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Release/0.5.0-beta, complete rewrite - #68

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ryandewolfe33 wants to merge 76 commits into
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ryandewolfe33:release/0.5.0-beta
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Release/0.5.0-beta, complete rewrite#68
ryandewolfe33 wants to merge 76 commits into
AleksanderWWW:mainfrom
ryandewolfe33:release/0.5.0-beta

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@ryandewolfe33

@ryandewolfe33 ryandewolfe33 commented Sep 3, 2026 •
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Complete re-write for version 0.5.0 to simplify structure and increase speed. Total disregard for backwards compatibility.

  • Main class is ABCD, stores parameters and has a .sample() method to generate a graph Redesign user interface #64
  • Returns an ABCDSample class that contains exporters and parameter measurements
  • New overlap features (ABCDoo) via parameters eta and rho in ABCD
  • All randomness through a global numpy rng Generator Handle seeding process better #65
  • ABCD.fit() to fit the parameters of an observed graph Fit params for observed graph. #66
  • Documentation ready for readthedocs
  • More tests
  • Benchmark tests to check for performance regression
  • Workflows moved entirely to uv
  • dev and docs dependencies moved to dependency-groups in pyproject, may cause problems with package versions.

Anything docker will probably break since I'm not sure how it works.

@ryandewolfe33
Add new interface via ABCD class
2fd6c65
@ryandewolfe33
Run black
7211d2b
@ryandewolfe33
Update README and demo
240fa05
@ryandewolfe33
Update changelog
ff6f00f
@ryandewolfe33
Formatting fixes for flake8
1ef6f1b
@ryandewolfe33
More formatting for flake
205cf2a
@ryandewolfe33
More formatting for flake
6fe9732
@ryandewolfe33
More formatting for flake
c2f8851
@ryandewolfe33
Remove src, tests, profiling
3dbb7b7
@ryandewolfe33
Update pyproject version, tools, and dependencies
ff1a6fe
@ryandewolfe33
Add configuration model and rewiring
b737ef8
@ryandewolfe33
Ignore .DS_store
841b6a4
@ryandewolfe33
Add chunglu model
276ecd8
@ryandewolfe33
Add community assignment for partitions and overlaps
4336194
@ryandewolfe33
Add function to split degrees among background and communities
5b29725
@ryandewolfe33
Add degree assignment and splitting
88e076e
@ryandewolfe33
Add degree and community samplers
af39a10
@ryandewolfe33
Try harder to fix community sizes
f615763
@ryandewolfe33
Make community size sums even
f1d2f78
@ryandewolfe33
Check sum of community degrees is even
7e1a4bf
@ryandewolfe33
Check total degree is even
3b2bcc9
@ryandewolfe33
Update ruff settings
4affb6b
@ryandewolfe33
Initial implemention of top level ABCD class
5f8f967
@ryandewolfe33
Update pre-commit hooks, remove mypy and switch to ruff
eb0e023
@ryandewolfe33
Update pyproject
30c86a7
@ryandewolfe33
Remove print statements
12345a7
@ryandewolfe33
Optimise split community degree
796c346
@ryandewolfe33
Simplify degree spliting
de9cdc5
@ryandewolfe33
Add seeds to tests
9a7842c
@ryandewolfe33
numbaify configuration model
4f7c598
ryandewolfe33 and others added 25 commits August 23, 2026 09:14
@ryandewolfe33
Feature/speed up assign degrees (#4)
bf89d06 
* Fix bug in rewiring and models, faster degree assignments

* Faster (and fixed?) degree assignment

* Can sample 100 000 node graph in 0.5s.
@ryandewolfe33
Update versions in ci workflow
5748827
@ryandewolfe33
Add fit function to ABCD (#5)
8dbc96c
@ryandewolfe33
Add upper limit on n
25c5a3a
@ryandewolfe33
Update docstrings and don't use rho in degrees without overlap
297f272
@ryandewolfe33
Update README and pyproject
4d15084
@ryandewolfe33
Bump version to beta
a5dddee
@ryandewolfe33
Fix overflow error in membership:
f6ba638
@ryandewolfe33
Add sphinx docs (#7)
77137e2 
* Start docs with index and API

* Getting started notebook

* Add outliers notebook

* Add overlap notebook

* Run overlap notebook through prek

* Add igraph notebook

* Add networkx benchmark

* Add networkx benchmark to index

* Add sknetwork benchmark

* Fix igraph benchmark import

* Update getting started headers

* Add how it works doc
@ryandewolfe33
Fix docs picture file format
a5fe9d4
@ryandewolfe33
Remove nbcompess from precommit
d69d317
@ryandewolfe33
Add fstar dependency to docs
ebe10d9
@ryandewolfe33
Remove outdated demo
a8c6e5f
@ryandewolfe33
Describe building docs in readme
9cb2f8f
@ryandewolfe33
Remove fstar dependency until added to pypi
dcb240f
@ryandewolfe33
Add more params to abcd tests
feec9cd
@ryandewolfe33
Refactor/remove powerlaw dependency (#9)
8eba604 
* Add custom powerlaw exponent estimator and remove powerlaw package

* Fix abcd_sample rho
@ryandewolfe33
Add benchmarks and ci workflow (#8)
ef33880 
* Add benchmarks and ci workflow

* Add pytest-benchmark to dev

* Move to dependency-groups in pyproject.toml

* Upgrade packages in lock

* Run everything with uv (and delete custom actions, specify everything in each workflow file)
@ryandewolfe33
Fix degree exponent validation message
1d04e44
@ryandewolfe33
Fix range in powerlaw fit
f1942dc
@ryandewolfe33
Wrtie progress bars through logger
0322890
@ryandewolfe33
Feature/better fit checks (#10)
4b348da 
* Fix doc typos in ABCD

* Add controls for fitting groups of parasm

* Add tests
@ryandewolfe33
Add ABCDe and clean up references in README
3ae52a0
@ryandewolfe33
Update changelog
707aa0b
@ryandewolfe33
Disable numba for coverage report
133d7d2
@ryandewolfe33
Rewire hashes edges as tuple (#11)
b05a6fe 
Hash edges as tuples instead of uint64 in rewire. Set up for general changes to make node dtype dynamic instead of uint32.
@ryandewolfe33
Refactor, models generate inplace (#12)
1da9288 
* Configuration model inplace option

* Add chung-lu model and update protocol

* Make abcd generate inplace
@ryandewolfe33
Refactor/degree assignment speed (#13)
83c7f0d 
* Use argpartiton in outlier degree assignment

* Special path for alpha=0
@ryandewolfe33
Dynamically assign node dtype at sample time (#14)
f2e71fd 
Instead of fixed uint32 (and thus maximum allowable node count), instead pick a dtype dynamically based on the number of nodes. Scipy requires int32/int64 for their pointer arrays, so there's not as much savings as anticipated
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