diff --git a/.github/workflows/nrn-modeldb-ci.yaml b/.github/workflows/nrn-modeldb-ci.yaml index 0b0a83c..053245a 100644 --- a/.github/workflows/nrn-modeldb-ci.yaml +++ b/.github/workflows/nrn-modeldb-ci.yaml @@ -98,6 +98,7 @@ jobs: - uses: actions/setup-python@v4 with: python-version: 3.9 + - name: Set models to run for PR run: | # For PRs we only have a few models for quick sanity checking. @@ -112,7 +113,9 @@ jobs: # 146030 -> curate_patterns # 244679 -> no entry in modeldb-run.yaml # rest: -> currently yielding differences in the pipeline - echo 'MODELS_TO_RUN=64195 22203 156120 51781 97868 22203 97756 97917 105507 136803 138379 138382 146030 244679 251881' >> $GITHUB_ENV + #echo 'MODELS_TO_RUN=64195 22203 156120 51781 97868 22203 97756 97917 105507 136803 138379 138382 146030 244679 251881' >> $GITHUB_ENV + #TODO - temporary run added python models + echo 'MODELS_TO_RUN=156039 194897 226422 186768 189922 195615 139421 144586 244412 39948 195569 249404 206400 144511 229276 151282 264834 151685' >> $GITHUB_ENV if: github.event_name == 'pull_request' && inputs.repo == '' - name: Install dependencies and project @@ -141,7 +144,7 @@ jobs: - name: Get ModelDB models if: steps.cache-models.outputs.cache-hit != 'true' run: getmodels - + - name: Run Models with NEURON V1 -> ${{ env.NEURON_V1 }} run: | # Install NEURON V1 diff --git a/modeldb/modeldb-run.yaml b/modeldb/modeldb-run.yaml index de34678..705bc9f 100644 --- a/modeldb/modeldb-run.yaml +++ b/modeldb/modeldb-run.yaml @@ -1181,12 +1181,115 @@ - verify_graph_() model_dir: mod_files # python models +# find * -name mosinit.py +156039: + python: true + run: + - import os; os.system("python mosinit.py"); quit(); + script: + - sed -i 's/h.tstop = 2500/h.tstop = 1500/g' mosinit.py # reduce sim time +194897: + python: true + run: + - import os; os.system("python main.py"); quit(); + script: + #reduce sim time (need to reduce more) + - sed -i "s/s.trainTime =/s.trainTime = 50#/g" network.py + - sed -i "s/testTime =/testTime = 50#/g" shared.py + - sed -i "s/tstop=mytstop=htmax=/tstop=mytstop=htmax= 50\/\//g" msarm.hoc +226422: + python: true + run: + - import os; os.system("python mosinit.py"); quit(); + script: + - sed -i 's/pyplot.show()/pyplot.show(block=False);pyplot.pause(1);pyplot.close();quit()/' MAT_Neuron_StepCurrent.py +186768: + python: true + run: + - import os; os.system("python mosinit.py"); quit(); + script: + - sed -i 's/tstop =/tstop = 100#/g' mosinit.py 189922: python: true run: - import os; os.system("python mosinit.py"); quit(); script: - - 2to3 -w . + - sed -i 's/plt.show()/plt.show(block=False);plt.pause(1);plt.close();quit()/' clay_mohit.py +195615: + python: true + run: + - import os; os.system("python sim.py PTcell.cfg"); quit(); + script: + - sed -i "s/baset = /baset = 2900.0#/g;s/tstop = 3000.0/tstop = 1000.0/g" PTcell.cfg # reduce sim time +139421: + python: true + run: + - import os; os.system("python mosinit.py"); quit(); + script: + - sed -i -e 's/tstop = /tstop = 10#/g' mosinit.py +144586: + python: true + run: + - import os; os.system("python mosinit.py"); quit(); + script: + - sed -i 's/nq = anet.randruns(/nq = anet.randruns(1000)#/g' mosinit.py +244412: + python: true + model_dir: mod_files + run: + - import os; os.system("python mosinit.py"); quit(); +39948: + python: true + run: + - import os; os.system("python mosinit.py"); quit(); +195569: + python: true + run: + - import os; os.system("python mosinit.py"); quit(); + script: + - sed -i 's/plt.show()/plt.show(block=False);plt.pause(1);plt.close()/g' fig2a_show.py +249404: + python: true + run: + - import os; os.system("python mosinit.py"); quit(); +206400: + python: true + run: + - import os; os.system("python mosinit.py"); quit(); + script: + - sed -i 's/pyl.show()/pyl.show(block=False);pyl.pause(1);pyl.close()/g' model.py +# find * -name run.py +144511: + python: true + run: + - import os; os.system("python run.py"); quit(); +229276: + model_dir: mechanisms + script: + - sed -i -e 's/tstop=/tstop=100\/\//g' createsimulation.hoc +151282: + python: true + model_dir: . + run: + - import os; os.system("python sim.py 1 1 100"); quit(); + script: + - sed -i 's/show()/show(block=False);pause(1);close()/g' sim.py +264834: + python: true + model_dir: mechanisms + run: + - import os; os.system("python run.py --plot trace"); quit(); + script: + # reduce sim time + - sed -i 's/,180)/,10)/g;s/,500)/,10)/g' run.py +151685: + python: true + model_dir: mod + run: + - import os; os.system("python run.py param/gamma_L5weak_L2weak.param"); quit(); + script: + - sed -i 's/from mpi4py/#from mpi4py/g' run.py + - sed -i "s/nrn.tstop =/nrn.tstop = 50#/g" run.py - sed -i'.bak' -e 's/plt.show()/plt.show(block=False);plt.pause(1);plt.close();quit()/' clay_mohit.py 251881: model_dir: mechanisms diff --git a/setup.py b/setup.py index 37ff596..1f3acc8 100644 --- a/setup.py +++ b/setup.py @@ -16,7 +16,7 @@ 'ipython', 'matplotlib', 'scipy', - '2to3', + 'h5py' ] with open('README.md', 'r', encoding='utf-8') as f: