update doc to avoid m2r building locally

.environment.yml

@@ -9,4 +9,5 @@ dependencies:
            - joblib
            - museotoolbox
            - psutil
+           - m2r
 

Makefile

@@ -43,13 +43,13 @@ uploadpypi :
 	twine upload dist/*
 
 doc :
-	m2r README.md
-	mv README.rst docs/source/
+	#m2r README.md
+	#mv README.rst docs/source/
 	cd docs/ && make html
 
 doc_full :
-	m2r README.md
-	mv README.rst docs/source/
+	#m2r README.md
+	#mv README.rst docs/source/
 	rm -rf docs/source/auto_examples/
 	rm -rf docs/source/modules/
 	rm -rf docs/build/

README.md

@@ -3,7 +3,6 @@
 [![Build status](https://api.travis-ci.com/nkarasiak/MuseoPheno.svg?branch=master)](https://travis-ci.com/nkarasiak/MuseoPheno)
 [![Downloads](https://pepy.tech/badge/museopheno)](https://pepy.tech/project/museopheno)
 
-
 ![MuseoPheno logo](https://github.com/nkarasiak/MuseoPheno/raw/master/metadata/MuseoPheno_logo_128.png)
 
 # MuseoPheno

docs/source/README.md

@@ -0,0 +1,54 @@
+[![Documentation status](https://readthedocs.org/projects/museopheno/badge/?version=latest)](https://museopheno.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/museopheno.svg)](https://badge.fury.io/py/museopheno)
+[![Build status](https://api.travis-ci.com/nkarasiak/MuseoPheno.svg?branch=master)](https://travis-ci.com/nkarasiak/MuseoPheno)
+[![Downloads](https://pepy.tech/badge/museopheno)](https://pepy.tech/project/museopheno)
+
+![MuseoPheno logo](https://github.com/nkarasiak/MuseoPheno/raw/master/metadata/MuseoPheno_logo_128.png)
+
+# MuseoPheno
+
+MuseoPheno aims to be a phenology toolbox for Satellite Image Time Series.
+The [documentation is hosted on readthedocs](https://museopheno.readthedocs.org/).
+
+# What does MuseoPheno do today ?
+
+MuseoPheno globally eases the way to smooth or compute spectral indices for time series.
+
+# Don't manage temporal information, MuseoPheno does it for you
+
+## Spectral indices
+
+Let's suppose you want to compute the NDVI, and you know how your bands are ordered in your raster.
+Just define your band order (it supposes your bands are stacked in the following order : band1, band2... for date 1, then band1, band2 for date 2 and so on...)
+then give MuseoPheno the expression "(B8-B4)/(B8+B4)", and the library will generate the NDVI for each date.
+
+So it takes only a few lines to go from your time series to a temporal spectral index. It is also as fast to produce the indice raster.
+
+You can see the [demo here with Leaf Chlorophyll Content](https://museopheno.readthedocs.io/en/latest/auto_examples/sensors/LeafChlorophyllContentFromS2TimeSeries.html).
+
+*Your index is not listed ?* It is very easy to add a new sensor or to add new index. Just follow the simple documentation.
+
+## Temporal resampling and smoothing
+
+It has never been so easy to temporaly resample a time series given an array. Just define the beginning date, the end date, and the delta between acquistion, then MuseoPheno will deal it for you.
+You need to smooth your new time series ? No problem, just use the SmoothSignal class.
+
+## Phenological metrics
+
+You can easilly compute phenological metrics (start of season, end of season) using the PhenologyMetrics class from the time_series module.
+
+
+# How do I install it ?
+A package is available on pip :
+`python3 -m pip install museopheno --user`
+
+Alternatively, you can install **museopheno** directly from the git :
+`python3 -m pip install git+https://github.com/nkarasiak/MuseoPheno.git --user`
+
+Feel free to remove the `--user` if you like to install the library for every user on the machine.
+
+# What is planning to do MuseoPheno ?
+
+- More temporal signal smoothing (Whittaker...)
+- Lot of examples... so feel free to add !
+- Add tests to check consistency and reliability.

docs/source/conf.py

@@ -37,21 +37,13 @@
 
 autoclass_content = 'both'
 
-source_parsers = {
-   '.md': 'recommonmark.parser.CommonMarkParser',
-}
-
 extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
     'sphinx_gallery.gen_gallery',
-    'nbsphinx'
-    #'sphinx.ext.linkcode',
-    #'sphinx.ext.doctest',
-    #'sphinx_automodapi.automodapi'
-    ]
+    'nbsphinx','m2r']
 
 autosummary_generate = True
 # numpydoc_show_class_members=False 

docs/source/index.rst

@@ -36,8 +36,8 @@ MuseoPheno documentation
    :target: https://pepy.tech/project/museopheno
    :alt: Downloads
 
-.. include:: README.rst
-    :start-line: 36
+.. mdinclude:: README.md
+   :start-line: 8
 
 .. toctree::
    :maxdepth: 2

docs/source/index.rst.save

@@ -0,0 +1,63 @@
+.. MuseoPheno documentation
+
+MuseoPheno documentation
+=============================
+
+.. sidebar:: About MuseoPheno
+
+    .. image:: https://github.com/nkarasiak.png?size=100
+       :alt: Nicolas Karasiak avatar
+       :class: avatar
+
+    :Author: `Nicolas Karasiak <http://www.karasiak.net>`_
+    :Source code: `github.com project <https://github.com/nkarasiak/MuseoPheno>`_
+    :Bug tracker: `github.com issues <https://github.com/nkarasiak/MuseoPheno/issues>`_
+    :Generated: |today|
+    :License: GPL v3
+    :Version: |release|
+
+
+.. image:: https://readthedocs.org/projects/museopheno/badge/?version=latest
+   :target: https://museopheno.readthedocs.io/en/latest/?badge=latest
+   :alt: Documentation status
+
+
+.. image:: https://badge.fury.io/py/museopheno.svg
+   :target: https://badge.fury.io/py/museopheno
+   :alt: PyPI version
+
+
+.. image:: https://api.travis-ci.com/nkarasiak/MuseoPheno.svg?branch=master
+   :target: https://travis-ci.com/nkarasiak/MuseoPheno
+   :alt: Build status
+
+
+.. image:: https://pepy.tech/badge/museopheno
+   :target: https://pepy.tech/project/museopheno
+   :alt: Downloads
+
+.. mdinclude:: README.md
+   :skip
+.. toctree::
+   :maxdepth: 2
+
+   self
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Examples gallery
+
+   auto_examples/index
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Documentation API
+
+   api
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

requirements-dev.txt

@@ -8,3 +8,4 @@ sphinx-rtd-theme
 ipykernel
 nbsphinx
 sphinx-gallery
+m2r