python311Packages.scikit-survival: 0.21.0 -> 0.22.1; fix build

[ghost]

Description of changes

update to 0.22.1 fixes broken build
https://github.com/sebp/scikit-survival/releases/tag/v0.22.1
https://github.com/sebp/scikit-survival/releases/tag/v0.22.0

https://hydra.nixos.org/build/239166746
ZHF: #265948

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
  • sandbox = relaxed
  • sandbox = true
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 23.11 Release Notes (or backporting 23.05 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md.

[ghost]

Result of nixpkgs-review run on x86_64-linux 1

4 packages built:

• python310Packages.scikit-survival
• python310Packages.scikit-survival.dist
• python311Packages.scikit-survival
• python311Packages.scikit-survival.dist

[natsukium]

Result of nixpkgs-review pr 266019 at a0370a3 run on aarch64-darwin 1

2 packages failed to build:

• python310Packages.scikit-survival
• python311Packages.scikit-survival

[wamserma]

Result of nixpkgs-review pr 266019 run on aarch64-linux 1

4 packages built:

• python310Packages.scikit-survival
• python310Packages.scikit-survival.dist
• python311Packages.scikit-survival
• python311Packages.scikit-survival.dist

[wamserma]

Result of nixpkgs-review pr 266019 run on aarch64-linux 1

Please adjust meta.broken.

[natsukium]

I don't think this is a significant error.
We just need to add this test to disabledTests as a flaky one.

>           return func(*args, **kwds)
E           AssertionError: 
E           Arrays are not almost equal to 5 decimals
E           alphas[22] [0].a mismatch
E           Mismatched elements: 1 / 1 (100%)
E           Max absolute difference: 2.79955566e-05
E           Max relative difference: 1.03381292e-12
E            x: array(27079905.88052)
E            y: array(27079905.8805)

=================================== FAILURES ===================================
_ TestCoxnetBaselineModel.test_baseline_predict[predict_cumulative_hazard_function-False] _

self = <test_coxnet.TestCoxnetBaselineModel object at 0x168aed4e0>
breast_cancer = (     X200726_at  ...  size
0     10.926361  ...   3.0
1     12.242090  ...   3.0
2     11.661716  ...   2.5
3     12.... True,  404.), (False, 2225.),
       (False, 2722.), (False, 1781.)],
      dtype=[('e.tdm', '?'), ('t.tdm', '<f8')]))
fn = 'predict_cumulative_hazard_function', normalize_options = False

    @pytest.mark.parametrize("fn", ["predict_survival_function", "predict_cumulative_hazard_function"])
    def test_baseline_predict(self, breast_cancer, fn, normalize_options):
        X, y = breast_cancer
    
        coxnet_1, coxnet_2, X_test, X_test_t = self._fit(X, y, normalize_options)
    
        time_points = np.unique(y["t.tdm"])
    
        for k, (a_1, a_2) in enumerate(zip(coxnet_1.alphas_, coxnet_2.alphas_)):
            pred_1 = getattr(coxnet_1, fn)(X_test, alpha=a_1)
            pred_2 = getattr(coxnet_2, fn)(X_test_t, alpha=a_2)
    
            for i, (f1, f2) in enumerate(zip(pred_1, pred_2)):
>               assert_array_almost_equal(f1.a, f2.a, 5, err_msg=f"alphas[{k}] [{i}].a mismatch")

tests/test_coxnet.py:1327: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/nix/store/ak3zf631ws2rwsl5qq0x3v7j18h0c2jj-python3-3.10.13/lib/python3.10/contextlib.py:79: in inner
    return func(*args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

args = (<function assert_array_almost_equal.<locals>.compare at 0x16996dd80>, 27079905.88052468, 27079905.880496684)
kwds = {'err_msg': 'alphas[22] [0].a mismatch', 'header': 'Arrays are not almost equal to 5 decimals', 'precision': 5, 'verbose': True}

    @wraps(func)
    def inner(*args, **kwds):
        with self._recreate_cm():
>           return func(*args, **kwds)
E           AssertionError: 
E           Arrays are not almost equal to 5 decimals
E           alphas[22] [0].a mismatch
E           Mismatched elements: 1 / 1 (100%)
E           Max absolute difference: 2.79955566e-05
E           Max relative difference: 1.03381292e-12
E            x: array(27079905.88052)
E            y: array(27079905.8805)

/nix/store/ak3zf631ws2rwsl5qq0x3v7j18h0c2jj-python3-3.10.13/lib/python3.10/contextlib.py:79: AssertionError

[ghost]

I don't think this is a significant error. We just need to add this test to disabledTests as a flaky one.

ok. i disabled it for darwin && aarch64 -- assuming it is deterministic and platform dependent as it passes aarch64 linux. waiting to see results from x64 darwin though after 7 hours build was still in the queue before last update.

[natsukium]

Result of nixpkgs-review pr 266019 at 20e41e0 run on x86_64-darwin 1

2 packages built successfully:

• python310Packages.scikit-survival
• python311Packages.scikit-survival