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Re-enable kikuchipy #65

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hakonanes
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We've just released kikuchipy v0.11.0 on PyPI, compatible with HyperSpy >= 2.2 (https://pypi.org/project/kikuchipy/).

I've therefore re-enabled kikuchipy here.

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ericpre commented Nov 11, 2024 

python -m pytest --pyargs kikuchipy
============================= test session starts ==============================
platform linux -- Python 3.11.10, pytest-8.3.3, pluggy-1.5.0
Matplotlib: 3.9.[2](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/11785534636/job/32826974375?pr=65#step:26:2)
Freetype: 2.12.1
rootdir: /home/runner/work/hyperspy-extensions-list/hyperspy-extensions-list
plugins: mpl-0.17.0, rerunfailures-14.0, xdist-[3](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/11785534636/job/32826974375?pr=65#step:26:3).6.1
collected 0 items

============================ no tests ran in 0.16s =============================

@hakonanes
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We don't package tests after changing to src-layout. I can look at including them in the next release.

@hakonanes
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pytest --pyargs kikuchipy won't discover any tests even though it is installed from GitHub because tests are not included in site-packages. We need to make a release where we include it in the tarball under kikuchipy/tests. So I'd skip testing it all together for now.

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ericpre commented Nov 12, 2024

Can you push a fix so that it can be tested when installing from github for now? The alternative would be to install in editable mode.
Anyway, this step is skipped because there is still a dependency issue with quaternion/orix/pyxem.

@hakonanes
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Can you push a fix so that it can be tested when installing from github for now?

Not sure how to do this, if it's at all possible? May be that an editable install is the only option.

Anyway, this step is skipped because there is still a dependency issue with quaternion/orix/pyxem.

Oh no, what's the issue?

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ericpre commented Nov 13, 2024

Not sure how to do this, if it's at all possible? May be that an editable install is the only option.

Update installation configuration to include the tests files? It doesn't need a release because we install from source?

Oh no, what's the issue?

from latest build: https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/11801796768/job/32875961663?pr=65

Fatal Python error: Segmentation fault

Thread 0x00007f181430e640 (most recent call first):
  File "/home/runner/miniconda3/envs/test/lib/python3.11/socket.py", line 294 in accept
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/pytest_rerunfailures.py", line 433 in run_server
  File "/home/runner/miniconda3/envs/test/lib/python3.11/threading.py", line 982 in run
  File "/home/runner/miniconda3/envs/test/lib/python3.11/threading.py", line [10](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/11801796768/job/32875961663?pr=65#step:28:11)45 in _bootstrap_inner
  File "/home/runner/miniconda3/envs/test/lib/python3.[11](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/11801796768/job/32875961663?pr=65#step:28:12)/threading.py", line 1002 in _bootstrap

Current thread 0x00007f1816[12](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/11801796768/job/32875961663?pr=65#step:28:13)4440 (most recent call first):
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/numba/np/ufunc/gufunc.py", line 279 in __call__
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/quaternion/quaternion.py", line 1282 in qu_multiply
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/quaternion/quaternion.py", line 207 in __mul__
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/quaternion/quaternion.py", line 1085 in outer
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/quaternion/rotation.py", line 385 in outer
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/quaternion/symmetry.py", line 396 in from_generators
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/quaternion/symmetry.py", line 566 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1[14](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/11801796768/job/32875961663?pr=65#step:28:15)7 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/quaternion/orientation_region.py", line 28 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1[17](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/11801796768/job/32875961663?pr=65#step:28:18)6 in _find_and_load
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/quaternion/misorientation.py", line 32 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/quaternion/orientation.py", line 31 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/quaternion/__init__.py", line 25 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1126 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/crystal_map/phase_list.py", line 33 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/crystal_map/crystal_map.py", line 25 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/orix/crystal_map/__init__.py", line 26 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/pyxem/utils/indexation_utils.py", line 29 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/pyxem/utils/calibration.py", line 28 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/pyxem/utils/__init__.py", line 39 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1126 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/pyxem/signals/common_diffraction.py", line 33 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/pyxem/signals/__init__.py", line 23 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1232 in _handle_fromlist
  File "/home/runner/miniconda3/envs/test/lib/python3.11/site-packages/pyxem/__init__.py", line 29 in <module>
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 940 in exec_module
  File "<frozen importlib._bootstrap>", line 690 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1176 in _find_and_load
  File "<frozen importlib._bootstrap>", line 1204 in _gcd_import
  File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed
  ...

Extension modules: markupsafe._speedups, numpy._core._multiarray_umath, numpy._core._multiarray_tests, numpy.linalg._umath_linalg, PIL._imaging, kiwisolver._cext, gmpy2.gmpy2, traits.ctraits, yaml._yaml, cytoolz.utils, cytoolz.itertoolz, cytoolz.functoolz, cytoolz.dicttoolz, cytoolz.recipes, psutil._psutil_linux, psutil._psutil_posix, scipy._lib._ccallback_c, numba.core.typeconv._typeconv, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt[19](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/11801796768/job/32875961663?pr=65#step:28:20)937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, numba._helperlib, numba._dynfunc, numba._dispatcher, numba.core.runtime._nrt_python, numba.np.ufunc._internal, numba.experimental.jitclass._box, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy._lib._uarray._uarray, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.fftpack.convolve, box.exceptions, work._ruamel_yaml, _ruamel_yaml, msgpack._cmsgpack, box.converters, box.box, box.box_list, box.config_box, box.from_file, box.shorthand_box, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, numba.mviewbuf, numba.types.itertools, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, skimage._shared.geometry, scipy.signal._sigtools, scipy.signal._max_len_seq_inner, scipy.signal._upfirdn_apply, scipy.signal._spline, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, scipy.signal._sosfilt, scipy.signal._spectral, scipy.special.cython_special, scipy.stats._stats, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy.stats._stats_pythran, scipy.stats._ansari_swilk_statistics, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._mvn, scipy.stats._rcont.rcont, scipy.stats._unuran.unuran_wrapper, scipy.signal._peak_finding_utils, sklearn.__check_build._check_build, sklearn.utils._isfinite, sklearn.utils.sparsefuncs_fast, sklearn.utils.murmurhash, sklearn.utils._openmp_helpers, sklearn.metrics.cluster._expected_mutual_info_fast, sklearn.preprocessing._csr_polynomial_expansion, sklearn.preprocessing._target_encoder_fast, sklearn.metrics._dist_metrics, sklearn.metrics._pairwise_distances_reduction._datasets_pair, sklearn.utils._cython_blas, sklearn.metrics._pairwise_distances_reduction._base, sklearn.metrics._pairwise_distances_reduction._middle_term_computer, sklearn.utils._heap, sklearn.utils._sorting, sklearn.metrics._pairwise_distances_reduction._argkmin, sklearn.metrics._pairwise_distances_reduction._argkmin_classmode, sklearn.utils._vector_sentinel, sklearn.metrics._pairwise_distances_reduction._radius_neighbors, sklearn.metrics._pairwise_distances_reduction._radius_neighbors_classmode, sklearn.metrics._pairwise_fast, sklearn.utils._fast_dict, sklearn.cluster._hierarchical_fast, sklearn.cluster._k_means_common, sklearn.cluster._k_means_elkan, sklearn.cluster._k_means_lloyd, sklearn.cluster._k_means_minibatch, sklearn.neighbors._partition_nodes, sklearn.neighbors._ball_tree, sklearn.neighbors._kd_tree, sklearn.utils.arrayfuncs, sklearn.utils._random, sklearn.utils._seq_dataset, sklearn.linear_model._cd_fast, _loss, sklearn._loss._loss, sklearn.svm._liblinear, sklearn.svm._libsvm, sklearn.svm._libsvm_sparse, sklearn.utils._weight_vector, sklearn.linear_model._sgd_fast, sklearn.linear_model._sag_fast, sklearn.decomposition._online_lda_fast, sklearn.decomposition._cdnmf_fast, sklearn.cluster._dbscan_inner, sklearn.cluster._hdbscan._tree, sklearn.cluster._hdbscan._linkage, sklearn.cluster._hdbscan._reachability, sklearn._isotonic, sklearn.tree._utils, sklearn.tree._tree, sklearn.tree._splitter, sklearn.tree._criterion, sklearn.neighbors._quad_tree, sklearn.manifold._barnes_hut_tsne, sklearn.manifold._utils, _cffi_backend (total: 194)
/home/runner/work/_temp/e0aebf4c-9008-4693-a0be-71eeb1a5e55f.sh: line 1:  48[35](https://github.com/hyperspy/hyperspy-extensions-list/actions/runs/11801796768/job/32875961663?pr=65#step:28:36) Segmentation fault      (core dumped) python -m pytest --pyargs pyxem

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@ericpre
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ericpre commented Nov 15, 2024

Sorry, my previous statement was most likely incorrect: the issue is with numpy 2.0 - possibly not orix/quaternion but with pyfai dependencies in pyxem?

@hakonanes
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Update installation configuration to include the tests files? It doesn't need a release because we install from source?

With pip install? I don't know how I can tell pip to include the tests/ directory from GitHub within site-packages/kikuchipy/tests for pytest to discover them.

@ericpre
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ericpre commented Nov 18, 2024

The build backend should be taking take of that.

@hakonanes
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Yes, and to do that I need to make a new post release. But you said I didn't need to, or did I misunderstand?

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@hakonanes @ericpre