Uniformize monorepo structure to OrdinaryDiffEq canonical style

.codecov.yml

@@ -0,0 +1 @@
+comment: false

.github/dependabot.yml

@@ -11,11 +11,9 @@ updates:
       - "/lib/CanonicalMoments"
       - "/lib/CanonicalMoments/docs"
       - "/lib/CanonicalMoments/examples"
-      - "/lib/CanonicalMoments/test"
       - "/lib/DiscreteMeasures"
       - "/lib/DiscreteMeasures/docs"
       - "/lib/OUQBase"
-      - "/lib/OUQBase/test"
     schedule:
       interval: "daily"
     groups:

.github/workflows/CI.yml

@@ -0,0 +1,107 @@
+name: CI
+on:
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - 'docs/**'
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - 'docs/**'
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    permissions:
+      actions: write
+      contents: read
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+    env:
+      # Pin the depot path so the registry-refresh step and the subsequent
+      # julia-actions/julia-{buildpkg,runtest} steps all read and write the
+      # same depot on self-hosted runners (where the runner may otherwise
+      # inject ~/github-runners/<name>/.julia for some steps but not others,
+      # causing "expected package X to be registered" failures when General is
+      # refreshed into ~/.julia but resolve happens against the per-runner
+      # depot).
+      JULIA_DEPOT_PATH: ~/.julia
+    strategy:
+      fail-fast: false
+      matrix:
+        group:
+          - Core
+        version:
+          - 'lts'
+          - '1'
+          - 'pre'
+    steps:
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@v3
+        with:
+          version: ${{ matrix.version }}
+      # Split cache restore/save by event to work around recurring GitHub
+      # Actions cache upload auth failures (Azure SAS "Server failed to
+      # authenticate the request"). PRs only restore from a recent main push
+      # cache; only main push runs write the cache. continue-on-error keeps a
+      # transient cache backend hiccup from flunking an otherwise green job.
+      - name: Cache Julia depot (push only — read+write)
+        if: github.event_name == 'push'
+        uses: julia-actions/cache@v3
+        continue-on-error: true
+        with:
+          cache-compiled: 'false'
+      - name: Cache Julia depot (PR — restore only)
+        if: github.event_name != 'push'
+        uses: actions/cache/restore@v5
+        continue-on-error: true
+        with:
+          path: |
+            ~/.julia/artifacts
+            ~/.julia/packages
+            ~/.julia/registries
+            ~/.julia/scratchspaces
+            ~/.julia/logs
+          # Primary key intentionally won't match (run_id is unique); the
+          # restore-keys prefix matches julia-actions/cache's key scheme
+          # `${cache-name};os=${runner.os};${matrix...}` so we pull the most
+          # recent cache from a main push for this same matrix cell.
+          key: julia-cache;workflow=${{ github.workflow }};job=${{ github.job }};os=${{ runner.os }};group=${{ matrix.group }};version=${{ matrix.version }};run_id=${{ github.run_id }};run_attempt=${{ github.run_attempt }}
+          restore-keys: |
+            julia-cache;workflow=${{ github.workflow }};job=${{ github.job }};os=${{ runner.os }};group=${{ matrix.group }};version=${{ matrix.version }};
+      - name: Develop local path deps (Julia < 1.11)
+        shell: julia --color=yes --project=. {0}
+        run: |
+          using Pkg
+          if VERSION < v"1.11.0-DEV.0"
+            toml = Pkg.TOML.parsefile("Project.toml")
+            if haskey(toml, "sources")
+              specs = Pkg.PackageSpec[]
+              for (dep, spec) in toml["sources"]
+                if spec isa Dict && haskey(spec, "path") && isdir(spec["path"])
+                  @info "Developing" dep spec["path"]
+                  push!(specs, Pkg.PackageSpec(path=spec["path"]))
+                end
+              end
+              isempty(specs) || Pkg.develop(specs)
+            end
+          end
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        with:
+          coverage: false
+          check_bounds: auto
+        env:
+          GROUP: ${{ matrix.group }}
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v6
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: lcov.info
+          fail_ci_if_error: false
+          disable_safe_directory: true

.github/workflows/DocPreviewCleanup.yml

@@ -0,0 +1,17 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: write
+
+jobs:
+  doc-preview-cleanup:
+    uses: "SciML/.github/.github/workflows/docs-preview-cleanup.yml@v1"
+    secrets: "inherit"

.github/workflows/Documentation.yml

@@ -0,0 +1,12 @@
+name: Documentation
+on:
+  push:
+    branches:
+      - main
+    tags: '*'
+  pull_request:
+jobs:
+  build-and-deploy-docs:
+    name: "Documentation"
+    uses: "SciML/.github/.github/workflows/documentation.yml@v1"
+    secrets: "inherit"

.github/workflows/Downgrade.yml

@@ -0,0 +1,24 @@
+name: Downgrade
+on:
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - 'docs/**'
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - 'docs/**'
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    name: "Downgrade"
+    uses: "SciML/.github/.github/workflows/downgrade.yml@v1"
+    with:
+      group: "Core"
+    secrets: "inherit"

.github/workflows/DowngradeSublibraries.yml

@@ -22,5 +22,6 @@ jobs:
     uses: "SciML/.github/.github/workflows/sublibrary-downgrade.yml@v1"
     secrets: "inherit"
     with:
-      julia-version: "1.10"
-      skip: "Pkg,TOML"
+      group-env-name: "OPTIMALUNCERTAINTYQUANTIFICATION_TEST_GROUP"
+      group-env-value: "Core"
+      # Every lib/* sublibrary is downgrade-tested (projects auto-discovered, no exclusions).

.github/workflows/Downstream.yml

@@ -0,0 +1,62 @@
+name: IntegrationTest
+on:
+  push:
+    branches: [main]
+    tags: [v*]
+  pull_request:
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    name: ${{ matrix.package.repo }}/${{ matrix.package.group }}/${{ matrix.julia-version }}
+    runs-on: ${{ matrix.os }}
+    env:
+      GROUP: ${{ matrix.package.group }}
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version: ['1.10']
+        os: [ubuntu-latest]
+        # OptimalUncertaintyQuantification.jl currently has no registered
+        # downstream consumers. The matrix is intentionally empty so this job
+        # is a no-op; add `{user: ..., repo: ..., group: ...}` entries here as
+        # downstream packages adopt it. An empty matrix skips the job cleanly
+        # rather than failing.
+        package: ${{ fromJSON('[]') }}
+
+    steps:
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@v3
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: x64
+      - name: Clone Downstream
+        uses: actions/checkout@v6
+        with:
+          repository: ${{ matrix.package.user }}/${{ matrix.package.repo }}
+          path: downstream
+      - name: Load this and run the downstream tests
+        shell: julia --color=yes --project=downstream {0}
+        run: |
+          using Pkg
+          try
+            Pkg.develop(map(path ->Pkg.PackageSpec.(;path="lib/$(path)"), readdir("./lib")));
+            Pkg.test(coverage=true)  # resolver may fail with test time deps
+          catch err
+            err isa Pkg.Resolve.ResolverError || rethrow()
+            # If we can't resolve that means this is incompatible by SemVer and this is fine
+            # It means we marked this as a breaking change, so we don't need to worry about
+            # mistakenly introducing a breaking change, as we have intentionally made one
+            @info "Not compatible with this release. No problem." exception=err
+            exit(0)  # Exit immediately, as a success
+          end
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v6
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: lcov.info
+          fail_ci_if_error: false
+          disable_safe_directory: true

.github/workflows/SublibraryCI.yml

@@ -19,4 +19,7 @@ concurrency:
 jobs:
   sublibraries:
     uses: "SciML/.github/.github/workflows/sublibrary-project-tests.yml@v1"
+    with:
+      group-env-name: OPTIMALUNCERTAINTYQUANTIFICATION_TEST_GROUP
+      check-bounds: auto
     secrets: "inherit"

.github/workflows/TagBot.yml

@@ -1,42 +1,9 @@
-name: TagBot
+name: "TagBot"
 on:
   issue_comment:
-    types:
-      - created
+    types: [created]
   workflow_dispatch:
-    inputs:
-      lookback:
-        default: "3"
-
-permissions:
-  actions: read
-  checks: read
-  contents: write
-  deployments: read
-  issues: read
-  discussions: read
-  packages: read
-  pages: read
-  pull-requests: read
-  repository-projects: read
-  security-events: read
-  statuses: read
-
 jobs:
-  TagBot-Subpackages:
-    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        package:
-          - CanonicalMoments
-          - DiscreteMeasures
-          - OUQBase
-    steps:
-      - name: Tag ${{ matrix.package }}
-        uses: JuliaRegistries/TagBot@v1
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
-          subdir: "lib/${{ matrix.package }}"
+  tagbot:
+    uses: "SciML/.github/.github/workflows/tagbot.yml@v1"
+    secrets: "inherit"

.gitignore

@@ -1,4 +1,14 @@
+*.jl.cov
+*.jl.*.cov
+*.jl.mem
+*.jl.*.mem
 Manifest.toml
-.vscode
+*/Manifest.toml
 *.DS_Store
-*/Manifest.toml
+.vscode
+profile.pb.gz
+.*.swp
+LocalPreferences.toml
+
+docs/build
+.claude/

_typos.toml → .typos.toml

@@ -1,3 +1,7 @@
+[default.extend-words]
+# Abbreviation for "Theorem" used in citation references (e.g. "Dette Thm 1.3.2").
+Thm = "Thm"
+
 [files]
 # Machine-generated Pluto.jl HTML exports; the only hits are author surnames
 # (e.g. "Fons van der Plas") in embedded boilerplate, not editable prose.

Project.toml

@@ -1,6 +1,31 @@
-[workspace]
-projects = [
-    "lib/CanonicalMoments",
-    "lib/DiscreteMeasures",
-    "lib/OUQBase"
-]
+name = "OptimalUncertaintyQuantification"
+uuid = "91ab1271-1799-4997-981e-07ad84422b0d"
+authors = ["Avinash Subramanian (JuliaHub), Benjamin Chung (JuliaHub), Adam Gerlach (AFRL)"]
+version = "0.1.0"
+
+[deps]
+CanonicalMoments = "58d2c334-1a3c-4862-bb37-9012b9e58a38"
+DiscreteMeasures = "7766d772-2108-41ee-a4bd-11c51440a39b"
+OUQBase = "01930cae-99d2-7439-8f4f-ace2ece9f1b9"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+
+[sources]
+CanonicalMoments = { path = "lib/CanonicalMoments" }
+DiscreteMeasures = { path = "lib/DiscreteMeasures" }
+OUQBase = { path = "lib/OUQBase" }
+
+[compat]
+julia = "1.10"
+CanonicalMoments = "0.1"
+DiscreteMeasures = "0.1"
+OUQBase = "0.1"
+Reexport = "1.2.2"
+SafeTestsets = "0.1"
+
+[extras]
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Pkg", "SafeTestsets", "Test"]

docs/Project.toml

@@ -0,0 +1,19 @@
+[deps]
+CanonicalMoments = "58d2c334-1a3c-4862-bb37-9012b9e58a38"
+DiscreteMeasures = "7766d772-2108-41ee-a4bd-11c51440a39b"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+OUQBase = "01930cae-99d2-7439-8f4f-ace2ece9f1b9"
+OptimalUncertaintyQuantification = "91ab1271-1799-4997-981e-07ad84422b0d"
+
+[sources]
+CanonicalMoments = {path = "../lib/CanonicalMoments"}
+DiscreteMeasures = {path = "../lib/DiscreteMeasures"}
+OUQBase = {path = "../lib/OUQBase"}
+OptimalUncertaintyQuantification = {path = ".."}
+
+[compat]
+CanonicalMoments = "0.1"
+DiscreteMeasures = "0.1"
+Documenter = "1"
+OUQBase = "0.1"
+OptimalUncertaintyQuantification = "0.1"