def show_comments(self):
# check for a good result, first
if len(self.comments) == 0:
print(UTIL.section_divider(' nothing to fix, yay! ', hchar='='))
print('')
return
print(UTIL.section_divider(' summary, please fix: ', hchar='='))
for cc in self.comments:
if len(cc) == 0: print('')
else:
if cc[0] == ' ': print(' %s' % cc)
else: print('* %s' % cc)
print('')
def show_python_lib_info(self, header=1):
# any extra libs to test beyone main ones
extralibs = ['matplotlib.pyplot']
verb = 3
if header: print(UTIL.section_divider('python libs', hchar='-'))
# itemize special libraries to test: PyQt4
self.test_python_lib_pyqt4(verb=verb)
print('')
# then go after any others
for plib in extralibs:
self.test_python_lib(plib, verb=verb)
print('')
for rootdir in ['/sw/bin', '/usr/local/bin']:
# hard to avoid related files, so search for expected names
pdirs = glob.glob('%s/python' % rootdir)
p1dirs = glob.glob('%s/python[0-9]' % rootdir)
p2dirs = glob.glob('%s/python[0-9].[0-9]' % rootdir)
pdirs.extend(p1dirs)
pdirs.extend(p2dirs)
if len(pdirs) > 0:
print('-- python binaries under %s:' % rootdir)
for pdir in pdirs:
if os.path.islink(pdir):
rstr = ' (sym link to %s)' % os.path.realpath(pdir)
else: rstr = ''
print(' %-20s%s' % (pdir, rstr))
print('')
def show_general_sys_info(self, header=1):
if header: print(UTIL.section_divider('general', hchar='-'))
print('architecture: %s' % tup_str(platform.architecture()))
print('system: %s' % platform.system())
print('release: %s' % platform.release())
print('version: %s' % platform.version())
# check distributions by type - now all over the place
self.os_dist = distribution_string() # save for later
print('distribution: %s' % self.os_dist)
print('number of CPUs: %s' % self.get_cpu_count())
# note shell, and if we are not in login shell
logshell = UTIL.get_login_shell()
curshell = UTIL.get_current_shell()
if logshell == curshell: note = ''
else: note = ' (current shell is %s)' % curshell
if logshell not in ['csh', 'tcsh']:
self.comments.append("login shell '%s', trusting user to translate" \
" code examples from 'tcsh'" % logshell)
print('apparent login shell: %s%s' % (logshell, note))
self.cur_shell = curshell
self.login_shell = logshell
self.set_shell_rc_file([logshell, curshell])
if self.home_file_exists(self.rc_file): fstr = 'exists'
else: fstr = 'does not exist'
print('shell RC file: %s (%s)' % (self.rc_file, fstr))
print('')
def show_function_help(flist):
from afnipy import afni_util as UTIL
for func in flist:
print(UTIL.section_divider('help for: %s' % func))
try:
fn = eval(func)
print(fn.__doc__)
except:
print("** not a valid function '%s'" % func)
def show_data_info(self, header=1):
"""checks that are specific to data
- class data existence and tree root
- assume $HOME if not found
- disk space under data root
- maybe check for mounted file system
- atlases (maybe just @Find TT_N27+tlrc?)
"""
if header: print(UTIL.section_divider('data checks', hchar='-'))
# locate various data trees, and possibly show recent history
rv = 0
rv += self.show_data_dir_info('AFNI_data6', 'history.txt')
rv += self.show_data_dir_info('AFNI_demos', 'history.txt')
rv += self.show_data_dir_info('suma_demo', 'README.archive_creation')
rv += self.show_data_dir_info('afni_handouts')
if rv: self.comments.append('insufficient data for AFNI bootcamp')
evar = 'AFNI_ATLAS_DIR'
tryenv = 0 # might suggest setting evar
haveenv = evar in os.environ
if haveenv: edir = os.environ[evar]
else: edir = ''
# look for atlases in multiple directories
atlas = 'TT_N27+tlrc'
if os.path.isfile('%s/%s.HEAD'%(edir,atlas)): glist = [edir]
else: glist = []
cmd = '@FindAfniDsetPath %s' % atlas
s, so, se = UTIL.limited_shell_exec(cmd, nlines=1)
if s: tryenv = 1 # failed
elif len(so) > 0: glist.append(so[0])
for ddir in ['/usr/share/afni/atlases', '/usr/local/afni/atlases']:
if os.path.isfile('%s/%s.HEAD'%(ddir,atlas)):
glist.append(ddir)
if tryenv:
self.comments.append('consider setting %s to %s' % (evar,ddir))
# fix to work with found after the fact
glist = UTIL.get_unique_sublist(glist)
if len(glist) == 0:
print('atlas : did not find %s' % atlas)
self.comments.append('possibly missing atlases')
else:
for ddir in glist:
print('atlas : found %-12s under %s' % (atlas, ddir))
if haveenv: print("\natlas var: %s = %s" % (evar, edir))
print('')
def show_os_specific(self, header=1):
"""checks that are specific to one OS or another"""
if self.system not in ['Linux', 'Darwin']: return
if header: print(UTIL.section_divider('OS specific', hchar='-'))
if self.system == 'Linux': self.show_spec_linux()
elif self.system == 'Darwin': self.show_spec_osx()
print('')
def show_path_vars(self, header=1):
print(UTIL.section_divider('env vars', hchar='-'))
for evar in ['PATH', 'PYTHONPATH', 'R_LIBS',
'LD_LIBRARY_PATH',
'DYLD_LIBRARY_PATH', 'DYLD_FALLBACK_LIBRARY_PATH']:
if evar in os.environ:
print("%s = %s\n" % (evar, os.environ[evar]))
elif evar.startswith('DY') and self.get_osx_ver() >= 11:
s, so = self.get_shell_value(self.cur_shell, evar)
print("%s (sub-shell) = %s" % (evar, so))
else:
print("%s = " % evar)
print('')
def check_dotfiles(self, show=0, pack=0):
global g_dotfiles
home = os.environ['HOME']
# get list of existing files
dfound = []
for dfile in g_dotfiles:
if os.path.isfile('%s/%s' % (home, dfile)):
dfound.append(dfile)
print('found under $HOME : %s' % dfile)
if show:
for dfile in dfound:
print(UTIL.section_divider(dfile, hchar='='))
print('%s\n' %
UTIL.read_text_file('%s/%s' % (home, dfile), lines=0))
if pack:
import shutil
package = self.dot_file_pack
pgz = '%s.tgz' % package
# maybe user included the extension
ext = package.find('.tgz')
if ext >= 0:
pgz = package
package = package[0:ext]
if os.path.exists(package) or os.path.exists('%s.tgz' % package):
print("** error: package dir '%s' or file '%s' already exists"\
% (package, pgz))
return 1
try:
os.mkdir(package)
except:
print("** failed to make dot file package dir '%s'" % package)
return 1
for dfile in dfound:
shutil.copy2('%s/%s' % (home, dfile), package)
os.system("tar cfz %s %s" % (pgz, package))
shutil.rmtree(package)
if os.path.exists(pgz): print('++ dot file package is in %s' % pgz)
else: print('** failed to make dot file packge %s' % pgz)
return 0
def show_env_vars(self, header=1):
print(UTIL.section_divider('env vars', hchar='-'))
for evar in ['PATH', 'PYTHONPATH', 'R_LIBS',
'LD_LIBRARY_PATH',
'DYLD_LIBRARY_PATH', 'DYLD_FALLBACK_LIBRARY_PATH']:
if evar in os.environ:
if self.verb > 2: print("-- SEV: getting var from current env ...")
print("%s = %s\n" % (evar, os.environ[evar]))
elif evar.startswith('DY') and self.get_osx_ver() >= 11:
if self.verb > 2:
print("-- SEV: get DY var from macos child env (cur shell)...")
s, so = self.get_shell_value(self.cur_shell, evar)
print("%s (sub-shell) = %s" % (evar, so))
else:
if self.verb > 2:
print("-- SEV: env var not set ...")
print("%s = " % evar)
print('')
self.check_for_bash_complete_under_zsh()
def process_args():
argv = sys.argv
if '-help' in argv or len(argv) < 2:
print(_g_main_help)
return 0
global argbase
# ------------------------------------------------------------
# main module has already been imported in global scope
# ------------------------------------------------------------
if argv[argbase] == '-eval':
eval(' '.join(argv[argbase+1:]))
return 0
elif argv[argbase] == '-exec':
exec(' '.join(argv[argbase+1:]))
return 0
elif argv[argbase] == '-funchelp':
from afnipy import afni_util as UTIL
for func in argv[argbase+1:]:
print(UTIL.section_divider('help for: %s' % func))
try:
fn = eval(func)
print(fn.__doc__)
except:
print("** not a valid function '%s'" % func)
# show_function_help(argv[argbase+1:])
return 0
elif argv[argbase] == '-lprint':
ret = eval(' '.join(argv[argbase+1:]))
print('\n'.join(['%s'%rent for rent in ret]))
return 0
elif argv[argbase] == '-print':
print(eval(' '.join(argv[argbase+1:])))
return 0
elif argv[argbase] == '-listfunc':
return process_listfunc(argv, argbase)
else:
print('** please see "afni_python_wrapper.py -help" for usage')
return 1
def show_general_afni_info(self, header=1):
print(UTIL.section_divider('AFNI and related program tests', hchar='-'))
self.afni_dir = self.get_afni_dir()
check_list = ['afni', 'afni label', 'AFNI_version.txt',
'python', 'R', 'tcsh']
nfound = self.check_for_progs(check_list, show_missing=1)
if nfound < len(check_list):
self.comments.append('failure under initial ' \
'"AFNI and related program tests"')
# make generic but pretty
print("instances of various programs found in PATH:")
proglist = ['afni', 'R', 'python', 'python2', 'python3']
ml = UTIL.max_len_in_list(proglist)
for prog in proglist:
rv, files = UTIL.search_path_dirs(prog, mtype=1)
if not rv:
if len(files) > 1: fstr = '\n '+'\n '.join(files)
elif len(files) > 0: fstr = ' (%s)' % files[0]
else: fstr = ''
print(' %-*s : %d %s' % (ml, prog, len(files), fstr))
if prog == 'afni':
if len(files) > 1:
self.comments.append("have multiple versions of AFNI in PATH")
if len(files) > 0:
if os.stat(files[0]).st_uid == 0:
self.comments.append("'afni' executable is owned by root")
print('')
# explicit python2 vs python3 check 7 Dec 2016
n2 = UTIL.num_found_in_path('python2', mtype=1)
n3 = UTIL.num_found_in_path('python3', mtype=1)
if n3 > 0 and n2 <= 0:
print("** have python3 but not python2")
print('')
# try select AFNI programs
print('testing ability to start various programs...')
ind = '%8s' % ' '
indn = '\n%8s' % ' '
proglist = ['afni', 'suma', '3dSkullStrip', 'uber_subject.py',
'3dAllineate', '3dRSFC', 'SurfMesh', '3dClustSim', '3dMVM']
fcount = 0
for prog in proglist:
st, so, se = BASE.shell_exec2('%s -help'%prog, capture=1)
# if 3dMVM, status will be 0 on failed library load (fix that, too)
if prog == '3dMVM' and not st:
mesg = ''.join(se)
if mesg.find('Error in dyn.load') >= 0:
st = 1
if st:
print(' %-20s : FAILURE' % prog)
print(ind + indn.join(se))
fcount += 1
else:
print(' %-20s : success' % prog)
# no OpenMP problem
if prog == '3dAllineate': self.ok_openmp = 1
print('')
pfailure = fcount == len(proglist)
if fcount > 0:
self.afni_fails = fcount
self.comments.append('AFNI programs show FAILURE')
# if complete failure, retry from exec dir
ascdir = UTIL.executable_dir()
if pfailure and self.afni_dir != ascdir:
fcount = 0
print('none working, testing programs under implied %s...' % ascdir)
for prog in proglist:
st, so, se = BASE.shell_exec2('%s/%s -help'%(ascdir,prog),capture=1)
if st:
print(' %-20s : FAILURE' % prog)
print(ind + indn.join(se))
fcount += 1
else: print(' %-20s : success' % prog)
print('')
if fcount < len(proglist):
self.comments.append('consider adding %s to your PATH' % ascdir)
# if afni_dir is not set, use ascdir
if self.afni_dir == '': self.afni_dir = ascdir
print('checking for R packages...')
cmd = 'rPkgsInstall -pkgs ALL -check'
st, so, se = BASE.shell_exec2(cmd, capture=1)
if st or len(se) < 2: okay = 0
else:
if se[1].startswith('++ Note:'): se = se[2:]
okay = 1
# do not require "verified", but fail on "not installed"
# (to avoid failing on 'unknown timezone' warnings)
for estr in se:
if estr != '' and estr.find('not installed') >= 0:
okay = 0 # any failure is terminal
break
if okay:
print(' %-20s : success' % cmd)
else:
print(' %-20s : FAILURE' % cmd)
print(ind + indn.join(se))
self.comments.append('missing R packages (see rPkgsInstall)')
print('')
status, cout = UTIL.exec_tcsh_command("R RHOME")
print('R RHOME : %s' % cout.strip())
print('')
print('checking for $HOME files...')
flist = ['.afnirc', '.sumarc', '.afni/help/all_progs.COMP']
for ff in flist:
if os.path.isfile('%s/%s'%(self.home_dir, ff)): fstr = 'found'
else: fstr = 'missing'
print(' %-25s : %s' % (ff, fstr))
# add to comments
if self.afni_dir:
ccc = 'run: cp %s/AFNI.afnirc ~/.afnirc' % self.afni_dir
else:
ccc = 'copy AFNI.afnirc to ~/.afnirc'
self.add_file_comment(None, '.afnirc', 'please %s' % ccc)
self.add_file_comment(None, '.sumarc',
'please run: "suma -update_env" for .sumarc')
self.add_file_comment(None, '.afni/help/all_progs.COMP',
'please run: apsearch -update_all_afni_help')
print('')
