Add/fsl eddy 5011 (#97)

* add: fsl eddy v5.0.11 pre-release

* fix: list cuda versions with commas

* enh: option to install fsl eddy 5.0.11 pre-release over fsl 5.0.10

* remove trailing whitespace

* fix: fsl apt deps + fsl tests

* remove eddy_openmp from test because it returns err code 1

README.md

@@ -55,6 +55,8 @@ Valid options for each software package are the keyword arguments for the class
 |                | license_path | Relative path to license file. If provided, this file will be copied into the Docker image. Must be within the build context. |
 |                | min | If true, install a version of FreeSurfer minimized for recon-all. See [freesurfer/freesurfer#70](https://github.com/freesurfer/freesurfer/issues/70). False by default. |
 | **FSL**** | version* | Any version for which binaries are provided. |
+|           | eddy_5011 | If true, use pre-release version of FSL eddy v5.0.11 |
+|           | eddy_5011_cuda | 6.5, 7.0, 7.5, 8.0; only valid if using eddy pre-release |
 |           | use_binaries | If true (default), use pre-compiled binaries. Building from source is not available now but might be added in the future. |
 |           | use_installer | If true, use FSL's Python installer. Only valid on CentOS images. |
 | **MINC** | version* | 1.9.15 |

neurodocker/generate.py

@@ -308,8 +308,8 @@ def _add_neurodocker_header(specs):
     """Return Dockerfile comment that references Neurodocker."""
     return ("# Generated by Neurodocker v{}."
             "\n#"
-            "\n# Thank you for using Neurodocker. If you discover any issues "
-            "\n# or ways to improve this software, please submit an issue or "
+            "\n# Thank you for using Neurodocker. If you discover any issues"
+            "\n# or ways to improve this software, please submit an issue or"
             "\n# pull request on our GitHub repository:"
             "\n#     https://github.com/kaczmarj/neurodocker"
             "\n#"

neurodocker/interfaces/fsl.py

@@ -33,21 +33,29 @@ class FSL(object):
     use_installer : bool
         If true, install FSL using FSL's Python installer. Only works on
         CentOS/RHEL (default false).
+    eddy_5011 : bool
+        If true, install pre-release of FSL eddy v5.0.11.
+    eddy_5011_cuda : {'6.5', '7.0', '7.5', '8.0'}
+        Version of CUDA for FSL eddy pre-release. Only applies if eddy_5011 is
+        true.
     check_urls : bool
         If true, raise error if a URL used by this class responds with an error
         code.
 
     Notes
     -----
-    Look into ReproNim/simple_workflow to learn how to install specific versions
-    of FSL on Debian (https://github.com/ReproNim/simple_workflow).
+    Look into ReproNim/simple_workflow to learn how to install specific
+    versions of FSL on Debian (https://github.com/ReproNim/simple_workflow).
     """
     def __init__(self, version, pkg_manager, use_binaries=True,
-                 use_installer=False, check_urls=True):
+                 use_installer=False, eddy_5011=False, eddy_5011_cuda=None,
+                 check_urls=True):
         self.version = LooseVersion(version)
         self.pkg_manager = pkg_manager
         self.use_binaries = use_binaries
         self.use_installer = use_installer
+        self.eddy_5011 = eddy_5011
+        self.eddy_5011_cuda = eddy_5011_cuda
         self.check_urls = check_urls
 
         self._check_args()
@@ -60,8 +68,11 @@ def _check_args(self):
         if self.use_binaries and self.use_installer:
             raise ValueError("More than one installation method specified.")
         if self.use_installer and self.pkg_manager != 'yum':
-            raise ValueError("FSL's Python installer works only on "
-                             "CentOS/RHEL-based systems.")
+            raise ValueError("FSL's Python installer works only on"
+                             " CentOS/RHEL-based systems.")
+        if self.version < LooseVersion('5.0.10') and self.eddy_5011:
+            raise ValueError("Pre-release of FSL eddy can only be installed"
+                             " with FSL v5.0.10.")
         return True
 
     def _create_cmd(self):
@@ -71,8 +82,9 @@ def _create_cmd(self):
                    "\n# FSL is non-free. If you are considering commerical use"
                    "\n# of this Docker image, please consult the relevant license:"
                    "\n# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence"
-                   "\n#-----------------------------------------------------------"
-                   "".format(self.version))
+                   "\n#-----------------------------------------------------------")
+        comment = comment.format(self.version)
+
         if self.use_binaries:
             url = self._get_binaries_url()
             cmd = self.install_binaries(url)
@@ -116,11 +128,14 @@ def _get_binaries_url(self):
         return url
 
     def _install_binaries_deps(self):
-        """Return command to install FreeSurfer dependencies. Use this for
-        FreeSurfer binaries, not if attempting to build FreeSurfer from source.
-        """
-        pkgs = {'apt': "bc dc",
-                'yum': "bc"}
+        """Return command to install FSL dependencies."""
+        pkgs = {'apt': ("bc dc libfontconfig1 libfreetype6 libgl1-mesa-dev"
+                        " libglu1-mesa-dev libgomp1 libice6 libmng1"
+                        " libxcursor1 libxft2 libxinerama1 libxrandr2"
+                        " libxrender1 libxt6"),
+                'yum': ("bc libGL libGLU libgomp libICE libjpeg libmng"
+                        " libpng12 libSM libX11 libXcursor libXext libXft"
+                        " libXinerama libXrandr libXt")}
 
         cmd = "{install}\n&& {clean}".format(**manage_pkgs[self.pkg_manager])
         return cmd.format(pkgs=pkgs[self.pkg_manager])
@@ -138,13 +153,16 @@ def install_binaries(self, url):
 
         if self.version >= LooseVersion('5.0.10'):
             fsl_python = "/opt/fsl/etc/fslconf/fslpython_install.sh"
-            cmd +=  "\n&& /bin/bash {} -q -f /opt/fsl".format(fsl_python)
+            cmd += "\n&& /bin/bash {} -q -f /opt/fsl".format(fsl_python)
+
+        if self.eddy_5011:
+            cmd += self._install_eddy_5011()
 
         ent_cmds = ["echo Some packages in this Docker container are non-free",
                     ("echo If you are considering commercial use of this"
                      " container, please consult the relevant license:"),
-                     "echo https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence",
-                     "source $FSLDIR/etc/fslconf/fsl.sh",]
+                    "echo https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence",
+                    "source $FSLDIR/etc/fslconf/fsl.sh"]
         cmd += "\n&& {}".format(_add_to_entrypoint(ent_cmds, with_run=False))
         cmd = indent("RUN", cmd)
 
@@ -153,3 +171,44 @@ def install_binaries(self, url):
         env_cmd = indent("ENV", env_cmd)
 
         return "\n".join((cmd, env_cmd))
+
+    def _get_eddy_5011_url(self):
+        """Return URL of FSL eddy 5.0.11 pre-release."""
+        # This function should probably be removed once FSL v5.0.11 is released
+        base_url = ("https://fsl.fmrib.ox.ac.uk/fsldownloads/patches/"
+                    "eddy-patch-fsl-5.0.11/centos6/")
+        cuda_versions = {
+            '6.5': 'eddy_cuda6.5',
+            '7.0': 'eddy_cuda7.0',
+            '7.5': 'eddy_cuda7.5',
+            '8.0': 'eddy_cuda8.0',
+        }
+        if self.eddy_5011_cuda is None:
+            filename = "eddy_openmp"
+        else:
+            filename = cuda_versions.get(self.eddy_5011_cuda, None)
+            if filename is None:
+                raise ValueError("Valid CUDA versions are {}"
+                                 .format(', '.join(cuda_versions.keys())))
+        return urljoin(base_url, filename)
+
+    def _install_eddy_5011(self):
+        """Return Dockerfile instructions to install FSL eddy v5.0.11
+        pre-release.
+        """
+        url = self._get_eddy_5011_url()
+
+        if self.check_urls:
+            check_url(url)
+
+        cmd = ('\n&& cd /opt/fsl/bin'
+               '\n&& rm -f eddy_openmp eddy_cuda*'
+               '\n&& echo "Downloading FSL eddy v5.0.11 pre-release ..."'
+               '\n&& curl -sSLO {}'
+               '\n&& chmod +x eddy_*').format(url)
+
+        filename = url.split('/')[-1]
+        if 'cuda' in filename:
+            cmd += '\n&& ln -sv {} eddy_cuda'.format(filename)
+
+        return cmd

neurodocker/interfaces/tests/test_fsl.py

@@ -33,17 +33,19 @@ def test_build_image_fsl_latest_pyinstaller_centos7(self):
         if push:
             utils.push_image(image_name)
 
-    def test_build_image_fsl_509_binaries_centos7(self):
+    def test_build_image_fsl_5010_binaries_centos7(self):
         """Install FSL binaries on CentOS 7."""
         specs = {'pkg_manager': 'yum',
                  'check_urls': True,
                  'instructions': [
-                    ('base', 'centos:7'),
-                    ('fsl', {'version': '5.0.9', 'use_binaries': True})
+                     ('base', 'centos:7'),
+                     ('fsl', {'version': '5.0.10',
+                              'use_binaries': True,
+                              'eddy_5011': True})
                  ]}
 
         df = Dockerfile(specs).cmd
-        dbx_path, image_name = utils.DROPBOX_DOCKERHUB_MAPPING['fsl-5.0.9_centos7']
+        dbx_path, image_name = utils.DROPBOX_DOCKERHUB_MAPPING['fsl-5.0.10_centos7']
         image, push = utils.get_image_from_memory(df, dbx_path, image_name)
 
         cmd = "bash /testscripts/test_fsl.sh"

neurodocker/interfaces/tests/utils.py

@@ -28,6 +28,9 @@
     'fsl-5.0.9_centos7': ('/Dockerfile.FSL-5.0.9_centos7',
                           'kaczmarj/fsl:5.0.9_centos7'),
 
+    'fsl-5.0.10_centos7': ('/Dockerfile.FSL-5.0.10_centos7',
+                           'kaczmarj/fsl:5.0.10_centos7'),
+
     'miniconda_centos7': ('/Dockerfile.Miniconda-latest_centos7',
                           'kaczmarj/miniconda:latest_centos7'),
 

neurodocker/neurodocker.py

@@ -21,7 +21,7 @@
 # https://stackoverflow.com/a/9028031/5666087
 class OrderedArgs(Action):
     def __call__(self, parser, namespace, values, option_string=None):
-        if not 'ordered_args' in namespace:
+        if 'ordered_args' not in namespace:
             setattr(namespace, 'ordered_args', [])
         previous = namespace.ordered_args
         previous.append((self.dest, values))
@@ -38,11 +38,11 @@ def list_of_kv(kv):
         l[1:] = ["=".join(l[1:])]
         return l
 
-    p.add_argument("-b", "--base", #required=True,
-                            help="Base Docker image. Eg, ubuntu:17.04")
-    p.add_argument("-p", "--pkg-manager", #required=True,
-                            choices=utils.manage_pkgs.keys(),
-                            help="Linux package manager.")
+    p.add_argument("-b", "--base",  # required=True,
+                   help="Base Docker image. Eg, ubuntu:17.04")
+    p.add_argument("-p", "--pkg-manager",  # required=True,
+                   choices=utils.manage_pkgs.keys(),
+                   help="Linux package manager.")
 
     # Arguments that should be ordered.
     p.add_argument('--add', action=OrderedArgs, nargs="+",
@@ -93,8 +93,7 @@ def list_of_kv(kv):
     p.add_argument('--no-print-df', dest='no_print_df', action="store_true",
                      help="Do not print the Dockerfile")
     p.add_argument("--no-check-urls", action="store_false", dest="check_urls",
-                        help=("Do not verify communication with URLs used in "
-                              "the build."))
+                   help="Do not verify communication with URLs used in the build.")
 
     _ndeb_servers = ", ".join(SUPPORTED_SOFTWARE['neurodebian'].SERVERS.keys())
 
@@ -145,7 +144,8 @@ def list_of_kv(kv):
             "Install SPM (and its dependency, Matlab Compiler Runtime). Valid"
             " keys are version and matlab_version."),
         "minc": (
-            "Install MINC. Valid keys is version (required). Only version 1.9.15 is supported at this time."),
+            "Install MINC. Valid keys is version (required). Only version"
+            " 1.9.15 is supported at this time."),
         "petpvc": (
             "Install PETPVC. Valid keys are version (required)."),
     }
@@ -165,21 +165,23 @@ def _add_reprozip_trace_arguments(parser):
     """Add arguments to `parser` for sub-command `reprozip-trace`."""
     p = parser
     p.add_argument('container',
-                        help="Running container in which to trace commands.")
+                   help="Running container in which to trace commands.")
     p.add_argument('commands', nargs='+', help="Command(s) to trace.")
     p.add_argument('--dir', '-d', dest="packfile_save_dir", default=".",
-                        help=("Directory in which to save pack file. Default "
-                              "is current directory."))
+                   help=("Directory in which to save pack file. Default "
+                         "is current directory."))
+
 
 def _add_reprozip_merge_arguments(parser):
     """Add arguments to `parser` for sub-command `reprozip-merge`."""
     p = parser
     p.add_argument('outfile', help="Filepath to merged pack file.")
     p.add_argument('pack_files', nargs='+', help="Pack files to merge.")
 
+
 def create_parser():
     """Return command-line argument parser."""
-    parser = ArgumentParser(description=__doc__, #add_help=False,
+    parser = ArgumentParser(description=__doc__,  # add_help=False,
                             formatter_class=RawDescriptionHelpFormatter)
 
     verbosity_choices = ('debug', 'info', 'warning', 'error', 'critical')
@@ -245,7 +247,7 @@ def reprozip_merge(namespace):
 
 def _validate_args(namespace):
     if (namespace.file is None and
-        (namespace.base is None or namespace.pkg_manager is None)):
+       (namespace.base is None or namespace.pkg_manager is None)):
         raise ValueError("-b/--base and -p/--pkg-manager are required if not"
                          " generating from JSON file.")
 
@@ -267,7 +269,7 @@ def main(args=None):
 
     subparser_functions = {'generate': generate,
                            'reprozip-trace': reprozip_trace,
-                           'reprozip-merge': reprozip_merge,}
+                           'reprozip-merge': reprozip_merge}
 
     if namespace.subparser_name not in subparser_functions.keys():
         print(__doc__)