Missing labels and captions in plots with default settings

Following workflow produced plots without labels or class colors (edited for brevity):

pyani index pyani_sample_genomes
pyani anim pyani_sample_genomes pyani_sample_genomes_anim
pyani plot --formats png,pdf pyani_sample_genomes_anim 1

Solution is to explicitly set labels and classes when call pyani anim,

pyani index pyani_sample_genomes
pyani anim pyani_sample_genomes pyani_sample_genomes_anim \
--labels pyani_sample_genomes/labels.txt --classes pyani_sample_genomes/classes.txt
pyani plot --formats png,pdf pyani_sample_genomes_anim 1

Would it make sense to have --labels and --classes default to $DIR/labels.txt and $DIR/classes.txt if present when run on input directory $DIR?

If no labels are given, would it make sense to use the filename stems as the default labels?

(I’m also puzzled why the classes and labels are tied to the run; I expected pyani index $DIR to record them from $DIR/labels.txt and $DIR/classes.txt)

[widdowquinn]

This is another thing that should go into the doumentation - the design goals and motivation for the database integration and how that affects the way we need to provide metadata for visualisation.

[widdowquinn]

I should really write this stuff down somewhere 😉