Merge https://github.com/Ferrite-FEM/Ferrite.jl

Author: kreutzheidephil

.git-blame-ignore-revs

@@ -1,2 +1,4 @@
 # `pre-commit run --all-files` (https://github.com/Ferrite-FEM/Ferrite.jl/pull/928)
 68e1ab15bea4618f76b9ed1d850e2ce33375e266
+# Apply Runic.jl formatting (https://github.com/Ferrite-FEM/Ferrite.jl/pull/1096)
+c50ce06f2261398ecfe6da4578e50baff88cf563

.github/workflows/Check.yml

@@ -10,14 +10,30 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
+        env:
+          # Skip runic-pre-commit since we use runic-action below instead
+          SKIP: runic
+
+  runic:
+    name: "Runic"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1.11'
+      - uses: julia-actions/cache@v2
+      - uses: fredrikekre/runic-action@v1
+        with:
+          version: "1.4" # Keep version in sync with .pre-commit-config.yaml
 
   explicit-imports:
     runs-on: ubuntu-latest
     name: "ExplicitImports.jl"
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       # - uses: julia-actions/setup-julia@v2
       #   with:
       #     version: '1'

.github/workflows/Documentation.yml

@@ -6,14 +6,14 @@ on:
     tags: ['*']
 jobs:
   docs:
-    name: Julia 1.11 - ubuntu-latest
+    name: Julia 1.12 - ubuntu-latest
     runs-on: ubuntu-latest
     timeout-minutes: 60
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: julia-actions/setup-julia@v2
         with:
-          version: '1.11'
+          version: '1.12'
       - uses: julia-actions/cache@v2
       - name: Install dependencies
         run: julia --project=docs -e 'using Pkg; Pkg.instantiate(); Pkg.precompile()'

.github/workflows/Downstream.yml

@@ -26,16 +26,17 @@ jobs:
           # - {user: 'Ferrite-FEM', repo: 'FerriteDistributed.jl'} # Requires more efforts to be updated to 1.0
           - {user: 'Ferrite-FEM', repo: 'FerriteGmsh.jl'}
           - {user: 'Ferrite-FEM', repo: 'FerriteMeshParser.jl'}
+          - {user: 'Ferrite-FEM', repo: 'FerriteInterfaceElements.jl'}
           # - {user: 'Ferrite-FEM', repo: 'FerriteViz.jl'} # Requires release
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.julia-version }}
       - uses: julia-actions/cache@v2
       # - uses: julia-actions/julia-buildpkg@v1
       - name: Clone Downstream
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: ${{ matrix.package.user }}/${{ matrix.package.repo }}
           path: downstream

.github/workflows/SpellCheck.yml

@@ -0,0 +1,13 @@
+name: Spell Check
+
+on: [pull_request]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v6
+      - name: Check spelling
+        uses: crate-ci/typos@v1.44.0

.github/workflows/Test.yml

@@ -9,18 +9,18 @@ jobs:
     name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     timeout-minutes: 40
-    continue-on-error: ${{ matrix.julia-version == 'nightly' }}
+    continue-on-error: ${{ matrix.julia-version == 'pre' }}
     strategy:
       matrix:
-        julia-version: ['1.10', '1', 'nightly']
+        julia-version: ['lts', '1', 'pre']
         os: ['ubuntu-latest']
         include:
           - os: windows-latest
             julia-version: '1'
           - os: macOS-latest
             julia-version: '1'
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.julia-version }}
@@ -34,12 +34,14 @@ jobs:
           Pkg.add("JET")
           Pkg.develop(path = pwd())
           include(joinpath(pwd(), "test/jet.jl"))
-        if: ${{ matrix.os == 'ubuntu-latest' && matrix.julia-version != 'nightly' }}
+        if: ${{ matrix.os == 'ubuntu-latest' && matrix.julia-version != 'pre' }}
       - uses: julia-actions/julia-processcoverage@v1
         with:
           directories: 'src,ext'
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
-          file: lcov.info
+          files: lcov.info
+          plugins: noop
+          disable_search: true
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -13,6 +13,7 @@ docs/src/examples/
 docs/src/tutorials/
 docs/src/howto/
 docs/src/gallery/
+docs/src/topics/downloaded_assets/
 docs/src/changelog.md
 *.DS_Store
 /Manifest.toml

.pre-commit-config.yaml

@@ -1,11 +1,17 @@
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+  - repo: 'https://github.com/pre-commit/pre-commit-hooks'
+    rev: v5.0.0
     hooks:
-     - id: check-added-large-files
-     - id: check-case-conflict
-     - id: check-toml
-     - id: check-yaml
-     - id: end-of-file-fixer
-     - id: mixed-line-ending
-     - id: trailing-whitespace
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+  - repo: 'https://github.com/fredrikekre/runic-pre-commit'
+    rev: v2.0.1
+    hooks:
+      - id: runic
+        additional_dependencies:
+          - 'Runic@1.4' # Keep version in sync with .github/workflows/Check.yml

.typos.toml

@@ -0,0 +1,21 @@
+[files]
+extend-exclude = ["*.svg", "*.toml"]
+
+[default.extend-words]
+ue = "ue"
+ba = "ba"
+nd = "nd"
+
+[type.qrtables]
+extend-glob = ["**/gaussquad_*_table.jl", "**/generate_quadrature.jl"]
+
+[type.qrtables.extend-words]
+Methode = "Methode"
+Numer = "Numer"
+Secrest = "Secrest"
+
+[type.feintro]
+extend-glob = ["**/fe_intro.md"]
+
+[type.feintro.extend-words]
+Strang = "Strang"

CHANGELOG.md

@@ -5,16 +5,76 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [Next] - xxxx-xx-xx
+
+## [v1.3.0] - 2026-01-09
+
+### Added
+ - New function `Ferrite.write_facetset` for exporting facet sets to VTK. ([#1132], [#1259])
+
+### Documentation
+ - Fix errors in incompressible elasticity tutorial. ([#1251])
+ - Add utility for downloading meshes (and other assets) for tutorials. ([#1037])
+
+## [v1.2.0] - 2025-11-14
+
+### Added
+ - Support for directly assembling to `SparseMatrixCSR` (from `SparseMatricesCSR.jl`). ([#864])
+ - Enhance `generate_grid` to support outputting line meshes embedded in two and three
+   spatial dimensions. ([#1122], [#1214])
+
+### Fixes
+ - Fix L2 projection of tensor fields on discontinuous interpolations. ([#1197], [#1198])
+ - Fix VTK output of tensor data in embedded domains. ([#1212], [#1213])
+ - Fix VTK nodal output for discontinuous output. ([#1194])
+ - Fix `facetskeleton` for mixed grids. ([#1223])
+ - Fix normal vector computation for boundary integration in embedded domains. ([#1226],
+   [#1235])
+ - Relax vector input type from `Vector` to `AbstractVector` in `evaluate_at_points!`.
+   ([#1183])
+- The result of grid coloring is now not dependent on iteration order of dictionaries and sets. This may change the coloring obtained from `create_coloring`
+  compared to previous Ferrite versions.
+
+### Documentation updates
+ - Extended assembly docs with information on how to support direct assembly into new matrix
+   types. ([#864])
+ - Add a list of research papers where Ferrite was used for simulations. Please add
+   your paper! ([#1221])
+ - Add section on global and local DoF numbering. ([#1089])
+ - Fix some typos and grammar ([#1210], [#1224], [#1228])
+
+## [v1.1.0] - 2025-05-01
+
+### Added
+ - New vector interpolations for H(div) and H(curl) spaces (`Nedelec`, `RaviartThomas`,
+   `BrezziDouglasMarini`). ([#1045],[#1162])
+ - New boundary condition type, `ProjectedDirichlet`, for H(div) and H(curl) interpolations. ([#1151])
+   It can be added to a constraint handler the same way as for a regular `Dirichlet`.
+ - Support for exporting discontinuous fields to VTK. ([#867])
+   This happens automatically when a DofHandler with a discontinuous field is used
+   to construct the `VTKGridFile`, but can be requested with the `write_discontinuous`
+   keyword argument.
+
+### Fixes
+ - `addboundaryfacetset` has been fixed for mixed grids. ([#1176])
+ -  `evaluate_at_grid_nodes` now respects the precision of the input dof vector. ([#1044])
 
 ### Removed
- - The deprecated third type parameter for interpolations have been removed. Old code which
-   tries to use three parameters will now throw the somewhat cryptic error:
+ - The deprecated third type parameter for interpolations has been removed. ([#1083])
+   Old code which tries to use three parameters will now throw the somewhat cryptic error:
    ```
    julia> Lagrange{2, RefCube, 1}()
    ERROR: too many parameters for type
    ```
-   ([#1083])
+
+### Documentation updates
+ - A comparison between different assembly strategies have been added to the docs. ([#1063])
+ - The affine constraints docs have been extended. ([#1146])
+
+### Other
+ - Ferrite now uses [Runic.jl](https://github.com/fredrikekre/Runic.jl) for code formatting.
+   ([#1096])
+ - Ferrite now supports `ForwardDiff` v1. ([#1178])
 
 ## [v1.0.0] - 2024-09-30
 
@@ -149,7 +209,7 @@ more discussion).
   - ip_function = Lagrange{2, RefTetrahedron, 2}()
   - ip_geometry = Lagrange{2, RefTetrahedron, 1}()
   - cv = CellScalarValues(qr, ip_function, ip_geometry)
-  + ip_function = Lagrange{2, RefTetrahedron, 2}()
+  + ip_function = Lagrange{RefTriangle, 2}()
   + cv = CellValues(qr, ip_function)
   ```
   and if you have quadratic (or higher order) elements in the grid you must now pass the
@@ -158,8 +218,8 @@ more discussion).
   qr = QuadratureRule(...)
   - ip_function = Lagrange{2, RefTetrahedron, 2}()
   - cv = CellScalarValues(qr, ip_function)
-  + ip_function = Lagrange{2, RefTetrahedron, 2}()
-  + ip_geometry = Lagrange{2, RefTetrahedron, 1}()
+  + ip_function = Lagrange{RefTriangle, 2}()
+  + ip_geometry = Lagrange{RefTriangle, 1}()
   + cv = CellValues(qr, ip_function, ip_geometry)
   ```
 
@@ -627,7 +687,7 @@ poking into Ferrite internals:
  - Fix grid coloring for cell sets with 0 or 1 cells. ([#600])
 ### Other improvements
  - Documentation improvements:
-    - Simplications and clarifications to hyperelasticity example. ([#591])
+    - Simplifications and clarifications to hyperelasticity example. ([#591])
     - Remove duplicate docstring entry for `vtk_point_data`. ([#602])
     - Update documentation about initial conditions. ([#601], [#604])
 
@@ -843,6 +903,8 @@ poking into Ferrite internals:
 [v0.3.13]: https://github.com/Ferrite-FEM/Ferrite.jl/releases/tag/v0.3.13
 [v0.3.14]: https://github.com/Ferrite-FEM/Ferrite.jl/releases/tag/v0.3.14
 [v1.0.0]: https://github.com/Ferrite-FEM/Ferrite.jl/releases/tag/v1.0.0
+[v1.1.0]: https://github.com/Ferrite-FEM/Ferrite.jl/releases/tag/v1.1.0
+[v1.2.0]: https://github.com/Ferrite-FEM/Ferrite.jl/releases/tag/v1.2.0
 [#352]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/352
 [#363]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/363
 [#378]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/378
@@ -1015,6 +1077,8 @@ poking into Ferrite internals:
 [#779]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/779
 [#835]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/835
 [#855]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/855
+[#864]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/864
+[#867]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/867
 [#880]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/880
 [#888]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/888
 [#914]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/914
@@ -1024,6 +1088,31 @@ poking into Ferrite internals:
 [#949]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/949
 [#953]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/953
 [#974]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/974
+[#1044]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1044
+[#1045]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1045
 [#1058]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1058
 [#1059]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1059
+[#1063]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1063
 [#1083]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1083
+[#1089]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1089
+[#1096]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1096
+[#1122]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1122
+[#1146]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1146
+[#1151]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1151
+[#1162]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1162
+[#1176]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1176
+[#1178]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1178
+[#1183]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1183
+[#1194]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1194
+[#1197]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1197
+[#1198]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1198
+[#1210]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1210
+[#1212]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1212
+[#1213]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1213
+[#1214]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1214
+[#1221]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1221
+[#1223]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1223
+[#1224]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1224
+[#1226]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1226
+[#1228]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1228
+[#1235]: https://github.com/Ferrite-FEM/Ferrite.jl/issues/1235