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Bump hyperspy>1.7.5 to ensure 3.12 compatibility #682

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TLCFEM opened this issue Sep 13, 2024 · 10 comments
Open

Bump hyperspy>1.7.5 to ensure 3.12 compatibility #682

TLCFEM opened this issue Sep 13, 2024 · 10 comments
Labels
maintenance This relates to package maintenance
Milestone
v0.10.1

Comments

@TLCFEM
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TLCFEM commented Sep 13, 2024

hyperspy==1.7.5 cannot be compiled in 3.12.

hyperspy==1.7.6 can be compiled and installed.

Maybe bump the version so that downstream packages can pick a compatible version.
@hakonanes
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Hi @TLCFEM, the HyperSpy version range in our config file is:

kikuchipy/setup.py

Line 149 in f4946c7

"hyperspy >= 1.7.3, < 2",

This means that you should be able to install kikuchipy v0.10 with HyperSpy 1.7.6. Are you not able to? If so, can you print your error output here?

@TLCFEM
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TLCFEM commented Sep 21, 2024

Hi @TLCFEM, the HyperSpy version range in our config file is:

kikuchipy/setup.py

Line 149 in f4946c7

"hyperspy >= 1.7.3, < 2",

This means that you should be able to install kikuchipy v0.10 with HyperSpy 1.7.6. Are you not able to? If so, can you print your error output here?

Resolver may pick a version that satisfies constraint but fail to install (<1.7.6).

@hakonanes
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Hm, OK, that's unfortunate. Can you paste the log you get in this situation?

@TLCFEM
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TLCFEM commented Sep 21, 2024

The dependency resolver could pick a version, say 1.7.5, due to other constraints in the downstream projects, not necessarily the exact hyperspy package. But eventually it ends up to pip install hyperspy==1.7.5 in 3.12.

Then you get.

      hyperspy/io_plugins/unbcf_fast.c: In function ‘__pyx_pf_8hyperspy_10io_plugins_10unbcf_fast_parse_to_numpy’:
      hyperspy/io_plugins/unbcf_fast.c:7318:3: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
       7318 |   __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_np); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 319, __pyx_L1_error)
            |   ^~~~~~~~~~~~~~~~~~~~~~~~~
      In file included from /home/theodore/.pyenv/versions/3.12.6/include/python3.12/dictobject.h:90,
                       from /home/theodore/.pyenv/versions/3.12.6/include/python3.12/Python.h:64,
                       from hyperspy/io_plugins/unbcf_fast.c:19:
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c:7367:3: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
       7367 |   __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_np); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 321, __pyx_L1_error)
            |   ^~~~~~~~~~~~~~~~~~~~~~~~~
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c:7423:3: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
       7423 |   __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_np); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 324, __pyx_L1_error)
            |   ^~~~~~~~~~~~~~~~~~~~~~~~~
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c:7479:3: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
       7479 |   __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_np); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 327, __pyx_L1_error)
            |   ^~~~~~~~~~~~~~~~~~~~~~~~~
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__pyx_pf___pyx_MemviewEnum___reduce_cython__’:
      hyperspy/io_plugins/unbcf_fast.c:9726:5: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
       9726 |     __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_Enum); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 13, __pyx_L1_error)
            |     ^~~~~~~~~~~~~~~~~~~~~~~~~
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c:9772:5: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
       9772 |     __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_pyx_unpickle_Enum); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 15, __pyx_L1_error)
            |     ^~~~~~~~~~~~~~~~~~~~~~~~~
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__pyx_memview_slice’:
      hyperspy/io_plugins/unbcf_fast.c:14909:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
      14909 |   if (unlikely(!Py_OptimizeFlag)) {
            |   ^~
      In file included from /home/theodore/.pyenv/versions/3.12.6/include/python3.12/Python.h:48:
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/pydebug.h:13:37: note: declared here
         13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
            |                                     ^~~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__pyx_pymod_exec_unbcf_fast’:
      hyperspy/io_plugins/unbcf_fast.c:22375:3: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
      22375 |   __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_sys); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
            |   ^~~~~~~~~~~~~~~~~~~~~~~~~
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_Raise’:
      hyperspy/io_plugins/unbcf_fast.c:23089:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’
      23089 |         PyObject* tmp_tb = tstate->curexc_traceback;
            |                                  ^~
      hyperspy/io_plugins/unbcf_fast.c:23092:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’
      23092 |             tstate->curexc_traceback = tb;
            |                   ^~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_get_tp_dict_version’:
      hyperspy/io_plugins/unbcf_fast.c:23575:5: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
      23575 |     return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0;
            |     ^~~~~~
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_get_object_dict_version’:
      hyperspy/io_plugins/unbcf_fast.c:23587:5: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
      23587 |     return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0;
            |     ^~~~~~
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_object_dict_version_matches’:
      hyperspy/io_plugins/unbcf_fast.c:23591:5: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
      23591 |     if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict)))
            |     ^~
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx__GetModuleGlobalName’:
      hyperspy/io_plugins/unbcf_fast.c:23608:5: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
      23608 |     __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
            |     ^~~~~~~~~~~~~~~~~~~~~~~
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_PyUnicode_Equals’:
      hyperspy/io_plugins/unbcf_fast.c:570:51: warning: implicit declaration of function ‘_PyUnicode_Ready’; did you mean ‘PyUnicode_READY’? [-Wimplicit-function-declaration]
        570 |                                               0 : _PyUnicode_Ready((PyObject *)(op)))
            |                                                   ^~~~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c:951:43: note: in definition of macro ‘unlikely’
        951 |   #define unlikely(x) __builtin_expect(!!(x), 0)
            |                                           ^
      hyperspy/io_plugins/unbcf_fast.c:23896:22: note: in expansion of macro ‘__Pyx_PyUnicode_READY’
      23896 |         if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0))
            |                      ^~~~~~~~~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_PyInt_AddObjC’:
      hyperspy/io_plugins/unbcf_fast.c:24458:51: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      24458 |         const digit* digits = ((PyLongObject*)op1)->ob_digit;
            |                                                   ^~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_CLineForTraceback’:
      hyperspy/io_plugins/unbcf_fast.c:24812:9: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
      24812 |         __PYX_PY_DICT_LOOKUP_IF_MODIFIED(
            |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c:24812:9: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
      24812 |         __PYX_PY_DICT_LOOKUP_IF_MODIFIED(
            |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      /home/theodore/.pyenv/versions/3.12.6/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_PyInt_As_int’:
      hyperspy/io_plugins/unbcf_fast.c:26039:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      26039 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      hyperspy/io_plugins/unbcf_fast.c:26094:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      26094 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_PyInt_As_uint32_t’:
      hyperspy/io_plugins/unbcf_fast.c:26235:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      26235 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      hyperspy/io_plugins/unbcf_fast.c:26290:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      26290 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_PyInt_As_uint64_t’:
      hyperspy/io_plugins/unbcf_fast.c:26431:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      26431 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      hyperspy/io_plugins/unbcf_fast.c:26486:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      26486 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_PyInt_As_uint16_t’:
      hyperspy/io_plugins/unbcf_fast.c:26703:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      26703 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      hyperspy/io_plugins/unbcf_fast.c:26758:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      26758 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_PyInt_As_long’:
      hyperspy/io_plugins/unbcf_fast.c:26975:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      26975 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      hyperspy/io_plugins/unbcf_fast.c:27030:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      27030 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_PyInt_As_char’:
      hyperspy/io_plugins/unbcf_fast.c:27209:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      27209 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      hyperspy/io_plugins/unbcf_fast.c:27264:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      27264 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      hyperspy/io_plugins/unbcf_fast.c: In function ‘__Pyx_PyIndex_AsSsize_t’:
      hyperspy/io_plugins/unbcf_fast.c:27615:45: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
      27615 |     const digit* digits = ((PyLongObject*)b)->ob_digit;
            |                                             ^~
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for hyperspy
  Building wheel for asciitree (pyproject.toml) ... done
  Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5034 sha256=23ca201993b8b2d33660c1be3744568ea5764b41fcf3629cfe2d183c1da389f5
  Stored in directory: /home/theodore/.cache/pip/wheels/a5/d7/98/f56ae733748cd0fa577172bda0e73e0b1f1793c98e09b9e458
Successfully built asciitree
Failed to build hyperspy
ERROR: Could not build wheels for hyperspy, which is required to install pyproject.toml-based projects

Somehow they probably have fixed it in 1.7.6, thus, to ensure successful installation, better bump up the version.

If the resolver fails to resolve, it will fail anyway so not a concern I guess.

@hakonanes
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hakonanes commented Sep 21, 2024 •
edited
Loading

Thanks, your output is from trying to install kikuchipy? From PyPI or conda-forge?

I cannot reproduce when installing kikuchipy v0.10 from PyPI in a clean conda environment:

> mamba create -n kp12 python=3.12 -y

Looking for: ['python=3.12']

conda-forge/osx-arm64                               11.9MB @  25.7MB/s  0.5s
conda-forge/noarch                                  16.5MB @  33.7MB/s  0.5s
default/osx-arm64                                             No change
default/noarch                                                No change
Transaction

  Prefix: /opt/homebrew/Caskroom/mambaforge/base/envs/kp12

  Updating specs:

   - python=3.12


  Package              Version  Build               Channel           Size
────────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────────

  + xz                   5.2.6  h57fd34a_0          conda-forge     Cached
  + libexpat             2.6.3  hf9b8971_0          conda-forge     Cached
  + ncurses                6.5  h7bae524_1          conda-forge     Cached
  + bzip2                1.0.8  h99b78c6_7          conda-forge     Cached
  + libffi               3.4.2  h3422bc3_5          conda-forge     Cached
  + libzlib              1.3.1  hfb2fe0b_1          conda-forge     Cached
  + ca-certificates  2024.8.30  hf0a4a13_0          conda-forge     Cached
  + readline               8.2  h92ec313_1          conda-forge     Cached
  + tk                  8.6.13  h5083fa2_1          conda-forge     Cached
  + libsqlite           3.46.1  hc14010f_0          conda-forge     Cached
  + openssl              3.3.2  h8359307_0          conda-forge     Cached
  + tzdata               2024a  h8827d51_1          conda-forge     Cached
  + python              3.12.6  h739c21a_0_cpython  conda-forge     Cached
  + wheel               0.44.0  pyhd8ed1ab_0        conda-forge     Cached
  + setuptools          74.1.2  pyhd8ed1ab_0        conda-forge     Cached
  + pip                   24.2  pyh8b19718_1        conda-forge     Cached

  Summary:

  Install: 16 packages

  Total download: 0 B

────────────────────────────────────────────────────────────────────────────



Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

To activate this environment, use

     $ mamba activate kp12

To deactivate an active environment, use

     $ mamba deactivate
> pip install kikuchipy
Collecting kikuchipy
  Downloading kikuchipy-0.10.0-py3-none-any.whl.metadata (13 kB)
Collecting dask>=2021.8.1 (from dask[array]>=2021.8.1->kikuchipy)
  Using cached dask-2024.9.0-py3-none-any.whl.metadata (3.7 kB)
Collecting diffpy.structure>=3 (from kikuchipy)
  Using cached diffpy.structure-3.2.1-py3-none-any.whl
Collecting diffsims>=0.5.2 (from kikuchipy)
  Downloading diffsims-0.6.0-py3-none-any.whl.metadata (6.2 kB)
Collecting hyperspy<2,>=1.7.3 (from kikuchipy)
  Downloading hyperspy-1.7.6.tar.gz (45.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.8/45.8 MB 9.1 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting h5py>=2.10 (from kikuchipy)
  Using cached h5py-3.11.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (2.5 kB)
Collecting imageio (from kikuchipy)
  Using cached imageio-2.35.1-py3-none-any.whl.metadata (4.9 kB)
Collecting matplotlib>=3.5 (from kikuchipy)
  Using cached matplotlib-3.9.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (11 kB)
Collecting numba>=0.57 (from kikuchipy)
  Using cached numba-0.60.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (2.7 kB)
Collecting numpy>=1.23.0 (from kikuchipy)
  Using cached numpy-2.1.1-cp312-cp312-macosx_14_0_arm64.whl.metadata (60 kB)
Collecting orix>=0.12.1 (from kikuchipy)
  Using cached orix-0.13.1-py3-none-any.whl.metadata (47 kB)
Collecting pooch>=1.3.0 (from kikuchipy)
  Using cached pooch-1.8.2-py3-none-any.whl.metadata (10 kB)
Collecting pyyaml (from kikuchipy)
  Using cached PyYAML-6.0.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (2.1 kB)
Collecting tqdm>=0.5.2 (from kikuchipy)
  Using cached tqdm-4.66.5-py3-none-any.whl.metadata (57 kB)
Collecting scikit-image>=0.16.2 (from kikuchipy)
  Using cached scikit_image-0.24.0-cp312-cp312-macosx_12_0_arm64.whl.metadata (14 kB)
Collecting scikit-learn (from kikuchipy)
  Using cached scikit_learn-1.5.2-cp312-cp312-macosx_12_0_arm64.whl.metadata (13 kB)
Collecting scipy>=1.7 (from kikuchipy)
  Using cached scipy-1.14.1-cp312-cp312-macosx_14_0_arm64.whl.metadata (60 kB)
Collecting click>=8.1 (from dask>=2021.8.1->dask[array]>=2021.8.1->kikuchipy)
  Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting cloudpickle>=3.0.0 (from dask>=2021.8.1->dask[array]>=2021.8.1->kikuchipy)
  Using cached cloudpickle-3.0.0-py3-none-any.whl.metadata (7.0 kB)
Collecting fsspec>=2021.09.0 (from dask>=2021.8.1->dask[array]>=2021.8.1->kikuchipy)
  Using cached fsspec-2024.9.0-py3-none-any.whl.metadata (11 kB)
Collecting packaging>=20.0 (from dask>=2021.8.1->dask[array]>=2021.8.1->kikuchipy)
  Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
Collecting partd>=1.4.0 (from dask>=2021.8.1->dask[array]>=2021.8.1->kikuchipy)
  Using cached partd-1.4.2-py3-none-any.whl.metadata (4.6 kB)
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Downloading entrypoints-0.4-py3-none-any.whl (5.3 kB)
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Building wheels for collected packages: hyperspy
  Building wheel for hyperspy (pyproject.toml) ... done
  Created wheel for hyperspy: filename=hyperspy-1.7.6-cp312-cp312-macosx_11_0_arm64.whl size=32576589 sha256=c711b39c78353827028af5bb9e2ce81a5026eed1c9bf02801caedd483efc9888
  Stored in directory: /Users/hakon/Library/Caches/pip/wheels/a1/47/5d/e5378eeba6d24d7b883baf7fbe9362061b6875acfb10212671
Successfully built hyperspy
Installing collected packages: wcwidth, pure-eval, ptyprocess, ply, mpmath, appdirs, zipp, urllib3, typing-extensions, traits, traitlets, tqdm, tornado, toolz, threadpoolctl, sympy, six, pyzmq, pyyaml, pyparsing, pygments, psutil, prompt-toolkit, prettytable, platformdirs, pillow, pexpect, parso, packaging, numpy, networkx, nest-asyncio, natsort, MarkupSafe, locket, llvmlite, kiwisolver, joblib, idna, fsspec, fonttools, executing, entrypoints, dill, decorator, debugpy, cycler, cloudpickle, click, charset-normalizer, certifi, appnope, transforms3d, tifffile, scipy, requests, python-dateutil, pycifrw, partd, numexpr, numba, matplotlib-inline, lazy_loader, jupyter-core, jinja2, jedi, importlib-metadata, imageio, h5py, flexparser, flexcache, contourpy, comm, asttokens, stack-data, sparse, scikit-learn, scikit-image, pooch, pint, matplotlib, jupyter-client, diffpy.structure, dask, matplotlib-scalebar, ipython, orix, ipykernel, ipyparallel, diffsims, hyperspy, kikuchipy
Successfully installed MarkupSafe-2.1.5 appdirs-1.4.4 appnope-0.1.4 asttokens-2.4.1 certifi-2024.8.30 charset-normalizer-3.3.2 click-8.1.7 cloudpickle-3.0.0 comm-0.2.2 contourpy-1.3.0 cycler-0.12.1 dask-2024.9.0 debugpy-1.8.5 decorator-5.1.1 diffpy.structure-3.2.1 diffsims-0.6.0 dill-0.3.8 entrypoints-0.4 executing-2.1.0 flexcache-0.3 flexparser-0.3.1 fonttools-4.53.1 fsspec-2024.9.0 h5py-3.11.0 hyperspy-1.7.6 idna-3.10 imageio-2.27.0 importlib-metadata-8.5.0 ipykernel-6.29.5 ipyparallel-8.8.0 ipython-8.27.0 jedi-0.19.1 jinja2-3.1.4 joblib-1.4.2 jupyter-client-8.6.3 jupyter-core-5.7.2 kikuchipy-0.10.0 kiwisolver-1.4.7 lazy_loader-0.4 llvmlite-0.43.0 locket-1.0.0 matplotlib-3.9.2 matplotlib-inline-0.1.7 matplotlib-scalebar-0.8.1 mpmath-1.3.0 natsort-8.4.0 nest-asyncio-1.6.0 networkx-3.3 numba-0.60.0 numexpr-2.10.1 numpy-1.26.4 orix-0.13.1 packaging-24.1 parso-0.8.4 partd-1.4.2 pexpect-4.9.0 pillow-10.0.1 pint-0.24.3 platformdirs-4.3.6 ply-3.11 pooch-1.8.2 prettytable-3.11.0 prompt-toolkit-3.0.47 psutil-6.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pycifrw-4.4.6 pygments-2.18.0 pyparsing-3.1.4 python-dateutil-2.9.0.post0 pyyaml-6.0.2 pyzmq-26.2.0 requests-2.32.3 scikit-image-0.22.0 scikit-learn-1.5.2 scipy-1.14.1 six-1.16.0 sparse-0.15.4 stack-data-0.6.3 sympy-1.13.3 threadpoolctl-3.5.0 tifffile-2024.9.20 toolz-0.12.1 tornado-6.4.1 tqdm-4.66.5 traitlets-5.14.3 traits-6.4.3 transforms3d-0.4.2 typing-extensions-4.12.2 urllib3-2.2.3 wcwidth-0.2.13 zipp-3.20.2
> pip list
Package             Version
------------------- -----------
appdirs             1.4.4
appnope             0.1.4
asttokens           2.4.1
certifi             2024.8.30
charset-normalizer  3.3.2
click               8.1.7
cloudpickle         3.0.0
comm                0.2.2
contourpy           1.3.0
cycler              0.12.1
dask                2024.9.0
debugpy             1.8.5
decorator           5.1.1
diffpy.structure    3.2.1
diffsims            0.6.0
dill                0.3.8
entrypoints         0.4
executing           2.1.0
flexcache           0.3
flexparser          0.3.1
fonttools           4.53.1
fsspec              2024.9.0
h5py                3.11.0
hyperspy            1.7.6
idna                3.10
imageio             2.27.0
importlib_metadata  8.5.0
ipykernel           6.29.5
ipyparallel         8.8.0
ipython             8.27.0
jedi                0.19.1
Jinja2              3.1.4
joblib              1.4.2
jupyter_client      8.6.3
jupyter_core        5.7.2
kikuchipy           0.10.0
kiwisolver          1.4.7
lazy_loader         0.4
llvmlite            0.43.0
locket              1.0.0
MarkupSafe          2.1.5
matplotlib          3.9.2
matplotlib-inline   0.1.7
matplotlib-scalebar 0.8.1
mpmath              1.3.0
natsort             8.4.0
nest-asyncio        1.6.0
networkx            3.3
numba               0.60.0
numexpr             2.10.1
numpy               1.26.4
orix                0.13.1
packaging           24.1
parso               0.8.4
partd               1.4.2
pexpect             4.9.0
Pillow              10.0.1
Pint                0.24.3
pip                 24.2
platformdirs        4.3.6
ply                 3.11
pooch               1.8.2
prettytable         3.11.0
prompt_toolkit      3.0.47
psutil              6.0.0
ptyprocess          0.7.0
pure_eval           0.2.3
PyCifRW             4.4.6
Pygments            2.18.0
pyparsing           3.1.4
python-dateutil     2.9.0.post0
PyYAML              6.0.2
pyzmq               26.2.0
requests            2.32.3
scikit-image        0.22.0
scikit-learn        1.5.2
scipy               1.14.1
setuptools          74.1.2
six                 1.16.0
sparse              0.15.4
stack-data          0.6.3
sympy               1.13.3
threadpoolctl       3.5.0
tifffile            2024.9.20
toolz               0.12.1
tornado             6.4.1
tqdm                4.66.5
traitlets           5.14.3
traits              6.4.3
transforms3d        0.4.2
typing_extensions   4.12.2
urllib3             2.2.3
wcwidth             0.2.13
wheel               0.44.0
zipp                3.20.2

@hakonanes
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hakonanes commented Sep 21, 2024 •
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OK, sorry, now I understand what you're telling me. I can reproduce in an environment with Python 3.12 and calling pip install kikuchipy hyperspy==1.7.5.

Can you explain how your resolver ends up using the non-3.12-compatible HyperSpy 1.7.5 instead of the compatible 1.7.6? Since kikuchipy is compatible with HyperSpy 1.7.6 for Python 3.12 and HyperSpy 1.7.3 for Python 3.8-11, I'm not sure I consider the problem you encounter to be the responsibility of kikuchipy. Rather, the package requiring HyperSpy < 1.7.6 should require Python <= 3.11.

@TLCFEM
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TLCFEM commented Sep 21, 2024 •
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The dependency resolver could pick a version, say 1.7.5, due to other constraints in the downstream projects, not necessarily the exact hyperspy package. But eventually it ends up to pip install hyperspy==1.7.5 in 3.12.

Installing kikuchipy alone does not raise error because the resolver picks 1.7.6.
But downstream projects would have more other constraints due to probably other packages as well, resolver is not bounded to pick the good versions.

I'm not sure I consider the problem you encounter to be the responsibility of kikuchipy.

No, it is not, it is hyperspy that shall have better constraints.
It's more like a quality of life fix, that could save some hassle for downstream projects.

@hakonanes
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Thank you for clarifying.

What we want is to update our dependencies so that HyperSpy 1.7.6 is required if the environment has Python >= 3.12. I didn't think this was easily done, but apparently it is with Hatch and their environment markers:

"hyperspy>=1.7.3,<2; python_version<'3.12'",
"hyperspy==1.7.6; python_version>='3.12'",

We will switch package configuration to use pyproject.toml and hatchling as build backend soon, which will enable this.

Also, note that kikuchipy will be compatible with HyperSpy v2 soon...

@hakonanes hakonanes added the maintenance This relates to package maintenance label Sep 21, 2024
@hakonanes hakonanes added this to the v0.10.1 milestone Sep 21, 2024
@TLCFEM
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TLCFEM commented Sep 21, 2024 

"hyperspy>=1.7.3,<2; python_version<'3.12'",
"hyperspy==1.7.6; python_version>='3.12'",

This also helps.

@hakonanes
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Indeed. I think this is better than requiring HyperSpy 1.7.6, less restrictive.

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