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Developer Installation

Dallinger is tested with Ubuntu 18.04 LTS, 16.04 LTS, 14.04 LTS and Mac OS X locally. If you are attempting to use Dallinger on Microsoft Windows, running Ubuntu in a virtual machine is the recommend method.

If you are interested in using Dallinger with Docker, read more :doc:`here <docker_setup>`.

Mac OS X

Install Python

Dallinger is written in the language Python. For it to work, you will need to have Python 2.7 installed, or alternatively Python 3.6 or higher. Python 3 is the preferred option. You can check what version of Python you have by running:

python --version

Note

You will also need to have pip installed. It is included in some of the later versions of Python 3, but not all. (pip is a package manager for Python packages, or modules if you like.) If you are using Python 3, you may find that you may need to use the pip3 command instead of pip where applicable in the instructions that follow.

Using Homebrew will install the latest version of Python and pip by default.

brew install python

This will install the latest Python3 and pip3.

You can also use the preinstalled Python in Mac OS X, currently Python 2.7 as of writing.

If you installed Python 3 with Homebrew, you should now be able to run the python3 command from the terminal. If the command cannot be found, check the Homebrew installation log to see if there were any errors. Sometimes there are problems symlinking Python 3 to the python3 command. If this is the case for you, look here for clues to assist you.

With the preinstalled Python in Mac OS X, you will need to install pip yourself. You can use:

sudo easy_install pip

Should that not work for whatever reason, you can search here for more clues.

Install Postgresql

On Mac OS X, we recommend installing using Homebrew:

brew install postgresql

Postgresql can then be started and stopped using:

brew services start postgresql
brew services stop postgresql

Create the databases

After installing Postgres, you will need to create two databases: one for your experiments to use, and a second to support importing saved experiments. It is recommended that you also create a database user.

Naviagate to a terminal and type:

createuser -P dallinger --createdb
(Password: dallinger)
createdb -O dallinger dallinger
createdb -O dallinger dallinger-import

The first command will create a user named dallinger and prompt you for a password. The second and third command will create the dallinger and dallinger-import databases, setting the newly created user as the owner.

You can optionally inspect your databases by entering psql dallinger. Inside psql you can use commands to see the roles and database tables:

\du
\l

To quit:

\q

If you get an error like the following:

createuser: could not connect to database postgres: could not connect to server:
    Is the server running locally and accepting
    connections on Unix domain socket "/tmp/.s.PGSQL.5432"?

then postgres is not running. Start postgres as described in the Install Postgresql section above.

Install Heroku

To run experiments locally or on the internet, you will need the Heroku Command Line Interface installed, version 3.28.0 or better. If you want to launch experiments on the internet, then you will also need a Heroku.com account, however this is not needed for local debugging.

To check which version of the Heroku CLI you have installed, run:

heroku --version

To install:

brew install heroku/brew/heroku

More information on the Heroku CLI is available at heroku.com along with alternative installation instructions, if needed.

Install Redis

Debugging experiments requires you to have Redis installed and the Redis server running.

brew install redis

Start Redis on Mac OS X with:

brew services start redis

You can find more details and other installation instructions at redis.com.

Install Git

Dallinger uses Git, a distributed version control system, for version control of its code. If you do not have it installed, you can install it as follows:

brew install git

Set up a virtual environment

Why use virtualenv?

Virtualenv solves a very specific problem: it allows multiple Python projects that have different (and often conflicting) requirements, to coexist on the same computer. If you want to understand this in detail, you can read more about it here.

Now let's set up a virtual environment by running the following commands:

If using Python 2.7 and pip:

pip install virtualenv
pip install virtualenvwrapper
export WORKON_HOME=$HOME/.virtualenvs
mkdir -p $WORKON_HOME
export VIRTUALENVWRAPPER_PYTHON=$(which python)
source $(which virtualenvwrapper.sh)

If using Python 3.x and pip3 (Python 3.7 in this example):

pip3 install virtualenv
pip3 install virtualenvwrapper
export WORKON_HOME=$HOME/.virtualenvs
mkdir -p $WORKON_HOME
export VIRTUALENVWRAPPER_PYTHON=$(which python3.7)
source $(which virtualenvwrapper.sh)

Now create the virtual environment using:

mkvirtualenv dlgr_env --python <specify_your_python_path_here>

Examples:

Using homebrew installed Python 3.7:

mkvirtualenv dlgr_env --python /usr/local/bin/python3.7

Using Python 2.7:

mkvirtualenv dlgr_env --python /usr/bin/python

Virtualenvwrapper provides an easy way to switch between virtual environments by simply typing: workon [virtual environment name].

The technical details:

These commands use pip/pip3, the Python package manager, to install two packages virtualenv and virtualenvwrapper. They set up an environmental variable named WORKON_HOME with a string that gives a path to a subfolder of your home directory (~) called Envs, which the next command (mkdir) then makes according to the path described in $WORKON_HOME (recursively, due to the -p flag). That is where your environments will be stored. The source command will run the command that follows, which in this case locates the virtualenvwrapper.sh shell script, the contents of which are beyond the scope of this setup tutorial. If you want to know what it does, a more in depth description can be found on the documentation site for virtualenvwrapper.

Finally, the mkvirtualenv makes your first virtual environment which you've named dlgr_env. We have explicitly passed it the location of the Python that the virtualenv should use. This Python has been mapped to the python command inside the virtual environment.

The how-to:

In the future, you can work on your virtual environment by running: Python 2.7

export VIRTUALENVWRAPPER_PYTHON=$(which python)
source $(which virtualenvwrapper.sh)
workon dlgr_env

Python 3.x

export VIRTUALENVWRAPPER_PYTHON=$(which python3.7)
source $(which virtualenvwrapper.sh)
workon dlgr_env

NB: To stop working in the virtual environment, run deactivate. To list all available virtual environments, run workon with no arguments.

If you plan to do a lot of work with Dallinger, you can make your shell execute the virtualenvwrapper.sh script everytime you open a terminal. To do that type:

Python 2.7

echo "export VIRTUALENVWRAPPER_PYTHON=$(which python)" >> ~/.bash_profile
echo "source $(which virtualenvwrapper.sh)" >> ~/.bash_profile

Python 3.x

echo "export VIRTUALENVWRAPPER_PYTHON=$(which python3.7)" >> ~/.bash_profile
echo "source $(which virtualenvwrapper.sh)" >> ~/.bash_profile

From then on, you only need to use the workon command before starting.

Install prerequisites for building documentation

To be able to build the documentation, you will need yarn.

Please follow the instructions here to install it.

Install Dallinger

Next, navigate to the directory where you want to house your development work on Dallinger. Once there, clone the Git repository using:

git clone https://github.com/Dallinger/Dallinger

This will create a directory called Dallinger in your current directory.

Change into your the new directory and make sure you are still in your virtual environment before installing the dependencies. If you want to be extra careful, run the command workon dlgr_env, which will ensure that you are in the right virtual environment.

cd Dallinger

Now we need to install the dependencies using pip:

pip install -r dev-requirements.txt

Next run setup.py with the argument develop:

pip install -e .[data]

Test that your installation works by running:

dallinger --version

Install the dlgr.demos sub-package

Both the test suite and the included demo experiments require installing the dlgr.demos sub-package in order to run. Install this in "develop mode" with the -e option, so that any changes you make to a demo will be immediately reflected on your next test or debug session.

From the root Dallinger directory you created in the previous step, run the installation command:

pip install -e demos

Next, you'll need :doc:`access keys for AWS, Heroku, etc. <aws_etc_keys>`.

Ubuntu

Install Python

Dallinger is written in the language Python. For it to work, you will need to have Python 2.7 installed, or alternatively Python 3.6 or higher. Python 3 is the preferred option. You can check what version of Python you have by running:

python --version

Note

You will also need to have pip installed. It is included in some of the later versions of Python 3, but not all. (pip is a package manager for Python packages, or modules if you like.) If you are using Python 3, you may find that you may need to use the pip3 command instead of pip where applicable in the instructions that follow.

Ubuntu 18.04 LTS ships with Python 3.6.

Ubuntu 16.04 LTS ships with Python 3.5, while Ubuntu 14.04 LTS ships with Python 3.4. In case you are using one of these distributions of Ubuntu, you can use dallinger with Python 2.7 or upgrade to the latest Python 3.x on your own.

(All three of these Ubuntu versions also provide a version of Python 2.7)

If you do not have Python 3 installed, you can install it from the Python website.

Also make sure you have the python headers installed. The python-dev package contains the header files you need to build Python extensions appropriate to the Python version you will be using. You will also need to install pip.

If using Python 2.7.x:

sudo apt-get install python-dev
sudo apt install -y python-pip

If using Python 3.x:

sudo apt-get install python3-dev
sudo apt install -y python3-pip

Install Postgresql

The lowest version of Postgresql that Dallinger v5 supports is 9.4.

This is fine for Ubuntu 18.04 LTS and 16.04 LTS as they ship with Postgresql 10.4 and 9.5 respectively, however Ubuntu 14.04 LTS ships with Postgresql 9.3

Postgres can be installed using the following instructions:

Ubuntu 18.04 LTS:

sudo apt-get update && sudo apt-get install -y postgresql postgresql-contrib

To run postgres, use the following command:

sudo service postgresql start

After that you'll need to run the following commands

sudo sed /etc/postgresql/10/main/pg_hba.conf -e 's/md5/trust/g' --in-place
sudo sed -e "s/[#]\?listen_addresses = .*/listen_addresses = '*'/g" -i '/etc/postgresql/10/main/postgresql.conf'
sudo service postgresql reload

Ubuntu 16.04 LTS:

sudo apt-get update && sudo apt-get install -y postgresql postgresql-contrib

To run postgres, use the following command:

service postgresql start

After that you'll need to run the following commands

sudo sed /etc/postgresql/9.5/main/pg_hba.conf -e 's/md5/trust/g' --in-place
sudo sed -e "s/[#]\?listen_addresses = .*/listen_addresses = '*'/g" -i '/etc/postgresql/9.5/main/postgresql.conf'
sudo service postgresql reload

Ubuntu 14.04 LTS:

Create the file /etc/apt/sources.list.d/pgdg.list and add a line for the repository:

sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt/ `lsb_release -cs`-pgdg main" >> /etc/apt/sources.list.d/pgdg.list'

Import the repository signing key, update the package lists and install postgresql:

wget -q https://www.postgresql.org/media/keys/ACCC4CF8.asc -O - | sudo apt-key add -
sudo apt-get update && sudo apt-get install -y postgresql postgresql-contrib

To run postgres, use the following command:

sudo service postgresql start

After that you'll need to run the following commands

sudo sed /etc/postgresql/10/main/pg_hba.conf -e 's/md5/trust/g' --in-place
sudo sed -e "s/[#]\?listen_addresses = .*/listen_addresses = '*'/g" -i '/etc/postgresql/10/main/postgresql.conf'
sudo service postgresql reload

Create the databases

Make sure that postgres is running. Switch to the postgres user:

sudo -u postgres -i

Run the following commands:

createuser -P dallinger --createdb
(Password: dallinger)
createdb -O dallinger dallinger
createdb -O dallinger dallinger-import
exit

The second command will create a user named dallinger and prompt you for a password. The third and fourth commands will create the dallinger and dallinger-import databases, setting the newly created user as the owner.

Finally restart postgresql:

sudo service postgresql reload

Install Heroku

To run experiments locally or on the internet, you will need the Heroku Command Line Interface installed, version 3.28.0 or better. If you want to launch experiments on the internet, then you will also need a Heroku.com account, however this is not needed for local debugging.

To check which version of the Heroku CLI you have installed, run:

heroku --version

To install:

sudo apt-get install curl
curl https://cli-assets.heroku.com/install.sh | sh

More information on the Heroku CLI is available at heroku.com along with alternative installation instructions, if needed.

Install Redis

Debugging experiments requires you to have Redis installed and the Redis server running.

sudo apt-get install -y redis-server

Start Redis on Ubuntu with:

sudo service redis-server start

You can find more details and other installation instructions at redis.com.

Install Git

Dallinger uses Git, a distributed version control system, for version control of its code. If you do not have it installed, you can install it as follows:

sudo apt install git

Set up a virtual environment

Why use virtualenv?

Virtualenv solves a very specific problem: it allows multiple Python projects that have different (and often conflicting) requirements, to coexist on the same computer. If you want to understand this in detail, you can read more about it here.

Now let's set up a virtual environment by running the following commands:

If using Python 2.7 and pip:

sudo pip install virtualenv
sudo pip install virtualenvwrapper
export WORKON_HOME=$HOME/.virtualenvs
mkdir -p $WORKON_HOME
source /usr/local/bin/virtualenvwrapper.sh

If using Python 3.x and pip3:

sudo pip3 install virtualenv
sudo pip3 install virtualenvwrapper
export WORKON_HOME=$HOME/.virtualenvs
mkdir -p $WORKON_HOME
export VIRTUALENVWRAPPER_PYTHON=/usr/bin/python3
source /usr/local/bin/virtualenvwrapper.sh

Now create the virtualenv using the mkvirtualenv command as follows:

If you are using Python 3 that is part of your Ubuntu installation (16.04 or 18.04):

mkvirtualenv dlgr_env --python /usr/bin/python3

If you are using Python 2 that is part of your Ubuntu installation:

mkvirtualenv dlgr_env --python /usr/bin/python

If you are using another Python version (eg. custom installed Python 3.x on Ubuntu 14.04):

mkvirtualenv dlgr_env --python <specify_your_python_path_here>

Virtualenvwrapper provides an easy way to switch between virtual environments by simply typing: workon [virtual environment name].

The technical details:

These commands use pip, the Python package manager, to install two packages virtualenv and virtualenvwrapper. They set up an environmental variable named WORKON_HOME with a string that gives a path to a subfolder of your home directory (~) called Envs, which the next command (mkdir) then makes according to the path described in $WORKON_HOME (recursively, due to the -p flag). That is where your environments will be stored. The source command will run the command that follows, which in this case locates the virtualenvwrapper.sh shell script, the contents of which are beyond the scope of this setup tutorial. If you want to know what it does, a more in depth description can be found on the documentation site for virtualenvwrapper.

Finally, the mkvirtualenv makes your first virtual environment which you've named dlgr_env. We have explicitly passed it the location of the Python that the virtualenv should use. This Python has been mapped to the python command inside the virtual environment.

The how-to:

In the future, you can work on your virtual environment by running:

source /usr/local/bin/virtualenvwrapper.sh
workon dlgr_env

NB: To stop working in the virtual environment, run deactivate. To list all available virtual environments, run workon with no arguments.

If you plan to do a lot of work with Dallinger, you can make your shell execute the virtualenvwrapper.sh script everytime you open a terminal. To do that:

echo "source /usr/local/bin/virtualenvwrapper.sh" >> ~/.bashrc

From then on, you only need to use the workon command before starting.

Install prerequisites for building documentation

To be able to build the documentation, you will need yarn.

Please follow the instructions here to install it.

Install Dallinger

Next, navigate to the directory where you want to house your development work on Dallinger. Once there, clone the Git repository using:

git clone https://github.com/Dallinger/Dallinger

This will create a directory called Dallinger in your current directory.

Change into your the new directory and make sure you are still in your virtual environment before installing the dependencies. If you want to be extra careful, run the command workon dlgr_env, which will ensure that you are in the right virtual environment.

cd Dallinger

Now we need to install the dependencies using pip:

pip install -r dev-requirements.txt

Next run setup.py with the argument develop:

pip install -e .[data]

Test that your installation works by running:

dallinger --version

Install the dlgr.demos sub-package

Both the test suite and the included demo experiments require installing the dlgr.demos sub-package in order to run. Install this in "develop mode" with the -e option, so that any changes you make to a demo will be immediately reflected on your next test or debug session.

From the root Dallinger directory you created in the previous step, run the installation command:

pip install -e demos

Next, you'll need :doc:`access keys for AWS, Heroku, etc. <aws_etc_keys>`.