BioCRNpyler Test

Workflow runs for BioCRNpyler Test

• Record the copyright header convention for new files

  completed successfully:
  BioCRNpyler Test#59:Commitcf6ddb4pushedbymurrayrm
  competition_bug-25Aug2026

  Aug 26, 20264m 29s
  More actions for workflow run 59

• Show resource competition in figure 4 by raising DNA to 10 nM

  completed successfully:
  BioCRNpyler Test#58:Commit771cd33pushedbymurrayrm
  competition_bug-25Aug2026

  Aug 26, 20263m 59s
  More actions for workflow run 58

• Set mRNA degradation from measured TX-TL lifetimes

  completed successfully:
  BioCRNpyler Test#57:Commitd5d3303pushedbymurrayrm
  competition_bug-25Aug2026

  Aug 25, 20264m 33s
  More actions for workflow run 57

• Skip the modules tutorial simulation when bioscrape is missing

  completed successfully:
  BioCRNpyler Test#56:Commit65f1632pushedbymurrayrm
  modules-16Aug2026

  Aug 21, 20264m 42s
  More actions for workflow run 56

• Use a fuller example in the modules tutorial

  failed:
  BioCRNpyler Test#55:Commit32d6d82pushedbymurrayrm
  modules-16Aug2026

  Aug 21, 20264m 37s
  More actions for workflow run 55

• address comments by @ayush9pandey

  completed successfully:
  BioCRNpyler Test#54:Commitdbd4fa4pushedbymurrayrm
  pure_update-01Jan2026

  Aug 21, 20264m 31s
  More actions for workflow run 54

• Leave a panel empty rather than raising when a species is absent

  completed successfully:
  BioCRNpyler Test#53:Commit80a7882pushedbymurrayrm
  pure_update-01Jan2026

  Aug 17, 20264m 32s
  More actions for workflow run 53

• remove the unused ndps argument from PURE

  completed successfully:
  BioCRNpyler Test#52:Commit23df6abpushedbymurrayrm
  pure_update-01Jan2026

  Aug 14, 20264m 44s
  More actions for workflow run 52

• deprecate BasicPURE and correct the PURE energy carrier documentation

  completed successfully:
  BioCRNpyler Test#51:Commit9e9e54apushedbymurrayrm
  pure_update-01Jan2026

  Aug 13, 20263m 24s
  More actions for workflow run 51

• treat an attribute passed as a string as a single attribute

  completed successfully:
  BioCRNpyler Test#50:Commit8f8d0b7pushedbymurrayrm
  pure_update-01Jan2026

  Aug 13, 20265m 14s
  More actions for workflow run 50

• add example of plot_all_species_containing to gfp_expression.py

  completed successfully:
  BioCRNpyler Test#49:Commiteb457cbpushedbymurrayrm
  pure_update-01Jan2026

  Aug 13, 20264m 42s
  More actions for workflow run 49

• Add attribution and AI drafting guidelines for coding agents

  completed successfully:
  BioCRNpyler Test#48:Commit94d080apushedbymurrayrm
  agents-13Aug2026

  Aug 13, 20264m 7s
  More actions for workflow run 48

• add AGENTS.md and CLAUDE.md files

  completed successfully:
  BioCRNpyler Test#47:Commitdf743aepushedbymurrayrm
  agents-13Aug2026

  Aug 13, 20264m 33s
  More actions for workflow run 47

• ruff format

  completed successfully:
  BioCRNpyler Test#46:Commit56ba17cpushedbymurrayrm
  pure_update-01Jan2026

  May 10, 20264m 37s
  More actions for workflow run 46

• ruff format

  completed successfully:
  BioCRNpyler Test#45:Commit2f14b63pushedbymurrayrm
  parameter_update-22Nov2025

  May 10, 20264m 33s
  More actions for workflow run 45

• working notebook that replaces gfp_expression.py

  failed:
  BioCRNpyler Test#44:Commit8702c07pushedbymurrayrm
  parameter_update-22Nov2025

  May 10, 20264m 16s
  More actions for workflow run 44

• working notebook that replaces gfp_expression.py

  failed:
  BioCRNpyler Test#43:Commit868de77pushedbymurrayrm
  parameter_update-22Nov2025

  May 10, 20264m 23s
  More actions for workflow run 43

• ruff format

  completed successfully:
  BioCRNpyler Test#42:Commit2f14b63pushedbymurrayrm
  parameter_update-22Nov2025

  May 10, 20264m 30s
  More actions for workflow run 42

• updated mechanisms and parameters for PURE

  completed successfully:
  BioCRNpyler Test#41:Commit7a12846pushedbymurrayrm
  pure_update-01Jan2026

  Mar 20, 20264m 30s
  More actions for workflow run 41

• updated mechanisms and parameters for PURE

  failed:
  BioCRNpyler Test#40:Commit6eb27e6pushedbymurrayrm
  pure_update-01Jan2026

  Mar 18, 20264m 27s
  More actions for workflow run 40

• new plotting routines: plot_all_containing, plot_gene_expression_data

  completed successfully:
  BioCRNpyler Test#39:Commit66f94a0pushedbymurrayrm
  pure_update-01Jan2026

  Feb 23, 20264m 45s
  More actions for workflow run 39

• create customizable PURE mixture

  failed:
  BioCRNpyler Test#38:Commit892bfc5pushedbymurrayrm
  pure_update-01Jan2026

  Feb 9, 20264m 19s
  More actions for workflow run 38

• convert parameter files to pure ASCII

  completed successfully:
  BioCRNpyler Test#37:Commit8869b5dpushedbymurrayrm
  parameter_update-22Nov2025

  Dec 29, 20254m 18s
  More actions for workflow run 37

• add default parameter_file for enzyme mechanisms

  completed successfully:
  BioCRNpyler Test#36:Commit32b4302pushedbymurrayrm
  parameter_update-22Nov2025

  Dec 28, 20254m 21s
  More actions for workflow run 36

• add default parameter_file for enzyme mechanisms

  completed successfully:
  BioCRNpyler Test#35:Commit087efbfpushedbymurrayrm
  parameter_update-22Nov2025

  Dec 28, 20254m 10s
  More actions for workflow run 35