feat: set sample config defaults

[uniqueg]

Fixes #53

Type of change

Please delete options that are not relevant.

• [ ] Bug fix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [ ] Documentation update

Checklist

Please carefully read these items and tick them off if the statements are true or do not apply.

• [ ] I have performed a self-review of my own code
• [ ] My code follows the existing coding style, lints and generates no new warnings
• [ ] I have added type annotations to all function/method signatures, and I have added type annotations for any local variables that are non-trivial, potentially ambiguous or might otherwise benefit from explicit typing.
• [ ] I have commented my code in hard-to-understand areas
• [ ] I have added Google-style docstrings to all new modules, classes, methods/functions or updated previously existing ones
• [ ] I have added tests that prove my fix is effective or that my feature works
• [ ] New and existing unit tests pass locally with my changes and I have not reduced the code coverage relative to the previous state
• [ ] I have updated any sections of the app's documentation that are affected by the proposed changes

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[codecov[bot]]

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (61f072d) 100.00% compared to head (3b961ab) 100.00%.

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #54 +/- ## ========================================= Coverage 100.00% 100.00% ========================================= Files 21 21 Lines 1026 1049 +23 ========================================= + Hits 1026 1049 +23 ``` | [Impacted Files](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/54?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab) | Coverage Δ | | |---|---|---| | [zarp/plugins/sample\_processors/defaults.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/54?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC9wbHVnaW5zL3NhbXBsZV9wcm9jZXNzb3JzL2RlZmF1bHRzLnB5) | `100.00% <100.00%> (ø)` | | | [zarp/samples/sample\_record\_processor.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/54?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC9zYW1wbGVzL3NhbXBsZV9yZWNvcmRfcHJvY2Vzc29yLnB5) | `100.00% <100.00%> (ø)` | | | [zarp/zarp.py](https://app.codecov.io/gh/zavolanlab/zarp-cli/pull/54?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-emFycC96YXJwLnB5) | `100.00% <100.00%> (ø)` | |

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[uniqueg]

Considering what you said yesterday regarding the time point at which defaults should be set and what I actually described in #53, this PR addresses/should address the following issue:

Set sample-specific defaults based on CLI arguments and the default config in ~/.zarp/user.yaml and apply them to all samples where that information is not yet available^†.

^† It is possible that the information is already available because users can also submit ZARP sample tables as sample references, full or partial, with individual rows/samples being complete or incomplete. And wherever metadata was supplied via a sample table, it should always trump any defaults, including those set via the CLI. Hence, we still wanna call .update() with overwrite set to False.

But what I had actually in mind when wiring the processor in the last position in zarp.zarp is something else:

To finalize the sample table for consumption in ZARP, where it (apparently, and unfortunately) cannot contain missing values (np.NaN), which instead have to be set to something like XXXXXXXXXXXXXXX (see example table in ZARP).

I'll create another issue for that. For this PR though, it means that the wiring in zarp.zarp should be changed such that the defaults block should be moved up, right after the initialization of the sample record processor.