Merge pull request #67 from wiheto/develop

0.5.2_prerelease

.travis.yml

@@ -2,12 +2,14 @@ language: python
 dist: xenial
 python:
   - "3.6"
-  - "3.6-dev"  # 3.6 development branch
+  - "3.8-dev"  # 3.6 development branch
+  - "3.7"
+  - "3.8"
 # command to install dependencies
 install:
   - pip install -r requirements.txt
   - python setup.py install
-  - pip install python-coveralls
+  - pip install coveralls
   - pip install pytest
   - pip install pytest-cov
   - sudo apt-get -y install python3-pyqt5

CHANGELOG.md

@@ -1,6 +1,26 @@
 # Changelog
 
-## V0.5.1
+## Version 0.5.2 (In development)
+
+### 0.5.2 Improvements
+
+Improved sidecar checking.
+
+Added is_jsonable to utils.
+
+### 0.5.2 Fixes
+
+Fixes the issues when shortest paths were trying to be derived on non existent time points (raised in #60)
+
+Fixing problem with df_to_array when time indices do not start at 0.
+
+Fixing problem with dataframe netshape when starttime !=0 (#61)
+
+coveralls resynced with travis (pip install python-coveralls replaced with pip install coveralls)
+
+### 0.5.2 Changes
+
+Removing wrong cased variables (e.g. netIN and TN from utils)
 
 ## Version 0.5.1
 

setup.py

@@ -2,12 +2,12 @@
 
 from setuptools import setup, find_packages
 
-version = "teneto/_version.py"
-verstrline = open(version, "rt").read()
-version = verstrline.split('"')[1]
+VERSION = "teneto/_version.py"
+VERSION = open(VERSION, "rt").read()
+VERSION = VERSION.split('"')[1]
 
 setup(name='teneto',
-      version=version,
+      version=VERSION,
       python_requires='>3.5',
       setup_requires=['pytest-runner'],
       tests_require=['pytest'],
@@ -30,10 +30,8 @@
       package_data={'': ['./teneto/data']},
       include_package_data=True,
       entry_points={
-          'console_scripts': ['teneto = teneto.__main__:main'
-                              ]
+          '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.'
-      )
+        Additional tools for temporal network analysis with neuroimaging contexts.')

teneto/__init__.py

@@ -6,8 +6,8 @@
 __author__ = "WHT (wiheto @ github)"
 #
 from ._version import __version__
+from .classes import TenetoBIDS, TemporalNetwork, TenetoWorkflow
 from . import networkmeasures
-from . import utils
 from . import plot
 from . import generatenetwork
 from . import timeseries
@@ -17,7 +17,7 @@
 from . import communitymeasures
 from . import communitydetection
 from . import neuroimagingtools
-from .classes import TenetoBIDS, TemporalNetwork, TenetoWorkflow
+from . import utils
 #del misc.teneto
 #del communitydetection.static.modularity_based_clustering
 __all__ = ['__version__', 'utils', 'networkmeasures', 'plot', 'generatenetwork',

teneto/_version.py

@@ -1 +1 @@
-__version__ = "0.5.1"
+__version__ = "0.5.2-dev-c"

teneto/classes/bids.py

@@ -1,17 +1,17 @@
-"""TenetoBIDS is a class which can be used to use Teneto functions with data organized with BIDS (neuroimaging data)."""
+"""TenetoBIDS is a class to use Teneto functions with data organized with BIDS (neuroimaging data)."""
 import os
-import bids
-import numpy as np
 import inspect
 import json
-from ..neuroimagingtools import load_tabular_file, get_sidecar
+import bids
+import importlib
+import numpy as np
 import pandas as pd
+from .. import __path__ as tenetopath
+from .. import __version__ as tenetoversion
+from ..neuroimagingtools import load_tabular_file, get_sidecar
 from .network import TemporalNetwork
-from teneto import __path__ as tenetopath
-from teneto import __version__ as tenetoversion
-import teneto
-
 
+# @check_neuro_packages(bids)
 class TenetoBIDS:
     """
     Class for analysing data in BIDS.
@@ -141,7 +141,9 @@ def run(self, run_func, input_params, output_desc=None, output_pipeline_name=Non
         """
         if exist_ok is not None:
             self.exist_ok = exist_ok
-
+        # Import teneto if it has not been already
+        if 'teneto' not in globals():
+            teneto = importlib.import_module('teneto')
         func = teneto
         for f in self.tenetobids_structure[run_func]['module'].split('.'):
             func = getattr(func, f)
@@ -244,16 +246,21 @@ def run(self, run_func, input_params, output_desc=None, output_pipeline_name=Non
                         input_params['confounds'] = 'Passed as argument'
                     if 'sidecar' in input_params:
                         input_params['sidecar'] = 'Loaded automatically via TenetoBIDS'
-                    sidecar['TenetoFunction']['Parameters'] = input_params
+                    # Loop through input params content and make any nparray input to list for sidecar
+                    sidecar['TenetoFunction']['Parameters'] = {}
+                    for key, value in input_params.items():
+                        if not teneto.utils.is_jsonable(value):
+                            if isinstance(input_params[key], np.ndarray):
+                                sidecar['TenetoFunction']['Parameters'][key] = input_params[key].tolist()
+                            else:
+                                print('Warning: Dropping input (' + key + ') from sidecar (not JSONable).')
+                        else:
+                            sidecar['TenetoFunction']['Parameters'][key] = input_params[key]
                 elif functype == 'on_sidecar':
                     sidecar = func(**input_params)
                     update_pipeline = False
                     save_path = f.dirname + '/'
                     save_name = f.filename
-                # Loop through sidecar content and make any nparray input to list
-                for n in sidecar.keys():
-                    if isinstance(sidecar[n], np.ndarray):
-                        sidecar[n] = sidecar[n].tolist()
                 # Save sidecar
                 with open(save_path + save_name.replace('.tsv', '.json'), 'w') as f:
                     json.dump(sidecar, f)
@@ -318,7 +325,7 @@ def get_run_options(self, for_selected=True):
                 for su in suffix:
                     if su in s:
                         funcs_filter.append(t)
-            funcs = list(set(funcs_filter))
+            funcs = sorted(list(set(funcs_filter)))
         return ', '.join(funcs)
 
     def update_bids_filter(self, filter_addons):