From 6ddb20d1f47318d1628e50beff7e60d1342bcc84 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 24 Jun 2026 03:23:36 +0000 Subject: [PATCH 01/12] Bump actions/checkout from 6 to 7 Bumps [actions/checkout](https://github.com/actions/checkout) from 6 to 7. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v6...v7) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/ci.yml | 8 ++++---- .github/workflows/ci_test_all.yml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2346bd28..73c095d0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,7 +16,7 @@ jobs: name: Format runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - uses: actions/setup-python@v6 with: python-version: '3.10' @@ -38,7 +38,7 @@ jobs: test-suite: tensorflow steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Setup Python uses: actions/setup-python@v6 @@ -86,7 +86,7 @@ jobs: needs: tests runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - uses: actions/setup-python@v6 with: python-version: '3.11' @@ -107,7 +107,7 @@ jobs: name: Distribution build runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - name: Build sdist & wheel run: pipx run --spec build pyproject-build - uses: actions/upload-artifact@v7 diff --git a/.github/workflows/ci_test_all.yml b/.github/workflows/ci_test_all.yml index 2a877f21..0c13ee29 100644 --- a/.github/workflows/ci_test_all.yml +++ b/.github/workflows/ci_test_all.yml @@ -18,7 +18,7 @@ jobs: runs-on: [ubuntu-latest] steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - uses: actions/setup-python@v6 with: From 42798512f7e08a36020636b47ed03da93f093ba3 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 24 Jun 2026 14:49:15 +0100 Subject: [PATCH 02/12] Update checkout action version in CI workflow --- .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 2346bd28..5fdc3b83 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,7 +16,7 @@ jobs: name: Format runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@v7 - uses: actions/setup-python@v6 with: python-version: '3.10' From e50eda08d2fc89541507ca1420f8954c4f5b6928 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 24 Jun 2026 15:15:33 +0100 Subject: [PATCH 03/12] To v0.4.15; run big test_all on 3.12 for now... --- .github/workflows/ci_test_all.yml | 2 +- .../api/export_format/ACT-R/addition.json | 2 +- .../api/export_format/ACT-R/addition.yaml | 2 +- .../source/api/export_format/ACT-R/count.json | 2 +- .../source/api/export_format/ACT-R/count.yaml | 2 +- .../source/api/export_format/ONNX/ab.json | 2 +- .../source/api/export_format/ONNX/ab.yaml | 2 +- .../source/api/export_format/ONNX/abc.json | 2 +- .../source/api/export_format/ONNX/abc.yaml | 2 +- .../api/export_format/ONNX/abc_basic-mdf.json | 2 +- .../api/export_format/ONNX/abc_basic-mdf.yaml | 2 +- .../source/api/export_format/ONNX/abcd.json | 2 +- .../source/api/export_format/ONNX/abcd.yaml | 2 +- .../api/export_format/PyTorch/inception.json | 2 +- .../export_format/PyTorch/mlp_pure_mdf.json | 2 +- .../export_format/PyTorch/mlp_pure_mdf.yaml | 2 +- .../PyTorch/simple_pytorch_to_mdf.json | 2 +- examples/ACT-R/addition.json | 2 +- examples/ACT-R/addition.yaml | 2 +- examples/ACT-R/count.json | 2 +- examples/ACT-R/count.yaml | 2 +- examples/MDF/ABCD.json | 2 +- examples/MDF/ABCD.yaml | 2 +- examples/MDF/Arrays.json | 2 +- examples/MDF/Arrays.yaml | 2 +- examples/MDF/NewtonCoolingModel.json | 2 +- examples/MDF/NewtonCoolingModel.yaml | 2 +- examples/MDF/ParametersFunctions.json | 2 +- examples/MDF/ParametersFunctions.yaml | 2 +- examples/MDF/RNN/IAF_net.json | 2 +- examples/MDF/RNN/IAF_net.yaml | 2 +- examples/MDF/RNN/IAF_net2.json | 2 +- examples/MDF/RNN/IAF_net2.yaml | 2 +- examples/MDF/RNN/IAF_net3.json | 2 +- examples/MDF/RNN/IAF_net3.yaml | 2 +- examples/MDF/RNN/IAFs.json | 2 +- examples/MDF/RNN/IAFs.yaml | 2 +- examples/MDF/RNN/RNNs.json | 2 +- examples/MDF/RNN/RNNs.yaml | 2 +- examples/MDF/Simple.bson | Bin 901 -> 901 bytes examples/MDF/Simple.json | 2 +- examples/MDF/Simple.yaml | 2 +- examples/MDF/States.json | 2 +- examples/MDF/States.yaml | 2 +- examples/MDF/SwitchedRLC_Circuit.json | 2 +- examples/MDF/SwitchedRLC_Circuit.yaml | 2 +- examples/MDF/abc_conditions.json | 2 +- examples/MDF/abc_conditions.yaml | 2 +- .../conditions/Composite_mdf_condition.json | 2 +- .../conditions/Composite_mdf_condition.yaml | 2 +- .../MDF/conditions/everyncalls_condition.json | 2 +- .../MDF/conditions/everyncalls_condition.yaml | 2 +- .../MDF/conditions/threshold_condition.json | 2 +- .../MDF/conditions/threshold_condition.yaml | 2 +- .../conditions/timeinterval_condition.json | 2 +- .../conditions/timeinterval_condition.yaml | 2 +- examples/MDF/networks/Net_acyclical.json | 2 +- examples/MDF/networks/Net_acyclical.yaml | 2 +- examples/ONNX/ab.json | 2 +- examples/ONNX/ab.yaml | 2 +- examples/ONNX/abc.json | 2 +- examples/ONNX/abc.yaml | 2 +- examples/ONNX/abc_basic-mdf.json | 2 +- examples/ONNX/abc_basic-mdf.yaml | 2 +- examples/ONNX/abcd.json | 2 +- examples/ONNX/abcd.yaml | 2 +- examples/PyTorch/MDF_PyTorch/ABCD.onnx | Bin 13274 -> 13274 bytes examples/PyTorch/MDF_PyTorch/ABCD_pytorch.py | 2 +- examples/PyTorch/MDF_PyTorch/Arrays.onnx | Bin 950 -> 950 bytes .../PyTorch/MDF_PyTorch/Arrays_pytorch.py | 2 +- examples/PyTorch/MDF_PyTorch/Simple.onnx | Bin 6277 -> 6277 bytes .../PyTorch/MDF_PyTorch/Simple_pytorch.py | 2 +- examples/PyTorch/inception.json | 2 +- examples/PyTorch/mlp_pure_mdf.json | 2 +- examples/PyTorch/mlp_pure_mdf.yaml | 2 +- examples/PyTorch/simple_pytorch_to_mdf.json | 2 +- src/modeci_mdf/__init__.py | 2 +- 77 files changed, 73 insertions(+), 73 deletions(-) diff --git a/.github/workflows/ci_test_all.yml b/.github/workflows/ci_test_all.yml index 2a877f21..113dbf0a 100644 --- a/.github/workflows/ci_test_all.yml +++ b/.github/workflows/ci_test_all.yml @@ -14,7 +14,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [ "3.13"] + python-version: [ "3.12"] runs-on: [ubuntu-latest] steps: diff --git a/docs/sphinx/source/api/export_format/ACT-R/addition.json b/docs/sphinx/source/api/export_format/ACT-R/addition.json index a288ed43..1572a4ce 100644 --- a/docs/sphinx/source/api/export_format/ACT-R/addition.json +++ b/docs/sphinx/source/api/export_format/ACT-R/addition.json @@ -1,7 +1,7 @@ { "addition": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "addition_graph": { "nodes": { diff --git a/docs/sphinx/source/api/export_format/ACT-R/addition.yaml b/docs/sphinx/source/api/export_format/ACT-R/addition.yaml index 7e6df724..65bd1ed4 100644 --- a/docs/sphinx/source/api/export_format/ACT-R/addition.yaml +++ b/docs/sphinx/source/api/export_format/ACT-R/addition.yaml @@ -1,6 +1,6 @@ addition: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: addition_graph: nodes: diff --git a/docs/sphinx/source/api/export_format/ACT-R/count.json b/docs/sphinx/source/api/export_format/ACT-R/count.json index 1f11da00..22d63756 100644 --- a/docs/sphinx/source/api/export_format/ACT-R/count.json +++ b/docs/sphinx/source/api/export_format/ACT-R/count.json @@ -1,7 +1,7 @@ { "count": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "count_graph": { "nodes": { diff --git a/docs/sphinx/source/api/export_format/ACT-R/count.yaml b/docs/sphinx/source/api/export_format/ACT-R/count.yaml index 8123bf7f..8cd4ee64 100644 --- a/docs/sphinx/source/api/export_format/ACT-R/count.yaml +++ b/docs/sphinx/source/api/export_format/ACT-R/count.yaml @@ -1,6 +1,6 @@ count: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: count_graph: nodes: diff --git a/docs/sphinx/source/api/export_format/ONNX/ab.json b/docs/sphinx/source/api/export_format/ONNX/ab.json index 71dad49f..b794dd5f 100644 --- a/docs/sphinx/source/api/export_format/ONNX/ab.json +++ b/docs/sphinx/source/api/export_format/ONNX/ab.json @@ -1,7 +1,7 @@ { "ONNX Model": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "main_graph": { "nodes": { diff --git a/docs/sphinx/source/api/export_format/ONNX/ab.yaml b/docs/sphinx/source/api/export_format/ONNX/ab.yaml index 8039d6f2..0373f730 100644 --- a/docs/sphinx/source/api/export_format/ONNX/ab.yaml +++ b/docs/sphinx/source/api/export_format/ONNX/ab.yaml @@ -1,6 +1,6 @@ ONNX Model: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: main_graph: nodes: diff --git a/docs/sphinx/source/api/export_format/ONNX/abc.json b/docs/sphinx/source/api/export_format/ONNX/abc.json index 45b433de..2d47a12f 100644 --- a/docs/sphinx/source/api/export_format/ONNX/abc.json +++ b/docs/sphinx/source/api/export_format/ONNX/abc.json @@ -1,7 +1,7 @@ { "ONNX Model": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "main_graph": { "nodes": { diff --git a/docs/sphinx/source/api/export_format/ONNX/abc.yaml b/docs/sphinx/source/api/export_format/ONNX/abc.yaml index 714367de..873597fd 100644 --- a/docs/sphinx/source/api/export_format/ONNX/abc.yaml +++ b/docs/sphinx/source/api/export_format/ONNX/abc.yaml @@ -1,6 +1,6 @@ ONNX Model: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: main_graph: nodes: diff --git a/docs/sphinx/source/api/export_format/ONNX/abc_basic-mdf.json b/docs/sphinx/source/api/export_format/ONNX/abc_basic-mdf.json index 793027f5..4f1c64af 100644 --- a/docs/sphinx/source/api/export_format/ONNX/abc_basic-mdf.json +++ b/docs/sphinx/source/api/export_format/ONNX/abc_basic-mdf.json @@ -1,7 +1,7 @@ { "ONNX Model": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "main_graph": { "nodes": { diff --git a/docs/sphinx/source/api/export_format/ONNX/abc_basic-mdf.yaml b/docs/sphinx/source/api/export_format/ONNX/abc_basic-mdf.yaml index ddabc3bc..5aa4dd24 100644 --- a/docs/sphinx/source/api/export_format/ONNX/abc_basic-mdf.yaml +++ b/docs/sphinx/source/api/export_format/ONNX/abc_basic-mdf.yaml @@ -1,6 +1,6 @@ ONNX Model: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: main_graph: nodes: diff --git a/docs/sphinx/source/api/export_format/ONNX/abcd.json b/docs/sphinx/source/api/export_format/ONNX/abcd.json index c84579a5..7d55c96e 100644 --- a/docs/sphinx/source/api/export_format/ONNX/abcd.json +++ b/docs/sphinx/source/api/export_format/ONNX/abcd.json @@ -1,7 +1,7 @@ { "ONNX Model": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "main_graph": { "nodes": { diff --git a/docs/sphinx/source/api/export_format/ONNX/abcd.yaml b/docs/sphinx/source/api/export_format/ONNX/abcd.yaml index beab1f98..890c27f2 100644 --- a/docs/sphinx/source/api/export_format/ONNX/abcd.yaml +++ b/docs/sphinx/source/api/export_format/ONNX/abcd.yaml @@ -1,6 +1,6 @@ ONNX Model: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: main_graph: nodes: diff --git a/docs/sphinx/source/api/export_format/PyTorch/inception.json b/docs/sphinx/source/api/export_format/PyTorch/inception.json index fc232e28..037884d5 100644 --- a/docs/sphinx/source/api/export_format/PyTorch/inception.json +++ b/docs/sphinx/source/api/export_format/PyTorch/inception.json @@ -1,7 +1,7 @@ { "InceptionBlocks": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "InceptionBlocksGraph": { "nodes": { diff --git a/docs/sphinx/source/api/export_format/PyTorch/mlp_pure_mdf.json b/docs/sphinx/source/api/export_format/PyTorch/mlp_pure_mdf.json index 22160972..797147cd 100644 --- a/docs/sphinx/source/api/export_format/PyTorch/mlp_pure_mdf.json +++ b/docs/sphinx/source/api/export_format/PyTorch/mlp_pure_mdf.json @@ -1,7 +1,7 @@ { "mlp_pure_mdf": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "mlp_pure_mdf": { "nodes": { diff --git a/docs/sphinx/source/api/export_format/PyTorch/mlp_pure_mdf.yaml b/docs/sphinx/source/api/export_format/PyTorch/mlp_pure_mdf.yaml index c8a37d9c..b3a07b34 100644 --- a/docs/sphinx/source/api/export_format/PyTorch/mlp_pure_mdf.yaml +++ b/docs/sphinx/source/api/export_format/PyTorch/mlp_pure_mdf.yaml @@ -1,6 +1,6 @@ mlp_pure_mdf: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: mlp_pure_mdf: nodes: diff --git a/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf.json b/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf.json index e6f03bf2..e4544c13 100644 --- a/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf.json +++ b/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf.json @@ -1,7 +1,7 @@ { "SimpleNet": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "SimpleNetGraph": { "nodes": { diff --git a/examples/ACT-R/addition.json b/examples/ACT-R/addition.json index a288ed43..1572a4ce 100644 --- a/examples/ACT-R/addition.json +++ b/examples/ACT-R/addition.json @@ -1,7 +1,7 @@ { "addition": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "addition_graph": { "nodes": { diff --git a/examples/ACT-R/addition.yaml b/examples/ACT-R/addition.yaml index 7e6df724..65bd1ed4 100644 --- a/examples/ACT-R/addition.yaml +++ b/examples/ACT-R/addition.yaml @@ -1,6 +1,6 @@ addition: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: addition_graph: nodes: diff --git a/examples/ACT-R/count.json b/examples/ACT-R/count.json index 1f11da00..22d63756 100644 --- a/examples/ACT-R/count.json +++ b/examples/ACT-R/count.json @@ -1,7 +1,7 @@ { "count": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "count_graph": { "nodes": { diff --git a/examples/ACT-R/count.yaml b/examples/ACT-R/count.yaml index 8123bf7f..8cd4ee64 100644 --- a/examples/ACT-R/count.yaml +++ b/examples/ACT-R/count.yaml @@ -1,6 +1,6 @@ count: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: count_graph: nodes: diff --git a/examples/MDF/ABCD.json b/examples/MDF/ABCD.json index 0d24f9da..1d19f2d7 100644 --- a/examples/MDF/ABCD.json +++ b/examples/MDF/ABCD.json @@ -1,7 +1,7 @@ { "ABCD": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "abcd_example": { "nodes": { diff --git a/examples/MDF/ABCD.yaml b/examples/MDF/ABCD.yaml index b6733a88..1ecba32a 100644 --- a/examples/MDF/ABCD.yaml +++ b/examples/MDF/ABCD.yaml @@ -1,6 +1,6 @@ ABCD: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: abcd_example: nodes: diff --git a/examples/MDF/Arrays.json b/examples/MDF/Arrays.json index 03477a69..44d06999 100644 --- a/examples/MDF/Arrays.json +++ b/examples/MDF/Arrays.json @@ -1,7 +1,7 @@ { "Arrays": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "array_example": { "nodes": { diff --git a/examples/MDF/Arrays.yaml b/examples/MDF/Arrays.yaml index ea200728..9ab8872f 100644 --- a/examples/MDF/Arrays.yaml +++ b/examples/MDF/Arrays.yaml @@ -1,6 +1,6 @@ Arrays: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: array_example: nodes: diff --git a/examples/MDF/NewtonCoolingModel.json b/examples/MDF/NewtonCoolingModel.json index 97b0b2b3..8a2557a1 100644 --- a/examples/MDF/NewtonCoolingModel.json +++ b/examples/MDF/NewtonCoolingModel.json @@ -1,7 +1,7 @@ { "NewtonCoolingModel": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "cooling_process": { "nodes": { diff --git a/examples/MDF/NewtonCoolingModel.yaml b/examples/MDF/NewtonCoolingModel.yaml index d1a29edc..d3d9ee71 100644 --- a/examples/MDF/NewtonCoolingModel.yaml +++ b/examples/MDF/NewtonCoolingModel.yaml @@ -1,6 +1,6 @@ NewtonCoolingModel: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: cooling_process: nodes: diff --git a/examples/MDF/ParametersFunctions.json b/examples/MDF/ParametersFunctions.json index 286b883d..92c1c55d 100644 --- a/examples/MDF/ParametersFunctions.json +++ b/examples/MDF/ParametersFunctions.json @@ -1,7 +1,7 @@ { "ParametersFunctions": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "params_funcs_example": { "nodes": { diff --git a/examples/MDF/ParametersFunctions.yaml b/examples/MDF/ParametersFunctions.yaml index 215418d6..30737c92 100644 --- a/examples/MDF/ParametersFunctions.yaml +++ b/examples/MDF/ParametersFunctions.yaml @@ -1,6 +1,6 @@ ParametersFunctions: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: params_funcs_example: nodes: diff --git a/examples/MDF/RNN/IAF_net.json b/examples/MDF/RNN/IAF_net.json index 23a2f1b6..7062654b 100644 --- a/examples/MDF/RNN/IAF_net.json +++ b/examples/MDF/RNN/IAF_net.json @@ -1,7 +1,7 @@ { "IAF_net": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "iaf_example": { "nodes": { diff --git a/examples/MDF/RNN/IAF_net.yaml b/examples/MDF/RNN/IAF_net.yaml index 0185b8cc..91878ae8 100644 --- a/examples/MDF/RNN/IAF_net.yaml +++ b/examples/MDF/RNN/IAF_net.yaml @@ -1,6 +1,6 @@ IAF_net: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: iaf_example: nodes: diff --git a/examples/MDF/RNN/IAF_net2.json b/examples/MDF/RNN/IAF_net2.json index 44e13307..ffd49836 100644 --- a/examples/MDF/RNN/IAF_net2.json +++ b/examples/MDF/RNN/IAF_net2.json @@ -1,7 +1,7 @@ { "IAF_net2": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "iaf_example": { "nodes": { diff --git a/examples/MDF/RNN/IAF_net2.yaml b/examples/MDF/RNN/IAF_net2.yaml index 44351dbe..6b049ca5 100644 --- a/examples/MDF/RNN/IAF_net2.yaml +++ b/examples/MDF/RNN/IAF_net2.yaml @@ -1,6 +1,6 @@ IAF_net2: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: iaf_example: nodes: diff --git a/examples/MDF/RNN/IAF_net3.json b/examples/MDF/RNN/IAF_net3.json index 092c9f99..af87c2d8 100644 --- a/examples/MDF/RNN/IAF_net3.json +++ b/examples/MDF/RNN/IAF_net3.json @@ -1,7 +1,7 @@ { "IAF_net3": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "iaf_example": { "nodes": { diff --git a/examples/MDF/RNN/IAF_net3.yaml b/examples/MDF/RNN/IAF_net3.yaml index 0d054295..d3ba4d8a 100644 --- a/examples/MDF/RNN/IAF_net3.yaml +++ b/examples/MDF/RNN/IAF_net3.yaml @@ -1,6 +1,6 @@ IAF_net3: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: iaf_example: nodes: diff --git a/examples/MDF/RNN/IAFs.json b/examples/MDF/RNN/IAFs.json index 4a02d147..db5b500d 100644 --- a/examples/MDF/RNN/IAFs.json +++ b/examples/MDF/RNN/IAFs.json @@ -1,7 +1,7 @@ { "IAFs": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "iaf_example": { "nodes": { diff --git a/examples/MDF/RNN/IAFs.yaml b/examples/MDF/RNN/IAFs.yaml index b114a055..b7ae2f7b 100644 --- a/examples/MDF/RNN/IAFs.yaml +++ b/examples/MDF/RNN/IAFs.yaml @@ -1,6 +1,6 @@ IAFs: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: iaf_example: nodes: diff --git a/examples/MDF/RNN/RNNs.json b/examples/MDF/RNN/RNNs.json index 608f55b1..f22ca9a2 100644 --- a/examples/MDF/RNN/RNNs.json +++ b/examples/MDF/RNN/RNNs.json @@ -1,7 +1,7 @@ { "RNNs": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "rnn_example": { "nodes": { diff --git a/examples/MDF/RNN/RNNs.yaml b/examples/MDF/RNN/RNNs.yaml index 04076c79..30f59a09 100644 --- a/examples/MDF/RNN/RNNs.yaml +++ b/examples/MDF/RNN/RNNs.yaml @@ -1,6 +1,6 @@ RNNs: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: rnn_example: nodes: diff --git a/examples/MDF/Simple.bson b/examples/MDF/Simple.bson index 48433c8c6650766c361b3a630de94f207a140479..c8e35f413840474ec8f9f8bd4d35e3f2aaabc14f 100644 GIT binary patch delta 12 TcmZo=Z)Km5z-YQLQH2=*7-s`` delta 12 TcmZo=Z)Km5z-Y2DQH2=*7-9o= diff --git a/examples/MDF/Simple.json b/examples/MDF/Simple.json index 6f5bfb70..a915780f 100644 --- a/examples/MDF/Simple.json +++ b/examples/MDF/Simple.json @@ -1,7 +1,7 @@ { "Simple": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "simple_example": { "nodes": { diff --git a/examples/MDF/Simple.yaml b/examples/MDF/Simple.yaml index 4e73e3d4..8c198014 100644 --- a/examples/MDF/Simple.yaml +++ b/examples/MDF/Simple.yaml @@ -1,6 +1,6 @@ Simple: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: simple_example: nodes: diff --git a/examples/MDF/States.json b/examples/MDF/States.json index 1be78346..3b2a0993 100644 --- a/examples/MDF/States.json +++ b/examples/MDF/States.json @@ -1,7 +1,7 @@ { "States": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "state_example": { "nodes": { diff --git a/examples/MDF/States.yaml b/examples/MDF/States.yaml index 327792fb..9613ded0 100644 --- a/examples/MDF/States.yaml +++ b/examples/MDF/States.yaml @@ -1,6 +1,6 @@ States: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: state_example: nodes: diff --git a/examples/MDF/SwitchedRLC_Circuit.json b/examples/MDF/SwitchedRLC_Circuit.json index 3b18562d..5c2ef12f 100644 --- a/examples/MDF/SwitchedRLC_Circuit.json +++ b/examples/MDF/SwitchedRLC_Circuit.json @@ -1,7 +1,7 @@ { "SwitchedRLC_Circuit": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "metadata": { "preferred_duration": 2, "preferred_dt": 0.001 diff --git a/examples/MDF/SwitchedRLC_Circuit.yaml b/examples/MDF/SwitchedRLC_Circuit.yaml index fc1f8a80..f105cad9 100644 --- a/examples/MDF/SwitchedRLC_Circuit.yaml +++ b/examples/MDF/SwitchedRLC_Circuit.yaml @@ -1,6 +1,6 @@ SwitchedRLC_Circuit: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 metadata: preferred_duration: 2 preferred_dt: 0.001 diff --git a/examples/MDF/abc_conditions.json b/examples/MDF/abc_conditions.json index 6b42fecd..58355ef1 100644 --- a/examples/MDF/abc_conditions.json +++ b/examples/MDF/abc_conditions.json @@ -1,7 +1,7 @@ { "abc_conditions": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "abc_conditions_example": { "nodes": { diff --git a/examples/MDF/abc_conditions.yaml b/examples/MDF/abc_conditions.yaml index e391b0e2..c377993d 100644 --- a/examples/MDF/abc_conditions.yaml +++ b/examples/MDF/abc_conditions.yaml @@ -1,6 +1,6 @@ abc_conditions: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: abc_conditions_example: nodes: diff --git a/examples/MDF/conditions/Composite_mdf_condition.json b/examples/MDF/conditions/Composite_mdf_condition.json index 878aaec7..a32e3cf2 100644 --- a/examples/MDF/conditions/Composite_mdf_condition.json +++ b/examples/MDF/conditions/Composite_mdf_condition.json @@ -1,7 +1,7 @@ { "Composite_mdf_condition": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "Composite_mdf_condition_example": { "nodes": { diff --git a/examples/MDF/conditions/Composite_mdf_condition.yaml b/examples/MDF/conditions/Composite_mdf_condition.yaml index 6140e478..b1d5e244 100644 --- a/examples/MDF/conditions/Composite_mdf_condition.yaml +++ b/examples/MDF/conditions/Composite_mdf_condition.yaml @@ -1,6 +1,6 @@ Composite_mdf_condition: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: Composite_mdf_condition_example: nodes: diff --git a/examples/MDF/conditions/everyncalls_condition.json b/examples/MDF/conditions/everyncalls_condition.json index 197e2977..27aebd4d 100644 --- a/examples/MDF/conditions/everyncalls_condition.json +++ b/examples/MDF/conditions/everyncalls_condition.json @@ -1,7 +1,7 @@ { "everyncalls_condition": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "everyncalls_example": { "nodes": { diff --git a/examples/MDF/conditions/everyncalls_condition.yaml b/examples/MDF/conditions/everyncalls_condition.yaml index c43d81a0..7736d12e 100644 --- a/examples/MDF/conditions/everyncalls_condition.yaml +++ b/examples/MDF/conditions/everyncalls_condition.yaml @@ -1,6 +1,6 @@ everyncalls_condition: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: everyncalls_example: nodes: diff --git a/examples/MDF/conditions/threshold_condition.json b/examples/MDF/conditions/threshold_condition.json index 27ac7fbc..b2e972e1 100644 --- a/examples/MDF/conditions/threshold_condition.json +++ b/examples/MDF/conditions/threshold_condition.json @@ -1,7 +1,7 @@ { "threshold_condition": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "threshold_example": { "nodes": { diff --git a/examples/MDF/conditions/threshold_condition.yaml b/examples/MDF/conditions/threshold_condition.yaml index 10a50e70..7f90a8b5 100644 --- a/examples/MDF/conditions/threshold_condition.yaml +++ b/examples/MDF/conditions/threshold_condition.yaml @@ -1,6 +1,6 @@ threshold_condition: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: threshold_example: nodes: diff --git a/examples/MDF/conditions/timeinterval_condition.json b/examples/MDF/conditions/timeinterval_condition.json index e22f7932..58ebddd2 100644 --- a/examples/MDF/conditions/timeinterval_condition.json +++ b/examples/MDF/conditions/timeinterval_condition.json @@ -1,7 +1,7 @@ { "timeinterval_condition": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "timeinterval_example": { "nodes": { diff --git a/examples/MDF/conditions/timeinterval_condition.yaml b/examples/MDF/conditions/timeinterval_condition.yaml index 2f539385..0100211e 100644 --- a/examples/MDF/conditions/timeinterval_condition.yaml +++ b/examples/MDF/conditions/timeinterval_condition.yaml @@ -1,6 +1,6 @@ timeinterval_condition: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: timeinterval_example: nodes: diff --git a/examples/MDF/networks/Net_acyclical.json b/examples/MDF/networks/Net_acyclical.json index c1be5e99..ac3ce346 100644 --- a/examples/MDF/networks/Net_acyclical.json +++ b/examples/MDF/networks/Net_acyclical.json @@ -1,7 +1,7 @@ { "Net_acyclical": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "Net_acyclical": { "nodes": { diff --git a/examples/MDF/networks/Net_acyclical.yaml b/examples/MDF/networks/Net_acyclical.yaml index 0be7ffc0..7514daad 100644 --- a/examples/MDF/networks/Net_acyclical.yaml +++ b/examples/MDF/networks/Net_acyclical.yaml @@ -1,6 +1,6 @@ Net_acyclical: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: Net_acyclical: nodes: diff --git a/examples/ONNX/ab.json b/examples/ONNX/ab.json index 71dad49f..b794dd5f 100644 --- a/examples/ONNX/ab.json +++ b/examples/ONNX/ab.json @@ -1,7 +1,7 @@ { "ONNX Model": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "main_graph": { "nodes": { diff --git a/examples/ONNX/ab.yaml b/examples/ONNX/ab.yaml index 8039d6f2..0373f730 100644 --- a/examples/ONNX/ab.yaml +++ b/examples/ONNX/ab.yaml @@ -1,6 +1,6 @@ ONNX Model: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: main_graph: nodes: diff --git a/examples/ONNX/abc.json b/examples/ONNX/abc.json index 45b433de..2d47a12f 100644 --- a/examples/ONNX/abc.json +++ b/examples/ONNX/abc.json @@ -1,7 +1,7 @@ { "ONNX Model": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "main_graph": { "nodes": { diff --git a/examples/ONNX/abc.yaml b/examples/ONNX/abc.yaml index 714367de..873597fd 100644 --- a/examples/ONNX/abc.yaml +++ b/examples/ONNX/abc.yaml @@ -1,6 +1,6 @@ ONNX Model: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: main_graph: nodes: diff --git a/examples/ONNX/abc_basic-mdf.json b/examples/ONNX/abc_basic-mdf.json index 793027f5..4f1c64af 100644 --- a/examples/ONNX/abc_basic-mdf.json +++ b/examples/ONNX/abc_basic-mdf.json @@ -1,7 +1,7 @@ { "ONNX Model": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "main_graph": { "nodes": { diff --git a/examples/ONNX/abc_basic-mdf.yaml b/examples/ONNX/abc_basic-mdf.yaml index ddabc3bc..5aa4dd24 100644 --- a/examples/ONNX/abc_basic-mdf.yaml +++ b/examples/ONNX/abc_basic-mdf.yaml @@ -1,6 +1,6 @@ ONNX Model: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: main_graph: nodes: diff --git a/examples/ONNX/abcd.json b/examples/ONNX/abcd.json index c84579a5..7d55c96e 100644 --- a/examples/ONNX/abcd.json +++ b/examples/ONNX/abcd.json @@ -1,7 +1,7 @@ { "ONNX Model": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "main_graph": { "nodes": { diff --git a/examples/ONNX/abcd.yaml b/examples/ONNX/abcd.yaml index beab1f98..890c27f2 100644 --- a/examples/ONNX/abcd.yaml +++ b/examples/ONNX/abcd.yaml @@ -1,6 +1,6 @@ ONNX Model: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: main_graph: nodes: diff --git a/examples/PyTorch/MDF_PyTorch/ABCD.onnx b/examples/PyTorch/MDF_PyTorch/ABCD.onnx index c772c3c37628dab071de54b3173e4acb4addf535..b05f48a6422db88776cb35e647507bfe7ca97cc7 100644 GIT binary patch delta 27 icmcbWek)ywgGGqFpt2;tC^<0?~ delta 27 icmZoQY&8_(U=d<3s4U4ZO3sjCHPSQHGuS9pECB#w{s#>J diff --git a/examples/PyTorch/MDF_PyTorch/Simple_pytorch.py b/examples/PyTorch/MDF_PyTorch/Simple_pytorch.py index e3875863..d9792093 100644 --- a/examples/PyTorch/MDF_PyTorch/Simple_pytorch.py +++ b/examples/PyTorch/MDF_PyTorch/Simple_pytorch.py @@ -1,5 +1,5 @@ """ -This script has been generated by modeci_mdf v0.4.14. +This script has been generated by modeci_mdf v0.4.15. It is an export of a MDF model (mdf.s - MDF stateful, i.e. full MDF allowing stateful parameters) to PyTorch """ diff --git a/examples/PyTorch/inception.json b/examples/PyTorch/inception.json index fc232e28..037884d5 100644 --- a/examples/PyTorch/inception.json +++ b/examples/PyTorch/inception.json @@ -1,7 +1,7 @@ { "InceptionBlocks": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "InceptionBlocksGraph": { "nodes": { diff --git a/examples/PyTorch/mlp_pure_mdf.json b/examples/PyTorch/mlp_pure_mdf.json index 22160972..797147cd 100644 --- a/examples/PyTorch/mlp_pure_mdf.json +++ b/examples/PyTorch/mlp_pure_mdf.json @@ -1,7 +1,7 @@ { "mlp_pure_mdf": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "mlp_pure_mdf": { "nodes": { diff --git a/examples/PyTorch/mlp_pure_mdf.yaml b/examples/PyTorch/mlp_pure_mdf.yaml index c8a37d9c..b3a07b34 100644 --- a/examples/PyTorch/mlp_pure_mdf.yaml +++ b/examples/PyTorch/mlp_pure_mdf.yaml @@ -1,6 +1,6 @@ mlp_pure_mdf: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.14 + generating_application: Python modeci-mdf v0.4.15 graphs: mlp_pure_mdf: nodes: diff --git a/examples/PyTorch/simple_pytorch_to_mdf.json b/examples/PyTorch/simple_pytorch_to_mdf.json index e6f03bf2..e4544c13 100644 --- a/examples/PyTorch/simple_pytorch_to_mdf.json +++ b/examples/PyTorch/simple_pytorch_to_mdf.json @@ -1,7 +1,7 @@ { "SimpleNet": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.14", + "generating_application": "Python modeci-mdf v0.4.15", "graphs": { "SimpleNetGraph": { "nodes": { diff --git a/src/modeci_mdf/__init__.py b/src/modeci_mdf/__init__.py index 79ee1392..83733d5c 100644 --- a/src/modeci_mdf/__init__.py +++ b/src/modeci_mdf/__init__.py @@ -13,4 +13,4 @@ MODECI_MDF_VERSION = "0.4" # Version of the Python module. -__version__ = "0.4.14" +__version__ = "0.4.15" From fa70085f4d6137c25623b8e2a3b48e40f7df0903 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 24 Jun 2026 16:28:56 +0100 Subject: [PATCH 04/12] More verbose install, for debug --- .github/workflows/ci_test_all.yml | 1 + test_all.sh | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci_test_all.yml b/.github/workflows/ci_test_all.yml index 113dbf0a..0511620b 100644 --- a/.github/workflows/ci_test_all.yml +++ b/.github/workflows/ci_test_all.yml @@ -37,6 +37,7 @@ jobs: - name: Run test script run: | + python -m pip install -U pip # pip install torch==2.8.0 # pinned to avoid issues with latest version taking up too much space... export NEURON_HOME=$pythonLocation ./test_all.sh diff --git a/test_all.sh b/test_all.sh index 506459d6..80e1bbf5 100755 --- a/test_all.sh +++ b/test_all.sh @@ -5,18 +5,18 @@ set -ex ## causing issues on GHA CI. df -h -pip install . --cache-dir=/home/runner/tmp --prefer-binary +python -m pip install -vvv . --cache-dir=/home/runner/tmp --prefer-binary df -h pip cache info pip cache purge df -h -pip install .[optional] --cache-dir=/home/runner/tmp --prefer-binary +python -m pip install -vvv .[optional] --cache-dir=/home/runner/tmp --prefer-binary df -h pip cache purge df -h -pip install .[all] --cache-dir=/home/runner/tmp --prefer-binary +python -m pip install -vvv .[all] --cache-dir=/home/runner/tmp --prefer-binary df -h From 020427b827098eeed2e816fe58a4f6d266b80164 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 24 Jun 2026 18:12:34 +0100 Subject: [PATCH 05/12] pip install psyneulink from https://github.com/PrincetonUniversity/PsyNeuLink, branch deve --- .github/workflows/ci_test_all.yml | 5 ++++- test_all.sh | 6 +++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci_test_all.yml b/.github/workflows/ci_test_all.yml index 0511620b..18776ad4 100644 --- a/.github/workflows/ci_test_all.yml +++ b/.github/workflows/ci_test_all.yml @@ -38,7 +38,10 @@ jobs: - name: Run test script run: | python -m pip install -U pip - # pip install torch==2.8.0 # pinned to avoid issues with latest version taking up too much space... + + # pip install psyneulink from https://github.com/PrincetonUniversity/PsyNeuLink, branch devel + pip install git+https://github.com/PrincetonUniversity/PsyNeuLink.git@devel + export NEURON_HOME=$pythonLocation ./test_all.sh diff --git a/test_all.sh b/test_all.sh index 80e1bbf5..e15b66ff 100755 --- a/test_all.sh +++ b/test_all.sh @@ -5,18 +5,18 @@ set -ex ## causing issues on GHA CI. df -h -python -m pip install -vvv . --cache-dir=/home/runner/tmp --prefer-binary +python -m pip install . --cache-dir=/home/runner/tmp --prefer-binary df -h pip cache info pip cache purge df -h -python -m pip install -vvv .[optional] --cache-dir=/home/runner/tmp --prefer-binary +python -m pip install .[optional] --cache-dir=/home/runner/tmp --prefer-binary df -h pip cache purge df -h -python -m pip install -vvv .[all] --cache-dir=/home/runner/tmp --prefer-binary +python -m pip install .[all] --cache-dir=/home/runner/tmp --prefer-binary df -h From ef59d7c7f932a5a565ad0b8c0f1c66bbd141bbff Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 22 Jul 2026 03:23:55 +0000 Subject: [PATCH 06/12] Bump pypa/gh-action-pypi-publish from 1.14.0 to 1.14.1 Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.14.0 to 1.14.1. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.14.0...v1.14.1) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .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 2346bd28..b69a1e2f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -113,7 +113,7 @@ jobs: - uses: actions/upload-artifact@v7 with: path: dist - - uses: pypa/gh-action-pypi-publish@v1.14.0 + - uses: pypa/gh-action-pypi-publish@v1.14.1 if: github.event_name == 'release' && github.event.action == 'published' with: user: __token__ From fc4929ea7dca6b0fb20dbdb8b1f3291a45bf5f65 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 22 Jul 2026 03:23:58 +0000 Subject: [PATCH 07/12] Bump actions/setup-python from 6 to 7 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 6 to 7. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v6...v7) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/ci.yml | 6 +++--- .github/workflows/ci_test_all.yml | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2346bd28..bb42bac7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -17,7 +17,7 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v6 - - uses: actions/setup-python@v6 + - uses: actions/setup-python@v7 with: python-version: '3.10' - uses: pre-commit/action@v3.0.1 @@ -41,7 +41,7 @@ jobs: - uses: actions/checkout@v6 - name: Setup Python - uses: actions/setup-python@v6 + uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} @@ -87,7 +87,7 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v6 - - uses: actions/setup-python@v6 + - uses: actions/setup-python@v7 with: python-version: '3.11' - name: Install uv and set the python version diff --git a/.github/workflows/ci_test_all.yml b/.github/workflows/ci_test_all.yml index 2a877f21..7cf0aa62 100644 --- a/.github/workflows/ci_test_all.yml +++ b/.github/workflows/ci_test_all.yml @@ -20,7 +20,7 @@ jobs: steps: - uses: actions/checkout@v6 - - uses: actions/setup-python@v6 + - uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} From 6ce1556031b83a17786f8d6a6822554ed8458ecd Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 22 Jul 2026 16:02:43 +0100 Subject: [PATCH 08/12] Fix formatting --- .github/workflows/ci_test_all.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_test_all.yml b/.github/workflows/ci_test_all.yml index 268683db..7212bbfe 100644 --- a/.github/workflows/ci_test_all.yml +++ b/.github/workflows/ci_test_all.yml @@ -41,7 +41,7 @@ jobs: # pip install psyneulink from https://github.com/PrincetonUniversity/PsyNeuLink, branch devel pip install git+https://github.com/PrincetonUniversity/PsyNeuLink.git@devel - + export NEURON_HOME=$pythonLocation ./test_all.sh From 72e6756e3cc051d82f253b58fd56028b90e31eb4 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 24 Jul 2026 17:32:53 +0100 Subject: [PATCH 09/12] Allow latest modelspec --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 48c49698..fe04d89d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -50,7 +50,7 @@ dependencies = [ "skl2onnx", "attrs>=21.1.0", "cattrs", - "modelspec<0.4,>=0.3.0", + "modelspec<0.5,>=0.3.0", "glom", ] From 252b803b2c0ab6751deb256269680d564450f535 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 29 Jul 2026 17:32:48 +0100 Subject: [PATCH 10/12] Test install latest psyneulink --- .github/workflows/ci_test_all.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci_test_all.yml b/.github/workflows/ci_test_all.yml index 9fe6e18b..5132e129 100644 --- a/.github/workflows/ci_test_all.yml +++ b/.github/workflows/ci_test_all.yml @@ -40,7 +40,7 @@ jobs: python -m pip install -U pip # pip install psyneulink from https://github.com/PrincetonUniversity/PsyNeuLink, branch devel - pip install git+https://github.com/PrincetonUniversity/PsyNeuLink.git@devel + pip install psyneulink export NEURON_HOME=$pythonLocation ./test_all.sh From c79ad07a9896055f62e0ae1f06517273e4269fc7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 5 Aug 2026 03:23:59 +0000 Subject: [PATCH 11/12] Bump pypa/gh-action-pypi-publish from 1.14.0 to 1.14.2 Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.14.0 to 1.14.2. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.14.0...v1.14.2) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.2 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .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 2346bd28..7e0a2fdb 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -113,7 +113,7 @@ jobs: - uses: actions/upload-artifact@v7 with: path: dist - - uses: pypa/gh-action-pypi-publish@v1.14.0 + - uses: pypa/gh-action-pypi-publish@v1.14.2 if: github.event_name == 'release' && github.event.action == 'published' with: user: __token__ From ad532017cd6aeb120b25a07263f56bdaa0b4bdb1 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 5 Aug 2026 09:17:25 +0100 Subject: [PATCH 12/12] Exclude tensorflow test on macos due to slowness --- .github/workflows/ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9d3f361e..ab654880 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -36,6 +36,8 @@ jobs: exclude: - os: windows-latest test-suite: tensorflow + - os: macos-latest + test-suite: tensorflow # too slow... steps: - uses: actions/checkout@v7