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Refactoring#51

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dufourc1 wants to merge 266 commits into
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refactoring
Draft

Refactoring#51
dufourc1 wants to merge 266 commits into
mainfrom
refactoring

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@dufourc1

@dufourc1 dufourc1 commented Feb 2, 2026 •
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Major refactoring to modernize the codebase, add support for decorated graphs (weighted, categorical edges), and improve documentation.

Core Architecture

  • New modular structure: Replaced monolithic implementations with SymArray.jl (fast symmetric arrays), GreedySuffStats.jl, and clean API layer
  • Preprocessor system: Unified edge type handling (binary, categorical, continuous) via preprocessor/
  • Pseudo sufficient statistics framework: Generic abstraction for different edge distributions in pseudo_suff_stats/
  • Removed: src/old/, deprecated src/UI.jl, legacy src/assignments/

Extensions

  • PythonOptimalTransport: srGW and fngw algorithms for partition alignment
  • BootstrapExt, LightMCExt, MakieExt: Optional functionality via weak dependencies

API Changes

# New high-level functions for different edge types
nethist_binary(A, k)      # Binary networks
nethist_categorical(A, k) # Discrete edge values
nethist_continuous(A, k)  # Real-valued edges

# Graphons.jl integration (re-exported)
# Hungarian algorithm for label alignment
# OT-based partition alignment methods

Documentation

  • Added tutorials: simple graphs, weighted networks, multiplex networks, temporal networks
  • Custom sufficient statistics example
  • Removed outdated internals/rules documentation

Infrastructure

  • Dependabot configuration
  • Benchmark PR workflow
  • CondaPkg.toml for Python dependencies

dufourc1 added 30 commits October 17, 2024 19:09
@dufourc1
add tests for assignments creation and swaps
a286874
@dufourc1
found fastest ll computation
c795929
@dufourc1
fix make data categorical
75e3f14
@dufourc1
remove useless memeory in BernoulliSwap
cc54cc4
@dufourc1
working cat assginment before switching to adj list
798ce65
@dufourc1
fix cat assignments
29f59cf
@dufourc1
clean
5bd3dd8
@dufourc1
clean bandwidth selection
d597330
@dufourc1
make docs work
d52a6b5
@dufourc1
add more docstrings
5d407ca
@dufourc1
format
4feb3d9
@dufourc1
add init rules
0fc312a
@dufourc1
add docs for init
cb668e5
@dufourc1
put first steps for clustering with higher dims
ea12c67
@dufourc1
using StatsAPI as it should be
6a8a13c
@dufourc1
handle categorical arrays and fix node labels
3ea8413
@dufourc1
format
ad9d78c
@dufourc1
bugfix: swap being overwritten when updating assignment
c3bd492
@dufourc1
remove debug statement
0c42955
@dufourc1
fix speed and correcteness issue in categorical case
0347062
@dufourc1
typo
82556fc
@dufourc1
first try to benchmark
d6ec72f
@dufourc1
add discretisation
42ffe61
@dufourc1
small api changes
77a3395
@dufourc1
remove unused import @turbo
45c9e40
@dufourc1
fix test to new api
45c1259
@dufourc1
other fit method
3149409
@dufourc1
add perm util function
d10db5b
@dufourc1
typo
5448040
@dufourc1
monkeypatch
dbde987
Copilot AI mentioned this pull request Feb 2, 2026
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@SDS-EPFL SDS-EPFL deleted a comment from Copilot AI Feb 2, 2026
@codecov

codecov Bot commented May 28, 2026 •
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Codecov Report

❌ Patch coverage is 17.05640% with 603 lines in your changes missing coverage. Please review.
✅ Project coverage is 17.05%. Comparing base (095a2c8) to head (99347d8).

Files with missing lines Patch % Lines
ext/PythonOptimalTransport/srGW.jl 0.00% 246 Missing ⚠️
src/GreedySuffStats.jl 0.00% 74 Missing ⚠️
src/utils/utils_node_labels.jl 0.00% 34 Missing ⚠️
src/api.jl 0.00% 32 Missing ⚠️
ext/LightMCExt.jl 0.00% 26 Missing ⚠️
src/pseudo_suff_stats/generic.jl 0.00% 26 Missing ⚠️
src/distributions/hist_dist.jl 0.00% 24 Missing ⚠️
src/config_rules/stop_rule.jl 0.00% 21 Missing ⚠️
ext/PythonOptimalTransport/alignment.jl 0.00% 17 Missing ⚠️
src/preprocessor/categorical.jl 0.00% 17 Missing ⚠️
... and 11 more
Additional details and impacted files 
@@             Coverage Diff             @@
##             main      #51       +/-   ##
===========================================
- Coverage   81.93%   17.05%   -64.88%     
===========================================
  Files          15       21        +6     
  Lines         465      727      +262     
===========================================
- Hits          381      124      -257     
- Misses         84      603      +519

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