001_intro

Abdul Sayyed — Fri, 10 Jul 2020 14:43:54 GMT

Jupyter note book basics¶

In [1]:

import os
print(os.name)
print(os.getcwd())
print(os.listdir( '.'))

posix
/home/sayyed/neuro-science/projects/nikola/mysite/notebooks
['002_intro.ipynb', '001_intro.ipynb', '002_basics.ipynb', '.ipynb_checkpoints', '005_intro.ipynb', '003_intro.ipynb', '004_intro.ipynb']

In [1]:

npm.install()

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-1-c09f0e0ad088> in <module>
----> 1 npm.install()

NameError: name 'npm' is not defined

Running code from different kernel¶

In [5]:

%%bash
which bash

/usr/bin/bash

In [6]:

%%HTML
<h4>This is html 4 heading </h4>

This is html 4 heading

In [ ]:

Checking-nipype-Installation

Abdul Sayyed — Fri, 10 Jul 2020 14:43:54 GMT

Checking `nipype` installation¶

There are number of ways to check its installation as shown below.

In [2]:

import nipype; print(nipype.__version__)

1.5.0

In [1]:

import nipype; nipype.test()

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/__init__.py in __call__(self, doctests, parallel)
     36         try:
---> 37             import pytest
     38         except ImportError:

ModuleNotFoundError: No module named 'pytest'

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
<ipython-input-1-bac8365228b1> in <module>
----> 1 import nipype; nipype.test()

~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/__init__.py in __call__(self, doctests, parallel)
     37             import pytest
     38         except ImportError:
---> 39             raise RuntimeError("py.test not installed, run: pip install pytest")
     40         args = []
     41         if not doctests:

RuntimeError: py.test not installed, run: pip install pytest

The above simply says that pytest is not installed and using the pip install it.
Installed pytest using pip install pytest and run the text again. When test is run it gives the following error.
Docs: https://docs.pytest.org/en/latest/warnings.html ======================================================== short test summary info ========================================================= ERROR ../../../../anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/documenter.py - ModuleNotFoundError: No module nam... ERROR ../../../../anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/apidoc/init.py - ModuleNotFoundError: No modul... ERROR ../../../../anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/apidoc/docstring.py - ModuleNotFoundError: No modu... !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 3 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ===================================================== 9 warnings, 3 errors in 57.98s =====================================================
The error above is related to the Sphinix package which comes with nipype. We wil see it later.

In [3]:

import nipype as ny
ny.get_info()

Out[3]:

{'pkg_path': '/home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype',
 'commit_source': 'archive substitution',
 'commit_hash': '%h',
 'nipype_version': '1.5.0',
 'sys_version': '3.8.2 | packaged by conda-forge | (default, Apr 24 2020, 08:20:52) \n[GCC 7.3.0]',
 'sys_executable': '/home/sayyed/anaconda3/envs/nipype/bin/python',
 'sys_platform': 'linux',
 'numpy_version': '1.18.5',
 'scipy_version': '1.5.0',
 'networkx_version': '2.4',
 'nibabel_version': '3.1.1',
 'traits_version': '6.1.0'}

Testing the installation¶

In [3]:

import nipype; nipype.test()

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/__init__.py in __call__(self, doctests, parallel)
     36         try:
---> 37             import pytest
     38         except ImportError:

ModuleNotFoundError: No module named 'pytest'

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
<ipython-input-3-bac8365228b1> in <module>
----> 1 import nipype; nipype.test()

~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/__init__.py in __call__(self, doctests, parallel)
     37             import pytest
     38         except ImportError:
---> 39             raise RuntimeError("py.test not installed, run: pip install pytest")
     40         args = []
     41         if not doctests:

RuntimeError: py.test not installed, run: pip install pytest

In [ ]:

1. I installed `pytest` using `pip install pytest` it rand the test and filed on `Sphinix extension`.
2. When tried to import `nilearn` it also threw an error of not finding this package.

In [4]:

import nipype; nipype.test()

============================= test session starts ==============================
platform linux -- Python 3.8.2, pytest-5.4.3, py-1.9.0, pluggy-0.13.1
rootdir: /home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype, inifile: pytest.ini
collected 2885 items / 2 errors / 2883 selected

==================================== ERRORS ====================================
________________ ERROR collecting sphinxext/apidoc/__init__.py _________________
/home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/apidoc/__init__.py:5: in <module>
    from sphinxcontrib.napoleon import (
E   ModuleNotFoundError: No module named 'sphinxcontrib.napoleon'
________________ ERROR collecting sphinxext/apidoc/docstring.py ________________
/home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/py/_path/local.py:704: in pyimport
    __import__(modname)
/home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/apidoc/__init__.py:5: in <module>
    from sphinxcontrib.napoleon import (
E   ModuleNotFoundError: No module named 'sphinxcontrib.napoleon'
=========================== short test summary info ============================
ERROR ../../../../../anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/apidoc/__init__.py
ERROR ../../../../../anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/sphinxext/apidoc/docstring.py
!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!
============================== 2 errors in 17.92s ==============================

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-4-bac8365228b1> in <module>
----> 1 import nipype; nipype.test()

~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/__init__.py in __call__(self, doctests, parallel)
     48             args.append("-n auto")
     49         args.append(os.path.dirname(__file__))
---> 50         pytest.main(args=args)
     51 
     52 

~/anaconda3/envs/nipype/lib/python3.8/site-packages/_pytest/config/__init__.py in main(args, plugins)
    122         else:
    123             try:
--> 124                 ret = config.hook.pytest_cmdline_main(
    125                     config=config
    126                 )  # type: Union[ExitCode, int]

~/anaconda3/envs/nipype/lib/python3.8/site-packages/pluggy/hooks.py in __call__(self, *args, **kwargs)
    284                     stacklevel=2,
    285                 )
--> 286         return self._hookexec(self, self.get_hookimpls(), kwargs)
    287 
    288     def call_historic(self, result_callback=None, kwargs=None, proc=None):

~/anaconda3/envs/nipype/lib/python3.8/site-packages/pluggy/manager.py in _hookexec(self, hook, methods, kwargs)
     91         # called from all hookcaller instances.
     92         # enable_tracing will set its own wrapping function at self._inner_hookexec
---> 93         return self._inner_hookexec(hook, methods, kwargs)
     94 
     95     def register(self, plugin, name=None):

~/anaconda3/envs/nipype/lib/python3.8/site-packages/pluggy/manager.py in <lambda>(hook, methods, kwargs)
     82             )
     83         self._implprefix = implprefix
---> 84         self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
     85             methods,
     86             kwargs,

    [... skipping hidden 3 frame]

~/anaconda3/envs/nipype/lib/python3.8/site-packages/_pytest/main.py in pytest_cmdline_main(config)
    238 
    239 def pytest_cmdline_main(config):
--> 240     return wrap_session(config, _main)
    241 
    242 

~/anaconda3/envs/nipype/lib/python3.8/site-packages/_pytest/main.py in wrap_session(config, doit)
    233                     session.exitstatus = exc.returncode
    234                 sys.stderr.write("{}: {}\n".format(type(exc).__name__, exc))
--> 235         config._ensure_unconfigure()
    236     return session.exitstatus
    237 

~/anaconda3/envs/nipype/lib/python3.8/site-packages/_pytest/config/__init__.py in _ensure_unconfigure(self)
    823         if self._configured:
    824             self._configured = False
--> 825             self.hook.pytest_unconfigure(config=self)
    826             self.hook.pytest_configure._call_history = []
    827         while self._cleanup:

~/anaconda3/envs/nipype/lib/python3.8/site-packages/pluggy/hooks.py in __call__(self, *args, **kwargs)
    284                     stacklevel=2,
    285                 )
--> 286         return self._hookexec(self, self.get_hookimpls(), kwargs)
    287 
    288     def call_historic(self, result_callback=None, kwargs=None, proc=None):

~/anaconda3/envs/nipype/lib/python3.8/site-packages/pluggy/manager.py in _hookexec(self, hook, methods, kwargs)
     91         # called from all hookcaller instances.
     92         # enable_tracing will set its own wrapping function at self._inner_hookexec
---> 93         return self._inner_hookexec(hook, methods, kwargs)
     94 
     95     def register(self, plugin, name=None):

~/anaconda3/envs/nipype/lib/python3.8/site-packages/pluggy/manager.py in <lambda>(hook, methods, kwargs)
     82             )
     83         self._implprefix = implprefix
---> 84         self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
     85             methods,
     86             kwargs,

    [... skipping hidden 3 frame]

~/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/conftest.py in pytest_unconfigure(config)
     42 def pytest_unconfigure(config):
     43     # Delete temp folder after session is finished
---> 44     shutil.rmtree(temp_folder)

~/anaconda3/envs/nipype/lib/python3.8/shutil.py in rmtree(path, ignore_errors, onerror)
    704             orig_st = os.lstat(path)
    705         except Exception:
--> 706             onerror(os.lstat, path, sys.exc_info())
    707             return
    708         try:

~/anaconda3/envs/nipype/lib/python3.8/shutil.py in rmtree(path, ignore_errors, onerror)
    702         # lstat()/open()/fstat() trick.
    703         try:
--> 704             orig_st = os.lstat(path)
    705         except Exception:
    706             onerror(os.lstat, path, sys.exc_info())

FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpqoloi4y8'

In [2]:

# Import the nipype module
import nipype
# Optional: Use the following lines to increase verbosity of output
nipype.config.set('logging', 'workflow_level', 'CRITICAL')
nipype.config.set('logging', 'interface_level', 'CRITICAL')
nipype.logging.update_logging(nipype.config)
# Run the test: Increase verbosity parameter for more info
nipype.test()

ERROR: usage: ipykernel_launcher.py [options] [file_or_dir] [file_or_dir] [...]
ipykernel_launcher.py: error: unrecognized arguments: --doctest-modules
  inifile: /home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype/pytest.ini
  rootdir: /home/sayyed/anaconda3/envs/nipype/lib/python3.8/site-packages/nipype

In [ ]:

Sayyed's blog (Posts about jupyter)

001_intro

Jupyter note book basics¶

Running code from different kernel¶

This is html 4 heading

Checking-nipype-Installation

Checking nipype installation¶

Testing the installation¶

Checking `nipype` installation¶