nosetests -v tamkin

[raghavven]

I ran the command 'pip install tamkin --user' and got the following lines.

Collecting tamkin Requirement already satisfied: molmod>=1.3.2 in ./.local/lib/python3.5/site-packages (from tamkin) (1.4.4) Requirement already satisfied: matplotlib>1.1 in /usr/lib/python3/dist-packages (from tamkin) (1.5.1) Requirement already satisfied: numpy>=1.0 in ./.local/lib/python3.5/site-packages (from tamkin) (1.16.4) Requirement already satisfied: nose>=0.11 in ./.local/lib/python3.5/site-packages (from tamkin) (1.3.7) Collecting scipy>=0.17.1 (from tamkin) Using cached https://files.pythonhosted.org/packages/14/49/8f13fa215e10a7ab0731cc95b0e9bb66cf83c6a98260b154cfbd0b55fb19/scipy-1.3.0-cp35-cp35m-manylinux1_x86_64.whl Requirement already satisfied: future in ./.local/lib/python3.5/site-packages (from molmod>=1.3.2->tamkin) (0.17.1) Requirement already satisfied: cython>=0.24.1 in ./.local/lib/python3.5/site-packages (from molmod>=1.3.2->tamkin) (0.29.12) Installing collected packages: scipy, tamkin Successfully installed scipy-1.3.0 tamkin-1.2.4

This looks like TAMkin has been successfully installed with other associated dependencies.

But when I run the command 'nosetests -v tamkin', it gives me an error saying

'The program 'nosetests' is currently not installed. You can install it by typing: sudo apt install python-nose'

Kindly advice how to go about it.

Thanks

[tovrstra]

I assume the install location of the nosetests program is not in your PATH. If you are working on a Linux system, you should make sure the following is added to your path: ${HOME}/.local/bin. This can be done by putting the following line in your .bashrc:

export PATH=${PATH}:${HOME}/.local/bin

It is slightly different (but similar) on a mac, but I don't know it by heart.

[raghavven]

Thank you for your kind reply Toon Verstraelen.

The 'nose' is located at /home/subbu/.local/lib/python3.5/site-packages. 'tamkin' and 'tamkin-1.2.4.dist-info' are also located at /home/subbu/.local/lib/python3.5/site-packages.

I pasted the following at the last line of '.bashrc' export PATH=${PATH}:/home/subbu/.local/lib/python3.5/site-packages/nose

And now when I run the command 'nosetests -v tamkin', I get the following error.

Failure: SyntaxError (invalid syntax (partf.py, line 1019)) ... ERROR

======================================================================
ERROR: Failure: SyntaxError (invalid syntax (partf.py, line 1019))
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/subbu/.local/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/home/subbu/.local/lib/python3.5/site-packages/nose/loader.py", line 407, in loadTestsFromName
    module = resolve_name(addr.module)
  File "/home/subbu/.local/lib/python3.5/site-packages/nose/util.py", line 312, in resolve_name
    module = __import__('.'.join(parts_copy))
  File "/home/subbu/.local/lib/python3.5/site-packages/tamkin/__init__.py", line 39, in <module>
    from tamkin.chemmod import *
  File "/home/subbu/.local/lib/python3.5/site-packages/tamkin/chemmod.py", line 42, in <module>
    from tamkin.partf import PartFun
  File "/home/subbu/.local/lib/python3.5/site-packages/tamkin/partf.py", line 1019
    print 'WARNING: molecule is too large (%i atoms > 10) to quickly estimate the rotational symmetry number.' % natom
                                                                                                             ^
SyntaxError: invalid syntax

----------------------------------------------------------------------
Ran 1 test in 0.004s

FAILED (errors=1)

Can you please advice how to overcome this error.

Thanks

[tovrstra]

Could you try the following line instead in .bashrc?

export PATH=${PATH}:/home/subbu/.local/bin

Normally, putting the directory with the python library into the PATH variable should not work.

[raghavven]

Thank you once again for your swift response.

I am new to the linux environment. I am not sure, if I am pasting things correctly in '.bashrc' file. So I have attached '.bashrc' file for your kind reference.

I pasted the following line at the end of the '.bashrc' file. 'export PATH=${PATH}:/home/subbu/.local/bin'

It gave me the same error.

Can you kindly help.

Thank you. .bashrc.txt

[tovrstra]

Oh, I should have looked more carefully at your error message. TAMkin is not ported yet to python 3, which is the cause here. Can you try using python 2 instead?

[raghavven]

Thank you for your valuable comment.

I ensured, numpy, scipy, matplotlib, molmod, nose and tamkin are all found inside python2.7

I ran the command 'nosetests tamkin' and after running a series of tests, it finally printed the following in the last two lines.

"Ran 126 tests in 99.491s

FAILED (errors=9, failures=10)"

Can you please help me overcome this.

Thanks.

[tovrstra]

Good, that is already an improvement. It all depends on which errors are failing. Can you run nosetests -v tamkin to get the detailed list of failing and passing tests? That should provide us with some hints on how to proceed.

[tovrstra]

TAMkin has become python 3 compatible as of version 1.2.6, which will be released today.