Merge pull request #33 from neuropsychology/0.2.0-Initial

0.2.0 - Many breaking changes. Beware!

.cache/v/cache/lastfailed

@@ -0,0 +1,7 @@
+{
+  "tests/test_bio.py::test_bio_process": true,
+  "tests/test_bio.py::test_read_acqknowledge": true,
+  "tests/test_miscellaneous.py::test_get_creation_date": true,
+  "tests/test_statistics.py::test_compute_BMI": true,
+  "tests/test_statistics.py::test_compute_dprime": true
+}

.travis.yml

@@ -16,7 +16,9 @@ install:
 
 script:
   - python setup.py install
-  - coverage run tests/tests.py
+  - coverage run tests/test_statistics.py
+  - coverage run tests/test_miscellaneous.py
+  - coverage run tests/test_bio.py
 
 after_success:
   - codecov

CHANGELOG.md

@@ -1,10 +1,26 @@
-## NEXT : 0.2
+## CURRENT : 0.2
+
+### Breaking changes
+- Many!!!
+- Append "complexity_" to all complexity function names (e.g., `entropy_shannon` -> `complexity_entropy_shannon`) (**since 0.2.0**) [#32](https://github.com/neuropsychology/NeuroKit.py/pull/32)
+- `read_acqknowledge` new parameter, `return_sampling_rate`. Default to False to keep old behaviour, but default will be changed to True in the future (**since 0.2.0**) [#32](https://github.com/neuropsychology/NeuroKit.py/pull/32)
+
+
+### New functions / parameters
+- Many!!!
+- `eeg_complexity`: First attempt to compute complexity features of epochs (**since 0.2.0**) [#32](https://github.com/neuropsychology/NeuroKit.py/pull/32)
+- `emg_process`: Computes linear envelope and activation (**since 0.2.0**) [#32](https://github.com/neuropsychology/NeuroKit.py/pull/32)
+
+### Major changes
+- Many!!!
+
+### Minor changes
+- Many!!!
 
-- Focus: EEG processing
 
 ---------
 
-## CURRENT : 0.1
+## 0.1
 
 ### Breaking changes
 - EventRelated functions for biosignals: complete overhaul (**since 0.1.93**) [#30](https://github.com/neuropsychology/NeuroKit.py/pull/30)

CONTRIBUTING.md

@@ -13,6 +13,7 @@
 ## Code
 - Authors of code contribution will be added within the [**contributor**](http://neurokit.readthedocs.io/en/latest/about.html#contributors) section within the documentation.
 - Authors of code contribution are invited to follow the [PEP 8](https://www.python.org/dev/peps/pep-0008/) style sheet to write some nice (and readable) python.
+- Contrary to Python recommandations, I prefer some nicely nested loops, rather than a one-liner ["that" for s if h in i for t in range("don't") if "understand" is False].
 - Please document and comment your code, so that the purpose of each step (or code line) is stated in a clear and understandable way.
 - Avoid unnecessary function splitting into smaller bits: it makes testing and reading of the code more difficult (as one must jump between functions and files to understand what's happening).
 - Avoid unnecessary use of "magic" functions (preceded by underscores, `_foo()`). I don't know I don't find them elegant. But it's personal. I might be wrong.

README.md

@@ -4,7 +4,16 @@
 
 
 # NeuroKit.py 
-[![pypi](https://img.shields.io/pypi/pyversions/neurokit.svg)](https://pypi.python.org/pypi/neurokit) [![pypi](https://img.shields.io/pypi/v/neurokit.svg)](https://pypi.python.org/pypi/neurokit) [![travis](https://travis-ci.org/neuropsychology/NeuroKit.py.svg?branch=master)](https://travis-ci.org/neuropsychology/NeuroKit.py) [![codecov](https://codecov.io/gh/neuropsychology/NeuroKit.py/branch/master/graph/badge.svg)](https://codecov.io/gh/neuropsychology/NeuroKit.py) [![Dependency Status](https://dependencyci.com/github/neuropsychology/NeuroKit.py/badge)](https://dependencyci.com/github/neuropsychology/NeuroKit.py) [![License](https://img.shields.io/pypi/l/neurokit.svg)](https://github.com/neuropsychology/NeuroKit.py/blob/master/LICENSE) [![Build status](https://ci.appveyor.com/api/projects/status/9w4qw55143xu1gei?svg=true)](https://ci.appveyor.com/project/DominiqueMakowski/neurokit-py)
+[![pypi](https://img.shields.io/pypi/pyversions/neurokit.svg)](https://pypi.python.org/pypi/neurokit) 
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/d5248bd8c8574e90b5c8fe0bf2030201)](https://www.codacy.com/app/DominiqueMakowski/NeuroKit.py?utm_source=github.com&utm_medium=referral&utm_content=neuropsychology/NeuroKit.py&utm_campaign=Badge_Grade) 
+[![pypi](https://img.shields.io/pypi/v/neurokit.svg)](https://pypi.python.org/pypi/neurokit) 
+[![travis](https://travis-ci.org/neuropsychology/NeuroKit.py.svg?branch=master)](https://travis-ci.org/neuropsychology/NeuroKit.py)
+[![codecov](https://codecov.io/gh/neuropsychology/NeuroKit.py/branch/master/graph/badge.svg)](https://codecov.io/gh/neuropsychology/NeuroKit.py) 
+[![Dependency Status](https://dependencyci.com/github/neuropsychology/NeuroKit.py/badge)](https://dependencyci.com/github/neuropsychology/NeuroKit.py) 
+[![License](https://img.shields.io/pypi/l/neurokit.svg)](https://github.com/neuropsychology/NeuroKit.py/blob/master/LICENSE) 
+[![Build status](https://ci.appveyor.com/api/projects/status/9w4qw55143xu1gei?svg=true)](https://ci.appveyor.com/project/DominiqueMakowski/neurokit-py) 
+[![Code Health](https://landscape.io/github/neuropsychology/NeuroKit.py/master/landscape.svg?style=flat)](https://landscape.io/github/neuropsychology/NeuroKit.py/master)
+
 
 A Python Toolbox for Statistics and Neurophysiological Signal Processing (EEG, EDA, ECG, EMG...).
 
@@ -32,6 +41,9 @@ Not working? [Check this out](http://neurokit.readthedocs.io/en/latest/tutorials
 
 
 ## Contribute
+
+Want to get involved in the developpment of an open-source software and improve neuroscience practice? **Join us!**
+
 - You need some help? You found a bug? You would like to request a new feature? 
   Just open an [issue](https://github.com/neuropsychology/NeuroKit.py/issues) :relaxed:
 - Want to add a feature? Correct a bug? You're more than welcome to contribute!
@@ -49,12 +61,11 @@ Not working? [Check this out](http://neurokit.readthedocs.io/en/latest/tutorials
 
 This package provides a high level integration of complex statistical routines for researchers and clinicians with not much experience in programming, statistics or signal theory.
 
-- **M/EEG**
-  - **[`read_eeg()`](http://neurokit.readthedocs.io/en/latest/documentation.html#read-eeg)**: Read and convert many EEG and MEG files to an [`mne.io.Raw`](http://martinos.org/mne/stable/generated/mne.io.Raw.html#mne.io.Raw) object
-  - Preprocessing: Under development
-  - ERP: Under development
-  - Time/Frequency: Under development
-  - Microstates: Under development
+- **[M/EEG](http://neurokit.readthedocs.io/en/latest/tutorials/EEG.html)** *(under developpment)*
+  - **[`eeg_erp()`](http://neurokit.readthedocs.io/en/latest/documentation.html#eeg_erp)**: Extract event-related potentials 
+  - **[`eeg_complexity()`](http://neurokit.readthedocs.io/en/latest/documentation.html#eeg_complexity)**: Compute entropy, fractal dimension, and complexity indices
+  - Time/Frequency: **SOON™**
+  - Microstates: **SOON™**
 - **[Biosignals](http://neurokit.readthedocs.io/en/latest/tutorials/Bio.html)**
   - **[`read_acqknowledge()`](http://neurokit.readthedocs.io/en/latest/documentation.html#read-acqknowledge)**: Load and convert Biopac:copyright:'s AcqKnowledge files to a dataframe
   - **[`ecg_process()`](http://neurokit.readthedocs.io/en/latest/documentation.html#ecg-process)**: Extract ECG features
@@ -74,15 +85,16 @@ This package provides a high level integration of complex statistical routines f
     - *Skin Conductance Responses (SCR) onsets, peaks, amplitudes, latencies, recovery times, ...*
   - **[`emg_process()`](http://neurokit.readthedocs.io/en/latest/documentation.html#emg-process)**: Extract EMG features
     - *Pulse onsets*
+    - *Linear envelope, muscle activation*
 - **Signal**
     - **[`complexity()`](http://neurokit.readthedocs.io/en/latest/documentation.html#complexity)**: Extract complexity/chaos indices, such as values of entropy (Shannon's, Sample and Multiscale), fractal dimension, Hurst and Lyapunov exponents and more
 - **Statistics**
   - **[`z_score()`](http://neurokit.readthedocs.io/en/latest/documentation.html#z-score)**: Normalize (scale and reduce) variables
   - **[`find_outliers()`](http://neurokit.readthedocs.io/en/latest/documentation.html#find_outliers)**: Identify outliers
-  - **[`dprime()`](http://neurokit.readthedocs.io/en/latest/documentation.html#dprime)**: Computes Signal Detection Theory (SDT) parameters (d', c, beta, a', b''d)
 - **Miscellaneous**
-  - **[`BMI()`](http://neurokit.readthedocs.io/en/latest/documentation.html#bmi)**: Compute the traditional body mass index (BMI), the new BMI, the Body Fat Percentage (BFP) and their interpretation
-
+  - **[`compute_dprime()`](http://neurokit.readthedocs.io/en/latest/documentation.html#compute_dprime)**: Computes Signal Detection Theory (SDT) parameters (d', c, beta, a', b''d)
+  - **[`compute_BMI()`](http://neurokit.readthedocs.io/en/latest/documentation.html#compute_bmi)**: Compute the traditional body mass index (BMI), the new BMI, the Body Fat Percentage (BFP) and their interpretation
+  - **[`compute_interoceptive_accuracy()`](http://neurokit.readthedocs.io/en/latest/documentation.html#compute_interoceptive_accuracy)**: Compute interoception accuracy according to Garfinkel et al., (2015).
 
 
 ## Citation

circle.yml

@@ -17,4 +17,11 @@ machine:
 
 dependencies:
   override:
+    - pip install codecov
     - pip install -r requirements.txt
+
+test:
+  override:
+    - coverage run tests/tests.py
+  post:
+    - codecov

docs/about.rst

@@ -1,7 +1,7 @@
 About
 #####
 
-NeuroKit is looking for devs, support and pretty much everything. Join the team by `contributing <https://github.com/neuropsychology/NeuroKit.py/blob/master/CONTRIBUTING.md>`_ :)
+NeuroKit is looking for developers, support and pretty much everything. Join the team by `contributing <https://github.com/neuropsychology/NeuroKit.py/blob/master/CONTRIBUTING.md>`_ :)
 
 Core Team
 ==========
@@ -13,7 +13,7 @@ Contributors
 
 - `Rhenan Bartels Ferreira <https://www.researchgate.net/profile/Rhenan_Ferreira>`_ (Brazil): HRV, Testing, RSP, RSA.
 - `Nate Vack <https://github.com/njvack>`_ (USA): Acqknowledge files reading.
-- `Vassilios Vonikakis <https://github.com/bbonik>`_ (USA): HRV preprocessing.
+- `Vassilios Vonikakis <https://github.com/bbonik>`_ (USA): HRV.
 
 Support
 ========
@@ -29,7 +29,7 @@ Credits
 
 Credits go to the authors of NeuroKit's dependencies.
 
-Publications using it
+Featured in
 =======================
 
 NeuroKit has been used in the following publications:

docs/documentation.rst

@@ -66,13 +66,9 @@ read_acqknowledge
 .. autofunction:: neurokit.read_acqknowledge
 
 
-EEG Processing
+EEG
 =====================
 
-read_eeg
---------------------
-
-.. autofunction:: neurokit.read_eeg
 
 
 eeg_add_channel
@@ -81,42 +77,51 @@ eeg_add_channel
 .. autofunction:: neurokit.eeg_add_channel
 
 
-
-eeg_add_events
+eeg_select_channels
 --------------------
 
-.. autofunction:: neurokit.eeg_add_events
+.. autofunction:: neurokit.eeg_select_channels
 
 
+eeg_select_electrodes
+-----------------------
 
-eeg_select_sensor_area
+.. autofunction:: neurokit.eeg_select_electrodes
+
+
+eeg_create_mne_events
 -------------------------
 
-.. autofunction:: neurokit.eeg_select_sensor_area
+.. autofunction:: neurokit.eeg_create_mne_events
 
+eeg_add_events
+-------------------------
 
+.. autofunction:: neurokit.eeg_add_events
 
-eeg_filter
---------------------
 
-.. autofunction:: neurokit.eeg_filter
+eeg_complexity
+-------------------------
 
-eeg_ica
---------------------
+.. autofunction:: neurokit.eeg_complexity
 
-.. autofunction:: neurokit.eeg_ica
 
+eeg_erp
+-------------------------
 
-eeg_name_frequencies
------------------------
+.. autofunction:: neurokit.eeg_erp
 
-.. autofunction:: neurokit.eeg_name_frequencies
 
-eeg_psd
----------------
+plot_eeg_erp
+-------------------------
+
+.. autofunction:: neurokit.plot_eeg_erp
 
-.. autofunction:: neurokit.eeg_psd
 
+plot_eeg_erp_topo
+-------------------------
+
+.. autofunction:: neurokit.plot_eeg_erp_topo
 
 
 Signal
@@ -128,10 +133,10 @@ find_events
 
 .. autofunction:: neurokit.find_events
 
-visually_check_events_in_signal
+plot_events_in_signal
 -----------------------------------
 
-.. autofunction:: neurokit.visually_check_events_in_signal
+.. autofunction:: neurokit.plot_events_in_signal
 
 create_epochs
 ---------------
@@ -146,37 +151,59 @@ complexity
 
 
 
+
+
+
+
+
 Statistics
 =====================
 
+
+mad
+---------------
+
+.. autofunction:: neurokit.mad
+
+
 z_score
 ---------------
 
 .. autofunction:: neurokit.z_score
 
-dprime
----------------
 
-.. autofunction:: neurokit.dprime
 
 find_outliers
 ---------------
 
 .. autofunction:: neurokit.find_outliers
 
-Miscellaneous
+
+normal_range
+---------------
+
+.. autofunction:: neurokit.normal_range
+
+
+
+
+
+
+
+
+Routines
 =====================
 
-BMI
+compute_dprime
 ---------------
 
-.. autofunction:: neurokit.BMI
+.. autofunction:: neurokit.compute_dprime
 
 
-find_closest_in_list
----------------------
+compute_BMI
+---------------
 
-.. autofunction:: neurokit.find_closest_in_list
+.. autofunction:: neurokit.compute_BMI
 
 
 
@@ -186,3 +213,57 @@ compute_interoceptive_accuracy
 .. autofunction:: neurokit.compute_interoceptive_accuracy
 
 
+
+
+
+
+Plot
+=====================
+
+plot_polarbar
+---------------
+
+.. autofunction:: neurokit.plot_polarbar
+
+
+
+
+Miscellaneous
+=====================
+
+
+find_following_duplicates
+----------------------
+
+.. autofunction:: neurokit.find_following_duplicates
+
+
+find_closest_in_list
+----------------------
+
+.. autofunction:: neurokit.find_closest_in_list
+
+
+Time
+----------------------
+
+.. autoclass:: neurokit.Time
+
+Data
+=====================
+
+
+find_creation_date
+----------------------
+
+.. autofunction:: neurokit.find_creation_date
+
+save_nk_object
+----------------------
+
+.. autofunction:: neurokit.save_nk_object
+
+read_nk_object
+----------------------
+
+.. autofunction:: neurokit.read_nk_object