alphapulldown-input-parser 0.2.0__tar.gz → 0.3.0__tar.gz

{alphapulldown_input_parser-0.2.0 → alphapulldown_input_parser-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: alphapulldown-input-parser
-Version: 0.2.0
+Version: 0.3.0
 Summary: Fold specification parser for AlphaPulldown
 Author-email: Kosinski Lab <alphapulldown@embl-hamburg.de>
 License: MIT

{alphapulldown_input_parser-0.2.0 → alphapulldown_input_parser-0.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "alphapulldown-input-parser"
-version = "0.2.0"
+version = "0.3.0"
 description = "Fold specification parser for AlphaPulldown"
 readme = "README.md"
 license = {text = "MIT"}

{alphapulldown_input_parser-0.2.0 → alphapulldown_input_parser-0.3.0}/src/alphapulldown_input_parser/parser.py

@@ -309,20 +309,48 @@ def expand_fold_specification(
         if not pf:
             continue
 
-        if pf.endswith(".json"):
-            path_pf = Path(pf)
+        tokens = [token.strip() for token in pf.split(":")]
+        base_token = tokens[0] if tokens else ""
+
+        # JSON inputs: support optional copy number, but no ranges.
+        if base_token.endswith(".json"):
+            path_pf = Path(base_token)
             json_path: Optional[str] = None
             for json_key in (path_pf.name, path_pf.stem):
                 json_path = index.json_path(json_key)
                 if json_path:
-                    formatted_folds.append({"json_input": json_path})
+                    # Handle optional copy number for JSON inputs.
+                    if len(tokens) == 1:
+                        copies = 1
+                    else:
+                        extra_tokens = tokens[1:]
+                        # Ranges (e.g. "1-10") are not supported for JSON feature files.
+                        if any("-" in tok for tok in extra_tokens):
+                            _format_error(
+                                spec,
+                                msg="Region ranges are not supported for JSON feature files.",
+                            )
+                        if len(extra_tokens) != 1:
+                            _format_error(
+                                spec,
+                                msg="JSON feature files support only an optional copy number.",
+                            )
+                        try:
+                            copies = int(extra_tokens[0])
+                        except ValueError:
+                            _format_error(
+                                spec,
+                                msg="Copy number for JSON feature file must be an integer.",
+                            )
+
+                    for _ in range(copies):
+                        formatted_folds.append({"json_input": json_path})
                     break
             if json_path:
                 continue
             missing_features.append(path_pf.name)
             continue
 
-        tokens = [token.strip() for token in pf.split(":")]
         if not tokens or not tokens[0]:
             _format_error(spec, msg="Protein token is empty.")
 

{alphapulldown_input_parser-0.2.0 → alphapulldown_input_parser-0.3.0}/src/alphapulldown_input_parser.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: alphapulldown-input-parser
-Version: 0.2.0
+Version: 0.3.0
 Summary: Fold specification parser for AlphaPulldown
 Author-email: Kosinski Lab <alphapulldown@embl-hamburg.de>
 License: MIT

{alphapulldown_input_parser-0.2.0 → alphapulldown_input_parser-0.3.0}/test/test_parser.py

@@ -211,6 +211,32 @@ def patch_feature_index(monkeypatch):
             None,
             id="json_in_multiple_dirs",
         ),
+        pytest.param(
+            ["protein1.json:3"],
+            ["dir1"],
+            "+",
+            {"pkl": {}, "json": {"protein1.json": "dir1/protein1.json"}},
+            [
+                [
+                    {"json_input": "dir1/protein1.json"},
+                    {"json_input": "dir1/protein1.json"},
+                    {"json_input": "dir1/protein1.json"},
+                ]
+            ],
+            None,
+            None,
+            id="json_with_copy_number",
+        ),
+        pytest.param(
+            ["protein1.json:1-10"],
+            ["dir1"],
+            "+",
+            {"pkl": {}, "json": {"protein1.json": "dir1/protein1.json"}},
+            None,
+            FormatError,
+            None,
+            id="json_with_range_not_supported",
+        ),
     ],
 )
 def test_parse_fold(