From 7e2d7eba07e1113d8072675548e0c4461c270658 Mon Sep 17 00:00:00 2001 From: hrani Date: Thu, 14 Mar 2024 17:43:39 +0530 Subject: [PATCH 1/5] fixed bug, nonContainerSet need to pass path, passing id --- simWrapMoose.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/simWrapMoose.py b/simWrapMoose.py index 634f848..b0be89b 100644 --- a/simWrapMoose.py +++ b/simWrapMoose.py @@ -302,7 +302,7 @@ def subsetItems( self, modelSubset ): doomed.update( dropSet ) else: indirectContainers.extend( getContainerTree(elm, kinpath)) - nonContainerSet.add( elm ) + nonContainerSet.add( elm.path ) #nonContainers.append( elm ) #print( 'isNotContainer' ) From 165717f585c2cad872a610f726cb011782dcd69d Mon Sep 17 00:00:00 2001 From: HarshaRani Date: Thu, 14 Mar 2024 17:50:52 +0530 Subject: [PATCH 2/5] Update findsim.yml Check for other version of python --- .github/workflows/findsim.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/findsim.yml b/.github/workflows/findsim.yml index 0ec8a34..0ae2284 100644 --- a/.github/workflows/findsim.yml +++ b/.github/workflows/findsim.yml @@ -21,7 +21,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [3.7] + python-version: [3.7,3.8,3.9,'3.10',3.11,3.12] # Steps represent a sequence of tasks that will be executed as part of the job steps: From 871fd9eb6dafdf64473f1b62589418f54246f5c7 Mon Sep 17 00:00:00 2001 From: HarshaRani Date: Thu, 14 Mar 2024 23:20:47 +0530 Subject: [PATCH 3/5] Update findsim.yml removed python-tk --- .github/workflows/findsim.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/findsim.yml b/.github/workflows/findsim.yml index 0ae2284..9baf8db 100644 --- a/.github/workflows/findsim.yml +++ b/.github/workflows/findsim.yml @@ -36,7 +36,7 @@ jobs: - name: Install dependencies run: | export DEBIAN_FRONTEND=noninteractive - sudo -E apt install python3-tk python-tk + sudo -E apt install python3-tk python -m pip install numpy matplotlib --user # Runs a set of commands using the runners shell - name: Build From 61736ee8869d026715cbcf6d9bc270bd8880a2a2 Mon Sep 17 00:00:00 2001 From: HarshaRani Date: Fri, 22 Mar 2024 16:46:36 +0530 Subject: [PATCH 4/5] Update findsim.yml setting up to install moose-core from git to get the latest version --- .github/workflows/findsim.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/findsim.yml b/.github/workflows/findsim.yml index 9baf8db..a759b3b 100644 --- a/.github/workflows/findsim.yml +++ b/.github/workflows/findsim.yml @@ -41,7 +41,7 @@ jobs: # Runs a set of commands using the runners shell - name: Build run: | - python -m pip install pymoose --pre --upgrade + python -m pip install git+https://github.com/BhallaLab/moose-core.git python -m pip install jsonschema - name: Test scripts run: ./test.sh From a3a61025137771ee0c38aced25c3dc6ae7d71151 Mon Sep 17 00:00:00 2001 From: HarshaRani Date: Fri, 22 Mar 2024 17:21:03 +0530 Subject: [PATCH 5/5] Update test.sh added solver --- test.sh | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test.sh b/test.sh index da3d8a8..581a2fd 100755 --- a/test.sh +++ b/test.sh @@ -6,7 +6,7 @@ set -x # virtualenv does not require --user PYTHON=$(which python) -$PYTHON findSim.py ./Curated/Jain2009_Fig3F.json --model models/synSynth7.g --map models/synSynth7_map.json -$PYTHON findSim.py ./Curated/Bhalla1999_Fig2B.json --model models/synSynth7.g --map models/synSynth7_map.json -$PYTHON findSim.py ./Curated/Gu2004_fig3B.json --model models/synSynth7.g --map models/synSynth7_map.json -$PYTHON findSim.py ./Curated/Bhalla1999_Fig4C.json --model models/synSynth7.g --map models/synSynth7_map.json +$PYTHON findSim.py ./Curated/Jain2009_Fig3F.json --model models/synSynth7.g --map models/synSynth7_map.json --solver LSODA +$PYTHON findSim.py ./Curated/Bhalla1999_Fig2B.json --model models/synSynth7.g --map models/synSynth7_map.json --solver LSODA +$PYTHON findSim.py ./Curated/Gu2004_fig3B.json --model models/synSynth7.g --map models/synSynth7_map.json --solver LSODA +$PYTHON findSim.py ./Curated/Bhalla1999_Fig4C.json --model models/synSynth7.g --map models/synSynth7_map.json --solver LSODA