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mattjj / pyhsmm

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Problems installing on Python 3.4 #71

Closed stevenwong closed 7 years ago

stevenwong commented 7 years ago

Hi all,

I'm using Anaconda's version of Python 3.4 and I get the following error:

(py34) C:\Users\swong32\Documents>pip install pyhsmm --trusted-host pypi.python.org
Collecting pyhsmm
  Downloading pyhsmm-0.1.6.tar.gz (491kB)
    100% |################################| 491kB 10.2MB/s
    Complete output from command python setup.py egg_info:
    C:\Program Files\Anaconda3\envs\py34\lib\site-packages\Cython\Distutils\old_build_ext.py:30: UserWarning: Cython.Distutils.old_build_ext does not properly handle dependencies and is deprecated.
      "Cython.Distutils.old_build_ext does not properly handle dependencies "
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\swong32\AppData\Local\Temp\pip-build-hrf3b39s\pyhsmm\setup.py", line 11, in <module>
        from urllib import urlretrieve
    ImportError: cannot import name 'urlretrieve'

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in C:\Users\swong32\AppData\Local\Temp\pip-build-hrf3b39s\pyhsmm\

I think it's because urllib.urlretrieve is now urllib.request.urlretrieve?

mattjj commented 7 years ago

Thanks for the find and diagnosis! I think I applied a fix using the future module, and I also added Python 3.4 to the .travis.yml file so that it gets tested.

Btw, that other warning that was printed seems to be this issue with cython.

stevenwong commented 7 years ago

Argh, more issues

Installed c:\program files\anaconda3\envs\py34\lib\site-packages\pyhsmm-0.1.6-py
3.4-win-amd64.egg
Processing dependencies for pyhsmm==0.1.6
Searching for pybasicbayes>=0.1.3
Reading https://pypi.python.org/simple/pybasicbayes/
Downloading https://pypi.python.org/packages/dd/a9/2e5270c591dcafb85ef91696179a5
f5620e683a7b6f35642ac6db1971209/pybasicbayes-0.2.1.tar.gz#md5=cee03ff871707a3adf
302ec850942783
Best match: pybasicbayes 0.2.1
Processing pybasicbayes-0.2.1.tar.gz
Writing C:\Users\swong32\AppData\Local\Temp\easy_install-ms7nxrn2\pybasicbayes-0
.2.1\setup.cfg
Running pybasicbayes-0.2.1\setup.py -q bdist_egg --dist-dir C:\Users\swong32\App
Data\Local\Temp\easy_install-ms7nxrn2\pybasicbayes-0.2.1\egg-dist-tmp-05cij7bl
C:\Program Files\Anaconda3\envs\py34\lib\site-packages\Cython\Distutils\old_buil
d_ext.py:30: UserWarning: Cython.Distutils.old_build_ext does not properly handl
e dependencies and is deprecated.
  "Cython.Distutils.old_build_ext does not properly handle dependencies "
Compiling pybasicbayes\util\cstats.pyx because it depends on C:\Program Files\An
aconda3\envs\py34\lib\site-packages\Cython\Includes\numpy\__init__.pxd.
[1/1] Cythonizing pybasicbayes\util\cstats.pyx

Error compiling Cython file:
------------------------------------------------------------
...
    tmp[0,0] = 0
    tmp.flat[1:] = np.cumsum(np.ravel(customers)[:_customers.size-1],dtype=tmp.d
type)
    cdef integral[:,::1] starts = tmp

    with nogil:
        for i in prange(_customers.shape[0]):
             ^
------------------------------------------------------------

pybasicbayes\util\cstats.pyx:70:14: Can only iterate over an iteration variable
C:\Users\swong32\AppData\Local\Temp\easy_install-ms7nxrn2\pybasicbayes-0.2.1\set
up.py:51: UserWarning: Failed to generate extension module code from Cython file
s
  warn('Failed to generate extension module code from Cython files')
Traceback (most recent call last):
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 156, in save_modules
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 197, in setup_context
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 246, in run_setup
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 276, in run
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 245, in runner
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 47, in _execfile
  File "C:\Users\swong32\AppData\Local\Temp\easy_install-ms7nxrn2\pybasicbayes-0
.2.1\setup.py", line 73, in <module>
    eigenpath = os.path.join('deps', 'Eigen')
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\core.py", line 148, i
n setup
    dist.run_commands()
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\dist.py", line 955, i
n run_commands
    self.run_command(cmd)
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\dist.py", line 974, i
n run_command
    cmd_obj.run()
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\bdist_egg.py", line 152, in run
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\cmd.py", line 313, in
 run_command
    self.distribution.run_command(command)
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\dist.py", line 974, i
n run_command
    cmd_obj.run()
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\egg_info.py", line 195, in run
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\egg_info.py", line 222, in find_sources
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\egg_info.py", line 306, in run
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\egg_info.py", line 335, in add_defaults
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\sdist.py", line 171, in add_defaults
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\cmd.py", line 299, in
 get_finalized_command
    cmd_obj.ensure_finalized()
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\cmd.py", line 107, in
 ensure_finalized
    self.finalize_options()
  File "C:\Users\swong32\AppData\Local\Temp\easy_install-ms7nxrn2\pybasicbayes-0
.2.1\setup.py", line 19, in finalize_options
    try:
AttributeError: 'dict' object has no attribute '__NUMPY_SETUP__'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "setup.py", line 123, in <module>
    cmdclass={'build_ext': build_ext, 'sdist': sdist, 'clean': clean})
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\core.py", line 148, i
n setup
    dist.run_commands()
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\dist.py", line 955, i
n run_commands
    self.run_command(cmd)
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\dist.py", line 974, i
n run_command
    cmd_obj.run()
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\install.py", line 67, in run
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\install.py", line 117, in do_egg_install
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\easy_install.py", line 409, in run
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\easy_install.py", line 645, in easy_install
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\easy_install.py", line 696, in install_item
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\easy_install.py", line 741, in process_distributio
n
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\pkg_resources\__init__.py", line 851, in resolve
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\pkg_resources\__init__.py", line 1123, in best_match
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\pkg_resources\__init__.py", line 1135, in obtain
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\easy_install.py", line 664, in easy_install
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\easy_install.py", line 694, in install_item
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\easy_install.py", line 875, in install_eggs
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\easy_install.py", line 1114, in build_and_install
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\easy_install.py", line 1100, in run_setup
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 249, in run_setup
  File "C:\Program Files\Anaconda3\envs\py34\lib\contextlib.py", line 77, in __e
xit__
    self.gen.throw(type, value, traceback)
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 197, in setup_context
  File "C:\Program Files\Anaconda3\envs\py34\lib\contextlib.py", line 77, in __e
xit__
    self.gen.throw(type, value, traceback)
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 168, in save_modules
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 143, in resume
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\pkg_resources\_vendor\six.py", line 685, in reraise
    raise value.with_traceback(tb)
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 156, in save_modules
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 197, in setup_context
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 246, in run_setup
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 276, in run
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 245, in runner
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\sandbox.py", line 47, in _execfile
  File "C:\Users\swong32\AppData\Local\Temp\easy_install-ms7nxrn2\pybasicbayes-0
.2.1\setup.py", line 73, in <module>
    eigenpath = os.path.join('deps', 'Eigen')
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\core.py", line 148, i
n setup
    dist.run_commands()
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\dist.py", line 955, i
n run_commands
    self.run_command(cmd)
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\dist.py", line 974, i
n run_command
    cmd_obj.run()
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\bdist_egg.py", line 152, in run
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\cmd.py", line 313, in
 run_command
    self.distribution.run_command(command)
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\dist.py", line 974, i
n run_command
    cmd_obj.run()
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\egg_info.py", line 195, in run
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\egg_info.py", line 222, in find_sources
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\egg_info.py", line 306, in run
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\egg_info.py", line 335, in add_defaults
  File "C:\Program Files\Anaconda3\envs\py34\lib\site-packages\setuptools-27.2.0
-py3.4.egg\setuptools\command\sdist.py", line 171, in add_defaults
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\cmd.py", line 299, in
 get_finalized_command
    cmd_obj.ensure_finalized()
  File "C:\Program Files\Anaconda3\envs\py34\lib\distutils\cmd.py", line 107, in
 ensure_finalized
    self.finalize_options()
  File "C:\Users\swong32\AppData\Local\Temp\easy_install-ms7nxrn2\pybasicbayes-0
.2.1\setup.py", line 19, in finalize_options
    try:
AttributeError: 'dict' object has no attribute '__NUMPY_SETUP__'