Merge pull request #11 from gridap/P4est_wrapper

amartinhuertas · web-flow · commit 268593cdd609 · 2021-09-21T18:15:25.000+10:00
P4est wrapper
diff --git a/Project.toml b/Project.toml
@@ -1,4 +1,4 @@
-name = "p4est_wrapper"
+name = "P4est_wrapper"
 uuid = "3743d7c0-8adf-11ea-380b-7d33b0ecc1da"
 authors = ["Victor Sande <vsande@cimne.upc.edu>", "Alberto F. Martin <alberto.martin@monash.edu>"]
 version = "0.1.0"
diff --git a/README.md b/README.md
@@ -1,20 +1,20 @@
-# p4est_wrapper
+# P4est_wrapper
 
 Julia wrappers for p4est library ([Parallel AMR on Forests of Octrees](http://www.p4est.org/))
 
-[![Build Status](https://github.com/gridap/p4est_wrapper.jl/workflows/CI/badge.svg?branch=master)](https://github.com/gridap/p4est_wrapper.jl/actions)
-[![Codecov](https://codecov.io/gh/gridap/p4est_wrapper.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/gridap/p4est_wrapper.jl)
+[![Build Status](https://github.com/gridap/P4est_wrapper.jl/workflows/CI/badge.svg?branch=master)](https://github.com/gridap/P4est_wrapper.jl/actions)
+[![Codecov](https://codecov.io/gh/gridap/P4est_wrapper.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/gridap/P4est_wrapper.jl)
 
 
 ## Basic Usage
 
 ```julia
 using MPI
-using p4est_wrapper
+using P4est_wrapper
 using Test
 
-sc_init(MPI.COMM_WORLD, Cint(true), Cint(true), C_NULL, p4est_wrapper.SC_LP_DEFAULT)
-p4est_init(C_NULL, p4est_wrapper.SC_LP_DEFAULT)
+sc_init(MPI.COMM_WORLD, Cint(true), Cint(true), C_NULL, P4est_wrapper.SC_LP_DEFAULT)
+p4est_init(C_NULL, P4est_wrapper.SC_LP_DEFAULT)
 unitsquare_connectivity = p4est_connectivity_new_unitsquare() 
 unitsquare_forest = p4est_new(MPI.COMM_WORLD, unitsquare_connectivity, 0, C_NULL, C_NULL) 
 ...
@@ -28,38 +28,38 @@ MPI.Finalize()
 
 ## Installation
 
-**p4est_wrapper.jl** itself is installed when you add and use it into another project.
+**P4est_wrapper.jl** itself is installed when you add and use it into another project.
 
 Please, ensure that your system fulfill the requirements.
 
 To include into your project form Julia REPL, use the following commands:
 
 ```
-pkg> add p4est_wrapper
-julia> using p4est_wrapper
+pkg> add P4est_wrapper
+julia> using P4est_wrapper
 ```
 
 If, for any reason, you need to manually build the project, write down the following commands in Julia REPL:
 ```
-pkg> add p4est_wrapper
-pkg> build p4est_wrapper
-julia> using p4est_wrapper
+pkg> add P4est_wrapper
+pkg> build P4est_wrapper
+julia> using P4est_wrapper
 ```
 
 ### Requirements
 
   - `p4est >= 2.2`
   - `MPI` 
 
-`p4est_wrapper` julia package requires `p4est` library ([Parallel AMR on Forests of Octrees](http://www.p4est.org/)), and (optionally) `MPI` to work correctly. 
+`P4est_wrapper` julia package requires `p4est` library ([Parallel AMR on Forests of Octrees](http://www.p4est.org/)), and (optionally) `MPI` to work correctly. 
   - Latests versions of julia `MPI` use artifacts to locally install a MPI distribution. You should take care with the compatibility (version/vendor/distribution) between the parallel `p4est` and `MPI` libraries. If you want julia `MPI` library to wrap your local MPI library, you must export `JULIA_MPI_BINARY="system"` before installing the package.
-  - Parallel `p4est` library can be manually installed in a custom path on your local machine. In order to succesfull describe your custom installation to be discovered by `p4est_wrapper`, you must export `P4EST_ROOT_DIR` environment variable pointing to the installation directory. If this environment variable is not available, and `julia >= 1.3`, `p4est_wrapper` will try to  use [`P4est_jll` artifact](https://github.com/JuliaBinaryWrappers/P4est_jll.jl), but you should take into account that this artifact is not for parallel computations (MPI not enabled). Finally, in other case `p4est_wrapper` will try to find the `p4est` library in the usual linux user library directory (`/usr/lib`).
+  - Parallel `p4est` library can be manually installed in a custom path on your local machine. In order to succesfull describe your custom installation to be discovered by `P4est_wrapper`, you must export `P4EST_ROOT_DIR` environment variable pointing to the installation directory. If this environment variable is not available, and `julia >= 1.3`, `P4est_wrapper` will try to  use [`P4est_jll` artifact](https://github.com/JuliaBinaryWrappers/P4est_jll.jl), but you should take into account that this artifact is not for parallel computations (MPI not enabled). Finally, in other case `P4est_wrapper` will try to find the `p4est` library in the usual linux user library directory (`/usr/lib`).
 
 #### Basic OpenMPI installation in debian based systems
 
 `MPI` can be obtained from the default repositories of your Debian-based OS by means of `apt` tool.
 
-Basic `MPI` installation in order to use it from `p4est_wrapper` julia package is as follows:
+Basic `MPI` installation in order to use it from `P4est_wrapper` julia package is as follows:
 
 ```
 apt-get update
@@ -102,8 +102,8 @@ Note: you need the following tools:
 
 ## Automated p4est wrapper generator
 
-`p4est_wrapper` bindings are automatically generated by using [Clang](https://github.com/JuliaInterop/Clang.jl) package.
+`P4est_wrapper` bindings are automatically generated by using [Clang](https://github.com/JuliaInterop/Clang.jl) package.
 
-To learn more about how it works, please read the README file at [gen directory](https://github.com/gridap/p4est_wrapper.jl/tree/master/gen).
+To learn more about how it works, please read the README file at [gen directory](https://github.com/gridap/P4est_wrapper.jl/tree/master/gen).
 
 
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,17 +1,17 @@
-using Documenter, p4est_wrapper
+using Documenter, P4est_wrapper
 
 makedocs(;
-    modules=[p4est_wrapper],
+    modules=[P4est_wrapper],
     format=Documenter.HTML(),
     pages=[
         "Home" => "index.md",
     ],
-    repo="https://github.com/gridap/p4est_wrapper.jl/blob/{commit}{path}#L{line}",
-    sitename="p4est_wrapper.jl",
+    repo="https://github.com/gridap/P4est_wrapper.jl/blob/{commit}{path}#L{line}",
+    sitename="P4est_wrapper.jl",
     authors="Víctor Sande <vsande@cimne.upc.edu>, Large Scale Scientific Computing",
     assets=String[],
 )
 
 deploydocs(;
-    repo="github.com/gridap/p4est_wrapper.jl",
+    repo="github.com/gridap/P4est_wrapper.jl",
 )
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,8 +1,8 @@
-# p4est_wrapper.jl
+# P4est_wrapper.jl
 
 ```@index
 ```
 
 ```@autodocs
-Modules = [p4est_wrapper]
+Modules = [P4est_wrapper]
 ```
diff --git a/src/P4est_wrapper.jl b/src/P4est_wrapper.jl
@@ -1,24 +1,24 @@
-module p4est_wrapper
+module P4est_wrapper
 
 ################################################################
 # Check correct installation
 ################################################################
 # Load in `deps.jl`, complaining if it does not exist
 const depsjl_path = joinpath(@__DIR__, "..", "deps", "deps.jl")
 if !isfile(depsjl_path)
-    error("p4est_wrapper was not build properly. Please run Pkg.build(\"p4est.jl\").")
+    error("P4est_wrapper was not build properly. Please run Pkg.build(\"p4est.jl\").")
 end
 include(depsjl_path)
 # Check if p4est library was found
 if(!P4EST_FOUND)
-    error("p4est_wrapper was not build properly. Please run Pkg.build(\"p4est.jl\").")
+    error("P4est_wrapper was not build properly. Please run Pkg.build(\"p4est.jl\").")
 end
 
 # Use library path from build process
 const p4est_lib = P4EST_LIB
 
 ################################################################
-# Use dependencies 
+# Use dependencies
 ################################################################
 using Libdl
 using MPI
@@ -32,7 +32,7 @@ export Ctm, Ctime_t, Cclock_t
 
 # Include P4EST bindings
 
-# The following file fix and/or complete 
+# The following file fix and/or complete
 # the automated generation of types and data structures
 include(joinpath(@__DIR__, "common_fixes.jl"))
 
@@ -56,7 +56,7 @@ include(joinpath(@__DIR__, "api_fixes.jl"))
 # Export everything starting with ...
 ################################################################
 foreach(names(@__MODULE__, all=true)) do s
-    if startswith(string(s), "sc") || startswith(string(s), "p4est") || startswith(string(s), "p6est") || startswith(string(s), "p8est") 
+    if startswith(string(s), "sc") || startswith(string(s), "p4est") || startswith(string(s), "p6est") || startswith(string(s), "p8est")
         @eval export $s
     end
 end
diff --git a/test/example_1.jl b/test/example_1.jl
@@ -1,5 +1,5 @@
 using MPI
-using p4est_wrapper
+using P4est_wrapper
 using Test
 
 # Initialize MPI if not initialized yet
@@ -38,17 +38,17 @@ const search_point_fn_c = @cfunction(search_point_fn, Cint, (Ptr{p4est_t}, p4est
 # Main program
 #############################################################################
 
-mpicomm = p4est_wrapper.P4EST_ENABLE_MPI ? MPI.COMM_WORLD : Cint(0)
+mpicomm = P4est_wrapper.P4EST_ENABLE_MPI ? MPI.COMM_WORLD : Cint(0)
 
 # Create a connectivity structure for the unit square.
-unitsquare_connectivity = p4est_connectivity_new_unitsquare() 
+unitsquare_connectivity = p4est_connectivity_new_unitsquare()
 @test unitsquare_connectivity != C_NULL
 
 # Create a new forest
-unitsquare_forest = p4est_new(mpicomm, unitsquare_connectivity, 0, C_NULL, C_NULL) 
+unitsquare_forest = p4est_new(mpicomm, unitsquare_connectivity, 0, C_NULL, C_NULL)
 @test unitsquare_forest != C_NULL
 
-# Register callback function to decide for refinement. 
+# Register callback function to decide for refinement.
 p4est_refine(unitsquare_forest, 1, my_refine_c, C_NULL)
 
 # Create a new sc_array
@@ -59,7 +59,7 @@ ptr_to_points_sc_array = sc_array_new_count(sizeof(point_t), 2)
 points_sc_array = ptr_to_points_sc_array[]
 @test points_sc_array.elem_count == 2 && points_sc_array.elem_size == sizeof(point_t)
 
-# Obtain reference to first point_t 
+# Obtain reference to first point_t
 ptr_to_points_array = Ptr{point_t}(sc_array_index(ptr_to_points_sc_array,0))
 @test ptr_to_points_array != C_NULL
 
diff --git a/test/example_2.jl b/test/example_2.jl
@@ -1,5 +1,5 @@
 using MPI
-using p4est_wrapper
+using P4est_wrapper
 using Test
 
 # Initialize MPI if not initialized yet
@@ -26,24 +26,24 @@ const my_refine_c = @cfunction(my_refine, Cint, (Ptr{p4est_t}, p4est_topidx_t, P
 # Main program
 #############################################################################
 
-mpicomm = p4est_wrapper.P4EST_ENABLE_MPI ? MPI.COMM_WORLD : Cint(0)
+mpicomm = P4est_wrapper.P4EST_ENABLE_MPI ? MPI.COMM_WORLD : Cint(0)
 
 # Create a connectivity structure for the unit square.
-unitsquare_connectivity = p4est_connectivity_new_unitsquare() 
+unitsquare_connectivity = p4est_connectivity_new_unitsquare()
 @assert Bool(p4est_connectivity_is_valid(unitsquare_connectivity))
 
 # Create a new forest
-unitsquare_forest = p4est_new(mpicomm, unitsquare_connectivity, sizeof(p4est_quadrant_t), C_NULL, C_NULL) 
+unitsquare_forest = p4est_new(mpicomm, unitsquare_connectivity, sizeof(p4est_quadrant_t), C_NULL, C_NULL)
 @test unitsquare_forest != C_NULL
 
-# Register callback function to decide for refinement. 
+# Register callback function to decide for refinement.
 p4est_refine(unitsquare_forest, 1, my_refine_c, C_NULL)
 
 # Equally partition the forest. The partition can be by element count or by a user-defined weight.
 p4est_partition(unitsquare_forest, 0, C_NULL);
 
-# Build the ghost layer. 
-ptr_to_p4est_ghost = p4est_ghost_new(unitsquare_forest, p4est_wrapper.P4EST_CONNECT_FULL)
+# Build the ghost layer.
+ptr_to_p4est_ghost = p4est_ghost_new(unitsquare_forest, P4est_wrapper.P4EST_CONNECT_FULL)
 p4est_ghost = ptr_to_p4est_ghost[]
 
 # Obtain ghost quadrants
@@ -56,7 +56,7 @@ for i=1:p4est_ghost.mpisize
         quadrant = ptr_ghost_quadrants[j+1]
         piggy3 = quadrant.p.piggy3
         @test Bool(p4est_quadrant_is_valid(ptr_ghost_quadrants+(sizeof(p4est_quadrant_t)*j)))
-        p4est_quadrant_print(p4est_wrapper.SC_LP_INFO, ptr_ghost_quadrants+(sizeof(p4est_quadrant_t)*j))
+        p4est_quadrant_print(P4est_wrapper.SC_LP_INFO, ptr_ghost_quadrants+(sizeof(p4est_quadrant_t)*j))
         print("(i, j, local_num, which_tree) ($(i),$(j),$(piggy3.local_num),$(piggy3.which_tree)) \n")
     end
 end
diff --git a/test/example_3.jl b/test/example_3.jl
@@ -1,5 +1,5 @@
 using MPI
-using p4est_wrapper
+using P4est_wrapper
 using Test
 
 # Initialize MPI if not initialized yet
@@ -27,8 +27,8 @@ const coarsen_flag = Cint(2)
 # back function to an array of ints with as many entries as forest quadrants. This call back function
 # initializes the quadrant->p.user_data void * pointer of all quadrants such that it
 # points to the corresponding entry in the global array mentioned in the previous sentence.
-function init_fn_callback_2d(forest_ptr::Ptr{p4est_t}, 
-                            which_tree::p4est_topidx_t, 
+function init_fn_callback_2d(forest_ptr::Ptr{p4est_t},
+                            which_tree::p4est_topidx_t,
                             quadrant_ptr::Ptr{p4est_quadrant_t})
     @assert which_tree == 0
     # Extract a reference to the first (and uniquely allowed) tree
@@ -45,8 +45,8 @@ end
 
 const init_fn_callback_2d_c = @cfunction(init_fn_callback_2d, Cvoid, (Ptr{p4est_t}, p4est_topidx_t, Ptr{p4est_quadrant_t}))
 
-function refine_callback_2d(::Ptr{p4est_t}, 
-                            which_tree::p4est_topidx_t, 
+function refine_callback_2d(::Ptr{p4est_t},
+                            which_tree::p4est_topidx_t,
                             quadrant_ptr::Ptr{p4est_quadrant_t})
     @assert which_tree == 0
     quadrant = quadrant_ptr[]
@@ -58,17 +58,17 @@ const refine_callback_2d_c = @cfunction(refine_callback_2d, Cint, (Ptr{p4est_t},
 # For each refined quadrant:
 #   num_calls is even -> leave untouched all children
 #   num_calls is odd  -> mark all children for coarsening
-function refine_replace_callback_2d(forest_ptr::Ptr{p4est_t}, 
-                                    which_tree::p4est_topidx_t, 
-                                    num_outgoing::Cint, 
-                                    outgoing_ptr::Ptr{Ptr{p4est_quadrant_t}}, 
-                                    num_incoming::Cint, 
+function refine_replace_callback_2d(forest_ptr::Ptr{p4est_t},
+                                    which_tree::p4est_topidx_t,
+                                    num_outgoing::Cint,
+                                    outgoing_ptr::Ptr{Ptr{p4est_quadrant_t}},
+                                    num_incoming::Cint,
                                     incoming_ptr::Ptr{Ptr{p4est_quadrant_t}})
     @assert which_tree   == 0
     @assert num_outgoing == 1
-    @assert num_incoming == p4est_wrapper.P4EST_CHILDREN
-    incoming = unsafe_wrap(Array, incoming_ptr, p4est_wrapper.P4EST_CHILDREN)
-    for quadrant_index = 1:p4est_wrapper.P4EST_CHILDREN
+    @assert num_incoming == P4est_wrapper.P4EST_CHILDREN
+    incoming = unsafe_wrap(Array, incoming_ptr, P4est_wrapper.P4EST_CHILDREN)
+    for quadrant_index = 1:P4est_wrapper.P4EST_CHILDREN
         quadrant = incoming[quadrant_index][]
         if (num_calls % 2 == 0)
             unsafe_store!(Ptr{Cint}(quadrant.p.user_data), nothing_flag, 1)
@@ -87,8 +87,8 @@ function coarsen_callback_2d(forest_ptr::Ptr{p4est_t},
                             quadrants_ptr::Ptr{Ptr{p4est_quadrant_t}})
     @assert which_tree == 0
     coarsen = Cint(1)
-    quadrants = unsafe_wrap(Array, quadrants_ptr, p4est_wrapper.P4EST_CHILDREN)
-    for quadrant_index = 1:p4est_wrapper.P4EST_CHILDREN
+    quadrants = unsafe_wrap(Array, quadrants_ptr, P4est_wrapper.P4EST_CHILDREN)
+    for quadrant_index = 1:P4est_wrapper.P4EST_CHILDREN
         quadrant = quadrants[quadrant_index][]
         coarsen = Cint(unsafe_wrap(Array, Ptr{Cint}(quadrant.p.user_data), 1)[] ==  coarsen_flag)
         if (!Bool(coarsen)) return coarsen end
@@ -119,9 +119,9 @@ end
 # Main program
 #############################################################################
 
-mpicomm = p4est_wrapper.P4EST_ENABLE_MPI ? MPI.COMM_WORLD : Cint(0)
-sc_init(mpicomm, Cint(true), Cint(true), C_NULL, p4est_wrapper.SC_LP_DEFAULT)
-p4est_init(C_NULL, p4est_wrapper.SC_LP_DEFAULT)
+mpicomm = P4est_wrapper.P4EST_ENABLE_MPI ? MPI.COMM_WORLD : Cint(0)
+sc_init(mpicomm, Cint(true), Cint(true), C_NULL, P4est_wrapper.SC_LP_DEFAULT)
+p4est_init(C_NULL, P4est_wrapper.SC_LP_DEFAULT)
 
 unitsquare_connectivity = p4est_connectivity_new_unitsquare()
 unitsquare_forest = p4est_new(mpicomm, unitsquare_connectivity, 0, C_NULL, C_NULL)
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,42 +1,42 @@
 using MPI
-using p4est_wrapper
+using P4est_wrapper
 using Test
 
 
 # Skip tests if library was not properly loaded
-if p4est_wrapper.P4EST_FOUND
+if P4est_wrapper.P4EST_FOUND
 
 
     nprocs = min(Sys.CPU_THREADS, 2)
     dir = dirname(@__FILE__)
     julia = Base.julia_cmd()
     mpiexec = MPI.mpiexec_path
-    @testset "Test SC bindings" begin 
+    @testset "Test SC bindings" begin
         cmd = `$mpiexec -n $nprocs --allow-run-as-root --tag-output $(julia) $(joinpath(dir, "test_sc_bindings.jl"))`
         @show cmd
         run(cmd)
     end
-    @testset "Test P4EST bindings" begin 
+    @testset "Test P4EST bindings" begin
         cmd = `$mpiexec -n $nprocs --allow-run-as-root --tag-output $(julia) $(joinpath(dir, "test_p4est_bindings.jl"))`
         @show cmd
         run(cmd)
     end
-    @testset "Test P8EST bindings" begin 
+    @testset "Test P8EST bindings" begin
         cmd = `$mpiexec -n $nprocs --allow-run-as-root --tag-output $(julia) $(joinpath(dir, "test_p8est_bindings.jl"))`
         @show cmd
         run(cmd)
     end
-    @testset "Example 1" begin 
+    @testset "Example 1" begin
         cmd = `$mpiexec -n $nprocs --allow-run-as-root --tag-output $(julia) $(joinpath(dir, "example_1.jl"))`
         @show cmd
         run(cmd)
     end
-    @testset "Example 2" begin 
+    @testset "Example 2" begin
         cmd = `$mpiexec -n $nprocs --allow-run-as-root --tag-output $(julia) $(joinpath(dir, "example_2.jl"))`
         @show cmd
         run(cmd)
     end
-    @testset "Example 3" begin 
+    @testset "Example 3" begin
         cmd = `$mpiexec -n $nprocs --allow-run-as-root --tag-output $(julia) $(joinpath(dir, "example_3.jl"))`
         @show cmd
         run(cmd)
diff --git a/test/test_p4est_bindings.jl b/test/test_p4est_bindings.jl
diff --git a/test/test_p8est_bindings.jl b/test/test_p8est_bindings.jl
diff --git a/test/test_sc_bindings.jl b/test/test_sc_bindings.jl

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name = "p4est_wrapper"`
	`1`	`+name = "P4est_wrapper"`
`2`	`2`	`uuid = "3743d7c0-8adf-11ea-380b-7d33b0ecc1da"`
`3`	`3`	`authors = ["Victor Sande <vsande@cimne.upc.edu>", "Alberto F. Martin <alberto.martin@monash.edu>"]`
`4`	`4`	`version = "0.1.0"`