Debugging Guide

Sometimes unexpected things happen. In this case, please, open an Issue and make sure to include the version of Hydrogen and Atom you are running. You can get this information by running atom --version from the command line.

Please, also include the output or a screenshot of the debug messages. To access the debug messages follow these steps:

  1. Open the Settings tab by pressing (ctrl-,), select the Hydrogen package (Packages --> Hydrogen), and tick Enable Debug Messages: hydrogen-settings

  2. Open the developer tools (View --> Developer --> Toggle Developer Tools or via shift-ctrl-i/cmd-alt-i): open-dev-tools

  3. Select the Console tab to see the debug logs and run the code causing the issue: dev-tools

Common Issues

Installation fails on Linux 32-bit

At the moment we don't ship prebuilts for 32-bit Linux. Hence you'll need some additional toolling to build from source:

  • python (v2.7 recommended, v3.x.x is not supported for building Hydrogen)
  • make
  • A proper C/C++ compiler toolchain, like GCC

Use your distribution's package manager to install.

If your default python is 3.x, you need to run instead PYTHON=python2.7 apm install hydrogen or change the default version for apm with apm config set python $(which python2.7) beforehand. You can still use 3.x versions of Python in Hydrogen, but it will only build with 2.x due to a longstanding issue with gyp.

No kernel for grammar XXX found

Hydrogen requires a Kernel to run code. Checkout for instructions on how to install the most popular kernels.

Atom won't pick up kernels inside a virtualenv unless Atom is launched as atom . within the virtualenv. The alternative is to create a kernel specifically for a virtualenv.

No kernel for grammar Python found error on Mac OS

First off, make sure that you run

python3 -m pip install ipykernel
python3 -m ipykernel install --user


jupyter --paths

shows IPython kernels you want to use.

Even after the above steps have been done successfully, if Hydrogen still keeps complaining the "No kernel for grammar Python found" error on Mac OS, this workaround may help you solve it.

Hydrogen doesn't show my results.

Again, there are a number of possible causes and solutions:

  • If the result bubble only shows check marks (see issues #61, #68, #73, #88):

    • solved by upgrading the jupyter version (see this comment );
  • If Hydrogen doesn't output any results for Atom version < 1.13 (see issue #326), check that you haven't disabled Use Shadow DOM under Settings > Editor. This option should be enabled.

  • If the spinner in the result bubble never stops (see issue #53): This is issue hasn't been seen recently. Please, post in issue #53 the details of your installation.

    Hydrogen stopped working after updating Atom

    Whenever your Atom is upgraded, the Hydrogen package needs to be rebuilt. Atom should prompt you to rebuild Hydrogen after upgrading. In case it doesn't, you can manually rebuild Hydrogen from the Panel that opens when executing Incompatible Packages: View via the command palette.

    You can also access this Panel by clicking on the tiny red bug icon at the bottom right of Atom.

    fullscreen-tiny-bug tiny-bug

    In case the Atom GUI Rebuild Packages button doesn't work, you can try running apm rebuild hydrogen (to rebuild) or apm install hydrogen (to reinstall) in the package directory then restarting Atom to resolve.

Setting environment variables on Windows

Hydrogen fails to import modules:

If hydrogen works for standard libraries but you encounter ModuleNotFoundError: No module named 'your_package' for custom installed packages, check that the path of the kernel you are using is the one specified in the windows PATH. Especially when using virtual environments like virtualenv and anaconda ensure that the corresponding python executables are set in the windows path.

To add the path, enter where python in the windows command line and chose the apporiate entry. Then, add it manually to the windows PATH, similarly as detailed below for the standard python path.

Hydrogen does not recognize python:

On Windows if Python is not added to your environment variables, Hydrogen won't be able to locate your Python installations (No kernel specs found).

Kernel specs not found

To solve this problem you need to add Python to your systems environment variables. This can be done in 2 ways:

  • During Python installation
  • Manually adding in the Environment variables

During Python installation:

While installing Python check Add Python to environment variables. It will do the rest of work for you!

Python setup Wizard

If you already have Python installed then you may not need to uninstall it just follow the steps:

  • Go to the Uninstall or Change a Program Menu
  • Select your Python version
  • Click on the Uninstall/Change button
  • Select Modify from the appeared menu
  • Click on Next
  • Check mark Add python to environment variables
  • And finish the installation process

Adding python to system environment variables

Manually adding Python to Environment variables:

You can also add Python to the environment variables manually

  • In Control Panel search for environment variables
  • Click on Edit system environment variables
  • Click on Environment variables
  • From the System variables tab select Path and click on Edit
  • Click on New and add C:\Program Files\Python36\Scripts\
  • Click on New again and add C:\Program Files\Python36\
  • Click on OK to finish, now your problem is fixed!

Adding environment Variables manually

You should see something like this,


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