Calculate the exact distance of binary codes with brute force in cyth…

…on (#211)

* add fast distance calculation for CSS codes with <= 64 qubits

* remove exact distance from surface code

* add pyx file forgotten before, also add > 64-qubit distance calculation

* choose distance method based on qubit number

* more distance calculations

* use c++

* revert to using c and fix array bug

* better test

* only brute-force distance up to n=64

* add cython distance calculation

* minor cleanup of _distance.pyx

* add type hint

* clean up build.py

* nit rearrangement

* typing fix

* rename functions

* ignore cython build artifacts

* fix typo

* fix typo

* typing fix and remove test.py file

* fix coverage

* modify error message to accomodate classical codes

* rename build.py to build-cython.py

* formatting fix

* add cython-lint options to pyproject.toml

* nit variable rename

* add calculation of distance for QuditCodes on <= 32 qubits

* fix coverage

* fix check for number of qubits

* remove debugging artifact

* typo fix

* one more typo

* rename get_gistance_subcode_64 to get_distance_sector_xz_64

* ctzll for gray code counter

* remove leading underscore from functions not accessible to python

* make rows_to_uint64 return a 2D array

* typecast

* type fix

* add comments

* add distance calculation for classical codes with arbitrary block lengths

* fix bug in QuditCode distance calculation

* add distance calculation for quantum codes with arbitrary block length

* some code rearranging

* balanced surface/toric codes

* Revert "balanced surface/toric codes"

This reverts commit 8d14312.

* properly balance surface and toric codes

* split off distance calculations by block length

* fix QuditCode distance calculation

* clean up weight_func construction

* renaming and comments

* add comment

* bugfix in QuditCode distance

* rename function

* add cython-lint to pyproject.toml

* more cleanup and helpful commenting

* add 128-bit classical code distance

* word

* minor bugfix for balanced CSS codes and warnings about runtime

* workflow update

* add cython language_level

* move language_level:3 and add comment

* increase timeout limit for the installation check

* fix string matching

.github/workflows/ci.yml

@@ -7,7 +7,7 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    types: [ opened, synchronize, reopened, ready_for_review ]  # these are the defaults, plus ready_for_review
+    types: [ opened, synchronize, reopened, ready_for_review ]  # defaults plus ready_for_review
     branches: [ main ]
   workflow_dispatch:
   workflow_call:
@@ -17,7 +17,7 @@ jobs:
     name: Installation check
     if: github.event.pull_request.draft == false
     runs-on: ubuntu-latest
-    timeout-minutes: 2
+    timeout-minutes: 3
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.11
@@ -27,7 +27,7 @@ jobs:
       - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
-          key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml', 'build-cython.py') }}
       - name: Install package and dependencies
         run: |
           python3 -m pip install --upgrade pip

.gitignore

@@ -20,3 +20,8 @@ __pycache__
 
 # sphinx documentation
 docs/build
+
+# cython build artifacts
+build
+*.c
+*.so

build-cython.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python3
+import os
+import shutil
+from distutils.command.build_ext import build_ext
+from distutils.core import Distribution, Extension
+
+import numpy
+from Cython.Build import cythonize
+
+
+def build_cython() -> None:
+    extension = Extension(
+        "*",
+        ["*/**/*.pyx"],
+        include_dirs=[numpy.get_include()],
+        extra_compile_args=["-O3", "-march=native", "-Wall"],
+    )
+    ext_modules = cythonize(extension, compiler_directives={"language_level": "3"})
+    distribution = Distribution(dict(ext_modules=ext_modules))
+
+    cmd = build_ext(distribution)
+    cmd.ensure_finalized()
+    cmd.run()
+
+    # copy *.so files to their respective *.pyx directories
+    for output in cmd.get_outputs():
+        relative_extension = os.path.relpath(output, cmd.build_lib)
+        shutil.copyfile(output, relative_extension)
+
+
+if __name__ == "__main__":
+    build_cython()

checks/pytest_.py

@@ -3,7 +3,14 @@
 
 import checks_superstaq
 
-EXCLUDE = ("checks/*.py", "experiments/*.py", "*/__init__.py", "docs/source/conf.py")
+EXCLUDE = (
+    "*/__init__.py",
+    "checks/*.py",
+    "examples/*.py",
+    "experiments/*.py",
+    "build-cython.py",
+    "docs/source/conf.py",
+)
 
 if __name__ == "__main__":
     exit(checks_superstaq.pytest_.run(*sys.argv[1:], exclude=EXCLUDE))

pyproject.toml

@@ -1,7 +1,11 @@
 [build-system]
-requires = ["poetry-core>=1.0.0"]
+requires = ["poetry-core>=1.0.0", "cython", "setuptools", "numpy"]
 build-backend = "poetry.core.masonry.api"
 
+[tool.poetry.build]
+generate-setup-file = false
+script = "build-cython.py"
+
 [tool.poetry]
 name = "qLDPC"
 version = "0.0.24"
@@ -23,7 +27,7 @@ classifiers = [
   "Topic :: Scientific/Engineering :: Mathematics",
   "Topic :: Scientific/Engineering :: Physics",
 ]
-include = ["qldpc/py.typed"]
+include = ["qldpc/py.typed", { path = "qldpc/**/*.so", format = "wheel" }]
 
 [tool.poetry.dependencies]
 python = "^3.10"
@@ -41,6 +45,7 @@ stim = ">=1.14.0"
 sympy = ">=1.12"
 
 checks-superstaq = { version = ">=0.5.34", optional = true }
+cython-lint = { version = ">=0.16.6", optional = true }
 
 [tool.poetry.extras]
 dev = ["checks-superstaq"]
@@ -75,3 +80,6 @@ exclude_lines = ["pragma: no cover", "if TYPE_CHECKING:"]
 
 [tool.coverage.run]
 include = ["./*"]
+
+[tool.cython-lint]
+max-line-length = 100