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python3Packages.clifford: fix tests #98404

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python3Packages.clifford: fix tests #98404

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drewrisinger
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Motivation for this change
  • Tests failed using nose.
  • Switched to pytest b/c that's what the official travis builds run.
  • Disabled slow and/or flaky tests as needed.
  • Changed patching from preConfigure to postPatch

ZHF: #97479

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.

@drewrisinger
python3Packages.clifford: fix tests
ca8f381 
* Tests failed using nose.
* Switched to pytest b/c that's what the official travis builds run.
* Disabled slow and/or flaky tests as needed.
* Changed patching from preConfigure to postPatch
@ofborg ofborg bot requested a review from costrouc September 21, 2020 16:25
jonringer
jonringer reviewed Sep 21, 2020
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not sure why, but it fails:

  clifford/test/test_cga.py .......x.......xx....x/nix/store/gnylh7dnvw9rcaz4y64f89z6x69rkcz2-pytest-check-hook/nix-support/setup-hook: line 40:    62 Aborted                 (core dumped) /nix/store/z65l1jqvxa58zzwwa3bvglb6asj4y8cv-python3-3.8.5/bin/python3.8 -m pytest -k "not test_iterative_model_match and not test_estimate_rotor and not test_estimate_motor and not test_array_control and not test_clustering and not test_write_and_read and not test_assign_objects_to_objects and not test_general_logarithm_conformal and not test_get_properties_of_sphere and not test_get_midpoint_between_lines" --pyargs clifford --benchmark-skip -m 'not veryslow'
cannot build derivation '/nix/store/gcfmri4ic7g7bsks63wbnzjhm3ca109z-env.drv': 1 dependencies couldn't be built
[1 built (1 failed), 0.0 MiB DL]
error: build of '/nix/store/gcfmri4ic7g7bsks63wbnzjhm3ca109z-env.drv' failed
https://github.com/NixOS/nixpkgs/pull/98404
1 package failed to build:
python38Packages.clifford

1 package built:
python37Packages.clifford

@risicle
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risicle commented Sep 21, 2020

Test failure on macos 10.14 for me with python 3.8:

============================= test session starts ==============================
platform darwin -- Python 3.8.5, pytest-5.4.3, py-1.9.0, pluggy-0.13.1
benchmark: 3.2.2 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /private/tmp/nix-build-python3.8-clifford-1.3.1.drv-0/clifford-1.3.1, inifile: setup.cfg
plugins: benchmark-3.2.2
collected 432 items / 47 deselected / 385 selected

clifford/test/test_algebra_initialisation.py sssssss                     [  1%]
clifford/test/test_aliases.py .........                                  [  4%]
clifford/test/test_bit_helpers.py ..                                     [  4%]
clifford/test/test_cga.py .......x.......xx....x/nix/store/kld0w0jn0iq86h0n5vnvbza3lkqrq1fk-pytest-check-hook/nix-support/setup-hook: line 40: 41866 Abort trap: 6           /nix/store/cp9nlaz4a24n8sp9f738ngdnrd19s4rp-python3-3.8.5/bin/python3.8 -m pytest -k "not test_iterative_model_match and not test_estimate_rotor and not test_estimate_motor and not test_array_control and not test_clustering and not test_write_and_read and not test_assign_objects_to_objects and not test_general_logarithm_conformal and not test_get_properties_of_sphere and not test_get_midpoint_between_lines" --pyargs clifford --benchmark-skip -m 'not veryslow'

@drewrisinger
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Test failure on macos 10.14 for me with python 3.8:

============================= test session starts ==============================
platform darwin -- Python 3.8.5, pytest-5.4.3, py-1.9.0, pluggy-0.13.1
benchmark: 3.2.2 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /private/tmp/nix-build-python3.8-clifford-1.3.1.drv-0/clifford-1.3.1, inifile: setup.cfg
plugins: benchmark-3.2.2
collected 432 items / 47 deselected / 385 selected

clifford/test/test_algebra_initialisation.py sssssss                     [  1%]
clifford/test/test_aliases.py .........                                  [  4%]
clifford/test/test_bit_helpers.py ..                                     [  4%]
clifford/test/test_cga.py .......x.......xx....x/nix/store/kld0w0jn0iq86h0n5vnvbza3lkqrq1fk-pytest-check-hook/nix-support/setup-hook: line 40: 41866 Abort trap: 6           /nix/store/cp9nlaz4a24n8sp9f738ngdnrd19s4rp-python3-3.8.5/bin/python3.8 -m pytest -k "not test_iterative_model_match and not test_estimate_rotor and not test_estimate_motor and not test_array_control and not test_clustering and not test_write_and_read and not test_assign_objects_to_objects and not test_general_logarithm_conformal and not test_get_properties_of_sphere and not test_get_midpoint_between_lines" --pyargs clifford --benchmark-skip -m 'not veryslow'

Strange @risicle, can replicate. investigating.

@risicle
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risicle commented Sep 21, 2020

The python 3.7 version fails for me too on linux x86_64:

============================= test session starts ==============================
platform linux -- Python 3.7.9, pytest-5.4.3, py-1.9.0, pluggy-0.13.1
benchmark: 3.2.2 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /build/clifford-1.3.1, inifile: setup.cfg
plugins: benchmark-3.2.2
collected 432 items / 47 deselected / 385 selected

clifford/test/test_algebra_initialisation.py sssssss                     [  1%]
clifford/test/test_aliases.py .........                                  [  4%]
clifford/test/test_bit_helpers.py ..                                     [  4%]
clifford/test/test_cga.py .......x.......xx....xxx.xx.                   [ 11%]
clifford/test/test_clifford.py ......................................... [ 22%]
.........................................                                [ 33%]
clifford/test/test_degenerate.py ....                                    [ 34%]
clifford/test/test_dg3c.py ..........                                    [ 36%]
clifford/test/test_dpga.py .......                                       [ 38%]
clifford/test/test_g3c_CUDA.py ssssssssssssss                            [ 42%]
clifford/test/test_g3c_tools.py .....F.................................. [ 52%]
...............................x............ssss                         [ 65%]
clifford/test/test_io.py .                                               [ 65%]
clifford/test/test_layout.py ......                                      [ 67%]
clifford/test/test_layout_helpers.py .............                       [ 70%]
clifford/test/test_parser.py .........                                   [ 72%]
clifford/test/test_tools.py ssss........                                 [ 75%]
clifford/test/test_tools_classify.py ................................... [ 84%]
...................................................                      [ 98%]
clifford/test/test_transformations.py .......                            [100%]

=================================== FAILURES ===================================
_____________ TestGeneralLogarithm.test_general_logarithm_rotation _____________

self = <clifford.test.test_g3c_tools.TestGeneralLogarithm object at 0x7fffd5841550>

    def test_general_logarithm_rotation(self):
        # Check we can reverse rotations
        for i in range(50):
            R = random_rotation_rotor()
            biv_2 = general_logarithm(R)
            biv_3 = ga_log(R)
>           assert_allclose(biv_2.value, biv_3.value)
E           AssertionError: 
E           Not equal to tolerance rtol=0.0001, atol=1e-06
E           
E           Mismatched elements: 3 / 32 (9.38%)
E           Max absolute difference: 1.18097551
E           Max relative difference: 0.99991057
E            x: array([-0.000000e+00, -0.000000e+00, -0.000000e+00, -0.000000e+00,
E                  -0.000000e+00, -0.000000e+00, -1.056186e-04, -7.419946e-05,
E                  -0.000000e+00, -0.000000e+00,  5.538197e-05, -0.000000e+00,...
E            y: array([ 0.      ,  0.      ,  0.      ,  0.      ,  0.      ,  0.      ,
E                  -1.181081, -0.829737,  0.      ,  0.      ,  0.61931 ,  0.      ,
E                   0.      ,  0.      ,  0.      ,  0.      ,  0.      ,  0.      ,...

clifford/test/test_g3c_tools.py:101: AssertionError
=============================== warnings summary ===============================
clifford/test/test_cga.py::test_from_points_construction[flat]
  /build/clifford-1.3.1/clifford/_multivector.py:262: RuntimeWarning: divide by zero encountered in true_divide
    newValue = self.value / other

clifford/test/test_cga.py::test_from_points_construction[flat]
clifford/test/test_clifford.py::TestBasicConformal41::test_categorization
  /build/clifford-1.3.1/clifford/_multivector.py:262: RuntimeWarning: invalid value encountered in true_divide
    newValue = self.value / other

clifford/test/test_cga.py::test_from_points_construction[flat]
  /build/clifford-1.3.1/clifford/_multivector.py:552: RuntimeWarning: invalid value encountered in subtract
    if (np.absolute(self.value - other.value) < _settings._eps).all():

clifford/test/test_io.py::TestParseMultivector::test_parse_multivector
  /build/clifford-1.3.1/clifford/test/test_io.py:16: UserWarning: Parentheses are not parsed, behavior may be surprising
    B = layout.parse_multivector(str(A))

-- Docs: https://docs.pytest.org/en/latest/warnings.html
=========================== short test summary info ============================
FAILED clifford/test/test_g3c_tools.py::TestGeneralLogarithm::test_general_logarithm_rotation
= 1 failed, 346 passed, 29 skipped, 47 deselected, 9 xfailed, 5 warnings in 344.41s (0:05:44) =

@drewrisinger
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drewrisinger commented Sep 27, 2020 •
edited

I rebuilt this on Friday via nix-review on Linux x86_64 (Windows Subsystem for Linux), and got a clean build. Not sure why this failed. Would anyone be able to try rebuilding?

1 package built:
python37Packages.clifford

EDIT: whoops, apparently must have missed the scroll up to get the python38Package.

@jonringer
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[1 built (1 failed), 2 copied (0.9 MiB), 0.2 MiB DL]
error: build of '/nix/store/71hk7918w2pmmv4p92ri4x4fvlbdk8d2-env.drv' failed
https://github.com/NixOS/nixpkgs/pull/98404
1 package failed to build:
python38Packages.clifford

1 package built:
python37Packages.clifford

unfortunately, the python38 failure isn't very useful:

/nix/store/gnylh7dnvw9rcaz4y64f89z6x69rkcz2-pytest-check-hook/nix-support/setup-hook: line 40:    62 Aborted                 (core dumped) /nix/store/z65l1jqvxa58zzwwa3bvglb6asj4y8cv-python3-3.8.5/bin/python...

@drewrisinger
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Closing because fixed in d65aba6

@drewrisinger drewrisinger deleted the zhf/py-clifford branch October 7, 2020 13:10
@jonringer
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jonringer commented Oct 7, 2020 •
edited

oh yea, sorry.

I just wanted to fix all the reverse dependencies

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