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Is a more extensive version checking necessary? #16
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Anyway, I have forked from Frank's head and committed my edits. |
Hi @JohnMCMa not sure if you are still working on this, but if there is an update let me know. Thanks! |
I'll try completing it, but I'd only have the time to start from late next week. John |
@JohnMCMa not any hurry, but glad to see you are still around |
Hey @cjfields, |
Hi @JohnMCMa I think we should set it to 2.2.3 if that's considered the base stable version (we can still support v1 but we should probably dissuade use of it since it's not actively developed). We'll of course need to actually evaluate v2.2.3 in tests; maybe something we should set up w/ Travis-CI at some future point. |
@cjfields |
@JohnMCMa to be honest, I would just stick with supporting a minimal version of v2.2.3, and stating that we no longer support older releases of v2 due to the unstable API (which would accomplish two things: reduce maintenance headache for us and push users to using more stable releases of primer3 v2). If it means we remove tags or replace older tags with newer ones I'm okay with that; we will just need to gauge how much fallout there would be in tests and update the tags as needed. |
It's less of an hassle than you'd expect. There're 174 tags that has been used at least once since v2.0.0, of which 133 are used in all versions. If we ignore 2.0.0, then between 2.2.0 and 2.3.7 there're 158 commonly used tags. Another option is just ignore all unstable versions, which means I'd only need to deal with 1.1.4, and 2.2.3 onwards. For the v2 part, this would leave 172 tags, of which 160 are common between 2.2.3 (strictly speaking 2.2.2) and 2.3.7. My quick skim of the release notes, however, shows there are more run-time arguments being deployed:
I sincerely hope nobody is seriously using anything older than 1.1.4/2.3.0, though. Attached is a census of the tags used in the 2.x.x branch. |
Hi @cjfields , I have actually coded what's on my mind right now; just I haven't synced it yet. |
@JohnMCMa not a problem. You may have guessed by my radio silence I've been a bit busy myself |
Looking back at primer3 2.2.3's release notes, I have noticed that even after 2.0.0 there has been quite a bit of changes among input tags:
2.2.0 added all the TH tags, SEQUENCE_PRIMER_OK_REGION_LIST, and "PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION, PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION have replaced
SEQUENCE_PRIMER_OVERLAP_POS and PRIMER_POS_OVERLAP_TO_END_DIST" (note the tag type change from PRIMER to SEQUENCE).
2.2.2 added PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE and PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE.
Looking even back, 1.1.X added PRIMER_TM_SANTALUCIA, PRIMER_SALT_CORRECTIONS, PRIMER_LOWERCASE_MASKING, PRIMER_DIVALENT_CONC, and PRIMER_DNTP_CONC over <1.0.X.
While I sincerely don't believe anyone would still be using version v<1.1.0, would it be necessary to allow a finer version check on the run script so that all input tags would be legal for the version of primer3 they're using? It is a straightforward change that I as an novice can do, but I wonder its necessity.
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