Does not compile without curl

[jbedo]

Building release 0.3.13 using python 3 fails due to a bug in setup.py:

Traceback (most recent call last):
  File "nix_run_setup", line 8, in <module>
    exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\\r\\n', '\\n'), __file__, 'exec'))
  File "setup.py", line 43, in <module>
    foo = foo.decode().strip().split()
AttributeError: 'str' object has no attribute 'decode'

Under python 3 there is no need to decode UTF-8 strings. Modifying the offending line to foo = foo.strip().split() resolves the problem.

[dpryan79]

Which version of python and were you using pip or python setup.py install? For example, under python 3.6 and 3.7 foo is a bytes object.

[jbedo]

Python 3.7.2, not using pip executed with python setup.py install.

[jbedo]

Should mention it's python setup.py install via the Nix build system (i.e., I didn't execute it directly).

[dpryan79]

I'll look into whether this changed in python 3.7.2, since it works as intended in 3.7.1. For what it's worth, this seems like a nice argument for "use conda for package management".

[dpryan79]

This seems to be an issue with Nix, because I just installed python 3.7.2 and ran python setup.py install --user with it without error. This is unsurprising since the aforementioned foo object is still a bytes object:

$ python
Python 3.7.2 | packaged by conda-forge | (default, Mar 20 2019, 01:46:52) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import subprocess
>>> foo, _ = subprocess.Popen(['curl-config', '--libs'], stdout=subprocess.PIPE).communicate()
>>> type(foo)
<class 'bytes'>
>>> foo
b'-lcurl\n'
>>> foo.decode().strip().split()
['-lcurl']

[jbedo]

Well, I use Nix not conda and consider it far superior :).

Package manager wars aside, that little test you did is interesting:

Python 3.7.2 (default, Dec 24 2018, 03:41:55)
[GCC 7.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import subprocess
>>> foo, _ = subprocess.Popen(['curl-config', '--libs'], stdout=subprocess.PIPE).communicate()
>>> type(foo)
<class 'bytes'>
>>> foo.decode().strip().split()
['-L/nix/store/mlnv0gkwszwc995b52ffnn57ig5cabpj-curl-7.64.0/lib', '-lcurl']
>>>

So you're right.

The problem actually seems to be that I didn't have curl-config exposed (i.e., the build fails without curl). I've verified that pyBigWig compiles fine with curl, and fails with the "no decode" error without.

[jbedo]

It also does correctly detect there's no curl-config, just fails anyway directly aftewards:

Either libcurl isn't installed, it didn't come with curl-config, or curl-config isn't in your $PATH. pyBigWig will be installed without support for remote files.
Traceback (most recent call last):
  File "nix_run_setup", line 8, in <module>
    exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\\r\\n', '\\n'), __file__, 'exec'))
  File "setup.py", line 43, in <module>
    foo = foo.decode().strip().split()
AttributeError: 'str' object has no attribute 'decode'
builder for '/nix/store/r9zxfh6sr6spd4m17naz4nryrscyl4d4-python3.7-pyBigWig-0.3.13.drv' failed with exit code 1
error: build of '/nix/store/r9zxfh6sr6spd4m17naz4nryrscyl4d4-python3.7-pyBigWig-0.3.13.drv' failed

[dpryan79]

Ah, that's the bug we're looking for then, thanks!

[dpryan79]

I'm pushing out version 0.3.14, which should fix this.

[dpryan79]

This should now be available in pypi.

[jbedo]

Confirmed resolved in 0.3.14, thanks!