Replace SciPy qhull dependence by DirectQhull.jl

thchr · Dec 1, 2022 · f3b1dd6 · f3b1dd6
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commit f3b1dd6
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Showing 3 changed files with 14 additions and 37 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -36,11 +36,7 @@ jobs:
             ${{ runner.os }}-test-
             ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@v1
-        env:
-          PYTHON: "" # the python version picked by PyCall.jl sometimes isn't Conda.jl's version, but the system's: this ensures that it is Conda.jl's
       - uses: julia-actions/julia-runtest@v1
-        env:
-          PYTHON: ""
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v1
         with:
@@ -54,8 +50,6 @@ jobs:
         with:
           version: '1'
       - uses: julia-actions/julia-buildpkg@v1
-        env:
-          PYTHON: ""
       - run: |
           julia --project=docs -e '
             using Pkg
@@ -67,10 +61,7 @@ jobs:
             using Documenter: doctest
             using Brillouin
             doctest(Brillouin)'
-        env:
-          PYTHON: ""
       - run: julia --project=docs docs/make.jl
         env:
-          PYTHON: ""
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
diff --git a/Project.toml b/Project.toml
@@ -1,21 +1,21 @@
 name = "Brillouin"
 uuid = "23470ee3-d0df-4052-8b1a-8cbd6363e7f0"
 authors = ["Thomas Christensen <tchr@mit.edu> and contributors"]
-version = "0.5.10"
+version = "0.5.11"
 
 [deps]
 Bravais = "ada6cbde-b013-4edf-aa94-f6abe8bd6e6b"
+DirectQhull = "c3f9d41a-afcb-471e-bc58-0b8d83bd86f4"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [compat]
 Bravais = "0.1.8"
+DirectQhull = "0.2"
 DocStringExtensions = "0.8, 0.9"
-PyCall = "1.92"
 Reexport = "1.0, 1.1, 1.2"
 Requires = "1.1"
 StaticArrays = "1.2"

diff --git a/src/WignerSeitz.jl b/src/WignerSeitz.jl
@@ -23,7 +23,7 @@ using LinearAlgebra:
     norm,
     dot,
     ×
-using PyCall
+import DirectQhull
 using DocStringExtensions
 
 import Base: getindex, size, IndexStyle, show, summary
@@ -32,20 +32,6 @@ import Base: getindex, size, IndexStyle, show, summary
 
 export Cell, wignerseitz, faces, vertices, reduce_to_wignerseitz
 
-# ---------------------------------------------------------------------------------------- #
-
-const PySpatial = PyNULL()
-function __init__()
-    # bringing in SciPy's Spatial module (for `Voronoi` and `ConvexHull`)
-    if PyCall.conda
-        copy!(PySpatial, pyimport_conda("scipy.spatial", "scipy"))
-    else
-        copy!(PySpatial, pyimport_e("scipy.spatial"))
-    end
-    ispynull(PySpatial) && @warn("scipy python package not found. " *
-                                 "WignerSeitz.wignerseitz is nonfunctional.")
-end
-
 # ---------------------------------------------------------------------------------------- #
 # STRUCTURES
 
@@ -130,15 +116,15 @@ function wignerseitz(basis::AVec{<:SVector{D,<:Real}};
         iszero(I) && (idx_cntr = idx)
     end
 
-    ispynull(PySpatial) && error("You need to install scipy for wignerseitz to work.")
-    vor = PySpatial.Voronoi(lattice) # voronoi tesselation of lattice
+    vor = DirectQhull.Voronoi(reduce(hcat, lattice)) # voronoi tesselation of lattice
 
     # grab all the vertices of the central voronoi region enclosing origo
-    verts_cntr =  # NB: offsets by 1 due to Julia 1-based vs. Python 0-based indexing
-        [vor.vertices[idx+1,:] for idx in vor.regions[vor.point_region[idx_cntr]+1]]
-
+    # [NB: offsets by 1 due to Julia 1-based vs. C++ 0-based indexing; 
+    #      see https://github.com/JuhaHeiskala/DirectQhull.jl/issues/7]
+    verts_cntr = vor.vertices[:, vor.regions[vor.point_region[idx_cntr]+1] .+ 1]
+
     # get convex hull of central vertices
-    hull = PySpatial.ConvexHull(verts_cntr)
+    hull = DirectQhull.ConvexHull(verts_cntr)
     c    = convert_to_cell(hull, basis)
     c    = reorient_normals!(c)
 
@@ -165,11 +151,11 @@ end
 # UTILITIES & SUBFUNCTIONS
 
 function convert_to_cell(hull, basis::AVec{<:SVector{D,<:Real}}) where D
-    vs′ = hull.points         # vertices
-    fs′ = hull.simplices .+ 1 # faces
+    vs′ = hull.points    # vertices
+    fs′ = hull.simplices # faces [NB: 1-based, cf. https://github.com/JuhaHeiskala/DirectQhull.jl/issues/7#issuecomment-1334411873]
 
-    vs = SVector{D, Float64}.(eachrow(vs′))
-    fs = Vector{Int}.(eachrow(fs′))
+    vs = SVector{D, Float64}.(eachcol(vs′))
+    fs = Vector{Int}.(eachcol(fs′))
     return Cell(vs, fs, SVector{D, SVector{D, Float64}}(basis), Ref(CARTESIAN))
 end