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Add examples to pypesto module #1561

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Add examples to pypesto module #1561

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PaulJonasJost
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I added the option to use examples directly in the Pypesto module.

Some thoughts for open discussion:

  • Currently, we load them from GitHub, thus needing an internet connection. Another option would be to include the files, though this might add unnecessary files to the package
  • Some examples describe a pipeline; for those, I have not added the usage of examples.
  • @dilpath there is the "testing" module that only contains two hierarchical examples. According to my gitblame these were created by you. Would it be ok to move this to the examples module as its own examples?

The examples for now have a petab_problem, an objective and a problem along with a small description. Happy for feedback, whether I missed something.

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codecov-commenter commented Mar 13, 2025

⚠️ Please install the 'codecov app svg image' to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

Attention: Patch coverage is 0% with 74 lines in your changes missing coverage. Please review.

Project coverage is 84.09%. Comparing base (6ba9cd3) to head (a1d29c7).
Report is 2 commits behind head on develop.

Files with missing lines Patch % Lines
pypesto/examples/example_class.py 0.00% 66 Missing ⚠️
pypesto/examples/examples.py 0.00% 7 Missing ⚠️
pypesto/examples/__init__.py 0.00% 1 Missing ⚠️

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Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #1561      +/-   ##
===========================================
- Coverage    84.49%   84.09%   -0.41%     
===========================================
  Files          163      166       +3     
  Lines        14034    14108      +74     
===========================================
+ Hits         11858    11864       +6     
- Misses        2176     2244      +68     

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dilpath commented Mar 13, 2025

* Currently, we load them from GitHub, thus needing an internet connection. Another option would be to include the files, though this might add unnecessary files to the package

Another option (unless this is what you meant) is it conditionally add it to the pacakge, like pip install pypesto[examples]

* @dilpath there is the "testing" module that only contains two hierarchical examples. According to my gitblame these were created by you. Would it be ok to move this to the examples module as its own examples?

Fine for me 👍

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