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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

❌ Patch coverage is 0% with 74 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.20%. Comparing base (c55a522) to head (f34453c).

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 ⚠️
❗ Your organization needs to install the Codecov GitHub app to enable full functionality.
Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #1561      +/-   ##
===========================================
- Coverage    84.85%   83.20%   -1.66%     
===========================================
  Files          163      166       +3     
  Lines        14029    14103      +74     
===========================================
- Hits         11905    11734     -171     
- Misses        2124     2369     +245     

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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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4 participants