FlepiMoP stable for older configurations

This release is the final one supporting older configurations (before the breaking-improvements branch was merged, so configuration files designed in 2023 or before). Compared to the alpha release, a bug for seeding new infections is fixed.

flepiMoP v1.2

flepimop pre-file and config structure revision that happened Feb 2024. This version was used for COVID-19 forecasting for the 2023-24 season.

flepiMoP v1.0.0

Near production-level, stable version of flepiMoP. This versions has substantial back compatibility and uses the 2022-23 config format.
In the next generation, redundant, deprecated code and components will be removed, substantial generalization revisions will be made, and file structures will be modified.

What's Changed

• force local_install.R to install flepicommon package first (since it's a dependency of the others). by @shauntruelove in #17
• fix hard-coded path to flepiMoP by @shauntruelove in #16
• Fix some installation things by @jcblemai in #18
• renamed "deathrates" to "outcome_scenarios" and "scenarios" to "npi_scenarios" by @alsnhll in #25
• Coviddata fix by @shauntruelove in #21
• Fixing ground truth covid data: by @shauntruelove in #30
• Spatial groups of NPI with the same values by @jcblemai in #28
• Little fixes by @jcblemai in #31
• R17 dev by @shauntruelove in #42
• fix bug where the build folder was not sent by @jcblemai in #44
• Config phase3 by @shauntruelove in #45
• Better error handling in the script to clean old AWS S3 intermediate files by @jcblemai in #46
• Postprocess snapshot dev by @saraloo in #47
• fix typo in select_outputs variable by @saraloo in #48
• Init files by @shauntruelove in #58
• Main fixvarerr by @shauntruelove in #59
• Init files by @jcblemai in #54
• Seeding fix by @jcblemai in #56
• fix pull of covid deaths data by @shauntruelove in #60
• Config.writer update by @shauntruelove in #61

Full Changelog: https://github.com/HopkinsIDD/flepiMoP/commits/v1.0.0-alpha