fslinstaller.py

#!/usr/bin/env python
#
# FSL installer script.
#
"""This is the FSL installation script. It can be used to install FSL, or
to update an existing FSL installation.  This script can be executed with
Python 2.7 or newer.
"""


from __future__ import print_function, division, unicode_literals

import functools      as ft
import os.path        as op
import subprocess     as sp
import textwrap       as tw
import                   argparse
import                   contextlib
import                   getpass
import                   hashlib
import                   json
import                   logging
import                   os
import                   platform
import                   re
import                   readline
import                   shlex
import                   shutil
import                   sys
import                   tempfile
import                   threading
import                   traceback

# TODO check py2/3
try:
    import urllib.request as urlrequest
except ImportError:
    import urllib as urlrequest

try:                import queue
except ImportError: import Queue as queue


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


log = logging.getLogger(__name__)


# this sometimes gets set to fslinstaller.pyc, so rstrip c
__absfile__ = op.abspath(__file__).rstrip('c')


__version__ = '1.4.1'
"""Installer script version number. This must be updated
whenever a new version of the installer script is released.
"""


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


FSL_INSTALLER_MANIFEST = 'https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/manifest.json'
"""URL to download the FSL installer manifest file from. The installer
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.

A custom manifest URL can be specified with the -a/--manifest command-line
option.
"""


FIRST_FSL_CONDA_RELEASE = '6.0.6'
"""Oldest conda-based FSL version that can be updated in-place by this
installer script. Versions older than this will need to be overwritten.
"""


@ft.total_ordering
class Version(object):
    """Class to represent and compare version strings.  Accepted version
    strings are of the form W.X.Y.Z, where W, X, Y, and Z are all integers.
    """
    def __init__(self, verstr):
        # Version identifiers for official FSL
        # releases will have up to four
        # components (X.Y.Z.W), but We accept
        # any number of (integer) components,
        # as internal releases may have more.
        components = []

        for comp in verstr.split('.'):
            try:              components.append(int(comp))
            except Exception: break

        self.components = components
        self.verstr     = verstr

    def __str__(self):
        return self.verstr

    def __eq__(self, other):
        for sn, on in zip(self.components, other.components):
            if sn != on:
                 return False
        return len(self.components) == len(other.components)

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


class Context(object):
    """Bag of information and settings created in main, and passed around
    this script.

    Several settings are lazily evaluated on first access, but once evaluated,
    their values are immutable.
    """

    def __init__(self, args):
        """Create the context with the argparse.Namespace object containing
        parsed command-line arguments.
        """

        self.args  = args
        self.shell = op.basename(os.environ.get('SHELL', 'sh')).lower()

        # These attributes are updated on-demand via
        # 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
        self.__need_admin     = None
        self.__admin_password = None

        # These attributes are set by main - exists is
        # a flag denoting whether the dest dir already
        # exists, and update is the version string of
        # the existing FSL installation if the user
        # has selected to update it, or None otherwise.
        self.exists = False
        self.update = None

        # If the destination directory already exists,
        # and the user chooses to overwrite it, it is
        # moved so that, if the installation fails, it
        # can be restored. The new path is stored
        # here - refer to overwrite_destdir.
        self.old_destdir = None

        # The download_fsl_environment function stores
        # the path to the FSL conda environment file,
        # list of conda channels, and versions of a
        # small set of "base" packages here.
        self.environment_file     = None
        self.environment_channels = None
        self.fsl_base_packages    = None

        # The config_logging function stores the path
        # to the fslinstaller log file here.
        self.logfile = None


    def finalise_settings(self):
        """Finalise values for all information and settings in the Context.
        """
        self.manifest
        self.platform
        self.cuda
        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
        installer manifest) for the target platform and requested FSL/CUDA
        versions.

        The returned dictionary has the following elements:
          - 'version'      FSL version.
          - 'platform':    Platform identifier (e.g. 'linux-64')
          - 'environment': Environment file to download
          - 'sha256':      Checksum of environment file
          - 'output':      Number of lines of expected output, for reporting
                           progress
          - 'cuda':        X.Y CUDA version, if a CUDA-enabled version of FSL
                           is to be installed.
        """

        if self.__build is not None:
            return self.__build

        # defaults to "latest" if
        # not specified by the user
        fslversion = self.args.fslversion

        if fslversion not in self.manifest['versions']:
            available = ', '.join(self.manifest['versions'].keys())
            raise Exception(
                'FSL version "{}" is not available - available '
                'versions: {}'.format(fslversion, available))

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

        # Find refs to all compatible builds,
        # separating the default (no CUDA) build
        # from CUDA-enabled builds. We assume
        # that there is only one default build
        # for each platform.
        default    = None
        candidates = []

        for build in self.manifest['versions'][fslversion]:
            if build['platform'] == self.platform:
                if build.get('cuda', None) is None:
                    default = build
                else:
                    candidates.append(build)

        if (default is None) and (len(candidates) == 0):
            raise Exception(
                'Cannot find a version of FSL matching platform '
                '{} and CUDA {}'.format(self.platform, self.cuda))

        # If we have CUDA (or the user has
        # specifically requested a CUDA build),
        # try and find a suitable build
        match = default
        if self.cuda is not None:
            candidates = sorted(candidates, key=lambda b: float(b['cuda']))

            for build in reversed(candidates):
                if self.cuda >= float(build['cuda']):
                    match = build
                    break
            else:
                available = [b['cuda'] for b in candidates]
                printmsg('Could not find a suitable FSL CUDA '
                         'build for CUDA version {} (available: '
                         '{}. Installing default (non-CUDA) '
                         'FSL build.'.format(self.cuda, available),
                         WARNING)
                printmsg('You can use the --cuda command-line option '
                         'to install a FSL build that is compatible '
                         'with a specific CUDA version', INFO)

        printmsg('FSL {} [CUDA: {}] selected for installation'.format(
            match['version'], match.get('cuda', 'n/a')))

        self.__build = match
        return match


    @property
    def destdir(self):
        """Installation directory. If not specified at the command line, the
        user is prompted to enter a directory.
        """

        if self.__destdir is not None:
            return self.__destdir

        # The loop below validates the destination directory
        # both when specified at commmand line or
        # interactively.  In either case, if invalid, the
        # user is re-prompted to enter a new destination.
        destdir = None
        if self.args.dest is not None: response = self.args.dest
        else:                          response = None

        while destdir is None:

            if response is None:
                printmsg('\nWhere do you want to install FSL?',
                         IMPORTANT, EMPHASIS)
                printmsg('Press enter to install to the default location '
                         '[{}]\n'.format(DEFAULT_INSTALLATION_DIRECTORY), INFO)
                response = prompt('FSL installation directory [{}]:'.format(
                    DEFAULT_INSTALLATION_DIRECTORY), QUESTION, EMPHASIS)
                response = response.rstrip(op.sep)

                if response == '':
                    response = DEFAULT_INSTALLATION_DIRECTORY

            response  = op.expanduser(op.expandvars(response))
            response  = op.abspath(response)
            parentdir = op.dirname(response)
            if op.exists(parentdir):
                destdir = response
            else:
                printmsg('Destination directory {} does not '
                         'exist!'.format(parentdir), ERROR)
                response = None

        self.__destdir = destdir
        return self.__destdir


    @property
    def need_admin(self):
        """Returns True if administrator privileges will be needed to install
        FSL.
        """
        if self.__need_admin is not None:
            return self.__need_admin
        parentdir = op.dirname(self.destdir)
        self.__need_admin = Context.check_need_admin(parentdir)
        return self.__need_admin


    @property
    def admin_password(self):
        """Returns the user's administrator password, prompting them if needed.
        """
        if self.__admin_password is not None:
            return self.__admin_password
        if self.__need_admin == False:
            return None
        self.__admin_password = Context.get_admin_password()


    @property
    def manifest(self):
        """Returns the FSL installer manifest as a dictionary. """
        if self.__manifest is None:
            self.__manifest = Context.download_manifest(self.args.manifest,
                                                        self.args.workdir)
        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') : 'macos-64',

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

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

        if key not in platforms:
            supported = ', '.join(['[{}, {}]' for s, c in platforms])
            raise Exception('This platform [{}, {}] is unrecognised or '
                            'unsupported! Supported platforms: {}'.format(
                                system, cpu, supported))

        return platforms[key]


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

        # see below - no_cuda is set to prevent unnecessary
        # attempts to call nvidia-smi more than once
        if getattr(Context.identify_cuda, 'no_cuda', False):
            return None

        try:
            output = Process.check_output('nvidia-smi')
        except Exception:
            Context.identify_cuda.no_cuda = True
            return None

        pat   = r'CUDA Version: (\S+)'
        lines = output.split('\n')
        for line in lines:
            match = re.search(pat, line)
            if match:
                cudaver = match.group(1)
                break
        else:
            # message for debugging - the output
            # will be present in the logfile
            log.debug('Could not parse nvidia-smi output')
            Context.identify_cuda.no_cuda = True
            return None

        return float(cudaver)


    @staticmethod
    def check_need_admin(dirname):
        """Returns True if dirname needs administrator privileges to write to,
        False otherwise.
        """
        # os.supports_effective_ids added in
        # python 3.3, so can't be used here
        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):
            proc = Process.sudo_popen(['true'], password, stdin=sp.PIPE)
            proc.communicate()
            return proc.returncode == 0

        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='')
            password = getpass.getpass('')
            valid    = validate_admin_password(password)

            if valid:
                printmsg('Password accepted', INFO)
                break
            else:
                printmsg('Incorrect password', WARNING)

        if not valid:
            raise Exception('Incorrect password')

        return password


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

        The manifest file is a JSON file. Lines beginning
        with a double-forward-slash are ignored. See test/data/manifes.json
        for an example.

        This function modifies the manifest structure by adding a 'version'
        attribute to all FSL build entries.
        """

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

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

        # Drop comments
        lines = [l for l in lines if not l.lstrip().startswith('//')]

        manifest = json.loads('\n'.join(lines))

        # Add "version" to every build
        for version, builds in manifest['versions'].items():
            if version == 'latest':
                continue
            for build in builds:
                build['version'] = version

        return manifest


# 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 = {
    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
}


def printmsg(msg='', *msgtypes, **kwargs):
    """Prints msg according to the ANSI codes provided in msgtypes.
    All other keyword arguments are passed through to the print function.

    :arg msgtypes: Message types to control formatting
    :arg log:      If True (default), the message is logged.

    All other keyword arguments are passed to the built-in print function.
    """
    logmsg   = kwargs.pop('log', msg != '')
    msgcodes = [ANSICODES[t] for t in msgtypes]
    msgcodes = ''.join(msgcodes)
    if logmsg:
        log.debug(msg)
    print('{}{}{}'.format(msgcodes, msg, ANSICODES[RESET]), **kwargs)
    sys.stdout.flush()


def prompt(prompt, *msgtypes, **kwargs):
    """Prompts the user for some input. msgtypes and kwargs are passed
    through to the printmsg function.
    """
    printmsg(prompt, *msgtypes, end='', log=False, **kwargs)

    if PY2: response = raw_input(' ').strip()
    else:   response = input(    ' ').strip()

    log.debug('%s: %s', prompt, response)

    return response


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(log=False)

    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', log=False)
        self.__last_spin = this

    def count(self, value):

        value = self.fmt(value)

        if self.label is None: line = '{} ...'.format(value)
        else:                  line = '{}{} ...'.format(value, self.label)

        printmsg(line, end='\r', log=False)

    def progress(self, value, total):

        value = min(value, total)

        # 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

        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 at the end
        width     = width - (len(suffix) + 5)
        completed = int(round(width * (value  / total)))
        remaining = width - completed
        progress  = '[{}{}] {}'.format('#' * completed,
                                       ' ' * remaining,
                                       suffix)

        printmsg(progress, end='', log=False)
        printmsg(' ', end='', log=False)
        self.spin()
        printmsg(end='\r', log=False)


    @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, so we try it but fall back to tput
        try:
            return os.get_terminal_size()[0]
        except Exception:
            pass

        try:
            result = sp.check_output(('tput', 'cols'))
            return int(result.strip())
        except Exception:
            return fallback


def isstr(s):
    """Returns True if s is a string, False otherwise, Works on python 2.7
    and >=3.3.
    """
    try:              return isinstance(s, basestring)
    except Exception: return isinstance(s, str)


@contextlib.contextmanager
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.
    """

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

    prevdir = os.getcwd()

    try:
        os.chdir(tmpdir)
        yield tmpdir

    finally:
        os.chdir(prevdir)
        if override_dir is None:
            shutil.rmtree(tmpdir)


def sha256(filename, check_against=None, blocksize=1048576):
    """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.
    """

    hashobj = hashlib.sha256()

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

    checksum = hashobj.hexdigest()

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

    return checksum


def download_file(url, destination, progress=None, blocksize=131072):
    """Download a file from url, saving it to destination. """

    def default_progress(downloaded, total):
        pass

    if progress is None:
        progress = default_progress

    log.debug('Downloading %s ...', url)

    # Path to local file
    if op.exists(url):
        url = 'file:' + urlrequest.pathname2url(op.abspath(url))

    req = None
    try:
        # py2: urlopen result cannot be
        # used as a context manager
        req = urlrequest.urlopen(url)
        with open(destination, 'wb') as outf:

            try:             total = int(req.headers['content-length'])
            except KeyError: total = None

            downloaded = 0

            progress(downloaded, total)
            while True:
                block = req.read(blocksize)
                if len(block) == 0:
                    break
                downloaded += len(block)
                outf.write(block)
                progress(downloaded, total)

    finally:
        if req:
            req.close()


class Process(object):
    """Container for a subprocess.Popen object, allowing non-blocking
    line-based access to its standard output and error streams via separate
    queues, while logging all outputs.

    Don't create a Process directly - use one of the following static methods:
     - Process.check_output
     - Process.check_call
     - Process.monitor_progress
    """


    def __init__(self, cmd, admin=False, ctx=None, log_output=True, **kwargs):
        """Run the specified command. Starts threads to capture stdout and
        stderr.

        :arg cmd:        Command to run - passed directly to subprocess.Popen
        :arg admin:      Run the command with administrative privileges
        :arg ctx:        The installer Context. Only used for admin password -
                         can be None if admin is False.
        :arg log_output: If True, the command and all of its stdout/stderr are
                         logged.
        :arg kwargs:     Passed to subprocess.Popen
        """

        self.ctx        = ctx
        self.cmd        = cmd
        self.admin      = admin
        self.log_output = log_output
        self.stdoutq    = queue.Queue()
        self.stderrq    = queue.Queue()

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

        self.popen = Process.popen(self.cmd, self.admin, self.ctx, **kwargs)

        # threads for consuming stdout/stderr
        self.stdout_thread = threading.Thread(
            target=Process.forward_stream,
            args=(self.popen.stdout, self.stdoutq, cmd, 'stdout', log_output))
        self.stderr_thread = threading.Thread(
            target=Process.forward_stream,
            args=(self.popen.stderr, self.stderrq, cmd, 'stderr', log_output))

        self.stdout_thread.daemon = True
        self.stderr_thread.daemon = True
        self.stdout_thread.start()
        self.stderr_thread.start()


    def wait(self):
        """Waits for the process to terminate, then waits for the stdout
        and stderr consumer threads to finish.
        """
        self.popen.wait()
        self.stdout_thread.join()
        self.stderr_thread.join()


    @property
    def returncode(self):
        """Process return code. Returns None until the process has terminated,
        and the stdout/stderr consumer threads have finished.
        """
        if self.popen.returncode is None: return None
        if self.stdout_thread.is_alive(): return None
        if self.stderr_thread.is_alive(): return None
        return self.popen.returncode


    @staticmethod
    def check_output(cmd, *args, **kwargs):
        """Behaves like subprocess.check_output. Runs the given command, then
        waits until it finishes, and return its standard output. An error
        is raised if the process returns a non-zero exit code.

        :arg cmd: The command to run, as a string
        """

        proc = Process(cmd, *args, **kwargs)
        proc.wait()

        if proc.returncode != 0:
            raise RuntimeError('This command returned an error: ' + cmd)

        stdout = ''
        while True:
            try:
                stdout += proc.stdoutq.get_nowait()
            except queue.Empty:
                break

        return stdout


    @staticmethod
    def check_call(cmd, *args, **kwargs):
        """Behaves like subprocess.check_call. Runs the given command, then
        waits until it finishes. An error is raised if the process returns a
        non-zero exit code.

        :arg cmd: The command to run, as a string
        """
        proc = Process(cmd, *args, **kwargs)
        proc.wait()
        if proc.returncode != 0:
            raise RuntimeError('This command returned an error: ' + cmd)


    @staticmethod
    def monitor_progress(cmd, total=None, *args, **kwargs):
        """Runs the given command(s), and shows a progress bar under the
        assumption that cmd will produce "total" number of lines of output.

        :arg cmd:   The commmand to run as a string, or a sequence of
                    multiple commands.
        :arg total: Total number of lines of standard output to expect.
        """
        if total is None: label = None
        else:             label = '%'

        if isstr(cmd): cmds = [cmd]
        else:          cmds =  cmd

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

            nlines = 0 if total else None

            for cmd in cmds:

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

                while proc.returncode is None:
                    try:
                        line    = proc.stdoutq.get(timeout=0.5)
                        nlines  = (nlines + 1) if total else None

                    except queue.Empty:
                        pass

                    prog.update(nlines, total)
                    proc.popen.poll()

                # force progress bar to 100% when finished
                if proc.returncode == 0:
                    prog.update(total, total)
                else:
                    raise RuntimeError('This command returned '
                                       'an error: ' + cmd)


    @staticmethod
    def forward_stream(stream, queue, cmd, streamname, log_output):
        """Reads lines from stream and pushes them onto queue until popen
        is finished. Logs every line.

        :arg stream:     stream to forward
        :arg queue:      queue.Queue to push lines onto
        :arg cmd:        string - the command that is running
        :arg streamname: string - 'stdout' or 'stderr'
        :arg log_output: If True, log all stdout/stderr.
        """

        while True:
            line = stream.readline().decode('utf-8')
            if line == '':
                break
            else:
                queue.put(line)
                if log_output:
                    log.debug(' [%s]: %s', streamname, line.rstrip())


    @staticmethod
    def popen(cmd, admin=False, ctx=None, **kwargs):
        """Runs the given command via subprocess.Popen, as administrator if
        requested.

        :arg cmd:    The command to run, as a string

        :arg admin:  Whether to run with administrative privileges

        :arg ctx:    The installer Context object. Only required if admin is
                     True.

        :arg kwargs: Passed to subprocess.Popen. stdin, stdout, and stderr
                     will be silently clobbered

        :returns:    The subprocess.Popen object.
        """

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

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

        cmd              = shlex.split(cmd)
        kwargs['stdin']  = sp.PIPE
        kwargs['stdout'] = sp.PIPE
        kwargs['stderr'] = sp.PIPE

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

        return proc


    @staticmethod
    def sudo_popen(cmd, password, **kwargs):
        """Runs "sudo cmd" using subprocess.Popen. Used by Process.popen.
        Assumes that kwargs contains stdin=sp.PIPE
        """

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


def list_available_versions(manifest):
    """Lists available FSL versions. """
    printmsg('Available FSL versions:', EMPHASIS)
    for version in manifest['versions']:
        if version == 'latest':
            continue
        printmsg(version, IMPORTANT, EMPHASIS)
        for build in 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 download_fsl_environment(ctx):
    """Downloads the environment specification file for the selected FSL
    version.

    If the (hidden) --environment option is provided, the specified file
    is used instead.

    Internal/development FSL versions may source packages from the internal
    FSL conda channel, which requires a username+password to authenticate.

    These are referred to in the environment file as ${FSLCONDA_USERNAME}
    and ${FSLCONDA_PASSWORD}.

    If the user has not provided a username+password on the command-line, they
    are prompted for them.
    """

    if ctx.args.environment is None:
        build        = ctx.build
        url          = build['environment']
        checksum     = build.get('sha256',        None)
        basepkgnames = build.get('base_packages', [])
    else:
        build        = {}
        url          = ctx.args.environment
        checksum     = None
        basepkgnames = []

    printmsg('Downloading FSL environment specification '
             'from {}...'.format(url))
    fname = url.split('/')[-1]
    download_file(url, fname)
    ctx.environment_file = op.abspath(fname)
    if (checksum is not None) and (not ctx.args.no_checksum):
        sha256(fname, checksum)

    # Environment files for internal/dev FSL versions
    # will list the internal FSL conda channel with
    # ${FSLCONDA_USERNAME} and ${FSLCONDA_PASSWORD}
    # as placeholders for the username/password.
    with open(fname, 'rt') as f:
        need_auth = '${FSLCONDA_USERNAME}' in f.read()

    # We need a username/password to access the internal
    # FSL conda channel. Prompt the user if they haven't
    # provided credentials.
    if need_auth and (ctx.args.username is None):
        printmsg('A username and password are required to install '
                 'this version of FSL.', WARNING, EMPHASIS)
        ctx.args.username = prompt('Username:').strip()
        ctx.args.password = getpass.getpass('Password: ').strip()

    # Conda expands environment variables within a
    # .condarc file, but *not* within an environment.yml
    # file. So to authenticate to our internal channel
    # without storing credentials anywhere in plain text,
    # we *move* the channel list from the environment.yml
    # file into $FSLDIR/.condarc.
    #
    # Here we extract the channels from the environment
    # file, and save them to ctx.environment_channels.
    # The install_miniconda function will then add the
    # channels to $FSLDIR/.condarc.
    #
    # A collection of "base" packages are installed
    # before any other packages. So we also extract the
    # version numbers of these base packages from the
    # environment file, and store them in the context.
    # Sort base package names from longest to shortest,
    # to avoid name conflicts (e.g. 'fsl-sub', and
    # 'fsl-sub_plugin_sge')
    basepkgnames = sorted(basepkgnames, key=len, reverse=True)
    copy         = '.' + op.basename(ctx.environment_file)
    channels     = []
    basepkgs     = {}

    shutil.move(ctx.environment_file, copy)
    with open(copy,                 'rt') as inf, \
         open(ctx.environment_file, 'wt') as outf:

        in_channels_section = False

        for line in inf:

            # start of channels list
            if line.strip() == 'channels:':
                in_channels_section = True
                continue

            if in_channels_section:
                # end of channels list
                if not line.strip().startswith('-'):
                    in_channels_section = False
                else:
                    channels.append(line.split()[-1])
                    continue

            # Save base package versions, as we
            # install them separately. Package
            # specs in the yml file are of the
            # form:
            #
            #   - <package> <version> [<build_variant>]
            for pkg in basepkgnames:
                if line.strip().startswith('- {} '.format(pkg)):
                    pkgver        = line.strip().split(' ', 2)[2]
                    basepkgs[pkg] = pkgver.replace(' ', '=')

            outf.write(line)

    ctx.environment_channels = channels
    ctx.fsl_base_packages    = basepkgs


def download_miniconda(ctx):
    """Downloads the miniconda/miniforge installer and saves it as
    "miniconda.sh".

    This function assumes that it is run within a temporary/scratch directory.
    """

    metadata = ctx.manifest['miniconda'][ctx.platform]
    url      = metadata['url']
    checksum = metadata['sha256']
    output   = metadata.get('output', '').strip()

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

    # Download
    printmsg('Downloading miniconda from {}...'.format(url))
    with Progress('MB', transform=Progress.bytes_to_mb) as prog:
        download_file(url, 'miniconda.sh', prog.update)
    if not ctx.args.no_checksum:
        sha256('miniconda.sh', checksum)


def install_miniconda(ctx):
    """Downloads the miniconda/miniforge installer, and installs it to the
    destination directory.

    This function assumes that it is run within a temporary/scratch directory.
    """

    metadata = ctx.manifest['miniconda'][ctx.platform]
    url      = metadata['url']
    checksum = metadata['sha256']
    output   = metadata.get('output', '').strip()

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

    # Install