Fix Makie.jl plotting behaviour within script and notebook environments, solves #4

.github/workflows/CI.yml

@@ -13,7 +13,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - name: Add GLMakie/XFVB dependencies
+        run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev libcairo2-dev libfreetype6-dev libffi-dev libjpeg-dev libpng-dev libz-dev
+      - name: Checkout
+        uses: actions/checkout@v4
       - name: Set up Julia
         uses: julia-actions/setup-julia@v1
         with:
@@ -33,11 +36,11 @@ jobs:
           conda activate test
           pip install -e .
 
-      - name: Run tests with coverage
+      - name: Run tests with xvfb
         shell: bash -l {0}
         run: |
           conda activate test
-          pytest --cov=battmo --cov-report=term-missing
+          xvfb-run -s "-screen 0 1024x768x24" pytest --cov=battmo --cov-report=term-missing
 
   release:
     name: Build and publish to PyPI

battmo/api/plotting.py

@@ -1,27 +1,31 @@
 import juliapkg
 from ..julia_import import jl
 import juliacall
+import time
+import asyncio
 
 
 def activate_plotting():
     try:
-        jl.seval("using WGLMakie; WGLMakie.activate!()")
+        jl.seval("using GLMakie; GLMakie.activate!()")
+
     except:
-        print("Unable to load WGLMakie. Have you called install_plotting()?")
+
+        print("Unable to load GLMakie. Have you called install_plotting()?")
 
         return False
     return True
 
 
 def install_plotting():
-    juliapkg.add("WGLMakie", "276b4fcb-3e11-5398-bf8b-a0c2d153d008")
+    juliapkg.add("GLMakie", "e9467ef8-e4e7-5192-8a1a-b1aee30e663a")
     juliapkg.resolve()
     activate_plotting()
     return True
 
 
 def uninstall_plotting():
-    juliapkg.rm("WGLMakie", "276b4fcb-3e11-5398-bf8b-a0c2d153d008")
+    juliapkg.rm("GLMakie", "e9467ef8-e4e7-5192-8a1a-b1aee30e663a")
     juliapkg.resolve()
     return True
 
@@ -30,43 +34,61 @@ def make_interactive():
     juliacall.interactive()
 
 
-def plot_dashboard(output, plot_type="simple"):
+async def keep_plot_dashboard_alive(*arg, **kwargs):
+    fig = jl.plot_dashboard(*arg, **kwargs)
+    while True:
+        jl.seval("yield()")
+        await asyncio.sleep(0.1)
+
+
+def plot_dashboard(*arg, **kwargs):
+
     if activate_plotting():
-        fig = jl.plot_dashboard(output, plot_type=plot_type)
 
-        if plot_type == "line":
-            jl.seval(
-                """
-                    println("Press Ctrl+C to stop plotting interactivity")
-                    while true
-                        sleep(0.1)
-                    end
-                    """
-            )
+        loop = asyncio.get_event_loop()
+
+        if loop.is_running():
+            # Notebook or already running loop
+            loop.create_task(keep_plot_dashboard_alive(*arg, **kwargs))
+        else:
+            # Script or no loop running - start a loop
+            asyncio.run(keep_plot_dashboard_alive(*arg, **kwargs))
 
-        make_interactive()
 
-    return fig
+async def keep_plot_output_alive(*arg, **kwargs):
+    fig = jl.plot_output(*arg, **kwargs)
+    while True:
+        jl.seval("yield()")
+        await asyncio.sleep(0.1)
 
 
 def plot_output(*arg, **kwargs):
     if activate_plotting():
-        fig = jl.plot_output(*arg, **kwargs)
-        make_interactive()
-        jl.seval("display(current_figure())")
-    return fig
+        try:
+            loop = asyncio.get_event_loop()
+            # Notebook or already running loop
+            loop.create_task(keep_plot_output_alive(*arg, **kwargs))
+
+        except RuntimeError:
+            # Script: no loop running, so start one
+            asyncio.run(keep_plot_output_alive(*arg, **kwargs))
+
+
+async def keep_plot_interactive_3d_alive(*arg, **kwargs):
+    fig = jl.plot_interactive_3d(*arg, **kwargs)
+    while True:
+        jl.seval("yield()")
+        await asyncio.sleep(0.1)
 
 
 def plot_interactive_3d(*arg, **kwargs):
     if activate_plotting():
-        fig = jl.plot_interactive_3d(*arg, **kwargs)
-        make_interactive()
-        jl.seval(
-            """
-                println("Press Ctrl+C to stop plotting interactivity")
-                while true
-                    sleep(0.1)
-                end
-                """
-        )
-    return fig
+        try:
+            loop = asyncio.get_event_loop()
+            # Notebook or already running loop
+            loop.create_task(keep_plot_interactive_3d_alive(*arg, **kwargs))
+
+        except RuntimeError:
+
+            # Script: no loop running, so start one
+            asyncio.run(keep_plot_interactive_3d_alive(*arg, **kwargs))

battmo/julia_import.py

@@ -40,9 +40,7 @@
 try:
     jl.seval(
         """
-    using BattMo, 
-    using Jutul:Jutul,get_1d_interpolator 
-    using WGLMakie
+    using BattMo, Jutul
     """
     )
 
@@ -53,12 +51,9 @@
         import Pkg
         Pkg.add("BattMo")
         Pkg.add("Jutul")
-        Pkg.add("WGLMakie")
         Pkg.instantiate()
 
-        using BattMo
-        using Jutul:Jutul,get_1d_interpolator 
-        using WGLMakie
+        using BattMo, Jutul
         """
     )
 

battmo/juliapkg.json

@@ -10,9 +10,9 @@
             "uuid": "2b460a1a-8a2b-45b2-b125-b5c536396eb9",
             "version": "0.4.6"
         },
-        "WGLMakie": {
-            "uuid": "276b4fcb-3e11-5398-bf8b-a0c2d153d008",
-            "version": "0.11.10"
+        "GLMakie": {
+            "uuid": "e9467ef8-e4e7-5192-8a1a-b1aee30e663a",
+            "version": "0.11.11"
         },
         "OpenSSL_jll": {
             "uuid": "458c3c95-2e84-50aa-8efc-19380b2a3a95",

examples/1d_simulation.py

@@ -1,30 +1,41 @@
-# Partial port of https://battmoteam.github.io/BattMo.jl/dev/tutorials/2_run_a_simulation
+# %%
 from battmo import *
 import plotly.express as px
 import pandas as pd
 import numpy as np
+import asyncio
 
+# %%
 # Load parameter sets
 cell_parameters = load_cell_parameters(from_default_set="chen_2020")
 cycling_protocol = load_cycling_protocol(from_default_set="cc_discharge")
 
+# %%
 # Have a quick look into what kind of cell we're dealing with
 quick_cell_check(cell_parameters)
 
+# %%
 # Setup model and simulation
 model = LithiumIonBattery()
 sim = Simulation(model, cell_parameters, cycling_protocol)
 output = solve(sim)
 
+# %%
 # Have a look into which output quantities are available
 print_info(output)
 
+# %%
 # Plot voltage curve
 time_series = output.time_series
 
 df = to_pandas(time_series)
 fig = px.line(df, x="Time", y="Voltage", title="Voltage curve")
 fig.show()
 
+
+# %%
 # Plot a dashboard
 plot_dashboard(output, plot_type="contour")
+
+
+# %%

examples/3d_simulation.py

@@ -1,8 +1,8 @@
-# Partial port of https://battmoteam.github.io/BattMo.jl/dev/tutorials/2_run_a_simulation
+# %%
 from battmo import *
 import plotly.express as px
 
-# Load parameter sets
+# %% Load parameter sets
 cell_parameters = load_cell_parameters(from_default_set="chen_2020")
 cycling_protocol = load_cycling_protocol(from_default_set="cc_discharge")
 model_settings = load_model_settings(from_default_set="p4d_cylindrical")
@@ -13,10 +13,12 @@
 cell_parameters["PositiveElectrode"]["CurrentCollector"]["TabWidth"] = 0.002
 simulation_settings["AngularGridPoints"] = 8
 
-# Setup model and simulation
+# %% Setup model and simulation
 model = LithiumIonBattery(model_settings=model_settings)
 sim = Simulation(model, cell_parameters, cycling_protocol, simulation_settings=simulation_settings)
 output = solve(sim)
 
-# Plot interative 3D results
+# %% Plot interative 3D results
 plot_interactive_3d(output)
+
+# %%