Persistence diagrams workflow

[raphaelreinauer]

New features:

• Automatic generation of PD dataset from standard graph datasets
• Persistence Diagram class with a lot of functionality like plotting
• Preprocessing for Persistence Diagrams
• New modular implementation of the Persformer

The whole pipeline as a tutorial is in examples/mutag_pipeline.ipynb

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[matteocao]

There are only very few small fixes to make mypy happy : would you mind please fixing them as well?

[matteocao]

almost there : once the CI passes, please have a look at my comments and also make sure that mypy has no issues (there are still a couple of minor things

Run mypy --ignore-missing-imports . || {
[9](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:10)
gdeep/data/preprocessors/min_max_scalar.py:54: error: "Dataset[Tuple[Tensor, Any]]" has no attribute "__iter__" (not iterable)
[10](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:11)
gdeep/data/datasets/persistence_diagrams_from_graphs_builder.py:8: error: Library stubs not installed for "requests" (or incompatible with Python 3.8)
[11](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:12)
gdeep/data/datasets/persistence_diagrams_from_graphs_builder.py:8: note: Hint: "python3 -m pip install types-requests"
[12](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:13)
gdeep/data/datasets/persistence_diagrams_from_graphs_builder.py:8: note: (or run "mypy --install-types" to install all missing stub packages)
[13](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:14)
gdeep/data/datasets/persistence_diagrams_from_graphs_builder.py:8: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
[14](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:15)
gdeep/data/datasets/base_dataloaders.py:209: error: Name "out" already defined on line 196
[15](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:16)
examples/mutag_pipeline.py:58: error: Name "pd" already defined on line 45
[16](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:17)
examples/mutag_pipeline.py:96: error: Incompatible types in assignment (expression has type "TransformingDataset[Tuple[OneHotEncodedPersistenceDiagram, int], Any]", variable has type "Subset[Tuple[OneHotEncodedPersistenceDiagram, int]]")
[17](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:18)
examples/mutag_pipeline.py:97: error: Incompatible types in assignment (expression has type "TransformingDataset[Tuple[OneHotEncodedPersistenceDiagram, int], Any]", variable has type "Subset[Tuple[OneHotEncodedPersistenceDiagram, int]]")
[18](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:19)
examples/mutag_pipeline.py:98: error: Incompatible types in assignment (expression has type "TransformingDataset[Tuple[OneHotEncodedPersistenceDiagram, int], Any]", variable has type "Subset[Tuple[OneHotEncodedPersistenceDiagram, int]]")
[19](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:20)
examples/mutag_pipeline.py:140: error: Incompatible types in assignment (expression has type "PersformerWrapper", variable has type "Persformer")
[20](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:21)
Found 8 errors in 4 files (checked 126 source files)
[21](https://github.com/giotto-ai/giotto-deep/runs/6919970264?check_suite_focus=true#step:6:22)
Type checking errors!

[raphaelreinauer]

There are only very few small fixes to make mypy happy : would you mind please fixing them as well?

Okay I fixed that!

[matteocao]

great work!