Skip to content
GitLab
Commit 81fd8b0a authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

ENH: Install FSL+shell/matlab configuration

parent 0f83f45b
Hide whitespace changes
Inline Side-by-side
fslinstaller.py
View file @ 81fd8b0a
......@@ -78,6 +78,12 @@ class BuildNotAvailable(Exception):
"""
class UnsupportedPlatform(Exception):
"""Exception raised by the identify_platform function if FSL is not
available on this platform.
"""
class Context(object):
"""Bag of information and settings created in main, and passed around
this script.
......@@ -91,7 +97,8 @@ class Context(object):
parsed command-line arguments.
"""
self.args = args
self.args = args
self.shell = op.basename(os.environ['SHELL'])
# These attributes are updated on-demand via
# the property accessors defined below, or all
......@@ -141,12 +148,11 @@ class Context(object):
@property
def build(self):
"""Returns a suitable FSL build (a dictionary entry from the FSL
installer manifest) for the target platform and CUDA version.
installer manifest) for the target platform and requested FSL/CUDA
versions.
"""
fslversion = self.args.fslversion
if fslversion is None:
fslversion = 'latest'
if fslversion not in self.manifest['versions']:
raise UnknownVersion(
......@@ -432,8 +438,8 @@ 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='', **kwargs)
return input().strip()
printmsg(prompt, *msgtypes, end='', **kwargs)
return input(' ').strip()
class Progress(object):
......@@ -687,16 +693,23 @@ def download_file(url, destination, progress=None, blocksize=1048576):
progress(downloaded, total)
except urllib.error.HTTPError as e:
raise DownloadFailed(f'A network error has occurred while '
f'trying to download {destname}') from e
raise DownloadFailed('A network error has occurred while trying '
'to download {}'.format(destname))
class Process(object):
"""Container for a subprocess.Popen object, allowing non-blocking access
to its standard output and error streams via separate queues.
"""Container for a subprocess.Popen object, allowing non-blocking
access to its standard output and error streams via separate queues.
"""
def __init__(self, ctx, cmd, admin, **kwargs):
"""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
"""
self.ctx = ctx
self.cmd = cmd
......@@ -793,6 +806,9 @@ class Process(object):
proc = Process(ctx, cmd, **kwargs)
nlines = 0
prog.update(nlines, total)
while proc.popen.returncode is None:
try:
......@@ -804,12 +820,6 @@ class Process(object):
prog.update(nlines, total)
class UnsupportedPlatform(Exception):
"""Exception raised by the identify_platform function if FSL is not
available on this platform.
"""
def list_available_versions(ctx):
"""Lists available FSL versions. """
printmsg('Available FSL versions:', EMPHASIS)
......@@ -834,7 +844,6 @@ def install_miniconda(ctx):
"""
metadata = ctx.manifest['installer']['miniconda'][ctx.platform]
url = metadata['url']
checksum = metadata['sha256']
output = metadata.get('output', '').strip()
......@@ -844,12 +853,13 @@ def install_miniconda(ctx):
# Download
printmsg('Downloading miniconda from {}...'.format(url))
# with Progress('MB', transform=Progress.bytes_to_mb) as prog:
# download_file(url, 'miniforge.sh', prog.update)
sha256('miniforge.sh', checksum)
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)
# Install
printmsg('Installing miniconda to {}...'.format(ctx.destdir))
printmsg('Installing miniconda at {}...'.format(ctx.destdir))
cmd = 'sh miniforge.sh -b -p {}'.format(ctx.destdir)
Process.monitor_progress(ctx, cmd, output, admin=ctx.need_admin)
......@@ -887,40 +897,167 @@ def install_miniconda(ctx):
with open('.condarc', 'wt') as f:
f.write(condarc)
Process.run(ctx, 'mv .condarc {}'.format(ctx.destdir, admin=ctx.need_admin))
Process.run(
ctx, 'cp .condarc {}'.format(ctx.destdir, admin=ctx.need_admin))
def install_fsl(ctx):
"""Install FSL into ctx.destdir (which is assumed to be a miniforge
"""Install FSL into ctx.destdir (which is assumed to be a miniconda
installation.
This function assumes that it is run within a temporary/scratch directory.
"""
builds = ctx.manifest['versions'][ctx.args.fslversion][ctx.platform]
for build in builds:
if ctx.cuda == build.get('cuda', None):
break
else:
raise
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)
if cudaver is not None:
filename = 'fsl-{}-{}-cuda-{}.yml'.format(fslversion,
platform,
cudaver)
def post_install_cleanup(ctx):
"""Cleans up the FSL directory after installation. """
conda = op.join(ctx.destdir, 'bin', 'conda')
cmd = conda + ' clean -y --all'
Process.run(ctx, cmd, output, admin=ctx.need_admin)
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()]
else:
filename = 'fsl-{}-{}.yml'.format(fslversion, platform)
lines = []
download_file(base + filename, 'environment.yml')
# replace block
try:
idx = lines.index(searchline)
lines = lines[:idx] + content + lines[idx + numlines:]
conda = op.join(destdir, 'bin', 'conda')
# append to end
except ValueError:
lines = lines + [''] + content
run(ctx, conda + ' env update -n base -f environment.yml',
admin=ctx.need_admin)
with open(filename, 'wt') as f:
f.write('\n'.join(lines))
def configure_environment(ctx):
def configure_shell(ctx):
"""Configures the user's shell environment (e.g. ~/.bash_profile). """
# TODO
pass
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)
def self_update(ctx):
......@@ -973,7 +1110,7 @@ def self_update(ctx):
download_file(ctx.manifest['installer']['url'], tmpf)
if not ctx.args.disable_checksum:
if not ctx.args.no_checksum:
sha256(tmpf, ctx.manifest['installer']['sha256'])
cmd = [sys.executable, tmpf] + sys.argv[1:]
......@@ -982,87 +1119,131 @@ def self_update(ctx):
def overwrite_destdir(ctx):
"""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.
"""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.
"""
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)
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)
printmsg('Deleting directory {}'.format(ctx.destdir), IMPORTANT)
Process.run(ctx, 'rm -r {}'.format(ctx.destdir), admin=ctx.need_admin)
def parse_args(argv=None):
"""Parse command-line arguments, returns an argparse.Namespace object. """
helps = {
'dest' : 'Install FSL into this folder (default: '
'{})'.format(DEFAULT_INSTALLATION_DIRECTORY),
'version' : 'Print installer version number and exit',
'disable_self_update' : 'Do not automatically update the installer '
'script',
'listversions' : 'List available versions of FSL',
'fslversion' : 'Download this specific version of FSL',
'cuda' : 'Install FSL for this CUDA version (default: '
'automatically detected)',
'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,
# Path to local installer manifest file
'manifest' : argparse.SUPPRESS,
'manifest' : argparse.SUPPRESS,
# Print debugging messages
'debug' : argparse.SUPPRESS,
'debug' : argparse.SUPPRESS,
# Disable SHA256 checksum validation of downloaded files
'disable_checksum' : argparse.SUPPRESS,
'no_checksum' : argparse.SUPPRESS,
# Store temp files in this directory (must already
# exist) rather than in a temporary directory
'workdir' : argparse.SUPPRESS,
# 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,
}
parser = argparse.ArgumentParser()
# regular options
parser.add_argument('-v', '--version', action='version',
version=__version__, help=helps['version'])
parser.add_argument('-D', '--debug', action='store_true',
help=helps['debug'])
parser.add_argument('-m', '--manifest', default=FSL_INSTALLER_MANIFEST,
help=helps['manifest'])
parser.add_argument('-u', '--disable_self_update', action='store_true',
help=helps['disable_self_update'])
parser.add_argument('-d', '--dest', metavar='DESTDIR',
help=helps['dest'])
parser.add_argument('-s', '--disable_checksum', action='store_true',
help=helps['disable_checksum'])
parser.add_argument('-w', '--workdir', help=helps['workdir'])
parser.add_argument('-o', '--overwrite', action='store_true',
help=helps['overwrite'])
parser.add_argument('-l', '--listversions', action='store_true',
help=helps['listversions'])
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'])
parser.add_argument('-V', '--fslversion', default='latest',
help=helps['version'])
parser.add_argument('-c', '--cuda', help=helps['cuda'])
# 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'])
args = parser.parse_args(argv)
logging.basicConfig()
if args.debug: logging.getLogger().setLevel(logging.DEBUG)
else: logging.getLogger().setLevel(logging.WARNING)
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)
return args
def main(argv=None):
"""Installer entry point. Downloads and installs miniconda and FSL, and
configures the user's environment.
"""
args = parse_args(argv)
ctx = Context(args)
if not args.disable_self_update:
if not args.no_self_update:
self_update(ctx)
printmsg('FSL installer version:', EMPHASIS, UNDERLINE, end='')
......@@ -1074,14 +1255,24 @@ def main(argv=None):
ctx.finalise_settings()
if op.exists(ctx.destdir):
overwrite_destdir(ctx)
with tempdir(args.workdir):
printmsg('Installing FSL into {}\n'.format(ctx.destdir), EMPHASIS)
if op.exists(ctx.destdir):
overwrite_destdir(ctx)
printmsg('\nInstalling FSL into {}\n'.format(ctx.destdir), EMPHASIS)
with tempdir(args.workdir):
install_miniconda(ctx)
#install_fsl(ctx)
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)
if __name__ == '__main__':
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment