jaqsi 0.1.0__tar.gz

jaqsi-0.1.0/.github/CODEOWNERS

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+/.github/ @stroblme @majafranz

jaqsi-0.1.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG]"
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here.

jaqsi-0.1.0/.github/ISSUE_TEMPLATE/code-health.md

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+---
+name: Code health
+about: Discovered code that should be improved?
+title: "[CH]"
+labels: ''
+assignees: ''
+
+---
+
+

jaqsi-0.1.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: "[FR]"
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

jaqsi-0.1.0/.github/dependabot.yml

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+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/dependabot-options-reference#about-the-dependabotyml-file
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    groups:
+      security-updates:
+        applies-to: "security-updates"
+        patterns:
+          - "*"
+      version-updates:
+        applies-to: "version-updates"
+        patterns:
+          - "*"
+    open-pull-requests-limit: 5
+    schedule:
+      day: "monday"
+      interval: "weekly"
+      time: "06:00"
+      timezone: "Europe/Amsterdam"
+    reviewers:
+      - "stroblme"
+    assignees:
+      - "stroblme"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      day: "monday"
+      interval: "weekly"
+      time: "06:00"
+      timezone: "Europe/Amsterdam"
+    reviewers:
+      - "stroblme"
+    assignees:
+      - "stroblme"

jaqsi-0.1.0/.github/workflows/dependabot-approve.yml

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+name: Dependabot auto-approve
+on: pull_request_target
+
+permissions:
+    pull-requests: write
+    contents: write
+
+jobs:
+    dependabot:
+        runs-on: ubuntu-latest
+        if: github.event.pull_request.user.login == 'dependabot[bot]' && github.repository == 'cirKITers/jaqsi'
+        steps:
+            - name: Dependabot metadata
+              id: metadata
+              uses: dependabot/fetch-metadata@25dd0e34f4fe68f24cc83900b1fe3fe149efef98
+              with:
+                  github-token: "${{ secrets.GITHUB_TOKEN }}"
+            - name: Approve a PR
+              run: gh pr review --approve "$PR_URL"
+              env:
+                  PR_URL: ${{github.event.pull_request.html_url}}
+                  GH_TOKEN: ${{secrets.GITHUB_TOKEN}}
+            - name: Enable auto-merge
+              run: gh pr merge --auto --squash "$PR_URL"
+              env:
+                  PR_URL: ${{github.event.pull_request.html_url}}
+                  GH_TOKEN: ${{secrets.GITHUB_TOKEN}}

jaqsi-0.1.0/.github/workflows/docs-publish.yml

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+name: Documentation on Publish
+on:
+  workflow_call:
+    inputs:
+      test-run-id:
+        required: true
+        type: string
+permissions:
+  contents: write
+  pages: write
+  id-token: write
+jobs:
+  test:
+    runs-on: self-hosted
+    if: ${{ github.ref != 'refs/heads/main' }}
+    steps:
+      - uses: actions/checkout@v7
+      - name: Install system dependencies
+        run: sudo apt-get update && sudo apt-get install -y gcc graphviz libgraphviz-dev pkg-config
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+          # cache: "uv"
+      - name: Install dependencies
+        run: pipx run uv sync --group docs
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      # - name: Setting up Cache
+      #   uses: actions/cache@v4
+      #   with:
+      #     key: mkdocs-material-${{ env.cache_id }}
+      #     path: .ci-cache
+      #     restore-keys: |
+      #       mkdocs-material-
+      - name: Build Docs
+        run: pipx run uv run zensical build --strict
+  deploy:
+    runs-on: self-hosted
+    if: ${{ github.ref == 'refs/heads/main' }}
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - uses: actions/configure-pages@v6
+      - uses: actions/checkout@v7
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+          # cache: "uv"
+      - name: Install dependencies
+        run: pipx run uv sync --group docs
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      # - name: Setting up Cache
+      #   uses: actions/cache@v4
+      #   with:
+      #     key: mkdocs-material-${{ env.cache_id }}
+      #     path: .ci-cache
+      #     restore-keys: |
+      #       mkdocs-material-
+      - name: Download a single artifact
+        uses: actions/download-artifact@v7
+        with:
+          name: coverage-report
+          run-id: ${{ inputs.test-run-id }}
+          path: docs/coverage/
+      - name: Build Docs
+        run: pipx run uv run zensical build --strict --clean
+      - uses: actions/upload-pages-artifact@v5
+        with:
+          path: site
+      - uses: actions/deploy-pages@v5
+        id: deployment

jaqsi-0.1.0/.github/workflows/docs.yml

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+name: Documentation
+on:
+  pull_request:
+    branches: ["main"]
+  workflow_call:
+    inputs:
+      test-run-id:
+        required: true
+        type: string
+permissions:
+  contents: write
+jobs:
+  test:
+    runs-on: self-hosted
+    if: ${{ github.ref != 'refs/heads/main' }}
+    steps:
+      - uses: actions/checkout@v7
+      - name: Install system dependencies
+        run: sudo apt-get update && sudo apt-get install -y gcc graphviz libgraphviz-dev pkg-config
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+          # cache: "uv"
+      - name: Install dependencies
+        run: pipx run uv sync --group docs
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      # - name: Setting up Cache
+      #   uses: actions/cache@v4
+      #   with:
+      #     key: mkdocs-material-${{ env.cache_id }}
+      #     path: .ci-cache
+      #     restore-keys: |
+      #       mkdocs-material-
+      - name: Build Docs
+        run: pipx run uv run zensical build --strict
+  deploy:
+    runs-on: self-hosted
+    if: ${{ github.ref == 'refs/heads/main' }}
+    steps:
+      - uses: actions/checkout@v7
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+          # cache: "uv"
+      - name: Install dependencies
+        run: pipx run uv sync --group docs
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      # - name: Setting up Cache
+      #   uses: actions/cache@v4
+      #   with:
+      #     key: mkdocs-material-${{ env.cache_id }}
+      #     path: .ci-cache
+      #     restore-keys: |
+      #       mkdocs-material-
+      - name: Download a single artifact
+        uses: actions/download-artifact@v7
+        with:
+          name: coverage-report
+          run-id: ${{ inputs.test-run-id }}
+          path: docs/coverage/
+      - name: Build Docs
+        run: pipx run uv run zensical build --strict
+      - name: Deploy
+        run: pipx run uv run zensical gh-deploy --force

jaqsi-0.1.0/.github/workflows/publish.yml

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+name: Publish
+on:
+  push:
+    branches: ["main"]
+permissions:
+  contents: write
+  pages: write
+  id-token: write
+jobs:
+  test-publish:
+    name: Trigger Expensive Tests
+    uses: ./.github/workflows/test-on-publish.yml
+  quality-publish:
+    name: Trigger Quality
+    uses: ./.github/workflows/quality-publish.yml
+  documentation-publish:
+    needs: test-publish
+    name: Trigger Documentation
+    uses: ./.github/workflows/docs-publish.yml
+    with:
+      test-run-id: ${{ github.run_id }}
+  release:
+    needs: [test-publish, quality-publish, documentation-publish]
+    name: Release
+    if: ${{ github.ref == 'refs/heads/main' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          fetch-tags: true
+          ssh-key: ${{ secrets.DEPLOY_KEY }}
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+          # cache: "uv"
+      - name: Compare tag and version
+        run: |
+          git fetch --tags
+          if [ "$(git tag | sort -g | tail -1)" = "$(pipx run uv version --short)" ]; then
+            echo "The tag and the version are the same, nothing to do."
+            echo "DORELEASE=false" >> $GITHUB_ENV
+          else
+            echo "The tag ($(git tag | sort -g | tail -1)) and the version ($(pipx run uv version --short)) differ, trigging a release."
+            echo "DORELEASE=true" >> $GITHUB_ENV
+          fi
+      # - name: Update Citation
+      #   if: env.DORELEASE == 'true'
+      #   run: |
+      #     sed -i "/^cff/! s/version:\s\S*/version: $(pipx run uv version --short)/" CITATION.cff
+      #     sed -i "s/date-released:\s\S*/date-released: $(date +'%Y-%m-%d')/" CITATION.cff
+      #     git config user.name github-actions[bot]
+      #     git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      #     git commit -am "Update Citation"
+      #     git push
+      #   env:
+      #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 
+      - name: Create Release & Tag
+        if: env.DORELEASE == 'true'
+        run: |
+          gh release create "$(pipx run uv version --short)" \
+          --repo="$GITHUB_REPOSITORY" \
+          --title="${GITHUB_REPOSITORY#*/} $(pipx run uv version --short)" \
+          --generate-notes
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Publish to PyPI
+        if: env.DORELEASE == 'true'
+        run: |
+          pipx run uv sync --group dev
+          pipx run uv build
+          pipx run uv publish --token ${{ secrets.PYPI_API_TOKEN }}

jaqsi-0.1.0/.github/workflows/quality-publish.yml

@@ -0,0 +1,24 @@
+name: Quality on Publish
+on:
+  workflow_call:
+permissions:
+  contents: read
+jobs:
+  quality:
+    runs-on: self-hosted
+    if: ${{ (github.actor != 'dependabot[bot]') }}
+    steps:
+      - uses: actions/checkout@v7
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+          # cache: "uv"
+      - name: Install dependencies
+        run: pipx run uv sync --group dev
+      - name: Lint with ruff
+        run: |
+          pipx run uv run ruff check jaqsi
+          pipx run uv run ruff check tests
+      - name: Running license check
+        run: pipx run uv run licensecheck --zero --license mit

jaqsi-0.1.0/.github/workflows/quality.yml

@@ -0,0 +1,25 @@
+name: Quality
+on:
+  pull_request:
+    branches: ["main"]
+permissions:
+  contents: read
+jobs:
+  quality:
+    runs-on: self-hosted
+    if: ${{ (github.actor != 'dependabot[bot]') }}
+    steps:
+      - uses: actions/checkout@v7
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+          # cache: "uv"
+      - name: Install dependencies
+        run: pipx run uv sync --group dev
+      - name: Lint with ruff
+        run: |
+          pipx run uv run ruff check jaqsi
+          pipx run uv run ruff check tests
+      - name: Running license check
+        run: pipx run uv run licensecheck --zero --license mit

jaqsi-0.1.0/.github/workflows/test-on-pr.yml

@@ -0,0 +1,27 @@
+name: Testing on PR
+on:
+  pull_request:
+    branches: ["main"]
+  workflow_call:
+  workflow_dispatch:
+permissions:
+  contents: write
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+jobs:
+  test-all:
+    runs-on: self-hosted
+    steps:
+      - uses: actions/checkout@v7
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+          # cache: "uv"
+      - name: Install dependencies
+        run: pipx run uv sync --group dev
+      - name: Test with pytest (no benchmark)
+        run: pipx run uv run pytest --cov=jaqsi --dist load -n 2 -m "not benchmark" -v
+      - name: Test with pytest (benchmark)
+        run: pipx run uv run pytest --cov=jaqsi -m "benchmark"

jaqsi-0.1.0/.github/workflows/test-on-publish.yml

@@ -0,0 +1,25 @@
+name: Testing on Publish
+on:
+  workflow_call:
+permissions:
+  contents: write
+jobs:
+  test-all:
+    runs-on: self-hosted
+    if: ${{ (github.actor != 'github-actions[bot]') }}
+    steps:
+      - uses: actions/checkout@v7
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.13"
+          # cache: "uv"
+      - name: Install dependencies
+        run: pipx run uv sync --group dev
+      - name: Test with pytest (no benchmark)
+        run: pipx run uv run pytest --cov=jaqsi --cov-report html --dist load -n 0 -m "not benchmark"
+      - name: Share coverage report
+        uses: actions/upload-artifact@v7
+        with:
+          name: coverage-report
+          path: htmlcov/

jaqsi-0.1.0/.gitignore

@@ -0,0 +1,185 @@
+.codegraph
+.vscode
+logs/
+tests_external/
+references
+
+# General files
+*.bkp
+tensorboard/
+
+# Test output
+*.tex
+
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
+# 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
+
+
+# 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/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.vscode/
+
+# 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/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python
+

jaqsi-0.1.0/.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.15.12
+  hooks:
+    # Run the linter.
+    - id: ruff-check
+      types_or: [ python, pyi ]
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi ]

jaqsi-0.1.0/CITATION.cff

@@ -0,0 +1,28 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: "Franz"
+    given-names: "Maja"
+    orcid: "https://orcid.org/0000-0002-2801-7192"
+  - family-names: "Strobl"
+    given-names: "Melvin"
+    orcid: "https://orcid.org/0000-0003-0229-9897"
+  - family-names: "Kuehn"
+    given-names: "Eileen"
+    orcid: "https://orcid.org/0000-0002-8034-8837"
+  - family-names: "van der Horst"
+    given-names: "Lucas"
+    orcid: "https://orcid.org/0009-0003-0609-9582"
+  - family-names: "Schillinger"
+    given-names: "Paul"
+    orcid: "https://orcid.org/0009-0009-1566-6220"
+  - family-names: "Hunz"
+    given-names: "Jonathan"
+  - family-names: "Wahl"
+    given-names: "Johannes"
+title: "JAQSI"
+version: 0.1.0
+date-released: 2026-09-01
+repository-code: "https://github.com/cirKITers/jaqsi"
+url: "https://cirkiters.github.io/jaqsi"
+license: MIT