A research change in 0.15 adds a "level" to certain technologies (such as "Mining Productivity"). This caused some issues in AR as "mining-productivity-1" remained marked as "not researched" after researching the technology, but the "level" increased to 2.
Long story short: Infinite and multi-level research isn't working as of version 3.0.1. I am looking into this, but I currently don't have a solution. For the time being AR will remove such technologies from the queue when it's done researching the first level.

Further testing revealed that upon completing level 1 of an infinite research, it did start on level 2, although the game displays level 1 as being researched. Rest assured, it isn't researching the same technology again, it's just a graphical issue in Factorio 0.15.2.

It seems that these issues are making a miscalculation on the option "Fewest Ingredients First". In my testing it keeps researching the same tech "Grenade damage" even tho it costs 8000 packs per 45s time instead of researching "Mining Productivity" which is costing 3300 packs per 60s time (360k packs instead of 180k packs)
Also with the mod "Crafting Speed Upgrade" from Klonan, it keeps researching that crafting speed since it takes 30s time but its not accounting the pack count of that, a lvl 57 takes 6397 packs and 6397x30s time for research while mining productivity 34 takes 3300 packs and 3300x60s time. It seems that its considering the time for the research instead of ammount of packs it consumes

Thanks for your feedback, I will look into it :)

I've uploaded a new version, although I can't say if it'll solve the issue you're experiencing. One thing though, the "fewest ingredients first" didn't mean "tech with least total science packs". It meant "tech with least types of science packs" (so it'll research all red science before it starts on red+green). It was a kinda confusing option that made more sense before the ingredient filter, so I've removed it in the last version.
Also, if you've prioritized any infinite techs, then the topmost prioritized tech will always be researched.

If it's still picking weird techs, then let me know. The formula for picking next tech (when you've not prioritized anything) is "<seconds per iteration> * <total science pack count per iteration> * <iterations>", the lower value should be picked first. If it doesn't do that, then something quite strange is going on.

Are you planning on adding support/an interface for mod-added research ingredients (e.g. Bob's Modules) in the new GUI? As is, with the removal of the custom ingredient box, AR can't touch those techs anymore.

I think what you're looking for are the new "Allowed research ingredients" toggle buttons. Research ingredients added by other mods such as Bob's Modules should show up there and you can disable those ingredients to prevent AR from starting any research that requires those ingredients.

No, I know that.

I guess it's a bug report as opposed to a question/suggestion, then -- https://puu.sh/vEvQG/873aebf22f.png

Strange. I tested this earlier and it worked, although I tested with Bob's Modules for 0.14 (just modified it to work with 0.15 for the testing). Guess there are some changes in the new version.

I'll take a look at it, thanks for letting me know!

Okay, this is really strange. I installed Bob's Modules and the new ingredients Bob's Modules add do show up in AR.
Does it happen when you start a new game? When you load a game?
If it happens when you load a game, was it a saved game that used to have an older version of AR? older version of BM?

Okay, yeah, it works in a new save. So I guess it gets cached somewhere?

The save in question was our initial foray into 0.15.
It's been having everything added in as it's updated. That means it started with nothing, added AR 3.0.0, then kept up with updates. I'd hazard a guess that the AR update with the filter came before the BM 0.15 update did, but I don't remember.

Oh, I think I know what's happened, and it needs fixing:
You added BM to a save that already had AR. AR only scans for technology ingredients once (it's for performance), then it's cached. Obviously it then won't pick up new ingredients by addons added later.
I'll see if I can get it fixed tomorrow.

Never mind, I fixed it.
Turns out I only needed to change three lines :)

I realized my fix was inferior; Whenever you add/remove/update mods then the ingredients filter will be reset. I'll fix this after work.

Now it should be fixed :)

I have been finding that even after unticking the announce completed research, I still get alerted. Are you able to take a look into this please? Cheers

Heya. I looked into it, but I'm not able to reproduce such an error.
I'm wondering, is it possible that you have another mod that announce a completed research?
Or perhaps you're thinking about the technology window that pops up when a research is completed? This one I can't control from the mod, but you can disable it by pressing "ESC" -> "Options" -> "Other" and unchecking "Technology window opens when research is completed"

2 bugs

Auto research doesn't always work with infinite research (maybe an infinite research checkbox that just researches each/the cheapest in turn once all other research is done?)

The tech tree is broken imo (https://forums.factorio.com/viewtopic.php?f=6&t=47945) and some of the prerequisites are hidden like you don't need to unlock a science pack for it to be demanded for by a research recipe easiest example is advanced oil processing that uses science pack 3 but doesn't at any point require advanced electronics to unlock science pack 3 could you add these hidden prerequisites

The second issue I won't add any fix for, that's something that must be fixed in the game. Basically I want this mod to be agnostic about technologies, the mod shouldn't know about any specific technologies and their dependencies, it should just work from a generic algorithm. This way the mod shouldn't break as easily as mods/patches modifies the tech tree.

The first issue I need a bit more explanation than "it doesn't work" :)
I haven't really tested infinite research that extensively, but it appears to work as intended. The ingredient cost increases for each level of infinite research and AR should then pick the the ingredient that requires the least amount of effort (which is ingredients multiplied by time). There's one issue that I'm aware of, but this I believe is a game bug: When AR selects the same research as the previous upon completion of a tech, the game will display the previous tech level. For example, I'm testing infinite research now and "Follower robot count" is the "least effort" tech. I've researched "Follower robot count" 9-14, but for each level the game claims I'm researching "Follower robot count 9". If I open the tech tree it does however display that "Follower robot count 15" is the next tech, so AR isn't researching the same tech over and over, it's just a display issue.

What I mean is that it doesn't auto research the infinite techs some of the time like now in one of my games it hasn't worked it hasn't selected a new technology to research I might not have all the ingredients ready to go but then look at what level I just achieved (okay admittedly that's using cheat mode but I get the same problem in regular play too) it just doesn't pick infinite technologies to research though they're all there. It could pick any one of them the settings are all the same as I use for regular research it just doesn't select one. On the other hand if I can get it to select one it will stick with it claiming it to be level 7 over and over and over until I reload the game it's not stuck thinking it's level 7 anymore and it doesn't continue that infinite research at all.

http://imgur.com/a/2A4c5

Hmm, that is strange, and I can't explain why AR won't pick a research in the image given.
I've not managed to reproduce this behavior, but I've never researched as far as Follower robot count 73. There's one thing you can do, it probably won't work, but it's the best suggestion I have at the moment: Load game without AR enabled, save the game, re-enable AR and load the game again (saved game should not list AR as one of the mods).

Reproduced by setting the research queue and then clearing it (or having it auto cleared cause the lower research completed.
I can get it to do one research by spam clicking research to queue until it sticks

Well, I'm stumbled by this issue. Do you have any other mods that interfere with research? You could try disabling other mods and see if that helps, but I'm afraid I don't have any more ideas as of what might be wrong. It doesn't really make any sense that AR should just stop setting up new techs for research, and when I can't reproduce it myself it's difficult to debug.

only mod I had enabled for the second test other than yours was creative mode to grab some creative labs, beacons and modules to speed cheat getting through the research and get to where the bug is for me, I started a new game and once I had the components I needed I disabled that too. I'll run it again without using even that and see what happens (it will take a lot longer though :) )

Creative mode shouldn't affect AR. If you have a savegame with this issue and can upload the file somewhere then I can take a look at it.