Release clean up

.readthedocs.yml

@@ -12,7 +12,5 @@ sphinx:
 
 formats: []
 
-python:
-  version: 3.6
-  install:
-    - requirements: doc/requirements.txt
+conda:
+  environment: environment.yml

Dockerfile

@@ -16,8 +16,9 @@ RUN apt-get update && \
     apt-get install -y cmake && \
     apt-get clean
 
-RUN git clone https://github.com/CEA-COSMIC/pysap.git && \
-    cd pysap && \
+RUN git clone https://github.com/CEA-COSMIC/pysap.git
+
+RUN cd pysap && \
     conda env create -f environment.yml
 
 ENV PATH /opt/conda/envs/pysap/bin:$PATH

README.rst

@@ -1,14 +1,11 @@
 
-|Travis|_ |Coveralls|_ |Python35|_ |Python36|_ |Python37|_ |Python38|_ |PyPi|_ |Doc|_ |CircleCI|_
+|CI|_ |Codecov|_ |Python36|_ |Python37|_ |Python38|_ |Python39|_ |PyPi|_ |Doc|_
 
-.. |Travis| image:: https://travis-ci.org/CEA-COSMIC/pysap.svg?branch=master
-.. _Travis: https://travis-ci.org/CEA-COSMIC/pysap
+.. |CI| image:: https://github.com/CEA-COSMIC/pysap/workflows/CI/badge.svg
+.. _CI: https://github.com/CEA-COSMIC/pysap/actions?query=workflow%3ACI
 
-.. |Coveralls| image:: https://coveralls.io/repos/CEA-COSMIC/pysap/badge.svg?branch=master&service=github
-.. _Coveralls: https://coveralls.io/github/CEA-COSMIC/pysap
-
-.. |Python35| image:: https://img.shields.io/badge/python-3.5-blue.svg
-.. _Python35: https://badge.fury.io/py/python-pySAP
+.. |Codecov| image:: https://codecov.io/gh/CEA-COSMIC/pysap/branch/master/graph/badge.svg?token=XHJIQXV7AX
+.. _Codecov: https://codecov.io/gh/CEA-COSMIC/pysap
 
 .. |Python36| image:: https://img.shields.io/badge/python-3.6-blue.svg
 .. _Python36: https://badge.fury.io/py/python-pySAP
@@ -19,23 +16,23 @@
 .. |Python38| image:: https://img.shields.io/badge/python-3.8-blue.svg
 .. _Python38: https://badge.fury.io/py/python-pySAP
 
+.. |Python39| image:: https://img.shields.io/badge/python-3.9-blue.svg
+.. _Python39: https://badge.fury.io/py/python-pySAP
+
 .. |PyPi| image:: https://badge.fury.io/py/python-pySAP.svg
 .. _PyPi: https://badge.fury.io/py/python-pySAP
 
 .. |Doc| image:: https://readthedocs.org/projects/python-pysap/badge/?version=latest
 .. _Doc: https://python-pysap.readthedocs.io/en/latest/?badge=latest
 
-.. |CircleCI| image:: https://circleci.com/gh/CEA-COSMIC/pysap.svg?style=svg
-.. _CircleCI: https://circleci.com/gh/CEA-COSMIC/pysap
-
 PySAP
 ======
 
 PySAP (Python Sparse data Analysis Package) is a Python module for **sparse data analysis** that offers:
 
 * A common API for astronomical and neuroimaging datasets.
 * Access to |link-to-sparse2d| executables with both wrappers and bindings.
-* Access to application specific plugins.
+* Access to application specific plug-ins.
 * A graphical user interface to play with the provided functions.
 
 .. |link-to-sparse2d| raw:: html
@@ -47,9 +44,13 @@ PySAP (Python Sparse data Analysis Package) is a Python module for **sparse data
 
   <img src="./doc/images/schema.jpg" width="250px">
 
-This package is the result of the COSMIC project, which is a collaboration between
+This package is the result of the |link-to-cosmic| project, which is a collaboration between
 the CEA Neurospin UNATI and CEA CosmoStat laboratories.
 
+.. |link-to-cosmic| raw:: html
+
+  <a href="http://cosmic.cosmostat.org/"
+  target="_blank">COSMIC</a>
 
 Important links
 ===============
@@ -58,7 +59,6 @@ Important links
 - API documentation (last stable release): https://python-pysap.readthedocs.io/
 - PySAP paper: https://arxiv.org/abs/1910.08465
 
-
 Dependencies
 ============
 
@@ -76,28 +76,48 @@ new issue.
 
 2. PySAP also requires the installation of the following third party software packages:
 
-* astropy
-* matplotlib
-* nibabel
-* numpy
-* scipy
-* progressbar2
-* pyqtgraph
-* PyWavelets
-* scikit-learn
+* scipy [==1.5.4]
+* numpy [==1.19.5]
+* matplotlib [==3.3.4]
+* astropy [==4.1]
+* nibabel [==3.2.1]
+* pyqtgraph [==0.11.1]
+* progressbar2 [==3.53.1]
+* scikit-learn [==0.24.1]
+* pybind11 [==2.6.2]
+* pyqt5 [==5.15.4]
+* PyWavelets [==1.1.1]
+
+Plug-Ins
+========
+
+PySAP currently supports the following plug-ins:
+
+* |link-to-pysap-astro| [==0.0.1]
+* |link-to-pysap-mri| [==0.3.0]
 
+.. |link-to-pysap-astro| raw:: html
+
+  <a href="https://github.com/CEA-COSMIC/pysap-astro"
+  target="_blank">PySAP-Astro</a>
+
+.. |link-to-pysap-mri| raw:: html
+
+  <a href="https://github.com/CEA-COSMIC/pysap-mri"
+  target="_blank">PySAP-MRI</a>
 
 Installation
 ============
 
 The installation of PySAP has been extensively tested on Ubuntu and macOS, however
-we cannot guarantee it will work on every operating system (e.g. Windows).
+we cannot guarantee it will work on every operating system (e.g. Windows). A Docker
+image is available (see below) for those unable to install PySAP directly.
 
 If you encounter any installation issues be sure to go through the following steps before opening a new issue:
 
-1. Check that that all of the installed all the dependencies listed above have been installed.
+1. Check that that all the dependencies listed above have been correctly installed.
 2. Read through all of the documentation provided, including the troubleshooting suggestions.
-3. Check if you problem has already been addressed in a previous issue.
+3. Check if your problem has already been addressed in a previous issue.
 
 Further instructions are available |link-to-install|.
 
@@ -144,6 +164,42 @@ or:
 
 As before, use the ``--user`` option if needed.
 
+Conda Environment
+-----------------
+
+A a conda ``environment.yml`` file is provided to facilitate the installation of
+the required PySAP dependencies along with some optional dependencies that
+provide additional features. To build the environment run:
+
+.. code-block:: bash
+
+  $ conda env create -f environment.yml
+
+Then to activate the environment run:
+
+.. code-block:: bash
+
+  $ conda activate pysap
+
+Finally, install PySAP following the instructions above.
+
+Docker Image
+------------
+
+A PySAP Docker image is available via DockerHub that includes the latest stable
+version of PySAP pre-installed. To install the image run:
+
+.. code-block:: bash
+
+  $ docker pull ceacosmic/pysap
+
+A Jupyter notebook can be launched using the Docker image as a backend and with
+access to the users current working directory as follows:
+
+.. code-block:: bash
+
+  $ docker run -p 8888:8888 -v ${PWD}:/home ceacosmic/pysap
+
 macOS
 -----