new backend

.JuliaFormatter.toml

@@ -1,74 +1,53 @@
-# base style
+# full list: https://domluna.github.io/JuliaFormatter.jl/dev/#Formatting-Options
+# style = "sciml"
 style = "yas"
-
-# number of spaces
-indent = 4
-
-# maximum lenght of line
 margin = 120
-
-# replace for i = [1:2] or i ∈ [1:2] with for i in [1:2]
 always_for_in = true
-
-# if true, add whitespace to typedef between , and <:
+normalize_line_endings = "unix"
+whitespace_in_kwargs = false
 whitespace_typedefs = false
-
-# f true, whitespace is added for binary operations in indices. Make this true
-# if you prefer arr[a + b] to arr[a+b]. Additionally, if there's a colon :
-# involved, parenthesis will be added to the LHS and RHS.
 whitespace_ops_in_indices = false
-
-# If true, superflous newlines will be removed. For example:
+format_markdown = false
+format_docstrings = true
+join_lines_based_on_source = true
 remove_extra_newlines = false
-
-# import A, B, C -> using A:A, Using B:B ...
-import_to_using = false
-
-# transform pipes |> to function calls
 pipe_to_function_call = false
-
-# transform f(x) = x definitons do full function... end blocks if line limit is exeded
-short_to_long_function_def = true
-
-# allways put return keyword at the end of functions
 always_use_return = false
 
-# (; a = 1) -> (; a=1)
-whitespace_in_kwargs = false
-
-# add ::Any to untyped fields
-annotate_untyped_fields_with_any = false
-
-# format docstrings with the same rules as the codebase
-format_docstrings = true
-
-# f the conditional E ? A : B exceeds the maximum margin converts it into the
-# equivalent if block:
-conditional_to_if = true
-
-# One of "unix" (normalize all \r\n to \n), "windows" (normalize all \n to
-# \r\n), "auto" (automatically choose based on which line ending is more common
-# in the file).
-normalize_line_endings = "auto"
-
-# comma after last element in multi line list?
-# trailing_comma = "nothing"
-
-# if there are linebreaks in argument lists in the source keep them like this
-join_lines_based_on_source = true
-
-# When set to true, submodule(s) appearing in the same file will be indented.
-indent_submodule = false
-
-# shot detials related to formatting
-verbose = true
-
-# also format markdown files?
-format_markdown = true
-
-# alignment rules
-# foo     = 1
-# foobar  = 2
-# stays like this
 align_assignment = true
+align_struct_field = true
+align_conditional = true
 align_pair_arrow = true
+align_matrix = true
+
+# ignore = ["docs/examples", "oldexamples", "test/oldtests"]
+
+# indent = 4,
+# margin = 92,
+# always_for_in = false,
+# for_in_replacement = "in",
+# whitespace_typedefs = false,
+# whitespace_ops_in_indices = false,
+# remove_extra_newlines = false,
+# import_to_using = false,
+# pipe_to_function_call = false,
+# short_to_long_function_def = false,
+# long_to_short_function_def = false,
+# always_use_return = false,
+# whitespace_in_kwargs = true,
+# annotate_untyped_fields_with_any = true,
+# format_docstrings = false,
+# align_struct_field = false,
+# align_conditional = false,
+# align_assignment = false,
+# align_pair_arrow = false,
+# conditional_to_if = false,
+# normalize_line_endings = "auto",
+# align_matrix = false,
+# trailing_comma = false,
+# trailing_zero = true,
+# indent_submodule = false,
+# separate_kwargs_with_semicolon = false,
+# surround_whereop_typeparameters = true,
+# variable_call_indent = []
+# short_circuit_to_if = false,

.github/workflows/CompatHelper.yml

@@ -1,7 +1,7 @@
 name: CompatHelper
 on:
   schedule:
-    - cron: '00 00 * * *'
+    - cron: 0 0 * * *
   workflow_dispatch:
 jobs:
   CompatHelper:

.github/workflows/Documentation.yaml

@@ -6,19 +6,35 @@ on:
       - main
     tags: '*'
   pull_request:
-
+  workflow_dispatch:
 jobs:
   build:
     runs-on: ubuntu-latest
+    permissions:
+      actions: write # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      contents: write
+      statuses: write
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
-          version: 1.6
-      - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
+          version: 1
+      - uses: julia-actions/cache@v2
+      - name: Configure doc environment
+        shell: julia --project=docs --color=yes {0}
+        run: |
+          using Pkg
+          Pkg.develop(PackageSpec(path=pwd()))
+          Pkg.instantiate()
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-        run: julia --project=docs/ docs/make.jl
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+      - name: Run doctests
+        shell: julia --project=docs --color=yes {0}
+        run: |
+          using Documenter: DocMeta, doctest
+          using NetworkDynamics
+          DocMeta.setdocmeta!(NetworkDynamics, :DocTestSetup, :(using NetworkDynamics); recursive=true)
+          doctest(NetworkDynamics)

.github/workflows/benchmark.yml

@@ -0,0 +1,48 @@
+name: Benchmark a pull request
+
+on:
+  pull_request:
+
+permissions:
+  pull-requests: write
+  actions: write
+  contents: read
+
+jobs:
+    run_benchmarks:
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v4
+              with:
+                fetch-depth: 0 # fetch all history
+            - uses: julia-actions/setup-julia@v2
+            - uses: julia-actions/cache@v2
+            - uses: julia-actions/julia-buildpkg@v1
+            - name: Run benchmarks
+              env:
+                JULIA_NUM_THREADS: auto
+              working-directory: benchmark
+              run: |
+                julia --color=yes ./run_benchmarks.jl -t ${{github.event.pull_request.head.ref}} -b ${{github.event.pull_request.base.ref}} --no-data-export --prefix ""
+                echo '### Benchmark Results' > body.md
+                echo '' >> body.md
+                echo '```' >> body.md
+                cat comparison.txt >> body.md
+                echo '```' >> body.md
+                echo '' >> body.md
+            - name: Upload plot
+              uses: actions/upload-artifact@v4
+              id: artifact-upload-step
+              with:
+                name: comparison.pdf
+                path: benchmark/comparison.pdf
+            - name: Link to graphic
+              run: |
+                echo '${{ steps.artifact-upload-step.outputs.artifact-url }}' >> benchmark/body.md
+            - uses: int128/hide-comment-action@v1 # hide all previous comments
+            - name: Comment on PR
+              uses: peter-evans/create-or-update-comment@v3
+              with:
+                issue-number: ${{ github.event.pull_request.number }}
+                body-path: benchmark/body.md

.github/workflows/tests.yml

@@ -4,52 +4,49 @@ on:
     branches:
       - main
   pull_request:
+  workflow_dispatch:
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
     runs-on: ${{ matrix.os }}
+    permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      actions: write
+      contents: read
     strategy:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
+          # - '1.6' TODO: replace with new LTS (1.10 probably)
           - '1'
+          - 'pre'
         os:
           - ubuntu-latest
           - macos-latest
           - windows-latest
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@latest
-      - run: |
-          git config --global user.name Tester
-          git config --global user.email [email protected]
-      - uses: julia-actions/julia-runtest@latest
-        continue-on-error: ${{ matrix.version == '1.2' }}
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v4
         with:
-          file: lcov.info
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
 
   pd-test:
     name: PowerDynamics.jl test - Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
     runs-on: ${{ matrix.os }}
+    permissions:
+      actions: write # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      contents: write
     strategy:
       fail-fast: false
       matrix:
@@ -60,13 +57,13 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: actions/checkout@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: actions/checkout@v4
         with:
           repository: JuliaEnergy/PowerDynamics.jl
           path: PowerDynamics.jl

.gitignore

@@ -3,11 +3,14 @@
 *.jl.mem
 deps/deps.jl
 .idea
-Manifest.toml
+Manifest*.toml
 scratch.jl
 docs/build
 bugs
 design_experiments
 benchmark/tune.json
 benchmark/*.md
 benchmark/*.data
+benchmark/*.txt
+/benchmark/*.pdf
+/docs/src/generated/