Merge pull request #1 from ghammad/develop

Develop

.gitignore

@@ -65,6 +65,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/source/_autosummary
 
 # PyBuilder
 target/

.gitlab-ci.yml

@@ -0,0 +1,54 @@
+# This file is a template, and might need editing before it works on your project.
+# Official language image. Look for the different tagged releases at:
+# https://hub.docker.com/r/library/python/tags/
+image: python:latest
+
+# Change pip's cache directory to be inside the project directory since we can
+# only cache local items.
+variables:
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache"
+
+# Pip's cache doesn't store the python packages
+# https://pip.pypa.io/en/stable/reference/pip_install/#caching
+#
+# If you want to also cache the installed packages, you have to install
+# them in a virtualenv and cache it as well.
+cache:
+  paths:
+    - .cache/pip
+    - venv/
+
+stages:
+  - build
+  - test
+  - deploy
+
+before_script:
+  - python -V               # Print out python version for debugging
+  - pip install virtualenv
+  - virtualenv venv
+  - source venv/bin/activate
+
+run:
+  stage: build
+  script:
+  - pip install -e .
+
+test:
+  stage: test
+  script:
+  - pip install pytest
+  - python -m pytest -vv --disable-pytest-warnings pyActigraphy/tests/
+  # - python setup.py test
+
+pages:
+  stage: deploy
+  script:
+  - pip install sphinx sphinx-bootstrap-theme
+  - cd docs ; make html
+  - mv build/html/ ../public/
+  artifacts:
+    paths:
+    - public
+  only:
+  - master

README.rst

@@ -0,0 +1,102 @@
+.. image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
+  :target: https://www.gnu.org/licenses/gpl-3.0
+.. image:: https://gitlab.com/ghammad/pyActigraphy/badges/master/pipeline.svg
+  :target: https://gitlab.com/ghammad/pyActigraphy/commits/master
+
+**pyActigraphy**
+================
+Open-source python package for actigraphy data analysis.
+
+
+This package is meant to provide a comprehensive set of tools to:
+
+* read actigraphy raw data files with various formats
+* calculate typical wake/sleep cycle-related variables (ex: IS, IV, ...)
+* perform complex analyses (ex: FDA, SSA, HMM, ...)
+
+Requirements
+============
+* python 3.X
+* joblib
+* pandas
+* numba
+* numpy
+* pyexcel
+* pyexcel-ods3
+* scipy
+* statsmodels
+
+Installation
+============
+In a (bash) shell, simply type:
+
+* For users:
+
+.. code-block:: shell
+
+  pip install pyActigraphy
+
+To update the package:
+
+.. code-block:: shell
+
+  pip install -U pyActigraphy
+
+It is strongly recommended to use the latest version of the pyActigraphy package.
+
+
+* For developers:
+
+.. code-block:: shell
+
+  git clone [email protected]:ghammad/pyActigraphy.git
+  cd pyActigraphy/
+  git checkout develop
+  pip install -e .
+
+Quick start
+===========
+
+The following example illustrates how to calculate the interdaily stability
+with the pyActigraphy package:
+
+.. code-block:: python
+
+  >>> import pyActigraphy
+  >>> rawAWD = pyActigraphy.io.read_raw_awd(fpath + 'SUBJECT_01.AWD')
+  >>> rawAWD.IS()
+  0.6900175913031027
+  >>> rawAWD.IS(freq='30min', binarize=True, threshold=4)
+  0.6245582891144925
+  >>> rawAWD.IS(freq='1H', binarize=False)
+  0.5257020914453097
+
+
+Contributing
+============
+
+There are plenty of ways to contribute to this package, including (but not limiting to):
+
+* report bugs (and, ideally, how to reproduce the bug)
+* suggest improvements
+* improve the documentation
+* hug or high-five the authors when you meet them!
+
+Authors
+=======
+
+* **Grégory Hammad** `@ghammad <https://github.com/ghammad>`_ - *Initial and main developer*
+* **Mathilde Reyt** `@ReytMathilde <https://github.com/ReytMathilde>`_
+
+See also the list of `contributors <https://github.com/ghammad/pyActigraphy/contributors>`_ who participated in this project.
+
+License
+=======
+
+This project is licensed under the GNU GPL-3.0 License - see the `LICENSE <LICENSE>`_ file for details
+
+Acknowledgments
+===============
+
+* **Aubin Ardois** `@aardoi <https://github.com/aardoi>`_ developed the first version of the MTN class during his internship at the CRC, in May-August 2018.
+* The CRC colleagues for their support, ideas, etc.

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = pyActigraphy
+SOURCEDIR     = source
+BUILDDIR      = ../../pyActigraphy-docs
+PDFBUILDDIR   = /tmp
+PDF           = ../manual.pdf
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(SPHINXOPTS) $(PDFBUILDDIR)/latex
+	make -C $(PDFBUILDDIR)/latex all-pdf
+	cp $(PDFBUILDDIR)/latex/*.pdf $(PDF)
+	@echo "pdflatex finished; see $(PDF)"
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=pyActigraphy
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/source/_templates/class.rst

@@ -0,0 +1,10 @@
+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :special-members: __contains__,__getitem__,__iter__,__len__,__add__,__sub__,__mul__,__div__,__neg__,__hash__
+
+   {% block methods %}
+   {% endblock %}

docs/source/_templates/function.rst

@@ -0,0 +1,10 @@
+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autofunction:: {{ objname }}
+
+.. raw:: html
+
+    <div style='clear:both'></div>