scitiff 0__tar.gz

scitiff-0/.copier-answers.yml

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+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: d704227
+_src_path: gh:scipp/copier_template
+description: Scientific tiff format for imaging experiments.
+max_python: '3.12'
+min_python: '3.10'
+namespace_package: ''
+nightly_deps: ''
+orgname: ess-dmsc-dram
+prettyname: SciTiff
+projectname: scitiff
+related_projects: Scipp,Plopp,ESSImaging,EasyImaging
+year: 2025

scitiff-0/.github/dependabot.yml

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+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"

scitiff-0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - release
+  pull_request:
+
+jobs:
+  formatting:
+    name: Formatting and static analysis
+    runs-on: 'ubuntu-24.04'
+    outputs:
+      min_python: ${{ steps.vars.outputs.min_python }}
+      min_tox_env: ${{ steps.vars.outputs.min_tox_env }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Get Python version for other CI jobs
+        id: vars
+        run: |
+          echo "min_python=$(< .github/workflows/python-version-ci)" >> "$GITHUB_OUTPUT"
+          echo "min_tox_env=py$(sed 's/\.//g' < .github/workflows/python-version-ci)" >> "$GITHUB_OUTPUT"
+      - uses: actions/setup-python@v5
+        with:
+          python-version-file: '.github/workflows/python-version-ci'
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --all-files
+      - uses: pre-commit-ci/lite-action@v1.1.0
+        if: always()
+        with:
+          msg: Apply automatic formatting
+
+  tests:
+    name: Tests
+    needs: formatting
+    strategy:
+      matrix:
+        os: ['ubuntu-24.04']
+        python:
+          - version: '${{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 }}
+    secrets: inherit
+
+  docs:
+    needs: tests
+    uses: ./.github/workflows/docs.yml
+    with:
+      publish: false
+      linkcheck: ${{ github.ref == 'refs/heads/main' }}
+      branch: ${{ github.head_ref == '' && github.ref_name || github.head_ref }}
+    secrets: inherit

scitiff-0/.github/workflows/docs.yml

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+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-24.04'
+    env:
+        ESS_PROTECTED_FILESTORE_USERNAME: ${{ secrets.ESS_PROTECTED_FILESTORE_USERNAME }}
+        ESS_PROTECTED_FILESTORE_PASSWORD: ${{ secrets.ESS_PROTECTED_FILESTORE_PASSWORD }}
+
+    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  # Skip linkcheck for now
+      #   if: ${{ inputs.linkcheck }}
+      - uses: actions/upload-artifact@v4
+        id: artifact-upload-step
+        with:
+          name: docs_html
+          path: html/
+      - run: echo "::notice::https://remote-unzip.deno.dev/${{ github.repository }}/artifacts/${{ steps.artifact-upload-step.outputs.artifact-id }}"
+
+      - uses: JamesIves/github-pages-deploy-action@v4.7.2
+        if: ${{ inputs.publish }}
+        with:
+          branch: gh-pages
+          folder: html
+          single-commit: true

scitiff-0/.github/workflows/nightly_at_main.yml

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+name: Nightly test at main branch
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '30 1 * * 1-5'
+
+jobs:
+  setup:
+    name: Setup variables
+    runs-on: 'ubuntu-24.04'
+    outputs:
+      min_python: ${{ steps.vars.outputs.min_python }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Get Python version for other CI jobs
+        id: vars
+        run: echo "min_python=$(< .github/workflows/python-version-ci)" >> "$GITHUB_OUTPUT"
+
+  tests:
+    name: Tests
+    needs: setup
+    strategy:
+      matrix:
+        os: ['ubuntu-24.04']
+        python:
+          - version: '${{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 }}
+    secrets: inherit

scitiff-0/.github/workflows/nightly_at_release.yml

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+name: Nightly tests at latest release
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 1 * * 1-5'
+
+jobs:
+  setup:
+    name: Setup variables
+    runs-on: 'ubuntu-24.04'
+    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)" >> "$GITHUB_OUTPUT"
+
+  tests:
+    name: Tests
+    needs: setup
+    strategy:
+      matrix:
+        os: ['ubuntu-24.04']
+        python:
+          - version: '${{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 }}
+    secrets: inherit

scitiff-0/.github/workflows/python-version-ci

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+3.10

scitiff-0/.github/workflows/release.yml

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+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-24.04'
+
+    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 --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-24.04'
+
+    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-24.04'
+    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
+
+  # Skipping conda upload until we have a token.
+  # upload_conda:
+  #   name: Deploy Conda
+  #   needs: [build_wheels, build_conda]
+  #   runs-on: 'ubuntu-24.04'
+  #   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 essdmsc --label main $(ls conda-package-noarch/*.tar.bz2)
+
+  docs:
+    # needs: [upload_conda, upload_pypi]
+    needs: [upload_pypi]
+    uses: ./.github/workflows/docs.yml
+    with:
+      publish: ${{ github.event_name == 'release' && github.event.action == 'published' }}
+    secrets: inherit
+
+  assets:
+    name: Upload docs
+    needs: docs
+    runs-on: 'ubuntu-24.04'
+    permissions:
+      contents: write  # This is needed so that the action can upload the asset
+    steps:
+    - uses: actions/download-artifact@v4
+    - name: Zip documentation
+      run: |
+        mv docs_html documentation-${{ 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

scitiff-0/.github/workflows/test.yml

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+name: Test
+
+on:
+  workflow_dispatch:
+    inputs:
+      os-variant:
+        default: 'ubuntu-24.04'
+        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-24.04'
+        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:
+  package-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 .
+      - run: python tests/package_test.py
+        name: Run package tests
+
+  test:
+    runs-on: ${{ inputs.os-variant }}
+    env:
+        ESS_PROTECTED_FILESTORE_USERNAME: ${{ secrets.ESS_PROTECTED_FILESTORE_USERNAME }}
+        ESS_PROTECTED_FILESTORE_PASSWORD: ${{ secrets.ESS_PROTECTED_FILESTORE_PASSWORD }}
+
+    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/

scitiff-0/.github/workflows/unpinned.yml

@@ -0,0 +1,41 @@
+name: Unpinned tests at latest release
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 2 * * 1'
+
+jobs:
+  setup:
+    name: Setup variables
+    runs-on: 'ubuntu-24.04'
+    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)" >> "$GITHUB_OUTPUT"
+
+  tests:
+    name: Tests
+    needs: setup
+    strategy:
+      matrix:
+        os: ['ubuntu-24.04']
+        python:
+          - version: '${{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 }}
+    secrets: inherit

scitiff-0/.github/workflows/weekly_windows_macos.yml

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+name: Windows and MacOS weekly tests
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 2 * * 1'
+
+jobs:
+  pytox:
+    name: Python and Tox env
+    runs-on: 'ubuntu-24.04'
+    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')" >> $GITHUB_OUTPUT
+  tests:
+    name: Tests
+    needs: pytox
+    strategy:
+      matrix:
+        os: ['macos-latest', 'windows-latest']
+        python:
+          - version: '${{needs.pytox.outputs.min_python}}'
+            tox-env: '${{needs.pytox.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
+      branch: ${{ github.head_ref == '' && github.ref_name || github.head_ref }}

scitiff-0/.gitignore

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+# Build artifacts
+build
+dist
+html
+.tox
+*.egg-info
+# we lock dependencies with pip-compile, not uv
+uv.lock
+
+*.sw?
+
+# Environments
+venv
+.venv
+
+# Caches
+.clangd/
+*.ipynb_checkpoints
+__pycache__/
+.vs/
+.virtual_documents
+.hypothesis
+.pytest_cache
+.mypy_cache
+docs/generated/
+.ruff_cache
+
+# Editor settings
+.idea/
+.vscode/
+
+# Data files
+*.data
+*.dat
+*.csv
+*.xye
+*.h5
+*.hdf5
+*.hdf
+*.nxs
+*.raw
+*.cif
+*.rcif
+*.ort
+*.zip
+*.sqw
+*.nxspe
+*.tiff
+*.tif

scitiff-0/.pre-commit-config.yaml

@@ -0,0 +1,54 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-illegal-windows-names
+      - 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: 0.7.1
+    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: v0.8.0
+    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: v2.3.0
+    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
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.7.3
+    hooks:
+      - id: actionlint
+        # Disable because of false-positive SC2046
+        args: ["-shellcheck="]

scitiff-0/.python-version

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