setup.py dependency checking detects unexpected dependencies

[sagetrac-sbarthelemy]

using sage 3.2.3, I'm trying to build a new module with a .pxd file containing this line

 #include "gmp.h"

note that the line is commented. The build fails with the following traceback

 sage -b

----------------------------------------------------------
sage: Building and installing modified Sage library files.


Installing c_lib
scons: `install' is up to date.
Updating Cython code....
Traceback (most recent call last):
  File "setup.py", line 503, in <module>
    queue = compile_command_list(ext_modules, deps)
  File "setup.py", line 463, in compile_command_list
    dep_file, dep_time = deps.newest_dep(f)
  File "setup.py", line 378, in newest_dep
    for f in self.all_deps(filename):
  File "setup.py", line 361, in all_deps
    deps.update(self.all_deps(f, path))
  File "setup.py", line 359, in all_deps
    for f in self.immediate_deps(filename):
  File "setup.py", line 341, in immediate_deps
    self._deps[filename] = self.parse_deps(filename)
  File "setup.py", line 331, in parse_deps
    raise IOError, "could not find dependency %s included in %s."%(path, filename)
IOError: could not find dependency gmp.h included in sage/geometry/cdd.pxd.
sage: There was an error installing modified sage library code.

There is probably a problem with the regexp on line 228 of setup.py. One can reprouce the bug with this snipet

dep_regex = re.compile(r'^ *(?:cimport +(\S+))|(?:from +(\S+) *cimport)|(?:include *[\'"]([^\'"]+)[\'"])', re.M)
m.groups()for m in dep_regex.finditer('#include "gmp.h"'):                      
    m.groups()                                                        

which results in

(None, None, 'gmp.h')

Component: build

Issue created by migration from https://trac.sagemath.org/ticket/5060

[sagetrac-cwitty]

comment:1

I think that modifying the regex like this (adding two '^' characters) will fix the problem. (It fixes the above test case, but I don't have time to do a real test, or submit a real patch, right now.)

r'^ *(?:cimport +(\S+))|^(?:from +(\S+) *cimport)|^(?:include *[\'"]([^\'"]+)[\'"])'

[sagetrac-sbarthelemy]

some more thoughts

1. the include keyword is deprecated cython doc,

2. the current regexp misses other cython patterns that involve dependancies:

cimport mod1, mod2

and

cdef extern from "toto.h":
    ....

Here is a first attempt to fix this,

import re
dep_regex = re.compile(r'^ *(?:(?:(?:(?:include)|(?:cdef +extern + from)) +[\'"]([^\'"]+)[\'"])|(?:from +(\w+) *cimport)|(?:cimport +([^ \t\n\r\f\v,]+)(?: *, *([^ \t\n\r\f\v,]+))*))',  re.MULTILINE)

teststr = """include "yes1.h"
include "yes2.h" 
 include "yes3.h"
 include 'yes4.h'
#include "no5.h"
 # include "no6.h"
cimport yes7
 cimport yes8 
#cimport no9
# cimport no10
from yes11 cimport toto
from yes12 cimport toto as tata
#from no13 cimport toto as tata
cdef extern from "yes14.h"
cimport yes15 , yes15b
cimport yes16, yes16b
cimport yes17, yes17b , yes17c

"""

print 'toto'
for m in dep_regex.finditer(teststr):
    print m.groups()

However, for some reason, it doesn't catch yes14.h nor yes17b. So this is not yet functional (nor elegant). Any suggestion is welcome.

[robertwb]

comment:4

Attachment: 5060-deps.patch.gz

The original bug was due to the fact that "^ *" was only required for the first grouping.

Given that more than one module could be cimported in a single statement, it took an extra loop in the parsing code as well.

[craigcitro]

comment:5

This looks good. Man, that is one serious regular expression.

[sagetrac-mabshoff]

comment:6

Merged in Sage 3.3.alpha2

Cheers,

Michael