Closed yunhuige closed 4 years ago
https://docs.python.org/2/library/2to3.html
Its a simple command e.g.,
--> 2to3 -v --add-suffix=3 --output-dir=~/ -n -w PosteriorSampler.py
lib2to3.main: Output in '~/' will mirror the input directory '' layout. RefactoringTool: Adding transformation: apply RefactoringTool: Adding transformation: asserts RefactoringTool: Adding transformation: basestring RefactoringTool: Skipping optional fixer: buffer RefactoringTool: Adding transformation: dict RefactoringTool: Adding transformation: except RefactoringTool: Adding transformation: exec RefactoringTool: Adding transformation: execfile RefactoringTool: Adding transformation: exitfunc RefactoringTool: Adding transformation: filter RefactoringTool: Adding transformation: funcattrs RefactoringTool: Adding transformation: future RefactoringTool: Adding transformation: getcwdu RefactoringTool: Adding transformation: has_key RefactoringTool: Skipping optional fixer: idioms RefactoringTool: Adding transformation: import RefactoringTool: Adding transformation: imports RefactoringTool: Adding transformation: imports2 RefactoringTool: Adding transformation: input RefactoringTool: Adding transformation: intern RefactoringTool: Adding transformation: isinstance RefactoringTool: Adding transformation: itertools RefactoringTool: Adding transformation: itertools_imports RefactoringTool: Adding transformation: long RefactoringTool: Adding transformation: map RefactoringTool: Adding transformation: metaclass RefactoringTool: Adding transformation: methodattrs RefactoringTool: Adding transformation: ne RefactoringTool: Adding transformation: next RefactoringTool: Adding transformation: nonzero RefactoringTool: Adding transformation: numliterals RefactoringTool: Adding transformation: operator RefactoringTool: Adding transformation: paren RefactoringTool: Adding transformation: print RefactoringTool: Adding transformation: raise RefactoringTool: Adding transformation: raw_input RefactoringTool: Adding transformation: reduce RefactoringTool: Adding transformation: renames RefactoringTool: Adding transformation: repr RefactoringTool: Skipping optional fixer: set_literal RefactoringTool: Adding transformation: standarderror RefactoringTool: Adding transformation: sys_exc RefactoringTool: Adding transformation: throw RefactoringTool: Adding transformation: tuple_params RefactoringTool: Adding transformation: types RefactoringTool: Adding transformation: unicode RefactoringTool: Adding transformation: urllib RefactoringTool: Skipping optional fixer: ws_comma RefactoringTool: Adding transformation: xrange RefactoringTool: Adding transformation: xreadlines RefactoringTool: Adding transformation: zip RefactoringTool: Refactoring PosteriorSampler.py RefactoringTool: Refactored PosteriorSampler.py --- PosteriorSampler.py (original) +++ PosteriorSampler.py (refactored) @@ -58,7 +58,7 @@
if not self.no_ref:
s = self.ensembles[0][0]
print '\n\n\n',s.sse,'\n\n\n'
print('\n\n\n',s.sse,'\n\n\n') if s.sse != 0: if self.use_exp_ref == True and self.use_gau_ref == True: self.build_gau_ref() @@ -84,18 +84,18 @@
for k in range(self.nensembles):
print 'Computing reference potentials for ensemble', k, 'of', self.nensembles, '...'
print('Computing reference potentials for ensemble', k, 'of', self.nensembles, '...') ensemble = self.ensembles[k]
# collect noe distributions across all structures
n = len(ensemble[0].restraints)
All = []
print 'n = ',n
print('n = ',n) distributions = [[] for j in range(n)] for s in ensemble: for j in range(len(s.restraints)):
print s.restraints[j].model
print(s.restraints[j].model) distributions[j].append( s.restraints[j].model ) All.append( s.restraints[j].model )
@@ -115,7 +115,7 @@
for k in range(self.nensembles):
print 'Computing Gaussian reference potentials for ensemble', k, 'of', self.nensembles, '...'
print('Computing Gaussian reference potentials for ensemble', k, 'of', self.nensembles, '...') ensemble = self.ensembles[k]
# collect noe distributions across All structures
@@ -154,10 +154,10 @@
s = self.ensembles[new_ensemble_index][new_state]
print 's = ',s
print('s = ',s)
result = s.free_energy + self.logZ
print 'Result =',result
print('Result =',result)
#result += (Nj+1.0)*np.log(self.sigma)
#if s.sse is not None: # trying to fix a future warning:"comparison to `None` will result in an elementwise object comparison in the future."
@@ -172,10 +172,10 @@
if verbose:
print 'state, f_sim', new_state, s.free_energy,
print 's.sse', s.sse, 's.Ndof', s.Ndof
print 's.sum_neglog_exp_ref', s.sum_neglog_exp_ref
print 's.sum_neglog_gau_ref', s.sum_neglog_gau_ref
print('state, f_sim', new_state, s.free_energy, end=' ')
print('s.sse', s.sse, 's.Ndof', s.Ndof)
print('s.sum_neglog_exp_ref', s.sum_neglog_exp_ref)
print('s.sum_neglog_gau_ref', s.sum_neglog_gau_ref) return result
@@ -282,7 +282,7 @@
self.n = len(ensemble[0].restraints)
print('self.ensemble[0] = ',self.ensemble[0]) self.restraints = len(self.ensemble[0].restraints)
self.allowed_sigma = allowed_sigma
@@ -517,11 +517,11 @@ """Reads a npz file"""
loaded = np.load(filename)
RefactoringTool: Writing converted PosteriorSampler.py to ~/PosteriorSampler.py3. RefactoringTool: Wrote changes to ~/PosteriorSampler.py3 RefactoringTool: Files that were modified: RefactoringTool: PosteriorSampler.py
FYI this is an old PosteriorSampler.py script.
2to3
branch):Script: https://github.com/vvoelz/biceps/blob/2to3/BICePs_2.0/2to3_conversion_test_02_09_2020/mp_lambdas.py
Log File of output: https://github.com/vvoelz/biceps/blob/2to3/BICePs_2.0/2to3_conversion_test_02_09_2020/mp_lambdas_02_09_2020.log
Note: not a end-to-end protocol for conversion —some minor alterations to depreciated modules etc.
2to3 -w -j 4 -n biceps -o ./biceps
reindent.py
(should be used after 2to3
)
#! /usr/bin/env python3
# Released to the public domain, by Tim Peters, 03 October 2000.
"""reindent [-d][-r][-v] [ path ... ]
-d (--dryrun) Dry run. Analyze, but don't make any changes to, files.
-r (--recurse) Recurse. Search for all .py files in subdirectories too.
-n (--nobackup) No backup. Does not make a ".bak" file before reindenting.
-v (--verbose) Verbose. Print informative msgs; else no output.
(--newline) Newline. Specify the newline character to use (CRLF, LF).
Default is the same as the original file.
-h (--help) Help. Print this usage information and exit.
Change Python (.py) files to use 4-space indents and no hard tab characters.
Also trim excess spaces and tabs from ends of lines, and remove empty lines
at the end of files. Also ensure the last line ends with a newline.
If no paths are given on the command line, reindent operates as a filter,
reading a single source file from standard input and writing the transformed
source to standard output. In this case, the -d, -r and -v flags are
ignored.
You can pass one or more file and/or directory paths. When a directory
path, all .py files within the directory will be examined, and, if the -r
option is given, likewise recursively for subdirectories.
If output is not to standard output, reindent overwrites files in place,
renaming the originals with a .bak extension. If it finds nothing to
change, the file is left alone. If reindent does change a file, the changed
file is a fixed-point for future runs (i.e., running reindent on the
resulting .py file won't change it again).
The hard part of reindenting is figuring out what to do with comment
lines. So long as the input files get a clean bill of health from
tabnanny.py, reindent should do a good job.
The backup file is a copy of the one that is being reindented. The ".bak"
file is generated with shutil.copy(), but some corner cases regarding
user/group and permissions could leave the backup file more readable than
you'd prefer. You can always use the --nobackup option to prevent this.
"""
__version__ = "1"
import tokenize
import os
import shutil
import sys
verbose = False
recurse = False
dryrun = False
makebackup = True
# A specified newline to be used in the output (set by --newline option)
spec_newline = None
def usage(msg=None):
if msg is None:
msg = __doc__
print(msg, file=sys.stderr)
def errprint(*args):
sys.stderr.write(" ".join(str(arg) for arg in args))
sys.stderr.write("\n")
def main():
import getopt
global verbose, recurse, dryrun, makebackup, spec_newline
try:
opts, args = getopt.getopt(sys.argv[1:], "drnvh",
["dryrun", "recurse", "nobackup", "verbose", "newline=", "help"])
except getopt.error as msg:
usage(msg)
return
for o, a in opts:
if o in ('-d', '--dryrun'):
dryrun = True
elif o in ('-r', '--recurse'):
recurse = True
elif o in ('-n', '--nobackup'):
makebackup = False
elif o in ('-v', '--verbose'):
verbose = True
elif o in ('--newline',):
if not a.upper() in ('CRLF', 'LF'):
usage()
return
spec_newline = dict(CRLF='\r\n', LF='\n')[a.upper()]
elif o in ('-h', '--help'):
usage()
return
if not args:
r = Reindenter(sys.stdin)
r.run()
r.write(sys.stdout)
return
for arg in args:
check(arg)
def check(file):
if os.path.isdir(file) and not os.path.islink(file):
if verbose:
print("listing directory", file)
names = os.listdir(file)
for name in names:
fullname = os.path.join(file, name)
if ((recurse and os.path.isdir(fullname) and
not os.path.islink(fullname) and
not os.path.split(fullname)[1].startswith("."))
or name.lower().endswith(".py")):
check(fullname)
return
if verbose:
print("checking", file, "...", end=' ')
with open(file, 'rb') as f:
try:
encoding, _ = tokenize.detect_encoding(f.readline)
except SyntaxError as se:
errprint("%s: SyntaxError: %s" % (file, str(se)))
return
try:
with open(file, encoding=encoding) as f:
r = Reindenter(f)
except IOError as msg:
errprint("%s: I/O Error: %s" % (file, str(msg)))
return
newline = spec_newline if spec_newline else r.newlines
if isinstance(newline, tuple):
errprint("%s: mixed newlines detected; cannot continue without --newline" % file)
return
if r.run():
if verbose:
print("changed.")
if dryrun:
print("But this is a dry run, so leaving it alone.")
if not dryrun:
bak = file + ".bak"
if makebackup:
shutil.copyfile(file, bak)
if verbose:
print("backed up", file, "to", bak)
with open(file, "w", encoding=encoding, newline=newline) as f:
r.write(f)
if verbose:
print("wrote new", file)
return True
else:
if verbose:
print("unchanged.")
return False
def _rstrip(line, JUNK='\n \t'):
"""Return line stripped of trailing spaces, tabs, newlines.
Note that line.rstrip() instead also strips sundry control characters,
but at least one known Emacs user expects to keep junk like that, not
mentioning Barry by name or anything <wink>.
"""
i = len(line)
while i > 0 and line[i - 1] in JUNK:
i -= 1
return line[:i]
class Reindenter:
def __init__(self, f):
self.find_stmt = 1 # next token begins a fresh stmt?
self.level = 0 # current indent level
# Raw file lines.
self.raw = f.readlines()
# File lines, rstripped & tab-expanded. Dummy at start is so
# that we can use tokenize's 1-based line numbering easily.
# Note that a line is all-blank iff it's "\n".
self.lines = [_rstrip(line).expandtabs() + "\n"
for line in self.raw]
self.lines.insert(0, None)
self.index = 1 # index into self.lines of next line
# List of (lineno, indentlevel) pairs, one for each stmt and
# comment line. indentlevel is -1 for comment lines, as a
# signal that tokenize doesn't know what to do about them;
# indeed, they're our headache!
self.stats = []
# Save the newlines found in the file so they can be used to
# create output without mutating the newlines.
self.newlines = f.newlines
def run(self):
tokens = tokenize.generate_tokens(self.getline)
for _token in tokens:
self.tokeneater(*_token)
# Remove trailing empty lines.
lines = self.lines
while lines and lines[-1] == "\n":
lines.pop()
# Sentinel.
stats = self.stats
stats.append((len(lines), 0))
# Map count of leading spaces to # we want.
have2want = {}
# Program after transformation.
after = self.after = []
# Copy over initial empty lines -- there's nothing to do until
# we see a line with *something* on it.
i = stats[0][0]
after.extend(lines[1:i])
for i in range(len(stats) - 1):
thisstmt, thislevel = stats[i]
nextstmt = stats[i + 1][0]
have = getlspace(lines[thisstmt])
want = thislevel * 4
if want < 0:
# A comment line.
if have:
# An indented comment line. If we saw the same
# indentation before, reuse what it most recently
# mapped to.
want = have2want.get(have, -1)
if want < 0:
# Then it probably belongs to the next real stmt.
for j in range(i + 1, len(stats) - 1):
jline, jlevel = stats[j]
if jlevel >= 0:
if have == getlspace(lines[jline]):
want = jlevel * 4
break
if want < 0: # Maybe it's a hanging
# comment like this one,
# in which case we should shift it like its base
# line got shifted.
for j in range(i - 1, -1, -1):
jline, jlevel = stats[j]
if jlevel >= 0:
want = have + (getlspace(after[jline - 1]) -
getlspace(lines[jline]))
break
if want < 0:
# Still no luck -- leave it alone.
want = have
else:
want = 0
assert want >= 0
have2want[have] = want
diff = want - have
if diff == 0 or have == 0:
after.extend(lines[thisstmt:nextstmt])
else:
for line in lines[thisstmt:nextstmt]:
if diff > 0:
if line == "\n":
after.append(line)
else:
after.append(" " * diff + line)
else:
remove = min(getlspace(line), -diff)
after.append(line[remove:])
return self.raw != self.after
def write(self, f):
f.writelines(self.after)
# Line-getter for tokenize.
def getline(self):
if self.index >= len(self.lines):
line = ""
else:
line = self.lines[self.index]
self.index += 1
return line
# Line-eater for tokenize.
def tokeneater(self, type, token, slinecol, end, line,
INDENT=tokenize.INDENT,
DEDENT=tokenize.DEDENT,
NEWLINE=tokenize.NEWLINE,
COMMENT=tokenize.COMMENT,
NL=tokenize.NL):
if type == NEWLINE:
# A program statement, or ENDMARKER, will eventually follow,
# after some (possibly empty) run of tokens of the form
# (NL | COMMENT)* (INDENT | DEDENT+)?
self.find_stmt = 1
elif type == INDENT:
self.find_stmt = 1
self.level += 1
elif type == DEDENT:
self.find_stmt = 1
self.level -= 1
elif type == COMMENT:
if self.find_stmt:
self.stats.append((slinecol[0], -1))
# but we're still looking for a new stmt, so leave
# find_stmt alone
elif type == NL:
pass
elif self.find_stmt:
# This is the first "real token" following a NEWLINE, so it
# must be the first token of the next program statement, or an
# ENDMARKER.
self.find_stmt = 0
if line: # not endmarker
self.stats.append((slinecol[0], self.level))
# Count number of leading blanks.
def getlspace(line):
i, n = 0, len(line)
while i < n and line[i] == " ":
i += 1
return i
if __name__ == '__main__':
main()
It will be good to have BICePs support Python3 since this is the trend and we must follow this up.