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ICB-DCM / pyABC

distributed, likelihood-free inference
https://pyabc.rtfd.io
BSD 3-Clause "New" or "Revised" License
205 stars 44 forks source link

Minor bug fixes #639

Closed arrjon closed 3 weeks ago

arrjon commented 1 month ago

Some minor bug fixes. These should be corrected in the main version too.

arrjon commented 1 month ago

Something with the petab seems to be the problem, working on it

stephanmg commented 4 weeks ago

@arrjon not sure what's the issue, thanks for spending time to debug this.

codecov-commenter commented 4 weeks ago

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Codecov Report

Attention: Patch coverage is 75.00000% with 4 lines in your changes missing coverage. Please review.

Project coverage is 84.30%. Comparing base (a322de3) to head (b0a1347). Report is 37 commits behind head on main.

Files with missing lines Patch % Lines
pyabc/petab/__init__.py 60.00% 2 Missing :warning:
pyabc/transition/local_transition.py 50.00% 2 Missing :warning:

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #639 +/- ## ========================================== - Coverage 84.35% 84.30% -0.06% ========================================== Files 141 141 Lines 8535 8544 +9 ========================================== + Hits 7200 7203 +3 - Misses 1335 1341 +6 ```

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arrjon commented 3 weeks ago

I changed the oldest python version from python 3.9 to 3.10 and updated the GitHub continous integration workflow. This helped with most of the failing tests.

arrjon commented 3 weeks ago

Adding | string to env.doc2path() forces Jinja2 to interpret the result as a string, which avoids _StrPath type issues in templates. This should resolve the TypeError by ensuring all path-related operations in nbsphinx_prolog handle paths as strings.

arrjon commented 3 weeks ago

In the migration test, incompatible numpy and pandas versions caused an error. This is fixed now.

arrjon commented 3 weeks ago

@stephanmg you can review now: only some tests for older python versions are sill in the status "expected" and never leave it (I think because they were part of the old CI workflow, but have been removed).