release 0.3 (#86)

* Adding release 0.3

* Fixing unit tests

* Try fix intersphinx

* Update mne_connectivity/tests/test_connectivity.py

Makefile

@@ -3,7 +3,7 @@
 # caution: testing won't work on windows, see README
 
 PYTHON ?= python
-PYTESTS ?= py.test
+PYTESTS ?= pytest
 CTAGS ?= ctags
 CODESPELL_SKIPS ?= "*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,plot_*.rst,*.rst.txt,*.html,gdf_encodes.txt"
 CODESPELL_DIRS ?= mne_connectivity/ doc/ examples/

doc/conf.py

@@ -220,7 +220,7 @@
     'mne-bids': ('https://mne.tools/mne-bids/dev/', None),
     'numpy': ('https://numpy.org/devdocs', None),
     'scipy': ('https://scipy.github.io/devdocs', None),
-    'matplotlib': ('https://matplotlib.org', None),
+    'matplotlib': ('https://matplotlib.org/stable', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/dev', None),
     'sklearn': ('https://scikit-learn.org/stable', None),
     'pyvista': ('https://docs.pyvista.org', None),

doc/install.rst

@@ -48,7 +48,7 @@ If you want to install a snapshot of the current development version, run:
 
 .. code-block:: bash
 
-   pip install --user -U https://api.github.com/repos/mne-tools/mne-connectivity/zipball/master
+   pip install --user -U https://api.github.com/repos/mne-tools/mne-connectivity/zipball/main
 
 To check if everything worked fine, the following command should not give any
 error messages:

doc/whats_new.rst

@@ -16,42 +16,30 @@ Here we list a changelog of MNE-connectivity.
 
 .. _current:
 
-Version 0.3 (Unreleased)
+Version 0.4 (Unreleased)
 ------------------------
 
 ...
 
 Enhancements
 ~~~~~~~~~~~~
 
-- Adding symmetric orthogonalization via :func:`mne_connectivity.symmetric_orth`, by `Eric Larson`_ (:gh:`36`)
-- Improved RAM usage for :func:`mne_connectivity.vector_auto_regression` by leveraging code from ``statsmodels``, by `Adam Li`_ (:gh:`46`)
-- Added :func:`mne_connectivity.select_order` for helping to select VAR order using information criterion, by `Adam Li`_ (:gh:`46`)
-- All connectivity functions retain ``events``, ``event_id`` and ``metadata`` from `mne.Epochs` objects as input and is stored as part of the connectivity object, by `Adam Li`_ (:gh:`58`)
-- Add spectral connectivity over time function :func:`mne_connectivity.spectral_connectivity_time`, by `Adam Li`_ (:gh:`67`)
-- Add conda installation, by `Adam Li`_ and `Richard Höchenberger`_ (:gh:`81`)
+-
 
 Bug
 ~~~
 
-- Fixed bug when saving connectivity with ``n_jobs`` greater than 1 from :func:`mne_connectivity.spectral_connectivity_epochs`, by `Adam Li`_ (:gh:`43`)
-- Fixed bug to allow saving complex data connectivity, by `Adam Li`_ (:gh:`43`)
-- Fixed bug to keep label orientation upright in :func:`mne_connectivity.viz.plot_connectivity_circle`, by `Alexander Kroner`_ (:gh:`60`)
+-
 
 API
 ~~~
 
-- Added ``h5netcdf`` as a requirement for saving connectivity data, by `Adam Li`_ (:gh:`43`)
-- Changed keyword argument ``model_order`` in :func:`mne_connectivity.vector_auto_regression` to ``lags`` to more align with statsmodels API, by `Adam Li`_ (:gh:`47`)
-- Add ``pandas`` as a requirement for dealing with metadata associated from the original Epochs file, by `Adam Li`_ (:gh:`58`)
-- Rename ``mne_connectivity.spectral_connectivity`` to :func:`mne_connectivity.spectral_connectivity_epochs`, by `Adam Li`_ (:gh:`69`)
+- 
 
 Authors
 ~~~~~~~
 
-* `Adam Li`_
-* `Eric Larson`_
-* `Alexander Kroner`_
+
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`
 

doc/whats_new_previous_releases.rst

@@ -7,6 +7,48 @@
 What was new in previous releases?
 ==================================
 
+Version 0.3 (2022-03-01)
+------------------------
+
+This version has bug fixes minor improvements in certain functions. A big change
+is the renaming of functions ``spectral_connectivity`` to ``spectral_connectivity_epochs``,
+which makes it explicit that the function operates over Epochs, rather then time.
+Importantly, we also provide a conda installation now.
+
+Enhancements
+~~~~~~~~~~~~
+
+- Adding symmetric orthogonalization via :func:`mne_connectivity.symmetric_orth`, by `Eric Larson`_ (:gh:`36`)
+- Improved RAM usage for :func:`mne_connectivity.vector_auto_regression` by leveraging code from ``statsmodels``, by `Adam Li`_ (:gh:`46`)
+- Added :func:`mne_connectivity.select_order` for helping to select VAR order using information criterion, by `Adam Li`_ (:gh:`46`)
+- All connectivity functions retain ``events``, ``event_id`` and ``metadata`` from `mne.Epochs` objects as input and is stored as part of the connectivity object, by `Adam Li`_ (:gh:`58`)
+- Add spectral connectivity over time function :func:`mne_connectivity.spectral_connectivity_time`, by `Adam Li`_ (:gh:`67`)
+- Add conda installation, by `Adam Li`_ and `Richard Höchenberger`_ (:gh:`81`)
+
+Bug
+~~~
+
+- Fixed bug when saving connectivity with ``n_jobs`` greater than 1 from :func:`mne_connectivity.spectral_connectivity_epochs`, by `Adam Li`_ (:gh:`43`)
+- Fixed bug to allow saving complex data connectivity, by `Adam Li`_ (:gh:`43`)
+- Fixed bug to keep label orientation upright in :func:`mne_connectivity.viz.plot_connectivity_circle`, by `Alexander Kroner`_ (:gh:`60`)
+
+API
+~~~
+
+- Added ``h5netcdf`` as a requirement for saving connectivity data, by `Adam Li`_ (:gh:`43`)
+- Changed keyword argument ``model_order`` in :func:`mne_connectivity.vector_auto_regression` to ``lags`` to more align with statsmodels API, by `Adam Li`_ (:gh:`47`)
+- Add ``pandas`` as a requirement for dealing with metadata associated from the original Epochs file, by `Adam Li`_ (:gh:`58`)
+- Rename ``mne_connectivity.spectral_connectivity`` to :func:`mne_connectivity.spectral_connectivity_epochs`, by `Adam Li`_ (:gh:`69`)
+
+Authors
+~~~~~~~
+People who contributed to this release (in alphabetical order):
+
+* `Adam Li`_
+* `Alexander Kroner`_
+* `Eric Larson`_
+* `Richard Höchenberger`_
+
 .. _changes_0_2:
 
 Version 0.2 (2021-09-07)

mne_connectivity/__init__.py

@@ -6,7 +6,7 @@
 #
 # License: BSD (3-clause)
 
-__version__ = '0.3dev0'
+__version__ = '0.3'
 
 from .base import (Connectivity, EpochConnectivity, EpochSpectralConnectivity,
                    EpochSpectroTemporalConnectivity, EpochTemporalConnectivity,

mne_connectivity/io.py

@@ -44,8 +44,8 @@ def _xarray_to_conn(array, cls_func):
     metadata = _prepare_read_metadata(metadata)
 
     # write event IDs
-    event_id_keys = array.attrs.pop('event_id_keys')
-    event_id_vals = array.attrs.pop('event_id_vals')
+    event_id_keys = np.atleast_1d(array.attrs.pop('event_id_keys')).tolist()
+    event_id_vals = np.atleast_1d(array.attrs.pop('event_id_vals')).tolist()
     event_id = {key: val for key, val in zip(event_id_keys, event_id_vals)}
     array.attrs['event_id'] = event_id