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-rw-r--r--.gitignore8
-rw-r--r--.gitmodules7
m---------cpuid0
-rw-r--r--flake.lock150
-rw-r--r--flake.nix198
m---------miasm0
-rw-r--r--nix.shell12
-rw-r--r--pyproject.toml64
-rw-r--r--reproducers/issue-508.c13
-rw-r--r--requirements.txt1
-rw-r--r--src/focaccia/__init__.py (renamed from focaccia/__init__.py)0
-rw-r--r--src/focaccia/arch/__init__.py (renamed from focaccia/arch/__init__.py)0
-rw-r--r--src/focaccia/arch/aarch64.py (renamed from focaccia/arch/aarch64.py)0
-rw-r--r--src/focaccia/arch/arch.py (renamed from focaccia/arch/arch.py)0
-rw-r--r--src/focaccia/arch/x86.py (renamed from focaccia/arch/x86.py)0
-rwxr-xr-xsrc/focaccia/cli.py (renamed from focaccia.py)0
-rw-r--r--src/focaccia/compare.py (renamed from focaccia/compare.py)0
-rw-r--r--src/focaccia/lldb_target.py (renamed from focaccia/lldb_target.py)0
-rw-r--r--src/focaccia/match.py (renamed from focaccia/match.py)0
-rw-r--r--src/focaccia/miasm_util.py (renamed from focaccia/miasm_util.py)0
-rw-r--r--src/focaccia/parser.py (renamed from focaccia/parser.py)0
-rw-r--r--src/focaccia/reproducer.py (renamed from focaccia/reproducer.py)0
-rw-r--r--src/focaccia/snapshot.py (renamed from focaccia/snapshot.py)0
-rw-r--r--src/focaccia/symbolic.py (renamed from focaccia/symbolic.py)0
-rw-r--r--src/focaccia/trace.py (renamed from focaccia/trace.py)0
-rw-r--r--src/focaccia/utils.py (renamed from focaccia/utils.py)0
-rw-r--r--tests/test_snapshot.py (renamed from test/test_snapshot.py)0
-rw-r--r--tests/test_sparse_memory.py (renamed from test/test_sparse_memory.py)0
-rwxr-xr-xtools/verify_qemu.py2
-rw-r--r--uv.lock227
30 files changed, 663 insertions, 19 deletions
diff --git a/.gitignore b/.gitignore
index ea2880a..29bd485 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,5 +14,9 @@ __pycache__/
 .gdbinit
 
 # Focaccia files
-qemu.sym
-qemu.trace
+*.sym
+*.trace
+
+# Nix
+result
+
diff --git a/.gitmodules b/.gitmodules
index a6d7f14..d74c6a5 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,4 @@
-[submodule "cpuid"]
-	path = cpuid
-	url = https://github.com/flababah/cpuid.py.git
+[submodule "miasm"]
+	path = miasm
+	url = git@github.com:taugoust/miasm.git
+
diff --git a/cpuid b/cpuid
deleted file mode 160000
-Subproject 335f97a08af46dda14a09f2e825dddbbe7e8177
diff --git a/flake.lock b/flake.lock
new file mode 100644
index 0000000..0343a0a
--- /dev/null
+++ b/flake.lock
@@ -0,0 +1,150 @@
+{
+  "nodes": {
+    "flake-utils": {
+      "inputs": {
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1731533236,
+        "narHash": "sha256-l0KFg5HjrsfsO/JpG+r7fRrqm12kzFHyUHqHCVpMMbI=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "11707dc2f618dd54ca8739b309ec4fc024de578b",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1749285348,
+        "narHash": "sha256-frdhQvPbmDYaScPFiCnfdh3B/Vh81Uuoo0w5TkWmmjU=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "3e3afe5174c561dee0df6f2c2b2236990146329f",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs-qemu-60": {
+      "locked": {
+        "lastModified": 1632168163,
+        "narHash": "sha256-iS3pBopSl0a2jAXuK/o0L+S86B9v9rnErsJHkNSdZRs=",
+        "owner": "nixos",
+        "repo": "nixpkgs",
+        "rev": "f8f124009497b3f9908f395d2533a990feee1de8",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nixos",
+        "repo": "nixpkgs",
+        "rev": "f8f124009497b3f9908f395d2533a990feee1de8",
+        "type": "github"
+      }
+    },
+    "pyproject-build-systems": {
+      "inputs": {
+        "nixpkgs": [
+          "nixpkgs"
+        ],
+        "pyproject-nix": [
+          "pyproject-nix"
+        ],
+        "uv2nix": [
+          "uv2nix"
+        ]
+      },
+      "locked": {
+        "lastModified": 1749519371,
+        "narHash": "sha256-UJONN7mA2stweZCoRcry2aa1XTTBL0AfUOY84Lmqhos=",
+        "owner": "pyproject-nix",
+        "repo": "build-system-pkgs",
+        "rev": "7c06967eca687f3482624250428cc12f43c92523",
+        "type": "github"
+      },
+      "original": {
+        "owner": "pyproject-nix",
+        "repo": "build-system-pkgs",
+        "type": "github"
+      }
+    },
+    "pyproject-nix": {
+      "inputs": {
+        "nixpkgs": [
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1746540146,
+        "narHash": "sha256-QxdHGNpbicIrw5t6U3x+ZxeY/7IEJ6lYbvsjXmcxFIM=",
+        "owner": "pyproject-nix",
+        "repo": "pyproject.nix",
+        "rev": "e09c10c24ebb955125fda449939bfba664c467fd",
+        "type": "github"
+      },
+      "original": {
+        "owner": "pyproject-nix",
+        "repo": "pyproject.nix",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs",
+        "nixpkgs-qemu-60": "nixpkgs-qemu-60",
+        "pyproject-build-systems": "pyproject-build-systems",
+        "pyproject-nix": "pyproject-nix",
+        "uv2nix": "uv2nix"
+      }
+    },
+    "systems": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    },
+    "uv2nix": {
+      "inputs": {
+        "nixpkgs": [
+          "nixpkgs"
+        ],
+        "pyproject-nix": [
+          "pyproject-nix"
+        ]
+      },
+      "locked": {
+        "lastModified": 1749170547,
+        "narHash": "sha256-zOptuFhTr9P0A+unFaOBFx5E5T6yx0qE8VrUGVrM96U=",
+        "owner": "pyproject-nix",
+        "repo": "uv2nix",
+        "rev": "7ae60727d4fc2e41aefd30da665e4f92ba8298f1",
+        "type": "github"
+      },
+      "original": {
+        "owner": "pyproject-nix",
+        "repo": "uv2nix",
+        "type": "github"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/flake.nix b/flake.nix
new file mode 100644
index 0000000..836a49e
--- /dev/null
+++ b/flake.nix
@@ -0,0 +1,198 @@
+{
+	description = "Focaccia: A Symbolic Tester for QEMU";
+
+	inputs = {
+		self.submodules = true;
+
+		nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+
+		nixpkgs-qemu-60.url = "github:nixos/nixpkgs/f8f124009497b3f9908f395d2533a990feee1de8";
+
+		flake-utils.url = "github:numtide/flake-utils";
+
+		pyproject-nix = {
+			url = "github:pyproject-nix/pyproject.nix";
+			inputs.nixpkgs.follows = "nixpkgs";
+		};
+
+		uv2nix = {
+			url = "github:pyproject-nix/uv2nix";
+			inputs.nixpkgs.follows = "nixpkgs";
+			inputs.pyproject-nix.follows = "pyproject-nix";
+		};
+
+		pyproject-build-systems = {
+			url = "github:pyproject-nix/build-system-pkgs";
+			inputs.uv2nix.follows = "uv2nix";
+			inputs.nixpkgs.follows = "nixpkgs";
+			inputs.pyproject-nix.follows = "pyproject-nix";
+		};
+	};
+
+	outputs = inputs@{
+		self,
+		uv2nix,
+		nixpkgs,
+		flake-utils,
+		pyproject-nix,
+		pyproject-build-systems,
+		...
+	}:
+	flake-utils.lib.eachDefaultSystem (system:
+	let
+		qemu-60 = inputs.nixpkgs-qemu-60.qemu;
+
+		# Refine nixpkgs used in flake to system arch
+		pkgs = import nixpkgs {
+			inherit system;
+		};
+
+		musl-pkgs = import nixpkgs {
+			inherit system;
+			crossSystem = {
+				config = "x86_64-unknown-linux-musl";
+			};
+		};
+
+		# Pin Python version
+		python = pkgs.python312;
+
+		# Define workspace root and load uv workspace metadata
+		workspace = uv2nix.lib.workspace.loadWorkspace { workspaceRoot = ./.; };
+
+		# Create an overlay for Nix that includes extracted Python packages declared as dependencies
+		# in uv
+		overlay = workspace.mkPyprojectOverlay { sourcePreference = "wheel"; };
+
+		editableOverlay = workspace.mkEditablePyprojectOverlay {
+			# Use environment variable
+			root = "$REPO_ROOT";
+
+			members = [ "focaccia" "miasm" ];
+		};
+
+		# Another overlay layer for flake-specific overloads
+		# This might be needed because uv does not have sufficient metadata
+		# Here, uv does include metadata about build systems used by each dependency
+		# Ergo we need to add a nativeBuildInput to miasm because it depends on setuptools for its
+		# installation
+		pyprojectOverrides = self: super: {
+			miasm = super.miasm.overrideAttrs (old: {
+				nativeBuildInputs = (old.nativeBuildInputs or []) ++ [ self.setuptools ];
+			});
+			cpuid = super.cpuid.overrideAttrs (old: {
+				nativeBuildInputs = (old.nativeBuildInputs or []) ++ [ self.setuptools ];
+			});
+		};
+
+		pyprojectOverridesEditable = self: super: {
+			miasm = super.miasm.overrideAttrs (old: {
+				nativeBuildInputs = (old.nativeBuildInputs or []) ++ [ self.setuptools ];
+
+				src = pkgs.lib.fileset.toSource {
+					root = old.src;
+					fileset = pkgs.lib.fileset.unions [
+						(old.src + "/pyproject.toml")
+						(old.src + "/README.md")
+						(old.src + "/miasm/__init__.py")
+					];
+				};
+			});
+
+			cpuid = super.cpuid.overrideAttrs (old: {
+				nativeBuildInputs = (old.nativeBuildInputs or []) ++ [ self.setuptools ];
+			});
+
+			focaccia = super.focaccia.overrideAttrs (old: {
+				nativeBuildInputs = (old.nativeBuildInputs or []) ++
+									self.resolveBuildSystem { editables = []; };
+
+				src = pkgs.lib.fileset.toSource {
+					root = old.src;
+					fileset = pkgs.lib.fileset.unions [
+						(old.src + "/pyproject.toml")
+						(old.src + "/README.md")
+						(old.src + "/src/focaccia/__init__.py")
+					];
+				};
+			});
+		};
+
+		# Build a set of Python packages
+		# The call to callPackage here uses the base package set from pyproject.nix
+		# We inherit the Python version to ensure that the packages have the same version
+		#
+		# The overrideScope here customizes the Python package set with an overlay defined by the
+		# composition of three overlay functions
+		pythonSet = (pkgs.callPackage pyproject-nix.build.packages { inherit python; }).
+					 overrideScope (pkgs.lib.composeManyExtensions [
+						 pyproject-build-systems.overlays.default
+						 overlay
+						 pyprojectOverrides 
+					 ]);
+
+		pythonSetEditable = pythonSet.overrideScope (
+			pkgs.lib.composeManyExtensions [
+				editableOverlay
+				pyprojectOverridesEditable
+			]
+		);
+
+		 # Create a Python venv with the default dependency group
+		 pythonEnv = pythonSet.mkVirtualEnv "focaccia-env" workspace.deps.default;
+
+		 # Create a Python venv with the default dependency group
+		 pythonDevEnv = pythonSetEditable.mkVirtualEnv "focaccia-env" workspace.deps.all;
+	in {
+		# Default package just builds Focaccia
+		packages.default = pythonDevEnv;
+
+		# Default app is just Focaccia
+		apps.default = {
+			type = "app";
+			program = "${self.packages.default}/bin/focaccia";
+		};
+
+		# Developer shell that includes Focaccia and QEMU
+		devShells = {
+			default = pkgs.mkShell {
+				packages = [
+					pythonDevEnv
+					pkgs.gdb
+					pkgs.git
+				];
+
+				env = {
+					UV_NO_SYNC = "1";
+					UV_PYTHON = python.interpreter;
+					UV_PYTHON_DOWNLOADS = "never";
+				};
+
+				shellHook = ''
+					unset PYTHONPATH
+
+					export REPO_ROOT=$(git rev-parse --show-toplevel)
+				'';
+			};
+
+			glibc = pkgs.mkShell {
+				packages = [
+					pythonEnv
+					pkgs.gdb
+					pkgs.gcc
+					pkgs.glibc.all
+				];
+			};
+
+			musl = pkgs.mkShell {
+				packages = [
+					pythonDevEnv
+					pkgs.gdb
+					musl-pkgs.gcc
+					musl-pkgs.pkg-config
+				];
+			};
+		};
+	});
+}
+
diff --git a/miasm b/miasm
new file mode 160000
+Subproject 13f9661aabe44ea4e4f147c32a344a1db128ab1
diff --git a/nix.shell b/nix.shell
deleted file mode 100644
index 00fef51..0000000
--- a/nix.shell
+++ /dev/null
@@ -1,12 +0,0 @@
-{ pkgs ? import <nixpkgs> {} }:
-pkgs.mkShell {
-    nativeBuildInputs = with pkgs; [
-        python311
-        python311Packages.pip
-        virtualenv
-
-        gcc gnumake binutils cmake ninja pkg-config
-        musl qemu swig4
-        gdb
-    ];
-}
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..5e16767
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,64 @@
+[project]
+name = "focaccia"
+version = "0.1.0"
+requires-python = "==3.12.*"
+description = "Symbolic Tester for QEMU"
+readme = {file = "README.md", content-type = "text/markdown"}
+authors = [
+	{name = "Theofilos Augoustis", email = "theofilos.augoustis@gmail.com"},
+	{name = "Christian Krinitsin", email="christian.krinitsin@tum.de"},
+	{name = "Sebastian Reimers", email="sebastian.reimers@in.tum.de"},
+	{name = "Nicola Crivellin", email="nicola.crivellin98@gmail.com"},
+	{name = "Alp Berkman", email="alpberkman@gmail.com"}
+]
+dependencies = [
+	"miasm",
+	"setuptools",
+	"lldb-python",
+	"cpuid @ git+https://github.com/taugoust/cpuid.py.git@master",
+]
+
+[project.optional-dependencies]
+dev = [
+	"ruff",
+	"black",
+	"pyright",
+]
+
+[project.scripts]
+focaccia = "focaccia:cli.main"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.uv.sources]
+miasm = { path = "./miasm" }
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.envs.default]
+dependencies = [
+	"ruff",
+	"black",
+	"pyright",
+]
+
+# Formatter
+[tool.black]
+line-length = 100
+target-version = ["py312"]
+
+[tool.ruff]
+line-length = 100
+exclude = ["__pycache__", "result"]
+src = ["src"]
+
+[tool.pyright]
+typeCheckingMode = "standard"
+reportMissingImports = true
+reportMissingTypeStubs = false
+useLibraryCodeForTypes = true
+executionEnvironments = [ {root = "src"} ]
+
diff --git a/reproducers/issue-508.c b/reproducers/issue-508.c
new file mode 100644
index 0000000..e143183
--- /dev/null
+++ b/reproducers/issue-508.c
@@ -0,0 +1,13 @@
+#include <stdio.h>
+
+int main() {
+  int mem = 0x12345678;
+  register long rax asm("rax") = 0x1234567812345678;
+  register int edi asm("edi") = 0x77777777;
+  asm("cmpxchg %[edi],%[mem]"
+      : [ mem ] "+m"(mem), [ rax ] "+r"(rax)
+      : [ edi ] "r"(edi));
+  long rax2 = rax;
+  printf("rax2 = %lx\n", rax2);
+}
+
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 220ba8b..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1 +0,0 @@
-miasm
diff --git a/focaccia/__init__.py b/src/focaccia/__init__.py
index e69de29..e69de29 100644
--- a/focaccia/__init__.py
+++ b/src/focaccia/__init__.py
diff --git a/focaccia/arch/__init__.py b/src/focaccia/arch/__init__.py
index 1797176..1797176 100644
--- a/focaccia/arch/__init__.py
+++ b/src/focaccia/arch/__init__.py
diff --git a/focaccia/arch/aarch64.py b/src/focaccia/arch/aarch64.py
index 2e510b9..2e510b9 100644
--- a/focaccia/arch/aarch64.py
+++ b/src/focaccia/arch/aarch64.py
diff --git a/focaccia/arch/arch.py b/src/focaccia/arch/arch.py
index ce5e532..ce5e532 100644
--- a/focaccia/arch/arch.py
+++ b/src/focaccia/arch/arch.py
diff --git a/focaccia/arch/x86.py b/src/focaccia/arch/x86.py
index fefab37..fefab37 100644
--- a/focaccia/arch/x86.py
+++ b/src/focaccia/arch/x86.py
diff --git a/focaccia.py b/src/focaccia/cli.py
index f0c6efe..f0c6efe 100755
--- a/focaccia.py
+++ b/src/focaccia/cli.py
diff --git a/focaccia/compare.py b/src/focaccia/compare.py
index 13f965c..13f965c 100644
--- a/focaccia/compare.py
+++ b/src/focaccia/compare.py
diff --git a/focaccia/lldb_target.py b/src/focaccia/lldb_target.py
index 1f31337..1f31337 100644
--- a/focaccia/lldb_target.py
+++ b/src/focaccia/lldb_target.py
diff --git a/focaccia/match.py b/src/focaccia/match.py
index be88176..be88176 100644
--- a/focaccia/match.py
+++ b/src/focaccia/match.py
diff --git a/focaccia/miasm_util.py b/src/focaccia/miasm_util.py
index a2cd025..a2cd025 100644
--- a/focaccia/miasm_util.py
+++ b/src/focaccia/miasm_util.py
diff --git a/focaccia/parser.py b/src/focaccia/parser.py
index c37c07a..c37c07a 100644
--- a/focaccia/parser.py
+++ b/src/focaccia/parser.py
diff --git a/focaccia/reproducer.py b/src/focaccia/reproducer.py
index 90e1378..90e1378 100644
--- a/focaccia/reproducer.py
+++ b/src/focaccia/reproducer.py
diff --git a/focaccia/snapshot.py b/src/focaccia/snapshot.py
index 1945d71..1945d71 100644
--- a/focaccia/snapshot.py
+++ b/src/focaccia/snapshot.py
diff --git a/focaccia/symbolic.py b/src/focaccia/symbolic.py
index 9aeff56..9aeff56 100644
--- a/focaccia/symbolic.py
+++ b/src/focaccia/symbolic.py
diff --git a/focaccia/trace.py b/src/focaccia/trace.py
index 094358f..094358f 100644
--- a/focaccia/trace.py
+++ b/src/focaccia/trace.py
diff --git a/focaccia/utils.py b/src/focaccia/utils.py
index c4f6a74..c4f6a74 100644
--- a/focaccia/utils.py
+++ b/src/focaccia/utils.py
diff --git a/test/test_snapshot.py b/tests/test_snapshot.py
index ddad410..ddad410 100644
--- a/test/test_snapshot.py
+++ b/tests/test_snapshot.py
diff --git a/test/test_sparse_memory.py b/tests/test_sparse_memory.py
index 4fd9cba..4fd9cba 100644
--- a/test/test_sparse_memory.py
+++ b/tests/test_sparse_memory.py
diff --git a/tools/verify_qemu.py b/tools/verify_qemu.py
index df9f83d..7402852 100755
--- a/tools/verify_qemu.py
+++ b/tools/verify_qemu.py
@@ -72,7 +72,7 @@ def try_remove(l: list, v):
 
 if __name__ == "__main__":
     prog = make_argparser()
-    prog.add_argument('--gdb', default='/bin/gdb',
+    prog.add_argument('--gdb', default='gdb',
                       help='GDB binary to invoke.')
     args = prog.parse_args()
 
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index 0000000..5f752bf
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