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catalystneuro / neuroconv

Create NWB files by converting and combining neural data in proprietary formats and adding essential metadata.
https://neuroconv.readthedocs.io
BSD 3-Clause "New" or "Revised" License
51 stars 21 forks source link

[Bug]: pyedflib installation issues #317

Closed bendichter closed 1 year ago

bendichter commented 1 year ago

What happened?

I am having trouble installing pyedflib on my M1 mac. Can we request support? And in the meantime, can we document this limitation on the EdfDataInterface and skip it in the tests for M1 macs?

Steps to Reproduce

pip install pyedflib

Traceback

$ pip install pyedflib
Collecting pyedflib
  Using cached pyEDFlib-0.1.30.tar.gz (1.7 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy>=1.9.1 in /Users/bendichter/opt/miniconda3/envs/neuroconv/lib/python3.9/site-packages (from pyedflib) (1.22.4)
Building wheels for collected packages: pyedflib
  Building wheel for pyedflib (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Building wheel for pyedflib (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [52 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.macosx-11.1-arm64-cpython-39
      creating build/lib.macosx-11.1-arm64-cpython-39/pyedflib
      copying pyedflib/version.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib
      copying pyedflib/highlevel.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib
      copying pyedflib/__init__.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib
      copying pyedflib/edfreader.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib
      copying pyedflib/edfwriter.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib
      creating build/lib.macosx-11.1-arm64-cpython-39/pyedflib/_extensions
      copying pyedflib/_extensions/__init__.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/_extensions
      creating build/lib.macosx-11.1-arm64-cpython-39/pyedflib/data
      copying pyedflib/data/_readers.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/data
      copying pyedflib/data/__init__.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/data
      creating build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests
      copying pyedflib/tests/test_edfwriter.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests
      copying pyedflib/tests/test_edfreader.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests
      copying pyedflib/tests/test_doc.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests
      copying pyedflib/tests/test_highlevel.py -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests
      copying pyedflib/data/test_generator.edf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/data
      creating build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
      copying pyedflib/tests/data/test_generator.edf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
      copying pyedflib/tests/data/test_subsecond.edf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
      copying pyedflib/tests/data/test_generator.bdf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
      copying pyedflib/tests/data/test_generator_datarec_generator_0_5.bdf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
      copying pyedflib/tests/data/test_generator_datarec_generator_2.bdf -> build/lib.macosx-11.1-arm64-cpython-39/pyedflib/tests/data
      running build_clib
      building 'c_edf' library
      creating build/temp.macosx-11.1-arm64-cpython-39
      creating build/temp.macosx-11.1-arm64-cpython-39/pyedflib
      creating build/temp.macosx-11.1-arm64-cpython-39/pyedflib/_extensions
      creating build/temp.macosx-11.1-arm64-cpython-39/pyedflib/_extensions/c
      clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/bendichter/opt/miniconda3/envs/neuroconv/include -arch arm64 -I/Users/bendichter/opt/miniconda3/envs/neuroconv/include -fPIC -O2 -isystem /Users/bendichter/opt/miniconda3/envs/neuroconv/include -arch arm64 -DPY_EXTENSION -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -Ipyedflib/_extensions/c -I/Users/bendichter/opt/miniconda3/envs/neuroconv/include/python3.9 -c pyedflib/_extensions/c/edflib.c -o build/temp.macosx-11.1-arm64-cpython-39/pyedflib/_extensions/c/edflib.o
      pyedflib/_extensions/c/edflib.c:39:9: warning: unknown pragma ignored [-Wunknown-pragmas]
      #pragma warning( disable : 4996 ) // ignore unsafe strncpy
              ^
      pyedflib/_extensions/c/edflib.c:40:9: warning: unknown pragma ignored [-Wunknown-pragmas]
      #pragma warning( disable : 4244 ) // ignore precision loss
              ^
      pyedflib/_extensions/c/edflib.c:2629:37: warning: format specifies type 'int' but the argument has type 'off_t' (aka 'long long') [-Wformat]
                      printf("filesize %d != %d*%d+%d ",ftello(inputfile),edfhdr->recordsize, edfhdr->datarecords, edfhdr->hdrsize);
                                       ~~               ^~~~~~~~~~~~~~~~~
                                       %lld
      pyedflib/_extensions/c/edflib.c:2629:75: warning: format specifies type 'int' but the argument has type 'long long' [-Wformat]
                      printf("filesize %d != %d*%d+%d ",ftello(inputfile),edfhdr->recordsize, edfhdr->datarecords, edfhdr->hdrsize);
                                                ~~                                            ^~~~~~~~~~~~~~~~~~~
                                                %lld
      4 warnings generated.
      /var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_648976sdlo/croot/python-split_1669299891106/_build_env/bin/llvm-ar rcs build/temp.macosx-11.1-arm64-cpython-39/libc_edf.a build/temp.macosx-11.1-arm64-cpython-39/pyedflib/_extensions/c/edflib.o
      error: command '/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_648976sdlo/croot/python-split_1669299891106/_build_env/bin/llvm-ar' failed: No such file or directory
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pyedflib
Failed to build pyedflib
ERROR: Could not build wheels for pyedflib, which is required to install pyproject.toml-based projects

Operating System

macOS

Python Executable

Conda

Python Version

3.9

Package Versions

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file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_4a509a63-68d9-468e-b7b9-f4d4ffac7351q0ounfrz/croots/recipe/imagesize_1657179503380/work importlib-metadata==5.1.0 iniconfig==1.1.1 interleave==0.2.1 ipykernel @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_7boejo_bxp/croots/recipe/ipykernel_1662361806503/work ipython @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_813bgy7kg6/croot/ipython_1668088123202/work ipython-genutils @ file:///tmp/build/80754af9/ipython_genutils_1606773439826/work ipywidgets @ file:///tmp/build/80754af9/ipywidgets_1634143127070/work iso8601==1.1.0 isoduration==20.11.0 jaraco.classes==3.2.3 jedi @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/croot-f1t6hma6/jedi_1644315882177/work Jinja2 @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_9fjgzv9ant/croot/jinja2_1666908141308/work joblib==1.1.1 json5 @ file:///tmp/build/80754af9/json5_1624432770122/work jsonpointer==2.3 jsonschema==4.17.1 jupyter @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_c96hs6nzjt/croots/recipe/jupyter_1659349054648/work jupyter-console @ file:///opt/conda/conda-bld/jupyter_console_1647002188872/work jupyter-server @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_20576569-56d2-46ec-9455-d266af658edbzbqhavnh/croots/recipe/jupyter_server_1658754492228/work jupyter_client @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_3bl8w897rj/croot/jupyter_client_1669040279222/work jupyter_core @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_9bflj8byfz/croot/jupyter_core_1668084444072/work jupyterlab @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_ebr25akxuh/croot/jupyterlab_1669368478002/work jupyterlab-pygments @ file:///tmp/build/80754af9/jupyterlab_pygments_1601490720602/work jupyterlab-widgets @ file:///tmp/build/80754af9/jupyterlab_widgets_1609884341231/work jupyterlab_server @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_bfh24ty__4/croot/jupyterlab_server_1669363632509/work keyring==23.11.0 keyrings.alt==4.2.0 kiwisolver==1.4.4 lazy-ops==0.2.0 locket @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_cb58d7ee-eabb-4e31-8a7c-68bb73b3bb2e3lthxgi7/croots/recipe/locket_1652903118916/work looseversion==1.0.3 lxml @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_71bcfe2b-fe7b-414a-9d7e-4f32bdd95f6d2vxca0jd/croots/recipe/lxml_1657545136492/work MarkupSafe @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_12c133f5-0720-4727-9c18-599a3af825723lzwham3/croots/recipe/markupsafe_1654597866058/work matplotlib==3.6.2 matplotlib-inline @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_f6fdc0hldi/croots/recipe/matplotlib-inline_1662014472341/work MEArec==1.8.0 MEAutility==1.5.1 mistune @ file:///Users/ktietz/demo/mc3/conda-bld/mistune_1629356075445/work mock @ file:///tmp/build/80754af9/mock_1607622725907/work more-itertools==9.0.0 msgpack==1.0.4 multidict==6.0.3 mypy-extensions==0.4.3 natsort==8.2.0 nbclassic @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_3btejl1i1y/croot/nbclassic_1668174982725/work nbclient @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_croot-08wgx75f/nbclient_1650373566605/work nbconvert @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_36au3u9s44/croot/nbconvert_1668450648628/work nbformat @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_94781rq_cg/croot/nbformat_1670352348390/work ndx-events==0.2.0 ndx-pose==0.1.1 ndx-sound==0.2.0 neo==0.11.1 nest-asyncio @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_croot-xymukih3/nest-asyncio_1649931465456/work networkx @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_933ef3b6-ee83-4587-8504-0a5b7ab57771x59ln7a7/croots/recipe/networkx_1657784101196/work -e git+https://github.com/catalystneuro/neuroconv.git@fe5d2aeefe8dd55eadb24d4a31f01bd0f2d5ac29#egg=neuroconv notebook @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_92n14lq88x/croot/notebook_1668179891126/work notebook_shim @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_f8mr1gjfb7/croot/notebook-shim_1668160580414/work numcodecs==0.10.2 numexpr @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_98sxk8lloi/croot/numexpr_1668713874222/work numpy==1.22.4 nwbinspector==0.4.20 opencv-python==4.6.0.66 openpyxl==3.0.10 packaging @ file:///tmp/build/80754af9/packaging_1637314298585/work pandas==1.5.2 pandocfilters @ file:///opt/conda/conda-bld/pandocfilters_1643405455980/work parameterized==0.8.1 parso @ file:///opt/conda/conda-bld/parso_1641458642106/work partd @ file:///opt/conda/conda-bld/partd_1647245470509/work pathspec==0.10.3 patool==1.12 pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work Pillow==9.2.0 platformdirs==2.6.0 pluggy==1.0.0 ply==3.11 probeinterface==0.2.16 prometheus-client @ file:///private/var/folders/nz/j6p8yfhx1mv_0grj5xl4650h0000gp/T/abs_25sgeyk0j5/croots/recipe/prometheus_client_1659455103277/work prompt-toolkit @ file:///tmp/build/80754af9/prompt-toolkit_1633440160888/work psutil==5.9.4 ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl pure-eval @ file:///opt/conda/conda-bld/pure_eval_1646925070566/work pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work pycryptodomex==3.15.0 pydantic==1.10.2 Pygments @ file:///opt/conda/conda-bld/pygments_1644249106324/work pyintan==0.3.0 pynwb==2.2.0 pyopenephys==1.1.6 pyOpenSSL @ 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Code of Conduct

bendichter commented 1 year ago

It looks like this as been reported here and it might be a Python 3.9 issue instead of an issue with the OS

CodyCBakerPhD commented 1 year ago

Still no word from GitHub on support M1 in the CI: https://github.com/actions/runner-images/issues/2187

so we can't verify that way if M1 is the issue vs. 3.9

With my own device(s) I can verify that 3.9 on Windows and Linux works fine, and 3.10 works fine on M1 Mac too

Able to replicate the issue with Python 3.9 on the M1 mac

CI currently tests this installation and usage on non-M1 macs for Python 3.8-3.11, so this is a specific M1 exclusion