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Fixes non omv tests #56

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merged 30 commits into from
Sep 21, 2023
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6c29f27
download an all active celltype
anujanegi Jun 29, 2022
ea71dc2
feat: configure an allactive cell type
anujanegi Jun 29, 2022
72080b9
init all active parsing
anujanegi Jun 29, 2022
ac7df4d
Merge
pgleeson Jun 29, 2022
3d411c7
Merge pull request #20 from anujanegi/all-active
pgleeson Jun 30, 2022
467b5b1
support for all-active Ra and Ca dynamics init and g_pas fixes
anujanegi Jun 30, 2022
818f00a
Merge branch 'experimental' into development
pgleeson Jun 30, 2022
af06fd4
Merge pull request #22 from anujanegi/all-active
pgleeson Jun 30, 2022
424b2a7
Test download of model files
pgleeson Jul 1, 2022
e1ad596
Temp generation of nml for all active
pgleeson Jul 1, 2022
d62c319
Fix issue with dependencies
pgleeson Jul 1, 2022
4568ed7
Merge pull request #2 from OpenSourceBrain/master
anujanegi Jul 1, 2022
f6ea3bb
CaDynamics all active
anujanegi Jul 4, 2022
4ed6472
Merge branch 'experimental' into development
pgleeson Jul 6, 2022
d984212
Merge branch 'master' into all-active
anujanegi Jul 6, 2022
bc4d89d
fix indent
anujanegi Jul 6, 2022
db6b55e
fix list appending
anujanegi Jul 6, 2022
b6211e2
cell files
anujanegi Jul 6, 2022
ebc08e1
Merge branch 'master' into development
pgleeson Jul 7, 2022
8316b07
Merge pull request #25 from anujanegi/all-active
pgleeson Jul 7, 2022
599beb1
Merge branch 'experimental' into development
pgleeson Jul 7, 2022
45af4b5
Merge branch 'master' into development
pgleeson Aug 18, 2023
f54eb9d
Remove dev model
pgleeson Aug 18, 2023
585ac5a
Remove more files
pgleeson Aug 18, 2023
6f816e6
Revert last few changes
pgleeson Aug 18, 2023
9c8d2b8
fix non omv tests
pgleeson Aug 18, 2023
28a478b
Test on 3.9 also
pgleeson Aug 18, 2023
6208ec8
Update non-omv.yml - test py3.9
pgleeson Sep 6, 2023
8fe15c6
Test pinnig allensdk==2.15.1
pgleeson Sep 6, 2023
e88a319
Restrict big download to neuron tests
pgleeson Sep 21, 2023
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10 changes: 5 additions & 5 deletions .github/workflows/non-omv.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,13 +14,13 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: [ 3.7, 3.8 ]
python-version: [ 3.7, 3.8, 3.9 ]

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}

Expand All @@ -30,7 +30,7 @@ jobs:

- name: Download some data
run: |
pip install allensdk
pip install allensdk==2.15.2

cd CellTypesDatabase/data
python download.py -test
Expand Down Expand Up @@ -90,7 +90,7 @@ jobs:
cd CellTypesDatabase/tune
git clone https://github.com/NeuralEnsemble/neurotune.git
cd neurotune/
python setup.py install
pip install .
cd ..
rm -rf neurotune
export NEURON_HOME=$pythonLocation
Expand Down
5 changes: 3 additions & 2 deletions .github/workflows/omv-ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -13,15 +13,15 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: [ 3.8 ]
python-version: [ 3.8, 3.9 ]
engine: ["NEURON:8.1", "PyNEURON:8.1", "jNeuroML", "jNeuroML_NEURON", "jNeuroML_NetPyNE", "jNeuroML_validate"]


steps:
- uses: actions/checkout@v3

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v3
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}

Expand All @@ -31,6 +31,7 @@ jobs:
pip install scipy sympy matplotlib cython pandas tables
- name: Download selected NEURON models
if: ${{ contains( matrix.engine, 'NEURON' ) }}
run: |
pip install allensdk # for NEURON models
cd CellTypesDatabase/models
Expand Down