def _namespace_to_specs(namespace):
"""Return dictionary of specifications from namespace."""
from neurodocker.generators.common import _installation_implementations
instructions = [('base', namespace.base)]
try:
for arg in namespace.ordered_args:
# TODO: replace try-except with stricter logic.
if arg[0] == 'install':
instructions.append(arg)
continue
try:
ii = (arg[0], {k: v for k, v in arg[1]})
except ValueError:
ii = arg
instructions.append(ii)
except AttributeError:
pass
# Convert string options that should be booleans to booleans.
for instruction, options in instructions:
if instruction in _installation_implementations.keys():
_string_vals_to_bool(options)
_string_vals_to_list(options)
return {
'pkg_manager': namespace.pkg_manager,
'instructions': instructions,
}
def _validate_software_options(self):
"""Raise ValueError if a key is present that does not belong in a
function's signature.
"""
for pkg, opts in self.specs['instructions']:
if pkg in _installation_implementations.keys():
func = _installation_implementations[pkg]
params = list(inspect.signature(func).parameters)
bad_opts = [opt for opt in opts if opt not in params]
if bad_opts:
bad_opts = ', '.join(bad_opts)
raise ValueError("Invalid option(s) found in instructions "
" key '{}': {}. Valid options are {}"
"".format(pkg, bad_opts, params))
def _namespace_to_specs(namespace):
"""Return dictionary of specifications from namespace."""
from neurodocker.generators.common import _installation_implementations
# instructions = [("base", namespace.base)]
instructions = []
try:
for arg in namespace.ordered_args:
# TODO: replace try-except with stricter logic.
if arg[0] == "install":
instructions.append(arg)
continue
try:
ii = (arg[0], {k: v for k, v in arg[1]})
except ValueError:
ii = arg
instructions.append(ii)
except AttributeError:
pass
# Convert string options that should be booleans to booleans.
for instruction, options in instructions:
if instruction in _installation_implementations.keys():
_string_vals_to_bool(options)
_string_vals_to_list(options)
specs = {
"pkg_manager": namespace.pkg_manager,
"instructions": instructions
}
# Add nd_freeze
nd_freeze_idx = _get_index_of_tuple_in_instructions(
"nd_freeze", specs["instructions"])
if nd_freeze_idx:
nd_freeze = specs["instructions"].pop(nd_freeze_idx)
specs["instructions"].insert(1, nd_freeze)
return specs
def _add_generate_common_arguments(parser):
p = parser
p.add_argument("-b",
"--base",
help="Base Docker image. E.g., debian:stretch")
p.add_argument("-p",
"--pkg-manager",
choices={'apt', 'yum'},
help="Linux package manager.")
p.add_argument(
'--add-to-entrypoint',
action=OrderedArgs,
help=("Add a command to the file /neurodocker/startup.sh, which is the"
" container's default entrypoint."))
p.add_argument(
'--copy',
action=OrderedArgs,
nargs="+",
help="Copy files into container. Use format <src>... <dest>")
p.add_argument(
'--install',
action=OrderedArgs,
nargs="+",
help=("Install system packages with apt-get or yum, depending on the"
" package manager specified."))
p.add_argument(
'--entrypoint',
action=OrderedArgs,
help="Set the container's entrypoint (Docker) / append to runscript"
" (Singularity)")
p.add_argument(
'-e',
'--env',
action=OrderedArgs,
nargs="+",
type=_list_of_kv,
help="Set environment variable(s). Use the format KEY=VALUE")
p.add_argument('-r',
'--run',
action=OrderedArgs,
help="Run a command when building container")
p.add_argument('--run-bash',
action=OrderedArgs,
help="Run a command in bash")
p.add_argument('-u',
'--user',
action=OrderedArgs,
help="Switch current user (creates user if necessary)")
p.add_argument('-w',
'--workdir',
action=OrderedArgs,
help="Set working directory")
# To generate from file.
p.add_argument(
'file',
nargs='?',
help="Generate file from JSON. Overrides other `generate` arguments")
p.add_argument('--json',
action="store_true",
help="Print Neurodocker JSON spec")
# Other arguments (no order).
p.add_argument(
'-o',
'--output',
dest="output",
help="If specified, save Dockerfile to file with this name.")
p.add_argument('--no-print',
dest='no_print',
action="store_true",
help="Do not print the generated file")
_ndeb_servers = ", ".join(
_installation_implementations['neurodebian']._servers.keys())
# Software package options.
pkgs_help = {
"all":
"Install software packages. Each argument takes a list of"
" key=value pairs. Where applicable, the default installation"
" behavior is to install by downloading and uncompressing"
" binaries. Some programs can be built from source.",
"afni":
"Install AFNI. Valid keys are version (required), method,"
" install_path, install_r, install_r_pkgs, install_python2,"
" and install_python3. Only the latest version and version"
" 17.2.02 are supported at this time.",
"ants":
"Install ANTs. Valid keys are version (required), method"
" install_path, cmake_opts, and make_opts. Version can be a "
" git commit hash if building from source.",
"convert3d":
"Install Convert3D. Valid keys are version (required),"
" method, and install_path.",
"dcm2niix":
"Install dcm2niix. Valid keys are version, method,"
" install_path, cmake_opts, and make_opts",
"freesurfer":
"Install FreeSurfer. Valid keys are version (required),"
" method, install_path, and exclude_paths. A FreeSurfer"
" license is required to run the software and is not"
" provided by Neurodocker.",
"fsl":
"Install FSL. Valid keys are version (required), method,"
" install_path, and exclude_paths.",
"matlabmcr":
"Install Matlab Compiler Runtime. Valid keys are version,"
" method, and install_path",
"miniconda":
"Install Miniconda. Valid keys are install_path,"
" env_name, conda_install, pip_install, conda_opts,"
" pip_opts, activate (default false), and version"
" (defaults to latest). The options conda_install and"
" pip_install accept strings of packages: conda_install="
'"python=3.6 numpy traits".',
"mrtrix3":
"Install MRtrix3. Valid keys are version (required),"
" method, and install_path",
"ndfreeze":
"Use the NeuroDebian command `nd_freeze` to freeze the apt"
" sources to a certain date. This will only have an effect"
" on Debian and NeuroDebian APT sources.",
"neurodebian":
"Add NeuroDebian repository. Valid keys are "
"os_codename (e.g., zesty), server (e.g., usa-nh), and"
" full (if true, use non-free packages). Valid download"
" servers are {}.".format(_ndeb_servers),
"spm12":
"Install SPM12 and its dependency, Matlab Compiler Runtime."
" Valid keys are version and install_path.",
"minc":
"Install MINC. Valid keys is version (required), method, and"
" install_path. Only version 1.9.15 is supported at this"
" time.",
"petpvc":
"Install PETPVC. Valid keys are version (required), method,"
" and install_path.",
"vnc":
"Install a VNC server. Valid keys are passwd (required),"
" start_at_runtime, and geometry."
}
pkgs = p.add_argument_group(title="software package arguments",
description=pkgs_help['all'])
for pkg in _installation_implementations.keys():
if pkg == '_header':
continue
flag = "--{}".format(pkg)
# MRtrix3 does not need any arguments by default.
nargs = "*" if pkg == "mrtrix3" else "+"
pkgs.add_argument(flag,
dest=pkg,
nargs=nargs,
action=OrderedArgs,
metavar="",
type=_list_of_kv,
help=pkgs_help[pkg])