Scvi scarches xgb

[LuckyMD]

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• This submission follows the guidelines in our Contributing document
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This PR will be evaluated on the basis of the following checks:

• The task addresses a valid open problem in single-cell analysis
• The latest version of master is merged and tested
• The methods/metrics are imported to __init__.py and were tested in the pipeline
• Method and metric decorators are annotated with paper title, year, author, code version, and date
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[LuckyMD]

Notes:

The following error in label encoding:

Traceback (most recent call last):
  File "/tmp/tmpc7ezwktc/test_method.py", line 31, in <module>
    test_method(*('label_projection', 'scarches_scanvi_xgb_all_genes', 'openproblems-python-scvi'), **{})
  File "/tmp/tmpc7ezwktc/test_method.py", line 12, in test_method
    adata = method(adata, test=True)
  File "/__w/SingleCellOpenProblems/SingleCellOpenProblems/openproblems/tools/decorators.py", line 80, in apply_method
    return func(*args, **kwargs)
  File "/__w/SingleCellOpenProblems/SingleCellOpenProblems/openproblems/tasks/label_projection/methods/scvi_tools.py", line 251, in scarches_scanvi_xgb_all_genes
    adata.obs["labels_pred"] = _scanvi_scarches(
  File "/__w/SingleCellOpenProblems/SingleCellOpenProblems/openproblems/tasks/label_projection/methods/scvi_tools.py", line 152, in _scanvi_scarches
    preds = _pred_xgb(adata, adata_train, adata_test, query_model, test=test)
  File "/__w/SingleCellOpenProblems/SingleCellOpenProblems/openproblems/tasks/label_projection/methods/scvi_tools.py", line 193, in _pred_xgb
    xgbc.fit(X_train, y_train)
  File "/usr/local/lib/python3.8/site-packages/xgboost/core.py", line 532, in inner_f
    return f(**kwargs)
  File "/usr/local/lib/python3.8/site-packages/xgboost/sklearn.py", line 1357, in fit
    raise ValueError(
ValueError: Invalid classes inferred from unique values of `y`.  Expected: [0 1 2 3 4], got ['0' '1' '2' '3' '4']

Tested:

• local install of xgboost 1.5.2 and 1.6.1 with different dataset but same prediction function -> works

Todo:

• get docker running locally to test the env
• Test integer label encoding