dcmqi 0.1.0__tar.gz

dcmqi-0.1.0/.copier-answers.yml

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+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: 2024.03.10
+_src_path: gh:scientific-python/cookie
+backend: skbuild
+email: lnuernberg@bwh.harvard.edu
+full_name: Leonard Nürnberg
+license: MIT
+org: ImagingDataCommons
+project_name: "dcmqi"
+project_short_description: Python distribution of the DCMQI library collection.
+url: "https://github.com/ImagingDataCommons/dcmqi-python-distributions"
+vcs: true

dcmqi-0.1.0/.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

dcmqi-0.1.0/.gitattributes

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+.git_archival.txt  export-subst

dcmqi-0.1.0/.github/CONTRIBUTING.md

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+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 `pipx run nox` to run it without installing, or `pipx install nox`.
+If you don't have pipx (pip for applications), then you can install with
+`pip install pipx` (the only case were installing an application with regular
+pip is reasonable). If you use macOS, then pipx and nox are both in brew, use
+`brew install pipx nox`.
+
+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 -- --serve  # 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
+python3 -m venv .venv
+source ./.venv/bin/activate
+pip install -v -e .[dev]
+```
+
+If you have the
+[Python Launcher for Unix](https://github.com/brettcannon/python-launcher), you
+can instead do:
+
+```bash
+py -m venv .venv
+py -m install -v -e .[dev]
+```
+
+# Post setup
+
+You should prepare pre-commit, which will help you by checking that commits pass
+required checks:
+
+```bash
+pip 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
+pytest
+```
+
+# Coverage
+
+Use pytest-cov to generate coverage reports:
+
+```bash
+pytest --cov=dcmqi
+```
+
+# Building docs
+
+You can build the docs using:
+
+```bash
+nox -s docs
+```
+
+You can see a preview with:
+
+```bash
+nox -s docs -- --serve
+```
+
+# Pre-commit
+
+This project uses pre-commit for all style checking. While you can run it with
+nox, this is such an important tool that it deserves to be installed on its own.
+Install pre-commit and run:
+
+```bash
+pre-commit run -a
+```
+
+to check all files.

dcmqi-0.1.0/.github/dependabot.yml

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

dcmqi-0.1.0/.github/matchers/pylint.json

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+{
+  "problemMatcher": [
+    {
+      "severity": "warning",
+      "pattern": [
+        {
+          "regexp": "^([^:]+):(\\d+):(\\d+): ([A-DF-Z]\\d+): \\033\\[[\\d;]+m([^\\033]+).*$",
+          "file": 1,
+          "line": 2,
+          "column": 3,
+          "code": 4,
+          "message": 5
+        }
+      ],
+      "owner": "pylint-warning"
+    },
+    {
+      "severity": "error",
+      "pattern": [
+        {
+          "regexp": "^([^:]+):(\\d+):(\\d+): (E\\d+): \\033\\[[\\d;]+m([^\\033]+).*$",
+          "file": 1,
+          "line": 2,
+          "column": 3,
+          "code": 4,
+          "message": 5
+        }
+      ],
+      "owner": "pylint-error"
+    }
+  ]
+}

dcmqi-0.1.0/.github/workflows/cd.yml

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+name: wheels
+
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  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
+
+  test_sdist:
+    name: Test SDist with python ${{ matrix.python }}
+    needs: [make_sdist]
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["3.8", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        name: Install Python ${{ matrix.python }}
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install dependencies
+        run: |
+          # pip install pytest pytest-cov
+          # Waiting pip supports `--only-deps=test`, explicitly extract the test dependencies
+          # See https://github.com/pypa/pip/issues/11440
+          pip install yq
+          tomlq -r '.project."optional-dependencies".test[]' pyproject.toml | xargs -d '\n' pip install
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist
+
+      - name: Install SDist
+        run: |
+          pip -V
+          pip install dist/*.tar.gz
+          rm -rf dist
+
+      - name: Test installed SDist
+        run: pytest ./tests
+
+  check_dist:
+    name: Check dist
+    needs: [build_wheels, make_sdist, test_sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: all
+
+      - run: pipx run twine check --strict all/*/*
+
+  build_wheels:
+    name: Wheel on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: pypa/cibuildwheel@v2.17.0
+        env:
+          CIBW_ARCHS_LINUX: "x86_64"
+          CIBW_BUILD: "cp312-*"
+          CIBW_SKIP: "*musllinux*"
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: wheelhouse/*.whl
+
+  upload_all:
+    needs: [check_dist]
+    environment: pypi
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

dcmqi-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  FORCE_COLOR: 3
+
+jobs:
+  pre-commit:
+    name: Format
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --hook-stage manual --all-files
+      - name: Run PyLint
+        run: |
+          echo "::add-matcher::$GITHUB_WORKSPACE/.github/matchers/pylint.json"
+          pipx run nox -s pylint
+
+  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: ["3.8", "3.12"]
+        runs-on: [ubuntu-latest, macos-latest, windows-latest]
+
+        include:
+          - python-version: pypy-3.10
+            runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - name: Install package
+        run: python -m pip install .[test]
+
+      - name: Test package
+        run: >-
+          python -m pytest -ra --cov --cov-report=xml --cov-report=term
+          --durations=20
+
+      # - name: Upload coverage report
+      #   uses: codecov/codecov-action@v4.1.0
+      #   with:
+      #     token: ${{ secrets.CODECOV_TOKEN }}

dcmqi-0.1.0/.gitignore

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+# 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
+
+# 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/
+
+# 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
+
+# dcmqi distributions
+src/dcmqi/dcmqi*

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

@@ -0,0 +1,98 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.16.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.5.0"
+    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/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    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: "v0.3.0"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: "v17.0.6"
+    hooks:
+      - id: clang-format
+        types_or: [c++, c, cuda]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.8.0"
+    hooks:
+      - id: mypy
+        files: src|tests
+        args: []
+        additional_dependencies:
+          - pytest
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.2.6"
+    hooks:
+      - id: codespell
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.9.0.6"
+    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: "v0.16"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.28.0"
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+      - id: check-readthedocs

dcmqi-0.1.0/.readthedocs.yaml

@@ -0,0 +1,18 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

dcmqi-0.1.0/CMakeLists.txt

@@ -0,0 +1,47 @@
+# Guided by the structure set-up by JC for the s5cmd python distributions project:
+# https://github.com/ImagingDataCommons/s5cmd-python-distributions/blob/56b84d679e3a14421ca4884406e825117eee4232/CMakeLists.txt
+
+cmake_minimum_required(VERSION 3.15...3.26)
+project(${SKBUILD_PROJECT_NAME} LANGUAGES NONE)
+
+# Set in the current scope the following variables:
+# - dcmqi_archive_url
+# - dcmqi_archive_sha256
+include(${CMAKE_CURRENT_SOURCE_DIR}/dcmqiUrls.cmake)
+
+#
+# Download & extract archive
+#
+set(download_dir "${PROJECT_BINARY_DIR}")
+set(extract_dir "${PROJECT_BINARY_DIR}/dcmqi-binary-distribution")
+include(FetchContent)
+FetchContent_Populate(dcmqi
+  URL ${dcmqi_archive_url}
+  URL_HASH SHA256=${dcmqi_archive_sha256}
+  DOWNLOAD_DIR ${download_dir}
+  SOURCE_DIR "${extract_dir}"
+  )
+
+#
+# Install executable
+#
+
+set(_permissions PERMISSIONS
+  OWNER_READ OWNER_WRITE OWNER_EXECUTE
+  GROUP_READ GROUP_EXECUTE
+  WORLD_READ WORLD_EXECUTE
+  )
+
+set(itkimage2segimage_executable_name "itkimage2segimage${CMAKE_EXECUTABLE_SUFFIX}")
+set(segimage2itkimage_executable_name "segimage2itkimage${CMAKE_EXECUTABLE_SUFFIX}")
+set(tid1500writer_executable_name "tid1500writer${CMAKE_EXECUTABLE_SUFFIX}")
+set(tid1500reader_executable_name "tid1500reader${CMAKE_EXECUTABLE_SUFFIX}")
+set(itkimage2paramap_executable_name "itkimage2paramap${CMAKE_EXECUTABLE_SUFFIX}")
+set(paramap2itkimage_executable_name "paramap2itkimage${CMAKE_EXECUTABLE_SUFFIX}")
+
+install(PROGRAMS ${extract_dir}/bin/${itkimage2segimage_executable_name} DESTINATION "dcmqi/bin" ${_permissions})
+install(PROGRAMS ${extract_dir}/bin/${segimage2itkimage_executable_name} DESTINATION "dcmqi/bin" ${_permissions})
+install(PROGRAMS ${extract_dir}/bin/${tid1500writer_executable_name} DESTINATION "dcmqi/bin" ${_permissions})
+install(PROGRAMS ${extract_dir}/bin/${tid1500reader_executable_name} DESTINATION "dcmqi/bin" ${_permissions})
+install(PROGRAMS ${extract_dir}/bin/${itkimage2paramap_executable_name} DESTINATION "dcmqi/bin" ${_permissions})
+install(PROGRAMS ${extract_dir}/bin/${paramap2itkimage_executable_name} DESTINATION "dcmqi/bin" ${_permissions})

dcmqi-0.1.0/LICENSE

@@ -0,0 +1,19 @@
+Copyright 2024 Leonard Nürnberg
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.