chore: run pre commit hooks

Author: DiogoRibeiro7

.pre-commit-config.yaml

@@ -1,35 +1,65 @@
+default_language_version:
+  python: python3.12
+
+exclude: |
+  (?x)(
+    ^\.venv/|
+    ^\.mypy_cache/|
+    ^\.pytest_cache/|
+    ^build/|
+    ^dist/|
+    ^docs/_build/|
+    ^migrations/
+  )
+
 repos:
-- repo: https://github.com/PyCQA/docformatter
-  rev: v1.7.5
-  hooks:
-  - id: docformatter
-    args: ["--wrap-summaries=100", "--wrap-descriptions=100"]
-    files: ^src/
-- repo: https://github.com/pycqa/isort
-  rev: 5.13.2
-  hooks:
-  - id: isort
-    files: ^src/
-    args: ["--profile", "black"]
-- repo: https://github.com/psf/black
-  rev: 24.8.0
-  hooks:
-  - id: black
-    files: ^src/
-- repo: https://github.com/pycqa/flake8
-  rev: 7.1.0
-  hooks:
-  - id: flake8
-    additional_dependencies: [flake8-docstrings]
-    files: ^src/
-    args: ["--max-line-length=100", "--extend-ignore=E203,W503,D401"]
-- repo: https://github.com/pycqa/pydocstyle
-  rev: 6.3.0
-  hooks:
-  - id: pydocstyle
-    files: ^src/
-- repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.10.0
-  hooks:
-  - id: mypy
-    files: ^src/
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.7          # use master until a 1.7.6+ release lands
+    hooks:
+      - id: docformatter
+        args: ["--wrap-summaries=100", "--wrap-descriptions=100"]
+        files: ^src/
+
+
+  - repo: https://github.com/pycqa/isort
+    rev: 6.0.1
+    hooks:
+      - id: isort
+        files: ^(src|tests)/
+        args: ["--profile", "black", "--line-length", "100"]
+
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+      - id: black
+        files: ^(src|tests)/
+        args: ["--line-length", "100"]
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.3.0
+    hooks:
+      - id: flake8
+        files: ^(src|tests)/
+        additional_dependencies:
+          - flake8-docstrings
+          # add plugins you like, e.g. flake8-bugbear
+          # - flake8-bugbear
+        args: ["--max-line-length=88", "--extend-ignore=E203,W503,D401"]
+
+  # Remove this if you keep flake8-docstrings above (to avoid duplicate checks)
+  # - repo: https://github.com/pycqa/pydocstyle
+  #   rev: 6.3.0
+  #   hooks:
+  #     - id: pydocstyle
+  #       files: ^(src|tests)/
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.17.1
+    hooks:
+      - id: mypy
+        files: ^src/
+        # Add stubs your project needs:
+        additional_dependencies:
+          - types-requests
+          - types-PyYAML
+        # If you have mypy.ini/pyproject.toml, it will be picked up automatically

src/ssspx/bench.py

@@ -117,21 +117,15 @@ def main(argv: List[str] | None = None) -> None:
         argv: Optional argument list for testing.
     """
     parser = argparse.ArgumentParser(description=__doc__)
-    parser.add_argument(
-        "--trials", type=int, default=1, help="Number of trials per configuration"
-    )
+    parser.add_argument("--trials", type=int, default=1, help="Number of trials per configuration")
     parser.add_argument(
         "--sizes",
         nargs="+",
         default=["10,20", "20,40"],
         help="Size pairs as n,m (e.g. 1000,5000). Defaults to a small demo.",
     )
-    parser.add_argument(
-        "--seed-base", type=int, default=0, help="Base seed for random graphs"
-    )
-    parser.add_argument(
-        "--out-csv", type=Path, help="Optional path to write per-trial CSV data"
-    )
+    parser.add_argument("--seed-base", type=int, default=0, help="Base seed for random graphs")
+    parser.add_argument("--out-csv", type=Path, help="Optional path to write per-trial CSV data")
     parser.add_argument(
         "--mem",
         action="store_true",

src/ssspx/cli.py

@@ -10,13 +10,7 @@
 from pathlib import Path
 from typing import List, Optional, Tuple
 
-from .exceptions import (
-    ConfigError,
-    GraphFormatError,
-    InputError,
-    NotSupportedError,
-    SSSPXError,
-)
+from .exceptions import ConfigError, GraphFormatError, InputError, NotSupportedError, SSSPXError
 from .export import export_dag_graphml, export_dag_json
 from .graph import Graph
 from .io import read_graph
@@ -110,26 +104,16 @@ def main(argv: Optional[List[str]] = None) -> int:
         default=None,
         help="Comma-separated list of source vertex ids",
     )
-    p.add_argument(
-        "--target", type=int, default=None, help="Target vertex id for path output"
-    )
+    p.add_argument("--target", type=int, default=None, help="Target vertex id for path output")
 
-    p.add_argument(
-        "--no-transform", action="store_true", help="Disable outdegree transform"
-    )
-    p.add_argument(
-        "--target-outdeg", type=int, default=4, help="Outdegree cap when transforming"
-    )
+    p.add_argument("--no-transform", action="store_true", help="Disable outdegree transform")
+    p.add_argument("--target-outdeg", type=int, default=4, help="Outdegree cap when transforming")
     p.add_argument("--frontier", choices=["block", "heap"], default="block")
 
     # Profiling + export
     p.add_argument("--profile", action="store_true", help="Enable cProfile")
-    p.add_argument(
-        "--profile-out", type=str, default=None, help="Dump .prof file to this path"
-    )
-    p.add_argument(
-        "--export-json", type=str, default=None, help="Write shortest-path DAG as JSON"
-    )
+    p.add_argument("--profile-out", type=str, default=None, help="Dump .prof file to this path")
+    p.add_argument("--export-json", type=str, default=None, help="Write shortest-path DAG as JSON")
     p.add_argument(
         "--export-graphml",
         type=str,
@@ -165,9 +149,7 @@ def main(argv: Optional[List[str]] = None) -> int:
         )
 
         stream = sys.stdout if args.log_json else sys.stderr
-        level = (
-            "info" if args.log_json and args.log_level == "warning" else args.log_level
-        )
+        level = "info" if args.log_json and args.log_level == "warning" else args.log_level
         logger = StdLogger(level=level, json_fmt=args.log_json, stream=stream)
 
         if args.sources is not None:
@@ -194,15 +176,11 @@ def main(argv: Optional[List[str]] = None) -> int:
             t0 = time.perf_counter()
             if args.profile:
                 with ProfileSession(dump_path=args.profile_out) as prof:
-                    solver = SSSPSolver(
-                        G, sources[0], config=cfg, logger=logger, sources=sources
-                    )
+                    solver = SSSPSolver(G, sources[0], config=cfg, logger=logger, sources=sources)
                     res = solver.solve()
                 sys.stderr.write(prof.report().to_text(lines=40))
             else:
-                solver = SSSPSolver(
-                    G, sources[0], config=cfg, logger=logger, sources=sources
-                )
+                solver = SSSPSolver(G, sources[0], config=cfg, logger=logger, sources=sources)
                 res = solver.solve()
             wall_ms = (time.perf_counter() - t0) * 1000.0
             _, peak = tracemalloc.get_traced_memory()
@@ -212,15 +190,11 @@ def main(argv: Optional[List[str]] = None) -> int:
             t0 = time.perf_counter()
             if args.profile:
                 with ProfileSession(dump_path=args.profile_out) as prof:
-                    solver = SSSPSolver(
-                        G, sources[0], config=cfg, logger=logger, sources=sources
-                    )
+                    solver = SSSPSolver(G, sources[0], config=cfg, logger=logger, sources=sources)
                     res = solver.solve()
                 sys.stderr.write(prof.report().to_text(lines=40))
             else:
-                solver = SSSPSolver(
-                    G, sources[0], config=cfg, logger=logger, sources=sources
-                )
+                solver = SSSPSolver(G, sources[0], config=cfg, logger=logger, sources=sources)
                 res = solver.solve()
             wall_ms = (time.perf_counter() - t0) * 1000.0
             peak_mib = None

src/ssspx/frontier.py

@@ -186,9 +186,7 @@ def pull(self) -> Tuple[Set[Vertex], Float]:
 
         got = self._consume_block_prefix(self._d0, self.M, chosen, pulled_keys)
         if got < self.M:
-            got += self._consume_block_prefix(
-                self._d1, self.M - got, chosen, pulled_keys
-            )
+            got += self._consume_block_prefix(self._d1, self.M - got, chosen, pulled_keys)
             new_bounds: List[Float] = []
             for blk in self._d1:
                 if blk:

src/ssspx/graph_numpy.py

@@ -25,9 +25,7 @@ def __post_init__(self) -> None:
         """Validate initialization arguments and allocate adjacency storage."""
         if not isinstance(self.n, int) or self.n <= 0:
             raise InputError("Graph.n must be a positive integer.")
-        self.adj: List[np.ndarray] = [
-            np.zeros((0, 2), dtype=float) for _ in range(self.n)
-        ]
+        self.adj: List[np.ndarray] = [np.zeros((0, 2), dtype=float) for _ in range(self.n)]
 
     def add_edge(self, u: Vertex, v: Vertex, w: Float) -> None:
         """Add a directed edge from ``u`` to ``v``."""

src/ssspx/io.py

@@ -135,11 +135,7 @@ def _read_graphml(path: Path) -> Tuple[int, EdgeList]:
         w_attr = edge.attrib.get("weight")
         if w_attr is None:
             data = edge.find(f"{ns}data[@key='w']")
-            w = (
-                float(data.text)
-                if (data is not None and data.text is not None)
-                else 1.0
-            )
+            w = float(data.text) if (data is not None and data.text is not None) else 1.0
         else:
             w = float(w_attr)
         edges.append((u, v, w))

src/ssspx/logger.py

@@ -50,9 +50,7 @@ def __init__(
     def _enabled(self, level: str) -> bool:  # pragma: no cover - thin wrapper
         return self._levels[level] >= self._levels.get(self.level, 20)
 
-    def log(
-        self, level: str, event: str, **fields: Any
-    ) -> None:  # pragma: no cover - simple I/O
+    def log(self, level: str, event: str, **fields: Any) -> None:  # pragma: no cover - simple I/O
         """Emit a log ``event`` at ``level`` with additional ``fields``."""
         if not self._enabled(level):
             return
@@ -69,8 +67,6 @@ def info(self, event: str, **fields: Any) -> None:  # pragma: no cover - passthr
         """Emit an ``INFO`` event."""
         self.log("info", event, **fields)
 
-    def debug(
-        self, event: str, **fields: Any
-    ) -> None:  # pragma: no cover - passthrough
+    def debug(self, event: str, **fields: Any) -> None:  # pragma: no cover - passthrough
         """Emit a ``DEBUG`` event."""
         self.log("debug", event, **fields)

src/ssspx/path.py

@@ -31,12 +31,7 @@ def reconstruct_path_basic(
     if source == target:
         return [source]
 
-    if (
-        target < 0
-        or target >= len(predecessors)
-        or source < 0
-        or source >= len(predecessors)
-    ):
+    if target < 0 or target >= len(predecessors) or source < 0 or source >= len(predecessors):
         raise ValueError("source/target out of range.")
 
     # Walk backwards from target to source

src/ssspx/solver.py

@@ -265,11 +265,7 @@ def _find_pivots(self, B: Float, S: Set[Vertex]) -> Tuple[Set[Vertex], Set[Verte
         children: Dict[Vertex, List[Vertex]] = {u: [] for u in W}
         for v in W:
             p = self.pred[v]
-            if (
-                p is not None
-                and p in W
-                and self.dhat[p] + self._weight(p, v) == self.dhat[v]
-            ):
+            if p is not None and p in W and self.dhat[p] + self._weight(p, v) == self.dhat[v]:
                 children[p].append(v)
 
         P: Set[Vertex] = set()
@@ -337,9 +333,7 @@ def _bmssp(self, level: int, B: Float, S: Set[Vertex]) -> Tuple[Float, Set[Verte
                         elif B_i_prime <= val < B_i:
                             K_pairs.append((v, val))
 
-            extra_pairs = [
-                (x, self.dhat[x]) for x in S_i if B_i_prime <= self.dhat[x] < B_i
-            ]
+            extra_pairs = [(x, self.dhat[x]) for x in S_i if B_i_prime <= self.dhat[x] < B_i]
             if K_pairs or extra_pairs:
                 D.batch_prepend(K_pairs + extra_pairs)
 
@@ -362,11 +356,7 @@ def solve(self) -> SSSPResult:
         _Bprime, _U = self._bmssp(top_level, B, S0)
 
         # If we transformed, compress distances back to original vertices (predecessors omitted).
-        if (
-            self.cfg.use_transform
-            and self._mapping is not None
-            and self._clone2orig is not None
-        ):
+        if self.cfg.use_transform and self._mapping is not None and self._clone2orig is not None:
             comp: List[Float] = [math.inf] * self._G_orig.n
             best_clone: List[int] = [-1] * self._G_orig.n
             for u_orig, clones in self._mapping.items():
@@ -405,11 +395,7 @@ def path(self, target_original: Vertex) -> List[Vertex]:
             raise AlgorithmError("Call solve() before requesting paths.")
 
         # No transform: reconstruct directly in original space
-        if (
-            not self.cfg.use_transform
-            or self._mapping is None
-            or self._clone2orig is None
-        ):
+        if not self.cfg.use_transform or self._mapping is None or self._clone2orig is None:
             src = self.root[target_original]
             if src < 0:
                 return []
@@ -420,9 +406,7 @@ def path(self, target_original: Vertex) -> List[Vertex]:
             raise AlgorithmError("target out of range for original graph.")
 
         if self._best_clone_for_orig is None:
-            raise AlgorithmError(
-                "Internal state missing best-clone cache. Call solve() first."
-            )
+            raise AlgorithmError("Internal state missing best-clone cache. Call solve() first.")
 
         start_clone = self._best_clone_for_orig[target_original]
         if start_clone < 0:

src/ssspx/transform.py

@@ -8,9 +8,7 @@
 from .graph import Float, Graph, Vertex
 
 
-def constant_outdegree_transform(
-    G: Graph, delta: int
-) -> Tuple[Graph, Dict[Vertex, List[Vertex]]]:
+def constant_outdegree_transform(G: Graph, delta: int) -> Tuple[Graph, Dict[Vertex, List[Vertex]]]:
     """Split vertices so that every vertex has out-degree at most ``delta``.
 
     The transformation replaces a vertex with a chain of clones. Each clone