From e788820923143975ecb6c346287860f1bd37bbc6 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 30 Jan 2024 15:27:24 +0000 Subject: [PATCH 1/8] List contents --- .github/workflows/omv-ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index b805894..65b57ff 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -45,6 +45,7 @@ jobs: omv install NEURON cd NEURON/test nrnivmodl ../channels + ls -alt - name: Run OMV tests on engine ${{ matrix.engine }} run: | From 633e355462856b55ed5e26e064a4871fa7d69ca9 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 30 Jan 2024 15:34:10 +0000 Subject: [PATCH 2/8] Test on more iterations --- .github/workflows/omv-ci.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 65b57ff..472452d 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -14,13 +14,14 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ 3.8, 3.9 ] + python-version: [ 3.8, 3.9, "3.10" ] engine: - jNeuroML_validate # - "NEURON:7.8.2" # slightly different spike times... - "NEURON:8.0.0" - "NEURON:8.0.2" - "NEURON:8.1" + - "NEURON:8.2.0" - jNeuroML - jNeuroML_NEURON - jNeuroML_NetPyNE From ffbaf03e285993996dd805a66f15dc11f6d64412 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 30 Jan 2024 15:50:34 +0000 Subject: [PATCH 3/8] Update gha action versions --- .github/workflows/non-omv-ci.yml | 4 ++-- .github/workflows/omv-ci.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/non-omv-ci.yml b/.github/workflows/non-omv-ci.yml index 29de27f..a0ebb79 100644 --- a/.github/workflows/non-omv-ci.yml +++ b/.github/workflows/non-omv-ci.yml @@ -17,10 +17,10 @@ jobs: python-version: [ 3.7, 3.9 ] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 472452d..238fb6b 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -27,10 +27,10 @@ jobs: - jNeuroML_NetPyNE steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} From 1de6a51c89231fb1570b98c591b0d8f454a48ab0 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 30 Jan 2024 16:04:30 +0000 Subject: [PATCH 4/8] Regenerated --- .gitignore | 2 ++ NeuroML2/CellBuilder.py | 4 ++- NeuroML2/LEMS_pyr_single_comp.xml | 43 +++++++++++++++---------------- 3 files changed, 26 insertions(+), 23 deletions(-) diff --git a/.gitignore b/.gitignore index cbfc544..d0bbab6 100644 --- a/.gitignore +++ b/.gitignore @@ -21,3 +21,5 @@ x86_64 NET_*.net.nml *.channel.nml arm64 +/NeuroML2/.ipynb_checkpoints +/NeuroML2/__pycache__ diff --git a/NeuroML2/CellBuilder.py b/NeuroML2/CellBuilder.py index 5054e7c..bfa73b1 100644 --- a/NeuroML2/CellBuilder.py +++ b/NeuroML2/CellBuilder.py @@ -11,7 +11,9 @@ from typing import List from neuroml import (Cell, Morphology, MembraneProperties, IntracellularProperties, BiophysicalProperties, Segment, SegmentGroup, Point3DWithDiam, SegmentParent, Member, InitMembPotential, Resistivity, SpecificCapacitance, NeuroMLDocument, IncludeType, ChannelDensity) # type: ignore # noqa -from pyneuroml.pynml import print_function # type: ignore + +def print_function(string): + print('CellBuilder: %s'%string) neuro_lex_ids = { diff --git a/NeuroML2/LEMS_pyr_single_comp.xml b/NeuroML2/LEMS_pyr_single_comp.xml index 2a6f761..1366b16 100644 --- a/NeuroML2/LEMS_pyr_single_comp.xml +++ b/NeuroML2/LEMS_pyr_single_comp.xml @@ -1,11 +1,11 @@ - + - + @@ -13,7 +13,7 @@ - + @@ -22,41 +22,40 @@ - + - - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + From fd0ea5d113bc7e4efd529a15acc62e79791dafc2 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 6 Feb 2024 17:16:21 +0000 Subject: [PATCH 5/8] Update omv-ci.yml --- .github/workflows/omv-ci.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 238fb6b..b5d3436 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -47,6 +47,10 @@ jobs: cd NEURON/test nrnivmodl ../channels ls -alt + + - name: Pip version info + run: | + pip list - name: Run OMV tests on engine ${{ matrix.engine }} run: | From ac33d09f08e9dc22391a147fefa9e47530ab7b69 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 6 Feb 2024 18:16:49 +0000 Subject: [PATCH 6/8] Update omv-ci.yml --- .github/workflows/omv-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index b5d3436..d6e4ea4 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -43,7 +43,7 @@ jobs: - name: Compile some mod files if: ${{ contains( matrix.engine, 'NEURON' ) }} run: | - omv install NEURON + omv install ${{ matrix.engine }} cd NEURON/test nrnivmodl ../channels ls -alt From 7885b1d7912ab05a0b1128238c063e8b5d83293c Mon Sep 17 00:00:00 2001 From: pgleeson Date: Fri, 31 May 2024 11:46:15 +0100 Subject: [PATCH 7/8] Test more versions --- .github/workflows/non-omv-ci.yml | 6 ++++-- .github/workflows/omv-ci.yml | 7 ++++--- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/.github/workflows/non-omv-ci.yml b/.github/workflows/non-omv-ci.yml index a0ebb79..07b7250 100644 --- a/.github/workflows/non-omv-ci.yml +++ b/.github/workflows/non-omv-ci.yml @@ -10,11 +10,13 @@ on: jobs: build: - runs-on: ubuntu-latest + name: Build for Python ${{ matrix.python-version }} on ${{ matrix.runs-on }} + runs-on: ${{ matrix.runs-on }} strategy: fail-fast: false matrix: - python-version: [ 3.7, 3.9 ] + python-version: [ "3.9", "3.10" ] + runs-on: [ubuntu-latest, macos-latest] steps: - uses: actions/checkout@v4 diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index d6e4ea4..02de1dc 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -9,12 +9,13 @@ on: jobs: build: - - runs-on: ubuntu-latest + + runs-on: ${{ matrix.runs-on }} strategy: fail-fast: false matrix: - python-version: [ 3.8, 3.9, "3.10" ] + python-version: [ 3.9, "3.10" ] + runs-on: [ubuntu-latest, macos-latest] engine: - jNeuroML_validate # - "NEURON:7.8.2" # slightly different spike times... From 17df3e63cdab0d27c13026cc52fdebac2225e3a0 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Fri, 31 May 2024 11:51:42 +0100 Subject: [PATCH 8/8] Fix macos for hdf5 --- .github/workflows/non-omv-ci.yml | 5 +++++ .github/workflows/omv-ci.yml | 7 ++++++- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/.github/workflows/non-omv-ci.yml b/.github/workflows/non-omv-ci.yml index 07b7250..6791429 100644 --- a/.github/workflows/non-omv-ci.yml +++ b/.github/workflows/non-omv-ci.yml @@ -26,6 +26,11 @@ jobs: with: python-version: ${{ matrix.python-version }} + - name: Install HDF5 for pytables on macos-latest + if: ${{ matrix.runs-on == 'macos-latest' }} + run: | + brew install hdf5 + - name: Run scripts run: | pip install pyneuroml diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml index 02de1dc..5670c4e 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -15,7 +15,6 @@ jobs: fail-fast: false matrix: python-version: [ 3.9, "3.10" ] - runs-on: [ubuntu-latest, macos-latest] engine: - jNeuroML_validate # - "NEURON:7.8.2" # slightly different spike times... @@ -26,6 +25,7 @@ jobs: - jNeuroML - jNeuroML_NEURON - jNeuroML_NetPyNE + runs-on: [ubuntu-latest, macos-latest] steps: - uses: actions/checkout@v4 @@ -35,6 +35,11 @@ jobs: with: python-version: ${{ matrix.python-version }} + - name: Install HDF5 for pytables on macos-latest + if: ${{ matrix.runs-on == 'macos-latest' }} + run: | + brew install hdf5 + - name: Install OMV run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation