[pyOpenSci - EiC Checks] Installation problems

Hi, I have some problems with the installation:

OS: macOS Sequoia 15 Python version: 3.10

Installation fails when I use your guide (pip install git+https://gitlab.com/astrogal/GALAssify.git) and when I install the package from PyPI directly with pip: (pip install galassify)

The error message is:

Collecting galassify
  Downloading galassify-1.0.1-py3-none-any.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 4.2 MB/s eta 0:00:00
Collecting pandas>=2.0
  Using cached pandas-2.2.3-cp310-cp310-macosx_10_9_x86_64.whl (12.6 MB)
Collecting PyConsoleMenu>=1.0
  Using cached PyConsoleMenu-1.0.4.tar.gz (5.2 kB)
  Preparing metadata (setup.py) ... done
Collecting matplotlib>=3.7
  Using cached matplotlib-3.9.2-cp310-cp310-macosx_10_12_x86_64.whl (7.9 MB)
Collecting PyQt5>=5.15
  Using cached PyQt5-5.15.11.tar.gz (3.2 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [22 lines of output]
      Traceback (most recent call last):
        File "/Users/szymonos/Documents/pyopensci/214-GALAssify/pyos214/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/Users/szymonos/Documents/pyopensci/214-GALAssify/pyos214/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/Users/szymonos/Documents/pyopensci/214-GALAssify/pyos214/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 152, in prepare_metadata_for_build_wheel
          whl_basename = backend.build_wheel(metadata_directory, config_settings)
        File "/private/var/folders/vv/zx11_2ts7tjfsny482gs54s80000gr/T/pip-build-env-s7gwvp4k/overlay/lib/python3.10/site-packages/sipbuild/api.py", line 28, in build_wheel
          project = AbstractProject.bootstrap('wheel',
        File "/private/var/folders/vv/zx11_2ts7tjfsny482gs54s80000gr/T/pip-build-env-s7gwvp4k/overlay/lib/python3.10/site-packages/sipbuild/abstract_project.py", line 74, in bootstrap
          project.setup(pyproject, tool, tool_description)
        File "/private/var/folders/vv/zx11_2ts7tjfsny482gs54s80000gr/T/pip-build-env-s7gwvp4k/overlay/lib/python3.10/site-packages/sipbuild/project.py", line 608, in setup
          self.apply_user_defaults(tool)
        File "/private/var/folders/vv/zx11_2ts7tjfsny482gs54s80000gr/T/pip-install-k2mf_16g/pyqt5_6c4f048fc1dd41e6929018e228e423fd/project.py", line 68, in apply_user_defaults
          super().apply_user_defaults(tool)
        File "/private/var/folders/vv/zx11_2ts7tjfsny482gs54s80000gr/T/pip-build-env-s7gwvp4k/overlay/lib/python3.10/site-packages/pyqtbuild/project.py", line 51, in apply_user_defaults
          super().apply_user_defaults(tool)
        File "/private/var/folders/vv/zx11_2ts7tjfsny482gs54s80000gr/T/pip-build-env-s7gwvp4k/overlay/lib/python3.10/site-packages/sipbuild/project.py", line 237, in apply_user_defaults
          self.builder.apply_user_defaults(tool)
        File "/private/var/folders/vv/zx11_2ts7tjfsny482gs54s80000gr/T/pip-build-env-s7gwvp4k/overlay/lib/python3.10/site-packages/pyqtbuild/builder.py", line 50, in apply_user_defaults
          raise PyProjectOptionException('qmake',
      sipbuild.pyproject.PyProjectOptionException
      [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.

Do you know what could be the reason for this failed build?

Hello @simon449, thank you very much for reporting this issue.

I'm trying to replicate the error using a docker-based macOS Sequoia 15 virtual machine with Python 3.10. Unfortunately, I'm not able to replicate the error. This is the output I get:

mrmanlu@QEMU Downloads % python3.10          
Python 3.10.11 (v3.10.11:7d4cc5aa85, Apr  4 2023, 19:05:19) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> ^D
mrmanlu@QEMU Downloads % python3.10 -m pip install git+https://gitlab.com/astrogal/GALAssify.git
Collecting git+https://gitlab.com/astrogal/GALAssify.git
  Cloning https://gitlab.com/astrogal/GALAssify.git to /private/var/folders/0r/5v5w1hb12r1gfhsrgkgrbqzm0000gn/T/pip-req-build-99dvltwq
  Running command git clone --filter=blob:none --quiet https://gitlab.com/astrogal/GALAssify.git /private/var/folders/0r/5v5w1hb12r1gfhsrgkgrbqzm0000gn/T/pip-req-build-99dvltwq
  Resolved https://gitlab.com/astrogal/GALAssify.git to commit 23e794c3ccb282008d8a428c8aa8cd3f70d1e550
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pandas>=2.0 (from galassify==1.0.1)
  Downloading pandas-2.2.3-cp310-cp310-macosx_10_9_x86_64.whl.metadata (89 kB)
Collecting PyQt5>=5.15 (from galassify==1.0.1)
  Downloading PyQt5-5.15.11-cp38-abi3-macosx_11_0_x86_64.whl.metadata (2.1 kB)
Collecting matplotlib>=3.7 (from galassify==1.0.1)
  Downloading matplotlib-3.9.2-cp310-cp310-macosx_10_12_x86_64.whl.metadata (11 kB)
Collecting astropy>=5.3 (from galassify==1.0.1)
  Downloading astropy-6.1.4-cp310-cp310-macosx_10_9_x86_64.whl.metadata (10 kB)
Collecting requests>=2.31 (from galassify==1.0.1)
  Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting Pillow>=9.5 (from galassify==1.0.1)
  Downloading pillow-10.4.0-cp310-cp310-macosx_10_10_x86_64.whl.metadata (9.2 kB)
Collecting PyConsoleMenu>=1.0 (from galassify==1.0.1)
  Downloading PyConsoleMenu-1.0.4.tar.gz (5.2 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting numpy>=1.23 (from astropy>=5.3->galassify==1.0.1)
  Downloading numpy-2.1.2-cp310-cp310-macosx_14_0_x86_64.whl.metadata (60 kB)
Collecting pyerfa>=2.0.1.1 (from astropy>=5.3->galassify==1.0.1)
  Downloading pyerfa-2.0.1.4-cp39-abi3-macosx_10_9_x86_64.whl.metadata (5.7 kB)
Collecting astropy-iers-data>=0.2024.8.27.10.28.29 (from astropy>=5.3->galassify==1.0.1)
  Downloading astropy_iers_data-0.2024.10.14.0.32.55-py3-none-any.whl.metadata (5.1 kB)
Collecting PyYAML>=3.13 (from astropy>=5.3->galassify==1.0.1)
  Downloading PyYAML-6.0.2-cp310-cp310-macosx_10_9_x86_64.whl.metadata (2.1 kB)
Collecting packaging>=19.0 (from astropy>=5.3->galassify==1.0.1)
  Downloading packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
Collecting contourpy>=1.0.1 (from matplotlib>=3.7->galassify==1.0.1)
  Downloading contourpy-1.3.0-cp310-cp310-macosx_10_9_x86_64.whl.metadata (5.4 kB)
Collecting cycler>=0.10 (from matplotlib>=3.7->galassify==1.0.1)
  Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib>=3.7->galassify==1.0.1)
  Downloading fonttools-4.54.1-cp310-cp310-macosx_10_9_universal2.whl.metadata (163 kB)
Collecting kiwisolver>=1.3.1 (from matplotlib>=3.7->galassify==1.0.1)
  Downloading kiwisolver-1.4.7-cp310-cp310-macosx_10_9_x86_64.whl.metadata (6.3 kB)
Collecting pyparsing>=2.3.1 (from matplotlib>=3.7->galassify==1.0.1)
  Downloading pyparsing-3.2.0-py3-none-any.whl.metadata (5.0 kB)
Collecting python-dateutil>=2.7 (from matplotlib>=3.7->galassify==1.0.1)
  Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas>=2.0->galassify==1.0.1)
  Downloading pytz-2024.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas>=2.0->galassify==1.0.1)
  Downloading tzdata-2024.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting PyQt5-sip<13,>=12.15 (from PyQt5>=5.15->galassify==1.0.1)
  Downloading PyQt5_sip-12.15.0-cp310-cp310-macosx_10_9_universal2.whl.metadata (421 bytes)
Collecting PyQt5-Qt5<5.16.0,>=5.15.2 (from PyQt5>=5.15->galassify==1.0.1)
  Downloading PyQt5_Qt5-5.15.15-py3-none-macosx_10_13_x86_64.whl.metadata (536 bytes)
Collecting charset-normalizer<4,>=2 (from requests>=2.31->galassify==1.0.1)
  Downloading charset_normalizer-3.4.0-cp310-cp310-macosx_10_9_x86_64.whl.metadata (34 kB)
Collecting idna<4,>=2.5 (from requests>=2.31->galassify==1.0.1)
  Downloading idna-3.10-py3-none-any.whl.metadata (10 kB)
Collecting urllib3<3,>=1.21.1 (from requests>=2.31->galassify==1.0.1)
  Downloading urllib3-2.2.3-py3-none-any.whl.metadata (6.5 kB)
Collecting certifi>=2017.4.17 (from requests>=2.31->galassify==1.0.1)
  Downloading certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB)
Collecting six>=1.5 (from python-dateutil>=2.7->matplotlib>=3.7->galassify==1.0.1)
  Downloading six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Downloading astropy-6.1.4-cp310-cp310-macosx_10_9_x86_64.whl (6.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.5/6.5 MB 18.8 MB/s eta 0:00:00
Downloading matplotlib-3.9.2-cp310-cp310-macosx_10_12_x86_64.whl (7.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.9/7.9 MB 18.0 MB/s eta 0:00:00
Downloading pandas-2.2.3-cp310-cp310-macosx_10_9_x86_64.whl (12.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.6/12.6 MB 23.5 MB/s eta 0:00:00
Downloading pillow-10.4.0-cp310-cp310-macosx_10_10_x86_64.whl (3.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.5/3.5 MB 20.0 MB/s eta 0:00:00
Downloading PyQt5-5.15.11-cp38-abi3-macosx_11_0_x86_64.whl (7.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.0/7.0 MB 20.6 MB/s eta 0:00:00
Downloading requests-2.32.3-py3-none-any.whl (64 kB)
Downloading astropy_iers_data-0.2024.10.14.0.32.55-py3-none-any.whl (1.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 14.2 MB/s eta 0:00:00
Downloading certifi-2024.8.30-py3-none-any.whl (167 kB)
Downloading charset_normalizer-3.4.0-cp310-cp310-macosx_10_9_x86_64.whl (125 kB)
Downloading contourpy-1.3.0-cp310-cp310-macosx_10_9_x86_64.whl (265 kB)
Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Downloading fonttools-4.54.1-cp310-cp310-macosx_10_9_universal2.whl (2.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 15.7 MB/s eta 0:00:00
Downloading idna-3.10-py3-none-any.whl (70 kB)
Downloading kiwisolver-1.4.7-cp310-cp310-macosx_10_9_x86_64.whl (65 kB)
Downloading numpy-2.1.2-cp310-cp310-macosx_14_0_x86_64.whl (6.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.9/6.9 MB 18.8 MB/s eta 0:00:00
Downloading packaging-24.1-py3-none-any.whl (53 kB)
Downloading pyerfa-2.0.1.4-cp39-abi3-macosx_10_9_x86_64.whl (341 kB)
Downloading pyparsing-3.2.0-py3-none-any.whl (106 kB)
Downloading PyQt5_Qt5-5.15.15-py3-none-macosx_10_13_x86_64.whl (39.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 39.1/39.1 MB 23.3 MB/s eta 0:00:00
Downloading PyQt5_sip-12.15.0-cp310-cp310-macosx_10_9_universal2.whl (122 kB)
Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB)
Downloading PyYAML-6.0.2-cp310-cp310-macosx_10_9_x86_64.whl (184 kB)
Downloading tzdata-2024.2-py2.py3-none-any.whl (346 kB)
Downloading urllib3-2.2.3-py3-none-any.whl (126 kB)
Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Building wheels for collected packages: galassify, PyConsoleMenu
  Building wheel for galassify (pyproject.toml) ... done
  Created wheel for galassify: filename=galassify-1.0.1-py3-none-any.whl size=3144379 sha256=7d3f442fc1951b63b6993f44060bc7f29032b96a0b655eba6802bd8cd26da6ce
  Stored in directory: /private/var/folders/0r/5v5w1hb12r1gfhsrgkgrbqzm0000gn/T/pip-ephem-wheel-cache-nq27_her/wheels/e4/9b/9d/e29186d0e0b5acaf315816fc417234d301b60626e5ea55f84b
  Building wheel for PyConsoleMenu (pyproject.toml) ... done
  Created wheel for PyConsoleMenu: filename=PyConsoleMenu-1.0.4-py3-none-any.whl size=6146 sha256=1b2d7de92443fd3d3890a7a8bc3e94497e3ef6142c03981da333c4e56469438b
  Stored in directory: /Users/mrmanlu/Library/Caches/pip/wheels/03/58/da/edc759515fa091c8955bb3270fbc5af9cdb6000a41267f4b19
Successfully built galassify PyConsoleMenu
Installing collected packages: pytz, PyQt5-Qt5, urllib3, tzdata, six, PyYAML, PyQt5-sip, pyparsing, PyConsoleMenu, Pillow, packaging, numpy, kiwisolver, idna, fonttools, cycler, charset-normalizer, certifi, astropy-iers-data, requests, python-dateutil, PyQt5, pyerfa, contourpy, pandas, matplotlib, astropy, galassify
  WARNING: The scripts f2py and numpy-config are installed in '/Library/Frameworks/Python.framework/Versions/3.10/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts fonttools, pyftmerge, pyftsubset and ttx are installed in '/Library/Frameworks/Python.framework/Versions/3.10/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script normalizer is installed in '/Library/Frameworks/Python.framework/Versions/3.10/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts pylupdate5, pyrcc5 and pyuic5 are installed in '/Library/Frameworks/Python.framework/Versions/3.10/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts fits2bitmap, fitscheck, fitsdiff, fitsheader, fitsinfo, samp_hub, showtable, volint and wcslint are installed in '/Library/Frameworks/Python.framework/Versions/3.10/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The script get_images_sdss is installed in '/Library/Frameworks/Python.framework/Versions/3.10/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed Pillow-10.4.0 PyConsoleMenu-1.0.4 PyQt5-5.15.11 PyQt5-Qt5-5.15.15 PyQt5-sip-12.15.0 PyYAML-6.0.2 astropy-6.1.4 astropy-iers-data-0.2024.10.14.0.32.55 certifi-2024.8.30 charset-normalizer-3.4.0 contourpy-1.3.0 cycler-0.12.1 fonttools-4.54.1 galassify-1.0.1 idna-3.10 kiwisolver-1.4.7 matplotlib-3.9.2 numpy-2.1.2 packaging-24.1 pandas-2.2.3 pyerfa-2.0.1.4 pyparsing-3.2.0 python-dateutil-2.9.0.post0 pytz-2024.2 requests-2.32.3 six-1.16.0 tzdata-2024.2 urllib3-2.2.3
mrmanlu@QEMU Downloads % galassify
zsh: command not found: galassify
mrmanlu@QEMU Downloads % python3.10 -m galassify                                                
/usr/local/bin/python3.10: No module named galassify.__main__; 'galassify' is a package and cannot be directly executed
mrmanlu@QEMU Downloads % python3.10 -m galassify.galassify
Matplotlib is building the font cache; this may take a moment.
INFO:    Generating the necessary files...
INFO:    The necessary files were created. 
INFO:    Now, open GALAssify with: galassify -i files/galaxies.csv -s files/output.csv -p img/ 
INFO:    If needed, you can download catalogue images by executing: get_images_sdss -i files/galaxies.csv -p img/ 
mrmanlu@QEMU Downloads % python3.10 -m galassify.galassify
INFO:   Reading from 'files/galaxies.csv' file... Done!
INFO:   Available groups: ['1' '2' '4']
INFO:   No group selected. Using all available by default.
INFO:    5 galaxies found in selected group(s).
Module pyds9 not found. DS9 interface is disabled.
2024-10-15 04:17:24.187 Python[2666:50622] +[IMKClient subclass]: chose IMKClient_Legacy

After executing the last command, the GUI is displayed as expected:

Looking at your output, it seems that the problem is related with PyQt 5.15. There exists some reports in stackOverflow asking about the same problem. For example: https://stackoverflow.com/questions/72085359/pip-install-pyqt5-tools-error-subprocess-exited-with-error

Are you installing the package inside a virtual environment? If not, please follow the guide about it written in the README.md, try to install the package inside this environment and then post your results. It will be helpfull in order to characterise this bug.

Thank you again for your report.

Regards, Manuel

P.S.: @andonij propose to ensure that libXt is installed. Please, check the Installation throubleshooting in the README.md file and tell us if it solved the problem. Thanks again!

Hi @Manalclay95

Thank you for pointing me to the possible reason why the installation has failed. I have found a solution, but unfortunately, it isn't the same as you have provided here

I will describe it below, maybe it will be helpful for you in the future, or you can copy & paste it into your docs.

---

MacOS and Python > 3.9 installation issues with pyQT 5.15

1. Upgrade pip (just in case).

pip install --upgrade pip

2. Install pyQT5

Related to: https://stackoverflow.com/questions/76113859/unable-to-install-pyqt5-on-macos

brew install qt5

Follow the instructions for installation; the last instructions show you how to update the .zshrc file.

3. Create virtual environment

4. Install the package with the command:

Related to: https://stackoverflow.com/questions/66546886/pip-install-stuck-on-preparing-wheel-metadata-when-trying-to-install-pyqt5

pip install git+https://gitlab.com/astrogal/GALAssify.git --config-settings --confirm-license= --verbose

When asked about the license, type yes. Installation can take some time because everything is compiled from scratch.

You can close the issue. I will update the pyOpenSci review accordingly

Hello again! We will use this issue to create a branch and update the README with the given instructions. We really appreciate all your help with this issue, Thank you!

created branch 13-pyopensci-eic-checks-installation-problems to address this issue

mentioned in merge request !24 (merged)

closed with merge request !24 (merged)

mentioned in commit 241f4efd

mentioned in commit 4a7ff20e