improve jupyter notebook

virtualcell · May 2, 2024 · 1ffe58e · 1ffe58e
1 parent 15e24d1
commit 1ffe58e
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Showing 6 changed files with 2,827 additions and 178 deletions.
diff --git a/.gitignore b/.gitignore
@@ -246,3 +246,5 @@ 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/
diff --git a/pythonData/example.ipynb b/pythonData/example.ipynb
diff --git a/pythonData/example_vcell_ui.png b/pythonData/example_vcell_ui.png
diff --git a/pythonData/poetry.lock b/pythonData/poetry.lock
diff --git a/pythonData/pyproject.toml b/pythonData/pyproject.toml
@@ -12,6 +12,8 @@ python = "^3.11"
 typer = "^0.9.0"
 numexpr = "^2.9.0"
 zarr = "^2.17.0"
+jupyter = "^1.0.0"
+matplotlib = "^3.8.3"
 
 
 [tool.poetry.group.dev.dependencies]

diff --git a/pythonData/tests/vcell_parsing_test.py b/pythonData/tests/vcell_parsing_test.py
@@ -51,7 +51,6 @@ def test_parse_vcelldata():
             data = pde_dataset.get_data(v.var_name, t)
             if data.size > 0 and v == "cytosol::RanC_cyt":
                 print(f"v={v}, t={t}, shape={data.shape}, min={np.min(data)}, max={np.max(data)}")
-    print("done")
 
 
 def test_function_parse():