CovsirPhy 3.0.0

All deprecated APIs were removed.
Milestone: https://github.com/lisphilar/covid19-sir/milestone/49?closed=1

What's Changed

• Deprecation for v3.0.0 by @lisphilar in #1261
• Run quality check workflow for all updates of default branch and pull requests by @lisphilar in #1264
• Refactoring Python files and tests, suppressing warning raised by a dependency by @lisphilar in #1269
• Stop tests with multiple CPUs to avoid un-necessary FAILED by @lisphilar in #1272
• fix: coverage report not created by @lisphilar in #1273
• update .github/workflows/**.yml to use "main" branch by @lisphilar in #1275
• exclude main branch from the targets of deleted after pull request closing by @lisphilar in #1276
• add automated rebase workflow by @lisphilar in #1277
• Bump optuna from 3.0.2 to 3.0.3 by @dependabot in #1279
• Bump numpy from 1.23.3 to 1.23.4 by @dependabot in #1280
• remove .html for deprecated classes and fix "APIs of GIS and DataEngineer class not documented" by @lisphilar in #1282
• update data/README.md to document the date ranges of Japan data by @lisphilar in #1284
• use type hints in APIs users will call: downloading, show type hint in documentation by @lisphilar in #1285
• Use type hint in APIs of dynamics and add pyright check to quality check workflow by @lisphilar in #1286
• use type hint in DatEngineer by @lisphilar in #1288
• revert test skip and use pandas 1.5.1 by @lisphilar in #1289
• Improve importing time and add make command for evaluation by @lisphilar in #1291
• Bump geopandas from 0.11.1 to 0.12.0 by @dependabot in #1293
• Bump pyarrow from 9.0.0 to 10.0.0 by @dependabot in #1294
• ignore pytest.PytestDeprecationWarning in tests by @lisphilar in #1296
• Bump pca from 1.8.3 to 1.8.4 by @dependabot in #1298
• Bump country-converter from 0.7.7 to 0.8.0 by @dependabot in #1299
• Bump autots from 0.5.0 to 0.5.1 by @dependabot in #1300
• Bump numpy from 1.23.4 to 1.23.5 by @dependabot in #1303
• Delegate error handling of colormap to Matplotlib by @lisphilar in #1310
• Bump certifi from 2022.9.24 to 2022.12.7 by @dependabot in #1311
• Bump geopandas from 0.12.1 to 0.12.2 by @dependabot in #1312
• Bump autots from 0.5.1 to 0.5.2 by @dependabot in #1313
• Bump numpy from 1.23.5 to 1.24.0 by @dependabot in #1315
• Bump optuna from 3.0.4 to 3.0.5 by @dependabot in #1316
• Bump autots from 0.5.2 to 0.5.3 by @dependabot in #1317
• Bump numpy from 1.24.0 to 1.24.1 by @dependabot in #1318
• Issue1319 by @lisphilar in #1320
• Bump pca from 1.8.5 to 1.8.6 by @dependabot in #1322
• Bump sphinx-autodoc-typehints from 1.19.5 to 1.21.4 by @dependabot in #1333
• Bump pyright from 1.1.285 to 1.1.290 by @dependabot in #1332
• Bump optuna from 3.0.5 to 3.1.0 by @dependabot in #1331
• Bump ipykernel from 6.19.4 to 6.20.2 by @dependabot in #1329
• Bump pillow from 9.3.0 to 9.4.0 by @dependabot in #1327
• Bump nbsphinx from 0.8.10 to 0.8.11 by @dependabot in #1326
• Bump pytest from 7.2.0 to 7.2.1 by @dependabot in #1325
• Bump requests from 2.28.1 to 2.28.2 by @dependabot in #1324
• Bump matplotlib from 3.6.2 to 3.6.3 by @dependabot in #1323
• Bump scipy from 1.8.1 to 1.10.0 by @dependabot in #1334
• Bump pandas from 1.5.2 to 1.5.3 by @dependabot in #1335
• Bump sphinx-autodoc-typehints from 1.21.4 to 1.21.7 by @dependabot in #1337
• Bump nbsphinx from 0.8.11 to 0.8.12 by @dependabot in #1336
• Bump sphinx-autodoc-typehints from 1.21.7 to 1.21.8 by @dependabot in #1338
• Bump ipykernel from 6.20.2 to 6.21.0 by @dependabot in #1341
• Bump pyarrow from 10.0.1 to 11.0.0 by @dependabot in #1340
• Bump pyright from 1.1.290 to 1.1.291 by @dependabot in #1339
• Bump sphinx-autodoc-typehints from 1.21.8 to 1.22 by @dependabot in #1342
• Bump pyright from 1.1.291 to 1.1.292 by @dependabot in #1343
• Bump nbsphinx from 0.8.10 to 0.8.12 by @dependabot in #1345
• close #1350 by @lisphilar in #1351
• Add Python 3.11 support by @lisphilar in #1297
• Bump numpy from 1.24.1 to 1.24.2 by @dependabot in #1352
• Bump pyright from 1.1.292 to 1.1.293 by @dependabot in #1353
• Bump sphinx-rtd-theme from 1.1.1 to 1.2.0 by @dependabot in #1354
• Bump ipython from 8.9.0 to 8.10.0 by @dependabot in #1355
• [Docs] update the last year in citation, 2020-2022 to 2020-2023 by @deepgohil in #1357
• close #1358 by updating Monkey Pox data URL by @lisphilar in #1359
• Bump matplotlib from 3.6.3 to 3.7.0 by @dependabot in #1361
• update citation section of README by @lisphilar in #1366
• [Docs] update the last year in citation, 2020-2022 to 2020-2023 #1356 by @mehrdadbn9 in #1364
• Bump typing-extensions from 4.4.0 to 4.5.0 by @dependabot in #1362
• Bump pyright from 1.1.293 to 1.1.294 by @dependabot in #1363
• Bump pca from 1.8.6 to 1.9.0 by @dependabot in #1365
• Bump pca from 1.9.0 to 1.9.1 by @dependabot in #1367
• Bump scipy from 1.10.0 to 1.10.1 by @dependabot in #1368
• Removed warning on README for using covsirphy with Google Colab by @Mihan786Chistie in #1369
• Bump pyright from 1.1.294 to 1.1.295 by @dependabot in #1370
• Bump markdown-it-py from 2.1.0 to 2.2.0 by @dependabot in #1371
• Bump pyright from 1.1.295 to 1.1.296 by @dependabot in #1372
• Bump autopep8 from 1.7.0 to 2.0.0 by @dependabot in #1375
• Bump pytest from 7.2.1 to 7.2.2 by @dependabot in #1379
• Bump myst-parser from 0.18.1 to 0.19.1 by @dependabot in #1378
• Bump pytest-cov from 3.0.0 to 4.0.0 by @dependabot in #1377
• Bump country-converter from 0.8.0 to 1.0.0 by @dependabot in #1380
• data: fix Japan vaccinaion aggregation method (1st, 2nd vaccinated) by @lisphilar in #1381
• Bump matplotlib from 3.7.0 to 3.7.1 by @dependabot in #1383
• Bump ipykernel from 6.21.2 to 6.21.3 by @dependabot in #1384
• Bump myst-parser from 0.19.1 to 1.0.0 by @dependabot in #1385
• data: revise vaccine data integration, add _4th and 5th columns by @lisphilar in #1386
• fix errors of pull request #1386 by @lisphilar in #1387
• Bump matplotlib from 3.7.0 to 3.7.1 by @dependabot in #1388
• Bump pyright from 1.1.296 to 1.1.298 by @dependabot in #1389
• Bump ipykernel from 6.21.2 to 6.21.3 by @dependabot in #1390
• Bump openpyxl from 3.1.1 to 3.1.2 by @dependabot in #1392
• Bump nbsphinx from 0.8.12 to 0.9.1 by @dependabot in #1393
• Bump pyright from 1.1.298 to 1.1.299 by @dependabot in #1394
• Bump ipykernel from 6.21.3 to 6.22.0 by @dependabot in #1395
• Bump ipywidgets from 8.0.4 to 8.0.5 by @dependabot in #1396
• Bump pyright from 1.1.299 to 1.1.300 by @dependabot in #1397
• Bump pca from 1.9.1 to 1.9.2 by @dependabot in #1398
• Bump ipywidgets from 8.0.5 to 8.0.6 by @dependabot in #1399
• Bump pyright from 1.1.300 to 1.1.301 by @dependabot in #1400
• Bump autots from 0.5.4 to 0.5.5 by @dependabot in #1403
• Bump pandas from 1.5.3 to 2.0.0 by @dependabot in #1402
• Bump pillow from 9.4.0 to 9.5.0 by @dependabot in #1401
• Bump pyright from 1.1.301 to 1.1.302 by @dependabot in #1404
• Bump optuna from 3.1.0 to 3.1.1 by @dependabot in #1405
• Bump loguru from 0.6.0 to 0.7.0 by @dependabot in #1406
• Bump autots from 0.5.5 to 0.5.6 by @dependabot in #1407
• Bump pytest from 7.2.2 to 7.3.0 by @dependabot in #1408
• Bump sphinx-autodoc-typehints from 1.22 to 1.23.0 by @dependabot in #1409
• Bump sphinx-copybutton from 0.5.1 to 0.5.2 by @dependabot in #1410
• Bump pytest from 7.3.0 to 7.3.1 by @dependabot in #1411
• Bump pyright from 1.1.302 to 1.1.303 by @dependabot in #1412
• Use pandas 2.0.0 and date_format argument of pandas.read_csv() by @lisphilar in #1414
• add DataEngineer().subset(get_dummies=True) as default by @lisphilar in #1416
• update version of cancel-workflow-action from 0.10.0 to 0.11.0 to fix warning in workflow by @lisphilar in #1418
• fix "ValueError: cannot insert City, already exists" when running notebook 01_data_preparation.ipynb by @lisphilar in #1420
• update DataDownloader to include 4th and 5th vaccination data for Japan by @lisphilar in #1421
• Bump pyright from 1.1.303 to 1.1.304 by @dependabot in #1422
• Bump pca from 1.9.2 to 2.0.0 by @dependabot in #1423
• Bump numpy from 1.24.2 to 1.24.3 by @dependabot in #1424
• Bump pandas from 2.0.0 to 2.0.1 by @dependabot in #1425
• Bump requests from 2.28.2 to 2.29.0 by @dependabot in #1426
• Bump pyright from 1.1.304 to 1.1.305 by @dependabot in #1427
• Bump pca from 2.0.0 to 2.0.1 by @dependabot in #1428
• Bump pyarrow from 11.0.0 to 12.0.0 by @dependabot in #1429
• Bump pyright from 1.1.305 to 1.1.306 by @dependabot in #1430
• Bump requests from 2.29.0 to 2.30.0 by @dependabot in #1431
• Bump geopandas from 0.12.2 to 0.13.0 by @dependabot in #1433
• Bump ipykernel from 6.22.0 to 6.23.0 by @dependabot in #1432
• Bump deptry from 0.8.0 to 0.10.0 by @dependabot in #1434
• Bump deptry from 0.10.0 to 0.10.1 by @dependabot in #1436
• Update deptry version to 0.11.0 and replace ignore_obsolute with ignore_unused by @lisphilar in #1440
• Bump sympy from 1.11.1 to 1.12 by @dependabot in #1441

New Contributors

• @deepgohil made their first contribution in #1357
• @mehrdadbn9 made their first contribution in #1364
• @Mihan786Chistie made their first contribution in #1369

Full Changelog: 2.28.0...3.0.0