machine from a port on the host machine. In the example below,
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# accessing "localhost:8080" will access port 80 on the guest machine.
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# config.vm.network "forwarded_port", guest: 80, host: 8080
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# Create a private network, which allows host-only access to the machine
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# using a specific IP.
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# config.vm.network "private_network", ip: "192.168.33.10"
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# Create a public network, which generally matched to bridged network.
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# Bridged networks make the machine appear as another physical device on
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# your network.
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# config.vm.network "public_network"
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# Share an additional folder to the guest VM. The first argument is
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# the path on the host to the actual folder. The second argument is
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# the path on the guest to mount the folder. And the optional third
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# argument is a set of non-required options.
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# config.vm.synced_folder "../data", "/vagrant_data"
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# Provider-specific configuration so you can fine-tune various
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# backing providers for Vagrant. These expose provider-specific options.
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# Example for VirtualBox:
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config.vm.provider "virtualbox" do |vb|
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# Display the VirtualBox GUI when booting the machine
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# vb.gui = true
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# Customize the amount of memory on the VM:
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vb.memory = "6144"
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end
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# View the documentation for the provider you are using for more
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# information on available options.
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# Define a Vagrant Push strategy for pushing to Atlas. Other push strategies
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# such as FTP and Heroku are also available. See the documentation at
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# https://docs.vagrantup.com/v2/push/atlas.html for more information.
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# config.push.define "atlas" do |push|
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# push.app = "YOUR_ATLAS_USERNAME/YOUR_APPLICATION_NAME"
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# end
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# Enable provisioning with a shell script. Additional provisioners such as
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# Puppet, Chef, Ansible, Salt, and Docker are also available. Please see the
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# documentation for more information about their specific syntax and use.
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config.vm.provision "shell", path: "setup.sh", privileged: false
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end

Diff for: vagrant/setup.sh

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sudo apt-get -y update
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sudo apt-get -y upgrade
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sudo apt-get -y install \
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build-essential \
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cython \
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git \
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libmysqlclient-dev \
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libhdf5-dev \
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libxml2-dev \
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libxslt1-dev \
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openjdk-8-jdk \
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python-dev \
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python-pip \
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python-h5py \
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python-matplotlib \
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python-mysqldb \
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python-scipy \
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python-numpy \
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python-wxgtk3.0 \
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python-zmq
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if ! cd $HOME/CellProfiler; then
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git clone https://github.com/CellProfiler/CellProfiler.git $HOME/CellProfiler
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fi
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sudo -H pip install --upgrade
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sudo -H pip install --editable $HOME/CellProfiler

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