Merge branch 'main' into spherical_shell

trixi-framework · Aug 7, 2024 · 31ec7a8 · 31ec7a8
2 parents a969339 + 7746a79
commit 31ec7a8
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diff --git a/.github/workflows/Invalidations.yml b/.github/workflows/Invalidations.yml
@@ -16,7 +16,7 @@ jobs:
     if: github.base_ref == github.event.repository.default_branch
     runs-on: ubuntu-latest
     steps:
-    - uses: julia-actions/setup-julia@v1
+    - uses: julia-actions/setup-julia@v2
       with:
         version: '1'
     - uses: actions/checkout@v4

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -47,25 +47,25 @@ jobs:
             arch: x64
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
         env:
           PYTHON: ""
       - uses: julia-actions/julia-runtest@v1
         env:
           PYTHON: ""
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: coverallsapp/github-action@master
+      - uses: coverallsapp/github-action@v2
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           flag-name: run-${{ matrix.version }}-${{ matrix.os }}-${{ matrix.arch }}
           parallel: true
           path-to-lcov: ./lcov.info
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: success() || failure() # upload artifacts even if tests have failed
         with:
           name: test-output-files-${{ matrix.version }}-${{ matrix.os }}-${{ matrix.arch }}
@@ -77,7 +77,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Coveralls Finished
-      uses: coverallsapp/github-action@master
+      uses: coverallsapp/github-action@v2
       with:
         github-token: ${{ secrets.GITHUB_TOKEN }}
         parallel-finished: true
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Trixi2Vtk"
 uuid = "bc1476a1-1ca6-4cc3-950b-c312b255ff95"
 authors = ["Michael Schlottke-Lakemper <[email protected]>", "Hendrik Ranocha <[email protected]>"]
-version = "0.3.13-pre"
+version = "0.3.17-DEV"
 
 [deps]
 Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
@@ -18,6 +18,6 @@ HDF5 = "0.14, 0.15, 0.16, 0.17"
 ProgressMeter = "1.3"
 StaticArrays = "0.12, 1.0"
 TimerOutputs = "0.5"
-Trixi = "0.5, 0.6"
+Trixi = "0.5, 0.6, 0.7, 0.8"
 WriteVTK = "1.7"
 julia = "1.7"
diff --git a/SECURITY.md b/SECURITY.md
@@ -0,0 +1,30 @@
+# Security Policy
+
+The Trixi.jl development team takes security issues seriously. We appreciate
+all efforts to responsibly disclose any security issues and will make every
+effort to acknowledge contributions.
+
+
+## Supported Versions
+
+The current stable release following the interpretation of
+[semantic versioning (SemVer)](https://julialang.github.io/Pkg.jl/dev/compatibility/#Version-specifier-format-1)
+used in the Julia ecosystem is supported with security updates.
+
+
+## Reporting a Vulnerability
+
+To report a security issue, please use the GitHub Security Advisory
+["Report a Vulnerability"](https://github.com/trixi-framework/Trixi2Vtk.jl/security/advisories/new)
+tab.
+
+We will send a response indicating the next steps in handling your report.
+After the initial reply to your report, we will keep you informed of the
+progress towards a fix and full announcement, and may ask for additional
+information or guidance.
+
+Please report security bugs in third-party modules directly to the person
+or team maintaining the module.
+
+Public notifications of vulnerabilities will be shared in community channels
+such as Slack.
diff --git a/test/Project.toml b/test/Project.toml
@@ -2,12 +2,14 @@
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 ReadVTK = "dc215faf-f008-4882-a9f7-a79a826fadc3"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Trixi = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
+UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [compat]
 Documenter = "0.27, 1"
 OrdinaryDiffEq = "6"
 ReadVTK = "0.1, 0.2"
-Trixi = "0.5, 0.6"
+Trixi = "0.5, 0.6, 0.7, 0.8"
diff --git a/test/test_2d.jl b/test/test_2d.jl
@@ -22,8 +22,8 @@ end
 
     @timed_testset "mesh data" begin
       # create the output file to be tested
-      @test_nowarn trixi2vtk(joinpath(outdir, "mesh_000010.h5"), output_directory=outdir)
-      outfilename = "mesh_000010_celldata.vtu"
+      @test_nowarn trixi2vtk(joinpath(outdir, "mesh_" * LEADING_ZEROS * "000010.h5"), output_directory=outdir)
+      outfilename = "mesh_" * LEADING_ZEROS * "000010_celldata.vtu"
       out_file = joinpath(outdir, outfilename)
 
       # save output file to `artifacts` to facilitate debugging of failing tests
@@ -38,8 +38,8 @@ end
 
     @timed_testset "solution celldata" begin
       # create the output file to be tested
-      @test_nowarn trixi2vtk(joinpath(outdir, "solution_000010.h5"), output_directory=outdir)
-      outfilename = "solution_000010_celldata.vtu"
+      @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000010.h5"), output_directory=outdir)
+      outfilename = "solution_" * LEADING_ZEROS * "000010_celldata.vtu"
       out_file = joinpath(outdir, outfilename)
 
       # save output file to `artifacts` to facilitate debugging of failing tests
@@ -54,8 +54,8 @@ end
 
     @timed_testset "reinterpolate with nonuniform data with VTU format" begin
       # Create and test output with reinterpolation (default options: `reinterpolate=true, data_is_uniform=false`)
-      @test_nowarn trixi2vtk(joinpath(outdir, "solution_000010.h5"), output_directory=outdir)
-      outfilename = "solution_000010.vtu"
+      @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000010.h5"), output_directory=outdir)
+      outfilename = "solution_" * LEADING_ZEROS * "000010.vtu"
       out_file = joinpath(outdir, outfilename)
 
       # save output file to `artifacts` to facilitate debugging of failing tests
@@ -70,8 +70,8 @@ end
 
     @timed_testset "reinterpolate with nonuniform data with VTI format" begin
       # Create and test output with reinterpolation (default options: `reinterpolate=true, data_is_uniform=false`)
-      @test_nowarn trixi2vtk(joinpath(outdir, "solution_000010.h5"), output_directory=outdir, format=:vti)
-      outfilename = "solution_000010.vti"
+      @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000010.h5"), output_directory=outdir, format=:vti)
+      outfilename = "solution_" * LEADING_ZEROS * "000010.vti"
       out_file = joinpath(outdir, outfilename)
 
       # save output file to `artifacts` to facilitate debugging of failing tests
@@ -86,8 +86,8 @@ end
 
     @timed_testset "do not reinterpolate with nonuniform data" begin
       # Create and test output without reinterpolation on LGL nodes
-      @test_nowarn trixi2vtk(joinpath(outdir, "solution_000010.h5"), output_directory=outdir, reinterpolate=false)
-      outfilename = "solution_000010.vtu"
+      @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000010.h5"), output_directory=outdir, reinterpolate=false)
+      outfilename = "solution_" * LEADING_ZEROS * "000010.vtu"
       out_file = joinpath(outdir, outfilename)
 
       # save output file to `artifacts` to facilitate debugging of failing tests
@@ -103,8 +103,8 @@ end
     @timed_testset "do not reinterpolate with uniform data" begin
       # Create and test output without reinterpolation on uniform nodes
       # OBS! This is a dummy test just to exercise code. The resulting plot will look weird.
-      @test_nowarn trixi2vtk(joinpath(outdir, "solution_000010.h5"), output_directory=outdir, reinterpolate=false, data_is_uniform=true)
-      outfilename = "solution_000010.vtu"
+      @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000010.h5"), output_directory=outdir, reinterpolate=false, data_is_uniform=true)
+      outfilename = "solution_" * LEADING_ZEROS * "000010.vtu"
       out_file = joinpath(outdir, outfilename)
 
       # save output file to `artifacts` to facilitate debugging of failing tests
@@ -120,7 +120,7 @@ end
     @timed_testset "attempt reinterpolate with uniform data" begin
       # Purposely request a bad configuration and check that an error message gets thrown
       # OBS! Only needs tested once across all mesh types and dimensions
-      @test_throws ArgumentError trixi2vtk(joinpath(outdir, "solution_000010.h5"), output_directory=outdir, data_is_uniform=true)
+      @test_throws ArgumentError trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000010.h5"), output_directory=outdir, data_is_uniform=true)
     end
   end
 
@@ -154,7 +154,7 @@ end
         #      that only needs to be tested once.
         @test_nowarn trixi2vtk(joinpath(outdir, "solution_00000*.h5"), output_directory=outdir)
 
-        outfilename = "solution_000001_celldata.vtu"
+        outfilename = "solution_" * LEADING_ZEROS * "000001_celldata.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests
@@ -169,8 +169,8 @@ end
 
       @timed_testset "reinterpolate with nonuniform data" begin
         # Create and test output with reinterpolation (default options: `reinterpolate=true, data_is_uniform=false`)
-        @test_nowarn trixi2vtk(joinpath(outdir, "solution_000001.h5"), output_directory=outdir)
-        outfilename = "solution_000001.vtu"
+        @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000001.h5"), output_directory=outdir)
+        outfilename = "solution_" * LEADING_ZEROS * "000001.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests
@@ -185,8 +185,8 @@ end
 
       @timed_testset "do not reinterpolate with nonuniform data" begin
         # Create and test output without reinterpolation on LGL nodes
-        @test_nowarn trixi2vtk(joinpath(outdir, "solution_000001.h5"), output_directory=outdir, reinterpolate=false)
-        outfilename = "solution_000001.vtu"
+        @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000001.h5"), output_directory=outdir, reinterpolate=false)
+        outfilename = "solution_" * LEADING_ZEROS * "000001.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests
@@ -202,8 +202,8 @@ end
       @timed_testset "do not reinterpolate with uniform data" begin
         # Create and test output without reinterpolation on uniform nodes
         # OBS! This is a dummy test just to exercise code. The resulting plot will look weird.
-        @test_nowarn trixi2vtk(joinpath(outdir, "solution_000001.h5"), output_directory=outdir, reinterpolate=false, data_is_uniform=true)
-        outfilename = "solution_000001.vtu"
+        @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000001.h5"), output_directory=outdir, reinterpolate=false, data_is_uniform=true)
+        outfilename = "solution_" * LEADING_ZEROS * "000001.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests
@@ -219,7 +219,7 @@ end
       @timed_testset "attempt VTI format on unsupported mesh type" begin
         # Purposely request a bad configuration and check that an error message gets thrown
         # OBS! Only needs tested once across all mesh types and dimensions
-        @test_throws ArgumentError trixi2vtk(joinpath(outdir, "solution_000001.h5"), output_directory=outdir, format=:vti)
+        @test_throws ArgumentError trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000001.h5"), output_directory=outdir, format=:vti)
       end
     end
 
@@ -245,8 +245,8 @@ end
 
       @timed_testset "solution celldata" begin
         # create the output file to be tested
-        @test_nowarn trixi2vtk(joinpath(outdir, "solution_000001.h5"), output_directory=outdir)
-        outfilename = "solution_000001_celldata.vtu"
+        @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000001.h5"), output_directory=outdir)
+        outfilename = "solution_" * LEADING_ZEROS * "000001_celldata.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests
@@ -261,8 +261,8 @@ end
 
       @timed_testset "reinterpolate with nonuniform data" begin
         # Create and test output with reinterpolation (default options: `reinterpolate=true, data_is_uniform=false`)
-        @test_nowarn trixi2vtk(joinpath(outdir, "solution_000001.h5"), output_directory=outdir)
-        outfilename = "solution_000001.vtu"
+        @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000001.h5"), output_directory=outdir)
+        outfilename = "solution_" * LEADING_ZEROS * "000001.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests
@@ -277,8 +277,8 @@ end
 
       @timed_testset "do not reinterpolate with nonuniform data" begin
         # Create and test output without reinterpolation on LGL nodes
-        @test_nowarn trixi2vtk(joinpath(outdir, "solution_000001.h5"), output_directory=outdir, reinterpolate=false)
-        outfilename = "solution_000001.vtu"
+        @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000001.h5"), output_directory=outdir, reinterpolate=false)
+        outfilename = "solution_" * LEADING_ZEROS * "000001.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests
@@ -294,8 +294,8 @@ end
       @timed_testset "do not reinterpolate with uniform data" begin
         # Create and test output without reinterpolation on uniform nodes
         # OBS! This is a dummy test just to exercise code. The resulting plot will look weird.
-        @test_nowarn trixi2vtk(joinpath(outdir, "solution_000001.h5"), output_directory=outdir, reinterpolate=false, data_is_uniform=true)
-        outfilename = "solution_000001.vtu"
+        @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000001.h5"), output_directory=outdir, reinterpolate=false, data_is_uniform=true)
+        outfilename = "solution_" * LEADING_ZEROS * "000001.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests
@@ -315,8 +315,8 @@ end
 
       @timed_testset "mesh data" begin
         # create the output file to be tested
-        @test_nowarn trixi2vtk(joinpath(outdir, "mesh_000005.h5"), output_directory=outdir)
-        outfilename = "mesh_000005_celldata.vtu"
+        @test_nowarn trixi2vtk(joinpath(outdir, "mesh_" * LEADING_ZEROS * "000005.h5"), output_directory=outdir)
+        outfilename = "mesh_" * LEADING_ZEROS * "000005_celldata.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests
@@ -331,8 +331,8 @@ end
 
       @timed_testset "solution celldata" begin
         # create the output file to be tested
-        @test_nowarn trixi2vtk(joinpath(outdir, "solution_000005.h5"), output_directory=outdir)
-        outfilename = "solution_000005_celldata.vtu"
+        @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000005.h5"), output_directory=outdir)
+        outfilename = "solution_" * LEADING_ZEROS * "000005_celldata.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests
@@ -347,8 +347,8 @@ end
 
       @timed_testset "reinterpolate with nonuniform data" begin
         # Create and test output with reinterpolation (default options: `reinterpolate=true, data_is_uniform=false`)
-        @test_nowarn trixi2vtk(joinpath(outdir, "solution_000005.h5"), output_directory=outdir)
-        outfilename = "solution_000005.vtu"
+        @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000005.h5"), output_directory=outdir)
+        outfilename = "solution_" * LEADING_ZEROS * "000005.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests
@@ -363,8 +363,8 @@ end
 
       @timed_testset "do not reinterpolate with nonuniform data" begin
         # Create and test output without reinterpolation on LGL nodes
-        @test_nowarn trixi2vtk(joinpath(outdir, "solution_000005.h5"), output_directory=outdir, reinterpolate=false)
-        outfilename = "solution_000005.vtu"
+        @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000005.h5"), output_directory=outdir, reinterpolate=false)
+        outfilename = "solution_" * LEADING_ZEROS * "000005.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests
@@ -380,8 +380,8 @@ end
       @timed_testset "do not reinterpolate with uniform data" begin
         # Create and test output without reinterpolation on uniform nodes
         # OBS! This is a dummy test just to exercise code. The resulting plot will look weird.
-        @test_nowarn trixi2vtk(joinpath(outdir, "solution_000005.h5"), output_directory=outdir, reinterpolate=false, data_is_uniform=true)
-        outfilename = "solution_000005.vtu"
+        @test_nowarn trixi2vtk(joinpath(outdir, "solution_" * LEADING_ZEROS * "000005.h5"), output_directory=outdir, reinterpolate=false, data_is_uniform=true)
+        outfilename = "solution_" * LEADING_ZEROS * "000005.vtu"
         out_file = joinpath(outdir, outfilename)
 
         # save output file to `artifacts` to facilitate debugging of failing tests