neurologic
commented
6 months ago I think I might have gotten it to work by starting with a new conda environment and doing pip install could-volume before pip install neuroglancer.
Open neurologic opened 6 months ago
neurologic
commented
6 months ago I think I might have gotten it to work by starting with a new conda environment and doing pip install could-volume before pip install neuroglancer.
william-silversmith
commented
6 months ago Huh, a couple odd things happening here. (a) for some reason your machine didn't find the fastremap-1.14.1-cp38-cp38-macosx_11_0_universal2.whl https://files.pythonhosted.org/packages/01/19/f5e90b1db6bde0c9f236bef8f47f1b29be712e87e95a63b84dd9312b2836/fastremap-1.14.1-cp38-cp38-macosx_11_0_universal2.whl on PyPI and tried to compile it from scratch (b) the pyx file should compile fine. Have you tried upgrading your cython version? pip install cython -U --force-reinstall
On Mon, Feb 19, 2024 at 1:56 PM neurologic @.***> wrote:
I think I might have gotten it to work by starting with a new conda environment and doing pip install could-volume before pip install neuroglancer.
— Reply to this email directly, view it on GitHub https://github.com/seung-lab/cloud-volume/issues/607#issuecomment-1953025122, or unsubscribe https://github.com/notifications/unsubscribe-auth/AATGQSLOBPHOSWNGZI7ZZ7DYUON7HAVCNFSM6AAAAABDIXSLMSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJTGAZDKMJSGI . You are receiving this because you are subscribed to this thread.Message ID: @.***>
OS: 14.1.2 Mac mini M1 chip
command tried: pip install cloud-volume
error:
Full Traceback
Collecting cloud-volume Using cached cloud_volume-8.29.1-py3-none-any.whl (238 kB) Collecting compressed-segmentation>=2.1.1 Using cached compressed_segmentation-2.2.2-cp38-cp38-macosx_10_9_x86_64.whl (178 kB) Requirement already satisfied: protobuf>=3.3.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (3.20.3) Requirement already satisfied: google-cloud-storage>=1.24.1 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (2.7.0) Requirement already satisfied: pyspng-seunglab>=1.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.1.1) Collecting python-jsonschema-objects>=0.3.3 Using cached python_jsonschema_objects-0.5.2-py2.py3-none-any.whl (29 kB) Requirement already satisfied: urllib3[brotli]>=1.25.7 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.26.14) Requirement already satisfied: python-dateutil in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (2.8.2) Collecting compresso>=3.0.0 Using cached compresso-3.2.2-cp38-cp38-macosx_10_9_x86_64.whl (330 kB) Requirement already satisfied: zfpc in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (0.1.2) Requirement already satisfied: simplejpeg in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.7.2) Requirement already satisfied: boto3>=1.4.7 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.24.28) Requirement already satisfied: DracoPy<2.0.0,>=1.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.4.0) Requirement already satisfied: posix-ipc>=1.0.4 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.1.1) Collecting cloud-files>=4.18.1 Using cached cloud_files-4.21.1-py3-none-any.whl (60 kB) Collecting gevent Using cached gevent-24.2.1-cp38-cp38-macosx_10_9_x86_64.whl Requirement already satisfied: jsonschema!=4.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (4.17.3) Collecting fastremap>=1.14.0 Using cached fastremap-1.14.1.tar.gz (44 kB) Preparing metadata (setup.py) ... done Requirement already satisfied: pysimdjson>=3.1.1 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (6.0.2) Requirement already satisfied: google-auth>=1.10.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (2.16.1) Requirement already satisfied: tenacity>=4.10.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (8.0.1) Collecting pathos Using cached pathos-0.3.2-py3-none-any.whl (82 kB) Requirement already satisfied: psutil in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (5.9.0) Requirement already satisfied: chardet>=3.0.4 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (4.0.0) Requirement already satisfied: json5 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (0.9.6) Requirement already satisfied: networkx in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (2.8.4) Requirement already satisfied: google-cloud-core>=1.1.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (2.3.2) Requirement already satisfied: numpy>=1.13.3 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.21.5) Requirement already satisfied: tqdm in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (4.64.1) Requirement already satisfied: Pillow>=4.2.1 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (9.3.0) Requirement already satisfied: six>=1.10.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.16.0) Requirement already satisfied: fpzip<2.0.0,>=1.2.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.2.3) Requirement already satisfied: requests>=2.22.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (2.28.1) Collecting crackle-codec Using cached crackle_codec-0.7.1-cp38-cp38-macosx_10_9_x86_64.whl (381 kB) Requirement already satisfied: botocore<1.28.0,>=1.27.28 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from boto3>=1.4.7->cloud-volume) (1.27.59) Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from boto3>=1.4.7->cloud-volume) (0.10.0) Requirement already satisfied: s3transfer<0.7.0,>=0.6.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from boto3>=1.4.7->cloud-volume) (0.6.0) Requirement already satisfied: rsa>=4.7.2 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (4.9) Requirement already satisfied: google-crc32c>=1.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (1.1.2) Requirement already satisfied: zstandard in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (0.18.0) Collecting deflate>=0.2.0 Using cached deflate-0.5.0-cp38-cp38-macosx_10_9_x86_64.whl (60 kB) Requirement already satisfied: click in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (8.0.4) Requirement already satisfied: brotli in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (1.1.0) Requirement already satisfied: orjson in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (3.9.14) Requirement already satisfied: fasteners in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (0.18) Requirement already satisfied: crc32c in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (2.3.post0) Requirement already satisfied: pytest in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from compressed-segmentation>=2.1.1->cloud-volume) (7.1.2) Requirement already satisfied: cachetools<6.0,>=2.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from google-auth>=1.10.0->cloud-volume) (5.3.0) Requirement already satisfied: pyasn1-modules>=0.2.1 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from google-auth>=1.10.0->cloud-volume) (0.2.8) Requirement already satisfied: google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.6 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from google-cloud-core>=1.1.0->cloud-volume) (2.8.1) Requirement already satisfied: google-resumable-media>=2.3.2 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from google-cloud-storage>=1.24.1->cloud-volume) (2.4.1) Requirement already satisfied: pkgutil-resolve-name>=1.3.10 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from jsonschema!=4.0->cloud-volume) (1.3.10) Requirement already satisfied: pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from jsonschema!=4.0->cloud-volume) (0.18.0) Requirement already satisfied: importlib-resources>=1.4.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from jsonschema!=4.0->cloud-volume) (5.2.0) Requirement already satisfied: attrs>=17.4.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from jsonschema!=4.0->cloud-volume) (22.1.0) Requirement already satisfied: Markdown>=2.4 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from python-jsonschema-objects>=0.3.3->cloud-volume) (3.4.1) Requirement already satisfied: inflection>=0.2 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from python-jsonschema-objects>=0.3.3->cloud-volume) (0.5.1) Collecting jsonschema!=4.0 Using cached jsonschema-4.21.1-py3-none-any.whl (85 kB) Collecting attrs>=17.4.0 Using cached attrs-23.2.0-py3-none-any.whl (60 kB) Collecting jsonschema-specifications>=2023.03.6 Using cached jsonschema_specifications-2023.12.1-py3-none-any.whl (18 kB) Requirement already satisfied: rpds-py>=0.7.1 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from jsonschema!=4.0->cloud-volume) (0.18.0) Collecting referencing>=0.28.4 Using cached referencing-0.33.0-py3-none-any.whl (26 kB) Requirement already satisfied: charset-normalizer<3,>=2 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from requests>=2.22.0->cloud-volume) (2.0.4) Requirement already satisfied: certifi>=2017.4.17 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from requests>=2.22.0->cloud-volume) (2022.12.7) Requirement already satisfied: idna<4,>=2.5 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from requests>=2.22.0->cloud-volume) (3.4) Requirement already satisfied: pybind11 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from crackle-codec->cloud-volume) (2.11.1) Requirement already satisfied: zope.event in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from gevent->cloud-volume) (5.0) Requirement already satisfied: greenlet>=2.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from gevent->cloud-volume) (2.0.1) Requirement already satisfied: zope.interface in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from gevent->cloud-volume) (5.4.0) Requirement already satisfied: ppft>=1.7.6.8 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pathos->cloud-volume) (1.7.6.8) Requirement already satisfied: pox>=0.3.4 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pathos->cloud-volume) (0.3.4) Collecting dill>=0.3.8 Using cached dill-0.3.8-py3-none-any.whl (116 kB) Collecting multiprocess>=0.70.16 Using cached multiprocess-0.70.16-py38-none-any.whl (132 kB) Requirement already satisfied: zfpy in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from zfpc->cloud-volume) (1.0.0) Requirement already satisfied: googleapis-common-protos<2.0dev,>=1.56.2 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.6->google-cloud-core>=1.1.0->cloud-volume) (1.57.0) Requirement already satisfied: cffi>=1.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from google-crc32c>=1.0.0->cloud-files>=4.18.1->cloud-volume) (1.15.1) Requirement already satisfied: zipp>=3.1.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from importlib-resources>=1.4.0->jsonschema!=4.0->cloud-volume) (3.11.0) Requirement already satisfied: importlib-metadata>=4.4 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from Markdown>=2.4->python-jsonschema-objects>=0.3.3->cloud-volume) (4.11.3) Requirement already satisfied: pyasn1<0.5.0,>=0.4.6 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pyasn1-modules>=0.2.1->google-auth>=1.10.0->cloud-volume) (0.4.8) Requirement already satisfied: iniconfig in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pytest->compressed-segmentation>=2.1.1->cloud-volume) (1.1.1) Requirement already satisfied: packaging in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pytest->compressed-segmentation>=2.1.1->cloud-volume) (22.0) Requirement already satisfied: pluggy<2.0,>=0.12 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pytest->compressed-segmentation>=2.1.1->cloud-volume) (1.0.0) Requirement already satisfied: py>=1.8.2 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pytest->compressed-segmentation>=2.1.1->cloud-volume) (1.11.0) Requirement already satisfied: tomli>=1.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pytest->compressed-segmentation>=2.1.1->cloud-volume) (2.0.1) Requirement already satisfied: setuptools in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from zope.event->gevent->cloud-volume) (65.6.3) Requirement already satisfied: pycparser in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cffi>=1.0.0->google-crc32c>=1.0.0->cloud-files>=4.18.1->cloud-volume) (2.21) Building wheels for collected packages: fastremap Building wheel for fastremap (setup.py) ... error error: subprocess-exited-with-error × python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [35 lines of output] /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/_distutils/extension.py:134: UserWarning: Unknown Extension options: 'language_level' warnings.warn(msg) /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer. warnings.warn( /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools. warnings.warn( /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running bdist_wheel running build running build_ext cythoning fastremap.pyx to fastremap.cpp Error compiling Cython file: ------------------------------------------------------------ ... elif (cx == sx and cy == sy and cz == sz): return [ image.tobytes(order) ] cdef cnp.ndarray[NUMBER] arr cdef list[cnp.ndarray[NUMBER]] array_grid = [ ^ ------------------------------------------------------------ fastremap.pyx:1369:30: Invalid type. building 'fastremap' extension creating build creating build/temp.macosx-10.9-x86_64-cpython-38 gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/kperks/opt/anaconda3/envs/ell/include -arch x86_64 -I/Users/kperks/opt/anaconda3/envs/ell/include -arch x86_64 -I/Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/numpy/core/include -I/Users/kperks/opt/anaconda3/envs/ell/include/python3.8 -c fastremap.cpp -o build/temp.macosx-10.9-x86_64-cpython-38/fastremap.o -std=c++11 -O3 -stdlib=libc++ -mmacosx-version-min=10.9 fastremap.cpp:1:2: error: Do not use this file, it is the result of a failed Cython compilation. #error Do not use this file, it is the result of a failed Cython compilation. ^ 1 error generated. error: command '/usr/bin/gcc' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for fastremap Running setup.py clean for fastremap Failed to build fastremap Installing collected packages: fastremap, dill, deflate, compresso, attrs, referencing, multiprocess, gevent, crackle-codec, pathos, jsonschema-specifications, compressed-segmentation, jsonschema, python-jsonschema-objects, cloud-files, cloud-volume Running setup.py install for fastremap ... error error: subprocess-exited-with-error × Running setup.py install for fastremap did not run successfully. │ exit code: 1 ╰─> [37 lines of output] /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/_distutils/extension.py:134: UserWarning: Unknown Extension options: 'language_level' warnings.warn(msg) /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer. warnings.warn( /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools. warnings.warn( /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running install [pbr] Generating AUTHORS [pbr] AUTHORS complete (0.0s) running build running build_ext cythoning fastremap.pyx to fastremap.cpp Error compiling Cython file: ------------------------------------------------------------ ... elif (cx == sx and cy == sy and cz == sz): return [ image.tobytes(order) ] cdef cnp.ndarray[NUMBER] arr cdef list[cnp.ndarray[NUMBER]] array_grid = [ ^ ------------------------------------------------------------ fastremap.pyx:1369:30: Invalid type. building 'fastremap' extension creating build creating build/temp.macosx-10.9-x86_64-cpython-38 gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/kperks/opt/anaconda3/envs/ell/include -arch x86_64 -I/Users/kperks/opt/anaconda3/envs/ell/include -arch x86_64 -I/Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/numpy/core/include -I/Users/kperks/opt/anaconda3/envs/ell/include/python3.8 -c fastremap.cpp -o build/temp.macosx-10.9-x86_64-cpython-38/fastremap.o -std=c++11 -O3 -stdlib=libc++ -mmacosx-version-min=10.9 fastremap.cpp:1:2: error: Do not use this file, it is the result of a failed Cython compilation. #error Do not use this file, it is the result of a failed Cython compilation. ^ 1 error generated. error: command '/usr/bin/gcc' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: legacy-install-failure × Encountered error while trying to install package. ╰─> fastremap note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.
Other version info: python 3.8.13 numpy 1.21.5
Steps tried:
pip install numpy pip install fastremap --no-binary :all:brew install gccand it seemed to workI am trying to install on an environment that already has numpy (I need to use cloudvolume simultaneously with other packages for handling the .jsons for my neurons -- in CREST format (from Alex Shapsoncoe). Not sure if that has to do with any issues.
I am new to working with this sort of data (though have been interacting with neuroglancer for a while now via python scripts, and I have used some example colab notebooks to interact with our cloudvolume mesh and skeleton data... I am trying to get it to work now on my local computer so that I can integrate it into the rest of the workflow I have... some of which I cannot reproduce on colab).
Let me know if you see any solutions I am not seeing. Thank you so much!
-Krista