python setup.py build_ext error: Cython.Compiler.Errors.CompileError: parse_bed.pyx

[bensutherland]

I am having trouble installing fastStructure (cloned today) on a MacOS (Ventura 13.5). I've followed all instructions from the README, and have installed all necessary dependencies. I can give details if needed, or if that would help please let me know.

The crash occurs when trying to compile the main cython scripts. Error message:

$ python setup.py build_ext --inplace
running build_ext
Compiling parse_bed.pyx because it changed.
[1/1] Cythonizing parse_bed.pyx
/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Cython/Compiler/Main.py:381:
FutureWarning: Cython directive 'language_level' not set, using '3str' for now
(Py3). This has changed from earlier releases! File:
/Users/bens/programs/fastStructure/parse_bed.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)

Error compiling Cython file:
------------------------------------------------------------
...
    checkB = bin(struct.unpack('<B', line)[0])[2:].zfill(8)[::-1]
    line = handle.read(1)
    checkC = bin(struct.unpack('<B', line)[0])[2:].zfill(8)[::-1]

    if checkA!="00110110" or checkB!="11011000":
        print "This is not a valid bed file"
              ^
------------------------------------------------------------

parse_bed.pyx:47:14: Syntax error in simple statement list
Traceback (most recent call last):
  File "setup.py", line 15, in <module>
    ext_modules = ext_modules
  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py",
line 151, in setup
    dist.run_commands()
  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py",
line 953, in run_commands
    self.run_command(cmd)
  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py",
line 972, in run_command
    cmd_obj.run()
  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/build_ext.py",
line 340, in run
    self.build_extensions()
  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/build_ext.py",
line 449, in build_extensions
    self.build_extension(ext)
  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Cython/Distutils/build_ext.py",
line 131, in build_extension
    ext,force=self.force, quiet=self.verbose == 0, **options
  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Cython/Build/Dependencies.py",
line 1154, in cythonize
    cythonize_one(*args)
  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Cython/Build/Dependencies.py",
line 1321, in cythonize_one
    raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: parse_bed.pyx

Some details: python /Library/Frameworks/Python.framework/Versions/2.7/bin/python2 GSL-2.7 installed from gnu.org numpy installed by pip Cython installed by pip /Library/Frameworks/Python.framework/Versions/2.7/bin/Cython

Thank you for any help.

[alleneli]

I'm having the exact same problem, was a solution found?

[bensutherland]

Hi @alleneli , Unfortunately no, I did not find a solution, and was not able to get the program to install.

[alleneli]

Shoot, I tried reverting to an older version of Cython that tends to work better with Python 2, but that led to another suite of issues.

If I make any progress I will report back here.

[pkmnsandy]

I found a workaround, someone created this: https://structure-threader.readthedocs.io/en/latest/ and it works perfectly in my M1 Mac.

[alleneli]

Awesome, thank you @pkmnsandy!

[David919110]

in parse_bed.pyx you need to put : Nbytes = Nindiv//4+(Nindiv%4>0)1 (double //), not Nbytes = Nindiv/4+(Nindiv%4>0)1, then in each .py file put print ( ), i.e. parentheses in each print

[ntakebay]

Original poster was using python 2, but if you are using python 3, you can try https://github.com/jashapiro/fastStructure/tree/py3 This fix wasn't incorporated into the main branch. But even with this py3 branch, I had to fix a couple additional things which David919110 suggested (missing parentheses for print () in fastStructure.pyx and parse_bed.pyx and specify integer division // instead of / in parse_bed.pyx. Here is the patch: fastStructure-py3.print.intDiv.patch :

diff -ru fastStructure-19e39d1161c2eb49e6137d2ab2449888bd04f7ec.orig/fastStructure.pyx fastStructure-19e39d1161c2eb49e6137d2ab2449888bd04f7ec/fastStructure.pyx
--- fastStructure-19e39d1161c2eb49e6137d2ab2449888bd04f7ec.orig/fastStructure.pyx       2015-10-15 12:34:35.000000000 -0800
+++ fastStructure-19e39d1161c2eb49e6137d2ab2449888bd04f7ec/fastStructure.pyx    2024-08-14 15:07:09.923564488 -0800
@@ -302,7 +302,7 @@

         if not len(newmasks)>=cv:
             wellmasked = False
-            print "Failed"
+            print("Failed")

     masks = newmasks[:cv]
     meandeviance = np.zeros((cv,), dtype=float)
diff -ru fastStructure-19e39d1161c2eb49e6137d2ab2449888bd04f7ec.orig/parse_bed.pyx fastStructure-19e39d1161c2eb49e6137d2ab2449888bd04f7ec/parse_bed.pyx
--- fastStructure-19e39d1161c2eb49e6137d2ab2449888bd04f7ec.orig/parse_bed.pyx   2015-10-15 12:34:35.000000000 -0800
+++ fastStructure-19e39d1161c2eb49e6137d2ab2449888bd04f7ec/parse_bed.pyx        2024-08-14 15:07:17.109669878 -0800
@@ -22,7 +22,7 @@
     Nindiv = i+1

     # Number of bytes to read in at a time
-    Nbytes = Nindiv/4+(Nindiv%4>0)*1
+    Nbytes = Nindiv//4+(Nindiv%4>0)*1

     # number of SNPs
     handle = open(file+'.bim','r')
@@ -45,7 +45,7 @@
     checkC = bin(struct.unpack('<B', line)[0])[2:].zfill(8)[::-1]

     if checkA!="00110110" or checkB!="11011000":
-        print "This is not a valid bed file"
+        print("This is not a valid bed file")
         handle.close()
         sys.exit(2)