Merge branch 'release/v0.3.9'

EtienneCmb · Jan 4, 2018 · 5b5b422 · 5b5b422
2 parents 79852a7 + 4662346
commit 5b5b422
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diff --git a/.travis.yml b/.travis.yml
@@ -47,7 +47,7 @@ install:
     # Install dependencies :
     - if [ "${TEST}" == "standard" ]; then
         pip install codecov pytest pytest-cov pytest-sugar pytest-travis-fold openpyxl;
-        pip install mne nibabel pandas;
+        pip install mne nibabel pandas tensorpac;
         pip install git+https://github.com/hbldh/lspopt.git#egg=lspopt;
       fi;
     - if [ "${TEST}" == "minimal" ]; then

diff --git a/Makefile b/Makefile
@@ -38,3 +38,8 @@ flake: clean-test
 
 examples: clean
 	@echo "NOT CONFIGURED YET"
+
+
+pypi:
+	@python setup.py register -r pypi
+	@python setup.py sdist upload -r pypi
diff --git a/README.rst b/README.rst
@@ -69,7 +69,7 @@ Modules
    :align:   center
 
 * `Brain <http://visbrain.org/brain.html>`_ : visualize EEG/MEG/Intracranial data, connectivity in a standard MNI 3D brain (see `Brain examples <http://visbrain.org/auto_examples/index.html#brain-examples>`_).
-* `Sleep <http://visbrain.org/sleep.html>`_ : visualize polysomnographic data and hypnogram edition (see `Sleep examples <http://visbrain.org/auto_examples/index.html#sleep-examples>`_).
+* `Sleep <http://visbrain.org/sleep.html>`_ : visualize and analyze polysomnographic sleep data (see `Sleep examples <http://visbrain.org/auto_examples/index.html#sleep-examples>`_).
 * `Signal <http://visbrain.org/signal.html>`_ : data-mining module for time-series inspection (see `Signal examples <http://visbrain.org/auto_examples/index.html#signal-examples>`_).
 * `Topo <http://visbrain.org/topo.html>`_ : display topographical maps (see `Topo examples <http://visbrain.org/auto_examples/index.html#topoplot-examples>`_).
 * `Figure <http://visbrain.org/figure.html>`_ : figure-layout for high-quality publication-like figures (see `Figure examples <http://visbrain.org/auto_examples/index.html#figure-examples>`_).

diff --git a/appveyor.yml b/appveyor.yml
@@ -20,7 +20,7 @@ install:
   # Activate testing environnement :
   - activate testenv
   # Install dependencies :
-  - pip install mne nibabel setuptools PyOpenGL PyOpenGL_accelerate pytest pytest-cov pytest-sugar pandas openpyxl
+  - pip install mne nibabel setuptools PyOpenGL PyOpenGL_accelerate pytest pytest-cov pytest-sugar pandas openpyxl tensorpac
   - pip install git+https://github.com/hbldh/lspopt.git#egg=lspopt
   # ------------------- VISBRAIN -------------------
   - pip install -e .

diff --git a/circle.yml b/circle.yml
@@ -43,7 +43,7 @@ dependencies:
       fi;
     - conda install -n circleenv --yes numpy scipy pip;
     - pip install codecov pytest pytest-cov pytest-travis-fold;
-    - pip install mne nibabel pandas openpyxl;
+    - pip install mne nibabel pandas openpyxl tensorpac;
     - pip install git+https://github.com/hbldh/lspopt.git#egg=lspopt;
     - ls -al /home/ubuntu/miniconda3;
     - ls -al /home/ubuntu/miniconda3/bin;

diff --git a/docs/brain.rst b/docs/brain.rst
@@ -79,15 +79,15 @@ The *Brain* graphical user interface is subdivided into three main parts :
 * **Colorbar canvas** (*hide by default*)
 * **Cross-sections canvas** (*hide by default*)
 
-.. note::
+.. .. note::
 
-   If you want to save the current GUI state (i.e. all buttons properties) and retrieve it later, use the menu File/Save/GUI config and File/Load/GUI config or the associated *Brain* method.
+..    If you want to save the current GUI state (i.e. all buttons properties) and retrieve it later, use the menu File/Save/GUI config and File/Load/GUI config or the associated *Brain* method.
    
-   **Examples**
-      * :ref:`sphx_glr_auto_examples_brain_13_load_gui_config.py`
+..    **Examples**
+..       * :ref:`sphx_glr_auto_examples_brain_13_load_gui_config.py`
 
-   **API**
-      * :ref:`LoadSaveConfig`
+..    **API**
+..       * :ref:`LoadSaveConfig`
 
 Settings panel tabs
 ^^^^^^^^^^^^^^^^^^^
@@ -146,18 +146,14 @@ MNI templates
 .. figure::  picture/picbrain/brain_templates.png
    :align:   center
 
-By default, *Brain* comes with three brain templates respectively B1 (with cerebellum), B2 and B3 (smoothest). But this list can be extended using those following functions :
-
-* :ref:`ConvertMeshData` : convert vertices and faces to be compatibles with *Brain*
-* :ref:`AddBrainTemplate` and :ref:`RemoveBrainTemplate` : using converted vertices and faces, add/remove the template to visbrain
+By default, *Brain* comes with three brain templates respectively B1 (with cerebellum), B2 and B3 (smoothest).
 
 Further brain templates can be downloaded `here <https://drive.google.com/open?id=0B6vtJiCQZUBvd0xfTHJqcHg2bTA>`_.
 
 .. note::
 
    **Examples**
-      * :ref:`sphx_glr_auto_examples_brain_11_convert_mesh_data.py`
-      * :ref:`sphx_glr_auto_examples_brain_02_add_brain_template.py`
+      * :ref:`sphx_glr_auto_examples_brain_02_brain_using_vertices.py`
 
    **API**
       * :ref:`BrainClass`
@@ -204,7 +200,6 @@ Both methods use a **radius** parameter and only vertices with an euclidian dist
    **Examples**
       * :ref:`sphx_glr_auto_examples_brain_03_sources.py`
       * :ref:`sphx_glr_auto_examples_brain_08_screenshot.py`
-      * :ref:`sphx_glr_auto_examples_brain_12_colorbar_control.py`
 
    **API**
       * :ref:`CortProj`
@@ -286,8 +281,6 @@ Cross-sections correspond to an axial, sagittal and coronal slice of the volume
       * :ref:`sphx_glr_auto_examples_brain_00_brain_control.py`
       * :ref:`sphx_glr_auto_examples_brain_10_add_nifti_volume.py`
 
-   **API**
-      * :ref:`VolCrossecApi`
 
 Region Of Interest (ROI)
 ^^^^^^^^^^^^^^^^^^^^^^^^
@@ -305,8 +298,6 @@ If a volume is provided with corresponding labels, ROIs can be extracted and the
       * :ref:`sphx_glr_auto_examples_brain_05_region_of_interest.py`
       * :ref:`sphx_glr_auto_examples_brain_08_screenshot.py`
 
-   **API**
-      * :ref:`RoiApi`
 
 3-D volume rendering
 ^^^^^^^^^^^^^^^^^^^^
@@ -322,8 +313,6 @@ If a volume is provided with corresponding labels, ROIs can be extracted and the
       * :ref:`sphx_glr_auto_examples_brain_00_brain_control.py`
       * :ref:`sphx_glr_auto_examples_brain_10_add_nifti_volume.py`
 
-   **API**
-      * :ref:`VolCrossecApi`
 
 Colorbar control
 ~~~~~~~~~~~~~~~~
@@ -342,7 +331,6 @@ The colorbar can be controlled for individual objects including :
 .. note::
 
    **Examples**
-      * :ref:`sphx_glr_auto_examples_brain_12_colorbar_control.py`
       * :ref:`sphx_glr_auto_examples_brain_08_screenshot.py`
 
    **API**

diff --git a/docs/changelog_futur.rst b/docs/changelog_futur.rst
@@ -6,6 +6,23 @@ Changelog and future directions
 Changelog
 ---------
 
+v0.3.8
+^^^^^^
+
+Visbrain
+~~~~~~~~
+
+* Added logging
+* Code improvements: PEP8 and flake8
+
+Sleep
+~~~~~
+
+* Simplified and improved user interface
+* Multitaper-based spectrogram (require `lspopt <https://github.com/hbldh/lspopt>`_ package, see doc)
+* Improved automatic spindles detection
+* Removed drag-and-drop method for hypnogram scoring
+
 v0.3.4
 ^^^^^^
 
@@ -28,9 +45,7 @@ Future directions
 Visbrain
 ^^^^^^^^
 
-* conda installation
-* Independent of the VisPy developer version for better installation (ST)
-* Code style improvements (flake8 and numpydoc) (ST)
+* Conda installation
 * New modules are planned (*Connect*, *Pictures*, *ERP*) (LT)
 
 Brain

diff --git a/docs/objects.rst b/docs/objects.rst
@@ -20,8 +20,7 @@ Here's the list of currently supported modules :
 * :ref:`CSObj`
 * :ref:`ImageObj`
 * :ref:`TFObj`
-* :ref:`SpecObj`
-* :ref:`MTObj`
+* :ref:`HypnoObj`
 
 Each object inherit to the following methods :
 
@@ -334,67 +333,41 @@ Time-frequency map object
 
 .. currentmodule:: visbrain.objects
 
-.. autoclass:: TimeFrequencyMapObj
+.. autoclass:: TimeFrequencyObj
   :members: set_data
 
     .. rubric:: Methods
 
     .. autosummary::
-        ~TimeFrequencyMapObj.set_data
+        ~TimeFrequencyObj.set_data
 
-.. include:: generated/visbrain.objects.TimeFrequencyMapObj.examples
+.. include:: generated/visbrain.objects.TimeFrequencyObj.examples
 .. raw:: html
 
     <div style='clear:both'></div>
 
 
-.. _SpecObj:
+.. _HypnoObj:
 
-Spectrogram object
-------------------
+Hypnogram object
+----------------
 
-.. figure::  picture/picobjects/pic_spec_obj.png
+.. figure::  picture/picobjects/pic_hypno_obj.png
    :align:   center
 
-   Spectrogram object example
+   Hypnogram object example
 
 .. currentmodule:: visbrain.objects
 
-.. autoclass:: SpectrogramObj
-  :members: set_data
-
-    .. rubric:: Methods
-
-    .. autosummary::
-        ~SpectrogramObj.set_data
-
-.. include:: generated/visbrain.objects.SpectrogramObj.examples
-.. raw:: html
-
-    <div style='clear:both'></div>
-
-
-.. _MTObj:
-
-Multi-taper object
-------------------
-
-.. figure::  picture/picobjects/pic_spec_obj.png
-   :align:   center
-
-   Multi-taper object example
-
-.. currentmodule:: visbrain.objects
-
-.. autoclass:: MultiTaperObj
-  :members: set_data
+.. autoclass:: HypnogramObj
+  :members: set_stage
 
     .. rubric:: Methods
 
     .. autosummary::
-        ~MultiTaperObj.set_data
+        ~HypnogramObj.set_stage
 
-.. include:: generated/visbrain.objects.MultiTaperObj.examples
+.. include:: generated/visbrain.objects.HypnogramObj.examples
 .. raw:: html
 
     <div style='clear:both'></div>
diff --git a/docs/picture/picobjects/pic_hypno_obj.png b/docs/picture/picobjects/pic_hypno_obj.png
diff --git a/docs/picture/picsleep/sleep_annotations.png b/docs/picture/picsleep/sleep_annotations.png
diff --git a/docs/picture/picsleep/sleep_filtering.png b/docs/picture/picsleep/sleep_filtering.png
diff --git a/docs/picture/picsleep/sleep_info.png b/docs/picture/picsleep/sleep_info.png
diff --git a/docs/picture/picsleep/sleep_livedit.png b/docs/picture/picsleep/sleep_livedit.png
diff --git a/docs/picture/picsleep/sleep_main.png b/docs/picture/picsleep/sleep_main.png
diff --git a/docs/picture/picsleep/sleep_open.png b/docs/picture/picsleep/sleep_open.png
diff --git a/docs/picture/picsleep/sleep_peak.png b/docs/picture/picsleep/sleep_peak.png
diff --git a/docs/picture/picsleep/sleep_rem.png b/docs/picture/picsleep/sleep_rem.png
diff --git a/docs/picture/picsleep/sleep_scoring.png b/docs/picture/picsleep/sleep_scoring.png
diff --git a/docs/picture/picsleep/sleep_scoring_table.png b/docs/picture/picsleep/sleep_scoring_table.png
diff --git a/docs/picture/picsleep/sleep_spectro_methods.png b/docs/picture/picsleep/sleep_spectro_methods.png
diff --git a/docs/picture/picsleep/sleep_spindles.png b/docs/picture/picsleep/sleep_spindles.png
diff --git a/docs/picture/picsleep/sleep_topo.png b/docs/picture/picsleep/sleep_topo.png