jsherfey
commented
8 years ago I think all functions in group one can be deleted.
- comparemodels, extractfeatures, and getfeatures were created for project-specific post-simulation analysis that is not generic enough to be included in the dnsim package.
- I remember creating prepare_spec, studydriver, and StudyDriverUI during development of the GUI, and it looks like they were subsequently fully incorporated into modeler(). It should be safe to remove these...
I'm in favor of removing all uninformative "graveyard code".
Jason
On Wed, Oct 7, 2015 at 3:22 PM, asoplata notifications@github.com wrote:
This is an issue for two little things, only concerning the "real" DNSIM code in dnsim/matlab/functions. The following functions do not seem to be used/called by anything else (some are interdependent, not that it matters), and I've never seen them used in any capacity like during instructional "how-to" scripts. We may have to update these functions when we make the post-SFN changes to the data structure, model structure, or the main control flow of the program IF they are necessary, but if they are not or are deprecated, we should delete them:
- comparemodels.m
- extractfeatures.m
- getfeatures.m
- prepare_spec.m (actually just a script, not a function)
- studydriver.m
- StudyDriverUI.m
In addition, after looking through the files in this subdirectory for functions that have a significant amount of commented-out code (especially at the end), I've found several files seem to have a large amount of this "graveyard code" as I call it. Given that versions of these files containing the commented-out code will still be present in the Git history, and we can clearly mark such a commit where they're removed, I think it's best to go ahead and remove most of the commented-out code in these files:
- biosimdriver.m
- dnsim2xpp.m
- MechanismBrowser.m
- modeler.m
- plotpow.m
- rk.m
- runsim.m
- write_dnsim_script.m
SO, my job for other people is to answer: Which files of the first group do we NOT want to delete (and therefore, when we make big architecture changes, have to port to the new formats/stuff), and is there any good reason, on a file-by-file basis, why the commented out code in the second group shouldn't be deleted?
— Reply to this email directly or view it on GitHub https://github.com/jsherfey/dnsim/issues/63.
asoplata
This is an issue for two little things, only concerning the "real" DNSIM code in
dnsim/matlab/functions. The following functions do not seem to be used/called by anything else (some are interdependent, not that it matters), and I've never seen them used in any capacity like during instructional "how-to" scripts. We may have to update these functions when we make the post-SFN changes to the data structure, model structure, or the main control flow of the program IF they are necessary, but if they are not or are deprecated, we should delete them:comparemodels.mextractfeatures.mgetfeatures.mprepare_spec.m(actually just a script, not a function)studydriver.mStudyDriverUI.mIn addition, after looking through the files in this subdirectory for functions that have a significant amount of commented-out code (especially at the end), I've found several files seem to have a large amount of this "graveyard code" as I call it. Given that versions of these files containing the commented-out code will still be present in the Git history, and we can clearly mark such a commit where they're removed, I think it's best to go ahead and remove most of the commented-out code in these files:
biosimdriver.mdnsim2xpp.mMechanismBrowser.mmodeler.mplotpow.mrk.mrunsim.mwrite_dnsim_script.mSO, my job for other people is to answer: Which files of the first group do we NOT want to delete (and therefore, when we make big architecture changes, have to port to the new formats/stuff), and is there any good reason, on a file-by-file basis, why the commented out code in the second group shouldn't be deleted?