Update tests for v0.3

[shinich1]

Before submitting, please check the following:

• Make sure you have tests for the new code and that test passes (run nox)
• If applicable, add a line to the [unreleased] part of CHANGELOG.md, following keep-a-changelog.
• Format added code by ruff
  • See CONTRIBUTING.md for more details
• Make sure the checks (github actions) pass.
• Check that the docs compile without errors (run make html in ./docs/ - you may need to install dependency for sphinx docs, see docs/requirements.txt.)

Then, please fill in below:

Context (if applicable):

Fix tests to account for the deprecations.

Description of the change:

• fixed test_pattern, test_transpiler. rename pattern.standardize, pattern.shift_signals argument names.
• removed CommandNode class which should also be deprecated.

Related issue:

[codecov]

Codecov Report

Attention: Patch coverage is 60.00000% with 6 lines in your changes missing coverage. Please review.

Please upload report for BASE (prepare-v03@3163e10). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
graphix/pattern.py	62.50%	3 Missing ⚠️
graphix/graphsim/rxgraphviews.py	66.66%	1 Missing ⚠️
graphix/sim/density_matrix.py	50.00%	1 Missing ⚠️
graphix/sim/statevec.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@              Coverage Diff               @@
##             prepare-v03     #232   +/-   ##
==============================================
  Coverage               ?   75.32%           
==============================================
  Files                  ?       38           
  Lines                  ?     5520           
  Branches               ?        0           
==============================================
  Hits                   ?     4158           
  Misses                 ?     1362           
  Partials               ?        0           

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[EarlMilktea]

@shinich1 I will directly push some changes to this branch for easier review. Watch out!

[EarlMilktea]

MEMO: Doc CI is failing. Could you fix it?