Detailed gene tracking #224
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This brings the functions in random.clj back into a working state, but there are other calls to random-plush-instruction-map that need to be updated. Calls to random-plush-genome-with-size do not need to be changed unless you want the flag to be set.
This does not break anything in random.clj, but it most assuredly breaks code elsewhere. WARNING: The breaking changes are probably not compiler errors and may show up in strange ways.
This commit is not tested.
This commit has not been tested, but it is essentially the same change as the previous commit so it should work fine.
I've only tested this function via the REPL. It is intended to be called on every individual after it is produced via an operator.
This macro is intended to make the code cleaner when you want to conditionally thread a value through several functions.
Using the or macro is so much cleaner than the anonymous function that I wrote.
Because the assoc was only being performed when the child wasn't oversized, and because revert-too-big-child doesn't always set the :genetic-operator, it was previously possible to produce children with no :genetic-operator.
The information is not readily useable in such a report, the UUIDs make the logs less readable, and they make the logs take more space in permanent storage.
…solution/detailed-gene-tracing-rebased The change by @lspector from representing genomes as vectors instead of lists modified many of the same spots in the code that the gene tracing did. This merge resolves all the conflicts in a way that preserves the intent of both changes.
This fixes errors that arise later when the autoconstruction code is interpreted and tries to manipulate the genomes as vectors which fails because *this* method turned all the vectors into lazy sequences.
…rebased This merge had one conflict. Lee moved the argmap into a separate file and I had added something to the argmap so I had to do the move manually.
Using forms built in to Clojure is preferred over custom code.
This will not make `git blame` more useful, but it will make the diff more readable when merging into master. The best thing to do would be to go back and modify commit 015d591 to not introduce the whitespace, but I'm not sure that we can do that at this point.
…rebased This brings in a whole bunch of new code (mainly operators) that will need to be adapted to work with the gene tracking before this can be merged to master.
This changes the code introduced in 015d591. I didn't do a `git revert` because it needed to be done manually.
Also, adjust formatting of this function so that it matches that on master.
They now use a consistent number of arguments (and the number is aligns with what random-plush-genome expects).
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This pull request brings in the code that allows one to track the individual transfer of genes. It can be enabled and disabled (default disabled) via the
:track-instruction-mapskey in the argmap. When it is enabled, each instruction map in each individual contains a:uuid. Genes also have a:parent-uuidthat refers the instruction map in previous generation that it was copied or mutated from (unless it was not copied or mutated from any previous gene in which case:parent-uuidis absent/null.The standard reports in
reports.cljhave been modified to hide this extra information. It is recommended to use EDN printing when this is enabled and while the CSV logging still works when EDN printing is enabled, the parsing is probably no fun.This also makes a small change to the way :genetic-operators is added. It was previously possible for an individual to have no
:genetic-operatorattached to it when a run was set to truncate children that exceed the size limit. (Commits 44382cd and (later) ceb92cf address this.)