From 1d0eaf633dcee8727c95735cb38982cc2fd2c1ce Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 10:35:14 +0100 Subject: [PATCH 1/5] Add test* to test branches --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f36109b..0c96292 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -2,9 +2,9 @@ name: Continuous builds on: push: - branches: [ master, development, experimental, modelspec ] + branches: [ master, development, experimental, modelspec, test* ] pull_request: - branches: [ master, development, experimental, modelspec ] + branches: [ master, development, experimental, modelspec, test* ] jobs: build: From e5fe0a695278944b617b13aba86ca1a5f5e03f27 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 10:35:21 +0100 Subject: [PATCH 2/5] Add dependabot --- .github/dependabot.yml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..28cb43e --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,14 @@ +# Source - https://stackoverflow.com/a/78380165 +# Posted by Stefan, modified by community. See post 'Timeline' for change history +# Retrieved 2026-04-14, License - CC BY-SA 4.0 + +# Set update schedule for GitHub Actions + +version: 2 +updates: + + - package-ecosystem: "github-actions" + directory: "/" + schedule: + # Check for updates to GitHub Actions every week + interval: "weekly" From 8ef0d50d02c7e89def0cd99a3396ad9243a2a48f Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 10:35:54 +0100 Subject: [PATCH 3/5] Update GHA versions --- .github/workflows/ci.yml | 4 ++-- .github/workflows/python-publish.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0c96292..2fc4251 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,9 +19,9 @@ jobs: HDF5_DISABLE_VERSION_CHECK: 1 steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml index 85cc411..912b67a 100644 --- a/.github/workflows/python-publish.yml +++ b/.github/workflows/python-publish.yml @@ -18,9 +18,9 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v7 - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v7 with: python-version: '3.x' - name: Install dependencies From f41a54211bcf4b9345fab7ed737b882bf954582e Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 11:12:44 +0100 Subject: [PATCH 4/5] Latest ci.yml --- .github/workflows/ci.yml | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2fc4251..2695aef 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10", "3.11"] + python-version: ["3.10", "3.11", "3.12", "3.13"] env: JNML_HOME: "/home/runner/work/NeuroMLlite/NeuroMLlite/jNeuroML" HDF5_DISABLE_VERSION_CHECK: 1 @@ -29,14 +29,12 @@ jobs: run: | python -m pip install --upgrade pip pip install flake8 + pip install setuptools==80 # needed for eden on Python 3.12... - name: Install NeuroMLlite and extra requirements run: | pip install . - pip install -r requirements-extra.txt - - #pip install 'numpy<=1.23.0' # temp fix, see https://github.com/OpenSourceBrain/osb-model-validation/issues/91 - + pip install .[dev] - name: Lint with flake8 run: | @@ -57,8 +55,7 @@ jobs: git clone https://github.com/NeuroML/pyNeuroML.git cd pyNeuroML git checkout $pynml_branch - pip install pandas==1.3.5 - pip install NEURON==8.2.2 # Specify version of neuron - 8.2.1 fails + pip install "NEURON>=8.2.2,<9.0.0" # Specify version of neuron - 8.2.1 fails #pip install -r requirements-dev.txt pip install . cd - @@ -93,7 +90,7 @@ jobs: - name: Install some simulators for testing run: | - #pip install cython + pip install "cython<3.1.0" # for nest... omv install NEURON pip install NetPyNE # strange issues on py3.7 with omv install... omv install PyNN @@ -108,6 +105,7 @@ jobs: #export HDF5_DISABLE_VERSION_CHECK=1 if [[ ${{ matrix.python-version }} != 2.7 ]]; then omv install PyNEST; fi #pip install h5py + omv list -V # list installed engines - name: Run pytest From 79bca3676eedda49fc3fc79ab64965f5bdb5c5b1 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 31 Jul 2026 11:40:52 +0100 Subject: [PATCH 5/5] Master not working with py3.13 yet --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2695aef..d572e4b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.10", "3.11", "3.12", "3.13"] + python-version: ["3.10", "3.11", "3.12"] env: JNML_HOME: "/home/runner/work/NeuroMLlite/NeuroMLlite/jNeuroML" HDF5_DISABLE_VERSION_CHECK: 1