Merge branch 'main' of github.com:gridap/GridapSolvers.jl into extensions

Author: JordiManyer

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

.github/workflows/CI.yml

@@ -27,18 +27,18 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Cache p4est
         id: cache-p4est
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
          path: ${{env.P4EST_ROOT_DIR}}
          key: ${{ runner.os }}-build-${{ env.P4EST_ROOT_DIR }}-
          restore-keys: |
            ${{ runner.os }}-build-${{ env.P4EST_ROOT_DIR }}-
            ${{ runner.os }}-build-
            ${{ runner.os }}-
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
@@ -106,7 +106,7 @@ jobs:
       - run: echo $PWD
       - run: julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.build(); Pkg.precompile()'
       - run: julia --project=. --color=yes --check-bounds=yes test/runtests.jl
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v5
         with:
           file: lcov.info
   docs:
@@ -115,8 +115,8 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
       - uses: julia-actions/julia-buildpkg@v1

.github/workflows/joss.yml

@@ -0,0 +1,24 @@
+name: Joss Paper
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft Compilation
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: joss_paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: joss_paper/paper.pdf

.gitignore

@@ -1,4 +1,4 @@
 .vscode
 Manifest.toml
 LocalPreferences.toml
-data
+data/*

CHANGELOG.md

@@ -0,0 +1,10 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## Previous versions
+
+A changelog is not maintained for older versions than 0.5.0.

Project.toml

@@ -1,7 +1,7 @@
 name = "GridapSolvers"
 uuid = "6d3209ee-5e3c-4db7-a716-942eb12ed534"
 authors = ["Santiago Badia <[email protected]>", "Jordi Manyer <[email protected]>", "Alberto F. Martin <[email protected]>", "Javier Principe <[email protected]>"]
-version = "0.4.1"
+version = "0.4.2"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
@@ -30,9 +30,9 @@ IterativeSolversExt = "IterativeSolvers"
 
 [compat]
 AbstractTrees = "0.4"
-BlockArrays = "0.16"
-FillArrays = "0.13, 1"
-Gridap = "0.18"
+BlockArrays = "1"
+FillArrays = "1"
+Gridap = "0.18.7"
 GridapDistributed = "0.4"
 GridapP4est = "0.3"
 GridapPETSc = "0.5"

README.md

@@ -4,7 +4,8 @@
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://gridap.github.io/GridapSolvers.jl/dev/)
 [![Build Status](https://github.com/gridap/GridapSolvers.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/gridap/GridapSolvers.jl/actions/workflows/CI.yml?query=branch%3Amain)
 [![Coverage](https://codecov.io/gh/gridap/GridapSolvers.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/gridap/GridapSolvers.jl)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13327414.svg)](https://zenodo.org/records/13327414)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13327414.svg)](https://doi.org/10.5281/zenodo.13327414)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.07162/status.svg)](https://doi.org/10.21105/joss.07162)
 
 GridapSolvers provides algebraic and non-algebraic solvers for the Gridap ecosystem, designed with High Performance Computing (HPC) in mind.
 
@@ -18,6 +19,14 @@ Solvers follow a modular design, where most blocks can be combined to produce PD
 - **Geometric Multigrid**: We provide a full-fledged geometric multigrid solver. Highly scalable adaptivity and redistribution of meshes, provided by `p4est` through `GridapP4est.jl`.
 - **PETSc interface**: Full access to PETSc algebraic solvers, through `GridapPETSc.jl`, with full interoperability with the rest of the aforementioned solvers.
 
+## Documentation and examples
+
+A (hopefully) comprehensive documentation is available at [https://gridap.github.io/GridapSolvers.jl/stable/](https://gridap.github.io/GridapSolvers.jl/stable/).
+
+A list of examples is available in the documentation. These include some very well known examples such as the Stokes, Incompressible Navier-Stokes and Darcy problems. The featured scripts are available in `test/Applications`.
+
+An example on how to use the library within an HPC cluster is available in `joss_paper/scalability`. The included example and drivers are used to generate the scalability results in our [JOSS paper](https://doi.org/10.21105/joss.07162).
+
 ## Installation
 
 GridapSolvers is a registered package in the official [Julia package registry](https://github.com/JuliaRegistries/General).  Thus, the installation of GridapSolvers is straight forward using the [Julia's package manager](https://julialang.github.io/Pkg.jl/v1/). Open the Julia REPL, type `]` to enter package mode, and install as follows
@@ -36,3 +45,32 @@ The previous installations steps will setup GridapSolvers to work using Julia's
 - [MPI.jl](https://juliaparallel.org/MPI.jl/stable/configuration/)
 - [GridapPETSc.jl](https://github.com/gridap/GridapPETSc.jl)
 - [GridapP4est.jl](https://github.com/gridap/GridapP4est.jl), and [P4est_wrapper.jl](https://github.com/gridap/p4est_wrapper.jl)
+
+## Citation
+
+In order to give credit to the `GridapSolvers` contributors, we simply ask you to cite the `Gridap` main project as indicated [here](https://github.com/gridap/Gridap.jl#how-to-cite-gridap) and the sub-packages you use as indicated in the corresponding repositories. Please, use the reference below in any publication in which you have made use of `GridapSolvers`:
+
+```
+@article{Manyer2024, 
+  doi = {10.21105/joss.07162}, 
+  url = {https://doi.org/10.21105/joss.07162}, 
+  year = {2024}, 
+  publisher = {The Open Journal}, 
+  volume = {9}, 
+  number = {102}, 
+  pages = {7162}, 
+  author = {Jordi Manyer and Alberto F. Martín and Santiago Badia}, 
+  title = {GridapSolvers.jl: Scalable multiphysics finite element solvers in Julia}, 
+  journal = {Journal of Open Source Software} 
+} 
+```
+
+## Contributing
+
+GridapSolvers is a collaborative project open to contributions. If you want to contribute, please take into account:
+
+  - Before opening a PR with a significant contribution, contact the project administrators by [opening an issue](https://github.com/gridap/GridapSolvers.jl/issues/new) describing what you are willing to implement. Wait for feedback from other community members.
+  - We adhere to the contribution and code-of-conduct instructions of the Gridap.jl project, available [here](https://github.com/gridap/Gridap.jl/blob/master/CONTRIBUTING.md) and [here](https://github.com/gridap/Gridap.jl/blob/master/CODE_OF_CONDUCT.md), resp.  Please, carefully read and follow the instructions in these files.
+  - Open a PR with your contribution.
+
+Want to help? We have [issues waiting for help](https://github.com/gridap/GridapSolvers.jl/labels/help%20wanted). You can start contributing to the GridapSolvers project by solving some of those issues.

docs/src/SolverInterfaces.md

@@ -26,5 +26,6 @@ CurrentModule = GridapSolvers.SolverInterfaces
   init!
   update!
   finalize!
+  set_depth!
   print_message
 ```

ext/GridapP4estExt/GridapP4estExt.jl

@@ -34,4 +34,24 @@ function P4estCartesianModelHierarchy(
   return mh
 end
 
+function GridapDistributed.DistributedAdaptedDiscreteModel(
+  model  :: GridapP4est.OctreeDistributedDiscreteModel,
+  parent :: GridapDistributed.DistributedDiscreteModel,
+  glue   :: AbstractArray{<:Gridap.Adaptivity.AdaptivityGlue};
+)
+  GridapDistributed.DistributedAdaptedDiscreteModel(
+    model.dmodel,parent,glue
+  )
+end
+
+function GridapDistributed.DistributedAdaptedDiscreteModel(
+  model  :: GridapP4est.OctreeDistributedDiscreteModel,
+  parent :: GridapP4est.OctreeDistributedDiscreteModel,
+  glue   :: AbstractArray{<:Gridap.Adaptivity.AdaptivityGlue};
+)
+  GridapDistributed.DistributedAdaptedDiscreteModel(
+    model.dmodel,parent.dmodel,glue
+  )
+end
+
 end # module

joss_paper/.gitignore

@@ -0,0 +1,3 @@
+paper.crossref
+paper.pdf
+demo