Merge branch 'master' of github.com:gridap/Gridap.jl into conforming-…

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gridap · Nov 8, 2024 · 273e52d · 273e52d
2 parents c442b98 + 06de5f7
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"
diff --git a/.github/workflows/Documenter.yml b/.github/workflows/Documenter.yml
@@ -0,0 +1,25 @@
+name: Documentation
+
+on: [push, pull_request]
+
+# Cancel redundant CI tests automatically
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1.10'
+      - uses: julia-actions/cache@v2
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
+        run: julia --project=docs/ docs/make.jl
diff --git a/.github/workflows/Downgrade.yml b/.github/workflows/Downgrade.yml
@@ -0,0 +1,37 @@
+name: Downgrade
+
+on: [pull_request, workflow_dispatch]
+
+# Cancel redundant CI tests automatically
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  downgrade:
+    name: Downgrade ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.8' # Needs to be lowest supported version
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)'
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-downgrade-compat@v1
+        with: # As per documentation, we exclude packages within the Julia standard library
+          skip: LinearAlgebra,SparseArrays,Random,Statistics,Test
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        with:
+          coverage: false
diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
@@ -0,0 +1,61 @@
+name: Benchmarks
+
+on:
+  workflow_dispatch:
+    inputs:
+      target:
+        description: 'Target branch'
+        required: true
+        type: string
+      base:
+        description: 'Base branch'
+        required: true
+        default: 'master'
+        type: string
+
+jobs:
+  benchmark:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os:
+          - ubuntu-latest
+        version:
+          - '1.10'
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+        with:
+            fetch-depth: 0
+      - run: |
+          git fetch --tags
+          git branch --create-reflog main origin/main
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v4
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - name: Install Gridap in main environment
+        run: julia -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Install dependencies
+        run: julia --project=benchmark/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Run benchmarks
+        run: julia --project=benchmark/ --color=yes benchmark/run_benchmarks.jl
+        env:
+          BM_BASE: ${{ github.event.inputs.base }}
+          BM_TARGET: ${{ github.event.inputs.target }}
+      - uses: actions/upload-artifact@v4
+        with:
+          name: benchmarks
+          path: benchmark/benchmark_results.md
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,97 +1,76 @@
 name: CI
-on: [push, pull_request]
+
+on: [push, pull_request, workflow_dispatch]
+
+# Cancel redundant CI tests automatically
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
-  test:
+  test: # Main CI tests
     name: Tests ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
-      matrix:
+      matrix: # Main tests for linux
         version:
           - '1.8'
+          - '1.9'
+          - '1.10'
         os:
           - ubuntu-latest
         arch:
           - x64
+        include: # Test macos/windows on latest LTS + x86 on ubuntu
+          - version: '1.10'
+            os: macos-latest
+            arch: aarch64
+          - version: '1.10'
+            os: windows-latest
+            arch: x64
+          - version: '1.10'
+            os: ubuntu-latest
+            arch: x86
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
+          verbose: true
           token: ${{ secrets.CODECOV_TOKEN }}
-          
+
   drivers:
     name: Drivers ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         version:
-          - '1.8'
+          - '1.10'
         os:
           - ubuntu-latest
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - run: |
           julia --color=yes --project=. --check-bounds=yes --depwarn=error -e '
             using Pkg; Pkg.instantiate()'
       - run: |
           julia --color=yes --project=. --check-bounds=yes --depwarn=error -e '
-            (1,) .== 1; include("test/GridapTests/runtests.jl")'
-
-  docs:
-    name: Documentation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: '1.8'
-      - run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()'
-#      - run: |
-#          julia --project=docs -e '
-#            using Documenter: doctest
-#            using Gridap
-#            doctest(Gridap)'
-      - run: julia --project=docs docs/make.jl
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+            include("test/GridapTests/runtests.jl")'
diff --git a/.github/workflows/ci_x86.yml b/.github/workflows/ci_x86.yml
diff --git a/NEWS.md b/NEWS.md
@@ -5,13 +5,26 @@ 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]
+## [0.18.7] - 2024-10-8
 
 ### Added
 
 - Added MacroFElements. These are defined as having the basis/dof-basis of a FESpace created on top of a RefinementRule. Since PR[#1024](https://github.com/gridap/Gridap.jl/pull/1024).
 - Added Barycentric refinement rule in 2D and 3D. Added Simplexify refinement rule. Since PR[#1024](https://github.com/gridap/Gridap.jl/pull/1024).
 - Added names to vector and tensor components in VTK exports, to avoid Paraview's automatic (sometimes wrong) guesses. See `TensorValues.indep_components_names`. Since PR[#1038](https://github.com/gridap/Gridap.jl/pull/1038).
+- Misc improvements of the `TensorValues` module:  See `TensorValues.indep_components_names`. Since PR[#1040](https://github.com/gridap/Gridap.jl/pull/1040).
+  - Documented all symbols exported by the module
+  - Improved and added test for some API function of `MultiValue` (general `diag` of 2nd order tensors, fixed `convert` of 3rd order tensors to SArray, avoid unwanted fallback of `num_components` on `MultiValue` types with undefined dimensions, more autodiff tests, better `double_contraction` API (prevent invalid operation giving indexing errors and enable valid operations)).
+  - Added a clear separation between the physical components access (`getindex`, `num_components`) and the numerical access to the stored independent components (`num_indep_components`, `indep_comp_getindex`) to enable using symmetric tensor types as unknown in FE Spaces.
+  - Implemented automatic differentiation `gradient` and `laplacian` for second order tensor, and `divergence` for third order tensors.
+  - Added `AbstractSymTensorValue`, an abstract type for second order symmetric tensors, and `SymTracelessTensorValue` (aliased to `QTensorValue`), a type for traceless symmetric tensors. `SymTensorValue` is now subtype of `AbstractSymTensorValue`.
+  - A convergence test for Poisson problem of `QTensorValue` unknown field validates the implementation.
+- Added support for benchmarking, through `PkgBenchmark.jl`. Since PR[#1039](https://github.com/gridap/Gridap.jl/pull/1039).
+- Added code quality tests, through `Aqua.jl`. Since PR[#1039](https://github.com/gridap/Gridap.jl/pull/1039).
+
+### Fixed
+
+- Fixed constructor of RungeKutta with only one solver. Since PR[#999](https://github.com/gridap/Gridap.jl/pull/999).
 
 ### Changed
 

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Gridap"
 uuid = "56d4f2e9-7ea1-5844-9cf6-b9c51ca7ce8e"
 authors = ["Santiago Badia <[email protected]>", "Francesc Verdugo <[email protected]>", "Alberto F. Martin <[email protected]>"]
-version = "0.18.6"
+version = "0.18.7"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
@@ -33,30 +33,37 @@ WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 
 [compat]
 AbstractTrees = "0.3.3, 0.4"
-BSON = "0.2.5, 0.3"
-BlockArrays = "0.12.12, 0.13, 0.14, 0.15, 0.16"
-Combinatorics = "1.0.0"
+Aqua = "0.8"
+BSON = "0.3.4"
+BlockArrays = "1"
+Combinatorics = "1"
 DataStructures = "0.18.13"
 DocStringExtensions = "0.8.1, 0.9"
-FastGaussQuadrature = "0.4.2, 1"
-FileIO = "1.2.2, 1.3, 1.4"
-FillArrays = "0.8.4, 0.9, 0.10, 0.11, 0.12, 0.13, 1"
-ForwardDiff = "0.10.10"
-JLD2 = "0.1.11, 0.3, 0.4, 0.5"
-JSON = "0.21.0"
+FastGaussQuadrature = "0.4.5, 1"
+FileIO = "1.5"
+FillArrays = "1.11"
+ForwardDiff = "0.10.14"
+JLD2 = "0.5"
+JSON = "0.21"
 LineSearches = "7.0.1"
-NLsolve = "4.3.0"
+LinearAlgebra = "1"
+NLsolve = "4.5.1"
 NearestNeighbors = "0.4.8"
-PolynomialBases = "0.4.12"
+PolynomialBases = "0.4.13"
 Preferences = "1.4"
-QuadGK = "2.3.1, 2.4"
+QuadGK = "2.4"
+Random = "1"
+SparseArrays = "1"
 SparseMatricesCSR = "0.6.4"
-StaticArrays = "0.12.1, 1.0"
-WriteVTK = "1.12.0"
-julia = "1.3"
+StaticArrays = "1.4"
+Statistics = "1"
+Test = "1"
+WriteVTK = "1.21.1"
+julia = "1.6"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["Aqua", "Test"]