feat(sql): make tree-sitter-sql a core dependency - #1
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A default install (uv tool install graphifyy / pipx install graphifyy) shipped without SQL parsing: tree-sitter-sql lived behind the [sql] extra, so every .sql file silently contributed nothing until the user found the extra or ran pipx inject (Graphify-Labs#1745). The grammar ships prebuilt abi3 wheels for every supported platform from 0.3.9, so the reason tree-sitter-dm stays optional does not apply. - promote tree-sitter-sql>=0.3.9,<0.4 into [project.dependencies]; keep the [sql] extra as an alias so existing install scripts resolve - drop .sql from _EXTRA_FOR_EXTENSION: a missing grammar now means a broken install, so the Graphify-Labs#1745 warning must not point at an extra - reword the extractor's missing-grammar error to say the install is incomplete and name the direct repair Bumps version to 0.9.49. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- new test_sql_core_dependency.py: tree-sitter-sql must sit in
[project.dependencies] with an upper bound, .sql must not map to an
optional extra, and a table/view/procedure corpus must produce
structural nodes plus contains/references/reads_from edges
- convert every importorskip("tree_sitter_sql") to a hard import: the
grammar is core now, so its absence must fail the suite, not skip it
- update the Graphify-Labs#1745 warning test: the dev environment now ships the
grammar, so genuine absence is simulated by blanking find_spec, and
the message must say "core dependency" instead of hinting at
graphifyy[sql]
Each packaging guard was mutation-tested (dep removed from pyproject,
.sql re-added to the extras map) and failed as required.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Remove the sql row from the optional-extras table, add an upgrade note (existing extra/pipx-inject users just run the normal upgrade), and add the 0.9.49 changelog entry. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Important
This repository does not receive automatic reviews because it has fewer than 10 stars. ⚙️ Run configurationConfiguration used: defaults Review profile: CHILL Plan: Team Run ID: 📝 WalkthroughWalkthroughSQL grammar support is now a constrained core dependency. The ChangesSQL dependency integration
Estimated code review effort: 2 (Simple) | ~15 minutes Merge Risk: 🟡 Moderate · up to SQL parsing will become available in default installations, but the current change still contains lint violations that may fail CI and gives users an unbounded repair command that could install an unsupported parser version. These are localized fixes required before merge. Suggested reviewers: 🚥 Pre-merge checks | ✅ 5✅ Passed checks (5 passed)
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Upstream cuts versions and batches changelog entries in maintainer commits (see 'chore: bump to 0.9.48'), so a contributor PR should not claim the next version number. Comments and messages now describe the grammar as a core dependency without naming a release.
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Inline comments:
In `@graphify/extractors/sql.py`:
- Around line 44-46: Update the missing-SQL-grammar error in the SQL extractor
to recommend pip install 'tree-sitter-sql>=0.3.9,<0.4', and update
test_extract_warns_when_sql_grammar_missing to assert that exact repair command.
In `@tests/test_extract.py`:
- Around line 3652-3655: In the test setup around the extract call, split each
semicolon-separated assignment and file write into its own statement line to
eliminate Ruff E702 violations. Keep the existing paths, file contents, and
extract invocation unchanged.
In `@tests/test_multilang.py`:
- Around line 460-472: Rename each ambiguous loop variable l to label in the
assertions at tests/test_multilang.py lines 460-472 and 661-663, and
tests/test_sql_core_dependency.py lines 90-91; update the corresponding
references while preserving the existing assertions.
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ℹ️ Review info
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Configuration used: defaults
Review profile: CHILL
Plan: Pro Plus
Run ID: c87571c5-6219-473a-93d4-4a5ee2dab79a
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uv.lockis excluded by!**/*.lock
📒 Files selected for processing (7)
README.mdgraphify/extract.pygraphify/extractors/sql.pypyproject.tomltests/test_extract.pytests/test_multilang.pytests/test_sql_core_dependency.py
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🟡 Changes recommended
The new SQL end-to-end test calls extract() without an isolated cache_root, which can write graphify-out/ under the working directory and cause cross-test interference.
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Pull request overview
This PR promotes tree-sitter-sql from an optional [sql] extra to a core dependency so default installs no longer silently skip .sql files, and updates warnings/docs/tests to reflect that SQL parsing must always be available.
Changes:
- Move
tree-sitter-sql>=0.3.9,<0.4into core dependencies while keeping thesqlextra as a compatibility alias. - Update missing-grammar messaging and remove
.sqlfrom_EXTRA_FOR_EXTENSIONso the Graphify-Labs#1745 warning no longer points users at an extra. - Convert SQL tests from
importorskipto hard imports and add a new packaging + end-to-end SQL extraction invariant test.
File summaries
| File | Description |
|---|---|
uv.lock |
Locks tree-sitter-sql as a core dependency and keeps the extra metadata consistent with the new pin. |
pyproject.toml |
Promotes tree-sitter-sql into [project.dependencies] and retains [project.optional-dependencies].sql as an alias. |
graphify/extract.py |
Removes .sql from _EXTRA_FOR_EXTENSION so missing SQL grammar is treated as a broken install, not a missing extra. |
graphify/extractors/sql.py |
Improves the “missing grammar” error text to reflect core-dependency status and a direct repair path. |
tests/test_sql_core_dependency.py |
Adds tests that pin the packaging invariant and validate end-to-end SQL node/edge emission. |
tests/test_multilang.py |
Converts SQL tests from skipping to failing when tree_sitter_sql is absent. |
tests/test_extract.py |
Updates the Graphify-Labs#1745 warning expectations and simulates missing grammar in a now-grammar-present dev environment. |
README.md |
Removes the sql extra from the install table and documents SQL as included by default. |
Review details
- Files reviewed: 7/8 changed files
- Comments generated: 1
- Review effort level: Lite
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Review findings on the fork PR: - The missing-grammar error now names pip install 'tree-sitter-sql>=0.3.9,<0.4' — the unpinned command could pull a grammar outside the supported range; the warning test asserts the pinned form. - The end-to-end corpus test now passes cache_root=tmp_path so it cannot write cache state under the working directory. - Renamed an ambiguous 'l' loop variable this PR introduced (E741); pre-existing occurrences upstream are left untouched to keep the diff scoped.
Owner
Author
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Review feedback addressed in 0eb61bc:
Skipped, with reason: the E702 semicolon lines in Validated: full suite |
…raphify-Labs#3150) The Objective-C field->type table is keyed by class node id, but the id-carrier rewrites (prefix strip, symbol canonicalisation, cache portability round-trip) never remapped those keys, so after graphify update the keys went stale and every self.field / obj.field method call missed resolution. Remap the table keys alongside the existing id remaps (in-process and in the cache round-trip); a dropped key can only cost a missed edge, never a phantom.
… a subclass (Graphify-Labs#3151) A method call through a field whose type is declared on an ancestor class, used from a subclass, did not resolve (the field-type table only held the class's own fields). Walk the inheritance chain (per-file for Java/C#, cross-file for Java/ObjC) to type the receiver, BFS with a seen-set so an inheritance cycle terminates. Target selection is unchanged (the single-definition guards stand), so this only widens receiver typing and never fabricates an edge; this.-only, and the binder refuses to guess on ambiguity.
…fy-Labs#3115) A PHP `new Foo()` emitted no edge. Add object_creation_expression to the PHP call types and emit a calls edge to the constructed class (namespaced names resolve to the last segment), consistent with the C# (Graphify-Labs#2998) and TypeScript (Graphify-Labs#3135) object-creation handling. Dynamic (new $var()), self/static/parent, and unknown external constructions fabricate nothing.
…raphify-Labs#3115) The fixtures embedded PHP namespace paths (\App\Bar, App\Command) as plain strings, so \A / \C were invalid escape sequences (SyntaxWarning now, SyntaxError in a future Python). Double the namespace backslashes; the \n newlines are unchanged.
…ify-Labs#3123) A type-only import (import type { T } from './m') produced an import edge like a value import, so type-only round-trips showed up as false import cycles. Stamp type_only on the module and symbol edges from type-only statements (correctly not firing for a mixed import { type A, B }, which keeps its value edge) and exclude stamped edges from find_import_cycles, mirroring the existing deferred-import exclusion.
…#3185) An `import(...)` used as a call type-argument (f<typeof import('mod')>()) could make the parser drop declarations that follow it. Rewrite the import-type to a byte-length- and newline-preserving placeholder before parsing so trailing declarations survive with exact source locations; the dynamic-import edge is still recovered by re-reading the original file. On the pinned tree-sitter-typescript (0.23.2) only the multiline form regresses today; the single-line/member/TSX tests guard against regressions on future grammar bumps.
…emap/ts-import-type batch
A sourceless legacy node now backfills its source_file from incident-edge provenance (only when real edge evidence exists, deterministic min, never fabricated), and a declined data JSON now emits a single file-identity node carrying source_file instead of nothing, so freshness/affected checks can see the file. No node is resurrected and config JSON does not double-add its file node.
…raphify-Labs#3129) A --project (committed/shared) install pinned the absolute interpreter path into the hook command, so the committed hook churned across machines. Emit a bare `graphify <sub>` command for project installs (resolved at hook-run time via the PATH/pin/uv-tool probes), while the global install still emits the absolute path (preserving the Windows VS Code Codex case). Uninstall still strips the bare command.
The prs MCP tools (list_prs, triage_prs, get_pr_impact) returned genuine failures (gh missing/unauth, unresolved PR) as success text. Raise a ToolError propagated as isError on both the 1.x and 2.x SDK paths, so a client sees the failure; an empty-but-successful result (0 PRs, PR with no changed files) is unaffected. Mirrors the Graphify-Labs#2725 MCP-error pattern.
get_node used a raw substring scan and returned an iteration-order match, so it could miss or mis-pick a node that get_neighbors resolves. Extract the shared tiered resolver (_resolve_single_node) and route get_node through it — deterministic tiered winner or an explicit ambiguity report, matching get_neighbors byte-for-byte; get_neighbors behavior and return shapes are unchanged.
Wire Razor .razor/.cshtml @inject/@using through the existing scope-aware C# type resolver instead of a bespoke path: @Inject emits a references edge to a sourceless stub, @using feeds scoping, and the type-resolution + stub-rewire passes now accept Razor sources. A cross-file injected type resolves to its real definition; an external/undeclared type fabricates nothing and a qualified inject does not mis-bind a same-named type. Partially addresses Graphify-Labs#3187: a bare @Inject of a type in a file-scoped namespace still dangles (same as a bare C# cross-namespace reference without a using), and implicit _Imports.razor global usings are not yet modeled — left as follow-up, so this does not auto-close the issue.
…stall/provenance batch
This reverts Graphify-Labs#3155 (b568488): the source_file backfill also fired on a shared external stub (e.g. a cross-file `Path` reference with no source_file), giving the stub a file identity so the orphan prune swept it when that one file was deleted even though another file still referenced it — regressing test_prune_sweeps_orphans. The fix needs to distinguish a legacy node that genuinely lost its provenance from an external stub that must stay sourceless; sending Graphify-Labs#3155 back as needs-work.
…ines (Graphify-Labs#3164) T-SQL routine idioms (CREATE OR ALTER, the PROC shorthand, bracket-delimited names like [dbo].[Get Widgets]) parse to tree-sitter ERROR nodes, so the routine names were lost. Hoist a single routine-recovery pattern covering all three forms and run it over a comment/string-masked copy of the file so commented-out or dynamic-SQL DDL cannot fabricate nodes; labels keep the raw bracketed text and plain CREATE PROCEDURE/FUNCTION is unchanged.
graphify --help omitted the real prs and provider commands and the export format list. Add them (verbatim from the dispatcher's own usage text), so every listed command/format exists and the export formats match the supported allow-list.
…ring Update the deepseek-v4-flash per-1M-token pricing (same units/ordering as neighboring models) and fix the build_merge docstring, which claimed it saved the graph back to disk; build_merge only reads the existing graph and returns the merged result — callers persist.
…(Win11 focus-steal) Add a comment warning against reverting the Windows detached spawn to DETACHED_PROCESS: DETACHED_PROCESS lets the child allocate its own console, which Windows 11 + Windows Terminal render as a visible focus-stealing window, so CREATE_NO_WINDOW is required.
…aphify-Labs#3190) A code-only watch/update rebuild never re-creates a semantic-backed document node, so an authored [[wikilink]] to such a doc resolved to a missing canonical id and reconcile silently dropped the edge. Re-parse each markdown source and repoint authored references edges onto a unique representative node for the target file (canonical id, else unique page node, else unique document node; ambiguous -> keep the existing edge), preserving links to the semantic tier across a code-only rebuild without resurrecting a deleted target.
… target (Graphify-Labs#3190) The reconcile relies on the extractor only stamping target_file when the link target exists on disk. Add a negative test: link text intact but the target file deleted must leave no reference edge and no edge pointing at the deleted document's node.
…help/pricing batch
Ships three batches: php new Foo() calls (Graphify-Labs#3115), inherited-field receivers (Graphify-Labs#3151), objc field-table remap (Graphify-Labs#3150), ts type-only-import cycles (Graphify-Labs#3123) and import-type args (Graphify-Labs#3185); razor @Inject cross-file (partial Graphify-Labs#3187), MCP prs isError + get_node resolver parity, project-scoped bare hook command (Graphify-Labs#3129); and T-SQL routine recovery (Graphify-Labs#3164), watch markdown->semantic reconcile (Graphify-Labs#3190), --help completeness, and a deepseek pricing fix. The Graphify-Labs#3155 provenance backfill was reverted (regressed the orphan prune). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…-Labs#3127) A god-node relation group capped at 20 targets showed no indication it was truncated; append a '…and N more' line (exact count, degree-sorted so the lowest-degree are dropped) only when the group actually exceeds the cap.
…Graphify-Labs#3148) The GRAPH_REPORT headline figures disagreed: shown-community count included empty communities the render loop skips, and the knowledge-gaps thin count used a hardcoded 3 beside a label printing min_community_size. Drive every figure from one _real_count predicate so the counts reconcile with what is actually rendered.
…d few (Graphify-Labs#3183) Only a handful of control tokens were defanged, so an attacker-chosen token outside the set (e.g. Llama-3 <|eot_id|>) could still reach the prompt. Generalize the neutraliser to match the control-token form (<|...|> and [/?INST|SYSTEM]) at the single _wrap_untrusted chokepoint; the bounded charset leaves legitimate content (|| , markdown tables, generics) untouched.
…prose (Graphify-Labs#3121) The hook-guard matched a search command appearing anywhere in the intercepted Bash string (a comment, a quoted -m message, an echo), firing false nudges. Match only an executed command position (start-of-segment after a shell operator, wrapper-aware), so prose lookalikes stay quiet while genuine pipes/&&/;/$() invocations still fire.
…L.md (Graphify-Labs#3144) When the installed SKILL.md has diverged (user edit or old version), back it up beside the install target before the atomic overwrite and print an actionable warning naming the stale path and the exact reinstall command; a clean up-to-date reinstall backs up nothing (no churn), and only the installed copy is touched, never the generated sources.
…bs#3190) Follow-up to Graphify-Labs#3191: an authored markdown link whose target basename is present in the graph but under a different spelling (e.g. Windows-case [[target]] vs TARGET.md) was dropped on a code-only rebuild. Preserve such an edge when its target node is still live in the merged graph, without loosening the deleted-target existence gate (a genuinely deleted target's node is evicted first, so it is never preserved).
On the default incremental path a semantic chunk that returned successfully but under-produced (prior semantic count > 1, fresh < prior) bypassed every guard, silently shrinking the graph. Flag that per-source shrink (computed only from fresh nodes, so a genuinely deleted file is never flagged) and route it through the existing shrink-guard refusal + manifest un-stamp so the source re-extracts next run; --allow-partial overrides. Does not touch the prune path.
… into one helper (Graphify-Labs#3203) The raw and clustered write paths carried a byte-identical ~27-line block differing only in whether the flag is read from merged or G.graph. Extract _handle_unverified_semantic_shrink so the two paths cannot drift; behavior-identical (the Graphify-Labs#3203 and prune-sweep suites pass).
…Labs#3192) Add a Robot Framework extractor using the official robot.api parser (pure-Python, optional [robot] extra), emitting suite/test/keyword nodes plus keyword-call, resource-import, and library edges. Keyword resolution is case/space/underscore-insensitive (RF's real semantics) and handles BDD prefixes and ${CURDIR}/${EXECDIR} path resolution; degrades to an actionable error when robotframework is absent.
…ollision (Graphify-Labs#3192) A user keyword named like an imported library (e.g. a keyword 'SeleniumLibrary') would mint the same id as the library stub. Namespace the stub id under robot_library so the two cannot collide; the display label keeps the raw library name.
…fy-Labs#1790) A plain JavaScript `class Dog extends Animal` produced no inherits edge — only the TypeScript extends_clause/implements_clause shapes were handled, not the bare identifier directly under class_heritage that JS emits. Fall back to reading heritage identifiers when no clause is present, so JS class inheritance is captured; a dynamic base (mixin call) yields nothing and TS is not double-emitted.
…raphify-Labs#1791) Only class_declaration was treated as a class type, so PHP interfaces, enums, and traits produced no node and no heritage edges. Add them as class-like containers (and walk the enum body) so their extends/implements/use heritage is captured as inherits/implements/ mixes_in edges to the right targets.
…hify-Labs#1794) A qualified Scala base (`extends pkg.Base with other.Trait`) parses as a stable_type_identifier (or generic_type wrapping one), which the heritage handler did not match, so the edge was dropped or targeted the full qualified string. Add a helper that takes the tail type name across all three shapes, emitting inherits for the first parent and mixes_in for the rest, with no package/generic-arg false edges.
…phify-Labs#1793) A qualified Kotlin supertype (`class Foo : com.example.Base()`) resolved to the first identifier (`com`), collapsing distinct bases onto a bogus node. Take the last segment of the user type (handling generics like `Container<String>` -> `Container`), so the edge targets the real base; simple and delegated supertypes are unaffected.
Ships two batches: the robot/defang/watch/semantic-guard set — Robot Framework extractor (Graphify-Labs#3192), generalized control-token defang (Graphify-Labs#3183), watch unresolved-link preservation (Graphify-Labs#3190), unverified-semantic-loss guard (Graphify-Labs#3203), hook-guard search detection (Graphify-Labs#3121), stale-SKILL.md backup (Graphify-Labs#3144), report/wiki count fixes (Graphify-Labs#3148/Graphify-Labs#3127); and a rescued batch of @Synvoya cross-language inheritance-edge corrections (JS Graphify-Labs#1790, PHP Graphify-Labs#1791, Scala Graphify-Labs#1792/Graphify-Labs#1794, Kotlin Graphify-Labs#1793, C# Graphify-Labs#1817, Go Graphify-Labs#1818) that had been buried in the backlog for ~7 weeks. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Problem
A default install (
uv tool install graphifyy/pipx install graphifyy) ships without SQL parsing:tree-sitter-sqllives behind the[sql]extra, so every.sqlfile silently contributes nothing until the user discovers the extra or runspipx inject(Graphify-Labs#1745).Change
tree-sitter-sql>=0.3.9,<0.4into[project.dependencies]. It ships prebuilt abi3 wheels for every supported platform (win/macOS/Linux glibc+musl, x86_64+arm64) from 0.3.9, so the default install stays toolchain-free — the reasontree-sitter-dmstays optional does not apply.[sql]extra as an alias so existing install scripts keep resolving..sqlfrom_EXTRA_FOR_EXTENSION; the missing-grammar error now says the install is incomplete and names the direct repair.tests/test_sql_core_dependency.pypins the packaging invariants and the end-to-end table/view/procedure node+edge shape; tenimportorskip("tree_sitter_sql")sites converted to hard imports so absence fails the suite instead of skipping.Verification
tree-sitter-sqlarrives transitively, SQL fixture repo produces structural nodes and edges.🤖 Generated with Claude Code
Summary by CodeRabbit
New Features
Bug Fixes
Documentation