What's Changed

• [WIP] Fix error during CI version push to PyPI by @Copilot in #1295
• Polish manuscript structure and methodology framing across Chapters 1–18 and Appendices A–E by @Copilot in #1292
• Add encoded multiedgelist roundtrip coverage without introducing markdown files by @Copilot in #1296
• Docs quality pass: clarify core how-to flows with concrete expected outputs by @Copilot in #1298
• Add focused DSL corner-case tests for empty query pipelines and QueryResult algebra by @Copilot in #1300
• Remove redundant runtime Cython dependency from package metadata by @Copilot in #1301
• Add targeted coverage for ergonomics helpers and profiling edge cases by @Copilot in #1302
• Improve semiring Pareto coverage with focused frontier-behavior tests by @Copilot in #1303
• Speed up synthetic generator hot paths by removing avoidable quadratic and allocation-heavy work by @Copilot in #1304
• Add 10 high-value missing tests across DSL v2, temporal, uncertainty, and plugin contracts by @Copilot in #1308
• Harden AGENTS.md claims with explicit validation boundaries by @Copilot in #1316
• Improve first-time contributor onboarding in README with enforceable guidance by @Copilot in #1318
• Document highest-impact new-user documentation gaps in roadmap by @Copilot in #1310
• Audit and tighten top-level public API exports (config + IO convenience aliases) by @Copilot in #1306
• Polish CLI help consistency for commands, defaults, and stdin usage by @Copilot in #1314
• Make QueryBuilder.explain_plan() effective and one-shot at execution time by @Copilot in #1319
• Remove unreachable branches in truncated power-law PDF paths by @Copilot in #1323
• Remove duplicate/overridden tests in multilayer visualization suite by @Copilot in #1322
• Add machine-facing agent API and structured DSL ergonomics for deterministic, low-ambiguity workflows by @Copilot in #1321
• Increase DSL QueryResult verification coverage for helper/property edge cases by @Copilot in #1324
• Stabilize UQ verification test and migrate to current uncertainty config API by @Copilot in #1325
• Add DSL guardrails for post-execute() misuse and clarify grouping lifecycle errors by @Copilot in #1326
• Add missing property coverage for multilayer edge aggregation invariants by @Copilot in #1327
• devx: add optional feature meta-extra, selftest optional coverage, and CI optional smoke lane by @Copilot in #1333
• Improve graph file linting for common edgelist/multiedgelist input pitfalls by @Copilot in #1331
• Polish DSL and example regressions by @SkBlaz in #1334
• Bump release to 1.1.6 across package, docs, and book surfaces by @Copilot in #1336
• Make selftest resilient to missing optional community dependency by @Copilot in #1340
• Make interactive visualization example optional-dependency-safe for examples verification by @Copilot in #1338
• Add native multilayer node-embedding support (state + physical targets) via existing py3plex embedding seams by @Copilot in #1342
• Improve sensitivity coverage with focused executor unit tests by @Copilot in #1343
• Increase optimizer submodule test coverage by @Copilot in #1344
• Add Python 3.13 to CI matrix and retire Python 3.8 lane by @Copilot in #1346
• Bump python-multipart from 0.0.22 to 0.0.26 in /gui/api by @dependabot[bot] in #1350
• Add high-ROI coverage targets: direct embeddings/legacy DSL tests, helper-level visualization+registry tests, and CI coverage job by @Copilot in #1347
• Bump project version to 1.1.7 across canonical release surfaces by @Copilot in #1352

Full Changelog: v1.1.51...v1.1.7

What's Changed

• Bumping library version for project by @Copilot in #1293

Full Changelog: v1.1.5...v1.1.51

What's Changed

• Add first-class embedding primitives across network API, DSL, graph_ops, and pipeline by @Copilot in #1270
• Refine AGENTS.md with current repository statistics and consistency fixes by @Copilot in #1271
• Make embeddings first-class across py3plex APIs: standardized result schema, richer EmbeddingResult ops, and deterministic cache/provenance by @Copilot in #1273
• Add PyPI download stats badge to README by @Copilot in #1274
• Consolidate examples/dsl_query_zoo into examples/dsl_zoo and update all path references by @Copilot in #1275
• Align AGENTS docs with current DSL API and repository state by @Copilot in #1276
• Align book version references with current source release (1.1.4) by @Copilot in #1277
• Repair book manuscript coherence: canonical metadata, honest claims, template case studies, and reference/path cleanup by @Copilot in #1279
• Add missing embeddings docs section to navigation and API reference by @Copilot in #1280
• Increase DSL embedding test coverage for builder/result edge paths by @Copilot in #1281
• Make version bump workflow canonical across library, docs, book, MCP, and citation by @Copilot in #1282
• Add first-class DSL workflows for link prediction and multilayer layer reduction by @Copilot in #1284
• Improve book onboarding ergonomics for DSL and visualization examples by @Copilot in #1285
• Improve ML embedding test coverage for result utilities and backend variants by @Copilot in #1287
• Stabilize book example execution in docs harness and fix dataset example layer introspection by @Copilot in #1286
• Rewrite book manuscript into a tighter technical handbook with reduced doc bloat and stronger analytical framing by @Copilot in #1289
• Enforce repository no-emoji policy and strengthen markdown guardrails by @Copilot in #1290

Full Changelog: v1.1.41...v1.1.5

What's Changed

• Switch PyPI publishing to OIDC trusted publishing (remove API token) by @Copilot in #1268

Full Changelog: v1.1.4...v1.1.41

What's Changed

• Identify and mitigate flaky tests with pytest-rerunfailures by @Copilot in #1196
• Align RST docs with source: Promote DSL v2.1 Builder API over legacy string DSL by @Copilot in #1197
• Add property tests for claims and counterfactual modules by @Copilot in #1198
• Remove duplicate flaky test documentation files by @Copilot in #1200
• Align examples with DSL v2 patterns from AGENTS.md by @Copilot in #1201
• Fix broken docs and enhance stub component documentation by @Copilot in #1203
• Add property-based tests for Leiden and Label Propagation community detection by @Copilot in #1202
• Remove redundant root-level markdown files by @Copilot in #1204
• Fix CI: Add --clear flag to cached uv venv commands by @Copilot in #1205
• Add runnable ergonomics demo script by @Copilot in #1208
• Fix broken PLUGIN_GUIDE.md references in documentation by @Copilot in #1207
• Add property tests for 9 critical modules (81+ tests) by @Copilot in #1206
• Fix 23 broken internal references in RST documentation by @Copilot in #1209
• Align book version references to 1.1.3 by @Copilot in #1210
• Add 56 tests for AutoCommunity subsystem coverage by @Copilot in #1211
• Update AGENTS.md with current repository state (v1.1.3) by @Copilot in #1212
• Verify documentation links and enforce markdown file count by @Copilot in #1213
• Improve test coverage: fix temporal_utils_extended tests, add utils.py deprecation tests by @Copilot in #1214
• Add ergonomic helpers to reduce boilerplate by 50-70% by @Copilot in #1216
• Fix inconsistencies in recently added algorithm implementations by @Copilot in #1215
• Fix type hints and exception handling consistency by @Copilot in #1217
• Consolidate DSL pattern documentation for faster onboarding by @Copilot in #1218
• Add docstrings to 10 advanced examples and fix error handling by @Copilot in #1219
• Update AGENTS.md to reflect v1.1.3 repository state by @Copilot in #1220
• [WIP] Improve test coverage for existing codebase by @Copilot in #1221
• Extend dsl_zoo with 19 missing DSL feature examples by @Copilot in #1223
• Refactor: Eliminate code duplication in layer name extraction by @Copilot in #1224
• Property test coverage: measure, fix, improve (9.65% → 15.20%) by @Copilot in #1226
• Update AGENTS.md repository statistics to current counts by @Copilot in #1227
• Fix outdated QueryResult API usage in book chapters by @Copilot in #1225
• feat: Query Algebra, Canonicalization & Equivalence Engine for the DSL by @Copilot in #1229
• Remove emojis from README by @Copilot in #1235
• Remove common DSL patterns section by @SkBlaz in #1236
• Add monotonic network_version mutation counter to multi_layer_network by @Copilot in #1233
• Book alignment: fix stale API names and capability claims in DSL chapters by @Copilot in #1238
• Add selection fast path for WHERE-only DSL queries by @Copilot in #1231
• Add first-class runtime capability discovery API (Python, CLI, MCP) by @Copilot in #1240
• Remove redundant AI-generated report txt files and tighten .gitignore by @Copilot in #1243
• feat: cost-based query optimizer layer between AST compilation and execution by @Copilot in #1242
• examples: consolidate folders, remove redundant dirs, strip emojis by @Copilot in #1244
• Add Network Experiment Registry with DSL v2 integration and CLI by @Copilot in #1246
• Update AGENTS.md with current repository statistics by @Copilot in #1247
• Add streaming / out-of-core query execution for multilayer networks by @Copilot in #1249
• Add first-class embeddings (NetMF) to DSL v2 with caching and provenance by @Copilot in #1251
• Update AGENTS.md repository statistics by @Copilot in #1252
• docs(AGENTS.md): sync with current repo state — new v1.2 modules and updated statistics by @Copilot in #1253
• Update AGENTS.md statistics for March 2026 by @Copilot in #1255
• perf: eliminate per-item getattr and redundant .keys() views in hot-path manipulators by @Copilot in #1254
• Add MetaPath2Vec embedding for heterogeneous/multilayer networks by @Copilot in #1257
• Refresh AGENTS.md with latest repo additions and March 2026 stats by @Copilot in #1258
• Polish rough source wording by fixing targeted typos in core comments/docstrings by @Copilot in #1259
• Bump library version metadata to 1.1.4 across package, docs, and citation surfaces by @Copilot in #1260
• docs: fix unexpected keyword arguments in random_multilayer_ER by @Daniel-A-GS in #1263
• some polishing by @SkBlaz in #1264
• Fix multiplex example by @SkBlaz in #1265
• Refresh AGENTS.md with current repo state and align repeated metadata by @Copilot in #1266

New Contributors

• @Daniel-A-GS made their first contribution in #1263

Full Changelog: v1.1.3...v1.1.4

What's Changed

• Add Successive Halving strategy for efficient AutoCommunity algorithm selection by @Copilot in #1079
• Add replica consistency and layer entropy metrics for multilayer community detection by @Copilot in #1081
• Add infomap as candidate algorithm to AutoCommunity by @Copilot in #1083
• Add property tests for 8 modules missing coverage by @Copilot in #1087
• Add SBM family as first-class algorithms with AutoCommunity, UQ, and Successive Halving integration by @Copilot in #1085
• Fix test failures and add coverage for counterfactual, claims, and paths modules by @Copilot in #1089
• Add DSL v2 support to py3plex-mcp server by @Copilot in #1091
• Add stratified perturbation for variance-reduced uncertainty quantification by @Copilot in #1093
• Implement compositional uncertainty quantification for DSL aggregate/summarize/ranking operations by @Copilot in #1095
• Add flagship example with AutoCommunity and multi-objective selection to README by @Copilot in #1097
• [WIP] Update AGENTS.md with DSL v2 specification by @Copilot in #1099
• Add Q.communities() DSL stage with integrated auto-detection and .nodes() chaining by @Copilot in #1101
• Add 35 DSL zoo examples with interlayer=True and summarise() support by @Copilot in #1103
• Remove redundant COMPOSITIONAL_UQ_SUMMARY.md and bump version to 1.1.2 by @Copilot in #1105
• Add comprehensive progress logging to DSL query execution pipeline by @Copilot in #1107
• Update flagship example to use Q.communities() DSL pattern with auto-included community info by @Copilot in #1109
• Add first-class joins and compiler-quality error diagnostics to DSL v2 by @Copilot in #1113
• Implement DSL v2 query planner with stage reordering, compute pushdown, and caching by @Copilot in #1111
• Implement native SBM family with UQ and AutoCommunity integration by @Copilot in #1115
• Add DSL-first benchmarking layer (B builder) for fair algorithm comparison by @Copilot in #1117
• Document recent DSL additions: field expressions, semiring algebra, compositional UQ by @Copilot in #1119
• Implement hierarchical flow-based community detection for multilayer networks by @Copilot in #1123
• Remove redundant implementation docs and backup files by @Copilot in #1125
• Fix KeyError in example_auto_select_uq.py for Pareto mode compatibility by @Copilot in #1131
• Handle SBM and UQ result types in AutoCommunity evaluation by @Copilot in #1129
• Replace deprecated np.matrix and DataFrame.append with modern APIs by @Copilot in #1127
• Implement Graph Programs as first-class compositional objects by @Copilot in #1121
• [WIP] Move contents from 'dsl' folder to 'dsl_zoo' by @Copilot in #1133
• DSL improvements - examples by @SkBlaz in #1135
• A few polishing fixes - community examples by @SkBlaz in #1134
• Add verification test suite for correctness, determinism, and regression prevention by @Copilot in #1137
• Add metamorphic and certificate-based verification infrastructure by @Copilot in #1139
• Implement deterministic UQ resolution with canonical schema and fail-fast validation by @Copilot in #1141
• Implement formal algebraic laws for UQ operations with fail-fast enforcement by @Copilot in #1143
• Implement unified diagnostic system with structured error reporting and query inspection by @Copilot in #1145
• RST documentation quality pass: clarity, consistency, and standards compliance by @Copilot in #1147
• Systematic ergonomics improvements: discoverability, pedagogical errors, multilayer semantics by @Copilot in #1151
• Add first-class algorithm requirements and compatibility diagnostics system with universal coverage, enforcement, and actionable conversion guidance by @Copilot in #1149
• Expand test coverage for DSL, UQ, null models, and I/O with 203 new tests enforcing documented guarantees by @Copilot in #1153
• Skip unnecessary layout computation in SBM workflows by @Copilot in #1155
• Add network type conversion methods with comprehensive test coverage by @Copilot in #1157
• Add comprehensive verification test framework with provenance-as-oracle, differential testing, and metamorphic transformations by @Copilot in #1159
• Update AGENTS.md with test coverage state and add 203 new tests for core, algorithms, and visualization modules by @Copilot in #1163
• Enforce round-trip guarantees in DSL v2 Builder API by @Copilot in #1165
• Cleanup: Remove redundant markdown and organize examples folder by @Copilot in #1169
• Implement Query Algebra: Compositional reasoning for DSL queries and results by @Copilot in #1167
• [WIP] Implement faster execution path for DSL v2 grouping by @Copilot in #1173
• Add approximate centrality algorithms to py3plex by @Copilot in #1171
• Expand AGENTS.md with comprehensive repository state and algorithm inventory by @Copilot in #1175
• Add Shapley-based attribution explanations to DSL v2 by @Copilot in #1177
• Add M builder for cross-network meta-analysis with fixed/random-effects models by @Copilot in #1179
• Align documentation between RST, AGENTS.md, and test coverage by @Copilot in #1181
• Implement Examples-as-Tests-as-Docs pipeline with CI enforcement by @Copilot in #1183
• Dynamics as first-class DSL citizen: D factory, deterministic n_jobs, UQ integration by @Copilot in #1185
• Implement end-to-end UQ propagation with selection probability tracking by @Copilot in #1187
• Bump python-multipart from 0.0.6 to 0.0.22 in /gui/api by @dependabot[bot] in #1190
• Implement zero-loss Arrow and Parquet interchange formats by @Copilot in #1189
• Remove 6 redundant test files by @Copilot in #1191
• Fix test collection errors and example failures for CI stability by @Copilot in #1193
• chore: bump version to 1.1.3 everywhere by @Copilot in #1195

New Contributors

• @dependabot[bot] made their first contribution in #1190

Full Changelog: v1.1.1...v1.1.3

Full Changelog: 1.1.1...v1.1.1

What's Changed

• Reorganize examples folder: move dangling files to topic subdirectories by @Copilot in #962
• Add optional progress logging for DSL query execution steps by @Copilot in #964
• Add property tests for DSL modules: executor, serializer, registries, AST, patterns, export, and result by @Copilot in #966
• Add .explain() DSL predicate for node-level explanations by @Copilot in #968
• Add Multilayer Stochastic Block Model implementation with variational inference by @Copilot in #970
• Add .explain() to flagship README example by @Copilot in #972
• Update AGENTS.md to reflect py3plex v1.1.0 feature set and repository state by @Copilot in #974
• Add endpoint properties and native aggregations to DSL v2 by @Copilot in #976
• Align version references to 1.1.0 across documentation and metadata by @Copilot in #978
• Fix RST formatting causing descriptive text to appear as ToC headings by @Copilot in #980
• Enable DSL progress logging by default and add property tests by @Copilot in #982
• Add first-class community support to DSL v2 by @Copilot in #984
• Add internal parallel execution for null models and uncertainty quantification by @Copilot in #986
• Add query provenance tracking to DSL v2 and legacy DSL by @Copilot in #988
• Add distributional community detection with uncertainty quantification by @Copilot in #992
• Implement counterfactual reasoning system distinct from uncertainty quantification by @Copilot in #994
• Implement semiring algebra layer for generic path computation and graph analysis by @Copilot in #990
• Implement provenance-complete reproducible query results with deterministic replay by @Copilot in #996
• Merge dplyr-style chainable API into DSL v2 builder by @Copilot in #998
• Implement probabilistic community detection with uncertainty quantification for DSL v2 by @Copilot in #1000
• Add Query Sensitivity Analysis: Test robustness of conclusions under perturbations by @Copilot in #1002
• Implement production-quality multilayer Leiden community detection with uncertainty quantification by @Copilot in #1008
• Implement robustness contracts for DSL v2 with auto-inference and typed failure modes by @Copilot in #1004
• Add Network Counterexample Generation with DSL v2 integration by @Copilot in #1010
• Implement inductive claim learning with DSL integration and counterexample falsification by @Copilot in #1012
• Rewrite AGENTS.md with comprehensive DSL v2 API reference and operational guidance by @Copilot in #1014
• Implement semiring algebra subsystem with bounded verification by @Copilot in #1016
• Implement PartitionUQ: First-class uncertainty quantification for community detection by @Copilot in #1018
• Implement SelectionUQ for probabilistic top-k rankings and filtered selections by @Copilot in #1020
• Implement single UQ execution spine and PartitionUQ MVP by @Copilot in #1022
• Implement AutoCommunity: automatic algorithm selection via most-wins decision engine by @Copilot in #1024
• Add examples for auto_select_community algorithm selection by @Copilot in #1026
• Update AGENTS.md and bump version to 1.1.1 by @Copilot in #1028
• Redesign AutoCommunity as multi-objective meta-algorithm with Pareto selection and uncertainty quantification by @Copilot in #1030
• [WIP] Add CI badge to display test count by @Copilot in #1034
• Implement hard-label propagation algorithms for multilayer networks by @Copilot in #1032
• Fix examples/communities execution and make layout computation optional by @Copilot in #1042
• Add DSLv2 auto community detection entrypoints: Q.communities().auto() and Q.nodes().community_auto() by @Copilot in #1038
• Fix test failures from domain-specific exception migration and conversion bugs by @Copilot in #1047
• Fix unnecessary layout computation in autocommunity execution by @Copilot in #1045
• [WIP] Add multilayer spectral clustering implementation by @Copilot in #1043
• Make uv the primary package manager by @Copilot in #1049
• Remove emojis and clean up examples by @Copilot in #1051
• Add graceful fallback for examples requiring missing datasets or image paths by @Copilot in #1057
• Refactor examples/ to 26 minimal, focused examples in 8 directories by @Copilot in #1059
• Align RST documentation with examples structure and integrate uv by @Copilot in #1063
• Add production-ready MCP server for AI agent integration by @Copilot in #1061
• Revert examples folder to comprehensive collection (170+ examples) by @Copilot in #1069
• Align RST documentation with repository contents and fix broken example references by @Copilot in #1071
• Improve example clarity with comprehensive docstrings and structured output by @Copilot in #1073
• AutoCommunity v2: Pareto-optimal multi-objective selection with UQ and null calibration by @Copilot in #1075
• Fix PDF artifacts and align documentation metadata by @Copilot in #1077

Full Changelog: 1.1.0...1.1.1

What's Changed

• Add uncertainty quantification examples for nullmodels and workflows by @Copilot in #938
• Expand selftest coverage to include uncertainty, nullmodels, DSL, workflows, and temporal features by @Copilot in #940
• Add 575 lines of tests for DSL error handling and serialization modules by @Copilot in #942
• Optimize DSL query execution by applying LIMIT before expensive computations by @Copilot in #944
• Add statistical verification tests for null models and uncertainty quantification by @Copilot in #946
• Replace generic exceptions with rich error messages and "did you mean?" suggestions by @Copilot in #948
• Add .mutate() method to builder DSL for row-wise transformations by @Copilot in #950
• Add coverage operator to flagship example with DSL operator documentation by @Copilot in #952
• Add 41 property tests for DSL module (43% coverage increase) by @Copilot in #954
• Add property tests for DSL operation order invariance and additional centrality measures by @Copilot in #956
• Add pymnet style multilayer visualization by @Copilot in #958
• Implement native multiplex routing with explicit layer-switching costs by @Copilot in #960

Full Changelog: 1.0.3...1.1.0

What's Changed

• Add uncertainty quantification and layer-level statistics to case studies by @Copilot in #895
• Book: Fix PDF structure, remove placeholder content, update security guidance by @Copilot in #897
• Add golden toy examples test suite for comprehensive py3plex validation by @Copilot in #899
• Fix documentation cross-references, code examples, and API consistency by @Copilot in #901
• Implement multilayer clustering coefficients (intra, multiplex, supra-adjacency) by @Copilot in #903
• Sync version strings to PyPI release 1.0.2 by @Copilot in #905
• More improvements by @SkBlaz in #906
• Fix broken math notation, editor notes, and contradictory guidance in documentation by @Copilot in #908
• Fix epidemic model math notation in Sphinx documentation by @Copilot in #910
• Verify documentation encoding cleanliness for v1.0.2 by @Copilot in #914
• Add test coverage for 5 untested core modules by @Copilot in #912
• some refurbishments by @SkBlaz in #915
• Docs update by @SkBlaz in #917
• Fix documentation artifacts: typos, version drift, Docker command consistency by @Copilot in #919
• Add more tests by @SkBlaz in #920
• Add documentation quality linter and standardize Docker commands by @Copilot in #922
• Fix PDF text-layer artifacts and Docker chapter inconsistencies in book sources by @Copilot in #924
• Remove forbidden Unicode artifacts from PDF_FIXES_SUMMARY.md by @Copilot in #926
• Fix licensing inconsistency and migrate documentation links to GitHub Pages by @Copilot in #928
• Remove legacy documentation warning from official docs by @Copilot in #930
• Add lossless cross-compatibility conversion layer for py3plex by @Copilot in #932
• chore: remove temporary documentation files and bump to v1.0.3 by @Copilot in #934
• Expand notebook demos with modern py3plex features by @Copilot in #936

Full Changelog: 1.0.2...1.0.3