ITKRemoteModuleBuildTestPackageAction

This project provides reusable GitHub Actions workflows to build, test, and package ITK external modules.

The Insight Toolkit (ITK) is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. More information is available on the ITK website or at the ITK GitHub homepage.

Table of Contents

• Motivation
• Usage
  • Example Usage
  • build-test-cxx Overview
  • build-test-package-python Overview
• Contributing
• Frequently Asked Questions
• Additional Notes
• Community Discussion
• License

Motivation

The ITK ecosystem is driven by community contributions in the form of external modules that provide expanded functionality. Chapter 9 of the ITK Software Guide, "How To Create A Module", details the process to extend ITK.

Continuous Integration (CI) is a best software practice wherein proposed code changes are automatically built and tested for quality assurance. The goal of ITKRemoteModuleBuildTestPackageAction is to minimize the CI development burden for community members by providing workflows for common building, testing, and packaging procedures.

In most cases community members can leverage ITKRemoteModuleBuildTestPackageAction in their external module projects for several advantages:

• Build procedures are provided as GitHub Actions (GHA) reusable workflow .yml files which integrate directly with GHA runners. These can be invoked for a given external module in its GitHub repository with minimal code.
• Build procedure updates are centralized. Rather than replicating build step updates directly in a custom build procedure for each external module, developers may simply update workflow commit tags to include process updates in external module CI. For example, updating a runner platform version from ubuntu-18.04 to ubuntu-20.04 would be introduced to ITKRemoteModuleBuildTestPackageAction once and then consumed by a variety of external modules by simply updating the ITKRemoteModuleBuildTestPackageAction commit hash accordingly.

Provided Workflows

Reusable workflow scripts are provided in the .github/workflows directory. Workflows are organized by target distribution:

• The build-test-cxx workflow provides processes for building a module from its C++ source code, running module tests, and then reporting those test results to CDash. The module is built and tested on Windows, Ubuntu, and MacOS platforms with provided GHA runners. Results are visible at the ITK CDash dashboard.
• The build-test-package-python workflow builds and packages external module Python wheels for Windows, Ubuntu, and MacOS platforms. The workflow uses build scripts provided at ITKPythonPackage.

Usage

ITKRemoteModuleBuildTestPackageAction may be used by ITK external modules that are hosted on GitHub to make use of GHA CI runners. The provided workflows assume that any build dependencies other than ITK will be fetched during the CMake build process.

Reusable workflows may be referenced inside an external module's .github/workflows/build-test-package.yml file to run when changes to the module are proposed. Input parameters may also be passed to the reusable workflow to guide the build/test procedure. See the inputs: field in any ITKRemoteModuleBuildTestPackageAction file for a list of parameters available for use.

More information on GitHub Actions reusable workflows is available in GitHub documentation.

Example Usage

An example GHA .yml file using ITKRemoteModuleBuildTestPackageAction workflows:

name: Build, test, package

on: [push,pull_request]

jobs:
  cxx-build-workflow:
    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@d4a5ce4f219b66b78269a15392e15c95f90e7e00
    with:
      itk-cmake-options: '-DITK_BUILD_DEFAULT_MODULES:BOOL=OFF -DITKGroup_Core:BOOL=ON'

  python-build-workflow:
    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@d4a5ce4f219b66b78269a15392e15c95f90e7e00
    secrets:
      pypi_password: ${{ secrets.pypi_password }}

The example above can be broken down line by line:

name: Build, test, package

The workflow name that will be used to group workflow runs under the "Action" tab on the external module's GitHub page.

on: [push, pull_request]

Run workflows every time a new commit is pushed or a pull request is entered on the module repository.

jobs:

The top-level jobs used to organize the run. Reusable workflows may provide multiple jobs.

  cxx-build-workflow:
    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@d4a5ce4f219b66b78269a15392e15c95f90e7e00

Tells GHA to fetch and run the build-test-cxx.yml workflow. A commit hash or tagged version may be provided.

    with:
      itk-cmake-options: '-DITK_BUILD_DEFAULT_MODULES:BOOL=OFF -DITKGroup_Core:BOOL=ON'

Passes input arguments to the reusable workflow. In this case the parameters provided in itk-cmake-options will be passed to the ITK configuration command so that only certain modules are built before the external module itself is subsequently built against ITK.

  python-build-workflow:
    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@d4a5ce4f219b66b78269a15392e15c95f90e7e00

Tells GHA to fetch and run the build-test-package-python.yml workflow. A commit hash or tagged version may be provided.

  secrets:
    pypi_password: ${{ secrets.pypi_password }}

Passes a secret from the external module repository to the workflow. In this case the pypi_password secret is required for automatically uploading Python wheel to the Python Package Index (PyPI) for distribution.

ITKSplitComponents is one example of an external module leveraging reusable workflows for continuous integration. Refer to ITKSplitComponent's GHA workflow

build-test-cxx Overview

The workflow defined in build-test-cxx.yml builds and tests the external module against a recent version of the Insight Toolkit. For efficiency, wrappings are not typically built as part of this workflow.

Several optional parameters are exposed to allow the external module to direct workflow execution.

• itk-git-tag: The git tag or commit hash to use to fetch ITK.

  with:
    itk-git-tag: 'v5.3.0'

• itk-cmake-options: CMake configuration parameters for building ITK as a prerequisite.

  with:
    itk-cmake-options: '-DITK_BUILD_DEFAULT_MODULES:BOOL=OFF'

• itk-module-deps: List of ITK remote module dependencies to build. Module name and git tag are passed to ITK to be fetched and built during the ITK build procedure. Note that the C++ build pipeline currently supports only modules that have a .remote.cmake entry under ITK/Modules/Remote. The list is colon-delimited and must be in order of subsequent dependencies, i.e. if module B depends on module A then module A must be listed first. A git tag or commit hash must be provided for each module entry. The list is formatted as module_A@tag:module_B@tag:.... Note that the "ITK" prefix is omitted for fetching remote modules.

  with:
    itk-module-deps: 'MeshToPolyData@3ad8f08:BSplineGradient@0.3.0'

• cmake-options: CMake configuration parameters for the module under test.

  with:
    cmake-options: '-DBUILD_EXAMPLES:BOOL=ON'

• warnings-to-ignore: Warning string patterns that should be ignored for CTest/CDash reporting. If the given warning text is found in build output then it should neither be reported as a warning nor result in a build "failure". The input to this parameter should be escaped with double quotations and multiple warnings should be separated by spaces.

  with:
    warnings-to-ignore: '\"libcleaver.a.*has no symbols\" \"libitkcleaver.*has no symbols\"'

• ctest-options: CTest command line interface (CLI) run options for the module under test. CTest options are described in CTest documentation. This parameter can be used to disable tests that are known to be broken, increase output verbosity, and more. Some options may be always enabled by default.

  with:
    ctest-options: '-E \"elastix_run_example_COMPARE_IM|elastix_run_3DCT_lung.MI.bspline.ASGD.001_COMPARE_TP\"'

build-test-package-python Overview

The workflow defined in build-test-package-python.yml builds and packages Python wrappings for the external module against a fixed version of the Insight Toolkit.

Several optional parameters are exposed to allow the external module to direct workflow execution.

• cmake-options: CMake configuration parameters for the module under test.

  with:
    cmake-options: '-DELASTIX_USE_OPENMP:BOOL=OFF'

• itk-wheel-tag: The GitHub release version tag for the ITKPythonBuilds archive to use. In order to efficiently package arbitrary ITK external modules within GitHub Actions runners time limits the Insight Software Consortium provides tagged ITK build caches at ITKPythonBuilds that correspond to pip-installable ITK releases on the Python Package Index. Setting this parameter will build the external module against a fixed ITK build cache corresponding to a certain ITK wheel release on PyPI. See ITKPythonBuilds/releases for a list of available tags to use.

  with:
    itk-wheel-tag: 'v5.3.0'

• itk-python-package-tag: The git tag or commit hash for ITKPythonPackage build scripts to use. The ITKPythonPackage repository contains scripts for building ITK wheels and ITK external module wheels for different Python versions on MacOS, Linux, and Windows target platforms. Setting this parameter will direct the workflow to use a certain script revision for building Python wheels. See available tags at ITKPythonPackage/releases.

  with:
    itk-python-package-tag: 'v5.3.0'

• itk-python-package-org: The GitHub organization to reference for fetching ITKPythonPackage build scripts. The central script repository is maintained on GitHub at InsightSoftwareConsortium/ITKPythonPackage. Setting this parameter will direct the workflow to fetch from an ITKPythonPackage fork on a different GitHub user's or organization's account. Using this parameter is discouraged for purposes other than testing ITKPythonPackage development branches.

  with:
    itk-python-package-org: 'InsightSoftwareConsortium'

• itk-module-deps: List of ITK remote module dependencies to build. Module name and git tag are iteratively fetched and built during the ITK build procedure. Modules need not be listed under ITK/Modules/Remote. The list is colon-delimited and must be in order of subsequent dependencies, i.e. if module B depends on module A then module A must be listed first. A git tag or commit hash must be provided for each module entry. The list is formatted as org/module_A@tag:org/module_B@tag:....

  with:
    itk-module-deps: 'InsightSoftwareConsortium/ITKMeshToPolyData@3ad8f08:InsightSoftwareConsortium/ITKBSplineGradient@0.3.0'

• python3-minor-versions: Array of Python 3.x wheel minor versions to target for building. The array follows JavaScript Object Notation (JSON) syntax and GHA jobs will launch in the order provided. One wheel is built per Python version and target platform. The first listed Python version may also be used for running Linux notebook tests if enabled. The default value is a list of currently supported Python versions ascending from oldest to newest.

  with:
    python3-minor-versions: '["7","8","9","10","11"]` # Builds for Python 3.7 through 3.11

• manylinux-platforms: Array of manylinux specialization build targets for Linux Python module wheels. Manylinux "provides a convenient way to distribute binary Python extensions as wheels on Linux"; see the manylinux README for more details. An array entry includes both the name of the manylinux specialization, which is related to the toolset to be used, and the platform architecture to target. All supported specialization and architecture pairs are enabled by default and listed in the example below, but can be disabled by removing them from the input array in the calling external module workflow. The array follows JavaScript Object Notation (JSON) syntax and GHA jobs will launch in the order provided. The array is formatted as '["-","-"]'.

  with:
    manylinux-platforms: '["_2_28-x64","2014-x64","_2_28-aarch64"]'

• test-notebooks: Boolean option to test Jupyter Notebook examples located in the examples/ directory of the external module. A requirements.txt file should be provided in either the external module root or binder/ directories to indicate notebook prerequisites for testing. The first Python version listed in python3-minor-versions will be used, i.e. if "9" is listed first then notebook tests will be run with Python 3.9. Default value is false, notebook tests may be enabled for a repository containing notebook examples by setting the value to true.

  with:
    test-notebooks: true

Contributing

Community contributions to ITKRemoteModuleBuildTestPackageAction are welcome!

Please read CONTRIBUTING.md for testing instructions and best practices before opening a pull request to contribute your changes. Also see ITK's contributing documentation for general best practices regarding ITK and external modules.

Workflow issues may be submitted to the ITKRemoteModuleBuildTestPackageAction issue tracker on GitHub.

Frequently Asked Questions

What target platforms and architectures are supported?

The build-test-cxx workflow supports building and running C++ tests on GitHub Actions runner images for Windows, Linux, and macOS. Image details are available here.

The build-test-package-python.yml workflow supports Python package generation for the following platforms and architectures:

• Windows 10 x86_64 platforms
• Windows 11 x86_64 platforms
• macOS 10.9+ x86_64 platforms
• macOS 11.0+ ARM64 platforms
• Linux glibc 2.17+ (E.g. Ubuntu 18.04+) x86_64 platforms
• Linux glibc 2.28+ (E.g. Ubuntu 20.04+) aarch64 (ARMv8) platforms

What should I do if my target platform/architecture does not appear on the list above?

itk-wasm is another experimental path for reproducible execution across architectures, with planned support for ITK external module Python distributions. Read more at https://wasm.itk.org/.

If the answers above do not meet your platform needs, please open an issue in the project issue tracker for discussion, and consider contributing either time or funding to support development. The ITK open source ecosystem is driven through contributions from its community members.

Additional Notes

ITKRemoteModuleBuildTestPackageAction aims to provide boilerplate to simplify CI processes for the majority of ITK C++ external modules. However, it may not be feasible to adapt reusable workflows to fit every project's needs, particularly in the case where build setup requires fetching project-specific third party dependencies before building.

If your project requires build steps not currently addressed by ITKRemoteModuleBuildTestPackageAction then consider doing one of the following:

1. Implement build setup steps in your project's CMake procedures in CMakeLists.txt such that building with CMake in a reusable workflow handles extraneous dependency retrieval steps.
2. Fork the workflows in ITKRemoteModuleBuildTestPackageAction for your project and manually replicate subsequent updates in your workflow.
3. Open a pull request to propose changes if the changes will generally benefit other external modules in the ITK ecosystem.
4. Open an issue on ITKRemoteModuleBuildTestPackageAction.

Community Discussion

Please direct general questions and discussions to the ITK Discourse forum.

License

ITKRemoteModuleBuildTestPackageAction is distributed under the Apache License 2.0 (see LICENSE)