Installation

Software requirements

This software is written in Python programming language, therefore you must have Python 3.8, 3.7, 3.6, 3.5 or 2.7 installed. In addition, the following third-party Python libraries are also required:

  • pip - Python package installer

  • setuptools - tools for installing Python packages

  • six - Python 2 and 3 compatibility library

  • NumPy - library for scientific computing with Python

  • matplotlib - Python plotting library

  • IPython - enhanced interactive Python shell

Standard Python releases can be obtained from https://www.python.org/downloads. The third-party libraries can be found at the Python Package Index or using any Internet search engine.

Another more convenient option is to obtain one of the science-oriented Python distributions such as Anaconda Python, Enthought Canopy or PythonXY, These distributions already include all the necessary libraries, so the required Python software can be all installed in one step.

On Linux operating systems the third-party libraries are usually included in a system software repository. For example on an Ubuntu Linux computer the software dependencies can be all installed with a single shell command

sudo apt-get install \
  python3-pip python3-setuptools python3-six \
  python3-numpy python3-matplotlib ipython3

This may be, of course, as well accomplished using the GUI driven Synaptic package manager. Other Linux distributions may use different software management tools, but the names of the necessary packages should be very similar to those above.

On Windows operating system, it may be necessary to add the C:\Python37 directory and the scripts directory C:\Python37\Scripts to the system PATH. Some Python distributions already do so as a part of their installation process. The easiest way to check is to start the Command Prompt, type there python and see if this starts the Python interpreter.

Alternately, if you want to run the diffpy.pdfgetx software with a specific version of Python, we recommend using a virtual environment, such as conda. For example, if you have Anaconda Python installed, you can create a conda virtual environment to install the software as follow

conda create --name pdfgetx_env numpy matplotlib ipython --python=3.8

You can choose the name of the environment and python version as you desire. You can choose any of the supported Python versions. Then, activate this environment and follow the instructions in the next section to install the software

conda activate pdfgetx_env

Installation

The diffpy.pdfgetx software is distributed as a Python wheel file, which can be obtained from the Columbia Technology Ventures. Once all the required software is in place, start the command prompt on Windows or a Unix terminal on Linux or Mac, navigate to the directory that contains the wheel file and execute the following command:

pip install ./diffpy.pdfgetx-VERSION.whl

Here VERSION needs to be replaced to match the actual filename. It is critical that pip installer is from a supported Python version otherwise the program would not work. On Linux and Mac operating systems the installation may need to run with root user privileges, for example, by prepending sudo to the command line above. If root access is not available, use the pip install options --user or --prefix to install the software to a user-writable directory.

The package provides three programs for PDF conversion, pdfgetx3, pdfgetn3 and pdfgets3. To check if they are correctly installed run

pdfgetx3 --version
pdfgetn3 --version
pdfgets3 --version

This should display the software version, which should agree with the VERSION string in the wheel package name. The installation also includes a plotdata command for an easy plotting of text data files. To verify if plotdata works, run the plotdata --version command. Finally, a comprehensive test of the installed software can be executed using

python -m diffpy.pdfgetx.tests.run

Note

Older versions of diffpy.pdfgetx use Python egg format instead of Python wheel. To install these use the easy_install command as follows:

python -m easy_install ./diffpy.pdfgetx-VERSION.egg

IPython magic command

These instructions are intended for IPython users who would like to integrate PDFgetX3, PDFgetN3 and PDFgetS3 into their IPython environment. If you don’t plan to customize IPython in such way you can safely skip this paragraph.

When pdfgetx3 or pdfgetn3 or pdfgets3 is run in interactive mode, it start IPython interactive shell and define an extra %pdfgetx3, %pdfgetn3 and %pdfgets3 magic commands within the IPython session. The IPython magic commands are not valid Python code, but work in a similar fashion as standard shell commands. The %pdfgetx3, %pdfgetn3 and %pdfgets3 magics can be thus used with the same options and arguments as if run from the shell. This is useful for processing more files, while preserving all plots or variables that were already created in an IPython session.

The %pdfgetx3, %pdfgetn3 and %pdfgets3 magic commands can be defined permanently so they are available in all IPython sessions. To set this up

  1. find the profile_default/ipython_config.py file and open it in a text editor. If that file does not exists, create it first by executing

    ipython profile create

  2. navigate to the paragraph that contains the c.InteractiveShellApp.extensions and add there the following line

    c.InteractiveShellApp.extensions = ['diffpy.pdfgetx.ipy_magics']

    There must be no leading indent, i.e., the text must start at the very first column.