GSoC visualisation improvements

[nilay-v3rma]

Updates:

1. Modularise the lignetwork.py file to a network package that contains lignetwork.py, network,js, network.css, network.html
2. Convert Fingerprint data to NetworkX graph object.
3. Coordinate Calculation to organize residues (protein and water) and ligand placements.
4. Tests for calculated coordinates.

[github-actions]

Type-checking report

Difference in type-hints coverage:

6a7,9
> │   ├── exports
> │   │   ├── [x] __init__.py
> │   │   └── [x] to_networkx.py
42a46,47
>     │   ├── [x] test_nx_graph_export.py
>     │   ├── [x] test_residue_coordinates.py
52c57
< Summary: 42/42 files have complete type hints (100.0%)
---
> Summary: 46/46 files have complete type hints (100.0%)

Overview

.
├── prolif
│   ├── [x] __init__.py
│   ├── [x] _version.py
│   ├── [x] datafiles.py
│   ├── [x] exceptions.py
│   ├── exports
│   │   ├── [x] __init__.py
│   │   └── [x] to_networkx.py
│   ├── [x] fingerprint.py
│   ├── [x] ifp.py
│   ├── interactions
│   │   ├── [x] __init__.py
│   │   ├── [x] base.py
│   │   ├── [x] constants.py
│   │   ├── [x] interactions.py
│   │   ├── [x] utils.py
│   │   └── [x] water_bridge.py
│   ├── [x] molecule.py
│   ├── [x] parallel.py
│   ├── [x] pickling.py
│   ├── plotting
│   │   ├── [x] __init__.py
│   │   ├── [x] barcode.py
│   │   ├── [x] complex3d.py
│   │   ├── network
│   │   │   ├── [x] __init__.py
│   │   │   └── [x] lignetwork.py
│   │   ├── [x] residues.py
│   │   └── [x] utils.py
│   ├── [x] rdkitmol.py
│   ├── [x] residue.py
│   ├── [x] typeshed.py
│   └── [x] utils.py
├── scripts
│   ├── [x] check_types.py
│   └── [x] test_build.py
└── tests
    ├── [x] __init__.py
    ├── [x] conftest.py
    ├── plotting
    │   ├── [x] __init__.py
    │   ├── [x] test_barcode.py
    │   ├── [x] test_complex3d.py
    │   ├── [x] test_network.py
    │   ├── [x] test_nx_graph_export.py
    │   ├── [x] test_residue_coordinates.py
    │   └── [x] test_residues.py
    ├── [x] test_fingerprint.py
    ├── [x] test_ifp.py
    ├── [x] test_interactions.py
    ├── [x] test_molecule.py
    ├── [x] test_pickling.py
    ├── [x] test_residues.py
    └── [x] test_utils.py

Summary: 46/46 files have complete type hints (100.0%)

Remaining errors

Poe => mypy .
Success: no issues found in 47 source files

[codecov]

Codecov Report

❌ Patch coverage is 25.21930% with 341 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.44%. Comparing base (185460c) to head (47eef6a).

Files with missing lines	Patch %	Lines
prolif/exports/to_networkx.py	0.00%	332 Missing ⚠️
prolif/plotting/network/lignetwork.py	94.26%	7 Missing ⚠️
prolif/exports/__init__.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           master     #303       +/-   ##
===========================================
- Coverage   95.10%   81.44%   -13.66%     
===========================================
  Files          23       25        +2     
  Lines        1878     2334      +456     
===========================================
+ Hits         1786     1901      +115     
- Misses         92      433      +341     

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