Fixes for failing unit tests

[smjoshiatglobus]

Main changes:

• Added support for elements of type SQ for unit tests. This has fixed some failing unit tests and I managed to remove several test files from the exclusion list.
• Fixed anonymization failures for RawDataElement type of elements, which are NamedTuple, issue Tag replacement fails during anonymization for structured reports #63
• Changed anonymized value for CS and some other types to all uppercase 'ANONYMIZED'. The CS VR type required uppercase characters per https://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_6.2-1
• Now the number of passing tests have increased from 313 to 397.

Other changes, mostly for development support:

• Added references to known issue X tags of VR == 'DA' not getting deleted #56 in tests code
• Added Pipfile for optional development setup using pipenv
• Added configuration for spell-checking using cspell and added custom dictionary.
• Fixed a typo (only one!)
• Formatted code in tests and example folders using black
• Suppressed some warnings from Sourcery

[smjoshiatglobus]

Just checking... anything you need from me for this pull request?

[pchoisel]

I'm not fond of removing tests because they fail. Let's leave them fail to remind us of the problem that needs fixing.
If this prevents merging, I'll change the related setting

[smjoshiatglobus]

Agreed! These were remnants from code no longer needed, since all (unexpectedly) failing tests are now removed. I have removed these lines in 2d53d34

[pchoisel]

This formatting feels weird, is it because of Flake8 ?

[smjoshiatglobus]

This comment suppresses couple of errors from Sourcery plugin: https://sourcery.ai/

[pchoisel]

@smjoshiatglobus Thank you for your work and sorry for the delay
I added a few comments to your modifications. Could you have a look and change what is needed ? Thanks !

[smjoshiatglobus]

@smjoshiatglobus Thank you for your work and sorry for the delay I added a few comments to your modifications. Could you have a look and change what is needed ? Thanks !

Thank you, @pchoisel, for the review. I have made a couple of changes and responded to your comments. Please re-review.

[pchoisel]

The changes look good to me !
Could you squash your commits about formatting, spell checking and issue linking ?

[smjoshiatglobus]

The changes look good to me ! Could you squash your commits about formatting, spell checking and issue linking ?

I am trying to learn squashing and worried that I am making it worse! I tried git rebase to squash the three commits on formatting. I am really confused about the commits now! I am not sure if I am doing the squash correctly. Can you please check/help?

[pchoisel]

I can see that the commit number increased instead of decreasing ^^
Here what I do when I want to squash commits:

• Backup my code in case I need to start again
• Input git rebase -i HEAD~N => you need to replace N with the number of commits you want to go "back in time". In your case, it will be 31. So input git rebase -i HEAD~31
• Git will display the 31 last commits in reverse order
• In front of each commit, you will see a word that will affect what will be done of the commit
• All you need to do is replace keep with squash for the commit you wish to squash and save the file

You can at all moment abort the rebase by doing git rebase --abort
At the end you will need to force push.

[smjoshiatglobus]

I can see that the commit number increased instead of decreasing ^^ Here what I do when I want to squash commits:

• Backup my code in case I need to start again
• Input git rebase -i HEAD~N => you need to replace N with the number of commits you want to go "back in time". In your case, it will be 31. So input git rebase -i HEAD~31
• Git will display the 31 last commits in reverse order
• In front of each commit, you will see a word that will affect what will be done of the commit
• All you need to do is replace keep with squash for the commit you wish to squash and save the file

You can at all moment abort the rebase by doing git rebase --abort At the end you will need to force push.

I create a separate branch to test this. I followed the steps you mentioned above. Instead of keep, I saw the word pick, which I retained.

There were several merge conflicts that I had to resolve. I have created draft PR #65 to show the changes. It still looks very clumsy! Sorry, I still don't know why there were so many merge conflicts.

I also created draft PR #66 with squashed commits. I am fine if you prefer to merge PR #66 and close this one.

[pchoisel]

Code merged in #66