OE IRC 11May06

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Harold: tada!

kchris: Hi!

Harold: Hi Karen

jrichter: Howdy, folks.

midori: yay, people!

Harold: the man

Alex_MGI: Hi

jrichter: The documentation finally got finished when I decided to remove the Complex Class Plugin from OBO-Edit. It was just a distraction anyway.

midori: whatever works ...

tberardi: Good morning!

pfey: hi All!

jrichter stands up in a gentlemanly manner

pfey: John, you are too fast for me - just had a lttle test-a-tete with beta19 last night, and now there's 20!

midori: 5:30 timestamp ... let's roll!

jrichter declines to respond, since there are so many possible innuendos...

Alex_MGI: Gonna be a quiet meeting.

jrichter: Midori, master of the agenda: tell us what to do!

midori: Jane & Jen are on holiday/agenda; as far as I know Amelia will be along

midori: Well, I've heard a crazy rumor that the documentation is done at last. Is it true???

jrichter: Indeed it is.

jrichter: I incorporated all the edit notes I could, although I think I've missed at least one person's suggestions.

jrichter: Great notes from Karen, by the way.

kchris: Thanks!

midori: There were two or three people assigned to read the whole thing through to make sure it makes sense ...

kchris: I think I learned a lot too, from working my way through the structural editing section!

jrichter: beta20 was released to incorporate the new docs, and all the bug fixes I did based on people's documentation notes.

jrichter: I added a whole new section to the introduction called "Basic Vocabulary" or something like that.

kchris: That should be good.

jrichter: It explains Terms/Classes, Properties/Relationship Types, Link/Relationships

midori: Yes, I saw it - very good move

jrichter: Karen's idea.

Alex_MGI: We're getting close to release then...

jrichter: Absolutely.

midori: I also spotted some typos in What is an OBO-Edit? and What is an ontology?

midori: Should I fix them (assuming my cvs access has resumed functioning...)?

jrichter: Please post 'em to the tracker. It's a very useful way for me to keep track of my documentation todo list.

midori: ok

jrichter: That way we don't end up replicating any work.

jrichter: I think we should give the docs a thorough perusal, do one last round of hardcore testing on OBO-Edit, and release.

jrichter: Which reminds me:

jrichter: Were there any objections to calling the first release "OBO-Edit 1.100"? I sent an email about this last night...

midori: I thought Alex's reply made sense ...

Harold: no

tberardi: I'm not sure why you don't want to call it OBO-Edit 1.0.

pfey: me neither, I think 1.0 is great and least confusing

Alex_MGI: I essentially agree.

jrichter: Because normally if a version number is succeeded by "beta", it means that it's a later release than the plain version number.

midori: I think 1.0 would be fine ... but I really have no strong feelings. You can number it 1 or 1111 or pi as long as it works

jrichter: Well, let's call it 1.0, but the next round of versions will be called 1.001-betaX

midori: ok

jrichter: And the next full release will be OBO-Edit 1.100. Is that okay?

Harold: How about THE OBO-Edit 1.0

tberardi: John, that sounds great.

midori: accept no substitutes!

gwg: sounds fine to me!

pfey: sounds good to me too

Harold: 1.0 is fine

rama: yeap, sounds good!

jrichter: Cool. Are there other agenda items, Midori? If not, I'd like to move to a discussion about planning OBO-Edit 1.1.

midori: Just a quick one: beta20 testing. Has anyone done any?

Alex_MGI: As far as versioning and planning goes, it would probably good to do more formal planning, such these things will be part of version 1.1.

Alex_MGI: such as

gwg says "not yet" to Midori

midori: I've just done load & save ....

Alex_MGI: Yes, I looked at the documentation and found some quirks which I have passed on to John.

midori: beta16 can read the beta20 output, no problem

kchris: I thought I was doing good that I had actually used beta19. I've only just loaded beta20 this morning...

Alex_MGI: Found one additional "Open" dialog box, where Save is expected.

pfey: same here

midori: There's just one thing, not even sure it's a problem:

Harold: Midori, I've tried an initial test, but it bombed loading the ontology, but it might be because I have installed it into a separate directory than OBO-Edit (which is where beta 16 is). I'm assuming that this is also why none of the figures show up in the docsl. I'll have to move it out into OBO-Edit

midori: beta20 is adding a bit to the part_of lines

jrichter: ?

jrichter: A little N?

midori: No, I mean in the output file - so instead of (e.g.) relationship: part_of GO:0005829 ! cytosol, we get

midori: relationship: part_of GO:0005829 {necessary=true} ! cytosol

jrichter: BAD!!!

Alex_MGI: Loads fine for me.

midori: (I noticed the little N, and I thought it was a nice touch)

kchris: beta20 loads fine for me too

Harold: again, I think it's my directory structure to keep it separate from OBO 16

midori: yeah, the extra {necessary=true} doesn't stop beta16 or beta20 from loading the file.

jrichter: Okay; I think I'm going to need to release beta21 again. I need to fix that output "bug" to avoid the huge diffs, and I need to fix the installer packaging so the docs appear.

jrichter: Not release "again", I guess, but I need to do a new release. It'll be done in under an hour.

kchris: I've got 16, 17, 18, 19, and now 20, each in their own directory, each launches fine

Harold: John, when I unpacked the mac version there was a flag about an unlicensed installer

jrichter: Oh, hell no. Did that happen to anyone else?

Harold: K- maybe it's the platform specific versions that do it; I haven't tried the platform-indpendent version

midori: I usually only use the platform-independent one ...

jrichter: This probably is easy enough to fix. I rebuild my system recently, and I bet InstallAnywhere just forgot the license info.

kchris: yea, I only ever use the platform independent, got frustrated with the Mac installer not working more than a year ago and quit ever downloading it

Harold: John, when I try to use the desktop icon, it repies sh:line 1: /Applications/OBO:

Harold: No such file or directory

jrichter: Harold - I'll test the mac installer before I post the next release today.

jrichter: If you want working docs immediately - download and unpack the platform independent installer.

jrichter: The docs are completely intact there.

Alex_MGI: As I noted, there are problems in the way screenshots get included for the documentation in the mac installer.

jrichter: Yeah. It looks like the file lists for the installer weren't updated correctly. That's one of the things I'll fix as soon as we're done here.

Harold: I just deleted the entirre 20 install, etc. and replaced it with the independent version

jrichter: We only have 10 minutes, so I'd like to discuss the process for planning version 1.1

kchris: John, I may have found a bug in cloning, but had a problem with the SF site last night when trying to post it. I'll post it now.

jrichter: (Thanks, k)

pfey: sorry I'm late - yes, the unlicensed installer message i got too!

jrichter: Oh, wait, we actually have 40 minutes. My bad. I still want to talk about version 1.1, tho.

tberardi: [I just tried installing the Windows version and got this message "This installer was created with an unlicensed version of InstallAnywhere."

midori: OK, shall we (a) watch out for beta21 and then (b) do the bare-bones tests on it?

jrichter: I think I need to update my serial number in InstallAnywhere. I'll look at it now.

jrichter: Yeah, Midori. beta21 is coming in a few hours. For now, download the platform independent version and use it to browse the docs.

midori: If it loads, etc. and these latest bugs are fixed, we'll move on to intensive testing.

rama: in beta20, i see the is_a icons but I don't see the part_of icons.

pfey: the platform independent version was fine for me

kchris: icon thing was also true for beta19

Harold: platfor independent seems to work, but the select button doesn't seem to exapnd the dag at the left anymore

Alex_MGI: I've got icons in B20.

midori: mine is ok on both counts (icons and expansion)

jrichter: I think the icon thing may be a result of deleting your .oboedit directory. You probably need to reassign part_of to an icon.

Harold: never mind, I had some filters turned on from a previous session

gwg: For the icon problem, I think it's just a case of specifying the correct name for the part-of relationship

gwg: ... like John says

rama: Yeap, that did it. I am seeing the part_of icons now. thanks for the tip.

midori: Anything more on testing? If not, we'll move on to plotting & scheming for 1.1.

Alex_MGI: When we do final testing, we'll need to do some installations on "virgin" machines, that have never seen OBO-Edit, to make sure everything gets installed correctly.

jrichter: You can simulate a virgin machine by deleting the .oboedit directory. That's the only place OBO-Edit writes configuration information.

jrichter: It doesn't use the windows registry or anything like that.

Alex_MGI: Okay. will do.

jrichter: Okay, moving on?

midori: OK by me.

jrichter: Here's how I think we should proceed on OBO 1.1 ...

jrichter: Let's use the sourceforge feature request tracker as our starting point.

jrichter: Anyone who has an idea for a new feature that they haven't posted, put it up there.

jrichter: Ideas can be as big or small as we like.

rama: Is it possible to have a Oboedit default, and a oboedit advanced option when we load? We need to define what is default and what is advanced.

jrichter: I thought the consensus was that we didn't want that kind of thing.

jrichter: Right?

rama: was there a consensus on that? Sorry, I missed that. Reason being????

tberardi: I don

kchris: I think we did agree that default vs advanced was not where we want to go right now

midori rummages through saved email ...

jrichter: I think people thought that we'd be better off focusing on documentation and general ease of use rather than breaking OBO-Edit into editing modes.

gwg: I think we kinda have an advanced and simple mode anyway

rama: I will look at the mail archives..

gwg: if you have it starting up without the link / complex filtering turned on, it is quite simple

jrichter: I know Suzi is dead against the idea, and she will be hard to convince.

gwg: and you don't have to use any of the plugins unless you specifically want to

midori: yup, found it ... we didn't want different modes set at the time of installation

rama: okay, lets move on!!

jrichter: But rama - if there are complex features you'd like to hide, put the specifics up on the feature request tracker. Maybe there's a way to hide those things without introducing a new mode.

jrichter: Anyway -

rama: Will do.

gwg: you could always hide things by putting them in the config manager

jrichter: I'd like OBO-Edit 1.1 to incorporate 10 or 15 new features, and 1 or 2 research project type goals.

midori: We can also use the documentation to help flag basic or advances features.

jrichter: Everyone should go through the feature request tracker in about a week, and pick their top 10 new features and send them to the mailing list.

midori: action item!

jrichter: We'll collate the lists, and come up with the new sets of features.

jrichter: Some requests will require more research. For example:

jrichter: I'd like to try to upgrade OBO-Edit's drag and drop capabilities. This will require a week or two of research to see if the Java 1.4.2 drag and drop spec is finally up to snuff. Also:

jrichter: I'd like to try out the "Editing with GraphViz" feature request. This probably isn't possible with GraphViz, but there are some cool new Java graph drawing tools out that might be used for a GraphViz-y editing mode. That'll take some research too.

kchris: I have a couple more basic requests, I just added them both the Feature REquests tracker.

jrichter: After we've had our mailing list discussion of what features to include, we can hammer out the final list over IRC.

jrichter: We may end up with way MORE than 15 new features, since some are really small. So when you mail your favorites out, include as many as you like.

jrichter: ALSO!

jrichter: If you see a feature request that you HATE and think would be destructive, send an email to the list so we can talk about it. If we agree we never want to do something like that, we'll just delete the request item.

jrichter: Okay, I'm done. Any thoughts/suggestions?

kchris: So, basically, everyone is supposed to look through the items on the Feature requests tracker, add any other suggestions, and then mail out their top picks?

jrichter: Yup. Also suggest unhelpful items on the list to delete.

jrichter: And big feature requests (like "Build an editor for the screen layout") are fine.

kchris: If we're done with defining the first task towards developing a plan for 1.1, then maybe we could go back and work out the next steps/timeline for the 1.0 release

Alex_MGI: Are there any major bugs remaining?

midori: I can't claim to have tested enough ... but I can only think of small ones

jrichter: (not that I know of...)

kchris: I think I found a significant bug with cloning this week, still need to submit the item.

kchris: My other bug was a pretty minor issue with a hotkey

gwg: what was the cloning bug, Karen?

kchris: I selected a group of 3 terms, 1 parent with 2 children, and cloned them

kchris: It looks to me like only 2 of the terms were created, and in looking at the OBO-Edit file, 1 of them might not have an ID

jrichter: !

midori: aaaaaaaaaaaaaaaaaugh

kchris: In addition, when I try to find them, searching for 'clone', the search only finds 1, even though I can see 2 on the screen

jrichter: Cloning is not designed to clone hierarchies all at once.

jrichter: I bet this problem happens when you try to clone a term and its child in one move.

jrichter: This is a cool bug. Please report it.

kchris: Yea, I tried last night, but the SF page gave me some problems, so I'll do it today

midori: I just tried it ... it only cloned the parent, but seems to have done so correctly.

jrichter: That cloning bug has a trivial fix - I could just force cloning to operate on one term at a time, if push comes to shove. But hopefully it can be fixed to clone hierarchies all at once.

kchris: The parent always works, it's one of the children that doesn't appear

midori: oh now, wait, it did try to clone one child as well ... so I must be getting the same behavior as Karen

kchris: For both of the 2 cloned terms that were created, the Text Editor Panel does not show an ID...

jrichter: I'm not sure I know what the correct behavior is in this case...

jrichter: Right now, "clone" means "create a duplicate term with all the parents, children and text attributes of the original".

jrichter: It seems we're using a more expansive definition of cloning now.

jrichter: Rather, we'd like to be using a more expansive definition.

jrichter: If you select a hierarchy of terms and say "clone" what do you expect to happen?

gwg: I would want the terms that I had selected to be cloned

midori: Let's make an executive decision. My suggestion: go with the force cloning to operate on one term at a time option for now, and put cloning hierarchies on the list of new features to consider for 1.1.

kchris: I still expected it to act on that same definition, but it might be creating cycles if that's what the red arrows mean.

gwg: if I'd selected a single term but one which had children, I'd just want the term selected to be cloned

gwg: can you do non-contiguous term selection in OBO-Edit?

jrichter: Let's take this to the email list. I'll send out a detailed discussion of this, because I think it's actually pretty complex.

pfey: agree with gwg

jrichter: gwg - Yes you can. On MacOS, command-click.

jrichter: On other OSes, ctrl-click.

midori: seems to be control-click on the mac as well; command-click equals right-click, and brings up the menu

kchris: I think MIdori's suggestion is fine, force clone to work on only one child. It sounds as if that's what John was thinking when he designed it, but the help said nothing about only one term, and with 3 contiguious terms selected, the 'clone' option appears on the right-click menu

jrichter: Oh, I intentionally made it clone multiple terms at once, but I was assuming those terms would be siblings, not related to each other.

gwg has to go to band practice and bids everyone a fond farewell

Harold: away

jrichter: It may be premature to relegate hierarchy cloning to the next release; it may be really simple to do.

jrichter: I humbly request permission to do a little research and then send out a report email.

kchris: I'll submit the bug report, you can see what you think is best

midori: all righty

jrichter: Actually, I think I'll force single-term cloning in the next beta release this afternoon, but I'll do research on the side. That way we get the best of both worlds.

jrichter: About deciding when we have a release...

jrichter: Let's say that in a week, everyone sends out an email saying "I sign off on this release" or "I sign of on this release when the following bugs have been addressed..."

kchris: What do we need to do with respect to the documentation? each person reread their section?

Alex_MGI: Whatever release is then current, I assume.

jrichter: Yes to Alex and Karen.

jrichter: Karen - I consider everyone's documentation section part of their bug-testing duties at this point.

jrichter: Midori - can you send out an email explaining that everyone needs to send out a sign-off email next week?

midori: We should also nudge the readers-of-all now that it's all there. It'll be good to have an overview.

midori: John - OK

jrichter: Anyone who doesn't send a signoff email will be considered to have opted-out of the approval process.

kchris: which means...

Harold I'm back

jrichter: Karen - They don't get to complain if OBO-Edit is released and they don't think it's ready.

jrichter: Okay, times up. Let's review action items...

kchris: So, you either have to send a sign-off email, or a "nope, not ready", no response is not acceptable

jrichter: Karen - more than that. If you say "not ready" you need to say what needs to be fixed before it IS ready.

kchris: agreed

jrichter: That way we have some way of working through a list of goals.

Harold: sounds good

jrichter: Action item - John releases beta21 with file writing fixes and installer documentation fixes

jrichter: Action item - Midori emails group about signoff emails

jrichter: (Let's call Thursday May 18th the deadline for that)

jrichter: Action item - John researches Karen's cloning bug

midori: One more thing about signoff: can someone request more time to make a decision, and if so, how long? (I'm a bit biased because I'll be away part of next week.)

jrichter: Midori - if that's a problem, let's just set the deadline back. I don't want to be able to extend this.

jrichter: (once a deadline is in place)

Alex_MGI: Good, I'm away at a meeting for most of the next week.

jrichter: Midori/Alex - A suggestion for a revised deadline?

midori: Will next chat be in two weeks? If so, that could also be the deadline.

Harold: so, the 25th

jrichter: Cool. May 25th IRC chat is the deadline.

Alex_MGI: Great

pfey: and always at the half hour?

jrichter: We can aim for a June 1st release for OBO-Edit.

midori: I like the connection to a chat.

midori: Petra - fine with me, so unless anyone else thinks it's terrible, yes.

rama: sounds good to me.

jrichter: If you CAN send your signoff email early, please do. That'll give me time to address bugs.

Alex_MGI: Fine with me.

kchris: sounds good to me

midori: and me

rama: quit

jrichter: Cool. Farewell, everyone. Excellent work.


midori: I'll send the transcript as usual.