Merge fork master: land chat ops, workspace FS, MolRec metrics UI - #12

Merged

Roy-Kid merged 320 commits into

MolCrafts:masterfrom

Aug 4, 2026

This pull request is big! We're only showing the most recent 250 commits

Commits on Jun 6, 2026

refactor(workspace): misc cleanup — dead slug helper, __import__, move_to guard (hardening P2-6)
Roy-Kid
committed
55ef734
perf(workflow): memoize task AST hash + cache compiled topology maps (hardening P2-5)
Roy-Kid
committed
2643402
refactor: typed RunContext.mark_failed replaces private _context.status poke (hardening P2-1)
Roy-Kid
committed
ebcf81d
feat(workspace): validate target references against the registry (hardening P2-4)
Roy-Kid
committed
d69391e
refactor(workflow): extract graph analysis from compiler.py (hardening P2-2)
Roy-Kid
committed
909c68f
refactor(workspace): remove run.py E402 block via TYPE_CHECKING _WorkflowLike (hardening P2-2)
Roy-Kid
committed
14f316b
refactor(workflow): split node.py into dispatch / cache / params (hardening P2-2)
Roy-Kid
committed
eeea8bd
refactor(workspace): extract RunContext to runcontext.py (hardening P2-2)
Roy-Kid
committed
891053b

Commits on Jun 7, 2026

perf(workflow): wake the dependency barrier via asyncio.Event, not busy-poll (hardening P0-3)
Roy-Kid
committed
d66709d

Commits on Jun 8, 2026

Commits on Jun 10, 2026

Commits on Jun 14, 2026

Commits on Jun 15, 2026

chore(repo): remove obsolete vscode-ext extension and stale top-level docs

Roy-Kid
and
claude
committed
4906fff
feat(cli): add `runs execute` command and run-duration column

Roy-Kid
and
claude
committed
abc950a
refactor(ui): migrate charts to plugins/molplot and add deltaf/editor/metrics plugins

Roy-Kid
and
claude
committed
aac3da4
refactor(ui): remove dead components and dedupe RunViewer/MolqRunViewer

Roy-Kid
and
claude
committed
1946752
feat(ui): multi-run metrics aggregation in Experiment view (multi-run-metrics-aggregation)

Roy-Kid
and
claude
committed
ef3a634

Commits on Jun 16, 2026

feat(ui): per-chart enlarge dialog + toolbar toggle in RunMetricsView (runinspector-metrics-molplot)

Roy-Kid
and
claude
committed
58bee78

Commits on Jun 19, 2026

feat(library): per-scope notes + literature with Zotero linking

Roy-Kid
and
claude
committed
135bb27
feat(vsc-ext): add VS Code extension scaffold

Roy-Kid
and
claude
committed
954eab8
chore: add harness worktree settings

Roy-Kid
and
claude
committed
129d889
Merge remote-tracking branch 'upstream/dev' into dev
Roy-Kid
committed
a74c6cd

Commits on Jun 20, 2026

Commits on Jun 21, 2026

feat(knowledge): add ConceptMeta + typed errors + layer import-guard (okf-01-02-meta-errors)

Roy-Kid
and
claude
committed
957eda3
feat(knowledge): add OKF Folder Concept-on-disk base (okf-01-03-folder)

Roy-Kid
and
claude
committed
d415f01
feat(knowledge): add OKF Library bundle façade (okf-01-04-library)

Roy-Kid
and
claude
committed
2fc026b
feat(knowledge): typed Concept hierarchy + concept-type registry (okf-02-concept-types)

Roy-Kid
and
claude
committed
7ecdb3b
feat(knowledge): typed _ops/ operational sidecar for Run hot state (okf-04-ops-sidecar)

Roy-Kid
and
claude
committed
efa2ed6
feat(knowledge): Library build_index + search over the Concept tree (okf-03-library-index)

Roy-Kid
and
claude
committed
2642261
feat(knowledge): Note + Reference concept types (okf-07-01-references)

Roy-Kid
and
claude
committed
211976a
feat(knowledge): read-only Zotero import → Reference concepts (okf-07-02-zotero)

Roy-Kid
and
claude
committed
c477864
docs(knowledge): add molexp.knowledge charter to CLAUDE.md ## Architecture (okf-05-01-architecture-charter)

Roy-Kid
and
claude
committed
499712c
feat(knowledge): run lifecycle — ownership, heartbeat, reaping (okf-05-02-run-lifecycle)

Roy-Kid
and
claude
committed
b619457
feat(knowledge): resume / rerun / cancel verbs on knowledge Run (okf-05-03-resume-rerun-cancel)

Roy-Kid
and
claude
committed
19efccd
feat(knowledge): injectable FileSystem seam for Folder/Library (okf-05-04-folder-filesystem-seam)

Roy-Kid
and
claude
committed
358b005
feat(knowledge): FileSystem.append_text — final pre-rehome parity gap (okf-05-05-filesystem-append)

Roy-Kid
and
claude
committed
51bdfd5
feat(knowledge): FileSystem read_bytes/write_bytes/remove — last parity primitives (okf-05-06-filesystem-bytes)

Roy-Kid
and
claude
committed
50a3c5c
docs(agent): realign agent.md to the current agent + harness surface

Roy-Kid
and
claude
committed
b9d1691
feat(harness): persist composed prompt + approval decided_at for provenance

Roy-Kid
and
claude
committed
80c161a
feat(agent): rehome Agent/AgentSession onto molexp.knowledge.Folder (okf agent-rehome)

Roy-Kid
and
claude
committed
d16c51a
feat(harness): fan out generated tests to one TestSpec per BoundTask

Roy-Kid
and
claude
committed
d2e068e
refactor(workflow): import atomic_write_json from molexp.atomicio, not the workspace shim (okf-05-07 prep)

Roy-Kid
and
claude
committed
bb6812f
feat(harness): add experiment-report review checkpoint to PlanMode

Roy-Kid
and
claude
committed
222de03
refactor(knowledge): reduce knowledge to the concept-type registry; drop the duplicate storage layer

Roy-Kid
and
claude
committed
beff737
refactor(harness): make planmode-alignment additions OOP + class-grouped tests

Roy-Kid
and
claude
committed
e71b46f
Revert "refactor(knowledge): reduce knowledge to the concept-type registry; drop the duplicate storage layer"
Roy-Kid
committed
ff915bd
feat(workspace): OKF index.md + markdown-link knowledge graph on Folder (wsokf-01)

Roy-Kid
and
claude
committed
508c57f
test(cli): fix two stale/brittle pre-existing test failures

Roy-Kid
and
claude
committed
4aaffab
chore: ruff format + lint repo-wide (format gate green)

Roy-Kid
and
claude
committed
8238768
docs(notes): record ApprovalGate instance-name rule; fix PlanMode stage count in CLAUDE.md

Roy-Kid
and
claude
committed
9a71c9e
feat(workspace): OKF meta.yaml concept marker + knowledge-registry reconstruction (wsokf-02)

Roy-Kid
and
claude
committed
efd9595
refactor(harness): TestSourceValidator class (validate_test_source -> OOP)

Roy-Kid
and
claude
committed
e57101a
feat(workspace): _ops/ operational sidecar on Run (wsokf-03)

Roy-Kid
and
claude
committed
6e58931
refactor(harness): convert validators + approval policy/event helpers to OOP classes

Roy-Kid
and
claude
committed
e849adb
refactor(cli): PlanRuntime class replaces _make_gateway/_make_executor factory functions

Roy-Kid
and
claude
committed
ab3b0ff
test(harness): group flat tests into Test<Subject> classes mirroring source

Roy-Kid
and
claude
committed
0404138
fix(types): make ty check src/ fully clean (34 pre-existing diagnostics)

Roy-Kid
and
claude
committed
02d5790
docs(harness): update stale make_final_report_approval_request reference in RunMode docstring

Roy-Kid
and
claude
committed
cbaae6d
feat(agent): Agent/AgentSession adopt OKF workspace.Folder (wsokf-06)

Roy-Kid
and
claude
committed
1f596fb
feat(workspace): OKF bundle façade Bundle over the Folder concept tree (wsokf-04)

Roy-Kid
and
claude
committed
09f36a5
feat(workspace,workflow,server,cli): read run hot-state from _ops/run.json (wsokf-07)

Roy-Kid
and
claude
committed
38c5bd0
feat(workspace): Note/Reference OKF concepts + Zotero importer (wsokf-05)

Roy-Kid
and
claude
committed
b42f4c9
fix(workspace): workspace-local ConceptMeta base for ReferenceMeta (wsokf-05)

Roy-Kid
and
claude
committed
128861f
refactor(knowledge): reduce molexp.knowledge to the concept-type registry (wsokf-09)

Roy-Kid
and
claude
committed
a746ef9
docs: sync on-disk layout to OKF (meta.yaml / _ops/run.json / flat agent)

Roy-Kid
and
claude
committed
739e665
docs(specs): index the wsokf chain (08 dropped)

Roy-Kid
and
claude
committed
7dde998
Merge branch 'dev' into workspace-okf
Roy-Kid
committed
882baf3
refactor(workspace): RunMetadata single source of truth — hot-state only in _ops (wsokf-10)

Roy-Kid
and
claude
committed
06caa85
refactor: remove the legacy per-scope Library now that OKF Concepts replace it (wsokf-11)

Roy-Kid
and
claude
committed
3937fbc

Commits on Jun 22, 2026

Commits on Jun 26, 2026

Commits on Jun 29, 2026

Commits on Jun 30, 2026

Commits on Jul 1, 2026

Commits on Jul 2, 2026

Commits on Jul 3, 2026

Commits on Jul 4, 2026

Commits on Jul 7, 2026

Bump docs theme dependency to 0.1.1
Roy-Kid
committed
fc0bbcf

Commits on Jul 10, 2026

Commits on Jul 17, 2026

feat(agent+ui): task modes, delete, gitignore walks, agent settings polish
Roy-Kid
committed
cbd3bb2
Merge branch 'feat/ui-runs-console' into dev
Roy-Kid
committed
5cf4b40
Merge branch 'docs/i18n-bilingual' into dev
Roy-Kid
committed
8508e08
Merge branch 'docs/examples-expand' into dev
Roy-Kid
committed
4cf42da
Merge branch 'chore/notes-sync' into dev
Roy-Kid
committed
e36a094
fix(agent): harden task_id paths, repair compaction fake, drop dead UI bits
Roy-Kid
committed
731a101
docs: bump molcrafts-zensical-theme to ≥0.2.2 and refresh manuals
Roy-Kid
committed
9b680d9
fix(tests): restore OpenAPI dump script and unstick CI gates
Roy-Kid
committed
6acf56a
fix(tests): skip molpy preview modules when molpy/molrs mismatch
Roy-Kid
committed
5ad3071
fix(preview): track molpy 0.8 — Frame lives in molrs
Roy-Kid
committed
ea6d9a5
fix(tests): stub MCP toolsets in agent session route suite
Roy-Kid
committed
a9266f7
ci: align pre-commit with CI (lint/test/ui) and hermetic CLI asserts
Roy-Kid
committed
186feee
chore: point META.build.test at the CI pytest command string
Roy-Kid
committed
3b0e64e

Commits on Jul 19, 2026

Commits on Jul 22, 2026

Commits on Jul 23, 2026

Commits on Jul 24, 2026

ci: prek + tox test gate; tox in pyproject dev
Roy-Kid
committed
dccf36b
fix(ci): restore CI/pre-commit parity with uv sync (drop tox-in-CI)
Roy-Kid
committed
16780a2
fix(ci): mark UI job advisory until molplot npm pin resolves
Roy-Kid
committed
82b40d9

Commits on Aug 3, 2026

Commits on Aug 4, 2026