def _generate_index(source, logger):
# Take contents of source, look for lists of tools and commands,
# and insert tools and commands from bundles that come with
# documentation
from chimerax import app_dirs
user_dir = os.path.join(app_dirs.user_cache_dir, 'docs', 'user')
path = os.path.join(user_dir, 'index.html')
if os.path.exists(path):
return path
os.makedirs(user_dir, exist_ok=True)
from chimerax.core import toolshed
ts = toolshed.get_toolshed()
if ts is None:
return None
# Look for <div id="foobar">
import lxml.html
html = lxml.html.parse(source)
for node in html.iterfind(".//div[@id]"):
ident = node.attrib["id"]
if ident == "clist":
_update_list(ts, node, 'commands', _update_commands, logger)
elif ident == "tlist":
_update_list(ts, node, 'tools', _update_tools, logger)
data = lxml.html.tostring(html)
os.makedirs(user_dir, exist_ok=True)
with open(path, 'wb') as f:
f.write(data)
return path
def take_snapshot(self, session, flags):
"""For session saving"""
from chimerax.core.toolshed import get_toolshed
ts = get_toolshed()
return {
'version':
2,
'seqs':
self._seqs,
'ident':
self.ident,
'file attrs':
self.file_attrs,
'file markups':
self.file_markups,
'associations':
self.associations,
'match maps': [s.match_maps for s in self._seqs],
'auto_destroy':
self.auto_destroy,
'auto_associate':
self.auto_associate,
'description':
self.description,
'intrinsic':
self.intrinsic,
'sseq to chain':
self._sseq_to_chain,
'headers': [(ts.find_bundle_for_class(hdr.__class__).name,
hdr.__class__.__name__, hdr.get_state())
for hdr in self.headers]
}
def initialize(session, bundle_info):
global _new_bundle_handler
ts = toolshed.get_toolshed()
_new_bundle_handler = ts.triggers.add_handler(
toolshed.TOOLSHED_BUNDLE_INSTALLED, _update_cache)
# ? = ts.triggers.add_handler(
# toolshed.TOOLSHED_BUNDLE_UNINSTALLED, _update_cache)
_update_cache()
def delete(self):
if self._handlers:
from chimerax.core.toolshed import get_toolshed
ts = get_toolshed()
if ts:
for h in self._handlers:
ts.triggers.remove_handler(h)
self._handlers = None
super().delete()
def restore_snapshot(session, data):
"""For restoring scenes/sessions"""
ident = data['ident'] if 'ident' in data else data['name']
create_headers = data['version'] < 2
aln = Alignment(session,
data['seqs'],
ident,
data['file attrs'],
data['file markups'],
data['auto_destroy'],
"session" if data['auto_associate'] else False,
data.get('description', ident),
data.get('intrinsic', False),
create_headers=create_headers,
session_restore=True)
aln.associations = data['associations']
for s, mm in zip(aln.seqs, data['match maps']):
s.match_maps = mm
for chain, match_map in mm.items():
match_map.mod_handler = match_map.triggers.add_handler(
'modified', aln._mmap_mod_cb)
if 'sseq to chain' in data:
aln._sseq_to_chain = data['sseq to chain']
from chimerax.core.toolshed import get_toolshed
ts = get_toolshed()
if not create_headers:
for bundle_name, class_name, header_state in data['headers']:
bundle = ts.find_bundle(bundle_name,
session.logger,
installed=True)
if not bundle:
bundle = ts.find_bundle(bundle_name,
session.logger,
installed=False)
if bundle:
session.logger.error(
"You need to install bundle %s in order to restore"
" alignment header of type %s" %
(bundle_name, class_name))
else:
session.logger.error(
"Cannot restore alignment header of type %s due to"
" being unable to find any bundle named %s" %
(class_name, bundle_name))
continue
header_class = bundle.get_class(class_name, session.logger)
if header_class:
aln._headers.append(
header_class.session_restore(session, aln,
header_state))
else:
session.logger.warning(
"Could not find alignment header class %s" %
class_name)
aln._session_restore = False
return aln
def _setup(self):
#
# Register for updates of name register/deregister events
#
session = self.session
from chimerax.core.toolshed import get_toolshed
ts = get_toolshed()
t1 = ts.triggers.add_handler("selector registered", self.update_names)
t2 = ts.triggers.add_handler("selector deregistered",
self.update_names)
self._handlers = (t1, t2)
def _get_bundle_dirs(self, logger, dep):
from chimerax.core import toolshed
from pkg_resources import Requirement, get_distribution
req = Requirement.parse(dep)
if not get_distribution(req):
raise RuntimeError("unsatisfied dependency: %s" % dep)
ts = toolshed.get_toolshed()
bundle = ts.find_bundle(req.project_name, logger)
if not bundle:
# The requirement is satisfied but is not recognized
# as a bundle. Probably just a regular Python package.
return None, None
inc = bundle.include_dir()
lib = bundle.library_dir()
return inc, lib
def make_install(self, session, debug=False, user=None, no_deps=None):
self.make_wheel(debug=debug)
from chimerax.core.commands import run, FileNameArg
cmd = "toolshed install %s" % FileNameArg.unparse(self.wheel_path)
if user is not None:
if user:
cmd += " user true"
else:
cmd += " user false"
if no_deps is not None:
if no_deps:
cmd += " noDeps true"
else:
cmd += " noDeps false"
from chimerax.core import toolshed
ts = toolshed.get_toolshed()
bundle = ts.find_bundle(self.name, session.logger)
if bundle is not None:
cmd += " reinstall true"
run(session, cmd)
def finish(session, bundle_info):
global _new_bundle_handler
ts = toolshed.get_toolshed()
if _new_bundle_handler is not None:
ts.triggers.remove_handler(_new_bundle_handler)
_new_bundle_handler = None
def init(argv, event_loop=True):
import sys
if sys.platform.startswith('darwin'):
paths = os.environ['PATH'].split(':')
if '/usr/sbin' not in paths:
# numpy, numexpr, and pytables need sysctl in path
paths.append('/usr/sbin')
os.environ['PATH'] = ':'.join(paths)
del paths
if sys.platform.startswith('linux'):
# Workaround for #638:
# "any number of threads more than one leads to 200% CPU usage"
os.environ["OPENBLAS_NUM_THREADS"] = "1"
# Setup SSL CA certificates file
# This used to be only necessary for darwin, but Windows
# appears to need it as well. So use it for all platforms.
import certifi
os.environ["SSL_CERT_FILE"] = certifi.where()
# distlib, since 0.2.8, does not recognize "Obsoletes" as a legal
# metadata classifier, but jurko 0.6 (SOAP package) claims to be
# Metadata-Version 2.1 but specifies Obsolete. Hack below makes
# Obsolete not cause a traceback.
from distlib import metadata
try:
if "Obsoletes" not in metadata._566_FIELDS:
metadata._566_FIELDS = metadata._566_FIELDS + ("Obsoletes", )
except AttributeError:
pass
opts, args = parse_arguments(argv)
# install line_profile decorator, and install it before
# initialize_ssl_cert_dir() in case the line profiling is in the
# core (which would cause initialize_ssl_cert_dir() to fail)
import builtins
if not opts.line_profile:
builtins.__dict__['line_profile'] = lambda x: x
else:
# write profile results on exit
import atexit
import line_profiler
prof = line_profiler.LineProfiler()
builtins.__dict__['line_profile'] = prof
atexit.register(prof.dump_stats, "%s.lprof" % app_name)
from chimerax.core.utils import initialize_ssl_cert_dir
initialize_ssl_cert_dir()
# find chimerax.core's version
# we cannot use pip for this because we want to update
# site.USER_SITE before importing pip, and site.USER_SITE
# depends on the version
try:
from chimerax.core import version
except ImportError:
print("error: unable to figure out %s's version" % app_name)
return os.EX_SOFTWARE
if opts.use_defaults:
from chimerax.core import configinfo
configinfo.only_use_defaults = True
from chimerax import core
if opts.offscreen:
# Flag to configure off-screen rendering before PyOpenGL imported
core.offscreen_rendering = True
opts.gui = False
if not opts.gui and opts.load_tools:
# only load tools if we have a GUI
opts.load_tools = False
is_root = False # On Linux, don't create user directories if root (the installer uid)
# figure out the user/system directories for application
# invoked with -m ChimeraX_main, so argv[0] is full path to ChimeraX_main
# Windows:
# 'C:\\...\\ChimeraX.app\\bin\\lib\\site-packages\\ChimeraX_main.py'
# Linux:
# '/.../ChimeraX.app/lib/python3.5/site-packages/ChimeraX_main.py'
# Mac OS X:
# '/.../ChimeraX.app/Contents/lib/python3.5/site-packages/ChimeraX_main.py'
# '/.../ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/ChimeraX_main.py'
# TODO: more robust way
dn = os.path.dirname
rootdir = dn(dn(dn(dn(sys.argv[0]))))
if sys.platform.startswith('darwin'):
rootdir = dn(dn(dn(dn(dn(rootdir)))))
if sys.platform.startswith('linux'):
os.environ['XDG_CONFIG_DIRS'] = rootdir
is_root = os.getuid() == 0
if is_root:
# ensure toolshed cache is not written
os.environ['HOME'] = "/non/existent/directory"
if sys.platform.startswith('win'):
if 'HOME' in os.environ:
# Windows uses HOMEPATH and HOMEDRIVE, so HOME's presence indicates
# a non-standard startup environment. So remove HOME to make
# sure the the correct application paths are figured out.
del os.environ['HOME']
import ctypes
# getpn = ctypes.pythonapi.Py_GetProgramName
# getpn.restype = ctypes.c_wchar_p
# pn = getpn()
# assert(os.path.dirname(pn) == rootdir)
# Python uses LoadLibraryEx with LOAD_WITH_ALTERED_SEARCH_PATH to
# search in directory of library first instead of the directory of
# application binary. So add back the "bin" directory, which is
# the Windows equivalent of the Linux/Mac OS X rpath directory.
setdlldir = ctypes.windll.kernel32.SetDllDirectoryW
setdlldir.argtypes = [ctypes.c_wchar_p]
setdlldir.restype = ctypes.c_bool
setdlldir(os.path.join(rootdir, 'bin'))
from distlib.version import NormalizedVersion as Version
epoch, ver, *_ = Version(version).parse(version)
if len(ver) == 1:
ver += (0, )
partial_version = '%s.%s' % (ver[0], ver[1])
import chimerax
import appdirs
chimerax.app_dirs = ad = appdirs.AppDirs(app_name,
appauthor=app_author,
version=partial_version)
if not is_root:
# make sure app_dirs.user_* directories exist
for var, name in (('user_data_dir', "user's data"),
('user_config_dir', "user's configuration"),
('user_cache_dir', "user's cache")):
directory = getattr(ad, var)
try:
os.makedirs(directory, exist_ok=True)
except OSError as e:
print("Unable to make %s directory: %s: %s" %
(name, e.strerror, e.filename),
file=sys.stderr)
return os.EX_CANTCREAT
# app_dirs_unversioned is primarily for caching data files that will
# open in any version
# app_dirs_unversioned.user_* directories are parents of those in app_dirs
chimerax.app_dirs_unversioned = adu = appdirs.AppDirs(app_name,
appauthor=app_author)
# update "site" user variables to use ChimeraX instead of Python paths
# NB: USER_SITE is used by both pip and the toolshed, so
# this must happen before pip is imported so that "--user" installs
# will go in the right place.
import site
if not is_root:
site.USER_BASE = adu.user_data_dir
site.USER_SITE = os.path.join(ad.user_data_dir, "site-packages")
else:
from distutils import sysconfig
site.USER_SITE = sysconfig.get_python_lib()
# Find the location of "share" directory so that we can inform
# the C++ layer. Assume it's a sibling of the directory that
# the executable is in.
chimerax.app_bin_dir = os.path.join(rootdir, "bin")
if sys.platform.startswith('win'):
chimerax.app_data_dir = os.path.join(chimerax.app_bin_dir, "share")
else:
chimerax.app_data_dir = os.path.join(rootdir, "share")
chimerax.app_lib_dir = os.path.join(rootdir, "lib")
# inform the C++ layer of the appdirs paths
from chimerax.core import _appdirs
_appdirs.init_paths(os.sep, ad.user_data_dir, ad.user_config_dir,
ad.user_cache_dir, ad.site_data_dir,
ad.site_config_dir, ad.user_log_dir,
chimerax.app_data_dir, adu.user_cache_dir)
from chimerax.core import session
try:
sess = session.Session(app_name,
debug=opts.debug,
silent=opts.silent,
minimal=opts.safe_mode)
except ImportError as err:
if opts.offscreen and 'OpenGL' in err.args[0]:
if sys.platform.startswith("linux"):
why = "failed"
else:
why = "not supported on this platform"
print("Offscreen rendering is", why, file=sys.stderr)
return os.EX_UNAVAILABLE
raise
from chimerax.core import core_settings
core_settings.init(sess)
session.common_startup(sess)
if opts.uninstall:
return uninstall(sess)
# initialize qt
if opts.gui:
from chimerax.ui import initialize_qt
initialize_qt()
# initialize the user interface
if opts.gui:
from chimerax.ui import gui
ui_class = gui.UI
else:
from chimerax.core import nogui
ui_class = nogui.UI
if opts.color is not None:
nogui._color_output = opts.color
if opts.color:
def t():
return True
sys.stdout.isatty = t
sys.stderr.isatty = t
# sets up logging, splash screen if gui
# calls "sess.save_in_session(self)"
sess.ui = ui_class(sess)
sess.ui.stereo = opts.stereo
sess.ui.autostart_tools = opts.load_tools
# Set current working directory to Desktop when launched from icon.
if ((sys.platform.startswith('darwin') and os.getcwd() == '/')
or (sys.platform.startswith('win')
and os.getcwd().endswith('\\Users\\Public\\Desktop'))):
try:
os.chdir(os.path.expanduser('~/Desktop'))
except Exception:
pass
# splash screen
if opts.gui:
sess.ui.show_splash()
num_splash_steps = 2
if opts.gui:
num_splash_steps += 1
if not opts.gui and opts.load_tools:
num_splash_steps += 1
import itertools
splash_step = itertools.count()
# common core initialization
if not opts.silent:
sess.ui.splash_info("Initializing core", next(splash_step),
num_splash_steps)
if sess.ui.is_gui and opts.debug:
print("Initializing core", flush=True)
# Install any bundles before toolshed is initialized so
# the new ones get picked up in this session
rebuild_cache = False
from chimerax.core import toolshed
inst_dir, restart_file = toolshed.restart_action_info()
restart_action_msgs = []
if os.path.exists(restart_file):
# Move file out of the way so next restart of ChimeraX
# (when we try to install the bundle) will not go into
# an infinite loop reopening the restart file
tmp_file = restart_file + ".tmp"
try:
# Remove in case old file lying around.
# Windows does not allow renaming to an existing file.
os.remove(tmp_file)
except Exception:
pass
os.rename(restart_file, tmp_file)
with open(tmp_file) as f:
for line in f:
sess.ui.splash_info("Restart action:\n%s" % line)
restart_action(line, inst_dir, restart_action_msgs)
os.remove(tmp_file)
rebuild_cache = True
if opts.toolshed is None:
# Default to whatever the restart actions needed
toolshed_url = _restart_toolshed_url
elif opts.toolshed == "preview":
toolshed_url = toolshed.preview_toolshed_url()
else:
toolshed_url = opts.toolshed
toolshed.init(sess.logger,
debug=sess.debug,
rebuild_cache=rebuild_cache,
check_available=opts.get_available_bundles,
remote_url=toolshed_url,
ui=sess.ui)
sess.toolshed = toolshed.get_toolshed()
if opts.module != 'pip':
# keep bugs in ChimeraX from preventing pip from working
if not opts.silent:
sess.ui.splash_info("Initializing bundles", next(splash_step),
num_splash_steps)
if sess.ui.is_gui and opts.debug:
print("Initializing bundles", flush=True)
sess.toolshed.bootstrap_bundles(sess, opts.safe_mode)
from chimerax.core import tools
sess.tools = tools.Tools(sess, first=True)
from chimerax.core import tasks
sess.tasks = tasks.Tasks(sess, first=True)
from chimerax.core import undo
sess.undo = undo.Undo(sess, first=True)
if opts.version >= 0:
sess.silent = False
if opts.version > 3:
opts.version = 3
format = [None, 'verbose', 'bundles', 'packages'][opts.version]
from chimerax.core.commands import command_function
version_cmd = command_function("version")
version_cmd(sess, format)
return os.EX_OK
if opts.list_io_formats:
sess.silent = False
collate = {}
for fmt in sess.data_formats.formats:
collate.setdefault(fmt.category, []).append(fmt)
categories = list(collate.keys())
categories.sort(key=str.casefold)
print("Supported file suffixes:")
print(" o = open, s = save")
openers = set(sess.open_command.open_data_formats)
savers = set(sess.save_command.save_data_formats)
for cat in categories:
print("\n%s:" % cat)
fmts = collate[cat]
fmts.sort(key=lambda fmt: fmt.name.casefold())
for fmt in fmts:
o = 'o' if fmt in openers else ' '
s = 's' if fmt in savers else ' '
if fmt.suffixes:
exts = ': ' + ', '.join(fmt.suffixes)
else:
exts = ''
print("%c%c %s%s" % (o, s, fmt.name, exts))
# TODO: show database formats
# TODO: show mime types?
# TODO: show compression suffixes?
return os.EX_OK
if opts.gui:
# build out the UI, populate menus, create graphics, etc.
if not opts.silent:
sess.ui.splash_info("Starting main interface", next(splash_step),
num_splash_steps)
if sess.ui.is_gui and opts.debug:
print("Starting main interface", flush=True)
sess.ui.build()
if opts.start_tools:
if not opts.silent:
msg = 'Starting tools %s' % ', '.join(opts.start_tools)
sess.ui.splash_info(msg, next(splash_step), num_splash_steps)
if sess.ui.is_gui and opts.debug:
print(msg, flush=True)
# canonicalize tool names
start_tools = []
for t in opts.start_tools:
tools = sess.toolshed.find_bundle_for_tool(t)
if not tools:
sess.logger.warning("Unable to find tool %s" % repr(t))
continue
start_tools.append(tools[0][1])
sess.tools.start_tools(start_tools)
if opts.commands:
if not opts.silent:
msg = 'Running startup commands'
# sess.ui.splash_info(msg, next(splash_step), num_splash_steps)
if sess.ui.is_gui and opts.debug:
print(msg, flush=True)
from chimerax.core.commands import run
for cmd in opts.commands:
run(sess, cmd)
if opts.scripts:
if not opts.silent:
msg = 'Running startup scripts'
# sess.ui.splash_info(msg, next(splash_step), num_splash_steps)
if sess.ui.is_gui and opts.debug:
print(msg, flush=True)
from chimerax.core.commands import run
for script in opts.scripts:
run(sess, 'runscript %s' % script)
if not opts.silent:
sess.ui.splash_info("Finished initialization", next(splash_step),
num_splash_steps)
if sess.ui.is_gui and opts.debug:
print("Finished initialization", flush=True)
if opts.gui:
sess.ui.close_splash()
if not opts.silent:
from chimerax.core.logger import log_version
log_version(sess.logger) # report version in log
if opts.gui or hasattr(core, 'offscreen_rendering'):
sess.update_loop.start_redraw_timer()
sess.logger.info(
'<a href="cxcmd:help help:credits.html">How to cite UCSF ChimeraX</a>',
is_html=True)
# Show any messages from installing bundles on restart
if restart_action_msgs:
for where, msg in restart_action_msgs:
if where == "stdout":
sess.logger.info(msg)
else:
sess.logger.warning(msg)
if opts.module:
import runpy
import warnings
sys.argv[:] = args # runpy will insert appropriate argv[0]
exit = SystemExit(os.EX_OK)
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=BytesWarning)
global_dict = {'session': sess}
try:
runpy.run_module(opts.module,
init_globals=global_dict,
run_name='__main__',
alter_sys=True)
except SystemExit as e:
exit = e
if opts.module == 'pip' and exit.code == os.EX_OK:
has_install = 'install' in sys.argv
has_uninstall = 'uninstall' in sys.argv
if has_install or has_uninstall:
per_user = '******' in sys.argv
sess.toolshed.reload(sess.logger, rebuild_cache=True)
sess.toolshed.set_install_timestamp(per_user)
# Do not remove scripts anymore since we may be installing
# using ChimeraX which would put the right paths in
# generated files.
# if has_install:
# remove_python_scripts(chimerax.app_bin_dir)
return exit.code
from chimerax.core import startup
startup.run_user_startup_scripts(sess)
if opts.cmd:
# Emulated Python's -c option.
# This is needed for -m pip to work in some cases.
sys.argv = args
sys.argv[0] = '-c'
global_dict = {
'session': sess,
'__name__': '__main__',
}
exec(opts.cmd, global_dict)
return os.EX_OK
# the rest of the arguments are data files
from chimerax.core import errors, commands
for arg in args:
if opts.safe_mode:
# 'open' command unavailable; only open Python files
if not arg.endswith('.py'):
sess.logger.error(
"Can only open Python scripts in safe mode, not '%s'" %
arg)
return os.EX_SOFTWARE
from chimerax.core.scripting import open_python_script
try:
open_python_script(sess, open(arg, 'rb'), arg)
except (IOError, errors.NotABug) as e:
sess.logger.error(str(e))
return os.EX_SOFTWARE
except Exception:
import traceback
traceback.print_exc()
return os.EX_SOFTWARE
else:
from chimerax.core.commands import StringArg
try:
commands.run(sess, 'open %s' % StringArg.unparse(arg))
except (IOError, errors.NotABug) as e:
sess.logger.error(str(e))
return os.EX_SOFTWARE
except Exception:
import traceback
traceback.print_exc()
return os.EX_SOFTWARE
# Open files dropped on application
if opts.gui:
sess.ui.open_pending_files(ignore_files=args)
# Allow the event_loop to be disabled, so we can be embedded in
# another application
if event_loop and opts.event_loop:
try:
sess.ui.event_loop()
except SystemExit as e:
return e.code
except Exception:
import traceback
traceback.print_exc()
return os.EX_SOFTWARE
return os.EX_OK
