Preparing 1.14.0 release #297
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Just needed to initialize the pointers in a better way for them to be passed across functions and objects. I won't pretend to understand why this works, only that it does work.
My initial fix unsynched the rules_map and the rules members of Hypothesis_Ruleset. This meant that when add_signal is called, only the Hypothesis_Rule's pointed to by the rules_map were updated and not the Hypothesis_Rule's in the rules vector. In this fix, the rules vector is now a vector of pointers to Hypothesis_Rules. See Lines 780 and 781 where both end up with the same (pointer) value stored.
Bug fixed: Previously in a scenario with multiple rules in the same response (increase or decrease) the last rule defined the max/min response value of behavior. Right now, it checks the min/max response value for all rules of the same behavior.
In the previous implementation, the last rule determined the maximum or minimum response of the behavior. In the current update, the behavior now checks for the maximum and minimum response in all rules. In cases where the minimum or maximum values do not exist, the system defaults to using the base value.
Adjust to the V0
… xml (intracellular=maboss) that will set the steepness of the hill function for each defined behavior. Standard value is 10 (very close to a step-like function)
This extends the functionality of plotting substrate heatmaps on SVG output: * Allows for all colormaps permitted in studio for visualizing substrate concentrations * Allows for configuration of this heatmap in the XML configuration file * updates all sample projects so that they can use this functionality just by enabling SVG substrate plots in the XML
Also, add the substrate element to the template project's SVG element in the config file. set to enabled="false" so as not to force this
disable_bugfix did not update based on the value of legacy_cell_defaults_copy previously. This fixes that for anyone still using the old, buggy version.
As discussed, the rule is defined as unique if the cell, behavior, signal, and response are equal. Previously, the test only included the signal; in this pull request, we have added the response test.
… specified in a .mat file CSVs (w/o headers) can be used for substrate ics. Substrate ICs from csv with headers. Now can include a header row in the CSV defining substrate ICs so that only a subset of substrates can be included for specification. If no header row is given, then it assumes the first n substrates are specified, which could be problematic? It issues a warning about that though.
Any behavior (as well as volume) can be set on a cell-by-cell basis drawn from a list of parameter distributions: uniform, loguniform, normal, lognormal, log10normal. See the template project after custom_data for how this can be implemented. Note: those are disabled to not change the base behavior of the template project. Checks are performed to ensure coherence (lower bounds <= upper bounds) and to make sure that truncated normals warn the user about how long they will take for draws. The main function, set_parameters_from_distributions() should be called immediately after load_cells_from_pugixml() and it will update the values of the loaded cells.
allow user to change max num (spring) attachments in xml
Added export of spring attachments
Fix bug in reading in rules.
Fix bug related to maximum/minimum saturation values and uniqueness test for rules
remove unwanted files; fix cancer_biorobots bug; etc.
Feat/minimal tests
Fix bug in matlab/read_MultiCellDS_xml.m
PhysiMeSS 1.0.1
Updated ruleset version in physiboss
fix typo in beta/test_plot_svgs_montage.py
set attack duration default to 30min
update copyright in core/*.h
update copyright in core/*.cpp update copyright in modules/*.h update copyright in modules/*.cpp
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