To v1.1.0; Update to jnml v0.12.3 jar

Generate pngs of tests in same dirs
NeuroML · Sep 19, 2023 · e4c7963 · e4c7963
1 parent 86fab33
commit e4c7963
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Showing 8 changed files with 33 additions and 24 deletions.
diff --git a/.gitignore b/.gitignore
@@ -157,3 +157,10 @@ arm64
 /examples/plot.py
 /tests/utils/test_rotation.net.nml
 /tests/utils/test_rotation.net.png
+/tests/analysis/test_analysis_if.png
+/tests/analysis/test_analysis_iv.png
+/tests/analysis/test_analysis_traces.png
+/tests/analysis/test_cell_analysis.cell.nml
+/tests/plot/test_schematic_plot_2d_test_cell_nml_xy.png
+/tests/plot/test_schematic_plot_2d_test_cell_nml_xz.png
+/tests/plot/test_schematic_plot_2d_test_cell_nml_yz.png
diff --git a/pyneuroml/__init__.py b/pyneuroml/__init__.py
@@ -8,7 +8,7 @@
     __version__ = importlib_metadata.version("pyNeuroML")
 
 
-JNEUROML_VERSION = "0.12.2"
+JNEUROML_VERSION = "0.12.3"
 
 # Define a logger for the package
 logging.basicConfig(

diff --git a/pyneuroml/lib/jNeuroML-0.12.3-jar-with-dependencies.jar b/pyneuroml/lib/jNeuroML-0.12.3-jar-with-dependencies.jar
diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = pyNeuroML
-version = 1.0.10
+version = 1.1.0
 author = Padraig Gleeson
 author_email = [email protected]
 url = https://github.com/NeuroML/pyNeuroML

diff --git a/test-ghactions.sh b/test-ghactions.sh
@@ -6,9 +6,11 @@ echo
 echo "################################################"
 echo "##   Running unit tests"
 
+
 # skip a few tests that segfault etc. on GH
 pytest --cov=pyneuroml -m "not localonly" .
 
+
 run_neuron_examples=false
 
 if [[ ($# -eq 1) && ($1 == '-neuron') ]]; then
@@ -106,7 +108,7 @@ echo
 echo "################################################"
 echo "##   Test export to PovRay"
 
- pynml-povray NML2_SingleCompHHCell.nml
+pynml-povray NML2_SingleCompHHCell.nml
 
 
 # Requires pyelectro, not in .travis.yml yet...

diff --git a/tests/analysis/test_cell_analysis.py b/tests/analysis/test_cell_analysis.py
@@ -38,16 +38,16 @@ def test_cell_analysis(self):
             c="-50.0mV",
             d="100pA",
         )
-        neuroml.writers.NeuroMLWriter.write(doc, "test_cell_analysis.cell.nml")
-        generate_current_vs_frequency_curve("test_cell_analysis.cell.nml",
+        neuroml.writers.NeuroMLWriter.write(doc, "tests/analysis/test_cell_analysis.cell.nml")
+        generate_current_vs_frequency_curve("tests/analysis/test_cell_analysis.cell.nml",
                                             "izh2007RS0",
                                             plot_voltage_traces=True,
                                             plot_iv=True,
                                             show_plot_already=False,
-                                            save_voltage_traces_to="test_analysis_traces.png",
-                                            save_if_figure_to="test_analysis_if.png",
-                                            save_iv_figure_to="test_analysis_iv.png"
+                                            save_voltage_traces_to="tests/analysis/test_analysis_traces.png",
+                                            save_if_figure_to="tests/analysis/test_analysis_if.png",
+                                            save_iv_figure_to="tests/analysis/test_analysis_iv.png"
                                             )
-        self.assertTrue(pathlib.Path("test_analysis_traces.png").is_file())
-        self.assertTrue(pathlib.Path("test_analysis_if.png").is_file())
-        self.assertTrue(pathlib.Path("test_analysis_iv.png").is_file())
+        self.assertTrue(pathlib.Path("tests/analysis/test_analysis_traces.png").is_file())
+        self.assertTrue(pathlib.Path("tests/analysis/test_analysis_if.png").is_file())
+        self.assertTrue(pathlib.Path("tests/analysis/test_analysis_iv.png").is_file())
diff --git a/tests/plot/test_morphology_plot.py b/tests/plot/test_morphology_plot.py
@@ -45,7 +45,7 @@ def test_2d_point_plotter(self):
         for nml_file in nml_files:
             ofile = pl.Path(nml_file).name
             for plane in ["xy", "yz", "xz"]:
-                filename = f"test_morphology_plot_2d_point_{ofile.replace('.', '_', 100)}_{plane}.png"
+                filename = f"tests/plot/test_morphology_plot_2d_point_{ofile.replace('.', '_', 100)}_{plane}.png"
                 # remove the file first
                 try:
                     pl.Path(filename).unlink()
@@ -70,7 +70,7 @@ def test_2d_plotter(self):
         for nml_file in nml_files:
             ofile = pl.Path(nml_file).name
             for plane in ["xy", "yz", "xz"]:
-                filename = f"test_morphology_plot_2d_{ofile.replace('.', '_', 100)}_{plane}.png"
+                filename = f"tests/plot/test_morphology_plot_2d_{ofile.replace('.', '_', 100)}_{plane}.png"
                 # remove the file first
                 try:
                     pl.Path(filename).unlink()
@@ -90,7 +90,7 @@ def test_2d_morphology_plotter_data_overlay(self):
             cell = nml_doc.cells[0]  # type: neuroml.Cell
             ofile = pl.Path(nml_file).name
             plane = "xy"
-            filename = f"test_morphology_plot_2d_{ofile.replace('.', '_', 100)}_{plane}_with_data.png"
+            filename = f"tests/plot/test_morphology_plot_2d_{ofile.replace('.', '_', 100)}_{plane}_with_data.png"
             # remove the file first
             try:
                 pl.Path(filename).unlink()
@@ -121,7 +121,7 @@ def test_2d_plotter_network(self):
         ofile = pl.Path(nml_file).name
         for plane in ["xy", "yz", "xz"]:
             filename = (
-                f"test_morphology_plot_2d_{ofile.replace('.', '_', 100)}_{plane}.png"
+                f"tests/plot/test_morphology_plot_2d_{ofile.replace('.', '_', 100)}_{plane}.png"
             )
             # remove the file first
             try:
@@ -139,7 +139,7 @@ def test_2d_constant_plotter_network(self):
         nml_file = "tests/plot/L23-example/TestNetwork.net.nml"
         ofile = pl.Path(nml_file).name
         for plane in ["xy", "yz", "xz"]:
-            filename = f"test_morphology_plot_2d_{ofile.replace('.', '_', 100)}_{plane}_constant.png"
+            filename = f"tests/plot/test_morphology_plot_2d_{ofile.replace('.', '_', 100)}_{plane}_constant.png"
             # remove the file first
             try:
                 pl.Path(filename).unlink()
@@ -162,7 +162,7 @@ def test_2d_schematic_plotter_network(self):
         nml_file = "tests/plot/L23-example/TestNetwork.net.nml"
         ofile = pl.Path(nml_file).name
         for plane in ["xy", "yz", "xz"]:
-            filename = f"test_morphology_plot_2d_{ofile.replace('.', '_', 100)}_{plane}_schematic.png"
+            filename = f"tests/plot/test_morphology_plot_2d_{ofile.replace('.', '_', 100)}_{plane}_schematic.png"
             # remove the file first
             try:
                 pl.Path(filename).unlink()
@@ -221,7 +221,7 @@ def test_3d_plotter_plotly(self):
         nml_files = ["tests/plot/Cell_497232312.cell.nml", "tests/plot/test.cell.nml"]
         for nml_file in nml_files:
             ofile = pl.Path(nml_file).name
-            filename = f"test_morphology_plot_3d_{ofile.replace('.', '_', 100)}.png"
+            filename = f"tests/plot/test_morphology_plot_3d_{ofile.replace('.', '_', 100)}.png"
             # remove the file first
             try:
                 pl.Path(filename).unlink()
@@ -249,7 +249,7 @@ def test_2d_schematic_plotter(self):
         for plane in ["xy", "yz", "xz"]:
             # olm cell
             filename = (
-                f"test_schematic_plot_2d_{olm_ofile.replace('.', '_', 100)}_{plane}.png"
+                f"tests/plot/test_schematic_plot_2d_{olm_ofile.replace('.', '_', 100)}_{plane}.png"
             )
             try:
                 pl.Path(filename).unlink()
@@ -266,7 +266,7 @@ def test_2d_schematic_plotter(self):
 
             # more complex cell
             filename = (
-                f"test_schematic_plot_2d_{ofile.replace('.', '_', 100)}_{plane}.png"
+                f"tests/plot/test_schematic_plot_2d_{ofile.replace('.', '_', 100)}_{plane}.png"
             )
             # remove the file first
             try:
@@ -295,7 +295,7 @@ def test_plot_segment_groups_curtain_plots(self):
         ofile = pl.Path(nml_file).name
 
         # more complex cell
-        filename = f"test_curtain_plot_2d_{ofile.replace('.', '_', 100)}.png"
+        filename = f"tests/plot/test_curtain_plot_2d_{ofile.replace('.', '_', 100)}.png"
         # remove the file first
         try:
             pl.Path(filename).unlink()
@@ -325,7 +325,7 @@ def test_plot_segment_groups_curtain_plots_with_data(self):
         ofile = pl.Path(nml_file).name
 
         # more complex cell
-        filename = f"test_curtain_plot_2d_{ofile.replace('.', '_', 100)}_withdata.png"
+        filename = f"tests/plot/test_curtain_plot_2d_{ofile.replace('.', '_', 100)}_withdata.png"
         # remove the file first
         try:
             pl.Path(filename).unlink()

diff --git a/tests/plot/test_plot.py b/tests/plot/test_plot.py
@@ -24,7 +24,7 @@ class TestPlot(BaseTestCase):
 
     def test_generate_plot(self):
         """Test generate_plot function."""
-        filename = "test_generate_plot.png"
+        filename = "tests/plot/test_generate_plot.png"
 
         # remove the file first
         try:
@@ -56,7 +56,7 @@ def test_generate_plot(self):
 
     def test_generate_interactive_plot(self):
         """Test generate_interactive_plot function."""
-        filename = "test_generate_interactive_plot.png"
+        filename = "tests/plot/test_generate_interactive_plot.png"
 
         # remove the file first
         try: