Documentation updates and bugfixes #171
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# Conflicts: # requirements.txt
# Conflicts: # immuneML/ml_methods/classifiers/BinaryFeatureClassifier.py
… for reports. Removed deprecated WeightsDistribution report.
minor adjustments to Repertoire object to make it easier/more consistent to retrieve relevant sequence info for new users
…ials for adding those. added some collapsing elements for long yaml sections.
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To do before reopening:
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… .readlines() even when .readline() was called earlier)
- class documentation: some formatting was missing
…nitions'/'instructions' for clarity) - general organisation related to YAML docs - marking experimental features consistently
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Documentation improvements:
Primarily: better documentation for developer tutorials
--- better intro ("why" should you integrate into immuneML)
--- rewritten tutorials in more detail
--- dummy examples of new components (SillyEncoder, Sillyclassifier, etc), with minimal clutter
Some re-organisation and revisiting of old docs
Improved/updated figures (e.g., explanation of YAML structure, valid YAML component combinations)
Reformatting of class docs (bold), added missing docs
Changes to e.g., MLMethod and DatasetEncoder interfaces to make integration of new components more streamlined
removed unfinished WeightsDistribution report that shouldnt have been there
simplified bits of code here and there (e.g. removing unused parameters, cleaning up utility methods)