Run doctest and fix old examples

[ricardoV94]

Description

Spinoff from #858

Related Issue

• Closes #
• Related to #

Checklist

• Checked that the pre-commit linting/style checks pass
• Included tests that prove the fix is effective or that the new feature works
• Added necessary documentation (docstrings and/or example notebooks)
• If you are a pro: each commit corresponds to a relevant logical change

Type of change

• New feature / enhancement
• Bug fix
• Documentation
• Maintenance
• Other (please specify):

[ricardoV94]

Only available via pip

[ricardoV94]

Doctests are working on the remote CI!

I couldn't find a way to trigger doctest locally automatically by playing with pyproject.toml so I didn't bother changing it.

I tried several flavors of:

[tool.pytest]
addopts = [
    "--durations=50",
    "--doctest-modules pytensor --ignore=pytensor/misc/check_duplicate_key.py --ignore=pytensor/link",
]
testpaths = [
    "pytensor",  # for doctests
    "tests/",
]

And then tested by seeing if this would return anything: pytest --collect-only | grep DoctestModule

So I've been using the explicit command (same that is in the CI) to run locally, which works

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 81.13%. Comparing base (7a00b88) to head (1634a2f).
Report is 164 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #865      +/-   ##
==========================================
+ Coverage   80.99%   81.13%   +0.14%     
==========================================
  Files         169      169              
  Lines       46939    46961      +22     
  Branches    11467    11478      +11     
==========================================
+ Hits        38019    38103      +84     
+ Misses       6713     6642      -71     
- Partials     2207     2216       +9     

Files with missing lines	Coverage Δ
pytensor/gradient.py	77.37% <ø> (ø)
pytensor/graph/basic.py	88.61% <ø> (ø)
pytensor/misc/pkl_utils.py	79.48% <ø> (ø)
pytensor/scalar/basic.py	80.33% <ø> (ø)
pytensor/sparse/basic.py	82.53% <ø> (ø)
pytensor/tensor/basic.py	88.59% <ø> (+0.12%)	⬆️
pytensor/tensor/extra_ops.py	88.60% <ø> (ø)
pytensor/tensor/math.py	90.43% <ø> (ø)
pytensor/tensor/random/utils.py	100.00% <ø> (ø)
pytensor/tensor/rewriting/math.py	89.42% <ø> (ø)
... and 4 more

... and 7 files with indirect coverage changes

[ricardoV94]

Ready for review

[OriolAbril]

I checked the pytest-sphinx readme and initially I wasn't able to see any extra feature with respect to pytest. It does seem that with either of them using a specific path for test files and --doctest-modules at the same time does not work.

I have tried locally to run

pytest --doctest-modules --ignore=pytensor/misc/check_duplicate_key.py pytensor --ignore=pytensor/link  --benchmark-skip

and got 30 tests to run. The found 31 because pytensor/sparse/basic.py::pytensor.sparse.basic.block_diag uses the testcode directive, which means pytest-sphinx is needed to parse that as a test. Everywhere else direct doctest syntax is used so pytest alone recognizes the other 30 tests without pytest-sphinx.

It might be better to modify the test in sparse/basic to use doctest syntax and not add the extra dependency

[ricardoV94]

In #858 I used pytest-sphinx as well, I like it more than the doctest approach? Is there a strong preference for not adding it as an extra-dependency on your side @OriolAbril?

[OriolAbril]

No, just trying to keep things simple given doctest directive is nearly equivalent to testcode+testoutput, the only difference being block vs line execution, but if using directives to separate test code and output helps then use the extension