Add program logger

[alexdewar]

Description

For various reasons, it's better to use a proper logging library rather than having print statements dotted throughout the code.

I've added env_logger as a dependency (it seems to be a conservative choice) and used it in a few places in the code. The default output will look something like this:

[2024-07-02T15:21:11Z INFO  muse2::simulation] Loading settings from "examples/simple/settings.toml"

We can always configure it later if we want it to look different.

Closes #91.

Type of change

• [ ] Bug fix (non-breaking change to fix an issue)
• [x] New feature (non-breaking change to add functionality)
• [ ] Refactoring (non-breaking, non-functional change to improve maintainability)
• [ ] Optimization (non-breaking change to speed up the code)
• [ ] Breaking change (whatever its nature)
• [ ] Documentation (improve or add documentation)

Key checklist

• [x] All tests pass: $ cargo test
• [x] The documentation builds and looks OK: $ cargo doc

Further checks

• [x] Code is commented, particularly in hard-to-understand areas
• [ ] Tests added that prove fix is effective or that feature works

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 59.09091% with 27 lines in your changes missing coverage. Please review.

Project coverage is 65.62%. Comparing base (387fd3b) to head (f00b7d0). Report is 4 commits behind head on main.

Files	Patch %	Lines
src/settings.rs	72.22%	15 Missing :warning:
src/main.rs	0.00%	8 Missing :warning:
src/log.rs	0.00%	3 Missing :warning:
src/simulation.rs	0.00%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #99 +/- ## =========================================== - Coverage 80.26% 65.62% -14.64% =========================================== Files 5 6 +1 Lines 76 96 +20 =========================================== + Hits 61 63 +2 - Misses 15 33 +18 ```

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[alexdewar]

@dalonsoa I've had another go, addressing your comments.

Now users can either set the logging level via an environment variable (MUSE2_LOG_LEVEL) or the settings.toml file, with the environment variable taking precedence (I figure it's probably handy to have this for debugging). As we want to be able to use the program logger to log progress as we load the various input files, we need to initialise the logger after reading settings.toml (so we know if the user has configured the log level or not), but before loading any of the CSV files. One option would have been to initialise the logger in the read_settings() function, but that seemed like a poor separation of concerns. Instead, I refactored the code so that reading the TOML file and reading the other files are carried out in two steps; in between them, we can extract the log level and set it. I've refactored settings.rs using a more idiomatic Rust style. Now the struct with the raw input data from settings.toml is called SettingsReader. It provides a method for accessing the log level and for converting it into a Settings struct, which is the higher-level representation of the model settings. I also followed a suggestion you made somewhere else about reading the settings in main(), then passing them as an argument to simulation::run(), which I think is cleaner.

[alexdewar]

Yeah :disappointed:. Part of the issue is that mocking in Rust is really hard, but also I've just been a bit lazy :stuck_out_tongue:. Some of the bits that are untested were untested before though, it's just that codecov is flagging them again because of the refactoring.

Honestly I'm not sure what the best approach is for testing in Rust. For little functions, it's easy enough to write a unit test, but for higher-level functions that call these little functions, it's hard to think of a sensible test. I guess maybe we just write functional tests for these ones?

[dalonsoa]

Yeah, I think rust encourages write code in small chunks that are easy to test. Anything bigger than that, looks more like an integration test.