fix (select): Rewrite detect_selection_mode function

@theHamsta Could you test that with the suggested changes made in nvim-treesitter (https://github.com/nvim-treesitter/nvim-treesitter/pull/4015)?
On my end, everything seems to be working well. In particular, I can do Vaf or vaf and it will respect the selection mode. If user has put a preference for selection mode in config, then config will take precedence.
Edit: ~I need to remove debug print statement.~
I also reintroduced the <cmd> instead of : in mapping. We could translate it directly to vim.keymap.set in this PR.

Works fine for me! Even with Vaf. <c-v>af also works even though the selection only gets visible after moving the cursor (I guess that's unrelated to your changes and maybe a Neovim bug).

af also works even though the selection only gets visible after moving the cursor

On my side, the seletion is visible right away, that's strange 🤔.

<c-v>af also works even though the selection only gets visible after moving the cursor

On my side, the seletion is visible right away, that's strange thinking.

As I said, to me it looked like a nvim bug. I'm using Nightly.

I use NVIM v0.9.0-dev-550+g3ea1524cf.

#344 happens again for me. I'm using Nvim 0.8.1. Maybe the <cmd> change is affecting this still.

I replaced old mapping with vim.keymap.set.
@kiyoon, have you tested with https://github.com/nvim-treesitter/nvim-treesitter/pull/4015?

For an obscure reason, <cmd> works correctly for repeat motion (ex. dap. (delete a parameter)), but with vim.keymap.set, it redoes the last basic action, i.e. if last parameter was 4 char long, it deletes 4 chars.

Whatever works is fine for me :sweat_smile:

I have been able to reproduce the visual glitch, but as you say it's only visual.
Well, when all is good for the changes in nvim-treesitter, this is ready to integrate.

I merged your upstream changes. I think this is ready then. @kiyoon can you merge when this is fine for you?

I merged your upstream changes. I think this is ready then. @kiyoon can you merge when this is fine for you?

Sure, sorry for the delay, I haven't been able to test yet. I will do within a day.

I noticed something that may be good to note for the future reference.
Prior to this update, the selection will be cancelled if there's no such statement in the file (e.g. calling @function.inner without any function will cancel the selection).
With this update, it will ignore the mapping and still keep the original selection.
The latter makes it more consistent to the default vim behaviour (vi( will not do anything if there's no parentheses)

Does it also help for incremental selection? What was the problem with it?

Does it also help for incremental selection? What was the problem with it?

I didn't test the incremental selection. I meant, it's a good change in behaviour that it makes it consistent to original vim. Thanks for your contribution!

There were some open issues with incremental selection that I couldn't reproduce.


rrd2whisper.py: Only suffix wsp files if required

Whisper files created by rrd2whisper should only be suffixed with the RRD data source name if more than one data source is defined in the RRD file.
Background: I converted a bunch of Munin RRDs into whisper format and all of the files were suffixed with _2 which was not especially convenient.

Coverage remained the same at 88.734% when pulling 37b6b0b6a3aa1fa8845fc8b5cf596a17db928796 on darrylring:master into 7c8702a7275c4e76af77e0869dd4114eb45e3d7e on graphite-project:master.

Never used rrd2whisper.py, but looks like a good addition. Any objections to merge?


Symlink command does not use directory flag.

symlinks:
 - symlink:
    - file: ~/git/vim
      link: ~/.vim
      directory: true

The correct implementation should append "/" to the remove command, as follows:

[x] before:
rm -frv ~/git/vim
[x] after:
rm -frv ~/git/vim/
delete symlink and directory it references.

Git-commit f67d354 completed this task.


safety auth redirected to localhost:49152

safety version:     3.1.0
Python version:   3.9.18
Operating System: Redhat

Description
safety auth launched browser and redirected to http://localhost:49152/?code=<hashcode with a length of 82>
What I Did
`safety auth` launched browser and redirected to `http://localhost:49152/?code=<hashcode with a length of 82>`
, then posted ``` 🛑 Error logging into Safety. Please try again, or use `safety auth -–help` for more information```

Hi @caot,
Thank you for bringing this up!
I’ve tested safety auth with the latest version, and everything seems to be working as expected. Unfortunately, I wasn’t able to recreate the issue you described. If the problem arises again, please don’t hesitate to reach out, and we’ll look into it further.


[Bug]: Kubernetes PodSecurityPolicy fails for Puppeteer container due to non-numeric user in Dockerfile

Minimal, reproducible example
// To reproduce this issue, run a puppeteer Docker container in a Kubernetes environment where PodSecurityPolicy requires runAsNonRoot.

Background
When deploying the Puppeteer container in a Kubernetes environment with a PodSecurityPolicy that enforces runAsNonRoot, the container fails to start because it cannot verify that the pptruser user is non-root. This is due to USER pptruser using a non-numeric username, which causes Kubernetes to be unable to verify the non-root status.
Suggested Solution: Use an environment variable (PPTRUSER_UID) and modify the Dockerfile to set USER to a numeric ID instead of the username:
ENV PPTRUSER_UID=10042

# Add pptruser.
RUN groupadd -r pptruser && useradd -u $PPTRUSER_UID -rm -g pptruser -G audio,video pptruser

USER $PPTRUSER_UID

Expectation
The Puppeteer container should start successfully in Kubernetes environments with PodSecurityPolicy set to runAsNonRoot, without violating the policy due to a non-numeric user.
Reality
The container fails to start due to a PodSecurityPolicy restriction when using a non-numeric username (pptruser), with the following error:
Error: container has runAsNonRoot and image has non-numeric user (pptruser),
cannot verify user is non-root

Puppeteer configuration file (if used)
No response
Puppeteer version
23.6.1
Node version
20.18.0
Package manager
npm
Package manager version
10.8.3
Operating system
Linux

Linking PR #13230 for reference.

Thanks for the PR!


False positive the pointer is nulled after the dereferencing

type User struct {
	Name *string
}

func DumpUserName(user *User) {
        // readnil.go:8:8: error: Potential nil panic detected. Observed nil flow from source to dereference point
        // readnil.go:8:8: field `Name` dereferenced
	a := *user.Name

        // readnil.go:9:14: literal `nil` assigned into field `Name`
	user.Name = nil
	_ = a
}

func DumpUserName2() {
	n := "ssss"
	u := User{Name: &n}
	DumpUserName(&u)
}

Detailed error information
readnil.go:8:8: error: Potential nil panic detected. Observed nil flow from source to dereference point:
- readnil.go:9:14: literal nil assigned into field Name
- readnil.go:8:8: field Name dereferenced
After dereferencing user.Name and assigning user.Name to nil, I don't think it should throw an error

set -experimental-struct-init=true, the error disappears.


[DOC] remove mxtheme from source tree

Description
Per vote feedback on 1.8, this PR removes mxtheme from the source tree so that it's not included in source releases.
Checklist
Essentials

[x] PR's title starts with a category (e.g. [BUGFIX], [MODEL], [TUTORIAL], [FEATURE], [DOC], etc)
[x] Changes are complete (i.e. I finished coding on this PR)
[x] All changes have test coverage
[x] Code is well-documented

Changes

[x] switch to mxtheme=0.3.14 pip package for doc build logic.

@mxnet-bot run ci [centos-gpu, windows-gpu]

@mxnet-bot run ci [windows-gpu]

@josephevans the master branch windows gpu tests are failing on the ONNX tests. Could you help take a look?

I found ways to override both the templates and css/js. I will attempt to include the changes through these overrides.


Downloading files from the new MDS with the Copernicusmarine Toolbox

The Motu-client no longer works.
I will add scripts to fetch both the BIO/PHYS  files using the Copernicusmarine Toolbox  (CMT).
A user guide about CMT can be found here: https://help.marine.copernicus.eu/en/articles/7970514-copernicus-marine-toolbox-installation

You need to specify the starting and end dates as well as your credential.

@AlfaAli I have requested a couple of changes  before it can be merged.


language-server: Simplify launch command to make it easier to use in other editors, like Sublime Text

https://github.com/BowlerHatLLC/vscode-as3mxml/wiki/How-to-use-the-ActionScript-and-MXML-language-server-with-Sublime-Text


get_absolute_url test will always fail for some models

This is probably more of a 'is this the right way to do it?' question rather than an actual bug.
I've got a model with the following:
def get_absolute_url(self):
    return reverse('product', kwargs={'slug': self.slug})

and the following url entry:
url(r'^(?P<slug>[\w-]+)/$', 'products.views.product', name='product')

Running smoke tests naively always fails as smoke tests will call it with a model that has no slug field set and thus slug is equal to '' which doesn't match the above rule.
I can think of two ways to get round this:

Subclass smoke tests and alter test_get_absolute_url so it supplies a slug
Subclass smoke tests and supply a fixture
Alter my model so that slug has a default value
Alter my url rule to url(r'^(?P[\w-]*)/$', 'products.views.product', name='product') - * instead of + will therefore match

1 and 2 mean that I'll need a different subclass for every model - this rather defeats the object of having a single generic smoketest for the admin
3 and 4 mean that I'm changing perfectly good code just to make a test pass which feels wrong too.
Is there another solution I've not thought of?

Here's another idea - the test should iterate through the model fields and look for subclasses on SlugField - if it finds one, it should instantiate the model with a random value for that field.
Some of my models have a url based on a field that aren't a subclass of slugfield however. I can't think of a generic solution short of randomly generating data for all models fields.

OK. Answering my own question (again) - I can set FIXTURE_DIRS to a dir only if tests are running.
But then test_get_absolute_url would have to be something like:
def test_get_absolute_url(self):
    for model, model_admin in self.modeladmins:
        if hasattr(model, 'get_absolute_url'):
            instance = model.objects.first()
            if not instance:
                instance = model(id=1)
            url = instance.get_absolute_url()

Is that a change that you'd consider including?

Yeah, I'd be fine with that, submit a PR.
In test_project, add a new model that uses a slug, get_absolute_url, etc. like you've described, and add a fixture file.

I've got that working.
I was planning to set FIXTURES_DIRS in my test_settings.py and use autoloading of inital_data. However initial_data is deprecated since 1.7 so I had another think.
I decided to add:
fixtures = ['django_admin_smoke_tests']
into AdminSiteSmokeTest. My thinking here is that it's a sensible default and you can always override it in a subclass if you don't like it. Any objections?
I'm a bit stuck on getting this plugged into your test project as 'main' isn't listed in INSTALLED_APPS so as far as I can tell, smoke tests is only testing auth.group and auth.user
And ff I add 'test_project.main' to INSTALLED_APPS I get model validation errors.
Have I missed something?

Any word on this?

Just pushed some fixes, sorry about that.

I updated the code and the README with another new solution.

Was the solution for this excluding apps from smoke tests? Or have I misunderstood.
I was really close to a proper solution - it was only this question: https://github.com/greyside/django-admin-smoke-tests/issues/2#issuecomment-112153317
that was still outstanding.

The best solution is to add fixtures with valid data for that model.


add: amfora-bin

[x]  Edit packagelist
[x]  Add initial pacscript
[x] Contact devs: ~~https://github.com/makeworld-the-better-one/amfora/issues/291~~
[x] Add maintainer to pacscript: resolved to @Henryws, https://github.com/makeworld-the-better-one/amfora/issues/291#issuecomment-1005295519

Mark it as ready, it's marked as a draft.


slurmctld not running

Hi,
Using the command
docker run -it -h ernie giovtorres/docker-centos7-slurm:17.02.9

the program 'slurmctld' is not running:
[root@ernie /]# supervisorctl status
munged                           RUNNING   pid 263, uptime 0:00:17
mysqld                           RUNNING   pid 491, uptime 0:00:13
slurmctld                        EXITED    Nov 13 12:50 PM
slurmd                           RUNNING   pid 262, uptime 0:00:17
slurmdbd                         RUNNING   pid 266, uptime 0:00:17

I am using docker 17.05.0-ce @ ubuntu 16.04.
Best regards,
Bernd

Hi Bernd,
It appears the database starts a little slower with ubuntu 16.04 and 17.06.2-ce (I couldn't find the deb package for 17.05.0-ce, but I was still able to replicate the problem).  slurmctld will fail to start if the database is not ready.  If you restart slurmctld (supervisorctl restart slurmctld), it should restart successfully.
I made some small adjustments in f34eb3c.  In a few minutes, you should be able to pull docker.io/giovtorres/docker-centos7-slurm:latest, which will be slurm 17.02.9.  Let me know if you have the same issue.
Thanks,
Giovanni

Thank you for your answer. The restart of slurmctld is working fine. But 'docker.io/giovtorres/docker-centos7-slurm:latest' containing slurm 17.11.0-0rc3 still fails to start slurmctld at boot.
Best regards,
Bernd

Did you run docker pull again? The image corresponding to the latest tag changed with this fix.  You'll have to pull down the updated image.

Yes, I had pulled the latest tag again. It contains your changes, but it is slurm 17.11.0-0rc3 and not 17.02.9 as you have mentioned above.

  I forgot to update the ENV after updating the supervisor.conf file.  I pushed updated tags and it just finished building on docker hub.  Give it a try now.

The version is now the mentioned one, but slurmctld is still not running after boot. I think we need something like an event listener to ensure that slurmctld starts after slurmdbd is finished.

Yeah, I think so.  I did something similar in a different project.  I was looking for other ways and came across this, but it wasn't very encouraging.
Feel free to submit a PR.  Otherwise, I'll look at the event listener docs over the next day or so.
Thanks.


Validation on Payment Page, can complete without filling in email & number

Also, let Jonny know validation criteria as part of handover

BUG: Validation works correctly now but form is submitting more than once if button is hammered


Fix Formatting

Fixes an issue with formatting.

Seems tabs.query doesn't accept callbacks.

Huh, I didn't see this locally. What version of Chrome are you using?

Oh, you know what, I did see this locally but I thought I reverted the use of the webextension-polyfill. Thanks for catching this!


Added university

@thushgithub I am sorry, I did not find any evidence to prove that this domain belongs to a university or  a college. I have to close the request without merging. Please ensure that you are familiar with this repository rules located at the bottom of this page before submitting a new request.


buid on iOS do not honor RCT_NO_LAUNCH_PACKAGER setup

🐛 Bug Report
Every time a build start for iOS, Xcode try to launch metro bundler. There is a flag to disable this behavior but is not honored
The script defined here [1] is using this condition
[ -z \"${RCT_NO_LAUNCH_PACKAGER+xxx}\" ]
and that never will resolve to null (-z), I think the correct check is
[ \"${RCT_NO_LAUNCH_PACKAGER+xxx}\"  = \"+xxx\" ]
[1] https://github.com/facebook/react-native/blob/master/React/React.xcodeproj/project.pbxproj#L4005
To Reproduce
Under Build Settings add an User Defined variable like
RCT_NO_LAUNCH_PACKAGER=1
close all terminals. Start a build, when React building starts, the metro bundler script is launched.
Expected Behavior
No terminal launched with metro bundler.
Environment
  React Native Environment Info:
    System:
      OS: macOS High Sierra 10.13.6
      CPU: (2) x64 Intel(R) Core(TM)2 Duo CPU     P8600  @ 2.40GHz
      Memory: 3.31 GB / 8.00 GB
      Shell: 3.2.57 - /bin/bash
    Binaries:
      Node: 8.11.3 - /usr/local/bin/node
      Yarn: 1.7.0 - /usr/local/bin/yarn
      npm: 6.8.0 - /usr/local/bin/npm
      Watchman: 4.9.0 - /usr/local/bin/watchman
    SDKs:
      iOS SDK:
        Platforms: iOS 12.1, macOS 10.14, tvOS 12.1, watchOS 5.1
    IDEs:
      Xcode: 10.1/10B61 - /usr/bin/xcodebuild
    npmPackages:
      react: 16.6.3 => 16.6.3
      react-native: 0.58.5 => 0.58.5
    npmGlobalPackages:
      react-native-cli: 2.0.1

Hello there 👋
By following the list of steps to reproduce, we can't actually see the reported bug on RN 0.59 so we'll close this issue. It may have something to do with your local setup, please double check that you are using the correct version of Android Studio / XCode / Android NDK / Yarn / etc.
Also, you may want to explore other ways to achieve that behaviour, like -> https://github.com/invertase/react-native-firebase/blob/master/tests/package.json#L86


Make output_type public in the output data structure

Following our discussion on a call, I'm suggesting that the output_type, now planned to be included in the obfuscated data structure (output_guard), is made public, similar to how tx_type is handled.
Below is the description of the issue and suggested change to the ALD.
Let's take some time to think about the implications.
Issue Type
[ ] bug report
[x] feature request (design)

Current Behavior
The current design keeps the output_type included in the output_guard_preimage and is delivered in the transaction data obfuscated. This means:

we're conflating two distinct mechanism - the exchange deposit obfuscation mechanism and the ALD's output_type discovery
we're limiting the discovery of output_type only if you have the remainder of the preimage (think: a query to get all outputs of certain type)
we're making the discovery of the owner of outputs harder (think: a query to get all outputs of all types belonging to someone - you need to know all the possible types)
we're making modifications to the decoding of an output harder - one needs the witness data (preimage) to discover the output type (think: changing the encoding of an output entirely)
we're making the so-called 1:1 binding more difficult: since output_type determines input_pointer_type, child chain/watcher wouldn't know how to store the output in their UTXO set. (1:1 binding makes UTXOset management easier and more abstract and also double-spend detection easier, see here for more info)
we're forcing ourselves to include things like confirmer_address in the output_guard_preimage too, thereby obfuscating it and leading to similar problems as written above

Expected Behavior
output_type is delivered similar to tx_type as the first n bit field of the structure (presumably RLP encodable array), in public. The obfuscation mechanism is set separate from the output_type typing - output_guard may contain either the hashed preimage or (hashed) owner's address, keeping the output_type the same. Then the witness to unlock such output may contain either the preimage (+other data if applicable) or the owners signature.
Motivation for Change
If the output_type is public:

we can dispatch do different decoding schemes if the current one turns out to be insufficient. An example of this is that we can then include confirm_address of an MVP output in the public section of the output data structure
we're keeping the two mechanisms (dispatch & obfuscation) separate
we still can have >1 output_type for a single creating tx_type, which seems to be required
we have the same dispatch/typing mechanism for output and transaction

LGTM

@boolafish what do you think about this one?

we can dispatch do different decoding schemes if the current one turns out to be insufficient.

Some implementation detail concerns. If a tx type has different output type with different decode schema, we need something more abstract on our current rlp encoding to output. The output itself (probably) need to be double encoded to be able to allow an array of arbitrary type (bytes) and decode on demand.
Otherwise, if we are using custom struct to be the type of the outputs array, we cannot have one array with two structs then we'd need to have multiple arrays and then it becomes a problem how we map the outputType from the array to the index in which array.
tx: {
    txType: uint256,
    outputTypes: [uint256, ...],
    inputs: [bytes32, ...],
    outputs: [bytes, ...],  <-- need to be same "type" for all outputs, so need to rlp encode the output itself?
    other fields....
}

So question, do we want to change our output encoding schema now? Quite likely some efforts on elixir side so I am not sure how heavy would that be. (btw, let's discuss this with #282 on what scope we'd like to do also according to our timeline, what can we do)

Some breaking changes with current smart contract codes and with previous design for DEX (that I've sensed)

One output type that can spent in both PaymentTx and DexSettlement. Previously, it was designed to be different output type.
We need a way to get confirm sig address. We lock in the code of using output guard to get confirm sig address now, need to change that to get from output. (I am thinking replacing existing OutputGuardHandler to become sth like OutputHandler instead, so it can do things via output guard or output as output guard would be part of output anyway.
How do we get exitTarget (the address to exit/withdraw fund to). Currently, we do it via OutputGuardHandler which each outputType has its implementation. However, if we are moving to one output type handling both scenario, where do we put the flag to differentiate? In the pre-image of output guard? Then do we hash the output guard for normal payment output as well?

Thanks! ooph, this looks like a substantial effort with the current impl :/. My gut tells me it's unlikely to go into the current immediate scope.
On top of this, just a couple of points I can relate to:

Quite likely some efforts on elixir side so I am not sure how heavy would that be

Abstract output handling hasn't yet landed on elixir side (actually, it would be good to see where this discussion is headed for a finalized version of this elixir impl.). Also, the current attempt to implement it there (wrongly) assumed that the output type is public, becaue of my incomplete knowledge, so it's probably actually less work with public output_type in elixir-omg. BTW, my wrong assumption was kinda done by extrapolating the tx_type mechanism.

breaking changes with (...) previous design for DEX
...
One output type that can spent in both PaymentTx and DexSettlement. Previously, it was designed to be different output type.

It would be good to double check against the DEX specs, but I think it's OK. I.e. it all boils down to whether the spending condition says :+1: or :-1:, prividing an API layer in between DEX protocol and this. But yea, revisiting would be necessary to make sure this holds water.

It would be good to double check against the DEX specs, but I think it's OK.

It need to be same type otherwise it would leak that the trader is doing DEX deposit.

Notes after the discussion w/ @kevsul @boolafish @paulperegud @Pongch :
tl;dr now only introduce output_type, punt the hard implementation stuff till new ExitGame (a future upgrade)
Implementation hurdles towards doing a full-fledged abstract output + output_type public in the contract:

opaque types missing in solidity (essentially what Andy posted above).

one solution: handling RLP encoded blobs instead of structs and decoding as late as possible sounds feasible and should not be too much gas.
alternative solution: same output structure for all output_types:output_type
output_guard - ....
token_standard <- new field, uint
token_contract_address - address
standard_specific_data - bytes
output_type_specific_data - bytes

This is a variation of the RLP encoded blobs - the blob (output_type_specific_data) sits as a field in a generic struct and is decoded only when needed (decided based on output_type) . This solves the confirm sig address being or not being there, still retaining the ability to define a solidity struct to hold the Output.

discovering exit target would require witness/preimage, but it does anyway so no biggie

Doing the full implementation along the lines of :point_up: seems unfeasible BUT:
output_type can be made public and put in the first item of the RLP encoded output structure.
The rest would stay the same, i.e. the structure would be fixed and we rely on the upgrade to a new ExitGame to provide full output type abstractness, possibly as outlined above.
We are thus able to make a cheap modification, that will provide the minimal future-proofing required and allow introduction of abstract output types later on.
It seems that the upgrade mechanism (new ExitGame) will be OK with processing an entirely new output data structure.
Kudos to @kevsul @boolafish @paulperegud  for realizing this.

There is one pending detail to decide on. There's 2 alternatives on passing output_type around:

as a first entry in an RLP encoded data for every output instance, i.e. encoded_output=RLP.encode(output_type, other_stuffs)
as a list in the second entry in the RLP encoded data for every tx instance, i.e. encoded_output=RLP.encode(other_stuffs), encoded_tx=RLP.encode(tx_type, [output_type1, output_type2, ...], other_stuffs)

When this is implemented, let's not forget to update RC MVP DEX and ALD specs that we might have fleshed out by then, which are, as of now, outside this repo.

There is one pending detail to decide on. There's 2 alternatives on passing output_type around:

as a first entry in an RLP encoded data for every output instance, i.e. encoded_output=RLP.encode(output_type, other_stuffs)
as a list in the second entry in the RLP encoded data for every tx instance, i.e. encoded_output=RLP.encode(other_stuffs), encoded_tx=RLP.encode(tx_type, [output_type1, output_type2, ...], other_stuffs)

The first option feels more natural to me, keeping the output type with the rest of the output data.
@boolafish was there a particular reason you proposed the second option?

@kevsul no really strong reason as I re-think, probably just my brain not working really well that time XD
Pros:

slightly more flexible, less assumption required. Assuming type to always be some first positions of tx make the remaining position of tx free of abstraction if we ever need that.
Potentially code wise it is more compatible with our existing one as we separate outputType from output now in everyplace.

Cons:
outputType is further away from the output itself so we always need to treat them kinda separated in a way....

to me, option (1.) has two benefits, expanding on what was stated above:

same typing mechanism for tx and output
output_type is still accessible, when we're processing an output instance, but have no access to the tx instance it came from; output data structure is self-contained

A downside of (1.) I can think of is this:

if one's really only interested in discovering the types of outputs, given a tx, going through outputs and having to RLP.decode() all of them just to fetch the first item is more gas-costly. But solving this particular problem is optimizable, if we're desperate to cut gas costs (RLP.decode_only_first_item())

output_type is still accessible, when we're processing an output instance, but have no access to the tx instance it came from; output data structure is self-contained

Yeah, encapsulating the outputType in the output is key for me. I'm strongly leaning towards this option - unless I come across anything that's clearly better the other way, I'm going to go with this one.


Implement Show and FromJson for tuple 8 to 16

rt

Pull Request Test Coverage Report for Build 3207
Details

10 of 153 (6.54%)  changed or added relevant lines in 2 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-2.4%) to 80.85%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

builtin/tuple_show.mbt
0
18
0.0%

json/tuple_fromjson.mbt
10
135
7.41%

Totals

Change from base Build 3206:
-2.4%

Covered Lines:
3956

Relevant Lines:
4893

💛  - Coveralls


doc: add guidance on new vs. literal usage

One thing I observed with new gophers, is having trouble judging is when to use new and when to take the address of struct literal.
Adding a bit of guidance in the wiki or effective_go.html would be quite useful.
Suggestion for guidance:

prefer the literal
if you don't initialize the struct with values, use new
if you did use new, don't initialize values later, prefer switching the code to a literal instead.

Or something at golang.org/s/style

Probably belongs in the style wiki page.

@adg I could add this to the style wiki, if you are ok with the suggestions itself. Then we can close this issue.

ok @adg It started a poll instead https://groups.google.com/forum/?fromgroups&nomobile=true#!topic/golang-nuts/OltVvy8T_ZM to get more feedback.

http://dave.cheney.net/2014/05/24/on-declaring-variables

@davecheney that blog post doesn't mention new at all. Did you mean to refer to another post?
I would not advise someone to switch from new(T) to &T{} or vice versa. The main piece of advice I agree with is your third point, which is not to use new followed by initializing fields with assignments. Not sure it really needs to be spelled out, though.


Hotplugs

[fix]Hotplugs: Show tunables for hotplugs without an enable/disable toggle.
I am a bit confused how hotplug settings work now with v11.
In v10 Intelliplug, AutoSMP and Bricked Hotplug had on/off toggles. I used Bricked Hotplug with my own settings. Now, in v11 i see the tunables for them without toggles, and a warning that more than 1 activated hotplug can cause problems.
Does it mean that Intelli,AutoSMP and Bricked are running at the same time now? Beacuse i can't disable Intelli and AutoSMP with a toggle. My CPU usage doesn't follow Bricked Hotplug settings. Last screenshot shows toggles in v10.

Yeah.  I need to revisit my logic for the hotplug section.
I had reports that sometimes th tunables wouldn't show for hotplugs that didn't have a toggle...  So I tried to fix that,  in doing so it seems that I broke things.

@Bender80 , could you tell me what you have for values in:
/sys/module/autosmp/parameters/enabled
/sys/kernel/autosmp/conf
and
/sys/kernel/msm_mpdecision/conf/enabled
/sys/kernel/bricked_hotplug/conf/enabled
and
/sys/module/intelli_plug/parameters/intelli_plug_active
/sys/kernel/intelli_plug/intelli_plug_active
You'll onlly have one path out of each set.
That, or send me a sysfsdump from the settings menu in app.

This was created with test version posted some minutes ago.
https://www.dropbox.com/s/bsbcvaed3dtc7qg/sysfsdump.txt?dl=0

New test build works fine.

Works better.... Still not 100% yet though.
The hotplugs functions section is really a mess and needs a rewrite like I did with the fragment itself... Unfortunately I don't have time for that at the moment.... So I'm just trying to hack together some fixes.

At least i have toggles for all hotplugs now. If i encounter bad behavior, i will use the backup of v10.

No worries.
I can tell you that the parameters for bricked won't work on the one I posted in my thread.... Though, I've already fixed that locally.

I don't know what you mean with "parameters for bricked won't work"
Values from bricked hotplug are saved in sys/kernel/msm_mpdecision
http://up.picr.de/25780077ka.jpg

Oh, I didn't figure they would. Hopefully they still do then with my local changes.
You know you're welcome to catch me on hangouts instead of chatting through here<EMAIL_ADDRESS>

I don't use Hangouts. It's not very popular in Germany. Like G+. Everyone uses Whatsapp or Crapbook here.

Sounds good, if everything's good then go ahead and close the issue.

And FYI, i deleted my xda account some weeks ago. It was getting worse and worse.  I decided that i have wasted too much time for the idiots. That's why i don't post in your thread or give thanks.

No worries man, I know that pain... It's a big part of the reason that I took a long hiatus from releasing any development work on XDA.  But, from a site operator perspective, more people = more ad money. So, I get it.
But it chases too many competent people off the site because they just get fed up with it.


Add ability to loop through the packages in a requirements.txt file

Is your feature request related to a problem? Please describe.
Being able to run this on a single package at a time is nice, but I’d like to be able to run it on a requirements.txt file so that I don’t have to check the packages one at a time.
Describe the solution you'd like
An update to the API that would allow a new option -r —requirements that would take a txt file as input. Something like
the-well-maintained-test -r ‘requirements.txt’

OR
the-well-maintained-test —requirements ‘requirements.txt’

Describe alternatives you've considered
Going through a requirements.txt file one package / library at a time

Closed with fc6b584


Verify that type constructor names contain contain module names

It seems that currently if multiple modules define a view of type Button the reconciler will treat them as views of the same type. We need to find a way to get a module-specific name for types of such views.

Closing as a duplicate of #218

Closing as a duplicate of #218


Fix HelmDelete command

HelmDelete was called with the namespace it needs to be called
with a chartname.  Also created a constant to make it more
obvious when called by the other Helm related commands.

[APPROVALNOTIFIER] This PR is NOT APPROVED
This pull-request has been approved by: john-a-joyce
To fully approve this pull request, please assign additional approvers.
We suggest the following additional approver: utka
If they are not already assigned, you can assign the PR to them by writing /assign @utka in a comment when ready.
The full list of commands accepted by this bot can be found here.
The pull request process is described here

Needs approval from an approver in each of these files:

tests/OWNERS

Approvers can indicate their approval by writing /approve in a comment
Approvers can cancel approval by writing /approve cancel in a comment

@john-a-joyce: The following test failed, say /retest to rerun them all:

Test name
Commit
Details
Rerun command

prow/e2e-simpleTests-cni.sh
d3f07761c133244bd005badaac22f334f983ea7e
link
/test e2e-simpleTests-cni

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.

@john-a-joyce: The following tests failed, say /retest to rerun them all:

Test name
Commit
Details
Rerun command

prow/e2e-simpleTests-cni.sh
d3f07761c133244bd005badaac22f334f983ea7e
link
/test e2e-simpleTests-cni

prow/istio-integ-k8s-tests.sh
d3f07761c133244bd005badaac22f334f983ea7e
link
/test istio-integ-k8s-tests

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.

@john-a-joyce: The following tests failed, say /retest to rerun them all:

Test name
Commit
Details
Rerun command

prow/e2e-simpleTests-cni.sh
d3f07761c133244bd005badaac22f334f983ea7e
link
/test e2e-simpleTests-cni

prow/istio-integ-k8s-tests.sh
d3f07761c133244bd005badaac22f334f983ea7e
link
/test istio-integ-k8s-tests

prow/istio-pilot-multicluster-e2e.sh
d3f07761c133244bd005badaac22f334f983ea7e
link
/test istio-pilot-multicluster-e2e

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.

@john-a-joyce: The following tests failed, say /retest to rerun them all:

Test name
Commit
Details
Rerun command

prow/istio-integ-k8s-tests.sh
d3f07761c133244bd005badaac22f334f983ea7e
link
/test istio-integ-k8s-tests

prow/istio-pilot-multicluster-e2e.sh
d3f07761c133244bd005badaac22f334f983ea7e
link
/test istio-pilot-multicluster-e2e

prow/e2e-simpleTests-cni.sh
f5f4bd954fde92154514ca51408c2ea65e358f0c
link
/test e2e-simpleTests-cni

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.

@john-a-joyce: The following tests failed, say /retest to rerun them all:

Test name
Commit
Details
Rerun command

prow/istio-pilot-multicluster-e2e.sh
d3f07761c133244bd005badaac22f334f983ea7e
link
/test istio-pilot-multicluster-e2e

prow/e2e-simpleTests-cni.sh
f5f4bd954fde92154514ca51408c2ea65e358f0c
link
/test e2e-simpleTests-cni

prow/istio-integ-k8s-tests.sh
f5f4bd954fde92154514ca51408c2ea65e358f0c
link
/test istio-integ-k8s-tests

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.

@john-a-joyce: The following tests failed, say /retest to rerun them all:

Test name
Commit
Details
Rerun command

prow/istio-pilot-multicluster-e2e.sh
d3f07761c133244bd005badaac22f334f983ea7e
link
/test istio-pilot-multicluster-e2e

prow/e2e-simpleTests-cni.sh
f5f4bd954fde92154514ca51408c2ea65e358f0c
link
/test e2e-simpleTests-cni

prow/istio-integ-k8s-tests.sh
f5f4bd954fde92154514ca51408c2ea65e358f0c
link
/test istio-integ-k8s-tests

prow/e2e-mixer-no_auth.sh
f5f4bd954fde92154514ca51408c2ea65e358f0c
link
/test e2e-mixer-no_auth

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.

@john-a-joyce: The following tests failed, say /retest to rerun them all:

Test name
Commit
Details
Rerun command

prow/istio-integ-k8s-tests.sh
f5f4bd954fde92154514ca51408c2ea65e358f0c
link
/test istio-integ-k8s-tests

prow/e2e-mixer-no_auth.sh
f5f4bd954fde92154514ca51408c2ea65e358f0c
link
/test e2e-mixer-no_auth

prow/e2e-simpleTests-cni.sh
565b7725fbe06a1bd36657db7fbb19de31770710
link
/test e2e-simpleTests-cni

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.

@john-a-joyce: The following tests failed, say /retest to rerun them all:

Test name
Commit
Details
Rerun command

prow/e2e-mixer-no_auth.sh
f5f4bd954fde92154514ca51408c2ea65e358f0c
link
/test e2e-mixer-no_auth

prow/e2e-simpleTests-cni.sh
565b7725fbe06a1bd36657db7fbb19de31770710
link
/test e2e-simpleTests-cni

prow/istio-integ-k8s-tests.sh
565b7725fbe06a1bd36657db7fbb19de31770710
link
/test istio-integ-k8s-tests

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.

@john-a-joyce: The following test failed, say /retest to rerun them all:

Test name
Commit
Details
Rerun command

prow/istio-pilot-multicluster-e2e.sh
28f87ebfd28f3153d96d4c1b10c2569b02a5d032
link
/test istio-pilot-multicluster-e2e

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.

Simple change hope so can review and approve

/lgtm
/approve

[APPROVALNOTIFIER] This PR is APPROVED
This pull-request has been approved by: john-a-joyce, utka
The full list of commands accepted by this bot can be found here.
The pull request process is described here

Needs approval from an approver in each of these files:

tests/OWNERS [utka]

Approvers can indicate their approval by writing /approve in a comment
Approvers can cancel approval by writing /approve cancel in a comment

@john-a-joyce: The following test failed, say /retest to rerun them all:

Test name
Commit
Details
Rerun command

prow/istio-pilot-multicluster-e2e.sh
28f87ebfd28f3153d96d4c1b10c2569b02a5d032
link
/test istio-pilot-multicluster-e2e

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.

@john-a-joyce: The following tests failed, say /retest to rerun them all:

Test name
Commit
Details
Rerun command

prow/istio-pilot-multicluster-e2e.sh
28f87ebfd28f3153d96d4c1b10c2569b02a5d032
link
/test istio-pilot-multicluster-e2e

prow/istio-integ-k8s-tests.sh
28f87ebfd28f3153d96d4c1b10c2569b02a5d032
link
/test istio-integ-k8s-tests

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository. I understand the commands that are listed here.


The bower can't fetch the dependent components of the polymer

I'm using Chrome Dev Editor to develop my apps on Chromebook. From yesterday, my Chrome Dev Editor app can't complete to run the "bower". Especially, the bower can't fetch the dependent components. When checking the console in the DevTools, I found the following output.
(I filed the issue as this ticket by the advice I heard at Chrome Dev Editor community on G+: http://goo.gl/t6Ph9A)
[WARNING] spark.bower_fetcher: Some dependencies could not be resolved and have been skipped.
To fix, modify "dependencies" key in your bower.json as outlined below:

  "core-media-query": "Polymer/core-media-query#^0.5", <== unrecognized dependency specification; replace with a supported one
    "core-overlay": "Polymer/core-overlay#^0.5", <== unrecognized dependency specification; replace with a supported one
    "font-roboto": "Polymer/font-roboto#^0.5", <== unrecognized dependency specification; replace with a supported one
    "polymer": "Polymer/polymer#^0.5", <== unrecognized dependency specification; replace with a supported one
    "core-a11y-keys": "Polymer/core-a11y-keys#^0.5", <== unrecognized dependency specification; replace with a supported one
    "core-focusable": "Polymer/core-focusable#^0.5", <== unrecognized dependency specification; replace with a supported one
    "core-icon": "Polymer/core-icon#^0.5", <== unrecognized dependency specification; replace with a supported one
    "paper-ripple": "Polymer/paper-ripple#^0.5", <== unrecognized dependency specification; replace with a supported one
    "paper-shadow": "Polymer/paper-shadow#^0.5", <== unrecognized dependency specification; replace with a supported one

This is a critical and fatal issue for developing Web application with Polymer as Chrome Dev Editor. I expect that this issue is caught by committers as quickly as possible.

I just investigated this issue. The Chrome Dev Editor is using the bower_semver library to check the version number of each dependent component written in bower.json.
https://github.com/dart-lang/chromedeveditor/blob/master/ide/web/lib/package_mgmt/bower_fetcher.dart#L571
The bower.json file of current Polymer components has like the following line:
"paper-ripple": "Polymer/paper-ripple#^0.5"

That is, the version number doesn't have the minor number. However, the bower_semver library expects the minor version number:
https://github.com/ussuri/bower_semver/blob/master/lib/src/patterns.dart#L11
Well, I think that we have two solutions:
(1) Committers of the Polymer add the minor version number against bower.json files of each Polymer copmonents.
(2) Committers of the bower_sember modify the pattern to check the version number without the minor number.
Can someone confirm my thinking above?

@yoichiro thanks for investigating this!
@gaurave Can you have look at this issue and confirm @yoichiro 's analysis?

I just ran into this as well.  I haven't investigated if the analysis above is correct, but can confirm that it is quite surprising, since bower install step claims to complete successfully.

@mmocny Yes, I confirmed that the bower said that the installing was successfully when I tried to run 'bower install', however, actually all dependent components could not be installed, and the error messages 'unrecognized dependency specification; replace with a supported one' was displayed in the DevTools console panel.

Here is a temporary workaround, in your project's bower.json file change the line
"paper-elements": "Polymer/paper-elements#latest"
to
"paper-elements": "Polymer/paper-elements#master"
If I had to guess, there is probably something amiss with the implementation of the #latest dependency spec in the bower module.

@brycethorup Thank you for the sharing the workaround. Actually, when I tried to use the workaround like the following, I could do the "bower install" successfully.
{
  "name": "...",
  "version": "1.0.0",
  "dependencies": {
    "jquery": "~1.11.2",
    "paper-toast": "Polymer/paper-toast#master",
    "paper-button": "Polymer/paper-button#master"
  }
}

However, the following definition failed as my report first:
{
  "name": "...",
  "version": "1.0.0",
  "dependencies": {
    "jquery": "~1.11.2",
    "paper-toast": "Polymer/paper-toast#~0.5.3",
    "paper-button": "Polymer/paper-button#~0.5.3"
  }
}

It seems that there is the problem when we specify the concrete version number or "latest". And, I guess that this problem causes the strict regular expression I reported above...

Looking into it, fix should be out soon

The issue is fixed. It will be available in the next release.

The issue is fixed and released. CDE will update itself. You can manually update it from
chrome://extensions page.

@gaurave Thank you so much!


fix metrics on Windowsuse dart pub instead of flutter pub

fix Windows metrics
use dart pub instead of flutter pub where needed

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

0 of 0   changed or added relevant lines in 0 files are covered.
1 unchanged line in 1 file lost coverage.
Overall coverage increased (+0.06%) to 88.614%

Files with Coverage Reduction
New Missed Lines
%

lib/src/subscription.dart
1
90.48%

Totals

Change from base Build<PHONE_NUMBER>:
0.06%

Covered Lines:
3222

Relevant Lines:
3636

💛  - Coveralls


Logging is thread sensetive

Messages reported to a task's logger from non-Gradle thread are not grouped in interactive command-line output and are not shown in build scans.
Consider the following build.gradle file:
task myTask() {
    doFirst {
        def log = logger
        log.error("Error from Gradle thread")
        def thread = Thread.start {
            log.error("Error from non-Gradle thread")
        }
        thread.join()
    }
}

The CLI output:
./gradlew myTask --scan
Error from non-Gradle thread

> Task :myTask
Error from Gradle thread

BUILD SUCCESSFUL in 0s
1 actionable task: 1 executed

Note that the non-Gradle thread error is shown before the task's output.
Also the error is not shown in the build scan at all https://scans.gradle.com/s/72wbcstydfouq/console-log
Maybe there are technical reasons for this behaviour, but I find it really unintuitive.
I would expect a correct grouping or a warning when a logger is used from different

@alexey-tsvetkov What's the real world use case for starting threads from a task?

@marcphilipp
We've been using RMI for Kotlin Compile Daemon. Messages from the compiler were received in an RMI thread.  I've fixed the issue on our side by collecting messages first and then reporting them all at once, but reporting messages as they arrive provided better UX. Now if the compiler stucks for some reason, a user would not be able to get any logs.
Also we have a way to run the compiler in-process. At first we ran it in a Gradle thread, but there was an issue with leaking thread local values, and the easiest fix was to run the compiler in a separate thread.
All in all, the workaround is pretty simple, but the underlying cause is very unintuitive.


Some question about your paper and code

Hi，I'm very interested in your work about Multi-scale Attention in Transformer. but I have some questions about your work：

In Appendix 2. DPB,  Why do i and j parameters range from 0 to 2G-1 instead of 0 to G-1？Besides，the inputs of DPB
module is (1-G+i, 1-G+j)， What is the reason for this setting? Why not just use i and j as inputs?

When I debug your code , I add a parameters due to I have only one 3090 with 24G memory， like this：

parser = argparse.ArgumentParser('CrossFormer training and evaluation script', add_help=False)
parser.add_argument('--cfg', type=str, required=True, metavar="FILE",
default='/configs/small_patch4_group7_224.yaml', help='path to config file')
parser.add_argument(
"--opts",
help="Modify config options by adding 'KEY VALUE' pairs. ",
default=None,
nargs='+'
)
# easy config modification
parser.add_argument('--batch-size', type=int, default=32, help="batch size for single GPU")
parser.add_argument('--data-set', type=str, default='flower', help='dataset to use')
parser.add_argument('--data-path', type=str, help='path to dataset', default='/media/data2/huzhen/flower_data')
parser.add_argument('--zip', action='store_true', help='use zipped dataset instead of folder dataset')
parser.add_argument('--cache-mode', type=str, default='part', choices=['no', 'full', 'part'],
help='no: no cache, '
'full: cache all data, '
'part: sharding the dataset into nonoverlapping pieces and only cache one piece')
parser.add_argument('--resume', help='resume from checkpoint', default='')
parser.add_argument('--accumulation-steps', type=int, help="gradient accumulation steps")
parser.add_argument('--use-checkpoint', action='store_true',
help="whether to use gradient checkpointing to save memory")
parser.add_argument('--amp-opt-level', type=str, default='native', choices=['native', 'O0', 'O1', 'O2'],
help='mixed precision opt level, if O0, no amp is used')
parser.add_argument('--output', default='./Flower_weights', type=str, metavar='PATH',
help='root of output folder, the full path is /<model_name>/ (default: output)')
parser.add_argument('--tag', help='tag of experiment')
parser.add_argument('--eval', action='store_true', help='Perform evaluation only')
parser.add_argument('--throughput', action='store_true', help='Test throughput only')
parser.add_argument('--num_workers', type=int, default=8, help="")
parser.add_argument('--mlp_ratio', type=int, default=4, help="")
parser.add_argument('--warmup_epochs', type=int, default=20, help="#epoches for warm up")
parser.add_argument("--local_rank", type=int, required=True, default=0, help='local rank for DistributedDataParallel')
parser.add_argument('--device', default='cuda:2',
help='device to use for training / testing')
args, unparsed = parser.parse_known_args()

but its report an error: 发生异常: SystemExit 2
The above is my parameter setting. Is there a problem?
I  sincerely hope I can receive for  your help！

DPB receives relative position as input. Take the case in 1-dimensional as an example: if the sequence length is G, the relation position of any two tokens ranges from [1-G, G-1], whose length is 2G-1. The case is similar for two-dimensional case. Absolute position bias uses i and j as input directly, while we use relative position bias. You may wish to read this paper (Self-attention with relative position representations) for their difference.

To run the model with 1 GPU, you could do this without changing any code:

CUDA_VISIBLE_DEVICES=0 python -u -m torch.distributed.launch --nproc_per_node 1 main.py --cfg configs/tiny_patch4_group7_224.yaml \
--batch-size 128 --data-path path_to_imagenet --output ./output

OK, thanks for your carefully reply。
The second point you mentioned is only about how to use a single GPU to train at the terminal.  But I want to ask  how to use a single GPU to debug the code,  because I want to know more details about the forward process of the model。
I set the cfg file address of the corresponding model in the ‘--cfg’ parameter in the main script, and  the ‘--local_ rank’ parameter is set to 0, as well as  a new parameter device is added to specify the GPU model used。

I have solved this question,  but when I debug the code，I find in the CrossFromerBlock。Even if it is distinguished whether SDA or LDA is used in each bottleneck, it does not seem to be reflected in the code,  like this：
`        G = self.group_size
if self.lsda_flag == 0: # 0 for SDA [bs, 112, 112, 96] -> [bs,16,16,7,7,96]
x = x.reshape(B, H // G, G, W // G, G, C).permute(0, 1, 3, 2, 4, 5)
else: # 1 for LDA [bs, 112, 112, 96] -> [bs,16,16,7,7,96]
x = x.reshape(B, G, H // G, G, W // G, C).permute(0, 2, 4, 1, 3, 5)
x = x.reshape(B * H * W // G2, G2, C) # [bs1616, 49, 96]
    # multi-head self-attention
    x = self.attn(x, mask=self.attn_mask)  # [num_groups*bs, 49, embed_dim]`

in my opinion，if SDA, The design of the code is consistent with that mentioned in the paper, and the feature map is divided into groups*groups（7x7），its have 'input size / 7' group. So  feature‘s shape  ：[bs, 112, 112, 96] -> [bs,16,16,7,7,96]  is  fully comply with the SDA mentioned in the paper. But In LDA ， I use CrossFormer-small model，so the LDA I is equal [8,4,2,1] 。
However, the same reshape operation as SDA is adopted，this is very puzzling to me。 As mentioned in the paper, it should
reshape ： x = x.reshape(B, I, H // I, I, W // I, C).permute(0, 2, 4, 1, 3, 5).
Can you tell me why this is done? Thanks ！


Fix vendor introduced with #275

gb vendor needs the new syntax for NewProject to work.

Thanks. I will add some tests so I don't break this again.


dchain module docs

This is a bit late (apologies), but this PR represents the docs tied around the new dchain module available for Prebid.js
The module code was already merged via https://github.com/prebid/Prebid.js/pull/7473
I would appreciate any feedback/word-smithing on this PR by interested parties, as describing  the business justifications and need for publishers is not exactly my forte.
If there's any other information needed or other back-end pages that need to be updated to properly reflect this page as a module in the new style of prebid.org, please let me know.  I tried to look around to current examples and past PRs, and I didn't believe anything else should be needed than cleanly defining the headers.

I think Jason's code covers Bret's concern.  I believe the module only establishes a dchain when the dchain is missing.


[FLINK-2152] Added zipWithIndex

This PR adds the zipWithIndex utility method to Flink's DataSetUtils as described in the mailing list discussion: http://apache-flink-mailing-list-archive.1008284.n3.nabble.com/The-correct-location-for-zipWithIndex-and-zipWithUniqueId-td6310.html.
The method could, in the future, be moved to DataSet.
@fhueske , @tillrohrmann , once we reach a conclusion for this one, I will also update #801 (I wouldn't like to fix unnecessary merge conflicts).
Once zipWIthUniqueIds is added, I could also explain the difference in the docs.

+1 to merge.

Good work @andralungu.
The data set utils are not working with the Scala API. Would be nice to support for Scala a syntax like
val ds: DataSet[String] = ...
val zipped: DataSet[(Long, String)] = ds.zipWithIndex

Hey @tillrohrmann ,
Sorry for the incredibly late reply. The last weeks have been very hectic.
Nevertheless, I'd like to properly finish and polish this issue very soon.
For that: I have addressed the Java comments, but I still have to provide support for Scala. I love this task because it really takes me out of my comfort zone: Gelly and Java. It's no secret that Scala is not my strongest point. Therefore, I'd like to use this thread to ask some rather trivial questions:
Before defining implicit methods and using pimp-my-lib, I need to wrap the Java function. Which should be easy right? Since there is a wrap method.
This being said, in org.apache.flink.api.scala, I created a DataSetUtils class. and wanted to call wrap(ju.countElements...). Apparently it does not let me. Can someone help me out with that?
Thanks!

Sorry for my late reply. Has everything worked out by now?
On Tue, Jun 23, 2015 at 2:43 PM, Andra Lungu<EMAIL_ADDRESS>wrote:

Hey @tillrohrmann https://github.com/tillrohrmann ,
Sorry for the incredibly late reply. The last weeks have been very hectic.
Nevertheless, I'd like to properly finish and polish this issue very soon.
For that: I have addressed the Java comments, but I still have to provide
support for Scala. I love this task because it really takes me out of my
comfort zone: Gelly and Java. It's no secret that Scala is not my strongest
point. Therefore, I'd like to use this thread to ask some rather trivial
questions:
Before defining implicit methods and using pimp-my-lib, I need to wrap the
Java function. Which should be easy right? Since there is a wrap method.
This being said, in org.apache.flink.api.scala, I created a DataSetUtils
class. and wanted to call wrap(ju.countElements...). Apparently it does not
let me. Can someone help me out with that?
Thanks!
—
Reply to this email directly or view it on GitHub
https://github.com/apache/flink/pull/832#issuecomment-114481973.

Actually, I get a weird compile error: it says missing Type parameter for the map in DataSet.scala...
I think this is because the map is overriden... and I haven't found the workaround just yet...
(The error is reproducible by calling testZipWithIndex)

Is it a type inference problem? Have you tried importing org.apache.flink.api.scala._ to see if that fixes it?

Uhmmm... flink.api.scala is imported. That's not the issue.

Seems like the problem was that the wrap was returning a DataSet[(java.lang.Long, T)]
If you change the map to .map { t => (t.f0.toLong, t.f1) } it should work.

Hey Theo,
Thanks a lot for finding my bug there ^^
PR updated to address the Java issues and to contain a  pimped Scala version of zipWithIndex :)

Hi, I added some minor comments about coding style in Scala test case. The rest things is okay.
I think we can merge this after fixing the style.

Perfectly valid comments, thanks! PR Updated.

Looks good :) merging

Oops! I forgot add "This closes #832" into commit message. I mistook because this is my first commit to upload Apache repository. Sorry. How can I fix it?

No problem ;)
In this case I would kindly ask @andralungu to close the issue manually.


Website down

Hi,
Just to make you aware, your website is down and inaccessible which means I, or anyone else, can't access any of the additional information/tutorials.

Fixed. Thanks for the heads up!


Mixpanel Source minor image correction

Cropped out browser chrome

done and merged internally. thanks for making the update @mohan-h


refactor: Base Rollup - migrate cbind routines to msgpack

### Tasks

Currently blocked by a memory type of issue while running yarn remake-bindings.

Currently blocked by a memory type of issue while running yarn remake-bindings. (See branch jm/2096-base-rollup-cbind-msgpack)

Solved by @ludamad


🗑 Deprecation promotion of toNegativeInt extension function to hidden level

📝 Description
We would like to promote the deprecation of the Number.toNegativeInt() extension function to a hidden level.
🔗 Dependencies
This issue is blocked by the following ones:

[ ] #469

✅ Checklist

[ ] Promote the deprecation of this declaration, update the public API binaries and the unreleased changelog.
[ ] Close this issue as completed and update tracking ones if present.

Another issue for this task will be created when ready.


[OSS-Releaser] Auto sync branch on GH

https://github.com/CrystallizeAPI/boilerplates/commit/3ca90c1cd36ead9dbc6969cd6b93d933d68b900f
merged manually


[Monitor-ingestion] remove error status

Packages impacted by this PR
@azure/monitor-ingestion
Issues associated with this PR
Describe the problem that is addressed by this PR
Removal of the status field entirely since -

Partial Failure and Failure Scenarios don't have any difference in terms of the code for processing the result object. No additional benefit gained from having an additional status type.
Between Success and Failure scenarios, the difference is that the success scenario will have an empty error field, which is very easy to determine without the need of the status field.

For the above two reasons, Python decided to drop the status field altogether. Wanted to discuss this proposal for Javascript. We'll probably need to update the docs/ Readme to incorporate this change.
What are the possible designs available to address the problem? If there are more than one possible design, why was the one in this PR chosen?
One alternative solution is to have the status field with "Success" and "Failure" types and drop just the "Partial Failure" status type.
Checklists

[ ] Added impacted package name to the issue description
[ ] Does this PR needs any fixes in the SDK Generator?** (If so, create an Issue in the Autorest/typescript repository and link it here)
[ ] Added a changelog (if necessary)

API change check
APIView has identified API level changes in this PR and created following API reviews.
azure-monitor-ingestion


I got error to start language server after update to laest version 1.0.3 with  mason.nvim

[platform]

windows 11 -> wsl -> ubuntu
[tool]
neovim 8.0.3

Settings need to be changed from volar 1.0.
nvim-lspconfig and mason-lspconfig seem to already support this, so please update your plug-in to the latest version.

https://github.com/neovim/nvim-lspconfig/commit/87c8c7ba29e8e07ef7e7d551d4e7a58345c50b9f
https://github.com/williamboman/mason-lspconfig.nvim/commit/0eb7cfefbd3a87308c1875c05c3f3abac22d367c


Make givens_matrix always return complex matrix

Summary
The test I added throws an error without this fix.
Details and comments

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

2 of 2 (100.0%)  changed or added relevant lines in 2 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage increased (+0.02%) to 85.888%

Totals

Change from base Build<PHONE_NUMBER>:
0.02%

Covered Lines:
17564

Relevant Lines:
20450

💛  - Coveralls

Done. It's at least a bugfix because it fixes the bug in BogoliubovTransform which I added a test for. I guess it's technically a breaking change, though I expect the user impact to be negligible.

Now that I think of it, I could also fix the bug without modifying the givens_matrix function. I think that's preferable, so I'll go ahead and do that.


Allow Bevy to start from non-main threads on supported platforms

Objective
Allow Bevy apps to run without requiring to start from the main thread.
This allows other projects and applications to do things like spawning a normal or scoped
thread and run Bevy applications there.
The current behaviour if you try this is a panic.
Solution
Allow this by default on platforms winit supports this behaviour on (x11, Wayland, Windows).

Changelog
Added

Added the ability to start Bevy apps outside of the main thread on x11, Wayland, Windows

can you add this for windows too?

Yeah, this seems acceptable. Just, users need to make sure any non-send resources get initialized in the same thread the app will live in (i.e. construct the app inside the new thread, don't add plugins in the main thread and then move it there).

I don't have any of the platforms impacted, but it should work as long as winit works 👍
I think it should be configurable by the user

I don't have any of the platforms impacted, but it should work as long as winit works 👍
I think it should be configurable by the user

I initially thought to make it configurable, but then I realized it only enables more flexiblity for the users of the affected platforms.
Since as far as I can tell it has no downsides, I see no point in not allowing any thread to start Bevy on platforms which support it.
Happy to make it configurable if you want to, in that case could you let me know which way to go:

Feature flag
A resource
A field on the winit plugin
Something else?

Imo this should be off by default, because a user may not realize that it works only on the platform they're developing on, and then run into issues later when running on a different platform.
I'm in favor of a field on the winit plugin.

Imo this should be off by default, because a user may not realize that it works only on the platform they're developing on, and then run into issues later when running on a different platform.
I'm in favor of a field on the winit plugin.

Good point, changed to this behavior now.

@james7132  there was some issues with docs, so changed the doc link slightly but kept it to local symbols.


staticLocalizationsNewMessages- Where is this coming from?

[Enter feedback here]
The reference of staticLocalizationsNewMessages is not clear as where this is coming from.

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: c40e1d02-821c-372a-6470-4850b5d04417
Version Independent ID: b7bd4543-5eba-c2b8-944e-be285f4455dc
Content: Localize sample apps (contains video) - Power Apps
Content Source: powerapps-docs/teams/localizing-sample-apps.md
Service: powerapps
GitHub Login: @joel-lindstrom
Microsoft Alias: saperlmu

Thanks for your comment, @anantharamakrishnans. This issue has been assigned to the doc author for review.

The sample app templates for Power Apps in Teams are now available in the Power Apps Teams Sample App Templates repository. Please use the latest version of the app templates, and if the problem persists, create a new issue.


Moved service config apis to MetadataExposable to allow for cli access

This is a pre-cursor to adding dynamic config get/set options to the cherami-admin cli. As a first step, the CRUD for service-config needs to be exposed through frontend for CLI access. This patch moves the service config APIs from MetadataService interface to MetadataExposable interface.

The latest stable version of thrift is 0.10.0 while the current generated files are from 0.9.3.
Will add my auto-generated files, once you merge your diff to re-generate all files from 0.10.0.

Abandoning this in favor of https://github.com/uber/cherami-thrift/pull/6


Create data collection group once on start document

With the exception of the barcode, which we can remove (see https://diamondlightsource.slack.com/archives/C048RD0KFFF/p1712327655071409), all the information in the data collection group is fixed at start document. Therefore we can:

Remove barcode reading from plans and setting in ispyb
Make a simple create_group function
The logic in activity_gated_start can then work out whether we need a group or not then make one (in the grid case we always want to and in rotation only sometimes)
Get the dcgid of either this new group or the old one and set this as the parent id
Never worry about groups again for the rest of the plan

The plot thickens... It looks like setting the barcode is just used to lookup the sampleID (see https://github.com/DiamondLightSource/hyperion/pull/1268#discussion_r1555570759). Even more so means we can remove it as we have the sampleId already!


Making sure that list of pods are loaded

Creating a backup of https://github.com/solid/solid-panes/pull/139 so that @timbl can give it a proper review later.

This is already merged into master, so I'll just close this issue.


layers: is_extension_added_token(VK_*_MAX_ENUM) returns false

Also implements the VkSamplerAddressMode variant in terms of the generic
variant, and adds a test to make sure that path is covered.
(Fixes #1770)

Thanks; will merge once I get a chance to run it through the build farm.

Seeing some odd failures in the farm on ShieldTV and PixelC.


UX Improvements

@whyrusleeping awesome script.
check out these commits. i suggest using git-rehost-ipfs as it's more git-ish.

sorry looks like we both changed it at the same time. i can resolve conflicts later.

nah, ill just take yours, more features!


rebar3.cmd fails with "system cannot find the file specified"

Windows 10. I usually run in Powershell, but I tried it in cmd.exe to make sure there wasn't some odd interaction.
C:\Users\rober>rebar3
The system cannot find the path specified.

I changed "echo off" to "echo on" to see where the failure was
D:\repos\channelserver\cb\channel>"C:\PROGRA~1\ERL100~1.1\bin\erl.exe" -noshell -eval "io:format(\"~s\", [filename:nativename(code:root_dir())])." -s init stop   1>C:\Users\rober\AppData\Local\Temp/erlroot.txt

D:\repos\channelserver\cb\channel>set erl_root=c:\PROGRA~1\ERL100~1.1

D:\repos\channelserver\cb\channel>dir /b "c:\PROGRA~1\ERL100~1.1"\erts*  1>C:\Users\rober\AppData\Local\Temp/ertsdir.txt

D:\repos\channelserver\cb\channel>set erts_bin_dir=c:\PROGRA~1\ERL100~1.1\erts-10.0\bin

D:\repos\channelserver\cb\channel>for %r in ("C:\ProgramData\chocolatey/Lib/Rebar3") do @(set rebar_escript_path=%~sr )
The system cannot find the path specified.

Version:
Chocolatey v0.10.8
rebar3 3.9.0 [Approved] Downloads cached for licensed users

Closed. I didn't figure it out, but I uninstalled everything and re-installed and it now works. I hope to be able to write a PowerShell version of this script to make it easier to work with on Windows. (Most people are scripting these days in PowerShell).


Autofix: How to reconnect to a PGVector document store?

To fix the issue of lost connections in the PostgreSQL document store, we'll add a retry mechanism that attempts to reconnect without reinitializing the entire store. This involves modifying the _create_connection method and adding a new _ensure_connection method.

[!CAUTION]
Disclaimer: This fix was created by Latta AI and you should never merge before you check the correctness of generated code!
The fix provided by Latta AI might not be complete and it can serve as an inspiration.

This bug was fixed for free by Latta AI - https://latta.ai/ourmission
If you no longer want Latta AI to attempt fixing issues on your repository, you can block this account.

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.Latta seems not to be a GitHub user. You need a GitHub account to be able to sign the CLA. If you have already a GitHub account, please add the email address used for this commit to your account.You have signed the CLA already but the status is still pending? Let us recheck it.


Support aarch64-linux

Hi! I was pointed to Bento as a simple and effective solution to deploying NixOS configurations. However, one of my servers is aarch64-linux and isn't supported by Bento (I can't run nix shell github:rapenne-s/bento).
It doesn't look like Bento depends on anything x86_64 specific. Could support be added easily?

Hello,
This is something that should be solved indeed. There is nothing x86-64 specific in Bentoo, the flake should be modified to support all architectures.

This should be fixed now


Torii graphql to use JOIN instead of subqueries to return custom types data

When querying for models with custom types there are inefficiencies due to how queries are executed. This ticket tracks this todo item here:
https://github.com/dojoengine/dojo/blob/c2687e8fd18a51bf5ed1e67997dd7db0853c5643/crates/torii/graphql/src/object/model_data.rs#L175
Parent query:
https://github.com/gianalarcon/dojo/blob/8de715d8691d987629948002fb8ba96d36b9990e/crates/torii/graphql/src/query/data.rs#L37

Hello, I'll be interested about working on this one :)

Sure! It's somewhat non-trivial as we build the graphql schema dynamically at runtime but feel free to reach out with any questions.
Here's the parent query: https://github.com/dojoengine/dojo/blob/b03bfb8d565d4d81b5afb98784d07741ca4d4f85/crates/torii/graphql/src/object/model_data.rs#L249

@azurwastaken are you still planning to work on this?

I can take this, we chatted offline and @azurwastaken will help with implementing some of the graphql testing

Hi team. Any updates for this issue.

Sure! It's somewhat non-trivial as we build the graphql schema dynamically at runtime but feel free to reach out with any questions.
Here's the parent query:
https://github.com/dojoengine/dojo/blob/b03bfb8d565d4d81b5afb98784d07741ca4d4f85/crates/torii/graphql/src/object/model_data.rs#L249

It seems like there is no parent query anymore. Now we have fn fetch_multiple_rows() instead
https://github.com/gianalarcon/dojo/blob/8de715d8691d987629948002fb8ba96d36b9990e/crates/torii/graphql/src/query/data.rs#L37
@broody Can you confirm it and update the issue? Thanks

It seems like there is no parent query anymore. Now we have fn fetch_multiple_rows() instead https://github.com/gianalarcon/dojo/blob/8de715d8691d987629948002fb8ba96d36b9990e/crates/torii/graphql/src/query/data.rs#L37
@broody Can you confirm it and update the issue? Thanks

Yeah, it's been generalized so could be used by all objects.
The challenge for model_data objects with nested types is after JOIN we get this flat sqlite row, connection_output will need to convert it properly to its value mapping with all the nested data.

@broody is this still active?

@broody is this still active?

Yes, we're gonna consolidate the queries from grpc and graphql which will resolve this issue.

Will close to have consolidation follow up in #1395.


Added support for skipping environment variables

When calling config('my_var') it is now possible to skip environment check.
That is useful when you have a common config var name or just want to skip environment variables altogether.
Per call skipping:
config = Config(RepositoryIni("myconfig.ini"))
ps1 = config("DISPLAY", default=True, cast=bool, skip_env=True)

Per config skipping:
config = Config(RepositoryIni("myconfig.ini"), skip_env=True)
home = config("HOME", default="128,13")

Use a prefix.


"Globed is incompatible with more tags"

globed is not compatible with a simplest mod ever that adds extra tags to levels, is it stupid?

yeah because more tags has some weird mode that causes globed to crash.


primitive query

Thanks for the pull request!
Pull requests should have these details:
What is this pull request?
Make concrete queries primitive, not hashable
Details/Features
List of features / major commits

Add ** to **
Remove ** from **
...

Additional dependencies (optional)
P.S. (optional)

Codecov Report

Merging #721 into feature/shared_model will not change coverage.
The diff coverage is n/a.

@@                  Coverage Diff                  @@
##           feature/shared_model     #721   +/-   ##
=====================================================
  Coverage                 43.49%   43.49%
=====================================================
  Files                       298      298
  Lines                     12022    12022
  Branches                   6599     6599
=====================================================
  Hits                       5229     5229
  Misses                      721      721
  Partials                   6072     6072

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 12d58e2...d0ca59e. Read the comment docs.


[Errno 2] No such file or directory: 'file.fastq' when using the --input_path argument

When specifying a input path, the path given to multiple steps of your script is only the filename which break the code cause it cant find the file in the adapt_find dir
[Errno 2] No such file or directory: 'GSM1608268.fastq'
Line 981 -> i added args.input_path + "/" +  before the f
line 154
line that launch cutadapt
etc
another thing i tried is adding
os.chdir(cwd)
I am able to fix it myself for myself but since i am not familiar with the overall organisation of your script i though id bring this issue for you so that you can fix it in a way that wont break anything else
so you have a better understanding of whats happening, here is a tree of my setup
adapt
--adapt_find
-----all the file of your git dir
--test
----in
--------fastq1
--------fastq2
----out
here is the command line
python adapt_find.py ILLUMINA --input_path path/to/adapt/test/in --output_path /path/to/adapt/test/out
and i run the line from /path/to/adapt/adapt_find

Another issue i run into is when i run the script on multiple files wether using the --input_path or --files argument, if multiple files are given and the list files is bigger than 1, the code is stuck forever after the first cutadapt file has been processed
Total number of input files = 2
Number of bigger files (>=10GB) = 0
Number of smaller files (<10 GB) = 2
number of CPU is 12
Processing 2 files
processing file GSM1948925.fastq
processing file GSM1608268.fastq
Median length of aligned sequences for filename - GSM1948925 is 8.0
Writing BLAST output
query  subject aligned_seq    adapter  adapter_length  aligned_length  evalue  qstart  sstart
0  19733     4731    AAGCTAAG   AAGCTAAG               8               8     1.4      20      24
1  13644     4731    AAGCTAAG   AAGCTAAG               8               8     1.3      20      24
2   8250     4731    AAGCTAAG   AAGCTAAG               8               8     1.5      20      24
3  12742     4731    AAGCTAAG   AAGCTAAG               8               8     1.4      20      24
4   7057     4657   ACCTCGGGC  ACCTCGGGC               9               9     0.4      17      20
Putative three prime end adapters for filename - GSM1948925 is
['GTATTAG', 'GCCAAAGC']
Three prime end adapter sequence for filename - GSM1948925 is GTATTAG
Trimming with CUTADAPT
cutadapt -q 20 -m 15 -M 50 -a GTATTAG -o /home/noxatras/Desktop/adapt/test1/out/good-mapping/GSM1948925_trimmed.fastq /home/noxatras/Desktop/adapt/test1/in/GSM1948925.fastq > /home/noxatras/Desktop/adapt/test1/out/aux_files/GSM1948925/GSM1948925_cutadapt.txt
[---------=8 ] 00:00:28     6,614,307 reads  @      4.3 µs/read;  13.84 M reads/minute
len of new_lst is GSM1948925 1764746
len of filtered list is GSM1948925 1177940
Empty DataFrame
Columns: [query, subject, aligned_seq, adapter, aligned_length, evalue, qstart, sstart]
Index: []
///i used ctrl c here after waiting a good 30 minutes////
^CProcess ForkPoolWorker-1:
Process ForkPoolWorker-7:
Traceback (most recent call last):
File "adapt_find.py", line 996, in
Process ForkPoolWorker-6:
result_list.append(pool.map(worker, [f for f in nasa ]))
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 651, in get
self.wait(timeout)
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 648, in wait
self._event.wait(timeout)
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/threading.py", line 552, in wait
Traceback (most recent call last):
Process ForkPoolWorker-4:
Traceback (most recent call last):
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 110, in worker
task = get()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/queues.py", line 351, in get
with self._rlock:
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/synchronize.py", line 95, in enter
return self._semlock.enter()
KeyboardInterrupt
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 110, in worker
task = get()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/queues.py", line 351, in get
with self._rlock:
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/synchronize.py", line 95, in enter
return self._semlock.enter()
KeyboardInterrupt
Process ForkPoolWorker-5:
Process ForkPoolWorker-3:
signaled = self._cond.wait(timeout)
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/threading.py", line 296, in wait
waiter.acquire()
KeyboardInterrupt
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 110, in worker
task = get()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/queues.py", line 351, in get
with self._rlock:
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/synchronize.py", line 95, in enter
return self._semlock.enter()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 110, in worker
task = get()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/queues.py", line 351, in get
with self._rlock:
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/synchronize.py", line 95, in enter
return self._semlock.enter()
KeyboardInterrupt
KeyboardInterrupt
Traceback (most recent call last):
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 110, in worker
task = get()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/queues.py", line 351, in get
with self._rlock:
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/synchronize.py", line 95, in enter
return self._semlock.enter()
KeyboardInterrupt
Traceback (most recent call last):
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 110, in worker
task = get()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/queues.py", line 352, in get
res = self._reader.recv_bytes()
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/connection.py", line 216, in recv_bytes
buf = self._recv_bytes(maxlength)
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/connection.py", line 407, in _recv_bytes
buf = self._recv(4)
File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/connection.py", line 379, in _recv
chunk = read(handle, remaining)
KeyboardInterrupt

When specifying a input path, the path given to multiple steps of your script is only the filename which break the code cause it cant find the file in the adapt_find dir [Errno 2] No such file or directory: 'GSM1608268.fastq'
Line 981 -> i added args.input_path + "/" + before the f line 154 line that launch cutadapt etc
another thing i tried is adding os.chdir(cwd)
I am able to fix it myself for myself but since i am not familiar with the overall organisation of your script i though id bring this issue for you so that you can fix it in a way that wont break anything else
so you have a better understanding of whats happening, here is a tree of my setup adapt --adapt_find -----all the file of your git dir --test ----in --------fastq1 --------fastq2 ----out
here is the command line python adapt_find.py ILLUMINA --input_path path/to/adapt/test/in --output_path /path/to/adapt/test/out and i run the line from /path/to/adapt/adapt_find

Hello. Thanks for pointing that out. I made some changes in December last year to fix the output path, unknowing to me it has created issues with input path, which  i  have fixed it now. Instead of adding args.input_path at several instances, i just made modifications to line no 77, so it works anywhere down the script. Please let me know if the latest version works for you with --input_path option.

Another issue i run into is when i run the script on multiple files wether using the --input_path or --files argument, if multiple files are given and the list files is bigger than 1, the code is stuck forever after the first cutadapt file has been processed
Total number of input files = 2 Number of bigger files (>=10GB) = 0 Number of smaller files (<10 GB) = 2 number of CPU is 12 Processing 2 files processing file GSM1948925.fastq processing file GSM1608268.fastq Median length of aligned sequences for filename - GSM1948925 is 8.0 Writing BLAST output query subject aligned_seq adapter adapter_length aligned_length evalue qstart sstart 0 19733 4731 AAGCTAAG AAGCTAAG 8 8 1.4 20 24 1 13644 4731 AAGCTAAG AAGCTAAG 8 8 1.3 20 24 2 8250 4731 AAGCTAAG AAGCTAAG 8 8 1.5 20 24 3 12742 4731 AAGCTAAG AAGCTAAG 8 8 1.4 20 24 4 7057 4657 ACCTCGGGC ACCTCGGGC 9 9 0.4 17 20
Putative three prime end adapters for filename - GSM1948925 is ['GTATTAG', 'GCCAAAGC'] Three prime end adapter sequence for filename - GSM1948925 is GTATTAG Trimming with CUTADAPT
cutadapt -q 20 -m 15 -M 50 -a GTATTAG -o /home/noxatras/Desktop/adapt/test1/out/good-mapping/GSM1948925_trimmed.fastq /home/noxatras/Desktop/adapt/test1/in/GSM1948925.fastq > /home/noxatras/Desktop/adapt/test1/out/aux_files/GSM1948925/GSM1948925_cutadapt.txt [---------=8 ] 00:00:28 6,614,307 reads @ 4.3 µs/read; 13.84 M reads/minute len of new_lst is GSM1948925 1764746 len of filtered list is GSM1948925 1177940 Empty DataFrame Columns: [query, subject, aligned_seq, adapter, aligned_length, evalue, qstart, sstart] Index: []
///i used ctrl c here after waiting a good 30 minutes////
^CProcess ForkPoolWorker-1: Process ForkPoolWorker-7: Traceback (most recent call last): File "adapt_find.py", line 996, in Process ForkPoolWorker-6: result_list.append(pool.map(worker, [f for f in nasa ])) File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 268, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 651, in get self.wait(timeout) File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 648, in wait self._event.wait(timeout) File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/threading.py", line 552, in wait Traceback (most recent call last): Process ForkPoolWorker-4: Traceback (most recent call last): File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 110, in worker task = get() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/queues.py", line 351, in get with self._rlock: File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/synchronize.py", line 95, in enter return self._semlock.enter() KeyboardInterrupt File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 110, in worker task = get() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/queues.py", line 351, in get with self._rlock: File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/synchronize.py", line 95, in enter return self._semlock.enter() KeyboardInterrupt Process ForkPoolWorker-5: Process ForkPoolWorker-3: signaled = self._cond.wait(timeout) File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/threading.py", line 296, in wait waiter.acquire() KeyboardInterrupt Traceback (most recent call last): Traceback (most recent call last): File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 110, in worker task = get() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/queues.py", line 351, in get with self._rlock: File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/synchronize.py", line 95, in enter return self._semlock.enter() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 110, in worker task = get() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/queues.py", line 351, in get with self._rlock: File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/synchronize.py", line 95, in enter return self._semlock.enter() KeyboardInterrupt KeyboardInterrupt Traceback (most recent call last): File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 110, in worker task = get() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/queues.py", line 351, in get with self._rlock: File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/synchronize.py", line 95, in enter return self._semlock.enter() KeyboardInterrupt Traceback (most recent call last): File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/pool.py", line 110, in worker task = get() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/queues.py", line 352, in get res = self._reader.recv_bytes() File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/connection.py", line 216, in recv_bytes buf = self._recv_bytes(maxlength) File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/connection.py", line 407, in _recv_bytes buf = self._recv(4) File "/home/noxatras/miniconda3/envs/adapt/lib/python3.7/multiprocessing/connection.py", line 379, in _recv chunk = read(handle, remaining) KeyboardInterrupt

The problem is not with --input_path or --files argument. I tested them with my small RNA FASTQ files with the latest version of adapt_find from github and it works fine with multiple files.  But based on your output log from your post, i presume what the problem might be. I could see that the FASTQ files you are using with GSM numbers correspond to these two entries (please check the GSM number after you open the link): https://www.ncbi.nlm.nih.gov/sra/?term=SRR1802156 and https://www.ncbi.nlm.nih.gov/sra/?term=SRR1802129 ? If it is so, those two entries correspond to ribosome RNA sequencing? adapt_find is trained only on sRNA datasets to identify adapter sequences, although it can also identify adapter sequences from single end ribosomal RNA sequencing files. However, adapt_find  is only customized to find whether input FASTQ files are already  adapter trimmed in sRNA libraries but not on single end ribosomal RNA sequencing. I assume the two
FASTQ files are already adapter trimmed RNA sequencing files. When you provide adapter trimmed small RNA FASTQ file as input to adapt_find, based on the length distribution, adapt find will detect as adapter trimmed file. I have not included any such checkpoint for ribosomal RNA sequencing file. It looks like to me you have used an adapter trimmed ribosomal RNA sequencing file as input. Therefore, for your input FASTQ files, the script will assume that the files have adapters and will look for adapters by creating query and subject files using a pre-defined criteria.  In such case, the common biological sequences was identified as adapters for the first FASTQ file. In the second file, i assume there was either no query and/or subject FASTA (no sequences after filtering) hence the resulting data frame is empty and as a result it hangs. There are checkpoints to check if a data frame is empty while processing the output from blast as data frame. But there is no checkpoint to check if the blast file is empty after reading the output blast file. I didn't have that checkpoint because hypothetically output from BLAST cannot be empty. My answer is based on the assumption that input FASTQ files are adapter trimmed rRNA sequencing FASTQ files. But if they are small RNA sequencing files, then can you please send the SRA link so that i can download and examine the issue?  if it is ribosomal RNA sequencing as i assume, then i will make changes to detect whether the input ribosomal RNA sequencing file is adapter trimmed or not.

For the input test I will try it tomorrow since I dont have my work computer with me right now
As for the 2nd issue i will confirm that I am trying to use adapt_find on ribosome profiling study,
Since I trying to re-analyse about 1.5k ribosome profiling files, I found your program pretty easy to include in my pipeline
In all my dataset, from a preliminary analysis, I seems to have both adapter reads and non-trimmed or partially trimmed read
Since Ribosome profiling usually consist of read between 20 to 40 nu and a lot of file have a fixed 51 to 151 nu distribution for all their read i assumed adapters were left
Initially i was thinking about running your program on all my file whether or not they had adaptor left and and parse the cutadapt stat result to decide wether or not the adaptor found and the trimming done is acceptable to see wether i use the pretrim fastq or post trim fastq to align with star
I hope this gave you enough context
If you can make it so it doesnt break between files i would be most grateful
Thank you for your time and help

UPDATE
I confirmed that your fix on the --input_path worked
Also, I was running the code from a local laptop and it seems like the stopping is due to my system breaking more than the code because now i am able to run 3 files in a row and it break on the 2nd batch (because i have less processes running at the same time)
heres a console log:
Total number of input files = 5
Number of bigger files (>=10GB) = 2
Number of smaller files (<10 GB) = 3
number of CPU is 12
Processing 3 files
processing file GSM2779672.fastq
processing file GSM1948925.fastq
processing file GSM1608268.fastq
is able to finish correctly this part
Working on bigger file(s) (file size greater than 10 GB)
processing file GSM3168233.fastq
processing file GSM2724036.fastq
stall here with the same error message when i keyboard interrupt
to solve this problem I will set it up so it calls each file one by one
Since your code seem to utilize multithreading and im using cpu cluster to run it, any idea how many cpu core i should assign for a job?
For the issues sake I will consider it resolved for now