V1 #4

andreafailla · 2025-11-19T12:21:12Z

No description provided.

Major changes: 1. Removed dependency on HALP. As a consequence, added self.edge_mapping and self.node_set_to_hyperedge to map arcs to ids. Node profiles are now mapped to self.node_profiles (node: tid: NProfile) and stars to self.stars (node: edge id set) 2. self.time_to_edge. Mapped tid: edge : event. Handling this mapping is the most expensive thing. Removing it gives a considerable boost in performance when creating large hypergraphs. Requires changing stream_interactions (the only function that really used it). 3. Stream_interactions. Can no longer simply iterate over time_to_edge. Now: If hedge_removal is False, it yields temporally ordered hyperedges (one iteration for each non-contiguous appearance). If hedge_removal is True, it instead (i) yields the first snapshot, (ii) for each subsequent instant, yields the additions checking that they are not present at the previous instant, then yields the removals checking that they are not present at the next instant. 4. Added a warning: hedge removal not implemented 5. add_nodes. Faster because it does not do time checks. Overwrites if the node already exists. (When working on it, therefore, add arcs first, then node attributes) 6. various bug fixes, incl. neighbors counting

… update related tests

- Created subdirectories: unit/, paths/, measures/, utils/, generators/, io/, viz/, integration/, fixtures/ - Added conftest.py with shared fixtures (rng, ash_factory, small_hg, matplotlib_agg) - Created fixtures/sample_hypergraphs.py with reusable test hypergraph factories - Moved all existing tests to appropriate subdirectories - Added 38 new tests: * measures/test_segregation.py: 16 tests for RWHS measures * integration/test_backends.py: 15 tests for Dense/Interval backend parity * integration/test_workflows.py: 7 end-to-end workflow tests - Fixed integration test API signatures - Copied hif_data to io/ subdirectory for I/O tests - All 189 tests passing (161 original + 28 new without duplicates) - Maintained 95% code coverage

- Implements multi-ego network extraction for temporal hypergraphs - Three extraction variants: standard, fractured (alpha), core (beta) - Three similarity measures: Jaccard, minimum overlapping, delta - Supports single snapshot and time window queries (start/end) - 28 comprehensive tests (all passing) - API consistent with ASH.star() and temporal conventions

- Convert docstrings from NumPy to Sphinx style (:param:, :return:) - Add docs/reference/multiego.rst with autosummary - Include multiego in docs/reference/reference.rst - All 28 tests passing - Consistent with ASH documentation standards

- Add conftest.py with shared fixtures - Create fixtures/sample_hypergraphs.py for reusable test data - Organize tests in subdirectories: integration/, measures/, viz/ - Add comprehensive integration tests (backends, workflows) - Add visualization tests (static and temporal) - Improve test isolation and maintainability - All 228 tests passing

- Update temporal parameters (start/end) to use Optional[int] for PEP 484 compliance - Add Optional to typing imports in s_centralities.py, projections.py, matrices.py - Fix s_eigenvector_centrality: add missing weight parameter - Fix s_load_centrality: correct docstring parameters - Improves IDE support, type checking, and code clarity - No behavioral changes, type system only - Affected: 15 functions across 3 modules - All tests pass (test_centralities.py, test_utils.py)

- Changed documentation theme from sphinx_rtd_theme to Furo for better logo visibility - Furo provides modern design with dark sidebar that makes the orange logo stand out - Fixed logo configuration to prevent duplication - Moved logo to _static directory for proper Furo integration - Reorganized reference.rst: moved multiego from Measures to its own MultiEgo section

- Add ash_model.viz.static: functions for static hypergraph visualization - plot_s_degrees: visualize s-degree distribution - plot_hyperedge_size_distribution: hyperedge size distribution - plot_degree_distribution: node degree distribution (log-log) - plot_s_ranks: s-rank distribution - Add ash_model.viz.temporal: functions for temporal hypergraph visualization - plot_hyperedge_activity_series: activity over time for hyperedges - plot_node_activity_series: activity over time for nodes - plot_node_presence_timeline: presence intervals for nodes - plot_hyperedge_presence_timeline: presence intervals for hyperedges - plot_interevent_time_distribution: time between consecutive events - plot_lifespan_distribution: lifespan distribution for nodes/hyperedges - Add docs/reference/viz.rst: comprehensive documentation with separate sections for static and temporal plots - Fixed docstring formatting issues to eliminate Sphinx warnings - Standardized parameter naming: 'normalize' (American English) across all functions

- Add generated autosummary documentation for multiego functions - Includes docs for delta_similarity, jaccard_similarity, minimum_overlap - Includes docs for get_core_multiego, get_multiego, get_fractures

- Remove same-timestamp edges: DAG now only creates edges from timestamp t to t' where t' > t - Each step in a time-respecting walk must happen at a strictly later timestamp - Optimize walk validation from O(n²) to O(n) by tracking prev_edge directly - Update temporal_s_dag to build only forward-in-time connections - Fix ping-pong detection to avoid redundant seq.index() calls Tests updated: - test_time_respecting_walks.py: All 5 tests passing with correct expectations - test_randwalks.py: Updated hypergraphs to use multi-timestamp scenarios - test_time_respecting_randwalks.py: Updated validation for strictly increasing timestamps Time-respecting walk constraints now correctly enforced: ✓ Each edge happens at a specific time t ✓ Can only move along edges that exist at that time ✓ Every next step must happen later in time (no backtracking, no same-time transitions)

Major improvements to time-respecting walks and random walks: **Time-Respecting Random Walks:** - Removed terminate_at_sink parameter (redundant with corrected logic) - Walks always terminate at temporal sinks (nodes with no forward neighbors) - Simplified API: walks stop automatically when no forward transitions exist - Updated docstring to reflect corrected behavior **Test Suite Enhancements:** - Added comprehensive test coverage for complex temporal networks - New test_complex_temporal_network: 11 hyperedges, 12 timestamps, 8 nodes - New test_larger_network_* tests: 15 hyperedges, 10 timestamps, 8 nodes - Tests verify walks spanning >2 timestamps with temporal diversity - Updated test expectations to match corrected time-respecting semantics **Test Improvements:** - test_time_respecting_walks.py: Added test_complex_temporal_network - test_time_respecting_randwalks.py: Added 3 comprehensive tests: * test_larger_network_node_walks (50 walks, length 8) * test_larger_network_edge_walks_long_paths (walks up to 10 steps) * test_larger_network_temporal_span_coverage (diversity metrics) - test_randwalks.py: Removed terminate_at_sink parameter usage **Coverage Statistics:** - Max timestamps tested: 12 (previously 5) - Max hyperedges tested: 15 (previously 5) - Max nodes tested: 8 (previously 4) - Temporal span: 6-10 timestamps (previously ~4) - All 38 tests in paths module passing

… features)

Copilot

Pull Request Overview

This PR represents a major version release (v1.0.0) of the ASH (Attributed Stream Hypergraph) library, introducing comprehensive tutorial notebooks, extensive documentation improvements, and important dependency updates.

Key changes:

Version bump from 0.1.0 to 1.0.0
Addition of 6 comprehensive tutorial notebooks covering all major library features
Complete documentation restructuring with improved organization and API references
Dependency updates including removal of deprecated halp library and addition of csrgraph

Reviewed Changes

Copilot reviewed 171 out of 180 changed files in this pull request and generated 48 comments.

Show a summary per file

File	Description
setup.py	Version bumped to 1.0.0, formatting standardized to double quotes
requirements.txt	Updated dependencies: removed halp/seaborn/pandas, added csrgraph, pinned numpy<2.0
environment.yml	New conda environment file with Python>=3.9 and key dependencies
tutorial/*.ipynb	6 new comprehensive tutorial notebooks (basics, attributes, walks, generators, I/O, multiego, segregation)
docs/tutorial.rst	Complete restructure referencing new tutorial notebooks with progressive organization
docs/reference/*.rst	Reorganized API documentation with improved structure and autosummary support
docs/conf.py	Major update: switched to Furo theme, added nbsphinx support, improved autodoc configuration
docs/requirements.txt	New documentation build dependencies including sphinx, furo, nbsphinx
ash_model/viz/static.py	Updated API calls from deprecated methods (get_node_set→nodes, get_degree→degree, get_s_degree→s_degree)
ash_model/utils/init.py	Updated imports reflecting module reorganization (matrices, projections, networkx, profiles)
conda/*	New conda build configuration files

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2025-11-19T12:28:59Z

conda/meta.yaml

+about:
+  home: https://github.com/GiulioRossetti/ASH
+  license: BSD-2-Clause
+  license_familY: BSD


Spelling error: "license_familY" should be "license_family" (lowercase 'y')

Copilot · 2025-11-19T12:28:59Z

tutorial/01-attribute_analysis.ipynb

+    "All methods in this module share the following characteristics:\n",
+    "1. They return results for all attributes;\n",
+    "2. Their return type is a dictionary, typically containing the attribute name (or value) and the corresponding score;\n",
+    "3. Imternally, they process <code>NProfile</code> objects. If you are not familiar with them, see the corresponding section in the \"basics\" tutorial notebook.\n",


Spelling error: "Imternally" should be "Internally"

Copilot · 2025-11-19T12:28:59Z

docs/reference/readwrite.rst

+~~~
+HIF (Hypergraph Interchange Format) is a file format designed for representing hypergraphs. It is particularly useful for storing and exchanging hypergraph data due to its simplicity and human-readability.
+
+Read more about HIF  `here <https://github.com/pszufe/HIF-standard/tree/main>`_ 


Extra space before "here" in the link text. Should be a single space after the period.

Copilot · 2025-11-19T12:29:00Z

ash_model/test/io/test_io.py

+            # file should either not exist or only header
+            lines = open(tf.name).read().splitlines()
+            # no header written (no nodes)
+            self.assertTrue(len(lines) in (0, 1))


assertTrue(a in b) cannot provide an informative message. Using assertIn(a, b) instead will give more informative messages.

Copilot · 2025-11-19T12:29:00Z

ash_model/test/paths/test_randwalks.py

+        # At least one short walk should be produced
+        self.assertGreaterEqual(len(walks), 1)
+        for w in walks:
+            self.assertTrue(len(w) >= 1)


assertTrue(a >= b) cannot provide an informative message. Using assertGreaterEqual(a, b) instead will give more informative messages.

Copilot · 2025-11-19T12:29:11Z

ash_model/test/integration/test_workflows.py

+"""Integration tests for complete analysis workflows."""
+
+import unittest
+import numpy as np


Import of 'np' is not used.

Copilot · 2025-11-19T12:29:11Z

ash_model/test/io/test_io.py

+
+    def test_hif_ash(self):
+        import fastjsonschema
+        import json


This import of module json is redundant, as it was previously imported on line 3.

Copilot · 2025-11-19T12:29:11Z

ash_model/classes/presence_store.py

+###############################################################################
+
+
+class _SnapshotMutable(set):


The class '_SnapshotMutable' does not override 'eq', but adds the new attribute _store.
The class '_SnapshotMutable' does not override 'eq', but adds the new attribute _time.

Copilot · 2025-11-19T12:29:12Z

ash_model/classes/node_profile.py



-class NProfile(object):
+class NProfile:


This class implements le, but does not implement lt or gt.

Copilot · 2025-11-19T12:29:12Z

ash_model/test/io/test_io.py

+        try:
+            write_profiles_to_csv(empty, tf.name)
+            # file should either not exist or only header
+            lines = open(tf.name).read().splitlines()


File is opened but is not closed.

…ions

andreafailla added 30 commits August 19, 2024 19:36

second major update (untested)

dbb2a09

Edge attrs

503f5ea

Typings, docs, black

9ab83ce

readability

ba5973e

changed tid parameters to start/end slice

d7deee3

json IO

c8b4af0

refactoring

b7589a0

ASH (tested)

c2ce5ce

Allow backend switch

808bf63

utils (tested)

c003281

support for high-performance computation of random walks

0430a89

Update test_ash.py

0a949d2

docs

2519608

test edits

ef51cfe

s_centralities (tested)

9166940

Update profile test and add utils init

3bd66ff

⚡️ improve performance

af764a1

🐛 fixed errors in method name

2818dca

🎨 Black formatting

129355a

🔧 Refactor ASH initialization to remove edge_attributes parameter and…

119fdbe

… update related tests

✅ Test walks and distances

738834a

✅ Test attribute analysis

5323988

✅ Test IO

22a6202

✅ Test paths

b83769d

✨ Introduce static random walks

70ce831

🎨 Black

8ebb1e9

✅ Test walks

eaf3b59

⚡️ Improved edge insertion on interval backend

47185db

✅ Test IO (temporal attributes)

4f52863

andreafailla added 23 commits September 22, 2025 10:23

🐛 handle networkx returning a generator from v3.13

30ef826

🐛 handle static hypergraphs

d55969f

🎨 Formatting

4d424d9

📝 Docs

d8f84c1

⚡️ Improve presence store

ab9952c

📝 docstring examples

4b82f2a

⚡️ Improve presence store

16f1671

✨ Added s parameter to random walks and rwhs

f91afc1

🩹 Patch & uniform randwalks and segregation API

47b740e

docs: add autosummary documentation for multiego module

04976d2

- Add generated autosummary documentation for multiego functions - Includes docs for delta_similarity, jaccard_similarity, minimum_overlap - Includes docs for get_core_multiego, get_multiego, get_fractures

update gitignore

3091d56

refactor: make start and end optional in multiego functions

fa711ed

Tutorials

731540f

Merge origin/features into main — prefer features (content taken from…

a2c0e82

… features)

andreafailla requested a review from Copilot November 19, 2025 12:21

Copilot started reviewing on behalf of andreafailla November 19, 2025 12:21 View session

Copilot finished reviewing on behalf of andreafailla November 19, 2025 12:22

Copilot AI reviewed Nov 19, 2025

View reviewed changes

Update requirements, and remove outdated test files and utility funct…

36abcbd

…ions

andreafailla merged commit e81f3e1 into main Nov 19, 2025
2 checks passed

andreafailla deleted the v1 branch November 19, 2025 12:59

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

V1 #4

V1 #4

Uh oh!

andreafailla commented Nov 19, 2025

Uh oh!

Copilot AI left a comment

Uh oh!

Copilot AI Nov 19, 2025

Uh oh!

Copilot AI Nov 19, 2025

Uh oh!

Copilot AI Nov 19, 2025

Uh oh!

Copilot AI Nov 19, 2025

Uh oh!

Copilot AI Nov 19, 2025

Uh oh!

Copilot AI Nov 19, 2025

Uh oh!

Copilot AI Nov 19, 2025

Uh oh!

Copilot AI Nov 19, 2025

Uh oh!

Copilot AI Nov 19, 2025

Uh oh!

Copilot AI Nov 19, 2025

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

		###############################################################################


		class _SnapshotMutable(set):

V1 #4

V1 #4

Uh oh!

Conversation

andreafailla commented Nov 19, 2025

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull Request Overview

Reviewed Changes

Uh oh!

Copilot AI Nov 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 19, 2025

Choose a reason for hiding this comment

Uh oh!

Copilot AI Nov 19, 2025

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants