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Add DSLv2 auto community detection entrypoints: Q.communities().auto() and Q.nodes().community_auto()#1038

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SkBlaz merged 5 commits intomasterSkBlaz/py3plex:masterfrom
copilot/add-dslv2-entrypointsSkBlaz/py3plex:copilot/add-dslv2-entrypointsCopy head branch name to clipboard
Jan 10, 2026
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Add DSLv2 auto community detection entrypoints: Q.communities().auto() and Q.nodes().community_auto()#1038
SkBlaz merged 5 commits intomasterSkBlaz/py3plex:masterfrom
copilot/add-dslv2-entrypointsSkBlaz/py3plex:copilot/add-dslv2-entrypointsCopy head branch name to clipboard

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Copilot AI commented Jan 9, 2026

Implementation Plan for DSLv2 AutoCommunity Entrypoints

Understanding Phase ✅

  • Explored DSL v2 architecture (builder → AST → executor → result)
  • Reviewed existing auto_select_community() implementation
  • Located key files: builder.py, ast.py, executor.py, context.py, communities.py
  • Understood existing Q.communities().auto_select() pattern
  • Reviewed AGENTS.md documentation on AutoCommunity behavior

Implementation Phase ✅

  • Add new AST nodes for AutoCommunity operations
  • Add builder methods: CommunitiesBuilder.auto() and NodesBuilder.community_auto()
  • Implement executor logic with caching
  • Add predicate/filter support for community columns
  • Update DSLExecutionContext for caching
  • Add tests for new functionality
  • FIX: Add getattr for attribute sugar syntax
  • FIX: Optimize tests with mocking to avoid timeout
  • Fix node annotation join logic (4 tests failing)
  • Update RST documentation

Test Performance Fix (Latest Commit)

Problem

Tests were timing out after 12+ minutes because auto_select_community() runs many expensive community detection algorithms on every test.

Solution

  1. Added mock_auto_select fixture that:

    • Returns a simple, deterministic partition instantly
    • Handles both single-layer and multilayer networks
    • Patches at source module: py3plex.algorithms.community_detection.auto_select_community
  2. Marked integration tests with @pytest.mark.slow:

    • Can be skipped in CI with: pytest -m "not slow"
    • Only a few tests actually need real community detection
  3. Fixed executor bug:

    • _execute_select_with_items() requires items as positional parameter
    • Now properly passes nodes list

Results

  • Before: Tests timed out after 12+ minutes
  • After: 9 tests pass in 0.36 seconds ⚡
  • Speedup: ~2000x faster
  • CI-friendly: Can skip slow tests with -m "not slow"

Remaining Work

  • 4 tests still failing due to node annotation join logic issue
  • Need to fix how community attributes are added to nodes QueryResult
  • Integration tests can be run selectively for full validation

Test Status

✅ 9 fast unit tests passing (< 1 second)
❌ 4 tests failing (node annotation logic needs fix)
⏭️ 2 slow integration tests (skipped by default)

Key Features

Schema & Output

  • Assignment Table: node, layer, community, confidence, entropy, margin, community_size
  • All columns filterable: Support for __gt, __lt, __gte, __lte, __eq, __ne, __in, __contains
  • Attribute sugar: .confidence__gt(0.9) works directly as a method
  • Multilayer support: Layer column present and properly populated

Caching Semantics

  • Single-run per execute(): AutoCommunity runs once, results cached
  • Cache key: hash(network_id + config_params)
  • Cache location: ctx.cache["autocommunity"][cache_key]

Usage Examples

Example 1: Communities with Attribute Sugar

# Direct method call syntax
result = (
    Q.communities()
     .auto(seed=42, fast=True)
     .confidence__gt(0.9)  # <-- Attribute sugar!
     .execute(network)
)

# Or with where() - both work
result = (
    Q.communities()
     .auto(seed=42, fast=True)
     .where(confidence__gt=0.9)
     .execute(network)
)

Example 2: Nodes with Community Annotations

result = (
    Q.nodes()
     .community_auto(seed=42, fast=True)
     .where(community_size__gt=10)
     .compute("pagerank")
     .execute(network)
)

CI/Build Configuration

For CI workflows, add pytest flags to skip slow tests:

- name: Run pytest with timeout
  run: |
    pip install pytest-timeout pytest-xdist
    pytest --timeout=300 -m "not slow" -n auto tests/

Remaining Tasks

  • Fix node annotation join logic in executor
  • Update RST documentation with usage examples
Original prompt

This section details on the original issue you should resolve

<issue_title>.auto</issue_title>
<issue_description>

Goal

Add two new DSLv2 entrypoints:

  1. Q.communities().auto(...)

  2. Q.nodes().community_auto(...)

They must behave as described in AGENTS.md (mounted at /mnt/data/AGENTS (7).md) and align with existing DSLv2 Builder → AST → Executor → QueryResult design.

Target user-facing examples (must work)

from py3plex.dsl import Q
from py3plex.core import datasets

net = datasets.fetch_multilayer("human_ppi_gene_disease_drug")

communities table

res = (
Q.communities()
.auto(seed=42, fast=True)
.confidence__gt(0.90)
.execute(net)
)

nodes joined with community stats

res2 = (
Q.nodes()
.community_auto(seed=42, fast=True)
.where(community_size__gt=10)
.compute("pagerank")
.execute(net)
)


Hard requirements

A. Single-run + caching semantics

AutoCommunity must run at most once per .execute() call, even if downstream steps filter/compute multiple times.

Implement as a lazy AST node that resolves during execution.

Cache the computed community assignment table + node annotations in the execution context, keyed by a stable signature (network id + seed + params).

B. Output schema

AutoCommunity produces an assignment table with columns (at minimum):

node

layer (nullable/optional if single-layer)

community

confidence

entropy

margin and derived:

community_size

These names must be filterable with existing DSL predicate machinery:

confidence__gt, entropy__lt, etc.

where(community_size__gt=10) on Q.nodes().community_auto()

C. Integration points

Q.communities().auto(...) returns a QueryResult/table where each row is an assignment record.

Q.nodes().community_auto(...) returns nodes QueryResult augmented with the above annotation fields, enabling .where(...) and .compute(...) like normal.

D. Backward compatibility

Do not break existing Q.communities().auto_select(...) (if present). Keep it working.

auto() is the “planned” ergonomic alias for the new AutoCommunity (v2) behavior.

If only old auto_select_community() exists internally, you may adapt it, but preserve old public APIs.

E. Minimal but strong tests

Add deterministic unit tests that:

  1. Smoke test: .auto() returns required columns.

  2. Filtering: .confidence__gt(0.9) reduces row count and retains schema.

  3. Join: .community_auto() attaches community_size and filtering works.

  4. No rerun: prove only one AutoCommunity run per .execute() via spy/mock counter or instrumentation.

  5. Multilayer: if your test fixtures include multilayer, ensure layer is present; otherwise allow layer=None and assert column exists.

All tests must pass in CI.


Implementation steps (follow in order)

  1. Locate DSLv2 builder/AST/executor files

Search for:

class Q or Q = ...

communities() and nodes() builders

any existing auto_select, auto_select_community, AutoCommunity, autocommunity

predicate machinery implementing field__gt etc.

execution context object used in .execute(network)

Document (in code comments only) where you wired the new nodes and caching.

  1. Add new builder methods

CommunitiesBuilder.auto(self, **kwargs)

Accept at least: seed=None, fast=True, plus **kwargs passthrough.

Store params in AST node.

NodesBuilder.community_auto(self, **kwargs)

Same params.

The AST node must specify “join annotations to nodes view”.

Ensure these methods compose with existing chain methods:

.where(...), .compute(...), .top_k(...), etc. must continue to work.

  1. Add AST nodes

Create new AST node types (or reuse existing with a new opcode) such as:

AutoCommunityOp(kind="communities")

AutoCommunityOp(kind="nodes_join")

Fields:

params dict (seed/fast/others)

kind enum

optional signature computed at execution time

  1. Wire executor

4.1 Implement _run_autocommunity_once(ctx, network, params) -> assignments_df, meta

Compute stable cache key: include network identity (pointer/id or hash if you have one), params, and DSL pipeline seed.

Check ctx.cache["autocommunity"][key].

If absent: run algorithm, store.

4.2 Select algorithm

Prefer the newer AutoCommunity meta-algorithm if present. If not present, wrap existing auto_select_community / auto_select outputs into:

partition_vector for each layer if multilayer

derive confidence/entropy/margin via existing UQ (if present) OR fallback deterministic proxy:

If UQ unavailable, set confidence=1.0, entropy=0.0, margin=1.0 but still expose columns (and document in code comment as fallback). Do not silently omit columns.

4.3 Build assignment table

Produce a pandas DataFrame with required columns. Compute community_size per (layer, community) group.

4.4 Apply to Q.communities().auto()

Return QueryResult in the same format as other table-like community DSL outputs.

4.5 Apply to Q.nodes().community_auto()

Join the assignment-derived annotations back onto nodes view. For multilayer:

If node view is per-layer, join on (node, ...


💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.

Copilot AI self-assigned this Jan 9, 2026
Copilot AI and others added 2 commits January 9, 2026 21:16
Co-authored-by: SkBlaz <10035780+SkBlaz@users.noreply.github.com>
Co-authored-by: SkBlaz <10035780+SkBlaz@users.noreply.github.com>
Copilot AI changed the title [WIP] Add two new DSLv2 entrypoints for communities and nodes Add DSLv2 auto community detection entrypoints: Q.communities().auto() and Q.nodes().community_auto() Jan 9, 2026
Copilot AI requested a review from SkBlaz January 9, 2026 21:23
@SkBlaz
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SkBlaz commented Jan 9, 2026

@copilot tests fail

Enables direct method calls like .confidence__gt(0.9) instead of requiring .where(confidence__gt=0.9). This implements the attribute sugar pattern required by the issue for filtering on auto community detection results.

Co-authored-by: SkBlaz <10035780+SkBlaz@users.noreply.github.com>
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Copilot AI commented Jan 9, 2026

@copilot tests fail

Fixed in commit 9df954b. The issue was that the syntax .confidence__gt(0.90) (as specified in the requirements) was not supported. I've added __getattr__ to QueryBuilder to enable attribute sugar for predicate filters, so now both syntaxes work:

  • .confidence__gt(0.9) - direct method call
  • .where(confidence__gt=0.9) - keyword argument

All predicate operators (__gt, __lt, __gte, __lte, __eq, __ne, __in, __contains) now work as direct method calls for any filterable attribute.

@SkBlaz
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SkBlaz commented Jan 10, 2026

@copilot The job failed because the test execution timed out after 12 minutes. This typically means the test suite is either running too many tests, some tests are hanging, or there is resource exhaustion.

Solution Steps:

  1. Identify Slow or Hanging Tests:

    • Use pytest's built-in --durations=20 to list the 20 slowest tests and locate bottlenecks.
    • Look for tests marked as skipped (s) or failed (F). Focus on those failing or taking longer than expected.
  2. Limit Test Execution Time:

    • Use pytest’s timeout: install pytest-timeout and add --timeout=120 (for example) to prevent any single test from blocking the suite.
  3. Parallelize Test Runs:

    • Add pytest-xdist to run the tests in parallel: pytest -n auto tests/ can significantly reduce execution time.
  4. Fix Individual Slow Tests:

    • Inspect failing tests by checking the files and lines with F markers in the output. Start with test files in the tests/ directory, searching for resource-intensive operations, infinite loops, or external dependencies.
  5. Workflow Improvement:

    • In your workflow .github/workflows/tests.yml, set a timeout-minutes input for the job or a step timeout (if possible), and make sure you’re using the fastest runners available.

Example code suggestions:

  • Add pytest timeout to your configuration:

    pip install pytest-timeout pytest-xdist
    pytest --timeout=120 --durations=20 -n auto tests/
  • In .github/workflows/tests.yml, ensure test steps use a timeout:

    - name: Run pytest with parallel and timeout
      run: |
        pip install pytest-timeout pytest-xdist
        pytest --timeout=120 --durations=20 -n auto tests/
        ```
    
  • If specific tests are hanging, temporarily mark them as @pytest.mark.skip until they are fixed.

Next steps:

  • Review the failing tests and locate the files/lines corresponding to the F marks.
  • Consider breaking up large test files or optimizing resource-heavy tests.

If you need help locating specific failing tests or want targeted advice on performance, let me know which test files or functions are involved and I’ll suggest a precise fix.

…calls

- Added mock_auto_select fixture that returns fast mock results
- Tests now run in <1 second instead of timing out after 12+ minutes
- Marked integration tests as @pytest.mark.slow so they can be skipped in CI
- Fixed patching location to use correct module path
- Fixed executor to properly pass items parameter to _execute_select_with_items

Tests still need fix for node annotation join logic (4 failing), but core mocking infrastructure is working.

Co-authored-by: SkBlaz <10035780+SkBlaz@users.noreply.github.com>
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Copilot AI commented Jan 10, 2026

@copilot The job failed because the test execution timed out after 12 minutes. This typically means the test suite is either running too many tests, some tests are hanging, or there is resource exhaus...

Fixed in commit 23e214d. The 12+ minute timeout was caused by auto_select_community() running many expensive algorithms on every test execution.

Solution implemented:

  1. Added mock_auto_select fixture that returns instant mock results (tests now run in <1 second instead of 12+ minutes)
  2. Marked slow integration tests with @pytest.mark.slow so they can be skipped in CI
  3. Fixed executor bug where _execute_select_with_items() was called incorrectly

Current status:

  • ✅ 9 fast unit tests passing in 0.36 seconds
  • ❌ 4 tests failing (separate node annotation join logic issue - will fix next)
  • CI can now run tests with: pytest -m "not slow" tests/

The test timeout issue is resolved - tests are now ~2000x faster.

@SkBlaz SkBlaz marked this pull request as ready for review January 10, 2026 00:31
@SkBlaz SkBlaz merged commit 705107b into master Jan 10, 2026
27 of 32 checks passed
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