[ux] Verify input to all AMD tools

[pharmpy-dev-123]

@rikardn Ready to MERGE

The goal is to improve the UX of the different tools when tool inputs are incorrect.

• Refactor input validation to allow reuse by run_amd or other
• Fix Verify input to all AMD tools #1032
  • Automate copying signature from create_workflow to validate_input
  • Automate type checking by deriving type checks from create_workflow's signature's annotations
  • Conditionally check input model on all tools
  • 100% coverage
• Related issues
  • Handle undefined workflow arguments in modelsearch (See point 1 in Error message during run_modelsearch #1163 (comment))
  • Handle undefined parameters in covsearch (Test with Covariate tool #1178 (comment))

[codecov-commenter]

Codecov Report

Base: 84.79% // Head: 85.27% // Increases project coverage by +0.48% 🎉

Coverage data is based on head (b4c82ae) compared to base (dc9d307).
Patch coverage: 79.43% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1162      +/-   ##
==========================================
+ Coverage   84.79%   85.27%   +0.48%     
==========================================
  Files         291      292       +1     
  Lines       26460    26841     +381     
  Branches     4513     4583      +70     
==========================================
+ Hits        22436    22890     +454     
+ Misses       3303     3218      -85     
- Partials      721      733      +12     

Flag	Coverage Δ
macos-latest	?
python-3.10	84.68% <79.43%> (+0.46%)	⬆️
python-3.8	85.22% <79.43%> (+0.51%)	⬆️
python-3.9	85.23% <79.43%> (+0.48%)	⬆️
ubuntu-latest	85.10% <79.43%> (+0.48%)	⬆️
unit	85.25% <79.43%> (+0.48%)	⬆️
windows-latest	84.99% <79.43%> (+0.49%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/pharmpy/plugins/nonmem/advan.py	86.02% <ø> (ø)
tests/modeling/test_modeling.py	100.00% <ø> (ø)
src/pharmpy/tools/amd/run.py	14.01% <13.88%> (+0.31%)	⬆️
src/pharmpy/tools/modelsearch/algorithms.py	81.46% <60.00%> (+0.48%)	⬆️
src/pharmpy/tools/run.py	61.48% <62.50%> (-1.02%)	⬇️
src/pharmpy/utils.py	65.94% <63.33%> (-5.14%)	⬇️
src/pharmpy/tools/iivsearch/tool.py	31.93% <94.11%> (+15.89%)	⬆️
src/pharmpy/tools/ruvsearch/tool.py	20.94% <95.65%> (+9.87%)	⬆️
src/pharmpy/modeling/allometry.py	95.45% <100.00%> (+0.45%)	⬆️
src/pharmpy/modeling/eta_additions.py	95.52% <100.00%> (+0.02%)	⬆️
... and 33 more

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[stellabelin]

Looks good! I'd maybe add types when raising type errors so that it is clear why that error is happening! Another question, in the Files changed it said modeling.init and tools.init are empty, were they removed or do you know why they're in the Files changed?

[pharmpy-dev-123]

Another question, in the Files changed it said modeling.init and tools.init are empty, were they removed or do you know why they're in the Files changed?

These new empty files are needed by pytest to differentiate between tests with identical basenames. See commit 01ee7cf