Covid19 Sir Versions Save

CovsirPhy: Python library for COVID-19 analysis with phase-dependent SIR-derived ODE models.

3.1.1

3 months ago

Fixed citation.

Related issue: [Docs] update the last year in citation, 2020-2023 to 2020-2024 #1598 Milestone: https://github.com/lisphilar/covid19-sir/milestone/54?closed=1

What's Changed

Full Changelog: https://github.com/lisphilar/covid19-sir/compare/3.1.0...3.1.1

3.1.0

3 months ago

Covsirphy dropped Python version 3.8 and added Python 3.12 support. Covsirphy version 3.1.0 support 3.9, 3.10, 3.11 and 3.12.

Milestone: https://github.com/lisphilar/covid19-sir/milestone/53?closed=1

  • [New] Drop Python 3.8 support #1591
  • [New] Add Python 3.12 support #1592
  • [Bug] UserWarning when plotting: The figure layout has changed to tight #1484
  • [Bug] FutureWarning with the behavior of DataFrame concatenation with empty or all-NA entries #1511
  • [Bug] FutureWarning: The default of observed=False is deprecated #1514
  • [Bug] FutureWarning: Series.getitem treating keys as positions is deprecated #1513
  • [Bug] FutureWarning: Setting an item of incompatible dtype is deprecated #1515
  • [Bug] FutureWarning: Series.getitem treating keys as positions is deprecated #1595
  • [Bug] FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '<FloatingArray> #1594
  • [Bug] DeprecationWarning: DataFrameGroupBy.apply operated on the grouping columns #1596
  • [Bug] tests failed with covsirphy.util.error.NotIncludedError: 'Population' was not included in the 'column list of raw data'. The dataframe has ISO3, Province, City, Date as columns. #1597
  • [Docs] fix URL expiration regarding pepy.tech #1504
  • [Docs] show data flow diagram of CovsirPhy on README #1507

What's Changed

Full Changelog: https://github.com/lisphilar/covid19-sir/compare/3.0.0...3.1.0

3.0.0

1 year ago

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

What's Changed

New Contributors

Full Changelog: https://github.com/lisphilar/covid19-sir/compare/2.28.0...3.0.0

2.28.0

1 year ago

Updates

  • [New] use logger #1242
  • [New] serialize ODEScenario object #1239
  • [Dev] use YAML issue templates #1232
  • [Dev] use deptry version 0.5.12 #1249
  • [Docs] update URL of installation guide in seculity policy #1251

Acknowledgement

Special thanks for users and developers!

Related issues and pull requests: https://github.com/lisphilar/covid19-sir/milestone/51?closed=1

What's Changed

Full Changelog: https://github.com/lisphilar/covid19-sir/compare/2.27.1...2.28.0

2.27.1

1 year ago

Data engineering

  • [Fix] DataDownloader().layer(databases=["google"]) updates mobility data although no longer updated #1223
  • [Fix] DataEngineer().subset(country=None) calculates total values without filling NAs #1222
  • [Fix] LinePlot().plot(), BarPlot().plot() raise incorrect error when un-expected colormap was specified #1228
  • [Fix] DataEngineer().diff() raises ValueError with pandas version 1.5.0 #1225

To handle warnings

  • [Fix] warning raised when tests #1227

Documentation

  • [Docs] documetation raises ValueError #1238
  • [Docs] fix broken URL for installation guide on README.md #1237
  • [Docs] update documentation for Monkeypox data downloading to use the lates file #1236

Acknowledgement

Special thanks for users and developers!

Related issues and pull requests: https://github.com/lisphilar/covid19-sir/milestone/50?closed=1

What's Changed

Full Changelog: https://github.com/lisphilar/covid19-sir/compare/2.27.0...2.27.1

2.27.0

1 year ago

Installation

  • [New] Drop Python 3.7 support #1146
  • [New] install all dependency automatically (especially with Python 3.10) by using pyarrow as the engine of reading CSV files #1159

Data engineering

  • [New] dataset regarding population #1180
  • [New] apply date range with DataEngineer().clean(kinds=["resample"], date_range=<tuple>) #1217
  • [Fix] UnicodeEncodeError when automated downloading #1160
  • [Deprecate] JapanData class #1179

Documentation

  • [Docs] how to analyze Monkeypox 2022 linelist data with SIR-derived models #1131
  • [Docs] add configuration file of Binder to open notebooks #1201
  • [Docs] remove input.py #1198
  • [Docs] fix terms in glossary list: trend analysis -> change point analysis #1216
  • [Docs] improve readability of API reference by updating titles and ignore internal classes #1208

For developers

  • [Revise] deptry 0.4.6 is available #1195
  • [Revise] use deptry version 0.5.0 #1207
  • [Revise] multiprocessing in tests #1203

Acknowledgement

Special thanks for users and developers!

Related issues and pull requests: https://github.com/lisphilar/covid19-sir/milestone/48?closed=1

What's Changed

Full Changelog: https://github.com/lisphilar/covid19-sir/compare/2.26.2...2.27.0

2.26.2

1 year ago

Data engineering

  • [Revise] change the default directory to save Natural Earth data #1190

Scenario analysis

  • [Fix] incorrect title of ODEScenario().compare_cases() #1192

ODE parameter prediction

  • [Fix] UnExpectedValueRangeError when phase appending after prediction #1188

For developers

  • [Fix] Running the unit tests clutters the project directory #1173
  • [Revise] Deptry 0.2.5 uses modified configuration #1174
  • [Revise] deptry 0.2.9 is available #1181
  • [Revise] confirm poetry envirenment activated before test #1177
  • [Revise] GitHub pages deployment with GitHub Actions #1184
  • [Revise] tests only with GitHub workflow #1185

Acknowledgement

Special thanks for users and developers!

Related issues and pull requests: https://github.com/lisphilar/covid19-sir/milestone/47

What's Changed

Full Changelog: https://github.com/lisphilar/covid19-sir/compare/2.26.1...2.26.2

2.26.1

1 year ago

Config

  • [Revise] re-organize pyproject.toml using dependency group #1144
  • [Revise] pyproject.toml contains obsolete dependencies #1161
  • [Revise] citation of CovsirPhy is confusing because we have two #1164

Scenario analysis

  • [Fix] UnExpectedValueError after appending a phase with under three days #1166

Acknowledgement

Special thanks for users and developers!

Related issues and pull requests: https://github.com/lisphilar/covid19-sir/milestone/46?closed=1

2.26.0

1 year ago

Config

  • [New] New support of Python 3.10 #1147

Data engineering

  • [Fix] Vaccinated_1st, _2nd and _3rd are included in the output of DataDownloader().layer() #1137

Dynamics

  • [New] progress bar with Dynamics().estimate_param() #1129
  • [Revise] use Optuna version 3.0.0+ #1143

ODE parameter prediction

  • [New] MLEngineer().pca() perform Principal Component Analysis (PCA) #1136
  • [New] Prediction of ODE parameters with indicators #477

Documentation

  • [Docs] update image in README with the latest version #1130
  • [Docs] not rendered bullet list from markdown and notebook #1132
  • [Docs] show favicon in documentation #1150

Acknowledgement

Special thanks for users and developers!

Related issues and pull requests: https://github.com/lisphilar/covid19-sir/milestone/45?closed=1

2.25.0

1 year ago

Breaking changes

  • [New] accept city-level data in analysis #1041
  • [New] change of data loading scheme: download datasets of selected location #1045
  • [New] DataEngineer class for data cleaning, transforming and complementing #1064

Most of classes were deprecated and new classes were created. Please refer to Documentation for tutorials of the new classes.

Others and documentation

  • [Fix] address format of county and province: province/country, not country/province #1059
  • [Fix] too much time to retrieve dataset from COVID-19 Data Hub #986
  • [Revise] stdout when downloading datasets from CovsirPhy/data project #1051
  • [Data] failed in ODE parameter estimation with Japan data: IndexError #1087
  • [Question/Docs] how to access S-R trend analysis statistical details #894

Acknowledgement

Special thanks for users and developers!

Related issues and pull requests: https://github.com/lisphilar/covid19-sir/milestone/44?closed=1