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Merged
pgleeson merged 19 commits into from
Aug 5, 2026
Merged

Update dependencies and improve GitHub Actions workflows #584

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202047e
Merge pull request #578 from ModECI/development
pgleeson May 27, 2026
a4e319d
Merge pull request #579 from ModECI/development
pgleeson May 28, 2026
6ddb20d
Bump actions/checkout from 6 to 7
dependabot[bot] Jun 24, 2026
4279851
Update checkout action version in CI workflow
pgleeson Jun 24, 2026
e50eda0
To v0.4.15; run big test_all on 3.12 for now...
pgleeson Jun 24, 2026
fa70085
More verbose install, for debug
pgleeson Jun 24, 2026
020427b
pip install psyneulink from https://github.com/PrincetonUniversity/Ps…
pgleeson Jun 24, 2026
ef59d7c
Bump pypa/gh-action-pypi-publish from 1.14.0 to 1.14.1
dependabot[bot] Jul 22, 2026
fc4929e
Bump actions/setup-python from 6 to 7
dependabot[bot] Jul 22, 2026
d6d78da
Merge branch 'dependabot/github_actions/actions/setup-python-7' into …
pgleeson Jul 22, 2026
6ce1556
Fix formatting
pgleeson Jul 22, 2026
72e6756
Allow latest modelspec
pgleeson Jul 24, 2026
a441424
Merge branch 'dependabot/github_actions/pypa/gh-action-pypi-publish-1…
pgleeson Jul 29, 2026
f1c39b6
Merge branch 'dependabot/github_actions/actions/checkout-7' into test…
pgleeson Jul 29, 2026
f74354c
Merge branch 'test_main' into nml_examples
pgleeson Jul 29, 2026
252b803
Test install latest psyneulink
pgleeson Jul 29, 2026
c79ad07
Bump pypa/gh-action-pypi-publish from 1.14.0 to 1.14.2
dependabot[bot] Aug 5, 2026
d2a8458
Merge remote-tracking branch 'origin/dependabot/github_actions/pypa/g…
pgleeson Aug 5, 2026
ad53201
Exclude tensorflow test on macos due to slowness
pgleeson Aug 5, 2026
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18 changes: 10 additions & 8 deletions .github/workflows/ci.yml
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Expand Up @@ -16,8 +16,8 @@ jobs:
name: Format
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- uses: actions/setup-python@v6
- uses: actions/checkout@v7
- uses: actions/setup-python@v7
with:
python-version: '3.10'
- uses: pre-commit/action@v3.0.1
Expand All @@ -36,12 +36,14 @@ jobs:
exclude:
- os: windows-latest
test-suite: tensorflow
- os: macos-latest
test-suite: tensorflow # too slow...

steps:
- uses: actions/checkout@v6
- uses: actions/checkout@v7

- name: Setup Python
uses: actions/setup-python@v6
uses: actions/setup-python@v7
with:
python-version: ${{ matrix.python-version }}

Expand Down Expand Up @@ -86,8 +88,8 @@ jobs:
needs: tests
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- uses: actions/setup-python@v6
- uses: actions/checkout@v7
- uses: actions/setup-python@v7
with:
python-version: '3.11'
- name: Install uv and set the python version
Expand All @@ -107,13 +109,13 @@ 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
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__
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12 changes: 8 additions & 4 deletions .github/workflows/ci_test_all.yml
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Expand Up @@ -14,13 +14,13 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: [ "3.13"]
python-version: [ "3.12"]
runs-on: [ubuntu-latest]

steps:
- uses: actions/checkout@v6
- uses: actions/checkout@v7

- uses: actions/setup-python@v6
- uses: actions/setup-python@v7
with:
python-version: ${{ matrix.python-version }}

Expand All @@ -37,7 +37,11 @@ jobs:

- name: Run test script
run: |
# pip install torch==2.8.0 # pinned to avoid issues with latest version taking up too much space...
python -m pip install -U pip

# pip install psyneulink from https://github.com/PrincetonUniversity/PsyNeuLink, branch devel
pip install psyneulink

export NEURON_HOME=$pythonLocation
./test_all.sh

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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/ACT-R/addition.json
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@@ -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": {
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/ACT-R/addition.yaml
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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:
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/ACT-R/count.json
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{
"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": {
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/ACT-R/count.yaml
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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:
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/ONNX/ab.json
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{
"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": {
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/ONNX/ab.yaml
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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:
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/ONNX/abc.json
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{
"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": {
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/ONNX/abc.yaml
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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:
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/ONNX/abc_basic-mdf.json
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{
"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": {
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/ONNX/abc_basic-mdf.yaml
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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:
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/ONNX/abcd.json
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{
"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": {
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/ONNX/abcd.yaml
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@@ -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:
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/PyTorch/inception.json
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@@ -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": {
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/PyTorch/mlp_pure_mdf.json
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@@ -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": {
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/PyTorch/mlp_pure_mdf.yaml
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@@ -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:
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2 changes: 1 addition & 1 deletion docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf.json
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@@ -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": {
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2 changes: 1 addition & 1 deletion examples/ACT-R/addition.json
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{
"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": {
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2 changes: 1 addition & 1 deletion examples/ACT-R/addition.yaml
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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:
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2 changes: 1 addition & 1 deletion examples/ACT-R/count.json
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{
"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": {
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2 changes: 1 addition & 1 deletion examples/ACT-R/count.yaml
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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:
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2 changes: 1 addition & 1 deletion examples/MDF/ABCD.json
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{
"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": {
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2 changes: 1 addition & 1 deletion examples/MDF/ABCD.yaml
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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:
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2 changes: 1 addition & 1 deletion examples/MDF/Arrays.json
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{
"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": {
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2 changes: 1 addition & 1 deletion examples/MDF/Arrays.yaml
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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:
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2 changes: 1 addition & 1 deletion examples/MDF/NewtonCoolingModel.json
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{
"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": {
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2 changes: 1 addition & 1 deletion examples/MDF/NewtonCoolingModel.yaml
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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:
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2 changes: 1 addition & 1 deletion examples/MDF/ParametersFunctions.json
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{
"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": {
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2 changes: 1 addition & 1 deletion examples/MDF/ParametersFunctions.yaml
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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:
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2 changes: 1 addition & 1 deletion examples/MDF/RNN/IAF_net.json
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{
"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": {
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2 changes: 1 addition & 1 deletion examples/MDF/RNN/IAF_net.yaml
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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:
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2 changes: 1 addition & 1 deletion examples/MDF/RNN/IAF_net2.json
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{
"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": {
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2 changes: 1 addition & 1 deletion examples/MDF/RNN/IAF_net2.yaml
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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:
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2 changes: 1 addition & 1 deletion examples/MDF/RNN/IAF_net3.json
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{
"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": {
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2 changes: 1 addition & 1 deletion examples/MDF/RNN/IAF_net3.yaml
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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:
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2 changes: 1 addition & 1 deletion examples/MDF/RNN/IAFs.json
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{
"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": {
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2 changes: 1 addition & 1 deletion examples/MDF/RNN/IAFs.yaml
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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:
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