pyworkflow 3.7.1 update dependency error message

[wlugmayr]

hi,

after the upgrade the user interface comes up without warning but during install the following error message appeared:

Installing collected packages: requests, pillow, numpy, configparser, matplotlib, scipion-pyworkflow Attempting uninstall: requests Found existing installation: requests 2.28.1 Uninstalling requests-2.28.1: Successfully uninstalled requests-2.28.1 Attempting uninstall: pillow Found existing installation: Pillow 9.2.0 Uninstalling Pillow-9.2.0: Successfully uninstalled Pillow-9.2.0 Attempting uninstall: numpy Found existing installation: numpy 1.23.0 Uninstalling numpy-1.23.0: Successfully uninstalled numpy-1.23.0 Attempting uninstall: configparser Found existing installation: configparser 5.2.0 Uninstalling configparser-5.2.0: Successfully uninstalled configparser-5.2.0 Attempting uninstall: matplotlib Found existing installation: matplotlib 3.5.2 Uninstalling matplotlib-3.5.2: Successfully uninstalled matplotlib-3.5.2 Attempting uninstall: scipion-pyworkflow Found existing installation: scipion-pyworkflow 3.6.0 Uninstalling scipion-pyworkflow-3.6.0: Successfully uninstalled scipion-pyworkflow-3.6.0 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. scipion-em 3.7.1 requires matplotlib<=3.5.2, but you have matplotlib 3.7.3 which is incompatible. scipion-em 3.7.1 requires Pillow<=9.2.0, but you have pillow 10.1.0 which is incompatible. Successfully installed configparser-6.0.0 matplotlib-3.7.3 numpy-1.24.4 pillow-10.1.0 requests-2.31.0 scipion-pyworkflow-3.7.0 scipion-pyworkflow was correctly updated.

$ scipion3 update Scipion v3.6.0 - Eugenius The package scipion-pyworkflow is up to date. Your version is 3.7.0 The package scipion-em is up to date. Your version is 3.7.1 The package scipion-app is up to date. Your version is 3.6.0 Scipion is up to date.

[azazellochg]

Could you post scipion3 pip list output please?

[azazellochg]

My guess you have a plugin that conflicts with the new core. Most likely xmipp-metadata or scipion-em-flexutils ..

[wlugmayr]

here are my installed plugins: scipion-em-aretomo 3.9.3 [X] scipion-em-chimera 3.4.0 [X] scipion-em-cistem 3.9.2 [X] scipion-em-cryocare 4.1.0 [X] scipion-em-dynamo 3.1.21 [X] scipion-em-eman2 3.6.1 [X] scipion-em-emantomo 3.3.1 [X] scipion-em-gctf 3.1.3 [X] scipion-em-imod 3.5.1 [X] scipion-em-isonet 3.0.1 [X] scipion-em-motioncorr 3.16.3 [X] scipion-em-novactf 3.2 [X] scipion-em-relion 5.0.0b8 [X] scipion-em-reliontomo 3.4.0 [X] scipion-em-sphire 3.2.2 [X] scipion-em-susantomo 3.0b4 [X] scipion-em-tomo 3.7.2 [X] scipion-em-tomo3d 3.1.2 [X] scipion-em-tomosegmemtv 3.1.2 [X] scipion-em-tomotwin 3.5 [X] scipion-em-tomoviz 3.1.4 [X] scipion-em-topaz 3.0.2 [X] scipion-em-warp 3.2.4 [X] scipion-em-xmipp 24.6.0.0 [X] scipion-em-xmipptomo 3.24.6.1 [X]

[wlugmayr]

Package Version

---

bibtexparser 1.2.0 biopython 1.79 certifi 2024.2.2 charset-normalizer 2.1.1 configparser 6.0.0 contourpy 1.1.1 cupy-cuda11x 12.3.0 cycler 0.12.1 distro 1.8.0 emtable 0.0.14 emtools 0.1.0 fastrlock 0.8.2 fonttools 4.51.0 future 1.0.0 h5py 3.8.0 idna 3.7 imageio 2.34.1 importlib-metadata 6.8.0 importlib_resources 6.4.0 joblib 1.4.0 kiwisolver 1.4.5 lazy_loader 0.4 littleutils 0.2.2 matplotlib 3.7.3 mrcfile 1.4.3 networkx 3.1 numpy 1.24.4 outdated 0.2.2 packaging 24.0 peppercorn 0.6 Pillow 10.1.0 pip 24.0 platformdirs 4.2.1 plotter 1.3.20 pooch 1.8.1 psutil 5.9.1 pymeshfix 0.14.1 pyparsing 3.1.2 PyQt5 5.15.10 PyQt5-Qt5 5.15.2 PyQt5-sip 12.13.0 python-dateutil 2.9.0.post0 pyvista 0.38.5 pyvistaqt 0.10.0 PyWavelets 1.4.1 QtPy 2.4.1 requests 2.31.0 scikit-image 0.20.0 scikit-learn 0.22 scipion-app 3.6.0 scipion-em 3.7.1 scipion-em-aretomo 3.9.3 scipion-em-chimera 3.4.0 scipion-em-cistem 3.9.2 scipion-em-cryocare 4.1.0 scipion-em-dynamo 3.1.21 scipion-em-eman2 3.6.1 scipion-em-emantomo 3.3.1 scipion-em-gctf 3.1.3 scipion-em-imod 3.5.1 scipion-em-isonet 3.0.1 scipion-em-motioncorr 3.16.3 scipion-em-novactf 3.2 scipion-em-relion 5.0.0b8 scipion-em-reliontomo 3.4.0 scipion-em-sphire 3.2.2 scipion-em-susantomo 3.0b4 scipion-em-tomo 3.7.2 scipion-em-tomo3d 3.1.2 scipion-em-tomosegmemtv 3.1.2 scipion-em-tomotwin 3.5 scipion-em-tomoviz 3.1.4 scipion-em-topaz 3.0.2 scipion-em-warp 3.2.4 scipion-em-xmipp 24.6.0.0 scipion-em-xmippBase 24.6.0.0 scipion-em-xmipptomo 3.24.6.1 scipion-pyworkflow 3.7.0 scipy 1.8.1 SCons 4.7.0 scooby 0.9.2 setuptools 69.5.1 six 1.16.0 tifffile 2021.11.2 tk_html_widgets 0.4.1 tkcolorpicker 2.1.3 typing_extensions 4.11.0 urllib3 1.26.18 vtk 9.3.0 wheel 0.43.0 xmltodict 0.13.0 zipp 3.18.1

[azazellochg]

For some reason, you have two outdated packages, tifffile and biopython. Both should get updated by new scipion-em. Could you update sequentially:

conda activate scipion3
pip install -U scipion-pyworkflow
pip install -U scipion-em
pip install -U scipion-app

and see if this gives any errors.

[wlugmayr]

the commands worked. here are the relevant log entries:

Installing collected packages: tifffile, biopython, scipion-em Attempting uninstall: tifffile Found existing installation: tifffile 2021.11.2 Uninstalling tifffile-2021.11.2: Successfully uninstalled tifffile-2021.11.2 Attempting uninstall: biopython Found existing installation: biopython 1.79 Uninstalling biopython-1.79: Successfully uninstalled biopython-1.79 Attempting uninstall: scipion-em Found existing installation: scipion-em 3.7.1 Uninstalling scipion-em-3.7.1: Successfully uninstalled scipion-em-3.7.1 Successfully installed biopython-1.81 scipion-em-3.8.0 tifffile-2023.7.10

[azazellochg]

Alright, then you should be good!