Added Docs and Codecov Improvements

.JuliaFormatter.toml

@@ -0,0 +1 @@
+style = "blue"

.github/workflows/CI.yml

@@ -39,6 +39,13 @@ jobs:
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+        if: matrix.version == '1.10' && matrix.os == 'ubuntu-latest'
+      - uses: codecov/codecov-action@v5
+        if: matrix.version == '1.10' && matrix.os == 'ubuntu-latest'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
   docs:
     name: Documentation
     runs-on: ubuntu-latest

CODE_OF_CONDUCT.md

@@ -0,0 +1,6 @@
+JuliaHealth Community Standards
+=========================
+
+The JuliaHealth community abides by the broader Julia Community Code of Conduct (CoC). You can find that CoC listed here: https://julialang.org/community/standards/
+
+If you have a conflict or concern that requires resolution, please contact the [Julia Community Stewards](https://julialang.org/community/stewards/).

CONTRIBUTING.md

@@ -0,0 +1,41 @@
+# Contributing Guidelines
+
+Thanks for taking the time to contribute to BloodFlowTrixi.jl! ❤️
+
+We appreciate your interest in improving this project. Before you start contributing, please take a moment to review the following guidelines.
+
+
+## Reporting Issues
+
+First off, we assume that you have read the available [Documentation](https://juliahealth.org/BloodFlowTrixi.jl/dev/).
+
+Before you report an issue, it is best to search for existing [Issues](https://github.com/JuliaHealth/BloodFlowTrixi.jl/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue.
+
+If you then still feel the need to report an issue, we recommend the following:
+
+- Open an [Issue on GitHub](https://github.com/JuliaHealth/BloodFlowTrixi.jl/issues/new).
+- Provide as much context as you can about what you're running into.
+- Provide project and platform versions, depending on what seems relevant.
+
+We will then take care of the issue as soon as possible.
+
+
+## How to Contribute
+
+- **Implement Code Changes**: Introduce your modifications, ensuring adherence to the [Julia Blue Style Guidelines](https://github.com/invenia/BlueStyle). For new features, include informative comments, docstrings, and consider enriching the documentation with relevant examples.
+
+- **Format Code**: This project uses JuliaFormatter with Blue style. Run formatting from the repository root using these steps:
+	- `julia --project=dev`
+	- `using JuliaFormatter`
+	- `format(".")`
+
+- **Validate Changes with Tests**: Execute existing tests to verify the compatibility of your alterations with the current functionality. If applicable, incorporate additional tests to validate your new contributions.
+
+- **Undergo Code Review**: Subject your code to review by maintainers, who will provide feedback and may request further adjustments before merging.
+
+
+## License
+
+By contributing to BloodFlowTrixi.jl, you agree that your contributions will be licensed under the [MIT License](LICENSE).
+
+Thank you for contributing to BloodFlowTrixi.jl! 🌟

Project.toml

@@ -1,7 +1,7 @@
 name = "BloodFlowTrixi"
 uuid = "7b46d5ad-635f-4b66-9393-904f183e39b5"
-version = "0.1.7"
 authors = ["yolhan83 <yolhan@laposte.net>"]
+version = "0.1.7"
 
 [deps]
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"

README.md

@@ -3,6 +3,7 @@
 [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliahealth.org/BloodFlowTrixi.jl/stable/)
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliahealth.org/BloodFlowTrixi.jl/dev/)
 [![Build Status](https://github.com/yolhan83/BloodFlowTrixi.jl/actions/workflows/CI.yml/badge.svg?branch=master)](https://github.com/yolhan83/BloodFlowTrixi.jl/actions/workflows/CI.yml?query=branch%3Amaster)
+[![Coverage](https://codecov.io/gh/JuliaHealth/BloodFlowTrixi.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaHealth/BloodFlowTrixi.jl)
 [![Aqua](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 
 **BloodFlowTrixi.jl** is a Julia package that implements one-dimensional (1D) and two-dimensional (2D) blood flow models for arterial circulation. These models are derived from the Navier-Stokes equations and were developed as part of my PhD research in applied mathematics, focusing on cardiovascular pathologies such as aneurysms and stenoses.
@@ -57,6 +58,10 @@ pkg> add Trixi
 pkg> add BloodFlowTrixi
 ```
 
+## Usage Examples
+
+For detailed usage examples and tutorials on how to use BloodFlowTrixi.jl, please visit the [Tutorial Documentation](https://juliahealth.org/BloodFlowTrixi.jl/stable/tuto/).
+
 # Simulations
 ![Alt Text](./docs/src/graph.gif)
 ![Alt Text](./docs/src/graph2d.gif)
@@ -80,6 +85,14 @@ pkg> add BloodFlowTrixi
 
 This package is licensed under the MIT license.
 
+## Contributing
+
+We welcome contributions from the community! If you find a bug, have a feature request, or want to improve the package, please:
+
+1. Check the [Contributing Guidelines](CONTRIBUTING.md)
+2. See the [Code of Conduct](CODE_OF_CONDUCT.md)
+3. Open a [new issue](https://github.com/JuliaHealth/BloodFlowTrixi.jl/issues) or [pull request](https://github.com/JuliaHealth/BloodFlowTrixi.jl/pulls)
+
 ## Acknowledgments
 
 This package was developed as part of my PhD research in applied mathematics in the IMATH laboratory and founded by the University of Toulon in France, focusing on mathematical modeling and numerical simulation of blood flow in arteries. 

dev/.gitignore

@@ -0,0 +1 @@
+/Manifest.toml

dev/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+
+[compat]
+JuliaFormatter = "2.3.0"

docs/make.jl

@@ -12,14 +12,7 @@ makedocs(;
         edit_link="master",
         assets=String[],
     ),
-    pages=[
-        "Home" => "index.md",
-        "Tutorial" => "tuto.md",
-        "Mathematics" => "math.md"
-    ],
+    pages=["Home" => "index.md", "Tutorial" => "tuto.md", "Mathematics" => "math.md"],
 )
 
-deploydocs(;
-    repo="github.com/JuliaHealth/BloodFlowTrixi.jl",
-    devbranch="master",
-)
+deploydocs(; repo="github.com/JuliaHealth/BloodFlowTrixi.jl", devbranch="master")

exemples/Model1D/exemple.jl

@@ -2,42 +2,34 @@ using Trixi
 using BloodFlowTrixi
 using OrdinaryDiffEq
 
-eq = BloodFlowEquations1D(; h = 0.1)
+eq = BloodFlowEquations1D(; h=0.1)
 
-mesh = TreeMesh(0.0, 40.0, 
-    initial_refinement_level = 4, 
-    n_cells_max = 10^4, 
-    periodicity = false)
+mesh = TreeMesh(0.0, 40.0; initial_refinement_level=4, n_cells_max=10^4, periodicity=false)
 
-bc = (;
-    x_neg = boundary_condition_pressure_in,
-    x_pos = Trixi.BoundaryConditionDoNothing()
-)
+bc = (; x_neg=boundary_condition_pressure_in, x_pos=Trixi.BoundaryConditionDoNothing())
 
-solver = DGSEM(polydeg = 2,
-    surface_flux = (flux_lax_friedrichs,flux_nonconservative),
-    volume_integral = VolumeIntegralFluxDifferencing((flux_lax_friedrichs,flux_nonconservative))
-    )
+solver = DGSEM(;
+    polydeg=2,
+    surface_flux=(flux_lax_friedrichs, flux_nonconservative),
+    volume_integral=VolumeIntegralFluxDifferencing((
+        flux_lax_friedrichs, flux_nonconservative
+    )),
+)
 
 semi = SemidiscretizationHyperbolic(
     mesh,
     eq,
     initial_condition_simple,
-    source_terms = source_term_simple,
-    solver,
-    boundary_conditions = bc
+    solver;
+    source_terms=source_term_simple,
+    boundary_conditions=bc,
 )
 
 tspan = (0.0, 0.3)
 ode = semidiscretize(semi, tspan)
 
-dt_adapt = StepsizeCallback(;cfl=0.5)
-analyse = AliveCallback(
-    alive_interval = 10,
-    analysis_interval = 100
-)
-cb = CallbackSet(
-    dt_adapt,analyse
-)
+dt_adapt = StepsizeCallback(; cfl=0.5)
+analyse = AliveCallback(; alive_interval=10, analysis_interval=100)
+cb = CallbackSet(dt_adapt, analyse)
 
-sol = solve(ode, SSPRK33(),dt = dt_adapt(ode),callback= cb)
+sol = solve(ode, SSPRK33(); dt=dt_adapt(ode), callback=cb)

exemples/Model1DOrd2/exemple.jl

@@ -2,48 +2,40 @@ using Trixi
 using BloodFlowTrixi
 using OrdinaryDiffEq
 
-eq = BloodFlowEquations1D(; h = 0.1)
+eq = BloodFlowEquations1D(; h=0.1)
 eq_ord2 = BloodFlowEquations1DOrd2(eq)
 
-mesh = TreeMesh(0.0, 40.0, 
-    initial_refinement_level = 4, 
-    n_cells_max = 10^4, 
-    periodicity = false)
+mesh = TreeMesh(0.0, 40.0; initial_refinement_level=4, n_cells_max=10^4, periodicity=false)
 
-bc_hypo = (;
-    x_neg = boundary_condition_pressure_in,
-    x_pos = Trixi.BoundaryConditionDoNothing()
-)
+bc_hypo = (; x_neg=boundary_condition_pressure_in, x_pos=Trixi.BoundaryConditionDoNothing())
 
 bc_parab = (;
-    x_neg = BoundaryConditionNeumann((x,t,eq) -> SVector(0.0,0,0,0,0)),
-    x_pos = BoundaryConditionNeumann((x,t,eq) -> SVector(0.0,0,0,0,0))
+    x_neg=BoundaryConditionNeumann((x, t, eq) -> SVector(0.0, 0, 0, 0, 0)),
+    x_pos=BoundaryConditionNeumann((x, t, eq) -> SVector(0.0, 0, 0, 0, 0)),
 )
 
-solver = DGSEM(polydeg = 2,
-    surface_flux = (flux_lax_friedrichs,flux_nonconservative),
-    volume_integral = VolumeIntegralFluxDifferencing((flux_lax_friedrichs,flux_nonconservative))
-    )
+solver = DGSEM(;
+    polydeg=2,
+    surface_flux=(flux_lax_friedrichs, flux_nonconservative),
+    volume_integral=VolumeIntegralFluxDifferencing((
+        flux_lax_friedrichs, flux_nonconservative
+    )),
+)
 
 semi = SemidiscretizationHyperbolicParabolic(
     mesh,
-    (eq,eq_ord2),
-    initial_condition_simple,
-    source_terms = source_term_simple_ord2,
+    (eq, eq_ord2),
+    initial_condition_simple;
+    source_terms=source_term_simple_ord2,
     solver,
-    boundary_conditions = (bc_hypo,bc_parab)
+    boundary_conditions=(bc_hypo, bc_parab),
 )
 
 tspan = (0.0, 0.3)
 ode = semidiscretize(semi, tspan)
 
-dt_adapt = StepsizeCallback(;cfl=0.5)
-analyse = AliveCallback(
-    alive_interval = 10,
-    analysis_interval = 100
-)
-cb = CallbackSet(
-    dt_adapt,analyse
-)
+dt_adapt = StepsizeCallback(; cfl=0.5)
+analyse = AliveCallback(; alive_interval=10, analysis_interval=100)
+cb = CallbackSet(dt_adapt, analyse)
 
-sol = solve(ode, SSPRK33(),dt = dt_adapt(ode),callback= cb)
+sol = solve(ode, SSPRK33(); dt=dt_adapt(ode), callback=cb)

exemples/Model2D/diexemple.jl

@@ -6,56 +6,53 @@ using StaticArrays, LinearAlgebra
 using QuadGK
 using LinearAlgebra
 
-eq = BloodFlowEquations2D(; h = 0.1)
-xyz_data = [SA[cos(0.2*si),sin(0.2*si),si] for si in range(0,40,100)]
+eq = BloodFlowEquations2D(; h=0.1)
+xyz_data = [SA[cos(0.2*si), sin(0.2*si), si] for si in range(0, 40, 100)]
 
 curve = interpolate_curve(xyz_data)
-L = curve.t[end-1]
+L = curve.t[end - 1]
 println("curve length : $L")
-BloodFlowTrixi.curvature(s) = norm(DataInterpolations.derivative(curve,s,2))
+BloodFlowTrixi.curvature(s) = norm(DataInterpolations.derivative(curve, s, 2))
 
 mesh = P4estMesh(
-    (1,2),
-    polydeg = 1,
-    periodicity = (true,false),
-    coordinates_min = (0.0,0.0),
-    coordinates_max = (2*pi,L),
-    initial_refinement_level = 4
+    (1, 2);
+    polydeg=1,
+    periodicity=(true, false),
+    coordinates_min=(0.0, 0.0),
+    coordinates_max=(2*pi, L),
+    initial_refinement_level=4,
 )
 
-bc = (;
-    y_neg = boundary_condition_pressure_in,
-    y_pos = Trixi.BoundaryConditionDoNothing()
-)
+bc = (; y_neg=boundary_condition_pressure_in, y_pos=Trixi.BoundaryConditionDoNothing())
 
-solver = DGSEM(polydeg = 1,
-    surface_flux = (flux_lax_friedrichs,flux_nonconservative),
-    volume_integral = VolumeIntegralFluxDifferencing((flux_lax_friedrichs,flux_nonconservative))
-    )
+solver = DGSEM(;
+    polydeg=1,
+    surface_flux=(flux_lax_friedrichs, flux_nonconservative),
+    volume_integral=VolumeIntegralFluxDifferencing((
+        flux_lax_friedrichs, flux_nonconservative
+    )),
+)
 
 semi = SemidiscretizationHyperbolic(
     mesh,
     eq,
     initial_condition_simple,
-    source_terms = source_term_simple,
-    solver,
-    boundary_conditions = bc
+    solver;
+    source_terms=source_term_simple,
+    boundary_conditions=bc,
 )
 
 tspan = (0.0, 0.3)
 ode = semidiscretize(semi, tspan)
 
-dt_adapt = StepsizeCallback(;cfl=0.5)
-analyse = AliveCallback(
-    alive_interval = 10,
-    analysis_interval = 100
-)
-cb = CallbackSet(
-    dt_adapt,analyse
-)
+dt_adapt = StepsizeCallback(; cfl=0.5)
+analyse = AliveCallback(; alive_interval=10, analysis_interval=100)
+cb = CallbackSet(dt_adapt, analyse)
 
-sol = solve(ode, SSPRK33(),dt = dt_adapt(ode),callback= cb,saveat = 0.03,save_everystep = false)
+sol = solve(
+    ode, SSPRK33(); dt=dt_adapt(ode), callback=cb, saveat=0.03, save_everystep=false
+)
 
 # artery center-line
 
-res = get3DData(eq,xyz_data,semi,sol,1)
+res = get3DData(eq, xyz_data, semi, sol, 1)