System Details:
macOS Version: macOS 13 Chip: Apple M2 Conda Version: 23.7.4 Python Version: 3.11 RELION Version: 5.0 PyQt5 Version: 5.15.9 Questions:
Why is PyQt5 failing to build metadata, and how can I fix this issue? Do I need to install qt or sip differently on macOS (ARM)? Is this related to the Conda environment using Python 3.11 instead of 3.10?
melchua@MacBook-Air ~ % conda activate relion
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
(relion) melchua@MacBook-Air ~ % cd relion
(relion) melchua@MacBook-Air relion % conda env update -f environment.yml
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
Collecting package metadata (repodata.json): done
Solving environment: done
Installing pip dependencies: - Ran pip subprocess with arguments:
['/Users/melchua/miniconda3/envs/relion-5.0/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/melchua/relion/condaenv.a1274g1p.requirements.txt', '--exists-action=b']
Pip subprocess output:
Collecting git+ (from -r /Users/melchua/relion/condaenv.a1274g1p.requirements.txt (line 22))
Cloning to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-5jmt46is
Resolved to commit 8727e78cf00ffcbb0cb3dd5918db987a13cf4f3a
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting git+ (from -r /Users/melchua/relion/condaenv.a1274g1p.requirements.txt (line 23))
Cloning to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-xjjpylws
Resolved to commit 7889199242ab8227c628df72ea396826ed50185e
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting git+ (from -r /Users/melchua/relion/condaenv.a1274g1p.requirements.txt (line 24))
Cloning to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-evq469a8
Resolved to commit d7d75e888635d5997b6183af77790d08cc6c7f26
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting git+ (from -r /Users/melchua/relion/condaenv.a1274g1p.requirements.txt (line 25))
Cloning to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-8npt2q95
Resolved to commit 14b2bc331768b67b3267397523de57c707fa1253
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting git+ (from -r /Users/melchua/relion/condaenv.a1274g1p.requirements.txt (line 26))
Cloning to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-0owgggtt
Resolved to commit ddd969038045c28c5f281353dd62e98afb57859c
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Processing /Users/melchua/relion
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting torch==2.0.1
Using cached torch-2.0.1-cp310-none-macosx_11_0_arm64.whl (55.8 MB)
Collecting torchvision==0.15.2
Using cached torchvision-0.15.2-cp310-cp310-macosx_11_0_arm64.whl (1.4 MB)
Collecting tqdm==4.65.0
Using cached tqdm-4.65.0-py3-none-any.whl (77 kB)
Collecting mrcfile==1.4.3
Using cached mrcfile-1.4.3-py2.py3-none-any.whl (43 kB)
Collecting starfile>=0.5.6
Using cached starfile-0.5.12-py3-none-any.whl (10 kB)
Collecting loguru==0.7.0
Using cached loguru-0.7.0-py3-none-any.whl (59 kB)
Collecting scikit-learn==1.3.0
Using cached scikit_learn-1.3.0-cp310-cp310-macosx_12_0_arm64.whl (9.5 MB)
Collecting umap-learn==0.5.3
Using cached umap-learn-0.5.3.tar.gz (88 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting matplotlib==3.7.2
Using cached matplotlib-3.7.2-cp310-cp310-macosx_11_0_arm64.whl (7.3 MB)
Collecting morphosamplers==0.0.13
Using cached morphosamplers-0.0.13-py3-none-any.whl (29 kB)
Collecting pydantic==1.10.18
Using cached pydantic-1.10.18-cp310-cp310-macosx_11_0_arm64.whl (2.3 MB)
Collecting napari[all]==0.4.18
Using cached napari-0.4.18-py3-none-any.whl (2.6 MB)
Collecting tsnecuda==3.0.1
Using cached tsnecuda-3.0.1-py3-none-any.whl (53.2 MB)
Collecting PyQt5==5.15.9
Using cached PyQt5-5.15.9.tar.gz (3.2 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
Pip subprocess error:
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
Running command git clone --filter=blob:none --quiet /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-5jmt46is
Running command git clone --filter=blob:none --quiet /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-xjjpylws
Running command git clone --filter=blob:none --quiet /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-evq469a8
Running command git clone --filter=blob:none --quiet /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-8npt2q95
Running command git clone --filter=blob:none --quiet /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-0owgggtt
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [25 lines of output]
pyproject.toml: line 7: using '[tool.sip.metadata]' to specify the project metadata is deprecated and will be removed in SIP v7.0.0, use '[project]' instead
Querying qmake about your Qt installation...
Traceback (most recent call last):
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 144, in prepare_metadata_for_build_wheel
hook = backend.prepare_metadata_for_build_wheel
AttributeError: module 'sipbuild.api' has no attribute 'prepare_metadata_for_build_wheel'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
main()
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 148, in prepare_metadata_for_build_wheel
whl_basename = backend.build_wheel(metadata_directory, config_settings)
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-build-env-tw3k0el0/overlay/lib/python3.10/site-packages/sipbuild/api.py", line 28, in build_wheel
project = AbstractProject.bootstrap('wheel',
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-build-env-tw3k0el0/overlay/lib/python3.10/site-packages/sipbuild/abstract_project.py", line 74, in bootstrap
project.setup(pyproject, tool, tool_description)
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-build-env-tw3k0el0/overlay/lib/python3.10/site-packages/sipbuild/project.py", line 645, in setup
self.update(tool)
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-install-8irt7wi9/pyqt5_fd2e5c57a5ea41b7914af6e97a8d3460/project.py", line 165, in update
raise UserException(
sipbuild.exceptions.UserException
[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.
failed
CondaEnvException: Pip failed
(relion) melchua@MacBook-Air relion % conda install -c conda-fe zstandard
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Users/melchua/miniconda3/envs/relion
added / updated specs:
- zstandard
The following packages will be downloaded:
package | build
---------------------------|-----------------
cffi-1.15.1 | py311hae827db_2 276 KB conda-fe
pycparser-2.21 | pyhd8ed1ab_0 100 KB conda-fe
python-3.11.0 |h93c2e33_0_cpython 14.9 MB conda-fe
python_abi-3.11 | 2_cp311 5 KB conda-fe
setuptools-65.5.1 | pyhd8ed1ab_0 731 KB conda-fe
zstandard-0.19.0 | py311he2be06e_0 562 KB conda-fe
------------------------------------------------------------
Total: 16.5 MB
The following NEW packages will be INSTALLED:
bzip2 conda-fe/osx-arm64::bzip2-1.0.8-h3422bc3_4
ca-certificates conda-fe/osx-arm64::ca-certificates-2022.9.24-h4653dfc_0
cffi conda-fe/osx-arm64::cffi-1.15.1-py311hae827db_2
libffi conda-fe/osx-arm64::libffi-3.4.2-h3422bc3_5
libsqlite conda-fe/osx-arm64::libsqlite-3.40.0-h76d750c_0
libzlib conda-fe/osx-arm64::libzlib-1.2.13-h03a7124_4
ncurses conda-fe/osx-arm64::ncurses-6.3-h07bb92c_1
openssl conda-fe/osx-arm64::openssl-3.0.7-h03a7124_0
pip conda-fe/noarch::pip-22.3.1-pyhd8ed1ab_0
pycparser conda-fe/noarch::pycparser-2.21-pyhd8ed1ab_0
python conda-fe/osx-arm64::python-3.11.0-h93c2e33_0_cpython
python_abi conda-fe/osx-arm64::python_abi-3.11-2_cp311
readline conda-fe/osx-arm64::readline-8.1.2-h46ed386_0
setuptools conda-fe/noarch::setuptools-65.5.1-pyhd8ed1ab_0
tk conda-fe/osx-arm64::tk-8.6.12-he1e0b03_0
tzdata conda-fe/noarch::tzdata-2022f-h191b570_0
wheel conda-fe/noarch::wheel-0.38.4-pyhd8ed1ab_0
xz conda-fe/osx-arm64::xz-5.2.6-h57fd34a_0
zstandard conda-fe/osx-arm64::zstandard-0.19.0-py311he2be06e_0
Proceed ([y]/n)? y
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
(relion) melchua@MacBook-Air relion % pip install --upgrade sip
Collecting sip
Using cached sip-6.10.0-1-py3-none-any.whl (2.6 MB)
Collecting packaging
Using cached packaging-24.2-py3-none-any.whl (65 kB)
Collecting setuptools>=69.5
Using cached setuptools-76.0.0-py3-none-any.whl (1.2 MB)
Installing collected packages: setuptools, packaging, sip
Attempting uninstall: setuptools
Found existing installation: setuptools 65.5.1
Uninstalling setuptools-65.5.1:
Successfully uninstalled setuptools-65.5.1
Successfully installed packaging-24.2 setuptools-76.0.0 sip-6.10.0
(relion) melchua@MacBook-Air relion % pip install PyQt5
Collecting PyQt5
Downloading PyQt5-5.15.11-cp38-abi3-macosx_11_0_arm64.whl (6.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.6/6.6 MB 2.6 MB/s eta 0:00:00
Collecting PyQt5-sip<13,>=12.15
Downloading PyQt5_sip-12.17.0-cp311-cp311-macosx_10_9_universal2.whl (122 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 122.7/122.7 kB 4.3 MB/s eta 0:00:00
Collecting PyQt5-Qt5<5.16.0,>=5.15.2
Downloading PyQt5_Qt5-5.15.16-py3-none-macosx_11_0_arm64.whl (37.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.1/37.1 MB 5.9 MB/s eta 0:00:00
Installing collected packages: PyQt5-Qt5, PyQt5-sip, PyQt5
Successfully installed PyQt5-5.15.11 PyQt5-Qt5-5.15.16 PyQt5-sip-12.17.0
(relion) melchua@MacBook-Air relion % conda env update -f environment.yml
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
Collecting package metadata (repodata.json): done
Solving environment: done
Installing pip dependencies: - Ran pip subprocess with arguments:
['/Users/melchua/miniconda3/envs/relion-5.0/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/melchua/relion/condaenv.sbi0htct.requirements.txt', '--exists-action=b']
Pip subprocess output:
Collecting git+ (from -r /Users/melchua/relion/condaenv.sbi0htct.requirements.txt (line 22))
Cloning to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-vffw4mxz
Resolved to commit 8727e78cf00ffcbb0cb3dd5918db987a13cf4f3a
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting git+ (from -r /Users/melchua/relion/condaenv.sbi0htct.requirements.txt (line 23))
Cloning to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-idx5vvk7
Resolved to commit 7889199242ab8227c628df72ea396826ed50185e
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting git+ (from -r /Users/melchua/relion/condaenv.sbi0htct.requirements.txt (line 24))
Cloning to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-vkp2a_ix
Resolved to commit d7d75e888635d5997b6183af77790d08cc6c7f26
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting git+ (from -r /Users/melchua/relion/condaenv.sbi0htct.requirements.txt (line 25))
Cloning to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-slmc2x98
Resolved to commit 14b2bc331768b67b3267397523de57c707fa1253
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting git+ (from -r /Users/melchua/relion/condaenv.sbi0htct.requirements.txt (line 26))
Cloning to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-z8sca1_6
Resolved to commit ddd969038045c28c5f281353dd62e98afb57859c
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Processing /Users/melchua/relion
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting torch==2.0.1
Using cached torch-2.0.1-cp310-none-macosx_11_0_arm64.whl (55.8 MB)
Collecting torchvision==0.15.2
Using cached torchvision-0.15.2-cp310-cp310-macosx_11_0_arm64.whl (1.4 MB)
Collecting tqdm==4.65.0
Using cached tqdm-4.65.0-py3-none-any.whl (77 kB)
Collecting mrcfile==1.4.3
Using cached mrcfile-1.4.3-py2.py3-none-any.whl (43 kB)
Collecting starfile>=0.5.6
Using cached starfile-0.5.12-py3-none-any.whl (10 kB)
Collecting loguru==0.7.0
Using cached loguru-0.7.0-py3-none-any.whl (59 kB)
Collecting scikit-learn==1.3.0
Using cached scikit_learn-1.3.0-cp310-cp310-macosx_12_0_arm64.whl (9.5 MB)
Collecting umap-learn==0.5.3
Using cached umap-learn-0.5.3.tar.gz (88 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting matplotlib==3.7.2
Using cached matplotlib-3.7.2-cp310-cp310-macosx_11_0_arm64.whl (7.3 MB)
Collecting morphosamplers==0.0.13
Using cached morphosamplers-0.0.13-py3-none-any.whl (29 kB)
Collecting pydantic==1.10.18
Using cached pydantic-1.10.18-cp310-cp310-macosx_11_0_arm64.whl (2.3 MB)
Collecting napari[all]==0.4.18
Using cached napari-0.4.18-py3-none-any.whl (2.6 MB)
Collecting tsnecuda==3.0.1
Using cached tsnecuda-3.0.1-py3-none-any.whl (53.2 MB)
Collecting PyQt5==5.15.9
Using cached PyQt5-5.15.9.tar.gz (3.2 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
Pip subprocess error:
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
Running command git clone --filter=blob:none --quiet /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-vffw4mxz
Running command git clone --filter=blob:none --quiet /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-idx5vvk7
Running command git clone --filter=blob:none --quiet /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-vkp2a_ix
Running command git clone --filter=blob:none --quiet /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-slmc2x98
Running command git clone --filter=blob:none --quiet /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-z8sca1_6
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [25 lines of output]
pyproject.toml: line 7: using '[tool.sip.metadata]' to specify the project metadata is deprecated and will be removed in SIP v7.0.0, use '[project]' instead
Querying qmake about your Qt installation...
Traceback (most recent call last):
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 144, in prepare_metadata_for_build_wheel
hook = backend.prepare_metadata_for_build_wheel
AttributeError: module 'sipbuild.api' has no attribute 'prepare_metadata_for_build_wheel'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
main()
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 148, in prepare_metadata_for_build_wheel
whl_basename = backend.build_wheel(metadata_directory, config_settings)
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-build-env-uym50ri9/overlay/lib/python3.10/site-packages/sipbuild/api.py", line 28, in build_wheel
project = AbstractProject.bootstrap('wheel',
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-build-env-uym50ri9/overlay/lib/python3.10/site-packages/sipbuild/abstract_project.py", line 74, in bootstrap
project.setup(pyproject, tool, tool_description)
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-build-env-uym50ri9/overlay/lib/python3.10/site-packages/sipbuild/project.py", line 645, in setup
self.update(tool)
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-install-in2203ks/pyqt5_42cc4e87898340ef9325f1fdcca53288/project.py", line 165, in update
raise UserException(
sipbuild.exceptions.UserException
[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.
failed
System Details:
macOS Version: macOS 13 Chip: Apple M2 Conda Version: 23.7.4 Python Version: 3.11 RELION Version: 5.0 PyQt5 Version: 5.15.9 Questions:
Why is PyQt5 failing to build metadata, and how can I fix this issue? Do I need to install qt or sip differently on macOS (ARM)? Is this related to the Conda environment using Python 3.11 instead of 3.10?
melchua@MacBook-Air ~ % conda activate relion
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
(relion) melchua@MacBook-Air ~ % cd relion
(relion) melchua@MacBook-Air relion % conda env update -f environment.yml
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
Collecting package metadata (repodata.json): done
Solving environment: done
Installing pip dependencies: - Ran pip subprocess with arguments:
['/Users/melchua/miniconda3/envs/relion-5.0/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/melchua/relion/condaenv.a1274g1p.requirements.txt', '--exists-action=b']
Pip subprocess output:
Collecting git+https://github/3dem/relion-classranker (from -r /Users/melchua/relion/condaenv.a1274g1p.requirements.txt (line 22))
Cloning https://github/3dem/relion-classranker to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-5jmt46is
Resolved https://github/3dem/relion-classranker to commit 8727e78cf00ffcbb0cb3dd5918db987a13cf4f3a
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting git+https://github/3dem/relion-blush (from -r /Users/melchua/relion/condaenv.a1274g1p.requirements.txt (line 23))
Cloning https://github/3dem/relion-blush to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-xjjpylws
Resolved https://github/3dem/relion-blush to commit 7889199242ab8227c628df72ea396826ed50185e
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting git+https://github/3dem/DynaMight (from -r /Users/melchua/relion/condaenv.a1274g1p.requirements.txt (line 24))
Cloning https://github/3dem/DynaMight to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-evq469a8
Resolved https://github/3dem/DynaMight to commit d7d75e888635d5997b6183af77790d08cc6c7f26
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting git+https://github/3dem/topaz (from -r /Users/melchua/relion/condaenv.a1274g1p.requirements.txt (line 25))
Cloning https://github/3dem/topaz to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-8npt2q95
Resolved https://github/3dem/topaz to commit 14b2bc331768b67b3267397523de57c707fa1253
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting git+https://github/3dem/model-angelo (from -r /Users/melchua/relion/condaenv.a1274g1p.requirements.txt (line 26))
Cloning https://github/3dem/model-angelo to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-0owgggtt
Resolved https://github/3dem/model-angelo to commit ddd969038045c28c5f281353dd62e98afb57859c
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Processing /Users/melchua/relion
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting torch==2.0.1
Using cached torch-2.0.1-cp310-none-macosx_11_0_arm64.whl (55.8 MB)
Collecting torchvision==0.15.2
Using cached torchvision-0.15.2-cp310-cp310-macosx_11_0_arm64.whl (1.4 MB)
Collecting tqdm==4.65.0
Using cached tqdm-4.65.0-py3-none-any.whl (77 kB)
Collecting mrcfile==1.4.3
Using cached mrcfile-1.4.3-py2.py3-none-any.whl (43 kB)
Collecting starfile>=0.5.6
Using cached starfile-0.5.12-py3-none-any.whl (10 kB)
Collecting loguru==0.7.0
Using cached loguru-0.7.0-py3-none-any.whl (59 kB)
Collecting scikit-learn==1.3.0
Using cached scikit_learn-1.3.0-cp310-cp310-macosx_12_0_arm64.whl (9.5 MB)
Collecting umap-learn==0.5.3
Using cached umap-learn-0.5.3.tar.gz (88 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting matplotlib==3.7.2
Using cached matplotlib-3.7.2-cp310-cp310-macosx_11_0_arm64.whl (7.3 MB)
Collecting morphosamplers==0.0.13
Using cached morphosamplers-0.0.13-py3-none-any.whl (29 kB)
Collecting pydantic==1.10.18
Using cached pydantic-1.10.18-cp310-cp310-macosx_11_0_arm64.whl (2.3 MB)
Collecting napari[all]==0.4.18
Using cached napari-0.4.18-py3-none-any.whl (2.6 MB)
Collecting tsnecuda==3.0.1
Using cached tsnecuda-3.0.1-py3-none-any.whl (53.2 MB)
Collecting PyQt5==5.15.9
Using cached PyQt5-5.15.9.tar.gz (3.2 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
Pip subprocess error:
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
Running command git clone --filter=blob:none --quiet https://github/3dem/relion-classranker /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-5jmt46is
Running command git clone --filter=blob:none --quiet https://github/3dem/relion-blush /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-xjjpylws
Running command git clone --filter=blob:none --quiet https://github/3dem/DynaMight /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-evq469a8
Running command git clone --filter=blob:none --quiet https://github/3dem/topaz /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-8npt2q95
Running command git clone --filter=blob:none --quiet https://github/3dem/model-angelo /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-0owgggtt
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [25 lines of output]
pyproject.toml: line 7: using '[tool.sip.metadata]' to specify the project metadata is deprecated and will be removed in SIP v7.0.0, use '[project]' instead
Querying qmake about your Qt installation...
Traceback (most recent call last):
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 144, in prepare_metadata_for_build_wheel
hook = backend.prepare_metadata_for_build_wheel
AttributeError: module 'sipbuild.api' has no attribute 'prepare_metadata_for_build_wheel'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
main()
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 148, in prepare_metadata_for_build_wheel
whl_basename = backend.build_wheel(metadata_directory, config_settings)
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-build-env-tw3k0el0/overlay/lib/python3.10/site-packages/sipbuild/api.py", line 28, in build_wheel
project = AbstractProject.bootstrap('wheel',
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-build-env-tw3k0el0/overlay/lib/python3.10/site-packages/sipbuild/abstract_project.py", line 74, in bootstrap
project.setup(pyproject, tool, tool_description)
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-build-env-tw3k0el0/overlay/lib/python3.10/site-packages/sipbuild/project.py", line 645, in setup
self.update(tool)
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-install-8irt7wi9/pyqt5_fd2e5c57a5ea41b7914af6e97a8d3460/project.py", line 165, in update
raise UserException(
sipbuild.exceptions.UserException
[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.
failed
CondaEnvException: Pip failed
(relion) melchua@MacBook-Air relion % conda install -c conda-fe zstandard
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Users/melchua/miniconda3/envs/relion
added / updated specs:
- zstandard
The following packages will be downloaded:
package | build
---------------------------|-----------------
cffi-1.15.1 | py311hae827db_2 276 KB conda-fe
pycparser-2.21 | pyhd8ed1ab_0 100 KB conda-fe
python-3.11.0 |h93c2e33_0_cpython 14.9 MB conda-fe
python_abi-3.11 | 2_cp311 5 KB conda-fe
setuptools-65.5.1 | pyhd8ed1ab_0 731 KB conda-fe
zstandard-0.19.0 | py311he2be06e_0 562 KB conda-fe
------------------------------------------------------------
Total: 16.5 MB
The following NEW packages will be INSTALLED:
bzip2 conda-fe/osx-arm64::bzip2-1.0.8-h3422bc3_4
ca-certificates conda-fe/osx-arm64::ca-certificates-2022.9.24-h4653dfc_0
cffi conda-fe/osx-arm64::cffi-1.15.1-py311hae827db_2
libffi conda-fe/osx-arm64::libffi-3.4.2-h3422bc3_5
libsqlite conda-fe/osx-arm64::libsqlite-3.40.0-h76d750c_0
libzlib conda-fe/osx-arm64::libzlib-1.2.13-h03a7124_4
ncurses conda-fe/osx-arm64::ncurses-6.3-h07bb92c_1
openssl conda-fe/osx-arm64::openssl-3.0.7-h03a7124_0
pip conda-fe/noarch::pip-22.3.1-pyhd8ed1ab_0
pycparser conda-fe/noarch::pycparser-2.21-pyhd8ed1ab_0
python conda-fe/osx-arm64::python-3.11.0-h93c2e33_0_cpython
python_abi conda-fe/osx-arm64::python_abi-3.11-2_cp311
readline conda-fe/osx-arm64::readline-8.1.2-h46ed386_0
setuptools conda-fe/noarch::setuptools-65.5.1-pyhd8ed1ab_0
tk conda-fe/osx-arm64::tk-8.6.12-he1e0b03_0
tzdata conda-fe/noarch::tzdata-2022f-h191b570_0
wheel conda-fe/noarch::wheel-0.38.4-pyhd8ed1ab_0
xz conda-fe/osx-arm64::xz-5.2.6-h57fd34a_0
zstandard conda-fe/osx-arm64::zstandard-0.19.0-py311he2be06e_0
Proceed ([y]/n)? y
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
(relion) melchua@MacBook-Air relion % pip install --upgrade sip
Collecting sip
Using cached sip-6.10.0-1-py3-none-any.whl (2.6 MB)
Collecting packaging
Using cached packaging-24.2-py3-none-any.whl (65 kB)
Collecting setuptools>=69.5
Using cached setuptools-76.0.0-py3-none-any.whl (1.2 MB)
Installing collected packages: setuptools, packaging, sip
Attempting uninstall: setuptools
Found existing installation: setuptools 65.5.1
Uninstalling setuptools-65.5.1:
Successfully uninstalled setuptools-65.5.1
Successfully installed packaging-24.2 setuptools-76.0.0 sip-6.10.0
(relion) melchua@MacBook-Air relion % pip install PyQt5
Collecting PyQt5
Downloading PyQt5-5.15.11-cp38-abi3-macosx_11_0_arm64.whl (6.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.6/6.6 MB 2.6 MB/s eta 0:00:00
Collecting PyQt5-sip<13,>=12.15
Downloading PyQt5_sip-12.17.0-cp311-cp311-macosx_10_9_universal2.whl (122 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 122.7/122.7 kB 4.3 MB/s eta 0:00:00
Collecting PyQt5-Qt5<5.16.0,>=5.15.2
Downloading PyQt5_Qt5-5.15.16-py3-none-macosx_11_0_arm64.whl (37.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.1/37.1 MB 5.9 MB/s eta 0:00:00
Installing collected packages: PyQt5-Qt5, PyQt5-sip, PyQt5
Successfully installed PyQt5-5.15.11 PyQt5-Qt5-5.15.16 PyQt5-sip-12.17.0
(relion) melchua@MacBook-Air relion % conda env update -f environment.yml
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
Collecting package metadata (repodata.json): done
Solving environment: done
Installing pip dependencies: - Ran pip subprocess with arguments:
['/Users/melchua/miniconda3/envs/relion-5.0/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/melchua/relion/condaenv.sbi0htct.requirements.txt', '--exists-action=b']
Pip subprocess output:
Collecting git+https://github/3dem/relion-classranker (from -r /Users/melchua/relion/condaenv.sbi0htct.requirements.txt (line 22))
Cloning https://github/3dem/relion-classranker to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-vffw4mxz
Resolved https://github/3dem/relion-classranker to commit 8727e78cf00ffcbb0cb3dd5918db987a13cf4f3a
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting git+https://github/3dem/relion-blush (from -r /Users/melchua/relion/condaenv.sbi0htct.requirements.txt (line 23))
Cloning https://github/3dem/relion-blush to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-idx5vvk7
Resolved https://github/3dem/relion-blush to commit 7889199242ab8227c628df72ea396826ed50185e
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting git+https://github/3dem/DynaMight (from -r /Users/melchua/relion/condaenv.sbi0htct.requirements.txt (line 24))
Cloning https://github/3dem/DynaMight to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-vkp2a_ix
Resolved https://github/3dem/DynaMight to commit d7d75e888635d5997b6183af77790d08cc6c7f26
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting git+https://github/3dem/topaz (from -r /Users/melchua/relion/condaenv.sbi0htct.requirements.txt (line 25))
Cloning https://github/3dem/topaz to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-slmc2x98
Resolved https://github/3dem/topaz to commit 14b2bc331768b67b3267397523de57c707fa1253
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting git+https://github/3dem/model-angelo (from -r /Users/melchua/relion/condaenv.sbi0htct.requirements.txt (line 26))
Cloning https://github/3dem/model-angelo to /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-z8sca1_6
Resolved https://github/3dem/model-angelo to commit ddd969038045c28c5f281353dd62e98afb57859c
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Processing /Users/melchua/relion
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting torch==2.0.1
Using cached torch-2.0.1-cp310-none-macosx_11_0_arm64.whl (55.8 MB)
Collecting torchvision==0.15.2
Using cached torchvision-0.15.2-cp310-cp310-macosx_11_0_arm64.whl (1.4 MB)
Collecting tqdm==4.65.0
Using cached tqdm-4.65.0-py3-none-any.whl (77 kB)
Collecting mrcfile==1.4.3
Using cached mrcfile-1.4.3-py2.py3-none-any.whl (43 kB)
Collecting starfile>=0.5.6
Using cached starfile-0.5.12-py3-none-any.whl (10 kB)
Collecting loguru==0.7.0
Using cached loguru-0.7.0-py3-none-any.whl (59 kB)
Collecting scikit-learn==1.3.0
Using cached scikit_learn-1.3.0-cp310-cp310-macosx_12_0_arm64.whl (9.5 MB)
Collecting umap-learn==0.5.3
Using cached umap-learn-0.5.3.tar.gz (88 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting matplotlib==3.7.2
Using cached matplotlib-3.7.2-cp310-cp310-macosx_11_0_arm64.whl (7.3 MB)
Collecting morphosamplers==0.0.13
Using cached morphosamplers-0.0.13-py3-none-any.whl (29 kB)
Collecting pydantic==1.10.18
Using cached pydantic-1.10.18-cp310-cp310-macosx_11_0_arm64.whl (2.3 MB)
Collecting napari[all]==0.4.18
Using cached napari-0.4.18-py3-none-any.whl (2.6 MB)
Collecting tsnecuda==3.0.1
Using cached tsnecuda-3.0.1-py3-none-any.whl (53.2 MB)
Collecting PyQt5==5.15.9
Using cached PyQt5-5.15.9.tar.gz (3.2 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
Pip subprocess error:
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.")
/Users/melchua/miniconda3/lib/python3.12/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
Running command git clone --filter=blob:none --quiet https://github/3dem/relion-classranker /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-vffw4mxz
Running command git clone --filter=blob:none --quiet https://github/3dem/relion-blush /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-idx5vvk7
Running command git clone --filter=blob:none --quiet https://github/3dem/DynaMight /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-vkp2a_ix
Running command git clone --filter=blob:none --quiet https://github/3dem/topaz /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-slmc2x98
Running command git clone --filter=blob:none --quiet https://github/3dem/model-angelo /private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-req-build-z8sca1_6
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [25 lines of output]
pyproject.toml: line 7: using '[tool.sip.metadata]' to specify the project metadata is deprecated and will be removed in SIP v7.0.0, use '[project]' instead
Querying qmake about your Qt installation...
Traceback (most recent call last):
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 144, in prepare_metadata_for_build_wheel
hook = backend.prepare_metadata_for_build_wheel
AttributeError: module 'sipbuild.api' has no attribute 'prepare_metadata_for_build_wheel'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
main()
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/Users/melchua/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 148, in prepare_metadata_for_build_wheel
whl_basename = backend.build_wheel(metadata_directory, config_settings)
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-build-env-uym50ri9/overlay/lib/python3.10/site-packages/sipbuild/api.py", line 28, in build_wheel
project = AbstractProject.bootstrap('wheel',
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-build-env-uym50ri9/overlay/lib/python3.10/site-packages/sipbuild/abstract_project.py", line 74, in bootstrap
project.setup(pyproject, tool, tool_description)
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-build-env-uym50ri9/overlay/lib/python3.10/site-packages/sipbuild/project.py", line 645, in setup
self.update(tool)
File "/private/var/folders/3s/2xryx8316mj8fwbryxd0z7d40000gp/T/pip-install-in2203ks/pyqt5_42cc4e87898340ef9325f1fdcca53288/project.py", line 165, in update
raise UserException(
sipbuild.exceptions.UserException
[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.
failed
1 Answer
Reset to default 1▎1. Version Compatibility Issues
PyQt5 may have compatibility issues with certain versions of Python. As of this writing, PyQt5 5.15.9 supports python up to version 3.10. If you are using Python 3.11, this could be the cause of the problem.
Solution: Try creating a new Conda environment with Python 3.10 and install PyQt5 there: conda create -n myenv python=3.10 conda activate myenv conda install pyqt=5.15.9
▎2. Installing Qt and SIP
PyQt5 depends on the Qt and SIP libraries. Make sure they are installed correctly. In Conda, this is usually done automatically, but there may be cases where you need to install them manually.
Solution: Try installing Qt and SIP via conda: conda install qt=5 sip
▎3. Conda Environment Issues
Sometimes issues can arise due to package conflicts in your conda environment.
Solution: Create a new environment with a minimal set of packages and add only the necessary ones: conda create -n newenv python=3.10 conda activate newenv conda install pyqt=5.15.9
▎4. System Dependencies
Make sure you have all the necessary dependencies installed to work with PyQt5 on macOS, especially for ARM architecture.