CurieNamespace catalog that is not a singleton and that uses curies

[kervel]

This PR introduces a new class CurieNamespaceCatalog that can convert between uries and curies using https://github.com/cthoyt/curies

Its main reason of existence is the detection of uri and curie synonyms in the given CurieNamespaces to create the converter in the correct way.

It is based on linkml #1244 with two modifications:

• use of curies package
• no use of classvars to store the catalog namespaces (so the catalog is not a singleton anymore)

This PR is needed to complete linkml/linkml#1257

after merging this PR, we will need to update poetry.lock (can't do it here or we will get merge conflicts)

[codecov-commenter]

Codecov Report

Merging #251 (814b03e) into main (b992fe0) will increase coverage by 0.61%.
The diff coverage is 70.70%.

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@@            Coverage Diff             @@
##             main     #251      +/-   ##
==========================================
+ Coverage   63.54%   64.16%   +0.61%     
==========================================
  Files          53       53              
  Lines        6117     6284     +167     
  Branches     1650     1701      +51     
==========================================
+ Hits         3887     4032     +145     
+ Misses       1774     1770       -4     
- Partials      456      482      +26     

Impacted Files	Coverage Δ
linkml_runtime/index/object_index.py	88.28% <12.50%> (-3.53%)	⬇️
linkml_runtime/dumpers/rdflib_dumper.py	94.94% <40.00%> (-2.97%)	⬇️
linkml_runtime/utils/context_utils.py	68.33% <50.00%> (-1.85%)	⬇️
linkml_runtime/utils/schemaview.py	83.29% <54.83%> (-3.11%)	⬇️
linkml_runtime/utils/curienamespace.py	93.44% <92.72%> (+8.82%)	⬆️
linkml_runtime/__init__.py	100.00% <100.00%> (ø)
linkml_runtime/utils/namespaces.py	73.37% <100.00%> (+2.48%)	⬆️
linkml_runtime/utils/yamlutils.py	79.44% <100.00%> (+1.29%)	⬆️

... and 1 file with indirect coverage changes

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[kervel]

i just discovered we also have "namespacegen.py" which generates a python file that ... can be used to do expand/compress. so i have the impression that we have 100 ways to fix the "how to expand/compress uri's" problems.

so for an outsider it would be a bit strange to say look with namespacegen you can generate a Namespace object (which doesn't use the Namespaces class , which also can serve the same purpose btw), but if you then use pythongen we won't use that file to do exactly this.

so we have:

• Namespaces class (now used in linkml) in linkml-runtime/utils/namespaces.py @hsolbrig seems you wrote a big part of that ? Couldn't we just use that one ?
• The NamespaceCatalog proposed in this PR, which is basically now a convenience to create a CurieConverter without figuring out what is a synonym of what.
• the output of linkml gen-namespaces.py which also generates a namespaces-like class, but the name is hardcoded to BiolinkNamespace

Update i tried to use Namespaces, it misses a few convenience functions: i have to deal with values that are uriorcurie which means they might be an uri or a curie. Namespaces doesn't have a function that goes from uriorcurie to uri or to curie, you have to know in advance if its an uri or a curie. I could add those instead of this PR.

[capsulecorplab]

Should we perhaps open an issue for implementing a Namespace function that goes from uriorcurie to uri or curie?

[amc-corey-cox]

@kervel I have moved the work on this PR into the repo branch curienamespace_index_catalogclass . If you would like to continue this work please re-open the PR on the mono-repo after the merge from that branch. We'll lift it over for you so it should take less effort. This will have a slight rename in the linkml repo but you will be able to re-open it there.