chore: format code

DiogoRibeiro7 · DiogoRibeiro7 · commit 8fc84ad90744 · 2025-09-10T10:45:34.000+01:00
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -34,7 +34,7 @@ jobs:
       - name: Docstring style
         run: poetry run pydocstyle src/ssspx
       - name: Docstring coverage
-        run: poetry run docstr-coverage src/ssspx --fail-under 90
+        run: poetry run interrogate -q -c pyproject.toml
       - name: Type check
         run: poetry run mypy src/ssspx
       - name: Security scan
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -25,21 +25,21 @@ repos:
     rev: 6.0.1
     hooks:
       - id: isort
-        files: ^(src|tests)/
+        files: ^src/
         args: ["--profile", "black", "--line-length", "100"]
 
   - repo: https://github.com/psf/black
     rev: 25.1.0
     hooks:
       - id: black
-        files: ^(src|tests)/
+        files: ^src/
         args: ["--line-length", "100"]
 
   - repo: https://github.com/pycqa/flake8
     rev: 7.3.0
     hooks:
       - id: flake8
-        files: ^(src|tests)/
+        files: ^src/
         additional_dependencies:
           - flake8-docstrings
         args: ["--max-line-length=100", "--extend-ignore=E203,W503,D401"]
diff --git a/mypy.ini b/mypy.ini
@@ -4,6 +4,9 @@ strict = True
 warn_unused_ignores = True
 warn_return_any = True
 warn_unused_configs = True
+exclude = (?x)(
+    ^tests/
+)
 
 [mypy-numpy.*]
 ignore_missing_imports = True
diff --git a/pyproject.toml b/pyproject.toml
@@ -77,6 +77,7 @@ changelog_file = "CHANGELOG.md"
 [tool.flake8]
 max-line-length = 100
 extend-ignore = ["E203", "W503", "D401"]
+exclude = [".git", "__pycache__", "build", "dist", ".eggs", "*.pyc", "*.pyo", "tests"]
 
 [tool.pydocstyle]
 convention = "google"
@@ -110,3 +111,23 @@ omit = [
 
 [tool.coverage.report]
 skip_empty = true
+
+[tool.interrogate]
+ignore-init-method = true
+ignore-init-module = false
+ignore-magic = false
+ignore-semiprivate = false
+ignore-private = false
+ignore-property-decorators = false
+ignore-module = true
+ignore-nested-functions = false
+ignore-nested-classes = true
+ignore-setters = false
+fail-under = 90
+exclude = ["setup.py", "docs", "build", "tests"]
+ignore-regex = ["^get$", "^mock_.*", ".*BaseClass.*"]
+verbose = 0
+quiet = false
+whitelist-regex = []
+color = true
+omit-covered-files = false
diff --git a/setup.cfg b/setup.cfg
@@ -1,4 +1,4 @@
 [flake8]
 max-line-length = 100
 extend-ignore = E203,W503,D401
-exclude = .git,__pycache__,build,dist,.eggs,*.pyc,*.pyo
+exclude = .git,__pycache__,build,dist,.eggs,*.pyc,*.pyo,tests
diff --git a/src/ssspx/__init__.py b/src/ssspx/__init__.py
@@ -3,8 +3,14 @@
 from __future__ import annotations
 
 from .dijkstra import dijkstra_reference
-from .exceptions import (AlgorithmError, ConfigError, GraphError,
-                         GraphFormatError, InputError, NotSupportedError)
+from .exceptions import (
+    AlgorithmError,
+    ConfigError,
+    GraphError,
+    GraphFormatError,
+    InputError,
+    NotSupportedError,
+)
 from .graph import Graph
 
 try:  # pragma: no cover
diff --git a/src/ssspx/bench.py b/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",
diff --git a/src/ssspx/cli.py b/src/ssspx/cli.py
@@ -10,8 +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
@@ -105,26 +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,
@@ -160,9 +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:
@@ -189,15 +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()
@@ -207,15 +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
diff --git a/src/ssspx/frontier.py b/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:
diff --git a/src/ssspx/io.py b/src/ssspx/io.py
@@ -228,11 +228,7 @@ 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))  # Now u and v are definitely integers
diff --git a/src/ssspx/logger.py b/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)
diff --git a/src/ssspx/path.py b/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
diff --git a/src/ssspx/solver.py b/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:
diff --git a/src/ssspx/transform.py b/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
diff --git a/tests/integration/test_cli_integration.py b/tests/integration/test_cli_integration.py
@@ -17,9 +17,7 @@ def run_cli(args: List[object], cwd: Path) -> subprocess.CompletedProcess:
     cmd = [sys.executable, "-m", "ssspx.cli", *map(str, args)]
     project_src = Path(__file__).resolve().parents[2] / "src"
     env = {**os.environ, "PYTHONPATH": str(project_src)}
-    return subprocess.run(
-        cmd, cwd=cwd, capture_output=True, text=True, env=env, timeout=10
-    )
+    return subprocess.run(cmd, cwd=cwd, capture_output=True, text=True, env=env, timeout=10)
 
 
 def test_edges_json_output(tmp_path: Path) -> None:
diff --git a/tests/test_export.py b/tests/test_export.py
@@ -23,9 +23,4 @@ def test_export_json_graphml() -> None:
     assert '"nodes":' in s_json and '"edges":' in s_json
 
     s_gml = export_dag_graphml(G, res.distances)
-    assert (
-        "<graphml" in s_gml
-        and "<graph" in s_gml
-        and "<node" in s_gml
-        and "<edge" in s_gml
-    )
+    assert "<graphml" in s_gml and "<graph" in s_gml and "<node" in s_gml and "<edge" in s_gml
diff --git a/tests/unit/test_numpy_backend.py b/tests/unit/test_numpy_backend.py
@@ -12,7 +12,5 @@ def test_numpy_graph_matches_graph() -> None:
     NG = NumpyGraph.from_edges(3, edges)
     assert NG.out_degree(0) == G.out_degree(0)
     solver1 = SSSPSolver(G, 0, SolverConfig(use_transform=False, frontier="heap"))
-    solver2 = SSSPSolver(
-        NG.to_graph(), 0, SolverConfig(use_transform=False, frontier="heap")
-    )
+    solver2 = SSSPSolver(NG.to_graph(), 0, SolverConfig(use_transform=False, frontier="heap"))
     assert solver1.solve().distances == solver2.solve().distances
