Issues with following demo

[bykovam]

I've experienced the following issues with running the demo so far:

1. Importing scanpy withput downgrading matplotlib to 3.4 produces this error:
   imported three packages: ---------------------------------------------------------------------------
   TypeError Traceback (most recent call last)
   Cell In[1], line 1
   ----> 1 import scanpy as sc
   2 import drug2cell as d2c
   3 import blitzgsea as blitz

File ~\Documents\Experimental_Venv\lib\site-packages\scanpy_init_.py:16
14 from . import tools as tl
15 from . import preprocessing as pp
---> 16 from . import plotting as pl
17 from . import datasets, logging, queries, external, get, metrics, experimental
19 from anndata import AnnData, concat

File ~\Documents\Experimental_Venv\lib\site-packages\scanpy\plotting_init_.py:1
----> 1 from ._anndata import (
2 scatter,
3 violin,
4 ranking,
5 clustermap,
6 tracksplot,
7 dendrogram,
8 correlation_matrix,
9 heatmap,
10 )
11 from ._dotplot import DotPlot, dotplot
12 from ._matrixplot import MatrixPlot, matrixplot

File ~\Documents\Experimental_Venv\lib\site-packages\scanpy\plotting_anndata.py:28
26 from .._utils import sanitize_anndata, _doc_params, _check_use_raw
27 from .._compat import Literal
---> 28 from . import _utils
29 from ._utils import scatter_base, scatter_group, setup_axes, check_colornorm
30 from ._utils import ColorLike, _FontWeight, _FontSize

File ~\Documents\Experimental_Venv\lib\site-packages\scanpy\plotting_utils.py:35
29 _FontSize = Literal[
30 'xx-small', 'x-small', 'small', 'medium', 'large', 'x-large', 'xx-large'
31 ]
32 VBound = Union[str, float, Callable[[Sequence[float]], float]]
---> 35 class _AxesSubplot(Axes, axes.SubplotBase, ABC):
36 """Intersection between Axes and SubplotBase: Has methods of both"""
39 # -------------------------------------------------------------------------------
40 # Simple plotting functions
41 # -------------------------------------------------------------------------------

TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases

2. targets["MHC CLASS II RECEPTOR ACTIVITY (GO:0032395)"] doesn't work anymore, it has to be targets["MHC class II receptor activity (GO:0032395)"]

3. Running
   #remove the score space object for illustration purposes
   #that it's really possible to run these functions with just the targets passed
   del adata.uns['drug2cell']

enrichment, plot_gsea_args = d2c.gsea(adata, targets=targets)
d2c.util.plot_gsea(enrichment, n=5, **plot_gsea_args)

without running beforehand %matplotlib notebook produces this error:

C:\Users\BYKOVAM\Documents\Experimental_Venv\lib\site-packages\drug2cell\util.py:143: UserWarning: Matplotlib is currently using module://matplotlib_inline.backend_inline, which is a non-GUI backend, so cannot show the figure.
fig.show()
C:\Users\BYKOVAM\Documents\Experimental_Venv\lib\site-packages\drug2cell\util.py:143: UserWarning: Matplotlib is currently using module://matplotlib_inline.backend_inline, which is a non-GUI backend, so cannot show the figure.
fig.show()
C:\Users\BYKOVAM\Documents\Experimental_Venv\lib\site-packages\drug2cell\util.py:143: UserWarning: Matplotlib is currently using module://matplotlib_inline.backend_inline, which is a non-GUI backend, so cannot show the figure.
fig.show()
C:\Users\BYKOVAM\Documents\Experimental_Venv\lib\site-packages\drug2cell\util.py:143: UserWarning: Matplotlib is currently using module://matplotlib_inline.backend_inline, which is a non-GUI backend, so cannot show the figure.
fig.show()
C:\Users\BYKOVAM\Documents\Experimental_Venv\lib\site-packages\drug2cell\util.py:143: UserWarning: Matplotlib is currently using module://matplotlib_inline.backend_inline, which is a non-GUI backend, so cannot show the figure.
fig.show()
C:\Users\BYKOVAM\Documents\Experimental_Venv\lib\site-packages\drug2cell\util.py:143: UserWarning: Matplotlib is currently using module://matplotlib_inline.backend_inline, which is a non-GUI backend, so cannot show the figure.
fig.show()
C:\Users\BYKOVAM\Documents\Experimental_Venv\lib\site-packages\drug2cell\util.py:143: UserWarning: Matplotlib is currently using module://matplotlib_inline.backend_inline, which is a non-GUI backend, so cannot show the figure.
fig.show()
C:\Users\BYKOVAM\Documents\Experimental_Venv\lib\site-packages\drug2cell\util.py:143: UserWarning: Matplotlib is currently using module://matplotlib_inline.backend_inline, which is a non-GUI backend, so cannot show the figure.
fig.show()

[ktpolanski]

Thank you very much for the heads up! Seems some stuff changed around since I put the package together

[ktpolanski]

Turns out that blitzGSEA now has the argument interactive_plot which creates figures that are .show()able within a notebook. I adjusted the syntax accordingly.

Before noticing that, I stumbled upon the following syntax for getting the figures to show en masse in a notebook. Will leave it here for posterity, just in case some changes make it desirable in the future.

from IPython.display import display

figs = d2c.util.plot_gsea(enrichment, n=5, **plot_gsea_args, interactive_plot=False)
for fig in figs:
    display(fig)