fushandchups/pyferret

The PyFerret program and Python module from NOAA/PMEL

PyFerret

The PyFerret Python module from NOAA/PMEL.
This repository is regularly synchronized with PyFerret repository at PMEL (the pyferret branch of the ferret project in the subversion repository at PMEL) using git-svn.

If you build Ferret from these source files, please note:
The site_specific.mk and external_functions/ef_utilites/site_specific.mk files in the repository have been renamed with a .in appended to the name. You must copy these files with the .in extensions to create files with the site_specific.mk name and edit the contents to configure these for your system. The site_specific.mk files will be ignored by git (the name was added to .gitignore) so your customized configuration files will not be added to your repository if you have cloned this repository.

Jupyter / iPython notebook

The latest ferretmagic module from Patrick Brockmann for using PyFerret with the iPython notebook can be obtained using pip install ferretmagic, or see http://pypi.python.org/pypi/ferretmagic. Note that this only installs the ferretmagic module for PyFerret; it does not install PyFerret.

Anaconda Installation - Linux, OS X, and Windows 10/bash

Download and install miniconda for your system. Note that Windows 10 bash must use the Linux version! The Python version in miniconda does not matter; pyferret only uses Python 2.7 and will install it in the pyferret environment.

Execute the following command on the terminal to install pyferret as well as ferret_datasets (the default Ferret/PyFerret datasets) into conda:

conda create -n FERRET -c conda-forge pyferret ferret_datasets --yes

To start using pyferret, execute the following command:

source activate FERRET

Once you are done working with pyferret you can leave this environment, if you wish, with the command:

source deactivate FERRET

In the commands above, FERRET is the environment name where pyferret is installed. You can change that to any name you like but we do not recommend installing pyferret in the root environment of miniconda. The main reason is to take advantage of the activate/deactivate script that will set up all the variables that pyferret needs. (You can test whether the pyferret environment is activated by issuing the command echo $FER_DATA and see if it returns a directory name.)

Installation from prebuilt tar.gz file

You will need to have the following packages installed using your software manager application, or using a command-line package installation program such as yum or apt-get (which needs to be run as the root user or using the sudo privilege escalation program.)

Required packages that may not already be installed:

• numpy or python-numpy (NumPy)
• libgfortran (Fortran library; if you install SciPy, it will be installed)
• PyQt4 or python-qt4 (Python binding for Qt4; may already be installed)

Highly recommended but optional packages:

• scipy or python-scipy (SciPy)
• pyshp or python-pyshp (PyShp for shapefile functions)

You may also wish to install the netcdf and nco packages to provide some useful programs for working with NetCDF files (such as ncdump and ncattted which are used in the benchmark tests).

If you do not have the Ferret standard datasets, they can be obtained from the NOAA-PMEL/FerretDatasets GitHub repo. The contents can be put extracted/cloned to whatever location desired.

Extract the PyFerret tar.gz file in the desired location. Starting with PyFerret v7, there is only one tar.gz file which extracts all its contents to a subdirectory that it creates (as apposed to Ferret which has separate fer_environment and fer_executables tar.gz files that extract into the current directory). If desired, at this time you can change the name of this subdirectory that was created.

Move into this PyFerret installation directory and run the bin/Finstall script to create the ferret_paths.sh, ferret_paths.csh, and pyferret scripts. The value of FER_DIR, the Ferret/PyFerret installation directory, should be this installation directory, which can be specified as . (a period) which means the current directory. (If FER_DIR is already defined for another Ferret/PyFerret installation, you will need to tell the script to use a new value.) For FER_DSETS, the Ferret standard datasets, specify the directory containing these datasets (which you may have created from the FerretDatasets github site mentioned above).

To run PyFerret, you first need to set the Ferret environment variables. This can be done by executing either . ferret_paths.sh (for Bourne-type shells; e.g., bash) or source ferret_paths.csh (for C-type shells; e.g. tcsh).

• Note: the pyferret script has recently been updated to automatically set the Ferret environment variables, if not already defined, using the appropriate ferret_paths script.

For more information on using PyFerret, see the Ferret and PyFerret documentation under http://ferret.pmel.noaa.gov/Ferret/documentation/ Information about the Ferret email users group, and archives of past discussions from the group (which should be searched prior to sending a question to the email users group) can be found at http://ferret.pmel.noaa.gov/Ferret/email-users-group

Building PyFerret from source

To build PyFerret from source code, please see the Building PyFerret instructions at http://ferret.pmel.noaa.gov/Ferret/documentation/pyferret/build-install/
Please note that the site_specific.mk and external_functions/ef_utilites/site_specific.mk files in the repository have been renamed with a .in appended to the name. You must copy these files with the .in extensions to create files with the site_specific.mk name and edit the contents to configure these for your system. The site_specific.mk files will be ignored by git (the name was added to .gitignore) so your customized configuration files will not be added to your repository if you have cloned this repository.