Various CI fixes (#62)

* Use the requirement files for installation of python packages * Use ci_requirements.txt only if it exists * Install also the required python packages for NMODL * Use MacOS 13 instead of 11 * Make sure that setuptools are installed for Python12 support * Recursively initialize submodules to include mod2c in macos-13 * Run CI on PRs on non-Mondays * Test latest release only on pushes to main and any PR * Add workaround for Brew packages --------- Co-authored-by: Goran Jelic-Cizmek <[email protected]>
neuronsimulator · Mar 19, 2024 · 96b8c0b · 96b8c0b
1 parent b346dd9
commit 96b8c0b
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diff --git a/.github/workflows/build-neuron.yml b/.github/workflows/build-neuron.yml
@@ -2,6 +2,9 @@ name: Scheduled NEURON CI
 
 on:
   push:
+    branches:
+      - main
+  pull_request:
   schedule:
     # Run at 2am every day
     - cron:  '0 2 * * *'
@@ -44,9 +47,10 @@ jobs:
         then
           # If we're not told to test a specific branch, test the default branch with neuron-nightly wheels
           values="{\"branch_or_tag\": \"\", \"default_wheel\": \"neuron-nightly\"}"
-          if [[ $(date +%u) == 1 ]]
+          if [[ $(date +%u) == 1 ]] || [[ ${{ github.event_name }} == 'pull_request' ]] || [[ ${{ github.event_name }} == 'push' ]]
           then
             # If it's a Monday, test the latest release (and latest released wheels) in addition
+            # Also test it on any PR, and any push to a PR
             tag_name="${{steps.get_latest_release.outputs.tag_name}}"
             values="${values}, {\"branch_or_tag\": \"${tag_name}\", \"default_wheel\": \"neuron==${tag_name}\"}"
           fi
@@ -74,10 +78,10 @@ jobs:
     strategy:
       matrix:
         os:
+        # GitHub Actions MacOS 13 runner
+        - { vm: macos-13, flavour: macOS }
         # GitHub Actions MacOS 12 runner
         - { vm: macos-12, flavour: macOS }
-        # GitHub Actions MacOS 11 runner
-        - { vm: macos-11, flavour: macOS }
         # CentOS7 Docker image
         - { vm: ubuntu-latest, container: "centos:7", flavour: redhat }
         # CentOS Stream 8 Docker image
@@ -136,7 +140,7 @@ jobs:
           if [ -n "${branch_or_tag}" ]; then BRANCH_OPT="--branch=${branch_or_tag}"; fi
           git clone --depth=1 --single-branch ${BRANCH_OPT} ${{github.server_url}}/${{github.repository_owner}}/nrn
           # Init submodules for testing purposes
-          cd nrn && git submodule update --init
+          cd nrn && git submodule update --init --recursive
 
       # When we run in Ubuntu/Fedora/Debian containers from Docker Hub then we
       # are root. This is different from when we use the GitHub Actions images

diff --git a/scripts/buildNeuron.sh b/scripts/buildNeuron.sh
@@ -25,8 +25,17 @@ export PYTHON=$(command -v python)
 export PYTHONPATH=$(${PYTHON} -c 'import site; print(":".join(site.getsitepackages()))')
 
 # Install extra dependencies for NEURON into the virtual environment.
-pip install --upgrade bokeh "cython<3" ipython matplotlib mpi4py numpy pytest \
-  pytest-cov scikit-build sympy
+pip install --upgrade -r nrn_requirements.txt
+if [[ -f ci_requirements.txt ]]; then
+  pip install --upgrade -r ci_requirements.txt
+else
+  pip install --upgrade plotly "ipywidgets>=7.0.0"
+fi
+if [[ -f external/nmodl/requirements.txt ]]; then
+  pip install --upgrade -r external/nmodl/requirements.txt
+fi
+# Needed for installation of older NEURON versions with Python 12
+pip install --upgrade setuptools
 
 # Set default compilers, but don't override preset values
 export CC=${CC:-gcc}

diff --git a/scripts/install_macOS.sh b/scripts/install_macOS.sh
@@ -1,3 +1,6 @@
+set -eux
+export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1
+export HOMEBREW_NO_INSTALL_UPGRADE=1
 brew install bison boost coreutils flex mpich ninja xz wget
 brew unlink mpich
 brew install openmpi