Sys bio model fixes part 2

[CodeByDrescher]

Fixes more problems found in Sys-bio models, including:

• Simulations with non-zero output start time
• Simulations with reaction names containing parenthesis missing from output
• Simulations using copasi annotations that would ignore certain parameters

[codecov]

Codecov Report

Attention: Patch coverage is 88.40580% with 8 lines in your changes missing coverage. Please review.

Project coverage is 89.30%. Comparing base (c1fa38c) to head (a635a27).
Report is 9 commits behind head on dev.

Files with missing lines	Patch %	Lines
biosimulators_copasi/core.py	82.60%	4 Missing ⚠️
biosimulators_copasi/data_model.py	91.30%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev      #76      +/-   ##
==========================================
- Coverage   89.50%   89.30%   -0.21%     
==========================================
  Files           6        6              
  Lines        1029     1047      +18     
==========================================
+ Hits          921      935      +14     
- Misses        108      112       +4     

Flag	Coverage Δ
unittests	89.30% <88.40%> (-0.21%)	⬇️

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[sonarqubecloud]

Quality Gate failed

Failed conditions
1 Security Hotspot

See analysis details on SonarCloud