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Installation without conda / Anaconda

Since this is development work, it might be good to create and run this in a virtual environment. Virtualenv and Virtual envwrapper eases management of virtual environments.

A virtualenv is not required to run PyGnome. But you may be working in an environment (on a corporate network, for example) that restricts your access to the system files on your computer. In such a case, you may require a virtualenv in order to freely install python packages in python's site-packages area. (site-packages is the standard place where python installers will put packages after building them)

You may also want to consider using conda environments -- see above.

There is C++/Cython code that must be built - you will need the correct C compiler and recent setuptools, etc. See "Installing With Anaconda" for more detail.

python.org

The following has been tested against Python 2.7

Linux (Tested in 64-bit, CentOS)

For Linux use appropriate package manager (yum on CentOS, apt-get on Ubuntu) to download/install binary dependencies.

Binary Dependencies

  1. setuptools is required.

    > sudo apt-get install python-setuptools ` `

  2. To compile Python extensions, you need the development libs for Python:

    > sudo apt-get install python-dev

  3. netCDF4 python module requires NetCDF libraries:

    libhdf5-serial-dev

    libnetcdf-dev

  4. The following python packages, documented in PyGnome's requirements.txt, may need to be manually installed.

Binaries for

Numpy and

Cython can be installed using apt-get.

Current binaries for these are sufficiently new: (Numpy >=1.11.0) and (Cython >= 0.24.1).

If you use virtualenv and apt-get to install these system site packages. Remember to use the --system-site-packages option when creating a new virtualenv so the system packages are available in the virtualenv.

Alternatively, pip install should also work. The following builds the latest packages in your virtualenv once the above dependencies are met:

> pip install numpy
> pip install cython
> pip install netCDF4

The remaining dependencies are python packages and can be installed using:

pip install -r requirements.txt

See Build PyGnome section below.

Windows 7 (64-bit, using VS-2008 express edition)

For compiling python extensions on Windows, you need the correct version of teh MS compiler: "Visual Studio 2008". Microsoft has made a versin of this compiler al properly set up for python extensions:

Microsoft Visual C++ Compiler for Python 2.7:

https://www.microsoft.com/en-us/download/details.aspx?id=44266

This compiler should work for both 32 bit and 64 bit Windows.

Binary Dependencies

Download and install the newest Windows executable distribution of Python 2.7 (note: we are not quite ready for Python 3.0) Make sure the distribution is named consistently with the Python environment you desire. For example, binaries ending in win64-py2.7.exe are for Python 2.7. (64-bit)

A number of the packages that GNOME depends on have very complex and brittle build processes, and depend on third-party libraries that can be a challenge to build.

Fortunately, Chris Gohlke's website contains pre-compiled binary distributions for many of these packages.

(The full list of dependent packages and their minimum versions can be found _in the file GNOME2/py__gnome/requirements.txt)

There are also more binary wheels available every day -- it's worth checking PyPi

Another option is to use a Python scientific distribution, such as Anaconda or Enthought Canopy

Here are the binary packages required:

  1. setuptools
  2. pip

At this point, we should test that pip is installed correctly. On command line invoke the following pip commands. These should show usage information for 'pip', and then a list of installed packages:

>  pip

Usage:
  pip <command> [options]

Commands:
  install                     Install packages.
  download                    Download packages.
  uninstall                   Uninstall packages.

> pip list
alabaster (0.7.9)
appnope (0.1.0)
awesome-slugify (1.6.5)
...
  1. numpy-MKL
  2. Cython
  3. Pillow
  4. 64-bit 1.0.6 version of netCDF4
  5. lxml - required for webgnome
  6. python-cjson - required for webgnome

The remaining dependencies are python packages and can be installed using the command:

> pip install -r requirements.txt

See Build PyGnome section below.

Windows 7 (64-bit, using VS-2008 express edition)

Building GNOME for 64 bit Windows is similar to the 32 bit Windows build, and has similar binary dependencies. There are however some extra steps you need to perform in order to build py_gnome.

Build PyGnome

  1. Clone the PyGnome repository:

    > git clone https://github.com/NOAA-ORR-ERD/PyGnome.git

  2. pip install all of GNOME's python package dependencies:

    > cd PyGnome/py_gnome
> pip install -r requirements.txt

  3. Install the Oil Library package. The OilLibary package is under active development along with py_gnome, so it's best to install that from source as well:

    https://github.com/NOAA-ORR-ERD/OilLibrary

  4. build the py_gnome module in develop mode first as install mode may still need some testing/work.

    The other option you may need is cleanall, which should clean the development environment -- good to do after puling new code from git.

  5. If this successfully completes, then run the unit tests:

    > py.test --runslow tests/unit_tests

Once all of the py_gnome unit tests pass, PyGnome is now built and ready to be put to use. You can use the gnome module inside your python scripts to set up a variety of modeling scenarios.

There are example full scripts in the py_gnome/scripts directory.