Remove unnecessary Mypy stub packages

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 = "3.5.0.20251001";
+            src = pkgs.fetchPypi {
+              pname = "types_networkx";
+              inherit version;
+              sha256 = "8e3c5c491ba5870d75e175751d70ddeac81df43caf2a64bae161e181f5e8ea7a";
+            };
+            pyproject = true;
+            nativeBuildInputs = [python.pkgs.setuptools];
+            propagatedBuildInputs = [python.pkgs.numpy];
+          };
           inherit (cli-wrapper-pkgs) cargoArtifacts probe-cli;
           libprobe = old-stdenv.mkDerivation rec {
             pname = "libprobe";
@@ -83,13 +95,13 @@
             doCheck = true;
             nativeCheckInputs = [
               old-pkgs.criterion
-              pkgs.include-what-you-use
+              pkgs.clang
               pkgs.clang-analyzer
               pkgs.clang-tools
-              pkgs.clang
               pkgs.compiledb
               pkgs.cppcheck
               pkgs.cppclean
+              pkgs.include-what-you-use
             ];
             checkPhase = ''
               # When a user buidls this WITHOUT build sandbox isolation, the libc files appear to come from somewhere different.
@@ -151,28 +163,26 @@
             };
             propagatedBuildInputs = [
               python.pkgs.networkx
-              python.pkgs.pygraphviz
+              python.pkgs.numpy
               python.pkgs.pydot
+              python.pkgs.pygraphviz
               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 = [
+              packages.types-networkx
+              pkgs.ruff
               python.pkgs.mypy
-              python.pkgs.types-pyyaml
               python.pkgs.types-tqdm
-              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 +200,11 @@
         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 {
@@ -213,18 +223,18 @@
                 packages.probe
                 (python.withPackages (ps:
                   with ps; [
+                    packages.probe-py
                     pytest
-                    pytest-timeout
                     pytest-asyncio
-                    packages.probe-py
+                    pytest-timeout
                   ]))
                 pkgs.buildah
-                pkgs.podman
-                pkgs.docker
+                pkgs.clang
                 pkgs.coreutils # so we can `probe record head ...`, etc.
+                pkgs.docker
                 pkgs.gnumake
-                pkgs.clang
                 pkgs.nix
+                pkgs.podman
               ]
               ++ pkgs.lib.lists.optional (system != "i686-linux" && system != "armv7l-linux") pkgs.jdk23_headless;
             buildPhase = ''
@@ -244,23 +254,22 @@
           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
+            packages.types-networkx
             pypkgs.ipython
+            pypkgs.mypy
+            pypkgs.pytest
             pypkgs.pytest-asyncio
+            pypkgs.pytest-timeout
+            pypkgs.types-tqdm
 
             # libprobe build time requirement
             pypkgs.pycparser
@@ -276,10 +285,10 @@
           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
@@ -292,14 +301,14 @@
               pkgs.clang-analyzer
               pkgs.clang-tools # must go after clang-analyzer
               pkgs.cppcheck
-              pkgs.gnumake
               pkgs.git
+              pkgs.gnumake
               pkgs.include-what-you-use
               old-pkgs.criterion # unit testing framework
 
               # Programs for testing
-              pkgs.nix
               pkgs.coreutils
+              pkgs.nix
 
               # For other lints
               pkgs.alejandra

libprobe/src/env.c

@@ -158,8 +158,10 @@ char* const* arena_copy_cmdline(struct ArenaDir* arena_dir, result_sized_mem cmd
         ptr += length + 1;
     }
 
+#ifndef NDEBUG
     ptr -= 1;
     ASSERTF(!*ptr, "'%s'", ptr);
+#endif
     argv_copy[argc] = NULL;
 
     return argv_copy;

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

@@ -86,7 +86,7 @@ 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)
+    return networkx.relabel_nodes(graph, dct) # type: ignore
 
 
 def serialize_graph(
@@ -96,10 +96,8 @@ def serialize_graph(
         cluster_labels: collections.abc.Mapping[str, str] = {},
 ) -> None:
     if name_mapper is None:
-        name_mapper = typing.cast(
-            typing.Callable[[_Node], str],
-            lambda node: graph.nodes(data=True)[node].get("id", str(node)),
-        )
+        def name_mapper(node: _Node) -> str:
+            return str(graph.nodes(data=True)[node].get("id", node))
     graph2 = map_nodes(name_mapper, graph)
     pydot_graph = networkx.drawing.nx_pydot.to_pydot(graph2)
 
@@ -376,7 +374,7 @@ 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()