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Sanitise input data#200

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alexdewar merged 48 commits intomainimperialCHEPI/healthgps:mainfrom sanitise_input_dataimperialCHEPI/healthgps:sanitise_input_dataCopy head branch name to clipboardAug 21, 2023

+1,609-626

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Commits on Aug 7, 2023

• Remove create_output_folder() function

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Commits on Aug 8, 2023

• Use std::filesystem::path cf. std::string in a few places

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• Drop support for v1 config files

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• load_configuration(): Remove some indentation

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• Make separate function for rebasing paths

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• Put new functions for loading JSON into configuration.cpp

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• Add ConfigurationError class and use in a few places

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• Remove unused field

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• Clean up and add extra error checking to config file loading

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Commits on Aug 9, 2023

• Remove superfluous helper functions

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• Fix: Seemingly MSVC isn't happy about casting filesystem::paths to strings

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• Move some functions out of configuration.cpp to program.cpp

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• Put functionality related to command-line args in own cpp file

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• Move some parsing functions into configuration_parsing.cpp

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• Put configuration parsing helper function defs into own header

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Commits on Aug 11, 2023

• Rename some functions and mark noexcept

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• Remove unused API version functionality

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• Move version.h.in to src/HealthGPS

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• Build most console functionality as lib for testability

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• Spelling

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• Add JSON (de)serialisation code for Interval<> class

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• Make SettingsInfo.age_range an IntegerInterval

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• Base OptionalRange on Interval class and rename

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• Add tests for some config code

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• Merge remote-tracking branch 'origin/main' into sanitise_input_data

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Commits on Aug 15, 2023

• Fix typo

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• Allow for parsing JSON objects to any map type with Identifier as key

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• Use default comparators cf. custom operator==

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• Add test for load_interventions

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• Make active intervention into an optional type

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• Add final tests for config code

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• MSVC resources file should live in HealthGPS.Console/

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• Remove unused var

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• Use different get_to overload in a couple of places

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• Explicitly convert to string to appease MSVC

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• Fix: Appease g++ v11 by not using structured bindings

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• Fix narrowing warning on MSVC

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Commits on Aug 16, 2023

• Fix: Interval class's members should be default-initialised

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• Fix/suppress bugprone-exception-escape clang-tidy warning

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• Fix: Use absolute cf. weakly canonical paths in rebase_valid_path()

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• Fix docstring warnings and rename a couple of args

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• Add docstrings to poco.h

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• Remove unused function definition

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• Add file-level documentation for several headers

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Commits on Aug 17, 2023

• range parameter doesn't need a default value

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Commits on Aug 18, 2023

• Revert "range parameter doesn't need a default value"

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Commits on Aug 21, 2023

• Remove special-casing for std::optional<Interval<T>>

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• Merge branch 'main' into sanitise_input_data

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