Merge branch 'main' into dependabot/github_actions/codecov/codecov-ac…

…tion-4
SKopecz · Mar 23, 2024 · f8549b8 · f8549b8
2 parents 0dd398c + 8edf2e2
commit f8549b8
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Showing 12 changed files with 259 additions and 54 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -59,7 +59,7 @@ jobs:
       - shell: bash
         run: |
           cp ./lcov.info ./lcov-${{ matrix.version }}-${{ github.run_id }}.info
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: lcov-${{ matrix.version }}-${{ github.run_id }}
           path: ./lcov-${{ matrix.version }}-${{ github.run_id }}.info
@@ -82,7 +82,7 @@ jobs:
       # At first, we check out the repository and download all artifacts
       # (and list files for debugging).
       - uses: actions/checkout@v4
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
       - run: ls -R
       # Next, we merge the individual coverage files and upload
       # the combined results to Coveralls.
@@ -106,7 +106,7 @@ jobs:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: ./lcov.info
       # Upload merged coverage data as artifact for debugging
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: lcov
           path: ./lcov.info

diff --git a/.github/workflows/Documenter.yml b/.github/workflows/Documenter.yml
@@ -38,7 +38,7 @@ jobs:
         with:
           version: '1'
           show-versioninfo: true
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:

diff --git a/.github/workflows/FormatCheck.yml b/.github/workflows/FormatCheck.yml
@@ -26,7 +26,7 @@ jobs:
         #
         # julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
         run: |
-          julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter"))'
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.45"))'
           julia  -e 'using JuliaFormatter; format(".", verbose = true)'
       - name: Format check
         run: |

diff --git a/.github/workflows/SpellCheck.yml b/.github/workflows/SpellCheck.yml
@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.16.23
+        uses: crate-ci/typos@v1.18.2
diff --git a/Project.toml b/Project.toml
@@ -10,7 +10,6 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SimpleUnPack = "ce78b400-467f-4804-87d8-8f486da07d0a"
@@ -29,4 +28,6 @@ Reexport = "1"
 SciMLBase = "2"
 SimpleUnPack = "1"
 SparseArrays = "1.7"
+StaticArrays = "1.5"
+SymbolicIndexingInterface = "0.2, 0.3"
 julia = "1.7"
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,7 +1,7 @@
 # PositiveIntegrators.jl
 
 The [Julia]() library
-[PositiveIntegrators.jl](https://github.com/ranocha/PositiveIntegrators.jl)
+[PositiveIntegrators.jl](https://github.com/SKopecz/PositiveIntegrators.jl)
 provides several time integration methods developed to preserve the positivity
 of numerical solutions.
 

diff --git a/examples/03_example_mprk22.jl b/examples/03_example_mprk22.jl
@@ -58,7 +58,7 @@ plot(p1, p2, p3, plot_title = "oop")
 # convergence order
 using DiffEqDevTools
 using PrettyTables
-convergence_tab_plot(linmod_op, [MPE(); MPRK22(0.5); MPRK22(1.0)])
+convergence_tab_plot(linmod_op, [MPE(); MPRK22(0.5); MPRK22(1.0)]; analytic = true)
 
 # in-place implementation
 function linmodP!(P, u, p, t)

diff --git a/examples/04_example_problemlibrary.jl b/examples/04_example_problemlibrary.jl
@@ -31,14 +31,16 @@ plot!(sol_linmod_MPE, idxs = (f2, 0, 1, 2))
 
 # convergence order
 # error based on analytic solution
-convergence_tab_plot(prob_pds_linmod, [MPE(), Euler()]; dts = 0.5 .^ (3:18),
-                     analytic = true, order_plot = true)
-savefig("figs/error_linmod_analytic.svg")
+sims = convergence_tab_plot(prob_pds_linmod, [MPE(), Euler()]; dts = 0.5 .^ (3:18),
+                            analytic = true, order_plot = true);
+@assert sims[1].𝒪est[:l∞] > 0.9
+#savefig("figs/error_linmod_analytic.svg")
 # error based on reference solution
 test_setup = Dict(:alg => Vern9(), :reltol => 1e-14, :abstol => 1e-14);
-convergence_tab_plot(prob_pds_linmod, [MPE(), Euler()], test_setup; dts = 0.5 .^ (3:18),
-                     order_plot = true)
-savefig("figs/error_linmod_reference.svg")
+sims = convergence_tab_plot(prob_pds_linmod, [MPE(), Euler()], test_setup;
+                            dts = 0.5 .^ (3:18), order_plot = true);
+@assert sims[1].𝒪est[:l∞] > 0.9
+#savefig("figs/error_linmod_reference.svg")
 
 ## nonlinear model ########################################################
 sol_nonlinmod = solve(prob_pds_nonlinmod, Tsit5());
@@ -49,10 +51,11 @@ plot(sol_nonlinmod, legend = :right)
 myplot!(sol_nonlinmod_MPE, "MPE")
 plot!(sol_nonlinmod_MPE, idxs = (f3, 0, 1, 2, 3))
 
-# convergence order 
+# convergence order
 test_setup = Dict(:alg => Vern9(), :reltol => 1e-14, :abstol => 1e-14)
-convergence_tab_plot(prob_pds_nonlinmod, [MPE(), Euler()], test_setup; dts = 0.5 .^ (3:17),
-                     order_plot = true)
+sims = convergence_tab_plot(prob_pds_nonlinmod, [MPE(), Euler()], test_setup;
+                            dts = 0.5 .^ (3:17), order_plot = true);
+@assert sims[1].𝒪est[:l∞] > 0.9
 
 ## robertson problem ######################################################
 sol_robertson = solve(prob_pds_robertson, Rosenbrock23());
@@ -74,10 +77,11 @@ myplot!(sol_brusselator_MPE, "MPE")
 plot!(sol_brusselator_MPE, idxs = (f_brusselator, 0, 1, 2, 3, 4, 5, 6),
       label = "f_brusselator")
 
-# convergence order 
+# convergence order
 test_setup = Dict(:alg => Vern9(), :reltol => 1e-14, :abstol => 1e-14)
-convergence_tab_plot(prob_pds_brusselator, [MPE()], test_setup; dts = 0.5 .^ (3:17),
-                     order_plot = true)
+sims = convergence_tab_plot(prob_pds_brusselator, [MPE()], test_setup; dts = 0.5 .^ (3:17),
+                            order_plot = true);
+@assert sims[1].𝒪est[:l∞] > 0.9
 
 ## SIR model ##############################################################
 sol_sir = solve(prob_pds_sir, Tsit5());
@@ -93,22 +97,23 @@ myplot!(sol_sir_Euler, "Euler")
 plot!(sol_sir_Euler, idxs = (f3, 0, 1, 2, 3), label = "f3")
 plot(p1, p2)
 
-# convergence order 
+# convergence order
 test_setup = Dict(:alg => Vern9(), :reltol => 1e-14, :abstol => 1e-14)
-convergence_tab_plot(prob_pds_sir, [MPE(), Euler()], test_setup; dts = 0.5 .^ (1:15),
-                     order_plot = true)
+sims = convergence_tab_plot(prob_pds_sir, [MPE(), Euler()], test_setup; dts = 0.5 .^ (1:15),
+                            order_plot = true);
+@assert sims[1].𝒪est[:l∞] > 0.9
 
 ## bertolazzi problem #####################################################
 sol_bertolazzi = solve(prob_pds_bertolazzi, TRBDF2());
 sol_bertolazzi_MPE = solve(prob_pds_bertolazzi, MPE(), dt = 0.01);
 
-# plot 
+# plot
 plot(sol_bertolazzi, legend = :right)
 myplot!(sol_bertolazzi_MPE, "MPE")
 ylims!((-0.5, 3.5))
 plot!(sol_bertolazzi_MPE, idxs = (f3, 0, 1, 2, 3))
 
-# convergence order 
+# convergence order
 test_setup = Dict(:alg => Rosenbrock23(), :reltol => 1e-8, :abstol => 1e-8)
 convergence_tab_plot(prob_pds_bertolazzi, [MPE(), ImplicitEuler()], test_setup;
                      dts = 0.5 .^ (10:15), order_plot = true)
@@ -123,16 +128,16 @@ myplot!(sol_npzd_MPE, "MPE")
 plot!(sol_npzd_MPE, idxs = (f_npzd, 0, 1, 2, 3, 4), label = "f_npzd")
 plot!(legend = :bottomright)
 
-# convergence order 
-# error should take all time steps into account, not only the final time! 
+# convergence order
+# error should take all time steps into account, not only the final time!
 test_setup = Dict(:alg => Rosenbrock23(), :reltol => 1e-14, :abstol => 1e-14)
-convergence_tab_plot(prob_pds_npzd, [MPE(), ImplicitEuler()], test_setup;
-                     dts = 0.5 .^ (5:17), order_plot = true)
+sims = convergence_tab_plot(prob_pds_npzd, [MPE(), ImplicitEuler()], test_setup;
+                            dts = 0.5 .^ (5:17), order_plot = true);
+@assert sims[1].𝒪est[:l∞] > 0.9
 
-### strat reac problem ####################################################
+### stratospheric reaction problem ####################################################
 sol_stratreac = solve(prob_pds_stratreac, TRBDF2(autodiff = false));
-#sol_stratreac_MPE = solve(prob_pds_stratreac, MPE(), dt = 25920.0);
-#tmp = reduce(hcat, sol_stratreac_MPE.u)
+# currently no solver for non-conservative PDS implemented
 
 tspan = prob_pds_stratreac.tspan
 u0 = prob_pds_stratreac.u0
@@ -171,12 +176,7 @@ ylims!((1.08e9, 1.1e9))
 
 p7 = plot(sol_stratreac, idxs = (g1, 0, 1, 2, 3, 4, 5, 6), xticks = [tspan[1], tspan[2]],
           legend = :outertop)
-#plot!(sol_stratreac_MPE.t,
-#      vec(mapslices((x) -> abs(x[1] + x[2] + 3 * x[3] + 2 * x[4] + x[5] + 2 * x[6] - linear_invariant_1) /
-#                           linear_invariant_1, tmp, dims = 1)))
 p8 = plot(sol_stratreac, idxs = (g2, 0, 1, 2, 3, 4, 5, 6),
           xticks = [tspan[1], tspan[2]], legend = :outertop)
-#plot!(sol_stratreac_MPE.t,
-#      vec(mapslices((x) -> abs(x[5] + x[6] - linear_invariant_2) / linear_invariant_2, tmp,
-#                    dims = 1)))
+
 plot(p1, p2, p3, p4, p5, p6, p7, p8)
diff --git a/examples/Project.toml b/examples/Project.toml
@@ -8,6 +8,7 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PositiveIntegrators = "d1b20bf0-b083-4985-a874-dc5121669aa5"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
 
 [compat]
@@ -17,3 +18,5 @@ LinearSolve = "2"
 OrdinaryDiffEq = "6"
 Plots = "1"
 PrettyTables = "2"
+StaticArrays = "1.5"
+SymbolicIndexingInterface = "0.2, 0.3"