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

Debian 8 and Ubuntu 16.04 LTS

Unfortunately, the versions of IPython provided in Debian's and Ubuntu's repositories are rather old and Hydrogen is unable to detect the kernel specs installed in your machine. To workaround this issue, Hydrogen provides the setting KernelSpec, where the user can declare the kernel specs manually. Find the KernelSpec setting in the Atom GUI by going to the Settings pane, click Packages, search for Hydrogen, and click the Hydrogen Settings button.

Below is an example KernelSpec for IPython 2 and 3:

  "kernelspecs": {
    "python2": {
      "spec": {
        "display_name": "Python 2",
        "language": "python",
        "argv": ["python2.7", "-m", "ipykernel", "-f", "{connection_file}"],
        "env": {}
    "python3": {
      "spec": {
        "display_name": "Python 3",
        "language": "python",
        "argv": ["python3.4", "-m", "ipykernel", "-f", "{connection_file}"],
        "env": {}

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 language X found, but I have a kernel for that language.

Currently, a recent version of Jupyter is required for Hydrogen to detect the available kernels automatically. Users can set kernels manually using the Hydrogen settings. See this section in the README for more details.

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.

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.

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