Issue #59: Import v0.0.3 from zenodo doi.

CONTRIBUTING.rst

@@ -10,7 +10,7 @@ We welcome contributions to Fiducial Registration Educational Demonstration.
 Reporting bugs and feature requests
 -----------------------------------
 
-Please create a new issue on https://github.com/UCL/scikit-surgeryfredwebapp/issues/new
+Please create a new issue on https://github.com/UCL/scikit-surgeryfred/issues/new
 
 When reporting a bug, please include:
 * The version of Fiducial Registration Educational Demonstration you are using
@@ -23,13 +23,13 @@ Fixing bugs or implement features
 
 The easiest way to contribute is to follow these guidelines:
 
-1. Look through the issues on https://github.com/UCL/scikit-surgeryfredwebapp/issues and assign the relevant issue to yourself. If there is not an existing issue that covers your work, please create one: https://github.com/UCL/scikit-surgeryfredwebapp/issues/new
+1. Look through the issues on https://github.com/UCL/scikit-surgeryfred/issues and assign the relevant issue to yourself. If there is not an existing issue that covers your work, please create one: https://github.com/UCL/scikit-surgeryfred/issues/new
 2. Read the design considerations below.
-3. Fork the repository: https://github.com/UCL/scikit-surgeryfredwebapp/forks/new
+3. Fork the repository: https://github.com/UCL/scikit-surgeryfred/forks/new
 4. Create a branch for your changes. The branch name should start with the issue number, followed by hyphen separated words describing the issue. For example: 1-update-contribution-guidelines
 5. Make your changes following the coding guidelines below.
 6. Commit and push your changes to your fork. The commit message should start with `Issue #<issue number>`, for example: "Issue #1: Fixed typo". Commit in small, related chunks. Review each commit and explain its purpose in the commit message.
-7. Submit a merge request: https://github.com/UCL/scikit-surgeryfredwebapp/merge_requests/new
+7. Submit a merge request: https://github.com/UCL/scikit-surgeryfred/merge_requests/new
 
 Design Considerations
 ---------------------

MANIFEST.in

@@ -0,0 +1,2 @@
+include versioneer.py
+include sksurgeryfred/_version.py

README.rst

@@ -1,34 +1,43 @@
 Fiducial Registration Educational Demonstration
 ===============================================
 
-.. image:: https://github.com/UCL/scikit-surgeryfredwebapp/raw/master/project-icon.png
+.. image:: https://github.com/UCL/scikit-surgeryfred/raw/master/project-icon.png
    :height: 128px
    :width: 128px
-   :target: https://github.com/UCL/scikit-surgeryfredwebapp
+   :target: https://github.com/UCL/scikit-surgeryfred
    :alt: Logo
 
-.. image:: https://github.com/UCL/scikit-surgeryfredwebapp/workflows/.github/workflows/ci.yml/badge.svg
-   :target: https://github.com/UCL/scikit-surgeryfredwebapp/actions
+.. image:: https://github.com/UCL/scikit-surgeryfred/workflows/.github/workflows/ci.yml/badge.svg
+   :target: https://github.com/UCL/scikit-surgeryfred/actions
    :alt: GitHub Actions CI status
 
-.. image:: https://coveralls.io/repos/github/UCL/scikit-surgeryfredwebapp/badge.svg?branch=master&service=github
-    :target: https://coveralls.io/github/UCL/scikit-surgeryfredwebapp?branch=master
+.. image:: https://coveralls.io/repos/github/UCL/scikit-surgeryfred/badge.svg?branch=master&service=github
+    :target: https://coveralls.io/github/UCL/scikit-surgeryfred?branch=master
     :alt: Test coverage
 
-.. image:: https://img.shields.io/badge/Cite-SciKit--Surgery-informational
-   :target: https://doi.org/10.1007/s11548-020-02180-5
-   :alt: The SciKit-Surgery paper
+.. image:: https://readthedocs.org/projects/scikit-surgeryfred/badge/?version=latest
+    :target: http://scikit-surgeryfred.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
 
 .. image:: https://zenodo.org/badge/269602581.svg
-   :target: https://zenodo.org/badge/latestdoi/269602581
-   :alt: DOI - Zenodo
+    :target: https://zenodo.org/badge/latestdoi/269602581
+    :alt: DOI - Zenodo
+
 
 Author: Stephen Thompson
 
-This is web app front end for the Fiducial Registration Educational Demonstration (SciKit-SurgeryFRED), part of the `SciKit-Surgery`_ software project, developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_, part of `University College London (UCL)`_.
+Fiducial Registration Educational Demonstration (SciKit-SurgeryFRED) is part of the `SciKit-Surgery`_ software project, developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_, part of `University College London (UCL)`_.
+
+Fiducial Registration Educational Demonstration is tested with Python 3.X
 
 Fiducial Registration Educational Demonstration is intended to be used as part of an online tutorial in using fiducial based registration. The tutorial covers the basic theory of fiducial based registration, which is used widely in image guided interventions. The tutorial aims to help the students develop an intuitive understanding of key concepts in fiducial based registration, including Fiducial Localisation Error, Fiducial Registration Error, and Target Registration Error. 
 
+::
+
+    python sksurgeryfred.py
+
+Please explore the project structure, and implement your own functionality.
+
 Citing
 ------
 If you use SciKit-SurgeryFRED in your research or teaching please cite it. Individual releases can be cited via the Zenodo tag. SciKit-Surgery should be cited as:
@@ -45,7 +54,38 @@ You can clone the repository using the following command:
 
 ::
 
-    git clone https://github.com/UCL/scikit-surgeryfredwebapp
+    git clone https://github.com/UCL/scikit-surgeryfred
+
+
+Running tests
+^^^^^^^^^^^^^
+Pytest is used for running unit tests:
+::
+
+    pip install pytest
+    python -m pytest
+
+
+Linting
+^^^^^^^
+
+This code conforms to the PEP8 standard. Pylint can be used to analyse the code:
+
+::
+
+    pip install pylint
+    pylint --rcfile=tests/pylintrc sksurgeryfred
+
+
+Installing
+----------
+
+You can pip install directly from the repository as follows:
+
+::
+
+    pip install git+https://github.com/UCL/scikit-surgeryfred
+
 
 
 Contributing
@@ -58,6 +98,7 @@ Useful links
 ^^^^^^^^^^^^
 
 * `Source code repository`_
+* `Documentation`_
 
 
 Licensing and copyright
@@ -74,12 +115,12 @@ Supported by `Wellcome`_ and `EPSRC`_.
 
 
 .. _`Wellcome EPSRC Centre for Interventional and Surgical Sciences`: http://www.ucl.ac.uk/weiss
-.. _`source code repository`: https://github.com/UCL/scikit-surgeryfredwebapp
+.. _`source code repository`: https://github.com/UCL/scikit-surgeryfred
 .. _`Documentation`: https://scikit-surgeryfred.readthedocs.io
 .. _`SciKit-Surgery`: https://github.com/UCL/scikit-surgery/wiki
 .. _`University College London (UCL)`: http://www.ucl.ac.uk/
 .. _`Wellcome`: https://wellcome.ac.uk/
 .. _`EPSRC`: https://www.epsrc.ac.uk/
-.. _`contributing guidelines`: https://github.com/UCL/scikit-surgeryfredwebapp/blob/master/CONTRIBUTING.rst
+.. _`contributing guidelines`: https://github.com/UCL/scikit-surgeryfred/blob/master/CONTRIBUTING.rst
 .. _`license file`: https://github.com/UCL/scikit-surgeryfred/blob/master/LICENSE
 

doc/.gitignore

@@ -0,0 +1,5 @@
+/sksurgeryfred.rst
+/sksurgeryfred.*.rst
+/modules.rst
+/versioneer.rst
+/build