fix: support Python 3.14 optional dependencies - #3490
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# Conflicts: # pyproject.toml
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🟡 Changes recommended
The optional-backend test can fail without its dependency, and documentation updates remain pending.
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Pull request overview
Updates Python 3.13/3.14 dependency handling, native Leiden support, dependency floors, and CI coverage.
Changes:
- Adds version-specific Leiden and tokenizer dependencies.
- Preserves isolated nodes in native Leiden partitions.
- Updates dependency locks, PostgreSQL extras, tests, and CI.
File summaries
| File | Summary | Review comments |
|---|---|---|
uv.lock |
Locks updated dependency resolutions. | — |
tests/test_serve.py |
Tests strict-warning imports. | — |
tests/test_cluster.py |
Tests native Leiden completeness. | Moderate (1 vote): Skip when the optional native backend is unavailable. |
tests/test_build_merge_hyperedges_and_prune.py |
Fixes a warning-producing docstring. | — |
tests/test_backend_extras.py |
Verifies PostgreSQL in [all]. |
— |
pyproject.toml |
Updates extras and dependency floors. | Nit (3 votes): Update documentation describing the Leiden extra as Python < 3.13 only. |
graphify/serve.py |
Suppresses tokenizer syntax warnings. | — |
graphify/cluster.py |
Restores omitted isolated nodes. | — |
.github/workflows/ci.yml |
Adds Python 3.13 and 3.14 CI jobs. | Nit (1 vote): Update README CI-version documentation. |
Review details
Suppressed comments (2)
.github/workflows/ci.yml:53
- The matrix now covers Python 3.13 and 3.14, but README.md:880 and README.md:907 still instruct contributors to use only Python 3.10/3.12 and say CI runs only those versions. Please update the local CI-parity and matrix documentation so it matches this workflow.
python-version: ["3.10", "3.12", "3.13", "3.14"]
tests/test_cluster.py:146
- This test only skips on Python <3.13, but
graspologic-nativeremains optional and is installed here only through theleiden/allextras (pyproject.toml:66-69, 108). On a Python 3.13+ development environment without those extras, this import raisesModuleNotFoundErrorand makes the suite fail before testing anything. Usepytest.importorskip("graspologic_native")so the test runs when the optional backend is present and otherwise follows the neighboring optional-backend test's skip behavior.
import graspologic_native # noqa: F401
- Files reviewed: 8/9 changed files
- Comments generated: 1
- Review effort level: Lite
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| leiden = [ | ||
| "graspologic; python_version < '3.13'", | ||
| "graspologic-native>=1.3.1,<2; python_version >= '3.13'", | ||
| ] |
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Fixed in c49db38. README now documents the version-specific Leiden backends, the Hebrew translation matches, and the local CI-parity documentation lists Python 3.10, 3.12, 3.13, and 3.14.
![graphify-labs[bot]](https://avatars.githubusercontent.com/in/4356270?s=60&v=4){kind=small}
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Graphify reviewed this change.
Worth a look — the grounded gate found no coupling regressions or blocking issues, but 2 advisory finding(s) below merit a look before merge.
Formal verification. 2 change(s) tested, no difference found (not proven).
Graphify review — findings
Adds Python 3.13 and 3.14 to the CI matrix and wires up the version-gated optional dependencies to make those interpreters work: graspologic-native for Leiden clustering on 3.13+ and jieba-py for Chinese segmentation on 3.14+. Fixes _native_leiden to return a complete partition by assigning each unclustered/isolated node its own community, so the 3.13+ native-only path runs Leiden instead of silently falling through to Louvain. Suppresses SyntaxWarning while importing jieba so graphify.serve stays importable under -W error::SyntaxWarning, and adds psycopg to the all extra.
Worth a look
- Test requires optional graspologic-native dependency —
tests/test_cluster.py:143· Escalate · medium- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review
- Test requires optional jieba dependency —
tests/test_serve.py:1131· Escalate · medium- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review
Analysis details — impact, health, verification
Impact & health
Graphify review
Impact — 906 functions depend on the 427 functions this change touches.
Health — this change adds coupling hotspots:
- new:
_rebuild_code()— 115 callers, 51 callees - new:
_query_graph_text()— 25 callers, 10 callees - new:
dispatch_command()— 2 callers, 124 callees - new:
_make_graph()— 33 callers, 6 callees - new:
cluster()— 61 callers, 3 callees - new:
run_pipeline()— 8 callers, 13 callees - new:
_score_query()— 15 callers, 6 callees - new:
make_inputs()— 14 callers, 5 callees - …and 20 more — each is listed as a finding
Verification — 906 functions in the blast radius were not formally verified this run (proofs are advisory here).
Gate & verification
graphify gate
PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.
Advisory (not blocking):
- verification_scope: 725 function(s) in the blast radius were not formally verified this run
Test selection
Test selection
266 of 266 test file(s) selected (100%) via static blast radius.
Escalated to a full run for safety — the selection is not trustworthy on its own (see below). CI should run the whole suite.
tests/test_affected_cli.py— full-run-safetytests/test_affected_member_seed.py— full-run-safetytests/test_agents_platform.py— full-run-safetytests/test_analyze.py— impact, full-run-safetytests/test_anthropic_custom_endpoint.py— full-run-safetytests/test_antigravity_install.py— full-run-safetytests/test_apm_fallback_version.py— full-run-safetytests/test_architecture_doc.py— full-run-safetytests/test_astro_extraction.py— full-run-safetytests/test_astro_import_ids.py— full-run-safetytests/test_atomic_canvas_export.py— full-run-safetytests/test_atomic_version_stamp.py— full-run-safetytests/test_atomic_writes.py— full-run-safetytests/test_backend_extras.py— impact, changed-test, full-run-safetytests/test_benchmark.py— impact, full-run-safetytests/test_benchmark_raw_graph.py— impact, full-run-safetytests/test_build.py— impact, full-run-safetytests/test_build_merge_hyperedges_and_prune.py— impact, changed-test, full-run-safetytests/test_build_merge_shrink_guard.py— full-run-safetytests/test_builtin_global_type_refs.py— full-run-safetytests/test_cache.py— full-run-safetytests/test_callflow_html.py— full-run-safetytests/test_cargo_introspect.py— full-run-safetytests/test_carried_hyperedge_remap.py— full-run-safetytests/test_case_sensitive_resolution.py— full-run-safetytests/test_charmap_encoding.py— full-run-safetytests/test_chunking.py— full-run-safetytests/test_cjs_module_extension.py— full-run-safetytests/test_claude_cli_backend.py— full-run-safetytests/test_claude_md.py— full-run-safetytests/test_cli_broken_pipe.py— full-run-safetytests/test_cli_export.py— impact, full-run-safetytests/test_cli_help.py— full-run-safetytests/test_cluster.py— impact, changed-test, full-run-safetytests/test_codebuddy.py— full-run-safetytests/test_community_hub_labels.py— impact, full-run-safetytests/test_community_labels_skill.py— full-run-safetytests/test_confidence.py— impact, full-run-safetytests/test_corrupt_graph_json.py— full-run-safetytests/test_cpp_nested_and_cli.py— full-run-safetytests/test_cpp_objc_cross_file_calls.py— full-run-safetytests/test_cpp_preprocess.py— full-run-safetytests/test_cross_extension_reexport_self_cycle.py— full-run-safetytests/test_cross_language_call_resolution.py— full-run-safetytests/test_cross_repo_member_calls.py— full-run-safetytests/test_cross_repo_shared_types.py— full-run-safetytests/test_csharp_call_site_generic_args.py— full-run-safetytests/test_csharp_enum_members.py— full-run-safetytests/test_csharp_field_generic_args.py— full-run-safetytests/test_csharp_generic_callsites.py— full-run-safety- … and 216 more
non-code file(s) changed (
.github/workflows/ci.yml,pyproject.toml,uv.lock) → running the full suite for safety (a code graph can't see config/fixture/data deps)
changed code file(s) with no mapped test (
.github/workflows/ci.yml,pyproject.toml) — a coverage gap or a missing link — running the full suite rather than only the selected tests
Selection is safe under the controlled-regression assumption; always-run tests + a periodic full run are the backstops. Advisory — it never changes the check verdict.
Formal verification
Could not verify: Could not verify build.
The verifier did not have enough to check build, so it is saying so rather than guessing. No false assurance is the whole point.
Guarantee: No guarantee either way, this is an honest abstention, not a pass.
Note: Reason: not verifiable: all 9 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly AttributeError — names the real obstacle, not a sampling gap)
Could not verify: Could not verify build\_merge.
The verifier did not have enough to check build\_merge, so it is saying so rather than guessing. No false assurance is the whole point.
Guarantee: No guarantee either way, this is an honest abstention, not a pass.
Note: Reason: parameter `graph_path` is annotated `str | Path | None` — outside the synthesizable primitive/collection set
No difference found (not proven): No behavior difference found in \_native\_leiden (not a proof).
The verifier ran both versions of \_native\_leiden on many inputs and saw identical behavior every time. Strong evidence the change is safe, but evidence, not a proof.
Guarantee: Empirical: differential testing (both versions run on many generated inputs). A divergence on an untested input remains possible, so this is 'no counterexample found', not 'proven equivalent'.
Note: An input the sampler did not try could still differ.
Could not verify: Could not verify extract\_rust.
The verifier did not have enough to check extract\_rust, so it is saying so rather than guessing. No false assurance is the whole point.
Guarantee: No guarantee either way, this is an honest abstention, not a pass.
Note: Reason: parameter `path` is annotated `Path` — outside the synthesizable primitive/collection set
No difference found (not proven): No behavior difference found in \_pinned\_python (not a proof).
The verifier ran both versions of \_pinned\_python on many inputs and saw identical behavior every time. Strong evidence the change is safe, but evidence, not a proof.
Guarantee: Empirical: differential testing (both versions run on many generated inputs). A divergence on an untested input remains possible, so this is 'no counterexample found', not 'proven equivalent'.
Note: An input the sampler did not try could still differ.
Could not verify: Could not verify install.
The verifier did not have enough to check install, so it is saying so rather than guessing. No false assurance is the whole point.
Guarantee: No guarantee either way, this is an honest abstention, not a pass.
Note: Reason: not verifiable: all 23 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly SystemExit — names the real obstacle, not a sampling gap)
Could not verify: Could not verify generate\_community\_labels.
The verifier did not have enough to check generate\_community\_labels, so it is saying so rather than guessing. No false assurance is the whole point.
Guarantee: No guarantee either way, this is an honest abstention, not a pass.
Note: Reason: non-vacuity: domain too small (only 1 distinct inputs exercised, need 3) — 'no divergence' would be near-vacuous
· 1 grounded finding(s) anchored inline below; 27 more finding(s) on lines outside this diff (see the check run).
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| def _partition(G: nx.Graph, resolution: float = 1.0) -> dict[str, int]: |
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_partition()
high coupling complexity (Ca·Ce = 12).
Grounded coupling-delta finding (deterministic), not an LLM guess.
There was a problem hiding this comment.
Graphify reviewed this change.
Worth a look — the grounded gate found no coupling regressions or blocking issues, but 1 advisory finding(s) below merit a look before merge.
Formal verification. 1 change(s) tested, no difference found (not proven).
Graphify review — findings
Adds Python 3.13 and 3.14 to the CI test matrix and provisions the corresponding native dependencies: graspologic-native for Leiden clustering on 3.13+ and jieba-py for Chinese segmentation on 3.14+. Fixes _native_leiden to return a complete partition by assigning each node the native binding omitted (e.g. isolated nodes) its own community, so the 3.13+ native-only path no longer silently falls through to Louvain. Suppresses SyntaxWarning while importing jieba in serve so the module stays importable under -W error::SyntaxWarning.
Worth a look
- Import-time warning suppression leaks across threads —
graphify/serve.py:21· Escalate · medium- agreed by 2 of 2 members but NOT verified (no proof, no reproducing execution) — consensus is not a verdict; needs human review
Analysis details — impact, health, verification
Impact & health
Graphify review
Impact — 908 functions depend on the 429 functions this change touches.
Health — this change adds coupling hotspots:
- new:
_rebuild_code()— 115 callers, 51 callees - new:
_query_graph_text()— 25 callers, 10 callees - new:
dispatch_command()— 2 callers, 124 callees - new:
_make_graph()— 33 callers, 6 callees - new:
cluster()— 61 callers, 3 callees - new:
run_pipeline()— 8 callers, 13 callees - new:
_score_query()— 15 callers, 6 callees - new:
make_inputs()— 14 callers, 5 callees - …and 20 more — each is listed as a finding
Verification — 908 functions in the blast radius were not formally verified this run (proofs are advisory here).
Gate & verification
graphify gate
PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.
Advisory (not blocking):
- verification_scope: 727 function(s) in the blast radius were not formally verified this run
Test selection
Test selection
268 of 268 test file(s) selected (100%) via static blast radius.
Escalated to a full run for safety — the selection is not trustworthy on its own (see below). CI should run the whole suite.
tests/test_affected_cli.py— full-run-safetytests/test_affected_member_seed.py— full-run-safetytests/test_agents_platform.py— full-run-safetytests/test_analyze.py— impact, full-run-safetytests/test_anthropic_custom_endpoint.py— full-run-safetytests/test_antigravity_install.py— full-run-safetytests/test_apm_fallback_version.py— full-run-safetytests/test_architecture_doc.py— full-run-safetytests/test_astro_extraction.py— full-run-safetytests/test_astro_import_ids.py— full-run-safetytests/test_atomic_canvas_export.py— full-run-safetytests/test_atomic_version_stamp.py— full-run-safetytests/test_atomic_writes.py— full-run-safetytests/test_backend_env_isolation.py— full-run-safetytests/test_backend_extras.py— impact, changed-test, full-run-safetytests/test_benchmark.py— impact, full-run-safetytests/test_benchmark_raw_graph.py— impact, full-run-safetytests/test_build.py— impact, full-run-safetytests/test_build_merge_hyperedges_and_prune.py— impact, changed-test, full-run-safetytests/test_build_merge_shrink_guard.py— full-run-safetytests/test_builtin_global_type_refs.py— full-run-safetytests/test_cache.py— full-run-safetytests/test_callflow_html.py— full-run-safetytests/test_cargo_introspect.py— full-run-safetytests/test_carried_hyperedge_remap.py— full-run-safetytests/test_case_sensitive_resolution.py— full-run-safetytests/test_charmap_encoding.py— full-run-safetytests/test_chunking.py— full-run-safetytests/test_cjs_module_extension.py— full-run-safetytests/test_claude_cli_backend.py— full-run-safetytests/test_claude_md.py— full-run-safetytests/test_cli_broken_pipe.py— full-run-safetytests/test_cli_export.py— impact, full-run-safetytests/test_cli_help.py— full-run-safetytests/test_cluster.py— impact, changed-test, full-run-safetytests/test_codebuddy.py— full-run-safetytests/test_community_hub_labels.py— impact, full-run-safetytests/test_community_labels_skill.py— full-run-safetytests/test_confidence.py— impact, full-run-safetytests/test_corrupt_graph_json.py— full-run-safetytests/test_cpp_nested_and_cli.py— full-run-safetytests/test_cpp_objc_cross_file_calls.py— full-run-safetytests/test_cpp_preprocess.py— full-run-safetytests/test_cross_extension_reexport_self_cycle.py— full-run-safetytests/test_cross_language_call_resolution.py— full-run-safetytests/test_cross_repo_member_calls.py— full-run-safetytests/test_cross_repo_shared_types.py— full-run-safetytests/test_csharp_call_site_generic_args.py— full-run-safetytests/test_csharp_enum_members.py— full-run-safetytests/test_csharp_field_generic_args.py— full-run-safety- … and 218 more
non-code file(s) changed (
.github/workflows/ci.yml,pyproject.toml,uv.lock) → running the full suite for safety (a code graph can't see config/fixture/data deps)
changed code file(s) with no mapped test (
.github/workflows/ci.yml,pyproject.toml) — a coverage gap or a missing link — running the full suite rather than only the selected tests
Selection is safe under the controlled-regression assumption; always-run tests + a periodic full run are the backstops. Advisory — it never changes the check verdict.
Formal verification
No difference found (not proven): No behavior difference found in \_native\_leiden (not a proof).
The verifier ran both versions of \_native\_leiden on many inputs and saw identical behavior every time. Strong evidence the change is safe, but evidence, not a proof.
Guarantee: Empirical: differential testing (both versions run on many generated inputs). A divergence on an untested input remains possible, so this is 'no counterexample found', not 'proven equivalent'.
Note: An input the sampler did not try could still differ.
· 1 grounded finding(s) anchored inline below; 27 more finding(s) on lines outside this diff (see the check run).
| return partition | ||
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| def _partition(G: nx.Graph, resolution: float = 1.0) -> dict[str, int]: |
There was a problem hiding this comment.
_partition()
high coupling complexity (Ca·Ce = 12).
Grounded coupling-delta finding (deterministic), not an LLM guess.
|
Addressed the review findings in
Verification: @copilot review |
There was a problem hiding this comment.
Graphify reviewed this change.
Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).
Formal verification. 1 change(s) tested, no difference found (not proven).
Graphify review — findings
Adds Python 3.13 and 3.14 to the CI matrix and packages version-gated backends so those interpreters get working native code: leiden now pulls graspologic-native on 3.13+ and chinese pulls jieba-py on 3.14+, with docs and the Windows skill updated to match. Fixes _native_leiden so nodes absent from the native partition (isolated nodes) are each assigned their own community, yielding a complete partition instead of dropping members and falling through to Louvain. Silences the SyntaxWarning from importing jieba in serve and bumps the pinned floors for setuptools, pypdf, and yt-dlp.
No blocking issues surfaced. 2 lower-confidence candidates did not survive cross-model review.
Analysis details — impact, health, verification
Impact & health
Graphify review
Impact — 1016 functions depend on the 537 functions this change touches.
Health — this change adds coupling hotspots:
- new:
_rebuild_code()— 115 callers, 51 callees - new:
_query_graph_text()— 25 callers, 10 callees - new:
dispatch_command()— 2 callers, 124 callees - new:
_make_graph()— 33 callers, 6 callees - new:
cluster()— 61 callers, 3 callees - new:
run_pipeline()— 8 callers, 13 callees - new:
_score_query()— 15 callers, 6 callees - new:
make_inputs()— 14 callers, 5 callees - …and 20 more — each is listed as a finding
Verification — 1016 functions in the blast radius were not formally verified this run (proofs are advisory here).
Gate & verification
graphify gate
PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.
Advisory (not blocking):
- verification_scope: 835 function(s) in the blast radius were not formally verified this run
Test selection
Test selection
268 of 268 test file(s) selected (100%) via static blast radius.
Escalated to a full run for safety — the selection is not trustworthy on its own (see below). CI should run the whole suite.
tests/test_affected_cli.py— full-run-safetytests/test_affected_member_seed.py— full-run-safetytests/test_agents_platform.py— full-run-safetytests/test_analyze.py— impact, full-run-safetytests/test_anthropic_custom_endpoint.py— full-run-safetytests/test_antigravity_install.py— full-run-safetytests/test_apm_fallback_version.py— full-run-safetytests/test_architecture_doc.py— full-run-safetytests/test_astro_extraction.py— full-run-safetytests/test_astro_import_ids.py— full-run-safetytests/test_atomic_canvas_export.py— full-run-safetytests/test_atomic_version_stamp.py— full-run-safetytests/test_atomic_writes.py— full-run-safetytests/test_backend_env_isolation.py— full-run-safetytests/test_backend_extras.py— impact, changed-test, full-run-safetytests/test_benchmark.py— impact, full-run-safetytests/test_benchmark_raw_graph.py— impact, full-run-safetytests/test_build.py— impact, full-run-safetytests/test_build_merge_hyperedges_and_prune.py— impact, changed-test, full-run-safetytests/test_build_merge_shrink_guard.py— full-run-safetytests/test_builtin_global_type_refs.py— full-run-safetytests/test_cache.py— full-run-safetytests/test_callflow_html.py— full-run-safetytests/test_cargo_introspect.py— full-run-safetytests/test_carried_hyperedge_remap.py— full-run-safetytests/test_case_sensitive_resolution.py— full-run-safetytests/test_charmap_encoding.py— full-run-safetytests/test_chunking.py— full-run-safetytests/test_cjs_module_extension.py— full-run-safetytests/test_claude_cli_backend.py— full-run-safetytests/test_claude_md.py— full-run-safetytests/test_cli_broken_pipe.py— full-run-safetytests/test_cli_export.py— impact, full-run-safetytests/test_cli_help.py— full-run-safetytests/test_cluster.py— impact, changed-test, full-run-safetytests/test_codebuddy.py— full-run-safetytests/test_community_hub_labels.py— impact, full-run-safetytests/test_community_labels_skill.py— full-run-safetytests/test_confidence.py— impact, full-run-safetytests/test_corrupt_graph_json.py— full-run-safetytests/test_cpp_nested_and_cli.py— full-run-safetytests/test_cpp_objc_cross_file_calls.py— full-run-safetytests/test_cpp_preprocess.py— full-run-safetytests/test_cross_extension_reexport_self_cycle.py— full-run-safetytests/test_cross_language_call_resolution.py— full-run-safetytests/test_cross_repo_member_calls.py— full-run-safetytests/test_cross_repo_shared_types.py— full-run-safetytests/test_csharp_call_site_generic_args.py— full-run-safetytests/test_csharp_enum_members.py— full-run-safetytests/test_csharp_field_generic_args.py— full-run-safety- … and 218 more
non-code file(s) changed (
.github/workflows/ci.yml,README.md,docs/translations/README.he-IL.md,graphify/skill-windows.md,pyproject.toml…) → running the full suite for safety (a code graph can't see config/fixture/data deps)
changed code file(s) with no mapped test (
.github/workflows/ci.yml,README.md,docs/translations/README.he-IL.md,graphify/skill-windows.md,pyproject.toml…) — a coverage gap or a missing link — running the full suite rather than only the selected tests
Selection is safe under the controlled-regression assumption; always-run tests + a periodic full run are the backstops. Advisory — it never changes the check verdict.
Formal verification
No difference found (not proven): No behavior difference found in \_native\_leiden (not a proof).
The verifier ran both versions of \_native\_leiden on many inputs and saw identical behavior every time. Strong evidence the change is safe, but evidence, not a proof.
Guarantee: Empirical: differential testing (both versions run on many generated inputs). A divergence on an untested input remains possible, so this is 'no counterexample found', not 'proven equivalent'.
Note: An input the sampler did not try could still differ.
· 1 grounded finding(s) anchored inline below; 27 more finding(s) on lines outside this diff (see the check run).
| return partition | ||
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| def _partition(G: nx.Graph, resolution: float = 1.0) -> dict[str, int]: |
There was a problem hiding this comment.
_partition()
high coupling complexity (Ca·Ce = 12).
Grounded coupling-delta finding (deterministic), not an LLM guess.
…tale skillgen windows test The #3490 lock predated its own setuptools>=83 / pypdf / yt-dlp floor bumps, so a frozen sync resolved setuptools 82.0.1 and the no-isolation wheel-build test failed. Regenerate the lock so it honors the floors. Also update the windows skill test: the troubleshooting item is now 'Skip Leiden' (graspologic -> graspologic-native gating), which #3490 changed in the fragment but not the test.
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Shipped in v0.9.60 — landed on |
Summary
graspologic-nativedirectly on Python 3.13+ while retaining the establishedgraspologicpath on older Pythonjieba-pydistribution on Python 3.14 and keep strict-warning imports clean[all]support and raise audited dependency floorsVerification
5562 passed, 14 skippedon CPython 3.14.7 against upstream 0.9.58ruff check graphify testsuv pip checkpip-audit: no known vulnerabilitiesSyntaxWarningimport checkPython itself was not downgraded or replaced.