[WIP] Packaging

[a-r-j]

Adding:

• versioneer for version management
• Travis CI
• Contributors and Contributor guidelines
• Dependabot
• PyPI release
• Misc badges

[codecov-io]

Codecov Report

Merging #54 (0e71a56) into graphein-api (6c946d9) will increase coverage by 24.46%.
The diff coverage is 36.18%.

@@                Coverage Diff                @@
##           graphein-api      #54       +/-   ##
=================================================
+ Coverage         19.33%   43.79%   +24.46%     
=================================================
  Files                25       41       +16     
  Lines              1583     2379      +796     
=================================================
+ Hits                306     1042      +736     
- Misses             1277     1337       +60     

Impacted Files	Coverage Δ
graphein/grn/config.py	0.00% <0.00%> (ø)
graphein/grn/edges.py	0.00% <0.00%> (ø)
graphein/grn/features/node_features.py	0.00% <0.00%> (ø)
graphein/grn/graphs.py	0.00% <0.00%> (ø)
graphein/grn/parse_regnetwork.py	0.00% <0.00%> (ø)
graphein/grn/parse_trrust.py	0.00% <0.00%> (ø)
graphein/protein/edges/intramolecular.py	22.68% <0.00%> (-13.59%)	⬇️
graphein/protein/edges/atomic.py	18.05% <14.28%> (+18.05%)	⬆️
graphein/protein/features/nodes/dssp.py	24.35% <22.03%> (+24.35%)	⬆️
graphein/protein/features/nodes/aaindex.py	40.90% <40.90%> (ø)
... and 52 more

---

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[Seanny123]

No need for f-string anymore, since no variable is being inserted?

Suggested change

	d[f"sequence"] = u.get_fasta_sequence(id)
	d["sequence"] = u.get_fasta_sequence(id)

[Seanny123]

This path is incorrect.

Suggested change

	"g = construct_graph(config=config, pdb_path=\"../examples/pdbs/3eiy.pdb\")"
	"g = construct_graph(config=config, pdb_path=\"../graphein/examples/pdbs/3eiy.pdb\")"

[Seanny123]

For my own notes:

Currently the TravisCI tests are failing because the tests are too slow. This is surprising to me, given they aren't using many resources on my machine. This might be solved with one of the pytest plugins which run tests in parallel. Alternatively, profiling ests/protein/test_graphs.py::test_sequence_features may be helpful.

[a-r-j]

For my own notes:

Currently the TravisCI tests are failing because the tests are too slow. This is surprising to me, given they aren't using many resources on my machine. This might be solved with one of the pytest plugins which run tests in parallel. Alternatively, profiling ests/protein/test_graphs.py::test_sequence_features may be helpful.

Hey @Seanny123 ! iirc this is due to the pre-trained ESM models being downloaded for use in the sequence features. Probably makes sense to remove that from tests.