Update config template and validations

change config bigscape.cutoff from float to string

transform config `root_dir` to full path.

src/nplinker/config.py

@@ -2,6 +2,7 @@
 from pathlib import Path
 from dynaconf import Dynaconf
 from dynaconf import Validator
+from nplinker.utils import transform_to_full_path
 
 
 # The Dynaconf library is used for loading NPLinker config file.
@@ -10,6 +11,7 @@
 # directory.
 # The loaded config data is available by importing this module and accessing the 'config' variable.
 
+__all__ = ["config"]
 
 # Locate the user's config file
 user_config_file = os.environ.get("NPLINKER_CONFIG_FILE", "nplinker.toml")
@@ -29,7 +31,9 @@
 validators = [
     # General settings
     ## `root_dir` value is transformed to a `pathlib.Path` object and must be a directory.
-    Validator("root_dir", required=True, cast=Path, condition=lambda v: v.is_dir()),
+    Validator(
+        "root_dir", required=True, cast=transform_to_full_path, condition=lambda v: v.is_dir()
+    ),
     Validator("mode", required=True, cast=lambda v: v.lower(), is_in=["local", "podp"]),
     ## `podp_id` must be set if `mode` is "podp"; must not be set if `mode` is "local".
     Validator("podp_id", required=True, when=Validator("mode", eq="podp")),
@@ -55,7 +59,7 @@
     ),
     # BigScape
     Validator("bigscape.parameters", required=True, is_type_of=str),
-    Validator("bigscape.cutoff", required=True, is_type_of=float),
+    Validator("bigscape.cutoff", required=True, is_type_of=str),
     # Scoring
     ## `scoring.methods` must be a list of strings and must contain at least one of the
     ## supported scoring methods.

src/nplinker/data/nplinker.toml

@@ -52,8 +52,9 @@ version = "3.1"
 parameters = "--mibig --clans-off --mix --include_singletons --cutoffs 0.30"
 # Which bigscape cutoff to use for NPLinker analysis.
 # There might be multiple cutoffs in bigscape output.
-# The default value is 0.30.
-cutoff = 0.30
+# Note that this value must be a string.
+# The default value is "0.30".
+cutoff = "0.30"
 
 
 [scoring]

src/nplinker/nplinker_default.toml

@@ -10,7 +10,7 @@ version = "3.1"
 
 [bigscape]
 parameters = "--mibig --clans-off --mix --include_singletons --cutoffs 0.30"
-cutoff = 0.30
+cutoff = "0.30"
 
 [scoring]
 methods = ["metcalf"]

tests/test_config.py

@@ -22,6 +22,6 @@ def test_config_demo1():
         config.bigscape.parameters
         == "--mibig --clans-off --mix --include_singletons --cutoffs 0.30"
     )
-    assert config.bigscape.cutoff == 0.30
+    assert config.bigscape.cutoff == "0.30"
 
     assert config.scoring.methods == ["metcalf"]