fslinstaller.py 40.1 KB
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#!/usr/bin/env python
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#
# FSL installer script.
#
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from __future__ import print_function, division, unicode_literals
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import functools      as ft
import os.path        as op
import subprocess     as sp
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import textwrap       as tw
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import                   os
import                   sys
import                   argparse
import                   contextlib
import                   getpass
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import                   hashlib
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import                   json
import                   logging
import                   platform
import                   shlex
import                   shutil
import                   tempfile
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import                   threading
import                   time
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# TODO check py2/3
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try:
    import                   urllib
    import urllib.parse   as urlparse
    import urllib.request as urlrequest
except ImportError:
    import urllib2 as urllib
    import urllib2 as urlparse
    import urllib2 as urlrequest
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try:                import queue
except ImportError: import Queue as queue


PY2 = sys.version[0] == '2'

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log = logging.getLogger(__name__)


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__version__ = '0.0.0'
"""Installer version number. This is automatically updated in release versions
whenever a new version is released.
"""


DEFAULT_INSTALLATION_DIRECTORY = '/usr/local/fsl'
"""Default FSL installation directory. """


FSL_INSTALLER_MANIFEST = 'http://18.133.213.73/installer/manifest,json'
"""URL to download the FSL installer manifest file from. The installer
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manifest file is a JSON file which contains information about available FSL
versions.

See the Context.download_manifest function, and an example manifest file
in test/data/manifest.json, for more details.
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"""


class InvalidPassword(Exception):
    """Exception raised by Context.get_admin_password if the user gives an
    incorrect password.
    """


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class UnknownVersion(Exception):
    """Exception raised by Context.build if the user has requested a FSL
    version that does not exist.
    """


class BuildNotAvailable(Exception):
    """Exception raised by Context.build if there is no available FSL version
    that matches the target platform and/or requested CUDA version.
    """


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class UnsupportedPlatform(Exception):
    """Exception raised by the identify_platform function if FSL is not
    available on this platform.
    """


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class Context(object):
    """Bag of information and settings created in main, and passed around
    this script.
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    Several settings are lazily evaluated on first access, but once evaluated,
    their values are immutable.
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    """

    def __init__(self, args):
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        """Create the context with the argparse.Namespace object containing
        parsed command-line arguments.
        """
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        self.args  = args
        self.shell = op.basename(os.environ['SHELL'])
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        # These attributes are updated on-demand via
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        # the property accessors defined below, or all
        # all updated via the finalise-settings method.
        self.__platform       = None
        self.__cuda           = None
        self.__manifest       = None
        self.__build          = None
        self.__destdir        = None
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        self.__need_admin     = None
        self.__admin_password = None
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    def finalise_settings(self):
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        """Finalise values for all information and settings in the Context.
        """
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        self.platform
        self.cuda
        self.manifest
        self.build
        self.destdir
        self.need_admin
        self.admin_password


    @property
    def platform(self):
        """The platform we are running on, e.g. "linux-64", "macos-64". """
        if self.__platform is None:
            self.__platform = Context.identify_platform()
        return self.__platform


    @property
    def cuda(self):
        """The available CUDA version, or a CUDA version requested by the user.
        """
        if self.__cuda is not None:
            return self.__cuda
        if self.args.cuda is not None:
            self.__cuda = self.args.cuda
        if self.__cuda is None:
            self.__cuda = Context.identify_cuda()
        return self.__cuda


    @property
    def build(self):
        """Returns a suitable FSL build (a dictionary entry from the FSL
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        installer manifest) for the target platform and requested FSL/CUDA
        versions.
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        """

        fslversion = self.args.fslversion

        if fslversion not in self.manifest['versions']:
            raise UnknownVersion(
                'FSL version {} is not available'.format(args.fslversion))

        if fslversion == 'latest':
            fslversion = self.manifest['versions']['latest']

        match = None

        for build in self.manifest['versions'][fslversion]:
            if build['platform']       == self.platform and \
               build.get('cuda', None) == self.cuda:
                match = build
                break
        else:
            raise BuildNotAvailable(
                'Cannot find a version of FSL matching platform '
                '{} and CUDA {}'.format(self.platform, self.cuda))

        return match
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    @property
    def destdir(self):
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        """Installation directory. If not specified at the command line, the
        user is prompted to enter a directory.
        """
        if self.args.dest is not None:
            self.__destdir = op.abspath(self.args.dest)
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        if self.__destdir is None:
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            while True:
                printmsg('Where do you want to install FSL?',
                         IMPORTANT, EMPHASIS)
                printmsg('Press enter to install to the default location [{}]'
                         .format(DEFAULT_INSTALLATION_DIRECTORY), INFO)
                response = prompt('FSL installation directory:', QUESTION)
                response = response.rstrip(op.sep)
                if response == '':
                    response = DEFAULT_INSTALLATION_DIRECTORY
                    break
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                response  = op.abspath(response)
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                parentdir = op.dirname(response)
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                if op.exists(parentdir):
                    break
                else:
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                    printmsg('Destination directory {} does not '
                             'exist!'.format(parentdir), ERROR)
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            self.__destdir = response
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        return self.__destdir


    @property
    def need_admin(self):
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        """Returns True if administrator privileges will be needed to install
        FSL.
        """
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        if self.__need_admin is not None:
            return self.__need_admin
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        parentdir = op.dirname(self.destdir)
        self.__need_admin = Context.check_need_admin(parentdir)
        return self.__need_admin
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    @property
    def admin_password(self):
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        """Returns the user's administrator password, prompting them if needed.
        """
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        if self.__admin_password is not None:
            return self.__admin_password
        if self.__need_admin == False:
            return None
        if self.__destdir is None:
            raise RuntimeError('Destination directory has not been set')
        self.__admin_password = Context.get_admin_password()


    @property
    def manifest(self):
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        """Returns the FSL installer manifest as a dictionary. """
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        if self.__manifest is None:
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            self.__manifest = Context.download_manifest(self.args.manifest,
                                                        self.args.workdir)
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        return self.__manifest


    @staticmethod
    def identify_platform():
        """Figures out what platform we are running on. Returns a platform
        identifier string - one of:

          - "linux-64" (Linux, x86_64)
          - "macos-64" (macOS, x86_64)
        """

        platforms = {
            ('linux',  'x86_64') : 'linux-64',
            ('darwin', 'x86_64') : 'linux-64',
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            # M1 builds (and possbily ARM for Linux)
            # will be added in the future
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            ('darwin', 'arm64')  : 'macos-64',
        }

        system = platform.system().lower()
        cpu    = platform.machine()
        key    = (system, cpu)

        if key not in platforms:
            raise UnsupportedPlatform()

        return platforms[key]


    @staticmethod
    def identify_cuda():
        """Identifies the CUDA version supported on the platform. Returns a
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        string containing the 'X.Y' CUDA version, or None if CUDA is not
        supported.
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        """

        try:
            output = sp.check_output('nvidia-smi')
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        except Exception:
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            return None

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        cudaver = '9.2'  # TODO
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        match   = None

        # Return the most suitable CUDA
        # version that we have a build for
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        available_cudas = ['9.2', '10.2', '11.1']
        for available in reversed(supported_cudas):
            if float(cudaver) <= float(available):
                match = available
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                break

        return match


    @staticmethod
    def check_need_admin(dirname):
        """Returns True if dirname needs administrator privileges to write to,
        False otherwise.
        """
        # TODO os.supports_effective_ids added in python 3.3
        return not os.access(dirname, os.W_OK | os.X_OK)


    @staticmethod
    def get_admin_password():
        """Prompt the user for their administrator password."""

        def validate_admin_password(password):
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            proc = sudo_popen(['true'], password)
            proc.communicate()
            return proc.returncode == 0
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        for attempt in range(3):
            if attempt == 0:
                msg = 'Your administrator password is needed to ' \
                      'install FSL: '
            else:
                msg = 'Your administrator password is needed to ' \
                      'install FSL [attempt {} of 3]:'.format(attempt + 1)
            printmsg(msg, IMPORTANT, end='', flush=True)
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            password = getpass.getpass('')
            valid    = validate_admin_password(password)

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            if valid:
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                printmsg('Password accepted', INFO)
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                break
            else:
                printmsg('Incorrect password', WARNING)
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        if not valid:
            raise InvalidPassword()

        return password


    @staticmethod
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    def download_manifest(url, workdir=None):
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        """Downloads the installer manifest file, which contains information
        about available FSL vesrions, and the most recent version number of the
        installer (this script).

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        The manifest file is a JSON file with the following structure (lines
        beginning with two forward-slashes are ignored):
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          {
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              "installer" : {
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                  // Latest version of installer script
                  "version" : "1.2.3",

                  // URL to download installer script
                  "url"     : "http://abc.com/fslinstaller.py"

                  // SHA256 checksum of installer script
                  "sha256"  : "ab238........."
              },
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              "versions" : {

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                  // Latest must be present, and must
                  // contain the version number of the
                  // latest release
                  "latest" : "6.1.0",
                  "6.1.0"  : {
                      'linux-64' : {
                          "environment" : "http;//abc.com/fsl-6.1.0-linux-64.yml",
                          "sha256"      : "ab23456...",
                      }
                      'macos-64' : {
                          "environment" : "http;//abc.com/fsl-6.1.0-macos-64.yml",
                          "sha256"      : "ab23456...",
                      }
                      'linux-64-cuda9.2' : {
                          "environment" : "http;//abc.com/fsl-6.1.0-linux-64-cuda9.2.yml",
                          "sha256"      : "ab23456...",
                      }
                      'linux-64-cuda10.2' : {
                          "environment" : "http;//abc.com/fsl-6.1.0-linux-64-cuda10.2.yml",
                          "sha256"      : "ab23456...",
                      }
                  }
                  "6.1.1" : {
                      ...
                  }
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              }
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          }
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        """

        log.debug('Downloading FSL installer manifest from %s', url)

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        with tempdir(workdir):
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            download_file(url, 'manifest.json')
            with open('manifest.json') as f:
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                lines = f.readlines()

        # Drop comments
        lines = [l for l in lines if not l.lstrip().startswith('//')]
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        return json.loads('\n'.join(lines))
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# List of modifiers which can be used to change how
# a message is printed by the printmsg function.
INFO      = 1
IMPORTANT = 2
QUESTION  = 3
PROMPT    = 4
WARNING   = 5
ERROR     = 6
EMPHASIS  = 7
UNDERLINE = 8
RESET     = 9
ANSICODES = {
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    INFO      : '\033[37m',         # Light grey
    IMPORTANT : '\033[92m',         # Green
    QUESTION  : '\033[36m\033[4m',  # Blue+underline
    PROMPT    : '\033[36m\033[1m',  # Bright blue+bold
    WARNING   : '\033[93m',         # Yellow
    ERROR     : '\033[91m',         # Red
    EMPHASIS  : '\033[1m',          # White+bold
    UNDERLINE : '\033[4m',          # Underline
    RESET     : '\033[0m',          # Used internally
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}


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def printmsg(msg='', *msgtypes, **kwargs):
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    """Prints msg according to the ANSI codes provided in msgtypes.
    All other keyword arguments are passed through to the print function.
    """
    msgcodes = [ANSICODES[t] for t in msgtypes]
    msgcodes = ''.join(msgcodes)
    print('{}{}{}'.format(msgcodes, msg, ANSICODES[RESET]), **kwargs)
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    sys.stdout.flush()
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def prompt(prompt, *msgtypes, **kwargs):
    """Prompts the user for some input. msgtypes and kwargs are passed
    through to the printmsg function.
    """
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    printmsg(prompt, *msgtypes, end='', **kwargs)
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    if PY2: return raw_input(' ').strip()
    else:   return input(    ' ').strip()
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class Progress(object):
    """Simple progress reporter. Displays one of the following:

       - If both a value and total are provided, a progress bar is shown
       - If only a value is provided, a cumulative count is shown
       - If nothing is provided, a spinner is shown.

    Use as a context manager, and call the update method to report progress,
    e,g:

        with Progress('%') as p:
            for i in range(100):
                p.update(i + 1, 100)
    """

    def __init__(self,
                 label='',
                 transform=None,
                 fmt='{:.1f}',
                 total=None,
                 width=None):
        """Create a Progress reporter.

        :arg label:     Units (e.g. "MB", "%",)

        :arg transform: Function to transform values (see e.g.
                        Progress.bytes_to_mb)

        :arg fmt:       Template string used to format value / total.

        :arg total:     Maximum value - overrides the total value passed to
                        the update method.

        :arg width:     Maximum width, if a progress bar is displayed. Default
                        is to automatically infer the terminal width (see
                        Progress.get_terminal_width).
        """

        if transform is None:
            transform = Progress.default_transform

        self.width     = width
        self.fmt       = fmt.format
        self.total     = total
        self.label     = label
        self.transform = transform

        # used by the spin function
        self.__last_spin = None

    @staticmethod
    def default_transform(val, total):
        return val, total

    @staticmethod
    def bytes_to_mb(val, total):
        if val   is not None: val   = val   / 1048576
        if total is not None: total = total / 1048576
        return val, total

    @staticmethod
    def percent(val, total):
        if val is None or total is None:
            return val, total
        return 100 * (val / total), 100

    def __enter__(self):
        return self

    def __exit__(self, *args, **kwargs):
        printmsg()

    def update(self, value=None, total=None):

        if total is None:
            total = self.total

        value, total = self.transform(value, total)

        if value is None and total is None:
            self.spin()
        elif value is not None and total is None:
            self.count(value)
        elif value is not None and total is not None:
            self.progress(value, total)

    def spin(self):

        symbols = ['|', '/', '-',  '\\']

        if self.__last_spin is not None: last = self.__last_spin
        else:                            last = symbols[-1]

        idx  = symbols.index(last)
        idx  = (idx + 1) % len(symbols)
        this = symbols[idx]

        printmsg(this, end='\r')
        self.__last_spin = this

    def count(self, value):
        value = self.fmt(value)
        line  = '{}{} ...'.format(value, self.label)
        printmsg(line, end='\r')

    def progress(self, value, total):

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        overflow = value > total
        value    = min(value, total)
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        # arbitrary fallback of 50 columns if
        # terminal width cannot be determined
        if self.width is None: width = Progress.get_terminal_width(50)
        else:                  width = self.width

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        fvalue = self.fmt(value)
        ftotal = self.fmt(total)
        suffix = '{} / {} {}'.format(fvalue, ftotal, self.label).rstrip()

        # +5: - square brackets around bar
        #     - space between bar and tally
        #     - space+spin in case of overflow
        width     = width - (len(suffix) + 5)
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        completed = int(round(width * (value  / total)))
        remaining = width - completed
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        progress  = '[{}{}] {}'.format('#' * completed,
                                       ' ' * remaining,
                                       suffix)
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        printmsg(progress, end='')
        if overflow:
            printmsg(' ', end='')
            self.spin()
        printmsg(end='\r')
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    @staticmethod
    def get_terminal_width(fallback=None):
        """Return the number of columns in the current terminal, or fallback
        if it cannot be determined.
        """
        # os.get_terminal_size added in python 3.3
        try:
            return int(sp.check_output('tput cols'.split()).strip())
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        except Exception:
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            return fallback


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@contextlib.contextmanager
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def tempdir(override_dir=None):
    """Returns a context manager which creates, changes into, and returns a
    temporary directory, and then deletes it on exit.

    If override_dir is not None, instead of creating and changing into a
    temporary directory, this function just changes into override_dir.
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    """

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    if override_dir is None: tmpdir = tempfile.mkdtemp()
    else:                    tmpdir = override_dir

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    prevdir = os.getcwd()

    try:
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        os.chdir(tmpdir)
        yield tmpdir
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    finally:
        os.chdir(prevdir)
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        if override_dir is None:
            shutil.rmtree(tmpdir)
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def memoize(f):
    """Decorator to memoize a function. """

    cache = f.cache = {}
    def g(*args, **kwargs):
        key = (f, tuple(args), frozenset(kwargs.items()))
        if key not in cache:
            cache[key] = f(*args, **kwargs)
        return cache[key]
    return g


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class ChecksumError(Exception):
    """Exception raised by the sha256 function if a file checksume does
    not match the expected checksum.
    """
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def sha256(filename, check_against=None, blocksize=1048576):
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    """Calculate the SHA256 checksum of the given file. If check_against
    is provided, it is compared against the calculated checksum, and an
    error is raised if they are not the same.
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    """

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    hashobj = hashlib.sha256()
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    with open(filename, 'rb') as f:
        while True:
            block = f.read(blocksize)
            if len(block) == 0:
                break
            hashobj.update(block)
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    checksum = hashobj.hexdigest()

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    if check_against is not None:
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        if checksum != check_against:
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            raise ChecksumError('File {} does not match expected checksum '
                                '({})'.format(filename, check_against))

    return checksum
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class DownloadFailed(Exception):
    """Exception type raised by the download_file function if a
    download fails for some reason.
    """
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def download_file(url, destination, progress=None, blocksize=1048576):
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    """Download a file from url, saving it to destination. """

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    def default_progress(downloaded, total):
        pass
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    if progress is None:
        progress = default_progress

    log.debug('Downloading %s ...', url)
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    try:
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        # py2: urlopen result cannot be
        # used as a context manager
        req = urlrequest.urlopen(url)
        with open(destination, 'wb') as outf:
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            try:             total = int(req.headers['content-length'])
            except KeyError: total = None

            downloaded = 0

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            progress(downloaded, total)
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            while True:
                block = req.read(blocksize)
                if len(block) == 0:
                    break
                downloaded += len(block)
                outf.write(block)
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                progress(downloaded, total)
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    except Exception:
        raise
        raise DownloadFailed('A network error has occurred while '
                             'trying to download {}'.format(url))
    finally:
        req.close()
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class Process(object):
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    """Container for a subprocess.Popen object, allowing non-blocking
    access to its standard output and error streams via separate queues.
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    """

    def __init__(self, ctx, cmd, admin, **kwargs):
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        """Run the specified command.

        :arg ctx:    The installer Context
        :arg cmd:    Command to run - passed directly to subprocess.Popen
        :arg admin:  Run the command with administrative privileges
        :arg kwargs: Passed to subprocess.Popen
        """
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        self.ctx     = ctx
        self.cmd     = cmd
        self.admin   = admin
        self.stdoutq = queue.Queue()
        self.stderrq = queue.Queue()
        self.popen   = Process.run(self.ctx, self.cmd, self.admin)
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        # threads for gathering stdout/stderr
        self.stdout_thread = threading.Thread(
            target=Process.forward_stream,
            args=(self.popen, self.popen.stdout, self.stdoutq))
        self.stderr_thread = threading.Thread(
            target=Process.forward_stream,
            args=(self.popen, self.popen.stderr, self.stderrq))
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        self.stdout_thread.daemon = True
        self.stderr_thread.daemon = True
        self.stdout_thread.start()
        self.stderr_thread.start()
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    @staticmethod
    def forward_stream(popen, stream, queue):
        """Runs cmd, and pushes lines from its stdout to the queue. """
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        while popen.returncode is None:
            line = stream.readline()
            popen.poll()
            if line == '':
                break
            else:
                queue.put(line)
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        # process finished, flush the stream
        line = stream.readline()
        while line != '':
            queue.put(line)
            line = stream.readline()
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    @staticmethod
    def sudo_popen(cmd, password, **kwargs):
        """Runs "sudo cmd" using subprocess.Popen.
        Assumes that kwargs contains stdin=sp.PIPE
        """

        cmd  = ['sudo', '-S', '-k'] + cmd
        proc = sp.Popen(cmd, **kwargs)
        proc.stdin.write('{}\n'.format(password))
        return proc


    @staticmethod
    def run(ctx, cmd, admin=False):
        """Starts the given command, as administrator if requested. Returns
        the subprocess.Popen object.
        """

        admin = admin and os.getuid() != 0

        if admin: password = ctx.password
        else:     password = None

        log.debug('Running %s [as admin: %s]', cmd, admin)

        cmd = shlex.split(cmd)

        # set universal_newlines to force text
        # based stdin/out on both py2 and py3
        kwargs = dict(stdin=sp.PIPE,
                      stdout=sp.PIPE,
                      stderr=sp.PIPE,
                      universal_newlines=True)

        if admin: proc = Process.sudo_popen(cmd, password, **kwargs)
        else:     proc = sp.Popen(          cmd, **kwargs)

        return proc


    @staticmethod
    def monitor_progress(ctx, cmd, total=None, **kwargs):
        """Creates a Process object to run cmd, and shows a progress bar
        under the assumption that cmd will produce "total" number of lines
        of output.
        """
        if total is None: label = None
        else:             label = '%'

        with Progress(label=label,
                      fmt='{:.0f}',
                      transform=Progress.percent) as prog:

            proc   = Process(ctx, cmd, **kwargs)
            nlines = 0
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            prog.update(nlines, total)

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            while proc.popen.returncode is None:

                try:
                    line = proc.stdoutq.get(timeout=1)
                except queue.Empty:
                    continue

                nlines += 1
                prog.update(nlines, total)
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def list_available_versions(ctx):
    """Lists available FSL versions. """
    printmsg('Available FSL versions:', EMPHASIS)
    for version in ctx.manifest['versions']:
        if version == 'latest':
            continue
        printmsg(version, IMPORTANT, EMPHASIS)
        for build in ctx.manifest['versions'][version]:
            if build.get('cuda', '').strip() != '':
                template = '  {platform} [CUDA {cuda}]'
            else:
                template = '  {platform}'
            printmsg(template.format(**build), EMPHASIS, end=' ')
            printmsg(build['environment'], INFO)


def install_miniconda(ctx):
    """Downloads the miniconda/miniforge installer, and installs it to the
    destination directory.
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    This function assumes that it is run within a temporary/scratch directory.
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    """

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    metadata = ctx.manifest['installer']['miniconda'][ctx.platform]
    url      = metadata['url']
    checksum = metadata['sha256']
    output   = metadata.get('output', '').strip()
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    if output == '': output = None
    else:            output = int(output)
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    # Download
    printmsg('Downloading miniconda from {}...'.format(url))
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    with Progress('MB', transform=Progress.bytes_to_mb) as prog:
        download_file(url, 'miniforge.sh', prog.update)
    if not ctx.args.no_checksum:
        sha256('miniforge.sh', checksum)
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    # Install
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    printmsg('Installing miniconda at {}...'.format(ctx.destdir))
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    cmd = 'sh miniforge.sh -b -p {}'.format(ctx.destdir)
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    Process.monitor_progress(ctx, cmd, output, admin=ctx.need_admin)

    # Create .condarc config file
    condarc = tw.dedent("""
    # Putting a .condarc file into the root environment
    # directory will override ~/.condarc if it exists,
    # but will not override a system condarc (e.g. at
    # /etc/condarc/condarc). There is currently no
    # workaround for this - see:
    #  - https://github.com/conda/conda/issues/8599
    #  - https://github.com/conda/conda/issues/8804

    # Try and make package downloads more robust
    remote_read_timeout_secs:    240
    remote_connect_timeout_secs: 20
    remote_max_retries:          10
    remote_backoff_factor:       5
    safety_checks:               warn

    # Channel priority is important. In older versions
    # of FSL we placed the FSL conda channel at the
    # bottom (lowest priority) for legacy reasons (to
    # ensure that conda-forge versions of e.g. VTK were
    # preferred over legacy FSL conda versions).
    #
    # https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html
    channel_priority: strict
    channels:
      - http://18.133.213.73/production/
      - conda-forge
      - defaults
    """)

    with open('.condarc', 'wt') as f:
        f.write(condarc)

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    Process.run(
        ctx, 'cp .condarc {}'.format(ctx.destdir, admin=ctx.need_admin))
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def install_fsl(ctx):
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    """Install FSL into ctx.destdir (which is assumed to be a miniconda
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    installation.
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    This function assumes that it is run within a temporary/scratch directory.
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    """

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    build    = ctx.build
    url      = build['environment']
    checksum = build['sha256']
    output   = build.get('output', None)

    if output == '': output = None
    else:            output = int(output)

    printmsg('Downloading FSL environment specification '
             'from {}...'.format(url))
    download_file(url, 'environment.yml')

    conda = op.join(ctx.destdir, 'bin', 'conda')
    cmd   = conda + ' env update -n base -f environment.yml'

    printmsg('Installing FSL into {}...'.format(ctx.destdir))

    env = os.environ.copy()
    env['FSL_CREATE_WRAPPER_SCRIPTS'] = '1'

    Process.monitor_progress(ctx, cmd, output, admin=ctx.need_admin, env=env)

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def post_install_cleanup(ctx):
    """Cleans up the FSL directory after installation. """

    conda = op.join(ctx.destdir, 'bin', 'conda')
    cmd   = conda + ' clean -y --all'

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    Process.run(ctx, cmd, admin=ctx.need_admin)
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def patch_file(filename, searchline, numlines, content):
    """Used by configure_shell and configure_matlab. Adds to, modifies,
    or creates the specified file.

    If a line matching searchline is found in the file, numlines (starting
    from searchline) are replaced with content.

    Otherwise, content is appended to the end of the file.
    """

    content = content.split('\n')

    if op.isfile(filename):
        with open(filename) as f:
            lines = [l.strip() for l in f.readlines()]
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        lines = []
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    # replace block
    try:
        idx   = lines.index(searchline)
        lines = lines[:idx] + content + lines[idx + numlines:]
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    # append to end
    except ValueError:
        lines = lines + [''] + content
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    with open(filename, 'wt') as f:
        f.write('\n'.join(lines))
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def configure_shell(ctx):
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    """Configures the user's shell environment (e.g. ~/.bash_profile). """
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    bourne_shells  = ['sh', 'bash', 'zsh', 'dash']
    csh_shells     = ['csh', 'tcsh']

    # we edit the first file that exists
    # in the list of candidate profile files,
    shell_profiles = {'sh'   : ['.profile'],
                      'bash' : ['.bash_profile', '.profile'],
                      'dash' : ['.bash_profile', '.profile'],
                      'zsh'  : ['.zprofile'],
                      'csh'  : ['.cshrc'],
                      'tcsh' : ['.tcshrc']}

    # Do not change the format of these configurations -
    # they are kept exactly as-is for compatibility with
    # legacy FSL installations, i.e. so we can modify
    # profiles with an existing configuration from older
    # FSL versions
    bourne_cfg = tw.dedent("""
    # FSL Setup
    FSLDIR={fsldir}
    PATH=${{FSLDIR}}/share/fsl/bin:${{PATH}}
    export FSLDIR PATH
    . ${{FSLDIR}}/etc/fslconf/fsl.sh
    """).format(fsldir=ctx.destdir)

    csh_cfg = tw.dedent("""
    # FSL Setup
    setenv FSLDIR {fsldir}
    setenv PATH ${{FSLDIR}}/share/fsl/bin:${{PATH}}
    source ${{FSLDIR}}/etc/fslconf/fsl.csh
    """).format(fsldir=ctx.destdir)

    if ctx.shell not in bourne_shells + csh_shells:
        printmsg('Shell {} not recognised - skipping environment '
                 'setup'.format(ctx.shell), WARNING, EMPHASIS)
        return

    if ctx.shell in bourne_shells: cfg = bourne_cfg
    else:                          cfg = csh_cfg

    # find the profile file to edit
    profile    = None
    candidates = [op.join(ctx.args.homedir, p)
                  for p in shell_profiles[ctx.shell]]
    for candidate in candidates:
        if op.isfile(candidate):
            profile = candidate
            break

    # if no candidate profile files
    # exist, fall back to the first one
    if profile is None:
        profile = candidates[0]

    printmsg('Adding FSL configuration to {}'.format(profile))

    patch_file(profile, '# FSL Setup', len(cfg.split('\n')), cfg)


def configure_matlab(ctx):
    """Creates/appends FSL configuration code to ~/Documents/MATLAB/startup.m.
    """

    # Do not change the format of this configuration -
    # see in-line comments in configure_shell.
    cfg = tw.dedent("""
    % FSL Setup
    setenv( 'FSLDIR', '{fsldir}' );
    setenv('FSLOUTPUTTYPE', 'NIFTI_GZ');
    fsldir = getenv('FSLDIR');
    fsldirmpath = sprintf('%s/etc/matlab',fsldir);
    path(path, fsldirmpath);
    clear fsldir fsldirmpath;
    """).format(fsldir=ctx.destdir)

    matlab_dir = op.expanduser(op.join(ctx.args.homedir, 'Documents', 'MATLAB'))
    startup_m  = op.join(matlab_dir, 'startup.m')

    if not op.exists(matlab_dir):
        os.makedirs(matlab_dir)

    printmsg('Adding FSL configuration to {}'.format(startup_m))

    patch_file(startup_m, '% FSL Setup', len(cfg.split('\n')), cfg)
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def self_update(ctx):
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    """Checks to see if a newer version of the installer (this script) is
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    available and if so, downloads it to a temporary file, and runs it in
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    place of this script.
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    """

    @ft.total_ordering
    class Version(object):
        """Class to hold and compare FSL installer version strings.  Version
        strings must be of the form X.Y.Z, where X, Y, and Z are all integers.
        """
        def __init__(self, verstr):
            major, minor, patch = verstr.split('.')[:3]
            self.verstr         = verstr
            self.major          = int(major)
            self.minor          = int(minor)
            self.patch          = int(patch)

        def __str__(self):
            return self.verstr

        def __eq__(self, other):
            return all((self.major == other.major,
                        self.minor == other.minor,
                        self.patch == other.patch))

        def __lt__(self, other):
            for p1, p2 in zip((self.major,  self.minor,  self.patch),
                              (other.major, other.minor, other.patch)):
                if p1 < p2: return True
                if p1 > p2: return False
            return False

    thisver   = Version(__version__)
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    latestver = Version(ctx.manifest['installer']['version'])
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    if latestver <= thisver:
        log.debug('Installer is up to date (this vesrion: %s, '
                  'latest version: %s)', thisver, latestver)
        return

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    log.debug('New version of installer is available '
              '(%s) - self-updating', latestver)
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    tmpf = tempfile.NamedTemporaryFile(delete=False)
    tmpf.close()
    tmpf = tmpf.name
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    download_file(ctx.manifest['installer']['url'], tmpf)
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    if not ctx.args.no_checksum:
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        sha256(tmpf, ctx.manifest['installer']['sha256'])
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    cmd = [sys.executable, tmpf] + sys.argv[1:]
    log.debug('Running new installer: %s', cmd)
    os.execv(sys.executable, cmd)
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def overwrite_destdir(ctx):
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    """Called by main if the destination directory already exists.  Asks the
    user if they want to overwrite it and, if they say yes, removes the
    existing destination directory. Otherwise exits.
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    """
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    if not ctx.args.overwrite:
        printmsg('Destination directory [{}] already exists!'
                 .format(ctx.destdir), WARNING, EMPHASIS)
        response = prompt('Do you want to overwrite it [N/y]?',
                          WARNING, EMPHASIS)
        if response.lower() not in ('y', 'yes'):
            printmsg('Aborting installation', ERROR, EMPHASIS)
            sys.exit(1)
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    printmsg('Deleting directory {}'.format(ctx.destdir), IMPORTANT)
    Process.run(ctx, 'rm -r {}'.format(ctx.destdir), admin=ctx.need_admin)


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def parse_args(argv=None):
    """Parse command-line arguments, returns an argparse.Namespace object. """

    helps = {
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        'version'      : 'Print installer version number and exit',
        'listversions' : 'List available FSL versions and exit',
        'dest'         : 'Install FSL into this folder (default: '
                         '{})'.format(DEFAULT_INSTALLATION_DIRECTORY),
        'overwrite'    : 'Delete destination directory without '
                         'asking, if it already exists',
        'no_env'       : 'Do not modify your shell or MATLAB configuration '
                         'implies --no_shell and --no_matlab)',
        'no_shell'     : 'Do not modify your shell configuration',
        'no_matlab'    : 'Do not modify your MATLAB configuration',
        'fslversion'   : 'Install this specific version of FSL',
        'cuda'         : 'Install FSL for this CUDA version (default: '
                         'automatically detected)',

        # Do not automatically update the installer script,
        'no_self_update' : argparse.SUPPRESS,
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        # Path to local installer manifest file
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        'manifest'       : argparse.SUPPRESS,
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        # Print debugging messages
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        'debug'          : argparse.SUPPRESS,
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        # Disable SHA256 checksum validation of downloaded files
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        'no_checksum'    : argparse.SUPPRESS,
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        # Store temp files in this directory
        # rather than in a temporary directory
        'workdir'        : argparse.SUPPRESS,

        # Treat this directory as user's home directory,
        # for the purposes of shell configuration. Must
        # already exist.
        'homedir'        : argparse.SUPPRESS,
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    }

    parser = argparse.ArgumentParser()
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    # regular options
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    parser.add_argument('-v', '--version', action='version',
                        version=__version__, help=helps['version'])
    parser.add_argument('-d', '--dest', metavar='DESTDIR',
                        help=helps['dest'])
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    parser.add_argument('-o', '--overwrite', action='store_true',
                        help=helps['overwrite'])
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    parser.add_argument('-l', '--listversions', action='store_true',
                        help=helps['listversions'])
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    parser.add_argument('-e', '--no_env', action='store_true',
                        help=helps['no_env'])
    parser.add_argument('-s', '--no_shell', action='store_true',
                        help=helps['no_shell'])
    parser.add_argument('-m', '--no_matlab', action='store_true',
                        help=helps['no_matlab'])
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    parser.add_argument('-V', '--fslversion', default='latest',
                        help=helps['version'])
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    parser.add_argument('-c', '--cuda', help=helps['cuda'])
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    # hidden options
    parser.add_argument('-k', '--no_checksum', action='store_true',
                        help=helps['no_checksum'])
    parser.add_argument('-w', '--workdir', help=helps['workdir'])
    parser.add_argument('-i', '--homedir', help=helps['homedir'],
                        default=op.expanduser('~'))
    parser.add_argument('-D', '--debug', action='store_true',
                        help=helps['debug'])
    parser.add_argument('-a', '--manifest', default=FSL_INSTALLER_MANIFEST,
                        help=helps['manifest'])
    parser.add_argument('-u', '--no_self_update', action='store_true',
                        help=helps['no_self_update'])

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    logging.basicConfig()
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    if args.debug: logging.getLogger().setLevel(logging.DEBUG)
    else:          logging.getLogger().setLevel(logging.WARNING)
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    args.homedir = op.abspath(args.homedir)

    if not op.isdir(args.homedir):
        printmsg('Home directory {} does not exist!'.format(args.homedir),
                 ERROR, EMPHASIS)
        sys.exit(1)

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    if os.getuid() == 0:
        printmsg('Running the installer script as root user - disabling '
                 'environment configuration', WARNING, EMPHASIS)
        args.no_env = True

    if args.no_env:
        args.no_shell  = True
        args.no_matlab = True

    if args.workdir is not None:
        args.workdir = op.abspath(args.workdir)
        if not op.exists(args.workdir):
            os.mkdir(args.workdir)

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    return args
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def main(argv=None):
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    """Installer entry point. Downloads and installs miniconda and FSL, and
    configures the user's environment.
    """
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    args = parse_args(argv)
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    ctx  = Context(args)

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    if not args.no_self_update:
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        self_update(ctx)
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    printmsg('FSL installer version:', EMPHASIS, UNDERLINE, end='')
    printmsg(' ' + __version__ + '\n')
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    if args.listversions:
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        list_available_versions(ctx)
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        sys.exit(0)

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    ctx.finalise_settings()

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    with tempdir(args.workdir):
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        if op.exists(ctx.destdir):
           overwrite_destdir(ctx)

        printmsg('\nInstalling FSL into {}\n'.format(ctx.destdir), EMPHASIS)
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        install_miniconda(ctx)
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        install_fsl(ctx)
        post_install_cleanup(ctx)

    if not args.no_shell:  configure_shell( ctx)
    if not args.no_matlab: configure_matlab(ctx)

    printmsg('\nFSL successfully installed\n', IMPORTANT)
    if not args.no_env:
        printmsg('Open a new terminal, or log out and log back in, '
                 'for the environment changes to take effect.', INFO)
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if __name__ == '__main__':
    sys.exit(main())