chore(ci,example): add examples to ci

Author: Casale Benjamin

.github/workflows/examples.yml

@@ -0,0 +1,55 @@
+name: Run Examples (after tests)
+
+on:
+  workflow_run:
+    workflows: ["Rust Test"]
+    types:
+      - completed
+
+jobs:
+  run_example:
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y cmake libhdf5-dev
+
+      - name: Install Rust
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          profile: minimal
+          override: true
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.7.11"
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Run examples
+        run: |
+          cargo run --release --example rust
+          cargo run --release --example rust_hist
+          uv run examples/python/example_python.py
+
+      - name: Archive output files
+        run: |
+          mkdir -p artefact
+          find examples/ -type f \( -name "*.svg" -o -name "*.png" -o -name "*.html" \) -exec cp --parents {} artefact/ \;
+          tar -cvf artefact.tar -C artefact .
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: example-artefact
+          path: artefact.tar

.github/workflows/rust_test.yml

@@ -1,10 +1,11 @@
 name: rust_test
 
 on:
+  workflow_call: {} 
   push:
     branches:
       - main
-      - test_ci
+      - "0.5"
     tags:
       - '*'
   pull_request:

.gitignore

@@ -72,3 +72,7 @@ docs/_build/
 
 # Pyenv
 .python-version
+
+*.htmlcov
+*.svg
+*.png

biomc_pp/main.py

@@ -4,7 +4,7 @@
 
 import timeit
 def test():
-    pp = biomc_pp.PostProcess("cstr","/home/benjamin/Documents/code/cpp/BioCMA-MCST/results/")
+    pp = biomc_pp.PostProcess("example0d","examples/")
     return pp.get_number_particle()
 
 def main():
@@ -14,7 +14,7 @@ def main():
     # c =results.get_spatial_average_concentration(0,biomc_pp.Phase.Liquid)
     # ctt =results.get_time_average_concentration(0,0,biomc_pp.Phase.Liquid)
 
-    pp = biomc_pp.PostProcess("test","/home_pers/casale/Documents/code/biomc/results/")
+    pp = biomc_pp.PostProcess("example0d","examples/")
 
     p = pp.get_growth_in_number()
 
@@ -53,5 +53,3 @@ def calculate_mean2():
 
 
 
-
-main()

examples/python/example_python.py

@@ -9,7 +9,7 @@
     X = pp.get_biomass_concentration()
     plt.plot(time,X)
     plt.title("Biomass concentration")
-    plt.savefig("./examples/out_py.png")
+    plt.savefig("./examples/out_python_2.png")
 
 
     n,c= pp.get_histogram(50,pp.n_export - 1, "nu_eff_2")
@@ -25,4 +25,4 @@
         alpha=0.7,
         color="blue",
     )
-    plt.show()
+    plt.savefig("./examples/out_python.png")