Scheduled CI builds for NEURON

This repository hosts scheduled GitHub Actions workflows that verify that the main NEURON repository can be built and run on a variety of common Linux distributions and macOS versions. The default branch of NEURON (and neuron-nightly wheel) is tested every night, and the latest tagged release (and corresponding neuron wheel) is tested once a week. At present Ubuntu 20.04, Ubuntu 22.04, Fedora 37, Fedora 38, CentOS7, CentOS Stream 8, CentOS Stream 9, Debian Bullseye (11), Debian Bookworm (12), macOS 11 and macOS 12 are tested.

The tested distributions are generally configured with the explicit name/version of the second-newest version of the distribution at the time, while a generic "latest" tag is used for the latest version (where available).

There is currently an exception for the CentOS family, where three versions are retained because the third-newest, CentOS7, is still in use on the BlueBrain5 system.

This means that when a new version of a distribution is released, we automatically start testing it. When this happens, the old second-newest version generally becomes the third-newest version, and must be manually updated via pull request. This is often an opportunity to drop some version-specific scripts. The fedora:latest build is particulally useful, as Fedora has a relatively fast release cadence and often includes cutting-edge compilers and library versions; this means we can often spot issues via this build before they trickle down to other CI configurations and users in the community.

The configuration of these builds serves as an up-to-date reference of how to build NEURON on each platform.

System package installation

The system packages needed on each platform are listed in the pair of scripts:

scripts/install_{flavour}_{container}.sh [this file may be missing if no container-specific setup is needed]
scripts/install_{flavour}.sh

Taking CentOS7 (a RedHat based distribution) as an example, the scripts install_redhat_centos:7.sh and install_redhat.sh install the required system packages that are not already included in the centos:7 image on Docker Hub.

Some of the content of these scripts is specific to the GitHub Actions environment in which they are regularly tested; this is commented in the following way:

# ---
# --- Begin GitHub-Actions-specific code ---
# ---
some_command_to_make_github_actions_work
# ---
# --- End GitHub-Actions-specific code ---
# ---

and need not be copied when these scripts are used as references for local installations.

Runtime environment

In a similar way, modifications to the runtime environment are listed in the scripts:

scripts/environment_{flavour}_{container}.sh [this may be missing]
scripts/environment_{flavour}.sh             [this may be missing]
scripts/environment.sh

In a local installation, you might prefer to place these commands in a ~/.bashrc or ~/.zshrc file.

When using RedHat-derived Linux distributions, such as Fedora and CentOS, some dependencies may be made available using Software Collections. These are enabled using the scl enable collection_name command, which launches a subshell and cannot trivially be included in the environmentXXX.sh scripts above. For interactive use, one can simply run

scl enable collection_name bash

to get a shell with the given collection enabled.

When running in GitHub Actions, the scl enable ... command is injected in the runUnprivileged.sh wrapper, based on SOFTWARE_COLLECTIONS_* environment modules set in the top-level YAML configuration. This is, for example, used to install a modern compiler toolchain on CentOS7.

Extra dependencies and NEURON installation

The installation of extra packages (via pip) and the installation of NEURON itself is steered by the buildNeuron.sh script. This closely mirrors the instructions in the main NEURON repository.

Azure wheels testing - Manual workflow

Given an Azure build (PR, master, ...), it is possible to test those specific wheels on the different platforms covered by this CI. The azure build publishes an artifact called drop, which contains all wheels built by the pipeline.

Here are the steps to follow:

• Retrieve the Azure drop url

  • From the azure build page, click on published:

    

  • then from the artifact page retrieve the drop download url:

    

• Launch the CI manually

  1. click on Actions tab
  2. click on Scheduled NEURON CI tab under Workflows
  3. click on Run workflow
  4. input Azure drop (artifacts) url and click Run workflow (leave NEURON branch to test) blank.

  

Testing a NEURON feature branch

By default the GitHub Actions workflow in this repository runs every night, and on modifications made to the nrn-build-ci repository itself. You can also use the same workflow to manually trigger testing a feature branch of NEURON, for example if you have a NEURON pull request that is fixing an issue identified by one of the scheduled builds in this repository. In that case, follow the instructions just above to launch a manual job, but instead of filling the Azure drop (artifacts) url, leave that blank and put the name of your NEURON feature branch in NEURON branch to test.