added new workflows

ReproNim · May 1, 2023 · e975219 · e975219
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diff --git a/.github/workflows/afni.yml 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', 'ubuntu:16.04', 'debian:bullseye-slim', 'debian:buster-slim', 'debian:stretch-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@v2
+        with:
+          python-version: "3.10"
+
+      - name: Install neurodocker
+        run: python -m pip install --editable .[dev]
+
+      - name: Generate Dockerfile
+        run: |
+
+          apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'ubuntu:16.04', 'debian:bullseye-slim', 'debian:buster-slim', 'debian:stretch-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
@@ -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', 'ubuntu:16.04', 'debian:bullseye-slim', 'debian:buster-slim', 'debian:stretch-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@v2
+        with:
+          python-version: "3.10"
+
+      - name: Install neurodocker
+        run: python -m pip install --editable .[dev]
+
+      - name: Generate Dockerfile
+        run: |
+
+          apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'ubuntu:16.04', 'debian:bullseye-slim', 'debian:buster-slim', 'debian:stretch-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/cat12.yml 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', 'ubuntu:16.04', 'debian:bullseye-slim', 'debian:buster-slim', 'debian:stretch-slim', 'fedora:36', 'centos:7']
+        version: ['r1933_R2017b']
+        method: ['binaries']
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+
+      - name: Install neurodocker
+        run: python -m pip install --editable .[dev]
+
+      - name: Generate Dockerfile
+        run: |
+
+          apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'ubuntu:16.04', 'debian:bullseye-slim', 'debian:buster-slim', 'debian:stretch-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
@@ -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', 'ubuntu:16.04', 'debian:bullseye-slim', 'debian:buster-slim', 'debian:stretch-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@v2
+        with:
+          python-version: "3.10"
+
+      - name: Install neurodocker
+        run: python -m pip install --editable .[dev]
+
+      - name: Generate Dockerfile
+        run: |
+
+          apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'ubuntu:16.04', 'debian:bullseye-slim', 'debian:buster-slim', 'debian:stretch-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
@@ -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', 'ubuntu:16.04', 'debian:bullseye-slim', 'debian:buster-slim', 'debian:stretch-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@v2
+        with:
+          python-version: "3.10"
+
+      - name: Install neurodocker
+        run: python -m pip install --editable .[dev]
+
+      - name: Generate Dockerfile
+        run: |
+
+          apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'ubuntu:16.04', 'debian:bullseye-slim', 'debian:buster-slim', 'debian:stretch-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
@@ -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', 'ubuntu:16.04', 'debian:bullseye-slim', 'debian:buster-slim', 'debian:stretch-slim', 'fedora:36', 'centos:7']
+        version: ['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@v2
+        with:
+          python-version: "3.10"
+
+      - name: Install neurodocker
+        run: python -m pip install --editable .[dev]
+
+      - name: Generate Dockerfile
+        run: |
+
+          apt_based=('ubuntu:22.04', 'ubuntu:18.04', 'ubuntu:16.04', 'debian:bullseye-slim', 'debian:buster-slim', 'debian:stretch-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 .