Dani Bodor

Cache CI environment so it doesn't need to be rebuilt each time

2

From [this blog post](https://blog.esciencecenter.nl/reduce-reuse-recycle-save-the-planet-one-github-action-at-a-time-4ab602255c3f). > # Reuse > > If you must run the CI, the best way to reduce its impact is limit the actual work that needs to...

Remove reduce

1

deeprankcore's dependency on reduce is buggy. we will instead use an external package for adding hydrogens to the pdb files (in development). all code relying on reduce should be removed...

Use pathlib or os.join method and global TEST_PATH variable consistently in test modules

1

From [this comment](https://github.com/DeepRank/deeprank-core/pull/387#pullrequestreview-1372515081) (see below for examples): > We can either: > > Use forward slashes (/) or commas (,) with pathlib functions - both options work. The Path() object...

Use actual pairing distances rather than physical distances to define potential energies

5

In #357 we decided to use distance cutoffs as a proxy for determining 1-3 and 1-4 pairing. A more precise way to determine this is using the adjacency matrix described...

Polarity-pair edge feature

1

We can consider adding an edge feature for polarity pairing (related to IRC node feature)

Investigate pdb2sql v0.5.3 error

3

In pdb2sql v0.5.3 a new check was created that is being triggered by deeprankcore/tools/target.py when the `StructureSimilarity` object is created. I have temporarily suppressed it in PR #333. We should...

Setting for random seeds

1

Would be nice if there can be setting for random seeds (for pytorch, numpy, random) to ensure consistency between experiments. Note that pdb2sql.transform.get_rot_axis_angle, also takes its own random

Unify `get_residue_contact_pairs()` from buildgraph.py by `get_IRCs()` from irc.py

1

The buildgraph function (exclusively used in some unit tests) already existed before I worked on irc feature. Later I discovered that I largely recreated that function. The one used created...

Explore options to store hdf5 files used by pytest externally

1

Currently, each time we change something about the features, there is a potential that the tests break because the files in tests/hdf5/ are no longer representative. At this point we...

Create unit tests for missing neuralnets

2

Currently, two modules from the neuralnets folder are not tested: - alignmentnet.py - ginet_nocluster.py Consider also resolving issue #259 while working on this issue.