[MRG] Adding release for 0.2. (#44)

* Adding release for 0.2. * Fixing tutorial. * Fixing tutorial. * Fixing docs. * Adding updated setup. * Fixed index. Co-authored-by: Adam Li <[email protected]> Co-authored-by: Adam Li <[email protected]>
mne-tools · Jun 7, 2021 · 7fb5ccb · 7fb5ccb
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diff --git a/Makefile b/Makefile
@@ -21,7 +21,6 @@ clean-build:
 
 clean-ctags:
 	rm -f tags
-	rm junit-results.xml
 
 clean: clean-build clean-so clean-ctags
 

diff --git a/Pipfile b/Pipfile
@@ -8,7 +8,7 @@ numpy = ">=1.20"
 scipy = ">=1.6"
 scikit-learn = ">=0.24"
 pandas = ">=1.2"
-mne = ">=0.22"
+mne = ">=0.23"
 mne-bids = ">=0.7"
 matplotlib = ">=3.3"
 joblib = ">=1.0.0"

diff --git a/Pipfile.lock b/Pipfile.lock
diff --git a/docs/conf.py b/docs/conf.py
@@ -119,7 +119,7 @@
 html_theme_options = {
     'icon_links': [
         dict(name='GitHub',
-             url='https://github.com/mne-tools/mne-bids',
+             url='https://github.com/mne-tools/mne-hfo',
              icon='fab fa-github-square'),
     ],
     # 'navbar_title': 'MNE-HFO',

diff --git a/docs/index.rst b/docs/index.rst
@@ -50,7 +50,7 @@ mne-hfo is a HFO-detection package in python.
    :caption: Useful Links
 
    mne-hfo @ PyPI <https://pypi.org/project/mne-hfo/>
-   Issue Tracker <https://github.com/adam2392/mne-hfo/issues>
+   Issue Tracker <https://github.com/mne-tools/mne-hfo/issues>
 
 
 Indices and tables

diff --git a/docs/tutorial.rst b/docs/tutorial.rst
@@ -12,7 +12,7 @@ This tutorial presents several HFO detectors: the Line Length detector, Root Mea
 
 
 .. toctree::
-   :maxdepth: 1
+   :maxdepth: 0
 
    tutorials/basic_compute_hfos
    tutorials/compute_hfos_on_fedele_dataset

diff --git a/docs/whats_new.rst b/docs/whats_new.rst
@@ -8,9 +8,9 @@ What's new?
 ===========
 
 .. currentmodule:: mne_hfo
-.. _changes_0_1:
+.. _changes_0_3:
 
-Version 0.1 (unreleased)
+Version 0.3 (unreleased)
 ------------------------
 
 xxx
@@ -23,40 +23,26 @@ Notable changes
 Authors
 ~~~~~~~
 
-* `Adam Li`_
-* `Patrick Myers`_
-
 Detailed list of changes
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
 Enhancements
 ^^^^^^^^^^^^
 
-- Added :func:`mne_hfo.compute_chs_hfo_rates` to compute HFO rates per unit of time for every channel, by `Adam Li`) (:gh:`13`)
-- Added :func:`mne_hfo.io.create_events_df` to generate a DataFrame of HFO events from ``Raw`` object, or dictionary of lists of HFO endpoints, by `Adam Li`_ (:gh:`7`)
-- Added :func:`mne_hfo.find_coincident_events` to compare two dicts that contain event information by `Patrick Myers`_ (:gh:`10`)
-- Added notebook to demo use of detection algorithms by `Patrick Myers`_ (:gh:`10`)
-- Vectorized detection overlap check to enhance scoring speed by `Patrick Myers`_ (:gh:`15`)
-- Added notebook to demo use of GridSearchCV to optimize detector performance by `Patrick Myers`_ (:gh:`15`)
-- Added module to compare detections and notebook to demo usage by `Patrick Myers`_ (:gh:`22`)
-- Added initial implementation of HilbertDetector by `Patrick Myers`_ (:gh:`23`)
-- Improve memory utilization by allowing parallelization of the entire workflow per channel by `Patrick Myers`_ (:gh:`38`)
+- xxx
 
 API changes
 ^^^^^^^^^^^
 
-- Added :func:`mne_hfo.io.events_to_annotations` to go from ``*events.tsv`` to ``*annotations.tsv`` files, by `Adam Li`_ (:gh:`10`)
-- Added :func:`mne_hfo.sklearn.make_Xy_sklearn` to format data into scikit-learn compatible data structures for the sake of running hyper-parameter searches with ``SearchCV`` functions, by `Adam Li`_ (:gh:`15`)
-- Separated postprocessing step into two discrete steps _threshold_statistic and _post_process_ch_hfos by `Patrick Myers`_ (:gh:`23`)
+- xxx
 
 Requirements
 ^^^^^^^^^^^^
 
-- Added ``tqdm``, ``joblib`` and ``pandas`` to requirements, by `Adam Li`_ (:gh:`7`)
+- xxx
 
 Bug fixes
 ^^^^^^^^^
-- Fixed channel name issue introduced by redundant type checks when using `fit_and_predict` by `Patrick Myers`_ (:gh:`15`)
 
 - xxx
 

diff --git a/docs/whats_new_previous_releases.rst b/docs/whats_new_previous_releases.rst
@@ -8,42 +8,61 @@ What was new in previous releases?
 ==================================
 
 .. currentmodule:: mne_hfo
-.. _changes_0_0:
+.. _changes_0_2:
 
-Version 0.0
+Version 0.2
 -----------
 
 Notable changes
 ~~~~~~~~~~~~~~~
 
--
+- Added the ``HilbertDetector`` and optimized its performance on long recordings
 
 Authors
 ~~~~~~~
 
 * `Adam Li`_
+* `Patrick Myers`_
 
 Detailed list of changes
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
+This release is the first one under the ``mne.tools`` umbrella. We introduced three core detectors that 
+we found were used and cited in the literature: Line Length, RMS and Hilbert detectors. We have organized 
+a roadmap for what future improvements would entail. In addition, we have added tutorials that are rendered 
+as jupyter notebooks, which walk through usage of the package to: i) load data from BIDS, ii) run a detection and 
+then iii) evaluate the efficacy using tools from ``scikit-learn``.
+
 Enhancements
 ^^^^^^^^^^^^
 
--
+- Added :func:`mne_hfo.compute_chs_hfo_rates` to compute HFO rates per unit of time for every channel, by `Adam Li`) (:gh:`13`)
+- Added :func:`mne_hfo.io.create_events_df` to generate a DataFrame of HFO events from ``Raw`` object, or dictionary of lists of HFO endpoints, by `Adam Li`_ (:gh:`7`)
+- Added :func:`mne_hfo.find_coincident_events` to compare two dicts that contain event information by `Patrick Myers`_ (:gh:`10`)
+- Added notebook to demo use of detection algorithms by `Patrick Myers`_ (:gh:`10`)
+- Vectorized detection overlap check to enhance scoring speed by `Patrick Myers`_ (:gh:`15`)
+- Added notebook to demo use of GridSearchCV to optimize detector performance by `Patrick Myers`_ (:gh:`15`)
+- Added module to compare detections and notebook to demo usage by `Patrick Myers`_ (:gh:`22`)
+- Added initial implementation of HilbertDetector by `Patrick Myers`_ (:gh:`23`)
+- Improve memory utilization by allowing parallelization of the entire workflow per channel by `Patrick Myers`_ (:gh:`38`)
+
 
 API changes
 ^^^^^^^^^^^
 
--
+- Added :func:`mne_hfo.io.events_to_annotations` to go from ``*events.tsv`` to ``*annotations.tsv`` files, by `Adam Li`_ (:gh:`10`)
+- Added :func:`mne_hfo.sklearn.make_Xy_sklearn` to format data into scikit-learn compatible data structures for the sake of running hyper-parameter searches with ``SearchCV`` functions, by `Adam Li`_ (:gh:`15`)
+- Separated postprocessing step into two discrete steps _threshold_statistic and _post_process_ch_hfos by `Patrick Myers`_ (:gh:`23`)
 
 Requirements
 ^^^^^^^^^^^^
 
--
+- Updated requirement version for ``mne`` to ``v0.23+``, by `Adam Li`_ (:gh:`44`)
+- Added ``tqdm``, ``joblib`` and ``pandas`` to requirements, by `Adam Li`_ (:gh:`7`)
 
 Bug fixes
 ^^^^^^^^^
 
--
+- Fixed channel name issue introduced by redundant type checks when using `fit_and_predict` by `Patrick Myers`_ (:gh:`15`)
 
 .. include:: authors.rst
diff --git a/mne_hfo/__init__.py b/mne_hfo/__init__.py
@@ -1,6 +1,6 @@
 """MNE software for computing HFOs from iEEG data."""
 
-__version__ = '0.2dev'
+__version__ = '0.2'
 
 from mne_hfo.detect import RMSDetector, LineLengthDetector, HilbertDetector
 from mne_hfo.hodetect import MorphologyDetector, CSDetector

diff --git a/setup.py b/setup.py
@@ -38,9 +38,9 @@
 DESCRIPTION = descr
 MAINTAINER = 'Adam Li'
 MAINTAINER_EMAIL = '[email protected]'
-URL = 'https://adam2392/mne-hfo/'
+URL = 'https://mne.tools/mne-hfo/stable/index.html'
 LICENSE = 'BSD (3-clause)'
-DOWNLOAD_URL = 'https://github.com/adam2392/mne-hfo.git'
+DOWNLOAD_URL = 'https://github.com/mne-tools/mne-hfo.git'
 VERSION = version
 
 if __name__ == "__main__":
@@ -56,8 +56,8 @@
           long_description_content_type='text/markdown',
           python_requires='~=3.6',
           install_requires=[
-              'mne >=0.22',
-              'mne-bids >= 0.6',
+              'mne >=0.23',
+              'mne-bids >= 0.7',
               'numpy >=1.14',
               'scipy >=0.18.1',
               'scikit-learn >= 0.23',
@@ -89,7 +89,7 @@
           packages=find_packages(),
           project_urls={
               'Documentation': URL,
-              'Bug Reports': 'https://github.com/adam2392/mne-hfo/issues',
-              'Source': 'https://github.com/adam2392/mne-hfo',
+              'Bug Reports': 'https://github.com/mne-tools/mne-hfo/issues',
+              'Source': 'https://github.com/mne-tools/mne-hfo',
           },
           )