Merge pull request #188 from gridap/release-0.7

Preparing release 0.7.0
gridap · Feb 13, 2020 · d2b7659 · d2b7659 · fverdugo · Feb 13, 2020
2 parents 82ccf12 + abd107b
commit d2b7659
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diff --git a/Manifest.toml b/Manifest.toml
@@ -100,9 +100,9 @@ version = "0.4.2"
 
 [[FileIO]]
 deps = ["Pkg"]
-git-tree-sha1 = "74585bf1f7ed7259e166011e89f49363d7fa89a6"
+git-tree-sha1 = "2c84c57aced468fa21763c66d3bef33adcd09ec7"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.2.1"
+version = "1.2.2"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays"]
@@ -195,9 +195,9 @@ version = "0.12.0"
 
 [[Parsers]]
 deps = ["Dates", "Test"]
-git-tree-sha1 = "0139ba59ce9bc680e2925aec5b7db79065d60556"
+git-tree-sha1 = "d112c19ccca00924d5d3a38b11ae2b4b268dda39"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "0.3.10"
+version = "0.3.11"
 
 [[Pkg]]
 deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
@@ -240,9 +240,9 @@ version = "0.2.0"
 
 [[Requires]]
 deps = ["UUIDs"]
-git-tree-sha1 = "999513b7dea8ac17359ed50ae8ea089e4464e35e"
+git-tree-sha1 = "d37400976e98018ee840e0ca4f9d20baa231dc6b"
 uuid = "ae029012-a4dd-5104-9daa-d747884805df"
-version = "1.0.0"
+version = "1.0.1"
 
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"

diff --git a/NEWS.md b/NEWS.md
@@ -4,6 +4,10 @@ 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).
 
+## [0.7.0] - 2020-02-13
+
+This version is a major refactoring of the project which is not summarized here for the sake of brevity. Most of the functionality of v0.6.0 is available in v0.7.0, but with a possibly slightly different API. See the changes in the sources of the Gridap Tutorials between versions 0.6.0 and 0.7.0 to effectively see the major changes in the API. 
+
 ## [0.6.0] - 2020-01-24
 ### Added
 - New `GenericRefFE`. Since commit [876ef1e](https://github.com/gridap/Gridap.jl/commit/c3c9010177432b8f07aaecf4a0baa4b93876ef1e)

diff --git a/Project.toml b/Project.toml
@@ -16,7 +16,6 @@ LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
 QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
-Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
@@ -27,14 +26,13 @@ BSON = "0.2.5"
 Combinatorics = "1.0.0"
 DocStringExtensions = "0.8.1"
 FastGaussQuadrature = "0.4.2"
-FileIO = "1.2.1"
+FileIO = "1.2.2"
 FillArrays = "0.8.4"
 JLD2 = "0.1.11"
 JSON = "0.21.0"
 LineSearches = "7.0.1"
 NLsolve = "4.3.0"
 QuadGK = "2.3.1"
-Reexport = "0.2.0"
 StaticArrays = "0.12.1"
 WriteVTK = "1.4.0"
 julia = "1.0"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,3 +1,6 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Gridap = "56d4f2e9-7ea1-5844-9cf6-b9c51ca7ce8e"
+
+[compat]
+Documenter = "0.24"
diff --git a/docs/make.jl b/docs/make.jl
@@ -8,16 +8,17 @@ pages = [
   "Gridap" => "Gridap.md",
   "Gridap.Helpers" => "Helpers.md",
   "Gridap.Inference" => "Inference.md",
+  "Gridap.Algebra" => "Algebra.md",
   "Gridap.Io" => "Io.md",
   "Gridap.TensorValues" => "TensorValues.md",
   "Gridap.Arrays" => "Arrays.md",
   "Gridap.Fields" => "Fields.md",
   "Gridap.Polynomials" => "Polynomials.md",
+  "Gridap.Integration" => "Integration.md",
   "Gridap.ReferenceFEs" => "ReferenceFEs.md",
   "Gridap.Geometry" => "Geometry.md",
-  "Gridap.Integration" => "Integration.md",
-  "Gridap.Algebra" => "Algebra.md",
   "Gridap.FESpaces" => "FESpaces.md",
+  "Gridap.MultiField" => "MultiField.md",
   "Gridap.Visualization" => "Visualization.md",
  ]
 

diff --git a/docs/src/Arrays.md b/docs/src/Arrays.md
@@ -138,6 +138,12 @@ LocalToGlobalPosNegArray
 LocalToGlobalPosNegArray(::AbstractArray{<:AbstractArray},::AbstractArray,::AbstractArray)
 ```
 
+### SubVector
+
+```@docs
+SubVector
+```
+
 ### Helpers
 
 ```@docs

diff --git a/docs/src/Geometry.md b/docs/src/Geometry.md
@@ -32,14 +32,25 @@ get_cell_shapefuns(trian::Triangulation)
 get_cell_map(trian::Triangulation)
 get_physical_coordinate(trian::Triangulation)
 ```
+### Integrating on a triangulation
+
+```@docs
+CellQuadrature
+CellQuadrature(array::AbstractArray{<:Quadrature})
+CellQuadrature(trian::Triangulation, degree::Integer)
+CellQuadrature(degree,polytopes::Vector{<:Polytope}, cell_types::AbstractVector)
+get_coordinates(quad::CellQuadrature)
+get_weights(quad::CellQuadrature)
+get_array(quad::CellQuadrature)
+integrate(cell_field,trian::Triangulation,quad::CellQuadrature)
+```
 
 ### TriangulationPortion
 
 ```@docs
 TriangulationPortion
 TriangulationPortion(oldtrian::Triangulation{Dc,Dp},cell_to_oldcell::Vector{Int}) where {Dc,Dp}
 ```
-
 ## BoundaryTriangulations
 
 ### Interface
@@ -96,6 +107,7 @@ compute_linear_grid(reffe::LagrangianRefFE)
 compute_reference_grid(reffe::LagrangianRefFE, nelems::Integer)
 Grid(::Type{ReferenceFE{d}},p::Polytope) where d
 GridTopology(grid::Grid)
+simplexify(grid::Grid)
 ```
 
 ### UnstructuredGrids
@@ -277,6 +289,13 @@ Grid(::Type{ReferenceFE{d}},model::DiscreteModel) where d
 Triangulation(::Type{ReferenceFE{d}},model::DiscreteModel) where d
 get_triangulation(model::DiscreteModel)
 get_polytopes(model::DiscreteModel)
+simplexify(model::DiscreteModel)
+```
+
+### DiscreteModelFromFile
+
+```@docs
+DiscreteModelFromFile(filename::AbstractString)
 ```
 
 ### UnstructuredDiscreteModels

diff --git a/docs/src/MultiField.md b/docs/src/MultiField.md
@@ -0,0 +1,10 @@
+
+```@meta
+CurrentModule = Gridap.MultiField
+```
+
+# Gridap.MultiField
+
+```@autodocs
+Modules = [MultiField,]
+```
diff --git a/docs/src/ReferenceFEs.md b/docs/src/ReferenceFEs.md
@@ -39,6 +39,8 @@ get_offsets(p::Polytope)
 get_offset(p::Polytope,d::Integer)
 get_faces(p::Polytope,dimfrom::Integer,dimto::Integer)
 get_face_vertices(p::Polytope,dim::Integer)
+get_face_coordinates(p::Polytope,d::Integer)
+get_face_dimranges(p::Polytope,d::Integer)
 get_reffaces(::Type{Polytope{d}},p::Polytope) where d
 get_face_type(p::Polytope,d::Integer)
 get_bounding_box(p::Polytope{D}) where D
@@ -201,6 +203,18 @@ is_S(reffe::LagrangianRefFE)
 SerendipityRefFE
 ```
 
+### PDiscRefFE
+
+```@docs
+PDiscRefFE
+```
+
+### RaviartThomasRefFE
+
+```@docs
+RaviartThomasRefFE
+```
+
 ### Pre-defined ReferenceFE instances
 
 ```@docs

diff --git a/docs/src/getting-started.md b/docs/src/getting-started.md
@@ -2,13 +2,11 @@
 
 ## Installation requirements
 
-At the moment, Gridap requires at least Julia version 1.1.
-
-Gridap has been tested on Linux and Mac Os operating systems.
+Gridap is tested on Linux, but it should be also possible to use it on Mac OS and Windows since it is written exclusively in Julia and it only depends on registered Julia packages.
 
 ## Installation
 
-Gridap is a registered package. Thus, the installation should be straight forward using the Julia's package manager [Pkg](https://julialang.github.io/Pkg.jl/v1/): open the Julia REPL (i.e., execute the `julia` binary), type `]` to enter package mode, and install Gridap as follows
+Gridap is a registered package. Thus, the installation should be straight forward using the Julia's package manager [Pkg](https://julialang.github.io/Pkg.jl/v1/). To this end, open the Julia REPL (i.e., execute the `julia` binary), type `]` to enter package mode, and install Gridap as follows
 
 ```julia
 pkg> add Gridap
@@ -21,6 +19,6 @@ For further information about how to install and manage Julia packages, see the
 
 ## Further steps
 
-We recommend to follow the [Gridap Tutorials](https://github.com/gridap/Tutorials) in order to get familiar with the library.
+We recommend to follow the [Gridap Tutorials](https://gridap.github.io/Tutorials/dev/) in order to get familiar with the library.
 
 
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -18,18 +18,16 @@ The library currently supports linear and nonlinear PDE systems for scalar and v
 
 * The first step for new users is to visit the [Getting Started](@ref) page.
 
+* A set of tutorials written as Jupyter notebooks and html pages are available [here](https://github.com/gridap/Tutorials).
+
 * The detailed documentation is in the [Manual](@ref) section.
 
 * Guidelines for developers of the Gridap project is found in the [Gridap wiki](https://github.com/gridap/Gridap.jl/wiki) page.
 
-## Tutorials
-
-In addition to these documentation pages, a set of tutorials written in Jupyter notebooks are available [here](https://github.com/gridap/Tutorials).
-
 ## Julia educational resources
 
 A basic knowledge of the Julia programming language is needed to use the Gridap package.
-Here, a list of resources to get started with this programming language.
+Here, one can find a list of resources to get started with this programming language.
 
 * First steps to learn Julia form the [Gridap wiki](https://github.com/gridap/Gridap.jl/wiki/Start-learning-Julia) page.
 * Official webpage [docs.julialang.org](https://docs.julialang.org/)
@@ -43,15 +41,16 @@ Pages = [
   "Helpers.md",
   "Inference.md",
   "Io.md",
+  "Algebra.md",
   "TensorValues.md",
   "Arrays.md",
   "Fields.md",
   "Polynomials.md",
+  "Integration.md",
   "ReferenceFEs.md",
   "Geometry.md",
-  "Integration.md",
-  "Algebra.md",
   "FESpaces.md",
+  "MultiField.md",
   "Visualization.md",
   ]
 ```

diff --git a/src/Arrays/SubVectors.jl b/src/Arrays/SubVectors.jl
@@ -1,4 +1,11 @@
 
+"""
+    struct SubVector{T,A<:AbstractVector{T}} <: AbstractVector{T}
+      vector::A
+      pini::Int
+      pend::Int
+    end
+"""
 struct SubVector{T,A<:AbstractVector{T}} <: AbstractVector{T}
   vector::A
   pini::Int

diff --git a/src/FESpaces/CLagrangianFESpaces.jl b/src/FESpaces/CLagrangianFESpaces.jl
@@ -1,11 +1,23 @@
 
+"""
+    struct CLagrangianFESpace{S} <: SingleFieldFESpace
+      grid::Grid
+      dof_to_node::Vector{Int}
+      dof_to_comp::Vector{Int8}
+      node_and_comp_to_dof::Vector{S}
+      # + private fields
+    end
+"""
 struct CLagrangianFESpace{S} <: SingleFieldFESpace
   space::UnsconstrainedFESpace
   grid::Grid
   dof_to_node::Vector{Int}
   dof_to_comp::Vector{Int8}
   node_and_comp_to_dof::Vector{S}
 
+  @doc """
+      CLagrangianFESpace(::Type{T},grid::Grid) where T
+  """
   function CLagrangianFESpace(::Type{T},grid::Grid) where T
     space, dof_to_node, dof_to_comp, node_and_comp_to_dof = _generate_clargangian_fespace(T,grid)
     S = eltype(node_and_comp_to_dof)

diff --git a/src/FESpaces/DivConformingFESpaces.jl b/src/FESpaces/DivConformingFESpaces.jl
@@ -1,4 +1,11 @@
 
+"""
+    DivConformingFESpace(
+      reffes::Vector{<:ReferenceFE},
+      model::DiscreteModel,
+      face_labeing::FaceLabeling,
+      dirichlet_tags)
+"""
 function DivConformingFESpace(
   reffes::Vector{<:ReferenceFE},
   model::DiscreteModel,

diff --git a/src/FESpaces/FESpacesWithLastDofRemoved.jl b/src/FESpaces/FESpacesWithLastDofRemoved.jl
@@ -1,6 +1,14 @@
 
+"""
+    struct FESpaceWithLastDofRemoved <: SingleFieldFESpace
+      space::SingleFieldFESpace
+    end
+"""
 struct FESpaceWithLastDofRemoved <: SingleFieldFESpace
   space::SingleFieldFESpace
+  @doc """
+      FESpaceWithLastDofRemoved(space::SingleFieldFESpace)
+  """
   function FESpaceWithLastDofRemoved(space::SingleFieldFESpace)
     s = "FESpaceWithLastDofRemoved can only be constructed from spaces without dirichlet dofs."
     @notimplementedif num_dirichlet_dofs(space) != 0 s

diff --git a/src/FESpaces/ZeroMeanFESpaces.jl b/src/FESpaces/ZeroMeanFESpaces.jl
@@ -1,10 +1,21 @@
 
+"""
+    struct ZeroMeanFESpace <: SingleFieldFESpace
+      # private fields
+    end
+"""
 struct ZeroMeanFESpace <: SingleFieldFESpace
   space::FESpaceWithLastDofRemoved
   vol_i::Vector{Float64}
   vol::Float64
 end
 
+"""
+    ZeroMeanFESpace(
+      space::SingleFieldFESpace,
+      trian::Triangulation,
+      quad::CellQuadrature)
+"""
 function ZeroMeanFESpace(
   space::SingleFieldFESpace,trian::Triangulation,quad::CellQuadrature)
 

diff --git a/src/Geometry/CellQuadratures.jl b/src/Geometry/CellQuadratures.jl
@@ -1,16 +1,22 @@
 """
+    struct CellQuadrature <: GridapType
+      array
+    end
 """
 struct CellQuadrature <: GridapType
   array
+  @doc """
+      CellQuadrature(array::AbstractArray{<:Quadrature})
+  """
   function CellQuadrature(array::AbstractArray{<:Quadrature})
     new(array)
   end
 end
 
 """
-    CellQuadrature(trian::Triangulation, degree)
+    CellQuadrature(trian::Triangulation, degree::Integer)
 """
-function CellQuadrature(trian::Triangulation, degree)
+function CellQuadrature(trian::Triangulation, degree::Integer)
   polytopes = map(get_polytope,get_reffes(trian))
   cell_type = get_cell_type(trian)
   CellQuadrature(degree,polytopes,cell_type)
@@ -35,6 +41,7 @@ function CellQuadrature(degree,polytopes::Vector{<:Polytope}, cell_types::Fill)
 end
 
 """
+    get_array(quad::CellQuadrature)
 """
 get_array(quad::CellQuadrature) = quad.array
 
@@ -81,7 +88,9 @@ function _get_weights(q::Fill{<:Quadrature})
 end
 
 """
-the `cell_field` is aligned with the cells in `trian`
+    integrate(cell_field,trian::Triangulation,quad::CellQuadrature)
+
+The `cell_field` is aligned with the cells in `trian`
 """
 function integrate(cell_field,trian::Triangulation,quad::CellQuadrature)
   cell_map = get_cell_map(trian)