Plan to add `mypy`

Add a check for mypy in

toqito/.github/workflows/build-test-actions.yml

Line 26 in 200f3dc

- name: Run tests

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

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

scipy/scipy#19502 (comment)

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.

@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.

toqito/toqito/state_props/sk_vec_norm.py

Lines 60 to 64 in ffa9165

    
           if isinstance(dim, int): 
        
               dim = np.array([dim, dim_xy / dim])  # pylint: disable=redefined-variable-type 
        
               if np.abs(dim[1] - np.round(dim[1])) >= 2 * dim_xy * np.finfo(float).eps: 
        
                   raise ValueError("If `dim` is a scalar, it must evenly divide the length of the state.") 
        
               dim[1] = int(np.round(dim[1]))

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.

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

Great!

To close this issue:

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.
Create a separate issue to add mypy back to the workflows after items 3 and 4 are fixed.
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.
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.

Alternative to mypy

https://pyre-check.org/

https://github.com/google/pytype

https://github.com/microsoft/pyright

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

	if isinstance(dim, int):
	dim = np.array([dim, dim_xy / dim]) # pylint: disable=redefined-variable-type
	if np.abs(dim[1] - np.round(dim[1])) >= 2 * dim_xy * np.finfo(float).eps:
	raise ValueError("If `dim` is a scalar, it must evenly divide the length of the state.")
	dim[1] = int(np.round(dim[1]))