More effectively use paths

src/biomappings/cli.py

@@ -3,6 +3,7 @@
 """The biomappings CLI."""
 
 import sys
+from pathlib import Path
 
 import click
 from more_click import run_app
@@ -23,12 +24,25 @@ def main():
 if get_git_hash() is not None:
 
     @main.command()
-    @click.option("--path", type=click.Path(), help="A predictions TSV file path")
-    def web(path):
+    @click.option("--predictions-path", type=click.Path(), help="A predictions TSV file path")
+    @click.option("--positives-path", type=click.Path(), help="A positives curation TSV file path")
+    @click.option("--negatives-path", type=click.Path(), help="A negatives curation TSV file path")
+    @click.option("--unsure-path", type=click.Path(), help="An unsure curation TSV file path")
+    def web(
+        predictions_path: Path,
+        positives_path: Path,
+        negatives_path: Path,
+        unsure_path: Path,
+    ):
         """Run the biomappings web app."""
         from .wsgi import get_app
 
-        app = get_app(predictions_path=path)
+        app = get_app(
+            predictions_path=predictions_path,
+            positives_path=positives_path,
+            negatives_path=negatives_path,
+            unsure_path=unsure_path,
+        )
         run_app(app, with_gunicorn=False)
 
     @main.command()

src/biomappings/resources/__init__.py

@@ -4,7 +4,6 @@
 
 import csv
 import itertools as itt
-import os
 from collections import defaultdict
 from pathlib import Path
 from typing import (
@@ -167,9 +166,9 @@ def target_curie(self) -> str:
         return f"{self.target_prefix}:{self.target_identifier}"
 
 
-def get_resource_file_path(fname) -> str:
+def get_resource_file_path(fname) -> Path:
     """Get a resource by its file name."""
-    return os.path.join(RESOURCE_PATH, fname)
+    return RESOURCE_PATH.joinpath(fname)
 
 
 def _load_table(fname) -> List[Dict[str, str]]:

src/biomappings/utils.py

@@ -4,16 +4,18 @@
 
 import os
 import re
+from pathlib import Path
 from subprocess import CalledProcessError, check_output  # noqa: S404
 from typing import Any, Mapping, Optional, Tuple
 
 import bioregistry
 
-HERE = os.path.dirname(os.path.abspath(__file__))
-RESOURCE_PATH = os.path.abspath(os.path.join(HERE, "resources"))
-DOCS = os.path.abspath(os.path.join(HERE, os.pardir, os.pardir, "docs"))
-IMG = os.path.join(DOCS, "img")
-DATA = os.path.join(DOCS, "_data")
+HERE = Path(__file__).parent.resolve()
+ROOT = HERE.parent.parent.resolve()
+RESOURCE_PATH = HERE.joinpath("resources")
+DOCS = ROOT.joinpath("docs")
+IMG = DOCS.joinpath("img")
+DATA = DOCS.joinpath("_data")
 
 OVERRIDE_MIRIAM = {
     # ITO is very messy (combines mostly numbers with a few