Add a function to compare the contents of two packets.

[plietar]

The new orderly_compare_packets function takes in two packet IDs and produces a diff of the two packets' contents. This includes a comparison of both the packets' metadata and of their files. The actual diff of the files is computed using the diffobj package.

A parameter of the function can be used to control which components of the packets are considered in the comparison, and take be one of "everything", "metadata", "files" and "artefacts".

This feature was requested as part of the epireview project, where one report's implementation got very messy and needs refactoring, but in the absence of any way of comparing two runs of the same report it is difficult to determine whether the refactor has any unexpected effect on the output.

[richfitz]

Thanks - this is looking great. Some broad comments about the comparison here, which I'm happy to litigate further in a conversation before you do any more implementation if you prefer!

[richfitz]

Why do we need to use stringr for this?

[plietar]

sub/gsub only perform a single substitution, where as we need to do many. I suppose I could compose calls and make one per replacement, but that's annoying to do in a general way. This was just easier.

[plietar]

diff <- orderly_compare_packets(p1, p2, root = root)
diff = list(root = root, metap1, metap2, ...)

class(diff) <- orderly_comparison

print(diff) --> summary view, no I/O
only list different field names, greyed out identical fields, ignore trivial fields (time, id, ...)

orderly_comparison_explain(diff, what # field name from metadata, verbose = FALSE)
orderly_comparison_explain()
# General purpose diff for unknown keys, we may have custom print outs for some of the keys, eg. files, dependencies, sessionInfo, ...
# verbose = TRUE might do file I/O using the saved root

S3 is.logical.orderly_comparison

[codecov]

Codecov Report

Attention: Patch coverage is 95.73171% with 7 lines in your changes missing coverage. Please review.

Project coverage is 99.26%. Comparing base (53cc972) to head (a3b6352).
Report is 42 commits behind head on main.

Files with missing lines	Patch %	Lines
R/compare.R	95.59%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #147      +/-   ##
==========================================
- Coverage   99.51%   99.26%   -0.25%     
==========================================
  Files          41       42       +1     
  Lines        3716     3957     +241     
==========================================
+ Hits         3698     3928     +230     
- Misses         18       29      +11     

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[plietar]

I think I’m mostly happy with the API now, except for the verbose argument that is a bit gross having 4 possible values.

The rendered output is a bit rough, especially when it comes to viewing the orderly specific metadata, but we can refine that over time.

[richfitz]

I've given this a quick whirl and I think this will be fun to try out today. I'll let people know it's subject to change but the overall idea is now pretty solid I think. Agree that handling of verbose is a bit gross, and will have a think about what we can do with that