def test_undef(self):
""" Tests CPreProcessor #undef preprocessing """
# This tests undef-ing both a defined and not-defined variable.
f = StringIO("MY_DEFINE\n#define MY_DEFINE Changed\nMY_DEFINE\n"
"#undef MY_DEFINE\nMY_DEFINE\n#undef NO_VARIABLE\n")
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(), "MY_DEFINE\nChanged\nMY_DEFINE")
def test_conservative_defines(self):
""" Tests CPreProcessor #define token replacement """
# Check that it does not replace tokens inside quotes
f = StringIO("'MY_VAR' is MY_VAR\n\"MY_VAR\" is MY_VAR still\n")
pp = CPreProcessor(f, defines=dict(MY_VAR='set'))
self.assertEqual(pp.read().strip(), "'MY_VAR' is set\n\"MY_VAR\" is set still")
f = StringIO("This is NOT_MY_VAR, but 'MY_VAR' is MY_VAR\n")
pp = CPreProcessor(f, defines=dict(MY_VAR='taken'))
self.assertEqual(pp.read().strip(), "This is NOT_MY_VAR, but 'MY_VAR' is taken")
def test_missing_include(self):
""" Tests CPreProcessor controllable behavior of missing #includes """
warnings.filterwarnings('error', category=PreProcessorWarning)
f = StringIO("#include \"nofile.h\"\n")
pp = CPreProcessor(f)
self.assertRaises(PreProcessorError, lambda: pp.read())
f.seek(0)
pp = CPreProcessor(f, notfound_fatal=False)
self.assertRaises(PreProcessorWarning, lambda: pp.read())
def test_ifndef(self):
""" Tests CPreProcessor #ifndef/#else#endif preprocessing """
f = StringIO('#ifndef MY_DEFINE\nMY_DEFINE is not set\n'
'#else\nPPVAR is set to MY_DEFINE\n#endif\n')
pp = CPreProcessor(f) # no defines
self.assertEqual(pp.read().strip(), 'MY_DEFINE is not set')
f.seek(0)
pp = CPreProcessor(f, defines=dict(MY_DEFINE='SUCCESS'))
self.assertEqual(pp.read().strip(), 'PPVAR is set to SUCCESS')
def test_not_implemented(self):
""" Test error catching for PP features not implemented """
f = StringIO('#define MYVAR 1\n#if (MYVAR == 1)\nCORRECT\n#endif')
pp = CPreProcessor(f)
self.assertRaises(NotImplementedError, lambda: pp.seek(10))
self.assertRaises(NotImplementedError, pp.read)
f = StringIO('#ifdef MYVAR\n#elif defined(NOTMYVAR)\n#else\nline\#endif')
pp = CPreProcessor(f)
self.assertRaises(NotImplementedError, pp.read)
def test_define(self):
""" Tests CPreProcessor #define preprocessing """
f = StringIO('#ifdef MY_DEFINE\nPPVAR is set to MY_DEFINE\n'
'#else\nMY_DEFINE is not set\n#endif\n'
'#define MY_DEFINE SUCCESS\n#ifdef MY_DEFINE\n'
'PPVAR is set to MY_DEFINE\n#else\nMY_DEFINE is not set\n'
'#endif\n')
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(),
'MY_DEFINE is not set\nPPVAR is set to SUCCESS')
def test_include_defines(self):
""" Tests CPreProcessor passing defines between included files """
pp = CPreProcessor(get_fn('pptest2/pptest1.h'))
self.assertEqual(pp.read().strip(), """\
pptest1 line 1
pptest2 line 1
pptest3 line 1
pptest1 line 2
pptest1 line 3
pptest3 line 1
pptest1 line 4""")
def test_simple_include(self):
""" Tests CPreProcessor simple #include directive """
pp = CPreProcessor(get_fn('pptest1/pptest1.h'))
self.assertEqual(pp.read().strip(), """\
pptest1 line 1
pptest2 line 1
pptest3 line 1
pptest2 line 2
pptest1 line 2
pptest3 line 1
pptest1 line 3""")
def test_undef(self):
""" Tests CPreProcessor #undef preprocessing """
# This tests undef-ing both a defined and not-defined variable.
f = StringIO("MY_DEFINE\n#define MY_DEFINE Changed\nMY_DEFINE\n"
"#undef MY_DEFINE\nMY_DEFINE\n#undef NO_VARIABLE\n")
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(), "MY_DEFINE\nChanged\nMY_DEFINE")
# Make sure undef does not occur where it shouldn't
f = StringIO('#define MYVAR something\n#ifdef NOVAR\n#undef MYVAR\n'
'#endif\nMYVAR')
with CPreProcessor(f) as pp:
self.assertEqual(pp.read().strip(), 'something')
def test_define_inside_ifdef(self):
""" Tests CPreProcessor #define inside #ifdef/#ifndef """
f = StringIO("#ifdef MY_DEFINE\n#define MY_DEFINE "
"Something\n#endif\nMY_DEFINE")
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(), "MY_DEFINE")
f = StringIO("#ifdef MY_DEFINE\n# define MY_DEFINE Something\n"
"#endif\nMY_DEFINE\n#ifndef MY_DEFINE\n"
"# define MY_DEFINE Something special\n#endif\n"
"MY_DEFINE")
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(), "MY_DEFINE\nSomething special")
def test_include_dir(self):
""" Tests CPreProcessor passing include directories to search """
f = StringIO('#include "pptest1.h"')
pp = CPreProcessor(f, includes=[get_fn('pptest1')])
self.assertEqual(pp.read().strip(), """\
pptest1 line 1
pptest2 line 1
pptest3 line 1
pptest2 line 2
pptest1 line 2
pptest3 line 1
pptest1 line 3""")
def test_bad_ifdef(self):
""" Tests CPreProcessor error processing of bad #ifdef/#ifndef """
f = StringIO("#ifdef\n#endif")
pp = CPreProcessor(f)
self.assertRaises(PreProcessorError, lambda: pp.read())
f = StringIO("#ifndef\n#endif")
pp = CPreProcessor(f)
self.assertRaises(PreProcessorError, lambda: pp.read())
f = StringIO("#ifdef SOME_VAR\ndangling ifdef\n\n\n")
pp = CPreProcessor(f)
self.assertRaises(PreProcessorError, lambda: pp.read())
warnings.filterwarnings('error', category=PreProcessorWarning)
f = StringIO("#ifdef SOME_VAR misplaced comments\n#endif\n")
pp = CPreProcessor(f)
self.assertRaises(PreProcessorWarning, lambda: pp.read())
f = StringIO("#ifdef SOME_VAR\n#endif misplaced comments\n")
pp = CPreProcessor(f)
self.assertRaises(PreProcessorWarning, lambda: pp.read())
def test_define(self):
""" Tests CPreProcessor #define preprocessing """
f = StringIO('#ifdef MY_DEFINE\nPPVAR is set to MY_DEFINE\n'
'#else\nMY_DEFINE is not set\n#endif\n'
'#define MY_DEFINE SUCCESS\n#ifdef MY_DEFINE\n'
'PPVAR is set to MY_DEFINE\n#else\nMY_DEFINE is not set\n'
'#endif\n')
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(),
'MY_DEFINE is not set\nPPVAR is set to SUCCESS')
warnings.filterwarnings('error', category=PreProcessorWarning)
f = StringIO('#define MYVAR something\nMYVAR\n#define MYVAR '
'something_else\nMYVAR')
with CPreProcessor(f) as pp:
self.assertRaises(PreProcessorWarning, pp.read)
warnings.filterwarnings('ignore', category=PreProcessorWarning)
f.seek(0)
with CPreProcessor(f) as pp:
self.assertEqual(pp.read().strip(), 'something\nsomething_else')
def test_nested_ifs(self):
""" Tests CPreProcessor nested #ifdef and #if """
f = StringIO("""
#ifdef MY_VAR
line 1
# if 1
line 2
# endif /* 1 */
#else /* ! MY_VAR */
# if 0
line 3
# else /* ! 0 */
line 4
# endif /* 0 */
#endif /* MY_VAR */
""")
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(), "line 4")
f.seek(0)
pp = CPreProcessor(f, defines=dict(MY_VAR=1))
self.assertEqual(pp.read().strip(), "line 1\nline 2")
def test_nested_ifs(self):
""" Tests CPreProcessor nested #ifdef and #if """
f = StringIO("""
#ifdef MY_VAR
line 1
# if 1
line 2
# endif /* 1 */
#else /* ! MY_VAR */
# if 0
line 3
# else /* ! 0 */
line 4
# endif /* 0 */
#endif /* MY_VAR */
""")
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(), "line 4")
f.seek(0)
pp = CPreProcessor(f, defines=dict(MY_VAR=1))
self.assertEqual(pp.read().strip(), "line 1\nline 2")
f = StringIO("""
#ifdef MY_VAR
# ifndef MY_VAR_2
MY_VAR defined... MY_VAR_2 not
# else
MY_VAR defined... MY_VAR_2 also
# endif
#endif
""")
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(), '')
f.seek(0)
pp = CPreProcessor(f, defines=dict(MY_VAR=1))
self.assertEqual(pp.read().strip(), '1 defined... MY_VAR_2 not')
f.seek(0)
pp = CPreProcessor(f, defines=dict(MY_VAR=1, MY_VAR_2=2))
self.assertEqual(pp.read().strip(), '1 defined... 2 also')
def test_if1_if0(self):
""" Tests CPreProcessor use of #if 1 and #if 0 to serve as comments """
f = StringIO('#if 1\n#ifdef MY_DEFINE\nPPVAR is set to MY_DEFINE\n'
'#else\nMY_DEFINE is not set\n#endif\n#endif\n')
pp = CPreProcessor(f) # no defines
self.assertEqual(pp.read().strip(), 'MY_DEFINE is not set')
f.seek(0)
pp = CPreProcessor(f, defines=dict(MY_DEFINE='SUCCESS'))
self.assertEqual(pp.read().strip(), 'PPVAR is set to SUCCESS')
f = StringIO('#if 0\n#ifdef MY_DEFINE\nPPVAR is set to MY_DEFINE\n'
'#else\nMY_DEFINE is not set\n#endif\n#endif\n')
pp = CPreProcessor(f) # no defines
self.assertFalse(pp.read().strip())
f.seek(0)
pp = CPreProcessor(f, defines=dict(MY_DEFINE='SUCCESS'))
self.assertFalse(pp.read().strip())
def test_bad_define_undef(self):
""" Tests CPreProcessor error processing of bad #define/#undef """
f = StringIO("#define\n")
pp = CPreProcessor(f)
self.assertRaises(PreProcessorError, lambda: pp.read())
f = StringIO("#undef\n")
pp = CPreProcessor(f)
self.assertRaises(PreProcessorError, lambda: pp.read())
warnings.filterwarnings('error', category=PreProcessorWarning)
f = StringIO('#undef VAR1 misplaced comments\n')
pp = CPreProcessor(f)
self.assertRaises(PreProcessorWarning, lambda: pp.read())
class GromacsFile(object):
"""
A GROMACS file that recognizes the ";" character as a 'comment' token. It
can be iterated over and generally treated like a file object, but only
spits out strings that have been truncated at its first comment character.
There is currently no way to recognize a ; as a _non_ comment character,
since allowing an escape character does not seem to be common practice and
would likely introduce negative performance implications.
Parameters
----------
fname : str or file-like
Name of the file to parse or file-like object to parse
defines : dict{str : str}, optional
List of defines for the preprocessed file, if any
includes : list of str, optional
List of include files. Default is taken from environment variables
GMXDATA or GMXBIN if they are set. Otherwise, it is looked for in /usr,
/usr/local, /opt, or /opt/local. If it is still not found, it is looked
for relative to whatever ``mdrun`` executable is in your path
notfound_fatal : bool, optional
If True, missing include files are fatal. If False, they are a warning.
Default is True
"""
def __init__(self, fname, **kwargs):
self._handle = CPreProcessor(fname, **kwargs)
self.closed = False
self.line_number = 0
def __iter__(self):
# Iterate over the file, treating an ending \ as a continuation
parts = []
for line in self._handle:
try:
idx = line.index(';')
if not parts:
yield '%s\n' % line[:idx]
else:
parts.append('%s' % line[:idx])
yield '%s\n' % ''.join(parts)
parts = []
except ValueError:
# There is no comment...
if line.rstrip('\r\n').endswith('\\'):
chars = list(reversed(line.rstrip('\r\n')))
del chars[chars.index('\\')]
parts.append('%s ' % ''.join(reversed(chars)))
elif parts:
parts.append(line)
yield ''.join(parts)
parts = []
else:
yield line
@property
def included_files(self):
return self._handle.included_files
def readline(self):
parts = []
self.line_number += 1
line = True
while line:
line = self._handle.readline()
try:
idx = line.index(';')
if not parts:
return '%s\n' % line[:idx]
else:
parts.append('%s' % line[:idx])
return '%s\n' % ''.join(parts)
except ValueError:
# There is no comment...
if line.rstrip('\r\n').endswith('\\'):
chars = list(reversed(line.rstrip('\r\n')))
del chars[chars.index('\\')]
parts.append('%s ' % ''.join(reversed(chars)))
elif parts:
parts.append(line)
return ''.join(parts)
else:
return line
def readlines(self):
return [line for line in self]
def read(self):
return ''.join(self.readlines())
def close(self):
self._handle.close()
self.closed = True
def __del__(self):
try:
self.closed or self._handle.close()
except AttributeError:
# It didn't make it out of the constructor
pass
def test_close(self):
""" Test closing file object before deleting it """
pp = CPreProcessor(get_fn('pptest1/pptest1.h'))
pp.close()
del pp
def test_if1_if0(self):
""" Tests CPreProcessor use of #if 1 and #if 0 to serve as comments """
f = StringIO('#if 1\n#ifdef MY_DEFINE\nPPVAR is set to MY_DEFINE\n'
'#else\nMY_DEFINE is not set\n#endif\n#endif\n')
pp = CPreProcessor(f) # no defines
self.assertEqual(pp.read().strip(), 'MY_DEFINE is not set')
f.seek(0)
pp = CPreProcessor(f, defines=dict(MY_DEFINE='SUCCESS'))
self.assertEqual(pp.read().strip(), 'PPVAR is set to SUCCESS')
f = StringIO('#if 0\n#ifdef MY_DEFINE\nPPVAR is set to MY_DEFINE\n'
'#else\nMY_DEFINE is not set\n#endif\n#endif\n')
pp = CPreProcessor(f) # no defines
self.assertFalse(pp.read().strip())
f.seek(0)
pp = CPreProcessor(f, defines=dict(MY_DEFINE='SUCCESS'))
self.assertFalse(pp.read().strip())
def test_nested_ifs(self):
""" Tests CPreProcessor nested #ifdef and #if """
f = StringIO("""
#ifdef MY_VAR
line 1
# if 1
line 2
# endif /* 1 */
#else /* ! MY_VAR */
# if 0
line 3
# else /* ! 0 */
line 4
# endif /* 0 */
#endif /* MY_VAR */
""")
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(), "line 4")
f.seek(0)
pp = CPreProcessor(f, defines=dict(MY_VAR=1))
self.assertEqual(pp.read().strip(), "line 1\nline 2")
f = StringIO("""
#ifdef MY_VAR
# ifndef MY_VAR_2
MY_VAR defined... MY_VAR_2 not
# else
MY_VAR defined... MY_VAR_2 also
# endif
#endif
""")
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(), '')
f.seek(0)
pp = CPreProcessor(f, defines=dict(MY_VAR=1))
self.assertEqual(pp.read().strip(), '1 defined... MY_VAR_2 not')
f.seek(0)
pp = CPreProcessor(f, defines=dict(MY_VAR=1, MY_VAR_2=2))
self.assertEqual(pp.read().strip(), '1 defined... 2 also')
def test_nested_defines(self):
""" Tests CPreProcessor nested #define token replacement """
f = StringIO("#define MY_VAR replace1\n#define MY_VAR2 MY_VAR\n"
"MY_VAR2\n")
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(), 'replace1')
def __init__(self, fname, **kwargs):
self._handle = CPreProcessor(fname, **kwargs)
self.closed = False
self.line_number = 0
class GromacsFile(object):
"""
A GROMACS file that recognizes the ";" character as a 'comment' token. It
can be iterated over and generally treated like a file object, but only
spits out strings that have been truncated at its first comment character.
There is currently no way to recognize a ; as a _non_ comment character,
since allowing an escape character does not seem to be common practice and
would likely introduce negative performance implications.
Parameters
----------
fname : str or file-like
Name of the file to parse or file-like object to parse
defines : dict{str : str}, optional
List of defines for the preprocessed file, if any
includes : list of str, optional
List of include files. Default is taken from environment variables
GMXDATA or GMXBIN if they are set. Otherwise, it is looked for in /usr,
/usr/local, /opt, or /opt/local. If it is still not found, it is looked
for relative to whatever ``mdrun`` executable is in your path
notfound_fatal : bool, optional
If True, missing include files are fatal. If False, they are a warning.
Default is True
"""
def __init__(self, fname, **kwargs):
self._handle = CPreProcessor(fname, **kwargs)
self.closed = False
self.line_number = 0
def __iter__(self):
# Iterate over the file, treating an ending \ as a continuation
parts = []
for line in self._handle:
try:
idx = line.index(';')
if not parts:
yield '%s\n' % line[:idx]
else:
parts.append('%s' % line[:idx])
yield '%s\n' % ''.join(parts)
parts = []
except ValueError:
# There is no comment...
if line.rstrip('\r\n').endswith('\\'):
chars = list(reversed(line.rstrip('\r\n')))
del chars[chars.index('\\')]
parts.append('%s ' % ''.join(reversed(chars)))
elif parts:
parts.append(line)
yield ''.join(parts)
parts = []
else:
yield line
@property
def included_files(self):
return self._handle.included_files
def readline(self):
parts = []
self.line_number += 1
line = True
while line:
line = self._handle.readline()
try:
idx = line.index(';')
if not parts:
return '%s\n' % line[:idx]
else:
parts.append('%s' % line[:idx])
return '%s\n' % ''.join(parts)
except ValueError:
# There is no comment...
if line.rstrip('\r\n').endswith('\\'):
chars = list(reversed(line.rstrip('\r\n')))
del chars[chars.index('\\')]
parts.append('%s ' % ''.join(reversed(chars)))
elif parts:
parts.append(line)
return ''.join(parts)
else:
return line
def readlines(self):
return [line for line in self]
def read(self):
return ''.join(self.readlines())
def close(self):
self._handle.close()
self.closed = True
def __del__(self):
try:
self.closed or self._handle.close()
except AttributeError:
# It didn't make it out of the constructor
pass
def test_nested_defines(self):
""" Tests CPreProcessor nested #define token replacement """
f = StringIO("#define MY_VAR replace1\n#define MY_VAR2 MY_VAR\n"
"MY_VAR2\n")
pp = CPreProcessor(f)
self.assertEqual(pp.read().strip(), 'replace1')
def __init__(self, fname, **kwargs):
self._handle = CPreProcessor(fname, **kwargs)
self.closed = False
self.line_number = 0