Require Julia 1.9

goerz · goerz · commit 954f4e1c436a · 2023-10-18T15:32:20.000-04:00
diff --git a/.coverage/.gitignore b/.coverage/.gitignore
@@ -0,0 +1 @@
+*.info
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -1,51 +1,58 @@
 name: CI
 on:
-  - push
-  - pull_request
+  push:
+    branches:
+      - master
+      - 'release-*'
+    tags:
+      - '*'
+  pull_request:
+    branches:
+      - master
 env:
   GKSwstype: 100
   JULIA_PKG_PRECOMPILE_AUTO: false
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    name: Test ${{ matrix.title }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        version:
-          - '1.6'
-        os:
-          - ubuntu-latest
-        arch:
-          - x64
+        include:
+          - title: 'Linux - Latest'
+            os: ubuntu-latest
+            version: '1'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
       - uses: julia-actions/cache@v1
-      - run: |
-          # Instantiate Pkg
+      - name: "Instantiate test environment"
+        run: |
           wget https://raw.githubusercontent.com/JuliaQuantumControl/JuliaQuantumControl/master/scripts/installorg.jl
           julia --project=test installorg.jl
-      - run: |
-          # Run tests
-          julia --project=test --color=auto --startup-file=yes --code-coverage="user" --depwarn="yes" --check-bounds="yes" -e 'include("test/runtests.jl")'
-      - run: |
-          # Run downstream "Krotov" tests
-          julia --project=test -e '
-            using Pkg
-            Pkg.test("Krotov", coverage=true)'
-      - run: |
-          # Run downstream "GRAPE" tests
-          julia --project=test -e '
-            using Pkg
-            Pkg.test("GRAPE", coverage=true)'
+      - name: "Run tests"
+        shell: julia --color=yes --project=test --code-coverage="@" --depwarn="yes" --check-bounds="yes" {0}
+        run: |
+          include(joinpath(pwd(), "test", "runtests.jl"))
+      - name: "Run downstream Krotov tests"
+        shell: julia --color=yes --project=test --code-coverage="@" --depwarn="yes" --check-bounds="yes" {0}
+        run: |
+          import Krotov
+          include(pkgdir(Krotov, "test", "runtests.jl"))
+      - name: "Run downstream GRAPE tests"
+        shell: julia --color=yes --project=test --code-coverage="@" --depwarn="yes" --check-bounds="yes" {0}
+        run: |
+          import GRAPE
+          include(pkgdir(GRAPE, "test", "runtests.jl"))
+      - name: "Summarize coverage"
+        shell: julia --project=test {0}
+        run: |
+          using QuantumControlTestUtils
+          show_coverage()
       - uses: julia-actions/julia-processcoverage@v1
-      - run: |
-          # Summarize coverage
-          julia --project=test -e 'using QuantumControlTestUtils; show_coverage();'
       - uses: codecov/codecov-action@v3
         with:
           files: lcov.info
@@ -55,36 +62,27 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1'
       - run: |
           # Install Python dependencies
           set -x
           /usr/bin/python3 -m pip install zip-files
-      - run: |
+      - name: "Instantiate test environment"
+        run: |
           # Instantiate Pkg
           wget https://raw.githubusercontent.com/JuliaQuantumControl/JuliaQuantumControl/master/scripts/installorg.jl
           install -m 600 -D /dev/null ~/.ssh/known_hosts
           ssh-keyscan -H github.com > ~/.ssh/known_hosts
           julia --project=test -e 'include("installorg.jl"); installorg(; github="develop")'
           # installing in develop mode enables proper "source" links in subpackage APIs
-      - run: cp test/*.toml docs/  # Prepare DrWatson
-      - run: |
-          # Run doctests
-          julia --project=test -e '
-            using Documenter: DocMeta, doctest
-            using QuantumControl
-            DocMeta.setdocmeta!(QuantumControl, :DocTestSetup, :(using QuantumControl); recursive=true)
-            doctest(QuantumControl)'
-      - run: |
-          # Make documentation
-          julia --project=test docs/make.jl
+      - name: "Build documentation"
+        run: julia --project=test docs/make.jl
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
-          JULIA_DEBUG: Documenter
       - name: Zip the HTML documentation
         run: zip-folder --debug --auto-root --outfile "docs.zip" docs/build
       - uses: actions/upload-artifact@v3
@@ -100,27 +98,26 @@ jobs:
     name: Codestyle
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1'
       - name: Get codestyle settings
         run: wget https://raw.githubusercontent.com/JuliaQuantumControl/JuliaQuantumControl/master/.JuliaFormatter.toml
       - name: Install JuliaFormatter and format
-        # This will use the latest version by default but you can set the version like so:
-        #
-        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+        shell: julia {0}
         run: |
-          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
-          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
-      - name: Format check
+          using Pkg
+          Pkg.add(PackageSpec(name="JuliaFormatter"))
+          using JuliaFormatter
+          format(".", verbose=true)
+      - name: Format Check
+        shell: julia {0}
         run: |
-          julia -e '
-          out = Cmd(`git diff --name-only`) |> read |> String
+          out = Cmd(`git diff -U0`) |> read |> String
           if out == ""
               exit(0)
           else
-              @error "Some files have not been formatted !!!"
-              write(stdout, out)
+              @error "Some files have not been formatted !!!\n\n$out"
               exit(1)
-          end'
+          end
diff --git a/Project.toml b/Project.toml
@@ -26,4 +26,4 @@ Krotov = ">=0.5.3"
 QuantumControlBase = ">=0.8.3"
 QuantumPropagators = ">=0.6.0"
 Zygote = "0.6"
-julia = "1.6"
+julia = "1.9"
diff --git a/docs/generate_api.jl b/docs/generate_api.jl
@@ -23,8 +23,13 @@ function get_local_members(pkg; all=true)
     ]
 end
 
-_parentmodule(m, pkg) = parentmodule(m)
-_parentmodule(m::Number, pkg) = pkg
+function _parentmodule(m, pkg)
+    try
+        parentmodule(m)
+    catch
+        return pkg
+    end
+end
 
 
 """Return a list of symbols for all the sub-modules of `pkg`.
diff --git a/docs/make.jl b/docs/make.jl
@@ -8,7 +8,7 @@ using QuantumControl.Functionals
 using QuantumControl.Generators
 using Pkg
 using Documenter
-using QuantumCitations
+using DocumenterCitations
 
 DocMeta.setdocmeta!(QuantumControl, :DocTestSetup, :(using QuantumControl); recursive=true)
 
@@ -24,9 +24,8 @@ include("generate_api.jl")
 
 bib = CitationBibliography(joinpath(@__DIR__, "src", "refs.bib"); style=:numeric)
 
-makedocs(
-    bib;
-    strict=("CI" in keys(ENV)),
+makedocs(;
+    plugins=[bib],
     authors=AUTHORS,
     sitename="QuantumControl.jl",
     format=Documenter.HTML(;
diff --git a/test/Project.toml b/test/Project.toml
@@ -7,34 +7,39 @@ CSVFiles = "5d742f6a-9f54-50ce-8119-2520741973ca"
 Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 GRAPE = "6b52fcaf-80fe-489a-93e9-9f92080510be"
 GRAPELinesearchAnalysis = "290eba36-e2d8-4488-81b6-f66cc44f2186"
 IOCapture = "b5f81e59-6552-4d32-b1f0-c071b021bf89"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
 Krotov = "b05dcdc7-62f6-4360-bf2c-0898bba419de"
+LBFGSB = "5be7bae1-8223-5378-bac3-9e7378a2f6e6"
+LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
 LocalCoverage = "5f6e1e16-694c-5876-87ef-16b5274f298e"
+Optim = "429524aa-4258-5aef-a3af-852621145aeb"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-QuantumCitations = "259add83-af3e-4603-9706-50e341d5574e"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 QuantumControl = "8a270532-f23f-47a8-83a9-b33d10cad486"
 QuantumControlBase = "f10a33bc-5a64-497c-be7b-6f86b4f0c2aa"
 QuantumControlTestUtils = "d3fd27c9-1dfb-4e67-b0c0-90d0d87a1e48"
 QuantumGradientGenerators = "a563f35e-61db-434d-8c01-8b9e3ccdfd85"
-QuantumOptics = "6e0679c1-51ea-5a7c-ac74-d61b76210b0c"
 QuantumPropagators = "7bf12567-5742-4b91-a078-644e72a65fc1"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
-Term = "22787eb5-b846-44ae-b979-8e399b8463ab"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TwoQubitWeylChamber = "cad078a0-0012-46f4-b55e-a945d44e115b"
 UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
+Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
-julia = "1.6"
+julia = "1.9"
+Documenter = "1.1"
diff --git a/test/clean.jl b/test/clean.jl
@@ -29,7 +29,8 @@ function clean(; distclean=false, _exit=true)
     append!(CLEAN, _glob(joinpath(ROOT, "docs", "src", "api"), ".md"))
     _push!(CLEAN, joinpath(ROOT, "coverage"))
     _push!(CLEAN, joinpath(ROOT, "docs", "build"))
-    _push!(CLEAN, joinpath(ROOT, "lcov.info"))
+    append!(CLEAN, _glob(ROOT, ".info"))
+    append!(CLEAN, _glob(joinpath(ROOT, ".coverage"), ".info"))
     ###########################################################################
 
     ###########################################################################
diff --git a/test/init.jl b/test/init.jl
@@ -5,7 +5,6 @@ unicodeplots()
 using JuliaFormatter
 using QuantumControlTestUtils: test, show_coverage, generate_coverage_html
 using LiveServer: LiveServer, serve, servedocs as _servedocs
-using Term
 include(joinpath(@__DIR__, "clean.jl"))
 
 function servedocs(; kwargs...)
