CompatHelper: bump compat for LazyArrays to 1, (keep existing compat)

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/CI.yml

@@ -27,12 +27,12 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+      - uses: actions/cache@v3
         env:
           cache-name: cache-artifacts
         with:
@@ -45,38 +45,31 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v2
+      - uses: codecov/codecov-action@v3
         with:
           files: lcov.info
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1'
       - run: |
           julia --project=docs -e '
             using Pkg
-            pkg"add https://github.com/jagot/Jagot.jl"'
-      - run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
             Pkg.instantiate()
-            pkg"build PyPlot"'
-        env:
-          PYTHON: ""
-      - run: julia --project=docs docs/make.jl
+            pkg"add https://github.com/jagot/Jagot.jl"'
+      - uses: julia-actions/julia-docdeploy@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
   doctests:
     name: Doctests
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1'

.gitignore

@@ -3,3 +3,5 @@
 *.jl.mem
 *~
 /docs/src/figures/
+Manifest.toml
+.CondaPkg

Project.toml

@@ -1,7 +1,7 @@
 name = "AtomicStructure"
 uuid = "e24b7630-0518-11e9-1346-1188d3abce50"
 authors = ["Stefanos Carlström <[email protected]>"]
-version = "0.1.7"
+version = "0.1.8"
 
 [deps]
 AngularMomentumAlgebra = "0bb1b1ac-0216-11e9-361b-bb110c659ce1"
@@ -40,22 +40,22 @@ WignerSymbols = "9f57e263-0b3d-5e2e-b1be-24f2bb48858b"
 [compat]
 AngularMomentumAlgebra = "0.1, 0.2, 0.3"
 ArnoldiMethod = "0.2"
-ArrayLayouts = "0.7, 0.8"
+ArrayLayouts = "0.7, 0.8, 1"
 AtomicLevels = "0.1.3"
 BandedMatrices = "0.16, 0.17"
-BlockBandedMatrices = "0.11"
+BlockBandedMatrices = "0.11, 0.12"
 CompactBases = "0.3.9"
 Compat = "3.27, 4"
 ContinuumArrays = "0.10, 0.11, 0.12"
 CoulombIntegrals = "0.1.1"
 Crayons = "4.0"
 EnergyExpressions = "0.1"
-FillArrays = "0.12, 0.13"
+FillArrays = "0.12, 0.13, 1"
 Formatting = "0.4"
 HalfIntegers = "1.3"
 IntervalSets = "0.5, 0.6, 0.7"
 IterativeSolvers = "0.9"
-LazyArrays = "0.22"
+LazyArrays = "0.22, 1"
 LineSearches = "7"
 Optim = "1.7"
 PrettyTables = "2"

docs/CondaPkg.toml

@@ -0,0 +1,2 @@
+[deps]
+matplotlib = ">=3"

docs/Project.toml

@@ -2,17 +2,30 @@
 AngularMomentumAlgebra = "0bb1b1ac-0216-11e9-361b-bb110c659ce1"
 AtomicLevels = "10933b4c-d60f-11e8-1fc6-bd9035a249a1"
 CompactBases = "2c0377a8-7469-4ebd-be0f-82e501f20078"
+CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
 ContinuumArrays = "7ae1f121-cc2c-504b-ac30-9b923412ae5c"
 CoulombIntegrals = "42e5845a-f9f1-11e8-0afe-795ea56ed153"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 EnergyExpressions = "f4b57a2e-27c7-11e9-0cb0-edd185b706f6"
 IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
-Jagot = "84fb645a-ffa8-56cf-983b-ade63a92b20c"
 LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
-PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
+PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
+PythonPlot = "274fc56d-3b97-40fa-a1cd-1b4a50311bf9"
 QuasiArrays = "c4ea9172-b204-11e9-377d-29865faadc5c"
 SolverTraces = "619b3e1a-df4a-11e8-3b0b-a997e0925a8d"
 
 [compat]
+AngularMomentumAlgebra = "0.1, 0.2, 0.3"
+AtomicLevels = "0.1.3"
+CompactBases = "0.3"
+CondaPkg = "0.2"
+ContinuumArrays = "0.10, 0.11, 0.12"
+CoulombIntegrals = "0.1.1"
 Documenter = "0.27"
+EnergyExpressions = "0.1"
+IntervalSets = "0.7"
+LazyArrays = "0.22, 1"
+PythonCall = "0.9"
+PythonPlot = "1"
+QuasiArrays = "0.9"
+SolverTraces = "0.1"

docs/plots.jl

@@ -1,11 +1,11 @@
-using PyPlot
+using PythonPlot
 using Jagot.plotting
 plot_style("ggplot")
 
-using PyCall
+using PythonCall
 Cycler = pyimport("cycler")
-plt.rc("axes", prop_cycle=(plt.rcParams["axes.prop_cycle"] +
-                           Cycler.cycler("linestyle", ["-","--",":","-.",":","-","--"])))
+pyplot.rc("axes", prop_cycle=(pyplot.rcParams["axes.prop_cycle"] +
+    Cycler.cycler("linestyle", ["-","--",":","-.",":","-","--"])))
 
 using Statistics
 using Random
@@ -23,29 +23,24 @@ function mean_color(color::String)
     mean([c.r,c.g,c.b])
 end
 
+mean_color(color::Py) = mean_color(pyconvert(String, color))
+
 lerp(a,b,t) = (1-t)*a + t*b
 
 mean_position(x, ϕ) = ϕ'*Diagonal(x)*ϕ/(ϕ'ϕ)
 
-function cfigure(fun::Function, figname; clear=true, tight=true, kwargs...)
-    figure(figname; kwargs...)
-    clear && clf()
-    fun()
-    tight && tight_layout()
-end
-
-function csubplot(fun::Function, args...; nox=false, noy=false)
-    ax = subplot(args...)
-    fun()
-    if nox
-        no_tick_labels(:x)
-        xlabel("")
-    end
-    if noy
-        no_tick_labels(:y)
-        ylabel("")
+function savedocfig(name,dir="figures")
+    fig = gcf()
+    filename = joinpath(@__DIR__, "src", dir, "$(name).svg")
+    savefig(filename,
+            transparent=true,
+            facecolor=fig.get_facecolor())
+    PythonPlot.close("all")
+    if isfile(filename)
+        println("Saved $(name) to $(filename)")
+    else
+        @warn "Saving $(name) to $(filename) failed"
     end
-    ax
 end
 
 function plot_orbitals(atom::Atom; nrplot=1000, plot_basis=false,
@@ -120,7 +115,7 @@ function hydrogen()
     gst = ground_state(nucleus)
     atom = Atom(R, [spin_configurations(gst)[1]], nucleus)
     plot_orbitals(atom)
-    savefig("docs/src/figures/hydrogen.svg")
+    savedocfig("hydrogen")
 end
 
 function helium()
@@ -142,7 +137,7 @@ function helium()
         end
         legend(framealpha=0.75,ncol=2)
     end
-    savefig("docs/src/figures/helium.svg")
+    savedocfig("helium")
 end
 
 function beryllium(grid_type)
@@ -153,7 +148,7 @@ function beryllium(grid_type)
     fock = Fock(atom)
     optimize!(fock,ω=0.999,ωmax=1-1e-3,scf_method=:arnoldi)
     plot_orbitals(atom)
-    savefig("docs/src/figures/beryllium-$(grid_type).svg")
+    savedocfig("beryllium-$(grid_type)")
 end
 
 macro echo(expr)
@@ -162,7 +157,8 @@ macro echo(expr)
 end
 
 @info "Documentation plots"
-mkpath("docs/src/figures")
+fig_dir = joinpath(@__DIR__, "src", "figures")
+mkpath(fig_dir)
 @echo hydrogen()
 @echo helium()
 @echo beryllium(:fedvr)