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Various fixes #604

Merged
merged 14 commits into from
May 9, 2023
Merged

Various fixes #604

merged 14 commits into from
May 9, 2023

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yannikschaelte
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@yannikschaelte yannikschaelte commented May 8, 2023

  • Update to Python 3.11, discard Python 3.8
  • Configure readthedocs build environment
  • Refactor API docs (add [+]; easier navigation)
  • Correct scipy intersphinx link
  • Turn simple files into submodules for cleaner import
  • Flake8 fixes of dict creation from key+value
  • Fix imports from correct submodule
  • Add docstrings to submodules
  • Fix dask sampler (change default pickling and use global function that it can pickle)
  • Fix column renaming in visserver
  • Fix package versions in migration test

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codecov-commenter commented May 8, 2023

Codecov Report

Merging #604 (ef02bbb) into develop (f51826b) will decrease coverage by 0.19%.
The diff coverage is 97.14%.

📣 This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more

@@             Coverage Diff             @@
##           develop     #604      +/-   ##
===========================================
- Coverage    86.92%   86.73%   -0.19%     
===========================================
  Files          130      139       +9     
  Lines         7931     7941      +10     
===========================================
- Hits          6894     6888       -6     
- Misses        1037     1053      +16     
Impacted Files Coverage Δ
pyabc/__init__.py 100.00% <ø> (ø)
pyabc/distance/pnorm.py 85.97% <ø> (ø)
pyabc/external/__init__.py 100.00% <ø> (ø)
pyabc/external/julia/__init__.py 100.00% <ø> (ø)
pyabc/external/r/__init__.py 100.00% <ø> (ø)
pyabc/parameters/parameters.py 84.21% <ø> (ø)
pyabc/petab/amici.py 81.48% <0.00%> (ø)
pyabc/random_choice/random_choice.py 100.00% <ø> (ø)
pyabc/sampler/__init__.py 100.00% <ø> (ø)
pyabc/sampler/dask_sampler.py 83.33% <ø> (-16.67%) ⬇️
... and 30 more

... and 1 file with indirect coverage changes

@yannikschaelte yannikschaelte merged commit abf43aa into develop May 9, 2023
11 checks passed
@yannikschaelte yannikschaelte deleted the fixes_ys branch May 9, 2023 10:07
yannikschaelte added a commit that referenced this pull request May 9, 2023
* Contour plots as a direct alternative to kernel density heat maps (#597)

* add contour plot

* add test

* fix C416 unnecessary dict comprehension

* Various fixes (#604)

* fix C416 unnecessary dict comprehension

* bump rtd python version

* update migration test

* fix .rtd file

* ensure jquery installed for [+] in docs

* ignore warnings

* refactor api docs

* fix typo

* update to py3.11

* fox

* extend migration time

* fix dask by global function; fix sqlalchemy update

* update migrate test with fixed versions

* fix visserver weird wrong rename

* update changelog
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2 participants