Feedback and comments from the replication of the tutorial02 by Sujon Hekim

[mxochicale]

Raising this one because "Authentication failed"

remote: Support for password authentication was removed on August 13, 2021. remote: Please see https://docs.github.com/en/get-started/getting-started-with-git/about-remote-repositories#cloning-with-https-urls for information on currently recommended modes of authentication. fatal: Authentication failed for 'https://github.com/mxochicale/scikit-surgerytutorial02-test.git/'

[mxochicale]

• [x] A good practice is to connect with GitHub is via Secure Shell Protocol (SSH), which I think is missing in the documentation. So, one can generate SSH keys as suggested here (or here). User also needs to "Adds a new SSH key to GitHub account."

Then do

cd sksurgeryspherefitting/
git init
git branch -m main
git add .
git commit -m "Initial commit of my sphere fitter"
git remote add origin git@github.com:mxochicale/sksurgeryspherefitting.git
git push origin main

Notes:

• [x] add vi reference for commands > https://www.redhat.com/sysadmin/introduction-vi-editor

• [x] do we really need pandoc for this tutorial?> lib doesnt seem to require pandoc so, we might like to update this line "scikit-surgery-sphere-fitting require pandoc: universal document converter pandoc_installation." but need to check because of sphinx. Might be fixed, so would need to check it.

• [x] this is confusing for new lines: "project_description [scikit-surgery-sphere-fitting is a Python package]: scikit-surgery-sphere-fitting implements a least squares sphere fitting algorithm, to read a vtk poly data file, a config file, and outputs the fitted sphere."

[mxochicale]

• [x] One useful command is also removing already merged branches using:

  git branch --merged | grep -i -v -E "master|main" | xargs git branch -d 

  Source: https://www.w3docs.com/snippets/git/how-to-delete-already-merged-git-branches.html

[mxochicale]

• [x] Instructions for virtual environment seems to not be clear, so perhaps we can add further instructions.

[mxochicale]

• [x] Add steps to make more visible this one "Edit the file pylintrc, which is in the tests directory. Near the top of the file is an entry called ignore, add “ui” to the list of things to ignore;" from https://scikit-surgerytutorial02.readthedocs.io/en/latest/06.1_Linting.html

[mxochicale]

• [x] Investigate why we get __main__.py, __init__.py that brings other linting errors https://github.com/mxochicale/scikit-surgerytutorial02-test

[mxochicale]

• [x] We might not need the commented lines, so we can just mention to remove them

  #def test_using_pytest_sksurgeryspherefitting():
  #    x = 1
  #    y = 2
  #    verbose = False
  #    multiply = False
  #
  #    expected_answer = 3
  #    assert run_demo(x, y, multiply, verbose) == expected_answer

[AbuAbdul1ah]

Error from tox -e lint on Window's computer

ERROR: Could not install packages due to an OSError: [Errno 2] No such file or directory: 'c:\users\musa_\onedrive\documents\sksurgeryspherefittingtest2\.tox\lint\lib\site-packages\virtualenv-20.23.1.dist-info\METADATA'

lint: exit 1 (41.91 seconds) C:\Users\musa_\OneDrive\Documents\sksurgeryspherefittingtest2> python -I -m pip install pylint -r requirements-dev.txt pid=11200 lint: FAIL code 1 (42.09 seconds) evaluation failed :( (42.70 seconds) (scikit-surgeryTUTORIAL02VE)

[mxochicale]

• [x] update version of requirements for vtk: vtk>=9.2.6 > aligning with https://github.com/SciKit-Surgery/scikit-surgerytutorial02/blob/master/requirements.txt

Remove version to avoid package version conflicts

     - vtk>=9.2.6
     - scikit-surgeryvtk>=2.0.1
     - scikit-surgeryimage
     - scikit-surgerycore

[mxochicale]

• [x] Select two vtp files and drop them into vtk_GeometryViewer

[mxochicale]

• [x] Update python version of For github actions, you will need to amend /.github/workflows/ci.yml using only python version 3.7

[mxochicale]

• [x] Further instructions on how the build is completed and how to commit new messages
• Test it out. Your documentation on readthedocs should now be automatically updated each time you push a commit to GitHub.

[mxochicale]

• [x] Not clear "readthedocs or WEISSLab " > in "Wait until the continuous integration tests have finished on WEISSLab. You should now be able to visit your code on readthedocs or WEISSLab and see three green boxes, showing that your code is tested (with 100% coverage) and that the docs are building. To anyone considering using your code this would be very encouraging."

[thompson318]

We used to build the docs on WEISSlab then push them to readthedocs. We don't do that anymore, they are built entirely on readthedocs, so remove all reference to weisslab.