Merge pull request #171 from esi-neuroscience/coherence

Coherence, big one

.coveragerc

@@ -0,0 +1,16 @@
+[run]
+branch = True
+source = syncopy
+
+[report]
+exclude_lines =
+    if self.debug:
+    if debug:
+    raise NotImplementedError
+    if __name__ == .__main__.:
+ignore_errors = True
+omit =
+    syncopy/tests/*
+    *conda2pip.py
+    *setup.py
+    test_*

.gitignore

@@ -69,3 +69,6 @@ requirements-test.txt
 
 # Editor-related stuff
 .vscode
+
+# Mac OS related stuff
+.DS_Store

.travis.yml

@@ -4,7 +4,6 @@ python:
 
 cache: pip
 
-# safelist
 branches:
   only:
   - master
@@ -16,6 +15,9 @@ install:
   - pip install -r requirements.txt
   - pip install -r requirements-test.txt
   - python setup.py -q install
-# command to run tests
+
 script:
-  - pytest -v
+  - pytest -v --cov=./
+
+after_success:
+  - bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports"

codecov.yml

@@ -0,0 +1,14 @@
+coverage:
+  status:
+    project:
+      default:
+        # Allow coverage to drop `threshold` percent in PRs to master/dev
+        target: auto
+        threshold: 5%
+        base: auto
+        branches:
+          - master
+          - dev
+        if_ci_failed: error #success, failure, error, ignore
+        informational: false
+        only_pulls: true

dev_frontend.py

@@ -0,0 +1,62 @@
+import numpy as np
+import scipy.signal as sci
+
+from syncopy.datatype import CrossSpectralData, padding, SpectralData, AnalogData
+from syncopy.connectivity.ST_compRoutines import cross_spectra_cF, ST_CrossSpectra
+from syncopy.connectivity.ST_compRoutines import cross_covariance_cF
+from syncopy.connectivity import connectivity
+from syncopy.specest import freqanalysis
+import matplotlib.pyplot as ppl
+
+from syncopy.shared.parsers import data_parser, scalar_parser, array_parser
+from syncopy.shared.tools import get_defaults
+from syncopy.datatype import SpectralData, padding
+
+from syncopy.tests.misc import generate_artificial_data
+tdat = generate_artificial_data(inmemory=True, seed=1230, nTrials=50, nChannels=5)
+
+foilim = [1, 30]
+# this still gives type(tsel) = slice :)
+sdict1 = {"trials": [0], 'channels' : ['channel1'], 'toi': np.arange(-1, 1, 0.001)}
+
+coherence = connectivity(data=tdat,
+                         foilim=None,
+                         output='pow',
+                         taper='dpss',
+                         tapsmofrq=5,
+                         foo = 3, # non-sensical 
+                         keeptrials=False)
+
+granger = connectivity(data=tdat,
+                       method='granger',
+                       foilim=[0, 50],
+                       output='pow',
+                       taper='dpss',
+                       tapsmofrq=5,                                 
+                       keeptrials=False)
+
+# D = SpectralData(dimord=['freq','test1','test2','taper'])
+# D2 = AnalogData(dimord=['freq','test1'])
+
+# a lot of problems here..
+# correlation = connectivity(data=tdat, method='corr', keeptrials=False, taper='df')
+
+
+# the hard wired dimord of the cF
+
+res = freqanalysis(data=tdat,
+                   method='mtmfft',
+                   samplerate=tdat.samplerate,
+#                   order_max=20,
+#                   foilim=foilim,
+#                   foi=np.arange(502),
+                   output='pow',
+#                   polyremoval=1,
+                   t_ftimwin=0.5,
+                   keeptrials=True,
+                   taper='dpss',
+                   nTaper = 19,
+                   tapsmofrq=5,
+                   keeptapers=True,
+                   parallel=False, # try this!!!!!!
+                   select={"trials" : [0,1]})

doc/source/user/data_handling.rst

@@ -22,19 +22,20 @@ Reading and writing data with Syncopy
     syncopy.load
     syncopy.save
 
-Functions for Editing Syncopy Data Objects
--------------------------------------------
-Defining trials, data selection and padding. 
+Functions for Inspecting/Editing Syncopy Data Objects
+-----------------------------------------------------
+Defining trials, data selection and padding.
 
 .. autosummary::
 
     syncopy.definetrial
+    syncopy.show
     syncopy.selectdata
     syncopy.padding
 
 Advanced Topics
 ---------------
-More information about Syncopy's data class structure and file format. 
+More information about Syncopy's data class structure and file format.
 
 .. toctree::
 

syncopy.yml

@@ -7,7 +7,7 @@ dependencies:
   - python >= 3.8, < 3.9
   - pip
   - numpy >= 1.10, < 2.0
-  - scipy >= 1.5, < 1.6
+  - scipy >= 1.5
   - h5py >= 2.9, < 3
   - matplotlib >= 3.3, < 3.5
   - tqdm >= 4.31
@@ -18,7 +18,7 @@ dependencies:
   - memory_profiler
   - numpydoc
   - sphinx_bootstrap_theme
-  - pytest
+  - pytest-cov
   - pylint
   - ipdb
   - tox