From 9587c136e3ddef0a0a9c653ff15fa5a5dedf65ed Mon Sep 17 00:00:00 2001 From: Repronim neurodocker bot Date: Fri, 15 Nov 2024 00:05:35 +0000 Subject: [PATCH] added new workflows --- .github/workflows/afni.yml | 64 +++++++++++++++++ .github/workflows/ants.yml | 62 ++++++++++++++++ .github/workflows/bids_validator.yml | 62 ++++++++++++++++ .github/workflows/cat12.yml | 63 +++++++++++++++++ .github/workflows/convert3d.yml | 62 ++++++++++++++++ .github/workflows/dcm2niix.yml | 62 ++++++++++++++++ .github/workflows/freesurfer.yml | 60 ++++++++++++++++ .github/workflows/fsl.yml | 62 ++++++++++++++++ .github/workflows/jq.yml | 62 ++++++++++++++++ .github/workflows/matlabmcr.yml | 62 ++++++++++++++++ .github/workflows/miniconda.yml | 60 ++++++++++++++++ .github/workflows/mricron.yml | 62 ++++++++++++++++ .github/workflows/mrtrix3.yml | 62 ++++++++++++++++ .github/workflows/spm12.yml | 62 ++++++++++++++++ docs/README.md | 102 +++++++++++++++++++++++++++ 15 files changed, 969 insertions(+) create mode 100644 .github/workflows/afni.yml create mode 100644 .github/workflows/ants.yml create mode 100644 .github/workflows/bids_validator.yml create mode 100644 .github/workflows/cat12.yml create mode 100644 .github/workflows/convert3d.yml create mode 100644 .github/workflows/dcm2niix.yml create mode 100644 .github/workflows/freesurfer.yml create mode 100644 .github/workflows/fsl.yml create mode 100644 .github/workflows/jq.yml create mode 100644 .github/workflows/matlabmcr.yml create mode 100644 .github/workflows/miniconda.yml create mode 100644 .github/workflows/mricron.yml create mode 100644 .github/workflows/mrtrix3.yml create mode 100644 .github/workflows/spm12.yml create mode 100644 docs/README.md diff --git a/.github/workflows/afni.yml b/.github/workflows/afni.yml new file mode 100644 index 00000000..59ad1587 --- /dev/null +++ b/.github/workflows/afni.yml @@ -0,0 +1,64 @@ +# This is file is automatically generated. Do not edit. +name: 'afni' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + afni: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['latest'] + method: ['binaries', 'source'] + afni_python: ['true', 'false'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --afni \ + version=${{ matrix.version }} \ + method=${{ matrix.method }} \ + install_python3=${{ matrix.afni_python }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/ants.yml b/.github/workflows/ants.yml new file mode 100644 index 00000000..978817a6 --- /dev/null +++ b/.github/workflows/ants.yml @@ -0,0 +1,62 @@ +# This is file is automatically generated. Do not edit. +name: 'ants' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + ants: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['2.4.3', '2.4.2', '2.4.1', '2.3.4', '2.3.2', '2.3.1', '2.3.0', '2.2.0', '2.1.0', '2.0.3', '2.0.0'] + method: ['binaries', 'source'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --ants \ + version=${{ matrix.version }} \ + method=${{ matrix.method }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/bids_validator.yml b/.github/workflows/bids_validator.yml new file mode 100644 index 00000000..fbf9e352 --- /dev/null +++ b/.github/workflows/bids_validator.yml @@ -0,0 +1,62 @@ +# This is file is automatically generated. Do not edit. +name: 'bids_validator' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + bids_validator: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['1.13.0', '1.12.0', '1.11.0', '1.10.0', '1.9.0'] + method: ['binaries'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --bids_validator \ + version=${{ matrix.version }} \ + method=${{ matrix.method }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/cat12.yml b/.github/workflows/cat12.yml new file mode 100644 index 00000000..a1565f93 --- /dev/null +++ b/.github/workflows/cat12.yml @@ -0,0 +1,63 @@ +# This is file is automatically generated. Do not edit. +name: 'cat12' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + cat12: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['r1933_R2017b', 'r2166_R2017b'] + method: ['binaries'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --matlabmcr method='binaries' version='2017b' \ + --cat12 \ + version=${{ matrix.version }} \ + method=${{ matrix.method }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/convert3d.yml b/.github/workflows/convert3d.yml new file mode 100644 index 00000000..59ca85be --- /dev/null +++ b/.github/workflows/convert3d.yml @@ -0,0 +1,62 @@ +# This is file is automatically generated. Do not edit. +name: 'convert3d' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + convert3d: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['nightly', '1.0.0'] + method: ['binaries'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --convert3d \ + version=${{ matrix.version }} \ + method=${{ matrix.method }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/dcm2niix.yml b/.github/workflows/dcm2niix.yml new file mode 100644 index 00000000..c77ccec4 --- /dev/null +++ b/.github/workflows/dcm2niix.yml @@ -0,0 +1,62 @@ +# This is file is automatically generated. Do not edit. +name: 'dcm2niix' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + dcm2niix: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['latest', 'v1.0.20201102', 'v1.0.20200331', 'v1.0.20190902'] + method: ['binaries', 'source'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --dcm2niix \ + version=${{ matrix.version }} \ + method=${{ matrix.method }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/freesurfer.yml b/.github/workflows/freesurfer.yml new file mode 100644 index 00000000..b16f27b7 --- /dev/null +++ b/.github/workflows/freesurfer.yml @@ -0,0 +1,60 @@ +# This is file is automatically generated. Do not edit. +name: 'freesurfer' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + freesurfer: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['7.4.1', '7.3.2', '7.3.1', '7.3.0', '7.2.0', '7.1.1', '7.1.1-min', '7.1.0', '6.0.1', '6.0.0', '6.0.0-min'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --freesurfer \ + version=${{ matrix.version }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/fsl.yml b/.github/workflows/fsl.yml new file mode 100644 index 00000000..dc2bb391 --- /dev/null +++ b/.github/workflows/fsl.yml @@ -0,0 +1,62 @@ +# This is file is automatically generated. Do not edit. +name: 'fsl' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + fsl: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['6.0.7.14', '6.0.7.8', '6.0.7.4', '6.0.7.1', '6.0.6.4', '6.0.6.3', '6.0.6.2', '6.0.6.1', '6.0.6', '6.0.5.2', '6.0.5.1', '6.0.5', '6.0.4', '6.0.3', '6.0.2', '6.0.1', '6.0.0', '5.0.11', '5.0.10', '5.0.9', '5.0.8'] + method: ['binaries'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --fsl \ + version=${{ matrix.version }} \ + method=${{ matrix.method }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/jq.yml b/.github/workflows/jq.yml new file mode 100644 index 00000000..02984a9f --- /dev/null +++ b/.github/workflows/jq.yml @@ -0,0 +1,62 @@ +# This is file is automatically generated. Do not edit. +name: 'jq' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + jq: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['1.6', '1.5'] + method: ['binaries', 'source'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --jq \ + version=${{ matrix.version }} \ + method=${{ matrix.method }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/matlabmcr.yml b/.github/workflows/matlabmcr.yml new file mode 100644 index 00000000..8e220d6a --- /dev/null +++ b/.github/workflows/matlabmcr.yml @@ -0,0 +1,62 @@ +# This is file is automatically generated. Do not edit. +name: 'matlabmcr' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + matlabmcr: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['2023b', '2023a', '2022b', '2022a', '2021b', '2021a', '2020b', '2020a', '2019b', '2019a', '2018b', '2018a', '2017b', '2017a', '2016b', '2016a', '2015b', '2015aSP1', '2015a', '2014a', '2014b', '2013b', '2013a', '2012b', '2012a', '2010a'] + method: ['binaries'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --matlabmcr \ + version=${{ matrix.version }} \ + method=${{ matrix.method }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/miniconda.yml b/.github/workflows/miniconda.yml new file mode 100644 index 00000000..e2e1ec61 --- /dev/null +++ b/.github/workflows/miniconda.yml @@ -0,0 +1,60 @@ +# This is file is automatically generated. Do not edit. +name: 'miniconda' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + miniconda: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['latest'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --miniconda \ + version=${{ matrix.version }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/mricron.yml b/.github/workflows/mricron.yml new file mode 100644 index 00000000..a9864581 --- /dev/null +++ b/.github/workflows/mricron.yml @@ -0,0 +1,62 @@ +# This is file is automatically generated. Do not edit. +name: 'mricron' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + mricron: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['1.0.20190902', '1.0.20190410', '1.0.20181114', '1.0.20180614', '1.0.20180404', '1.0.20171220'] + method: ['binaries'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --mricron \ + version=${{ matrix.version }} \ + method=${{ matrix.method }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/mrtrix3.yml b/.github/workflows/mrtrix3.yml new file mode 100644 index 00000000..c547c085 --- /dev/null +++ b/.github/workflows/mrtrix3.yml @@ -0,0 +1,62 @@ +# This is file is automatically generated. Do not edit. +name: 'mrtrix3' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + mrtrix3: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['3.0.4', '3.0.3', '3.0.2', '3.0.1', '3.0.0'] + method: ['binaries', 'source'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --mrtrix3 \ + version=${{ matrix.version }} \ + method=${{ matrix.method }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/.github/workflows/spm12.yml b/.github/workflows/spm12.yml new file mode 100644 index 00000000..c389dfb5 --- /dev/null +++ b/.github/workflows/spm12.yml @@ -0,0 +1,62 @@ +# This is file is automatically generated. Do not edit. +name: 'spm12' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +on: + push: + branches: ["test_docker_build"] + +jobs: + + spm12: + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + base_image: ['ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim', 'fedora:36', 'centos:7'] + version: ['r7771', 'r7487', 'r7219', 'r6914', 'r6685', 'r6472', 'r6225'] + method: ['binaries'] + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.11" + + - name: Install neurodocker + run: python -m pip install --editable .[dev] + + - name: Generate Dockerfile + run: | + + apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'debian:bullseye-slim', 'debian:buster-slim') + if [[ " ${apt_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="apt" + fi + + yum_based=('fedora:36', 'centos:7') + if [[ " ${yum_based[*]} " =~ ${{ matrix.base_image }} ]]; then + pkg_manager="yum" + fi + + neurodocker \ + generate docker \ + --base-image=${{ matrix.base_image }} \ + --pkg-manager=${pkg_manager} \ + --yes \ + --spm12 \ + version=${{ matrix.version }} \ + method=${{ matrix.method }} \ + > Dockerfile_tmp + + cat Dockerfile_tmp + + - name: Build the Docker image + run: docker build -f Dockerfile_tmp . diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 00000000..8cadd3b1 --- /dev/null +++ b/docs/README.md @@ -0,0 +1,102 @@ + +# Build dashboard + +- [afni](#afni) +- [ants](#ants) +- [bids_validator](#bids_validator) +- [cat12](#cat12) +- [convert3d](#convert3d) +- [dcm2niix](#dcm2niix) +- [freesurfer](#freesurfer) +- [fsl](#fsl) +- [jq](#jq) +- [matlabmcr](#matlabmcr) +- [mricron](#mricron) +- [mrtrix3](#mrtrix3) +- [spm12](#spm12) +- [miniconda](#miniconda) + +## afni + +[afni workflow](https://github.com/ReproNim/neurodocker/actions/workflows/afni.yml) + +![afni build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=afni) + +## ants + +[ants workflow](https://github.com/ReproNim/neurodocker/actions/workflows/ants.yml) + +![ants build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=ants) + +## bids_validator + +[bids_validator workflow](https://github.com/ReproNim/neurodocker/actions/workflows/bids_validator.yml) + +![bids_validator build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=bids_validator) + +## cat12 + +[cat12 workflow](https://github.com/ReproNim/neurodocker/actions/workflows/cat12.yml) + +![cat12 build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=cat12) + +## convert3d + +[convert3d workflow](https://github.com/ReproNim/neurodocker/actions/workflows/convert3d.yml) + +![convert3d build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=convert3d) + +## dcm2niix + +[dcm2niix workflow](https://github.com/ReproNim/neurodocker/actions/workflows/dcm2niix.yml) + +![dcm2niix build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=dcm2niix) + +## freesurfer + +[freesurfer workflow](https://github.com/ReproNim/neurodocker/actions/workflows/freesurfer.yml) + +![freesurfer build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=freesurfer) + +## fsl + +[fsl workflow](https://github.com/ReproNim/neurodocker/actions/workflows/fsl.yml) + +![fsl build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=fsl) + +## jq + +[jq workflow](https://github.com/ReproNim/neurodocker/actions/workflows/jq.yml) + +![jq build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=jq) + +## matlabmcr + +[matlabmcr workflow](https://github.com/ReproNim/neurodocker/actions/workflows/matlabmcr.yml) + +![matlabmcr build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=matlabmcr) + +## mricron + +[mricron workflow](https://github.com/ReproNim/neurodocker/actions/workflows/mricron.yml) + +![mricron build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=mricron) + +## mrtrix3 + +[mrtrix3 workflow](https://github.com/ReproNim/neurodocker/actions/workflows/mrtrix3.yml) + +![mrtrix3 build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=mrtrix3) + +## spm12 + +[spm12 workflow](https://github.com/ReproNim/neurodocker/actions/workflows/spm12.yml) + +![spm12 build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=spm12) + +## miniconda + +[miniconda workflow](https://github.com/ReproNim/neurodocker/actions/workflows/miniconda.yml) + +![miniconda build status](http://github-actions.40ants.com/ReproNim/neurodocker/matrix.svg?branch=test_docker_build&only=miniconda) +