CompatHelper: bump compat for ArnoldiMethod to 0.4, (keep existing co…

…mpat) (#7) * CompatHelper: bump compat for ArnoldiMethod to 0.4, (keep existing compat) * Updated CompatHelper workflow * Add new compat entry for Statistics * Updated TagBot workflow * Bump version * Imports of targets from ArnoldiMethod.jl * Transitioned documentation plot to Python{Call,Plot} * Upgraded Documenter compat * Fix test --------- Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Stefanos Carlström <[email protected]>
jagot · Feb 23, 2024 · 11975c4 · 11975c4 · jagot · Feb 23, 2024
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -51,7 +51,7 @@ jobs:
       - run: |
           julia --project=docs -e '
             using Pkg
-            pkg"add PyCall PyPlot https://github.com/jagot/Jagot.jl.git https://github.com/jagot/PyPlotRecipes.jl.git Colors SpecialFunctions LinearAlgebra"
+            pkg"add PythonCall PythonPlot https://github.com/jagot/Jagot.jl.git Colors SpecialFunctions LinearAlgebra"
             Pkg.develop(PackageSpec(path=pwd()))
             Pkg.instantiate()'
         env:

diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
@@ -3,14 +3,43 @@ on:
   schedule:
     - cron: 0 0 * * *
   workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml
@@ -4,6 +4,22 @@ on:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
@@ -12,4 +28,6 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
+          # Edit the following line to reflect the actual name of the GitHub Secret containing your private key
           ssh: ${{ secrets.DOCUMENTER_KEY }}
+          # ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}
diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,5 @@
 /docs/build/
 /docs/site/
 /docs/src/figures/
+/docs/Manifest.toml
+.CondaPkg/
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "MatrixPolynomials"
 uuid = "bd52c179-449c-4965-a404-68b29a447f4b"
 authors = ["Stefanos Carlström <[email protected]>"]
-version = "0.1.2"
+version = "0.1.3"
 
 [deps]
 ArnoldiMethod = "ec485272-7323-5ecc-a04f-4719b315124d"
@@ -14,11 +14,12 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 UnicodeFun = "1cfade01-22cf-5700-b092-accc4b62d6e1"
 
 [compat]
-ArnoldiMethod = "0.2.0"
+ArnoldiMethod = "0.2.0, 0.4"
 Compat = "3.26.0, 4"
 Formatting = "0.4"
 Parameters = "0.12"
 SpecialFunctions = "1.3, 2"
+Statistics = "1"
 UnicodeFun = "0.4"
 julia = "1.3"
 

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -2,4 +2,4 @@
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 
 [compat]
-Documenter = "0.25"
+Documenter = "1"
diff --git a/docs/make.jl b/docs/make.jl
@@ -14,10 +14,11 @@ makedocs(;
         "Newton polynomials" => "newton_polynomials.md",
         "φₖ functions" => "phi_functions.md",
     ],
-    repo="https://github.com/jagot/MatrixPolynomials.jl/blob/{commit}{path}#L{line}",
+    repo=Remotes.GitHub("jagot", "MatrixPolynomials.jl"),
     sitename="MatrixPolynomials.jl",
     authors="Stefanos Carlström <[email protected]>",
     doctest=false,
+    checkdocs=:exports
 )
 
 deploydocs(;

diff --git a/docs/plots.jl b/docs/plots.jl
@@ -1,4 +1,4 @@
-using PyPlot
+using PythonPlot
 using Jagot.plotting
 plot_style("ggplot")
 

diff --git a/docs/src/divided_differences.md b/docs/src/divided_differences.md
@@ -56,7 +56,7 @@ i.e. the first row of the function ``f`` applied to the matrix
 &&&&\zeta_j}.
 \end{equation}
 ```
-The right-eigenvectors are given by [Opitz]
+The right-eigenvectors are given by [^Opitz]
 ```math
 \begin{equation}
 \label{eqn:div-diff-mat-right-eigen}
@@ -268,12 +268,6 @@ MatrixPolynomials.propagate_div_diff_sin_cos
     propagators. Computing, 80(2), 189–201. [DOI:
     10.1007/s00607-007-0227-1](http://dx.doi.org/10.1007/s00607-007-0227-1)
 
-[^Kandolf]: Kandolf, P., Ostermann, A., & Rainer, S. (2014). A
-    residual based error estimate for Leja interpolation of matrix
-    functions. Linear Algebra and its Applications, 456(nil),
-    157–173. [DOI:
-    10.1016/j.laa.2014.04.023](http://dx.doi.org/10.1016/j.laa.2014.04.023)
-
 [^McCurdy]: McCurdy, A. C., Ng, K. C., & Parlett,
     B. N. (1984). Accurate computation of divided differences of the
     exponential function. Mathematics of Computation, 43(168),

diff --git a/docs/src/funcv.md b/docs/src/funcv.md
@@ -10,6 +10,7 @@ LinearAlgebra.mul!(w, funcv::MatrixPolynomials.FuncV, v)
 
 ```@docs
 MatrixPolynomials.spectral_range
+MatrixPolynomials.hermitian_spectral_range
 ```
 
 ### Shapes

diff --git a/docs/src/leja.md b/docs/src/leja.md
@@ -34,12 +34,12 @@ interpolation points.
 
 MatrixPolynomials.jl provides two methods for generating the Leja
 points, [`MatrixPolynomials.Leja`](@ref) and
-[`MatrixPolynomials.FastLeja`](@ref). The figure below illustrates the
-distribution of Leja points using both methods, on the line
-``[-2,2]``, for the [`MatrixPolynomials.Leja`](@ref), an underlying
-discretization of 1000 points was employed, and 10 Leja points were
-generated. The lower part of the plot shows the estimation of the
-[capacity](https://en.wikipedia.org/wiki/Capacity_of_a_set),
+[`MatrixPolynomials.FastLeja`](@ref)[^Baglama]. The figure below
+illustrates the distribution of Leja points using both methods, on the
+line ``[-2,2]``, for the [`MatrixPolynomials.Leja`](@ref), an
+underlying discretization of 1000 points was employed, and 10 Leja
+points were generated. The lower part of the plot shows the estimation
+of the [capacity](https://en.wikipedia.org/wiki/Capacity_of_a_set),
 calculated as
 ```math
 C(\{\zeta_{1:m}\}) \approx

diff --git a/docs/src/newton_polynomials.md b/docs/src/newton_polynomials.md
@@ -1,4 +1,5 @@
 # Newton polynomials
+[^Kandolf]
 
 ```@docs
 MatrixPolynomials.NewtonPolynomial
@@ -13,3 +14,10 @@ LinearAlgebra.mul!(w, nmp::MatrixPolynomials.NewtonMatrixPolynomial, A, v)
 MatrixPolynomials.NewtonMatrixPolynomialDerivative
 MatrixPolynomials.φₖResidualEstimator
 ```
+## Bibliography
+
+[^Kandolf]: Kandolf, P., Ostermann, A., & Rainer, S. (2014). A
+    residual based error estimate for Leja interpolation of matrix
+    functions. Linear Algebra and its Applications, 456(nil),
+    157–173. [DOI:
+    10.1016/j.laa.2014.04.023](http://dx.doi.org/10.1016/j.laa.2014.04.023)
diff --git a/src/MatrixPolynomials.jl b/src/MatrixPolynomials.jl
@@ -3,6 +3,7 @@ module MatrixPolynomials
 using Parameters
 using LinearAlgebra
 using ArnoldiMethod
+using ArnoldiMethod: SR, SI, LR, LI
 using SpecialFunctions
 const Γ = gamma
 const lnΓ = loggamma

diff --git a/test/newton.jl b/test/newton.jl
@@ -100,7 +100,7 @@ end
     @testset "Matrix polynomials" begin
         @testset "Inhomogeneous coupled ODEs, $kind" for (kind,m,tol) in [(:real,43,1e-12), (:complex,60,1e-12)]
             n = 10 # Number of ODEs
-            Y₀ = 1.0*ones(n)
+            Y₀ = 1.0*ones(kind == :real ? Float64 : ComplexF64, n)
             G = -3*ones(n) # Inhomogeneous terms
 
             n_discr = 1000 # Number of points spanning eigenspectrum interval