PDM + Meson Build System

.gitattributes

@@ -1,2 +1 @@
-poetry.lock linguist-generated=true
-src/cynetdiff/models.cpp linguist-generated=true
+pdm.lock linguist-generated=true

.github/workflows/benchmark.yml

@@ -8,28 +8,19 @@ on:
     branches: ["*"]
 
 jobs:
-  build:
+  benchmark:
     runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ["3.12"]
-        poetry-version: ["1.8.5"]
-
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - uses: abatilo/actions-poetry@v2
+      - name: Setup PDM
+        uses: pdm-project/setup-pdm@v4
         with:
-          poetry-version: ${{ matrix.poetry-version }}
+          python-version: "3.12"
+          cache: true
 
       - name: Install dependencies
-        run: poetry install --with dev,benchmark
+        run: pdm install -G test,build
 
-      - name: Benchmark with pytest-benchmark
-        run: poetry run pytest --benchmark-only --benchmark-warmup-iterations=0 benchmarks/test_benchmark.py
+      - name: Run benchmarks
+        run: pdm run pytest benchmarks

.github/workflows/docs.yml

@@ -1,9 +1,10 @@
 name: docs
 # Based on https://squidfunk.github.io/mkdocs-material/publishing-your-site/
 on:
-  push:
-    tags:
-      - "v*.*.*"
+  workflow_dispatch:
+  release:
+    types:
+      - published
 permissions:
   contents: write
 jobs:
@@ -16,17 +17,14 @@ jobs:
           git config user.name github-actions[bot]
           git config user.email 41898282+github-actions[bot]@users.noreply.github.com
       - uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
-      - uses: abatilo/actions-poetry@v2
-        with:
-          poetry-version: 1.8.2
+      - name: Setup PDM
+        uses: pdm-project/setup-pdm@v4
       - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
       - uses: actions/cache@v3
         with:
           key: mkdocs-material-${{ env.cache_id }}
           path: .cache
           restore-keys: |
             mkdocs-material-
-      - run: poetry install --with docs
-      - run: poetry run mkdocs gh-deploy --force
+      - run: pdm install -G docs --no-self
+      - run: pdm run mkdocs gh-deploy --force

.github/workflows/lint.yml

@@ -10,35 +10,28 @@ on:
     branches: ["*"]
 
 jobs:
-  ci:
-    strategy:
-      matrix:
-        python-version: ["3.12"]
-        poetry-version: ["1.8.1"]
-        os: [ubuntu-latest]
-    runs-on: ${{ matrix.os }}
+  lint:
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-        with:
-          submodules: recursive
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
 
-      - uses: abatilo/actions-poetry@v2
+      - name: Setup PDM
+        uses: pdm-project/setup-pdm@v4
         with:
-          poetry-version: ${{ matrix.poetry-version }}
+          python-version: "3.10"
+          cache: true
+
       - name: Install dependencies
-        run: poetry install --with dev,benchmark
+        run: pdm install -G lint --no-self
 
       - name: Run ruff lint check
-        run: poetry run ruff check .
+        run: pdm run ruff check .
 
       - name: Run ruff format check
-        run: poetry run ruff format --check .
+        run: pdm run ruff format --check .
 
       - name: Run Cython lint
-        run: poetry run cython-lint .
+        run: pdm run cython-lint .
 
       - name: Run mypy
-        run: poetry run mypy .
+        run: pdm run mypy .

.github/workflows/publish.yml

@@ -1,15 +1,63 @@
 # Automatically publishes version of the package on tagged release
+# Largely copied from https://learn.scientific-python.org/development/guides/gha-wheels/
 name: publish
 on:
-  push:
-    tags:
-      - "v*.*.*"
+  workflow_dispatch:
+  release:
+    types:
+      - published
+  pull_request:
+    paths:
+      - .github/workflows/publish.yml
+
 jobs:
-  build:
+  make_sdist:
+    name: Make SDist
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Build and publish to pypi
-        uses: JRubics/[email protected]
+
+      - name: Build SDist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
         with:
-          pypi_token: ${{ secrets.PYPI_TOKEN }}
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  build_wheels:
+    name: Wheel on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # TODO add back windows-latest, when I can fix it
+        os: [ubuntu-latest, macos-13, macos-14]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v6
+
+      - uses: pypa/[email protected]
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}
+          path: wheelhouse/*.whl
+
+  upload_all:
+    needs: [build_wheels, make_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/tests.yml

@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: tests
 
 on:
@@ -10,28 +7,19 @@ on:
     branches: ["*"]
 
 jobs:
-  build:
+  test:
     runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
-        poetry-version: ["1.8.1"]
-
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - uses: abatilo/actions-poetry@v2
+      - name: Setup PDM
+        uses: pdm-project/setup-pdm@v4
         with:
-          poetry-version: ${{ matrix.poetry-version }}
+          python-version: "3.10"
+          cache: true
 
       - name: Install dependencies
-        run: poetry install --with dev
+        run: pdm install -G test,build
 
-      - name: Test with pytest
-        run: poetry run pytest
+      - name: Run tests
+        run: pdm run pytest

.gitignore

@@ -112,7 +112,11 @@ venv
 
 # Cython
 *.html
+*.cpp
+*.c
 
 speed/
 
 get_graph_hashes.py
+
+.pdm-python

.vscode/settings.json

@@ -12,6 +12,9 @@
     "editor.defaultFormatter": "tamasfe.even-better-toml",
     "editor.formatOnSave": true
   },
+  "[json][yaml]": {
+    "editor.formatOnSave": true
+  },
   "files.trimTrailingWhitespace": true,
   "files.insertFinalNewline": true,
   "files.trimFinalNewlines": true,

demo/demo_backend.py

@@ -300,7 +300,7 @@ def plot_num_nodes_activated(
                 )
                 for i in range(max_length)
             ]
-            lower_quartile, upper_quartile = zip(*iqr_values)
+            lower_quartile, upper_quartile = zip(*iqr_values, strict=True)
 
             for y in mean_infected:
                 plt.axhline(y=y, color=colors[idx], linestyle="--", alpha=0.2)

meson.build

@@ -0,0 +1,48 @@
+project('cynetdiff', 'cython', 'c',
+  meson_version : '>= 1.1',
+  default_options : ['warning_level=3']
+)
+
+python = import('python').find_installation('python3', pure: false)
+
+if python.language_version().version_compare('< 3.10')
+  error('Requires Python >= 3.10')
+endif
+
+python_dep = python.dependency()
+
+# https://numpy.org/doc/2.0/reference/random/examples/cython/meson.build.html
+_numpy_abs = run_command(python, ['-c',
+    'import os; os.chdir(".."); import numpy; print(os.path.abspath(numpy.get_include() + "../../.."))'],
+    check: true).stdout().strip()
+
+cc = meson.get_compiler('c')
+
+npymath_path = _numpy_abs / '_core' / 'lib'
+npy_include_path = _numpy_abs / '_core' / 'include'
+npyrandom_path = _numpy_abs / 'random' / 'lib'
+npymath_lib = cc.find_library('npymath', dirs: npymath_path)
+npyrandom_lib = cc.find_library('npyrandom', dirs: npyrandom_path)
+
+numpy_dep = dependency('numpy', required: true)
+
+package_name = 'cynetdiff'
+# Path to your Python package sources relative to meson.build
+package_source_dir = 'src' / package_name
+
+# Install the Cython extension module
+python.extension_module(
+    'models',
+    package_source_dir / 'models.pyx',
+    dependencies: [npyrandom_lib, python_dep, numpy_dep],
+    override_options : ['cython_language=cpp'],
+    install: true,
+    subdir: 'cynetdiff',
+    cpp_args: ['-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION', '-Wno-pedantic'],
+)
+
+# Install pure python files
+install_subdir(
+  package_source_dir,
+  install_dir: python.get_install_dir()
+)