Reduced dependencies and added `check_packages` decorator

[jolespin]

I forked https://github.com/wiheto/teneto and added that to my GitHub. After that I adjusted files that loaded bids, nilearn, and templateflow.

There were more files that I needed to adjust than ones in utils as shown below. Any function using one of those packages I had to add check_packages decorator or else there will be an import error.

# Version: 0.5.2-dev-c
(base) jespinozlt2-osx:teneto jespinoz$ grep -E -r "nilearn|templateflow|bids" teneto/ | grep ".py"
teneto//timeseries/remove_confounds.py:import nilearn
teneto//timeseries/remove_confounds.py:    Removes specified confounds using nilearn.signal.clean
teneto//timeseries/remove_confounds.py:        Dictionary of kawgs to pass to nilearn.signal.clean
teneto//timeseries/remove_confounds.py:    # nilearn works with time,node data
teneto//timeseries/remove_confounds.py:    cleaned_timeseries = nilearn.signal.clean(
teneto//classes/bids.py:import bids
teneto//classes/bids.py:# @check_neuro_packages(bids)
teneto//classes/bids.py:    bids_dir : str
teneto//classes/bids.py:        the directory that is in the bids_dir/derivatives/<selected_pipeline>/.
teneto//classes/bids.py:        With this, the input for netin with be from bids_dir/derivatives/[teneto-]tvc/,
teneto//classes/bids.py:        and the input for communities will be from bids_dir/derivatives/[teneto-]coms/.
teneto//classes/bids.py:    bids_filter : dict
teneto//classes/bids.py:    def __init__(self, bids_dir, selected_pipeline, bids_filter=None, bidsvalidator=False,
teneto//classes/bids.py:            self.BIDSLayout = bids.BIDSLayout(bids_dir, derivatives=True)
teneto//classes/bids.py:        self.bids_dir = bids_dir
teneto//classes/bids.py:        if bids_filter is None:
teneto//classes/bids.py:            self.bids_filter = {}
teneto//classes/bids.py:            self.bids_filter = bids_filter
teneto//classes/bids.py:        with open(tenetopath[0] + '/config/tenetobids/tenetobids_description.json') as f:
teneto//classes/bids.py:            self.tenetobids_description = json.load(f)
teneto//classes/bids.py:        self.tenetobids_description['PipelineDescription']['Version'] = tenetoversion
teneto//classes/bids.py:        with open(tenetopath[0] + '/config/tenetobids/tenetobids_structure.json') as f:
teneto//classes/bids.py:            self.tenetobids_structure = json.load(f)
teneto//classes/bids.py:    #    bids.
teneto//classes/bids.py:    def update_bids_layout(self):
teneto//classes/bids.py:        self.BIDSLayout = bids.BIDSLayout(self.bids_dir, derivatives=True)
teneto//classes/bids.py:            bids_dir/teneto-[output_pipeline]/
teneto//classes/bids.py:        output_pipeline_path = self.bids_dir + '/derivatives/' + output_pipeline
teneto//classes/bids.py:        datainfo = self.tenetobids_description.copy()
teneto//classes/bids.py:        self.update_bids_layout()
teneto//classes/bids.py:    def run(self, run_func, input_params, output_desc=None, output_pipeline_name=None, bids_filter=None, update_pipeline=True, exist_ok=None):
teneto//classes/bids.py:            For any other input that needs to be loaded loaded within the teneto_bidsstructure (communities, events, confounds),
teneto//classes/bids.py:            you can pass the value "bids" if they can be found within the current selected_pipeline.
teneto//classes/bids.py:            If they are found within a different selected_pipeline, type "bids_[selected_pipeline]".
teneto//classes/bids.py:        for f in self.tenetobids_structure[run_func]['module'].split('.'):
teneto//classes/bids.py:        functype = self.tenetobids_structure[run_func]['functype']
teneto//classes/bids.py:                        self.tenetobids_structure[run_func.split('.')[-1]]['output'])
teneto//classes/bids.py:                    save_path = self.bids_dir + '/derivatives/' + output_pipeline
teneto//classes/bids.py:                    # Probably should check the output type in tenetobidsstructure
teneto//classes/bids.py:            # Create new bids_filter dictionary that only contains sub/ses/run/task as other tags are dropped.
teneto//classes/bids.py:            bids_filter = dict(self.bids_filter)
teneto//classes/bids.py:            self.bids_filter = {}
teneto//classes/bids.py:            bids_filters_allowed = ['subject', 'ses', 'run', 'task']
teneto//classes/bids.py:            [self.update_bids_filter({'f': bids_filter[f]}) for f in bids_filters_allowed if f in bids_filter.keys()]
teneto//classes/bids.py:        self.update_bids_layout()
teneto//classes/bids.py:        Uses information in selected_pipeline and the bids layout and shows the files that will be processed when calling TenetoBIDS.run().
teneto//classes/bids.py:            filters = self.tenetobids_structure[output]['input']
teneto//classes/bids.py:        filters.update(self.bids_filter)
teneto//classes/bids.py:        funcs = self.tenetobids_structure.keys()
teneto//classes/bids.py:                s = self.tenetobids_structure[t]['input']['suffix']
teneto//classes/bids.py:    def update_bids_filter(self, filter_addons):
teneto//classes/bids.py:        """Updates TenetoBIDS.bids_filter
teneto//classes/bids.py:            dictionary that updates TenetoBIDS.bids_filter
teneto//classes/bids.py:        self.bids_filter.update(filter_addons)
teneto//classes/bids.py:    def get_confounds(self, bidsfile, confound_filters=None):
teneto//classes/bids.py:        bidsfile : BIDSDataFile or BIDSImageFile
teneto//classes/bids.py:        file_entities = bidsfile.get_entities()
teneto//classes/bids.py:    def load_data(self, bids_filter=None):
teneto//classes/bids.py:        bids_filter : dict
teneto//classes/bids.py:            default is None. If set, load data will load all files found by the bids_filter.
teneto//classes/bids.py:        if bids_filter is None:
teneto//classes/bids.py:            filters = dict(self.bids_filter)
teneto//classes/bids.py:            filters.update(bids_filter)
teneto//classes/bids.py:    def load_file(self, bidsfile):
teneto//classes/bids.py:        bidsfile : BIDSDataFile or BIDSImageFile
teneto//classes/bids.py:        sidecar = get_sidecar(bidsfile.dirname + '/' + bidsfile.filename)
teneto//classes/bids.py:            if hasattr(bidsfile, 'get_image'):
teneto//classes/bids.py:                data = bidsfile.get_image()
teneto//classes/bids.py:            elif hasattr(bidsfile, 'get_df'):
teneto//classes/bids.py:                # This can be changed if/when pybids is updated. Assumes index_col=0 in tsv file
teneto//classes/bids.py:                    bidsfile.dirname + '/' + bidsfile.filename)
teneto//classes/__init__.py:from .bids import TenetoBIDS
teneto//neuroimagingtools/fmriutils.py:import templateflow.api as tf
teneto//neuroimagingtools/fmriutils.py:from nilearn.input_data import NiftiLabelsMasker
teneto//neuroimagingtools/fmriutils.py:from .bidsutils import load_tabular_file
teneto//neuroimagingtools/fmriutils.py:        Specify which atlas you want to use (see github.com/templateflow/)
teneto//neuroimagingtools/fmriutils.py:        **kwargs for nilearn functions.
teneto//neuroimagingtools/fmriutils.py:    These functions make use of nilearn. Please cite templateflow and nilearn if used in a publicaiton.
teneto//neuroimagingtools/fmriutils.py:                         Run: templateflow.api.TF_LAYOUT.get_descs(atlas=' +
teneto//neuroimagingtools/bidsutils.py:def drop_bids_suffix(fname):
teneto//neuroimagingtools/__init__.py:from .bidsutils import drop_bids_suffix, \
teneto//neuroimagingtools/__init__.py:__all__ = ['make_parcellation', 'drop_bids_suffix',

I also adjusted the setup.py:

"""General setup for module."""

from setuptools import setup, find_packages

VERSION = "teneto/_version.py"
VERSION = open(VERSION, "rt").read()
VERSION = VERSION.split('"')[1]

setup(name='teneto',
      version=VERSION,
      python_requires='>3.5',
      setup_requires=['pytest-runner'],
      tests_require=['pytest'],
      install_requires=[
          ## Required
          'statsmodels>=0.8.0',
          'networkx>=2.0',
          'python-louvain>=0.13',
          'pandas>=0.21',
          'scipy>=1.4.1',
          'numpy>=1.16.1',
          "matplotlib >=3.1",
          ## Optional for neural
          #'nilearn>=0.6.0',
          #'pybids>=0.9',
          #'templateflow>=0.4.1',
          ],
      description='Temporal network tools',
      packages=find_packages(),
      author='William Hedley Thompson',
      author_email='hedley@startmail.com',
      url='https://www.github.com/wiheto/teneto',
      download_url='https://github.com/wiheto/teneto/archive/0.3.3.tar.gz',
      package_data={'': ['./teneto/data']},
      include_package_data=True,
      entry_points={
          'console_scripts': ['teneto = teneto.__main__:main']
      },
      long_description='Temporal network tools. \
        A package for deriving, analysing and plotting temporal network representations. \
        Additional tools for temporal network analysis with neuroimaging contexts.')

and requirements.txt

scipy>=1.4.1
numpy>=1.16.1
#scikit-learn>=0.20.3
#seaborn==0.8.1
matplotlib>=3.1.0
pandas>=0.21
#python-igraph>=0.7.1
#louvain >= 0.6.1
statsmodels>=0.8.0
networkx>=2.0
python-louvain>=0.13
#tables>=3.4.4
#scikit-optimize>=0.5.2
#pybids==0.9.5
#nilearn>=0.6.1
#templateflow>=0.4.1rc5

[wiheto]

All looks good. I'll merge this soon cause there is a couple of things I need to add regarding documentation and Travis CI installing all the neuropackages.

Thanks for this!

[jolespin]

Awesome! Thanks for proceeding with this. I'll need to look at Travis CI documentation as I'm quite new to PR requests on GitHub. This is one of my firsts.

[wiheto]

I’ll do the next step very very soon and this will be accepted. You don’t need to do anything more here at all. But to explain what I need to do (if you are curious): travis uses the requirements.txt to install the software and run the tests. So the settings file (.travis.cli) file needs a to be told to install the additional requirements, otherwise tests will fail cause the software for the neuro tests is missing. It’s a very small thing to fix, but that’s basically it.

There’s a few other things I want to check as well, such as the dockerfile. All minor things.

Congratulations on one of your first PRs! Happy that you contributed to teneto.

29 maj 2020 kl. 16:19 skrev Josh L. Espinoza notifications@github.com:

 Awesome! Thanks for proceeding with this. I'll need to look at Travis CI documentation as I'm quite new to PR requests on GitHub. This is one of my firsts.

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[wiheto]

Ok, LGTM. Thanks for contributing! One thing I need to fix soon is a way to add all contributors to the zenodo DOI. I'll send you a message sometime in the near future about this.

[wiheto]

I'm sorry but all these changes have been removed the neuro requirements are going to be kept for some time. As it stood, the PR did not import the packages correctly into globals and all tests using these packages were broken. If you can fix this, I'll be happy to include it, but until then, I'm removing the functionality and the three neuropackages will remain in the requirements.