[DATALAD RUNCMD] run precommit

=== Do not change lines below === { "chain": [], "cmd": "pre-commit run -a", "exit": 1, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^
ReproNim · Aug 22, 2023 · 974e8c9 · 974e8c9
1 parent 4d291a1
commit 974e8c9
Show file tree

Hide file tree

Showing 5 changed files with 45 additions and 45 deletions.
diff --git a/docs/user_guide/cli.rst b/docs/user_guide/cli.rst
@@ -71,13 +71,13 @@ neurodocker generate docker
                                 does not exist)
 
     --workdir TEXT               Set the working directory
-    --yes                        Reply yes to all prompts for agreeing to any 
+    --yes                        Reply yes to all prompts for agreeing to any
                                 alerts that a neurodocker template might have.
-                                The alert messages will still be printed but 
+                                The alert messages will still be printed but
                                 no confirmation is necessary from the user.
 
-    --json                       Output instructions as JSON. This can be used	
-                                to generate Dockerfiles or Singularity recipes	
+    --json                       Output instructions as JSON. This can be used
+                                to generate Dockerfiles or Singularity recipes
                                 with Neurodocker.
 
     --_header KEY=VALUE          Add _header
@@ -93,7 +93,7 @@ neurodocker generate docker
                                     - install_python3 [default: false]
                                     options for method=source
                                     - version [required]
-                                    - repo [default: https://github.com/afni/afni.git]	
+                                    - repo [default: https://github.com/afni/afni.git]
                                     - install_path [default: /opt/afni-{{ self.version }}]
                                     - install_r_pkgs [default: false]
                                     - install_python3 [default: false]
@@ -176,14 +176,14 @@ neurodocker generate docker
                                     options for method=source
                                     - version [required]
 
-    --matlabmcr KEY=VALUE        Add matlabmcr	
+    --matlabmcr KEY=VALUE        Add matlabmcr
                                     method=[binaries]
                                     options for method=binaries
-                                    - version [required]	
-                                        version=[2021b|2021a|2020b|2020a|2019b|2019a|2018b|2018a|2017b|2017a|2016b|2016a|2015b|2015aSP1|2015a|2014b|2014a|2013b|2013a|2012b|2012a|2010a]	
-                                    - curl_opts [default: ]	
-                                    - install_path [default: /opt/MCR-{{ self.version }}]	
-  
+                                    - version [required]
+                                        version=[2021b|2021a|2020b|2020a|2019b|2019a|2018b|2018a|2017b|2017a|2016b|2016a|2015b|2015aSP1|2015a|2014b|2014a|2013b|2013a|2012b|2012a|2010a]
+                                    - curl_opts [default: ]
+                                    - install_path [default: /opt/MCR-{{ self.version }}]
+
     --minc KEY=VALUE             Add minc
                                     method=[binaries]
                                     options for method=binaries
@@ -240,13 +240,13 @@ neurodocker generate docker
                                     - os_codename [required]
                                     - full_or_libre [default: full]
 
-    --niftyreg KEY=VALUE         Add niftyreg	
-                                    method=[source]	
-                                    options for method=source	
-                                    - version [required]	
-                                    - repo [default: https://github.com/KCL-BMEIS/niftyreg]	
-                                    - install_path [default: /opt/niftyreg-{{ self.version }}]	
-                                    - cmake_opts [default: -DCMAKE_INSTALL_PREFIX={{ self.install_path }} -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF]	
+    --niftyreg KEY=VALUE         Add niftyreg
+                                    method=[source]
+                                    options for method=source
+                                    - version [required]
+                                    - repo [default: https://github.com/KCL-BMEIS/niftyreg]
+                                    - install_path [default: /opt/niftyreg-{{ self.version }}]
+                                    - cmake_opts [default: -DCMAKE_INSTALL_PREFIX={{ self.install_path }} -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF]
                                     - make_opts [default: -j1]
 
     --petpvc KEY=VALUE           Add petpvc

diff --git a/neurodocker/templates/afni.yaml b/neurodocker/templates/afni.yaml
@@ -64,12 +64,12 @@ binaries:
     - which
     - xorg-x11-fonts-misc
     - xorg-x11-server-Xvfb
-    - wget 
-    - mesa-dri-drivers 
-    - mesa-libGLw 
-    - which 
-    - unzip 
-    - ncurses-compat-libs 
+    - wget
+    - mesa-dri-drivers
+    - mesa-libGLw
+    - which
+    - unzip
+    - ncurses-compat-libs
     debs:
       - http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb
       - http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb

diff --git a/neurodocker/templates/ants.yaml b/neurodocker/templates/ants.yaml
@@ -10,7 +10,7 @@ binaries:
   urls:
     # Official binaries are provided as of 2.4.1 (https://github.com/ANTsX/ANTs/releases)
     "2.4.3": https://github.com/ANTsX/ANTs/releases/download/v2.4.3/ants-2.4.3-centos7-X64-gcc.zip
-    "2.4.2": https://github.com/ANTsX/ANTs/releases/download/v2.4.2/ants-2.4.2-centos7-X64-gcc.zip   
+    "2.4.2": https://github.com/ANTsX/ANTs/releases/download/v2.4.2/ants-2.4.2-centos7-X64-gcc.zip
     "2.4.1": https://github.com/ANTsX/ANTs/releases/download/v2.4.1/ants-2.4.1-centos7-X64-gcc.zip
     # Binaries prior to 2.4.x were compiled by Jakub Kaczmarzyk (https://github.com/kaczmarj)
     "2.3.4": https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz

diff --git a/neurodocker/templates/cat12.yaml b/neurodocker/templates/cat12.yaml
@@ -13,7 +13,7 @@ binaries:
       install_path: /opt/CAT12-{{ self.version }}
   urls:
     r1933_R2017b: http://www.neuro.uni-jena.de/cat12/CAT12.8_r1933_R2017b_MCR_Linux.zip
-    r2166_R2017b: http://www.neuro.uni-jena.de/cat12/CAT12.8.2_r2166_R2017b_MCR_Linux.zip 
+    r2166_R2017b: http://www.neuro.uni-jena.de/cat12/CAT12.8.2_r2166_R2017b_MCR_Linux.zip
   dependencies:
     apt:
     - ca-certificates
@@ -43,4 +43,4 @@ binaries:
     {{ self.install_path }}/spm12 function exit
     # Fix m file
     rm {{ self.install_path }}/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_long_main.m
-    cp {{ self.install_path }}/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_long_main.txt {{ self.install_path }}/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_long_main.m
+    cp {{ self.install_path }}/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_long_main.txt {{ self.install_path }}/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_long_main.m
diff --git a/neurodocker/templates/minc.yaml b/neurodocker/templates/minc.yaml
@@ -31,17 +31,17 @@ binaries:
     - libgomp1
     - libjpeg62
     - unzip
-    - octave 
-    - libglu1-mesa 
-    - libgl1-mesa-glx 
-    - perl 
-    - imagemagick 
-    - bc 
-    - ed 
-    - libc6 
-    - libstdc++6 
-    - gdebi-core 
-    - binutils 
+    - octave
+    - libglu1-mesa
+    - libgl1-mesa-glx
+    - perl
+    - imagemagick
+    - bc
+    - ed
+    - libc6
+    - libstdc++6
+    - gdebi-core
+    - binutils
     - git
     yum:
     - curl
@@ -57,12 +57,12 @@ binaries:
     - unzip
     - octave
     - mesa-dri-drivers
-    - epel-release 
-    - glibc 
-    - libstdc++ 
-    - ImageMagick 
-    - perl 
-    - binutils 
+    - epel-release
+    - glibc
+    - libstdc++
+    - ImageMagick
+    - perl
+    - binutils
     - git
   env:
     MINC_TOOLKIT: "{{ self.install_path }}"
@@ -81,7 +81,7 @@ binaries:
     cd /
     # ar allows to extract the debian package so we can also install this in centos based OSs.
     curl {{ self.urls[self.version] }} -o minc.deb && ar p minc.deb data.tar.gz | tar zx && rm minc.deb
-    ln -s /opt/minc/{{ self.version }} {{ self.install_path }} 
+    ln -s /opt/minc/{{ self.version }} {{ self.install_path }}
     git clone https://github.com/CAIsr/volgenmodel-nipype.git {{ self.install_path }}/volgenmodel-nipype/
     curl -fL http://packages.bic.mni.mcgill.ca/tgz/beast-library-1.1.tar.gz \
     | tar -xz -C {{ self.install_path }}/share