Merge pull request #11 from ProjectTorreyPines/format

Adds a format check using a configuration file and a GitHub Action to check format on push and PR with master and dev branches. The configuration file `.JuliaFormatter.toml` and the github workflow file `.github/workflows/format_check.yml` can be copied as it is to any other GitHub repo to recreate the same functionality.

.JuliaFormatter.toml

@@ -0,0 +1,27 @@
+align_assignment = true
+align_conditional = true
+align_matrix = true
+align_pair_arrow = true
+align_struct_field = true
+always_for_in = true
+always_use_return = true
+annotate_untyped_fields_with_any = false
+conditional_to_if = true
+for_in_replacement = "∈"
+format_docstrings = true
+import_to_using = true
+indent = 4
+indent_submodule = true
+join_lines_based_on_source = true
+long_to_short_function_def = true
+margin = 88
+normalize_line_endings = "unix"
+pipe_to_function_call = true
+remove_extra_newlines = true
+separate_kwargs_with_semicolon = true
+surround_whereop_typeparameters = true
+trailing_comma = true
+whitespace_in_kwargs = false
+whitespace_ops_in_indices = false
+whitespace_typedefs = true
+yas_style_nesting = true

.github/workflows/format_check.yml

@@ -0,0 +1,36 @@
+name: Format Check
+
+on:
+  push:
+    branches: ["master", "dev", "format"]
+  pull_request:
+    branches: ["master", "dev"]
+jobs:
+  check:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1.9.3]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v1
+      - name: Install JuliaFormatter and format
+        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'

README.md

@@ -1,2 +1,5 @@
 # GGDUtils
+
+![Format Check](https://github.com/ProjectTorreyPines/GGDUtils.jl/actions/workflows/format_check.yml/badge.svg)
+
 Package holding utilities for Generalized Grid Description (GGD) objects in IMAS datastructure. Primary goals are interpolation and core profile extrapolation.

src/GGDUtils.jl

@@ -3,58 +3,60 @@ module GGDUtils
 import NearestNeighbors: KDTree, knn
 import StaticArrays: SVector
 import Statistics: mean
-import OMAS
+using OMAS: OMAS
 import SOLPS2IMAS: get_subset_space, get_grid_subset_with_index
 using RecipesBase
-import ColorSchemes
+using ColorSchemes: ColorSchemes
 
 export interp
 export get_kdtree
 export project_prop_on_subset!
 
-
 include("recipes.jl")
 
-
 function get_kdtree(space::OMAS.edge_profiles__grid_ggd___space)
     grid_nodes = space.objects_per_dimension[1].object
     grid_faces = space.objects_per_dimension[3].object
-    grid_faces = [cell for cell in grid_faces if length(cell.nodes) == 4]
-    grid_centers = [SVector{2}(mean([grid_nodes[node].geometry for node in cell.nodes])) for cell in grid_faces]
+    grid_faces = [cell for cell ∈ grid_faces if length(cell.nodes) == 4]
+    grid_centers = [
+        SVector{2}(mean([grid_nodes[node].geometry for node ∈ cell.nodes])) for
+        cell ∈ grid_faces
+    ]
     return KDTree(grid_centers; leafsize=10)
 end
 
-
 function interp(prop, kdtree::KDTree)
     function get_interp_val(x::Number, y::Number)
         nearest_indices, distances = knn(kdtree, Array([x, y]), 4)
-        v1, v2, v3, v4 = [prop.values[ii] for ii in nearest_indices]
+        v1, v2, v3, v4 = [prop.values[ii] for ii ∈ nearest_indices]
         d1, d2, d3, d4 = distances
-        return ((v1 * d2 * d3 * d4 + d1 * v2 * d3 * d4
-                 + d1 * d2 * v3 * d4 + d1 * d2 * d3 * v4)
-                /
-                (d2 * d3 * d4 + d1 * d3 * d4
-                 + d1 * d2 * d4 + d1 * d2 * d3))
+        return (
+            (
+                v1 * d2 * d3 * d4 + d1 * v2 * d3 * d4
+                + d1 * d2 * v3 * d4 + d1 * d2 * d3 * v4
+            )
+            /
+            (d2 * d3 * d4 + d1 * d3 * d4
+             + d1 * d2 * d4 + d1 * d2 * d3)
+        )
     end
     function get_interp_val(x::Vector{Float64}, y::Vector{Float64})
         if length(x) != length(y)
             error("Length of the two axes are not equal")
         else
-            return [get_interp_val(x[ii], y[ii]) for ii in eachindex(x)]
+            return [get_interp_val(x[ii], y[ii]) for ii ∈ eachindex(x)]
         end
     end
     function get_interp_val(xy::Vector{Tuple{Float64, Float64}})
-        return [get_interp_val(xy[ii]...) for ii in eachindex(xy)]
+        return [get_interp_val(xy[ii]...) for ii ∈ eachindex(xy)]
     end
     return get_interp_val
 end
 
-
 function interp(prop, space::OMAS.edge_profiles__grid_ggd___space)
     return interp(prop, get_kdtree(space))
 end
 
-
 """
     get_subset_centers(space::OMAS.edge_profiles__grid_ggd___space,
                             subset::OMAS.edge_profiles__grid_ggd___grid_subset)
@@ -66,50 +68,64 @@ function get_subset_centers(space::OMAS.edge_profiles__grid_ggd___space,
     subset::OMAS.edge_profiles__grid_ggd___grid_subset)
     subset_space = get_subset_space(space, subset.element)
     grid_nodes = space.objects_per_dimension[1].object
-    return [Tuple(mean([grid_nodes[node].geometry for node in obj.nodes])) for obj in subset_space]
+    return [
+        Tuple(mean([grid_nodes[node].geometry for node ∈ obj.nodes])) for
+        obj ∈ subset_space
+    ]
 end
 
-
+#! format: off
 """
-    project_prop_on_subset!(prop, from_subset::OMAS.edge_profiles__grid_ggd___grid_subset,
-                                 to_subset::OMAS.edge_profiles__grid_ggd___grid_subset;
-                                 space::OMAS.edge_profiles__grid_ggd___space)
+    project_prop_on_subset!(prop,
+    from_subset::OMAS.edge_profiles__grid_ggd___grid_subset,
+    to_subset::OMAS.edge_profiles__grid_ggd___grid_subset,
+    space::OMAS.edge_profiles__grid_ggd___space)
 
-This function can be used to add another instance on a property vector representing the value
-in a new subset that can be taken as a projection from an existing larger subset.
+This function can be used to add another instance on a property vector representing the
+value in a new subset that can be taken as a projection from an existing larger subset.
 Arguments:
-prop: A property like electrons.density that is a vector of objects with fields coefficients,
-      grid_index, grid_subset_index, and values. The different instances in the vector correspond
-      to different grid_subset for which the property is provided.
-from_subset: grid_subset object which is already represented in the property instance. grid subset
-             with index 5 is populated in electrons.density already if the values for all cells are
-             present.
-to_subset: grid_subset which is either a smaller part of from_subset (core, sol, idr, odr) but has
-           same dimensions as from_subset
+prop: A property like electrons.density that is a vector of objects with fields
+      coefficients, grid_index, grid_subset_index, and values. The different instances
+      in the vector correspond to different grid_subset for which the property is
+      provided.
+from_subset: grid_subset object which is already represented in the property instance.
+             grid subset with index 5 is populated in electrons.density already if the
+             values for all cells are present.
+to_subset: grid_subset which is either a smaller part of from_subset (core, sol, idr,
+           odr) but has same dimensions as from_subset
            OR
-           is smaller in dimension that goes through the from_subset (core_boundary, separatix etc.)
-space: (optional) space object in grid_ggd is required only when from_subset is higher dimensional
-       than to_subset.
+           is smaller in dimension that goes through the from_subset (core_boundary,
+           separatix etc.)
+space: (optional) space object in grid_ggd is required only when from_subset is
+       higher dimensional than to_subset.
 Returns:
-NOTE: This function ends in ! which means it updates prop argument in place. But for the additional
-utility, this function also returns a tuple
-to_subset_centers, to_prop.values (when from_subset dimension is greater than to_subset dimension)
-to_subset_ele_obj_inds, to_prop.values (when from_subset dimension is same as to_subset dimension)
+NOTE: This function ends in ! which means it updates prop argument in place. But for
+the additional utility, this function also returns a tuple
+(to_subset_centers, to_prop.values) when from_subset dimension is greater than
+                                    to_subset dimension
+OR
+(to_subset_ele_obj_inds, to_prop.values) when from_subset dimension is same as
+                                         to_subset dimension)
 Descriptions:
-to_subset_centers: center of cells or center of edges of the to_subset where property values are
-                   defined and stored
-to_subset_ele_obj_inds: Indices of the elements of to_subset where property values are deined and
-                        stored
-to_prop.values: The projected values of the properties added to prop object in a new instance
+to_subset_centers: center of cells or center of edges of the to_subset where property
+                   values are defined and stored
+to_subset_ele_obj_inds: Indices of the elements of to_subset where property values are
+                        defined and stored
+to_prop.values: The projected values of the properties added to prop object in a new
+                instance
 """
-function project_prop_on_subset!(prop, from_subset::OMAS.edge_profiles__grid_ggd___grid_subset,
-                                 to_subset::OMAS.edge_profiles__grid_ggd___grid_subset,
-                                 space::OMAS.edge_profiles__grid_ggd___space)
-    if from_subset.element[1].object[1].dimension == to_subset.element[1].object[1].dimension
+#! format: on
+function project_prop_on_subset!(prop,
+    from_subset::OMAS.edge_profiles__grid_ggd___grid_subset,
+    to_subset::OMAS.edge_profiles__grid_ggd___grid_subset,
+    space::OMAS.edge_profiles__grid_ggd___space)
+    if from_subset.element[1].object[1].dimension ==
+       to_subset.element[1].object[1].dimension
         return project_prop_on_subset!(prop, from_subset, to_subset)
-    elseif from_subset.element[1].object[1].dimension > to_subset.element[1].object[1].dimension
+    elseif from_subset.element[1].object[1].dimension >
+           to_subset.element[1].object[1].dimension
         from_prop = nothing
-        for p in prop
+        for p ∈ prop
             if p.grid_subset_index == from_subset.identifier.index
                 from_prop = p
                 break
@@ -132,11 +148,11 @@ function project_prop_on_subset!(prop, from_subset::OMAS.edge_profiles__grid_ggd
     end
 end
 
-
-function project_prop_on_subset!(prop, from_subset::OMAS.edge_profiles__grid_ggd___grid_subset,
-                                 to_subset::OMAS.edge_profiles__grid_ggd___grid_subset)
+function project_prop_on_subset!(prop,
+    from_subset::OMAS.edge_profiles__grid_ggd___grid_subset,
+    to_subset::OMAS.edge_profiles__grid_ggd___grid_subset)
     from_prop = nothing
-    for p in prop
+    for p ∈ prop
         if p.grid_subset_index == from_subset.identifier.index
             from_prop = p
             break
@@ -145,34 +161,39 @@ function project_prop_on_subset!(prop, from_subset::OMAS.edge_profiles__grid_ggd
     if isnothing(from_prop)
         println("from_subset not represented in the property yet")
     end
-    if from_subset.element[1].object[1].dimension == to_subset.element[1].object[1].dimension
+    if from_subset.element[1].object[1].dimension ==
+       to_subset.element[1].object[1].dimension
         resize!(prop, length(prop) + 1)
         to_prop = prop[end]
         to_prop.grid_index = from_prop.grid_index
         to_prop.grid_subset_index = to_subset.identifier.index
-        from_subset_ele_obj_inds = [ele.object[1].index for ele in from_subset.element]
-        to_subset_ele_obj_inds = [ele.object[1].index for ele in to_subset.element]
+        from_subset_ele_obj_inds = [ele.object[1].index for ele ∈ from_subset.element]
+        to_subset_ele_obj_inds = [ele.object[1].index for ele ∈ to_subset.element]
         if to_subset_ele_obj_inds ⊆ from_subset_ele_obj_inds
             from_ele_inds = []
-            for to_ele_obj_ind in to_subset_ele_obj_inds
-                for (from_ele_ind, from_ele_obj_ind) in enumerate(from_subset_ele_obj_inds)
+            for to_ele_obj_ind ∈ to_subset_ele_obj_inds
+                for (from_ele_ind, from_ele_obj_ind) ∈
+                    enumerate(from_subset_ele_obj_inds)
                     if from_ele_obj_ind == to_ele_obj_ind
                         append!(from_ele_inds, from_ele_ind)
                     end
                 end
             end
-            filtered_values = [from_prop.values[from_ele_ind] for from_ele_ind in from_ele_inds]
-            resize!(to_prop.values, length(filtered_values)) 
+            filtered_values =
+                [from_prop.values[from_ele_ind] for from_ele_ind ∈ from_ele_inds]
+            resize!(to_prop.values, length(filtered_values))
             to_prop.values = filtered_values
             return to_subset_ele_obj_inds, to_prop.values
         else
-            error("to_subset does not lie entirely inside from_subset. Projection not possible.")
+            error("to_subset does not lie entirely inside from_subset. Projection ",
+                "not possible.",
+            )
         end
     else
         error("Dimensions of from_subset and to_subset do not match. Provide keyword ",
-              "argument space if you want to project to a smaller dimension as space ",
-              "information is required for that. Use\n",
-              "project_prop_on_subset!(prop, from_subset, to_subset; space=space)")
+            "argument space if you want to project to a smaller dimension as space ",
+            "information is required for that. Use\n",
+            "project_prop_on_subset!(prop, from_subset, to_subset; space=space)")
     end
 end