Add copy_network, merge_networks, merge_scopes (closes #221) - #507

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dotsdl wants to merge 49 commits into

mainfrom

Commits on Sep 16, 2025

Add unimplemented merge_networks
ianmkenney
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1484de4

Commits on Sep 27, 2025

Make assemble_network chainable
ianmkenney
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40cb0ab
Partial implementation of merge_networks
ianmkenney
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30e7dd3

Commits on Sep 28, 2025

Merge remote-tracking branch 'origin/main' into an_merge
ianmkenney
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fc8656e

Commits on Sep 29, 2025

Make _validate_extends_tasks and create_tasks chainable
ianmkenney
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865a46f

Commits on Oct 7, 2025

Commits on Oct 16, 2025

Commits on Oct 20, 2025

Add comments to merge_networks
ianmkenney
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f19985f
Merge remote-tracking branch 'origin/main' into an_merge
ianmkenney
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c6edcd4

Commits on Nov 12, 2025

Typo fix and formatting
dotsdl
committed
9374b9b

Commits on Mar 16, 2026

Merge branch 'main' into an_merge
dotsdl
authored
6b98cb0

Commits on Jun 8, 2026

Expose merge_networks on the user-facing client and API

dotsdl
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claude
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6859746
Refactor merge_networks using KeyedChain.decode_subchains

dotsdl
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claude
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7e3f5d1
Bump gufe to >=1.8.0 in test and server env files

dotsdl
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claude
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df3a180
Merge branch 'main' into an_merge
dotsdl
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eb3c532
Address PR #507 review: PERFORMS wiring, state parameter, optimizations

dotsdl
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claude
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d0bf4ec

Commits on Jun 9, 2026

Pin gufe to =1.8.0 across all conda env files

dotsdl
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claude
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5a92fbc

Commits on Jun 23, 2026

Merge branch 'main' into an_merge
dotsdl
authored
beaf68c

Commits on Jun 26, 2026

Bump gufe / openfe / feflow to align with feflow 0.2.1 release

dotsdl
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claude
committed
b63474e
Fix merge_networks tests' scope auth; revert docs.yml gufe bump

dotsdl
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claude
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61a9f04
Add copy_network, merge_scopes; fix PERFORMS reachability bug

dotsdl
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claude
committed
e6b7aa6

Commits on Jun 27, 2026

Fix inverted EXTENDS direction in _TransformationData.to_subgraph

dotsdl
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6192d08
Memoize Task Nodes in to_subgraph so EXTENDS endpoints share identity

dotsdl
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claude
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f69f36f

Commits on Jul 2, 2026

Document Strategy and TaskRestartPattern non-preservation

dotsdl
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128ef9e

Commits on Jul 5, 2026

Document merge_networks, copy_network, merge_scopes in user guide

dotsdl
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claude
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a9b89df
Assert AlchemicalNetwork dedup in test_copy_network

dotsdl
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564ce40
Cover fan-in case in test_merge_scopes_creates_new_networks_in_target

dotsdl
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claude
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e8f5c37
Merge branch 'main' into an_merge
dotsdl
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94fda30
Add store-level test_copy_network with partial-preload target

dotsdl
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claude
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c5bc737

Commits on Jul 6, 2026

Split merge/copy docs into own user guide page

dotsdl
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dce5b16
Restrict merge/copy Task carry-over to complete status

dotsdl
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ef44334
Trim stale actioning caveats from merge/copy docstrings

dotsdl
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1e210f4
Link NonTransformation in merge/copy user guide

dotsdl
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claude
committed
ee1318a

Commits on Jul 7, 2026

Merge branch 'main' into an_merge
dotsdl
authored
435e41b

Commits on Jul 8, 2026

Merge branch 'main' into an_merge
dotsdl
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6a50050

Commits on Jul 14, 2026

Docs simplification.
dotsdl
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ea94afa
Address final review: qualname guards, state preservation, hygiene

dotsdl
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a31c8e5

Commits on Jul 16, 2026

Gate EXTENDS parent on task_statuses in update_task_trees

dotsdl
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7ccd708

Commits on Jul 17, 2026

Revert "Gate EXTENDS parent on task_statuses in update_task_trees"
dotsdl
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ca37a68
Merge branch 'main' into an_merge
dotsdl
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7f20a2c

Commits on Jul 20, 2026

Address mikemhenry review: 4 items on merge/copy machinery

dotsdl
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claude
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135fd62

Commits on Jul 21, 2026

Update merge/copy tests for active-only source policy

dotsdl
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claude
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08a6c69