Parallelisation improvements

[cbouy]

A few things for parallel analysis:

• Fixes using more cores slows down the fingerprint analysis #316: some adjustments to the number of processes spawned by default (capping to 10 for trajectories by default)
• Implements a queue-based strategy for trajectories, works better than the original "chunk"-based strategy for large files
• Adds some heuristics to chose between the chunk and queue strategies
• Adds some docs to explain those changes
• Enables parallel processing for WaterBridge

[github-actions]

Type-checking report

Difference in type-hints coverage:

47a48
>     ├── [x] test_parallel.py
52c53
< Summary: 42/42 files have complete type hints (100.0%)
---
> Summary: 43/43 files have complete type hints (100.0%)

Overview

.
├── prolif
│   ├── [x] __init__.py
│   ├── [x] _version.py
│   ├── [x] datafiles.py
│   ├── [x] exceptions.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_residues.py
    ├── [x] test_fingerprint.py
    ├── [x] test_ifp.py
    ├── [x] test_interactions.py
    ├── [x] test_molecule.py
    ├── [x] test_parallel.py
    ├── [x] test_pickling.py
    ├── [x] test_residues.py
    └── [x] test_utils.py

Summary: 43/43 files have complete type hints (100.0%)

Remaining errors

Poe => mypy .
Success: no issues found in 43 source files

[codecov]

Codecov Report

❌ Patch coverage is 93.10345% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 95.07%. Comparing base (c3bcee1) to head (8674f29).
⚠️ Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
prolif/parallel.py	91.66%	5 Missing ⚠️
prolif/fingerprint.py	93.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #324      +/-   ##
==========================================
- Coverage   95.11%   95.07%   -0.05%     
==========================================
  Files          23       23              
  Lines        1885     1950      +65     
==========================================
+ Hits         1793     1854      +61     
- Misses         92       96       +4     

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