diff --git a/.zenodo.json b/.zenodo.json index c7c6f8eb..ce2dee0e 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -8,6 +8,11 @@ "affiliation": "Applied Mathematics, University of Hamburg, Germany", "name": "Lampert, Joshua", "orcid": "0009-0007-0971-6709" + }, + { + "affiliation": "Numerical Mathematics, Johannes Gutenberg University Mainz, Germany", + "name": "Ranocha, Hendrik", + "orcid": "0000-0002-3456-2277" } ], "access_right": "open" diff --git a/CITATION.bib b/CITATION.bib index e7f70104..86612bca 100644 --- a/CITATION.bib +++ b/CITATION.bib @@ -1,7 +1,7 @@ @misc{lampert2023dispersive, title={{D}ispersive{S}hallow{W}ater.jl: {S}tructure-preserving numerical methods for dispersive shallow water models}, - author={Lampert, Joshua}, + author={Lampert, Joshua and Ranocha, Hendrik}, year={2023}, month={10}, howpublished={\url{https://github.com/JoshuaLampert/DispersiveShallowWater.jl}}, diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..83abdd1d --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,129 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, religion, or sexual identity +and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or + advances of any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email + address, without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to +[Joshua Lampert](mailto:joshua.lampert@uni-hamburg.de) or +[Hendrik Ranocha](mailto:mail@ranocha.de). +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +[version 2.0](https://www.contributor-covenant.org/version/2/0/code_of_conduct.html). + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the +[FAQ](https://www.contributor-covenant.org/faq). +[Translations](https://www.contributor-covenant.org/translations) +are also available there. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..26b01307 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,55 @@ +# Contributing + +DispersiveShallowWater.jl is an open-source project and we are very happy to accept contributions +from the community. Please feel free to +[open issues](https://github.com/JoshuaLampert/DispersiveShallowWater.jl/issues/new/choose) +or submit patches (preferably as +[pull requests](https://github.com/JoshuaLampert/DispersiveShallowWater.jl/pulls)) +any time. + +DispersiveShallowWater.jl and its contributions are licensed under the MIT license (see +[LICENSE](LICENSE)). As a contributor, you certify that all your +contributions are in conformance with the *Developer Certificate of Origin +(Version 1.1)*, which is reproduced below. + +## Developer Certificate of Origin (Version 1.1) +The following text was taken from +[https://developercertificate.org](https://developercertificate.org): + + Developer Certificate of Origin + Version 1.1 + + Copyright (C) 2004, 2006 The Linux Foundation and its contributors. + 1 Letterman Drive + Suite D4700 + San Francisco, CA, 94129 + + Everyone is permitted to copy and distribute verbatim copies of this + license document, but changing it is not allowed. + + + Developer's Certificate of Origin 1.1 + + By making a contribution to this project, I certify that: + + (a) The contribution was created in whole or in part by me and I + have the right to submit it under the open source license + indicated in the file; or + + (b) The contribution is based upon previous work that, to the best + of my knowledge, is covered under an appropriate open source + license and I have the right under that license to submit that + work with modifications, whether created in whole or in part + by me, under the same open source license (unless I am + permitted to submit under a different license), as indicated + in the file; or + + (c) The contribution was provided directly to me by some other + person who certified (a), (b) or (c) and I have not modified + it. + + (d) I understand and agree that this project and the contribution + are public and that a record of the contribution (including all + personal information I submit with it, including my sign-off) is + maintained indefinitely and may be redistributed consistent with + this project or the open source license(s) involved. diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 00000000..d868a4a6 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,49 @@ +# Changelog + +DispersiveShallowWater.jl follows the interpretation of +[semantic versioning (semver)](https://julialang.github.io/Pkg.jl/dev/compatibility/#Version-specifier-format-1) +used in the Julia ecosystem. Notable changes will be documented in this file +for human readability. + + +## Changes in the v0.4 lifecycle + +#### Added +- The `SerreGreenNaghdiEquations1D` were added for different types of bathymetry ([#127], [#135]). +- The `HyperbolicSerreGreenNaghdiEquations1D` were added for different types of bathymetry ([#139]). +- The abstract interface `AbstractShallowWaterEquations` was added to unify several + systems such as the `SerreGreenNaghdiEquations1D`, the `BBMBBMEquations1D`, and the + `SvärdKalischEquations1D` ([#127]). + +## Changes when updating to v0.4 from v0.3.x + +#### Changed +- Use `ArrayPartition` from RecursiveArrayTools.jl to store the solution of the `ODEProblem` ([#118]). + +## Changes in the v0.3 lifecycle + +#### Added +- Add possibility to pass vector of `Ns` to `convergence_test` ([#113]). +- Performance improvements by using factorized matrices for linear systems solves ([#108], [#112], [#114]). +- Reflecting boundary conditions are added for the BBM-BBM equations ([#104], [#109]). +- Fix for the `BBMBBMVariableEquations1D`, where the still water surface was neglected leading + to a bug in the Dingemans setup ([#91]). + +## Changes when updating to v0.3 from v0.2.x + +#### Changed +- Add keyword argument `start_from` when plotting `AnalysisCallback` ([#87]). +- Manufactured solution for Svärd-Kalisch equations uses a variable bathymetry ([#84]). + +## Changes in the v0.2 lifecycle + +#### Added +- Add `SummaryCallback` ([#75]). + +## Changes when updating to v0.2 from v0.1.x + +#### Changed +- The code from the master thesis of Joshua Lampert was separated ([#69]). +- Add support for source terms ([#65]). +- A higher order interpolation is used when plotting the solution at a value `x` outside + the grid ([#64]). diff --git a/README.md b/README.md index 67e1e569..c0327188 100644 --- a/README.md +++ b/README.md @@ -65,7 +65,7 @@ You can directly refer to DispersiveShallowWater.jl as @misc{lampert2023dispersive, title={{D}ispersive{S}hallow{W}ater.jl: {S}tructure-preserving numerical methods for dispersive shallow water models}, - author={Lampert, Joshua}, + author={Lampert, Joshua and Ranocha, Hendrik}, year={2023}, month={10}, howpublished={\url{https://github.com/JoshuaLampert/DispersiveShallowWater.jl}}, @@ -75,9 +75,12 @@ You can directly refer to DispersiveShallowWater.jl as ## Authors -The package is developed and maintained by Joshua Lampert (University of Hamburg). -Some parts of this repository are based on parts of [Dispersive-wave-schemes-notebooks. A Broad Class of Conservative Numerical Methods for Dispersive Wave Equations](https://github.com/ranocha/Dispersive-wave-schemes-notebooks) -by Hendrik Ranocha, Dimitrios Mitsotakis and David Ketcheson. The code structure is inspired by [Trixi.jl](https://github.com/trixi-framework/Trixi.jl/). +The package is mainly developed and maintained by Joshua Lampert (University of Hamburg) +with contributions from Hendrik Ranocha (Johannes Gutenberg University Mainz). +Some parts of this repository are based on parts of +[Dispersive-wave-schemes-notebooks. A Broad Class of Conservative Numerical Methods for Dispersive Wave Equations](https://github.com/ranocha/Dispersive-wave-schemes-notebooks) +by Hendrik Ranocha, Dimitrios Mitsotakis and David Ketcheson. +The code structure is inspired by [Trixi.jl](https://github.com/trixi-framework/Trixi.jl/). ## License and contributing diff --git a/SECURITY.md b/SECURITY.md new file mode 100644 index 00000000..b5e8c1c0 --- /dev/null +++ b/SECURITY.md @@ -0,0 +1,30 @@ +# Security Policy + +The DispersiveShallowWater.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/JoshuaLampert/DispersiveShallowWater.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/docs/Project.toml b/docs/Project.toml index a7b1e702..76e53476 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,4 +1,5 @@ [deps] +Changelog = "5217a498-cd5d-4ec6-b8c2-9b85a09b6e3e" Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" @@ -6,6 +7,7 @@ SummationByPartsOperators = "9f78cca6-572e-554e-b819-917d2f1cf240" TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284" [compat] +Changelog = "1" Documenter = "1" OrdinaryDiffEq = "6.49.1" Plots = "1.9" diff --git a/docs/make.jl b/docs/make.jl index 8503ee40..f6ca1870 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,6 +1,7 @@ using Documenter using DispersiveShallowWater using TrixiBase +using Changelog: Changelog # Dynamically replace all files in subdirectories of the source directory to include all files in these subdirectories # This way they don't need to be listed explicitly @@ -32,6 +33,56 @@ DocMeta.setdocmeta!(DispersiveShallowWater, :DocTestSetup, :(using DispersiveSha recursive = true) DocMeta.setdocmeta!(TrixiBase, :DocTestSetup, :(using TrixiBase); recursive = true) +# Copy some files from the repository root directory to the docs and modify them +# as necessary +# Based on: https://github.com/ranocha/SummationByPartsOperators.jl/blob/0206a74140d5c6eb9921ca5021cb7bf2da1a306d/docs/make.jl#L27-L41 +open(joinpath(@__DIR__, "src", "code_of_conduct.md"), "w") do io + # Point to source file + println(io, + """ + ```@meta + EditURL = "https://github.com/JoshuaLampert/DispersiveShallowWater.jl/blob/main/CODE_OF_CONDUCT.md" + ``` + """) + # Write the modified contents + println(io, "# [Code of Conduct](@id code-of-conduct)") + println(io, "") + for line in eachline(joinpath(dirname(@__DIR__), "CODE_OF_CONDUCT.md")) + println(io, "> ", line) + end +end + +open(joinpath(@__DIR__, "src", "contributing.md"), "w") do io + # Point to source file + println(io, + """ + ```@meta + EditURL = "https://github.com/JoshuaLampert/DispersiveShallowWater.jl/blob/main/CONTRIBUTING.md" + ``` + """) + # Write the modified contents + for line in eachline(joinpath(dirname(@__DIR__), "CONTRIBUTING.md")) + line = replace(line, "[LICENSE](LICENSE)" => "[License](@ref)") + println(io, line) + end +end + +# Create changelog +Changelog.generate(Changelog.Documenter(), # output type + joinpath(@__DIR__, "..", "NEWS.md"), # input file + joinpath(@__DIR__, "src", "changelog_tmp.md"); # output file + repo = "JoshuaLampert/DispersiveShallowWater.jl", # default repository for links + branch = "main",) +# Fix edit URL of changelog +open(joinpath(@__DIR__, "src", "changelog.md"), "w") do io + for line in eachline(joinpath(@__DIR__, "src", "changelog_tmp.md")) + if startswith(line, "EditURL") + line = "EditURL = \"https://github.com/JoshuaLampert/DispersiveShallowWater.jl/blob/main/NEWS.md\"" + end + println(io, line) + end +end + makedocs(; modules = [DispersiveShallowWater, TrixiBase], authors = "Joshua Lampert ", @@ -52,6 +103,9 @@ makedocs(; "TrixiBase" => "ref-trixibase.md", "DispersiveShallowWater" => "ref.md", ], + "Changelog" => "changelog.md", + "Contributing" => "contributing.md", + "Code of Conduct" => "code_of_conduct.md", "License" => "license.md", ])