Dani Bodor

Refactor duplicate code

4

- utils/graph.py: build_atomic_graph / build_residue_graph - features/surfacearea.py: - add_sasa_for_residues and add_sasa_for_atoms - add_sasa and and_bsa can be fused - test_surfacearea has duplicate code - query.py: - SingleResidueVariantResidueQuery and SingleResidueVariantAtomicQuery -...

Split current test_trainer into test_trainer and test_neuralnets

1

test_trainer should tests core Trainer class functionality, e.g. missing network and dataset equivalence. test_neuralnets should test each network from neuralnets subpackage. These are largely the tests that are currently using...

- pdb1tff.ent: is looking for a residue at position 6 on chain A, but it doesn't exist in the .ent file - [ ] either remove entry 20 from the...

ci: improve release workflow

6

An automated workflow can be triggered from the [Actions tab](https://github.com/DeepRank/deeprank2/actions) (once this is merged to main) that creates a draft GitHub release. The draft release (notes) can be edited if...

fix #635

re-order `add_feature` arguments

3

The function is currently defined by default as follows: ```python def add_features( pdb_path: str, # noqa: ARG001 graph: Graph, single_amino_acid_variant: SingleResidueVariant | None = None, # noqa: ARG001 ) ->...

This request is made in response to an [answer](https://stackoverflow.com/a/78834381) I received on StackOverflow ### Is your feature request related to a problem? Please describe. I have a python package where...

Improvements to PyPi listing/pyproject.toml

1

On the [PyPi page](https://pypi.org/project/deeprank2/) for this project: - the image from the README is not displayed properly - the author field shows all the authors from pyproject that do not...

docs: improve dev readme

2

For neurogym, I based the dev readme on the one from this package, but found some errors or explanations that were unclear. I now fixed the readme here as well....

Expand to ``use-implicit-booleaness-not-len`` to catch `len(iterable) == 0` and `>0`

16

### Current problem [C1802](https://pylint.readthedocs.io/en/latest/user_guide/messages/convention/use-implicit-booleaness-not-len.html) currently catches this Examples 1&2 (currently caught by rule C1802) ```py fruits = ["orange", "apple"] vegetables = [] if len(fruits): print(fruits) if not len(vegetables): print(vegetables) ```...