CI

.github/dependabot.yml

@@ -7,3 +7,10 @@ updates:
       interval: daily
     labels:
       - automerge
+  - package-ecosystem: pip
+    directory: "/"
+    open-pull-requests-limit: 1
+    schedule:
+      interval: daily
+    labels:
+      - automerge

.github/workflows/ci.yml

@@ -12,7 +12,8 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  NPROC: '2' # Number of Julia processes to run the notebooks
+  NPROC: '3' # Number of Julia processes to run the notebooks
+  PY_VER: '3.12'
   CACHE_NUM: '1'
   JULIA_NUM_THREADS: 'auto'
   JULIA_CONDAPKG_BACKEND: 'Null'
@@ -24,12 +25,20 @@ jobs:
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
-    - name: Setup micromamba
-      uses: mamba-org/setup-micromamba@v1
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      id: cp
       with:
-        environment-file: environment.yml
-        cache-environment: true
-        post-cleanup: all
+        python-version: ${{ env.PY_VER }}
+    - name: Cache pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ${{ env.pythonLocation }}
+        key: ${{ runner.os }}-pip-${{ steps.cp.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
+    - name: Install python packages
+      if: ${{ steps.cache-pip.outputs.cache-hit != 'true' }}
+      run: pip install -r requirements.txt
     - name: Read Julia version
       uses: SebRollen/[email protected]
       id: read_toml
@@ -41,9 +50,9 @@ jobs:
         wget -O /tmp/jill.sh https://raw.githubusercontent.com/abelsiqueira/jill/main/jill.sh
         bash /tmp/jill.sh --version ${{ steps.read_toml.outputs.value }} -y
         echo "$HOME/.local/bin" >> $GITHUB_PATH
-    - name: Restore Julia packages
+    - name: Cache Julia packages
       uses: actions/cache/restore@v3
-      id: cache
+      id: cache-julia
       with:
         path: |
           ~/.julia
@@ -52,26 +61,24 @@ jobs:
         restore-keys: |
           ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-
     - name: Install Julia packages
-      shell: micromamba-shell {0}
+      if: ${{ steps.cache-julia.outputs.cache-hit != 'true' }}
       run: |
         julia --color=yes -e 'using Pkg; Pkg.add(["PrettyTables", "Literate"])'
-        julia --project=@. --color=yes -e 'using Pkg, Dates; Pkg.instantiate(); Pkg.gc(collect_delay=Day(1))'
+        julia --project=@. --color=yes -e 'using Pkg, Dates; Pkg.instantiate(); Pkg.resolve(); Pkg.precompile(); Pkg.gc(collect_delay=Day(0))'
     - name: Save Julia packages
       uses: actions/cache/save@v3
-      if: ${{ steps.cache.outputs.cache-hit != 'true' }}
+      if: ${{ steps.cache-julia.outputs.cache-hit != 'true' }}
       with:
         path: |
           ~/.julia
           !~/.julia/registries
-        key: ${{ steps.cache.outputs.cache-primary-key }}
+        key: ${{ steps.cache-julia.outputs.cache-primary-key }}
     - name: Run program
-      shell: micromamba-shell {0}
       env:
         JULIA_PROJECT: '@.'
         GKSwstype: '100'
       run: julia --color=yes -p ${{ env.NPROC }} literate.jl
     - name: Build website
-      shell: micromamba-shell {0}
       run: jupyter-book build docs/
     - name: Upload pages artifact
       if: ${{ github.ref == 'refs/heads/main' }}

.github/workflows/linkcheck.yml

@@ -14,13 +14,28 @@ on:
 
 env:
   DIR: 'docs'
+  PY_VER: '3.12'
 
 jobs:
   linkcheck:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        id: cp
+        with:
+          python-version: ${{ env.PY_VER }}
+      - name: Cache pip
+        uses: actions/cache@v3
+        id: cache-pip
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ runner.os }}-pip-${{ steps.cp.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
+      - name: Install python packages
+        if: ${{ steps.cache-pip.outputs.cache-hit != 'true' }}
+        run: pip install -r requirements.txt
       - name: Setup Julia
         uses: julia-actions/setup-julia@v1
       - name: Convert literate notebooks to markdown files
@@ -33,28 +48,10 @@ jobs:
           for (root, dirs, files) in walkdir(pwd())
             for file in files
               if endswith(file, ".jl")
-                Literate.markdown(joinpath(root, file); mdstrings=true, flavor = Literate.CommonMarkFlavor())
+                nb = joinpath(root, file)
+                Literate.notebook(nb, dirname(nb); mdstrings=true, execute=false)
               end
             end
           end
-      - name: Restore lychee cache
-        id: restore-cache
-        uses: actions/cache/restore@v3
-        with:
-          path: .lycheecache
-          key: cache-lychee-${{ github.sha }}
-          restore-keys: cache-lychee-
-      - name: Lychee Checker
-        uses: lycheeverse/[email protected]
-        id: lychee
-        with:
-          fail: true
-          args: '--accept 200,204,429 --verbose --no-progress --cache --max-cache-age 1d ${{ env.DIR }}'
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Save lychee cache
-        uses: actions/cache/save@v3
-        if: always()
-        with:
-          path: .lycheecache
-          key: ${{ steps.restore-cache.outputs.cache-primary-key }}
+      - name: Check links
+        run: jupyter-book build ${DIR} --builder linkcheck

.github/workflows/update-manifest.yml

@@ -28,6 +28,8 @@ jobs:
         uses: actions/checkout@v4
       - name: Setup Julia
         uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
       - name: Update Julia dependencies
         env:
           JULIA_PKG_PRECOMPILE_AUTO: '0'

literate.jl

@@ -6,7 +6,7 @@ using PrettyTables
 end
 
 basedir = "docs"
-config = Dict("mdstrings" => true, "execute" => true, "flavor" => Literate.CommonMarkFlavor())
+config = Dict("mdstrings" => true, "execute" => true)
 
 nbs = String[]
 
@@ -21,9 +21,7 @@ end
 
 # Execute the notebooks in worker processes
 ts = pmap(nbs; on_error=ex->NaN) do nb
-    cd(dirname(nb)) do
-        @elapsed Literate.markdown(basename(nb); config)
-    end
+    @elapsed Literate.notebook(nb, dirname(nb); config)
 end
 
 pretty_table([nbs ts], header=["Notebook", "Elapsed (s)"])
@@ -34,12 +32,10 @@ for (nb, t) in zip(nbs, ts)
         println("Debugging notebook: ", nb)
         try
             withenv("JULIA_DEBUG" => "Literate") do
-                cd(dirname(nb)) do
-                    Literate.markdown(basename(nb); config)
-                end
+                Literate.notebook(nb, dirname(nb); config)
             end
         catch e
-            println("An error occured: ", e)
+            println(e)
         end
     end
 end

requirements.txt

@@ -0,0 +1,3 @@
+# matplotlib==3.8.2
+jupyter-book==0.15.1
+docutils!=0.18.*,!=0.19.*