Pecanpy

Bug fixes and minor changes.

What's Changed
* [TYPO FIX] Update README.md by cakiki in https://github.com/krishnanlab/PecanPy/pull/159
* add n2vplusplus experimental feature by RemyLau in https://github.com/krishnanlab/PecanPy/pull/190
* fix tests by RemyLau in https://github.com/krishnanlab/PecanPy/pull/191
* fix doc by RemyLau in https://github.com/krishnanlab/PecanPy/pull/213
* add typing_extensions dependency by RemyLau in https://github.com/krishnanlab/PecanPy/pull/244
* Update pecanpy.py by aviswaroop in https://github.com/krishnanlab/PecanPy/pull/284
* Update graph.py by aviswaroop in https://github.com/krishnanlab/PecanPy/pull/283
* Update experimental.py by aviswaroop in https://github.com/krishnanlab/PecanPy/pull/282
* Update sparse_rw.py by aviswaroop in https://github.com/krishnanlab/PecanPy/pull/281
* Update dense_rw.py by aviswaroop in https://github.com/krishnanlab/PecanPy/pull/280
* Update test_graph.py by aviswaroop in https://github.com/krishnanlab/PecanPy/pull/285

New Contributors
* cakiki made their first contribution in https://github.com/krishnanlab/PecanPy/pull/159
* aviswaroop made their first contribution in https://github.com/krishnanlab/PecanPy/pull/284

Dependencies
* Bump pytest from 7.1.2 to 7.1.3 by dependabot in https://github.com/krishnanlab/PecanPy/pull/144
* Bump nptyping from 2.2.0 to 2.3.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/142
* Bump tox from 3.25.1 to 3.26.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/150
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/151
* Bump sphinx from 5.1.1 to 5.2.3 by dependabot in https://github.com/krishnanlab/PecanPy/pull/157
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/154
* Bump mypy from 0.971 to 0.981 by dependabot in https://github.com/krishnanlab/PecanPy/pull/153
* Bump pytest-cov from 3.0.0 to 4.0.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/156
* Bump mypy from 0.981 to 0.982 by dependabot in https://github.com/krishnanlab/PecanPy/pull/158
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/160
* Bump numba from 0.56.2 to 0.56.3 by dependabot in https://github.com/krishnanlab/PecanPy/pull/161
* Bump sphinx from 5.2.3 to 5.3.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/162
* Bump pytest-xdist from 2.5.0 to 3.0.2 by dependabot in https://github.com/krishnanlab/PecanPy/pull/163
* Bump tox from 3.26.0 to 3.27.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/165
* Bump pytest from 7.1.3 to 7.2.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/164
* Bump numba from 0.56.3 to 0.56.4 by dependabot in https://github.com/krishnanlab/PecanPy/pull/168
* Bump mypy from 0.982 to 0.990 by dependabot in https://github.com/krishnanlab/PecanPy/pull/167
* Bump sphinx-rtd-theme from 1.0.0 to 1.1.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/166
* Bump nptyping from 2.3.1 to 2.4.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/174
* Bump tox from 3.27.0 to 3.27.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/171
* Bump mypy from 0.990 to 0.991 by dependabot in https://github.com/krishnanlab/PecanPy/pull/170
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/172
* Bump numba-progress from 0.0.3 to 0.0.4 by dependabot in https://github.com/krishnanlab/PecanPy/pull/169
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/175
* Bump pre-commit from 2.20.0 to 2.21.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/188
* Bump tox from 3.27.1 to 4.0.18 by dependabot in https://github.com/krishnanlab/PecanPy/pull/189
* Bump gensim from 4.2.0 to 4.3.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/187
* Bump pytest-xdist from 3.0.2 to 3.1.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/177
* Bump sphinx from 5.3.0 to 6.0.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/194
* Bump tox from 4.0.18 to 4.1.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/195
* Bump sphinx from 6.0.0 to 6.1.3 by dependabot in https://github.com/krishnanlab/PecanPy/pull/205
* Bump tox from 4.1.1 to 4.2.8 by dependabot in https://github.com/krishnanlab/PecanPy/pull/206
* Bump pytest from 7.2.0 to 7.2.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/208
* Bump tox from 4.2.8 to 4.3.2 by dependabot in https://github.com/krishnanlab/PecanPy/pull/209
* Bump tox from 4.3.2 to 4.3.4 by dependabot in https://github.com/krishnanlab/PecanPy/pull/210
* Bump tox from 4.3.4 to 4.3.5 by dependabot in https://github.com/krishnanlab/PecanPy/pull/211
* Bump pre-commit from 2.21.0 to 3.0.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/212
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/221
* Bump pytest-xdist from 3.1.0 to 3.3.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/248
* Bump mypy from 0.991 to 1.3.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/246
* Bump nptyping from 2.4.1 to 2.5.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/227
* Bump pre-commit from 3.0.0 to 3.3.2 by dependabot in https://github.com/krishnanlab/PecanPy/pull/247
* Bump tox from 4.3.5 to 4.5.2 by dependabot in https://github.com/krishnanlab/PecanPy/pull/245
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/255
* Bump pytest from 7.2.1 to 7.3.2 by dependabot in https://github.com/krishnanlab/PecanPy/pull/254
* Bump numba-progress from 0.0.4 to 1.0.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/252
* Bump parameterized from 0.8.1 to 0.9.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/250
* Bump numba from 0.56.4 to 0.57.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/249
* Bump pytest-cov from 4.0.0 to 4.1.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/251
* Bump mypy from 1.3.0 to 1.4.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/260
* Bump tox from 4.5.2 to 4.6.3 by dependabot in https://github.com/krishnanlab/PecanPy/pull/259
* Bump typing-extensions from 4.6.2 to 4.6.3 by dependabot in https://github.com/krishnanlab/PecanPy/pull/258
* Bump pre-commit from 3.3.2 to 3.3.3 by dependabot in https://github.com/krishnanlab/PecanPy/pull/257
* Bump gensim from 4.3.0 to 4.3.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/256
* Bump numba from 0.57.0 to 0.57.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/262
* Bump pytest from 7.3.2 to 7.4.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/261
* Bump mypy from 1.4.0 to 1.4.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/263
* Bump typing-extensions from 4.6.3 to 4.7.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/265
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/266
* Bump tox from 4.6.3 to 4.6.4 by dependabot in https://github.com/krishnanlab/PecanPy/pull/267
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/268
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/269
* Bump numba-progress from 1.0.0 to 1.1.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/273
* Bump mypy from 1.4.1 to 1.5.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/271
* Bump tox from 4.6.4 to 4.8.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/272
* Bump gensim from 4.3.1 to 4.3.2 by dependabot in https://github.com/krishnanlab/PecanPy/pull/277
* Bump tox from 4.8.0 to 4.10.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/276
* Bump mypy from 1.5.0 to 1.5.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/275
* Bump tox from 4.10.0 to 4.11.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/279
* Bump pre-commit from 3.3.3 to 3.4.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/287
* Bump pytest from 7.4.0 to 7.4.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/286
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/288
* Bump tox from 4.11.1 to 4.11.2 by dependabot in https://github.com/krishnanlab/PecanPy/pull/290
* Bump pytest from 7.4.1 to 7.4.2 by dependabot in https://github.com/krishnanlab/PecanPy/pull/289
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/292
* Bump tox from 4.11.2 to 4.11.3 by dependabot in https://github.com/krishnanlab/PecanPy/pull/291
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/294
* Bump typing-extensions from 4.7.1 to 4.8.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/293
* Bump numba from 0.57.1 to 0.58.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/295
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/296
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/297
* Bump mypy from 1.5.1 to 1.6.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/298
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/302
* Bump pre-commit from 3.4.0 to 3.5.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/299
* Bump numba from 0.58.0 to 0.58.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/301
* Bump mypy from 1.6.0 to 1.6.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/300
* Bump pytest from 7.4.2 to 7.4.3 by dependabot in https://github.com/krishnanlab/PecanPy/pull/303
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/306
* Bump pytest-xdist from 3.3.1 to 3.5.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/307
* Bump mypy from 1.6.1 to 1.7.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/308
* Bump tox from 4.11.3 to 4.11.4 by dependabot in https://github.com/krishnanlab/PecanPy/pull/309
* Bump typing-extensions from 4.8.0 to 4.9.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/310
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/312
* Bump mypy from 1.7.1 to 1.8.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/313
* Bump pytest from 7.4.3 to 7.4.4 by dependabot in https://github.com/krishnanlab/PecanPy/pull/315
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/314
* Bump pre-commit from 3.5.0 to 3.6.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/311

**Full Changelog**: https://github.com/krishnanlab/PecanPy/compare/v2.0.8...v2.0.9

What's Changed
* update: move dev requirements into setup.cfg by RemyLau in https://github.com/krishnanlab/PecanPy/pull/147
* set up bump2version by RemyLau in https://github.com/krishnanlab/PecanPy/pull/148
* update numba by RemyLau in https://github.com/krishnanlab/PecanPy/pull/149


**Full Changelog**: https://github.com/krishnanlab/PecanPy/compare/v2.0.7...v2.0.8

What's Changed
* Require ``numba<0.56``

What's Changed
* update the current import by PascalSun in https://github.com/krishnanlab/PecanPy/pull/113
* Support scipy CSR (implicit node IDs) by RemyLau in https://github.com/krishnanlab/PecanPy/pull/124
* Fix RTD by RemyLau in https://github.com/krishnanlab/PecanPy/pull/128

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

New Contributors
* PascalSun made their first contribution in https://github.com/krishnanlab/PecanPy/pull/113

**Full Changelog**: https://github.com/krishnanlab/PecanPy/compare/v2.0.5...v2.0.6

Update dependencies and project metadata.

What's Changed
* Create dependabot.yml by RemyLau in https://github.com/krishnanlab/PecanPy/pull/84
* Bump pre-commit from 2.16.0 to 2.17.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/89
* Bump tox from 3.24.4 to 3.24.5 by dependabot in https://github.com/krishnanlab/PecanPy/pull/87
* Bump twine from 3.4.1 to 3.8.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/86
* Bump black from 21.12b0 to 22.1.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/85
* Update dependabot.yml by RemyLau in https://github.com/krishnanlab/PecanPy/pull/90
* Bump mypy from 0.931 to 0.942 by dependabot in https://github.com/krishnanlab/PecanPy/pull/92
* Bump pytest from 6.2.5 to 7.1.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/91
* Bump twine from 3.8.0 to 4.0.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/95
* Bump pre-commit from 2.17.0 to 2.18.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/96
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/97
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/100
* Bump tox from 3.24.5 to 3.25.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/99
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/krishnanlab/PecanPy/pull/101
* Bump nptyping from 1.4.4 to 2.0.0 by dependabot in https://github.com/krishnanlab/PecanPy/pull/98
* Bump pytest from 7.1.1 to 7.1.2 by dependabot in https://github.com/krishnanlab/PecanPy/pull/102
* Bump mypy from 0.942 to 0.950 by dependabot in https://github.com/krishnanlab/PecanPy/pull/103
* Bump nptyping from 2.0.0 to 2.0.1 by dependabot in https://github.com/krishnanlab/PecanPy/pull/104

New Contributors
* dependabot made their first contribution in https://github.com/krishnanlab/PecanPy/pull/89
* pre-commit-ci made their first contribution in https://github.com/krishnanlab/PecanPy/pull/97

**Full Changelog**: https://github.com/krishnanlab/PecanPy/compare/v2.0.3...v2.0.5

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 https://github.com/krishnanlab/PecanPy/pull/63
* Save as edgelist file by RemyLau in https://github.com/krishnanlab/PecanPy/pull/64
* Refactor test graph by RemyLau in https://github.com/krishnanlab/PecanPy/pull/65
* Pass delimiter through when using cli by justinlboyer in https://github.com/krishnanlab/PecanPy/pull/66
* Upgrade dependencies; minor renaming by RemyLau in https://github.com/krishnanlab/PecanPy/pull/68
* Fix directed graph to_csr by RemyLau in https://github.com/krishnanlab/PecanPy/pull/69
* Random seed for random walk generation by RemyLau in https://github.com/krishnanlab/PecanPy/pull/71
* Static typing and format fixes by RemyLau in https://github.com/krishnanlab/PecanPy/pull/77
* Attach random seed to gensim word2vec by RemyLau in https://github.com/krishnanlab/PecanPy/pull/78
* Refactor n2v walk by RemyLau in https://github.com/krishnanlab/PecanPy/pull/81
* Refactor typing by RemyLau in https://github.com/krishnanlab/PecanPy/pull/82

New Contributors
* justinlboyer made their first contribution in https://github.com/krishnanlab/PecanPy/pull/66

**Full Changelog**: https://github.com/krishnanlab/PecanPy/compare/v2.0.2...v2.0.3