Merge pull request #112 from finsberg/code-autolink

Code autolink

Author: finsberg

.github/workflows/build_docs.yml

@@ -18,9 +18,6 @@ jobs:
     container: ghcr.io/fenics/dolfinx/lab:v0.9.0
     env:
       PUBLISH_DIR: ./_build/html
-      DISPLAY: ":99.0"
-      PYVISTA_TRAME_SERVER_PROXY_PREFIX: "/proxy/"
-      PYVISTA_TRAME_SERVER_PROXY_ENABLED: "True"
       PYVISTA_OFF_SCREEN: false
       PYVISTA_JUPYTER_BACKEND: "html"
 
@@ -29,10 +26,13 @@ jobs:
         uses: actions/checkout@v5
 
       - name: Install dependencies for pyvista
-        run: apt-get update && apt-get install -y libgl1-mesa-dev xvfb
+        run: apt-get update && apt-get install -y libxrender1
 
       - name: Install dependencies
-        run: python3 -m pip install ".[docs]"
+        run: |
+          python3 -m pip install -r https://raw.githubusercontent.com/scientificcomputing/scifem/refs/heads/main/build-requirements.txt
+          python3 -m pip install scifem --no-build-isolation
+          python3 -m pip install ".[docs]"
 
       - name: Build docs
         run: jupyter book build -W --keep-going .

.github/workflows/test_package_coverage.yml

@@ -24,13 +24,9 @@ jobs:
     steps:
       - uses: actions/checkout@v5
 
-      - name: Install development version of scifem
-        if : ${{ matrix.container == 'ghcr.io/fenics/dolfinx/dolfinx:nightly' }}
-        run: |
-          python3 -m pip install git+https://github.com/scientificcomputing/scifem.git --no-build-isolation
-
       - name: Install package
         run: |
+          python3 -m pip install -r https://raw.githubusercontent.com/scientificcomputing/scifem/refs/heads/main/build-requirements.txt
           python3 -m pip install scifem --no-build-isolation
           python3 -m pip install .[test]
 

_config.yml

@@ -40,12 +40,29 @@ sphinx:
             - fmt: py
 
     suppress_warnings: ["mystnb.unknown_mime_type", "bibtex.duplicate_citation"]
-    html_js_files:
-      - https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js
+    codeautolink_concat_default: True
+    intersphinx_mapping:
+      basix : ["https://docs.fenicsproject.org/basix/main/python/", null]
+      ffcx : ["https://docs.fenicsproject.org/ffcx/main/", null]
+      ufl : ["https://docs.fenicsproject.org/ufl/main/", null]
+      dolfinx : ["https://docs.fenicsproject.org/dolfinx/main/python", null]
+      petsc4py: ["https://petsc.org/release/petsc4py", null]
+      mpi4py: ["https://mpi4py.readthedocs.io/en/stable", null]
+      numpy: ["https://numpy.org/doc/stable/", null]
+      matplotlib: ["https://matplotlib.org/stable/", null]
+      pyvista: ["https://docs.pyvista.org/", null]
+      packaging: ["https://packaging.pypa.io/en/stable/", null]
+      gotranx: ["https://finsberg.github.io/gotranx/", null]
+      cardiac_geometries: ["https://computationalphysiology.github.io/cardiac-geometriesx/", null]
+
+
   extra_extensions:
   - 'sphinx.ext.autodoc'
   - 'sphinx.ext.napoleon'
   - 'sphinx.ext.viewcode'
   - 'sphinxcontrib.bibtex'
+  - 'sphinx_copybutton'
+  - 'sphinx_codeautolink'
+  - 'sphinx.ext.intersphinx'
 
 exclude_patterns: [".pytest_cache/*", ".github/*", ".tox/*", "third_party/*"]

demo/benchmark/problem1.py

@@ -125,7 +125,6 @@ def dirichlet_bc(
 except ImportError:
     print("Pyvista is not installed")
 else:
-    pyvista.start_xvfb()
     V = dolfinx.fem.functionspace(mesh, ("Lagrange", 1, (mesh.geometry.dim,)))
     uh = dolfinx.fem.Function(V)
     uh.interpolate(problem.u)

demo/benchmark/problem2.py

@@ -155,7 +155,6 @@
 except ImportError:
     print("Pyvista is not installed")
 else:
-    pyvista.start_xvfb()
     V = dolfinx.fem.functionspace(geometry.mesh, ("Lagrange", 1, (geometry.mesh.geometry.dim,)))
     uh = dolfinx.fem.Function(V)
     uh.interpolate(problem.u)

demo/benchmark/problem3.py

@@ -129,7 +129,6 @@
 except ImportError:
     print("Pyvista is not installed")
 else:
-    pyvista.start_xvfb()
     V = dolfinx.fem.functionspace(geometry.mesh, ("Lagrange", 1, (geometry.mesh.geometry.dim,)))
     uh = dolfinx.fem.Function(V)
     uh.interpolate(problem.u)

demo/biv_ellipsoid.py

@@ -127,7 +127,6 @@
 except ImportError:
     print("Pyvista is not installed")
 else:
-    pyvista.start_xvfb()
     V = dolfinx.fem.functionspace(geometry.mesh, ("Lagrange", 1, (geometry.mesh.geometry.dim,)))
     uh = dolfinx.fem.Function(V)
     uh.interpolate(problem.u)

demo/lv_ellipsoid.py

@@ -95,7 +95,6 @@
 except ImportError:
     print("Pyvista is not installed")
 else:
-    pyvista.start_xvfb()
     V = dolfinx.fem.functionspace(geometry.mesh, ("Lagrange", 1, (geometry.mesh.geometry.dim,)))
     uh = dolfinx.fem.Function(V)
     uh.interpolate(problem.u)

demo/time_dependent_land_circ_biv.py

@@ -72,7 +72,7 @@
     material=material,
     active=active_model,
     compressibility=comp_model,
-    viscoelasticity=viscoeleastic_model,
+    # viscoelasticity=viscoeleastic_model,
 )
 
 alpha_epi = pulse.Variable(

demo/unit_cube.py

@@ -122,9 +122,6 @@ def dirichlet_bc(
 except ImportError:
     print("Pyvista is not installed")
 else:
-
-    pyvista.start_xvfb()
-
     # Create plotter and pyvista grid
     p = pyvista.Plotter()