cyclebane 24.5.0__tar.gz

cyclebane-24.5.0/.copier-answers.yml

@@ -0,0 +1,13 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: 9bb9876
+_src_path: gh:scipp/copier_template
+description: Transform directed acyclic graphs using map-reduce and groupby operations
+max_python: '3.12'
+min_python: '3.10'
+namespace_package: ''
+nightly_deps: networkx/networkx
+orgname: scipp
+prettyname: Cyclebane
+projectname: cyclebane
+related_projects: Sciline
+year: 2024

cyclebane-24.5.0/.github/dependabot.yml

@@ -0,0 +1,13 @@
+version: 2
+updates:
+  # Note: We are not listing package-ecosystem: "github-actions". This causes
+  # noise in all template instances. Instead dependabot.yml in scipp/copier_template
+  # triggers updates of github-actions in the *template*. We then use `copier update`
+  # in template instances.
+  - package-ecosystem: "pip"
+    directory: "/requirements"
+    schedule:
+      interval: "daily"
+    allow:
+      - dependency-name: "scipp"
+        dependency-type: "direct"

cyclebane-24.5.0/.github/workflows/ci.yml

@@ -0,0 +1,56 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - release
+  pull_request:
+
+jobs:
+  formatting:
+    name: Formatting and static analysis
+    runs-on: 'ubuntu-22.04'
+    outputs:
+      min_python: ${{ steps.vars.outputs.min_python }}
+      min_tox_env: ${{ steps.vars.outputs.min_tox_env }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Get Python version for other CI jobs
+        id: vars
+        run: |
+          echo "min_python=$(cat .github/workflows/python-version-ci)" >> $GITHUB_OUTPUT
+          echo "min_tox_env=py$(cat .github/workflows/python-version-ci | sed 's/\.//g')" >> $GITHUB_OUTPUT
+      - uses: actions/setup-python@v5
+        with:
+          python-version-file: '.github/workflows/python-version-ci'
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --all-files
+      - uses: pre-commit-ci/lite-action@v1.0.2
+        if: always()
+        with:
+          msg: Apply automatic formatting
+
+  tests:
+    name: Tests
+    needs: formatting
+    strategy:
+      matrix:
+        os: ['ubuntu-22.04']
+        python:
+          - version: '${{needs.formatting.outputs.min_python}}'
+            tox-env: '${{needs.formatting.outputs.min_tox_env}}'
+    uses: ./.github/workflows/test.yml
+    with:
+      os-variant: ${{ matrix.os }}
+      python-version: ${{ matrix.python.version }}
+      tox-env: ${{ matrix.python.tox-env }}
+
+  docs:
+    needs: tests
+    uses: ./.github/workflows/docs.yml
+    with:
+      publish: false
+      linkcheck: ${{ contains(matrix.variant.os, 'ubuntu') && github.ref == 'refs/heads/main' }}
+      branch: ${{ github.head_ref == '' && github.ref_name || github.head_ref }}

cyclebane-24.5.0/.github/workflows/docs.yml

@@ -0,0 +1,73 @@
+name: Docs
+
+on:
+  workflow_dispatch:
+    inputs:
+      publish:
+        default: false
+        type: boolean
+      version:
+        default: ''
+        required: false
+        type: string
+      branch:
+        description: 'Branch/tag with documentation source. If not set, the current branch will be used.'
+        default: ''
+        required: false
+        type: string
+  workflow_call:
+    inputs:
+      publish:
+        default: false
+        type: boolean
+      version:
+        default: ''
+        required: false
+        type: string
+      branch:
+        description: 'Branch/tag with documentation source. If not set, the current branch will be used.'
+        default: ''
+        required: false
+        type: string
+      linkcheck:
+        description: 'Run the link checker. If not set the link checker will not be run.'
+        default: false
+        required: false
+        type: boolean
+
+env:
+  VERSION: ${{ inputs.version }}
+
+jobs:
+  docs:
+    name: Build documentation
+    runs-on: 'ubuntu-22.04'
+    steps:
+      - run: sudo apt install --yes graphviz pandoc
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.branch == '' && github.ref_name || inputs.branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          fetch-depth: 0  # history required so cmake can determine version
+      - uses: actions/setup-python@v5
+        with:
+          python-version-file: '.github/workflows/python-version-ci'
+      - run: python -m pip install --upgrade pip
+      - run: python -m pip install -r requirements/ci.txt
+      - run: tox -e releasedocs -- ${VERSION}
+        if: ${{ inputs.version != '' }}
+      - run: tox -e docs
+        if: ${{ inputs.version == '' }}
+      - run: tox -e linkcheck
+        if: ${{ inputs.linkcheck }}
+      - uses: actions/upload-artifact@v4
+        with:
+          name: docs_html
+          path: html/
+
+      - uses: JamesIves/github-pages-deploy-action@v4.6.1
+        if: ${{ inputs.publish }}
+        with:
+          branch: gh-pages
+          folder: html
+          single-commit: true

cyclebane-24.5.0/.github/workflows/nightly_at_main.yml

@@ -0,0 +1,33 @@
+name: Nightly test at main branch
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '30 1 * * 1-5'
+
+jobs:
+  setup:
+    name: Setup variables
+    runs-on: 'ubuntu-22.04'
+    outputs:
+      min_python: ${{ steps.vars.outputs.min_python }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Get Python version for other CI jobs
+        id: vars
+        run: echo "min_python=$(cat .github/workflows/python-version-ci)" >> $GITHUB_OUTPUT
+
+  tests:
+    name: Tests
+    needs: setup
+    strategy:
+      matrix:
+        os: ['ubuntu-22.04']
+        python:
+          - version: '${{needs.setup.outputs.min_python}}'
+            tox-env: 'nightly'
+    uses: ./.github/workflows/test.yml
+    with:
+      os-variant: ${{ matrix.os }}
+      python-version: ${{ matrix.python.version }}
+      tox-env: ${{ matrix.python.tox-env }}

cyclebane-24.5.0/.github/workflows/nightly_at_release.yml

@@ -0,0 +1,40 @@
+name: Nightly tests at latest release
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 1 * * 1-5'
+
+jobs:
+  setup:
+    name: Setup variables
+    runs-on: 'ubuntu-22.04'
+    outputs:
+      min_python: ${{ steps.vars.outputs.min_python }}
+      release_tag: ${{ steps.release.outputs.release_tag }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # history required so we can determine latest release tag
+      - name: Get last release tag from git
+        id: release
+        run: echo "release_tag=$(git describe --tags --abbrev=0 --match '[0-9]*.[0-9]*.[0-9]*')" >> $GITHUB_OUTPUT
+      - name: Get Python version for other CI jobs
+        id: vars
+        run: echo "min_python=$(cat .github/workflows/python-version-ci)" >> $GITHUB_OUTPUT
+
+  tests:
+    name: Tests
+    needs: setup
+    strategy:
+      matrix:
+        os: ['ubuntu-22.04']
+        python:
+          - version: '${{needs.setup.outputs.min_python}}'
+            tox-env: 'nightly'
+    uses: ./.github/workflows/test.yml
+    with:
+      os-variant: ${{ matrix.os }}
+      python-version: ${{ matrix.python.version }}
+      tox-env: ${{ matrix.python.tox-env }}
+      checkout_ref: ${{ needs.setup.outputs.release_tag }}

cyclebane-24.5.0/.github/workflows/python-version-ci

@@ -0,0 +1 @@
+3.10

cyclebane-24.5.0/.github/workflows/release.yml

@@ -0,0 +1,113 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash -l {0}  # required for conda env
+
+jobs:
+  build_conda:
+    name: Conda build
+    runs-on: 'ubuntu-22.04'
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+          fetch-depth: 0  # history required so setuptools_scm can determine version
+
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: build-env
+          create-args: >-
+            conda-build
+            boa
+      - run: conda mambabuild --channel conda-forge --channel scipp --no-anaconda-upload --override-channels --output-folder conda/package conda
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: conda-package-noarch
+          path: conda/package/noarch/*.tar.bz2
+
+  build_wheels:
+    name: Wheels
+    runs-on: 'ubuntu-22.04'
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # history required so setuptools_scm can determine version
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version-file: '.github/workflows/python-version-ci'
+
+      - run: python -m pip install --upgrade pip
+      - run: python -m pip install -r requirements/wheels.txt
+
+      - name: Build wheels
+        run: python -m build
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+  upload_pypi:
+    name: Deploy PyPI
+    needs: [build_wheels, build_conda]
+    runs-on: 'ubuntu-22.04'
+    environment: release
+    permissions:
+      id-token: write
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v4
+      - uses: pypa/gh-action-pypi-publish@v1.8.14
+
+  upload_conda:
+    name: Deploy Conda
+    needs: [build_wheels, build_conda]
+    runs-on: 'ubuntu-22.04'
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/download-artifact@v4
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: upload-env
+          # frozen python due to breaking removal of 'imp' in 3.12
+          create-args: >-
+            anaconda-client
+            python=3.11
+      - run: anaconda --token ${{ secrets.ANACONDATOKEN }} upload --user scipp --label main $(ls conda-package-noarch/*.tar.bz2)
+
+  docs:
+    needs: [upload_conda, upload_pypi]
+    uses: ./.github/workflows/docs.yml
+    with:
+      publish: ${{ github.event_name == 'release' && github.event.action == 'published' }}
+    secrets: inherit
+
+  assets:
+    name: Upload docs
+    needs: docs
+    runs-on: 'ubuntu-22.04'
+    permissions:
+      contents: write  # This is needed so that the action can upload the asset
+    steps:
+    - uses: actions/download-artifact@v4
+    - name: Zip documentation
+      run: |
+        mv docs_html documentation-${{ github.ref_name }}
+        zip -r documentation-${{ github.ref_name }}.zip documentation-${{ github.ref_name }}
+    - name: Upload release assets
+      uses: svenstaro/upload-release-action@v2
+      with:
+        file: ./documentation-${{ github.ref_name }}.zip
+        overwrite: false

cyclebane-24.5.0/.github/workflows/test.yml

@@ -0,0 +1,61 @@
+name: Test
+
+on:
+  workflow_dispatch:
+    inputs:
+      os-variant:
+        default: 'ubuntu-22.04'
+        type: string
+      python-version:
+        type: string
+      tox-env:
+        default: 'test'
+        type: string
+      pip-recipe:
+        default: 'requirements/ci.txt'
+        type: string
+      coverage-report:
+        default: false
+        type: boolean
+      checkout_ref:
+        default: ''
+        type: string
+  workflow_call:
+    inputs:
+      os-variant:
+        default: 'ubuntu-22.04'
+        type: string
+      python-version:
+        type: string
+      tox-env:
+        default: 'test'
+        type: string
+      pip-recipe:
+        default: 'requirements/ci.txt'
+        type: string
+      coverage-report:
+        default: false
+        type: boolean
+      checkout_ref:
+        default: ''
+        type: string
+
+jobs:
+  test:
+    runs-on: ${{ inputs.os-variant }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.checkout_ref }}
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ inputs.python-version }}
+      - run: python -m pip install --upgrade pip
+      - run: python -m pip install -r ${{ inputs.pip-recipe }}
+      - run: tox -e ${{ inputs.tox-env }}
+      - uses: actions/upload-artifact@v4
+        if: ${{ inputs.coverage-report }}
+        with:
+          name: CoverageReport
+          path: coverage_html/

cyclebane-24.5.0/.github/workflows/unpinned.yml

@@ -0,0 +1,40 @@
+name: Unpinned tests at latest release
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 2 * * 1'
+
+jobs:
+  setup:
+    name: Setup variables
+    runs-on: 'ubuntu-22.04'
+    outputs:
+      min_python: ${{ steps.vars.outputs.min_python }}
+      release_tag: ${{ steps.release.outputs.release_tag }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # history required so we can determine latest release tag
+      - name: Get last release tag from git
+        id: release
+        run: echo "release_tag=$(git describe --tags --abbrev=0 --match '[0-9]*.[0-9]*.[0-9]*')" >> $GITHUB_OUTPUT
+      - name: Get Python version for other CI jobs
+        id: vars
+        run: echo "min_python=$(cat .github/workflows/python-version-ci)" >> $GITHUB_OUTPUT
+
+  tests:
+    name: Tests
+    needs: setup
+    strategy:
+      matrix:
+        os: ['ubuntu-22.04']
+        python:
+          - version: '${{needs.setup.outputs.min_python}}'
+            tox-env: 'unpinned'
+    uses: ./.github/workflows/test.yml
+    with:
+      os-variant: ${{ matrix.os }}
+      python-version: ${{ matrix.python.version }}
+      tox-env: ${{ matrix.python.tox-env }}
+      checkout_ref: ${{ needs.setup.outputs.release_tag }}

cyclebane-24.5.0/.gitignore

@@ -0,0 +1,40 @@
+# Build artifacts
+build
+dist
+html
+.tox
+*.egg-info
+
+*.sw?
+
+# Environments
+venv
+
+# Caches
+.clangd/
+*.ipynb_checkpoints
+__pycache__/
+.vs/
+.virtual_documents
+.hypothesis
+.pytest_cache
+.mypy_cache
+docs/generated/
+
+# Editor settings
+.idea/
+.vscode/
+
+# Data files
+*.data
+*.dat
+*.csv
+*.xye
+*.h5
+*.hdf5
+*.hdf
+*.nxs
+*.raw
+*.cif
+*.rcif
+*.ort

cyclebane-24.5.0/.pre-commit-config.yaml

@@ -0,0 +1,46 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-json
+        exclude: asv.conf.json
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-yaml
+        exclude: conda/meta.yaml
+      - id: detect-private-key
+      - id: trailing-whitespace
+        args: [ --markdown-linebreak-ext=md ]
+        exclude: '\.svg'
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.0
+    hooks:
+      - id: nbstripout
+        types: [ "jupyter" ]
+        args: [ "--drop-empty-cells",
+                "--extra-keys 'metadata.language_info.version cell.metadata.jp-MarkdownHeadingCollapsed cell.metadata.pycharm'" ]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.3
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+        types_or: [ python, pyi, jupyter ]
+      - id: ruff-format
+        types_or: [ python, pyi ]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-no-eval
+      - id: python-no-log-warn
+      - id: python-use-type-annotations
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+      - id: text-unicode-replacement-char

cyclebane-24.5.0/CODE_OF_CONDUCT.md

@@ -0,0 +1,134 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+scipp[at]ess.eu.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
+

cyclebane-24.5.0/CONTRIBUTING.md

@@ -0,0 +1,20 @@
+## Contributing to Cyclebane
+
+Welcome to the developer side of Cyclebane!
+
+Contributions are always welcome.
+This includes reporting bugs or other issues, submitting pull requests, requesting new features, etc.
+
+If you need help with using Cyclebane or contributing to it, have a look at the GitHub [discussions](https://github.com/scipp/cyclebane/discussions) and start a new [Q&A discussion](https://github.com/scipp/cyclebane/discussions/categories/q-a) if you can't find what you are looking for.
+
+For bug reports and other problems, please open an [issue](https://github.com/scipp/cyclebane/issues/new) in GitHub.
+
+You are welcome to submit pull requests at any time.
+But to avoid having to make large modifications during review or even have your PR rejected, please first open an issue first to discuss your idea!
+
+Check out the subsections of the [Developer documentation](https://scipp.github.io/cyclebane/developer/index.html) for details on how Cyclebane is developed.
+
+## Code of conduct
+
+This project is a community effort, and everyone is welcome to contribute.
+Everyone within the community is expected to abide by our [code of conduct](https://github.com/scipp/cyclebane/blob/main/CODE_OF_CONDUCT.md).