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HenriquesLab / ZeroCostDL4Mic

ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy
MIT License
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Splinedist failing to install dependencies #328

Open PennyJClarke opened 2 months ago

PennyJClarke commented 2 months ago

Describe the bug When I open the colab workbook having saved it to my drive, and I run the first cell to 'Play to install SplineDist dependencies' the installation fails based on the version of numpy.

To Reproduce Steps to reproduce the behavior:

  1. Go to Splinedist 2D notebook
  2. Save to drive or run the colab before saving to drive, the same issue persists
  3. Scroll down to 'Play to install SplineDist dependencies' and run the cell
  4. See error below:

Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (1.26.4) Collecting numpy Downloading numpy-2.1.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.9/60.9 kB 1.7 MB/s eta 0:00:00 Downloading numpy-2.1.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.3/16.3 MB 25.3 MB/s eta 0:00:00 Installing collected packages: numpy Attempting uninstall: numpy Found existing installation: numpy 1.26.4 Uninstalling numpy-1.26.4: Successfully uninstalled numpy-1.26.4 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. cudf-cu12 24.4.1 requires numpy<2.0a0,>=1.23, but you have numpy 2.1.1 which is incompatible. cupy-cuda12x 12.2.0 requires numpy<1.27,>=1.20, but you have numpy 2.1.1 which is incompatible. gensim 4.3.3 requires numpy<2.0,>=1.18.5, but you have numpy 2.1.1 which is incompatible. ibis-framework 8.0.0 requires numpy<2,>=1, but you have numpy 2.1.1 which is incompatible. numba 0.60.0 requires numpy<2.1,>=1.22, but you have numpy 2.1.1 which is incompatible. pandas 2.1.4 requires numpy<2,>=1.22.4; python_version < "3.11", but you have numpy 2.1.1 which is incompatible. pytensor 2.25.4 requires numpy<2,>=1.17.0, but you have numpy 2.1.1 which is incompatible. rmm-cu12 24.4.0 requires numpy<2.0a0,>=1.23, but you have numpy 2.1.1 which is incompatible. scikit-learn 1.3.2 requires numpy<2.0,>=1.17.3, but you have numpy 2.1.1 which is incompatible. tensorflow 2.17.0 requires numpy<2.0.0,>=1.23.5; python_version <= "3.11", but you have numpy 2.1.1 which is incompatible. thinc 8.2.5 requires numpy<2.0.0,>=1.19.0; python_version >= "3.9", but you have numpy 2.1.1 which is incompatible. Successfully installed numpy-2.1.1 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 71.3/71.3 kB 2.1 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 450.7/450.7 kB 16.9 MB/s eta 0:00:00 error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. Installing build dependencies ... error error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 193.6/193.6 kB 10.4 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 191.9/191.9 kB 16.4 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 136.8/136.8 kB 12.4 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 102.7 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 698.1/698.1 kB 47.5 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.6/78.6 kB 7.4 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.9/89.9 kB 8.3 MB/s eta 0:00:00 Building wheel for reikna (setup.py) ... done 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. albucore 0.0.16 requires numpy>=1.24, but you have numpy 1.23.5 which is incompatible. albumentations 1.4.15 requires numpy>=1.24.4, but you have numpy 1.23.5 which is incompatible. bigframes 1.17.0 requires numpy>=1.24.0, but you have numpy 1.23.5 which is incompatible. chex 0.1.86 requires numpy>=1.24.1, but you have numpy 1.23.5 which is incompatible. pandas-stubs 2.1.4.231227 requires numpy>=1.26.0; python_version < "3.13", but you have numpy 1.23.5 which is incompatible. xarray 2024.9.0 requires numpy>=1.24, but you have numpy 1.23.5 which is incompatible. ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 63.2 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Building wheel for wget (setup.py) ... done ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.3/58.3 kB 2.3 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 206.4/206.4 kB 7.1 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Building wheel for PTable (setup.py) ... done Cloning into 'splinedist'... remote: Enumerating objects: 290, done. remote: Counting objects: 100% (81/81), done. remote: Compressing objects: 100% (40/40), done. remote: Total 290 (delta 54), reused 51 (delta 40), pack-reused 209 (from 1) Receiving objects: 100% (290/290), 4.76 MiB | 27.05 MiB/s, done. Resolving deltas: 100% (105/105), done.

Expected behavior To run the installation of dependencies to run the notebook.

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