fixed bugs in points models

[LucaMarconato]

Fixed bugs and added tests:

• fixed bug (appearing with MERSCOPE data and described also here). In the case in which a dataframe is passed to PointsModel.parse() and the dataframe contains both x and another_x, and coordinates[x] = 'another_x, then the final parsed dataframe would contain the original column x and not another_x as expected. Added tests.
• fixed bug where if coordinates.keys() are x and y, but the dataframe contains a z column, the z column is added to the metadata and the get_axis_names() would return x, y, z instead of x, y. Now the z column is not added. Added tests.
• fixed bug same as above, but the parser gets a np.ndarray instead. I.e. if the parser receives a 2D array but the annotation dataframe contains z, now z is not added. Added tests.
• PointsModels.parse() for dataframes now takes the paramter coordinates as optional. In such a case, if x, y, or x, y, z, are in the dataframe, it is assumed, respectively that coordinates is {'x': 'x', 'y': 'y'} and {'x': 'x', 'y': 'y, 'z', 'z''}. This improves the ergonomics of the parser and closes PointsModel default argument for coordinates #228. Added tests.

[codecov]

Codecov Report

Merging #322 (fc923be) into main (cdddb8b) will decrease coverage by 0.03%.
The diff coverage is 81.81%.

❗ Current head fc923be differs from pull request most recent head 4d6de6e. Consider uploading reports for the commit 4d6de6e to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #322      +/-   ##
==========================================
- Coverage   90.75%   90.72%   -0.03%     
==========================================
  Files          36       36              
  Lines        4630     4638       +8     
==========================================
+ Hits         4202     4208       +6     
- Misses        428      430       +2     

Impacted Files	Coverage Δ
src/spatialdata/models/models.py	86.14% <81.81%> (-0.21%)	⬇️

... and 2 files with indirect coverage changes