Merge pull request #1162 from virtualcell/1161-simularium-zarr

save finite volume simulation results as zarr

.github/workflows/CI-full.yml

@@ -81,6 +81,12 @@ jobs:
         poetry install
         poetry run python -m pytest
 
+    - name: build vcelldata package
+      run: |
+        cd pythonData
+        poetry install
+        poetry run python -m pytest
+
     - name: setup java 17 with maven cache
       uses: actions/setup-java@v3
       with:

.github/workflows/NightlyBMDB_CLI.yml

@@ -73,6 +73,12 @@ jobs:
           poetry install
           poetry run python -m pytest
 
+      - name: build vcelldata package
+        run: |
+          cd pythonData
+          poetry install
+          poetry run python -m pytest
+
       - name: Setup Java for Build
         uses: actions/setup-java@v2
         with:

.github/workflows/ci_cd.yml

@@ -65,6 +65,12 @@ jobs:
           poetry install
           poetry run python -m pytest
 
+      - name: build vcelldata package
+        run: |
+          cd pythonData
+          poetry install
+          poetry run python -m pytest
+
       - name: setup java 17 with maven cache
         uses: actions/setup-java@v3
         with:
@@ -148,6 +154,12 @@ jobs:
           poetry install
           poetry run python -m pytest
 
+      - name: build vcelldata package
+        run: |
+          cd pythonData
+          poetry install
+          poetry run python -m pytest
+
       - name: setup java 17 with maven cache
         uses: actions/setup-java@v3
         with:
@@ -225,6 +237,12 @@ jobs:
           poetry install
           poetry run python -m pytest
 
+      - name: build vcelldata package
+        run: |
+          cd pythonData
+          poetry install
+          poetry run python -m pytest
+
       - name: setup java 17 with maven cache
         uses: actions/setup-java@v3
         with:

.github/workflows/nightly-model-testing.yml

@@ -74,6 +74,12 @@ jobs:
           poetry install
           poetry run python -m pytest
 
+      - name: build vcelldata package
+        run: |
+          cd pythonData
+          poetry install
+          poetry run python -m pytest
+
       - name: setup java 17 with maven cache
         uses: actions/setup-java@v3
         with:

.gitignore

@@ -236,3 +236,15 @@ webapp-ng/.nx/
 localsolvers/mac64/GNUSparseFile.0/
 
 webapp-ng/.nvmrc
+
+pythonData/test_data/SimID_946368938_0__0.simtask.xml
+pythonData/test_data/SimID_946368938_0_.functions
+pythonData/test_data/SimID_946368938_0_.fvinput
+pythonData/test_data/SimID_946368938_0_.hdf5
+pythonData/test_data/SimID_946368938_0_.mesh
+pythonData/test_data/SimID_946368938_0_.meshmetrics
+pythonData/test_data/SimID_946368938_0_.subdomains
+pythonData/test_data/SimID_946368938_0_.vcg
+pythonData/test_data/SimID_946368938_mathmodel.vcml
+
+pythonData/test_data/zarr/

pythonData/README.md

@@ -0,0 +1 @@
+readme ... coming soon