repository transfer (#156)

* repository transfer

* format

* relax work-precision time tests

* allow bigger tolerance on macOS

---------

Co-authored-by: Stefan Kopecz <[email protected]>

Author: ranocha

.github/workflows/DocPreviewCleanup.yml

@@ -8,7 +8,7 @@ jobs:
   doc-preview-cleanup:
     # Do not run on forks to avoid authorization errors
     # Source: https://github.community/t/have-github-action-only-run-on-master-repo-and-not-on-forks/140840/18
-    if: github.repository_owner == 'SKopecz'
+    if: github.repository_owner == 'NumericalMathematics'
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch

CITATION.bib

@@ -4,5 +4,5 @@ @misc{PositiveIntegrators.jl
   author={Kopecz, Stefan and Lampert, Joshua and Ranocha, Hendrik},
   year={2023},
   doi={10.5281/zenodo.10868393},
-  url={https://github.com/SKopecz/PositiveIntegrators.jl}
+  url={https://github.com/NumericalMathematics/PositiveIntegrators.jl}
 }

Project.toml

@@ -1,7 +1,7 @@
 name = "PositiveIntegrators"
 uuid = "d1b20bf0-b083-4985-a874-dc5121669aa5"
 authors = ["Stefan Kopecz, Hendrik Ranocha, and contributors"]
-version = "0.2.11-DEV"
+version = "0.2.11"
 
 [deps]
 FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"

README.md

@@ -1,10 +1,10 @@
 # PositiveIntegrators.jl
 
-[![Docs-stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://SKopecz.github.io/PositiveIntegrators.jl/stable)
-[![Docs-dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://SKopecz.github.io/PositiveIntegrators.jl/dev)
-[![Build Status](https://github.com/SKopecz/PositiveIntegrators.jl/workflows/CI/badge.svg)](https://github.com/SKopecz/PositiveIntegrators.jl/actions?query=workflow%3ACI)
-[![Codecov](https://codecov.io/gh/SKopecz/PositiveIntegrators.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/SKopecz/PositiveIntegrators.jl)
-[![Coveralls](https://coveralls.io/repos/github/SKopecz/PositiveIntegrators.jl/badge.svg?branch=main)](https://coveralls.io/github/SKopecz/PositiveIntegrators.jl?branch=main)
+[![Docs-stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://NumericalMathematics.github.io/PositiveIntegrators.jl/stable)
+[![Docs-dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://NumericalMathematics.github.io/PositiveIntegrators.jl/dev)
+[![Build Status](https://github.com/NumericalMathematics/PositiveIntegrators.jl/workflows/CI/badge.svg)](https://github.com/NumericalMathematics/PositiveIntegrators.jl/actions?query=workflow%3ACI)
+[![Codecov](https://codecov.io/gh/NumericalMathematics/PositiveIntegrators.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/NumericalMathematics/PositiveIntegrators.jl)
+[![Coveralls](https://coveralls.io/repos/github/NumericalMathematics/PositiveIntegrators.jl/badge.svg?branch=main)](https://coveralls.io/github/NumericalMathematics/PositiveIntegrators.jl?branch=main)
 [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 [![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://opensource.org/licenses/MIT)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10868393.svg)](https://doi.org/10.5281/zenodo.10868393)
@@ -20,12 +20,12 @@ by
   modified Patankar-Runge-Kutta (MPRK) schemes
 
 Please find more information online in the
-[documentation](https://skopecz.github.io/PositiveIntegrators.jl/stable).
+[documentation](https://NumericalMathematics.github.io/PositiveIntegrators.jl/stable).
 
 
 ## Installation
 
-[PositiveIntegrators.jl](https://github.com/SKopecz/PositiveIntegrators.jl)
+[PositiveIntegrators.jl](https://github.com/NumericalMathematics/PositiveIntegrators.jl)
 is a registered Julia package. Thus, you can install it from the Julia REPL via
 ```julia
 julia> using Pkg; Pkg.add("PositiveIntegrators")
@@ -40,7 +40,7 @@ julia> using Pkg; Pkg.update("PositiveIntegrators")
 ## Referencing
 
 If you use
-[PositiveIntegrators.jl](https://github.com/SKopecz/PositiveIntegrators.jl)
+[PositiveIntegrators.jl](https://github.com/NumericalMathematics/PositiveIntegrators.jl)
 for your research, please cite it using the bibtex entry
 ```bibtex
 @misc{PositiveIntegrators.jl,
@@ -49,16 +49,16 @@ for your research, please cite it using the bibtex entry
   author={Kopecz, Stefan and Lampert, Joshua and Ranocha, Hendrik},
   year={2023},
   doi={10.5281/zenodo.10868393},
-  url={https://github.com/SKopecz/PositiveIntegrators.jl}
+  url={https://github.com/NumericalMathematics/PositiveIntegrators.jl}
 }
 ```
 
 
 ## License and contributing
 
 This project is licensed under the MIT license
-(see [License](https://github.com/SKopecz/PositiveIntegrators.jl/blob/main/LICENSE)).
+(see [License](https://github.com/NumericalMathematics/PositiveIntegrators.jl/blob/main/LICENSE)).
 Since it is an open-source project, we are very happy to accept contributions
 from the community. Please refer to the section
-[Contributing](https://github.com/SKopecz/PositiveIntegrators.jl/blob/main/CONTRIBUTING.md)
+[Contributing](https://github.com/NumericalMathematics/PositiveIntegrators.jl/blob/main/CONTRIBUTING.md)
 for more details.

SECURITY.md

@@ -14,7 +14,7 @@ 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/SKopecz/PositiveIntegrators.jl/security/advisories/new)
+["Report a Vulnerability"](https://github.com/NumericalMathematics/PositiveIntegrators.jl/security/advisories/new)
 tab.
 
 We will send a response indicating the next steps in handling your report.

docs/make.jl

@@ -18,11 +18,12 @@ DocMeta.setdocmeta!(PositiveIntegrators,
 # as necessary
 open(joinpath(@__DIR__, "src", "license.md"), "w") do io
     # Point to source license file
-    println(io, """
-    ```@meta
-    EditURL = "https://github.com/SKopecz/PositiveIntegrators.jl/blob/main/LICENSE"
-    ```
-    """)
+    println(io,
+            """
+```@meta
+EditURL = "https://github.com/NumericalMathematics/PositiveIntegrators.jl/blob/main/LICENSE"
+```
+""")
     # Write the modified contents
     println(io, "# License")
     println(io, "")
@@ -37,7 +38,7 @@ open(joinpath(@__DIR__, "src", "code_of_conduct.md"), "w") do io
     println(io,
             """
             ```@meta
-            EditURL = "https://github.com/SKopecz/PositiveIntegrators.jl/blob/main/CODE_OF_CONDUCT.md"
+            EditURL = "https://github.com/NumericalMathematics/PositiveIntegrators.jl/blob/main/CODE_OF_CONDUCT.md"
             ```
             """)
     # Write the modified contents
@@ -51,11 +52,12 @@ end
 
 open(joinpath(@__DIR__, "src", "contributing.md"), "w") do io
     # Point to source license file
-    println(io, """
-    ```@meta
-    EditURL = "https://github.com/SKopecz/PositiveIntegrators.jl/blob/main/CONTRIBUTING.md"
-    ```
-    """)
+    println(io,
+            """
+```@meta
+EditURL = "https://github.com/NumericalMathematics/PositiveIntegrators.jl/blob/main/CONTRIBUTING.md"
+```
+""")
     # Write the modified contents
     println(io, "# Contributing")
     println(io, "")
@@ -69,7 +71,7 @@ end
 makedocs(modules = [PositiveIntegrators],
          sitename = "PositiveIntegrators.jl",
          format = Documenter.HTML(prettyurls = get(ENV, "CI", nothing) == "true",
-                                  canonical = "https://SKopecz.github.io/PositiveIntegrators.jl/stable"),
+                                  canonical = "https://NumericalMathematics.github.io/PositiveIntegrators.jl/stable"),
          # Explicitly specify documentation structure
          pages = [
              "Home" => "index.md",
@@ -95,6 +97,6 @@ makedocs(modules = [PositiveIntegrators],
              "License" => "license.md"
          ])
 
-deploydocs(repo = "github.com/SKopecz/PositiveIntegrators.jl",
+deploydocs(repo = "github.com/NumericalMathematics/PositiveIntegrators.jl",
            devbranch = "main",
            push_preview = true)

docs/src/faq.md

@@ -3,7 +3,7 @@
 ## Sparse matrices
 
 You can use sparse matrices for the linear systems arising in
-[PositiveIntegrators.jl](https://github.com/SKopecz/PositiveIntegrators.jl),
+[PositiveIntegrators.jl](https://github.com/NumericalMathematics/PositiveIntegrators.jl),
 as described, e.g., in the [tutorial on linear advection](@ref tutorial-linear-advection).
 However, you need to make sure that you do not change the sparsity pattern
 of the production term matrix since we assume that the structural nonzeros

docs/src/heat_equation_dirichlet.md

@@ -58,7 +58,7 @@ In addition, all production and destruction terms not listed are zero.
 
 Now we are ready to define a [`PDSProblem`](@ref) and to solve this
 problem with a method of
-[PositiveIntegrators.jl](https://github.com/SKopecz/PositiveIntegrators.jl) or
+[PositiveIntegrators.jl](https://github.com/NumericalMathematics/PositiveIntegrators.jl) or
 [OrdinaryDiffEq.jl](https://docs.sciml.ai/OrdinaryDiffEq/stable/).
 In the following we use ``N = 100`` nodes and the time domain ``t \in [0,1]``.
 Moreover, we choose the initial condition

docs/src/heat_equation_neumann.md

@@ -50,7 +50,7 @@ and destruction terms ``d_{i,j} = p_{j,i}``. In addition, all production and des
 
 Now we are ready to define a [`ConservativePDSProblem`](@ref) and to solve this
 problem with a method of
-[PositiveIntegrators.jl](https://github.com/SKopecz/PositiveIntegrators.jl) or
+[PositiveIntegrators.jl](https://github.com/NumericalMathematics/PositiveIntegrators.jl) or
 [OrdinaryDiffEq.jl](https://docs.sciml.ai/OrdinaryDiffEq/stable/).
 In the following we use ``N = 100`` nodes and the time domain ``t \in [0,1]``.
 Moreover, we choose the initial condition

docs/src/index.md

@@ -1,14 +1,14 @@
 # PositiveIntegrators.jl
 
 The [Julia](https://julialang.org) library
-[PositiveIntegrators.jl](https://github.com/SKopecz/PositiveIntegrators.jl)
+[PositiveIntegrators.jl](https://github.com/NumericalMathematics/PositiveIntegrators.jl)
 provides several time integration methods developed to preserve the positivity
 of numerical solutions.
 
 
 ## Installation
 
-[PositiveIntegrators.jl](https://github.com/SKopecz/PositiveIntegrators.jl)
+[PositiveIntegrators.jl](https://github.com/NumericalMathematics/PositiveIntegrators.jl)
 is a registered Julia package. Thus, you can install it from the Julia REPL via
 ```julia
 julia> using Pkg; Pkg.add("PositiveIntegrators")
@@ -88,7 +88,7 @@ tspan = (0.0, 10.0) # time span
 prob = PDSProblem(P, d, u0, tspan)
 nothing #hide
 ```
-Now that the problem has been created, we can solve it with any method of [PositiveIntegrators.jl](https://github.com/SKopecz/PositiveIntegrators.jl). In the following, we use the method `MPRK22(1.0)`. In addition, we could also use any method provided by [OrdinaryDiffEq.jl](https://docs.sciml.ai/OrdinaryDiffEq/stable/), but these might possibly generate negative approximations.
+Now that the problem has been created, we can solve it with any method of [PositiveIntegrators.jl](https://github.com/NumericalMathematics/PositiveIntegrators.jl). In the following, we use the method `MPRK22(1.0)`. In addition, we could also use any method provided by [OrdinaryDiffEq.jl](https://docs.sciml.ai/OrdinaryDiffEq/stable/), but these might possibly generate negative approximations.
 
 ```@example LotkaVolterra
 sol = solve(prob, MPRK22(1.0))
@@ -132,7 +132,7 @@ The corresponding production matrix ``\mathbf P`` is
 \mathbf P(S,I,R) = \begin{pmatrix}0 & 0 & 0\\ \frac{β S I}{N} & 0 & 0\\ 0 & γ I & 0\end{pmatrix}.
 ```
 
-The following example shows how to implement the above SIR model with ``\beta=0.4, \gamma=0.04``, initial conditions ``S(0)=997, I(0)=3, R(0)=0`` and time domain ``(0, 100)`` using `ConservativePDSProblem` from [PositiveIntegrators.jl](https://github.com/SKopecz/PositiveIntegrators.jl).
+The following example shows how to implement the above SIR model with ``\beta=0.4, \gamma=0.04``, initial conditions ``S(0)=997, I(0)=3, R(0)=0`` and time domain ``(0, 100)`` using `ConservativePDSProblem` from [PositiveIntegrators.jl](https://github.com/NumericalMathematics/PositiveIntegrators.jl).
 
 ```@example SIR
 using PositiveIntegrators
@@ -158,7 +158,7 @@ tspan = (0.0, 100.0); # time span
 prob = ConservativePDSProblem(P, u0, tspan)
 nothing # hide
 ```
-Since the SIR model is not only conservative but also positive, we can use any scheme from [PositiveIntegrators.jl](https://github.com/SKopecz/PositiveIntegrators.jl) to solve it. Here we use `MPRK22(1.0)`.
+Since the SIR model is not only conservative but also positive, we can use any scheme from [PositiveIntegrators.jl](https://github.com/NumericalMathematics/PositiveIntegrators.jl) to solve it. Here we use `MPRK22(1.0)`.
 Please note that any method from [OrdinaryDiffEq.jl](https://docs.sciml.ai/OrdinaryDiffEq/stable/) can be used as well, but might possibly generate negative approximations.
 
 ```@example SIR
@@ -186,7 +186,7 @@ for your research, please cite it using the bibtex entry
   author={Kopecz, Stefan and Lampert, Joshua and Ranocha, Hendrik},
   year={2023},
   doi={10.5281/zenodo.10868393},
-  url={https://github.com/SKopecz/PositiveIntegrators.jl}
+  url={https://github.com/NumericalMathematics/PositiveIntegrators.jl}
 }
 ```