directedstructure 0.1.1__tar.gz

directedstructure-0.1.1/.copier-answers.yml

@@ -0,0 +1,14 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: 2025.11.21-25-gad4434f
+_src_path: gh:scientific-python/cookie
+backend: skbuild
+docs: sphinx
+email: mjerdee@santafe.edu
+full_name: Maximilian Jerdee
+license: MIT
+org: maxjerdee
+project_name: directedstructure
+project_short_description: Infer communities, hierarchies, and their connection in
+    directed graphs
+url: https://github.com/maxjerdee/directedstructure
+vcs: true

directedstructure-0.1.1/.git_archival.txt

@@ -0,0 +1,3 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

directedstructure-0.1.1/.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

directedstructure-0.1.1/.github/CONTRIBUTING.md

@@ -0,0 +1,77 @@
+See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed
+description of best practices for developing scientific packages.
+
+[spc-dev-intro]: https://learn.scientific-python.org/development/
+
+# Quick development
+
+The fastest way to start with development is to use nox. If you don't have nox,
+you can use `uvx nox` to run it without installing, or `uv tool install nox`. If
+you don't have uv, you can
+[install it a variety of ways](https://docs.astral.sh/uv/getting-started/installation/),
+including with pip, pipx, brew, and just downloading the binary (single file).
+
+To use, run `nox`. This will lint and test using every installed version of
+Python on your system, skipping ones that are not installed. You can also run
+specific jobs:
+
+```console
+$ nox -s lint  # Lint only
+$ nox -s tests  # Python tests
+$ nox -s docs  # Build and serve the docs
+$ nox -s build  # Make an SDist and wheel
+```
+
+Nox handles everything for you, including setting up an temporary virtual
+environment for each run.
+
+# Setting up a development environment manually
+
+You can set up a development environment by running:
+
+```bash
+uv sync
+```
+
+# Pre-commit
+
+You should prepare pre-commit or prek, which will help you by checking that
+commits pass required checks:
+
+```bash
+uv tool install pre-commit # or brew install pre-commit on macOS
+pre-commit install # Will install a pre-commit hook into the git repo
+```
+
+You can also/alternatively run `pre-commit run` (changes only) or
+`pre-commit run --all-files` to check even without installing the hook.
+
+# Testing
+
+Use pytest to run the unit checks:
+
+```bash
+uv run pytest
+```
+
+# Coverage
+
+Use pytest-cov to generate coverage reports:
+
+```bash
+uv run pytest --cov=directedstructure
+```
+
+# Building docs
+
+You can build and serve the docs using:
+
+```bash
+nox -s docs
+```
+
+You can build the docs only with:
+
+```bash
+nox -s docs --non-interactive
+```

directedstructure-0.1.1/.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

directedstructure-0.1.1/.github/release.yml

@@ -0,0 +1,5 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot[bot]
+      - pre-commit-ci[bot]

directedstructure-0.1.1/.github/workflows/cd.yml

@@ -0,0 +1,95 @@
+name: wheels
+
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+  pull_request:
+    paths:
+      - .github/workflows/cd.yml
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  make_sdist:
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Build SDist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v6
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  build_wheels:
+    name: Wheel on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+          - ubuntu-24.04-arm
+          - windows-latest
+          - windows-11-arm
+          - macos-15-intel
+          - macos-latest
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - uses: astral-sh/setup-uv@v7
+
+      - uses: pypa/cibuildwheel@v3.3
+        env:
+          CIBW_BUILD: cp310-* cp311-* cp312-* cp313-*
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: wheelhouse/*.whl
+
+  upload_all:
+    needs: [build_wheels, make_sdist]
+    environment: pypi
+    permissions:
+      id-token: write
+      attestations: write
+      contents: read
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/download-artifact@v7
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - name: Generate artifact attestations
+        uses: actions/attest-build-provenance@v3
+        with:
+          subject-path: "dist/*"
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          # Remember to tell (test-)pypi about this repo before publishing
+          # Remove this line to publish to PyPI
+          repository-url: https://test.pypi.org/legacy/

directedstructure-0.1.1/.github/workflows/ci.yml

@@ -0,0 +1,77 @@
+name: CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this variable to be set to any value.
+  # Set it to 3 to support 8-bit color graphics (256 colors per channel)
+  # for libraries that care about the value set.
+  FORCE_COLOR: 3
+
+jobs:
+  pre-commit:
+    name: Format
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.x"
+
+      - uses: astral-sh/setup-uv@v7
+
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --hook-stage manual --all-files
+      - name: Run Pylint
+        run: uvx nox -s pylint -- --output-format=github
+
+  checks:
+    name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
+    needs: [pre-commit]
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        runs-on: [ubuntu-latest, windows-latest, macos-latest, macos-15-intel]
+
+        include:
+          - python-version: "pypy-3.11"
+            runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - uses: astral-sh/setup-uv@v7
+
+      - name: Install package
+        run: uv sync
+
+      - name: Test package
+        run: >-
+          uv run pytest -ra --cov --cov-report=xml --cov-report=term
+          --durations=20
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

directedstructure-0.1.1/.github/workflows/release.yml

@@ -0,0 +1,114 @@
+name: release
+
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+  pull_request:
+    paths:
+      - .github/workflows/cd.yml
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  make_sdist:
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Build SDist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  build_wheels:
+    name: Wheel on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-14, ubuntu-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Install system dependencies for Pillow (Ubuntu)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libjpeg-dev
+
+      - name: Install correct numpy version
+        run: python -m pip install "numpy==2.0.2"
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.20
+
+      # Building all wheels for Python 3.10-3.13
+      - name: Build Wheel
+        env:
+          CIBW_BUILD: cp310-* cp311-* cp312-* cp313-*
+          CIBW_ARCHS_WINDOWS: AMD64
+          CIBW_BEFORE_ALL_LINUX: |
+            if command -v apk &> /dev/null; then
+              apk add --no-cache jpeg-dev zlib-dev
+            elif command -v yum &> /dev/null; then
+              yum install -y libjpeg-devel zlib-devel
+            elif command -v apt-get &> /dev/null; then
+              apt-get update && apt-get install -y libjpeg-dev zlib1g-dev
+            fi
+          CIBW_TEST_REQUIRES: pytest
+          CIBW_TEST_COMMAND: pytest {project}/tests
+        run: cibuildwheel --output-dir wheelhouse
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: wheelhouse/*.whl
+
+  upload_all:
+    needs: [build_wheels, make_sdist]
+    environment: pypi
+    permissions:
+      id-token: write
+      attestations: write
+      contents: read
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - name: Generate artifact attestations
+        uses: actions/attest-build-provenance@v1.4.1
+        with:
+          subject-path: "dist/*"
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          # Remember to tell (test-)pypi about this repo before publishing
+          # repository-url: https://test.pypi.org/legacy/
+          repository-url: https://upload.pypi.org/legacy/
+          username: __token__
+          # password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          verbose: true

directedstructure-0.1.1/.gitignore

@@ -0,0 +1,188 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# setuptools_scm
+src/*/_version.py
+
+
+# ruff
+.ruff_cache/
+
+# OS specific stuff
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Common editor files
+*~
+*.swp

directedstructure-0.1.1/.pre-commit-config.yaml

@@ -0,0 +1,104 @@
+ci:
+  autoupdate_commit_msg: "chore(deps): update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+  autoupdate_schedule: "monthly"
+
+exclude: ^.cruft.json|.copier-answers.yml$
+
+repos:
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.20.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==25.*]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v6.0.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: "v3.7.4"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.14.11"
+    hooks:
+      - id: ruff-check
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: "v21.1.8"
+    hooks:
+      - id: clang-format
+        types_or: [c++, c, cuda]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.19.1"
+    hooks:
+      - id: mypy
+        files: src|tests|noxfile.py
+        args: []
+        additional_dependencies:
+          - nox
+          - pytest
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.4.1"
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli; python_version<'3.11'
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.11.0.1"
+    hooks:
+      - id: shellcheck
+
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+        exclude: .pre-commit-config.yaml
+
+  - repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: "v0.6.13"
+    hooks:
+      - id: cmake-format
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.24.1"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.36.0"
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+      - id: check-readthedocs