relative path interpretation for manifests is a little fubar

[ctb]

(this is what is triggering the problem in #3048 (comment))

with the following directory structure:

annie-test-1/sig.csv
annie-test-1/sig.zip
annie-test-2/mf.csv

mf.csv built by doing:

sourmash sig check annie-test-1/sig.zip --picklist annie-test-1/sig.csv:md5:md5 -m annie-test-2/mf.csv

then mf.csv looks like this:

# SOURMASH-MANIFEST-VERSION: 1.0
internal_location,md5,md5short,ksize,moltype,num,scaled,n_hashes,with_abundance,name,filename
annie-test-1/sig.zip,c11126d0591db94cd3d1c8568499375f,c11126d0,31,DNA,0,1000,1478,False,"CP001941.1 Aciduliprofundum boonei T469, complete genome",1.fa

and then

sourmash sig cat annie-test-2/mf.csv -o /dev/null -d

yields

sourmash.exceptions.IndexNotLoaded: Cannot load sourmash index: annie-test-2/annie-test-1/sig.zip

more info soon

related to:

• standalone manifests and storage and internal_location - what do we recommend? #3008
• how to support lazy/streaming load with standard sourmash functions: standalone manifests #3023
• can we turn picklists + collections into manifests? #3048

[ctb]

The problem in the code is here:

https://github.com/sourmash-bio/sourmash/blob/latest/src/sourmash/save_load.py#L162-L171

here:

https://github.com/sourmash-bio/sourmash/blob/latest/src/sourmash/index/__init__.py#L1157-L1158

and here:

https://github.com/sourmash-bio/sourmash/blob/latest/src/sourmash/index/__init__.py#L1188-L1192

basically, the prefix is set from the dirname of the manifest, and then prepended wilhe-nilhe to the internal_locations of the rows in the manifest.

A workaround that @AnneliektH used successfully was to build the manifest with sig check using absolute paths to the zip files.

[ctb]

see discussion in #3048 (comment); once #3054 is merged, solution will be to use sourmash sig check --relpath.