alphapulldown-input-parser 0.1.0__tar.gz → 0.3.0__tar.gz

{alphapulldown_input_parser-0.1.0 → alphapulldown_input_parser-0.3.0}/LICENSE

@@ -1,10 +1,6 @@
 MIT License
 
-<<<<<<< HEAD
-Copyright (c) 2024 Kosinski Lab
-=======
 Copyright (c) 2025 KosinskiLab
->>>>>>> f65396f8370fada264ee798bbeb0666d4c5726d3
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{alphapulldown_input_parser-0.1.0 → alphapulldown_input_parser-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: alphapulldown-input-parser
-Version: 0.1.0
+Version: 0.3.0
 Summary: Fold specification parser for AlphaPulldown
 Author-email: Kosinski Lab <alphapulldown@embl-hamburg.de>
 License: MIT

{alphapulldown_input_parser-0.1.0 → alphapulldown_input_parser-0.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "alphapulldown-input-parser"
-version = "0.1.0"
+version = "0.3.0"
 description = "Fold specification parser for AlphaPulldown"
 readme = "README.md"
 license = {text = "MIT"}

alphapulldown_input_parser-0.3.0/src/alphapulldown_input_parser/parser.py

@@ -0,0 +1,478 @@
+"""Standalone parser for AlphaPulldown fold specifications."""
+
+from __future__ import annotations
+
+import warnings
+from dataclasses import dataclass
+from itertools import product
+from pathlib import Path
+from typing import Dict, Iterable, List, NamedTuple, Optional, Sequence, Tuple, Union
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+
+def _deduplicate_preserve_order(items: Iterable[str]) -> Tuple[str, ...]:
+    """Return a tuple containing the first occurrence of every item."""
+    return tuple(dict.fromkeys(items))
+
+
+def _strip_path_and_extension(value: str) -> str:
+    return Path(value).stem
+
+
+def _format_error(spec: str, msg: str | None = None) -> None:
+    """Mirror the historical AlphaPulldown error message."""
+    base = f"Your format: {spec} is wrong. The program will terminate."
+    detail = f" {msg}" if msg else ""
+    raise FormatError(f"{base}{detail}")
+
+
+def _read_nonempty_lines(path: Path) -> List[str]:
+    with path.open(mode="r", encoding="utf-8") as handle:
+        return [line.strip() for line in handle if line.strip()]
+
+
+# ---------------------------------------------------------------------------
+# Core data structures
+# ---------------------------------------------------------------------------
+
+
+class FormatError(ValueError):
+    """Raised when a fold specification cannot be parsed."""
+
+
+@dataclass(frozen=True)
+class Region:
+    """1-based closed interval over the protein sequence."""
+
+    start: int
+    end: int
+
+    def __post_init__(self) -> None:
+        if self.start < 1 or self.end < 1:
+            raise ValueError("Region boundaries must be positive integers (1-based).")
+        if self.start > self.end:
+            raise ValueError("Region start must not exceed region end.")
+
+
+@dataclass(frozen=True)
+class RegionSelection:
+    """Container describing the region selection for a fold."""
+
+    regions: Tuple[Region, ...] | None = None
+
+    @property
+    def is_all(self) -> bool:
+        return self.regions is None
+
+    @classmethod
+    def all(cls) -> "RegionSelection":
+        return cls(regions=None)
+
+
+# Either {"json_input": "/path/to.json"} or {"CHAIN_A": RegionSelection(...)}
+FoldEntry = Dict[str, Union[str, RegionSelection]]
+
+
+class ExpandResult(NamedTuple):
+    formatted_folds: List[FoldEntry]
+    missing_features: List[str]
+
+
+# ---------------------------------------------------------------------------
+# Fold dataset
+# ---------------------------------------------------------------------------
+
+
+@dataclass
+class FoldDataset:
+    """Container encapsulating parsed fold specifications."""
+
+    fold_specifications: Tuple[str, ...]
+    sequences_by_origin: Dict[str, Tuple[str, ...]]
+    sequences_by_fold: Dict[str, Tuple[str, ...]]
+
+    @property
+    def unique_sequences(self) -> Tuple[str, ...]:
+        ordered: List[str] = []
+        for spec in self.fold_specifications:
+            ordered.extend(self.sequences_by_fold.get(spec, ()))
+        return _deduplicate_preserve_order(ordered)
+
+    def symlink_local_files(self, output_directory: Union[str, Path]) -> None:
+        output = Path(output_directory).expanduser().resolve()
+        output.mkdir(parents=True, exist_ok=True)
+        for file in self.sequences_by_origin.get("local", ()):
+            source = Path(file).expanduser()
+            target = output / Path(file).name
+            if target.exists() or target.is_symlink():
+                target.unlink()
+            target.symlink_to(source)
+
+    @classmethod
+    def from_fold_specifications(
+        cls,
+        fold_specifications: Sequence[str],
+        *,
+        protein_delimiter: str = "+",
+    ) -> "FoldDataset":
+        normalized_specs: List[str] = []
+        sequences_by_fold: Dict[str, Tuple[str, ...]] = {}
+        referenced_sequences: List[str] = []
+
+        for specification in fold_specifications:
+            tokens = [
+                token.strip()
+                for token in specification.split(protein_delimiter)
+                if token.strip()
+            ]
+            if not tokens:
+                continue
+
+            normalized_tokens: List[str] = []
+            per_fold_sequences: List[str] = []
+            for token in tokens:
+                parts = [part.strip() for part in token.split(":")]
+                protein_reference = parts[0]
+                referenced_sequences.append(protein_reference)
+
+                base_name = _strip_path_and_extension(protein_reference)
+                per_fold_sequences.append(base_name)
+                suffix_components = [part for part in parts[1:] if part]
+                normalized_tokens.append(
+                    ":".join([base_name, *suffix_components]) if suffix_components else base_name
+                )
+
+            normalized_spec = protein_delimiter.join(normalized_tokens)
+            normalized_specs.append(normalized_spec)
+            sequences_by_fold[normalized_spec] = _deduplicate_preserve_order(per_fold_sequences)
+
+        unique_inputs = _deduplicate_preserve_order(referenced_sequences)
+        sequences_by_origin: Dict[str, List[str]] = {"uniprot": [], "local": []}
+        for sequence in unique_inputs:
+            path = Path(sequence).expanduser()
+            has_separator = "/" in sequence or "\\" in sequence
+            has_suffix = path.suffix != ""
+            exists = path.exists() and (path.is_file() or path.is_symlink())
+            is_local = exists and (has_separator or has_suffix)
+            if is_local:
+                sequences_by_origin["local"].append(str(path.resolve()))
+            else:
+                sequences_by_origin["uniprot"].append(sequence)
+
+        return cls(
+            fold_specifications=_deduplicate_preserve_order(normalized_specs),
+            sequences_by_origin={
+                key: tuple(values) for key, values in sequences_by_origin.items()
+            },
+            sequences_by_fold=sequences_by_fold,
+        )
+
+    @classmethod
+    def from_file(
+        cls,
+        filepath: Union[str, Path],
+        *,
+        protein_delimiter: str = "+",
+    ) -> "FoldDataset":
+        path = Path(filepath).expanduser().resolve()
+        specifications = _deduplicate_preserve_order(_read_nonempty_lines(path))
+        return cls.from_fold_specifications(
+            specifications,
+            protein_delimiter=protein_delimiter,
+        )
+
+# ---------------------------------------------------------------------------
+# Feature index
+# ---------------------------------------------------------------------------
+
+
+@dataclass(frozen=True)
+class FeatureIndex:
+    """Pre-indexed feature availability for faster lookups."""
+
+    pkl: Dict[str, Tuple[str, ...]]
+    json: Dict[str, str]
+
+    def has_pkl(self, name: str) -> bool:
+        return name in self.pkl
+
+    def json_path(self, name: str) -> Optional[str]:
+        return self.json.get(name)
+
+
+def _build_feature_index(directories: Sequence[Path]) -> FeatureIndex:
+    pkl: Dict[str, List[str]] = {}
+    json_files: Dict[str, str] = {}
+
+    for directory in directories:
+        if not directory.is_dir():
+            continue
+        for entry in directory.iterdir():
+            if not entry.is_file():
+                continue
+            filename = entry.name
+            if filename.endswith(".json"):
+                keys = {entry.name, entry.stem}
+                for key in keys:
+                    json_files.setdefault(key, str(entry))
+            elif filename.endswith(".pkl"):
+                base = filename[:-4]
+                keys = {base, entry.name, entry.stem}
+                for key in keys:
+                    pkl.setdefault(key, []).append(str(entry))
+            elif filename.endswith(".pkl.xz"):
+                base = filename[:-7]
+                keys = {base, entry.name, Path(filename[:-3]).stem}
+                for key in keys:
+                    pkl.setdefault(key, []).append(str(entry))
+
+    return FeatureIndex(
+        # deduplicate paths while preserving order
+        pkl={name: tuple(dict.fromkeys(paths)) for name, paths in pkl.items()},
+        json=json_files,
+    )
+
+
+# ---------------------------------------------------------------------------
+# Expansion helpers
+# ---------------------------------------------------------------------------
+
+
+def _extract_copy_and_regions(tokens: Sequence[str], spec: str) -> Tuple[int, Sequence[str]]:
+    """Return copy count and the remaining region tokens."""
+    if len(tokens) > 1:
+        try:
+            return int(tokens[1]), tokens[2:]
+        except ValueError:
+            pass
+        try:
+            return int(tokens[-1]), tokens[1:-1]
+        except ValueError:
+            pass
+    return 1, tokens[1:]
+
+
+def _parse_regions(region_tokens: Sequence[str], spec: str) -> RegionSelection:
+    """Parse optional region tokens into a RegionSelection."""
+    if not region_tokens:
+        return RegionSelection.all()
+    regions: List[Region] = []
+    for tok in region_tokens:
+        parts = tok.split("-")
+        if len(parts) != 2:
+            _format_error(spec, msg=f"Region token '{tok}' is not of form start-stop.")
+        try:
+            start, end = map(int, parts)
+        except ValueError:
+            _format_error(spec, msg=f"Region token '{tok}' contains non-integer bounds.")
+        try:
+            regions.append(Region(start=start, end=end))
+        except ValueError as exc:
+            _format_error(spec, msg=str(exc))
+    return RegionSelection(regions=tuple(regions))
+
+
+# ---------------------------------------------------------------------------
+# Expansion logic
+# ---------------------------------------------------------------------------
+
+
+def expand_fold_specification(
+    spec: str,
+    features_directory: Iterable[str],
+    protein_delimiter: str,
+    *,
+    feature_index: FeatureIndex | None = None,
+) -> ExpandResult:
+    """Expand a single fold specification into fold entries.
+
+    Example:
+        >>> expand_fold_specification("protA:1-10+protB", ["/features"], "+", feature_index=index)
+
+    Returns:
+        ExpandResult with fold entries and missing feature names. Pure function.
+    """
+
+    index = feature_index
+    if index is None:
+        directories = tuple(Path(d).expanduser().resolve() for d in features_directory)
+        index = _build_feature_index(directories)
+
+    formatted_folds: List[FoldEntry] = []
+    missing_features: List[str] = []
+
+    for raw_pf in spec.split(protein_delimiter):
+        pf = raw_pf.strip()
+        if not pf:
+            continue
+
+        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:
+                    # 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
+
+        if not tokens or not tokens[0]:
+            _format_error(spec, msg="Protein token is empty.")
+
+        name = tokens[0]
+        name_path = Path(name)
+        name_candidates = [
+            name,
+            name_path.name,
+            name_path.stem,
+        ]
+        # copy count can be either second or last token
+        number, region_tokens = _extract_copy_and_regions(tokens, spec)
+        regions = _parse_regions(region_tokens, spec)
+
+        # try different name representations against prebuilt index
+        canonical_name = next((candidate for candidate in name_candidates if index.has_pkl(candidate)), None)
+        if canonical_name is None:
+            missing_features.append(name)
+            continue
+
+        for _ in range(number):
+            formatted_folds.append({canonical_name: regions})
+
+    return ExpandResult(formatted_folds=formatted_folds, missing_features=missing_features)
+
+
+def parse_fold(
+    input_list: List[str],
+    features_directory: Iterable[str],
+    protein_delimiter: str,
+) -> List[List[FoldEntry]]:
+    """Parse a list of fold specifications into folding jobs.
+
+    Example:
+        >>> parse_fold(["protA+protB"], ["/features"], "+")
+
+    Returns:
+        List of jobs (each job is a list of FoldEntry). Pure function.
+    """
+
+    directories = tuple(features_directory)
+    directory_labels = [str(d) for d in directories]
+    directory_paths = tuple(Path(d).expanduser().resolve() for d in directories)
+    feature_index = _build_feature_index(directory_paths)
+
+    all_folding_jobs: List[List[FoldEntry]] = []
+    missing_features = set()
+
+    for spec in input_list:
+        result = expand_fold_specification(
+            spec=spec,
+            features_directory=directories,
+            protein_delimiter=protein_delimiter,
+            feature_index=feature_index,
+        )
+        missing_features.update(result.missing_features)
+        if result.formatted_folds:
+            all_folding_jobs.append(result.formatted_folds)
+
+    if missing_features:
+        raise FileNotFoundError(f"{sorted(missing_features)} not found in {directory_labels}")
+
+    return all_folding_jobs
+
+
+# ---------------------------------------------------------------------------
+# Public API
+# ---------------------------------------------------------------------------
+
+
+def generate_fold_specifications(
+    input_files: Sequence[Union[str, Path]],
+    *,
+    delimiter: str = "+",
+    exclude_permutations: bool = True,
+    output_path: Optional[Union[str, Path]] = None,
+) -> List[str]:
+    """Compute the Cartesian product of specification files.
+
+    Args:
+        input_files: Paths to text files containing one specification per line.
+        delimiter: Delimiter used to join the combination into a specification string.
+        exclude_permutations: When True, filter out combinations that are permutations
+            of entries that already appear.
+        output_path: Optional destination to persist the resulting specifications.
+
+    Returns:
+        List of joined specification strings.
+    """
+
+    paths = [Path(p).expanduser().resolve() for p in input_files]
+    lines_per_file: List[List[str]] = []
+    for path in paths:
+        lines = _read_nonempty_lines(path)
+        if not lines:
+            warnings.warn(
+                f"Input file '{path}' contains no specifications; skipping combination generation.",
+                RuntimeWarning,
+            )
+            return []
+        lines_per_file.append(lines)
+
+    if not lines_per_file:
+        combinations: List[Tuple[str, ...]] = []
+    else:
+        combinations_iter = product(*lines_per_file)
+        seen: set[Tuple[str, ...]] = set()
+        combinations = []
+        for combo in combinations_iter:
+            typed_combo = tuple(map(str, combo))
+            if exclude_permutations:
+                normalized = tuple(sorted(typed_combo))
+                if normalized in seen:
+                    continue
+                seen.add(normalized)
+            combinations.append(typed_combo)
+
+    specifications = [delimiter.join(combo) for combo in combinations]
+
+    if output_path:
+        output = Path(output_path).expanduser().resolve()
+        output.parent.mkdir(parents=True, exist_ok=True)
+        output.write_text("\n".join(specifications) + ("\n" if specifications else ""), encoding="utf-8")
+
+    return specifications

{alphapulldown_input_parser-0.1.0 → 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: 0.1.0
+Version: 0.3.0
 Summary: Fold specification parser for AlphaPulldown
 Author-email: Kosinski Lab <alphapulldown@embl-hamburg.de>
 License: MIT

{alphapulldown_input_parser-0.1.0 → 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(

alphapulldown_input_parser-0.1.0/src/alphapulldown_input_parser/parser.py

@@ -1,273 +0,0 @@
-"""Standalone parser for AlphaPulldown fold specifications."""
-
-from __future__ import annotations
-
-import warnings
-from dataclasses import dataclass
-from itertools import product
-from pathlib import Path
-from typing import Dict, Iterable, List, NamedTuple, Optional, Sequence, Tuple, Union
-
-
-class FormatError(ValueError):
-    """Raised when a fold specification cannot be parsed."""
-
-
-def _format_error(spec: str, msg: str | None = None) -> None:
-    """Mirror the historical AlphaPulldown error message."""
-    base = f"Your format: {spec} is wrong. The program will terminate."
-    detail = f" {msg}" if msg else ""
-    raise FormatError(f"{base}{detail}")
-
-
-@dataclass(frozen=True)
-class Region:
-    """Closed interval over the protein sequence."""
-
-    start: int
-    end: int
-
-    def __post_init__(self) -> None:
-        if self.start < 0 or self.end < 0:
-            raise ValueError("Region boundaries must be non-negative integers.")
-        if self.start > self.end:
-            raise ValueError("Region start must not exceed region end.")
-
-
-@dataclass(frozen=True)
-class RegionSelection:
-    """Container describing the region selection for a fold."""
-
-    regions: Tuple[Region, ...] | None = None
-
-    @property
-    def is_all(self) -> bool:
-        return self.regions is None
-
-    @classmethod
-    def all(cls) -> "RegionSelection":
-        return cls(regions=None)
-
-
-FoldEntry = Dict[str, Union[str, RegionSelection]]
-
-
-class ExpandResult(NamedTuple):
-    formatted_folds: List[FoldEntry]
-    missing_features: List[str]
-
-
-@dataclass(frozen=True)
-class FeatureIndex:
-    """Pre-indexed feature availability for faster lookups."""
-
-    pkl: Dict[str, Tuple[str, ...]]
-    json: Dict[str, str]
-
-    def has_pkl(self, name: str) -> bool:
-        return name in self.pkl
-
-    def json_path(self, name: str) -> Optional[str]:
-        return self.json.get(name)
-
-
-def _build_feature_index(directories: Sequence[Path]) -> FeatureIndex:
-    pkl: Dict[str, List[str]] = {}
-    json_files: Dict[str, str] = {}
-
-    for directory in directories:
-        if not directory.is_dir():
-            continue
-        for entry in directory.iterdir():
-            if not entry.is_file():
-                continue
-            filename = entry.name
-            if filename.endswith(".json"):
-                json_files.setdefault(filename, str(entry))
-            elif filename.endswith(".pkl"):
-                base = filename[:-4]
-                pkl.setdefault(base, []).append(str(entry))
-            elif filename.endswith(".pkl.xz"):
-                base = filename[:-7]
-                pkl.setdefault(base, []).append(str(entry))
-
-    return FeatureIndex(
-        pkl={name: tuple(paths) for name, paths in pkl.items()},
-        json=json_files,
-    )
-
-
-def _extract_copy_and_regions(tokens: Sequence[str], spec: str) -> Tuple[int, Sequence[str]]:
-    """Return copy count and the remaining region tokens."""
-    if len(tokens) > 1:
-        try:
-            return int(tokens[1]), tokens[2:]
-        except ValueError:
-            pass
-        try:
-            return int(tokens[-1]), tokens[1:-1]
-        except ValueError:
-            pass
-    return 1, tokens[1:]
-
-
-def _parse_regions(region_tokens: Sequence[str], spec: str) -> RegionSelection:
-    """Parse optional region tokens into a RegionSelection."""
-    if not region_tokens:
-        return RegionSelection.all()
-    regions: List[Region] = []
-    for tok in region_tokens:
-        parts = tok.split("-")
-        if len(parts) != 2:
-            _format_error(spec, msg=f"Region token '{tok}' is not of form start-stop.")
-        try:
-            start, end = map(int, parts)
-        except ValueError:
-            _format_error(spec, msg=f"Region token '{tok}' contains non-integer bounds.")
-        try:
-            regions.append(Region(start=start, end=end))
-        except ValueError as exc:
-            _format_error(spec, msg=str(exc))
-    return RegionSelection(regions=tuple(regions))
-
-
-def expand_fold_specification(
-    spec: str,
-    features_directory: Iterable[str],
-    protein_delimiter: str,
-    *,
-    feature_index: FeatureIndex | None = None,
-) -> ExpandResult:
-    """Expand a single fold specification.
-
-    Returns a tuple of (formatted_folds, missing_features).
-    """
-
-    index = feature_index
-    if index is None:
-        directories = tuple(Path(d).expanduser().resolve() for d in features_directory)
-        index = _build_feature_index(directories)
-
-    formatted_folds: List[FoldEntry] = []
-    missing_features: List[str] = []
-
-    for pf in spec.split(protein_delimiter):
-        if pf.endswith(".json"):
-            json_name = pf
-            json_path = index.json_path(json_name)
-            if json_path:
-                formatted_folds.append({"json_input": json_path})
-            else:
-                missing_features.append(json_name)
-            continue
-
-        tokens = pf.split(":")
-        if not tokens or not tokens[0]:
-            _format_error(spec, msg="Protein token is empty.")
-
-        name = tokens[0]
-        number, region_tokens = _extract_copy_and_regions(tokens, spec)
-        regions = _parse_regions(region_tokens, spec)
-
-        if not index.has_pkl(name):
-            missing_features.append(name)
-            continue
-
-        for _ in range(number):
-            formatted_folds.append({name: regions})
-
-    return ExpandResult(formatted_folds=formatted_folds, missing_features=missing_features)
-
-
-def parse_fold(
-    input_list: List[str],
-    features_directory: Iterable[str],
-    protein_delimiter: str,
-) -> List[List[FoldEntry]]:
-    """Parse a list of fold specifications into folding jobs."""
-
-    directories = tuple(features_directory)
-    directory_labels = [str(d) for d in directories]
-    directory_paths = tuple(Path(d).expanduser().resolve() for d in directories)
-    feature_index = _build_feature_index(directory_paths)
-
-    all_folding_jobs: List[List[FoldEntry]] = []
-    missing_features = set()
-
-    for spec in input_list:
-        result = expand_fold_specification(
-            spec=spec,
-            features_directory=directories,
-            protein_delimiter=protein_delimiter,
-            feature_index=feature_index,
-        )
-        missing_features.update(result.missing_features)
-        if result.formatted_folds:
-            all_folding_jobs.append(result.formatted_folds)
-
-    if missing_features:
-        raise FileNotFoundError(f"{sorted(missing_features)} not found in {directory_labels}")
-
-    return all_folding_jobs
-
-
-def _read_nonempty_lines(path: Path) -> List[str]:
-    with path.open(mode="r", encoding="utf-8") as handle:
-        return [line.strip() for line in handle if line.strip()]
-
-
-def generate_fold_specifications(
-    input_files: Sequence[Union[str, Path]],
-    *,
-    delimiter: str = "+",
-    exclude_permutations: bool = True,
-    output_path: Optional[Union[str, Path]] = None,
-) -> List[str]:
-    """Compute the Cartesian product of specification files.
-
-    Args:
-        input_files: Paths to text files containing one specification per line.
-        delimiter: Delimiter used to join the combination into a specification string.
-        exclude_permutations: When True, filter out combinations that are permutations
-            of entries that already appear.
-        output_path: Optional destination to persist the resulting specifications.
-
-    Returns:
-        List of joined specification strings.
-    """
-
-    paths = [Path(p).expanduser().resolve() for p in input_files]
-    lines_per_file: List[List[str]] = []
-    for path in paths:
-        lines = _read_nonempty_lines(path)
-        if not lines:
-            warnings.warn(
-                f"Input file '{path}' contains no specifications; skipping combination generation.",
-                RuntimeWarning,
-            )
-            return []
-        lines_per_file.append(lines)
-
-    combinations = list(product(*lines_per_file)) if lines_per_file else []
-
-    if exclude_permutations:
-        filtered: List[Tuple[str, ...]] = []
-        seen: set[Tuple[str, ...]] = set()
-        for combo in combinations:
-            normalized = tuple(sorted(map(str, combo)))
-            if normalized in seen:
-                continue
-            seen.add(normalized)
-            filtered.append(tuple(map(str, combo)))
-        combinations = filtered
-    else:
-        combinations = [tuple(map(str, combo)) for combo in combinations]
-
-    specifications = [delimiter.join(combo) for combo in combinations]
-
-    if output_path:
-        output = Path(output_path).expanduser().resolve()
-        output.parent.mkdir(parents=True, exist_ok=True)
-        output.write_text("\n".join(specifications) + ("\n" if specifications else ""), encoding="utf-8")
-
-    return specifications