Add workflow for reproducing results and update results due to changes in the underlying ldrb package

Author: finsberg

.github/workflows/reproduce_results.yml

@@ -0,0 +1,56 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Reproduce results
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+
+    # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+  workflow_call:
+
+
+jobs:
+  run:
+    runs-on: ubuntu-22.04
+    container:
+      image: ghcr.io/scientificcomputing/fenics-gmsh:2023-08-16
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Cache
+        id: cache
+        uses: actions/cache@v3
+        with:
+          path: |
+            ~/.cache/pip
+          key: cache_v1
+          restore-keys: |
+            cache_v1
+
+      - name: Install dependencies
+        run: python3 -m pip install -r requirements.txt
+
+      - name: Download data
+        run: cd data && bash download_data.sh && cd ..
+
+      - name: Run pre-processing
+        run: cd code && python3 pre_processing.py && cd ..
+
+      - name: Run simulation
+        run: cd code && python3 run_fiber_generation.py && cd ..
+
+      - name: Postprocess
+        run: cd code && python3 postprocess.py && cd ..
+
+      - name: Upload artifact
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          path: |
+            ./data/mesh
+            ./code/results
+          if-no-files-found: error

code/postprocess.py

@@ -64,7 +64,7 @@ def check_results(features_path: Path, features: dict):
     # Check each (key, value) pair in the features and check they are
     # within machine precision
     for key in expected_features.keys():
-        if not np.isclose(expected_features[key], features[key]):
+        if not np.isclose(expected_features[key], features[key], rtol=1e-8):
             logger.error(f"{key}: {expected_features[key]}!={features[key]}")
             reproducible = False
 

code/results/features_01.json

@@ -1,7 +1,7 @@
 {
   "size": 4713,
-  "min": -0.9986740049294516,
-  "max": 0.9997579018328593,
-  "mean": 0.08134810142530069,
-  "std": 0.5715906050031196
+  "min": -0.9989439046376276,
+  "max": 0.9997658401474652,
+  "mean": -0.001603664479271975,
+  "std": 0.5773480419933641
 }

code/results/features_02.json

@@ -1,7 +1,7 @@
 {
   "size": 139263,
-  "min": -0.9999307486841351,
-  "max": 0.99999840073201,
-  "mean": 0.05442689976746109,
-  "std": 0.5747791279396253
+  "min": -0.9999985280667274,
+  "max": 0.9999988537980897,
+  "mean": -0.07252592808131289,
+  "std": 0.57277685148967
 }

data/download_data.sh

@@ -1,5 +1,6 @@
 #!/usr/bin/env bash
 
 # Removing the dl=0 from the end of the shared link from dropbox
-curl -L https://www.dropbox.com/s/6bkbw6v269dyfie/data.tar -o data.tar
+# curl -L https://www.dropbox.com/s/6bkbw6v269dyfie/data.tar -o data.tar
+wget https://www.dropbox.com/s/6bkbw6v269dyfie/data.tar
 tar -xvf data.tar