Merge branch 'main' of https://github.com/charmoniumQ/PROBE into data…

…flow_graph

.gitignore

@@ -13,3 +13,5 @@
 **/.directory
 **/.Trash*
 **/desktop.ini
+
+probe_log

Justfile

@@ -12,25 +12,43 @@ check-ruff:
     #ruff format --check probe_src # TODO: uncomment
     ruff check probe_src
 
+check-format-rust:
+    env --chdir probe_src/probe_frontend cargo fmt --check
+
+fix-format-rust:
+    env --chdir probe_src/probe_frontend cargo fmt
+
+check-clippy:
+    env --chdir probe_src/probe_frontend cargo clippy
+
+fix-clippy:
+    env --chdir probe_src/probe_frontend cargo clippy --fix --allow-staged
+
 check-mypy:
-    MYPYPATH=probe_src mypy --strict --package arena
-    MYPYPATH=probe_src mypy --strict --package probe_py
+    mypy --strict --package probe_py.manual
+    mypy --strict --package probe_py.generated
     mypy --strict probe_src/libprobe
 
-compile-libprobe:
+compile-lib:
     make --directory=probe_src/libprobe all
 
-test-ci: compile-libprobe
-    make --directory=probe_src/tests/c all
-    cd probe_src && python -m pytest .
+compile-cli:
+    env --chdir=probe_src/probe_frontend cargo build --release
 
-test-dev: compile-libprobe
+compile-tests:
     make --directory=probe_src/tests/c all
-    cd probe_src && python -m pytest . --failed-first --maxfail=1
+
+compile: compile-lib compile-cli compile-tests
+
+test-ci: compile-lib
+     pytest probe_src
+
+test-dev: compile-lib
+    pytest probe_src --failed-first --maxfail=1
 
 check-flake:
     nix flake check --all-systems
 
-pre-commit: fix-format-nix fix-ruff check-mypy check-flake compile-libprobe test-dev
+pre-commit: fix-format-nix   fix-ruff   fix-format-rust   fix-clippy   compile check-mypy             test-dev
 
-on-push: check-format-nix check-ruff check-mypy check-flake compile-libprobe test-ci
+on-push:    check-format-nix check-ruff check-format-rust check-clippy compile check-mypy check-flake test-ci

flake.nix

@@ -1,51 +1,127 @@
 {
-  inputs.flake-utils.url = "github:numtide/flake-utils";
+  inputs = {
+    nixpkgs = {
+      url = "github:NixOS/nixpkgs/nixpkgs-unstable";
+    };
+    flake-utils = {
+      url = "github:numtide/flake-utils";
+    };
+
+    crane = {
+      url = "github:ipetkov/crane";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+
+    advisory-db = {
+      url = "github:rustsec/advisory-db";
+      flake = false;
+    };
+
+    rust-overlay = {
+      url = "github:oxalica/rust-overlay";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+  };
 
   outputs = {
     self,
     nixpkgs,
     flake-utils,
-  }:
-    flake-utils.lib.eachDefaultSystem (
-      system: let
-        pkgs = nixpkgs.legacyPackages.${system};
-        inherit (pkgs) lib;
-        python312-debug = pkgs.python312.overrideAttrs (oldAttrs: {
-          configureFlags = oldAttrs.configureFlags ++ ["--with-pydebug"];
-          # patches = oldAttrs.patches ++ [ ./python.patch ];
-        });
-        export-and-rename = pkg: file-pairs:
-          pkgs.stdenv.mkDerivation {
-            pname = "${pkg.pname}-only-bin";
+    rust-overlay,
+    ...
+  }@inputs: let
+    supported-systems = [
+      "x86_64-linux"
+      "i686-linux"
+      "aarch64-linux"
+      "armv7l-linux"
+    ];
+  in
+    flake-utils.lib.eachSystem supported-systems (system: let
+      pkgs = import nixpkgs {
+        inherit system;
+        overlays = [(import rust-overlay)];
+      };
+      python = pkgs.python312;
+      frontend = (import ./probe_src/probe_frontend/frontend.nix) ({ inherit system pkgs python; } // inputs);
+    in {
+        packages = rec {
+          probe-bundled = let
+            # libprobe is a "private" package
+            # It is only used in probe-bundled
+            # TODO: The only public package should probably be probe-bundled and probe-py.
+            libprobe = pkgs.stdenv.mkDerivation rec {
+              pname = "libprobe";
+              version = "0.1.0";
+              src = ./probe_src/libprobe;
+              makeFlags = [ "INSTALL_PREFIX=$(out)" "SOURCE_VERSION=${version}" ];
+              buildInputs = [
+                (pkgs.python312.withPackages (pypkgs: [
+                  pypkgs.pycparser
+                ]))
+              ];
+            };
+          in pkgs.stdenv.mkDerivation rec {
+            pname = "probe-bundled";
+            version = "0.1.0";
             dontUnpack = true;
-            version = pkg.version;
-            buildInputs = [pkg];
-            buildPhase =
-              builtins.concatStringsSep
-              "\n"
-              (builtins.map
-                (pairs: "install -D ${pkg}/${builtins.elemAt pairs 0} $out/${builtins.elemAt pairs 1}")
-                file-pairs);
+            dontBuild = true;
+            nativeBuildInputs = [ pkgs.makeWrapper ];
+            installPhase = ''
+              mkdir $out $out/bin
+              makeWrapper \
+                ${self.packages.${system}.probe-cli}/bin/probe \
+                $out/bin/probe \
+                --set __PROBE_LIB ${libprobe}/lib
+            '';
           };
-      in {
-        packages = {
-          python-dbg = python312-debug;
-        };
+          probe-py-manual = python.pkgs.buildPythonPackage rec {
+            pname = "probe_py.manual";
+            version = "0.1.0";
+            pyproject = true;
+            build-system = [
+              python.pkgs.flit-core
+            ];
+            src = ./probe_src/python;
+            propagatedBuildInputs = [
+              self.packages.${system}.probe-py-generated
+              python.pkgs.networkx
+              python.pkgs.pygraphviz
+              python.pkgs.pydot
+              python.pkgs.rich
+              python.pkgs.typer
+            ];
+            pythonImportsCheck = [ pname ];
+          };
+          default = probe-bundled;
+        } // frontend.packages;
+        # TODO: Run pytest tests in Nix checks
+        checks = self.packages.${system} // frontend.checks;
         devShells = {
-          default = pkgs.mkShell {
+          default = frontend.devShells.default.overrideAttrs (oldAttrs: rec {
+            shellHook = ''
+              pushd $(git rev-parse --show-toplevel)
+              source ./setup_devshell.sh
+              popd
+            '';
             buildInputs =
-              [
-                (pkgs.python312.withPackages (pypkgs: [
-                  pypkgs.psutil
+              oldAttrs.buildInputs ++ [
+                (python.withPackages (pypkgs: [
+                  # probe_py.manual runtime requirements
+                  pypkgs.networkx
+                  pypkgs.pygraphviz
+                  pypkgs.pydot
+                  pypkgs.rich
                   pypkgs.typer
-                  pypkgs.pycparser
+
+                  # probe_py.manual "dev time" requirements
+                  pypkgs.psutil
                   pypkgs.pytest
                   pypkgs.mypy
-                  pypkgs.pygraphviz
-                  pypkgs.networkx
                   pypkgs.ipython
-                  pypkgs.pydot
-                  pypkgs.rich
+
+                  # libprobe build time requirement
+                  pypkgs.pycparser
                 ]))
                 # (export-and-rename python312-debug [["bin/python" "bin/python-dbg"]])
                 pkgs.which
@@ -67,12 +143,12 @@
               )
               ++ (
                 # while xdot isn't marked as linux only, it has a dependency (xvfb-run) that is
-                if builtins.elem system lib.platforms.linux
+                if builtins.elem system pkgs.lib.platforms.linux
                 then [pkgs.xdot]
                 else []
               );
-          };
+          });
         };
-      }
+       }
     );
 }