Develop has several issues

[vikramalva]

Forwarding, selection etc. are broken. I have no free time to test the Toolkit presently and I am afraid we are just accumulating bugs. Please urgently reset the Toolkit to: https://github.com/zy4/Toolkit/commit/4f9b7f09e0a92ac5d7ac2fb84878cd0478dfda41.

[vikramalva]

Some issues that I found within 5-10 minutes of testing:

[vikramalva]

[vikramalva]

Positioning of the menu and unnecessary scrollbars

UPDATE: should be fixed now - Felix

[vikramalva]

I will just stop here, but there are several others.

[vikramalva]

Toolbar is missing..

[zy4]

are you planning to push to production today? Because otherwise I can fix all of these today. There will always be bugs like this but this is no reason to panic. As far as I can see, these bugs are css and off-by-one-errors but nothing special. And regarding the workflow: if you really need to change something today, let's say some update message, you can simply merge a separate branch on rye and push it back to master. But these big commits needed to get merged because otherwise we can hardly proceed in other big tasks like the frontend rewrite. The reason for this being that simply Felix was working on files which I deleted in the other branch!

[zy4]

Plus I squashed all of the recent commits so that reverting (not resetting) is easy.

[vikramalva]

No, but I can only start to test the Toolkit again after I return to Germany. And when I return I will have to hit the ground running to deal with other important deadlines. All search tools are essentially broken. Clicking on the visualization map doesn't take me to the alignments. When I select sequences on a different page of the data table and subsequently go somewhere else they are not remembered. If I select one sequence and hit foward, not one but but many are forwarded. There many other issues. I would prefer to have Master in a clean state and we should revert back to my last commit.

[zy4]

There is some trade-off to be paid: you saw the size of the merges. Either we have a very painful process to resolve merge conflicts (and you would have to test thrice or more times the whole toolkit) or we run through some mild debugging which I would completely do myself. Again: if you need to push to master, just modify in a different branch and merge it. If you need to merge a bugfix which exists only in master: just git cherry-pick and push back to master.

Master will be clean this evening. These are minor bugs.

[vikramalva]

I just pushed IE related changes to Rye and had to do it via a not so straightforward process. I could of course merge bug fixes directly to master on Rye through new branches, but this would result in many unwanted issues. I may not be able to push back to master easily without doing a pull.

[zy4]

they were merged first, you could just pull them from master via git cherry-pick commithash

I see your points and from your perspective it is understandable to me that:

• you want developers to invest more time in manual testing since you don't have this time (we'll find a solution for this. You could write a check-list or so)
• you want to be involved in breaking and design-related changes

From a developer's perspective, I made my points quite clear. We are under heavy construction, still. This is due to the fact that the current code base is not extensible. Only to the price of following all the anti-patterns.

As for pushing back, you can do the following: git push origin master:newbranchname But in this case I see no point in doing so because you would not add anything new to master, you are just behind.

[vikramalva]

My only aim is to keep master as clean as possible and we should test branches thoroughly before merging them to master to avoid this sort of situations.

[vikramalva]

Loading is broken:

[zy4]

Should we set up a "develop" branch then? How can we speed up code reviewing?

[zy4]

We can do something like https://github.com/zurb/foundation-sites They have the "develop" branch as main protected branch and master is separate.

[vikramalva]

Good idea! That way I would not need to test Master thoroughly so often.

[zy4]

I am going to set it up later. We need to find some workflow for the time when we make it open-source, anyways.

[vikramalva]

Selection and forwarding for all search tools are broken; Please compare with production. There seems to be no real correlation between what is selected and what is forwarded. Selection syn between data tables and alignments is broken for all search tools. If one selects a hit on any page of the data table, they should also be selected in the alignments section. I think I would need days of tests to have all of this working again.

[vikramalva]

Please have the HEAD of the develop branch point to https://github.com/zy4/Toolkit/commit/2904f1bdfb1862b4b0ca56e945a1682595157bc8. We could push all important fixes directly to the develop branch.

[felixgabler]

Mental note: Maybe we should also think about implementing tests in the frontend. Forwarding, selecting and more could be tested in a more automated fashion to make it easier for all of us. There has to be a way to rid us of the unnecessary function testing to some degree.

vikramalva notifications@github.com schrieb am Mi., 10. Jan. 2018, 15:07:

Please have the HEAD of the develop branch point to 2904f1b https://github.com/zy4/Toolkit/commit/2904f1bdfb1862b4b0ca56e945a1682595157bc8. We could push all important fixed directly to the develop branch.

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[zy4]

What about css, though?

[felixgabler]

I hope that there will not be such a big refactoring in the near future. Furthermore CSS is quickly tested. Or at least quicker than all of the js.

Seung-Zin Nam notifications@github.com schrieb am Mi., 10. Jan. 2018, 15:25:

What about css, though?

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[zy4]

Please have the HEAD of the develop branch point to 2904f1b. We could push all important fixes directly to the develop branch.

you mean HEAD of master, right?

[vikramalva]

Yes head of master. And I meant we could push import fixes directly to master, while most other stuff should go through the develop branch.

[vikramalva]

I found a bug in PSI-BLAST on production that must have crept recently; I had tested these things thoroughly in the past.

Hit 1 reappears again after hit 500. We should try to fix this soon, before fixing the others. https://toolkit.tuebingen.mpg.de/#/jobs/10165566

[zy4]

For me it does not repeat

[vikramalva]

I tested it more and it doesn't happen every time. Something to keep in mind.

[zy4]

I think this is due to side-effects which I was about to reduce.

[zy4]

branches are set up

[zy4]

Could you sbt-release since you pushed to production?

[vikramalva]

To the current master on GitHub?

[zy4]

I already did it. It's alright! We should just keep up the workflow...

[felixgabler]

I have a question about the missing toolbar. Do we really want to show it for smaller devices? We already have a off-canvas menu for these cases

[zy4]

I also think that it should not be there

[vikramalva]

I find it really practical to have, as I use the Toolkit in a browser window half the size of my screen and I don't want to always use the off-canvas menu for this. I would therefore like have it.

[felixgabler]

We could reduce the breakpoint to only hide it for small screens but display it for medium-sized ones.

vikramalva notifications@github.com schrieb am Do., 11. Jan. 2018, 18:54:

I find it really practical to have, as I use the Toolkit in a browser window half the size of my screen and I don't want to always use the off-canvas menu for this. I would therefore like have it.

[image: toolbar1] https://user-images.githubusercontent.com/20257466/34839047-9c2a9b94-f700-11e7-91d1-fd8bb13e4186.png

[image: toolbar2] https://user-images.githubusercontent.com/20257466/34839060-a41245dc-f700-11e7-9ece-4803f394ee57.png

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[vikramalva]

Isn't it this way on production?

[zy4]

Clicking on the visualization map doesn't take me to the alignments

this bug was settled outside of our codebase - it is in hhviz.pl wondering whether we should include this into the repo because there is javascript code embedded

[vikramalva]

Sure and I should mention that it used by HHblits, HHpred and HHomp. Also, clicking on a bar at the bottom of the map should load all unloaded alignments up until the alignment corresponding to that bar, as on production.

[vikramalva]

I think the map is also broken for PSI-BLAST, which uses a different script.

[felixgabler]

If it is already this way, we should think about reworking our responsiveness. I will look into it

[vikramalva]

Also, don't try to further optimize the size for mobile devices. I and @anjestephens spent quite some time on this and fixed the smallest size such that the results page of various tools are not broken. We don't want to spend time on optimizing the pages of every single tool for mobile devices.

[anjestephens]

I don't know if I did everything right to get up to date but I have issues as well. (The tabs are not generated, the content is limited to the input field)

[felixgabler]

Are there still issues?

[zy4]

@anjestephens please try to execute sbt clean and sbt cleanFiles @felixgabler yes, I am going to fix them this WE.

[anjestephens]

@zy4 Actually I freshly cloned the project because I had merging issues and thought it was time to refresh anyways. But I'll try that.

[vikramalva]

@felixgabler most of the issues (e.g. with selection and forwarding) that I reported earlier still exist. There are some CSS issues too.

[zy4]

@anjestephens ... also clear the browser cache if you haven't already

[zy4]

@vikramalva can you check again? If something is still missing / not working, please open a separate issue for it.

[felixgabler]

If I understand correctly, all the issues have been singled out into separate issues. Forwarding/Selecting into the checkbox component (#260) and css into #265. If this is correct, we could close this issue