Merge pull request #208 from EmmaRenauld/documentation

Update the documentation

Makefile

@@ -1,10 +1,20 @@
-flake8:
-	@if command -v flake8 > /dev/null; then \
-		echo "Running flake8"; \
-		flake8 flake8 --ignore N802,N806 `find . -name \*.py | grep -v setup.py | grep -v /doc/`; \
-	else \
-		echo "flake8 not found, please install it!"; \
-		exit 1; \
-	fi;
-	@echo "flake8 passed"
+# Minimal makefile for Sphinx documentation
+#
 
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# 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)

README.rst

@@ -19,6 +19,7 @@ Links
 =====
 
 * `Getting started: installation and download <https://dwi-ml.readthedocs.io/en/latest/getting_started.html>`_
+* `Complete documentation with a step-by-step process explanation <https://dwi-ml.readthedocs.io/en/latest/>`_
 * `Contribute/Submit a patch <https://github.com/scil-vital/dwi_ml/blob/master/CONTRIBUTING.rst>`_
 * `Issue tracking <https://github.com/scil-vital/dwi_ml/issues>`_
 
@@ -29,19 +30,6 @@ DWI_ML is a toolkit for Diffusion Magnetic Resonance Imaging (dMRI) analysis
 using machine learning and deep learning methods. It is mostly focused on the
 tractography derivatives of dMRI.
 
-**Here is the usual workflow for people using dwi_ml**:
-
-1. `Organize your data <https://dwi-ml.readthedocs.io/en/latest/data_organization.html>`_. If your data is organized as expected, the following steps will be much easier.
-
-2. `Preprocess your data <https://dwi-ml.readthedocs.io/en/latest/preprocessing.html>`_.
-   - Preprocess your diffusion data using Tractoflow
-   - Preprocess your tractogram using RecoBundlesX
-
-3. `Create your own project with DWI_ML <https://dwi-ml.readthedocs.io/en/latest/processing.html>`_.
-   - Create your own repository for your project.
-   - Copy our scripts from ``please_copy_and_adapt``. Adapt based on your needs.
-   - Train your ML algorithm
-   - If needed, create your tracking algorithm based on your results.
 
 License
 =======