Underworld-Technical-Notes · lmoresi · Sep 2, 2026 · Sep 2, 2026 · Sep 2, 2026 · Sep 2, 2026
diff --git a/.github/workflows/deposit-ready.yml b/.github/workflows/deposit-ready.yml
@@ -31,7 +31,19 @@ jobs:
 
       - name: Which notes have no DOI
         id: pending
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
+          # A request that is already OPEN counts as asked. deposit-queue.txt
+          # only records what has been merged, so without this the workflow
+          # re-asks on every metadata change and the same note accumulates
+          # requests -- four for one note, before this was noticed. Duplicate
+          # reminders are how a reminder becomes something you scroll past.
+          gh pr list --state open --limit 100 --json title \
+            --jq '.[] | select(.title | startswith("Deposit: ")) |
+                  .title | sub("^Deposit: "; "")' \
+            | tr ',' '\n' | tr -d ' ' | sed '/^$/d' > .already-asked || true
+          echo "already asked: $(tr '\n' ' ' < .already-asked)"
           SLUGS=$(pixi run -q python3 -c "
           import sys; sys.path.insert(0, 'scripts'); import deposit
           queued = set()
@@ -41,8 +53,13 @@ jobs:
                   if line: queued.add(line)
           except FileNotFoundError:
               pass
+          try:
+              queued.update(l.strip() for l in open('.already-asked') if l.strip())
+          except FileNotFoundError:
+              pass
           print(','.join(s for s in deposit.pending() if s not in queued))
           ")
+          rm -f .already-asked
           echo "slugs=${SLUGS}" >> "$GITHUB_OUTPUT"
           echo "not yet queued: ${SLUGS:-none}"
 

diff --git a/.github/workflows/outstanding.yml b/.github/workflows/outstanding.yml
@@ -0,0 +1,88 @@
+name: outstanding
+
+# Every step of publishing here is deliberate: a person merges the request to
+# deposit, a person merges the identifiers that come back. That is the right
+# design, and its failure mode is that a step simply does not happen and
+# nothing says so. A deposit sat unrecorded for a fortnight because the only
+# thing that would have complained was the NEXT deposit -- which is the worst
+# possible moment to find out.
+#
+# So this asks the question on a schedule instead of relying on anyone
+# remembering to. It maintains ONE issue: opened when something is
+# outstanding, edited while it stays outstanding, closed when it clears. It
+# never opens a second one, and it says nothing at all when there is nothing
+# to say.
+
+on:
+  schedule:
+    # Mondays, 22:00 UTC -- Tuesday morning in Canberra, so the week starts
+    # with the list rather than ending with it.
+    - cron: '0 22 * * 1'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  issues: write
+  pull-requests: read
+
+concurrency:
+  group: outstanding
+  cancel-in-progress: false
+
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          cache: true
+
+      - name: What is half-finished
+        id: check
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          set +e
+          pixi run -q python3 scripts/outstanding.py > report.txt
+          echo "count=$?" >> "$GITHUB_OUTPUT"
+          set -e
+          cat report.txt
+          {
+            echo "## Outstanding"
+            echo '```'
+            cat report.txt
+            echo '```'
+          } >> "$GITHUB_STEP_SUMMARY"
+
+      - name: Open, update or close the one issue
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          TITLE="Publishing steps not finished"
+          NUM=$(gh issue list --state open --limit 50 \
+                  --json number,title \
+                  --jq ".[] | select(.title == \"$TITLE\") | .number" | head -1)
+
+          if [ "${{ steps.check.outputs.count }}" = "0" ]; then
+            if [ -n "$NUM" ]; then
+              gh issue close "$NUM" \
+                --comment "Nothing outstanding as of $(date -u +%Y-%m-%d). Closed automatically."
+              echo "closed #$NUM"
+            else
+              echo "nothing outstanding, no issue open -- saying nothing"
+            fi
+            exit 0
+          fi
+
+          BODY=$(printf '%s\n\n```\n%s\n```\n\n%s\n' \
+            "Steps that were started and not finished. Regenerated each Monday by the \`outstanding\` workflow; run \`pixi run outstanding\` to see the same thing locally." \
+            "$(cat report.txt)" \
+            "This issue closes itself when the list is empty.")
+
+          if [ -n "$NUM" ]; then
+            gh issue edit "$NUM" --body "$BODY"
+            echo "updated #$NUM"
+          else
+            gh issue create --title "$TITLE" --body "$BODY"
+          fi
diff --git a/articles/2-11-scaling/metadata.yml b/articles/2-11-scaling/metadata.yml
@@ -16,6 +16,7 @@ version: 1.0.0
 legacy_doi: 10.59350/3wz3c-c8w65
 archive_doi: 10.6084/m9.figshare.33193458
 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
 license: CC-BY-4.0
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diff --git a/articles/30-years-of-citcom-ellipsis-and-underworld/metadata.yml b/articles/30-years-of-citcom-ellipsis-and-underworld/metadata.yml
@@ -13,6 +13,7 @@ version: 1.0.0
 legacy_doi: 10.59350/hsp06-ag431
 archive_doi: 10.6084/m9.figshare.33193530
 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
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diff --git a/articles/adding-zotero-references-to-a-webpage/metadata.yml b/articles/adding-zotero-references-to-a-webpage/metadata.yml
@@ -13,6 +13,7 @@ version: 1.0.0
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 archive_doi: 10.6084/m9.figshare.33193416
 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
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diff --git a/articles/ai-and-scientific-software-what-we-learned-rebuilding-underworld3/metadata.yml b/articles/ai-and-scientific-software-what-we-learned-rebuilding-underworld3/metadata.yml
@@ -13,6 +13,7 @@ version: 1.0.0
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 archive_doi: 10.6084/m9.figshare.33193560
 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
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 legacy_paths:

diff --git a/articles/alaska-moho-model-reproducible-research-with-containers/metadata.yml b/articles/alaska-moho-model-reproducible-research-with-containers/metadata.yml
@@ -13,6 +13,7 @@ version: 1.0.0
 legacy_doi: 10.59350/pn8gh-98592
 archive_doi: 10.6084/m9.figshare.33193410
 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
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 legacy_paths:

diff --git a/articles/build-conda-packages/metadata.yml b/articles/build-conda-packages/metadata.yml
@@ -13,6 +13,7 @@ version: 1.0.0
 legacy_doi: 10.59350/7x9h6-y1x53
 archive_doi: 10.6084/m9.figshare.33193440
 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
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diff --git a/articles/compressible-convection-in-cartesian-coordinates-in-underworld3/metadata.yml b/articles/compressible-convection-in-cartesian-coordinates-in-underworld3/metadata.yml
@@ -13,6 +13,7 @@ version: 1.0.0
 legacy_doi: 10.59350/g4ysn-pv176
 archive_doi: 10.6084/m9.figshare.33193527
 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
 license: CC-BY-4.0
 canonical_path: /compressible-convection-in-cartesian-coordinates-in-underworld3/
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diff --git a/articles/constitutive-models-in-symbolic-form/metadata.yml b/articles/constitutive-models-in-symbolic-form/metadata.yml
@@ -33,4 +33,5 @@ source: ghost-migration
 ghost_uuid: 137d7c0a-1a6b-412b-a605-069137faac95
 repository_record_id: 33193590
 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
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diff --git a/articles/craton-formation-and-the-onset-of-plate-tectonics/metadata.yml b/articles/craton-formation-and-the-onset-of-plate-tectonics/metadata.yml
@@ -13,6 +13,7 @@ version: 1.0.0
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 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
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diff --git a/articles/finding-particles-in-a-distributed-unstructured-mesh/metadata.yml b/articles/finding-particles-in-a-distributed-unstructured-mesh/metadata.yml
@@ -31,4 +31,5 @@ source: ghost-migration
 ghost_uuid: 1b9677b5-5308-4c90-a192-d29aad4000b7
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 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
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diff --git a/articles/free-surface-in-underworld/metadata.yml b/articles/free-surface-in-underworld/metadata.yml
@@ -13,6 +13,7 @@ version: 1.0.0
 legacy_doi: 10.59350/1a3e6-3v712
 archive_doi: 10.6084/m9.figshare.33193503
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+archived_version: 1.0.0
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diff --git a/articles/getting-started-60-seconds-to-underworld/metadata.yml b/articles/getting-started-60-seconds-to-underworld/metadata.yml
@@ -12,6 +12,7 @@ version: 1.0.0
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 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
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diff --git a/articles/getting-started-with-pull-requests/metadata.yml b/articles/getting-started-with-pull-requests/metadata.yml
@@ -13,6 +13,7 @@ version: 1.0.0
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+archived_version: 1.0.0
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diff --git a/articles/how-many-processors-should-we-use-to-solve-problem-x/metadata.yml b/articles/how-many-processors-should-we-use-to-solve-problem-x/metadata.yml
@@ -16,6 +16,7 @@ version: 1.0.0
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+archived_version: 1.0.0
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diff --git a/articles/how-to-install-underworld-on-mac-osx-big-sur-apple-silicon-m1/metadata.yml b/articles/how-to-install-underworld-on-mac-osx-big-sur-apple-silicon-m1/metadata.yml
@@ -13,6 +13,7 @@ version: 1.0.0
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 archive_doi: 10.6084/m9.figshare.33193455
 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
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diff --git a/articles/how-underworld3-turns-sympy-into-c/metadata.yml b/articles/how-underworld3-turns-sympy-into-c/metadata.yml
@@ -38,4 +38,5 @@ source: ghost-migration
 ghost_uuid: ba7cc108-239e-4371-8182-2316f9e2cf7c
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 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
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diff --git a/articles/ismip-hom-benchmark-experiments-using-underworld/metadata.yml b/articles/ismip-hom-benchmark-experiments-using-underworld/metadata.yml
@@ -12,6 +12,7 @@ version: 1.0.0
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+archived_version: 1.0.0
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diff --git a/articles/mesh-variables-and-petsc-vectors-keeping-arrays-in-sync/metadata.yml b/articles/mesh-variables-and-petsc-vectors-keeping-arrays-in-sync/metadata.yml
@@ -30,4 +30,5 @@ source: ghost-migration
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diff --git a/articles/moving-the-mesh-without-remaking-it/metadata.yml b/articles/moving-the-mesh-without-remaking-it/metadata.yml
@@ -37,4 +37,5 @@ source: native
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+archived_version: 1.0.0
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diff --git a/articles/new-features-of-the-surface-coupling-framework-in-underworld-2/metadata.yml b/articles/new-features-of-the-surface-coupling-framework-in-underworld-2/metadata.yml
@@ -31,4 +31,5 @@ source: ghost-migration
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diff --git a/articles/our-journey-from-underworld2-to-underworld3/metadata.yml b/articles/our-journey-from-underworld2-to-underworld3/metadata.yml
@@ -41,4 +41,5 @@ source: ghost-migration
 ghost_uuid: 6bfa4eab-e83e-4a57-8246-5c6ae2ecc353
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 archived_at: 2026-08-10T04:19:43Z
+archived_version: 1.0.0
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diff --git a/articles/particles-in-underworld3/metadata.yml b/articles/particles-in-underworld3/metadata.yml
@@ -31,4 +31,5 @@ source: ghost-migration
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diff --git a/articles/physical-units-in-computational-geodynamics/metadata.yml b/articles/physical-units-in-computational-geodynamics/metadata.yml
@@ -33,4 +33,5 @@ source: ghost-migration
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diff --git a/articles/running-underworld-in-a-browser/metadata.yml b/articles/running-underworld-in-a-browser/metadata.yml
@@ -20,6 +20,7 @@ archive_doi: 10.6084/m9.figshare.33216996
 repository_provider: figshare
 repository_record_id: 33216996
 archived_at: 2026-08-31T17:36:06Z
+archived_version: 1.1.0
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 subjects:
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diff --git a/articles/scaling-in-underworld/metadata.yml b/articles/scaling-in-underworld/metadata.yml
@@ -19,6 +19,7 @@ version: 1.0.0
 legacy_doi: 10.59350/qvgm0-yz754
 archive_doi: 10.6084/m9.figshare.33193452
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+archived_version: 1.0.0
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diff --git a/articles/self-updating-repositories/metadata.yml b/articles/self-updating-repositories/metadata.yml
@@ -13,6 +13,7 @@ version: 1.0.0
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diff --git a/articles/setting-up-full-multigrid/metadata.yml b/articles/setting-up-full-multigrid/metadata.yml
@@ -39,4 +39,5 @@ source: native
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diff --git a/articles/setting-up-underworld-dependencies/metadata.yml b/articles/setting-up-underworld-dependencies/metadata.yml
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diff --git a/articles/shear-bands-with-dilatancy-modelled-with-underworld/metadata.yml b/articles/shear-bands-with-dilatancy-modelled-with-underworld/metadata.yml
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diff --git a/articles/stress-recovery-in-underworld/metadata.yml b/articles/stress-recovery-in-underworld/metadata.yml
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diff --git a/articles/symbolic-time-derivatives-in-underworld3/metadata.yml b/articles/symbolic-time-derivatives-in-underworld3/metadata.yml
@@ -32,4 +32,5 @@ source: ghost-migration
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diff --git a/articles/the-dynamics-of-continental-accretion/metadata.yml b/articles/the-dynamics-of-continental-accretion/metadata.yml
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diff --git a/articles/underworld-2/metadata.yml b/articles/underworld-2/metadata.yml
@@ -13,6 +13,7 @@ version: 1.0.0
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diff --git a/articles/underworld-and-docker-part-1/metadata.yml b/articles/underworld-and-docker-part-1/metadata.yml
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diff --git a/articles/underworld-and-docker-part-2/metadata.yml b/articles/underworld-and-docker-part-2/metadata.yml
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diff --git a/articles/underworld-and-singularity/metadata.yml b/articles/underworld-and-singularity/metadata.yml
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diff --git a/articles/underworld-low-fat-cloud/metadata.yml b/articles/underworld-low-fat-cloud/metadata.yml
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