Linux developer install#

These are the install instructions for Linux/developer.

Install Python#

First, you will need to download a scientific Python distribution. We strongly recommend Anaconda. Be warned, your computer comes with a version of Python already installed; but this pre-installed version does NOT have everything you will need to run PmagPy, so you will still need to download Anaconda.

  • Download and install Anaconda Python 3.

  • In general, if you run into errors with your Anaconda Python environment, it can save time to simply uninstall and reinstall.

  • Open your command line (Terminal). See this Cookbook section for more information on finding your command line.

  • Create and activate a new conda Python environment with some required packages:

    conda create -n pmagpy_env future wxPython cartopy pandas matplotlib requests jupyter
conda activate pmagpy_env
pip install --user --upgrade pip setuptools
conda install conda-forge::python-wget

  • You have now created a new environment called “pmagpy_env” and activated it. This gives you a Python environment with the packages you need to run PmagPy programs. Each time you want to use PmagPy, you will open your Terminal and then run:

    conda activate pmagpy_env

    You can also deactivate the environment using:

    conda deactivate

    You must always activate your pmagpy environment when you open a new Terminal window if you want to use PmagPy in that window. To learn more about managing conda environments, etc., see the Anaconda documentation and cheatsheet.

  • When running these commands you may see some warnings about dependencies, but you can just ignore them!

  • If a package fails to install, you may need to use “sudo”: i.e., sudo pip install scripttest. You will then be asked for your computer password.

Install wxPython#

Next, you need to install wxPython.

Most recently (on Ubuntu 18.04.2), I’ve had success with simply running:

conda install wxPython

However, in the past this didn’t work and still may not work for all Linux distributions. Try the above command first, and if that fails, try working through the instructions below.

  • The following is a list of wxPython dependencies for Ubuntu 16.04 (this list may be redundant or incomplete, depending on your specific OS):

    pip install libtiff

sudo apt-get install libgtk-3-dev freeglut3-dev libgstreamer1.0-0 gstreamer1.0-plugins-base gstreamer1.0-plugins-good gstreamer1.0-plugins-bad gstreamer1.0-plugins-ugly gstreamer1.0-libav gstreamer1.0-doc gstreamer1.0-tools libgstreamer-plugins-base0.10-dev

sudo apt-get install dpkg-dev build-essential libjpeg-dev  libtiff-dev libsdl1.2-dev   libnotify-dev  freeglut3 freeglut3-dev libsm-dev libwebkitgtk-3.0-dev libxtst-dev python-dev libpng-dev

sudo apt-get install libwebkit2gtk-4.0-dev libsdl2-dev

    Carefully read through this page and look for a compatible wheel for your distribution. Download the appropriate wheel and then install it:

    pip install wxPython-4.0.1-cp35-cp35m-linux_x86_64.whl

    Be sure to replace the wheel name above with the actual wheel you downloaded.

    Or install the wheel from the download site directly:

    pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-16.04 wxPython

    Again, you will need the replace the link above with the link appropriate for your OS.

  • If you aren’t able to find a wheel that works, try these instructions

Test your python#

Run python on your command line.

You should see something like this:

Python 3.6.1 |Anaconda custom (x86_64)| (default, May 11 2017, 13:04:09)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>

If you don’t see that, go back and reinstall Anaconda.

Once you have successfully started the python interactive prompt, try:

import wx

You may have an error like this:

ImportError: libwx_gtk3u_core-3.0.so.0: cannot open shared object file: No such file or directory

If so, exit the python interpreter (quit()) and try:

export LD_LIBRARY_PATH=~/anaconda3/lib/python3.6/site-packages/wx/

(If you are using a non-Anaconda Python, your path to wx may be different).

Try again to import wx. If it now works, you may want to add that line to the end of your .bashrc file so that you don’t have to specify the path each time.

For more details about this issue, see this explanation and this Github issue for more information.

Install PmagPy#

Here are the steps to clone and install PmagPy.

  • You must use bash as your shell (not csh, zsh, etc.). You can make sure you are using bash with the command:

    printenv SHELL

    If your result is not “/bin/bash”, you will need to reset it. See this question for more details.

  • Download and install git

  • Navigate to the directory where you want to put the PmagPy folder, then run:

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

  • You should now have a full local copy of the PmagPy repository. Change directories into PmagPy:

    cd PmagPy

  • Next, you need to add PmagPy to your PATH so that the PmagPy programs can be called from any directory. Try running:

    python dev_setup.py install

  • If you have problems with the install, run python dev_setup.py -h for more information. You can also set your PATH manually if dev_setup.py fails.

  • After completing the developer install, you should restart your command line.

Test PmagPy#

Test core functionality:

  • On your command line, type “python” to start the interpreter. You will import pmagpy and then run a simple calculation. Importing pmagpy may take over a minute the first time, so be patient! It will be much faster in subsequent runs.

    >>> from pmagpy import pmag
>>> pmag.angle([350.0,10.0],[320.0,20.0])
array([30.59060998])
>>>

Test the GUIs:

  • On the command line, open Pmag GUI by running:

    pmag_gui.py

If you get an error about “pythonw”, you may need to link “python” to “pythonw” with a command like:

ln -s ~/anaconda3/bin/python3 ~/anaconda3/bin/pythonw

If you get any other errors, or if any of the test commands don’t work, go back and carefully follow the install instructions to make sure you didn’t miss a step. If you still have a problem, try the Troubleshooting section. If you don’t find an answer there, check out the existing Github issues and create a new one if necessary.

Finishing up#

Accessing example data files:

There are many data files used in the examples of programs and for use with the textbook Essentials of Paleomagnetism. You can find these in PmagPy/data_files.

Keeping PmagPy up-to-date#

You will want to stay up to date with PmagPy development. To update your developer install, you will just need to navigate to the PmagPy directory and run:

git pull

This will grab all of the latest code from Github, and will be immediately available to you.