Fixed mypy sp check guidelines #4887

Rishab87 · 2025-03-02T07:54:12Z

Description

Fixing mypy sp check guidelines

Some major changes I did:

In src/pybamm/expression_tree/binary_operators.py I've replaced self.__ class __ in line 131 with new_instance because earlier when we were using self.__ class __ it showed a third arg was not getting passed:
```
error: Missing positional argument "right_child" in call to "BinaryOperator"  [call-arg]
```
but this function was always getting called from instance of its child classes which don't need to pass 3 arguments, so i
thought it was better to make a new_instance method which can be overrided in child classes
In src/pybamm/expression_tree/broadcasts.py I've forced child classes of Broadcast to implement _unary_new_copy because earlier we were using self.broadcast_domain in this function in Broadcast class but it does not have any attribute self.broadcast_domain, this function was only getting called by instance of their child classes which has self.broadcast_domain property.
In tests/unit/test_expression_tree/test_operations/test_copy.py in test_symbol_create_copy_new_children test I've added an extra argument perform_simplifications=False to create_copy method to ensure 100% coverage of new_instance methods.

Related to #3489

Type of change

Please add a line in the relevant section of CHANGELOG.md to document the change (include PR #)

Important checks:

Please confirm the following before marking the PR as ready for review:

No style issues: nox -s pre-commit
All tests pass: nox -s tests
The documentation builds: nox -s doctests
Code is commented for hard-to-understand areas
Tests added that prove fix is effective or that feature works

Rishab87 · 2025-03-02T07:55:08Z

Still 25 mypy errors are left, drafting this so that its easier to communicate changes

agriyakhetarpal

Thanks, I've triggered the workflows! I haven't reviewed all the files, because I understand that the PR is still a draft and you have yet to complete the changes.

Checking https://learn.scientific-python.org/development/guides/repo-review/?repo=pybamm-team/pybamm, a few more rules where we have problems have popped up. So we shouldn't mark this PR as one that closes the linked issue. Could you please replace the "Fixes" keyword in the PR description with "Related to"?

It is also possible to add sp-repo-review as a pre-commit hook so that new rules will be checked on every commit. I think we should investigate that and add it if running the checks is not too slow. I'm also curious to hear what @Saransh-cpp has to say about this.

docs/conf.py

codecov · 2025-03-02T12:35:27Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.70%. Comparing base (8f91615) to head (e1b1aec).
Report is 1 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4887      +/-   ##
===========================================
- Coverage    98.71%   98.70%   -0.01%     
===========================================
  Files          304      304              
  Lines        23509    23542      +33     
===========================================
+ Hits         23207    23238      +31     
- Misses         302      304       +2

☔ View full report in Codecov by Sentry.
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Saransh-cpp · 2025-03-02T13:17:14Z

It would be great to have repo-review as a pre-commit hook! @agriyakhetarpal maybe you can create a new independent issue for that?

Rishab87 · 2025-03-03T04:38:11Z

I've changed the PR description to related to and I also think it would be great to have a pre-commit hook for sp-check-guidelines, I'll investigate its speed after this PR is done

Rishab87 · 2025-03-03T08:44:54Z

I've fixed the remaining errors too

Saransh-cpp

Thanks for taking this up, @Rishab87! See my comment below about splitting this PR.

CHANGELOG.md

Saransh-cpp · 2025-03-03T13:53:41Z

pyproject.toml

@@ -252,6 +252,10 @@ concurrency = ["multiprocessing"]
 ignore_missing_imports = true
 allow_redefinition = true
 disable_error_code = ["call-overload", "operator"]
+strict = false


Given how big this PR is, it would actually be better to split it into multiple PRs, each one adding a new config option in pyproject.toml.

ok so should I go ahead then and make a PR on one of the config first? or edit this one accordingly?

You can keep this PR for one config, and add other configs in subsequent PRs.

ok I'll create seperate PRs for different configs and then keep this one for the end, I think that would be faster for me

I noticed many of the warn_unreachable error depends on errors from enable_error_code config, they're related to each other and their are total of 77 errors out of which 57 are from enable_error_code so I think creating a seperate PR would still be almost as big as this one, so should I still proceed with it?

Yes, I think anything that reduces the diff and keeps this PR scoped to a specific change (or a few of them) would be great. Thanks for investigating!

I've created the PR with just enable_error_code config: #4891, sorry for the delay lab tests going on

Co-authored-by: Saransh Chopra <[email protected]>

into sp-check-guidelines

kratman · 2025-03-03T20:44:40Z

examples/scripts/SPM_compare_particle_grid.py

@@ -48,7 +49,7 @@
    disc.process_model(model)

 # solve model
-solutions = [None] * len(models)
+solutions: Any = [None] * len(models)


Shouldn't this be something like list[Any]?

yess, I'll change that

agriyakhetarpal

Thanks, @Rishab87! It is not fully clear from some of the changes as to why they were made, could you please highlight them and tell us what was fixed where? Some changes also seem to change the logic in a few places; documenting it is important.

agriyakhetarpal · 2025-03-07T21:36:48Z

examples/scripts/heat_equation.py

@@ -106,7 +106,7 @@ def T_exact(x, t):
 # Plot ------------------------------------------------------------------------
 x_nodes = mesh["rod"].nodes  # numerical gridpoints
 xx = np.linspace(0, 2, 101)  # fine mesh to plot exact solution
-plot_times = np.linspace(0, 1, 5)
+plot_times: np.ndarray = np.linspace(0, 1, 5)


This should be npt.NDArray (see #4899).

changed this

agriyakhetarpal · 2025-03-07T21:38:46Z

src/pybamm/expression_tree/binary_operators.py

+    # Check right is pybamm Symbol
+    if not isinstance(right, pybamm.Symbol):


Could you please explain why this check was modified?

I was getting

error: Left operand of "and" is always true [redundant-expr]

but I think now this should not be modified, this seems weird that its not showing this for right symbol as its also going through the same checks above

agriyakhetarpal · 2025-03-07T21:39:38Z

src/pybamm/expression_tree/binary_operators.py

+    def _new_instance(self, left: pybamm.Symbol, right: pybamm.Symbol) -> pybamm.Symbol:
+        return Power(left, right)
+


Why do we need new _new_instance methods? Could you document this in an inline comment somewhere, or add it in the PR description (better)?

I've added new_instance because earlier when we were using __ class __ it showed a third arg was not getting passed:

error: Missing positional argument "right_child" in call to "BinaryOperator" [call-arg]

but this function was always getting called from child classes of BinaryOperator which don't need to pass 3 arguments, so i thought it was better to make a new_instance method which can be overirded in child classes

so should I update the PR description or think of some other approach?

And for broadcasts.py self.broadcast_domain was not defined in parent class they were params of child classes and _unary_new_copy function was getting called from child class instance always so I just overrided this function in child classes, apart from these changes all other changes are mostly type changes

…sp-check-guidelines

Rishab87 · 2025-03-09T05:27:37Z

@agriyakhetarpal Thanks for the review, I've left comments for the major changes, should I write these major changes in PR description too?

agriyakhetarpal · 2025-03-10T06:30:16Z

@agriyakhetarpal Thanks for the review, I've left comments for the major changes, should I write these major changes in PR description too?

Yes, please do!

Rishab87 · 2025-03-10T09:50:42Z

@agriyakhetarpal I've updated the PR description, can you please review it?

Rishab87 added 2 commits March 1, 2025 19:35

changes in pyproject.toml

ad17bc6

fixed around 40 mypy errors

ba437d6

agriyakhetarpal reviewed Mar 2, 2025

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docs/conf.py Outdated Show resolved Hide resolved

agriyakhetarpal mentioned this pull request Mar 2, 2025

Examine usage of repo-review tools as pre-commit hooks #4888

Closed

fixed remaining issues

77863b8

Rishab87 marked this pull request as ready for review March 3, 2025 08:37

Rishab87 requested a review from a team as a code owner March 3, 2025 08:37

fixed issue in py 3.9 and modified tests

5413828

Saransh-cpp requested changes Mar 3, 2025

View reviewed changes

Rishab87 and others added 3 commits March 3, 2025 19:33

Update CHANGELOG.md

f7beff0

Co-authored-by: Saransh Chopra <[email protected]>

minor changes

fba51e2

Merge branch 'sp-check-guidelines' of https://github.com/Rishab87/PyBaMM

fef8148

into sp-check-guidelines

kratman reviewed Mar 3, 2025

View reviewed changes

Rishab87 mentioned this pull request Mar 4, 2025

Added mypy enable_error_code sp check guideline #4891

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agriyakhetarpal reviewed Mar 7, 2025

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Rishab87 added 2 commits March 9, 2025 09:59

Merge branch 'develop' of https://github.com/pybamm-team/PyBaMM into …

f5f6d50

…sp-check-guidelines

minor changes

e1b1aec

		# Check right is pybamm Symbol
		if not isinstance(right, pybamm.Symbol):

		def _new_instance(self, left: pybamm.Symbol, right: pybamm.Symbol) -> pybamm.Symbol:
		return Power(left, right)

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Fixed mypy sp check guidelines #4887

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Description

Some major changes I did:

Type of change

Important checks:

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