README.md

C-PAC/.github README

This directory contains Dockerfiles, scripts, requirements files, and workflow configurations for this repository's GitHub Actions.

When updating these files, please update this README as necessary.

The workflows directory contains the configurations for the Actions themselves. The other directories support these configs.

flowchart TD
    subgraph Dockerfiles
      base[base-.*]

      cpacdockerfiles["C-PAC.develop-(?!lite).*"]

      cpaclitedockerfile[C-PAC.develop-lite.*]

      stagedockerfiles[AFNI.*\nANTs.*\nc3d.*\nconnectome-workbench.*\nFSL.*\nICA-AROMA.*\nmsm.*]

      ubuntudockerfiles[Ubuntu.*]
    end
    subgraph scripts
      get_package_id.py
      get_pr_base_shas
      local_ghcr
    end
    subgraph smoke_test_participant.yml
      smoke_test_human
      smoke_test_nhp
      smoke_test_rodent
    end
    subgraph stage_requirements
      .*.txt
    end
    subgraph workflows
      subgraph build_stages.yml

        ubuntu[[Ubnutu]]-->stages[[stages]]-->build-base[[build-base]]

      end
      subgraph build_C-PAC.yml
        bCPAC[[C-PAC]]
      end
      subgraph build_and_test.yml
        Circle_tests[[Circle_tests]]
      
        C-PAC[[C-PAC]]-->bCPAC
        C-PAC-->Circle_tests
        C-PAC-->smoke-tests-participant
        C-PAC-->C-PAC-lite

        C-PAC-lite[[C-PAC-lite]]-->bCPAC
        C-PAC-lite-->Circle_tests
        C-PAC-lite-->smoke-tests-participant

        C-PAC-ABCD-HCP[[C-PAC-ABCD-HCP]]-->bCPAC
        C-PAC-ABCD-HCP-->Circle_tests
        C-PAC-ABCD-HCP-->smoke-tests-participant

        C-PAC-fMRIPrep[[C-PAC-fMRIPrep-LTS]]-->bCPAC
        C-PAC-fMRIPrep-->Circle_tests
        C-PAC-fMRIPrep-->smoke-tests-participant

        smoke-tests-participant[[smoke-tests-participant]]
      end

      on_push.yml-->build_stages.yml

      delete_images.yml
    end

    subgraph yaml_template[CPAC/utils/configuration/yaml_template.py]

      update_all_preconfigs[[update_all_preconfigs]]
    end

    base<-->build-base

    Circle_tests-->CircleCI((Run tests on Circle CI))

    build_stages.yml-->build_and_test.yml

    on_push.yml<-->get_pr_base_shas
    on_push.yml-->update_all_preconfigs

    cpacdockerfiles<-->C-PAC
    cpacdockerfiles<-->C-PAC-ABCD-HCP
    cpacdockerfiles<-->C-PAC-fMRIPrep

    cpaclitedockerfile<-->C-PAC-lite

    delete>delete branch]-->delete_images.yml

    delete_images.yml<-->get_package_id.py

    build-base<-->local_ghcr
    bCPAC<-->local_ghcr
    stages<-->local_ghcr

    push>git push]-->on_push.yml

    smoke-tests-participant-->smoke_test_human
    smoke-tests-participant-->smoke_test_nhp
    smoke-tests-participant-->smoke_test_rodent

    stagedockerfiles<-->stages

    build-base<-->.*.txt

    ubuntudockerfiles<-->ubuntu

Loading

In this Mermaid flowchart, these shapes are used:

concept	shape
directory	subgraph
file	rectangle ([]) or subgraph
workflow job	subprocess ([[]])
trigger action	asymetric (>])
external API	circle ((()))

Multistage builds

C-PAC images are built in stages like

flowchart LR

OS["operating system"] --> deps["versioned dependencies"]
deps --> base["base image"]
base --> CPAC["C-PAC version"]

Loading

See fcp-indi.github.io/docs/nightly/developer/installation for more information about C-PAC's use of multistage builds.

GitHub Actions will dynamically skip building stages based on when a stage's Dockerfile or a workflow file was last modified. To force a stage to rebuild, include

[rebuild ${DOCKERFILE_BASENAME}]

in a commit message and push. For example, to rebuild ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free, include

[rebuild Ubuntu.bionic-non-free]

in the commit message. For this to work, all of these must be true:

1. The Dockerfile is listed in a

   strategy:
     matrix:
       Dockerfile: 

   in a job in a workflow file.

2. The Dockerfile exists.

3. The commit message including

   [rebuild ${DOCKERFILE_BASENAME}]

   is for the most recent commit when pushing to GitHub.