OSX pip install#

These are the install instructions for OSX/pip.

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.

  • Note: if you already installed Anaconda Python, and then you upgrade to OSX Catalina, you may need to reinstall Anaconda. 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.

Test your python#

To make sure that you have installed Python successfully, type python on your command line. You should see something like this:

Python 3.7.10 (default, Feb 26 2021, 10:16:00)
[Clang 10.0.0 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.

(Press control-D to exit)

Install PmagPy#

  • Install pmagpy and pmagpy-cli:

    pip install --upgrade pmagpy --no-deps
pip install --upgrade pmagpy-cli --no-deps

  • If you are getting weird install errors, try uninstalling and then force reinstalling with this:

    pip uninstall pmagpy pmagpy-cli
pip install pmagpy --upgrade --no-deps --force-reinstall --no-cache-dir
pip install pmagpy-cli --upgrade --no-deps --force-reinstall --no-cache-dir

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_anaconda

Remember that the program may be very slow to initialize the first time! You may also need to resize the GUI window. If the program doesn’t open or you get an error message, 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 may want to copy the data files to your Desktop or another convenient location. To do this, navigate on the command line to your desired destination folder (for help, see this Cookbook section). Then, use the command:

move_data_files.py

This will copy all of the PmagPy example files to your current directory. NB: If you have a developer install, you can simply navigate to PmagPy/data_files, and move_data_files.py will not be needed.

Keeping PmagPy up-to-date#

To stay up to date with new features and bug fixes, you should periodically update both PmagPy packages.

pip install pmagpy --upgrade --no-deps

To check the currently installed version number for pmagpy (or any other Python package), run:

conda list

If you ever need to uninstall pmagpy or pmagpy-cli:

pip uninstall pmagpy

or

pip uninstall pmagpy-cli