dvpimg 0.0.1a36__tar.gz

dvpimg-0.0.1a36/.bumpversion.ini

@@ -0,0 +1,21 @@
+[bumpversion]
+current_version = 0.0.1-alpha36
+commit = true
+tag = true
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)-(?P<release>[a-z]+)(?P<build>\d+)
+serialize = 
+	{major}.{minor}.{patch}-{release}{build}
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:part:release]
+values = 
+	alpha
+	beta
+	rc
+	final
+
+[bumpversion:part:build]
+first_value = 1

dvpimg-0.0.1a36/.codecov.yaml

@@ -0,0 +1,6 @@
+coverage:
+  status:
+    project:
+      default:
+        target: 80%
+        threshold: 1%

dvpimg-0.0.1a36/.github/release.yaml

@@ -0,0 +1,16 @@
+# .github/release.yml
+
+changelog:
+  exclude:
+    labels:
+      - bump-version
+  categories:
+    - title: 🚀 Features
+      labels:
+        - enhancement
+    - title: ⛓️‍💥 Breaking Changes
+      labels:
+        - breaking-change
+    - title: 📎 Other Changes
+      labels:
+        - "*"

dvpimg-0.0.1a36/.github/workflows/build.yaml

@@ -0,0 +1,32 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  package:
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+      - name: Install build dependencies
+        run: python -m pip install --upgrade pip wheel twine build
+      - name: Build package
+        run: python -m build
+      - name: Check package
+        run: twine check --strict dist/*.whl

dvpimg-0.0.1a36/.github/workflows/bump-version.yaml

@@ -0,0 +1,143 @@
+name: Version Bump
+
+on:
+  pull_request:
+    types: [closed]
+    branches:
+      - main
+  workflow_dispatch:
+    inputs:
+      bump:
+        description: "Select version bump type"
+        required: true
+        default: patch
+        type: choice
+        options:
+          - major
+          - minor
+          - patch
+          - release
+          - build
+
+jobs:
+  bump-version:
+    name: bump-version
+    permissions:
+      contents: write
+      pull-requests: write # Add this permission for creating PRs
+
+    # Run if PR merged or manually triggered
+    if: (github.event_name == 'pull_request' && github.event.pull_request.merged == true) || (github.event_name == 'workflow_dispatch')
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.GITHUB_TOKEN }} # Ensure we have push permissions
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install bump2version and packaging
+        run: pip install bump2version packaging
+
+      - name: Authenticate GitHub CLI
+        run: |
+          echo "${{ secrets.PR_WRITE }}" | gh auth login --with-token
+
+      - name: Set up git config
+        shell: bash
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
+          git config --global user.name "${GITHUB_ACTOR}"
+          git config -l
+
+      - name: Determine bump type
+        id: bump
+        run: |
+          if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then
+            # Manual trigger: use input
+            echo "bump=${{ github.event.inputs.bump }}" >> $GITHUB_OUTPUT
+          else
+            # PR merge: determine bump from labels
+            # Use environment variable to safely handle JSON with special characters
+            echo "Labels: $LABELS_JSON"
+            if echo "$LABELS_JSON" | grep -q '"name": *"update-major"'; then
+              echo "bump=major" >> $GITHUB_OUTPUT
+            elif echo "$LABELS_JSON" | grep -q '"name": *"update-minor"'; then
+              echo "bump=minor" >> $GITHUB_OUTPUT
+            elif echo "$LABELS_JSON" | grep -q '"name": *"update-patch"'; then
+              echo "bump=patch" >> $GITHUB_OUTPUT
+            elif echo "$LABELS_JSON" | grep -q '"name": *"update-release"'; then
+              echo "bump=release" >> $GITHUB_OUTPUT
+            elif echo "$LABELS_JSON" | grep -q '"name": *"update-build"'; then
+              echo "bump=build" >> $GITHUB_OUTPUT
+            else
+              echo "bump=none" >> $GITHUB_OUTPUT
+            fi
+          fi
+        env:
+          LABELS_JSON: ${{ toJson(github.event.pull_request.labels) }}
+
+      - name: Preview version bump
+        if: steps.bump.outputs.bump != 'none'
+        run: |
+          BUMP_TYPE="${{ steps.bump.outputs.bump }}"
+          echo "Previewing version bump: $BUMP_TYPE"
+          bump2version --config-file .bumpversion.ini --dry-run --list $BUMP_TYPE
+
+      - name: Bump version
+        id: b2v
+        if: steps.bump.outputs.bump != 'none'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          BUMP_TYPE="${{ steps.bump.outputs.bump }}"
+
+          # Create a new branch for manual bump
+          BRANCH="bump/${BUMP_TYPE}-$(date +%Y%m%d%H%M%S)"
+          git checkout -b $BRANCH
+
+          # Perform the version bump
+          bump2version --config-file .bumpversion.ini $BUMP_TYPE
+
+          # Push the branch with tags
+          git push origin $BRANCH --tags
+
+          # Output branch name for PR step
+          echo "branch_name=$BRANCH" >> $GITHUB_OUTPUT
+          echo "Branch created: $BRANCH"
+
+          NEW_VERSION=$(grep -oP '(?<=^current_version = ).*' .bumpversion.ini)
+          echo "new_version=$NEW_VERSION" >> $GITHUB_OUTPUT
+
+      - name: Create Pull Request (manual dispatch only)
+        if: steps.bump.outputs.bump != 'none'
+        run: |
+          # Create PR using GitHub CLI
+          gh pr create \
+            --base main \
+            --head "${{ steps.b2v.outputs.branch_name }}" \
+            --title "Version bump (${{ steps.bump.outputs.bump }}) → ${{ steps.b2v.outputs.new_version }}" \
+            --body "## Automated Version Bump
+
+            This PR bumps the version using the **${{ steps.bump.outputs.bump }}** strategy.
+
+            ### Changes
+            - Version bumped via \`bump2version\`
+            - New version: ${{ steps.b2v.outputs.new_version }}
+            - Configuration file: \`.bumpversion.ini\`
+
+            ### Type
+            - Bump type: \`${{ steps.bump.outputs.bump }}\`
+            "
+
+          # Set Labels
+          pr_url=$(gh pr view "${{ steps.b2v.outputs.branch_name }}" --json url -q .url)
+          gh pr edit "$pr_url" --add-label "automated" --add-label "bump-version"

dvpimg-0.0.1a36/.github/workflows/main.yaml

@@ -0,0 +1,44 @@
+name: Formatting + Linting
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  Formatting:
+    if: >
+      github.event_name != 'pull_request' ||
+      (
+        !contains(join(fromJSON(toJSON(github.event.pull_request.labels)).*.name), 'bump-version')
+      )
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Formatting
+        uses: super-linter/super-linter@v7
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: main
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          VALIDATE_SNAKEMAKE_SNAKEFMT: true
+          VALIDATE_YAML_PRETTIER: true
+
+  Linting:
+    if: >
+      github.event_name != 'pull_request' ||
+      (
+        !contains(join(fromJSON(toJSON(github.event.pull_request.labels)).*.name), 'bump-version')
+      )
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Lint workflow
+        uses: snakemake/snakemake-github-action@v2
+        with:
+          directory: ./workflow
+          snakefile: workflow/Snakefile
+          args: "--lint"

dvpimg-0.0.1a36/.github/workflows/release-please.yaml

@@ -0,0 +1,20 @@
+on:
+  workflow_dispatch:
+  # push:
+  #   branches:
+  #     - main
+
+permissions:
+  contents: write
+  pull-requests: write
+
+name: release-please
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: googleapis/release-please-action@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          release-type: go # just keep a changelog, no version anywhere outside of git tags

dvpimg-0.0.1a36/.github/workflows/release-pypi.yaml

@@ -0,0 +1,31 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/dvpimg
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+      - run: pip install build
+      - run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

dvpimg-0.0.1a36/.github/workflows/test.yaml

@@ -0,0 +1,76 @@
+name: Test
+
+permissions:
+  actions: read
+  contents: read
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: "3.12"
+
+    name: Python ${{ matrix.python }}
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+      MPLBACKEND: Agg # Non-interactive matplotlib backend
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python with uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "latest"
+          enable-cache: false
+          cache-dependency-glob: "**/pyproject.toml"
+
+      - name: Set up Python ${{ matrix.python }}
+        run: uv python install ${{ matrix.python }}
+
+      - name: Install development dependencies
+        run: |
+          uv venv
+          uv pip install -e ".[dev,test]"
+
+      - name: Run unit tests
+        run: |
+          uv run coverage run -m pytest -v --color=yes
+          uv run coverage report --ignore-errors
+
+      #   - name: Run functional tests
+      #     run: |
+      #       hatch run dev:test-functional --tb=short -v
+
+      #   - name: Validate pipeline consistency
+      #     run: |
+      #       hatch run workflow:dry-run
+      #     continue-on-error: true
+
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

dvpimg-0.0.1a36/.gitignore

@@ -0,0 +1,235 @@
+results/**
+resources/**
+logs/**
+.snakemake
+.snakemake/**
+.test/results/*
+workflow/notebooks/.ipynb_checkpoints/**
+**/.Rhistory
+**/*.Rproj
+**/.Rproj.user/**
+**/.RData
+**/Rplots.pdf
+
+
+# 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
+#poetry.toml
+
+# 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 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/
+
+# 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/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Claude
+#  Claude Code specific files and settings
+.claude/**
+
+# MacOS
+.DS_Store
+
+# Plots
+*.png
+*.jpeg
+*.pdf
+*.html
+
+# Large files
+*.zarr
+*.hdf5
+*.h5ad
+
+# Logs
+*.out
+*.err
+
+# Claude Code documentation
+CLAUDE.md
+REPOSITORY_REFERENCE.md

dvpimg-0.0.1a36/.pre-commit-config.yaml

@@ -0,0 +1,52 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        exclude: .bumpversion.ini
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.5.0
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.3
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: local
+    hooks:
+      - id: snakemake-lint
+        name: Lint with snakemake
+        language: system
+        entry: bash -c 'cd "$(git rev-parse --show-toplevel)/workflow" && snakemake --lint || echo "[Warning] snakemake --lint reported issues, but commit will proceed."'
+
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

dvpimg-0.0.1a36/.snakemake-workflow-catalog.yaml

@@ -0,0 +1,11 @@
+# configuration of display in snakemake workflow catalog: https://snakemake.github.io/snakemake-workflow-catalog
+
+usage:
+  mandatory-flags:
+    desc: # describe your flags here in a few sentences
+    flags: # put your flags here
+  software-stack-deployment:
+    conda: true # whether pipeline works with '--sdm conda'
+    apptainer: true # whether pipeline works with '--sdm apptainer/singularity'
+    apptainer+conda: true # whether pipeline works with '--sdm conda apptainer/singularity'
+    report: true # whether creation of reports using 'snakemake --report report.zip' is supported