Merge branch 'main' into edit_tutorial_contents

Author: hexaeder

.github/workflows/cleanup_stale_docpreview.yml

@@ -0,0 +1,87 @@
+name: Cleanup stale doc Previews
+
+on:
+  schedule:
+    - cron: '0 2 * * *'  # Run daily at 2 AM UTC
+  workflow_dispatch:      # Allow manual trigger
+
+concurrency:
+  group: doc-preview-cleanup
+  cancel-in-progress: false
+
+jobs:
+  cleanup-closed-pr-previews:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: read
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+          fetch-depth: 0
+
+      - name: Clean up closed PR previews
+        run: |
+          echo "Starting preview cleanup..."
+
+          deleted_previews=""
+
+          # Find all preview directories
+          if [ -d "previews" ]; then
+            shopt -s nullglob
+            for preview_dir in previews/PR*; do
+              if [ -d "$preview_dir" ]; then
+                # Extract PR number
+                pr_number=$(echo "$preview_dir" | sed 's/previews\/PR//')
+
+                # Validate PR number is numeric
+                if ! [[ "$pr_number" =~ ^[0-9]+$ ]]; then
+                  echo "Skipping invalid directory: $preview_dir"
+                  continue
+                fi
+
+                # Check PR state via GitHub API
+                api_response=$(curl -s -w "%{http_code}" -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+                  "https://api.github.com/repos/${{ github.repository }}/pulls/$pr_number")
+
+                http_code="${api_response: -3}"
+                json_response="${api_response%???}"
+
+                if [ "$http_code" != "200" ] && [ "$http_code" != "404" ]; then
+                  echo "API error for PR #$pr_number: HTTP $http_code"
+                  echo "Response: $json_response"
+                  exit 1
+                fi
+
+                pr_state=$(echo "$json_response" | jq -r '.state // "not_found"')
+
+                if [ "$pr_state" = "closed" ] || [ "$pr_state" = "not_found" ]; then
+                  echo "Delete $preview_dir (PR #$pr_number is $pr_state)"
+                  deleted_previews="$deleted_previews $preview_dir"
+
+                  git rm -rf "$preview_dir"
+                else
+                  echo "Keeping $preview_dir (PR #$pr_number is open)"
+                fi
+
+                sleep 1
+              fi
+            done
+            shopt -u nullglob
+          fi
+
+          # Commit and clean history if any previews were deleted
+          if [ -n "$deleted_previews" ]; then
+            echo "Clean up history for:$deleted_previews"
+
+            git config user.name "Documenter.jl"
+            git config user.email "[email protected]"
+            git commit -m "delete previews"
+            git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+            echo "Force push changes to upstream repo"
+            git push --force origin gh-pages-new:gh-pages
+          else
+            echo "No previews to clean up"
+          fi

.github/workflows/docpreviewcleanup.yml

@@ -145,6 +145,7 @@ jobs:
     permissions:
       actions: write # needed to allow julia-actions/cache to proactively delete old caches that it has created
       contents: write
+      pull-requests: read
     strategy:
       fail-fast: false
       matrix:
@@ -164,9 +165,36 @@ jobs:
       - name: Load Julia packages from cache
         id: julia-cache
         uses: julia-actions/cache@v2
+      - name: Extract OpPoDyn branch from PR
+        id: extract-branch
+        run: |
+          if [[ "${{ github.event_name }}" == "pull_request" ]]; then
+            PR_DATA=$(curl -s -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+                             -H "Accept: application/vnd.github.v3+json" \
+                             "https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}")
+            PR_TITLE=$(echo "$PR_DATA" | jq -r '.title')
+            PR_BODY=$(echo "$PR_DATA" | jq -r '.body')
+            # Combine title and body for searching
+            PR_TEXT="$PR_TITLE $PR_BODY"
+
+            # Look for [oppodyn:branch-name] pattern (case insensitive)
+            BRANCH_MATCH=$(echo "$PR_TEXT" | grep -i -o "\[oppodyn:[^]]*\]" | head -n1)
+            if [[ -n "$BRANCH_MATCH" ]]; then
+              BRANCH_NAME=$(echo "$BRANCH_MATCH" | sed 's/\[[Oo][Pp][Pp][Oo][Dd][Yy][Nn]:\([^]]*\)\]/\1/i')
+              echo "Found OpPoDyn branch specification: $BRANCH_NAME"
+              echo "oppodyn_branch=$BRANCH_NAME" >> $GITHUB_OUTPUT
+            else
+              echo "No OpPoDyn branch specified, using main"
+              echo "oppodyn_branch=main" >> $GITHUB_OUTPUT
+            fi
+          else
+            echo "Not a pull request, using main branch"
+            echo "oppodyn_branch=main" >> $GITHUB_OUTPUT
+          fi
       - uses: actions/checkout@v4
         with:
           repository: JuliaEnergy/OpPoDyn.jl
+          ref: ${{ steps.extract-branch.outputs.oppodyn_branch }}
           path: OpPoDyn
       - name: Run OpPoDyn tests
         shell: julia --project=testenv --color=yes {0}

.github/workflows/tests.yml

@@ -1,5 +1,19 @@
 # NetworkDynamics Release Notes
 
+## v0.10.1 Changelog
+- [#294](https://github.com/JuliaDynamics/NetworkDynamics.jl/pull/294) add linear stability analysis functions: `isfixpoint`, `jacobian_eigenvals`, and `is_linear_stable` with support for both ODE and DAE systems
+- [#283](https://github.com/JuliaDynamics/NetworkDynamics.jl/pull/283) add automatic sparsity detection using `get_jac_prototype` and `set_jac_prototype!`
+- [#285](https://github.com/JuliaDynamics/NetworkDynamics.jl/pull/285) rename `delete_initconstraint!` -> `delete_initconstaints!` and `delete_initformula!` -> `delete_initformulas!`
+
+## v0.10 Changelog
+- **BREAKING**: the interface initialization of components has changed: it is now split up in two versions, mutating and non mutating version. Also it errors now if the tolerance bounds are violated. See docs on initialization for more details.
+
+- new `get_graph(::Network)` method to extract graph object from nw
+- **improved Initialization System**: Added comprehensive initialization formulas and constraints system:
+  - added `@initformula` to add explicit algebraic init equations for specific variables
+  - added `@initconstraint` to add additional constraints for the component initialization
+- allow access edges via Pairs, i.e. `EIndex(1=>2,:a)` references variable `:a` in edge from vertex 1 to 2. Works also with unique names of vertices like `EIndex(:a=>:b)` [#281](https://github.com/JuliaDynamics/NetworkDynamics.jl/pull/281).
+
 ## v0.9 Changelog
 ### Main changes in this release
 NetworkDynamics v0.9 is a complete overhaul of the previous releases of NetworkDynamics.

NEWS.md

@@ -1,7 +1,7 @@
 name = "NetworkDynamicsInspector"
 uuid = "0a4713f2-d58f-43f2-b63b-1b5d5ee4e65a"
 authors = ["Hans Würfel <[email protected]>"]
-version = "0.1.6"
+version = "0.1.8"
 
 [deps]
 Bonito = "824d6782-a2ef-11e9-3a09-e5662e0c26f8"
@@ -32,12 +32,12 @@ ColorSchemes = "3.29.0"
 Colors = "0.13.0"
 Downloads = "1.6.0"
 Electron = "6"
-GraphMakie = "0.5.14"
+GraphMakie = "0.6"
 Graphs = "1.12.0"
-NetworkDynamics = "0.9.13"
+NetworkDynamics = "0.9.13, 0.10"
 Observables = "0.5.5"
 OrderedCollections = "1.8.0"
 PrecompileTools = "1.2.1"
 SciMLBase = "2.75.1"
-WGLMakie = "0.11"
+WGLMakie = "0.13"
 julia = "1.10"

NetworkDynamicsInspector/Project.toml

@@ -1,7 +1,7 @@
 name = "NetworkDynamics"
 uuid = "22e9dc34-2a0d-11e9-0de0-8588d035468b"
 authors = ["Frank Hellmann <[email protected]>, Michael Lindner <[email protected]>, Hans Würfel <[email protected]"]
-version = "0.9.18"
+version = "0.10.1"
 
 [deps]
 ArgCheck = "dce04be8-c92d-5529-be00-80e4d2c0e197"
@@ -14,6 +14,7 @@ Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 Mixers = "2a8e4939-dab8-5edc-8f64-72a8776f13de"
 NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
@@ -37,15 +38,17 @@ TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+RuntimeGeneratedFunctions = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"
+SparseConnectivityTracer = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
 SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [extensions]
 NetworkDynamicsCUDAExt = ["CUDA", "Adapt"]
 NetworkDynamicsDataFramesExt = ["DataFrames"]
 NetworkDynamicsMTKExt = ["ModelingToolkit", "SymbolicUtils", "Symbolics"]
+NetworkDynamicsSparsityExt = ["SparseConnectivityTracer", "RuntimeGeneratedFunctions"]
 NetworkDynamicsSymbolicsExt = ["Symbolics", "MacroTools"]
 
 [compat]
@@ -74,8 +77,10 @@ PrecompileTools = "1.2.1"
 Printf = "1.10.0"
 Random = "1"
 RecursiveArrayTools = "3.27.0"
+RuntimeGeneratedFunctions = "0.5.15"
 SciMLBase = "2"
 SparseArrays = "1"
+SparseConnectivityTracer = "0.6, 1"
 Static = "1.1.1"
 StaticArrays = "1.9.4"
 SteadyStateDiffEq = "2.2.0"

Project.toml

@@ -26,10 +26,10 @@ NetworkDynamics = {path = ".."}
 AbstractTrees = "0.4.5"
 ArgParse = "1.2.0"
 CUDA = "≥0.0.1"
-CairoMakie = "0.13.1"
+CairoMakie = "0.15"
 Chairmarks = "1.3.1"
 Graphs = "≥0.0.1"
-Makie = "0.22.1"
+Makie = "0.24"
 NetworkDynamics = "≥0.0.1"
 OrderedCollections = "1.7.0"
 PkgBenchmark = "0.2.12"

benchmark/Project.toml

@@ -3,6 +3,7 @@ name = "ND.jl docs"
 [deps]
 Bonito = "824d6782-a2ef-11e9-3a09-e5662e0c26f8"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+Chairmarks = "0ca39b1e-fe0b-4e98-acfc-b1656634c4de"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
@@ -27,24 +28,20 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SimpleWeightedGraphs = "47aef6b3-ad0c-573a-a1e2-d07658019622"
+SparseConnectivityTracer = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 StyledStrings = "f489334b-da3d-4c2e-b8f0-e476e12c162b"
 SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
 
-[sources.Bonito]
-rev = "master"
-url = "https://github.com/SimonDanisch/Bonito.jl"
-
-[sources.NetworkDynamics]
-path = ".."
-
-[sources.NetworkDynamicsInspector]
-path = "../NetworkDynamicsInspector"
+[sources]
+NetworkDynamics = {path = ".."}
+NetworkDynamicsInspector = {path = "../NetworkDynamicsInspector"}
 
 [compat]
 Bonito = "≥0.0.1"
-CairoMakie = "0.13.1"
+CairoMakie = "0.15"
+Chairmarks = "1.3.1"
 DataFrames = "≥0.0.1"
 DataInterpolations = "7, 8"
 DiffEqCallbacks = "4.2.2"
@@ -53,7 +50,7 @@ Documenter = "1.8.0"
 DocumenterInterLinks = "1"
 DynamicQuantities = "1.4.0"
 Electron = "≥0.0.1"
-GraphMakie = "0.5.13"
+GraphMakie = "0.6"
 Graphs = "≥0.0.1"
 LaTeXStrings = "1.4.0"
 Literate = "2.20.1"
@@ -69,6 +66,7 @@ Printf = "≥0.0.1"
 Random = "≥0.0.1"
 SciMLBase = "≥0.0.1"
 SimpleWeightedGraphs = "1.4.0"
+SparseConnectivityTracer = "≥0.0.1"
 StableRNGs = "1.0.2"
 StaticArrays = "≥0.0.1"
 StyledStrings = "≥0.0.1"