fgbio failing silently on generation of UMI consensus reads

New batch of samples, identical formatting, set-up, config to previous batch, which ran successfully. The UMI config is fastq_name.
Successful log file snippet looks like this:
[2017-10-25T16:55Z] INFO:umis.umis:Processed 16459742 alignments.
[2017-10-25T16:55Z] Index BAM file: 5628-sort.bam
[2017-10-25T16:57Z] UMI consensus fastq generation
[2017-10-25T16:57Z] [2017/10/25 17:57:13 | FgBioMain | Info] Executing GroupReadsByUmi from fgbio version 0.2.1-SNAPSHOT as<EMAIL_ADDRESS>on JRE 1.8.0_121-b15 with snappy
[2017-10-25T16:57Z] [2017/10/25 17:57:13 | FgBioMain | Info] Executing CallMolecularConsensusReads from fgbio version 0.2.1-SNAPSHOT as<EMAIL_ADDRESS>on JRE 1.8.0_121-b15 with snappy

Unsuccessful run log output is truncated:
[2017-11-21T11:44Z] INFO:umis.umis:Processed 19514399 alignments.
[2017-11-21T11:44Z] Index BAM file: 2935-sort.bam
[2017-11-21T12:13Z] UMI consensus fastq generation

fgbio was called (from command log):
[2017-11-21T11:44Z] /gpfs/igmmfs01/eddie/bioinfsvice/ameynert/software/bcbio/galaxy/../anaconda/bin/samtools index -@ 4 /gpfs/igmmfs01/eddie/HGS-OvarianCancerB/work/2017-11-17.100ng-2935/align/2935/2935-sort.bam /gpfs/igmmfs01/eddie/HGS-OvarianCancerB/work/2017-11-17.100ng-2935/bcbiotx/tmpSpFTXE/2935-sort.bam.bai
[2017-11-21T12:13Z] unset JAVA_HOME && fgbio -Xms2g -Xmx8g -XX:+UseSerialGC --tmp-dir /gpfs/igmmfs01/eddie/HGS-OvarianCancerB/work/2017-11-17.100ng-2935/bcbiotx/tmpXGBn7V --async-io=true --compression=0 GroupReadsByUmi --edits=1 --min-map-q=1 -t RX -s adjacency -i /gpfs/igmmfs01/eddie/HGS-OvarianCancerB/work/2017-11-17.100ng-2935/align/2935/2935-sort.bam | fgbio -Xms2g -Xmx8g -XX:+UseSerialGC --tmp-dir /gpfs/igmmfs01/eddie/HGS-OvarianCancerB/work/2017-11-17.100ng-2935/bcbiotx/tmpXGBn7V --async-io=true --compression=0 CallMolecularConsensusReads --min-input-base-quality=2 --min-reads=1 --max-reads=100000 --output-per-base-tags=false --sort-order=:none: -i /dev/stdin -o /dev/stdout | fgbio -Xms2g -Xmx8g -XX:+UseSerialGC --tmp-dir /gpfs/igmmfs01/eddie/HGS-OvarianCancerB/work/2017-11-17.100ng-2935/bcbiotx/tmpXGBn7V --async-io=true --compression=0 FilterConsensusReads --min-reads=1 --min-base-quality=13 -r /gpfs/igmmfs01/eddie/bioinfsvice/ameynert/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa -i /dev/stdin -o /dev/stdout | bamtofastq collate=1 T=/gpfs/igmmfs01/eddie/HGS-OvarianCancerB/work/2017-11-17.100ng-2935/align/2935/2935-sort-cumi-1-bamtofastq-tmp F=/gpfs/igmmfs01/eddie/HGS-OvarianCancerB/work/2017-11-17.100ng-2935/bcbiotx/tmpXGBn7V/2935-sort-cumi-1.fq.gz F2=/gpfs/igmmfs01/eddie/HGS-OvarianCancerB/work/2017-11-17.100ng-2935/bcbiotx/tmpXGBn7V/2935-sort-cumi-2.fq.gz tags=cD,cM,cE gz=1

I see there was a commit on 7 Oct to use a new version of fgbio; possibly this is the cause.

Alison;
Thanks much for this report. I've been trying to reproduce and haven't been able to replicate this. It's running cleanly for me with the recent fgbio release (0.4.0) and the latest code. What behavior do you see if the problematic run? Does it hang at this point? What does the output directory align/2935/ look like? Are any consensus files being generated? Thanks for any additional information you can provide to help track what is going on.

It doesn't hang at all - the job exits with no errors. No consensus FASTQ is generated. Work directory contents look like this:
.:
total 0
drwx--S--- 3 ameyner2 igmm_datastore_HGS-OvarianCancerB 512 Nov 21 10:24 align
drwx--S--- 2 ameyner2 igmm_datastore_HGS-OvarianCancerB 512 Nov 21 10:24 align_prep
drwx--S--- 4 ameyner2 igmm_datastore_HGS-OvarianCancerB 512 Nov 21 12:13 bcbiotx
drwx--S--- 2 ameyner2 igmm_datastore_HGS-OvarianCancerB 512 Nov 21 10:23 checkpoints_parallel
drwx--S--- 2 ameyner2 igmm_datastore_HGS-OvarianCancerB 512 Nov 21 10:23 log
drwx--S--- 2 ameyner2 igmm_datastore_HGS-OvarianCancerB 512 Nov 21 10:23 provenance

./align:
total 0
drwx--S--- 2 ameyner2 igmm_datastore_HGS-OvarianCancerB 512 Nov 21 12:12 2935

./align/2935:
total 1.8G
-rw------- 1 ameyner2 igmm_datastore_HGS-OvarianCancerB 1.8G Nov 21 11:44 2935-sort.bam
-rw------- 1 ameyner2 igmm_datastore_HGS-OvarianCancerB 4.6M Nov 21 12:12 2935-sort.bam.bai

./align_prep:
total 256K
lrwxrwxrwx 1 ameyner2 igmm_datastore_HGS-OvarianCancerB  98 Nov 21 10:24 2935_2935_R1.fastq.gz -> ../../../../../../../exports/igmm/eddie/HGS-OvarianCancerB/reads/2017-11-17.100ng/2935_R1.fastq.gz
-rw------- 1 ameyner2 igmm_datastore_HGS-OvarianCancerB 13K Nov 21 10:24 2935_2935_R1.fastq.gz.gbi
lrwxrwxrwx 1 ameyner2 igmm_datastore_HGS-OvarianCancerB  98 Nov 21 10:24 2935_2935_R2.fastq.gz -> ../../../../../../../exports/igmm/eddie/HGS-OvarianCancerB/reads/2017-11-17.100ng/2935_R2.fastq.gz
-rw------- 1 ameyner2 igmm_datastore_HGS-OvarianCancerB 13K Nov 21 10:24 2935_2935_R2.fastq.gz.gbi

./bcbiotx:
total 0
drwx--S--- 2 ameyner2 igmm_datastore_HGS-OvarianCancerB 512 Nov 21 10:23 tmpGWWFKP
drwx--S--- 2 ameyner2 igmm_datastore_HGS-OvarianCancerB 512 Nov 21 12:13 tmpXGBn7V

./bcbiotx/tmpGWWFKP:
total 0

./bcbiotx/tmpXGBn7V:
total 0

./checkpoints_parallel:
total 0

./log:
total 512K
-rw------- 1 ameyner2 igmm_datastore_HGS-OvarianCancerB 3.0K Nov 21 12:13 bcbio-nextgen-commands.log
-rw------- 1 ameyner2 igmm_datastore_HGS-OvarianCancerB 134K Nov 21 12:13 bcbio-nextgen-debug.log
-rw------- 1 ameyner2 igmm_datastore_HGS-OvarianCancerB  937 Nov 21 10:24 bcbio-nextgen.log

./provenance:
total 256K
-rw------- 1 ameyner2 igmm_datastore_HGS-OvarianCancerB 895 Nov 21 10:23 data_versions.csv
-rw------- 1 ameyner2 igmm_datastore_HGS-OvarianCancerB 832 Nov 21 10:23 programs.txt

Alison -- thanks for the details. I'm not sure what is going on and why bcbio doesn't catch the error. Is it possible to share the BAM file with me off list (https://github.com/chapmanb/) and I can try to reproduce? I guess the changes to either fgbio or adding in the separate FilterConsensusReads step are causing some kind of issue.
Practically, bcbio should fail after this step with the missing fastq consensus reads, is that right? I want to be sure it's not continuing on with processing; silent failures and skips are very bad.
Thanks again for helping to debug.

Sorry Brad, I'm not allowed to share any of these out of the EU. Could ask Miika in Cambridge?
Yes, an error message of some sort would be appropriate.

If I can be of help we can download the data on our UK cluster where Brad also has access. Would that help Alison?

Thank you, Miika, that would be very helpful, since you're on this project anyway. Can I send you the FASTQ for one of the samples that worked under 1.0.5 and for a sample that didn't work under 1.0.6? The raw FASTQ was produced identically, as far as I know, and I have processed it into bcbio-ready FASTQ with the same scripts, and the files look the same to me in terms of structure.
--
Alison Meynert
<EMAIL_ADDRESS>MRC Human Genetics Unit
MRC IGMM
University of Edinburgh
Western General Hospital
Crewe Road, Edinburgh EH4 2XU
United Kingdom

From: Miika Ahdesmaki<EMAIL_ADDRESS>Sent: 23 November 2017 12:55:08
To: chapmanb/bcbio-nextgen
Cc: MEYNERT Alison; Author
Subject: Re: [chapmanb/bcbio-nextgen] fgbio failing silently on generation of UMI consensus reads (#2167)
If I can be of help we can download the data on our UK cluster where Brad also has access. Would that help Alison?
—
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Reply to this email directly, view it on GitHubhttps://github.com/chapmanb/bcbio-nextgen/issues/2167#issuecomment-346611216, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AGbyA7O9xqxbNUCZAhyE1mJRqVtv73ajks5s5WssgaJpZM4Ql4VF.
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Hi Alison,
That would work for me.  I can provide a Box folder if necessary.

About 3.5Gb total for 4 FASTQ files with the UMIs in the headers (as generated by the bcbio UMI pre-processing scripts).
--
Alison Meynert
<EMAIL_ADDRESS>MRC Human Genetics Unit
MRC IGMM
University of Edinburgh
Western General Hospital
Crewe Road, Edinburgh EH4 2XU
United Kingdom

From: Miika Ahdesmaki<EMAIL_ADDRESS>Sent: 23 November 2017 15:34:41
To: chapmanb/bcbio-nextgen
Cc: MEYNERT Alison; Author
Subject: Re: [chapmanb/bcbio-nextgen] fgbio failing silently on generation of UMI consensus reads (#2167)
Hi Alison,
That would work for me.  I can provide a Box folder if necessary.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHubhttps://github.com/chapmanb/bcbio-nextgen/issues/2167#issuecomment-346648026, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AGbyA7HEf7uzUy9Z5FkQkYvHA3AmIwKDks5s5ZCRgaJpZM4Ql4VF.
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Alison and Miika;
Thanks so much for the help making the data available. I ran these and have, I guess, good and bad news all rolled into one: these worked for me with the latest development version (1.0.7a-05fc3c9, but I don't think the specific revision matters) and fgbio (0.4.0). So it's bad I can't reproduce and offer any suggestions but good that a potential path to getting running cleanly is to upgrade either bcbio or fgbio and then run. I wish I had a better clue about the underlying behavior but hope this provides a useful path forward to getting your analysis finished. Thanks again for all the help debugging and please let me know if upgrading does not fix the problem.

I was still seeing the issue on the development version, but now think I've solved this by bumping the fgbio default memory request to Xms4g and Xmx8g explicitly in postalign.py. That's what I had specified in my galaxy YAML config as default jvm_opts, so I'm not sure why they weren't feeding through to fgbio.

Alison;
Thanks for continuing to debug this and for the additional details. I've been trying to replicate this here by running with both lower and higher memory and all I can manage to do is trigger memory errors and failures from fgbio, not any type of silent skipping. I'm totally baffled as to what I'm missing to reproduce the problem.
What memory specification do you get if you don't change it directly in postalign.py? What are you specifying in bcbio_system.yaml? Maybe if I can debug what is going on there that will give some more clues. Thanks again for helping with testing and debugging.

Brad, it appears to be something peculiar to our cluster. I have it working interactively on a standalone node with an unedited postalign.py from release 1.0.6, using 8 cores and Xms2g Xmx4g. When I submit the same job to the cluster (standard SGE Linux, using a bash script wrapping a call to bcbio_nextgen.py -t local) it's failing. I am totally puzzled.

 I'm not sure if SGE does this (not on our system) - from experience Slurm eagerly does.
Could also ask the system administrators to monitor the nodes for memory use during the failure?

Alison;
Thanks for following up and sorry about this inconsistent behavior. I'd definitely like to squash this if we can figure out the underlying cause. bcbio should error out if the jobs get killed by the scheduler, and I'm not sure how they'd continue on without the consensus output. If you can understand the behavior on your system I'd be keen to add in checks to try and avoid continuing and at least raise the correct error if things fail. Thanks much for the help debugging this.

Brad, I'll check into that. I know we have previously had issues with Java memory requirements and the system mis-interpreting how much memory is actually available.

Thanks, closing this as it is stale and there has been a bunch of fgbio work since then, so it is likely to not be an issue. Please re-open if I am mistaken.


[Low Priority] Wrangler update message has a broken documentation link

🐛 Bug Report
Environment

operating system: macOS Big Sur
output of rustc -V:
output of node -v:
output of wrangler -V:
contents of wrangler.toml

Steps to reproduce
Run any Wrangler action while on an out of date version of Wrangler
What did you expect to see?
What did you see instead?

The docs link in the update message is no longer current for updating the CLI:
https://developers.cloudflare.com/workers/quickstart#updating-the-cli
The current documentation is here:
https://developers.cloudflare.com/workers/cli-wrangler/install-update#update

thanks for the report. Would you mind sending a PR to fix that?

As far as I can tell from the source code, this has already been updated.


Add secure powers generation for simd

This change is

#930  👈 (View in Graphite)
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Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 91.49%. Comparing base (060f0e4) to head (3057bea).

Additional details and impacted files
@@            Coverage Diff             @@
##              dev     #930      +/-   ##
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+ Coverage   91.47%   91.49%   +0.01%
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Merge activity

Dec 18, 5:58 AM EST: A user started a stack merge that includes this pull request via Graphite.


"BEIUȘ" is a locality in "BIHOR" county

Description
Check that the locality is displayed in the search bar in accordance with Act 2 02/16/1968

Precondition
Empty the search bar after every step

Steps 1
Acces to the link https://peviitor-ro.github.io/ui.orase/
Expected result
The page opens

Steps 2
Write " Delani"
Expected result
In the drop down menu you find " Delani, BIHOR(BEIUS)"
Test Data
Delani


luci-app-ddns: fix next_update error

Fix the error that next_update sometimes display Verify

@jow- Cloud you please merge this PR? I've been testing it for a month, and it shows that verify has been fixed, and it doesn't happen again.


Bump the push tag to 5.0.0-RC

What does this PR change?
Bump the tag used by the push script to RC.
This needs to be accepted with https://build.suse.de/request/show/328222
Test coverage

No tests: only internal changes

[x] DONE

Links
Relate(s): https://github.com/SUSE/spacewalk/issues/23744

[x] DONE

Changelogs
Make sure the changelogs entries you are adding are compliant with https://github.com/uyuni-project/uyuni/wiki/Contributing#changelogs and https://github.com/uyuni-project/uyuni/wiki/Contributing#uyuni-projectuyuni-repository
If you don't need a changelog check, please mark this checkbox:

[ ] No changelog needed

If you uncheck the checkbox after the PR is created, you will need to re-run changelog_test (see below)
Before you merge
Check How to branch and merge properly!

@juliogonzalez feel free to delete the branch when merged. I pushed directly a branch on uyuni-tools instead of using my fork so, if needed, you can push even if I'm not around.


Pull in design system for UI

Not just one task but a placeholder to remind us to do this!

Closed in https://github.com/cds-snc/url-shortener/pull/216


New open source app example

Hi! Thanks for taking the time to contribute! Could you please provide a description of your changes? It's easier on the maintainers and helpful for those who reference this pull request in the future. Thanks!

Done! Sorry, this was my first pull request ever :_)

this was my first pull request ever

That's awesome! So excited that you contributed here :tada: :pizza:


Added The Kadane's Algorithm

Description 📜
Calculation of maximum subarray sum in an efficient manner!
Fixes #2359

Type of change 📝

[ ] Au#dio (Should be in mp3 format Includes speech clarity, Concise ,Low distortion)
[ ] Vi#deo (Animations, screen-recordings, presentations and regular explanatory films are all possibilties etc)
[x] Documentation (Content Creation in the form of codes or tutorials)
[ ] Other (If you choose other, Please mention changes below)

Domain of Contribution 📊

[ ] Android Dev #(Flutter)
[ ] Android Dev #(Java)
[ ] Android Dev #(Kotlin)
[ ] Backend Dev #(Java)
[ ] Backend Dev #(.NET)
[ ] Backend Dev #(PHP)
[ ] Backend Dev #(Python)
[ ] C/#CPP
[x] Competitive Programming
[ ] Cyber #Security
[ ] DS#A
[ ] Data#base
[ ] Datascience with #Python
[ ] Datascience with #R
[ ] Frontend Dev #HTML/CSS/JS
[ ] Frontend Dev #React/Angular/Vue
[ ] Go#lang
[ ] Interview #Prep
[ ] Java_#Domain
[ ] Java#Script
[ ] ME#RN
[ ] Machine #Learning
[ ] Open #Source
[ ] Python_#Domain
[ ] Ru#st
[ ] Statis#tics
[ ] UI/#UX

Checklist ✅

[x] I follow Contributing Guidelines & Code of conduct of this project.
[x] I have performed a self-review of my own code or work.
[x] I have commented my code, particularly in hard-to-understand areas.
[x] My changes generates no new warnings.
[x] I'm GWOC'21 contributor

Hey @akshat12000, someone is already working on Kadane's algorithm. You can view it here. So this is a duplicate PR so I won't be able to review or merge it. Please close this PR.


Should log claim be part of the individual vaults

In the new architecture, should the logClaim function be part of the vault code, or rather be in the registry contract. I think the latter makes more sense but not sure.

I see no argument either way. It's in the vault now, let's leave it in the vault :)

makes sense to me it's in the vault contract since it's connected to a specific vault, but i don't feel strongly about that either :)


doc: please include a local copy of the IRIS logo

In order to make the generated HTML documentation fully functional offline please include a local copy of the IRIS logo instead of fetching it at runtime, here:
https://github.com/iris-edu/libmseed/blob/master/doc/footer.html#L4
I think that's the only line to change. I understand the documentation is meant to be pushed to GitHub pages, however a copy of the generated HTML files is going to be included as a Debian/Ubuntu package for offline reference. Think of the people doing field work in Antarctica :-)

Done in 497dff7343cdcf42e40b24781761d53fdc0ac991


浏览器扩展

啥时候给个Eage浏览器的扩展呀

@suxiangyv Hi dear. please speak English here so I can understand your issue.

I hope Microsoft Edge can also have this plugin

@suxiangyv Hi dear. you can use the extension for Edge using chrome web store. because Edge is also a Chromium Browser however I will add it to Microsoft Edge Store ( this is duplicate of #31 )


Improvement Suggestion: Accurate "True" Metrics on Validation Set

Keras.metrics current implementation averages metrics in batchwise averages. I think there should be an option to cache the intermediate output and compute accurate metrics at the end of epoch for the entire validation set. This would unlock metrics such as AUC, Precision, Recall, etc...
The hacky solution that I have used thus far (included below):

Remove validation generator from fit_generator

Create a custom callback that takes a list of custom metric functions and the validation generator. At the end of the epoch hack the accurate metrics to the metrics log.

This is completely undesirable as it runs against the default Keras API. I was hoping to make this an option in evaluate_generator.
The callback (single metric) looks like (1.5x slower than predict on generator...):
class TrueMetrics(keras.callbacks.Callback):

    def __init__(self, gen_handle, func, name):
        ''' Constructor for True Metrics.

        :param gen_handle: Generator - data to compute metric.
        :param func: Function - metric(y_pred, y_true).
        :param mode: String - 'best' defined by 'min' or 'max'.
        :param name: String - metric name.
        '''
        self.gen_handle = gen_handle
        self.func = func
        self.name = name
        self.score = None

    def on_epoch_end(self, epoch, logs={}):
        ''' On epoch end compute the metrics on entire generator.

        :param epoch: Keras epoch - required input (unused).
        :param log: Keras logs - required input.
        '''

        # Batch and epoch params
        batch_size = self.gen_handle.batch_size
        n_samples = self.gen_handle.n_samples
        steps_per_epoch = self.gen_handle.steps_per_epoch

        # Create empty placeholder arrays
        output_shape = list(self.model.output_shape)

        # Replace 'None' with # Samples
        output_shape[0] = batch_size * steps_per_epoch
        y_true = np.squeeze(np.zeros(output_shape))
        y_pred = np.squeeze(np.zeros(output_shape))

        for ind, batch in enumerate(self.gen_handle.generate()):

            # Grab batch components
            X_batch = batch[0]
            y_true_batch = batch[1]

            # Compute the output on the batch
            y_pred_batch = self.model.predict_on_batch(X_batch)

            # Create ind
            start = ind * batch_size
            # Safeguard against improper sizing on last batch
            stop = start + y_pred_batch.shape[0]

            # Add the batch output to the placeholder arrays
            y_true[start:stop] = np.squeeze(y_true_batch)
            y_pred[start:stop] = np.squeeze(y_pred_batch)

            # Check for last batch
            if ind + 1 == steps_per_epoch:
                break

        # Trim batch padding
        y_true = y_true[:n_samples]
        y_pred = y_pred[:n_samples]

        # Compute metric
        self.score = self.func(y_true, y_pred)
        # Hack - write metric to logs for {ModelCheckpoint, EarlyStopping, etc...}
        logs[self.name] = np.float64(self.score)  #np.float64 for TensorBoard

Note: I am using a custom generator under the hood in this callback.

Any progress here?
Would especially be advantaged from efficient [statefully] optimisation on specificity & sensitivity.

Yes, you can use Stateful metrics.


constrain payday based on approval

Once new terms (#3390) and approval process (#3395) land, we need to constrain payday to only process payments for approved receivers.

---
Want to back this issue? **[Post a bounty on it!](https://www.bountysource.com/issues/14250675-constrain-payday-based-on-approval?utm_campaign=plugin&utm_content=tracker%2F85909&utm_medium=issues&utm_source=github)** We accept bounties via [Bountysource](https://www.bountysource.com/?utm_campaign=plugin&utm_content=tracker%2F85909&utm_medium=issues&utm_source=github).

Done in #3414!

Done in #3414!

Not exactly, we still haven't constrained the payout phase.

Good point.

The last part of this is #3450.

We have constrained payday based on approval for team owners, what's left is payroll - that is part of https://github.com/gratipay/gratipay.com/milestones/Payroll. Closing this.


Git parameters superfluous when image is hard coded

Hi,
Template very useful Thanks.
One issue when trying to re-use

ecs-refarch-continuous-deployment.yaml has a bunch of parameters to supply your own repository. But .... within templates/service.yaml the amazon image is hard coded. When you switch to providing your own github project as parameters it actually has no effect (the amazon namespace is universally available in docker-hub. So what happens is you build your own project then use the amazon image at the last stage =) )

ContainerDefinitions:
        - Name: simple-app
          Image: amazon/amazon-ecs-sample
          EntryPoint:

I think it needs to be a parameter

Second suggestion is not to override the entry point as part of the task def and allow the entry point provided as part of docker image to run by default

G

The GitHubRepo is used to configure the pipeline -- the initial task definition that has the Docker image configured is just a placeholder until the pipeline's first execution. Make sense?
I don't know about your second point - I think I took the task definition whole cloth from here. What's the benefit of changing it?

Thanks for quick response

Think there may have been two things going on. My deploy stage of the pipeline was still running at 35 minutes. When I hit the service I saw the 'hello world' page from the  amazon/amazon-ecs-sample image. I assumed I had not replaced something correctly (rather than it being a default until the pipeline runs). Is it more intuitive to have the container blank till the first deploy?

Is there repetition in having the task-def defined in both the the task-def.json in addition to the cloud formation template?

I guess my question is whether the task-def from git will replace the cloud formation specification once the first pipeline runs.

I'm not sure why your pipeline would be running for 35 minutes.
As to the intuitive question - I'm not sure. CloudFormation requires the service to come up healthily and since we're deploying this service, using its configuration seemed natural. The instructions mention to commit a change to the index to watch it go through the pipeline which was is the intent of the reference architecture.
In this pipeline, the only thing that changes is the image field in the task definition via CodePipeline. The task definition in git is not used.

I'm not sure why your pipeline would be running for 35 minutes.

To begin with I replicated using the launch stack from the page so I know it is me not you =). The only change I have made are running under a different account and also from the command line as opposed to console.  I killed it after 35 minutes so it did not get a chance.

The task definition in git is not used.

Thanks. Was grepping to understand if it had an impact.
Thanks for your help - will close this one


Listening again on getPositionStream does not immediately trigger retrieval of the location

🐛 Bug Report
After cancelling a subscription on getPositionStream, when I start a listener again, it does not immediately tries to get the location, but waits according to how it is specified on the LocationOptions when the stream was created.
Expected behavior
Every time a new listener is attached to the same stream, it should start with immediately getting the location. Just like it does when the first listener subscribes.
Note: I experience this behaviour on other packages like cloud_firestore
Reproduction steps

Listen to the getPositionStream with timeInterval: 60000. Save the stream as a broadcast stream and the subscription into a variable. (getPositionStream(locationOptions).asBroadcastStream())
a) Observe that as soon as the listener is set up, the location is retrieved.
Cancel the subscription with subscription.cancel();
Start listening to the saved stream again.
b) Observe that the next update comes when the one minute interval is reached. Not immediately at subscription.

Configuration
Version: 5.0.0
Platform:

[x] :robot: Android

I think this is by design, have a look at this article in the Dart repo: https://github.com/dart-lang/sdk/issues/18588


Can't compile with Xcode 11 for iOS 13

I saw this has been fixed in #211 and has been merged in master but there's no new release yet.
Installing directly from master branch works though but would prefer to have a payment lib fixed on a version rather than on the master branch. As for now I'm using this workaround.
npm i --save react-native-in-app-utils@chirag04/react-native-in-app-utils#master

Same here, would be great to have this on a release.
In case anyone needs a yarn equivalent
yarn add react-native-in-app-utils@chirag04/react-native-in-app-utils#master

I think this is specific to Xcode 13 because I am experiencing this with Xcode 13 and iOS12 simulator.

published in 6.0.2

Thanks @chirag04 🙏


Debug console output from multiple debugging processes always appears in the currently active debug console

I've found that when running multiple debugger processes at the same time, the console output from all processes ends up in whatever debug console window I happen to have open.
I set up a simple demo repository that can be used to demonstrate the issue fairly easily:
https://github.com/hoylemd/vscode-ruby-console-debug-demo
How to:

clone that repo
open up a workspace in the clones repo directory
install the vscode-rdbg extension if it's not already active
Run the 'hickory(rdbg)' debug configuration
immediately also run the 'dickory(rdbg)' debug configuration

You'll see the output from both processes appear in whatever debug console window you have open, they're prefixed with their names so you can tell which is which.
e.g.

The same issue appears in the ruby_lsp extension, I'll log a similar issue under that and link it here: https://github.com/Shopify/vscode-ruby-lsp/issues/714
@st0012 on the Ruby DX slack server had this to say about it, which may be helpful in fixing the issue:

Yeah I think it’s probably because the extension always passes the active debug console to functions that run debuggee processes.

duplicate with https://github.com/ruby/vscode-rdbg/issues/111
(please reopen if it's wrong)


dbt run, test, seed, etc. counts exclude disabled models but include tests that depend on disabled models

Describe the bug
When running dbt compile, dbt run, dbt test, etc., a count of objects in the dbt project are provided, like this:
Found 45 models, 252 tests, 0 snapshots, 0 analyses, 123 macros, 0 operations, 0 seed files, 57 sources

This count excludes dbt models which are disabled, but includes tests which depend on disabled models. This is confusing and inconsistent.
Steps To Reproduce
Create a model and some associated schema tests that are related to the model. Execute dbt compile and look at the counts for the models and tests in the project, e.g.
Found 45 models, 252 tests, 0 snapshots, 0 analyses, 123 macros, 0 operations, 0 seed files, 57 sources

Disable the model. Run dbt compile and observe the number of objects associated with the project. The number of models will have decreased by one but the number of tests will have remained constant even though some of the tests depend on the disabled model, e.g.:
Found 44 models, 252 tests, 0 snapshots, 0 analyses, 123 macros, 0 operations, 0 seed files, 57 sources

Expected behavior
The more immediate behavior to fix the bug would be to exclude tests that are disabled from the count of objects generated from dbt commands. So in the scenario above, assuming that two tests depend on the disabled model, the count of objects after disabling the model should exclude these two tests and be:
Found 44 models, 250 tests, 0 snapshots, 0 analyses, 123 macros, 0 operations, 0 seed files, 57 sources

A more helpful longer-term approach might be to include and count both enabled and disabled objects, such as:
Found 44 enabled models, 1 disabled model, 250 enabled tests, 2 disabled tests, 0 snapshots, 0 analyses, 123 macros, 0 operations, 0 seed files, 57 sources

I understand that there are a lot of mechanical reasons why it is difficult to count disabled models. But given that disabled tests are already being lumped in with enabled tests in the counts, it should hopefully not be that hard to at least call out the number of enabled vs. disabled tests as per the following:
Found 44 models, 250 enabled tests, 2 disabled tests, 0 snapshots, 0 analyses, 123 macros, 0 operations, 0 seed files, 57 sources

Screenshots and log output
Already above.
System information
Which database are you using dbt with?
Snowflake
The output of dbt --version:
installed version: 0.14.2
   latest version: 0.14.2

Up to date!

The operating system you're using:
Mac OS Mojave 10.14.5
The output of python --version:
Python 2.7.10

Thanks @jrandrews! I'd be very interested in merging a PR that excludes disabled models from this resource count log line. Is that something you'd be interested in submitting a patch for? I believe the operative lines of code are around here:
https://github.com/fishtown-analytics/dbt/blob/31e085b7df015eac92faee4912fa481d1085c4b9/core/dbt/ui/printer.py#L90-L106

Thanks @jrandrews! I'd be very interested in merging a PR that excludes disabled models from this resource count log line. Is that something you'd be interested in submitting a patch for? I believe the operative lines of code are around here:
https://github.com/fishtown-analytics/dbt/blob/31e085b7df015eac92faee4912fa481d1085c4b9/core/dbt/ui/printer.py#L90-L106

The code invoked for compile stats is https://github.com/fishtown-analytics/dbt/blob/e51c942e91a94936f68f2965963d3b46f1257658/core/dbt/compilation.py#L34-L54
Not sure that this is a case of simply filtering out the test nodes in that function, I think the issue lies in a higher level function. From the digging I've done so far it, created manifests exclude disabled models, but includes the tests for them. Here is where disabled models are filtered out: https://github.com/fishtown-analytics/dbt/blob/e51c942e91a94936f68f2965963d3b46f1257658/core/dbt/parser/util.py#L79-L96
This is my first contribution so very new to the codebase, keen for thoughts @drewbanin.

hey @NiallRees - I lost track of this one!
This change looks like it would be simple, but it's actually pretty complicated!! There's a lot going on here that's not super obvious.
Take a look at this method:
https://github.com/fishtown-analytics/dbt/blob/8cd8705d67627e8f701afb5f5490d553e76f3dfa/core/dbt/compilation.py#L204-L207
This is where the "stats" that are printed out get generated. In this case, test nodes that reference disabled models will have the property node.config.enabled set to False. This happens in the parsing code, check it out here:
https://github.com/fishtown-analytics/dbt/blob/8cd8705d67627e8f701afb5f5490d553e76f3dfa/core/dbt/parser/util.py#L200-L209
So, I think we can add some logic to this stats generating method to check where node.config.enabled is False, then exclude those nodes from the count. One small problem is that certain node types (like macros) don't have config properties! We could address that by:

using something like getattr(node, 'config', None) (not ideal)
using a conditional to check the node's resource type, eg (pseudocode):

if node.resource_type in [NodeTypes.model, NodeTypes.test, NodeTypes.snapshot, ....] \
   and not node.config.enabled:
  pass
else:
  stats[node.resource_type] += 1

Happy to follow up here if you have any questions or thoughts - let me know!

@drewbanin Submitted a PR here: https://github.com/fishtown-analytics/dbt/pull/2026


Implement self-consistent gap calculation

Pull Request Test Coverage Report for Build<PHONE_NUMBER>3
Details

4 of 14 (28.57%)  changed or added relevant lines in 3 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-2.1%) to 97.924%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

src/quant_met/mean_field/self_consistency.py
2
4
50.0%

src/quant_met/mean_field/base_hamiltonian.py
1
9
11.11%

Totals

Change from base Build<PHONE_NUMBER>6:
-2.1%

Covered Lines:
474

Relevant Lines:
484

💛  - Coveralls


Randomise results

Add a button which allows the user to randomise the meal and drink results if not happy.
Possible suggestions: 'not happy with your meal/drink, click here to change'

We will need to add a button to take back to search area if not happy with choice

We have decided to have only one button which redirects the user to the search form.


Cloudflare Error: DNS points to prohibited IP

I'm trying to use: https://brucelawson.github.io/manifest/
With the URL: https://www.ssense.com/
That web services uses your "crossorigin.me" and I get: Error: DNS points to prohibited IP
Possible reason (where example.com is SSENSE):
"your web server is proxying requests to "www.example.com," but because Cloudflare has been activated for that DNS record, the web server is proxying those requests to a DNS record that resolves to Cloudflare IPs, resulting in cyclical requests and the "DNS points to prohibited IP" error screen with the IP of your web server's proxy IP. Web servers should be configured to resolve www.example.com to the internal NAT-ed IP, if applicable,  or the public IP of the origin web server to prevent the problem."
Source:
https://support.cloudflare.com/hc/en-us/articles/200171826-Why-am-I-getting-an-error-message-of-DNS-points-to-Prohibited-IP-Error-1001
Help?

Want to back this issue? Post a bounty on it! We accept bounties via Bountysource.

Still happening?

@technoboy10 Yes.

@connerbw Thanks, I'll see if I can find out what's up.

Looks like the issue is caused by accessing a site that's using CloudFlare. Further discussion will be on #92.


TypeError: apply_overlay() takes 3 positional arguments but 4 were given

Getting the error in the title when trying to "inpaint only masked" on the new FORGE UI. Im aware this was made for AUTO but because it's deprecated now with everyone switching over and the UIs are very similar I'd love a fix. Seems to work fine otherwise.
Console log
Traceback (most recent call last):
File "F:\stable diffusion\FORGE\webui\modules\call_queue.py", line 57, in f
res = list(func(*args, **kwargs))
File "F:\stable diffusion\FORGE\webui\modules\call_queue.py", line 36, in f
res = func(*args, **kwargs)
File "F:\stable diffusion\FORGE\webui\modules\img2img.py", line 235, in img2img
processed = process_images(p)
File "F:\stable diffusion\FORGE\webui\modules\processing.py", line 749, in process_images
res = process_images_inner(p)
File "F:\stable diffusion\FORGE\webui\extensions\sdwebui-nai-api\nai_api_gen\nai_api_processing.py", line 115, in process_images_patched
results = modules.processing.process_images_pre_patch_4_nai(p)
File "F:\stable diffusion\FORGE\webui\modules\processing.py", line 813, in process_images_inner
p.scripts.process(p)
File "F:\stable diffusion\FORGE\webui\extensions\sdwebui-nai-api\nai_api_gen\nai_api_processing.py", line 107, in process_patched
script.nai_image_processsing(p, *args) # Sets p.nai_processed if images have been processed
File "F:\stable diffusion\FORGE\webui\extensions\sdwebui-nai-api\nai_api_gen\nai_api_script.py", line 421, in nai_image_processsing
if not self.use_batch_processing: self.nai_generate_images(p, *args, **kwargs)
File "F:\stable diffusion\FORGE\webui\extensions\sdwebui-nai-api\nai_api_gen\nai_api_script.py", line 490, in nai_generate_images
self.get_batch_images(p, getparams, save_images = isimg2img and getattr(p,"inpaint_full_res",False) and shared.opts.data.get('nai_api_save_fragments', False), save_suffix ="-nai-init-image" if do_local_img2img > 0 else "" ,overlay = inpaint_mode == 1 or getattr(p,"inpaint_full_res",False))
File "F:\stable diffusion\FORGE\webui\extensions\sdwebui-nai-api\nai_api_gen\nai_api_script.py", line 605, in get_batch_images
image = apply_overlay(self.images[i],  (self.crop[0], self.crop[1], self.crop[2]-self.crop[0], self.crop[3]-self.crop[1]), 0, self.init_masked)
TypeError: apply_overlay() takes 3 positional arguments but 4 were given

No idea what FORGE is, but the same issue occurs with the A1111 dev branch, just added a fix for it which should resolve this issue

its quite literally just auto but better cause it has newest optimizations https://github.com/lllyasviel/stable-diffusion-webui-forge
Thanks anyways


Coverage

Adds coverage analysis using travis and coveralls.io.

Hee je hebt function.py.new meegecommit :)
On Mon, Jan 4, 2016 at 10:44 AM, Joost van Zwieten<EMAIL_ADDRESS>
wrote:

Adds coverage analysis using travis and coverage.io
https://coveralls.io/github/joostvanzwieten/nutils.
You can view, comment on, or merge this pull request online at:
https://github.com/nutils/nutils/pull/88
Commit Summary

add coverage analysis to Makefile
fix cmdline parsing of tests when using coverage
let travis do coverage analysis

File Changes

A .coveragerc
https://github.com/nutils/nutils/pull/88/files#diff-0 (2)
M .gitignore
https://github.com/nutils/nutils/pull/88/files#diff-1 (1)
M .travis.yml
https://github.com/nutils/nutils/pull/88/files#diff-2 (6)
M Makefile https://github.com/nutils/nutils/pull/88/files#diff-3
(21)
M tests/init.py
https://github.com/nutils/nutils/pull/88/files#diff-4 (9)
A tests/function.py.new
https://github.com/nutils/nutils/pull/88/files#diff-5 (297)
A tests/index.py.num
https://github.com/nutils/nutils/pull/88/files#diff-6 (141)

Patch Links:

https://github.com/nutils/nutils/pull/88.patch
https://github.com/nutils/nutils/pull/88.diff

—
Reply to this email directly or view it on GitHub
https://github.com/nutils/nutils/pull/88.

shit
On 4 January 2016 at 10:53, Gertjan van Zwieten<EMAIL_ADDRESS>wrote:

Hee je hebt function.py.new meegecommit :)
On Mon, Jan 4, 2016 at 10:44 AM, Joost van Zwieten <
<EMAIL_ADDRESS>
wrote:

Adds coverage analysis using travis and coverage.io
https://coveralls.io/github/joostvanzwieten/nutils.
You can view, comment on, or merge this pull request online at:
https://github.com/nutils/nutils/pull/88
Commit Summary

add coverage analysis to Makefile
fix cmdline parsing of tests when using coverage
let travis do coverage analysis

File Changes

A .coveragerc
https://github.com/nutils/nutils/pull/88/files#diff-0 (2)
M .gitignore
https://github.com/nutils/nutils/pull/88/files#diff-1 (1)
M .travis.yml
https://github.com/nutils/nutils/pull/88/files#diff-2 (6)
M Makefile https://github.com/nutils/nutils/pull/88/files#diff-3
(21)
M tests/init.py
https://github.com/nutils/nutils/pull/88/files#diff-4 (9)
A tests/function.py.new
https://github.com/nutils/nutils/pull/88/files#diff-5 (297)
A tests/index.py.num
https://github.com/nutils/nutils/pull/88/files#diff-6 (141)

Patch Links:

https://github.com/nutils/nutils/pull/88.patch
https://github.com/nutils/nutils/pull/88.diff

—
Reply to this email directly or view it on GitHub
https://github.com/nutils/nutils/pull/88.

—
Reply to this email directly or view it on GitHub
https://github.com/nutils/nutils/pull/88#issuecomment-168627178.

The recursive make trick in the coverage target is a bit dirty, but it works and does not duplicate code like test3.


Using the resolve command with bob requires additional arguments

If you call bob with the resolve command it expects the --email and --auth values to be set even if the dependencies are public. It's ok to pass any kind of bogus e-mail and auth token.

Fixed in https://github.com/aglitchman/defold-playable-ads/commit/65c892d0aa20b9c26df06c98a353ba613d687f79


Enable configurable Jaeger sampling strategies (with defaults)

This PR is a partner of https://github.com/weaveworks/common/pull/87.
This commit adds runtime configuration env vars to allow each system that's Jaeger-enabled to specify its own sampling strategy and parameters. We chose defaults of jaeger.SamplerTypeRateLimiting and 10.0 to yield an intuitive default behavior of "send ~10 traces per second to the collector". Other strategies are certainly usable here, however, and I'd happily entertain different default behaviors.
To test this independent of the state of the weaveworks/common PR referenced above, you can add these lines to your local Cortex repo's Gopkg.toml:
[[override]]
  name = "github.com/weaveworks/common"
  source = "github.com/Fresh-Tracks/weaveworks-common"
  revision = "e6856c7a5d16d9525051dc8daf3ce5399e5a9384"

With this, a dep ensure && make make should result in a sane build (Makefile runs dep ensure - handy!).

Looking a bit closer, would it be better to collapse the environment variable retrieval and parsing into tracing.New() and just call it without args from the various Cortex components? Turns it into a one-line change per Cortex component to enable tracing, and DRYs things up a bit more.

Done deal! Thanks for the feedback!

Needs a vendoring update before it'll actually work. Reverting in #707. @cboggs

:+1: New PR incoming shortly!


How to get 'padded.dat' in bert.py when constructing graph

When using the following scipt to make the graphs, a FileNotFoundError encountered.
python3 -m graph_construction.bert
In graph_construction/bert.py, padded.dat and attention_mask.dat are needed.
def read_data(graph_dir):
    padded = np.memmap(graph_dir + 'padded.dat', dtype=int, shape=(89123, 512))
    attention_mask = np.memmap(graph_dir + 'attention_mask.dat', dtype=int, shape=(89123, 512))
    input_ids = torch.tensor(padded).to('cuda')
    attn_mask = torch.tensor(attention_mask).to('cuda')
    return input_ids, attn_mask

How to generate padded.dat and attention_mask.dat? I am curious about how to use bert to analyze the EHR data. Could you share the related code? Thank you very much.

Hello! Sorry it took a while to respond as it was the weekend. If you would like access to the graphs without needing those files, you can just download it by request from here: https://drive.google.com/drive/folders/1yWNLhGOTPhu6mxJRjKCgKRJCJjuToBS4?usp=sharing
To make those files from scratch, you would need to run eICU-GNN-LSTM/src/dataloader/convert.py. I will add that to the documentation!
Let us know if you have any other problems


Preparation for 0.3.0

No more snapshots.

Current coverage is 79.13%

Merging #195 into master will increase coverage by +0.16% as of 8631280

Powered by Codecov. Updated on successful CI builds.

In build.sbt, replace scalaJSStage in Global := FastOptStage by scalaJSUseRhino in Global := false. Typical breaking change of 0.6.5 -> 0.6.6, as highlighted in the release notes.

@sjrd Thanks, but that doesn't seem to help. The strange thing is that I'd been able to run the tests locally until this morning (they were slow, but I could live with that), and the only change here that seems at all possibly relevant is the Shapeless version.

Just confirmed that changing the Shapeless version back to the 2.3.0 snapshot fixes the Scala.js tests.


NullPointerException in response.header(String, int)

spark.http.matching.ResponseWrapper needs to override this method spark.Response.header(String, int) and call the delegate to add the int Header; otherwise this method throws a NullPointerException
java.lang.NullPointerException: null
at spark.Response.header(Response.java:166)

Yes, I believe you are right. I fixed the code in the unofficial release-5, which I'm planning to release within the next week (if all goes smoothly).


Doubt not issue ( can't resolve module woff within css file )

I tried to use @font-face and the loader style-loader along with url loader and file loader for fonts but it still shows some weird error
Code
CSS File
@font-face {
  font-family: 'fontello';
  src: url('../../sass/fonts/fontello/fontello-webfont.woff2') format('woff2'),
       url('../../sass/fonts/fontello/fontello-webfont.woff') format('woff');
  font-weight: normal;
  font-style: normal;
}

Webpack.Cient.js
     { test: /\.(woff|woff2|ttf|eot|svg|png|jpg|gif)(.*)?$/,
      loader: 'file?name=asset/[name].[ext]'
    },
    {
      test: /\.css/,
      loader: 'style-loader!css-loader',
    }```

**ERROR**

Module not found: Error: Can't resolve '../../sass/fonts/fontello/fontello-webfont.woff2' in '/home/sairam/Downloads/goin/goin/src/modules/goin_theme/client/css'

It looks like you just deleted our lovely crafted issue template. It was there for good reasons. Please help us solving your issue by answering the questions asked in this template. I'm closing this. Please open a new issue with filled issue template. Also make sure your issue is not a question. Questions should be posted on Stack Overflow.


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unable to load Material Theme and font

There is a issue with the Material Theme for a longer time now - is there any fix to this?
The Material Theme issue is perfectly described in this post; unable to load Material Theme #567
I also noticed that I am not able to load any fonts; for example the Fira Code font:

What am I doing wrong?
Thanks alot!

+1

Are these fonts installed to the client machine? The fonts are rendered in your browser, so only fonts on your computer can be used.

I have the fonts installed I'm using them in my current local vs code installation but over in web its not working, Plus I can't get the ligatures to work with Roboto or Fira code

I have Fira Code installed on my local machine and my config.json set to the following and both the font and ligatures work:
{
    "editor.fontFamily": "'Fira Code', 'Droid Sans Mono', 'monospace', monospace, 'Droid Sans Fallback'",
    "editor.fontLigatures": true
}

Tested in Chromium and Firefox. Try restarting your browser to see if it helps, as your browser could be caching the font list.

Thanks, @deansheather,
I got it fixed, not sure what happened there but Fira code works now, Roboto is still not working but I'm happy with it, I'll keep this thread posted in case I see something off,


[SPARK-32344][SQL] Unevaluable expr is set to FIRST/LAST ignoreNullsExpr in distinct aggregates

What changes were proposed in this pull request?

This PR intends to fix a bug of distinct FIRST/LAST aggregates in v2.4.6/v3.0.0/master;
scala> sql("SELECT FIRST(DISTINCT v) FROM VALUES 1, 2, 3 t(v)").show()
...
Caused by: java.lang.UnsupportedOperationException: Cannot evaluate expression: false#37
  at org.apache.spark.sql.catalyst.expressions.Unevaluable$class.eval(Expression.scala:258)
  at org.apache.spark.sql.catalyst.expressions.AttributeReference.eval(namedExpressions.scala:226)
  at org.apache.spark.sql.catalyst.expressions.aggregate.First.ignoreNulls(First.scala:68)
  at org.apache.spark.sql.catalyst.expressions.aggregate.First.updateExpressions$lzycompute(First.scala:82)
  at org.apache.spark.sql.catalyst.expressions.aggregate.First.updateExpressions(First.scala:81)
  at org.apache.spark.sql.execution.aggregate.HashAggregateExec$$anonfun$15.apply(HashAggregateExec.scala:268)

A root cause of this bug is that the Aggregation strategy replaces a foldable boolean ignoreNullsExpr expr with a Unevaluable expr (AttributeReference) for distinct FIRST/LAST aggregate functions. But, this operation cannot be allowed because the Analyzer has checked that it must be foldabe;
https://github.com/apache/spark/blob/ffdbbae1d465fe2c710d020de62ca1a6b0b924d9/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/expressions/aggregate/First.scala#L74-L76
So, this PR proposes to change a vriable for IGNORE NULLS  from Expression to Boolean to avoid the case.
Why are the changes needed?

Bugfix.
Does this PR introduce any user-facing change?

No.
How was this patch tested?

Added a test in DataFrameAggregateSuite.

Test build #126038 has started for PR 29143 at commit 0e30a25.

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This patch merges cleanly.
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cc: @cloud-fan @viirya @dongjoon-hyun

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I think the description is out-of-dated. Can you also update the description?

Test build #126057 has finished for PR 29143 at commit 92f5b7d.

This patch fails Spark unit tests.
This patch merges cleanly.
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Looks like related failure.

Test build #126056 has finished for PR 29143 at commit a83de82.

This patch fails Spark unit tests.
This patch merges cleanly.
This patch adds the following public classes (experimental):
case class First(child: Expression, ignoreNulls: Boolean)
case class Last(child: Expression, ignoreNulls: Boolean)

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Ah, I see. Seems like I need to update the golden files..

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Test build #126086 has finished for PR 29143 at commit 66bf522.

This patch fails due to an unknown error code, -9.
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retest this please

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Merged to master and branch-3.0.

@HyukjinKwon This shoulbe be backported to branch-2.4, too, for the 2.4.7 release?

@maropu, sure feel free to port it back!

okay, I will. Thanks for the check, @HyukjinKwon

+1, late LGTM. Thank you all.


YARN-11073: avoid unnecessary preemption for tiny queues under certain corner cases

Description of PR
When running a Hive job in a low-capacity queue on an idle cluster, preemption kicked in to preempt job containers even though there's no other job running and competing for resources.
Let's take this scenario as an example:
cluster resource : <Memory:168GB, VCores:48>
queue_low: min_capacity 1%
queue_mid: min_capacity 19%
queue_high: min_capacity 80%
CapacityScheduler with DRF

During the fifo preemption candidates selection process, the preemptableAmountCalculator needs to first "computeIdealAllocation" which depends on each queue's guaranteed/min capacity. A queue's guaranteed capacity is currently calculated as "Resources.multiply(totalPartitionResource, absCapacity)", so the guaranteed capacity of queue_low is:
queue_low: <Memory: (168*0.01)GB, VCores:(48*0.01)> = <Memory:1.68GB, VCores:0.48>, but since the Resource object takes only Long values, these Doubles values get casted into Long, and then the final result becomes <Memory:1GB, VCores:0>
Because the guaranteed capacity of queue_low is 0, its normalized guaranteed capacity based on active queues is also 0 based on the current algorithm in "resetCapacity". This eventually leads to the continuous preemption of job containers running in queue_low.
In order to work around this corner case, "resetCapacity" needs to consider a couple new scenarios:
if the sum of absoluteCapacity/minCapacity of all active queues is zero, we should normalize their guaranteed capacity evenly: 1.0f / num_of_queues
if the sum of pre-normalized guaranteed capacity values (MB or VCores) of all active queues is zero, meaning we might have several queues like queue_low whose capacity value got casted into 0, we should normalize evenly as well like the first scenario (if they are all tiny, it really makes no big difference, for example, 1% vs 1.2%).
if one of the active queues has a zero pre-normalized guaranteed capacity value but its absoluteCapacity/minCapacity is not zero, then we should normalize based on the weight of their configured queue absoluteCapacity/minCapacity. This is to make sure queue_low gets a small but fair normalized value when queue_mid is also active.
minCapacity / (sum_of_min_capacity_of_active_queues)
How was this patch tested?
The patch was tested on a small cluster with queues configured to be same as the scenario described above, verified that

containers running in a low-capacity queue didn't get preempted when the cluster is idle
preemption kicked in properly in the low-capacity queue when cluster is busy (heavy usage in high-capacity queues)

For code changes:

[ ] Does the title or this PR starts with the corresponding JIRA issue id (e.g. 'HADOOP-17799. Your PR title ...')?
[ ] Object storage: have the integration tests been executed and the endpoint declared according to the connector-specific documentation?
[ ] If adding new dependencies to the code, are these dependencies licensed in a way that is compatible for inclusion under ASF 2.0?
[ ] If applicable, have you updated the LICENSE, LICENSE-binary, NOTICE-binary files?

@aajisaka

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fix(controller): ignore KeyError on delete

In some odd cases, etcd keys no longer exist from manual intervention.
That should not stop resources from being destroyed, however, as it is
assumed that the etcd key does not exist (which is what was intended,
anyways).
closes #3357

I agree that the rest of cleanup should proceed after a KeyError in this case. Code LGTM.

Code LGTM


Missing python requirement - PIL

Immediately after install, this code failed:
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from IPython.display import SVG
import time
print(time.asctime())

with the following error:
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/usr/local/lib/python3.5/site-packages/rdkit/Chem/Draw/IPythonConsole.py in <module>()
     42 try:
---> 43     import Image
     44 except ImportError:

ImportError: No module named 'Image'

During handling of the above exception, another exception occurred:

ImportError                               Traceback (most recent call last)
<ipython-input-1-5f71ef0713a1> in <module>()
      1 from rdkit import Chem
----> 2 from rdkit.Chem.Draw import IPythonConsole
      3 from IPython.display import SVG
      4 import time
      5 print(time.asctime())

/usr/local/lib/python3.5/site-packages/rdkit/Chem/Draw/IPythonConsole.py in <module>()
     43     import Image
     44 except ImportError:
---> 45     from PIL import Image
     46
     47 from IPython.display import SVG

ImportError: No module named 'PIL'

This error was immediately fixed with pip install pillow, so my best guess is there's a problem with the requirements.txt file in the project.

How did you install the RDKit?

Brew install --with-python3. It installed to my brew Python 2.7.12 and brew Python 3.5.2_2

Great. Thanks.

So I sort of lied, because I ran python3 -m pip install pillow to fix the problem in Python 3. I don't know if there's a problem on Python 2. Sorry about the double post, but I can't edit on GitHub mobile :)

@cthoyt this can be closed now, right?


Improvement adjust priority of materialized view match rule

Proposed changes

when the query can match mv, it is also allowed to match the base index.
prioritize using non-base index
prioritize using index with where clause
prioritize using index with pre agg

Further comments
If this is a relatively large or complex change, kick off the discussion at<EMAIL_ADDRESS>by explaining why you chose the solution you did and what alternatives you considered, etc...

run buildall

run buildall

run buildall


Record and document how much gas is used by the relayer over some period of time

We should monitor the relayer to see how much gas is used to get a better idea of how much is used and provide a more detailed look into relayer cost.

This is a duplicate to: https://github.com/celestiaorg/quantum-gravity-bridge/issues/181
So I'll close this one


[Windows] Updating AzurecosmoDB checksum and Removing m2repositry in AndriodSDK

Description
Image generation failed due to checksum issues with Azure Cosmos DB and problems with the m2repository in the Android SDK. This PR addresses the checksum issue and removes the m2repository from the Android SDK after the image generation passes successfully.
Related issue:
Check list

[ ] Related issue / work item is attached
[ ] Tests are written (if applicable)
[ ] Documentation is updated (if applicable)
[ ] Changes are tested and related VM images are successfully generated

/azp win19

/azp run windows2022


Set up a build tool to bundle all the JavaScript code on the site into one file

As an end user I want a fast load experience. Add a build tool to bundle everything into one file that can be loaded quickly.

Resolved!


ApolloProvider.provide() is deprecated. Use the 'apolloProvider' option instead...

Version
v4.0.0-rc.1
Reproduction link
https://cmty.app/nuxt/issues/new?type=bug-report&repo=apollo-module
Steps to reproduce
Get a fresh nuxt install
Install / Config Apollo Module
Run the app
What is expected ?
To run smoothly as it was few days ago
What is actually happening?
Two error messages:
apolloProvider.prefetchAll is not a function
that is due to:
.provide() is deprecated. Use the 'apolloProvider' option instead with the provider object directly.
Additional comments?
Installed dependencies:
nuxtjs/apollo : 4.0.0-rc1
nuxtjs/axios : 5.3.1
nuxtjs/component-cache : 1.1.2
nuxtjs/pwa : 2.0.8
nuxt : 1.4.1
This could be possible after this vue-apollo commit: https://github.com/Akryum/vue-apollo/commit/62829e4a969532f8a4568302ff6f89286cde5b77
Some changes may be needed @ .nuxt/apollo-module.js

This bug report is available on Nuxt community (#c136)

The error is gone on my end when I remove provide() method. Have a look at this :
new Vue({
  el: '#app',
  provide: apolloProvider,
  router,
  render: h => h(App)
})

Can you guys try this PR and see if it fixes the issue: https://github.com/nuxt-community/apollo-module/pull/158

Fixed, thanks a lot for both of you

@DuyguKeskek  where is this piece if code you removed ?

@heshamelmasry77  This is old Code
new Vue({   el: '#app',   // Inject apolloProvider for components to use.   provide: apolloProvider.provide(),   render: h => h(App) })
And this is new codigo
new Vue({   el: '#app',   // Inject apolloProvider for components to use.   apolloProvider,   render: h => h(App) })


Add simple helm chart for deployment of Egeria to kubernetes

In #273 a simple docker image was added which is self-build from source
Docker images work well for a single component of an application environment, but we need much more for a real environment. there are multiple moving parts such as egeria itself, kafka, perhaps ranger, atlas, gaian & others.
This issue will target creation of a basic helm chart to deploy egeria.
Given a working kubernetes cluster, and helm installed (tiller on the backend) - such as on docker for mac, IBM cloud private or many other environments, the intent is that such a chart could be deployed with
helm add repo xxxx
helm install egeria-basic-cluster
or similar, with a 'values.yaml' optionally offering additional configuration
Also of note - #177 added instructions on creating a 2 node in-memory repository using docker compose. This works well in a local environment, but is more awkward for deployment to cloud environments, and not portable across all.
Once a simple proof point is in place we can consider additional charts (which can depend on other charts) , points of variability, and the publishing of required images to make for an easy end user experience be it for demos, development, education etc.

Added simple egeria chart & documentation
Note - currently whilst this deploys Egeria in-memory, and kafka - they are not immediately configured to work together. this still requires use of the Admin API
I have also checked in charts for

ranger -- we already used the prior docker version in previous demos
vdc-open -- this is work in progress, to incorporate other components needed for vdc demo. It will not contain non-open components. It may be split into further charts.

Neither of these are quite as clean, and need a few updates but are included


background will beat.

When the setting height is small, the month mode and the week mode switch, the selected background will beat.

I see what you mean, if you do have a small height for your tiles, it might not be the result you expect. I would recommend setting a minimum height of 24 to prevent any wrong behavior. Let me know if that works for you or not.


Can't see added tasks

I can't see my tasks (sorry for this poor gif):

What did I miss this time?

The issue what that I used ~ in LEAF_TASKS_PATH. Everything works. Thanks:)

🤔 Hmm yes ~ doesn't get expanded in environment variables. It's customary to do something like LEAF_TASKS_PATH=$HOME in that case. I'll leave this open with the intent to add a note to the README.

[ ] Add note to README about how to refer to home directory in LEAF_TASKS_PATH.


Using RGB Strips with Limitlessled

Home Assistant release (hass --version):
.57.2
Python release (python3 --version):
3.5.3
Component/platform:
limitlessled
Description of problem:
Hello, I need some help setting one of these up. I got MiLight iBox like the one HERE. And I got an RGB led strip controller, like the one HERE. Everything works as expected via the app, however, I can't get Home Assistant to control it. Here's the yaml code:
  - platform: limitlessled
    bridges:
      - host: <IP_ADDRESS>
        groups:
        - number: 1
          name: MasterBed

Does anyone know why this isn't working? I know the IP address is correct. The only thing I can think of is that I am using an RGB LED controller, and all the docs only seem to mention RGBW. Is there anything that I can do to get this working with Home Assistant?
If this is something that is yet to be implemented, then I am more than willing to take some packet caps if that would help.

Any error messages?

@dramamoose unfortunately there are no error messages. My theory is that the wrong packets are being sent.

Hi
I have the exact same problem as you. maybe "version: ?" must be correct


Snippet for getting the last updated time for a pull request.

There is a snippet that shows how to list PRs, but not how to get the 'last updated' time for them.
Looking at the calls made by Azure DevOps, this is a separate call:
POST /_apis/visits/artifactStatsBatch?includeUpdatesSinceLastVisit=True
How can I do the same using the C# library?
I couldn't find documentation for 'artifact stats'.

Would also like to be able to see this. I've noticed that the GitHub API has lastUpdated field on a Pull Request which is updated whenever anything on that PR changes.


Add getters for stakeholder by wallet and issuer_assigned_id

What?

Adding more getters for stakeholders based on fields other than the mongo UUID.

Also conditionally check for the WalletAlreadyExists(address) selector (0x789a109e) in the /add-wallet endpoint so it can more gracefully handle the contract error and return a successful response.

Why?
One use case that we want to support is being able to find or create a stakeholder starting from a User external to the TAP system.
Screenshots (optional)

Reviewing tonight.


why has white？？

why has white？？

Your question is not clear. Please post questions in the Discussions tab. Also, a full reproduction on CodePen or Repl.it (for larger repros) would help us find your mistake.
One explanation for the white color could be that the noise texture contains white pixels that aren't full white (i.e. not RGB 255, 255, 255 but may 250, 250, 250).

Your question is not clear. Please post questions in the Discussions tab. Also, a full reproduction on CodePen or Repl.it (for larger repros) would help us find your mistake.
One explanation for the white color could be that the noise texture contains white pixels that aren't full white (i.e. not RGB 255, 255, 255 but may 250, 250, 250).

Your question is not clear. Please post questions in the Discussions tab. Also, a full reproduction on CodePen or Repl.it (for larger repros) would help us find your mistake.
One explanation for the white color could be that the noise texture contains white pixels that aren't full white (i.e. not RGB 255, 255, 255 but may 250, 250, 250).

 Please post questions in the Discussions tab. Also, a full reproduction on CodePen or Repl.it (for larger repros) would help us find your mistake.
One explanation for the white color could be that the noise texture contains white pixels that aren't full white (i.e. not RGB 255, 255, 255 but may 250, 250, 250).

Otherwise it looks like linear interpolation problem, "texture2D" doesnt actually return a pixel from texture, it interpolates 4 pixels into one color

Did you by any chance enabled mipmapping (search "mipmap" in your code) ?

Try this
tex1 = vec4(0., 0., 0., 1.);


Explicitly pass the kubeconfig file to kubectl

Do not try to pass the kubeconfig in the KUBECONFIG env var: it can be problematic. Just use the --kubeconfig argument of kubectl

I'm still evaluating the root cause of this problem. It looks like the envvar really exists on the until and onlyif contexts....

The problem in this case is the subshell $().

Just to provide more context. In the update orchestration nodes were left in SchedulingDisabled status (all of them). We are doing a drain before rebooting them, but then the update orchestration despite being successful had:
                        ID: kubelet
                  Function: caasp_cmd.run
                      Name: kubectl uncordon 9e8ed6f15c754766ac64e6ee620890fe.infra.caasp.local

                    Result: True
                   Comment: onlyif execution failed
                   Started: 15:37:44.208830
                  Duration: 495.543 ms
                   Changes:


fix IIS Web site link

Q
A

Is bugfix?
✔

New feature?
✔/❌

Breaks BC?
✔/❌

Tests pass?
✔/❌

Fixed issues
https://github.com/yiisoft/yii2/issues/18704

@bizley, I think not, this link is the 2nd item in the list

Oh, right. I've added the same one, lol, sorry. I can see that the original link was somehow different (at least the version of it at archive.org) but this might do. Is there a chance to fix this for other languages as well?

Oh, right. I've added the same one, lol, sorry. I can see that the original link was somehow different (at least the version of it at archive.org) but this might do. Is there a chance to fix this for other languages as well?

I looked before doing PR
This fix is only in the en version

Thanks.


[FEAT REQ]: Close tooltip using the escape key

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
I can't see from the docs whether it's possible to escape a tooltip and close it. If so, I would be happy to help address this.
Describe the solution you'd like
A clear and concise description of what you want to happen.
Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.
Additional context
Add any other context or screenshots about the feature request here.

Are you referring to being able to close the tooltip by pressing the escape key? If so, this feature is yet to be implemented.
Feel free to submit a PR if you'd like. I suggest for it to be disabled by default, and enabled using a prop called closeOnEscape.

Awesome thanks!!!


Update showcase.md

hey, thanks for the contribution! our showcase list was getting really long and i wanted to specifically highlight new things that other sites in the showcase haven't yet, hope you understand :')


[feature](regress test) regression test support run in docker

Support run regress test suites in docker.  Each suite can setup multiple docker clusters and execute sql commands inside the docker. Each docker is a independent env,  it will not affect other suites. Then we can add complicated test suites,  like  add/remove/start/stop/restart backends.
example usage:
suite("test_chaos_example") {
    // This is a docker
    docker {
        sql """create table tb1 (k int) DISTRIBUTED BY HASH(k) BUCKETS 10"""
        sql """insert into tb1 values (1),(2),(3)"""

        cluster.checkBeIsAlive(2, true)

        // stop backend 2, 3
        cluster.stopBackends(2, 3)
        // wait be lost heartbeat
        Thread.sleep(6000)

        cluster.checkBeIsAlive(2, false)

        test {
            sql """insert into tb1 values (4),(5),(6)"""

            // REPLICA_FEW_ERR
            exception "errCode = 3,"
        }
    }

    // run another docker
    def options = new ClusterOptions()
    // add fe config items
    options.feConfigs = ["example_conf_k1=v1", "example_conf_k2=v2"]
    // contains 5 backends
    options.beNum = 5
    // each backend has 3 disks
    options.beDiskNum = 3
    // This is an another docker
    docker (options) {
        sql """create table tb1 (k int) DISTRIBUTED BY HASH(k) BUCKETS 10 properties ("replication_num"="5")"""
    }
}

To  use docker function in regression test,  need three steps:

Build doris fe and be;
Build a image using docker file docker/runtime/doris-compose/Dockerfile;
Special docker image  item image in file regression-conf.groovy or regression-conf-custom.groovy. The image is generated by step 2.

The image should be build with Docker file docker/runtime/doris-compose/Dockerfile.
Proposed changes
Issue Number: close #xxx

Further comments
If this is a relatively large or complex change, kick off the discussion at<EMAIL_ADDRESS>by explaining why you chose the solution you did and what alternatives you considered, etc...

run buildall

run buildall

run buildall

run buildall


Add link to napari/docs in Readme file.

Fixes/Closes

Closes #
Description
Adds a link to napari/docs in Readme.

cc @dgmccart
References

Type of change

[ ] Bug-fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[x] This change requires a documentation update

How has this been tested?

[ ] example: the test suite for my feature covers cases x, y, and z
[ ] example: all tests pass with my change
[ ] example: I check if my changes works with both PySide and PyQt backends
as there are small differences between the two Qt bindings.

Final checklist:

[x] My PR is the minimum possible work for the desired functionality
[ ] I have commented my code, particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation
[ ] I have added tests that prove my fix is effective or that my feature works
[ ] If I included new strings, I have used trans. to make them localizable.
For more information see our translations guide.

I think the first link people should see is the one to the docs at https://napari.org. I don't think it makes sense to remove that, since it should be one of the first things people look at.
Second, there is also a "tutorials" section of the README that will also need updating. Perhaps that, or the "contributing" section are better places to put the information and link to https://github.com/napari/docs

Genevieve, I added that information back in.  I agree with you.  I moved the information about contributing to the contributing section. I don't know what needs to be updated in the tutorial section.  It basically refers people to the tutorials on napari.org.

@psobolewskiPhD I made one final change. (There's almost always a way to make a doc a little bit better!)  Please approve this again, if you think it's worthy.
Thanks,
Nadalyn

Docs build was failing so I've reran checks (might take a while). The doc build error looked unrelated (something about tomli_w and npe2 docs), but we should make sure before merge.


DB setup coroutine never awaited

One gets a "coroutine never awaited" runtime warning from a very simple script such as this one:
import cassio

if __name__ == '__main__':
  cassio.init(database_id="...", token="...")
  cassio.table.MetadataVectorCassandraTable(table="my_table", vector_dimension=10)

The warning is:
RuntimeWarning: coroutine 'MetadataMixin.adb_setup' was never awaited
  self.db_setup()
RuntimeWarning: Enable tracemalloc to get the object allocation traceback

Fixed by #135


learn monolog-cascade

https://github.com/theorchard/monolog-cascade

blocked by https://github.com/kamilsk/Common/issues/20


DNS over HTTPS enhancement - Add CAA and SOA records - related to issue #7

CAA responses are going to be fun. See below for pointers on handling the decode.
curl -H 'accept: application/dns-json' 'https://cloudflare-dns.com/dns-query?name=yahoo.com&type=CAA'
curl -H 'accept: application/dns-json' 'https://cloudflare-dns.com/dns-query?name=yahoo.com&type=SOA'
For CAA, using this example data response:
"data": "\# 21 00 05 69 73 73 75 65 67 6c 6f 62 61 6c 73 69 67 6e 2e 63 6f 6d"
which decodes to "issue globalsign.com"
From the above example: The decimal number '21' identifies how many following hex byte pairs to expect. The next two hex byte pairs '\x00 05' identifies the number of hex bytes to decode into the first word where '\x69 73 73 75 65' decodes to ascii as 'issue'. The remaining hex bytes '\x67 6c 6f 62 61 6c 73 69 67 6e 2e 63 6f 6d' decode to ascii as 'globalsign.com'.
So the CAA bubble in this case would contain "issue globalsign.com"
For SOA, Just display the returned text in an SOA bubble.

Added the types to the DNS data dictionary, converting CAA hex into readable text


[Bug] Exhentai doesn't load some thumbnails

Device information

Tachiyomi version: v8.7.4-AZ
Android version: 11
Device: Samsung Galaxy A50

Steps to reproduce

Search something on Exhentai

Expected behavior
All thumbnails load
Actual behavior
Some thumbnails don't load
Other details
Opening the gallery, waiting for the thumbnail to load, and backing out sometimes fixes the issue for that gallery for that search.

Same problem, Huawei MediaPad M5. Observed behaviour is that more you search more  thumbs fails to load. Chapters themself load perfectly.

Can confirm that it seems to be the case. When there's nothing in the search bar, thumbnails load fine. The more terms you search for, though, the more thumbnails go missing

Same problem with LG G8, I've tried clearing cache, cookies, relogging, reinstalling, switchign to the DEV version, and messing around with "e-hentai" settings. There doesn't seem to be any discussion about this out side of this bug report. I've also noticed that Using E-hentai the same results will load perfectly fine, its only on EX where its bugged. However EX its self seems fine, its only in the App that fails to load thumbnails.
I tried to see if the fork SY had the same issues but according to its one now closed bug report it was fixed by relogging and resetting some settings. I don't want to sound like that guy, but considering there haven't been any activity from az4521 in months I'm starting to believe that this is abandoned. However SY insist on using that god awful List format when viewing E/EX hentai with no option to change it to Grid like with AZ, so I'm pretty much stuck with this because I rather have no thumbnails then SY telling me how I can/can't view the site.

Some details from my end (S21 Ultra, up to date on all updates):

it seems to affect older (presumably previously loaded?) thumbnails at a higher rate?
only affects exhentai
new galleries are unaffected until some time passes and they too lose thumbnails
galleries can often (but not always?) get their thumbnail back if you manually reload that individual entry, also eventually goes away
started a while ago, not sure exactly when

Attempted unsuccessful fixes:

clearing chapter cache
relogging + toggling ehentai settings (from: https://github.com/jobobby04/TachiyomiSY/issues/855) [unless I did it wrong? vague instructions]
clearing cookies
switching internet sources (2 independent wi-fi networks and mobile internet)

Unattempted fixes:

clearing database (seems to crash/stall at every attempt, probably just has too much in there [I do not have a problem I'll admit to at this time])
app reinstall

Re: App Abandoned (@T3hFyrefly):

Az is very much alive
he's fumo-posting almost every day
he saw your message and got self-conscious
this app has never been frequently maintained to begin with outside of widespread bugs, which is part of why it has the decrepit UI we all know and love

Ongoing fix attempts:

changing my github profile picture to a standard issue illicit fumo to elicit a dev response
procurement of more powerful fumo images to elicit more effective neuron activation
astrology and essential oils

Didn't mean to sound rude, his website just happened to be in 404 mode when I wrote that, so I assumed even if he was alive some IRL stuff happened.

 Initially not all of the thumbnails would load and currently none of the thumbnails load. Unless I'm using a VPN.  If I'm using a VPN every thumbnail loads.


move orphan validation into the import process

changed back to motasem code
moved nik validation of orphan into orphan importer
invalid orphans now show in error screen on import

Coverage decreased (-0.82%) to 98.79% when pulling c58a2108a906ca3d155b583618cb1905cc0e489f on PurityControl:orphan-validation-on-import into 02e7cb9b8501866c945d19c7742d06320ef0f162 on AgileVentures:develop.


Add RDO decision for partition splitting

Start of work on issue #44.
Partitions with block sizes above 8x8 (achieved by raising the value at lib.rs:708) will cause desynchronization.

This needs to rebased.

@tdaede Done, sorry for the messy history.

Done and added comparisons between default and best-performing speed parameters.

I have re-squashed with fixes to @ycho's comments and some more improvements to reduce duplicated code and remove RD cost computations from rdo_partition_decision for a performance and negligible precision improvement.

LGTM with ycho's comments addressed. Make sure to "squash and merge".

LGTM with my recommended manual rust formatting!


[BUG] All Word file's preview not working

OS: Win10
Extension Version: V3.4.4
VSCode: 1.95.3

The preview for Word files (*.docx, *.xlsx, .pdf) and Image files (.png, *.jpg, ...) is not working.
I remember this happening when I updated VSCode.

OS: Win10
Extension Version: V3.4.4
VSCode: 1.95.3

The preview for Word files (*.docx, *.xlsx, .pdf) and Image files (.png, *.jpg, ...) is not working. I remember this happening when I updated VSCode.

the error is caused by the latest version V3.4.4.The current solution is rollback version V3.4.3 and turn off zhe auto-update

Actually, opening, previewing file is not working at the current update. Roll back to the very previous one would help/

The preview for .csv file is not working too,Roll back to v3.4.3 can preview .csv file

me tool.

Fixed in version 7.4.5.


add .join({ wrap: fn })

I need this for implementing throttling in Dat Desktop.

Codecov Report

Merging #155 into master will increase coverage by 0.04%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #155      +/-   ##
==========================================
+ Coverage   87.59%   87.63%   +0.04%
==========================================
  Files           6        6
  Lines         274      275       +1
==========================================
+ Hits          240      241       +1
  Misses         34       34

Impacted Files
Coverage Δ

dat.js
90.8% <100%> (+0.1%)
:arrow_up:

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i'm not sure this is a good idea yet, let me test this in desktop first

this pattern isn't as nice as discovery swarm reads some custom props on the underlying stream. a throttle implementation would look something like this:
const wrap = function (stream) {
  // this is the normal throttle logic
  const input = throttle(speed)
  const output = throttle(speed)

  input.pipe(stream).pipe(output)
  const throttled = duplex(input, output)

  // this is all the extra plumbing you have to do
  stream.on('error', throttled.emit.bind(throttled, 'error'))
  stream.on('handshake', throttled.emit.bind(throttled, 'handshake'))

  throttled.destroy = stream.destroy.bind(stream)

  Object.defineProperty(throttled, 'id', { get: () => stream.id })
  Object.defineProperty(throttled, 'remoteId', { get: () => stream.remoteId })

  return throttled
}
dat.joinNetwork({ wrap })

instead, this module (and thus also discovery-swarm) should let you connect streams yourself. I'm thinking about something like:
disc({
  connect: (local, remote) => {
    local.pipe(throttle(speed)).pipe(remote).pipe(throttle(speed)).pipe(local)
  }
})

this is possible now through https://github.com/mafintosh/discovery-swarm/pull/29#event-1118506654 which floats in automatically :)

oh, so, I forgot to close this issue! Just pass { connect } to .join() :)

Ha I couldn't tell if it was still needed =)


Tweak syntax highlighting prompt detection

The terminal prompt was using the same class as double-quoted SQL
strings in the new version of the syntax highlighter, which was causing
the prompt detection code to inadvertently remove double-quoted SQL
strings.
Teach the prompt detection code to double-check that the prompt it's
removing is actually at the beginning of the code block and only
contains the prompt character ($) or (<) to avoid accidentally removing
strings.

This change is

Online preview: http://cockroach-docs-review.s3-website-us-east-1.amazonaws.com/a4291160d5edd27df6d1ffe46c18d1ea5b27a059/


Use JSON markdown blocks in docs

The comments aren't supported in JSON, that's why there are shown as red.
An option may be to use an other block code, like YAML (or something else, don't know if there is JSON5).

This pull request didn't trigger Jenkins as its author isn't in the whitelist.
An organization member must perform one of the following:

To have this branch tested by Jenkins, use the "ok to test" command.
To have a one time test done, use the "test this please" command.

Those commands are simple Github comments of the format: "jenkins: COMMAND"

Hmm, yeah, the fact that it's not valid json is going to be a problem I suspect.
jsonc or json5 would work on Github but pygment doesn't seem to support either as a format.
yaml may do the trick as it's a superset of json, I just don't know how well the coloring will be with that.

We can also use js instead of json, and replace # comments to //

Switching to json or js has now made github do a better job at validating things, showing a number of issues that we should probably fix as part of this.

Looks good, thanks!


Code cleanup: fixup linting issues

You now get a clean run through pylint.
I've also gone through the pylint ignores
and updated them based on what's appropriate
for this project.
I've also changed make check to have pylint
check everything.  It was previously only checking
for errors.

@stealthycoin Should be good to look at again.  I wasn't using the same commit off the master branch for pylint, and the newer version has a few errors I wasn't accounting for.

Codecov Report

Merging #327 into master will increase coverage by 0.21%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #327      +/-   ##
==========================================
+ Coverage   89.13%   89.34%   +0.21%
==========================================
  Files          18       18
  Lines        1905     1906       +1
  Branches      231      231
==========================================
+ Hits         1698     1703       +5
+ Misses        152      149       -3
+ Partials       55       54       -1

Impacted Files
Coverage Δ

chalice/policy.py
91.89% <100%> (+0.11%)
:arrow_up:

chalice/local.py
94.17% <100%> (+0.05%)
:arrow_up:

chalice/deploy/packager.py
90.83% <100%> (+0.07%)
:arrow_up:

chalice/cli/factory.py
86.31% <100%> (ø)
:arrow_up:

chalice/utils.py
88.88% <100%> (ø)
:arrow_up:

chalice/app.py
95.13% <100%> (ø)
:arrow_up:

chalice/package.py
97.05% <100%> (ø)
:arrow_up:

chalice/analyzer.py
89.37% <100%> (+1.33%)
:arrow_up:

chalice/deploy/deployer.py
80.47% <100%> (+0.09%)
:arrow_up:

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surfaced links to Cloud swarm connect options

What's changed

Surfaced links to Cloud swarm connect topics to highlight the Docker for Mac and Windows menu options

Related
#3594
Signed-off-by: Victoria Bialas<EMAIL_ADDRESS>

LGTM


quiet mode arg being passed when loading model

Codecov Report
Base: 78.03% // Head: 78.04% // Increases project coverage by +0.01% :tada:

Coverage data is based on head (43a4813) compared to base (328d892).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #620      +/-   ##
==========================================
+ Coverage   78.03%   78.04%   +0.01%
==========================================
  Files         178      178
  Lines       30588    30549      -39
==========================================
- Hits        23868    23842      -26
+ Misses       6720     6707      -13

Impacted Files
Coverage Δ

resqpy/model/_model.py
90.03% <100.00%> (ø)

resqpy/olio/simple_lines.py
40.16% <0.00%> (-0.49%)
:arrow_down:

resqpy/derived_model/_add_faults.py
91.58% <0.00%> (-0.47%)
:arrow_down:

resqpy/olio/keyword_files.py
48.29% <0.00%> (-0.36%)
:arrow_down:

resqpy/model/_forestry.py
78.83% <0.00%> (-0.22%)
:arrow_down:

resqpy/fault/_gcs_functions.py
63.83% <0.00%> (-0.12%)
:arrow_down:

resqpy/time_series/_from_nexus_summary.py
90.90% <0.00%> (-0.10%)
:arrow_down:

resqpy/olio/factors.py
97.05% <0.00%> (-0.09%)
:arrow_down:

resqpy/lines/_polyline.py
85.07% <0.00%> (-0.07%)
:arrow_down:

resqpy/olio/vdb.py
55.52% <0.00%> (-0.07%)
:arrow_down:

... and 17 more

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