From ba7a8ca4b4819fe18d12ebc46ec68bbdfbbd2bfa Mon Sep 17 00:00:00 2001
From: Nick Ponomarev <wowasterdev@gmail.com>
Date: Mon, 22 Jun 2026 15:21:55 +0300
Subject: [PATCH 01/11] Fix links in matrices.yaml

---
 matrices.yaml | 33 ++++++++++++++++-----------------
 1 file changed, 16 insertions(+), 17 deletions(-)

diff --git a/matrices.yaml b/matrices.yaml
index df68757..7494eaf 100644
--- a/matrices.yaml
+++ b/matrices.yaml
@@ -50,8 +50,8 @@
     - fsharp
   reorder: true
   link: https://suitesparse-collection-website.herokuapp.com/MM/DIMACS10/coAuthorsCiteseer.tar.gz
-# SSSP - find 50K vertices matrix and test (Andrews_positive.mtx)
-- name: Andrews_positive
+# SSSP - find 50K vertices matrix and test (Andrews.mtx)
+- name: Andrews
   enabled: true
   algorithm: sssp
   tools:
@@ -60,8 +60,8 @@
     - lagraph
     - fsharp
   reorder: false
-  link: https://sparse.tamu.edu/Andrews/Andrews
-- name: Andrews_positive
+  link: https://suitesparse-collection-website.herokuapp.com/MM/Andrews/Andrews.tar.gz
+- name: Andrews
   enabled: true
   algorithm: sssp
   tools:
@@ -70,7 +70,7 @@
     - lagraph
     - fsharp
   reorder: true
-  link: https://sparse.tamu.edu/Andrews/Andrews
+  link: https://suitesparse-collection-website.herokuapp.com/MM/Andrews/Andrews.tar.gz
 # TC - only small matrices
 # Small matrices ==> every algorithm for vine comparison
 - name: gr_30_30
@@ -83,7 +83,7 @@
     - fsharp
     - vine
   reorder: false
-  link: https://sparse.tamu.edu/HB/gr_30_30
+  link: https://suitesparse-collection-website.herokuapp.com/MM/HB/gr_30_30.tar.gz
 - name: gr_30_30
   enabled: true
   algorithm: bfs
@@ -94,7 +94,7 @@
     - fsharp
     - vine
   reorder: true
-  link: https://sparse.tamu.edu/HB/gr_30_30
+  link: https://suitesparse-collection-website.herokuapp.com/MM/HB/gr_30_30.tar.gz
 - name: Trefethen_2000
   enabled: true
   algorithm: bfs
@@ -105,7 +105,7 @@
     - fsharp
     - vine
   reorder: false
-  link: https://sparse.tamu.edu/JGD_Trefethen/Trefethen_2000
+  link: https://suitesparse-collection-website.herokuapp.com/MM/JGD_Trefethen/Trefethen_2000.tar.gz
 - name: Trefethen_2000
   enabled: true
   algorithm: bfs
@@ -116,7 +116,7 @@
     - fsharp
     - vine
   reorder: true
-  link: https://sparse.tamu.edu/JGD_Trefethen/Trefethen_2000
+  link: https://suitesparse-collection-website.herokuapp.com/MM/JGD_Trefethen/Trefethen_2000.tar.gz
 - name: gr_30_30
   enabled: true
   algorithm: sssp
@@ -127,7 +127,7 @@
     - fsharp
     - vine
   reorder: false
-  link: https://sparse.tamu.edu/HB/gr_30_30
+  link: https://suitesparse-collection-website.herokuapp.com/MM/HB/gr_30_30.tar.gz
 - name: gr_30_30
   enabled: true
   algorithm: sssp
@@ -138,7 +138,7 @@
     - fsharp
     - vine
   reorder: true
-  link: https://sparse.tamu.edu/HB/gr_30_30
+  link: https://suitesparse-collection-website.herokuapp.com/MM/HB/gr_30_30.tar.gz
 - name: Trefethen_2000
   enabled: true
   algorithm: sssp
@@ -149,7 +149,7 @@
     - fsharp
     - vine
   reorder: false
-  link: https://sparse.tamu.edu/JGD_Trefethen/Trefethen_2000
+  link: https://suitesparse-collection-website.herokuapp.com/MM/JGD_Trefethen/Trefethen_2000.tar.gz
 - name: Trefethen_2000
   enabled: true
   algorithm: sssp
@@ -160,7 +160,7 @@
     - fsharp
     - vine
   reorder: true
-  link: https://sparse.tamu.edu/JGD_Trefethen/Trefethen_2000
+  link: https://suitesparse-collection-website.herokuapp.com/MM/JGD_Trefethen/Trefethen_2000.tar.gz
 - name: gr_30_30
   enabled: true
   algorithm: tc
@@ -171,7 +171,7 @@
     - fsharp
     - vine
   reorder: false
-  link: https://sparse.tamu.edu/HB/gr_30_30
+  link: https://suitesparse-collection-website.herokuapp.com/MM/HB/gr_30_30.tar.gz
 - name: gr_30_30
   enabled: true
   algorithm: tc
@@ -182,7 +182,7 @@
     - fsharp
     - vine
   reorder: true
-  link: https://sparse.tamu.edu/HB/gr_30_30
+  link: https://suitesparse-collection-website.herokuapp.com/MM/HB/gr_30_30.tar.gz
 - name: Trefethen_2000
   enabled: true
   algorithm: tc
@@ -192,6 +192,5 @@
     - lagraph
     - fsharp
   reorder: false
-  link: https://sparse.tamu.edu/JGD_Trefethen/Trefethen_2000
-
+  link: https://suitesparse-collection-website.herokuapp.com/MM/JGD_Trefethen/Trefethen_2000.tar.gz
 # Trefethen_2000 is not reordered for tc because it makes everything much worse

From 9812fa5a8be8cbef66563d6e4b17f2c070aed97e Mon Sep 17 00:00:00 2001
From: Nick Ponomarev <wowasterdev@gmail.com>
Date: Mon, 22 Jun 2026 15:23:44 +0300
Subject: [PATCH 02/11] Add unified interface with download command

---
 main.py                      | 25 ++++++++--
 pyproject.toml               |  1 +
 scripts/download_matrices.py | 92 ------------------------------------
 src/__init__.py              |  0
 src/common.py                | 36 ++++++++++++++
 src/download.py              | 60 +++++++++++++++++++++++
 src/type_aliases.py          | 27 +++++++++++
 uv.lock                      | 16 +++++++
 8 files changed, 162 insertions(+), 95 deletions(-)
 delete mode 100644 scripts/download_matrices.py
 create mode 100644 src/__init__.py
 create mode 100644 src/common.py
 create mode 100644 src/download.py
 create mode 100644 src/type_aliases.py

diff --git a/main.py b/main.py
index 288bbe4..8fbadc1 100644
--- a/main.py
+++ b/main.py
@@ -1,6 +1,25 @@
-def main():
-    print("Hello from graph-benchmarks!")
+import logging
+
+import typer
+from rich.logging import RichHandler
+
+from src.download import app as download_app
+
+app = typer.Typer()
+app.add_typer(download_app)
+
+log_file_handler = logging.FileHandler("log.txt")
+
+FORMAT = "%(message)s"
+logging.basicConfig(
+    level="NOTSET",
+    format=FORMAT,
+    datefmt="[%X]",
+    handlers=[RichHandler(), log_file_handler],
+)
+
+log = logging.getLogger("rich")
 
 
 if __name__ == "__main__":
-    main()
+    app()
diff --git a/pyproject.toml b/pyproject.toml
index c5f1024..5a6d6b8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,6 +5,7 @@ description = "Add your description here"
 readme = "README.md"
 requires-python = ">=3.13"
 dependencies = [
+    "dataclass-wizard[yaml]>=0.39.1",
     "ipykernel>=7.2.0",
     "matplotlib>=3.10.8",
     "pandas>=3.0.2",
diff --git a/scripts/download_matrices.py b/scripts/download_matrices.py
deleted file mode 100644
index a209794..0000000
--- a/scripts/download_matrices.py
+++ /dev/null
@@ -1,92 +0,0 @@
-from pathlib import Path
-import shutil
-from typing import Annotated
-
-import requests
-import typer
-import yaml
-
-
-def get_matrices(path: Path) -> dict[str, str]:
-    with open(path, "r", encoding="utf-8") as m_file:
-        matrices = yaml.safe_load(m_file)
-    enabled_matrices = filter(lambda matrix: matrix["enabled"], matrices)
-    return dict(
-        map(
-            lambda matrix: ((matrix["name"], matrix["link"])),
-            enabled_matrices,
-        )
-    )
-
-
-def download_matrix(tmp_path: Path, url: str) -> Path:
-    matrix = requests.get(url, allow_redirects=True)
-    filename = url.split("/")[-1]
-    full_path = tmp_path / filename
-    with open(full_path, "wb+") as f:
-        f.write(matrix.content)
-    return full_path
-
-
-def unpack_matrix(matrix_archive_path: Path, matrices_path: Path) -> None:
-    shutil.unpack_archive(matrix_archive_path, matrix_archive_path.parent)
-    paths_to_copy = list(
-        Path(matrix_archive_path.parent).glob(
-            f"**/{matrix_archive_path.name.split('.')[0]}.mtx"
-        )
-    )
-    for path in paths_to_copy:
-        output = shutil.copy(path, matrices_path)
-        print("Wrote", output)
-
-
-def main(
-    matrices_spec_path: Annotated[
-        Path,
-        typer.Option(
-            exists=True,
-            file_okay=True,
-            dir_okay=False,
-            readable=True,
-            resolve_path=True,
-        ),
-    ] = Path("matrices.yaml"),
-    matrices_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("matrices"),
-    tmp_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("tmp"),
-):
-    print("Reading matrices spec from", matrices_spec_path)
-    matrices = get_matrices(matrices_spec_path)
-    print("Enabled matrices:", ", ".join(matrices.keys()))
-
-    tmp_path.mkdir(exist_ok=True)
-    matrices_path.mkdir(exist_ok=True)
-
-    temp_paths = []
-    for name, link in matrices.items():
-        print("Downloading", name)
-        downloaded_path = download_matrix(tmp_path, link)
-        temp_paths.append(downloaded_path)
-    for matrix in temp_paths:
-        unpack_matrix(matrix, matrices_path)
-
-
-if __name__ == "__main__":
-    typer.run(main)
diff --git a/src/__init__.py b/src/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/common.py b/src/common.py
new file mode 100644
index 0000000..5cd6f58
--- /dev/null
+++ b/src/common.py
@@ -0,0 +1,36 @@
+from dataclasses import dataclass
+from enum import StrEnum, auto
+from pathlib import Path
+from typing import List
+
+from dataclass_wizard import YAMLWizard
+import yaml
+
+
+class Algorithm(StrEnum):
+    BFS = auto()
+    SSSP = auto()
+    TC = auto()
+
+
+class Tool(StrEnum):
+    NETWORKX = auto()
+    FSHARP = auto()
+    INPLA = auto()
+    LAGRAPH = auto()
+    VINE = auto()
+
+
+@dataclass
+class Matrix(YAMLWizard):
+    name: str
+    enabled: bool
+    algorithm: Algorithm
+    tools: list[Tool]
+    reorder: bool
+    link: str
+
+
+def get_enabled_matrices(matrices_spec_path: Path) -> list[Matrix]:
+    matrices: List[Matrix] = Matrix.from_yaml_file(matrices_spec_path)  # type: ignore
+    return list(filter(lambda matrix: matrix.enabled, matrices))
diff --git a/src/download.py b/src/download.py
new file mode 100644
index 0000000..f0eea20
--- /dev/null
+++ b/src/download.py
@@ -0,0 +1,60 @@
+import logging
+from pathlib import Path
+import shutil
+
+import requests
+import typer
+
+from .common import Matrix, get_enabled_matrices
+from .type_aliases import DirPathOption, FilePathOption
+
+app = typer.Typer()
+log = logging.getLogger("rich")
+
+
+def download_matrix(matrix: Matrix, tmp_path: Path) -> Path:
+    matrix_resp = requests.get(matrix.link, allow_redirects=True)
+    filename = matrix.link.split("/")[-1]
+    full_path = tmp_path / filename
+    with open(full_path, "wb+") as f:
+        f.write(matrix_resp.content)
+    return full_path
+
+
+def unpack_matrix(matrix_archive_path: Path, matrices_path: Path) -> None:
+    shutil.unpack_archive(matrix_archive_path, matrix_archive_path.parent)
+    paths_to_copy = list(
+        Path(matrix_archive_path.parent).glob(
+            f"**/{matrix_archive_path.name.split('.')[0]}.mtx"
+        )
+    )
+    for path in paths_to_copy:
+        output = shutil.copy(path, matrices_path)
+        log.info("Unpacked to %s", output)
+
+
+@app.command()
+def download(
+    matrices_spec_path: FilePathOption = Path("matrices.yaml"),
+    matrices_path: DirPathOption = Path("matrices"),
+    tmp_path: DirPathOption = Path("tmp"),
+):
+    log.info("Reading matrices spec from %s", matrices_spec_path)
+    matrices = get_enabled_matrices(matrices_spec_path)
+    matrix_names = list(map(lambda matrix: matrix.name, matrices))
+    log.info("Enabled matrices: %s", set(matrix_names))
+
+    log.info("Creating %s", tmp_path)
+    tmp_path.mkdir(exist_ok=True)
+    log.info("Creating %s", tmp_path)
+    matrices_path.mkdir(exist_ok=True)
+
+    for matrix in matrices:
+        if (matrices_path / (matrix.name + ".mtx")).exists():
+            log.info("%s already downloaded, skipping", matrix.name)
+            continue
+
+        log.info("Downloading %s", matrix.name)
+        matrix_archive_path = download_matrix(matrix, tmp_path)
+        log.info("Unpacking %s", matrix_archive_path)
+        unpack_matrix(matrix_archive_path, matrices_path)
diff --git a/src/type_aliases.py b/src/type_aliases.py
new file mode 100644
index 0000000..be802f4
--- /dev/null
+++ b/src/type_aliases.py
@@ -0,0 +1,27 @@
+from pathlib import Path
+from typing import Annotated
+
+import typer
+
+
+FilePathOption = Annotated[
+    Path,
+    typer.Option(
+        exists=True,
+        file_okay=True,
+        dir_okay=False,
+        readable=True,
+        resolve_path=True,
+    ),
+]
+
+DirPathOption = Annotated[
+    Path,
+    typer.Option(
+        file_okay=False,
+        dir_okay=True,
+        readable=True,
+        writable=True,
+        resolve_path=True,
+    ),
+]
diff --git a/uv.lock b/uv.lock
index f2eae2d..6183221 100644
--- a/uv.lock
+++ b/uv.lock
@@ -242,6 +242,20 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/e7/05/c19819d5e3d95294a6f5947fb9b9629efb316b96de511b418c53d245aae6/cycler-0.12.1-py3-none-any.whl", hash = "sha256:85cef7cff222d8644161529808465972e51340599459b8ac3ccbac5a854e0d30", size = 8321, upload-time = "2023-10-07T05:32:16.783Z" },
 ]
 
+[[package]]
+name = "dataclass-wizard"
+version = "0.39.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/36/ea/6b2811092feecbe9d672e3641196ac5fcbec6664074da5dec8b9fd9b9059/dataclass_wizard-0.39.1.tar.gz", hash = "sha256:1679948ed7c62103f40b34df97d03b35e6b2ad50f58173fdbe30074e2e4730f2", size = 361190, upload-time = "2026-01-06T03:30:57.054Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/27/a0/a221942b3fbbafaea4e211744d298366b6a9712c1aa336b05fc1c865ac0c/dataclass_wizard-0.39.1-py3-none-any.whl", hash = "sha256:3324e59eca705882eb34e2b3989b2beadd8c2b523e6269d4002cf1a4a5bf703b", size = 215344, upload-time = "2026-01-06T03:30:54.915Z" },
+]
+
+[package.optional-dependencies]
+yaml = [
+    { name = "pyyaml" },
+]
+
 [[package]]
 name = "debugpy"
 version = "1.8.20"
@@ -315,6 +329,7 @@ name = "graph-benchmarks"
 version = "0.1.0"
 source = { virtual = "." }
 dependencies = [
+    { name = "dataclass-wizard", extra = ["yaml"] },
     { name = "ipykernel" },
     { name = "matplotlib" },
     { name = "pandas" },
@@ -326,6 +341,7 @@ dependencies = [
 
 [package.metadata]
 requires-dist = [
+    { name = "dataclass-wizard", extras = ["yaml"], specifier = ">=0.39.1" },
     { name = "ipykernel", specifier = ">=7.2.0" },
     { name = "matplotlib", specifier = ">=3.10.8" },
     { name = "pandas", specifier = ">=3.0.2" },

From e72ef287f943bdc9a8800be6d94b4afcd71317a0 Mon Sep 17 00:00:00 2001
From: Nick Ponomarev <wowasterdev@gmail.com>
Date: Mon, 22 Jun 2026 16:01:21 +0300
Subject: [PATCH 03/11] Add prepare-matrices to unified interface

---
 main.py                      |  2 +
 pyproject.toml               |  2 +
 scripts/make_positive_int.py | 38 -----------------
 scripts/prepare_matrices.py  | 75 --------------------------------
 src/common.py                | 10 +++++
 src/download.py              |  5 ++-
 src/prepare_matrices.py      | 83 ++++++++++++++++++++++++++++++++++++
 uv.lock                      | 52 ++++++++++++++++++++++
 8 files changed, 152 insertions(+), 115 deletions(-)
 delete mode 100644 scripts/make_positive_int.py
 delete mode 100644 scripts/prepare_matrices.py
 create mode 100644 src/prepare_matrices.py

diff --git a/main.py b/main.py
index 8fbadc1..f3c45fe 100644
--- a/main.py
+++ b/main.py
@@ -4,9 +4,11 @@
 from rich.logging import RichHandler
 
 from src.download import app as download_app
+from src.prepare_matrices import app as prepare_matrices_app
 
 app = typer.Typer()
 app.add_typer(download_app)
+app.add_typer(prepare_matrices_app)
 
 log_file_handler = logging.FileHandler("log.txt")
 
diff --git a/pyproject.toml b/pyproject.toml
index 5a6d6b8..d63f8be 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,5 +12,7 @@ dependencies = [
     "pyyaml>=6.0.3",
     "requests[socks]>=2.33.1",
     "scipy>=1.17.1",
+    "scipy-stubs>=1.18.0.0",
+    "toolz>=1.1.0",
     "typer>=0.24.1",
 ]
diff --git a/scripts/make_positive_int.py b/scripts/make_positive_int.py
deleted file mode 100644
index 297d5a9..0000000
--- a/scripts/make_positive_int.py
+++ /dev/null
@@ -1,38 +0,0 @@
-from pathlib import Path
-from typing import Annotated
-
-from scipy.sparse import coo_array
-from scipy.io import mmread, mmwrite
-import typer
-
-
-def make_nonnegative_int(matrix: coo_array):
-    matrix = matrix.trunc()
-    min_element = matrix.min()
-    if min_element < 0:
-        to_add = abs(min_element)
-        matrix.data += to_add
-        matrix.eliminate_zeros()
-    return matrix
-
-
-def main(
-    matrix_path: Annotated[
-        Path,
-        typer.Argument(
-            exists=True,
-            file_okay=True,
-            dir_okay=False,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ],
-):
-    matrix = mmread(matrix_path, spmatrix=True)
-    nonnegative_int_matrix = make_nonnegative_int(matrix)
-    mmwrite(matrix_path, nonnegative_int_matrix, field="integer")
-
-
-if __name__ == "__main__":
-    typer.run(main)
diff --git a/scripts/prepare_matrices.py b/scripts/prepare_matrices.py
deleted file mode 100644
index ac8dd08..0000000
--- a/scripts/prepare_matrices.py
+++ /dev/null
@@ -1,75 +0,0 @@
-from pathlib import Path
-import subprocess
-from typing import Annotated
-
-import typer
-import yaml
-
-from common import BenchMatrix, BenchmarkType
-
-
-def main(
-    matrices_spec_path: Annotated[
-        Path,
-        typer.Option(
-            exists=True,
-            file_okay=True,
-            dir_okay=False,
-            readable=True,
-            resolve_path=True,
-        ),
-    ] = Path("matrices.yaml"),
-    matrices_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("matrices"),
-    inpla_bench_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("tools") / "QTreeInpla",
-):
-    with open(matrices_spec_path, "r", encoding="utf-8") as m_file:
-        matrices: list[BenchMatrix] = yaml.safe_load(m_file)
-    enabled_matrices = list(filter(lambda matrix: matrix["enabled"], matrices))
-
-    print("*** Making matrices nonnegative int ***")
-    enabled_matrix_names = set(map(lambda matrix: matrix["name"], enabled_matrices))
-    for matrix_name in enabled_matrix_names:
-        matrix_path = matrices_path / (matrix_name + ".mtx")
-        subprocess.run(
-            ["uv", "run", Path("scripts") / "make_positive_int.py", matrix_path],
-            check=True,
-        )
-        print("Made nonnegative int matrix", matrix_path)
-    print("")
-
-    print("*** Reordering matrices ***")
-    matrices_to_reorder = list(
-        filter(lambda matrix: matrix["reorder"], enabled_matrices)
-    )
-    for matrix in matrices_to_reorder:
-        subprocess.run(
-            [
-                "uv",
-                "run",
-                inpla_bench_path / "scripts" / "simple_mtx_reordering.py",
-                matrices_path / (matrix["name"] + ".mtx"),
-            ],
-            check=True,
-        )
-
-
-if __name__ == "__main__":
-    typer.run(main)
diff --git a/src/common.py b/src/common.py
index 5cd6f58..78e4d84 100644
--- a/src/common.py
+++ b/src/common.py
@@ -1,9 +1,11 @@
 from dataclasses import dataclass
 from enum import StrEnum, auto
+from operator import attrgetter
 from pathlib import Path
 from typing import List
 
 from dataclass_wizard import YAMLWizard
+from toolz.itertoolz import unique
 import yaml
 
 
@@ -34,3 +36,11 @@ class Matrix(YAMLWizard):
 def get_enabled_matrices(matrices_spec_path: Path) -> list[Matrix]:
     matrices: List[Matrix] = Matrix.from_yaml_file(matrices_spec_path)  # type: ignore
     return list(filter(lambda matrix: matrix.enabled, matrices))
+
+
+def get_unique_by_name_matrices(matrices: list[Matrix]) -> list[Matrix]:
+    return list(unique(matrices, attrgetter("name")))
+
+
+def get_matrix_base_name(matrix: Matrix) -> str:
+    return matrix.name + ("_reordered" if matrix.reorder else "")
diff --git a/src/download.py b/src/download.py
index f0eea20..86e52c1 100644
--- a/src/download.py
+++ b/src/download.py
@@ -5,7 +5,7 @@
 import requests
 import typer
 
-from .common import Matrix, get_enabled_matrices
+from .common import Matrix, get_enabled_matrices, get_unique_by_name_matrices
 from .type_aliases import DirPathOption, FilePathOption
 
 app = typer.Typer()
@@ -41,8 +41,9 @@ def download(
 ):
     log.info("Reading matrices spec from %s", matrices_spec_path)
     matrices = get_enabled_matrices(matrices_spec_path)
+    matrices = get_unique_by_name_matrices(matrices)
     matrix_names = list(map(lambda matrix: matrix.name, matrices))
-    log.info("Enabled matrices: %s", set(matrix_names))
+    log.info("Enabled matrices: %s", matrix_names)
 
     log.info("Creating %s", tmp_path)
     tmp_path.mkdir(exist_ok=True)
diff --git a/src/prepare_matrices.py b/src/prepare_matrices.py
new file mode 100644
index 0000000..310f5b3
--- /dev/null
+++ b/src/prepare_matrices.py
@@ -0,0 +1,83 @@
+import logging
+from pathlib import Path
+
+import scipy.sparse as sp
+import typer
+from scipy.io import mmread, mmwrite
+
+from .common import Matrix, get_enabled_matrices, get_unique_by_name_matrices
+from .type_aliases import DirPathOption, FilePathOption
+
+app = typer.Typer()
+log = logging.getLogger("rich")
+
+
+def make_coo_array_nonnegative_int(matrix):
+    matrix = matrix.trunc()
+    min_element = matrix.min()
+    if min_element < 0:
+        to_add = abs(min_element)
+        matrix.data += to_add
+        matrix.eliminate_zeros()
+    return matrix
+
+
+def make_matrix_nonnegative_int(matrices_path: Path, matrix: Matrix):
+    matrix_path = matrices_path / (matrix.name + ".mtx")
+    matrix_array = mmread(matrix_path, spmatrix=False)
+    nonnegative_int_matrix = make_coo_array_nonnegative_int(matrix_array)
+    mmwrite(matrix_path, nonnegative_int_matrix, field="integer")
+
+
+# Based on https://github.com/Lamagraph/QTreeInpla/blob/main/scripts/simple_mtx_reordering.py
+def reorder_rcm_array(matrix_array):
+    """
+    Переупорядочивание с помощью обратного алгоритма Катхилла-Макки (RCM).
+    Возвращает перестановку для строк и столбцов (одна и та же).
+    """
+    # Симметризуем структуру ненулевых элементов
+    matrix_array_bin = (matrix_array != 0).astype(int)  # type: ignore
+    matrix_array_sym = (matrix_array_bin + matrix_array_bin.T) > 0
+    matrix_array_sym = matrix_array_sym.tocsr()
+    matrix_array_sym.setdiag(0)  # убираем петли (диагональ)
+    matrix_array_sym.eliminate_zeros()
+
+    # Вычисляем перестановку RCM
+    perm = sp.csgraph.reverse_cuthill_mckee(matrix_array_sym, symmetric_mode=True)
+    return perm
+
+
+def reorder_rcm_matrix(matrices_path: Path, matrix: Matrix):
+    matrix_path = matrices_path / (matrix.name + ".mtx")
+    matrix_array = mmread(matrix_path, spmatrix=False).tocsr()
+    if matrix_array.shape[0] != matrix_array.shape[1]:
+        log.warning("Rectangle matrix detected. Only rows will be reordered.")
+    perm = reorder_rcm_array(matrix_array)
+    if matrix_array.shape[0] == matrix_array.shape[1]:
+        matrix_array_reordered = matrix_array[perm, :][:, perm]
+    else:
+        matrix_array_reordered = matrix_array[perm, :]
+
+    mmwrite(matrix_path, matrix_array_reordered)
+
+
+@app.command()
+def prepare_matrices(
+    matrices_spec_path: FilePathOption = Path("matrices.yaml"),
+    matrices_path: DirPathOption = Path("matrices"),
+):
+    log.info("Reading matrices spec from %s", matrices_spec_path)
+    matrices = get_enabled_matrices(matrices_spec_path)
+    matrices_unique = get_unique_by_name_matrices(matrices)
+
+    log.info("Making matrices nonnegative int")
+    for matrix in matrices_unique:
+        log.info("Making %s nonnegative", matrix.name)
+        make_matrix_nonnegative_int(matrices_path, matrix)
+
+    matrices_for_reorder = list(filter(lambda matrix: matrix.reorder, matrices))
+    matrices_for_reorder = get_unique_by_name_matrices(matrices_for_reorder)
+    log.info("Creating reordered matrices")
+    for matrix in matrices_for_reorder:
+        log.info("Creating reorder of %s", matrix.name)
+        reorder_rcm_matrix(matrices_path, matrix)
diff --git a/uv.lock b/uv.lock
index 6183221..119fbeb 100644
--- a/uv.lock
+++ b/uv.lock
@@ -336,6 +336,8 @@ dependencies = [
     { name = "pyyaml" },
     { name = "requests", extra = ["socks"] },
     { name = "scipy" },
+    { name = "scipy-stubs" },
+    { name = "toolz" },
     { name = "typer" },
 ]
 
@@ -348,6 +350,8 @@ requires-dist = [
     { name = "pyyaml", specifier = ">=6.0.3" },
     { name = "requests", extras = ["socks"], specifier = ">=2.33.1" },
     { name = "scipy", specifier = ">=1.17.1" },
+    { name = "scipy-stubs", specifier = ">=1.18.0.0" },
+    { name = "toolz", specifier = ">=1.1.0" },
     { name = "typer", specifier = ">=0.24.1" },
 ]
 
@@ -665,6 +669,33 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/58/78/548fb8e07b1a341746bfbecb32f2c268470f45fa028aacdbd10d9bc73aab/numpy-2.4.4-cp314-cp314t-win_arm64.whl", hash = "sha256:ba203255017337d39f89bdd58417f03c4426f12beed0440cfd933cb15f8669c7", size = 10566643, upload-time = "2026-03-29T13:21:34.339Z" },
 ]
 
+[[package]]
+name = "numpy-typing-compat"
+version = "20260602.2.4"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "numpy" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/fc/73/e331473d3db84a8e8883ac07bfd63a8ce9eb7196acbb672bda1f5b8d3294/numpy_typing_compat-20260602.2.4.tar.gz", hash = "sha256:e4eb661f312a7ad5805677967d5879e04fd7b97627fe910121ce7b1f43aa748c", size = 4603, upload-time = "2026-06-02T15:52:38.572Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/f8/a8/94811eedac4cef5ef7df4b24e06715fa371724782e86a4573f5d172c8473/numpy_typing_compat-20260602.2.4-py3-none-any.whl", hash = "sha256:78d33917d5f6921f8d1c549db347a5b8d9768853e36796b08208c81f5b620977", size = 5879, upload-time = "2026-06-02T15:52:33.214Z" },
+]
+
+[[package]]
+name = "optype"
+version = "0.18.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/99/51/51dc9b1009e020f44703933d4d1ee3429c647c026ce7806b37ee2b257998/optype-0.18.0.tar.gz", hash = "sha256:ea10dee61b15ca299ed0d97025d362585c4dfc5481159bb999a1d0d414bbcb04", size = 59967, upload-time = "2026-06-07T22:13:17.534Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/5b/91/2b064a117cb2593bc3eb04ee994134ca2a6bf2162c92961769947e3258cc/optype-0.18.0-py3-none-any.whl", hash = "sha256:91822ed8516e7a4f225ba53d30f291776c35f31553fb952d7cda98286679c5a6", size = 73410, upload-time = "2026-06-07T22:13:16.324Z" },
+]
+
+[package.optional-dependencies]
+numpy = [
+    { name = "numpy" },
+    { name = "numpy-typing-compat" },
+]
+
 [[package]]
 name = "packaging"
 version = "26.1"
@@ -1075,6 +1106,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/07/39/338d9219c4e87f3e708f18857ecd24d22a0c3094752393319553096b98af/scipy-1.17.1-cp314-cp314t-win_arm64.whl", hash = "sha256:200e1050faffacc162be6a486a984a0497866ec54149a01270adc8a59b7c7d21", size = 25489165, upload-time = "2026-02-23T00:22:29.563Z" },
 ]
 
+[[package]]
+name = "scipy-stubs"
+version = "1.18.0.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "optype", extra = ["numpy"] },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/e5/9b/6cb11393563241c79b74e035c1d697329d1dce1635565e40b0085d56a2fe/scipy_stubs-1.18.0.0.tar.gz", hash = "sha256:a1fc917da66e4d338998839170e218754a669f6455c24243890a1e572bde98f6", size = 402538, upload-time = "2026-06-19T10:56:39.57Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/e9/b4/82d4de656500722dea533151b88f926672341b46289cc31eb2e2c1c7c1d7/scipy_stubs-1.18.0.0-py3-none-any.whl", hash = "sha256:872ec1066a75feb5c5d8451231e8f7826d08d53fb806c526abd5f97bb1ba29fb", size = 608175, upload-time = "2026-06-19T10:56:37.905Z" },
+]
+
 [[package]]
 name = "shellingham"
 version = "1.5.4"
@@ -1107,6 +1150,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/f1/7b/ce1eafaf1a76852e2ec9b22edecf1daa58175c090266e9f6c64afcd81d91/stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695", size = 24521, upload-time = "2023-09-30T13:58:03.53Z" },
 ]
 
+[[package]]
+name = "toolz"
+version = "1.1.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/11/d6/114b492226588d6ff54579d95847662fc69196bdeec318eb45393b24c192/toolz-1.1.0.tar.gz", hash = "sha256:27a5c770d068c110d9ed9323f24f1543e83b2f300a687b7891c1a6d56b697b5b", size = 52613, upload-time = "2025-10-17T04:03:21.661Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/fb/12/5911ae3eeec47800503a238d971e51722ccea5feb8569b735184d5fcdbc0/toolz-1.1.0-py3-none-any.whl", hash = "sha256:15ccc861ac51c53696de0a5d6d4607f99c210739caf987b5d2054f3efed429d8", size = 58093, upload-time = "2025-10-17T04:03:20.435Z" },
+]
+
 [[package]]
 name = "tornado"
 version = "6.5.5"

From 9c2a1a820a7aa08abe84062c164267ed43f82fb9 Mon Sep 17 00:00:00 2001
From: Nick Ponomarev <wowasterdev@gmail.com>
Date: Fri, 26 Jun 2026 11:33:50 +0300
Subject: [PATCH 04/11] Use modern syntax for type aliases

---
 src/type_aliases.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/type_aliases.py b/src/type_aliases.py
index be802f4..2bde500 100644
--- a/src/type_aliases.py
+++ b/src/type_aliases.py
@@ -4,7 +4,7 @@
 import typer
 
 
-FilePathOption = Annotated[
+type FilePathOption = Annotated[
     Path,
     typer.Option(
         exists=True,
@@ -15,7 +15,7 @@
     ),
 ]
 
-DirPathOption = Annotated[
+type DirPathOption = Annotated[
     Path,
     typer.Option(
         file_okay=False,

From cdd20aa358df33cda1b1220118e0692cd368c204 Mon Sep 17 00:00:00 2001
From: Nick Ponomarev <wowasterdev@gmail.com>
Date: Fri, 26 Jun 2026 19:16:48 +0300
Subject: [PATCH 05/11] Fix renaming after reordering

---
 src/prepare_matrices.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/prepare_matrices.py b/src/prepare_matrices.py
index 310f5b3..6c5f4b1 100644
--- a/src/prepare_matrices.py
+++ b/src/prepare_matrices.py
@@ -1,4 +1,5 @@
 import logging
+import os
 from pathlib import Path
 
 import scipy.sparse as sp
@@ -57,7 +58,8 @@ def reorder_rcm_matrix(matrices_path: Path, matrix: Matrix):
         matrix_array_reordered = matrix_array[perm, :][:, perm]
     else:
         matrix_array_reordered = matrix_array[perm, :]
-
+    name, ext = os.path.splitext(matrix_path)
+    matrix_path = name + "_reordered" + ext
     mmwrite(matrix_path, matrix_array_reordered)
 
 

From eb5b07086a00bbcafbe0db75b75474ec2fc1601a Mon Sep 17 00:00:00 2001
From: Nick Ponomarev <wowasterdev@gmail.com>
Date: Fri, 26 Jun 2026 19:17:01 +0300
Subject: [PATCH 06/11] Bump all dependencies

---
 uv.lock | 526 +++++++++++++++++++++++++++-----------------------------
 1 file changed, 252 insertions(+), 274 deletions(-)

diff --git a/uv.lock b/uv.lock
index 119fbeb..45df208 100644
--- a/uv.lock
+++ b/uv.lock
@@ -39,11 +39,11 @@ wheels = [
 
 [[package]]
 name = "certifi"
-version = "2026.2.25"
+version = "2026.6.17"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/af/2d/7bf41579a8986e348fa033a31cdd0e4121114f6bce2457e8876010b092dd/certifi-2026.2.25.tar.gz", hash = "sha256:e887ab5cee78ea814d3472169153c2d12cd43b14bd03329a39a9c6e2e80bfba7", size = 155029, upload-time = "2026-02-25T02:54:17.342Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/c9/c7/424b75da314c1045981bd9777432fad05a9e0c69daa4ed7e308bbaffe405/certifi-2026.6.17.tar.gz", hash = "sha256:024c88eeec92ca068db80f02b8b07c9cef7b9fe261d1d535abfd5abd6f6af432", size = 134594, upload-time = "2026-06-17T10:31:07.894Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/9a/3c/c17fb3ca2d9c3acff52e30b309f538586f9f5b9c9cf454f3845fc9af4881/certifi-2026.2.25-py3-none-any.whl", hash = "sha256:027692e4402ad994f1c42e52a4997a9763c646b73e4096e4d5d6db8af1d6f0fa", size = 153684, upload-time = "2026-02-25T02:54:15.766Z" },
+    { url = "https://files.pythonhosted.org/packages/ef/2f/c5464532e965badff2f4c4c1a3a83f5697f0d7c407ed0cda44aaa99bb451/certifi-2026.6.17-py3-none-any.whl", hash = "sha256:2227dcbaafe0d2f59279d1762ddddc37783ed4354594f194ffc31d20f41fc3db", size = 133289, upload-time = "2026-06-17T10:31:06.348Z" },
 ]
 
 [[package]]
@@ -148,18 +148,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/db/8f/61959034484a4a7c527811f4721e75d02d653a35afb0b6054474d8185d4c/charset_normalizer-3.4.7-py3-none-any.whl", hash = "sha256:3dce51d0f5e7951f8bb4900c257dad282f49190fdbebecd4ba99bcc41fef404d", size = 61958, upload-time = "2026-04-02T09:28:37.794Z" },
 ]
 
-[[package]]
-name = "click"
-version = "8.3.1"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "colorama", marker = "sys_platform == 'win32'" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/3d/fa/656b739db8587d7b5dfa22e22ed02566950fbfbcdc20311993483657a5c0/click-8.3.1.tar.gz", hash = "sha256:12ff4785d337a1bb490bb7e9c2b1ee5da3112e94a8622f26a6c77f5d2fc6842a", size = 295065, upload-time = "2025-11-15T20:45:42.706Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/98/78/01c019cdb5d6498122777c1a43056ebb3ebfeef2076d9d026bfe15583b2b/click-8.3.1-py3-none-any.whl", hash = "sha256:981153a64e25f12d547d3426c367a4857371575ee7ad18df2a6183ab0545b2a6", size = 108274, upload-time = "2025-11-15T20:45:41.139Z" },
-]
-
 [[package]]
 name = "colorama"
 version = "0.4.6"
@@ -258,28 +246,28 @@ yaml = [
 
 [[package]]
 name = "debugpy"
-version = "1.8.20"
+version = "1.8.21"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/e0/b7/cd8080344452e4874aae67c40d8940e2b4d47b01601a8fd9f44786c757c7/debugpy-1.8.20.tar.gz", hash = "sha256:55bc8701714969f1ab89a6d5f2f3d40c36f91b2cbe2f65d98bf8196f6a6a2c33", size = 1645207, upload-time = "2026-01-29T23:03:28.199Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/f2/aa/12037145b7a56eaa5b29b41872f7a21b538e807e13f32c4d3c46e59be084/debugpy-1.8.21.tar.gz", hash = "sha256:a3c53278e84c94e11bd87c53970ec391d1a67396c8b22609fcac576520e611a6", size = 1697577, upload-time = "2026-06-01T19:30:35.156Z" }
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+    { url = "https://files.pythonhosted.org/packages/96/8d/1080ee4c231f361b6ce4470d556c8c435b67c7e0753aaa641497ee92f88b/traitlets-5.15.1-py3-none-any.whl", hash = "sha256:770a53705f84b81ac107e83a1b3328ff2dae16094d8fc3cfc004e4b22dfd8e92", size = 85858, upload-time = "2026-06-03T12:26:04.395Z" },
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-version = "0.24.1"
+version = "0.26.7"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "annotated-doc" },
-    { name = "click" },
+    { name = "colorama", marker = "sys_platform == 'win32'" },
     { name = "rich" },
     { name = "shellingham" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/f5/24/cb09efec5cc954f7f9b930bf8279447d24618bb6758d4f6adf2574c41780/typer-0.24.1.tar.gz", hash = "sha256:e39b4732d65fbdcde189ae76cf7cd48aeae72919dea1fdfc16593be016256b45", size = 118613, upload-time = "2026-02-21T16:54:40.609Z" }
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+wheels = [
+    { url = "https://files.pythonhosted.org/packages/24/25/2201973529af2c954de0bb725323c3aaed6d7f0ceee8f550dec9185df013/typer-0.26.7-py3-none-any.whl", hash = "sha256:5c87cfbc5d34491c5346ebf49c23e18d56ccb863268d3a8d592b26087c2f5e58", size = 122456, upload-time = "2026-06-03T07:18:05.732Z" },
+]
+
+[[package]]
+name = "typing-extensions"
+version = "4.15.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/72/94/1a15dd82efb362ac84269196e94cf00f187f7ed21c242792a923cdb1c61f/typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466", size = 109391, upload-time = "2025-08-25T13:49:26.313Z" }
 wheels = [
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+    { url = "https://files.pythonhosted.org/packages/18/67/36e9267722cc04a6b9f15c7f3441c2363321a3ea07da7ae0c0707beb2a9c/typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548", size = 44614, upload-time = "2025-08-25T13:49:24.86Z" },
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 [[package]]
@@ -1211,18 +1189,18 @@ wheels = [
 
 [[package]]
 name = "urllib3"
-version = "2.6.3"
+version = "2.7.0"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/c7/24/5f1b3bdffd70275f6661c76461e25f024d5a38a46f04aaca912426a2b1d3/urllib3-2.6.3.tar.gz", hash = "sha256:1b62b6884944a57dbe321509ab94fd4d3b307075e0c2eae991ac71ee15ad38ed", size = 435556, upload-time = "2026-01-07T16:24:43.925Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/53/0c/06f8b233b8fd13b9e5ee11424ef85419ba0d8ba0b3138bf360be2ff56953/urllib3-2.7.0.tar.gz", hash = "sha256:231e0ec3b63ceb14667c67be60f2f2c40a518cb38b03af60abc813da26505f4c", size = 433602, upload-time = "2026-05-07T16:13:18.596Z" }
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+    { url = "https://files.pythonhosted.org/packages/7f/3e/5db95bcf282c52709639744ca2a8b149baccf648e39c8cc87553df9eae0c/urllib3-2.7.0-py3-none-any.whl", hash = "sha256:9fb4c81ebbb1ce9531cce37674bbc6f1360472bc18ca9a553ede278ef7276897", size = 131087, upload-time = "2026-05-07T16:13:17.151Z" },
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 [[package]]
 name = "wcwidth"
-version = "0.6.0"
+version = "0.8.1"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/35/a2/8e3becb46433538a38726c948d3399905a4c7cabd0df578ede5dc51f0ec2/wcwidth-0.6.0.tar.gz", hash = "sha256:cdc4e4262d6ef9a1a57e018384cbeb1208d8abbc64176027e2c2455c81313159", size = 159684, upload-time = "2026-02-06T19:19:40.919Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/49/b4/51fe890511f0f242d07cb1ebe6a5b6db417262b9d2568b460347c57d95cc/wcwidth-0.8.1.tar.gz", hash = "sha256:faf5b4a5366a72dc49cad48cdf21f52bdf63bdda995178e483ba247ff79089b9", size = 1466072, upload-time = "2026-06-08T05:57:23.146Z" }
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+    { url = "https://files.pythonhosted.org/packages/bd/6e/95b0e537de1f4d4301f76f944642c6da50d1511cc7b3d64dc418a66c7509/wcwidth-0.8.1-py3-none-any.whl", hash = "sha256:f453740b1e4a4f3291faa37944c555d71056c4da08d59809b307ef4feba695c8", size = 323092, upload-time = "2026-06-08T05:57:21.413Z" },
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From 3c5c9578cac19d7a674e8410307c1401a11a3149 Mon Sep 17 00:00:00 2001
From: Nick Ponomarev <wowasterdev@gmail.com>
Date: Fri, 26 Jun 2026 19:55:43 +0300
Subject: [PATCH 07/11]  Add lagraph benchmark

---
 main.py                   |   4 +-
 scripts/run_lagraph.py    | 266 --------------------------------------
 src/benchmark/__init__.py |   7 +
 src/benchmark/lagraph.py  | 144 +++++++++++++++++++++
 src/common.py             | 113 +++++++++++++++-
 src/type_aliases.py       |   4 +-
 6 files changed, 267 insertions(+), 271 deletions(-)
 delete mode 100644 scripts/run_lagraph.py
 create mode 100644 src/benchmark/__init__.py
 create mode 100644 src/benchmark/lagraph.py

diff --git a/main.py b/main.py
index f3c45fe..e4b85fc 100644
--- a/main.py
+++ b/main.py
@@ -5,10 +5,12 @@
 
 from src.download import app as download_app
 from src.prepare_matrices import app as prepare_matrices_app
+from src.benchmark import app as benchmark_app
 
-app = typer.Typer()
+app = typer.Typer(no_args_is_help=True)
 app.add_typer(download_app)
 app.add_typer(prepare_matrices_app)
+app.add_typer(benchmark_app, name="benchmark")
 
 log_file_handler = logging.FileHandler("log.txt")
 
diff --git a/scripts/run_lagraph.py b/scripts/run_lagraph.py
deleted file mode 100644
index df1f0fb..0000000
--- a/scripts/run_lagraph.py
+++ /dev/null
@@ -1,266 +0,0 @@
-from datetime import datetime
-import json
-import os
-from pathlib import Path
-import subprocess
-from typing import Annotated
-
-import typer
-import yaml
-
-from common import (
-    BenchMatrix,
-    BenchmarkType,
-    get_matrix_base_name,
-    get_matrix_filename_mtx,
-)
-
-
-def make_GraphBLAS(dependencies_path: Path):
-    subprocess.run(["make"], cwd=dependencies_path / "GraphBLAS", check=True)
-
-
-def check_GraphBLAS(dependencies_path: Path):
-    subprocess.run(["make", "check"], cwd=dependencies_path / "GraphBLAS", check=True)
-
-
-def make_LAGraph(dependencies_path: Path):
-    subprocess.run(["make"], cwd=dependencies_path / "LAGraph", check=True)
-
-
-def check_LAGraph(dependencies_path: Path):
-    subprocess.run(["make", "test"], cwd=dependencies_path / "LAGraph", check=True)
-
-
-def make_benchmarks(dependencies_path: Path, lagraph_bench_path: Path):
-    (lagraph_bench_path / "build").mkdir(exist_ok=True)
-    cc_common_args = [
-        "-I",
-        str(dependencies_path / "GraphBLAS" / "Include"),
-        "-I",
-        str(dependencies_path / "LAGraph" / "include"),
-        "-L",
-        str(dependencies_path / "GraphBLAS" / "build"),
-        "-L",
-        str(dependencies_path / "LAGraph" / "build" / "src"),
-        "-lgraphblas",
-        "-llagraph",
-        "-Wl,-rpath=" + str(dependencies_path / "GraphBLAS" / "build"),
-        "-Wl,-rpath=" + str(dependencies_path / "LAGraph" / "build" / "src"),
-        "-O3",
-        "-g",
-    ]
-    subprocess.run(
-        ["cc", "src/lagraph_bfs.c", "-o", "build/lagraph_bfs"] + cc_common_args,
-        cwd=lagraph_bench_path,
-        check=True,
-    )
-    subprocess.run(
-        ["cc", "src/lagraph_sssp.c", "-o", "build/lagraph_sssp"] + cc_common_args,
-        cwd=lagraph_bench_path,
-        check=True,
-    )
-    subprocess.run(
-        ["cc", "src/lagraph_triangles.c", "-o", "build/lagraph_tc"] + cc_common_args,
-        cwd=lagraph_bench_path,
-        check=True,
-    )
-
-
-def run_lagraph(
-    lagraph_bench_path: Path,
-    matrices_path: Path,
-    matrix: BenchMatrix,
-    thread_count: int,
-) -> str:
-    run_res = subprocess.run(
-        [
-            Path("build") / ("lagraph_" + matrix["algorithm"]),
-            matrices_path / get_matrix_filename_mtx(matrix),
-        ],
-        cwd=lagraph_bench_path,
-        capture_output=True,
-        text=True,
-        env={"OMP_NUM_THREADS": str(thread_count)},
-    )
-    if run_res.returncode != 0:
-        print(
-            "Process",
-            run_res.args,
-            "exited with code",
-            run_res.returncode,
-            end="",
-            flush=True,
-        )
-    return run_res.stdout
-
-
-def run_lagraph_many_times(
-    lagraph_bench_path: Path,
-    matrices_path: Path,
-    matrix: BenchMatrix,
-    run_count: int,
-    thread_count: int,
-) -> list[str]:
-    result = []
-    print("Running with", thread_count, "threads. Run: ", end="")
-    for i in range(run_count):
-        print(i + 1, "...", sep="", end="", flush=True)
-        result.append(
-            run_lagraph(lagraph_bench_path, matrices_path, matrix, thread_count)
-        )
-    print("")
-    return result
-
-
-def run_experiment(
-    lagraph_bench_path: Path,
-    matrices_path: Path,
-    matrix: BenchMatrix,
-    run_count: int,
-    thread_count: int,
-) -> dict[int, list[str]]:
-    if thread_count <= 0:
-        result = dict()
-
-        nproc = os.cpu_count()
-        if nproc is None:
-            raise RuntimeError("Cannot get nproc")
-        thread_counts = [1] + list(range(2, nproc + 1, 2))
-
-        for thread_count in thread_counts:
-            result[thread_count] = run_lagraph_many_times(
-                lagraph_bench_path, matrices_path, matrix, run_count, thread_count
-            )
-
-        return result
-    else:
-        result = run_lagraph_many_times(
-            lagraph_bench_path, matrices_path, matrix, run_count, thread_count
-        )
-        return {thread_count: result}
-
-
-def run_experiments(
-    lagraph_bench_path: Path,
-    matrices_path: Path,
-    run_count: int,
-    thread_count: int,
-    lagraph_matrices: list[BenchMatrix],
-):
-    results: dict[str, dict[str, dict[int, list[str]]]] = {
-        "bfs": dict(),
-        "sssp": dict(),
-        "tc": dict(),
-    }
-    for matrix in lagraph_matrices:
-        base_name = get_matrix_base_name(matrix)
-        print("Benchmarking", matrix["algorithm"], "on", base_name)
-        results[matrix["algorithm"]][base_name] = run_experiment(
-            lagraph_bench_path, matrices_path, matrix, run_count, thread_count
-        )
-        print("")
-
-    return results
-
-
-def main(
-    matrices_spec_path: Annotated[
-        Path,
-        typer.Option(
-            exists=True,
-            file_okay=True,
-            dir_okay=False,
-            readable=True,
-            resolve_path=True,
-        ),
-    ] = Path("matrices.yaml"),
-    matrices_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("matrices"),
-    dependencies_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("dependencies"),
-    lagraph_bench_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("tools/lagraph-bench"),
-    raw_results_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("results") / "raw",
-    check: Annotated[bool, typer.Option()] = False,
-    run_count: Annotated[int, typer.Option] = 20,
-    thread_count: Annotated[int, typer.Option] = 0,
-):
-    print("*** Making GraphBLAS ***")
-    make_GraphBLAS(dependencies_path)
-    print("")
-    if check:
-        print("*** Checking GraphBLAS ***")
-        check_GraphBLAS(dependencies_path)
-        print("")
-
-    print("*** Making LAGraph ***")
-    make_LAGraph(dependencies_path)
-    print("")
-    if check:
-        print("*** Checking LAGraph ***")
-        check_LAGraph(dependencies_path)
-        print("")
-
-    print("*** Making benchmarks ***")
-    make_benchmarks(dependencies_path, lagraph_bench_path)
-    print("")
-
-    with open(matrices_spec_path, "r", encoding="utf-8") as m_file:
-        matrices: list[BenchMatrix] = yaml.safe_load(m_file)
-    enabled_matrices = filter(lambda matrix: matrix["enabled"], matrices)
-    lagraph_matrices = list(
-        filter(lambda matrix: "lagraph" in matrix["tools"], enabled_matrices)
-    )
-
-    print("*** Running experiments ***")
-    results = run_experiments(
-        lagraph_bench_path, matrices_path, run_count, thread_count, lagraph_matrices
-    )
-    print("")
-
-    print("*** Writing results ***")
-    raw_results_path.mkdir(parents=True, exist_ok=True)
-    results_path = raw_results_path / (
-        datetime.now().astimezone().isoformat(timespec="minutes") + "_lagraph.json"
-    )
-    with open(results_path, "w", encoding="utf-8") as r_file:
-        json.dump(results, r_file)
-    print("Wrote to", str(results_path))
-
-
-if __name__ == "__main__":
-    typer.run(main)
diff --git a/src/benchmark/__init__.py b/src/benchmark/__init__.py
new file mode 100644
index 0000000..88d68ab
--- /dev/null
+++ b/src/benchmark/__init__.py
@@ -0,0 +1,7 @@
+import typer
+
+from .lagraph import app as lagraph_app
+
+app = typer.Typer(no_args_is_help=True)
+
+app.add_typer(lagraph_app)
diff --git a/src/benchmark/lagraph.py b/src/benchmark/lagraph.py
new file mode 100644
index 0000000..33d1406
--- /dev/null
+++ b/src/benchmark/lagraph.py
@@ -0,0 +1,144 @@
+import logging
+from pathlib import Path
+import subprocess
+from typing import Annotated
+
+import typer
+
+from ..common import (
+    Matrix,
+    Tool,
+    comma_separated_str_to_int_list,
+    get_enabled_matrices,
+    get_matrix_filename_mtx,
+    run_benchmarks,
+    write_results,
+)
+from ..type_aliases import DirPathOption, FilePathOption
+
+app = typer.Typer()
+log = logging.getLogger("rich")
+
+
+def build_GraphBLAS(dependencies_path: Path):
+    subprocess.run(["make"], cwd=dependencies_path / "GraphBLAS", check=True)
+
+
+def check_GraphBLAS(dependencies_path: Path):
+    subprocess.run(["make", "check"], cwd=dependencies_path / "GraphBLAS", check=True)
+
+
+def build_LAGraph(dependencies_path: Path):
+    subprocess.run(["make"], cwd=dependencies_path / "LAGraph", check=True)
+
+
+def check_LAGraph(dependencies_path: Path):
+    subprocess.run(["make", "test"], cwd=dependencies_path / "LAGraph", check=True)
+
+
+def build_benchmarks(dependencies_path: Path, lagraph_bench_path: Path):
+    (lagraph_bench_path / "build").mkdir(exist_ok=True)
+    cc_common_args = [
+        "-I",
+        str(dependencies_path / "GraphBLAS" / "Include"),
+        "-I",
+        str(dependencies_path / "LAGraph" / "include"),
+        "-L",
+        str(dependencies_path / "GraphBLAS" / "build"),
+        "-L",
+        str(dependencies_path / "LAGraph" / "build" / "src"),
+        "-lgraphblas",
+        "-llagraph",
+        "-Wl,-rpath=" + str(dependencies_path / "GraphBLAS" / "build"),
+        "-Wl,-rpath=" + str(dependencies_path / "LAGraph" / "build" / "src"),
+        "-O3",
+        "-g",
+    ]
+    subprocess.run(
+        ["cc", "src/lagraph_bfs.c", "-o", "build/lagraph_bfs"] + cc_common_args,
+        cwd=lagraph_bench_path,
+        check=True,
+    )
+    subprocess.run(
+        ["cc", "src/lagraph_sssp.c", "-o", "build/lagraph_sssp"] + cc_common_args,
+        cwd=lagraph_bench_path,
+        check=True,
+    )
+    subprocess.run(
+        ["cc", "src/lagraph_triangles.c", "-o", "build/lagraph_tc"] + cc_common_args,
+        cwd=lagraph_bench_path,
+        check=True,
+    )
+
+
+def run_lagraph(
+    matrix: Matrix,
+    thread_count: int,
+    *,
+    lagraph_bench_path: Path,
+    matrices_path: Path,
+) -> subprocess.CompletedProcess[str]:
+    return subprocess.run(
+        [
+            Path("build") / ("lagraph_" + matrix.algorithm),
+            matrices_path / get_matrix_filename_mtx(matrix),
+        ],
+        cwd=lagraph_bench_path,
+        capture_output=True,
+        text=True,
+        env={"OMP_NUM_THREADS": str(thread_count)},
+    )
+
+
+@app.command()
+def lagraph(
+    matrices_spec_path: FilePathOption = Path("matrices.yaml"),
+    matrices_path: DirPathOption = Path("matrices"),
+    dependencies_path: DirPathOption = Path("dependencies"),
+    lagraph_bench_path: DirPathOption = Path("tools/lagraph-bench"),
+    raw_results_path: DirPathOption = Path("results") / "raw",
+    check: Annotated[bool, typer.Option()] = False,
+    run_count: Annotated[int, typer.Option] = 20,
+    thread_counts: Annotated[str | None, typer.Option()] = None,
+):
+    log.info("Building GraphBLAS")
+    build_GraphBLAS(dependencies_path)
+    log.info("Successfully built GraphBLAS")
+
+    if check:
+        log.info("Checking GraphBLAS")
+        check_GraphBLAS(dependencies_path)
+        log.info("Successfully checked GraphBLAS")
+
+    log.info("Building LAGraph")
+    build_LAGraph(dependencies_path)
+    log.info("Successfully built LAGraph")
+    if check:
+        log.info("Checking LAGraph")
+        check_LAGraph(dependencies_path)
+        log.info("Successfully checked LAGraph")
+
+    log.info("Building benchmarks")
+    build_benchmarks(dependencies_path, lagraph_bench_path)
+    log.info("Successfully built LAGraph")
+
+    matrices = get_enabled_matrices(matrices_spec_path)
+    matrices = list(filter(lambda matrix: Tool.LAGRAPH in matrix.tools, matrices))
+
+    # parser doesn't work
+    # see https://github.com/fastapi/typer/discussions/1393
+    thread_counts_t = comma_separated_str_to_int_list(thread_counts)
+    logging.info(
+        "Starting LAGraph benchmarks with thread counts: %s",
+        thread_counts_t,
+    )
+    results = run_benchmarks(
+        matrices,
+        thread_counts_t,
+        run_count,
+        run_lagraph,
+        matrices_path=matrices_path,
+        lagraph_bench_path=lagraph_bench_path,
+    )
+
+    write_results(results, raw_results_path, Tool.LAGRAPH)
diff --git a/src/common.py b/src/common.py
index 78e4d84..6ebfa0f 100644
--- a/src/common.py
+++ b/src/common.py
@@ -1,12 +1,20 @@
 from dataclasses import dataclass
+from datetime import datetime
 from enum import StrEnum, auto
+import json
+import logging
 from operator import attrgetter
+import os
 from pathlib import Path
-from typing import List
+import subprocess
+from typing import Callable, Concatenate, List, TypedDict
 
 from dataclass_wizard import YAMLWizard
 from toolz.itertoolz import unique
-import yaml
+
+type RunToolCallable = Callable[
+    Concatenate[Matrix, int, ...], subprocess.CompletedProcess[str]
+]
 
 
 class Algorithm(StrEnum):
@@ -33,6 +41,13 @@ class Matrix(YAMLWizard):
     link: str
 
 
+# @dataclass would be fancier, but would require many setattrs and getattrs
+class Results(TypedDict):
+    bfs: dict[str, dict[int, list[str]]]
+    sssp: dict[str, dict[int, list[str]]]
+    tc: dict[str, dict[int, list[str]]]
+
+
 def get_enabled_matrices(matrices_spec_path: Path) -> list[Matrix]:
     matrices: List[Matrix] = Matrix.from_yaml_file(matrices_spec_path)  # type: ignore
     return list(filter(lambda matrix: matrix.enabled, matrices))
@@ -44,3 +59,97 @@ def get_unique_by_name_matrices(matrices: list[Matrix]) -> list[Matrix]:
 
 def get_matrix_base_name(matrix: Matrix) -> str:
     return matrix.name + ("_reordered" if matrix.reorder else "")
+
+
+def get_matrix_filename_mtx(matrix: Matrix) -> str:
+    return get_matrix_base_name(matrix) + ".mtx"
+
+
+def comma_separated_str_to_int_list(str: str | None) -> list[int] | None:
+    if str is None:
+        return None
+    else:
+        tmp = list(map(lambda x: int(x), str.split(",")))
+        return tmp
+
+
+def run_tool_many_times(
+    matrix: Matrix,
+    thread_count: int,
+    run_count: int,
+    run_tool: RunToolCallable,
+    **kwargs,
+):
+    results = []
+    logging.info("Running with %s threads", thread_count)
+    for i in range(run_count):
+        logging.info("Starting run %s", i)
+        result = run_tool(matrix, thread_count, **kwargs)
+        if result.returncode != 0:
+            logging.warning(
+                "Process %s exited with code %s",
+                result.args,
+                result.returncode,
+            )
+        results.append(result.stdout)
+    return results
+
+
+def run_benchmark(
+    matrix: Matrix,
+    thread_counts: list[int] | None,
+    run_count: int,
+    run_tool: RunToolCallable,
+    **kwargs,
+):
+    if thread_counts is None:
+        nproc = os.cpu_count()
+        if nproc is None:
+            raise RuntimeError("Cannot get nproc")
+        thread_counts = [1] + list(range(2, nproc + 1, 2))
+
+    result: dict[int, list[str]] = dict()
+
+    for thread_count in thread_counts:
+        result[thread_count] = run_tool_many_times(
+            matrix, thread_count, run_count, run_tool, **kwargs
+        )
+
+    return result
+
+
+def run_benchmarks(
+    matrices: list[Matrix],
+    thread_counts: list[int] | None,
+    run_count: int,
+    run_tool: RunToolCallable,
+    **kwargs,
+):
+    results: Results = {
+        "bfs": dict(),
+        "sssp": dict(),
+        "tc": dict(),
+    }
+
+    for matrix in matrices:
+        base_name = get_matrix_base_name(matrix)
+        logging.info("Benchmarking %s on %s", matrix.algorithm, base_name)
+        results[str(matrix.algorithm)][base_name] = run_benchmark(
+            matrix, thread_counts, run_count, run_tool, **kwargs
+        )
+
+    return results
+
+
+def write_results(results: Results, raw_results_path: Path, tool: Tool):
+    raw_results_path.mkdir(parents=True, exist_ok=True)
+    results_path = raw_results_path / (
+        datetime.now().astimezone().isoformat(timespec="minutes")
+        + "_"
+        + str(tool)
+        + ".json"
+    )
+    with open(results_path, "w", encoding="utf-8") as r_file:
+        json.dump(results, r_file)
+
+    logging.info("Successfully wrote results to %s", results_path)
diff --git a/src/type_aliases.py b/src/type_aliases.py
index 2bde500..be802f4 100644
--- a/src/type_aliases.py
+++ b/src/type_aliases.py
@@ -4,7 +4,7 @@
 import typer
 
 
-type FilePathOption = Annotated[
+FilePathOption = Annotated[
     Path,
     typer.Option(
         exists=True,
@@ -15,7 +15,7 @@
     ),
 ]
 
-type DirPathOption = Annotated[
+DirPathOption = Annotated[
     Path,
     typer.Option(
         file_okay=False,

From 3856e92d97b35bdc0eb504fc0592746650c5de49 Mon Sep 17 00:00:00 2001
From: Nick Ponomarev <wowasterdev@gmail.com>
Date: Sun, 28 Jun 2026 20:56:29 +0300
Subject: [PATCH 08/11] Add get_enabled_matrices_for_tool helper

---
 src/benchmark/lagraph.py | 5 ++---
 src/common.py            | 7 +++++++
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/benchmark/lagraph.py b/src/benchmark/lagraph.py
index 33d1406..13f1814 100644
--- a/src/benchmark/lagraph.py
+++ b/src/benchmark/lagraph.py
@@ -9,7 +9,7 @@
     Matrix,
     Tool,
     comma_separated_str_to_int_list,
-    get_enabled_matrices,
+    get_enabled_matrices_for_tool,
     get_matrix_filename_mtx,
     run_benchmarks,
     write_results,
@@ -122,8 +122,7 @@ def lagraph(
     build_benchmarks(dependencies_path, lagraph_bench_path)
     log.info("Successfully built LAGraph")
 
-    matrices = get_enabled_matrices(matrices_spec_path)
-    matrices = list(filter(lambda matrix: Tool.LAGRAPH in matrix.tools, matrices))
+    matrices = get_enabled_matrices_for_tool(matrices_spec_path, Tool.LAGRAPH)
 
     # parser doesn't work
     # see https://github.com/fastapi/typer/discussions/1393
diff --git a/src/common.py b/src/common.py
index 6ebfa0f..c66d79f 100644
--- a/src/common.py
+++ b/src/common.py
@@ -53,6 +53,13 @@ def get_enabled_matrices(matrices_spec_path: Path) -> list[Matrix]:
     return list(filter(lambda matrix: matrix.enabled, matrices))
 
 
+def get_enabled_matrices_for_tool(matrices_spec_path: Path, tool: Tool) -> list[Matrix]:
+    matrices: List[Matrix] = Matrix.from_yaml_file(matrices_spec_path)  # type: ignore
+    return list(
+        filter(lambda matrix: matrix.enabled and (tool in matrix.tools), matrices)
+    )
+
+
 def get_unique_by_name_matrices(matrices: list[Matrix]) -> list[Matrix]:
     return list(unique(matrices, attrgetter("name")))
 

From af3d81dd5b5cb7d23be2398c8f88aaba7d1b0da2 Mon Sep 17 00:00:00 2001
From: Nick Ponomarev <wowasterdev@gmail.com>
Date: Sun, 28 Jun 2026 21:42:23 +0300
Subject: [PATCH 09/11] Add FSharp benchmark

---
 scripts/run_fsharp.py     | 210 --------------------------------------
 src/benchmark/__init__.py |   2 +
 src/benchmark/fsharp.py   | 171 +++++++++++++++++++++++++++++++
 src/common.py             |   2 +-
 4 files changed, 174 insertions(+), 211 deletions(-)
 delete mode 100644 scripts/run_fsharp.py
 create mode 100644 src/benchmark/fsharp.py

diff --git a/scripts/run_fsharp.py b/scripts/run_fsharp.py
deleted file mode 100644
index fe71093..0000000
--- a/scripts/run_fsharp.py
+++ /dev/null
@@ -1,210 +0,0 @@
-from datetime import datetime
-import json
-from pathlib import Path
-import re
-import subprocess
-from typing import Annotated
-
-import typer
-import yaml
-
-from common import BenchMatrix, BenchmarkType, get_matrix_filename_mtx
-
-
-def get_file_by_algorithm(fsharp_bench_path: Path, algorithm: BenchmarkType):
-    base = fsharp_bench_path / "QuadTree.Benchmark"
-    match algorithm:
-        case BenchmarkType.BFS:
-            return base / "BFS.fs"
-        case BenchmarkType.SSSP:
-            return base / "SSSP.fs"
-        case BenchmarkType.TC:
-            return base / "Triangles.fs"
-
-
-def clean_symlinks(fsharp_bench_path: Path):
-    data_dir = fsharp_bench_path / "QuadTree.Benchmark" / "data"
-    links_to_clean = data_dir.glob("*.mtx")
-    for file in links_to_clean:
-        file.unlink()
-        print("Cleaned", file)
-
-
-def symlink_matrices(
-    fsharp_matrices: list[BenchMatrix], matrices_path: Path, fsharp_bench_path: Path
-):
-    for matrix in fsharp_matrices:
-        file_path = matrices_path / get_matrix_filename_mtx(matrix)
-        dst_path = (
-            fsharp_bench_path
-            / "QuadTree.Benchmark"
-            / "data"
-            / get_matrix_filename_mtx(matrix)
-        )
-        dst_path.symlink_to(file_path)
-        print("Symlinked", file_path, "to", dst_path)
-
-
-def patch_benchmark(
-    fsharp_bench_path: Path,
-    fsharp_matrices: list[BenchMatrix],
-    algorithm: BenchmarkType,
-):
-    matrices = filter(lambda matrix: matrix["algorithm"] == algorithm, fsharp_matrices)
-    filenames_quoted = map(
-        lambda matrix: '"' + get_matrix_filename_mtx(matrix) + '"', matrices
-    )
-    filenames_str = "[<Params(" + ", ".join(filenames_quoted) + ")>]"
-    with open(
-        get_file_by_algorithm(fsharp_bench_path, algorithm), "r", encoding="utf-8"
-    ) as f:
-        file = f.read()
-    file_edited = re.sub(r"\[<Params\(.*\)>]", filenames_str, file)
-    with open(
-        get_file_by_algorithm(fsharp_bench_path, algorithm), "w", encoding="utf-8"
-    ) as f:
-        f.write(file_edited)
-    print(
-        "Patched",
-        get_file_by_algorithm(fsharp_bench_path, algorithm),
-        "with",
-        filenames_str,
-    )
-
-
-def patch_benchmarks(fsharp_bench_path: Path, fsharp_matrices: list[BenchMatrix]):
-    patch_benchmark(fsharp_bench_path, fsharp_matrices, BenchmarkType.BFS)
-    patch_benchmark(fsharp_bench_path, fsharp_matrices, BenchmarkType.SSSP)
-    patch_benchmark(fsharp_bench_path, fsharp_matrices, BenchmarkType.TC)
-
-
-def main(
-    matrices_spec_path: Annotated[
-        Path,
-        typer.Option(
-            exists=True,
-            file_okay=True,
-            dir_okay=False,
-            readable=True,
-            resolve_path=True,
-        ),
-    ] = Path("matrices.yaml"),
-    matrices_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("matrices"),
-    fsharp_bench_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("tools") / "QTreeFSharp",
-    raw_results_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("results") / "raw",
-    reset_tree: Annotated[bool, typer.Option()] = False,
-):
-    if reset_tree:
-        print("*** Reset QTreeFSharp ***")
-        subprocess.run(["git", "restore", "."], cwd=fsharp_bench_path, check=True)
-        print("")
-
-    with open(matrices_spec_path, "r", encoding="utf-8") as m_file:
-        matrices: list[BenchMatrix] = yaml.safe_load(m_file)
-    enabled_matrices = filter(lambda matrix: matrix["enabled"], matrices)
-    fsharp_matrices = list(
-        filter(lambda matrix: "fsharp" in matrix["tools"], enabled_matrices)
-    )
-
-    print("*** Cleaning symlinks ***")
-    clean_symlinks(fsharp_bench_path)
-    print("")
-
-    print("*** Symlinking matrices ***")
-    symlink_matrices(fsharp_matrices, matrices_path, fsharp_bench_path)
-    print("")
-
-    print("*** Patching benchmarks ***")
-    patch_benchmarks(fsharp_bench_path, fsharp_matrices)
-    print("")
-
-    print("*** Running experiments ***")
-    subprocess.run(
-        [
-            "dotnet",
-            "run",
-            "--configuration",
-            "Release",
-            "--project",
-            "QuadTree.Benchmark",
-            "--",
-            "--filter",
-            "*",
-            "--exporters",
-            "json",
-        ],
-        cwd=fsharp_bench_path,
-        check=True,
-    )
-    print("")
-
-    print("*** Writing results ***")
-    raw_results_path.mkdir(parents=True, exist_ok=True)
-    results_path = raw_results_path / (
-        datetime.now().astimezone().isoformat(timespec="minutes") + "_fsharp.json"
-    )
-    results = dict()
-
-    results_dir = fsharp_bench_path / "BenchmarkDotNet.Artifacts" / "results"
-    bfs_results_json = (
-        results_dir / "QuadTree.Benchmarks.BFS.Benchmark-report-full-compressed.json"
-    )
-    try:
-        with open(bfs_results_json, "r", encoding="utf-8") as f:
-            results["bfs"] = json.load(f)
-    except FileNotFoundError:
-        results["vfs"] = ""
-
-    sssp_results_json = (
-        results_dir / "QuadTree.Benchmarks.SSSP.Benchmark-report-full-compressed.json"
-    )
-    try:
-        with open(sssp_results_json, "r", encoding="utf-8") as f:
-            results["sssp"] = json.load(f)
-    except FileNotFoundError:
-        results["sssp"] = ""
-
-    tc_results_json = (
-        results_dir
-        / "QuadTree.Benchmarks.Triangles.Benchmark-report-full-compressed.json"
-    )
-    try:
-        with open(tc_results_json, "r", encoding="utf-8") as f:
-            results["tc"] = json.load(f)
-    except FileNotFoundError:
-        results["tc"] = ""
-
-    with open(results_path, "w", encoding="utf-8") as r_file:
-        json.dump(results, r_file)
-    print("Wrote to", str(results_path))
-
-
-if __name__ == "__main__":
-    typer.run(main)
diff --git a/src/benchmark/__init__.py b/src/benchmark/__init__.py
index 88d68ab..a65768c 100644
--- a/src/benchmark/__init__.py
+++ b/src/benchmark/__init__.py
@@ -1,7 +1,9 @@
 import typer
 
 from .lagraph import app as lagraph_app
+from .fsharp import app as fsharp_app
 
 app = typer.Typer(no_args_is_help=True)
 
 app.add_typer(lagraph_app)
+app.add_typer(fsharp_app)
diff --git a/src/benchmark/fsharp.py b/src/benchmark/fsharp.py
new file mode 100644
index 0000000..11c821e
--- /dev/null
+++ b/src/benchmark/fsharp.py
@@ -0,0 +1,171 @@
+import json
+import logging
+from pathlib import Path
+import re
+import subprocess
+from typing import Annotated
+
+import typer
+
+from ..common import (
+    Algorithm,
+    Matrix,
+    Tool,
+    get_enabled_matrices_for_tool,
+    get_matrix_filename_mtx,
+    get_unique_by_name_matrices,
+    write_results,
+    Results,
+)
+from ..type_aliases import DirPathOption, FilePathOption
+
+app = typer.Typer()
+log = logging.getLogger("rich")
+
+
+DOTNETBENCHMARK_RUN_COMMAND = [
+    "dotnet",
+    "run",
+    "--configuration",
+    "Release",
+    "--project",
+    "QuadTree.Benchmark",
+    "--",
+    "--filter",
+    "*",
+    "--exporters",
+    "json",
+]
+
+
+def get_fsharp_algorithm_name(algorithm: Algorithm) -> str:
+    match algorithm:
+        case Algorithm.BFS:
+            return "BFS"
+        case Algorithm.SSSP:
+            return "SSSP"
+        case Algorithm.TC:
+            return "Triangles"
+
+
+def get_benchmark_project_path(fsharp_bench_path: Path) -> Path:
+    return fsharp_bench_path / "QuadTree.Benchmark"
+
+
+def get_benchmark_project_data_path(fsharp_bench_path: Path) -> Path:
+    return get_benchmark_project_path(fsharp_bench_path) / "data"
+
+
+def clean_symlinks(fsharp_bench_path: Path) -> None:
+    data_dir = get_benchmark_project_data_path(fsharp_bench_path)
+    links_to_clean = data_dir.glob("*.mtx")
+    for file in links_to_clean:
+        log.info("Removing %s", file)
+        file.unlink()
+
+
+def symlink_matrices(
+    matrices: list[Matrix], matrices_path: Path, fsharp_bench_path: Path
+) -> None:
+    matrices_unique = get_unique_by_name_matrices(matrices)
+    for matrix in matrices_unique:
+        file_path = matrices_path / get_matrix_filename_mtx(matrix)
+        dst_path = get_benchmark_project_data_path(
+            fsharp_bench_path
+        ) / get_matrix_filename_mtx(matrix)
+        log.info("Symlinking %s to %s", file_path, dst_path)
+        dst_path.symlink_to(file_path)
+
+
+def get_file_by_algorithm(fsharp_bench_path: Path, algorithm: Algorithm) -> Path:
+    return get_benchmark_project_path(fsharp_bench_path) / (
+        get_fsharp_algorithm_name(algorithm) + ".fs"
+    )
+
+
+def patch_benchmark(
+    matrices: list[Matrix], fsharp_bench_path: Path, algorithm: Algorithm
+) -> None:
+    matrices_t = filter(lambda matrix: matrix.algorithm == algorithm, matrices)
+    filenames_quoted = map(
+        lambda matrix: '"' + get_matrix_filename_mtx(matrix) + '"', matrices_t
+    )
+    filenames_str = "[<Params(" + ", ".join(filenames_quoted) + ")>]"
+    file_to_path = get_file_by_algorithm(fsharp_bench_path, algorithm)
+    with open(file_to_path, "r", encoding="utf-8") as f:
+        file = f.read()
+    file_edited = re.sub(r"\[<Params\(.*\)>]", filenames_str, file)
+    log.info(
+        "Patching %s with %s",
+        file_to_path,
+        filenames_str,
+    )
+    with open(file_to_path, "w", encoding="utf-8") as f:
+        f.write(file_edited)
+
+
+def patch_benchmarks(matrices: list[Matrix], fsharp_bench_path: Path) -> None:
+    for algorithm in Algorithm:
+        patch_benchmark(matrices, fsharp_bench_path, algorithm)
+
+
+def collect_result_of_algorithm(
+    results: Results, fsharp_bench_path: Path, algorithm: Algorithm
+) -> None:
+    log.info("Collecting %s results", algorithm.name)
+    results_dir = fsharp_bench_path / "BenchmarkDotNet.Artifacts" / "results"
+    results_json = results_dir / (
+        "QuadTree.Benchmarks."
+        + get_fsharp_algorithm_name(algorithm)
+        + ".Benchmark-report-full-compressed.json"
+    )
+    try:
+        with open(results_json, "r", encoding="utf-8") as f:
+            results[str(algorithm)] = json.load(f)
+    except FileNotFoundError:
+        results[str(algorithm)] = ""
+
+
+def collect_results(results: Results, fsharp_bench_path: Path) -> None:
+    for algorithm in Algorithm:
+        collect_result_of_algorithm(results, fsharp_bench_path, algorithm)
+
+
+@app.command()
+def fsharp(
+    matrices_spec_path: FilePathOption = Path("matrices.yaml"),
+    matrices_path: DirPathOption = Path("matrices"),
+    fsharp_bench_path: DirPathOption = Path("tools") / "QTreeFSharp",
+    raw_results_path: DirPathOption = Path("results") / "raw",
+    clean_benchmark: Annotated[bool, typer.Option()] = False,
+):
+    if clean_benchmark:
+        log.info("Cleaning QTreeFSharp")
+        subprocess.run(["git", "restore", "."], cwd=fsharp_bench_path, check=True)
+
+    matrices = get_enabled_matrices_for_tool(matrices_spec_path, Tool.FSHARP)
+
+    log.info("Removing matrices in QTreeFSharp")
+    clean_symlinks(fsharp_bench_path)
+
+    log.info("Symlinking matrices to QTreeFSharp")
+    symlink_matrices(matrices, matrices_path, fsharp_bench_path)
+
+    log.info("Enabling matrices in QTreeFSharp")
+    patch_benchmarks(matrices, fsharp_bench_path)
+
+    log.info("Starting QTreeFSharp benchmark")
+    subprocess.run(
+        DOTNETBENCHMARK_RUN_COMMAND,
+        cwd=fsharp_bench_path,
+        check=True,
+    )
+
+    results: Results = {
+        "bfs": dict(),
+        "sssp": dict(),
+        "tc": dict(),
+    }
+    collect_results(results, fsharp_bench_path)
+
+    write_results(results, raw_results_path, Tool.FSHARP)
diff --git a/src/common.py b/src/common.py
index c66d79f..448a9a1 100644
--- a/src/common.py
+++ b/src/common.py
@@ -157,6 +157,6 @@ def write_results(results: Results, raw_results_path: Path, tool: Tool):
         + ".json"
     )
     with open(results_path, "w", encoding="utf-8") as r_file:
-        json.dump(results, r_file)
+        json.dump(results, r_file, indent=4)
 
     logging.info("Successfully wrote results to %s", results_path)

From b9a9a875654f12748b1dbb1e35dfd171aef53786 Mon Sep 17 00:00:00 2001
From: Nick Ponomarev <wowasterdev@gmail.com>
Date: Sun, 28 Jun 2026 22:02:17 +0300
Subject: [PATCH 10/11] Add NetworkX benchmark

---
 scripts/run_networkx.py   | 128 --------------------------------------
 src/benchmark/__init__.py |   2 +
 src/benchmark/networkx.py |  69 ++++++++++++++++++++
 3 files changed, 71 insertions(+), 128 deletions(-)
 delete mode 100644 scripts/run_networkx.py
 create mode 100644 src/benchmark/networkx.py

diff --git a/scripts/run_networkx.py b/scripts/run_networkx.py
deleted file mode 100644
index 845700b..0000000
--- a/scripts/run_networkx.py
+++ /dev/null
@@ -1,128 +0,0 @@
-from datetime import datetime
-from pathlib import Path
-import shutil
-import subprocess
-from typing import Annotated
-
-import typer
-import yaml
-
-from common import BenchMatrix, get_matrix_filename_mtx
-
-
-def prepare_environment(nx_bench_path: Path):
-    subprocess.run(["uv", "sync"], cwd=nx_bench_path, check=True)
-
-
-def clean_symlinks(nx_bench_path: Path):
-    bfs_to_clean = (nx_bench_path / "bfs").glob("**/*.mtx")
-    for file in bfs_to_clean:
-        file.unlink()
-        print("Cleaned", file)
-    sssp_to_clean = (nx_bench_path / "sssp").glob("**/*.mtx")
-    for file in sssp_to_clean:
-        file.unlink()
-        print("Cleaned", file)
-    tc_to_clean = (nx_bench_path / "tc").glob("**/*.mtx")
-    for file in tc_to_clean:
-        file.unlink()
-        print("Cleaned", file)
-
-
-def symlink_matrices(
-    matrices_spec_path: Path, matrices_path: Path, nx_bench_path: Path
-):
-    with open(matrices_spec_path, "r", encoding="utf-8") as m_file:
-        matrices: list[BenchMatrix] = yaml.safe_load(m_file)
-    enabled_matrices = filter(lambda matrix: matrix["enabled"], matrices)
-    networkx_matrices = filter(
-        lambda matrix: "networkx" in matrix["tools"], enabled_matrices
-    )
-    for matrix in networkx_matrices:
-        file_path = matrices_path / get_matrix_filename_mtx(matrix)
-        dst_path = (
-            nx_bench_path / (matrix["algorithm"]) / get_matrix_filename_mtx(matrix)
-        )
-        dst_path.symlink_to(file_path)
-        print("Symlinked", file_path, "to", dst_path)
-
-
-def run_benchmarks(nx_bench_path: Path):
-    subprocess.run(["uv", "run", "pytest"], cwd=nx_bench_path, check=True)
-
-
-def main(
-    matrices_spec_path: Annotated[
-        Path,
-        typer.Option(
-            exists=True,
-            file_okay=True,
-            dir_okay=False,
-            readable=True,
-            resolve_path=True,
-        ),
-    ] = Path("matrices.yaml"),
-    matrices_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("matrices"),
-    nx_bench_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("tools/nx-benchmarks"),
-    raw_results_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("results") / "raw",
-):
-    print("*** Preparing NetworkX ***")
-    prepare_environment(nx_bench_path)
-    print("")
-
-    print("*** Cleaning symlinks ***")
-    clean_symlinks(nx_bench_path)
-    print("")
-
-    print("*** Symlinking matrices ***")
-    symlink_matrices(matrices_spec_path, matrices_path, nx_bench_path)
-    print("")
-
-    print("*** Running experiments ***")
-    run_benchmarks(nx_bench_path)
-    print("")
-
-    print("*** Writing results ***")
-    json_files = sorted(
-        (nx_bench_path / "results").glob("**/*.json"),
-        key=lambda p: p.stat().st_mtime,
-        reverse=True,
-    )
-    latest_json = json_files[0]
-    raw_results_path.mkdir(parents=True, exist_ok=True)
-    results_path = raw_results_path / (
-        datetime.now().astimezone().isoformat(timespec="minutes") + "_networkx.json"
-    )
-    shutil.copy(latest_json, results_path)
-    print("Wrote to", str(results_path))
-
-
-if __name__ == "__main__":
-    typer.run(main)
diff --git a/src/benchmark/__init__.py b/src/benchmark/__init__.py
index a65768c..9e8e643 100644
--- a/src/benchmark/__init__.py
+++ b/src/benchmark/__init__.py
@@ -2,8 +2,10 @@
 
 from .lagraph import app as lagraph_app
 from .fsharp import app as fsharp_app
+from .networkx import app as networkx_app
 
 app = typer.Typer(no_args_is_help=True)
 
 app.add_typer(lagraph_app)
 app.add_typer(fsharp_app)
+app.add_typer(networkx_app)
diff --git a/src/benchmark/networkx.py b/src/benchmark/networkx.py
new file mode 100644
index 0000000..3aaae37
--- /dev/null
+++ b/src/benchmark/networkx.py
@@ -0,0 +1,69 @@
+from datetime import datetime
+import logging
+from pathlib import Path
+import shutil
+import subprocess
+
+import typer
+
+from ..common import (
+    Matrix,
+    Tool,
+    get_enabled_matrices_for_tool,
+    get_matrix_filename_mtx,
+)
+from ..type_aliases import DirPathOption, FilePathOption
+
+app = typer.Typer()
+log = logging.getLogger("rich")
+
+
+def clean_symlinks(nx_bench_path: Path):
+    matrices_to_clean = nx_bench_path.glob("**/*.mtx")
+    for file in matrices_to_clean:
+        log.info("Removing %s", file)
+        file.unlink()
+
+
+def symlink_matrices(matrices: list[Matrix], matrices_path: Path, nx_bench_path: Path):
+    for matrix in matrices:
+        file_path = matrices_path / get_matrix_filename_mtx(matrix)
+        dst_path = nx_bench_path / (matrix.algorithm) / get_matrix_filename_mtx(matrix)
+        log.info("Symlinking %s to %s", file_path, dst_path)
+        dst_path.symlink_to(file_path)
+
+
+@app.command()
+def networkx(
+    matrices_spec_path: FilePathOption = Path("matrices.yaml"),
+    matrices_path: DirPathOption = Path("matrices"),
+    nx_bench_path: DirPathOption = Path("tools/nx-benchmarks"),
+    raw_results_path: DirPathOption = Path("results") / "raw",
+):
+    log.info("Setting up NetworkX")
+    subprocess.run(["uv", "sync"], cwd=nx_bench_path, check=True)
+
+    log.info("Removing matrices in NetworkX")
+    clean_symlinks(nx_bench_path)
+
+    matrices = get_enabled_matrices_for_tool(matrices_spec_path, Tool.NETWORKX)
+
+    log.info("Symlinking matrices to NetworkX")
+    symlink_matrices(matrices, matrices_path, nx_bench_path)
+
+    log.info("Starting NetworkX benchmark")
+    subprocess.run(["uv", "run", "pytest"], cwd=nx_bench_path, check=True)
+
+    json_files = sorted(
+        (nx_bench_path / "results").glob("**/*.json"),
+        key=lambda p: p.stat().st_mtime,
+        reverse=True,
+    )
+    latest_json = json_files[0]
+    raw_results_path.mkdir(parents=True, exist_ok=True)
+    results_path = raw_results_path / (
+        datetime.now().astimezone().isoformat(timespec="minutes") + "_networkx.json"
+    )
+    shutil.copy(latest_json, results_path)
+
+    logging.info("Successfully wrote results to %s", results_path)

From c90d1bb53a4d2e4b8cba09209ee45d8f4556cf28 Mon Sep 17 00:00:00 2001
From: Nick Ponomarev <wowasterdev@gmail.com>
Date: Tue, 30 Jun 2026 16:26:41 +0300
Subject: [PATCH 11/11] Add inpla benchmark

---
 scripts/run_inpla.py      | 297 --------------------------------------
 src/benchmark/__init__.py |   2 +
 src/benchmark/inpla.py    | 137 ++++++++++++++++++
 src/common.py             |   4 +
 4 files changed, 143 insertions(+), 297 deletions(-)
 delete mode 100644 scripts/run_inpla.py
 create mode 100644 src/benchmark/inpla.py

diff --git a/scripts/run_inpla.py b/scripts/run_inpla.py
deleted file mode 100644
index 6487e8e..0000000
--- a/scripts/run_inpla.py
+++ /dev/null
@@ -1,297 +0,0 @@
-from datetime import datetime
-import json
-import os
-from pathlib import Path
-import resource
-import subprocess
-from typing import Annotated
-
-import typer
-import yaml
-
-from common import (
-    BenchMatrix,
-    get_matrix_base_name,
-    get_matrix_filename_in,
-    get_matrix_filename_mtx,
-)
-
-
-def make_inpla(inpla_path: Path):
-    subprocess.run(["make", "clean"], cwd=inpla_path, check=True)
-    subprocess.run(["make"], cwd=inpla_path, check=True)
-    subprocess.run(["make", "clean"], cwd=inpla_path, check=True)
-    subprocess.run(["make", "thread"], cwd=inpla_path, check=True)
-
-
-def check_inpla(inpla_path: Path, inpla_bench_path: Path):
-    subprocess.run(
-        ["dotnet", "fsi", "test.fsx", inpla_path / "inpla"],
-        cwd=inpla_bench_path,
-        check=True,
-    )
-
-
-def convert_matrix_to_inpla(
-    matrix: BenchMatrix,
-    matrices_path: Path,
-    inpla_bench_path: Path,
-):
-    subprocess.run(
-        [
-            Path("scripts") / "mtx_to_experiment.fsx",
-            matrices_path / get_matrix_filename_mtx(matrix),
-            matrix["algorithm"],
-        ],
-        cwd=inpla_bench_path,
-        check=True,
-    )
-
-
-def convert_matrices_to_inpla(
-    inpla_matrices: list[BenchMatrix],
-    matrices_path: Path,
-    inpla_bench_path: Path,
-):
-
-    for matrix in inpla_matrices:
-        convert_matrix_to_inpla(matrix, matrices_path, inpla_bench_path)
-
-
-def run_inpla(
-    inpla_path: Path,
-    inpla_bench_path: Path,
-    thread_count: int,
-    matrix_path: Path,
-    memory_limit_for_1_thread: int,
-) -> str:
-    resource.setrlimit(
-        resource.RLIMIT_STACK, (resource.RLIM_INFINITY, resource.RLIM_INFINITY)
-    )
-    run_res = subprocess.run(
-        [
-            inpla_path / "inpla",
-            "-t",
-            str(thread_count),
-            "-f",
-            matrix_path,
-            "-Xms",
-            str(memory_limit_for_1_thread // thread_count),
-        ],
-        cwd=inpla_bench_path,
-        capture_output=True,
-        text=True,
-    )
-    if run_res.returncode != 0:
-        print(
-            "Process",
-            run_res.args,
-            "exited with code",
-            run_res.returncode,
-            end=" ",
-            flush=True,
-        )
-    return run_res.stdout
-
-
-def run_inpla_many_times(
-    inpla_path: Path,
-    inpla_bench_path: Path,
-    run_count: int,
-    thread_count: int,
-    matrix_path: Path,
-    memory_limit_for_1_thread: int,
-) -> list[str]:
-    result = []
-    print("Running with", thread_count, "threads. Run: ", end="")
-    for i in range(run_count):
-        print(i + 1, "...", sep="", end="", flush=True)
-        result.append(
-            run_inpla(
-                inpla_path,
-                inpla_bench_path,
-                thread_count,
-                matrix_path,
-                memory_limit_for_1_thread,
-            )
-        )
-    print("")
-    return result
-
-
-def run_experiment(
-    inpla_path: Path,
-    inpla_bench_path: Path,
-    run_count: int,
-    thread_count: int,
-    matrix_path: Path,
-    memory_limit_for_1_thread: int,
-) -> dict[int, list[str]]:
-    if thread_count <= 0:
-        result = dict()
-
-        nproc = os.cpu_count()
-        if nproc is None:
-            raise RuntimeError("Cannot get nproc")
-        thread_counts = [1] + list(range(2, nproc + 1, 2))
-
-        for thread_count in thread_counts:
-            result[thread_count] = run_inpla_many_times(
-                inpla_path,
-                inpla_bench_path,
-                run_count,
-                thread_count,
-                matrix_path,
-                memory_limit_for_1_thread,
-            )
-
-        return result
-    else:
-        result = run_inpla_many_times(
-            inpla_path,
-            inpla_bench_path,
-            run_count,
-            thread_count,
-            matrix_path,
-            memory_limit_for_1_thread,
-        )
-        return {thread_count: result}
-
-
-def run_experiments(
-    inpla_path: Path,
-    inpla_bench_path: Path,
-    run_count: int,
-    thread_count: int,
-    inpla_matrices: list[BenchMatrix],
-    memory_limit_for_1_thread: int,
-):
-    results: dict[str, dict[str, dict[int, list[str]]]] = {
-        "bfs": dict(),
-        "sssp": dict(),
-        "tc": dict(),
-    }
-    for matrix in inpla_matrices:
-        filename_base = get_matrix_base_name(matrix)
-        matrix_path = (
-            inpla_bench_path
-            / ("experiments_" + matrix["algorithm"])
-            / get_matrix_filename_in(matrix)
-        )
-        print("Benchmarking", matrix["algorithm"], "on", filename_base)
-        results[matrix["algorithm"]][filename_base] = run_experiment(
-            inpla_path,
-            inpla_bench_path,
-            run_count,
-            thread_count,
-            matrix_path,
-            memory_limit_for_1_thread,
-        )
-        print("")
-
-    return results
-
-
-def main(
-    matrices_spec_path: Annotated[
-        Path,
-        typer.Option(
-            exists=True,
-            file_okay=True,
-            dir_okay=False,
-            readable=True,
-            resolve_path=True,
-        ),
-    ] = Path("matrices.yaml"),
-    matrices_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("matrices"),
-    inpla_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("dependencies") / "inpla",
-    inpla_bench_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("tools") / "QTreeInpla",
-    raw_results_path: Annotated[
-        Path,
-        typer.Option(
-            file_okay=False,
-            dir_okay=True,
-            readable=True,
-            writable=True,
-            resolve_path=True,
-        ),
-    ] = Path("results") / "raw",
-    check: Annotated[bool, typer.Option()] = False,
-    run_count: Annotated[int, typer.Option] = 5,
-    thread_count: Annotated[int, typer.Option] = 0,
-    memory_limit_for_1_thread: Annotated[
-        int,
-        typer.Option(
-            help="Compute by formula ((desired heap size in GiB) * 2**30 / (88+16) / 1.2), default for 128 GiB machines"
-        ),
-    ] = 1032444062,
-):
-    print("*** Making inpla ***")
-    make_inpla(inpla_path)
-    print("")
-    if check:
-        print("*** Checking inpla ***")
-        check_inpla(inpla_path, inpla_bench_path)
-        print("")
-
-    with open(matrices_spec_path, "r", encoding="utf-8") as m_file:
-        matrices: list[BenchMatrix] = yaml.safe_load(m_file)
-    enabled_matrices = filter(lambda matrix: matrix["enabled"], matrices)
-    inpla_matrices = list(
-        filter(lambda matrix: "inpla" in matrix["tools"], enabled_matrices)
-    )
-
-    print("*** Converting matrices for inpla ***")
-    convert_matrices_to_inpla(inpla_matrices, matrices_path, inpla_bench_path)
-    print("")
-
-    print("*** Running experiments ***")
-    results = run_experiments(
-        inpla_path,
-        inpla_bench_path,
-        run_count,
-        thread_count,
-        inpla_matrices,
-        memory_limit_for_1_thread,
-    )
-    print("")
-
-    print("*** Writing results ***")
-    raw_results_path.mkdir(parents=True, exist_ok=True)
-    results_path = raw_results_path / (
-        datetime.now().astimezone().isoformat(timespec="minutes") + "_inpla.json"
-    )
-    with open(results_path, "w", encoding="utf-8") as r_file:
-        json.dump(results, r_file)
-    print("Wrote to", str(results_path))
-
-
-if __name__ == "__main__":
-    typer.run(main)
diff --git a/src/benchmark/__init__.py b/src/benchmark/__init__.py
index 9e8e643..dc601c9 100644
--- a/src/benchmark/__init__.py
+++ b/src/benchmark/__init__.py
@@ -3,9 +3,11 @@
 from .lagraph import app as lagraph_app
 from .fsharp import app as fsharp_app
 from .networkx import app as networkx_app
+from .inpla import app as inpla_app
 
 app = typer.Typer(no_args_is_help=True)
 
 app.add_typer(lagraph_app)
 app.add_typer(fsharp_app)
 app.add_typer(networkx_app)
+app.add_typer(inpla_app)
diff --git a/src/benchmark/inpla.py b/src/benchmark/inpla.py
new file mode 100644
index 0000000..f852adf
--- /dev/null
+++ b/src/benchmark/inpla.py
@@ -0,0 +1,137 @@
+import logging
+from pathlib import Path
+import resource
+import subprocess
+from typing import Annotated
+
+import typer
+
+
+from ..common import (
+    Matrix,
+    Tool,
+    comma_separated_str_to_int_list,
+    get_enabled_matrices_for_tool,
+    get_matrix_filename_in,
+    get_matrix_filename_mtx,
+    run_benchmarks,
+    write_results,
+)
+from ..type_aliases import DirPathOption, FilePathOption
+
+app = typer.Typer()
+log = logging.getLogger("rich")
+
+
+def make_inpla(inpla_path: Path) -> None:
+    subprocess.run(["make", "clean"], cwd=inpla_path, check=True)
+    subprocess.run(["make"], cwd=inpla_path, check=True)
+    subprocess.run(["make", "clean"], cwd=inpla_path, check=True)
+    subprocess.run(["make", "thread"], cwd=inpla_path, check=True)
+
+
+def check_inpla(inpla_path: Path, inpla_bench_path: Path) -> None:
+    subprocess.run(
+        ["dotnet", "fsi", "test.fsx", inpla_path / "inpla"],
+        cwd=inpla_bench_path,
+        check=True,
+    )
+
+
+def convert_matrices_to_inpla(
+    inpla_matrices: list[Matrix],
+    matrices_path: Path,
+    inpla_bench_path: Path,
+) -> None:
+    for matrix in inpla_matrices:
+        subprocess.run(
+            [
+                Path("scripts") / "mtx_to_experiment.fsx",
+                matrices_path / get_matrix_filename_mtx(matrix),
+                matrix.algorithm,
+            ],
+            cwd=inpla_bench_path,
+            check=True,
+        )
+
+
+def run_inpla(
+    matrix: Matrix,
+    thread_count: int,
+    *,
+    inpla_path: Path,
+    inpla_bench_path: Path,
+    memory_limit_for_1_thread: int,
+) -> subprocess.CompletedProcess[str]:
+    resource.setrlimit(
+        resource.RLIMIT_STACK, (resource.RLIM_INFINITY, resource.RLIM_INFINITY)
+    )
+    matrix_path = (
+        inpla_bench_path
+        / ("experiments_" + matrix.algorithm)
+        / get_matrix_filename_in(matrix)
+    )
+    return subprocess.run(
+        [
+            inpla_path / "inpla",
+            "-t",
+            str(thread_count),
+            "-f",
+            matrix_path,
+            "-Xms",
+            str(memory_limit_for_1_thread // thread_count),
+        ],
+        cwd=inpla_bench_path,
+        capture_output=True,
+        text=True,
+    )
+
+
+@app.command()
+def inpla(
+    matrices_spec_path: FilePathOption = Path("matrices.yaml"),
+    matrices_path: DirPathOption = Path("matrices"),
+    inpla_path: DirPathOption = Path("dependencies") / "inpla",
+    inpla_bench_path: DirPathOption = Path("tools") / "QTreeInpla",
+    raw_results_path: DirPathOption = Path("results") / "raw",
+    check: Annotated[bool, typer.Option()] = False,
+    run_count: Annotated[int, typer.Option] = 5,
+    thread_counts: Annotated[str | None, typer.Option()] = None,
+    memory_limit_for_1_thread: Annotated[
+        int,
+        typer.Option(
+            help="Compute by formula ((desired heap size in GiB) * 2**30 / (88+16) / 1.2), default for 128 GiB machines"
+        ),
+    ] = 1032444062,
+):
+    logging.info("Building inpla")
+    make_inpla(inpla_path)
+    logging.info("Successfully built inpla")
+
+    if check:
+        logging.info("Checking inpla")
+        check_inpla(inpla_path, inpla_bench_path)
+        logging.info("Successfully checked inpla")
+
+    matrices = get_enabled_matrices_for_tool(matrices_spec_path, Tool.INPLA)
+
+    logging.info("Converting matrices for inpla")
+    convert_matrices_to_inpla(matrices, matrices_path, inpla_bench_path)
+
+    # parser doesn't work
+    # see https://github.com/fastapi/typer/discussions/1393
+    thread_counts_t = comma_separated_str_to_int_list(thread_counts)
+    logging.info(
+        "Starting inpla benchmarks with thread counts: %s",
+        thread_counts_t,
+    )
+    results = run_benchmarks(
+        matrices,
+        thread_counts_t,
+        run_count,
+        run_inpla,
+        inpla_path=inpla_path,
+        inpla_bench_path=inpla_bench_path,
+        memory_limit_for_1_thread=memory_limit_for_1_thread,
+    )
+    write_results(results, raw_results_path, Tool.INPLA)
diff --git a/src/common.py b/src/common.py
index 448a9a1..eded1a8 100644
--- a/src/common.py
+++ b/src/common.py
@@ -72,6 +72,10 @@ def get_matrix_filename_mtx(matrix: Matrix) -> str:
     return get_matrix_base_name(matrix) + ".mtx"
 
 
+def get_matrix_filename_in(matrix: Matrix) -> str:
+    return get_matrix_base_name(matrix) + ".in"
+
+
 def comma_separated_str_to_int_list(str: str | None) -> list[int] | None:
     if str is None:
         return None