merging c+11 changes with master branch #25
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The cygwin version of NFsim needs certain DLLs to run. I also removed what is presumably a backup version of the appveyor yaml file.
I must be making some small syntactical mistake.
The DLLs are in the expected directory on appveyor (C:\cygwin64\bin), so it's unclear why it can't find them to copy them. With this commit, I'm explicitly copying them instead of relying on the wildcards to do it.
This file doesn't exist in the 32bit version of cygwin.
Also, removed outdated references and a duplicated section.
I had forgotten to remove the old html pages that linked to the ftp site where we were hosting nfsim before the move to bintray.
If you looked at the travis logs, it looks like the only thing the osx_install script was doing anything in the osx_install script was the brew update, so I removed it and added that one line to travis.yml. It's not even clear if that one line is necessary.
Added few lines to print reaction details for specific molecules and reactions. Realized why endocleavage at stall was not working properly. See the notes in data/sim180620.
This code is buggy for TASEP since it ignores state changes of trailing ribosomes that are stacked behind a leading ribosome but are not bonded to it. To solve this problem, I am going to look at the MappingSet of mRNA molecules to identify the spatial region around the state change and include any associated bonded molecules in the product list. Will involve introducing notion of a polymer molecule and spatial states.
PySB, BioNetGen have also been modified to be able to specify polymeric sites on molecules, their type, location, and interaction distance.
The ribosome that has collided at the stall site is not able to move subsequently. Needs fixing.
Also updated README listing major lessons learned. Need to figure out how reactantTemplates are assigned for each reactionClass instance.
The reactions match between the old exhaustive search and the new polymerneighborhood search. No random printing to screen. Transcription is failing in the polymerNeighborhood search. But this should be a fixable problem.
But the neighborhood search on its own did not improve speed significantly. See README.org from today for details. I will come back to this at a later time.
updated validation for windows
including windows dll's for proper bundling
dll requirement for windows is confirmed
was missing a "[" if no operations were present
Ubuntu binary not working under WsL at least, testing different version
Merging branch made to address seg fault in Issue 37
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