Type errors and missing pino package..

Error 1

Argument of type '_INTERNAL_ElysiaLoggerPlugin<_INTERNAL_ElysiaLoggerPluginAutoLoggingState>' is not assignable to parameter of type 'Promise<{ default: (elysia: Elysia<any, any>) => Elysia<any, ElysiaInstance>; }>'.
      Type 'Elysia<"", { request: { log: pino.Logger<Options>; }; store: _INTERNAL_ElysiaLoggerPluginAutoLoggingState; }>' is missing the following properties from type 'Promise<{ default: (elysia: Elysia<any, any>) => Elysia<any, ElysiaInstance>; }>': then, catch, finally, [Symbol.toStringTag]ts(2769)

Argument of type '_INTERNAL_ElysiaLoggerPlugin<_INTERNAL_ElysiaLoggerPluginAutoLoggingState>' is not assignable to parameter of type 'Promise<{ default: (elysia: Elysia<any, any>) => Elysia<any, ElysiaInstance>; }>'.
      Type 'Elysia<"", { request: { log: pino.Logger<Options>; }; store: _INTERNAL_ElysiaLoggerPluginAutoLoggingState; }>' is missing the following properties from type 'Promise<{ default: (elysia: Elysia<any, any>) => Elysia<any, ElysiaInstance>; }>': then, catch, finally, [Symbol.toStringTag]ts(2769)

Error 2
bun start
$ bun run src/index.ts

error: Cannot find package "pino" from<EMAIL_ADDRESS>error: script "start" exited with code 1 (SIGHUP)

Info
Bun version: 1.0.6
@bogeychan/elysia-logger version: 0.0.12
vscode: 1.83.1
os: AlmaLinux 9.2

Hi 👋
thanks for reporting!
I can't reproduce both errors on my end. Can you send me your tsconfig.json and elysia version pls?

Based on your screenshot, I'm assuming you're doing something like this, right?
import { createPinoLogger } from '@bogeychan/elysia-logger';

const log = createPinoLogger();

const app = new Elysia()
  .use(
    log.into({
      autoLogging: true
    })
  )
  .get('/', () => '')

tsconfig.json
{
        "compilerOptions": {
                "lib": ["ESNext"],
                "module": "esnext",
                "target": "esnext",
                "moduleResolution": "bundler",
                "moduleDetection": "force",
                "allowImportingTsExtensions": true,
                "noEmit": true,
                "composite": true,
                "strict": true,
                "downlevelIteration": true,
                "skipLibCheck": true,
                "jsx": "preserve",
                "allowSyntheticDefaultImports": true,
                "forceConsistentCasingInFileNames": true,
                "allowJs": true,
                "types": [
                        "bun-types" // add Bun global
                ]
        }
}

"elysia": "^0.6.23"

Oh, you're using an older elysia version.
the plugin requires at least:
https://github.com/bogeychan/elysia-logger/blob/f1f3e89c4a5a1606f920c4de50ebc0129f442a9f/package.json#L36
The plugin won't be backward compatible until elysia becomes stable.

Thank you for the response, I will check it out!

So the errors from vscode is gone. But compilation errors still occurs.
Here is the error:
[myuser@ificluster chord-node]$ bun start
$ bun run src/index.ts
error: Cannot find package "pino" from<EMAIL_ADDRESS>error: script "start" exited with code 1 (SIGHUP)

package.json:
{
  "name": "node",
  "module": "index.ts",
  "type": "module",
  "scripts": {
    "start": "bun run src/index.ts",
    "compile": "bun build src/index.ts --compile --outfile=dist/chordnode",
    "cleanup": "/share/ifi/cleanup.sh",
    "list-all": "/share/ifi/list-cluster-static.sh",
    "list-available": "/share/ifi/available-nodes.sh"
  },
  "devDependencies": {
    "bun-types": "latest"
  },
  "peerDependencies": {
    "typescript": "^5.0.0"
  },
  "dependencies": {
    "@bogeychan/elysia-logger": "^0.0.12",
    "@elysiajs/swagger": "^0.7.3",
    "commander": "^11.1.0",
    "elysia": "^0.7.17"
  }
}

bun.lockdb:
# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
# yarn lockfile v1
# bun ./bun.lockb --hash: 8DB69B4C21831BAC-c5505adc448c6336-D5C3E1D2F05551B6-1ddf090cffd074fd

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can't reproduce it with your package.json and tsconfig.json... is pino actually installed? Can you check if there's a pino folder under node_modules?
And try to reinstall everything and clear the bun install cache before:
rm -fr node_modules/ bun.lockb ~/.bun/install/cache/ && bun install

Bun 1.0.7 released yesterday including a few fixes related to bun install. Try to upgrade bun

closed this issue due to inactivity, feel free to reopen it or create a new one.


Leaky functions: localise all variables except output

Functions should be well-encapsulated; they should not declare any unnecessary non-local variables. Any non-local variables declared must be catalogued as outputs in the function documentation. All existing functions should be reviewed to ensure compliance.

Similarly, each function should pre-clear any potential outputs from memory when it is called to ensure that the output values return empty if the function fails (and are not populated by residual values from elsewhere in the module/utility or from previous calls to the same function).


Angular Gridster instead of jquery-sortable

For a more consistent layout I propose angular-gridster as a replacement for angular-ui-sortable

Agree with above. Would suggest add layout control by users. Packery also a good choice. Glad to help if needed to push some changes.

I'm going to give ng-sortable a try for v1.0.0... it looks like it has matured a fair amount in the last six months.

ng-sortable hase the same problem as angular-ui-sortable. if the cells are not equal sizes the layout is messed up. for example angular-gridster has relative cell-sizes which makes the layout more consistent.

Yeah, I gave it a shot and it was not too pretty... will give gridster another look. My beef with gridster is that it has fixed height for all elements :-/ this can be pretty hard to deal with for certain widget content.

removing this from the 1.0.0 milestone as this is probably achievable using a custom dashboard template. If someone else wants to add this option, i am open to PRs.

We choose to switch to Gridster in our project, so I forked this repo and made the changes. It's working pretty fine I'd say. https://github.com/SC5/malhar-angular-dashboard
Disclaimer: haven't touched to tests (possibly broken), haven't touched to demo (completely broken), switched to Foundation instead of Bootstrap (just because we're using it in our project). In case someone chooses to try our version, feel free to contact us for guidance.

Hi artoliukkonen!
I am interested in the gridster fork but my project uses bootstrap. Could you please tell me what changes are required to make it work as gridster/bootstrap instead of gridster/foundation.
Also what is the possibility of getting the demo application to work. This is simplified version and will help a lot. Thanks.


Enhancemente/fix discounts

Se fixea descuentos en congrats

Codecov Report

:exclamation: No coverage uploaded for pull request base (feature/congrats-templating@2fb16fd). Click here to learn what that means.
The diff coverage is 26.92%.

@@                      Coverage Diff                       @@
##             feature/congrats-templating     #767   +/-   ##
==============================================================
  Coverage                               ?   27.88%
==============================================================
  Files                                  ?      312
  Lines                                  ?    19897
  Branches                               ?     1846
==============================================================
  Hits                                   ?     5549
  Misses                                 ?    13698
  Partials                               ?      650

Impacted Files
Coverage Δ

...ymentresult/components/PaymentMethodComponent.java
51.85% <ø> (ø)

...com/mercadopago/paymentresult/components/Body.java
40.67% <0%> (ø)

...dopago/paymentresult/props/PaymentMethodProps.java
54.76% <14.28%> (ø)

...cadopago/paymentresult/props/TotalAmountProps.java
50% <14.28%> (ø)

...paymentresult/components/TotalAmountComponent.java
61.9% <45.45%> (ø)

Continue to review full report at Codecov.

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Add a way to tell the client to blob upload large async inputs when the runnable queue is full.

One thing I had to think through when writing this simple PR is the nuance around how we plan to handle multiple inputs passed into FunctionMap. While we currently only pass in one input for experimental_spawn, we should have a reasonable behavior for the future. Let's say the client passes in 3 inputs, and the second one is too large. We would then send back a response containing 3 items - the first and third would just contain the index and nothing else (we wouldn't create those inputs). The second would contain the index and requires_blob_upload = true. This would inform the client of which inputs they should upload before trying again.

Deleting in favor of creating a new RPC.


Added Dutch localization file

Thanks :-)

Hi! Thanks for your contribution!
Can you add this translation that come with V2 soon ?
https://github.com/Alex-D/Trumbowyg/blob/master/src/trumbowyg.js#L36
Thanks again! :)

Added the missing string "removeFormat".

You could be proud of your contribution =D

You can be proud of this plugin! Thanks for your work. ;-)


fix: Unhandled Connection Closing in websocker_server_awaitable.cpp

This PR fixes #2778

Thank you for the PR,
The problem seems to be in this line: https://github.com/boostorg/beast/blob/192b7d5a43a7a95dd29df8b08cff635fb14ad9a6/example/websocket/server/awaitable/websocket_server_awaitable.cpp#L81
It continues to loop if ec == websocket::error::closed which leads to an operation_aborted error. I would suggest put the  whole loop inside try catch block so it will break out of loop if an exception throws, something like:
    try
    {
        for(;;)
        {
            // This buffer will hold the incoming message
            beast::flat_buffer buffer;

            // Read a message
            co_await ws.async_read(buffer);

            // Echo the message back
            ws.text(ws.got_text());
            co_await ws.async_write(buffer.data());
        }
    }
    catch(const boost::system::system_error & se)
    {
        if (se.code() != websocket::error::closed)
            throw;
    }

And check if exception_ptr is not null (as your current code does).

Thanks for the suggestion.


BUG: App gets stuck with dragging an element

I am not sure what leads to this state, but sometimes I end up with arrows that still have an elementId in their startBinding property, however, the element they were bound to no longer exists. In such a case, if you start to drag the arrow, you cannot let go.
This is the simplest case of such an element: https://excalidraw.com/#json=5kcNHN-i6LwVtGudc4ELB,Es27vQIuj7QY_YcZPs9p_g
This becomes very frustrating when this arrow is grouped with other objects such as in this case: https://excalidraw.com/#json=Tt8ze8blbLtOAM0QtBHw1,G0OaV0UnGE9DK6P7Lcnf9Q
The only way to stop dragging is to double-click to enter the text editor and then press escape.
https://github.com/excalidraw/excalidraw/assets/14358394/9a00e4f8-0f57-4565-80ca-ad8a4cf6b1f3
If in the below I set "startBinding: null, the issue does not happen.
{
  "type": "excalidraw",
  "version": 2,
  "source": "https://excalidraw.com",
  "elements": [
  		{
			"type": "arrow",
			"version": 2296,
			"versionNonce": 613623198,
			"index": "b0vV",
			"isDeleted": false,
			"id": "-wM53QBFbd2mecyjTrYRI",
			"fillStyle": "solid",
			"strokeWidth": 1,
			"strokeStyle": "dashed",
			"roughness": 0,
			"opacity": 100,
			"angle": 0,
			"x": -55,
			"y": 135,
			"strokeColor": "black",
			"backgroundColor": "transparent",
			"width": 0,
			"height": 109,
			"seed":<PHONE_NUMBER>,
			"groupIds": [],
			"frameId": null,
			"roundness": null,
			"boundElements": [],
			"updated":<PHONE_NUMBER>728,
			"link": null,
			"locked": false,
			"startBinding": {
				"elementId": "xw25sQBsbd2mecyjTrYHA",
				"focus": -0.022693576407543894,
				"gap": 15.681219937390892
			},
			"endBinding": null,
			"lastCommittedPoint": null,
			"startArrowhead": null,
			"endArrowhead": null,
			"points": [
				[
					0,
					0
				],
				[
					0,
					109
				]
			]
		}
  ],
  "appState": {
    "gridSize": null,
    "viewBackgroundColor": "#ffffff"
  },
  "files": {}
}


serialization: GetRecord method identifier fix

UUID was being serialized into the record identifier on the final XML instead of the pid_value, see: https://zenodo.org/oai2d?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai:zenodo.org:167082

@jirikuncar It looks like it was intended (and tested for in the unit test), however it's not how it was serialized in the legacy Zenodo.

I think the build error can likely be fixed by just upgrading to sphinx>=1.5.1

@krzysztof there should be 2 commits - first one fixing the serialization and second one bumping the Sphinx version.

@jirikuncar This needs to be merged and requires a release: https://github.com/inveniosoftware/requirements-builder/pull/24


Fix typo in date time section of Jetcaster README

Fixes typo in README.md
Data -> Date

Thanks Ben!


Question about fragment lengths

Hi all,
I am new to RNAseq analysis and I ran bcbio-nextgen on a set of 11 case and 11 control datasets. I used bcbio.rnaseq summarize to generate a report.
I noticed that I have zeros for the fragment.length.mean values in the table for almost all my samples (5 out of my 22 samples have a value ranging from 77 to 101).
Since I have paired-end reads, I expected there to be non-zero values. I am also a bit confused as to why some samples have values and most don't.
Do I need to be concerned about the zero fragment-lengths? If yes, how do I go about diagnosing this?
Thanks for any advice you may have!
~Lina

Hi Lina,
I am looking into the code. It seems we check that internally.
I would make sure that in the project-summary.yaml file the numbers are the same. Maybe the error is in the parsing?
If not, we get the first 1000 reads, and calculate the median. Can you take one of those samples with  0 and check the first reads of the BAM file to see if those reads has paired reads mapped?
In case, you see reads where their pairs are not mapped, you can look at the samtools stats inside the QC folders for each sample and check the first lines to see if you can note some difference in the stats related to paired reads.
let's see if that helps us to know what is going one.
cheers

Hi Lorena,
Thanks for the quick reply!
I checked the project-summary.yaml file and the parsing looks ok (i.e. the values in that file correspond to the table I got in the summary report).
Then I went ahead and truncated the bam file for one of the "zero-fragment-length" samples to the first 1000 alignments and ran samtools flagstat on it:
1000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
1000 + 0 mapped (100.00%:-nan%)
1000 + 0 paired in sequencing
666 + 0 read1
334 + 0 read2
448 + 0 properly paired (44.80%:-nan%)
1000 + 0 with itself and mate mapped
0 + 0 singletons (0.00%:-nan%)
421 + 0 with mate mapped to a different chr
4 + 0 with mate mapped to a different chr (mapQ>=5)

I also found this file: final/13_D/qc/bamtools/bamtools_stats.txt
cat bamtools_stats.txt

**********************************************
Stats for BAM file(s):
**********************************************

Total reads:       79531382
Mapped reads:      79531382     (100%)
Forward strand:    39771278     (50.007%)
Reverse strand:    39760104     (49.993%)
Failed QC:         0    (0%)
Duplicates:        0    (0%)
Paired-end reads:  79531382     (100%)
'Proper-pairs':    59129662     (74.3476%)
Both pairs mapped: 79531382     (100%)
Read 1:            39765691
Read 2:            39765691
Singletons:        0    (0%)
Average insert size (absolute value): 287031
Median insert size (absolute value): 181

Are the average and/or median insert sizes related to the fragment lengths, or are these completely different values?

It should be median. Maybe you have overlapped reads then. Can you check some of the reads manually to see if the two reads overlaps? maybe is that. i can check further the function.

What's the best way to check if they overlap? (sorry, total n00b here :-P)
Can I determine this from samtools view output?

yep!
just samtools view and you will see where the paired reads is mapped in the same line. I think column9 is the one we use.

On Apr 6, 2016, at 2:47 PM, lfaller<EMAIL_ADDRESS>wrote:
What's the best way to check if they overlap? (sorry, total n00b here :-P)
Can I determine this from samtools view output?
—
You are receiving this because you commented.
Reply to this email directly or view it on GitHub https://github.com/chapmanb/bcbio-nextgen/issues/1312#issuecomment-206510379

Ok! Here is some (truncated) samtools view output:
NS500401:21:HMNK2BGXX:1:12104:11946:14608       385     1       11695   1       75M     2       114358998       0       AGTGATTTGGGCTGGGGCCTGGCCATGTGTATTTTTTTAAATTTCCACTGATGTTTTTGCTGCATGGCCG
NS500401:21:HMNK2BGXX:1:21203:18510:19986       129     1       11869   50      75M     2       114359007       0       GTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCA
NS500401:21:HMNK2BGXX:2:11210:15503:19135       417     1       11891   3       75M     =       12033   216     CTTTGACCTCTTCTTTCTGTTCATGTGTATCTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACTGGGCC
NS500401:21:HMNK2BGXX:4:23404:6980:4808 355     1       11900   3       75M     =       12030   204     CTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGG     AAAAAE
NS500401:21:HMNK2BGXX:2:12105:16535:5164        419     1       11913   1       75M     =       12033   194     ATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTG
NS500401:21:HMNK2BGXX:1:23306:13958:14563       99      1       11981   3       75M     =       12041   135     GGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTG
NS500401:21:HMNK2BGXX:4:23404:6980:4808 403     1       12030   3       74M     =       11900   -204    GCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGG      EEEEEE
NS500401:21:HMNK2BGXX:2:11210:15503:19135       337     1       12033   3       74M     =       11891   -216    GGCCTGTGCCAGGGTGGAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGAT
NS500401:21:HMNK2BGXX:2:12105:16535:5164        339     1       12033   1       74M     =       11913   -194    GGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGAT
NS500401:21:HMNK2BGXX:1:23306:13958:14563       147     1       12041   3       75M     =       11981   -135    CCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTCCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTG
NS500401:21:HMNK2BGXX:4:13410:7058:9240 385     1       12067   0       75M     =       21547051        21535054        GGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTG
NS500401:21:HMNK2BGXX:4:21511:16851:11242       385     1       12173   0       55M385N19M      2       114357705       0       GAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTGTGTG
NS500401:21:HMNK2BGXX:4:21511:16851:11242       385     1       12173   0       55M385N19M      15      102517859       0       GAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTGTGTG
NS500401:21:HMNK2BGXX:4:21511:16851:11242       417     1       12173   0       55M385N19M      =       13237   1139    GAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTGTGTGGTGATGCC
NS500401:21:HMNK2BGXX:4:21511:16851:11242       417     1       12173   0       55M385N19M      16      62918   0       GAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTGTGTGGTGATGCC
NS500401:21:HMNK2BGXX:1:11206:13796:19415       99      1       12569   1       75M     =       12635   141     GTGATGTGTGGGCCCACCGGCCCCAGGCTCCTGTCTCCCCCCAGGTGTGTGGTGATGCCAGGCATGCCCTTCCCC
NS500401:21:HMNK2BGXX:4:21503:9214:6192 65      1       12596   1       70M     12      92865   0       CTCCTGTCTCCCCCCAGGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCTCCAGAGCTGC  AAAAAEEEEEEEEE
NS500401:21:HMNK2BGXX:1:11206:13796:19415       147     1       12635   1       75M     =       12569   -141    CCCTTCCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCC
NS500401:21:HMNK2BGXX:2:22307:3091:9114 129     1       12647   0       73M     2       114357694       0       ATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAG
NS500401:21:HMNK2BGXX:2:22307:3091:9114 385     1       12647   0       73M     12      92291   0       ATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAG       AAAAAE
NS500401:21:HMNK2BGXX:2:22307:3091:9114 385     1       12647   0       73M     15      102517848       0       ATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAG
NS500401:21:HMNK2BGXX:2:22307:3091:9114 417     1       12647   0       73M     =       13250   676     ATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAG       AAAAAE
NS500401:21:HMNK2BGXX:4:23509:2921:1600 433     1       12828   3       72M     =       87491341        87478588        TGATCTTCCCTGTGATGTCATCTGGAGCCCTGCTGCTTGCGGTGGCCTATAAAGCCTCCTAGTCTGGCTC
NS500401:21:HMNK2BGXX:4:21511:16851:11242       337     1       13237   0       75M     =       12173   -1139   CCAAAGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACATGCTGTTGGC

Some of the values in column 9 are zeros. Is that ok?

I see,
It seems that when the read is in another chromosome then the TLEN is set to 0 and then if we calculate the median, it goes down. In the previous report you can see that 50% of them are in different chromosome, at least for the first 1000. I would do samtools stats BAM of the whole bam to check if this is only on the top or not.
I think the solution would be to ignore the 0 when calculating. As well, when is spliced the value is super high, so not realistic, should be ignored as well.
Maybe something happened with those samples? the counts distribution are the same? or any other metric in the report that makes then be together?
I will change this in the code. So for now, you can ignore the ones that says 0 or super big, and look at the other values. It seems like 150-200

On Apr 6, 2016, at 2:51 PM, lfaller<EMAIL_ADDRESS>wrote:
Ok! Here is some (truncated) samtools view output:
NS500401:21:HMNK2BGXX:1:12104:11946:14608       385     1       11695   1       75M     2       114358998       0       AGTGATTTGGGCTGGGGCCTGGCCATGTGTATTTTTTTAAATTTCCACTGATGTTTTTGCTGCATGGCCG
NS500401:21:HMNK2BGXX:1:21203:18510:19986       129     1       11869   50      75M     2       114359007       0       GTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCA
NS500401:21:HMNK2BGXX:2:11210:15503:19135       417     1       11891   3       75M     =       12033   216     CTTTGACCTCTTCTTTCTGTTCATGTGTATCTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACTGGGCC
NS500401:21:HMNK2BGXX:4:23404:6980:4808 355     1       11900   3       75M     =       12030   204     CTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGG     AAAAAE
NS500401:21:HMNK2BGXX:2:12105:16535:5164        419     1       11913   1       75M     =       12033   194     ATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTG
NS500401:21:HMNK2BGXX:1:23306:13958:14563       99      1       11981   3       75M     =       12041   135     GGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTG
NS500401:21:HMNK2BGXX:4:23404:6980:4808 403     1       12030   3       74M     =       11900   -204    GCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGG      EEEEEE
NS500401:21:HMNK2BGXX:2:11210:15503:19135       337     1       12033   3       74M     =       11891   -216    GGCCTGTGCCAGGGTGGAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGAT
NS500401:21:HMNK2BGXX:2:12105:16535:5164        339     1       12033   1       74M     =       11913   -194    GGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGAT
NS500401:21:HMNK2BGXX:1:23306:13958:14563       147     1       12041   3       75M     =       11981   -135    CCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTCCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTG
NS500401:21:HMNK2BGXX:4:13410:7058:9240 385     1       12067   0       75M     =       21547051        21535054        GGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTG
NS500401:21:HMNK2BGXX:4:21511:16851:11242       385     1       12173   0       55M385N19M      2       114357705       0       GAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTGTGTG
NS500401:21:HMNK2BGXX:4:21511:16851:11242       385     1       12173   0       55M385N19M      15      102517859       0       GAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTGTGTG
NS500401:21:HMNK2BGXX:4:21511:16851:11242       417     1       12173   0       55M385N19M      =       13237   1139    GAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTGTGTGGTGATGCC
NS500401:21:HMNK2BGXX:4:21511:16851:11242       417     1       12173   0       55M385N19M      16      62918   0       GAAAGATTGGAGGAAAGATGAGTGACAGCATCAACTTCTCTCACAACCTAGGCCAGTGTGTGGTGATGCC
NS500401:21:HMNK2BGXX:1:11206:13796:19415       99      1       12569   1       75M     =       12635   141     GTGATGTGTGGGCCCACCGGCCCCAGGCTCCTGTCTCCCCCCAGGTGTGTGGTGATGCCAGGCATGCCCTTCCCC
NS500401:21:HMNK2BGXX:4:21503:9214:6192 65      1       12596   1       70M     12      92865   0       CTCCTGTCTCCCCCCAGGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCTCCAGAGCTGC  AAAAAEEEEEEEEE
NS500401:21:HMNK2BGXX:1:11206:13796:19415       147     1       12635   1       75M     =       12569   -141    CCCTTCCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCC
NS500401:21:HMNK2BGXX:2:22307:3091:9114 129     1       12647   0       73M     2       114357694       0       ATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAG
NS500401:21:HMNK2BGXX:2:22307:3091:9114 385     1       12647   0       73M     12      92291   0       ATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAG       AAAAAE
NS500401:21:HMNK2BGXX:2:22307:3091:9114 385     1       12647   0       73M     15      102517848       0       ATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAG
NS500401:21:HMNK2BGXX:2:22307:3091:9114 417     1       12647   0       73M     =       13250   676     ATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAG       AAAAAE
NS500401:21:HMNK2BGXX:4:23509:2921:1600 433     1       12828   3       72M     =       87491341        87478588        TGATCTTCCCTGTGATGTCATCTGGAGCCCTGCTGCTTGCGGTGGCCTATAAAGCCTCCTAGTCTGGCTC
NS500401:21:HMNK2BGXX:4:21511:16851:11242       337     1       13237   0       75M     =       12173   -1139   CCAAAGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACATGCTGTTGGC
Some of the values in column 9 are zeros. Is that ok?
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Ok! Thanks for helping me out! I will ignore the fragment lengths for now.
I am just now going through the report and trying to understand every part of it ;-)
I think the counts distributions look pretty similar across the samples. Is this the figure you are thinking of?

What other plots could I look at to try and see if the samples look ok?

As a side note, we are moving to another way to give basic QC metrics with multiqc, but this is happening in the devel version. ")
About the boxplot, yest, that's fine for raw counts before normalization.

Ok cool, I'll definitely check out the new QC metrics once they are live :)
Thanks!!

I modified bcbio.rnaseq to use the samtools value, hope this helps in the future.

great, thanks!!


Defaults of the HTTPManager

Change the defaults of the HTTPManager to the most-secure variants of all options.

In order to do this, the defaults within the program should change.
The HTTPManager and the web.config is just a way to change the defaults.


Update publish action

[x] Make action deploy to testpypi on release with manual trigger to pypi
[x] Fix concurrency bugs due to #50
[x] Fix unit test bug not detecting user key

@yuxqiu

Log: https://github.com/TrueLearnAI/truelearn/actions/runs/4548246898/jobs/8019079308
Its failing when the publish action calls it, I think this is to do with the fact that we are doing a workflow call, so the environment may not be the same?

I have a question about concurrency. From Github Doc, it seems that it's unnecessary for us to add a suffix after group: ${{ github.workflow }}-${{ github.ref }}. What's the problem that you encountered?

@yuxqiu  Log: https://github.com/TrueLearnAI/truelearn/actions/runs/4548246898/jobs/8019079308 Its failing when the publish action calls it, I think this is to do with the fact that we are doing a workflow call, so the environment may not be the same?

Let me investigate this issue.

I have a question about concurrency. From Github Doc, it seems that it's unnecessary for us to add a suffix after group: ${{ github.workflow }}-${{ github.ref }}. What's the problem that you encountered?

The problem is if all the workflows are in the same group, they effectively cancel eachother. By appending that text we get the desired behaviour as stated in #50 by assigning each workflow to its own respective group, where currently in-progress runs of the same workflow are cancelled if new commits have been made.
Concurrency ensures that only a single job or workflow using the same concurrency group will run at a time. A concurrency group can be any string or expression. The expression can use any context except for the secrets context. You can also specify concurrency at the workflow level. When a concurrent job or workflow is queued, if another job or workflow using the same concurrency group in the repository is in progress, the queued job or workflow will be pending. Any previously pending job or workflow in the concurrency group will be canceled. To also cancel any currently running job or workflow in the same concurrency group, specify cancel-in-progress: true.

@yuxqiu  Log: https://github.com/TrueLearnAI/truelearn/actions/runs/4548246898/jobs/8019079308 Its failing when the publish action calls it, I think this is to do with the fact that we are doing a workflow call, so the environment may not be the same?

This thing looks strange because if WIKIFIER_API_KEY is None, the test would be skipped. However, since it is not skipped here, this means that there is some value in this variable. But based on the output, this is not a valid value.
So, where does it come from? 😕

@yuxqiu  Log: https://github.com/TrueLearnAI/truelearn/actions/runs/4548246898/jobs/8019079308 Its failing when the publish action calls it, I think this is to do with the fact that we are doing a workflow call, so the environment may not be the same?

This thing looks strange because if WIKIFIER_API_KEY is None, the test would be skipped. However, since it is not skipped here, this means that there is some value in this variable. But based on the output, this is not a valid value.
So, where does it come from? 😕

I have found the cause: actions/runner#1490

@yuxqiu  Log: https://github.com/TrueLearnAI/truelearn/actions/runs/4548246898/jobs/8019079308 Its failing when the publish action calls it, I think this is to do with the fact that we are doing a workflow call, so the environment may not be the same?

This thing looks strange because if WIKIFIER_API_KEY is None, the test would be skipped. However, since it is not skipped here, this means that there is some value in this variable. But based on the output, this is not a valid value.
So, where does it come from? 😕
Resolved 🚀 , we have this beatiful info about environments on GitHub, but you cant have it all eh

I have a question about concurrency. From Github Doc, it seems that it's unnecessary for us to add a suffix after group: ${{ github.workflow }}-${{ github.ref }}. What's the problem that you encountered?

The problem is if all the workflows are in the same group, they effectively cancel eachother. By appending that text we get the desired behaviour as stated in #50 by assigning each workflow to its own respective group, where currently in-progress runs of the same workflow are cancelled if new commits have been made. To see a more precise reason: immich-app/immich#1820 ( We experience a deadlock )
Concurrency ensures that only a single job or workflow using the same concurrency group will run at a time. A concurrency group can be any string or expression. The expression can use any context except for the secrets context. You can also specify concurrency at the workflow level. When a concurrent job or workflow is queued, if another job or workflow using the same concurrency group in the repository is in progress, the queued job or workflow will be pending. Any previously pending job or workflow in the concurrency group will be canceled. To also cancel any currently running job or workflow in the same concurrency group, specify cancel-in-progress: true.

I see. So, to solve this problem, we just need to add a suffix to the concurrency group in python_publish.yml because it calls other workflows and then the other workflows inherit its github.workflow.
But, do you think we need to add suffixes for other workflows? It doesn't seem very necessary except for the sake of consistency.

It doesn't seem to work?

It doesn't seem to work?

yep doesnt work

Approved 🚀


Work around dosfstools 4.2's FAT label check

See the commits for the issue with the new dosfstools 4.2 label check. This PR
works around the issue since fixing it in FatFS looks riskier than keeping the
current behavior.

Test 032 is failing with the missing boot sector label also.  Removing the label as in 074 fixes it.


LineFormatter outputs \n instead of new line

Monolog v1.22.0 on php PHP 7.0.8-0ubuntu<IP_ADDRESS>
Not sure where I'm going wrong.  Even the simplest case of running the following in the php -a CLI interpreter:
function throwException(\Monolog\Logger $logger)
{
    $e = new Exception("test exception");
    $logger->error("exception logged", [$e]);
}

$logger = new \Monolog\Logger("Default");
$handler = new \Monolog\Handler\StreamHandler("php://stdout", \Monolog\Logger::DEBUG);
$formatter = new \Monolog\Formatter\LineFormatter();
$formatter->includeStacktraces(true);
$handler->setFormatter($formatter);
$logger->pushHandler($handler);

throwException($logger);

outputs everything on one line as follows:
[2017-02-16 16:58:49] Default.ERROR: exception logged ["[object] (Exception(code: 0): test exception at php shell code:3)\n[stacktrace]\n#0 php shell code(1): throwException(Object(Monolog\\Logger))\n#1 {main}"] []

Hi @Seldaek thanks for the backport/fix but it doesn't seem to have resolved the problem.
I'm now on the version the fix is tagged-against (1.22.1) (the below from composer.lock):
            "name": "monolog/monolog",
            "version": "1.22.1",
            "source": {
                "type": "git",
                "url": "https://github.com/Seldaek/monolog.git",
                "reference": "1e044bc4b34e91743943479f1be7a1d5eb93add0"
            },

but running the code in the ticket still outputs everything on the same line.

Ah yeah sorry I forgot to clarify here, but Really you shouldn't just pass [$e] as context info.. If you pass ['exception' => $e] you follow PSR-3 standards, and a lot of handlers and stuff will work better, and it outputs a json object as opposed to a json array, in which case the fix kicks in and converts the new lines.

Ah excellent, thank you.  I haven't read the PSR-3 standards - I'll go and do that now :)
(and you're right, the code above works fine once I've updated as you suggest!).

PSR-3 doesn't do a whole lot, but standardizing the exception key is a good thing IMO, as it allows all the tooling to know where to expect exceptions, and generally speaking it's a good idea to "name" your context data to have more context as to how to read the context data.. :)

You're spot-on - and I do it for the others, just not Exceptions (I guess because the class names are normally suffixed Exception).  I got away with it using log4php because the PSR-3 wrapper checked each context arg to see if it was an instanceof Exception.
For those finding this ticket, PSR-3 is indeed very explicit:

If an Exception object is passed in the context data, it MUST be in the 'exception' key.


Resource exhausted: OOM when allocating tensor with shape[32,512,3072] and type float on

i have trouble with run the run_race.py. I google it and decrease the --train_batch_size from 32 to 8,but it didn't work.
i use a GTX 1660TI with cuda10.
here is my parameter:
--albert_config_file=/home/dy/Project/ALBERT/albert_base/albert_config.json
--output_dir=/home/dy/Project/ALBERT/output_dir
--data_dir=/home/dy/Project/ALBERT
--init_checkpoint=/home/dy/Project/ALBERT/albert_base/model.ckpt-best
--train_file=/home/dy/Project/ALBERT/train_file/train
--eval_file=/home/dy/Project/ALBERT/eval_file/eval
--vocab_file=/home/dy/Project/ALBERT/albert_base/30k-clean.vocab
--spm_model_file=/home/dy/Project/ALBERT/albert_base/30k-clean.model
--max_seq_length=512
--max_qa_length=128
--do_train
--do_eval
--train_batch_size=8
--eval_batch_size=8
--learning_rate=1e-5
--train_step=12000
--warmup_step=1000
--save_checkpoints_steps=100
if you need know anything orther,just let me know.
im appreciate any help!

i have trouble with run the run_race.py. I google it and decrease the --train_batch_size from 32 to 8,but it didn't work.
i use a GTX 1660TI with cuda10.
here is my parameter:
--albert_config_file=/home/dy/Project/ALBERT/albert_base/albert_config.json
--output_dir=/home/dy/Project/ALBERT/output_dir
--data_dir=/home/dy/Project/ALBERT
--init_checkpoint=/home/dy/Project/ALBERT/albert_base/model.ckpt-best
--train_file=/home/dy/Project/ALBERT/train_file/train
--eval_file=/home/dy/Project/ALBERT/eval_file/eval
--vocab_file=/home/dy/Project/ALBERT/albert_base/30k-clean.vocab
--spm_model_file=/home/dy/Project/ALBERT/albert_base/30k-clean.model
--max_seq_length=512
--max_qa_length=128
--do_train
--do_eval
--train_batch_size=8
--eval_batch_size=8
--learning_rate=1e-5
--train_step=12000
--warmup_step=1000
--save_checkpoints_steps=100
if you need know anything orther,just let me know.
im appreciate any help!

by the way,what does max_qa_length mean? is there any different bettwen max_seq_length and max_qa_length?

Resource exhausted means you do not have enough memory on your device.
[32,512,3072] indicates that your batch size is 32, which is the default. Are you sure that your flags are being passed to run_race.py correctly?
See run_race.py for definition of max_qa_length:
flags.DEFINE_integer(
    "max_qa_length", 128,
    "The maximum total input sequence length after WordPiece tokenization. "
    "Sequences longer than this will be truncated, and sequences shorter "
    "than this will be padded.")

very thank you for your reply. i have checked the flags,but finding nothing wrong as i see .
i try to clear the output_dir and try to run run_race.py again. it turn out to a new error as following:
`Traceback (most recent call last):
File "/home/dy/Project/ALBERT/run_race.py", line 457, in
tf.app.run()
File "/home/dy/anaconda3/envs/albert/lib/python3.6/site-packages/tensorflow_core/python/platform/app.py", line 40, in run
_run(main=main, argv=argv, flags_parser=_parse_flags_tolerate_undef)
File "/home/dy/anaconda3/envs/albert/lib/python3.6/site-packages/absl/app.py", line 299, in run
_run_main(main, args)
File "/home/dy/anaconda3/envs/albert/lib/python3.6/site-packages/absl/app.py", line 250, in _run_main
sys.exit(main(argv))
File "/home/dy/Project/ALBERT/run_race.py", line 260, in main
FLAGS.train_file, FLAGS.max_qa_length)
File "/home/dy/Project/ALBERT/race_utils.py", line 263, in file_based_convert_examples_to_features
max_seq_length, tokenizer, max_qa_length)
File "/home/dy/Project/ALBERT/race_utils.py", line 233, in convert_single_example
tf.logging.info("tokens: {}".format(" ".join(tokens)))
TypeError: sequence item 373: expected str instance, bytes found
Process finished with exit code 1
`
before fix this error, i want to assure  what is the all.txt file in RACE dataset exactly is?
i can't find it in RACE dataset .i download the RACE dataset at race
here is the all.txt how it be used in race_utils.py:
def read_examples(self, data_dir):
"""Read examples from RACE json files."""
examples = []
for level in ["middle", "high"]:
if level == "middle" and self.high_only: continue
if level == "high" and self.middle_only: continue
cur_dir = os.path.join(data_dir, level)
  cur_path = os.path.join(cur_dir, "all.txt")
  with tf.gfile.Open(cur_path) as f:
    for line in f:
      cur_data = json.loads(line.strip())

      answers = cur_data["answers"]
      options = cur_data["options"]
      questions = cur_data["questions"]
      context = self.process_text(cur_data["article"])

      for i in range(len(answers)):
        label = ord(answers[i]) - ord("A")
        qa_list = []

        question = self.process_text(questions[i])
        for j in range(4):
          option = self.process_text(options[i][j])

          if "_" in question:
            qa_cat = question.replace("_", option)
          else:
            qa_cat = " ".join([question, option])

          qa_list.append(qa_cat)

        examples.append(
            InputExample(
                example_id=cur_data["id"],
                context_sentence=context,
                start_ending=None,
                endings=[qa_list[0], qa_list[1], qa_list[2], qa_list[3]],
                label=label
            )
        )

return examples


nfs-utils, rpcbind: Update packages to fix nfs3 test

Unbreaks the NFSv3 test, which has started to fail since the staging merge due to rpc.mountd segfaulting: http://hydra.nixos.org/build/23867058/nixlog/1/raw. I don't know particularly why it was broken there, but updating the packages seems to make it work.

Actually only updating nfs-utils is enough. I don't know if the rpcbind update from 0.x to 1.x is smart, and their webpage is down due to sourceforge being down.

Tested, it resolves my issues. Thanks!

I can't find any reference to 1.0.7 version outside of our pull requests, and there's no 1.0.7 version on SourceForge; http://downloads.sourceforge.net/project/rpcbind/rpcbind/1.0.7/rpcbind-1.0.7.tar.bz2 gives me 404.

cc @matthiasbeyer ; where have you found it?

@abbradar I found the package update on monitor.nixos.org.

I have a feeling that it's actually 0.1.7 and upstream maintainer made a mistype at some point, as evidenced by last entries in ChangeLog for 0.2.3 and 0.1.7.

0.2.3

2008-11-19 Steve Dickson<EMAIL_ADDRESS>   * Version 0.1.7 released.

0.1.7

2008-11-19 Steve Dickson<EMAIL_ADDRESS>   * Version 1.0.7 released.

Yeah looks like it. I wonder how the monitor discovered that url...

OK, it indeed looks so, and 0.2.3 was released in 2015.05 so it should be newer than 2008.11 anyway ^_^. it's interesting how monitor.nixos.org found this version, since upstream maintainer have removed it from SourceForge (though it remains on mirrors). Reverted an update.


Ansible build fails to generate webpack resources

The Ansible tasks at the end of the Arches deployment role starts the Arches server and then tries to run the webpack build_development. The webpack command appears to crash the Arches server. However if the server is restarted manually and then the webpack command rerun manually it works as expected.

Updated the fossils Auth Required middleware to bypass the check/redirect if it comes from the localhost and is a node fetch.

Fixed issue by:

correcting the formatting of the ALLOWED_HOSTS value
adding the IP address to the exception list for the Fossils required auth middleware
sleeping after starting the arches server to allow the process to start before the session ends


removed The Vim Blog

What does this PR do?
Remove resource(s)
For resources
The Vim Blog
Description
Linked podcast is a politics podcast
Why is this valuable (or not)?
Not related to free programming books
How do we know it's really free?
For book lists, is it a book? For course lists, is it a course? etc.
Checklist:

[ ] Read our contributing guidelines
[ ] Search for duplicates.
[ ] Include author(s) and platform where appropriate.
[ ] Put lists in alphabetical order, correct spacing.
[ ] Add needed indications (PDF, access notes, under construction)

Follow-up

Check the status of GitHub Actions and resolve any reported warnings!

Remember to tick the checklist next time

Tracking Info
Podcast was added at #4458 and url fixed previously by #6152 after


Add helper from_package to load package datasets

Can we add a helper (e.g. from_package()) that would essentially load data in this regard:
data(dataset, package = "package_name")

I know the pipable way to do this (e.g. inside tbl_store()) would be package_name::dataset, but if we wanted to do this for github packages to get the most updated data that should be an option too. The function could wrap from_github() perhaps if we requested the get the remote version instead of local version of the package.

This is a great idea! Will look into getting this implemented.


Typescript

This is a work-in-progress just for exploratory purposes. Not sure if TS is the way forward for us but I thought that this would be a worth-while exercise.
The html option in grunt-ts (the plugin that Dojo uses) looks like it might be a work around for the dojo/text! AMD plugin.

Yay. Fun.

For another day...


Remove ascii tea

Let's say goodbye to ASCII tea. Thank you for your service!
                (  )   (   )  )
                 ) (   )  (  (
                 ( )  (    ) )
                 _____________
                <_____________> ___
                |             |/ _ \
                |               | | |
                |               |_| |
             ___|             |\___/
            /    \___________/    \
            \_____________________/

It's like tearing my heart out, man :sob: :broken_heart:


Ammonite fails to recognize lazy concatenation operator for Streams

I am using Ammonite REPL version 0.8.0.
I pasted the following code in Ammonite shell:
val fact:Stream[BigInt] =
   1 #::
   fact.zip(
        Stream.from(2))
   .map(x => x._1 * x._2)

Ammonite gives error on the second line (specifically the concatenation operator):
cmd0.sc:2: value #:: is not a member of Int
I started the Scala REPL and pasted the same code. It works fine. The Scala REPL is using Scala version 2.11.8.

You need to wrap it in parens otherwise statement-inference does the wrong thing
val fact:Stream[BigInt] = {
   1 #::
   fact.zip(
        Stream.from(2))
   .map(x => x._1 * x._2)
}

Unfortunate but unlikely to ever get fixed


Fix Bugs found with TPCC

This PR fixes these bugs:

Cast expressions in updates (Reviewer: @lmwnshn)
Offsets in Limit and OrderBy plan nodes (Reviewer: @17zhangw )
Distinct and Static Aggregates (Reviewer: @pmenon).

For TPCC, I think the only bug left is the insert order one. This PR can run all queries except for New Order (it has out of order inserts).

Adding myself as reviewer just so I can push the merge conflict fix.

I fixed the merge conflict, but when running check-tpl locally I'm seeing static-agg.tpl seemingly run forever.

Scratch that, static-agg.tpl took forever but it finished.

It looks like this PR was always failing on SelectTest::testSelectAlias in our junit test, which seems to be a true positive? I don't see this failure showing up in other PRs, and the error still exists after merged into master. @amlatyrngom @mbutrovich


Unnecessary Rebuilds

I just added to  debugPrint('${widget.message.id} rebuilt'); to MessageView  build method .
The logs i obtained then.
https://user-images.githubusercontent.com/88256165/228053504-507ae548-96e4-4fd1-bcb6-7bc4664ddf44.mp4
Each message even which are outside the viewPort are getting rebuilt, that causes huge memory consumption.

I figured out the problem, SingleChildScrollView is the responsible widget.
https://github.com/SimformSolutionsPvtLtd/flutter_chatview/blob/dc4a2f032f79ddc1b0b5c9b4bb9f6375f7f687bc/lib/src/widgets/chat_groupedlist_widget.dart#L161
Since the _chatStreamBuilder method is embedded inside SingleChildScrollView so it builds each items at once, which in context with performance is not so good solution.
I tried removing SingleChildScrollView like this.
GestureDetector(
      onHorizontalDragUpdate: (details) => isEnableSwipeToSeeTime
          ? showPopUp
              ? null
              : _onHorizontalDrag(details)
          : null,
      onHorizontalDragEnd: (details) => isEnableSwipeToSeeTime
          ? showPopUp
              ? null
              : _animationController?.reverse()
          : null,
      onTap: widget.onChatListTap,
      child: Column(
        children: [
          Flexible(
            child: _animationController != null
                ? AnimatedBuilder(
                    animation: _animationController!,
                    builder: (context, child) {
                      return _chatStreamBuilder;
                    },
                  )
                : _chatStreamBuilder,
          ),
          TypingIndicator(
            typeIndicatorConfig: widget.typeIndicatorConfig,
            chatBubbleConfig: chatBubbleConfig?.inComingChatBubbleConfig,
            showIndicator: showTypingIndicator,
            profilePic: profileCircleConfig?.profileImageUrl,
          ),
          SizedBox(
            height: MediaQuery.of(context).size.width *
                (widget.replyMessage.message.isNotEmpty ? 0.3 : 0.14),
          ),
        ],
      ),
    );

https://github.com/SimformSolutionsPvtLtd/flutter_chatview/blob/dc4a2f032f79ddc1b0b5c9b4bb9f6375f7f687bc/lib/src/widgets/chat_groupedlist_widget.dart#L274
- physics: const NeverScrollableScrollPhysics(),
+ controller: widget.scrollController,

After making these changes guess what, it worked nicely.
Note
Using this method performance can be improved until an extent but, scrollingToReplyMessages will take a lot of time because GroupedListView is built on top of ListView.builders. I suggest using   scrollable_positioned_list or scrollable_positioned_list_extended(with helper methods like scrollToMax extent and notification listeners)  inside custom fork of GroupedList we  can reach to threaded messages instantly.

@Yogesh-Dubey-Ayesavi  Thanks for pointing out these issues. We had planned for this performance improvement, but you suggested some changes, I will try those and give feedback on this


Where is the .clang-format for this repository?

Hi. I have used a bit of code here and would like to contribute back (a little bit of refactoring for the shape fitter if the repository owner does not mind). Then, I notice I can not find an open clang-formatter anywhere though the log said clang-formatter has been applied.
https://github.com/Autoware-AI/core_perception/blob/f14a0ca32d57ab87477cd5fb3e96656320bc497e/lidar_fake_perception/CHANGELOG.rst#180-2018-08-31
If able, can you add an open format for clang-formatter, which makes it easier for contributors?
Sorry if it is wrong to label this issue as "bug" :)

Closed by #9.


Fix _RegexParser build when using 5.6 host tools

Add a type annotation to allow a --bootstrap=hosttools compiler build to work with a Swift 5.6 compiler.
Resolves #451

@swift-ci please test


event.detail is incorrect and inconsistent between dart2js and dartium

If the event contains a JSON object containing a proxy to a Dart object, the result:
 - is null in dartium, but not null in JS.
 - in JS it returns an map containing the JsObject for the proxy, rather than the unwrapped object.
Here is a simple example that can repro this problem:
<body>
  <script>
  function fire(item)  {
    var event = new CustomEvent('my-event', {detail: {item: item}});
    document.body.dispatchEvent(event);
  }
  </script>
  <script type="application/dart" src="index.dart"></script>
  <script src="packages/browser/dart.js"></script>
index.dart:
  import 'dart:html';
  import 'dart:js';
  main() {
    document.body.on['my-event'].listen((e) {
      if (e.detail != null) {
        var d = e.detail["item"];
        print('0: ${d}, type: ${d.runtimeType}');
      } else {
        print('0: null');
      }
      var d = new JsObject.fromBrowserObject(e)['detail']['item'];
      print('1: $d, type: ${d.runtimeType}');
    });
    context['fire'].apply([new _Foo()]);
  }
  class _Foo { int id = 3; }
In dartium, this prints '0: null', in dart2js it prints '0: [object Object], type: JSObject ', where the object happens to be the JsObject proxy for _Foo
The second line prints the same result in both: 1: Instance of '_Foo', type: \_Foo. I expect there result to always be like this line.
This is related to bug 19315, but I'd like to make sure we track separately the inconsistency between the two implementations today.

Dartium is no longer supported.


Add support for uploading local application dependencies to HDFS

Now we could upload local application dependencies to stage server. However stage server might be a single point of failure or have performance issue. We plan to deploy Kubernetes and HDFS together, and it will be better to add support for uploading application dependencies to HDFS.

SubmittedDependencyUploader and KubernetesSparkDependencyDownloadInitContainer are tightly coupled with stage server. It is not easy to add other uploader(e.g. HDFS). I propose to refactor them in this way:

Add function configureContainers in SubmittedDependencyUploader. Then all uploader related things are done in configureContainers.
Deal with different download servers(e.g. stage server/HDFS/...) in KubernetesSparkDependencyDownloadInitContainer instead of stage server only.

cc @mccheah @liyinan926 @foxish @ash211


remove without_storage_info from pallet-collective

Closes #14323
Changelog:

[x] migration to storage v5 and test
[x] bounded the Voting StorageMap by putting BoundedVec for ayes and nays in the Vote struct
[x] bounded the Members storage by putting BoundedVec
[x] use Bounded<Call> instead of Hash to represent calls
[x] removed the Proposal and ProposalOf storages, everything relies now on the Vote map + preimage to store long calls
[x] Voting is now a CountedStorageMap, to handle the MaxProposals bound
[x] update mock & test for pallet collective
[x] update mock & test for pallet utility
[x] update trait ProposalProvider to use Bounded<Call> instead of Hash
[x] update mock & test for pallet alliance
[x] update kitchensink runtime
[x] fix weights & re-run benchmarks(?)

Cumulus companion: cumulus#2761 here
Polkadot companion: polkadot#7400 here

The CI pipeline was cancelled due to failure one of the required jobs.
Job name: cargo-check-each-crate
Logs: https://gitlab.parity.io/parity/mirrors/substrate/-/jobs/2972871

The CI pipeline was cancelled due to failure one of the required jobs.
Job name: cargo-check-benches
Logs: https://gitlab.parity.io/parity/mirrors/substrate/-/jobs/2972857

The CI pipeline was cancelled due to failure one of the required jobs.
Job name: cargo-check-each-crate-macos
Logs: https://gitlab.parity.io/parity/mirrors/substrate/-/jobs/2985023

The CI pipeline was cancelled due to failure one of the required jobs.
Job name: cargo-check-each-crate-macos
Logs: https://gitlab.parity.io/parity/mirrors/substrate/-/jobs/2992861

The CI pipeline was cancelled due to failure one of the required jobs.
Job name: cargo-check-each-crate-macos
Logs: https://gitlab.parity.io/parity/mirrors/substrate/-/jobs/3001349

@ggwpez benchmarks must be re-ran, but I'm not sure about how the bot works and if I'm allowed to call it.

bot bench $ pallet dev pallet-collective

Sorry I am quite busy rn, will try to take a look tomorrow.

The CI pipeline was cancelled due to failure one of the required jobs.
Job name: test-linux-stable
Logs: https://gitlab.parity.io/parity/mirrors/substrate/-/jobs/3176625

The CI pipeline was cancelled due to failure one of the required jobs.
Job name: test-linux-stable
Logs: https://gitlab.parity.io/parity/mirrors/substrate/-/jobs/3176623

The CI pipeline was cancelled due to failure one of the required jobs.
Job name: test-linux-stable
Logs: https://gitlab.parity.io/parity/mirrors/substrate/-/jobs/3176624

The CI pipeline was cancelled due to failure one of the required jobs.
Job name: cargo-check-each-crate
Logs: https://gitlab.parity.io/parity/mirrors/substrate/-/jobs/3193121

The CI pipeline was cancelled due to failure one of the required jobs.
Job name: cargo-check-benches
Logs: https://gitlab.parity.io/parity/mirrors/substrate/-/jobs/3193107

The CI pipeline was cancelled due to failure one of the required jobs.
Job name: test-linux-stable
Logs: https://gitlab.parity.io/parity/mirrors/substrate/-/jobs/3196295

Addressed in #14585


Update rest-client

Merge of reauth token in UserSessionInfoProvider so reauth isn't lost
Reset of retry count so retries aren't missed
Update to how ClientInfo strings are generated

I can't see what the code is for UserSessionInfoProvider.mergeReauthToken so I can't really review.  Is there someone better that could?

Yea, that was code reviewed. This was refactor moving the code to mergeReauthToken to be reused in BridgeJavaSDK. I left the unit tests covering this in AccountDAO so we're good


[CRASH] Wen pasting a koravex setup with cut tool

Error running event cut-and-paste::on_put_item (ID 9)

LuaEntry API call when LuaEntry was invalid

stack traceback:
__cut-and-paste__/control.lua:308: in function <__cut-and-paste__/control.lua:268>

Thanks for addressing this


Incorrect highlighting using enum values as class member names

Using the following source (valid in at least TypeScript 1.6):
enum Hello {
	A,
	B
}

class World {
	normal() {
		let x = 5;
		console.log("hello");
	}

	[Hello.A]() {
		let x = 5;
		console.log("hello");
	}
}

This causes very strange highlighting in the body of the method declaration:

Closing as tmLanguage issues are now tracked at https://github.com/Microsoft/TypeScript-TmLanguage


Add devcontainer support

Enables one-click launching of devcontainers (e.g. with GitHub Codespaces or VSCode remote containers), with all dependencies automatically installed.
I'm currently using this personally to speed up working with meltingpot, but figured others may find it helpful given how popular devcontainers are becoming (especially Codespaces)?
It should also help reduce support requests, for setup related issues.

Thanks for the review @jagapiou !


Stern not displaying logs as expected

What happened:
When I use stern -n istio-operator . I expect to see all logs in the istio-operator namespace. Unfortunately it doesn't seem to want to do that and only outputs the container creation log message.
What you expected to happen:
All logs would be in the output.
How to reproduce it (as minimally and precisely as possible):

Deploy istio-operator to a kubernetes cluster
Use stern -n istio-operator .

Anything else we need to know?:
Output from stern:
jdfalk@ws1 ➜  ~ () stern -A istio-operator
+ istio-operator istio-operator-58795db644-db9tx › istio-operator
^C

Output from kubectl log -n istio-system deployment/istio-operator -f:
jdfalk@cube-1763 ➜  ~ () kl -n istio-operator deployment/istio-operator -f
2021-08-03T18:43:14.945273Z	info	leader election cm: istio-operator-lock
2021-08-03T18:43:14.945545Z	info	ControlZ available at <IP_ADDRESS>:9876
2021-08-03T18:43:15.995931Z	info	klog	Throttling request took 1.041510984s, request: GET:https://redacted:443/apis/scheduling.k8s.io/v1?timeout=32s
2021-08-03T18:43:18.701882Z	info	Creating operator metrics exporter
2021-08-03T18:43:18.702030Z	info	Registering Components.
2021-08-03T18:43:18.702133Z	info	installer	Adding controller for IstioOperator.
2021-08-03T18:43:18.702230Z	info	installer	Controller added
2021-08-03T18:43:18.702257Z	info	Starting the Cmd.
2021-08-03T18:43:18.702460Z	info	klog	attempting to acquire leader lease istio-operator/istio-operator-lock...
2021-08-03T18:43:40.715124Z	info	klog	successfully acquired lease istio-operator/istio-operator-lock
2021-08-03T18:43:40.718690Z	info	proto: tag has too few fields: "-"
2021-08-03T18:43:45.032501Z	info	installer	Reconciling IstioOperator
2021-08-03T18:43:45.034028Z	info	installer	Updating IstioOperator
2021-08-03T18:43:45.146172Z	info	installer	Detecting third-party JWT support

Environment:

stern version (use stern --version): version: 1.20.0
OS (e.g: cat /etc/os-release): Mac OS 11.5.2
Install tools (e.g: Homebrew): Homebrew
Others:

I tried to reproduce the problem by following the steps below, but was unable to do so.
$ stern --version
version: 1.20.0
commit: 0f9402d4c7c11f343dab140e7461817e21f3a9e8
built at: 2021-08-13T01:32:22Z

$ kind version
kind v0.11.1 go1.16.4 linux/amd64

$ kind create cluster --image=kindest/node:v1.22.1

$ kubectl version
Client Version: version.Info{Major:"1", Minor:"22", GitVersion:"v1.22.0", GitCommit:"c2b5237ccd9c0f1d600d3072634ca66cefdf272f", GitTreeState:"clean", BuildDate:"2021-08-04T18:03:20Z", GoVersion:"go1.16.6", Compiler:"gc", Platform:"linux/amd64"}
Server Version: version.Info{Major:"1", Minor:"22", GitVersion:"v1.22.1", GitCommit:"632ed300f2c34f6d6d15ca4cef3d3c7073412212", GitTreeState:"clean", BuildDate:"2021-08-25T19:54:13Z", GoVersion:"go1.16.7", Compiler:"gc", Platform:"linux/amd64"}

$ wget https://github.com/istio/istio/releases/download/1.11.2/istioctl-1.11.2-linux-amd64.tar.gz
$ tar xvzf ./istioctl-1.11.2-linux-amd64.tar.gz
$ ./istioctl version
no running Istio pods in "istio-system"
1.11.2

$ ./istioctl operator init
Installing operator controller in namespace: istio-operator using image: docker.io/istio/operator:1.11.2
Operator controller will watch namespaces: istio-system
✔ Istio operator installed
✔ Installation complete

$ stern -n istio-operator .
+ istio-operator-6547bf56c-nl4gs › istio-operator
istio-operator-6547bf56c-nl4gs istio-operator 2021-09-07T12:57:38.585565Z       info    ControlZ available at <IP_ADDRESS>:9876
istio-operator-6547bf56c-nl4gs istio-operator 2021-09-07T12:57:38.585976Z       info    leader election cm: istio-operator-lock
istio-operator-6547bf56c-nl4gs istio-operator 2021-09-07T12:57:38.887945Z       info    Creating operator metrics exporter
istio-operator-6547bf56c-nl4gs istio-operator 2021-09-07T12:57:38.888276Z       info    Registering Components.
istio-operator-6547bf56c-nl4gs istio-operator 2021-09-07T12:57:38.888524Z       info    installer       Adding controller for IstioOperator.
istio-operator-6547bf56c-nl4gs istio-operator 2021-09-07T12:57:38.888781Z       info    installer       Controller added
istio-operator-6547bf56c-nl4gs istio-operator 2021-09-07T12:57:38.888838Z       info    Starting the Cmd.
istio-operator-6547bf56c-nl4gs istio-operator 2021-09-07T12:57:38.889299Z       info    klog    attempting to acquire leader lease istio-operator/istio-operator-lock...
istio-operator-6547bf56c-nl4gs istio-operator 2021-09-07T12:57:38.898265Z       info    klog    successfully acquired lease istio-operator/istio-operator-lock

By default, stern only outputs logs from 48h ago. Is it possible that there were no logs output newer than that?
$ stern -h | grep -- --since
  -s, --since duration             Return logs newer than a relative duration like 5s, 2m, or 3h. (default 48h0m0s)

You might be right about the time. I'll try it the next time I am seeing weird results like that.


Possible removal of RabbitMQ resources

Rabbit Hole is a complete Go library for managing RabbitMQ resources. I'm going to look into making them Terraform resources and then possibly remove the existing RabbitMQ Waffles resources.

Again why? It seems to me that having extra resources is a good thing.

Everything in #177 is applicable here, too. One extra thing specific to RabbitMQ is that a previous version of Waffles had more RabbitMQ resources than there are now. The caveat was that they required Augeas.
A few weeks ago I stripped down Waffles and Augeas was one of the things that got cut. I haven't found a good reason to bring it back yet.
If more RabbitMQ resources would be added to Waffles, I'd be more inclined to use the RabbitMQ management API rather than interacting with RabbitMQ's wacky config file syntax.

These are going to stay, too, though I might try to alter them a bit to use the Management REST API. I've just finished a bunch of work with Terraform and RabbitHole and it was a breeze to use.


AdminBro Custom Component fails when deployed

Describe the bug
Transpiled AdminBro custom components break in production. While I'm not entirely sure why this occurs, my project runs as expected post-transpilation locally, but the component does not render when deployed to the Google App Engine.
Installed libraries and their versions
"@admin-bro/design-system": "^1.7.0",
"@admin-bro/express": "^3.0.1",
"@admin-bro/mongoose": "^1.1.0",
"@babel/cli": "^7.10.5",
"@babel/core": "^7.10.5",
"@babel/node": "^7.10.5",
"@babel/plugin-proposal-export-default-from": "^7.10.4",
"@babel/plugin-transform-runtime": "^7.10.5",
"@babel/preset-env": "^7.10.4",
"@babel/register": "^7.10.5",
"@babel/runtime": "^7.10.5",
"admin-bro": "^3.3.1",

To Reproduce
Our project structure is as follows, and the AdminBro call may be found in server/routes/admin.js:
.babelrc
server/
server/admin/dashboard.jsx
server/routes/admin.js
package.json
package-lock.json

server/routes/admin.js:
export const adminPortal = (app) => {
  AdminBro.registerAdapter(AdminBroMongoose);
  const adminBro = new AdminBro({
    resources: [
      Resource1,
      Resource2
    ],
    rootPath: "/admin",
    branding: {
      companyName: "Name",
      logo: "image.jpg",
    },
    dashboard: {
      component: AdminBro.bundle("../admin/dashboard"),
    },
  });
  const router = AdminBroExpress.buildRouter(adminBro);
  app.use(adminBro.options.rootPath, VerifyRedirectToken, router);
  logger.info({
    message: `Admin router configured!`,
  });
};

The contents of the .babelrc are as follows, and the transpile command is be invoked as throughbabel -d ./build ./server -s:
{
    "presets": [
      "@babel/preset-env",
      "@babel/preset-react"
    ],
    "plugins": [
      "@babel/plugin-proposal-class-properties",
      "@babel/plugin-proposal-export-default-from",
      "@babel/plugin-transform-runtime"
    ]
}

The error encountered may be found below:
[Error] Failed to load resource: the server responded with a status of 500 () (components.bundle.js, line 0)
[Error] Refused to execute https://[DOMAIN]/admin/frontend/assets/components.bundle.js as script because "X-Content-Type-Options: nosniff" was given and its Content-Type is not a script MIME type.
[Error] Failed to load resource: The file “purify.js.map” couldn’t be opened because there is no such file. (purify.js.map, line 0)

Expected behavior
When the transpile command is run locally, the dashboard component renders. However, the same fails on the App Engine. The .entry.js file is as follows and it is the same file both locally, and on the remote deployment:
AdminBro.UserComponents = {}
import Component1 from '../build/admin/dashboard'
AdminBro.UserComponents.Component1 = Component1

Additional context
This was not a problem earlier when our project had a bundle.js file within the .adminbro/ directory. However, we deleted that file since it seemed to be caching the versions of the .jsx files and were hindering development.

could be related https://github.com/SoftwareBrothers/admin-bro/issues/751?

Closing this issue as it was related to running a snippet similar to the one below:
if (process.env.ENV !== "test") {
    if (process.env.NODE_ENV === "production") {
      adminBro.initialize();
    } else {
      adminBro.watch();
    }
  }


Issue-Release 0.7.0.

Automated Review Comments
Issues in package-lock.json:

(4, 'Hardcoded string found')
(8, 'Hardcoded string found')
(9, 'Hardcoded string found')
(14, 'Hardcoded string found')
(15, 'Line exceeds 80 characters')
(15, 'Hardcoded string found')
(16, 'Line exceeds 80 characters')
(16, 'Hardcoded string found')
(17, 'Hardcoded string found')
(18, 'Line exceeds 80 characters')
(18, 'Hardcoded string found')
(19, 'Line exceeds 80 characters')
(19, 'Hardcoded string found')
(20, 'Hardcoded string found')
(24, 'Line exceeds 80 characters')
(24, 'Hardcoded string found')
(27, 'Hardcoded string found')
(28, 'Line exceeds 80 characters')
(28, 'Hardcoded string found')
(29, 'Line exceeds 80 characters')
(29, 'Hardcoded string found')
(30, 'Hardcoded string found')
(31, 'Line exceeds 80 characters')
(31, 'Hardcoded string found')
(32, 'Line exceeds 80 characters')
(32, 'Hardcoded string found')
(33, 'Hardcoded string found')
Issues in package.json:
(3, 'Hardcoded string found')
(4, 'Hardcoded string found')
(5, 'Hardcoded string found')
(6, 'Line exceeds 80 characters')
(6, 'Hardcoded string found')
(7, 'Hardcoded string found')
(8, 'Hardcoded string found')
(12, 'Hardcoded string found')
(16, 'Hardcoded string found')
(17, 'Hardcoded string found')

I got it.


Cleanup the amount of strategies?

The current amount of strategies may be a bit overkill. A lot of these were added simply to see how they'd perform but never cleaned up. Perhaps it would be a good thing to go for quality instead of quantity. The backtester could be a good tool to help refine some of the better performing ones.

The amount of strategies was cleaned up in develop. A lot of these strategies were only present because I found them online somewhere. Backtesting never really gave a decent result for a lot of them. Therefore they have been removed for now. If someone has a strategy that can provide decent consistent results feel free to PR it in.


Use the vulnerabity in-toto predicate for vulnerability  attestations instead of the one in cosign

Description

We added a new predicate type in in-toto for vulnerability attestations inspired on the initial predicate type defined in cosign for vulnerabilities.

yes, I'll work on this shortly.


Decimal DIV changes

This PR deals with the changes to the Decimal DIV in cudf.
There is a bug in rapidsai/cudf#7435 where it's returning a Decimal col when a BOOL8 col is expected. I have commented on the PR https://github.com/rapidsai/cudf/pull/7435#issuecomment-792217382
Signed-off-by: Raza Jafri<EMAIL_ADDRESS>

@gerashegalov have I addressed all your concerns? PTAL

@revans2 can you take a look at this PR.

@revans2 I have addressed your concerns. Knowing what I know now, the math is pretty much just adding the r.scale to the outputType.scale so after div is called we end up with outputType.scale.

@revans2 can you check my math on the tagExprForGpu method?

FYI the new cudf has just been built and deployed to snapshot

build

build