time integration methods and multirate infinitesimal split methods (#43)

* add RootedTrees API reference * use RungeKuttaMethod, AdditiveRungeKuttaMethod * update CI * WIP: MultirateInfinitesimalSplitMethod * fix some type instabilities * another type stability fix * polynomial multiplication is fast * reexport Polynomial and add first tests * test for MIS methods Co-authored-by: OsKnoth <[email protected]> * update CI to use parallel coveralls * fix typo * fix typo * increase test coverage * mode=PKGMODE_MANIFEST for Pkg.status in the docs * fix typo * fix typo * add TODO note Co-authored-by: OsKnoth <[email protected]>
ranocha · Jan 17, 2022 · dd0e0e1 · dd0e0e1
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -11,11 +11,18 @@ on:
 jobs:
   test:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        group:
+          - Core
+        version:
+          - '1'
+          - '1.6'
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
-          version: 1
+          version: ${{ matrix.version }}
       - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
         env:
@@ -49,7 +56,73 @@ jobs:
       - uses: codecov/codecov-action@v1
         with:
           file: lcov.info
+      # The standard setup of Coveralls is just annoying for parallel builds, see, e.g.,
+      # https://github.com/trixi-framework/Trixi.jl/issues/691
+      # https://github.com/coverallsapp/github-action/issues/47
+      # https://github.com/coverallsapp/github-action/issues/67
+      # This standard setup is reproduced below for completeness.
+      # - uses: coverallsapp/github-action@master
+      #   with:
+      #     github-token: ${{ secrets.GITHUB_TOKEN }}
+      #     flag-name: run-${{ matrix.version }}-${{ github.run_id }}
+      #     parallel: true
+      #     path-to-lcov: ./lcov.info
+      # Instead, we use a more tedious approach:
+      # - Store all individual coverage files as artifacts (directly below)
+      # - Download and merge individual coverage reports in another step
+      # - Upload only the merged coverage report to Coveralls
+      - shell: bash
+        run: |
+          cp ./lcov.info ./lcov-${{ matrix.version }}-${{ github.run_id }}.info
+      - uses: actions/upload-artifact@v2
+        with:
+          name: lcov-${{ matrix.version }}-${{ github.run_id }}
+          path: ./lcov-${{ matrix.version }}-${{ github.run_id }}.info
+
+  finish:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      # The standard setup of Coveralls is just annoying for parallel builds, see, e.g.,
+      # https://github.com/trixi-framework/Trixi.jl/issues/691
+      # https://github.com/coverallsapp/github-action/issues/47
+      # https://github.com/coverallsapp/github-action/issues/67
+      # This standard setup is reproduced below for completeness.
+      # - name: Coveralls Finished
+      #   uses: coverallsapp/github-action@master
+      #   with:
+      #     github-token: ${{ secrets.GITHUB_TOKEN }}
+      #     parallel-finished: true
+      # Instead, we use the more tedious approach described above.
+      # At first, we check out the repository and download all artifacts
+      # (and list files for debugging).
+      - uses: actions/checkout@v2
+      - uses: actions/download-artifact@v2
+      - run: ls -R
+      # Next, we merge the individual coverage files and upload
+      # the combined results to Coveralls.
+      - name: Merge lcov files using Coverage.jl
+        shell: julia --color=yes {0}
+        run: |
+          using Pkg
+          Pkg.activate(temp=true)
+          Pkg.add("Coverage")
+          using Coverage
+          coverage = LCOV.readfolder(".")
+          for cov in coverage
+            cov.filename = replace(cov.filename, "\\" => "/")
+          end
+          coverage = merge_coverage_counts(coverage)
+          @show covered_lines, total_lines = get_summary(coverage)
+          LCOV.writefile("./lcov.info", coverage)
       - uses: coverallsapp/github-action@master
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: ./lcov.info
+      # Upload merged coverage data as artifact for debugging
+      - uses: actions/upload-artifact@v2
+        with:
+          name: lcov
+          path: ./lcov.info
+      # That's it
+      - run: echo "Finished testing BSeries"
diff --git a/Project.toml b/Project.toml
@@ -7,14 +7,16 @@ version = "0.1.17-pre"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+Polynomials = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 RootedTrees = "47965b36-3f3e-11e9-0dcf-4570dfd42a8c"
 
 [compat]
 Latexify = "0.15"
 OrderedCollections = "1"
+Polynomials = "2.0.23"
 Reexport = "1"
 Requires = "1"
-RootedTrees = "2.6.3"
+RootedTrees = "2.8.3"
 julia = "1.6"
diff --git a/docs/src/api_reference.md b/docs/src/api_reference.md
@@ -1,4 +1,6 @@
-# BSeries.jl API
+# API reference
+
+## BSeries.jl API
 
 ```@meta
 CurrentModule = BSeries
@@ -8,3 +10,12 @@ CurrentModule = BSeries
 Modules = [BSeries]
 ```
 
+## RootedTrees.jl API
+
+```@meta
+CurrentModule = RootedTrees
+```
+
+```@autodocs
+Modules = [RootedTrees]
+```
diff --git a/docs/src/benchmarks.md b/docs/src/benchmarks.md
@@ -104,7 +104,8 @@ using InteractiveUtils
 versioninfo()
 
 using Pkg
-Pkg.status(["BSeries", "RootedTrees", "SymEngine", "SymPy", "Symbolics"])
+Pkg.status(["BSeries", "RootedTrees", "SymEngine", "SymPy", "Symbolics"],
+           mode=PKGMODE_MANIFEST)
 nothing # hide
 ```
 

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,10 +1,14 @@
 # BSeries.jl
 
-The Julia library
 [BSeries.jl](https://github.com/ranocha/BSeries.jl)
-is work in progress. Nevertheless, we follow semantic versioning. Thus, you can
-safely use the package right now. Extended documentation will be provided in the
-future.
+is a collection of functionality around
+[B-series](https://en.wikipedia.org/wiki/Butcher_group)
+in [Julia](https://julialang.org/). See for example
+
+- Philippe Chartier, Ernst Hairer, Gilles Vilmart (2010)
+  Algebraic Structures of B-series.
+  Foundations of Computational Mathematics
+  [DOI: 10.1007/s10208-010-9065-1](https://doi.org/10.1007/s10208-010-9065-1)
 
 BSeries.jl re-exports everything from
 [RootedTrees.jl](https://github.com/SciML/RootedTrees.jl).
@@ -13,6 +17,20 @@ you should also include it explicitly in your project dependencies
 to track breaking changes, since the version numbers of RootedTrees.jl
 and BSeries.jl are not necessarily synchronized.
 
+The main API of BSeries.jl consists of the following components.
+
+- B-series behave like `AbstractDict`s mapping
+  (abstract) `RootedTree`s to coefficients.
+- The B-series of time integration methods such as Runge-Kutta methods
+  can be constructed by the function [`bseries`](@ref).
+- The algebraic structures of the composition law and the substitution law are
+  implemented via [`compose`](@ref) and [`substitute`](@ref).
+- Backward error analysis can be performed via
+  [`modified_equation`](@ref)s and [`modifying_integrator`](@ref)s.
+
+Further information is provided in the following tutorials and
+API documentation.
+
 
 ## Installation