merge LinkFinder to MetcalfScoring class (#248)

* merge LinkFinder to MetcalfScoring class

The actual role of LinkFinder is to calculate metcalf score, so it makes more sense to merge its functions to MetcalfScoring class

* remove LinkFinder

* move unit tests of LinkFinder

* update static typings

* Delete conftest.py

* create temporary root dir only in the places that require  it

* update fixture scopes

* Update test_metcalf_scoring.py

caplog cannot capture all logs, so remove the assertions.

* update pytest dist value to loadgroup

This option is much faster and easier to control the group of tests for same worker.

* fix repeatings

pyproject.toml

@@ -87,8 +87,10 @@ namespaces = true # enable data directory to be identified
 
 [tool.pytest.ini_options]
 minversion = "6.0"
-# pytest options: -ra: show summary info for all test outcomes; -n auto: run tests in parallel; --dist loadscope: distribute tests by loading scope
-addopts = "-ra -n auto --dist loadscope"    
+# -ra: show summary info for all test outcomes; 
+# -n auto: run tests in parallel; 
+# --dist loadgroup: sends tests marked with 'xdist_group' to the same worker
+addopts = "-ra -n auto --dist loadgroup"    
 testpaths = ["tests/unit"]
 
 [tool.coverage.run]

src/nplinker/scoring/linking/__init__.py

@@ -1,8 +1,7 @@
 from .data_links import LINK_TYPES
 from .data_links import DataLinks
-from .link_finder import LinkFinder
 from .utils import calc_correlation_matrix
 from .utils import isinstance_all
 
 
-__all__ = ["DataLinks", "LINK_TYPES", "LinkFinder", "calc_correlation_matrix", "isinstance_all"]
+__all__ = ["DataLinks", "LINK_TYPES", "calc_correlation_matrix", "isinstance_all"]