Getting Started :: Coding For Chemists

0. Installing Python

authors@codingforchemistsbook.com (Benjamin Lear and Christopher Johnson) — Tue, 03 Jun 2025 00:00:00 +0000

Installation of Python We strongly recommend following the procedure outlined here to get a working Python installation that will work with this book1 and set you up well for ongoing Python work in your chemistry career!2 Download the most recent official release of Python https://www.python.org/ that is appropriate for your computer and install it. On Windows PCs, make sure to check the box to add the Python executables to your PATH during the first few screens of the installer (before clicking “Install”).

1. Installing Python Libraries

authors@codingforchemistsbook.com (Benjamin Lear and Christopher Johnson) — Tue, 03 Jun 2025 00:00:00 +0000

Installation of libraries needed for this book Open a command line: On Windows PCs, press the Windows key, then type cmd and press Enter. On Macs, hold the “command” key, press the space bar, and type Terminal, then press “return.” Your base Python installation includes the program pip to install packages. On Windows PCs, the command for pip is just pip On Macs, the command for pip is most often pip3 In the command line that you just opened type the appropriate command, which should give you an output that looks like: C:\Users\Chris>pip Usage: pip [options] Commands: install Install packages. download Download packages. uninstall Uninstall packages. freeze Output installed packages in requirements format. inspect Inspect the python environment. list List installed packages. show Show information about installed packages. check Verify installed packages have compatible dependencies. config Manage local and global configuration. If you get this, or something like it, then pip is working correctly and you are ready to install packages. If not, you will need to troubleshoot.

2. Testing your Installation

authors@codingforchemistsbook.com (Benjamin Lear and Christopher Johnson) — Tue, 03 Jun 2025 00:00:00 +0000

Testing your Python environment Download the file plotly_test.py to your Downloads folder. Open a command prompt (Windows - press the Windows key, type cmd.exe, and press Enter; Macs - Hold the “command” key, press the space bar, type Terminal, and press return). Type cd ~/Downloads and press enter. Run the plotly_test.py script (Windows - type python.exe plotly_test.py and press Enter; Macs - type python3 plotly_test.py and press return). After a few seconds, two things should happen: 1.) you should see a browser window open with a plot of a sine wave it it; 2.) a new file image named test.png containing the same plot should appear in your Downloads folder.1 If both of these things happen, then your installation works fine. Sometimes, the image file will not be generated, often coinciding with a message in the command line to run plotly_get_chrome. You can usually simply type plotly_get_chrome into this same command line and go back to step 6.4 above, and things should work now. ↩︎

3. Making the Python Installation Convenient

authors@codingforchemistsbook.com (Benjamin Lear and Christopher Johnson) — Tue, 03 Jun 2025 00:00:00 +0000

Making the Python installation more convenient As installed, you will need to open a command line and type spyder every time you want to use Spyder. This can be annoying, so you can make a shortcut that you can open from your desktop or quick launch: On Windows PCs: Right-click on your desktop background and click New->Shortcut in the menu that pops up. A dialog box will appear that asks you to type the location of the item (in this case, the executable file for spyder). You can find this by going to the command line and typing where spyder to reveal the location of the spyder executable. You should get a long line of text that starts with C:\ and ends with spyder.exe that you can highlight with your mouse and copy by pressing “Ctrl C” on your keyboard. Paste this line of text into the text entry box in the dialog for the shortcut and click “Next” to continue. The dialog will now prompt you to give the shortcut a name. You can choose whatever you want, but we recommned calling it Spyder! Type in Spyder and click “Finish” to make the shortcut. (optional) The shortcut should appear but it has a generic icon. You can add the proper icon by right clicking on the shortcut and clicking “Properties” in the menu that pops up. A dialog box should appear that has a button labeled “Change Icon…” that, when clicked, allows you to specify a file with the icon image to use. In this new dialog box, click “Browse…” to bring up a file explorer window that you can use to find the icon file. In this window, click This PC in the taskbar to the left and then in the search box in the top right, type “windows_app_icon” and press Enter. It may take a bit of time for Windows to find it, but you should eventually get a file that has the spyder logo (A black S and a red spider web). Click Open, then OK, then OK again to finish, and you should now see the shortcut on your desktop. On a Mac: We are still working on this. . . You can also add a link to Spyder in your Start menu in Windows. This will have the secondary effect of making it possible to launch Spyder by pressing your Windows key and typing “spyder” as a quick method. Right click your Spyder shortcut that you just made and, in the popup menu that appears, click “Pin to Start” to make a Start menu shortcut. Now you can even delete your desktop shortcut if you want, and Spyder will remain in the Start menu!