Merge pull request #419 from JuliaMolSim/remove_warnings

Suppress conditional package load warnings

.github/workflows/CompatHelper.yaml

@@ -10,7 +10,7 @@ jobs:
     steps:
       - uses: julia-actions/setup-julia@latest
         with:
-          version: 1.3
+          version: 1.5
       - name: Pkg.add("CompatHelper")
         run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
       - name: CompatHelper.main()

.github/workflows/ci.yaml

@@ -22,10 +22,10 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - {version: '1.4',   os: ubuntu-latest,  payload: serial}
-          - {version: '1.4',   os: macOS-latest,   payload: serial}
-          - {version: '1.4',   os: windows-latest, payload: serial}
-          - {version: '1.4',   os: ubuntu-latest,  payload: mpi   }
+          - {version: '1.5',   os: ubuntu-latest,  payload: serial}
+          - {version: '1.5',   os: macOS-latest,   payload: serial}
+          - {version: '1.5',   os: windows-latest, payload: serial}
+          - {version: '1.5',   os: ubuntu-latest,  payload: mpi   }
           - {version: nightly, os: ubuntu-latest,  payload: serial}
     env:
       PYTHON: ""  # Force using Conda in PyCall
@@ -95,7 +95,7 @@ jobs:
         run: pip install ase pymatgen
       - uses: julia-actions/setup-julia@v1
         with:
-          version: '1.4'
+          version: '1.5'
       - uses: actions/cache@v1
         env:
           cache-name: cache-artifacts

Project.toml

@@ -65,7 +65,7 @@ StaticArrays = "0.12, 1"
 TimerOutputs = "0.5.6"
 Unitful = "1"
 UnitfulAtomic = "1"
-julia = "1.4"
+julia = "1.5"
 spglib_jll = "1.15"
 
 [extras]

README.md

@@ -47,7 +47,7 @@ For getting started with DFTK, see our documentation:
 - [Tutorial](https://juliamolsim.github.io/DFTK.jl/dev/guide/tutorial/)
 - [Examples](https://juliamolsim.github.io/DFTK.jl/dev/#example-index-1)
 
-Note that at least **Julia 1.4** is required.
+Note that at least **Julia 1.5** is required.
 
 ## Support and citation
 DFTK is mostly developed as part of academic research.

docs/src/guide/installation.md

@@ -3,7 +3,7 @@
 In case you don't have a working Julia installation yet, first
 [download the Julia binaries](https://julialang.org/downloads/)
 and follow the [Julia installation instructions](https://julialang.org/downloads/platform/).
-At least **Julia 1.4** is required for DFTK.
+At least **Julia 1.5** is required for DFTK.
 
 Afterwards you can install DFTK
 [like any other package](https://julialang.github.io/Pkg.jl/v1/getting-started/)

docs/src/index.md

@@ -15,6 +15,7 @@ Our performance is of the same order of magnitude as much larger production
 codes such as [Abinit](https://www.abinit.org/),
 [Quantum Espresso](http://quantum-espresso.org/) and
 [VASP](https://www.vasp.at/).
+DFTK's source code is [publicly available on github](https://dftk.org).
 
 ## [Package features](@id package-features)
 * Methods and models:

src/external/etsf_nanoquanta.jl

@@ -3,7 +3,6 @@
 
 export EtsfFolder
 
-using NCDatasets
 import JSON
 
 struct EtsfFolder

src/external/jld2io.jl

@@ -1,5 +1,3 @@
-import JLD2
-
 """
 Adds simplistic checkpointing to a DFTK self-consistent field calculation.
 """

src/external/load_from_python.jl

@@ -6,8 +6,9 @@ function load_lattice(T, pyobj::PyObject)
     ase = pyimport_e("ase")
 
     if !ispynull(mg)
-        mg_supported = (mg.Structure, mg.Lattice)
-        if any(pyisinstance(pyobj, s) for s in mg_supported)
+        Lattice   = pyimport("pymatgen.core.lattice").Lattice
+        Structure = pyimport("pymatgen.core.structure").Structure
+        if any(pyisinstance(pyobj, s) for s in (Lattice, Structure))
             return load_lattice_pymatgen(T, pyobj)
         end
     end
@@ -27,8 +28,10 @@ function load_atoms(T, pyobj::PyObject)
     mg = pyimport_e("pymatgen")
     ase = pyimport_e("ase")
 
-    if !ispynull(mg) && pyisinstance(pyobj, mg.Structure)
-        return load_atoms_pymatgen(T, pyobj)
+    if !ispynull(mg)
+        if pyisinstance(pyobj, pyimport("pymatgen.core.structure").Structure)
+            return load_atoms_pymatgen(T, pyobj)
+        end
     end
     if !ispynull(ase) && pyisinstance(pyobj, ase.Atoms)
         return load_atoms_ase(T, pyobj)

src/external/pymatgen.jl

@@ -4,15 +4,14 @@
 function pymatgen_lattice(lattice::AbstractArray)
     # Notice: Pymatgen uses rows as lattice vectors, so we unpeel
     # our lattice column by column. The default unit in pymatgen is Ångström
-    mg = pyimport("pymatgen")
+    Lattice = pyimport("pymatgen.core.lattice").Lattice
     bohr_to_A = 1 / austrip(1u"Å")
-    mg.Lattice([Array(bohr_to_A .* lattice[:, i]) for i in 1:3])
+    Lattice([Array(bohr_to_A .* lattice[:, i]) for i in 1:3])
 end
 pymatgen_lattice(model::Model) = pymatgen_lattice(model.lattice)
 
 
 function pymatgen_structure(model_or_lattice, atoms)
-    mg = pyimport("pymatgen")
     pylattice = pymatgen_lattice(model_or_lattice)
 
     n_species = sum(length(pos) for (spec, pos) in atoms)
@@ -28,17 +27,19 @@ function pymatgen_structure(model_or_lattice, atoms)
     end
     @assert ispec == n_species + 1
 
-    mg.Structure(pylattice, pyspecies, pypositions)
+    Structure = pyimport("pymatgen.core.structure").Structure
+    Structure(pylattice, pyspecies, pypositions)
 end
 pymatgen_structure(model::Model) = pymatgen_structure(model, model.atoms)
 
 
 function load_lattice_pymatgen(T, pyobj::PyObject)
-    mg = pyimport("pymatgen")
+    Structure = pyimport("pymatgen.core.structure").Structure
+    Lattice   = pyimport("pymatgen.core.lattice").Lattice
 
-    if pyisinstance(pyobj, mg.Structure)
+    if pyisinstance(pyobj, Structure)
         load_lattice_pymatgen(T, pyobj.lattice)
-    elseif pyisinstance(pyobj, mg.Lattice)
+    elseif pyisinstance(pyobj, Lattice)
         lattice = Matrix{T}(undef, 3, 3)
         for i in 1:3, j in 1:3
             lattice[i, j] = austrip(get(get(pyobj.matrix, j-1), i-1) * u"Å")
@@ -55,7 +56,7 @@ Load a DFTK-compatible atoms representation from a supported pymatgen object.
 All atoms are using a Coulomb model.
 """
 function load_atoms_pymatgen(T, pyobj::PyObject)
-    @assert pyisinstance(pyobj, pyimport("pymatgen").Structure)
+    @assert pyisinstance(pyobj, pyimport("pymatgen.core.structure").Structure)
     map(unique(pyobj.species)) do spec
         coords = [s.frac_coords for s in pyobj.sites if s.specie == spec]
         ElementCoulomb(spec.number) => coords

src/external/vtkio.jl

@@ -1,5 +1,3 @@
-import WriteVTK: vtk_grid, vtk_save
-
 @doc raw"""
     save_scfres(filename, scfres, Val(:vtk))
 
@@ -30,7 +28,7 @@ function save_scfres_master(filename::AbstractString, scfres::NamedTuple, ::Val{
     for (idcs, r) in zip(CartesianIndices(basis.fft_size), r_vectors_cart(basis))
         grid[:, Tuple(idcs)...] = r
     end
-    vtkfile = vtk_grid(filename, grid)
+    vtkfile = WriteVTK.vtk_grid(filename, grid)
 
     # Storing the bloch waves
     if save_ψ
@@ -67,5 +65,5 @@ function save_scfres_master(filename::AbstractString, scfres::NamedTuple, ::Val{
         vtkfile[key] = value
     end
 
-    only(vtk_save(vtkfile))
+    only(WriteVTK.vtk_save(vtkfile))
 end

src/plotting.jl

@@ -1,5 +1,3 @@
-import Plots
-
 # This is needed to flag that the plots-dependent code has been loaded
 const PLOTS_LOADED = true
 

test/external_pymatgen.jl

@@ -6,8 +6,8 @@ using UnitfulAtomic
 using PyCall
 
 py"""
-import numpy as np
-import pymatgen as mg
+from pymatgen.core.lattice import Lattice
+from pymatgen.core.structure import Structure
 """
 
 @testset "Lattice DFTK -> pymatgen -> DFTK" begin
@@ -18,7 +18,7 @@ end
 
 @testset "Lattice pymatgen -> DFTK -> pymatgen" begin
     data = randn(9)
-    reference = py"mg.Lattice($data)"
+    reference = py"Lattice($data)"
     output = pymatgen_lattice(load_lattice(reference))
     output = py"$output.matrix.ravel()" .+ 0
     @test data ≈ output atol=1e-14
@@ -41,11 +41,11 @@ end
 
 @testset "Structure pymatgen -> DFTK -> pymatgen" begin
     data = randn(9)
-    reflattice = py"mg.Lattice($data)"
+    reflattice = py"Lattice($data)"
     species = [1, 1, 6, 6, 6, 8]
     positions = [randn(3), randn(3), randn(3), randn(3), randn(3), randn(3)]
 
-    reference = py"mg.Structure($reflattice, $species, $positions)"
+    reference = py"Structure($reflattice, $species, $positions)"
     atoms = load_atoms(reference)
     @test length(atoms) == 3
     @test all(at isa ElementCoulomb for (at, positions) in atoms)