Merge pull request #7 from bids-apps/6.0.1

[REL] 6.0.1

.circleci/config.yml

@@ -0,0 +1,47 @@
+---
+version: 2.1
+jobs:
+  build:
+    machine:
+      # https://circleci.com/developer/machine/image/ubuntu-2204
+      image: ubuntu-2204:2022.10.2
+    steps:
+    - checkout
+    - run:
+        name: build docker image
+        command: |
+          wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/circleci/build_docker.sh
+          bash build_docker.sh
+    - persist_to_workspace:
+        root: /home/circleci
+        paths:
+        - docker/image.tar
+
+  deploy:
+    machine:
+      image: ubuntu-2204:2022.10.2
+    steps:
+    - attach_workspace:
+        at: /tmp/workspace
+    - run: docker load -i /tmp/workspace/docker/image.tar
+    - run:
+        name: push to dockerhub
+        command: |
+          wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/circleci/push_docker.sh
+          bash push_docker.sh
+
+workflows:
+  build_deploy:
+    jobs:
+    - build:
+        filters:
+          branches:
+            only: master
+    - deploy:
+        context:
+        - dockerhub
+        requires:
+        - build
+        filters:
+          branches:
+            only: master

.hadolint.yaml

@@ -0,0 +1,9 @@
+---
+ignored:
+- DL3002
+- DL3006
+- DL3008
+- DL4006
+- SC2015
+- SC2016
+- SC2028

.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+---
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.3.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-json
+  - id: check-added-large-files
+  - id: check-case-conflict
+  - id: check-merge-conflict
+
+
+- repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+  rev: 0.2.2
+  hooks:
+  - id: yamlfmt
+    args: [--mapping, '2', --sequence, '2', --offset, '0']
+
+
+- repo: https://github.com/hadolint/hadolint
+  rev: v2.12.0
+  hooks:
+  - id: hadolint-docker
+    name: Lint Dockerfiles
+    description: Runs hadolint Docker image to lint Dockerfiles
+    language: docker_image
+    types: [dockerfile]
+    entry: ghcr.io/hadolint/hadolint hadolint
+
+ci:
+  skip: [hadolint-docker]

Dockerfile

@@ -1,22 +1,86 @@
-FROM bids/base_validator
-
-RUN apt-get update && \
-    apt-get install -y curl && \
-    curl -sSL http://neuro.debian.net/lists/trusty.us-ca.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
-    apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9 && \
-    apt-get update && \
-    apt-get remove -y curl && \
-    apt-get install -y fsl-core=5.0.9-3~nd14.04+1 && \
-    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+# Generated by Neurodocker and Reproenv.
 
+FROM bids/base_validator
+ENV FSLDIR="/opt/fsl-6.0.1" \
+    PATH="/opt/fsl-6.0.1/bin:$PATH" \
+    FSLOUTPUTTYPE="NIFTI_GZ" \
+    FSLMULTIFILEQUIT="TRUE" \
+    FSLTCLSH="/opt/fsl-6.0.1/bin/fsltclsh" \
+    FSLWISH="/opt/fsl-6.0.1/bin/fslwish" \
+    FSLLOCKDIR="" \
+    FSLMACHINELIST="" \
+    FSLREMOTECALL="" \
+    FSLGECUDAQ="cuda.q"
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           bc \
+           ca-certificates \
+           curl \
+           dc \
+           file \
+           libfontconfig1 \
+           libfreetype6 \
+           libgl1-mesa-dev \
+           libgl1-mesa-dri \
+           libglu1-mesa-dev \
+           libgomp1 \
+           libice6 \
+           libopenblas-base \
+           libxcursor1 \
+           libxft2 \
+           libxinerama1 \
+           libxrandr2 \
+           libxrender1 \
+           libxt6 \
+           nano \
+           sudo \
+           wget \
+    && rm -rf /var/lib/apt/lists/* \
+    && echo "Downloading FSL ..." \
+    && mkdir -p /opt/fsl-6.0.1 \
+    && curl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.1-centos6_64.tar.gz \
+    | tar -xz -C /opt/fsl-6.0.1 --strip-components 1 \
+    && echo "Installing FSL conda environment ..." \
+    && bash /opt/fsl-6.0.1/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.1 \
+    && echo "Downgrading deprecation module per https://github.com/kaczmarj/neurodocker/issues/271#issuecomment-514523420" \
+    && /opt/fsl-6.0.1/fslpython/bin/conda install -n fslpython -c conda-forge -y deprecation==1.* \
+    && echo "Removing bundled with FSLeyes libz likely incompatible with the one from OS" \
+    && rm -f /opt/fsl-6.0.1/bin/FSLeyes/libz.so.1
 
-# Configure environment
-ENV FSLDIR=/usr/share/fsl/5.0
-ENV FSLOUTPUTTYPE=NIFTI_GZ
-ENV PATH=/usr/lib/fsl/5.0:$PATH
-ENV FSLMULTIFILEQUIT=TRUE
-ENV POSSUMDIR=/usr/share/fsl/5.0
-ENV LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
-ENV FSLTCLSH=/usr/bin/tclsh
-ENV FSLWISH=/usr/bin/wish
-ENV FSLOUTPUTTYPE=NIFTI_GZ
+# Save specification to JSON.
+RUN printf '{ \
+  "pkg_manager": "apt", \
+  "existing_users": [ \
+    "root" \
+  ], \
+  "instructions": [ \
+    { \
+      "name": "from_", \
+      "kwds": { \
+        "base_image": "bids/base_validator" \
+      } \
+    }, \
+    { \
+      "name": "env", \
+      "kwds": { \
+        "FSLDIR": "/opt/fsl-6.0.1", \
+        "PATH": "/opt/fsl-6.0.1/bin:$PATH", \
+        "FSLOUTPUTTYPE": "NIFTI_GZ", \
+        "FSLMULTIFILEQUIT": "TRUE", \
+        "FSLTCLSH": "/opt/fsl-6.0.1/bin/fsltclsh", \
+        "FSLWISH": "/opt/fsl-6.0.1/bin/fslwish", \
+        "FSLLOCKDIR": "", \
+        "FSLMACHINELIST": "", \
+        "FSLREMOTECALL": "", \
+        "FSLGECUDAQ": "cuda.q" \
+      } \
+    }, \
+    { \
+      "name": "run", \
+      "kwds": { \
+        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    bc \\\\\\n    ca-certificates \\\\\\n    curl \\\\\\n    dc \\\\\\n    file \\\\\\n    libfontconfig1 \\\\\\n    libfreetype6 \\\\\\n    libgl1-mesa-dev \\\\\\n    libgl1-mesa-dri \\\\\\n    libglu1-mesa-dev \\\\\\n    libgomp1 \\\\\\n    libice6 \\\\\\n    libopenblas-base \\\\\\n    libxcursor1 \\\\\\n    libxft2 \\\\\\n    libxinerama1 \\\\\\n    libxrandr2 \\\\\\n    libxrender1 \\\\\\n    libxt6 \\\\\\n    nano \\\\\\n    sudo \\\\\\n    wget\\nrm -rf /var/lib/apt/lists/*\\necho \\"Downloading FSL ...\\"\\nmkdir -p /opt/fsl-6.0.1\\ncurl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.1-centos6_64.tar.gz \\\\\\n| tar -xz -C /opt/fsl-6.0.1 --strip-components 1 \\necho \\"Installing FSL conda environment ...\\"\\nbash /opt/fsl-6.0.1/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.1\\necho \\"Downgrading deprecation module per https://github.com/kaczmarj/neurodocker/issues/271#issuecomment-514523420\\"\\n/opt/fsl-6.0.1/fslpython/bin/conda install -n fslpython -c conda-forge -y deprecation==1.*\\necho \\"Removing bundled with FSLeyes libz likely incompatible with the one from OS\\"\\nrm -f /opt/fsl-6.0.1/bin/FSLeyes/libz.so.1" \
+      } \
+    } \
+  ] \
+}' > /.reproenv.json
+# End saving to specification to JSON.

Makefile

@@ -0,0 +1,9 @@
+.PHONY: Dockerfile
+
+Dockerfile:
+	docker run --rm -i kaczmarj/neurodocker:0.9.1 \
+		generate docker \
+			--base-image bids/base_validator \
+			--pkg-manager apt \
+			--yes \
+			--fsl method=binaries version=6.0.1 > Dockerfile