Plan to add `mypy`

[purva-thakre]

Add a check for mypy in https://github.com/vprusso/toqito/blob/200f3dc7a2178174d4ad6846f84686bc89c4c0ce/.github/workflows/build-test-actions.yml#L26

Right now, ~/toqito$ mypy . fails due to following:

build/lib/tests/test_matrices/test_gell_mann.py:4: error: Skipping analyzing "scipy.sparse": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/tests/test_matrices/test_gell_mann.py:4: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
build/lib/tests/test_matrices/test_pauli.py:4: error: Skipping analyzing "scipy.sparse": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/channels/reduction.py:4: error: Skipping analyzing "scipy.sparse": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/matrices/gell_mann.py:5: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/matrices/gen_gell_mann.py:6: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/matrices/iden.py:4: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/matrices/pauli.py:6: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/matrix_props/sk_norm.py:8: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/perms/antisymmetric_projection.py:6: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/perms/perm_sign.py:6: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/perms/permute_systems.py:9: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/perms/symmetric_projection.py:5: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/state_metrics/fidelity.py:4: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/state_metrics/matsumoto_fidelity.py:4: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/state_props/entanglement_of_formation.py:5: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/states/ghz.py:4: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/states/max_entangled.py:4: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/states/max_mixed.py:4: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
build/lib/toqito/states/w_state.py:4: error: Skipping analyzing "scipy": module is installed, but missing library stubs or py.typed marker  [import-untyped]
toqito/channel_metrics/fidelity_of_separability.py: error: Source file found twice under different module names: "channel_metrics.fidelity_of_separability" and "toqito.channel_metrics.fidelity_of_separability"

Found 20 errors in 20 files (errors prevented further checking)

scipy is not in typeshed as suggested by mypy's docs.

https://mypy.readthedocs.io/en/stable/config_file.html#config-file https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-library-stubs-or-py-typed-marker https://mypy.readthedocs.io/en/stable/stubs.html#stub-files https://mypy.readthedocs.io/en/stable/error_code_list.html#error-codes-enabled-by-default https://stackoverflow.com/a/64122820 https://stackoverflow.com/a/73390971 https://mypy.readthedocs.io/en/stable/config_file.html#using-a-pyproject-toml-file

[purva-thakre]

It might be better to ignore scipy related warnings/errors raised by mypy.

https://github.com/scipy/scipy/issues/19502#issuecomment-1806386197

[purva-thakre]

The same issue in scipy also applies to toqito. So, we will have to

• option 1: ignore all modules in toqito.same_module or
• option 2: generate stubs for each and every module in toqito.

https://mypy.readthedocs.io/en/stable/stubs.html#stub-files

How scipy ignores all issues related to [import-untyped] modules in their package: https://github.com/scipy/scipy/blob/fcf7b652bc27e47d215557bda61c84d19adc3aae/mypy.ini

To work on either of the above options, need to first fix toqito/channel_metrics/fidelity_of_separability.py: error: Source file found twice under different module names: "channel_metrics.fidelity_of_separability" and "toqito.channel_metrics.fidelity_of_separability". The same error is applied to all toqito.some_module. Might be related to how mypy finds the import path.

https://mypy.readthedocs.io/en/stable/running_mypy.html#how-imports-are-found

Edit: Ignoring all module is installed, but missing library stubs or py.typed marker, issues that need to be fixed are in the attached file mypy_errors.txt. It might be better to create a PR per module or per function.

[purva-thakre]

@vprusso FYI I am un-assigning myself from this issue.

I believe trying to fix some of the errors in the txt file might require a major refactor considering quite a few functions allow multiple types of inputs and same variable is re-assigned a different value/type based on these inputs.

For example, the following lines are flagged by mypy due to the redefinition. We disabled pylint warnings for the same.

https://github.com/vprusso/toqito/blob/ffa9165ed5f851c9a286f1d5821ac220e3850991/toqito/state_props/sk_vec_norm.py#L60-L64

state_props/sk_vec_norm.py:61: error: Incompatible types in assignment (expression has type "ndarray[Any, dtype[Any]]", variable has type "int | list[int]")  [assignment]
state_props/sk_vec_norm.py:62: error: Value of type "int" is not indexable  [index]
state_props/sk_vec_norm.py:64: error: Unsupported target for indexed assignment ("int")  [index]
state_props/sk_vec_norm.py:64: error: Value of type "int" is not indexable  [index]

What if we defined one private method per allowed option for an input? Then we could call these in the main function sk_vector_norm.

[vprusso]

Sounds good, that's completely reasonable. Thanks for the heads up, @purva-thakre !

[purva-thakre]

Great!

To close this issue:

1. Add mypy to github workflows: Fix Source file found twice under different module names, ignore toqito's stub issues similar to scipy, comment out mypy lines in the workflow after fixing the quickly fixable errors.
2. Create a separate issue to add mypy back to the workflows after items 3 and 4 are fixed.
3. Create a separate issue for an itemized list of which functions require a refactor to fix mypy errors. Fix each item with a new PR.
4. Create a separate issue to generate stub files for all modules in toqito. Remove the file where mypy was ignoring import errors related to toqito's modules.

[purva-thakre]

Alternative to mypy

https://pyre-check.org/

https://github.com/google/pytype

https://github.com/microsoft/pyright

[purva-thakre]

Figured out a nice workaround to understanding what type mypy expects.

In some .py file, add from typing import reveal_type as an import. Then use reveal_type to print the type of the output. This makes sure we are using types consistent with what's expected by mypy.

Note: We will have to use --explicit-package-bases when running mypy in some directory because it gets confused with two modules having similarly named files.

https://mypy.readthedocs.io/en/stable/command_line.html#import-discovery