Updating documentation from review #25

[mxochicale]

Miscellaneous

List of items to update in a new branches

• [x] Add hyperlink for body of evidence in "There is a substantial body of evidence that thinking before coding leads to better code." at https://scikit-surgerytutorial02.readthedocs.io/en/latest/04_Planning.html
• [x] git commit -m "Issue #1 added some functional requirements" in https://scikit-surgerytutorial02.readthedocs.io/en/latest/04_Planning.html might be simplified using git commit -m "added some functional requirements (#1)"
• [x] pylint --rcfile=tests/pylintrc scikitsurgeryspherefitting is not mentioned in https://scikit-surgerytutorial02.readthedocs.io/en/latest/06.1_Linting.html which might be good to incorporate
• [x] Do we need .gitlab-ci.yml?
• [x] It is a bit confusion to me to have project_name [My New Project]: scikit-surgery-sphere-fitting and project_slug [scikit-surgery-sphere-fitting]: sksurgeryspherefitting at https://scikit-surgerytutorial02.readthedocs.io/en/latest/01_Starting_Out.html, also repository path, license and UCL license should be added in the docs. See further info for slug: https://github.com/audreyfeldroy/cookiecutter-pypackage/issues/487
• [x] Figures are from weiss gitlab which require to be updated to github : https://scikit-surgerytutorial02.readthedocs.io/en/latest/01_Starting_Out.html and others to section 06.
• [x] More updates with figure at https://scikit-surgerytutorial02.readthedocs.io/en/latest/08_Documentation.html
• [x] tests/test_sksurgeryspherefitting_demo.py https://scikit-surgerytutorial02.readthedocs.io/en/latest/07_UserInterface.html is missing a tab, the following one should work:

  
  # coding=utf-8

"""scikit-surgery-sphere-fitting tests"""

from sksurgeryspherefitting.ui.sksurgeryspherefitting_demo import run_demo

def test_fit_sphere_least_squares_demo(): model_name = 'data/CT_Level_1.vtp' output_name = 'out_temp.vtp'

run_demo(model_name, output_name)

* [x] Command test that is useful for me: `pylint --rcfile=tests/pylintrc scikitsurgeryspherefitting`
* [x] `source .tox/py36/bin/activate` might be not necesary when using conda env covering all dependencies at https://scikit-surgerytutorial02.readthedocs.io/en/latest/07_UserInterface.html
* [x] Not sure how to run vtk viewer, just managed: 

wget https://github.com/thompson318/scikit-surgery-sphere-fitting/raw/master/data/US_Sphere_2.vtp

(scikit-surgery-VE) miguel@smartliveri4i-Alienware-13-R3:~/repositories/SciKit-Surgery/scikit-surgery-sphere-fitting$ python sksurgeryspherefitting.py data/CT_Level_1.vtp -o sphere.vtp Result is (array([136.571217 , 151.97335771, -95.51789211, 8.11853981]), 2) (scikit-surgery-VE) miguel@smartliveri4i-Alienware-13-R3:~/repositories/SciKit-Surgery/scikit-surgery-sphere-fitting$ python sksurgeryspherefitting.py data/US_Sphere_2.vtp -o sphere.vtp Result is (array([252.96783239, 216.57631804, 270.37878929, 596.29375964]), 2)

   Steve recommends to use: https://kitware.github.io/vtk-js/examples/GeometryViewer.html 

* [x] Incomplete install_requires in `. Open it and edit it. The most important thing to do is to update the “install_requires" ` https://scikit-surgerytutorial02.readthedocs.io/en/latest/09_Releaseing.html

_Originally posted by @mxochicale in https://github.com/SciKit-Surgery/scikit-surgerytutorial02/issues/25#issuecomment-1280888442_

[mxochicale]

• [x] We might like to add brief description to create conda env as step 1 in "https://scikit-surgerytutorial02.readthedocs.io/en/latest/01_Starting_Out.html"

  
  ## cd $HOME/repositories/code/conda/create-virtual-environments
  ## conda list -n *VE # show list of installed packages
  ## conda update -n base -c defaults conda  ## UPDATE CONDA
  ## conda env create -f *VE.yml                      ## INSTALL
  ## conda env update --file *VE.yml --prune      ## UPDATE
  ## conda activate *VE                                       ## ACTIVATE
  ## conda remove -n *VE --all                            ## REMOVE

name: scikit-surgery-VE channels:

• defaults
• conda-forge #vtk; tox; notebook; jupyter_contrib_nbextensions; tqdm
• anaconda #coverage; scipy; ipython dependencies:
• python=3.7
• cookiecutter>=1.7.3
• numpy>=1.21.5
• scipy>=1.7.3
• tox>=3.26.0
• pytest>=7.1.2
• pylint>=2.14.5
• vtk>=9.0.3
• pip>=22.2.2
• coverage>=6.3.2
• pip:
  • scikit-surgeryvtk>=1.0.6
  • scikit-surgeryimage>=0.10.1
  • scikit-surgerycore>=0.6.10

* [x] Also, other dependencies like pandoc: Do I need `Pandoc wasn't found.` for tox -e docs
  * `scikit-surgery-VE; pip pandoc` don't work
  * in the terminal `sudo apt install pandoc`  > `docs: commands succeeded congratulations :)`

[mxochicale]

Meeting 1:1 w/Steve 19-Oct-2022 at 11:00

• [x] To run tox in the repo /scikit-surgerytutorial02
• [x] conda env can be added in a new page, subjection or link at the 06_Testing.rst
• [x] Add a pandoc link for other dependencies in the 01_Starting_Out and where tox -e docs is 08_Documentation
• [x] To address https://github.com/SciKit-Surgery/scikit-surgerytutorial02/issues/22 in a separate branch/PR

[mxochicale]

• [x] fix the rendering section of requirements https://scikit-surgerytutorial02.readthedocs.io/en/latest/01_Starting_Out.html :

https://scikit-surgerytutorial02.readthedocs.io/en/latest/01_Starting_Out.html