refactor NPLinker class (#256)

* remove unused property `metadata`

* refactor private data containers and relevant methods

* remove legacy code for saving data

* change the variable of default database folder to package level

* update config related code

* uniform the names of scoring methods

* refactor `NPLinker.get_links` method

- remove unused method `scoring_method`
- refactor the method `get_links`

* Delete test_nplinker_scoring.py

* reorder methods and properties of NPLinker class

* fix returned value type

* update integration tests

- simplify the `conftest.py`
- remove unused functions
- add tests for `get_link`

* fix mypy errors

src/nplinker/__init__.py

@@ -1,4 +1,5 @@
 import logging
+from pathlib import Path
 
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())
@@ -8,6 +9,11 @@
 __version__ = "2.0.0-alpha.1"
 
 
+# The path to the NPLinker application database directory
+NPLINKER_APP_DATA_DIR = Path(__file__).parent / "data"
+del Path
+
+
 def setup_logging(level: str = "INFO", file: str = "", use_console: bool = True) -> None:
     """Setup logging configuration for the ancestor logger "nplinker".
 
@@ -22,7 +28,7 @@ def setup_logging(level: str = "INFO", file: str = "", use_console: bool = True)
     from rich.console import Console
     from rich.logging import RichHandler
 
-    # Get the acncestor logger "nplinker"
+    # Get the ancestor logger "nplinker"
     logger = logging.getLogger(__name__)
     logger.setLevel(level)
 

src/nplinker/loader.py

@@ -1,8 +1,8 @@
 import logging
 import os
-from importlib.resources import files
 from deprecated import deprecated
 from dynaconf import Dynaconf
+from nplinker import NPLINKER_APP_DATA_DIR
 from nplinker import defaults
 from nplinker.genomics.antismash import AntismashBGCLoader
 from nplinker.genomics.bigscape import BigscapeGCFLoader
@@ -23,8 +23,6 @@
 
 logger = logging.getLogger(__name__)
 
-NPLINKER_APP_DATA_DIR = files("nplinker").joinpath("data")
-
 
 class DatasetLoader:
     """Class to load all data.
@@ -228,9 +226,10 @@ def _load_class_info(self):
             True if everything completes
         """
         # load Class_matches with mibig info from data
-        mibig_class_file = NPLINKER_APP_DATA_DIR.joinpath(
-            "MIBiG2.0_compounds_with_AS_BGC_CF_NPC_classes.txt"
+        mibig_class_file = (
+            NPLINKER_APP_DATA_DIR / "MIBiG2.0_compounds_with_AS_BGC_CF_NPC_classes.txt"
         )
+
         self.class_matches = ClassMatches(mibig_class_file)  # noqa
 
         # run canopus if canopus_dir does not exist