LoLab-VU / pysb

75%

master: 79%

LAST BUILD ON BRANCH v1.6.0

branch: v1.6.0

CHANGE BRANCH

x

Reset

• v1.6.0
• JamesPino-patch-1
• add_python2_to_travis
• alias_components
• appveyorfix
• asv
• benchmarking
• bidirectional_fix
• bngSSASimulator
• bng_read_expr_from_gdat
• bng_simulator
• bngconsole
• bngl_import
• boole2rules
• celery
• cupsoda
• cupsoda_logging
• cupsoda_py3
• cupsoda_simulator
• cytoscapejs
• dae
• dev
• dev_may2017
• drug_binding_macro
• duplicate_sites
• dupsites_localfxns
• ems_monintegrator
• export_compartments
• fast_exprs
• fast_netfiles
• fix_solver_verbose
• gpu_ssa
• hybrid_particle_population
• influence_nets
• is_equivalent_to
• kappatests
• kasimPy3errorfix
• lassie
• lcs
• master
• more_docs
• multi
• new_revrule_op
• nfsim
• pysbflat_matchonce
• remove_pygraphiv_add_dot
• remove_pygraphviz_dep_render_network
• rule_function
• sensitivity_analysis
• simclass_LAH
• simcls_stochkit
• simres_hdf5
• simulatorclass
• sphinxfix
• sphinxver
• stochkit
• synth_without_initials
• test2-rebase-cupsoda
• update_sensitivity_tool
• v1.7.0
• v1.9.0
• v1.9.1

Build # 795

Build Type

push

travis-ci

Committed by web-flow

Commit Message

Fix Kappa 4 multiple agent synthesis (#339)

In Kappa 4, a Ghost agent (placeholder 'dot') must be used to make
the two sides of a reaction rule match. For example, the following
two agent synthesis rule:

    Rule('synthesize_A_and_B', M() + None + None >> M() + A() + B(), k)

This was previously failing (one None was silently dropped). This
has been fixed by modifying ReactionPattern.__add__ and implementing
__radd__. The only caveat is with multiple leading Nones, which will
need to be in parentheses to avoid a TypeError from adding two Nones:

    None + (None + M())

This should also be avoidable by reordering the agents to put the
Nones last, as in the original example.

Fixes: #338

Run Details

6431 of 8598 relevant lines covered (74.8%)

1.49 hits per line