What’s new?
Coming soon
The comma project started in March 2023 and ended on February 2024. It was developed by a team of research software engineers led by Eva Viviani at the Netherlands eScience center with a grant awarded to Dr Kristina Thompson (Wageningen university).
Further info about this project can be found in the relative `RSD: https://research-software-directory.org/projects/covid-19-mitigation-policies`_
Changelog
All notable changes to the codebase are documented in this file.
1.1.3
Released on February 19, 2024
Main changes
In PR #78 by @n400peanuts:
New features in agents, new lockdown files. The rest of the code has been refactored for clarity and maintainance purposes. Tutorials have been edited to extensively show two different examples: hard vs easy lockdown.
1.1.2
Released on December 6, 2023
Main changes
Features
In PR #76 by @n400peanuts:
Integration of the long covid type of situation in the individual class
Addition of the get_covid_status among the methods in the individual class
is_recovered() method now has been adjusted to integrate long-covid type of recovery
Change of the data repository to the RIVM website (cumulative positive tests) in the hypothesis class
Issue about having an additional method to work out positive cases for days that are not in data – solved, this is integrated into the RIVM data already
Hypothesis class does not require anymore the following methods: get_file_paths() and filter_dates
Hypothesis class now has adjusted methods for get_covid_data() and get_positive_cases() to account for the RIVM cumulative tests data
Model class now accounts for municipality_code rather than ‘location’
Tests
In PR #76 by @n400peanuts:
Added test for long covid with test_long_covid
Added test for testing positivity to COVID with test_positivity
tests test_filter_dates_on_boundary, test_filter_dates_within_range and file_list have all been removed, as the new data collection from RIVM does not require anymore the functions filter_dates
tests test_range_error and test_get_covid_data have been changed to include the new RIVM website and type of data
tests test_scaling and test_location_not_in_dataset changed to include the new RIVM website and type of data
1.1.1
Released on November 21, 2023
Main changes
Refactor
refactor: hypothesis class focuses now on data validation and preparation for the model PR #75 by @n400peanuts
refactor: model class now requires only initialisation and run, no more setup() PR #75 by @n400peanuts
refactor: individual class better interacts with the model and hypothesis class PR #75 by @n400peanuts
1.1.0
Released on October 18, 2023
Main changes
Features
Comma now integrates positivity to COVID-19 in the model Commit [2ff9a2c] in PR #73 by @n400peanuts
New documentation about the implementation of the positivity to COVID-19 PR #48 by @n400peanuts
Models can be set with a specific seed to ensure reproducibility Commit [3a9419] in PR #73 by @n400peanuts
Code formatted with Black
Tests
Added tests for Hypothesis class Commit [5636c9] in PR #73 by @n400peanuts
Added test for Individual “test_actions_when_positive” Commit [] in PR #73 by @n400peanuts
Refactored test for Model module to have higher tolerance and test all data types in dataframe Commit [8e007] in PR #73 by @n400peanuts
1.0.0
Released on August 29, 2023
Main changes
Refactor
refactor: generate agents with the IPF sampling and refactor individual class in PR #60 by @n400peanuts
refactor: generate agents by sampling from the param_individual.json in PR #22 by @jiqicn
refactor: create model class in PR #18 by @n400peanuts
refactor: create individual class in PR #17 by @jiqicn
refactor: add new actions effects on mental health matrices in PR #72 by @Astrid-p
Features
feat: add tutorial notebook in PR #43 by @n400peanuts