frheault
commented
2 years ago I always use the -e option. Otherwise, I never got that error.
I will try to get someone else with a Mac to test.
Open neurolabusc opened 2 years ago
frheault
commented
2 years ago I always use the -e option. Otherwise, I never got that error.
I will try to get someone else with a Mac to test.
neurolabusc
commented
2 years ago My computer uses the Apple Silicon M1 CPU.
$git clone --branch testing_script https://github.com/frheault/tractography_file_format.git
$ cd tractography_file_format
$ pip3 install -e .
Obtaining file:///Users/chrisrorden/Downloads/tractography_file_format
Preparing metadata (setup.py) ... done
Requirement already satisfied: dipy>=1.2.0 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from tractography-file-format==0.0.0) (1.5.0)
Requirement already satisfied: nibabel>=3.0.0 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from tractography-file-format==0.0.0) (3.2.2)
Requirement already satisfied: PyYAML>=5.3.1 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from tractography-file-format==0.0.0) (6.0)
Requirement already satisfied: h5py>=2.8.0 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from dipy>=1.2.0->tractography-file-format==0.0.0) (3.6.0)
Requirement already satisfied: tqdm>=4.30.0 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from dipy>=1.2.0->tractography-file-format==0.0.0) (4.62.3)
Requirement already satisfied: scipy>=1.1 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from dipy>=1.2.0->tractography-file-format==0.0.0) (1.7.3)
Requirement already satisfied: packaging>=14.3 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from nibabel>=3.0.0->tractography-file-format==0.0.0) (21.3)
Requirement already satisfied: numpy>=1.14 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from nibabel>=3.0.0->tractography-file-format==0.0.0) (1.22.2)
Requirement already satisfied: setuptools in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from nibabel>=3.0.0->tractography-file-format==0.0.0) (60.5.0)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from packaging>=14.3->nibabel>=3.0.0->tractography-file-format==0.0.0) (3.0.7)
Installing collected packages: tractography-file-format
Attempting uninstall: tractography-file-format
Found existing installation: tractography-file-format 0.0.0
Uninstalling tractography-file-format-0.0.0:
Successfully uninstalled tractography-file-format-0.0.0
Running setup.py develop for tractography-file-format
Successfully installed tractography-file-format-0.0.0
$ cd scripts
$ python tff_convert_tractogram.py ~/IFOF_L.trk ~/IFOF_L.trx
zsh: segmentation fault python tff_convert_tractogram.py ~/IFOF_L.trk ~/IFOF_L.trx
fionaEyoung
commented
2 years ago I attempted to replicate on my M1 MBP and didn't get a segmentation fault.
$ git clone --branch testing_script https://github.com/frheault/tractography_file_format.git
$ pip3 install .
Successfully installed Cython-0.29.28 aiohttp-3.8.1 aiosignal-1.2.0 async-timeout-4.0.2 charset-normalizer-2.0.12 dipy-1.6.0.dev0 frozenlist-1.3.0 fury-0.8.0.post416+g5059a52 multidict-6.0.2 tractography-file-format-0.0.0 vtk-9.1.0 wslink-1.6.1 yarl-1.7.2
$ cd scripts
$ python3 tff_convert_tractogram.py ~/AF_left.trk ~/test.trxOS: macOS Big Sur v11.1
neurolabusc
commented
2 years ago I still get the fault. I tried removing all the components you installed.
$ pip3 uninstall Cython aiohttp aiosignal async-timeout charset-normalizer dipy frozenlist fury multidict tractography-file-format vtk wslink yarl
$ git clone --branch testing_script https://github.com/frheault/tractography_file_format.git
$ cd tractography_file_format
$ pip3 install .
$ cd scripts
$ python3 tff_convert_tractogram.py ~/AF_left.trk ~/test.trx
zsh: segmentation fault python3 tff_convert_tractogram.py ~/IFOF_L.trk IFO.trx
$sw_vers
ProductName: macOS
ProductVersion: 11.6.5
BuildVersion: 20G527
$sysctl -n hw.model
MacBookAir10,1I get the same crash if I attempt to import the library:
> python
Python 3.9.9 | packaged by conda-forge | (main, Dec 20 2021, 02:41:07)
[Clang 11.1.0 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> print('hola')
hola
>>> from tractography_file_format.workflows import convert_tractogram
zsh: segmentation fault python3
arokem
commented
2 years ago Are both/either of you using Anaconda Python? If one is and the other isn't that could also be a cause.
On Fri, Apr 29, 2022 at 11:07 AM Chris Rorden @.***> wrote:
I still get the fault. I tried removing all the components you installed.
$ pip3 uninstall Cython aiohttp aiosignal async-timeout charset-normalizer dipy frozenlist fury multidict tractography-file-format vtk wslink yarl $ git clone --branch testing_script https://github.com/frheault/tractography_file_format.git $ cd tractography_file_format $ pip3 install . $ cd scripts $ python3 tff_convert_tractogram.py ~/AF_left.trk ~/test.trx zsh: segmentation fault python3 tff_convert_tractogram.py ~/IFOF_L.trk IFO.trx $sw_vers ProductName: macOS ProductVersion: 11.6.5 BuildVersion: 20G527 $sysctl -n hw.model MacBookAir10,1
I get the same crash if I attempt to import the library:
python Python 3.9.9 | packaged by conda-forge | (main, Dec 20 2021, 02:41:07) [Clang 11.1.0 ] on darwin Type "help", "copyright", "credits" or "license" for more information.
print('hola') hola from tractography_file_format.workflows import convert_tractogram zsh: segmentation fault python3
— Reply to this email directly, view it on GitHub https://github.com/tee-ar-ex/trx/issues/23#issuecomment-1113586070, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAA46NX57MV6QGZSBI4U7P3VHQQNTANCNFSM5T3YUZPQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
neurolabusc
commented
2 years ago I was:
$ conda --version
conda 4.12.0
$ conda list
# packages in environment at /Users/chrisrorden/miniforge3:
#
# Name Version Build Channel
aiohttp 3.8.1 pypi_0 pypi
aiosignal 1.2.0 pypi_0 pypi
aom 3.3.0 h07bb92c_1 conda-forge
appdirs 1.4.4 pypi_0 pypi
async-timeout 4.0.2 pypi_0 pypi
attrs 21.4.0 pypi_0 pypi
beautifulsoup4 4.11.1 pypi_0 pypi
bjdata 0.3.3 pypi_0 pypi
blosc 1.21.0 h9f76cd9_0 conda-forge
brotli 1.0.9 h1c322ee_7 conda-forge
brotli-bin 1.0.9 h1c322ee_7 conda-forge
brotlipy 0.7.0 py39h5161555_1003 conda-forge
brunsli 0.1 h9f76cd9_0 conda-forge
bvbabel 0.1.0 pypi_0 pypi
bzip2 1.0.8 h3422bc3_4 conda-forge
c-ares 1.18.1 h3422bc3_0 conda-forge
c-blosc2 2.0.4 h0095615_1 conda-forge
ca-certificates 2021.10.8 h4653dfc_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
certifi 2021.10.8 py39h2804cbe_2 conda-forge
cffi 1.15.0 py39h52b1de0_0 conda-forge
cfitsio 4.1.0 hd4f5c17_0 conda-forge
charls 2.3.4 hbdafb3b_0 conda-forge
charset-normalizer 2.0.12 pypi_0 pypi
cloudpickle 2.0.0 pyhd8ed1ab_0 conda-forge
codespell 2.1.0 pypi_0 pypi
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
commonmark 0.9.1 pypi_0 pypi
conda 4.12.0 py39h2804cbe_0 conda-forge
conda-package-handling 1.7.3 py39h5161555_1 conda-forge
cryptography 37.0.1 pypi_0 pypi
curl 7.82.0 hb0e6552_0 conda-forge
cycler 0.10.0 pypi_0 pypi
cython 0.29.28 pypi_0 pypi
cytoolz 0.11.2 py39hb18efdd_2 conda-forge
dask 2022.4.1 pypi_0 pypi
dcmstack 0.8.0 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
dicom 0.9.9.post1 pypi_0 pypi
dicom2nifti 2.3.3 pypi_0 pypi
dipy 1.6.0.dev0 pypi_0 pypi
double-conversion 3.2.0 hbdafb3b_0 conda-forge
eigen 3.4.0 hc021e02_0 conda-forge
euclid 1.2 pypi_0 pypi
expat 2.4.8 h6b3803e_0 conda-forge
ffmpeg 4.3.2 h38cfed3_3 conda-forge
filelock 3.6.0 pypi_0 pypi
fonttools 4.33.3 pypi_0 pypi
freetype 2.10.4 h17b34a0_1 conda-forge
frozenlist 1.3.0 pypi_0 pypi
fsspec 2022.3.0 pyhd8ed1ab_0 conda-forge
fury 0.8.0.post416+g5059a52 pypi_0 pypi
gdown 4.4.0 pypi_0 pypi
gettext 0.19.8.1 h049c9fb_1008 conda-forge
giflib 5.2.1 h27ca646_2 conda-forge
gl2ps 1.4.2 h17b34a0_0 conda-forge
glcontext 2.3.6 pypi_0 pypi
glew 2.1.0 h9f76cd9_2 conda-forge
gmp 6.2.1 h9f76cd9_0 conda-forge
gnutls 3.6.13 h706517b_1 conda-forge
h5py 3.6.0 nompi_py39hd982b79_100 conda-forge
hdf4 4.2.15 h0ef36ac_3 conda-forge
hdf5 1.12.1 nompi_hf9525e8_104 conda-forge
icu 70.1 h6b3803e_0 conda-forge
idna 3.3 pypi_0 pypi
imagecodecs 2022.2.22 py39h9494253_1 conda-forge
imageio 2.13.3 pypi_0 pypi
jbig 2.1 h3422bc3_2003 conda-forge
jdata 0.4.0 pypi_0 pypi
jinja2 3.1.2 pypi_0 pypi
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h3422bc3_0 conda-forge
jsoncpp 1.9.5 hc021e02_1 conda-forge
jxrlib 1.1 h27ca646_2 conda-forge
kiwisolver 1.3.2 pypi_0 pypi
krb5 1.19.3 hf9b2bbe_0 conda-forge
lame 3.100 h27ca646_1001 conda-forge
lcms2 2.12 had6a04f_0 conda-forge
lerc 3.0 hbdafb3b_0 conda-forge
libaec 1.0.6 hbdafb3b_0 conda-forge
libavif 0.9.3 h1c322ee_1 conda-forge
libblas 3.9.0 12_osxarm64_openblas conda-forge
libbrotlicommon 1.0.9 h1c322ee_7 conda-forge
libbrotlidec 1.0.9 h1c322ee_7 conda-forge
libbrotlienc 1.0.9 h1c322ee_7 conda-forge
libcblas 3.9.0 12_osxarm64_openblas conda-forge
libcurl 7.82.0 hb0e6552_0 conda-forge
libcxx 12.0.1 h168391b_1 conda-forge
libdeflate 1.10 h3422bc3_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libev 4.33 h642e427_1 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libgfortran 5.0.0.dev0 11_0_1_hf114ba7_23 conda-forge
libgfortran5 11.0.1.dev0 hf114ba7_23 conda-forge
libiconv 1.16 h642e427_0 conda-forge
liblapack 3.9.0 12_osxarm64_openblas conda-forge
libnetcdf 4.8.1 nompi_h96a3436_101 conda-forge
libnghttp2 1.47.0 he723fca_0 conda-forge
libogg 1.3.4 h27ca646_1 conda-forge
libopenblas 0.3.18 openmp_h5dd58f0_0 conda-forge
libpng 1.6.37 hf7e6567_2 conda-forge
libssh2 1.10.0 hb80f160_2 conda-forge
libtheora 1.1.1 h3422bc3_1005 conda-forge
libtiff 4.3.0 h77dc3b6_3 conda-forge
libvorbis 1.3.7 h9f76cd9_0 conda-forge
libwebp 1.2.2 h0d20362_0 conda-forge
libwebp-base 1.2.2 h3422bc3_1 conda-forge
libxcb 1.13 h9b22ae9_1004 conda-forge
libxml2 2.9.12 h97d9dda_2 conda-forge
libzip 1.8.0 h3887732_1 conda-forge
libzlib 1.2.11 hee7b306_1013 conda-forge
libzopfli 1.0.3 h9f76cd9_0 conda-forge
llvm-openmp 12.0.1 hf3c4609_1 conda-forge
locket 1.0.0 pypi_0 pypi
loguru 0.6.0 py39h2804cbe_1 conda-forge
lxml 4.8.0 pypi_0 pypi
lz4-c 1.9.3 hbdafb3b_1 conda-forge
markupsafe 2.1.1 pypi_0 pypi
matplotlib 3.4.3 pypi_0 pypi
matplotlib-base 3.5.1 py39h5aa4fe7_0 conda-forge
meshio 5.3.4 pypi_0 pypi
mne 1.0.2 pypi_0 pypi
moderngl 5.6.4 pypi_0 pypi
multidict 6.0.2 pypi_0 pypi
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
ncurses 6.2 h9aa5885_4 conda-forge
nettle 3.6 hc6a1b29_0 conda-forge
networkx 2.8 pypi_0 pypi
nibabel 3.2.1 pypi_0 pypi
nilearn 0.9.1 pypi_0 pypi
numexpr 2.8.1 pypi_0 pypi
numpy 1.22.3 pypi_0 pypi
numpy-stl 2.16.3 pypi_0 pypi
openh264 2.1.1 habe5f53_0 conda-forge
openjpeg 2.4.0 h062765e_1 conda-forge
openssl 1.1.1n h90dfc92_0 conda-forge
packaging 21.0 pypi_0 pypi
pandas 1.3.2 pypi_0 pypi
partd 1.2.0 pyhd8ed1ab_0 conda-forge
patsy 0.5.2 pyhd8ed1ab_0 conda-forge
pillow 8.3.2 pypi_0 pypi
pip 22.0.4 pypi_0 pypi
pooch 1.6.0 pypi_0 pypi
proj 8.2.1 h2d984c1_0 conda-forge
pthread-stubs 0.4 h27ca646_1001 conda-forge
pugixml 1.11.4 hbdafb3b_0 conda-forge
pycosat 0.6.3 py39h5161555_1009 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydicom 2.3.0 pypi_0 pypi
pyfqmr 0.1.1 pypi_0 pypi
pyglet 1.5.23 pypi_0 pypi
pygments 2.12.0 pypi_0 pypi
pymesh 1.0.2 pypi_0 pypi
pyopenssl 22.0.0 pypi_0 pypi
pyparsing 3.0.8 pypi_0 pypi
pysocks 1.7.1 py39h2804cbe_4 conda-forge
pytables 3.7.0 py39h086b50d_0 conda-forge
python 3.9.9 h70c1b39_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-utils 3.1.0 pypi_0 pypi
python_abi 3.9 2_cp39 conda-forge
pytz 2021.1 pypi_0 pypi
pywavelets 1.2.0 pypi_0 pypi
pyyaml 6.0 py39hb18efdd_4 conda-forge
readline 8.1 hedafd6a_0 conda-forge
requests 2.27.1 pyhd8ed1ab_0 conda-forge
rich 12.3.0 pypi_0 pypi
ruamel_yaml 0.15.80 py39h5161555_1006 conda-forge
scikit-image 0.19.0 pypi_0 pypi
scikit-learn 1.0.2 py39hef7049f_0 conda-forge
scipy 1.8.0 pypi_0 pypi
seaborn 0.11.2 pypi_0 pypi
setuptools 60.5.0 py39h2804cbe_0 conda-forge
simpleitk 2.1.1.2 pypi_0 pypi
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.8 hc88da5d_3 conda-forge
soupsieve 2.3.2.post1 pypi_0 pypi
sqlite 3.37.0 h72a2b83_0 conda-forge
statsmodels 0.13.2 py39h20ef057_0 conda-forge
tbb 2021.5.0 h3e96240_1 conda-forge
tbb-devel 2021.5.0 h3e96240_1 conda-forge
threadpoolctl 3.1.0 pypi_0 pypi
tifffile 2021.11.2 pypi_0 pypi
tk 8.6.12 he1e0b03_0 conda-forge
toolz 0.11.2 pyhd8ed1ab_0 conda-forge
torch 1.11.0 pypi_0 pypi
tqdm 4.64.0 pypi_0 pypi
trimesh 3.11.2 pypi_0 pypi
typing-extensions 4.2.0 pypi_0 pypi
tzdata 2021e he74cb21_0 conda-forge
unicodedata2 14.0.0 py39hb18efdd_1 conda-forge
urllib3 1.26.9 pypi_0 pypi
utfcpp 3.2.1 hce30654_0 conda-forge
vtk 9.1.0 pypi_0 pypi
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
wslink 1.6.1 pypi_0 pypi
wxpython 4.1.1 pypi_0 pypi
x264 1!161.3030 h3422bc3_1 conda-forge
xorg-libxau 1.0.9 h27ca646_0 conda-forge
xorg-libxdmcp 1.1.3 h27ca646_0 conda-forge
xz 5.2.5 h642e427_1 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
yarl 1.7.2 pypi_0 pypi
yyjson 0.3.1 pypi_0 pypi
zfp 0.5.5 hcfdfaf5_8 conda-forge
zlib 1.2.11 hee7b306_1013 conda-forge
zstd 1.5.2 h861e0a7_0 conda-forgedeactivating condo and attempting to a clean install did not go well:
pip3 install -e .
DEPRECATION: Configuring installation scheme with distutils config files is deprecated and will no longer work in the near future. If you are using a Homebrew or Linuxbrew Python, please see discussion at https://github.com/Homebrew/homebrew-core/issues/76621
Obtaining file:///Users/chrisrorden/Downloads/tractography_file_format
Preparing metadata (setup.py) ... done
Collecting fury@ git+https://github.com/frheault/fury.git@5059a529#egg=fury
Cloning https://github.com/frheault/fury.git (to revision 5059a529) to /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-sw_3v8ui/fury_82af4cb13191472cbc8c4364b907d666
Running command git clone --filter=blob:none --quiet https://github.com/frheault/fury.git /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-sw_3v8ui/fury_82af4cb13191472cbc8c4364b907d666
WARNING: Did not find branch or tag '5059a529', assuming revision or ref.
Running command git checkout -q 5059a529
Resolved https://github.com/frheault/fury.git to commit 5059a529
Preparing metadata (setup.py) ... done
Collecting dipy@ git+https://github.com/frheault/dipy.git@4e192c5c6#egg=dipy
Cloning https://github.com/frheault/dipy.git (to revision 4e192c5c6) to /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-sw_3v8ui/dipy_204ef0147cf94966a3dc2123d8da3c95
Running command git clone --filter=blob:none --quiet https://github.com/frheault/dipy.git /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-sw_3v8ui/dipy_204ef0147cf94966a3dc2123d8da3c95
WARNING: Did not find branch or tag '4e192c5c6', assuming revision or ref.
Running command git checkout -q 4e192c5c6
Resolved https://github.com/frheault/dipy.git to commit 4e192c5c6
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [8 lines of output]
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-sw_3v8ui/dipy_204ef0147cf94966a3dc2123d8da3c95/setup.py", line 34, in <module>
from cythexts import cyproc_exts, get_pyx_sdist
File "/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-sw_3v8ui/dipy_204ef0147cf94966a3dc2123d8da3c95/cythexts.py", line 7, in <module>
from packaging.version import Version
ModuleNotFoundError: No module named 'packaging'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.@neurolabusc for the clean env there is a ModuleNotFoundError: No module named 'packaging' that can be solved doing a pip install packaging first. This is coming from Dipy and I can't fix that (I don't know how)
When I get out of isolation I will do some testing on a Mac with and without Anancoda and hopefully replicate your error.
neurolabusc
commented
2 years ago It still fails:
pip3 install -e .
DEPRECATION: Configuring installation scheme with distutils config files is deprecated and will no longer work in the near future. If you are using a Homebrew or Linuxbrew Python, please see discussion at https://github.com/Homebrew/homebrew-core/issues/76621
Obtaining file:///Users/chrisrorden/Downloads/tractography_file_format
Preparing metadata (setup.py) ... done
Collecting fury@ git+https://github.com/frheault/fury.git@5059a529#egg=fury
Cloning https://github.com/frheault/fury.git (to revision 5059a529) to /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/fury_be8c2ba98456401aade12b83137e594f
Running command git clone --filter=blob:none --quiet https://github.com/frheault/fury.git /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/fury_be8c2ba98456401aade12b83137e594f
WARNING: Did not find branch or tag '5059a529', assuming revision or ref.
Running command git checkout -q 5059a529
Resolved https://github.com/frheault/fury.git to commit 5059a529
Preparing metadata (setup.py) ... done
Collecting dipy@ git+https://github.com/frheault/dipy.git@4e192c5c6#egg=dipy
Cloning https://github.com/frheault/dipy.git (to revision 4e192c5c6) to /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/dipy_6ced980d2e844f4db296afe414d769da
Running command git clone --filter=blob:none --quiet https://github.com/frheault/dipy.git /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/dipy_6ced980d2e844f4db296afe414d769da
WARNING: Did not find branch or tag '4e192c5c6', assuming revision or ref.
Running command git checkout -q 4e192c5c6
Resolved https://github.com/frheault/dipy.git to commit 4e192c5c6
Preparing metadata (setup.py) ... done
Collecting gdown>=4.*
Using cached gdown-4.4.0-py3-none-any.whl
Collecting tqdm
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Building wheels for collected packages: dipy, fury, h5py
Building wheel for dipy (setup.py) ... error
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/opt/homebrew/lib/python3.9/site-packages/setuptools/dist.py:506: UserWarning: Normalizing '1.6.0dev0' to '1.6.0.dev0'
warnings.warn(tmpl.format(**locals()))
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-11-arm64-3.9
creating build/lib.macosx-11-arm64-3.9/dipy
copying dipy/conftest.py -> build/lib.macosx-11-arm64-3.9/dipy
copying dipy/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy
copying dipy/pkg_info.py -> build/lib.macosx-11-arm64-3.9/dipy
copying dipy/info.py -> build/lib.macosx-11-arm64-3.9/dipy
creating build/lib.macosx-11-arm64-3.9/dipy/tests
copying dipy/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/tests
copying dipy/tests/scriptrunner.py -> build/lib.macosx-11-arm64-3.9/dipy/tests
copying dipy/tests/test_scripts.py -> build/lib.macosx-11-arm64-3.9/dipy/tests
creating build/lib.macosx-11-arm64-3.9/dipy/align
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copying dipy/align/metrics.py -> build/lib.macosx-11-arm64-3.9/dipy/align
copying dipy/align/scalespace.py -> build/lib.macosx-11-arm64-3.9/dipy/align
copying dipy/align/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/align
copying dipy/align/imaffine.py -> build/lib.macosx-11-arm64-3.9/dipy/align
copying dipy/align/imwarp.py -> build/lib.macosx-11-arm64-3.9/dipy/align
copying dipy/align/reslice.py -> build/lib.macosx-11-arm64-3.9/dipy/align
copying dipy/align/_public.py -> build/lib.macosx-11-arm64-3.9/dipy/align
creating build/lib.macosx-11-arm64-3.9/dipy/align/tests
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copying dipy/align/tests/test_imwarp.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/test_metrics.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/test_vector_fields.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/test_sumsqdiff.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/test_whole_brain_slr.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/test_transforms.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/test_scalespace.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/test_api.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/test_streamlinear.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/test_imaffine.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/test_crosscorr.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/test_parzenhist.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
copying dipy/align/tests/test_reslice.py -> build/lib.macosx-11-arm64-3.9/dipy/align/tests
creating build/lib.macosx-11-arm64-3.9/dipy/core
copying dipy/core/optimize.py -> build/lib.macosx-11-arm64-3.9/dipy/core
copying dipy/core/rng.py -> build/lib.macosx-11-arm64-3.9/dipy/core
copying dipy/core/gradients.py -> build/lib.macosx-11-arm64-3.9/dipy/core
copying dipy/core/profile.py -> build/lib.macosx-11-arm64-3.9/dipy/core
copying dipy/core/graph.py -> build/lib.macosx-11-arm64-3.9/dipy/core
copying dipy/core/subdivide_octahedron.py -> build/lib.macosx-11-arm64-3.9/dipy/core
copying dipy/core/ndindex.py -> build/lib.macosx-11-arm64-3.9/dipy/core
copying dipy/core/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/core
copying dipy/core/wavelet.py -> build/lib.macosx-11-arm64-3.9/dipy/core
copying dipy/core/geometry.py -> build/lib.macosx-11-arm64-3.9/dipy/core
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copying dipy/core/sphere_stats.py -> build/lib.macosx-11-arm64-3.9/dipy/core
creating build/lib.macosx-11-arm64-3.9/dipy/core/tests
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copying dipy/core/tests/test_rng.py -> build/lib.macosx-11-arm64-3.9/dipy/core/tests
copying dipy/core/tests/test_ndindex.py -> build/lib.macosx-11-arm64-3.9/dipy/core/tests
copying dipy/core/tests/test_optimize.py -> build/lib.macosx-11-arm64-3.9/dipy/core/tests
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copying dipy/core/tests/test_graph.py -> build/lib.macosx-11-arm64-3.9/dipy/core/tests
copying dipy/core/tests/test_geometry.py -> build/lib.macosx-11-arm64-3.9/dipy/core/tests
copying dipy/core/tests/test_gradients.py -> build/lib.macosx-11-arm64-3.9/dipy/core/tests
copying dipy/core/tests/test_subdivide_octahedron.py -> build/lib.macosx-11-arm64-3.9/dipy/core/tests
creating build/lib.macosx-11-arm64-3.9/dipy/direction
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copying dipy/direction/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/direction
creating build/lib.macosx-11-arm64-3.9/dipy/direction/tests
copying dipy/direction/tests/test_prob_direction_getter.py -> build/lib.macosx-11-arm64-3.9/dipy/direction/tests
copying dipy/direction/tests/test_bootstrap_direction_getter.py -> build/lib.macosx-11-arm64-3.9/dipy/direction/tests
copying dipy/direction/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/direction/tests
copying dipy/direction/tests/test_peaks.py -> build/lib.macosx-11-arm64-3.9/dipy/direction/tests
copying dipy/direction/tests/test_pmf.py -> build/lib.macosx-11-arm64-3.9/dipy/direction/tests
creating build/lib.macosx-11-arm64-3.9/dipy/tracking
copying dipy/tracking/metrics.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking
copying dipy/tracking/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking
copying dipy/tracking/mesh.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking
copying dipy/tracking/streamline.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking
copying dipy/tracking/life.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking
copying dipy/tracking/utils.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking
copying dipy/tracking/learning.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking
copying dipy/tracking/local_tracking.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking
copying dipy/tracking/_utils.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking
creating build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/test_utils.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/test_track_volumes.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/test_metrics.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/test_mesh.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/test_stopping_criterion.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/test_streamline.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/test_learning.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/test_distances.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/test_tracking.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/test_life.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/test_fbc.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
copying dipy/tracking/tests/test_propagation.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/tests
creating build/lib.macosx-11-arm64-3.9/dipy/tracking/benchmarks
copying dipy/tracking/benchmarks/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/benchmarks
copying dipy/tracking/benchmarks/bench_streamline.py -> build/lib.macosx-11-arm64-3.9/dipy/tracking/benchmarks
creating build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/fwdti.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/qtdmri.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/dti.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/shm.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/qti.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/odf.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/forecast.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/mapmri.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/rumba.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/dsi.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/msdki.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/multi_voxel.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/cache.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/shore.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/utils.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/mcsd.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/dki_micro.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/csdeconv.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/ivim.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/gqi.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/dki.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/base.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/sfm.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
copying dipy/reconst/cross_validation.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst
creating build/lib.macosx-11-arm64-3.9/dipy/reconst/benchmarks
copying dipy/reconst/benchmarks/bench_csd.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/benchmarks
copying dipy/reconst/benchmarks/bench_bounding_box.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/benchmarks
copying dipy/reconst/benchmarks/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/benchmarks
copying dipy/reconst/benchmarks/bench_squash.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/benchmarks
copying dipy/reconst/benchmarks/bench_vec_val_sum.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/benchmarks
copying dipy/reconst/benchmarks/bench_peaks.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/benchmarks
creating build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_dki_micro.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_utils.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_multi_voxel.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_cross_validation.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_dti.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_shm.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_qti.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_shore_odf.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_eudx_dg.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_odf.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_forecast.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_shore_metrics.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_dsi.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_reco_utils.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_fwdti.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_csdeconv.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_gqi.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_qtdmri.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_mcsd.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_dki.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_vec_val_vect.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_mapmri.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_sfm.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_msdki.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_rumba.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_peak_finding.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_dsi_metrics.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_cache.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_shore.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_ivim.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
copying dipy/reconst/tests/test_dsi_deconv.py -> build/lib.macosx-11-arm64-3.9/dipy/reconst/tests
creating build/lib.macosx-11-arm64-3.9/dipy/io
copying dipy/io/peaks.py -> build/lib.macosx-11-arm64-3.9/dipy/io
copying dipy/io/pickles.py -> build/lib.macosx-11-arm64-3.9/dipy/io
copying dipy/io/gradients.py -> build/lib.macosx-11-arm64-3.9/dipy/io
copying dipy/io/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/io
copying dipy/io/stateful_tractogram.py -> build/lib.macosx-11-arm64-3.9/dipy/io
copying dipy/io/streamline.py -> build/lib.macosx-11-arm64-3.9/dipy/io
copying dipy/io/utils.py -> build/lib.macosx-11-arm64-3.9/dipy/io
copying dipy/io/vtk.py -> build/lib.macosx-11-arm64-3.9/dipy/io
copying dipy/io/dpy.py -> build/lib.macosx-11-arm64-3.9/dipy/io
copying dipy/io/bvectxt.py -> build/lib.macosx-11-arm64-3.9/dipy/io
copying dipy/io/image.py -> build/lib.macosx-11-arm64-3.9/dipy/io
creating build/lib.macosx-11-arm64-3.9/dipy/io/tests
copying dipy/io/tests/test_utils.py -> build/lib.macosx-11-arm64-3.9/dipy/io/tests
copying dipy/io/tests/test_io_gradients.py -> build/lib.macosx-11-arm64-3.9/dipy/io/tests
copying dipy/io/tests/test_streamline.py -> build/lib.macosx-11-arm64-3.9/dipy/io/tests
copying dipy/io/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/io/tests
copying dipy/io/tests/test_io.py -> build/lib.macosx-11-arm64-3.9/dipy/io/tests
copying dipy/io/tests/test_io_peaks.py -> build/lib.macosx-11-arm64-3.9/dipy/io/tests
copying dipy/io/tests/test_stateful_tractogram.py -> build/lib.macosx-11-arm64-3.9/dipy/io/tests
copying dipy/io/tests/test_dpy.py -> build/lib.macosx-11-arm64-3.9/dipy/io/tests
creating build/lib.macosx-11-arm64-3.9/dipy/viz
copying dipy/viz/gmem.py -> build/lib.macosx-11-arm64-3.9/dipy/viz
copying dipy/viz/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/viz
copying dipy/viz/regtools.py -> build/lib.macosx-11-arm64-3.9/dipy/viz
copying dipy/viz/app.py -> build/lib.macosx-11-arm64-3.9/dipy/viz
copying dipy/viz/projections.py -> build/lib.macosx-11-arm64-3.9/dipy/viz
copying dipy/viz/panel.py -> build/lib.macosx-11-arm64-3.9/dipy/viz
creating build/lib.macosx-11-arm64-3.9/dipy/viz/tests
copying dipy/viz/tests/test_apps.py -> build/lib.macosx-11-arm64-3.9/dipy/viz/tests
copying dipy/viz/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/viz/tests
copying dipy/viz/tests/test_viz_import.py -> build/lib.macosx-11-arm64-3.9/dipy/viz/tests
copying dipy/viz/tests/test_fury.py -> build/lib.macosx-11-arm64-3.9/dipy/viz/tests
copying dipy/viz/tests/test_regtools.py -> build/lib.macosx-11-arm64-3.9/dipy/viz/tests
creating build/lib.macosx-11-arm64-3.9/dipy/testing
copying dipy/testing/spherepoints.py -> build/lib.macosx-11-arm64-3.9/dipy/testing
copying dipy/testing/memory.py -> build/lib.macosx-11-arm64-3.9/dipy/testing
copying dipy/testing/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/testing
copying dipy/testing/decorators.py -> build/lib.macosx-11-arm64-3.9/dipy/testing
creating build/lib.macosx-11-arm64-3.9/dipy/testing/tests
copying dipy/testing/tests/test_decorators.py -> build/lib.macosx-11-arm64-3.9/dipy/testing/tests
copying dipy/testing/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/testing/tests
copying dipy/testing/tests/test_memory.py -> build/lib.macosx-11-arm64-3.9/dipy/testing/tests
copying dipy/testing/tests/test_testing.py -> build/lib.macosx-11-arm64-3.9/dipy/testing/tests
creating build/lib.macosx-11-arm64-3.9/dipy/boots
copying dipy/boots/resampling.py -> build/lib.macosx-11-arm64-3.9/dipy/boots
copying dipy/boots/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/boots
creating build/lib.macosx-11-arm64-3.9/dipy/data
copying dipy/data/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/data
copying dipy/data/fetcher.py -> build/lib.macosx-11-arm64-3.9/dipy/data
creating build/lib.macosx-11-arm64-3.9/dipy/data/tests
copying dipy/data/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/data/tests
copying dipy/data/tests/test_data.py -> build/lib.macosx-11-arm64-3.9/dipy/data/tests
copying dipy/data/tests/test_fetcher.py -> build/lib.macosx-11-arm64-3.9/dipy/data/tests
creating build/lib.macosx-11-arm64-3.9/dipy/utils
copying dipy/utils/tripwire.py -> build/lib.macosx-11-arm64-3.9/dipy/utils
copying dipy/utils/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/utils
copying dipy/utils/optpkg.py -> build/lib.macosx-11-arm64-3.9/dipy/utils
copying dipy/utils/_importlib.py -> build/lib.macosx-11-arm64-3.9/dipy/utils
copying dipy/utils/deprecator.py -> build/lib.macosx-11-arm64-3.9/dipy/utils
copying dipy/utils/parallel.py -> build/lib.macosx-11-arm64-3.9/dipy/utils
copying dipy/utils/multiproc.py -> build/lib.macosx-11-arm64-3.9/dipy/utils
copying dipy/utils/arrfuncs.py -> build/lib.macosx-11-arm64-3.9/dipy/utils
creating build/lib.macosx-11-arm64-3.9/dipy/utils/tests
copying dipy/utils/tests/test_tripwire.py -> build/lib.macosx-11-arm64-3.9/dipy/utils/tests
copying dipy/utils/tests/test_deprecator.py -> build/lib.macosx-11-arm64-3.9/dipy/utils/tests
copying dipy/utils/tests/test_multiproc.py -> build/lib.macosx-11-arm64-3.9/dipy/utils/tests
copying dipy/utils/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/utils/tests
copying dipy/utils/tests/test_parallel.py -> build/lib.macosx-11-arm64-3.9/dipy/utils/tests
copying dipy/utils/tests/test_arrfuncs.py -> build/lib.macosx-11-arm64-3.9/dipy/utils/tests
copying dipy/utils/tests/test_omp.py -> build/lib.macosx-11-arm64-3.9/dipy/utils/tests
creating build/lib.macosx-11-arm64-3.9/dipy/segment
copying dipy/segment/mask.py -> build/lib.macosx-11-arm64-3.9/dipy/segment
copying dipy/segment/clustering.py -> build/lib.macosx-11-arm64-3.9/dipy/segment
copying dipy/segment/tissue.py -> build/lib.macosx-11-arm64-3.9/dipy/segment
copying dipy/segment/bundles.py -> build/lib.macosx-11-arm64-3.9/dipy/segment
copying dipy/segment/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/segment
copying dipy/segment/threshold.py -> build/lib.macosx-11-arm64-3.9/dipy/segment
copying dipy/segment/metric.py -> build/lib.macosx-11-arm64-3.9/dipy/segment
creating build/lib.macosx-11-arm64-3.9/dipy/segment/benchmarks
copying dipy/segment/benchmarks/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/segment/benchmarks
copying dipy/segment/benchmarks/bench_quickbundles.py -> build/lib.macosx-11-arm64-3.9/dipy/segment/benchmarks
creating build/lib.macosx-11-arm64-3.9/dipy/segment/tests
copying dipy/segment/tests/test_metric.py -> build/lib.macosx-11-arm64-3.9/dipy/segment/tests
copying dipy/segment/tests/test_bundles.py -> build/lib.macosx-11-arm64-3.9/dipy/segment/tests
copying dipy/segment/tests/test_adjustment.py -> build/lib.macosx-11-arm64-3.9/dipy/segment/tests
copying dipy/segment/tests/test_mask.py -> build/lib.macosx-11-arm64-3.9/dipy/segment/tests
copying dipy/segment/tests/test_feature.py -> build/lib.macosx-11-arm64-3.9/dipy/segment/tests
copying dipy/segment/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/segment/tests
copying dipy/segment/tests/test_quickbundles.py -> build/lib.macosx-11-arm64-3.9/dipy/segment/tests
copying dipy/segment/tests/test_mrf.py -> build/lib.macosx-11-arm64-3.9/dipy/segment/tests
copying dipy/segment/tests/test_qbx.py -> build/lib.macosx-11-arm64-3.9/dipy/segment/tests
copying dipy/segment/tests/test_clustering.py -> build/lib.macosx-11-arm64-3.9/dipy/segment/tests
creating build/lib.macosx-11-arm64-3.9/dipy/sims
copying dipy/sims/phantom.py -> build/lib.macosx-11-arm64-3.9/dipy/sims
copying dipy/sims/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/sims
copying dipy/sims/voxel.py -> build/lib.macosx-11-arm64-3.9/dipy/sims
creating build/lib.macosx-11-arm64-3.9/dipy/sims/tests
copying dipy/sims/tests/test_voxel.py -> build/lib.macosx-11-arm64-3.9/dipy/sims/tests
copying dipy/sims/tests/test_phantom.py -> build/lib.macosx-11-arm64-3.9/dipy/sims/tests
copying dipy/sims/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/sims/tests
creating build/lib.macosx-11-arm64-3.9/dipy/stats
copying dipy/stats/analysis.py -> build/lib.macosx-11-arm64-3.9/dipy/stats
copying dipy/stats/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/stats
creating build/lib.macosx-11-arm64-3.9/dipy/stats/tests
copying dipy/stats/tests/test_analysis.py -> build/lib.macosx-11-arm64-3.9/dipy/stats/tests
copying dipy/stats/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/stats/tests
creating build/lib.macosx-11-arm64-3.9/dipy/denoise
copying dipy/denoise/non_local_means.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise
copying dipy/denoise/patch2self.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise
copying dipy/denoise/localpca.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise
copying dipy/denoise/noise_estimate.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise
copying dipy/denoise/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise
copying dipy/denoise/adaptive_soft_matching.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise
copying dipy/denoise/gibbs.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise
copying dipy/denoise/nlmeans.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise
creating build/lib.macosx-11-arm64-3.9/dipy/denoise/tests
copying dipy/denoise/tests/test_ascm.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise/tests
copying dipy/denoise/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise/tests
copying dipy/denoise/tests/test_noise_estimate.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise/tests
copying dipy/denoise/tests/test_non_local_means.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise/tests
copying dipy/denoise/tests/test_nlmeans.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise/tests
copying dipy/denoise/tests/test_lpca.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise/tests
copying dipy/denoise/tests/test_kernel.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise/tests
copying dipy/denoise/tests/test_patch2self.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise/tests
copying dipy/denoise/tests/test_gibbs.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise/tests
copying dipy/denoise/tests/test_denoise.py -> build/lib.macosx-11-arm64-3.9/dipy/denoise/tests
creating build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/mask.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/reconst.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/multi_io.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/combined_workflow.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/align.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/io.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/flow_runner.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/stats.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/workflow.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/segment.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/denoise.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/viz.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/tracking.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/base.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
copying dipy/workflows/docstring_parser.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows
creating build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_stats.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/workflow_tests_utils.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_docstring_parser.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_reconst_ivim.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_reconst_dki.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_masking.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_iap.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_io.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_reconst_dti.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_workflow.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_tracking.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_viz.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_align.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_reconst_mapmri.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_reconst_csa_csd.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_segment.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
copying dipy/workflows/tests/test_denoise.py -> build/lib.macosx-11-arm64-3.9/dipy/workflows/tests
creating build/lib.macosx-11-arm64-3.9/dipy/nn
copying dipy/nn/histo_resdnn.py -> build/lib.macosx-11-arm64-3.9/dipy/nn
copying dipy/nn/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/nn
copying dipy/nn/model.py -> build/lib.macosx-11-arm64-3.9/dipy/nn
creating build/lib.macosx-11-arm64-3.9/dipy/nn/tests
copying dipy/nn/tests/test_tf.py -> build/lib.macosx-11-arm64-3.9/dipy/nn/tests
copying dipy/nn/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/dipy/nn/tests
copying dipy/nn/tests/test_histo_resdnn.py -> build/lib.macosx-11-arm64-3.9/dipy/nn/tests
creating build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/test_ui_text_block.npz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/ScannerVectors_GQI101.txt -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/small_64D.bvals.npy -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/aniso_vox.nii.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/55dir_grad.bvec -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/evenly_distributed_sphere_642.npz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/tdesign45.txt -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/fib1.pkl.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/func_discrete.nii.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/grad_514.txt -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/dsi4169_b_table.txt -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/life_matlab_weights.npy -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/evenly_distributed_sphere_724.npz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/dipy_colormaps.json -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/EuDX_small_25.trk -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/small_101D.bvec -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/tracks300.trk -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/C.npy -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/life_matlab_rmse.npy -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/small_64D.gradients.npy -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/small_101D.bval -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/gtab_3shell.txt -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/repulsion724.npz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/small_25.nii.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/55dir_grad.bval -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/test_piesno.nii.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/cb_2.npz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/gtab_isbi2013_2shell.txt -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/fib2.pkl.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/C3.pkl.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/small_64D.bval -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/func_coef.nii.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/repulsion100.npz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/small_101D.nii.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/eg_3voxels.pkl -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/C1.pkl.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/evenly_distributed_sphere_362.npz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/small_64D.nii -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/small_25.bvec -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/t1_coronal_slice.npy -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/fib0.pkl.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/gtab_taiwan_dsi.txt -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/small_64D.bvec -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/S0_10slices.nii.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/record_horizon.log.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/small_25.bval -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/sphere_grad.txt -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/dsi515_b_table.txt -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/repulsion200.npz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/circle.npy -> build/lib.macosx-11-arm64-3.9/dipy/data/files
copying dipy/data/files/ascm_out_test.nii.gz -> build/lib.macosx-11-arm64-3.9/dipy/data/files
running build_ext
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/dipy_6ced980d2e844f4db296afe414d769da/setup.py", line 245, in <module>
main(**extra_setuptools_args)
File "/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/dipy_6ced980d2e844f4db296afe414d769da/setup.py", line 177, in main
setup(name=info.NAME,
File "/opt/homebrew/lib/python3.9/site-packages/setuptools/__init__.py", line 155, in setup
return distutils.core.setup(**attrs)
File "/opt/homebrew/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 148, in setup
return run_commands(dist)
File "/opt/homebrew/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 163, in run_commands
dist.run_commands()
File "/opt/homebrew/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 967, in run_commands
self.run_command(cmd)
File "/opt/homebrew/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/opt/homebrew/lib/python3.9/site-packages/wheel/bdist_wheel.py", line 299, in run
self.run_command('build')
File "/opt/homebrew/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/opt/homebrew/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/opt/homebrew/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/opt/homebrew/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/opt/homebrew/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/dipy_6ced980d2e844f4db296afe414d769da/cythexts.py", line 14, in run
raise RuntimeError(msg)
RuntimeError: Need cython>=0.29.24 to build extensions but cannot import "Cython"
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for dipy
Running setup.py clean for dipy
Building wheel for fury (setup.py) ... done
Created wheel for fury: filename=fury-0.8.0.post416+g5059a52-py3-none-any.whl size=380600 sha256=e361e2757150039bf449b5e4c43d1bd6700aa61f637bf4cae99b7071b4185618
Stored in directory: /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-ephem-wheel-cache-y81j8slb/wheels/1f/59/cb/927f9ac22ab4ca5bbb7d091fd9395f820ebc66d84a81829df1
Building wheel for h5py (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for h5py (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [124 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-11-arm64-3.9
creating build/lib.macosx-11-arm64-3.9/h5py
copying h5py/h5py_warnings.py -> build/lib.macosx-11-arm64-3.9/h5py
copying h5py/version.py -> build/lib.macosx-11-arm64-3.9/h5py
copying h5py/__init__.py -> build/lib.macosx-11-arm64-3.9/h5py
copying h5py/ipy_completer.py -> build/lib.macosx-11-arm64-3.9/h5py
creating build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/files.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/compat.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/__init__.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/selections.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/dataset.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/vds.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/selections2.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/group.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/datatype.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/attrs.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/dims.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/base.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
copying h5py/_hl/filters.py -> build/lib.macosx-11-arm64-3.9/h5py/_hl
creating build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_dimension_scales.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_attribute_create.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_file_image.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/conftest.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_h5f.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_dataset_getitem.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_group.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_errors.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_dataset_swmr.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_slicing.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_h5pl.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_attrs.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/__init__.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_attrs_data.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_h5t.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_big_endian_file.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_h5p.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_h5o.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_datatype.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/common.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_dataset.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_file.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_selections.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_dtype.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_h5.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_file2.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_completions.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_filters.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_base.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
copying h5py/tests/test_objects.py -> build/lib.macosx-11-arm64-3.9/h5py/tests
creating build/lib.macosx-11-arm64-3.9/h5py/tests/data_files
copying h5py/tests/data_files/__init__.py -> build/lib.macosx-11-arm64-3.9/h5py/tests/data_files
creating build/lib.macosx-11-arm64-3.9/h5py/tests/test_vds
copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.macosx-11-arm64-3.9/h5py/tests/test_vds
copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.macosx-11-arm64-3.9/h5py/tests/test_vds
copying h5py/tests/test_vds/__init__.py -> build/lib.macosx-11-arm64-3.9/h5py/tests/test_vds
copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.macosx-11-arm64-3.9/h5py/tests/test_vds
copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.macosx-11-arm64-3.9/h5py/tests/data_files
copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.macosx-11-arm64-3.9/h5py/tests/data_files
copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.macosx-11-arm64-3.9/h5py/tests/data_files
running build_ext
Loading library to get build settings and version: libhdf5.dylib
********************************************************************************
Summary of the h5py configuration
HDF5 include dirs: []
HDF5 library dirs: []
HDF5 Version: (1, 12, 1)
MPI Enabled: False
ROS3 VFD Enabled: False
Rebuild Required: True
********************************************************************************
Executing api_gen rebuild of defs
Executing cythonize()
[ 1/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/_conv.pyx
[ 2/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/_errors.pyx
[ 3/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/_objects.pyx
[ 4/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/_proxy.pyx
[ 5/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/_selector.pyx
[ 6/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/defs.pyx
[ 7/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5.pyx
[ 8/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5a.pyx
[ 9/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5ac.pyx
[10/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5d.pyx
[11/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5ds.pyx
[12/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5f.pyx
[13/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5fd.pyx
[14/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5g.pyx
[15/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5i.pyx
[16/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5l.pyx
[17/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5o.pyx
[18/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5p.pyx
[19/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5pl.pyx
[20/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5r.pyx
[21/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5s.pyx
[22/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5t.pyx
[23/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/h5z.pyx
[24/24] Cythonizing /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/utils.pyx
building 'h5py.defs' extension
creating build/temp.macosx-11-arm64-3.9
creating build/temp.macosx-11-arm64-3.9/private
creating build/temp.macosx-11-arm64-3.9/private/var
creating build/temp.macosx-11-arm64-3.9/private/var/folders
creating build/temp.macosx-11-arm64-3.9/private/var/folders/4p
creating build/temp.macosx-11-arm64-3.9/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn
creating build/temp.macosx-11-arm64-3.9/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T
creating build/temp.macosx-11-arm64-3.9/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx
creating build/temp.macosx-11-arm64-3.9/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d
creating build/temp.macosx-11-arm64-3.9/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk -DH5_USE_18_API -DNPY_NO_DEPRECATED_API=0 -I./h5py -I/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/lzf -I/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/lzf/lzf -I/opt/homebrew/Cellar/python@3.9/3.9.12/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/include -I/opt/homebrew/Cellar/python@3.9/3.9.12/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/defs.c -o build/temp.macosx-11-arm64-3.9/private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/defs.o
In file included from /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-gaj2h2vx/h5py_f4018f9caa414bfd84ce03de4ad6736d/h5py/defs.c:740:
./h5py/api_compat.h:27:10: fatal error: 'hdf5.h' file not found
#include "hdf5.h"
^~~~~~~~
1 error generated.
error: command '/usr/bin/clang' 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 h5py
Successfully built fury
Failed to build dipy h5py
ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projectsI don't own a Mac, so I don't know why and partially remember, but I once solved that with brew install hdf5
The underlying error of the segfault will be hard to identify. There is an import from the viz module, which means VTK. I am 90% sure it's from VTK or something related to graphics.
EDIT: When I get my hands on a Mac Monday, I will note what I did from scratch and write it in the README.md Having a Windows, Mac, and Linux installation will be useful.
fionaEyoung
commented
2 years ago I once solved that with
brew install hdf5
This sounds very familiar. I also had huge issues getting dipy installed on my M1, that eventually was at least part of the solution.
I don't use anaconda, I use homebrew python.
neurolabusc
commented
2 years ago I was able to get pip3 install -e . to install cleanly without conda after getting hdf5 installed using this kludge since the default brew command failed. Now I am getting the following errors:
python3 ./tff_convert_tractogram.py ~/IFOF_L.trk ~/IFOF.trx
Traceback (most recent call last):
File "/Users/chrisrorden/Downloads/tractography_file_format/scripts/./tff_convert_tractogram.py", line 14, in <module>
from tractography_file_format.workflows import convert_tractogram
File "/Users/chrisrorden/Downloads/tractography_file_format/tractography_file_format/__init__.py", line 2, in <module>
from .utils import *
File "/Users/chrisrorden/Downloads/tractography_file_format/tractography_file_format/utils.py", line 8, in <module>
from dipy.io.stateful_tractogram import StatefulTractogram
File "/opt/homebrew/lib/python3.9/site-packages/dipy/io/__init__.py", line 5, in <module>
from .bvectxt import (read_bvec_file, ornt_mapping, reorient_vectors,
File "/opt/homebrew/lib/python3.9/site-packages/dipy/io/bvectxt.py", line 5, in <module>
from dipy.core import gradients
File "/opt/homebrew/lib/python3.9/site-packages/dipy/core/gradients.py", line 5, in <module>
from scipy.linalg import inv, polar
File "/opt/homebrew/lib/python3.9/site-packages/scipy/linalg/__init__.py", line 198, in <module>
from ._misc import *
File "/opt/homebrew/lib/python3.9/site-packages/scipy/linalg/_misc.py", line 3, in <module>
from .blas import get_blas_funcs
File "/opt/homebrew/lib/python3.9/site-packages/scipy/linalg/blas.py", line 213, in <module>
from scipy.linalg import _fblas
ImportError: dlopen(/opt/homebrew/lib/python3.9/site-packages/scipy/linalg/_fblas.cpython-39-darwin.so, 2): Library not loaded: @rpath/libopenblas.0.dylib
Referenced from: /opt/homebrew/lib/python3.9/site-packages/scipy/linalg/_fblas.cpython-39-darwin.so
Reason: image not foundIs there a way to get the functionality without all of these dependencies? Now that I have attempted to install via both conda and non-conda my system hard disk shows it getting filled with all things Python.
frheault
commented
2 years ago Dipy and Nibabel and VTK are required for the scripts and the utilities, so there no way around it.
You probably need brew install openblas lapack now.
Conda probably installed all of that (and a lot more), but it's weird Conda didn't work as it was.
I'm sorry I don't have a recipe for you, I'm not a Mac user and I don't know what's going on with Conda.
@fionaEyoung Is there something special about M1?
neurolabusc
commented
2 years ago Does not look
brew reinstall openblas lapack
==> Downloading https://ghcr.io/v2/homebrew/core/openblas/manifests/0.3.20
Already downloaded: /Users/chrisrorden/Library/Caches/Homebrew/downloads/f2d61ce797d723fc51e0172f9f30e3454c38301e0ac094222ca5fa081f5cd2d3--openblas-0.3.20.bottle_manifest.json
==> Downloading https://ghcr.io/v2/homebrew/core/openblas/blobs/sha256:a08b76f9d
Already downloaded: /Users/chrisrorden/Library/Caches/Homebrew/downloads/485cd15a9b761c24206551fc8e2c254103951bc055fdf84d9660a8fc61657f49--openblas--0.3.20.arm64_big_sur.bottle.tar.gz
==> Reinstalling openblas
==> Pouring openblas--0.3.20.arm64_big_sur.bottle.tar.gz
🍺 /opt/homebrew/Cellar/openblas/0.3.20: 23 files, 56.1MB
==> Running `brew cleanup openblas`...
Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP.
Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`).
==> Downloading https://ghcr.io/v2/homebrew/core/lapack/manifests/3.10.1
Already downloaded: /Users/chrisrorden/Library/Caches/Homebrew/downloads/7995608582d3d85c4bf4da5932b7ae698598deb9a20123dc81db6c7a0ddcad5f--lapack-3.10.1.bottle_manifest.json
==> Downloading https://ghcr.io/v2/homebrew/core/lapack/blobs/sha256:fcba5f25c50
Already downloaded: /Users/chrisrorden/Library/Caches/Homebrew/downloads/5043664b594fd0689ad4bbd2a6cc8f74ac6ad7d06193809ea0222d3ed1d04472--lapack--3.10.1.arm64_big_sur.bottle.tar.gz
==> Reinstalling lapack
==> Pouring lapack--3.10.1.arm64_big_sur.bottle.tar.gz
==> Caveats
lapack is keg-only, which means it was not symlinked into /opt/homebrew,
because macOS provides LAPACK in Accelerate.framework.
For compilers to find lapack you may need to set:
export LDFLAGS="-L/opt/homebrew/opt/lapack/lib"
export CPPFLAGS="-I/opt/homebrew/opt/lapack/include"
For pkg-config to find lapack you may need to set:
export PKG_CONFIG_PATH="/opt/homebrew/opt/lapack/lib/pkgconfig"
==> Summary
🍺 /opt/homebrew/Cellar/lapack/3.10.1: 29 files, 8.9MB
==> Running `brew cleanup lapack`...
==> Caveats
==> lapack
lapack is keg-only, which means it was not symlinked into /opt/homebrew,
because macOS provides LAPACK in Accelerate.framework.
For compilers to find lapack you may need to set:
export LDFLAGS="-L/opt/homebrew/opt/lapack/lib"
export CPPFLAGS="-I/opt/homebrew/opt/lapack/include"
For pkg-config to find lapack you may need to set:
export PKG_CONFIG_PATH="/opt/homebrew/opt/lapack/lib/pkgconfig"
scripts > python3 ./tff_convert_tractogram.py ~/IFOF_L.trk ~/IFO.trx
Traceback (most recent call last):
File "/Users/chrisrorden/Downloads/tractography_file_format/scripts/./tff_convert_tractogram.py", line 14, in <module>
from tractography_file_format.workflows import convert_tractogram
File "/Users/chrisrorden/Downloads/tractography_file_format/tractography_file_format/__init__.py", line 2, in <module>
from .utils import *
File "/Users/chrisrorden/Downloads/tractography_file_format/tractography_file_format/utils.py", line 8, in <module>
from dipy.io.stateful_tractogram import StatefulTractogram
File "/opt/homebrew/lib/python3.9/site-packages/dipy/io/__init__.py", line 5, in <module>
from .bvectxt import (read_bvec_file, ornt_mapping, reorient_vectors,
File "/opt/homebrew/lib/python3.9/site-packages/dipy/io/bvectxt.py", line 5, in <module>
from dipy.core import gradients
File "/opt/homebrew/lib/python3.9/site-packages/dipy/core/gradients.py", line 5, in <module>
from scipy.linalg import inv, polar
File "/opt/homebrew/lib/python3.9/site-packages/scipy/linalg/__init__.py", line 198, in <module>
from ._misc import *
File "/opt/homebrew/lib/python3.9/site-packages/scipy/linalg/_misc.py", line 3, in <module>
from .blas import get_blas_funcs
File "/opt/homebrew/lib/python3.9/site-packages/scipy/linalg/blas.py", line 213, in <module>
from scipy.linalg import _fblas
ImportError: dlopen(/opt/homebrew/lib/python3.9/site-packages/scipy/linalg/_fblas.cpython-39-darwin.so, 2): Library not loaded: @rpath/libopenblas.0.dylib
Referenced from: /opt/homebrew/lib/python3.9/site-packages/scipy/linalg/_fblas.cpython-39-darwin.so
Reason: image not found@arokem Do you have an idea?
This all comes from Dipy, is it Python3.9? M1 CPU? Is it the way I fetch a specific branch of Dipy in the setup.py
skoudoro
commented
2 years ago We do not provide wheels or tried with ARM64 yet for DIPY.
So, on macOS, I recommend using Rosetta for now (the x86_64 emulator). we need to check if all DIPY dependencies work with ARM64 which seems to not be the case now.
I did not follow the thread above so I am not sure if homebrew or conda is using the rosetta environment or ARM64 environment.
Also, do not forget that OpenGL "is not working" on the ARM64 architecture of the mac M1, you need to use the rosetta environment. VTK works only in the rosetta environment. They did not integrate vulkan/moltenvk and it will take quite some time for them to do it. This implies that the VTK reader can be problematic for quite a long time if you do not implement your own.
frheault
commented
2 years ago Well, this seems to explain why everything is breaking, thank you for the information. I had no idea there were so many underlying issues!
fionaEyoung
commented
2 years ago @neurolabusc does this help?
neurolabusc
commented
2 years ago @skoudoro thanks for all your insightful comments. I do want to take issue with your comment OpenGL "is not working" on the ARM64 architecture of the mac M1. You can try out the M1 builds of MRIcroGL and Surfice and see that Apple's OpenGL drivers for the M1 provide excellent performance. Indeed, I can compile MRIcroGL for either Metal API or OpenGL, and have chosen OpenGL since the performance is just as good. Apple's M1 OpenGL driver appears to be an abstraction to Metal. I have only discovered a couple of edge cases where OpenGL features do not have a Metal equivalent.
neurolabusc
commented
2 years ago I wonder if the DIPY developers could revisit this issue.
arokem
commented
2 years ago
- Homebrew supports native VTK 9.1.
Does this mean that Mac-bound DIPY users would have to install VTK with homebrew for DIPY to work? That might cause some environment messes (e.g., for conda users), no?
skoudoro
commented
2 years ago Thank you for pinging us @neurolabusc. I will look into it today or tomorrow.
it seems that our core dependencies (h5py, NumPy, scipy) and some optional dependencies (like VTK) have a wheel on PyPI for native support of macOS with python 3.9.
For some of them, the wheels are missing for python 3.10 so it will work only on python 3.9 for now.
So the goal is to check if all the tests passed with the current version of DIPY and arm64.
skoudoro
commented
2 years ago dipy-1.5.0-cp39-cp39-macosx_11_0_arm64.whl and dipy-1.5.0-cp39-cp39-macosx_10_9_universal2.whl have been created as you can see here
it should now work now natively on mac M1 with python 3.9. I do not have this machine so can you try it and give us an update @neurolabusc? (VTK should work also with pip install vtk)
Thanks!
neurolabusc
commented
2 years ago Any ideas?
$ python3 --version
Python 3.9.9
$ git clone --branch testing_script https://github.com/frheault/tractography_file_format.git
$ cd tractography_file_format
$ pip3 install -e .
Obtaining file:///Users/chrisrorden/src/tractography_file_format
Preparing metadata (setup.py) ... done
Collecting fury@ git+https://github.com/frheault/fury.git@5059a529#egg=fury
Cloning https://github.com/frheault/fury.git (to revision 5059a529) to /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-6txnxi8f/fury_9d902ee9c4a2496ba0234eb19a77f02b
Running command git clone --filter=blob:none --quiet https://github.com/frheault/fury.git /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-6txnxi8f/fury_9d902ee9c4a2496ba0234eb19a77f02b
WARNING: Did not find branch or tag '5059a529', assuming revision or ref.
Running command git checkout -q 5059a529
Resolved https://github.com/frheault/fury.git to commit 5059a529
Preparing metadata (setup.py) ... done
Collecting dipy@ git+https://github.com/frheault/dipy.git@4e192c5c6#egg=dipy
Cloning https://github.com/frheault/dipy.git (to revision 4e192c5c6) to /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-6txnxi8f/dipy_b1f71c0acf9a486ca7be04f8ad391233
Running command git clone --filter=blob:none --quiet https://github.com/frheault/dipy.git /private/var/folders/4p/cxb1ys0s4wz6dh3rtj22pq8w0000gn/T/pip-install-6txnxi8f/dipy_b1f71c0acf9a486ca7be04f8ad391233
WARNING: Did not find branch or tag '4e192c5c6', assuming revision or ref.
Running command git checkout -q 4e192c5c6
fatal: unable to access 'https://github.com/frheault/dipy.git/': LibreSSL SSL_connect: SSL_ERROR_SYSCALL in connection to github.com:443
Resolved https://github.com/frheault/dipy.git to commit 4e192c5c6
Preparing metadata (setup.py) ... done
Requirement already satisfied: gdown>=4.* in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from tractography-file-format==0.0.0) (4.4.0)
Requirement already satisfied: six in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from gdown>=4.*->tractography-file-format==0.0.0) (1.16.0)
Requirement already satisfied: requests[socks] in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from gdown>=4.*->tractography-file-format==0.0.0) (2.27.1)
Requirement already satisfied: beautifulsoup4 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from gdown>=4.*->tractography-file-format==0.0.0) (4.11.1)
Requirement already satisfied: filelock in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from gdown>=4.*->tractography-file-format==0.0.0) (3.6.0)
Requirement already satisfied: tqdm in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from gdown>=4.*->tractography-file-format==0.0.0) (4.64.0)
Requirement already satisfied: nibabel>=3.0.0 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from dipy@ git+https://github.com/frheault/dipy.git@4e192c5c6#egg=dipy->tractography-file-format==0.0.0) (3.2.2)
Requirement already satisfied: h5py>=2.8.0 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from dipy@ git+https://github.com/frheault/dipy.git@4e192c5c6#egg=dipy->tractography-file-format==0.0.0) (3.6.0)
Requirement already satisfied: numpy>=1.15 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from fury@ git+https://github.com/frheault/fury.git@5059a529#egg=fury->tractography-file-format==0.0.0) (1.23.0)
Requirement already satisfied: scipy>=1.0 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from fury@ git+https://github.com/frheault/fury.git@5059a529#egg=fury->tractography-file-format==0.0.0) (1.8.0)
Requirement already satisfied: vtk>=9.1.0 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from fury@ git+https://github.com/frheault/fury.git@5059a529#egg=fury->tractography-file-format==0.0.0) (9.1.0)
Requirement already satisfied: pillow>=5.4.1 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from fury@ git+https://github.com/frheault/fury.git@5059a529#egg=fury->tractography-file-format==0.0.0) (9.1.0)
Requirement already satisfied: packaging>=17.0 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from fury@ git+https://github.com/frheault/fury.git@5059a529#egg=fury->tractography-file-format==0.0.0) (21.3)
Requirement already satisfied: setuptools in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from fury@ git+https://github.com/frheault/fury.git@5059a529#egg=fury->tractography-file-format==0.0.0) (60.5.0)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from packaging>=17.0->fury@ git+https://github.com/frheault/fury.git@5059a529#egg=fury->tractography-file-format==0.0.0) (3.0.8)
Requirement already satisfied: soupsieve>1.2 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from beautifulsoup4->gdown>=4.*->tractography-file-format==0.0.0) (2.3.2.post1)
Requirement already satisfied: idna<4,>=2.5 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from requests[socks]->gdown>=4.*->tractography-file-format==0.0.0) (3.3)
Requirement already satisfied: charset-normalizer~=2.0.0 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from requests[socks]->gdown>=4.*->tractography-file-format==0.0.0) (2.0.12)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from requests[socks]->gdown>=4.*->tractography-file-format==0.0.0) (1.26.9)
Requirement already satisfied: certifi>=2017.4.17 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from requests[socks]->gdown>=4.*->tractography-file-format==0.0.0) (2021.10.8)
Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /Users/chrisrorden/miniforge3/lib/python3.9/site-packages (from requests[socks]->gdown>=4.*->tractography-file-format==0.0.0) (1.7.1)
Installing collected packages: tractography-file-format
Running setup.py develop for tractography-file-format
Successfully installed tractography-file-format-0.0.0
$ cd scripts
$ python3 tff_convert_tractogram.py ~/IFOF_L.trk ~/IFOF_L.trx
zsh: segmentation fault python3 tff_convert_tractogram.py ~/IFOF_L.trk ~/IFOF_L.trx@skoudoro just tried again, with same results as June. Anything else I can do?
skoudoro
commented
2 years ago Hi @neurolabusc,
Sorry, I did not try yet to fork the repo and introspect in detail this command line to see where it fails exactly.
Since you have no issue with the installation anymore, I was assuming that someone else will look at that. I am not sure what is the reason for the segfault (if it is coming from trx, dipy, vtk or something else). I hope I will be able to reproduce it.
I will look into it next week and keep you updated, I am currently not available this week.
skoudoro
commented
2 years ago My mac is too old and I can not generate the error, everything is working as expected. I am currently trying to have access to an M1.
neurolabusc
commented
2 years ago @skoudoro I would suggest you ask for cloud credits from brainhack_cloud or use the free tier this will give you access to Ampere Altera A1 ARM-based CPUs.
For your needs, I do not even think you need docker, you can simply create and launch an instance and SSH into the CPU. Here are the instructions. You can create multiple instances using Oracle (rpm-based) or Ubuntu (Debian-based 18.04-22.04) distributions. You can choose between ARM (A1) and x86-64 (Xeon and Ryzen) instances, so you can validate your solution across architectures. I am happy to have a zoom meeting to help get you up and running.
skoudoro
commented
2 years ago Hi @neurolabusc,
I just got a new M1 and try this. it worked as expected, no segmentation fault. I only difference I see is:
you use this repo https://github.com/frheault/tractography_file_format.git
and I use the official https://github.com/tee-ar-ex/trx-python
I am not sure that the repo you are using is up to date.
I hope it helps, keep me updated
skoudoro
commented
2 years ago @frheault, can you tell us if you continue to update https://github.com/frheault/tractography_file_format.git or we should just forget it?
neurolabusc
commented
2 years ago @skoudoro well spotted. Thanks for following up on this. It does seem like the installer(s) do not correctly identify all the dependencies - things worked if I manually installed them. Is there a way we could resolve these? Regardless, I think you can close this issue as you have resolved my core issue.
$ cd trx-python
$ pip3 install -e .
...
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
nilearn 0.9.2 requires joblib>=0.15, which is not installed.
nilearn 0.9.2 requires lxml, which is not installed.
nilearn 0.9.2 requires pandas>=1.0, which is not installed.
nilearn 0.9.2 requires scikit-learn>=0.22, which is not installed.
$ pip3 install scikit-learn
$ pip3 install pandas
$ pip3 install lxml
$ pip3 install -e .
$ cd scripts
$ python tff_convert_tractogram.py ~/IFOF_L.trk ~/IFOF_L.trxIt does seem like the installer(s) do not correctly identify all the dependencies - things worked if I manually installed them. Is there a way we could resolve these?
I had the same problem concerning the dependencies, I had to do it manually.
I think #36 is fixing those problems so it should be better when this PR is merged.
arokem
commented
2 years ago @frheault, can you tell us if you continue to update https://github.com/frheault/tractography_file_format.git or we should just forget it?
That repository is now set to automatically redirect here. So, this repository supersedes it completely. I believe that you can still pull from the old URL, so you don't necessarily have to update the remotes on your local machine.
Recent versions of the
testing_scriptbranch fail on my macOS M1 computer. Earlier commits work correctly. I am eager to try out the new features (options to save indices and positions as 32-bit values). There is no documentation on installation, so perhaps I am doing something wrong. Can you replicate this behavior (assuming a valid TRK file in the home directory):