Add scripts for running sensitivity analysis

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/build_docs.yml

@@ -0,0 +1,36 @@
+name: Build documentation
+
+on:
+  pull_request:
+    branches: [main]
+  workflow_call:
+  workflow_dispatch:
+
+env:
+  DEB_PYTHON_INSTALL_LAYOUT: deb_system
+  DISPLAY: ":99.0"
+
+jobs:
+
+  build:
+    runs-on: ubuntu-22.04
+    container: ghcr.io/scientificcomputing/fenics-gmsh:2023-02-20
+    env:
+      PUBLISH_DIR: ./docs/_build/html
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install ".[docs, gui]"
+
+      - name: Build docs
+        run: make docs
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ${{ env.PUBLISH_DIR }}

.github/workflows/convergence-test.yml

@@ -0,0 +1,71 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Run convergence test
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - "!*"
+    tags:
+      - "v*"
+
+
+jobs:
+  job_1:
+    name: run convergence tests
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        dx: [0.1, 0.2, 0.4]
+        dt: [0.05]
+        include:
+          - dt: 0.025
+            dx: 0.2
+          - dt: 0.1
+            dx: 0.2
+
+
+    container:
+      image: ghcr.io/scientificcomputing/fenics-gmsh:2023-02-20
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install -e "."
+
+      - name: Run benchmark with dx = ${{ matrix.dx }} and dt = ${{ matrix.dt }}
+        run: python3 -m simcardems.benchmark run convergence_test --dt=${{ matrix.dt }} --dx=${{ matrix.dx }} --sha=${{ github.sha }}
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: "results-${{ matrix.dx }}-${{ matrix.dt }}"
+          path: convergence_test/results_dx*.json
+
+  job_2:
+    name: Download repost and upload to gist
+    needs: job_1
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/download-artifact@v4
+        with:
+          path: convergence_test
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: python3 -m pip install requests
+
+      - name: Print files
+        run: python3 scripts/upload-data.py convergence_test --token=${{ secrets.CONV_TOKEN }}

.github/workflows/deploy_docs.yml

@@ -0,0 +1,41 @@
+name: Publish documentation
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+
+  build:
+    uses: ./.github/workflows/build_docs.yml
+
+  deploy:
+    needs: build
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/docker-image.yml

@@ -25,29 +25,29 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@369eb591f429131d6889c46b94e711f089e6ca96
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: true

.github/workflows/main.yml

@@ -10,11 +10,11 @@ jobs:
       image: ghcr.io/scientificcomputing/fenics-gmsh:2023-02-20
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Cache
         id: cache-primes
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: |
             ~/.cache/instant
@@ -34,12 +34,18 @@ jobs:
         run: |
           python3 -m pytest
 
-      - name: Coverage report
-        uses: codecov/codecov-action@v3
-        if: github.ref == 'refs/heads/main'
+      - name: Extract Coverage
+        run: |
+          python3 -m coverage report | sed 's/^/    /' >> $GITHUB_STEP_SUMMARY
+          python3 -m coverage json
+          export TOTAL=$(python3 -c "import json;print(json.load(open('coverage.json'))['totals']['percent_covered_display'])")
+          echo "total=$TOTAL" >> $GITHUB_ENV
+
+      - name: Upload HTML report.
+        uses: actions/upload-artifact@v4
         with:
-          fail_ci_if_error: true
-          files: ./coverage.xml
+          name: html-report
+          path: htmlcov
 
       - name: Install pypa/build
         run: >-

.pre-commit-config.yaml

@@ -25,11 +25,6 @@ repos:
     hooks:
       - id: flake8
 
-  - repo: https://github.com/asottile/add-trailing-comma
-    rev: v2.4.0
-    hooks:
-      - id: add-trailing-comma
-
   - repo: https://github.com/asottile/setup-cfg-fmt
     rev: v2.2.0
     hooks:

demos/stiffness_sensitivity.py

@@ -0,0 +1,76 @@
+# # Simple demo
+#
+# In this demo we show the most simple usage of the `simcardems` library using the python API.
+#
+# Import the necessary libraries
+#
+
+from pathlib import Path
+import simcardems
+import matplotlib.pyplot as plt
+import numpy as np
+
+here = Path(__file__).absolute().parent
+geometry_path = here / "geometries/slab.h5"
+geometry_schema_path = here / "geometries/slab.json"
+
+
+def run(outdir: Path, a: float = 2.28):
+    outdir.mkdir(exist_ok=True, parents=True)
+    results_file = outdir.joinpath("results.h5")
+    if results_file.exists():
+        values = np.load(outdir.joinpath("values.npy"), allow_pickle=True).item()
+
+        t = values["time"]
+        lmbda = values["mechanics"]["lambda"]
+        return t, lmbda
+    config = simcardems.Config(
+        outdir=outdir,
+        geometry_path=geometry_path,
+        geometry_schema_path=geometry_schema_path,
+        coupling_type="fully_coupled_ORdmm_Land",
+        T=1000,
+        material_parameter_a=a,
+    )
+    runner = simcardems.Runner(config)
+    runner.solve(T=config.T, save_freq=config.save_freq, show_progress_bar=True)
+
+    loader = simcardems.datacollector.DataLoader(results_file)
+    values = simcardems.postprocess.extract_traces(loader, reduction="center")
+    np.save(outdir.joinpath("values.npy"), values)
+
+    t = values["time"]
+    lmbda = values["mechanics"]["lambda"]
+    fig, ax = plt.subplots()
+    ax.plot(t, lmbda)
+    ax.set_xlabel("Time [ms]")
+    ax.set_ylabel("Lambda")
+    ax.set_title(f"Material parameter a = {a}")
+    fig.savefig(outdir.joinpath(f"lambda_{a}.png"))
+
+    return t, lmbda
+    # simcardems.postprocess.plot_state_traces(outdir.joinpath("results.h5"), "center")
+
+
+def main():
+    outdir = here / "results_stiffness_sensitivity"
+    fig, ax = plt.subplots()
+    a_default = 2.28
+    for a in [
+        a_default / 4.0,
+        a_default / 2.0,
+        a_default,
+        a_default * 2.0,
+        a_default * 4.0,
+    ]:
+        t, lmbda = run(outdir=outdir / f"a_{a}", a=a)
+        ax.plot(t, lmbda, label=f"a = {a}")
+    ax.legend()
+    ax.set_xlabel("Time [ms]")
+    ax.set_ylabel("Lambda")
+    ax.set_title("Stiffness sensitivity")
+    fig.savefig(outdir / "stiffness_sensitivity.png")
+
+
+if __name__ == "__main__":
+    main()