Remove mypy stubs

README.md

@@ -138,7 +138,6 @@ probe export --help
   - `probe_py/probe_py`: Main package to be imported or run.
   - `probe_py/pyproject.toml`: Definition of main package and dependencies.
   - `probe_py/tests`: Python unittests, i.e., `from probe_py import foobar; test_foobar()`; Run `just test-py`.
-  - `probe_py/mypy_stubs`: "Stub" files that tell Mypy how to check untyped library code. Should be added to `$MYPYPATH` by `nix develop`.
 - `tests`: End-to-end opaque-box tests. They will be run with Pytest, but they will not test Python directly; they should always `subprocess.run(["probe", ...])`. Additionally, some tests have to be manually invoked.
 - `docs`: Documentation and papers.
 - `benchmark`: Programs and infrastructure for benchmarking.

flake.nix

@@ -55,6 +55,18 @@
         old-stdenv = pkgs.overrideCC pkgs.stdenv new-clang-old-glibc;
       in rec {
         packages = rec {
+          types-networkx = python.pkgs.buildPythonPackage rec {
+            pname = "types-networkx";
+            version = "3.5.0.20251104";
+            src = pkgs.fetchPypi {
+              pname = "types_networkx";
+              inherit version;
+              sha256 = "0ae55ff562126dcb7dc6bf0b716a2333b69d5ff6fbcb7f768916eb8bd09fc0c9";
+            };
+            pyproject = true;
+            nativeBuildInputs = [python.pkgs.setuptools];
+            propagatedBuildInputs = [python.pkgs.numpy];
+          };
           inherit (cli-wrapper-pkgs) cargoArtifacts probe-cli;
           libprobe = old-stdenv.mkDerivation rec {
             pname = "libprobe";
@@ -151,28 +163,29 @@
             };
             propagatedBuildInputs = [
               python.pkgs.networkx
-              python.pkgs.pygraphviz
+              python.pkgs.numpy
               python.pkgs.pydot
               python.pkgs.rich
-              python.pkgs.typer
-              python.pkgs.xdg-base-dirs
               python.pkgs.sqlalchemy
-              python.pkgs.pyyaml
-              python.pkgs.numpy
               python.pkgs.tqdm
+              python.pkgs.typer
+              python.pkgs.xdg-base-dirs
             ];
             nativeCheckInputs = [
               python.pkgs.mypy
-              python.pkgs.types-pyyaml
+              python.pkgs.pytest
+              python.pkgs.pytest-asyncio
+              python.pkgs.pytest-timeout
               python.pkgs.types-tqdm
+              types-networkx
               pkgs.ruff
             ];
             checkPhase = ''
               runHook preCheck
               #ruff format --check probe_src # TODO: uncomment
               ruff check .
               python -c 'import probe_py'
-              MYPYPATH=$src/mypy_stubs:$MYPYPATH mypy --strict --package probe_py
+              mypy --strict --package probe_py
               runHook postCheck
             '';
           };
@@ -190,11 +203,11 @@
         checks = {
           inherit
             (cli-wrapper.checks."${system}")
+            probe-workspace-audit
             probe-workspace-clippy
+            probe-workspace-deny
             probe-workspace-doc
             probe-workspace-fmt
-            probe-workspace-audit
-            probe-workspace-deny
             probe-workspace-nextest
             ;
           fmt-nix = pkgs.stdenv.mkDerivation {
@@ -213,6 +226,7 @@
                 packages.probe
                 (python.withPackages (ps:
                   with ps; [
+                    packages.probe-py
                     pytest
                     pytest-timeout
                     pytest-asyncio
@@ -244,23 +258,22 @@
           probe-python = python.withPackages (pypkgs: [
             # probe_py.manual runtime requirements
             pypkgs.networkx
+            pypkgs.numpy
             pypkgs.pydot
             pypkgs.rich
-            pypkgs.typer
             pypkgs.sqlalchemy
-            pypkgs.xdg-base-dirs
-            pypkgs.pyyaml
-            pypkgs.numpy
             pypkgs.tqdm
+            pypkgs.typer
+            pypkgs.xdg-base-dirs
 
             # probe_py.manual "dev time" requirements
-            pypkgs.types-tqdm
-            pypkgs.types-pyyaml
-            pypkgs.pytest
-            pypkgs.pytest-timeout
-            pypkgs.mypy
             pypkgs.ipython
+            pypkgs.mypy
+            pypkgs.pytest
             pypkgs.pytest-asyncio
+            pypkgs.pytest-timeout
+            pypkgs.types-tqdm
+            packages.types-networkx
 
             # libprobe build time requirement
             pypkgs.pycparser
@@ -276,10 +289,10 @@
           shellPackages =
             [
               # Rust tools
-              pkgs.cargo-deny
               pkgs.cargo-audit
-              pkgs.cargo-machete
+              pkgs.cargo-deny
               pkgs.cargo-hakari
+              pkgs.cargo-machete
 
               # Replay tools
               pkgs.buildah
@@ -298,8 +311,8 @@
               old-pkgs.criterion # unit testing framework
 
               # Programs for testing
-              pkgs.nix
               pkgs.coreutils
+              pkgs.nix
 
               # For other lints
               pkgs.alejandra

probe_py/probe_py/dataflow_graph.py

@@ -301,4 +301,4 @@ def shorten_path(input: pathlib.Path) -> str:
                 data["shape"] = "rectangle"
                 data["id"] = str(hash(node))
     for a, b in cycle:
-        dataflow_graph.edges[a, b]["color"] = "red"  # type: ignore
+        dataflow_graph.edges[a, b]["color"] = "red"

probe_py/probe_py/graph_utils.py

@@ -15,14 +15,11 @@
 _Node = typing.TypeVar("_Node")
 
 
-_CoNode = typing.TypeVar("_CoNode", covariant=True)
-
-
 @dataclasses.dataclass(frozen=True)
-class Segment(typing.Generic[_CoNode]):
-    dag_tc: ReachabilityOracle[_CoNode]
-    upper_bound: frozenset[_CoNode]
-    lower_bound: frozenset[_CoNode]
+class Segment(typing.Generic[_Node]):
+    dag_tc: ReachabilityOracle[_Node]
+    upper_bound: frozenset[_Node]
+    lower_bound: frozenset[_Node]
 
     def __post_init__(self) -> None:
         assert self.upper_bound
@@ -38,15 +35,15 @@ def __post_init__(self) -> None:
         assert not unbounded, \
             f"{unbounded} in self.lower_bound is not a descendant of any in {self.upper_bound=}"
 
-    def nodes(self) -> collections.abc.Iterable[_CoNode]:
+    def nodes(self) -> collections.abc.Iterable[_Node]:
         return self.dag_tc.nodes_between(self.upper_bound, self.lower_bound)
 
-    def overlaps(self, other: Segment[_CoNode]) -> bool:
+    def overlaps(self, other: Segment[_Node]) -> bool:
         assert self.dag_tc is other.dag_tc
         return bool(frozenset(self.nodes()) & frozenset(other.nodes()))
 
     @staticmethod
-    def union(segments: typing.Sequence[Segment[_CoNode]]) -> Segment[_CoNode]:
+    def union(segments: typing.Sequence[Segment[_Node]]) -> Segment[_Node]:
         assert segments
         dag_tc = segments[0].dag_tc
         assert all(segment.dag_tc is dag_tc for segment in segments)
@@ -86,7 +83,8 @@ def map_nodes(
 ) -> networkx.DiGraph[_Node2]:
     dct = {node: function(node) for node in graph.nodes()}
     assert util.all_unique(dct.values()), util.duplicates(dct.values())
-    return networkx.relabel_nodes(graph, dct)
+    ret = typing.cast("networkx.DiGraph[_Node2]", networkx.relabel_nodes(graph, dct))
+    return ret
 
 
 def serialize_graph(
@@ -233,7 +231,7 @@ def create(dag: networkx.DiGraph[_Node]) -> ReachabilityOracle[_Node]:
 
     @abc.abstractmethod
     def is_reachable(self, u: _Node, v: _Node) -> bool:
-        pass
+        ...
 
     @abc.abstractmethod
     def nodes_between(
@@ -321,6 +319,7 @@ def non_ancestors(
             candidates: collections.abc.Iterable[_Node],
             lower_bounds: collections.abc.Iterable[_Node],
     ) -> collections.abc.Iterable[_Node]:
+        "Return all candidates that are not ancestors of any element in lower_bounds."
         return frozenset({
             candidate
             for candidate in candidates
@@ -335,6 +334,7 @@ def non_descendants(
             candidates: collections.abc.Iterable[_Node],
             upper_bounds: collections.abc.Iterable[_Node],
     ) -> collections.abc.Iterable[_Node]:
+        "Return all candidates that are not descendent of any element in upper_bounds."
         return frozenset({
             candidate
             for candidate in candidates
@@ -376,7 +376,7 @@ def add_edge(self, source: _Node, target: _Node) -> None:
 
 
 def get_faces(
-        planar_graph: networkx.PlanarEmbedding[_Node], # type: ignore
+        planar_graph: networkx.PlanarEmbedding[_Node],
 ) -> frozenset[tuple[_Node, ...]]:
     faces = set()
     covered_half_edges = set()