From 7ac61f3b78ea0acb15574b6f961c9c439566992c Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 13 Aug 2024 14:26:35 +0100 Subject: [PATCH 1/5] Ignoring full download cell files --- .gitignore | 85 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 85 insertions(+) diff --git a/.gitignore b/.gitignore index 18aeafd..fd64537 100644 --- a/.gitignore +++ b/.gitignore @@ -486,3 +486,88 @@ arm64 /CellTypesDatabase/models/NeuroML2/489932597.net.nml /CellTypesDatabase/models/NeuroML2/491517388.net.nml /CellTypesDatabase/models/NeuroML2/496930338.net.nml + +CellTypesDatabase/models/476630516/ +CellTypesDatabase/models/476637723/ +CellTypesDatabase/models/476637747/ +CellTypesDatabase/models/476637796/ +CellTypesDatabase/models/476679102/ +CellTypesDatabase/models/477313251/ +CellTypesDatabase/models/477510918/ +CellTypesDatabase/models/477510985/ +CellTypesDatabase/models/477838913/ +CellTypesDatabase/models/477839613/ +CellTypesDatabase/models/477876559/ +CellTypesDatabase/models/477878284/ +CellTypesDatabase/models/477878554/ +CellTypesDatabase/models/477880244/ +CellTypesDatabase/models/478045081/ +CellTypesDatabase/models/478045202/ +CellTypesDatabase/models/478045226/ +CellTypesDatabase/models/478047588/ +CellTypesDatabase/models/478047618/ +CellTypesDatabase/models/478048947/ +CellTypesDatabase/models/478513407/ +CellTypesDatabase/models/478513415/ +CellTypesDatabase/models/478513437/ +CellTypesDatabase/models/478513441/ +CellTypesDatabase/models/478809612/ +CellTypesDatabase/models/478809991/ +CellTypesDatabase/models/479234441/ +CellTypesDatabase/models/479427443/ +CellTypesDatabase/models/479694359/ +CellTypesDatabase/models/479694384/ +CellTypesDatabase/models/479694856/ +CellTypesDatabase/models/479695152/ +CellTypesDatabase/models/480056382/ +CellTypesDatabase/models/480361288/ +CellTypesDatabase/models/480613522/ +CellTypesDatabase/models/480624051/ +CellTypesDatabase/models/480624126/ +CellTypesDatabase/models/480624251/ +CellTypesDatabase/models/480624414/ +CellTypesDatabase/models/480630211/ +CellTypesDatabase/models/480630395/ +CellTypesDatabase/models/480630857/ +CellTypesDatabase/models/480631048/ +CellTypesDatabase/models/480631187/ +CellTypesDatabase/models/480631286/ +CellTypesDatabase/models/480632564/ +CellTypesDatabase/models/480633479/ +CellTypesDatabase/models/482524837/ +CellTypesDatabase/models/482529696/ +CellTypesDatabase/models/482583564/ +CellTypesDatabase/models/482934212/ +CellTypesDatabase/models/483066358/ +CellTypesDatabase/models/483106906/ +CellTypesDatabase/models/483109057/ +CellTypesDatabase/models/483156585/ +CellTypesDatabase/models/484620556/ +CellTypesDatabase/models/484628276/ +CellTypesDatabase/models/485476031/ +CellTypesDatabase/models/485510712/ +CellTypesDatabase/models/485513184/ +CellTypesDatabase/models/485513255/ +CellTypesDatabase/models/485591776/ +CellTypesDatabase/models/485602029/ +CellTypesDatabase/models/485720616/ +CellTypesDatabase/models/485904766/ +CellTypesDatabase/models/485909125/ +CellTypesDatabase/models/485909152/ +CellTypesDatabase/models/486052435/ +CellTypesDatabase/models/486144663/ +CellTypesDatabase/models/486508647/ +CellTypesDatabase/models/486508758/ +CellTypesDatabase/models/486556597/ +CellTypesDatabase/models/486556714/ +CellTypesDatabase/models/486558444/ +CellTypesDatabase/models/486909496/ +CellTypesDatabase/models/488462783/ +CellTypesDatabase/models/488462965/ +CellTypesDatabase/models/488759006/ +CellTypesDatabase/models/488763268/ +CellTypesDatabase/models/489931686/ +CellTypesDatabase/models/489932183/ +CellTypesDatabase/models/489932435/ +CellTypesDatabase/models/489932597/ +CellTypesDatabase/models/491517388/ \ No newline at end of file From c9b69e1491dde1a0dcc31fae3cd991acc39ae6df Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 12 Nov 2025 18:35:34 +0000 Subject: [PATCH 2/5] Update Python version matrix in CI workflow --- .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 1cf0eb5..b3b7879 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ 3.8, 3.9 ] + python-version: [ 3.9, 3.12 ] engine: ["NEURON:8.1", "PyNEURON:8.1", "jNeuroML", "jNeuroML_NEURON", "jNeuroML_NetPyNE", "jNeuroML_validate"] From d0607dfd81a12f20b734b7678c86b731512b8d40 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 14 Nov 2025 16:52:58 +0000 Subject: [PATCH 3/5] Upgrade setuptools for compatibility with Neuron --- .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 b3b7879..3b82fe8 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -29,6 +29,7 @@ jobs: run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation pip install scipy sympy matplotlib cython pandas tables + pip install setuptools --upgrade # needed for Neuron on py 3.12 - name: Download selected NEURON models if: ${{ contains( matrix.engine, 'NEURON' ) }} From a42cc27aa1c57bcf9299596199757cea0bd58a33 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 14 Nov 2025 17:20:45 +0000 Subject: [PATCH 4/5] Change Python version from 3.12 to 3.11 Updated Python version in CI workflow to 3.11. --- .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 3b82fe8..765be5c 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ 3.9, 3.12 ] + python-version: [ 3.9, 3.11 ] # allensdk doesn't work with py 3.12... engine: ["NEURON:8.1", "PyNEURON:8.1", "jNeuroML", "jNeuroML_NEURON", "jNeuroML_NetPyNE", "jNeuroML_validate"] From 3046628ee1217ebda75a8edd4984064e9895ddd9 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 25 Nov 2025 17:32:02 +0000 Subject: [PATCH 5/5] Also test latest Neuron versions --- .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 765be5c..c525175 100644 --- a/.github/workflows/omv-ci.yml +++ b/.github/workflows/omv-ci.yml @@ -14,7 +14,7 @@ jobs: fail-fast: false matrix: python-version: [ 3.9, 3.11 ] # allensdk doesn't work with py 3.12... - engine: ["NEURON:8.1", "PyNEURON:8.1", "jNeuroML", "jNeuroML_NEURON", "jNeuroML_NetPyNE", "jNeuroML_validate"] + engine: ["NEURON", "PyNEURON", "NEURON:8.1", "PyNEURON:8.1", "jNeuroML", "jNeuroML_NEURON", "jNeuroML_NetPyNE", "jNeuroML_validate"] steps: