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. At present Ubuntu 18.04, Ubuntu 20.04, Fedora 32, Fedora 33, CentOS7, CentOS8, Debian Buster (10) and macOS 10.15 are tested.

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.