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YosefLab / PopV

MIT License
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Package installation issue in Colab #15

Closed nagendraKU closed 1 year ago

nagendraKU commented 1 year ago

Trying to install the popv package in the colab notebook with

!pip install --quiet git+https://github.com/czbiohub/PopV

produces the following installation error. This prevents popv from being imported and the notebook is not functional anymore.

Cloning into 'PopV'...
remote: Enumerating objects: 397, done.
remote: Counting objects: 100% (141/141), done.
remote: Compressing objects: 100% (91/91), done.
remote: Total 397 (delta 77), reused 78 (delta 40), pack-reused 256
Receiving objects: 100% (397/397), 77.03 MiB | 17.59 MiB/s, done.
Resolving deltas: 100% (197/197), done.
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done

|████████████████████████████████| 588.3 MB 20 kB/s 
     |████████████████████████████████| 296 kB 63.7 MB/s 
     |████████████████████████████████| 24.9 MB 89.4 MB/s 
     |████████████████████████████████| 78 kB 8.2 MB/s 
     |████████████████████████████████| 1.1 MB 63.7 MB/s 
     |████████████████████████████████| 97 kB 8.7 MB/s 
     |████████████████████████████████| 761 kB 86.0 MB/s 
     |████████████████████████████████| 5.8 MB 77.4 MB/s 
     |████████████████████████████████| 4.5 MB 82.0 MB/s 
     |████████████████████████████████| 182 kB 101.4 MB/s 
     |████████████████████████████████| 237 kB 88.3 MB/s 
     |████████████████████████████████| 8.8 MB 87.5 MB/s 
     |████████████████████████████████| 1.1 MB 38.2 MB/s 
     |████████████████████████████████| 647 kB 92.3 MB/s 
     |████████████████████████████████| 88 kB 7.9 MB/s 
     |████████████████████████████████| 1.6 MB 57.9 MB/s 
     |████████████████████████████████| 386 kB 80.5 MB/s 
     |████████████████████████████████| 85 kB 5.8 MB/s 
     |████████████████████████████████| 96 kB 6.2 MB/s 
     |████████████████████████████████| 51 kB 8.5 MB/s 
     |████████████████████████████████| 512 kB 91.2 MB/s 
     |████████████████████████████████| 85 kB 4.9 MB/s 
     |████████████████████████████████| 292 kB 93.8 MB/s 
     |████████████████████████████████| 727 kB 81.6 MB/s 
     |████████████████████████████████| 708 kB 102.4 MB/s 
     |████████████████████████████████| 154 kB 80.0 MB/s 
     |████████████████████████████████| 77 kB 8.1 MB/s 
     |████████████████████████████████| 197 kB 66.6 MB/s 
     |████████████████████████████████| 1.7 MB 91.2 MB/s 
     |████████████████████████████████| 439 kB 103.7 MB/s 
     |████████████████████████████████| 6.0 MB 72.0 MB/s 
     |████████████████████████████████| 7.6 MB 84.9 MB/s 
     |████████████████████████████████| 66 kB 5.9 MB/s 
     |████████████████████████████████| 8.3 MB 70.4 MB/s 
     |████████████████████████████████| 1.3 MB 71.8 MB/s
Building wheel for popv (PEP 517) ... done
  Building wheel for onclass (setup.py) ... done
  Building wheel for fbpca (setup.py) ... done
  Building wheel for annoy (setup.py) ... done
  Building wheel for intervaltree (setup.py) ... done
  Building wheel for docrep (setup.py) ... done
  Building wheel for ml-collections (setup.py) ... done
  Building wheel for umap-learn (setup.py) ... done
  Building wheel for pynndescent (setup.py) ... done
  Building wheel for sentence-transformers (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.
yellowbrick 1.5 requires scikit-learn>=1.0.0, but you have scikit-learn 0.24.2 which is incompatible.
gym 0.25.2 requires importlib-metadata>=4.8.0; python_version < "3.10", but you have importlib-metadata 4.2.0 which is incompatible.
googleapis-common-protos 1.57.0 requires protobuf!=3.20.0,!=3.20.1,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0dev,>=3.19.5, but you have protobuf 3.19.0 which is incompatible.
google-colab 1.0.0 requires ipython~=7.9.0, but you have ipython 8.7.0 which is incompatible.
google-cloud-translate 3.8.4 requires protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0dev,>=3.19.5, but you have protobuf 3.19.0 which is incompatible.
google-cloud-language 2.6.1 requires protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0dev,>=3.19.5, but you have protobuf 3.19.0 which is incompatible.
google-cloud-firestore 2.7.2 requires protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0dev,>=3.19.5, but you have protobuf 3.19.0 which is incompatible.
google-cloud-datastore 2.9.0 requires protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0dev,>=3.19.5, but you have protobuf 3.19.0 which is incompatible.
google-cloud-bigquery 3.3.6 requires protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0dev,>=3.19.5, but you have protobuf 3.19.0 which is incompatible.
google-cloud-bigquery-storage 2.16.2 requires protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0dev,>=3.19.5, but you have protobuf 3.19.0 which is incompatible.
canergen commented 1 year ago

This error shouldn't prevent the tool from installing. You need to restart Colab after installing PopV (Colab imports modules upon start-up and needs to do this again when upgrading those modules). However, I will post in this thread when a redeveloped version has pretrained models (current branch fast_popv as the dataset links are not valid anymore (switch to Zenodo to allow better reproducibility). ETA is next week. Zenodo is slow currently, which is the main factor currently.

canergen commented 1 year ago

All changes are merged into main. There is a second tutorial still missing showing application to a dataset without an existing ontology.