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mxochicale committed Jul 14, 2023
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Expand Up @@ -3,22 +3,25 @@ Python Template

.. image:: https://github.com/SciKit-Surgery/PythonTemplate/workflows/.github/workflows/ci.yml/badge.svg
:target: https://github.com/SciKit-Surgery/PythonTemplate/actions
:alt: GitHub Actions CI statuss
:alt: GitHub Actions CI status


Python Template is a Cookiecutter template for creating a python project. When used with `Cookiecutter`_.
Python Template will create a fully working python "Hello world" project with unit tests, GitHub Actions/GitLab CI, linting, PyPi distribution and sphinx documentation.
Python Template is a Cookiecutter template for creating a python project.
When used with `Cookiecutter`_ Python Template will create a fully working python "Hello world" project with unit tests,
GitHub Actions/GitLab CI, linting, PyPi distribution and sphinx documentation.

Purpose
~~~~~~~
Python Template was developed by the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_,
to assist researchers in the development of small but well engineered stofware components. It has been
widely used in the development of `scikit-surgery`_, but can be used as a starting point for any
Python project.

The template supports and encourages well engineered software by helping researchers with
standard software development tasks (`Software Process`_). The table below
lists standard development tasks and how the Python Template helps to deliver them.
standard software development tasks (`Software Process`_).

How the Python Template helps to deliver standard development tasks
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The table below lists standard development tasks and how the Python Template helps to deliver them.
Paying heed to the following tasks at the earliest stage of development should support the
creation of well defined, maintainable, well documented, and well tested code.

Expand Down Expand Up @@ -70,7 +73,10 @@ creation of well defined, maintainable, well documented, and well tested code.
| bugs | repository host. |
+-------------------------+--------------------------------------------------------------+

Whilst every effort has been made to automate tasks where possible, it is up to the researcher consider software requirements, write documentation, and create unit tests. Templates for each of these tasks are provided, so after creating your project, please take a little time before you start coding to think about what you want your software to achieve, and write it down in the file doc/requirements.rst.
Whilst every effort has been made to automate tasks where possible, it is up to the researcher consider software
requirements, write documentation, and create unit tests.
Templates for each of these tasks are provided, so after creating your project, please take a little time before you
start coding to think about what you want your software to achieve, and write it down in the file doc/requirements.rst.

How to use
~~~~~~~~~~
Expand All @@ -91,7 +97,8 @@ Similarly, you can install your VE using `mambaforce`_ by replacing conda with m

cookiecutter https://github.com/SciKit-Surgery/PythonTemplate.git

3. Answer the questions to configure your template (press enter to choose defaults), for further details on available answers see "List of Parameters" below.
3. Answer the questions to configure your template (press enter to choose defaults), for further details on available
answers see "List of Parameters" below.

4. Create a local git repository for your new project and commit the files.

Expand All @@ -106,14 +113,17 @@ Note: make sure you use "git add ." not "git add * " to pick up hidden files lik

5. Create a new project on GitHub (or Weisslab/CmicLab/Gitlab), making sure the URL matches what you set in step 3.

6. Add a remote in order to link your local repository to your GitHub repository and push the files across. NOTE: use the SSH form of the repository URL so you can use SSH key authentication (so you don't have to enter a username and password)
6. Add a remote in order to link your local repository to your GitHub repository and push the files across.
NOTE: use the SSH form of the repository URL so you can use SSH key authentication
(so you don't have to enter a username and password).

::

git remote add origin [email protected]:JoanneBloggs/MyNewProject.git
git push origin master

7. If using GitHub or WeissLAb, and assuming your URLs are all correct, GitHub Actions/GitLab CI should automatically run tests for your project.
7. If using GitHub or WeissLAb, and assuming your URLs are all correct, GitHub Actions/GitLab CI should automatically
run tests for your project.

8. You can verify your project has been set up correctly by installing and running tox.

Expand All @@ -124,7 +134,8 @@ Note: make sure you use "git add ." not "git add * " to pick up hidden files lik
tox
cd ..

tox runs several different stages, including pytest for unit tests and pylint for check for PEP8 linting. These can also be run independently:
tox runs several different stages, including pytest for unit tests and pylint for check for PEP8 linting.
These can also be run independently:

::

Expand All @@ -134,7 +145,8 @@ tox runs several different stages, including pytest for unit tests and pylint fo



9. Take a moment to write some software requirements, and populate the README file with a basic description of what you want to do, then start coding.
9. Take a moment to write some software requirements, and populate the README file with a basic description of
what you want to do, then start coding.


List of parameters for cookiecutter
Expand Down Expand Up @@ -184,17 +196,18 @@ List of parameters for cookiecutter

Authors: Tom Doel, Stephen Thompson, Matt Clarkson, Thomas Dowrick, Mian Ahmad, Miguel Xochicale

Python Template was developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_ in `University College London (UCL)`_.
Python Template was developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_ in
`University College London (UCL)`_.


Contributing
^^^^^^^^^^^^
~~~~~~~~~~~~

Please see the `contributing guidelines`_.


Useful links
^^^^^^^^^^^^
~~~~~~~~~~~~

* `pip`_
* `python`_
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