v2.0.9

Bug fixes and minor changes.

What's Changed

• [TYPO FIX] Update README.md by @cakiki in #159
• add n2vplusplus experimental feature by @RemyLau in #190
• fix tests by @RemyLau in #191
• fix doc by @RemyLau in #213
• add typing_extensions dependency by @RemyLau in #244
• Update pecanpy.py by @aviswaroop in #284
• Update graph.py by @aviswaroop in #283
• Update experimental.py by @aviswaroop in #282
• Update sparse_rw.py by @aviswaroop in #281
• Update dense_rw.py by @aviswaroop in #280
• Update test_graph.py by @aviswaroop in #285

New Contributors

• @cakiki made their first contribution in #159
• @aviswaroop made their first contribution in #284

Dependencies

• Bump pytest from 7.1.2 to 7.1.3 by @dependabot in #144
• Bump nptyping from 2.2.0 to 2.3.1 by @dependabot in #142
• Bump tox from 3.25.1 to 3.26.0 by @dependabot in #150
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #151
• Bump sphinx from 5.1.1 to 5.2.3 by @dependabot in #157
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #154
• Bump mypy from 0.971 to 0.981 by @dependabot in #153
• Bump pytest-cov from 3.0.0 to 4.0.0 by @dependabot in #156
• Bump mypy from 0.981 to 0.982 by @dependabot in #158
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #160
• Bump numba from 0.56.2 to 0.56.3 by @dependabot in #161
• Bump sphinx from 5.2.3 to 5.3.0 by @dependabot in #162
• Bump pytest-xdist from 2.5.0 to 3.0.2 by @dependabot in #163
• Bump tox from 3.26.0 to 3.27.0 by @dependabot in #165
• Bump pytest from 7.1.3 to 7.2.0 by @dependabot in #164
• Bump numba from 0.56.3 to 0.56.4 by @dependabot in #168
• Bump mypy from 0.982 to 0.990 by @dependabot in #167
• Bump sphinx-rtd-theme from 1.0.0 to 1.1.1 by @dependabot in #166
• Bump nptyping from 2.3.1 to 2.4.1 by @dependabot in #174
• Bump tox from 3.27.0 to 3.27.1 by @dependabot in #171
• Bump mypy from 0.990 to 0.991 by @dependabot in #170
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #172
• Bump numba-progress from 0.0.3 to 0.0.4 by @dependabot in #169
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #175
• Bump pre-commit from 2.20.0 to 2.21.0 by @dependabot in #188
• Bump tox from 3.27.1 to 4.0.18 by @dependabot in #189
• Bump gensim from 4.2.0 to 4.3.0 by @dependabot in #187
• Bump pytest-xdist from 3.0.2 to 3.1.0 by @dependabot in #177
• Bump sphinx from 5.3.0 to 6.0.0 by @dependabot in #194
• Bump tox from 4.0.18 to 4.1.1 by @dependabot in #195
• Bump sphinx from 6.0.0 to 6.1.3 by @dependabot in #205
• Bump tox from 4.1.1 to 4.2.8 by @dependabot in #206
• Bump pytest from 7.2.0 to 7.2.1 by @dependabot in #208
• Bump tox from 4.2.8 to 4.3.2 by @dependabot in #209
• Bump tox from 4.3.2 to 4.3.4 by @dependabot in #210
• Bump tox from 4.3.4 to 4.3.5 by @dependabot in #211
• Bump pre-commit from 2.21.0 to 3.0.0 by @dependabot in #212
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #221
• Bump pytest-xdist from 3.1.0 to 3.3.1 by @dependabot in #248
• Bump mypy from 0.991 to 1.3.0 by @dependabot in #246
• Bump nptyping from 2.4.1 to 2.5.0 by @dependabot in #227
• Bump pre-commit from 3.0.0 to 3.3.2 by @dependabot in #247
• Bump tox from 4.3.5 to 4.5.2 by @dependabot in #245
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #255
• Bump pytest from 7.2.1 to 7.3.2 by @dependabot in #254
• Bump numba-progress from 0.0.4 to 1.0.0 by @dependabot in #252
• Bump parameterized from 0.8.1 to 0.9.0 by @dependabot in #250
• Bump numba from 0.56.4 to 0.57.0 by @dependabot in #249
• Bump pytest-cov from 4.0.0 to 4.1.0 by @dependabot in #251
• Bump mypy from 1.3.0 to 1.4.0 by @dependabot in #260
• Bump tox from 4.5.2 to 4.6.3 by @dependabot in #259
• Bump typing-extensions from 4.6.2 to 4.6.3 by @dependabot in #258
• Bump pre-commit from 3.3.2 to 3.3.3 by @dependabot in #257
• Bump gensim from 4.3.0 to 4.3.1 by @dependabot in #256
• Bump numba from 0.57.0 to 0.57.1 by @dependabot in #262
• Bump pytest from 7.3.2 to 7.4.0 by @dependabot in #261
• Bump mypy from 1.4.0 to 1.4.1 by @dependabot in #263
• Bump typing-extensions from 4.6.3 to 4.7.1 by @dependabot in #265
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #266
• Bump tox from 4.6.3 to 4.6.4 by @dependabot in #267
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #268
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #269
• Bump numba-progress from 1.0.0 to 1.1.0 by @dependabot in #273
• Bump mypy from 1.4.1 to 1.5.0 by @dependabot in #271
• Bump tox from 4.6.4 to 4.8.0 by @dependabot in #272
• Bump gensim from 4.3.1 to 4.3.2 by @dependabot in #277
• Bump tox from 4.8.0 to 4.10.0 by @dependabot in #276
• Bump mypy from 1.5.0 to 1.5.1 by @dependabot in #275
• Bump tox from 4.10.0 to 4.11.1 by @dependabot in #279
• Bump pre-commit from 3.3.3 to 3.4.0 by @dependabot in #287
• Bump pytest from 7.4.0 to 7.4.1 by @dependabot in #286
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #288
• Bump tox from 4.11.1 to 4.11.2 by @dependabot in #290
• Bump pytest from 7.4.1 to 7.4.2 by @dependabot in #289
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #292
• Bump tox from 4.11.2 to 4.11.3 by @dependabot in #291
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #294
• Bump typing-extensions from 4.7.1 to 4.8.0 by @dependabot in #293
• Bump numba from 0.57.1 to 0.58.0 by @dependabot in #295
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #296
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #297
• Bump mypy from 1.5.1 to 1.6.0 by @dependabot in #298
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #302
• Bump pre-commit from 3.4.0 to 3.5.0 by @dependabot in #299
• Bump numba from 0.58.0 to 0...

v2.0.8

What's Changed

• update: move dev requirements into setup.cfg by @RemyLau in #147
• set up bump2version by @RemyLau in #148
• update numba by @RemyLau in #149

Full Changelog: v2.0.7...v2.0.8

v2.0.7

What's Changed

• Require numba<0.56

v2.0.6

What's Changed

• update the current import by @PascalSun in #113
• Support scipy CSR (implicit node IDs) by @RemyLau in #124
• Fix RTD by @RemyLau in #128

Auto dependency version bumps

• Bump mypy from 0.950 to 0.960 by @dependabot in #109
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #106
• Bump numba from 0.55.1 to 0.55.2 by @dependabot in #111
• Bump numba-progress from 0.0.2 to 0.0.3 by @dependabot in #112
• Bump pre-commit from 2.18.1 to 2.19.0 by @dependabot in #107
• Bump twine from 4.0.0 to 4.0.1 by @dependabot in #114
• Bump gensim from 4.1.2 to 4.2.0 by @dependabot in #105
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #117
• Bump nptyping from 2.0.1 to 2.1.3 by @dependabot in #120
• Bump mypy from 0.960 to 0.961 by @dependabot in #116
• Bump black from 22.1.0 to 22.6.0 by @dependabot in #123
• Bump nptyping from 2.1.3 to 2.2.0 by @dependabot in #121
• Bump tox from 3.25.0 to 3.25.1 by @dependabot in #125
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #127
• Bump pre-commit from 2.19.0 to 2.20.0 by @dependabot in #130
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #131
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #134
• Bump mypy from 0.961 to 0.971 by @dependabot in #132
• Bump sphinx from 5.0.2 to 5.1.0 by @dependabot in #133

New Contributors

• @PascalSun made their first contribution in #113

Full Changelog: v2.0.5...v2.0.6

v2.0.5

Update dependencies and project metadata.

What's Changed

• Create dependabot.yml by @RemyLau in #84
• Bump pre-commit from 2.16.0 to 2.17.0 by @dependabot in #89
• Bump tox from 3.24.4 to 3.24.5 by @dependabot in #87
• Bump twine from 3.4.1 to 3.8.0 by @dependabot in #86
• Bump black from 21.12b0 to 22.1.0 by @dependabot in #85
• Update dependabot.yml by @RemyLau in #90
• Bump mypy from 0.931 to 0.942 by @dependabot in #92
• Bump pytest from 6.2.5 to 7.1.1 by @dependabot in #91
• Bump twine from 3.8.0 to 4.0.0 by @dependabot in #95
• Bump pre-commit from 2.17.0 to 2.18.1 by @dependabot in #96
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #97
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #100
• Bump tox from 3.24.5 to 3.25.0 by @dependabot in #99
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #101
• Bump nptyping from 1.4.4 to 2.0.0 by @dependabot in #98
• Bump pytest from 7.1.1 to 7.1.2 by @dependabot in #102
• Bump mypy from 0.942 to 0.950 by @dependabot in #103
• Bump nptyping from 2.0.0 to 2.0.1 by @dependabot in #104

New Contributors

• @dependabot made their first contribution in #89
• @pre-commit-ci made their first contribution in #97

Full Changelog: v2.0.3...v2.0.5

v2.0.3 Minor bug fixes and changes

TL;DR

• AdjLst fixes and save edgelist file
• Specify delimiter for edgelist file (thanks to @justinlboyer !)
• Random seeds for random walk generation

What's Changed

• Test PecanPy, fix AdjLst from_mat, and SparseGraph num_edges by @RemyLau in #63
• Save as edgelist file by @RemyLau in #64
• Refactor test graph by @RemyLau in #65
• Pass delimiter through when using cli by @justinlboyer in #66
• Upgrade dependencies; minor renaming by @RemyLau in #68
• Fix directed graph to_csr by @RemyLau in #69
• Random seed for random walk generation by @RemyLau in #71
• Static typing and format fixes by @RemyLau in #77
• Attach random seed to gensim word2vec by @RemyLau in #78
• Refactor n2v walk by @RemyLau in #81
• Refactor typing by @RemyLau in #82

New Contributors

• @justinlboyer made their first contribution in #66

Full Changelog: v2.0.2...v2.0.3

First order walks and major refactoring

Summary

New features

• Implemented fast and memory efificent first-order walk modes PreCompFirstOrder and FirstOrderUnweighted (when p = q = 1, or even faster when the graph is unweighted)
• Added new gamma hyperparameter for node2vec+

Others

• Setup automated testing
• Refactor graph objects

What's Changed

• Refactor graph by @RemyLau in #43
• Refactor graph construction by @RemyLau in #50
• Test cli and remove deprecated options by @RemyLau in #51
• Refactor rwgraph by @RemyLau in #52
• First order walk by @RemyLau in #53
• Automated testing by @RemyLau in #56
• Fix windows by @RemyLau in #57
• Cleanup configs by @RemyLau in #58
• Gamma hyperparam by @RemyLau in #60

Full Changelog: v2.0.1...v2.0.2

Progress bar and csr graph read/write

New features

• Progress bar via numba-progress, enable by specifying --verbose
• Read and write CSR sparse graph as .npz (with the convention of .csr.npz for csr graph and .dense.npz for dense graph)
• Convert weighted dense graph to unweighted dense graph

Minor changes

• Refactor Timer
• Enforce BLACK formatting

Node2vec+

• Node2vec+ implementation.
• Several fixes of node2vec with improved usage of PecanPy from Python script.

Improve doc and major bugs fixed

• Improved the documentation of the package and hosted on readthedoc
• Enforced coding style consistency through flake
• Fixed bug in setting in-out bias according to q
• Fixed gensim.word2vec keywords back compatibility for gensim 4.0.1