Release PreCICE.jl v2.4.0 (#38)

* Change version

* Correct TagBot

* Try _ to seperate PreCICE from bindings version

* Seperate bindings version with a `-`

* Change version to release candidate `2.4.0-0-rc1`

* Add formatter workflow (#31)

* Update README

* Add formatter workflow

* Format every current file

* New line at the end of the file

* Revert README changes

* Run format on each push on all branches

* Update README with general repository and troubleshooting (#30)

* Update README

* Minor edits to README

Co-authored-by: Ishaan Desai <ishaandesai@gmail.com>

* Fix bug: readScalarData returns wrong value (#33)

* Fix wrong transposes (#35)

* Add tests for Package functions (#32)

* Update README

* Add formatter workflow

* Format every current file

* New line at the end of the file

* Revert README changes

* Run format on each push on all branches

* [WIP] Set up testing for all functions

* [WIP] Set up testing for all functions

* Correct some errors and types

* Use string compare and debugging

* Debugging

* Undo Integer convert

* Don't use range for 1.6 compat

* integer to Cint

* Merge develop into testing

* Seperate Functioncall tests

* Add info message where to run `make`

* Format

* Move function tests back to the rest

* Undo documentation changes for now unchanged functions

* Add user info where to run `make`

* Update test workflow to include function tests

* Undo changes to workflow and Fix runtests

* Update Readme

* Test excluding julia x86 architecture

* Test running tests manually

* Undo workflow changes

* Compile Fake solverdummy

* Install make in workflow

* no sudo

* make instead of build essential

* update and apt

* Add info on how to compile fake SolveIinterface.c

* Change command in user info

* Update README.md

Co-authored-by: Ishaan Desai <ishaandesai@gmail.com>

* Update README.md

Co-authored-by: Ishaan Desai <ishaandesai@gmail.com>

* Review Changes

Co-authored-by: Ishaan Desai <ishaandesai@gmail.com>

* Remove meshName from arguments (#36)

* Remove meshName from arguments

* Remove MeshName from solverdummy test

* Format

* Fix tests (#37)

* Fix tests

* Remove unecessary comment

* Update version number

Co-authored-by: Ishaan Desai <ishaandesai@gmail.com>

.github/workflows/build-and-test.yml

@@ -41,5 +41,15 @@ jobs:
       - name: Build Package
         uses: julia-actions/julia-buildpkg@v1
 
+      - name: install make
+        run: |
+         apt update
+         apt install make
+
+      - name: Build Fake Solverinterface
+        run: |
+          cd test
+          make
+
       - name: Run tests
         uses: julia-actions/julia-runtest@v1

.github/workflows/format.yml

@@ -0,0 +1,36 @@
+name: format-check
+
+on: 
+  push
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1.6.0]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v1
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

.gitignore

@@ -3,3 +3,6 @@ binarybuilder
 solverdummy/*.log
 solverdummy/*.json
 solverdummy/precice-run/
+*.o
+*.so
+deps/build.log

Project.toml

@@ -1,7 +1,7 @@
 name = "PreCICE"
 uuid = "57fbd4af-5cc3-4712-aac0-6930e7658184"
 authors = ["preCICE <https://precice.org/> and contributors"]
-version = "0.0.1"
+version = "2.4.0"
 
 [compat]
 julia = "1.6"

README.md

@@ -8,44 +8,53 @@ This package provides Julia language bindings for the C++ library [preCICE](http
 
 ## Adding and using the package
 
-You can use the Julia bindings for preCICE by adding them as a package in a Julia environment or also directly including the package in a Julia script. For both type of usages you need to have preCICE installed on the system. For preCICE installation you can look at the [installation documentation](https://precice.org/installation-overview.html). 
+The Julia bindings for preCICE can be used by either by adding them as a package in a Julia environment or also directly including the package in a Julia script. For both type of usages preCICE needs to be installed on the system. For preCICE installation, have a look at the [installation documentation](https://precice.org/installation-overview.html).
 
-### Adding the package using the repository link
+### Adding the package
 
 Add the Julia bindings to the Julia environment in the following way:
 
 ```julia
 julia> ]
-pkg> add https://github.com/precice/julia-bindings.git 
+pkg> add PreCICE 
 Then exit the package mode with 🔙 or Ctrl + c
 julia> using PreCICE
 ```
 
 Alternatively you can also include the package in a Julia script in the following way:
 
 ```julia
-import Pkg; Pkg.add(url="https://github.com/precice/julia-bindings.git")
+import Pkg; Pkg.add("PreCICE")
 using PreCICE
 ```
 
 ### Adding the package from a local folder
 
 If you have cloned or downloaded the Julia bindings on your local machine, add the Julia bindings to your Julia environment in the following way:
 
-```julia
+```julia-repl
 julia> ]
 pkg> add <path-to-repository>
 Then exit the package mode with 🔙 or Ctrl + c
 julia> using PreCICE
 ```
 
-## Adding the package when preCICE is installed at a custom path
+Alternatively, you can install a specific branch of this repository with the following command:
+```julia-repl
+pkg> add https://github.com/precice/PreCICE.jl#<branch-name>
+```
 
-If you installed preCICE at a custom path, errors of the form ```ERROR: could not load library "/..."``` can occur after adding the Julia bindings package.
+## Troubleshooting
 
-Set your custom path through the environment variable `PRECICE_JL_BINARY` and rebuild this package:
+If preCICE is installed at a custom path, errors of the form ```ERROR: could not load library "/..."``` can occur after adding the Julia bindings package. Make sure the preCICE library is in the system library path through `echo $LD_LIBRARY_PATH` and otherwise update the variable with the correct path.
 
-```julia
+```bash
+~$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path-to-precice.so>
+```
+
+A different way to fix this error is to set the custom path of the preCICE installation through the environment variable `PRECICE_JL_BINARY`. Afterwards you need to rebuild this package:
+
+```julia-repl
 ~$ export PRECICE_JL_BINARY=/usr/lib/x86_64-linux-gnu/
 ~$ julia (--project)
 julia> ]
@@ -56,27 +65,29 @@ julia> using PreCICE
 
 ## Usage
 
-You can look at [solverdummy](https://github.com/precice/julia-bindings/tree/main/solverdummy) as an example of how to use the Julia bindings for preCICE.
-
-## Testing new features that are on branches of this repository
+The [solverdummy](https://github.com/precice/julia-bindings/tree/main/solverdummy) shows an example of how to use the Julia bindings for preCICE.
 
-To use a certain branch of this package, add `#branchname` after the package url, for example if the branch `mpi-parallelization` is to be tested:
+## Testing PreCICE.jl
 
-```julia
+To test the bindings, run:
+```julia-repl
 julia> ]
-pkg> add https://github.com/precice/julia-bindings.git#mpi-parallelization
-Then exit the package mode with 🔙 or Ctrl + c
-julia> using PreCICE
+pkg> test PreCICE
 ```
 
+This checks if the preCICE bindings can be found and accessed correctly.
+You can also test the full functionality of PreCICE.jl. If not set up, the output of the previous test shows an info on what command you need to execute. It will be along the lines of:
+```
+cd /home/<user>/.julia/packages/PreCICE/<code>/test && make
+```
+After this, you can run the tests again, resulting individual 22 tests being executed.
+
 ## Dependencies
 
 This package works with official Julia binaries listed below. See the [Platform Specific Instructions for official Binaries](https://julialang.org/downloads/platform/)  or [Julia's documentation](https://docs.julialang.org/en/v1/manual/getting-started/) if you are not sure how to download them.
 
 ## Supported versions
 
-The package is tested for Julia versions `1.6.0`, `1.6.5`, `1.7.0` and the two newest [Julia releases](https://github.com/JuliaLang/julia/releases).
-
-Versions prior to `v1.6.0` are not supported.
+The package is tested for Julia versions `1.6.0`, `1.6.5`, `1.7.0` and the two newest [Julia releases](https://github.com/JuliaLang/julia/releases). Julia versions prior to `v1.6.0` are not supported.
 
 [Unofficial Julia binaries](https://julialang.org/downloads/platform/#platform_specific_instructions_for_unofficial_binaries) may not be compatible.

deps/build.jl

@@ -1,4 +1,4 @@
-if VERSION<v"1.6"
+if VERSION < v"1.6"
     error("Julia version $VERSION not compatible with PreCICE Adapter")
 end
 
@@ -10,10 +10,10 @@ if haskey(ENV, "PRECICE_JL_BINARY")
     try
         Libc.Libdl.dlopen(libprecice)
         push!(Libc.Libdl.DL_LOAD_PATH, libprecice)
-    catch e 
+    catch e
         @warn "could not load custom preCICE binary at location: $libprecice"
         @warn "will search the system locations for a valid library."
         throw(e)
     end
-    
+
 end

solverdummy/README.md

@@ -2,13 +2,13 @@ This is a minimal working example for using preCICEC.jl with Julia. The solverdu
 
 From this directory, run 
 ```
-julia ./solverdummy.jl ./precice-config.xml SolverOne MeshOne
+julia ./solverdummy.jl ./precice-config.xml SolverOne
 ```
 
 or 
 
 ```
-julia ./solverdummy.jl ./precice-config.xml SolverTwo MeshTwo
+julia ./solverdummy.jl ./precice-config.xml SolverTwo
 ```
 
 respectively.

solverdummy/solverdummy.jl

@@ -3,8 +3,10 @@ using PreCICE
 commRank = 0
 commSize = 1
 
-if size(ARGS, 1) < 2
-    println("ERROR: pass config path, solver name and mesh name, example: julia solverdummy.jl ./precice-config.xml SolverOne MeshOne")
+if size(ARGS, 1) < 1
+    @error(
+        "ERROR: pass config path and solver name, example: julia solverdummy.jl ./precice-config.xml SolverOne",
+    )
     exit(1)
 end
 
@@ -15,15 +17,17 @@ solverName = ARGS[2]
 if solverName == "SolverOne"
     meshName = "MeshOne"
     dataWriteName = "dataOne"
-    dataReadName  = "dataTwo"
+    dataReadName = "dataTwo"
 else
     meshName = "MeshTwo"
-    dataReadName  = "dataOne"
+    dataReadName = "dataOne"
     dataWriteName = "dataTwo"
 end
 
 
-println("""DUMMY: Running solver dummy with preCICE config file "$configFileName", participant name "$solverName", and mesh name "$meshName" """)
+println(
+    """DUMMY: Running solver dummy with preCICE config file "$configFileName", participant name "$solverName", and mesh name "$meshName" """,
+)
 PreCICE.createSolverInterface(solverName, configFileName, commRank, commSize)
 
 meshID = PreCICE.getMeshID(meshName)
@@ -33,53 +37,53 @@ dimensions = PreCICE.getDimensions()
 numberOfVertices = 3
 
 
-readDataID  = PreCICE.getDataID(dataReadName, meshID)
+readDataID = PreCICE.getDataID(dataReadName, meshID)
 writeDataID = PreCICE.getDataID(dataWriteName, meshID)
 
 writeData = zeros(numberOfVertices, dimensions)
 
-vertices = Array{Float64, 2}(undef, numberOfVertices, dimensions)
+vertices = Array{Float64,2}(undef, numberOfVertices, dimensions)
 
-for i in 1:numberOfVertices, j in 1:dimensions
-        vertices[i,j] = i
+for i = 1:numberOfVertices, j = 1:dimensions
+    vertices[i, j] = i
 end
 
 vertexIDs = PreCICE.setMeshVertices(meshID, vertices)
 
 let # setting local scope for dt outside of the while loop
 
-dt = PreCICE.initialize()
-readData = zeros(numberOfVertices, dimensions)
+    dt = PreCICE.initialize()
+    readData = zeros(numberOfVertices, dimensions)
 
-while PreCICE.isCouplingOngoing()
-
-    if PreCICE.isActionRequired(PreCICE.actionWriteIterationCheckpoint())
-        println("DUMMY: Writing iteration checkpoint")
-        PreCICE.markActionFulfilled(PreCICE.actionWriteIterationCheckpoint())
-    end
+    while PreCICE.isCouplingOngoing()
 
-    if PreCICE.isReadDataAvailable()
-        readData = PreCICE.readBlockVectorData(readDataID, vertexIDs) 
-    end
+        if PreCICE.isActionRequired(PreCICE.actionWriteIterationCheckpoint())
+            println("DUMMY: Writing iteration checkpoint")
+            PreCICE.markActionFulfilled(PreCICE.actionWriteIterationCheckpoint())
+        end
 
-    for i in 1:numberOfVertices,j in 1:dimensions
-        writeData[i,j] = readData[i,j] + 1.0
-    end
+        if PreCICE.isReadDataAvailable()
+            readData = PreCICE.readBlockVectorData(readDataID, vertexIDs)
+        end
 
-    if PreCICE.isWriteDataRequired(dt)
-        PreCICE.writeBlockVectorData(writeDataID, vertexIDs, writeData)
-    end
+        for i = 1:numberOfVertices, j = 1:dimensions
+            writeData[i, j] = readData[i, j] + 1.0
+        end
 
-    dt = PreCICE.advance(dt)
+        if PreCICE.isWriteDataRequired(dt)
+            PreCICE.writeBlockVectorData(writeDataID, vertexIDs, writeData)
+        end
 
-    if PreCICE.isActionRequired(PreCICE.actionReadIterationCheckpoint())
-        println("DUMMY: Reading iteration checkpoint")
-        PreCICE.markActionFulfilled(PreCICE.actionReadIterationCheckpoint())
-    else
-        println("DUMMY: Advancing in time")
-    end
+        dt = PreCICE.advance(dt)
 
-end # while
+        if PreCICE.isActionRequired(PreCICE.actionReadIterationCheckpoint())
+            println("DUMMY: Reading iteration checkpoint")
+            PreCICE.markActionFulfilled(PreCICE.actionReadIterationCheckpoint())
+        else
+            println("DUMMY: Advancing in time")
+        end
+
+    end # while
 
 end # let