enabling ignore tests

Closes #1830 .
Changes
(Please provide a brief description of the changes here.)
Checklist

[ ] I ran Unit Tests locally.
[ ] CHANGELOG.md updated with one line description of the fix, and a link to the original issue if available.

For significant contributions please make sure you have completed the following items:

[ ] Design discussion issue #
[ ] Changes in public surface reviewed

The PR will trigger build, unit tests, and functional tests automatically. Please follow these instructions to build and test locally.
Notes for authors:

FxCop and other analyzers will fail the build. To see these errors yourself, compile localy using the Release configuration.

Notes for reviewers:

We support comment build triggers

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For reference, some of these classes weren't compiling which is why we marked them "out of date".
Here is the former PR: #1827

@eddynaka I see that only 6 tests are failing out of the dozen or so that were in those classes.
I propose we split this into two parts;

First,
If you can mark these tests to be conditionally ignored in NET45 only.
That will let us immediately enable all the others which improves our overall test coverage!

Second,
Create a PR to investigate just these 6 tests.

@eddynaka I see that only 6 tests are failing out of the dozen or so that were in those classes.
I propose we split this into two parts;

First,
If you can mark these tests to be conditionally ignored in NET45 only.
That will let us immediately enable all the others which improves our overall test coverage!
Second,
Create a PR to investigate just these 6 tests.

OK! will do that!


Relationships edit page incorrectly states source/destination filters are Queryset filters instead of Filterset filters

Environment

Python version: n/a
Nautobot version: 1.3.3

Steps to Reproduce

Browse to https://nautobot/extras/relationships/add/
Create a new relationship with a source type "dcim | interface"
Enter a source filter with related objects filters such as  {"device__site__name__in": ["HQ"]} )
Click create

Expected Behavior
Since information text below "Source filter" and "Destination filter" textboxes state "Queryset filter matching the applicable source objects of the selected type. Enter in JSON format.", expected Queryset filter to be accepted

Observed Behavior
Results in an error
'device__site__name__in' is not a valid filter parameter for dcim.Interface object
Per @glennmatthews, relationships source/destination filters are actually Filterset filters rather than Queryset filters.
Info text should be modified to reflect that.

Would be good to make this explicit in the documentation as well.


Use node-pre-gyp to distribute pre-built binaries

On a test machine, brings the installation time down from ~63s to ~11s

@darora this is awesome. @pyramation I see you've merged it, do you plan on doing a release? We'd love to test this out in our CI to reduce compilation times in our pnpm install

please try and test it! @darora and I have released a new version 13.2.4
https://github.com/pyramation/libpg-query-node/commit/23526c7db6f20885bf8a5bfb1c306a098bc1f313

@pyramation any way I can help the release on pgsql-parser to use this new version? It's quite difficult for me to override at a 3 level depth.

@pyramation I was able to force it, but still got
.../node_modules/libpg-query install: node-pre-gyp WARN Pre-built binaries not installable for<EMAIL_ADDRESS>and<EMAIL_ADDRESS>(node-v83 ABI, glibc) (falling back to source compile with node-gyp)

@maschwenk try now?
We'll be making a new release for pgsql-parser this week to pick this up

@maschwenk @darora I just published the other module just in case
<EMAIL_ADDRESS>


Broken app label: 8x8

What's wrong with the app label?
Currently getting a "need to provide 'downloadURL'" error. Have looked at the URL and can see it just goes to a support page. Have found that this is the download page with the download link located there (https://support-portal.8x8.com/helpcenter/viewArticle.html?d=8bff4970-6fbf-4daf-842d-8ae9b533153d)
Installomator version
Installomator v. 10.7beta, date 2024-11-21
Installomator log
2024-11-29 16:59:56 : REQ   : 8x8 : ################## Start Installomator v. 10.7beta, date 2024-11-21
2024-11-29 16:59:56 : INFO  : 8x8 : ################## Version: 10.7beta
2024-11-29 16:59:56 : INFO  : 8x8 : ################## Date: 2024-11-21
2024-11-29 16:59:56 : INFO  : 8x8 : ################## 8x8
2024-11-29 16:59:59 : ERROR : 8x8 : need to provide 'downloadURL'

After looking through the Issues. There is a fix under this issue that has resolved it for me: #1684.


Add "Displayed Status" column to report status table on About page

Should just display the "Status" we link to on the search page.

@hancush Or is this what we mean?

@antidipyramid Yes, your interpretation in your screenshot is correct!

@shrayshray Deployed to the live site


Fix assert_equal arguments order in README

Fixed order of the arguments of assert_equal that was supposed to reverse.

Makes sense.


Removed keyword arguments from calls into enclave

Signed-off-by: Jamie Jason<EMAIL_ADDRESS>

What is the motivation for moving to positional arguments?

Swig seems to be puking on it.

Want to get a fix in so @aludvik can proceed.  I personally like keyword arguments so will revisit to see if there is a better fix than simply going to positional arguments.

@aludvik Was having problem with pickle and enclave wait certificate object.  Backed out a change that affected that.
If this works, will migrate any necessary changes to master.


--kerberos5i-rw and others missing option

--kerberos5i-rw
--kerberos5i-r
and all the other kerberos options look like they need a false | true set for them and the docs don't indicate that. If you don't indicate true | false you get error: "argument --kerberos5i-rw: expected one argument"
Would be nice to have an example of how to configure a krb encrypted volume from the CLI. There are a lot of dependencies for the commands that aren't noted.
"Parameter allowed-clients needs to be set when protocol-type is NFSv4.1"
So I set the allowed-clients to <IP_ADDRESS>/0
Parameter rule-index needs to be set when protocol-type is NFSv4.1
So i set the --rule-index to 1
(BadRequest) Mismatch between KerberosEnabled flag value and ExportPolicyRule's access type parameter values.
I'm stuck here. I don't know wht "ExportPolicyRule" is. I guessed and set "--policy-enforced true" but that didn't work.
As it stands now the command I am issuing is: az netappfiles volume create -g $rg --account-name $account --pool-name $pool --name $volname --location $region --usage-threshold 100 --file-path $volname --vnet $vnet --subnet $subnet --protocol-types NFSv4.1 --allowed-clients 0.0.00/0 --rule-index 1 --kerberos-enabled true --kerberos5i-rw true --policy-enforced true
...but it's failing and I am stuck with whatever this ExportPolicyRule setting is. Nothing in the docs indicating what that is.

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

ID: 298ada99-369a-1c65-50ca-617931d26b7a
Version Independent ID: 5fbd1cdf-e27f-8ffe-1c72-14f5d9e186f1
Content: az netappfiles volume
Content Source: latest/docs-ref-autogen/netappfiles/volume.yml
GitHub Login: @rloutlaw
Microsoft Alias: routlaw

route to service team


Nonblock<TcpListener> is not properly closed when going out of scope

Starting from this code, running on Linux-3.18.9:
extern crate mio;

fn main() {
    let listener = ::mio::tcp::listen(&"<IP_ADDRESS>:8000".parse().unwrap()).unwrap();

    loop {
        match listener.accept() {
            Ok(Some(_)) => break,
            Ok(None) => continue,
            Err(e) => panic!("{:?}", e)
        }
    }
}

At first execution, once a client is connected, the program quits. The client properly sees the connection being closed.
However, if you try to re-run the program right after, you get this error:
thread '<main>' panicked at
    'called `Result::unwrap()` on an `Err` value: Error { repr: Os(98) }'

And you have to wait for around 1 or 2 minutes before being able to run int again successfully.
On Linux error 98 is for Address already in use, so my guess is that for some reason the file descriptor is not properly closed.
Also, it seems to be properly closed if the program is killed with ^C before any client connects.
As neither TcpListener nor NonBlock<TcpListener> provides a close() method, I guess this is not expected behavior ?

Hi there.
This is normal behavior. What you probably want to do is set the reuse address socket option. More info about it here. I think the echo server tests show how to set it.
It may be worth setting it by default though.


[Feature]: Animate transition of resolving a three (revealed card moving into player hand)

Feature Summary
You cannot currently see which card an opponent selected when they pick a card from the scrap with a 3. We should use an animated transition to clarify this interaction
Detailed Description
Currently, when a player selects a card from the scrap with a 3 you can't see which card was selected, and the resolution looks similar to drawing a card:
https://github.com/cuttle-cards/cuttle/assets/6520704/edab2336-96ab-4f19-bc7a-4f6f88adf9e2
We should clarify this interaction by revealing the selected card on top of the scrap pile and transitioning it towards the hand of the player that played the three. To do this we should update the socket event sent via Game.publish() in api/controllers/game/resolve-three.js so that it includes the card being moved like
      Game.publish([fullGame.id], {
        change: 'resolveThree',
        game: fullGame,
        victory,
        chosenCardId: req.body.cardId
      });

That way the frontend can know which specific card to animate in the scrap. Then we should add data to the GameStore for cardSelectedFromScrap which we could use to render and animate the selected card. We should then define a new processResolveThree function in the gameStore.js store which behaves similarly to processScuttle by setting the new cardSelectedFromScrap value to the card that was just picked, then setting a timeout and after the delay, unsetting cardSelectedFromScrap and updating the rest of the game object so that card triggers its leave animation and disappears.
Then we should update the DOM in GameView.vue so that the Scrap area can temporarily display the cardSelectedFromScrap as a <GameCard>  and animate it up-and-right or down-and-right at a diagonal using new transition classes similar to the ones used on the hands, points etc. The card should have it's leave transition to be up-and-right if moving into the opponent hand and down-and-right if moving into the player hand.
This way we will have a much smoother, clearer interaction that makes it easy to tell which card was selected when your opponent plays a 3.

Got this


expose Writer via Output

Hi!
A small feature request:
Can the FlagSet's Writer be exposed via Output method, as it is done in original Go's flag package.
Example use case:
You have special usage function which is printing both 'defaults' (as returned via FlagUsages) and your custom message. You want to print custom message to the same writer as PrintDefaults does it, and you don't know which one is it.
Not artificial example - a popular practice is that the writer is either stderr when user typed wrong flags, or stdout for -h; but, the logic to decide it doesn't belong to the usage function where you'd want to use it, right

Related: #220 and #241

Yep, merging any of these would do it

Solved by #220, thx guys


Error connecting to Aurora DB using the "Amazon RDS" profile

Hi,
I'm trying to connect to an Aurora DB provisioned in the Asia Pacific (Sydney) region using SSL - using the "Amazon RDS" profile from a node application hosted on Tanzu platform (PCF). However, getting the following error:
"Error: unable to get local issuer certificate"
Here's my config:
       {
            host: process.env.DB_HOST_NAME,
            user: process.env.DB_USER,
            password: process.env.DB_PASSWORD,
            database: process.env.DB_NAME,
            multipleStatements: true,
            ssl: "Amazon RDS"
        }

When  I try to use the "rejectUnauthorized" to false, the connection succeeds. Also, Java applications are able to successfully connect and so does npm applications when trying to run db migrations using the db-migrate package (specifying ssl to true). Any idea what I could be doing wrong?

Hi, sorry you are having trouble. It looks like the cert is in the module, but they do change over time. What version of this module are you using? Recently the certs were updated.

Gotcha. I believe you need the updated certs in 2.18.0 for that region now as RDS continues to migrate to the new 2024 certs.

That works. Thanks @dougwilson


YouTube Premium has no ads

I can't tell if this issue is a joke or not :D

I have tries it for a month. It ended on the 14th.

Now the ff bookmarklet is back in action!


esp_hid_host's BT classic part does not work (IDFGH-11236)

Answers checklist.

[X] I have read the documentation ESP-IDF Programming Guide and the issue is not addressed there.
[X] I have updated my IDF branch (master or release) to the latest version and checked that the issue is present there.
[X] I have searched the issue tracker for a similar issue and not found a similar issue.

IDF version.
v5.0.4
Espressif SoC revision.
ESP32-S3 (revision v0.2)
Operating System used.
Linux
How did you build your project?
Command line with idf.py
If you are using Windows, please specify command line type.
None
Development Kit.
Third party custom board
Power Supply used.
USB
What is the expected behavior?
I expected the esp_hid_host demo to  successfully find and pair with a BT classic HID device such as Logitech K380 used for testing.
What is the actual behavior?
The esp_hid_host demo fails to find the BT classic devices in pairing mode.
Steps to reproduce.

Build, flash and monitor esp_hid_host example
2.
Put the BT Classic HID device into pairing mode (in my case it was a Logitech K380)
3.
Reset the ESP32-S3
4.
The demo fails to find anything
Debug Logs.
I (24) boot: ESP-IDF v5.0.4 2nd stage bootloader
I (24) boot: compile time 07:17:04
I (25) boot: Multicore bootloader
I (27) boot: chip revision: v0.2
I (30) boot.esp32s3: Boot SPI Speed : 80MHz
I (35) boot.esp32s3: SPI Mode       : DIO
I (40) boot.esp32s3: SPI Flash Size : 2MB
I (45) boot: Enabling RNG early entropy source...
I (50) boot: Partition Table:
I (54) boot: ## Label            Usage          Type ST Offset   Length
I (61) boot:  0 nvs              WiFi data        01 02 00009000 00006000
I (68) boot:  1 phy_init         RF data          01 01 0000f000 00001000
I (76) boot:  2 factory          factory app      00 00 00010000 00100000
I (83) boot: End of partition table
I (88) esp_image: segment 0: paddr=00010020 vaddr=3c080020 size=236b4h (145076) map
I (122) esp_image: segment 1: paddr=000336dc vaddr=3fc97000 size=03638h ( 13880) load
I (125) esp_image: segment 2: paddr=00036d1c vaddr=40374000 size=092fch ( 37628) load
I (136) esp_image: segment 3: paddr=00040020 vaddr=42000020 size=7fd40h (523584) map
I (231) esp_image: segment 4: paddr=000bfd68 vaddr=4037d2fc size=09c28h ( 39976) load
I (247) boot: Loaded app from partition at offset 0x10000
I (248) boot: Disabling RNG early entropy source...
I (259) cpu_start: Multicore app
I (259) cpu_start: Pro cpu up.
I (259) cpu_start: Starting app cpu, entry point is 0x4037535c
0x4037535c: call_start_cpu1 at /home/meow/esp/esp-idf_v5/components/esp_system/port/cpu_start.c:143

I (0) cpu_start: App cpu up.
I (278) cpu_start: Pro cpu start user code
I (278) cpu_start: cpu freq: 160000000 Hz
I (278) cpu_start: Application information:
I (281) cpu_start: Project name:     esp_hid_host
I (286) cpu_start: App version:      1
I (291) cpu_start: Compile time:     Oct 13 2023 07:16:59
I (297) cpu_start: ELF file SHA256:  d14f1a81ac64e854...
I (303) cpu_start: ESP-IDF:          v5.0.4
I (307) cpu_start: Min chip rev:     v0.0
I (312) cpu_start: Max chip rev:     v0.99
I (317) cpu_start: Chip rev:         v0.2
I (322) heap_init: Initializing. RAM available for dynamic allocation:
I (329) heap_init: At 3FC9E5E0 len 0004B130 (300 KiB): DRAM
I (335) heap_init: At 3FCE9710 len 00005724 (21 KiB): STACK/DRAM
I (342) heap_init: At 3FCF0000 len 00008000 (32 KiB): DRAM
I (348) heap_init: At 600FE010 len 00001FD8 (7 KiB): RTCRAM
I (355) spi_flash: detected chip: gd
I (359) spi_flash: flash io: dio
W (363) spi_flash: Detected size(8192k) larger than the size in the binary image header(2048k). Using the size in the binary image header.
I (376) coexist: coexist rom version e7ae62f
I (381) app_start: Starting scheduler on CPU0
I (386) app_start: Starting scheduler on CPU1
I (386) main_task: Started on CPU0
I (396) main_task: Calling app_main()
I (406) ESP_HIDH_DEMO: setting hid gap, mode:1
I (406) BLE_INIT: BT controller compile version [963cad4]
I (416) phy_init: phy_version 610,2bff4c8,Jul 27 2023,20:22:14
I (456) system_api: Base MAC address is not set
I (456) system_api: read default base MAC address from EFUSE
I (456) BLE_INIT: Bluetooth MAC:

I (496) ESP_HIDH_DEMO: SCAN...
I (496) main_task: Returned from app_main()
BLE: aa:bb:cc:dd:ee:ff, RSSI: -91, UUID: 0x0000, APPEARANCE: 0x0000, ADDR_TYPE: 'RANDOM'
BLE: aa:bb:cc:dd:ee:ff, RSSI: -93, UUID: 0x0000, APPEARANCE: 0x0000, ADDR_TYPE: 'RANDOM'
BLE: aa:bb:cc:dd:ee:ff, RSSI: -62, UUID: 0x0000, APPEARANCE: 0x0000, ADDR_TYPE: 'RANDOM'
BLE: aa:bb:cc:dd:ee:ff, RSSI: -88, UUID: 0x0000, APPEARANCE: 0x0000, ADDR_TYPE: 'PUBLIC'
BLE: aa:bb:cc:dd:ee:ff, RSSI: -90, UUID: 0x0000, APPEARANCE: 0x0000, ADDR_TYPE: 'PUBLIC', NAME: 'U-AC7BC6'
I (5496) ESP_HIDH_DEMO: SCAN: 0 results

More Information.
No response

Hi @ImproperCatGirl,
Thanks for your reporting. ESP32-S3 does not support Classic Bluetooth, you can think about using ESP32.

I could not find any Classic Bluetooth devices either using an Arduino Nano ESP32 which is also based on ESP32-S3 and that would explain why. That's really too bad cause I bought those thinking they did support Classic Bluetooth (BR/EDR). 🤦♂


Rename exported global from hyperapp to Hyperapp.

This is a proposal only relevant to CDN users. If you are using ES5 or ES6 via a module bundler, etc., you have nothing to worry about.
Before
🚫 const { h, app } = hyperapp

After
✅ const { h, app } = Hyperapp

Related: https://github.com/hyperapp/hyperapp/issues/352

I like hyperapp. It's so minimal and tiny. Hyperapp looks like it should be HyperApp then.

I like hyperapp. It's so minimal and tiny.

Agree.

Hyperapp looks like it should be HyperApp then.

Not really. It's a matter of perspective. "Hyperapp" is a whole word.
@lazarljubenovic Now, the real issue is that then what do you name the router?
HyperappRouter > hyperappRouter
/cc @lukejacksonn @zaceno

"Hyperapp" is a whole word.

The ligature ha from the logo made it two words in my head. Can't unsee it now. :sweat_smile:

It is probably worth making clear that, for any apps/demos that rely on the window.hyperapp namespace already (codepens especially officials and forks), this is a breaking change.
I prefer hyperapp and therefore would support hyperappRouter on the grounds of, same advantages less disruption.

I'm not a fan of using snake_case as the primary case, but what about using _ as a separator between hyperapp and package name? It would make it obvious that it's somehow related, yet not as related as multiple words on the right.
For example.
hyperappMyAwesomeThing

Not only that hyperapp is not immediately visible as a separate entity, even the right part of the word is not. You have to read the whole thing and midway through realize that "hyperapp my awesome--" doesn't make sense, so it's actually "hyperapp [pause] my awesome thing".
Compare with this.
hyperapp_myAwesomeThing

You immediately see both hyperapp and myAwesomeThing.

The thing which would confuse people it that most commonly used packages would probably have a single word, like hyperapp_router. This might lead developers to a wrong conclusion that the convention is to use snake case all the way: hyperapp_router_my_awesome_thing, which is again not desirable because we do not see name of the package closer together.
I'm reading too much into this, right? :sweat_smile:

By the way, do we have any statistics of how often people use CDN?  The way I see it, only experienced users would prefer a CDN. I know it sounds contradictory at a first glance, because setting up the build system is more advanced, but I think that with all the seed projects, people prefer having a build pipeline which allows them to use JSX.

@lazarljubenovic I think the most common use of CDN is for codepen examples and similar. I feel pretty certain any real project will be using npm and a build system of some kind.

@lazarljubenovic The thing which would confuse people...
I don't see anyone confused with React, ReactRedux, ReduxThunk or ReactRouter.

In a unexpected turn of events, I'm closing here and https://github.com/hyperapp/hyperapp/issues/352 and leaving things the way they are!


How to change text colors?

Hey, how do I change the color of NORMAL and line count texts(foreground color)?
Also, how to convert 16 colors to 256 colorspace?
i.e. I'm currently doing
let s:cterm01 = "00"
how to change it do
let s:cterm01 = 234(or whatever equivalent number is)?

I don't understand. You can change the normal highlighting via :hi Normal ... The colors of the statusline are pretty much defined by the airline-theme you are using.  I don't understand what you mean with :let s:cterm01...

I'm talking about the themes, where I'm defining colors. I'm trying to port base16 darktooth, but enable to set the NORMAL and line count text colors from inside the base16_darktooth.vim file. How to do that?

the NORMAL should be highlighting group airline_a (bold) and the wordcount is airline_z highlighting group.

Can you link a theme as an example?


Node.js grpc does not have close function for connection?

Cannot find any method to close the client connection from node grpc.

Would be nice with an answer. The close method on the Channel class don't seem to be closing the connection right away.

@edvinerikson Actually there is only a getClientChannel method in client class, I don't see any method about closing connection anyway.

getClientChannel(client).close(); works for me. Some docs about it would be nice though

+1

As of<EMAIL_ADDRESS>you can now use the function grpc.closeClient(client) to close a client connection.

@murgatroid99 can i see code example grpc.closeClient?

@gih2yun What's confusing (not mocking, actual question)? grpc is the module, and client is the client GRPC has generated with your custom functions.

@tejasmanohar Thanks for response.
My code calling grpc.closeClient failed  intermittently.
  var client = new my.GrpcService('<IP_ADDRESS>:1234', grpc.credentials.createInsecure());
  var request = new my.RequestObject();
  request.name = req.body.name;
  request.exec_cmd = req.body.exec_cmd;
  client.someGrpcMethod(request, function(err, r) {
   grpc.closeClient(client); // <======== this line
   // blah
   // blah
  });

I think above code is not correct.
Where is the best position to call grpc.closeClient()?
I'll test to call in proess.nextTick at the end of callback function.
How do you think about?

Haven't used the method yet. Looks ok if you want to close the client right after a single call. This looks ok to me. What was the error?

That should work just fine. What failure are you seeing?


Modify Calico e2e Yaml manifests

What this PR does / why we need it:
Modified Calico CNI configuration to use images from quay.io instead of docker.io. This to prevent image pull errors during e2e runs.
Which issue(s) this PR fixes (optional, in fixes #<issue number>(, fixes #<issue_number>, ...) format, will close the issue(s) when PR gets merged):
N/A
How Has This Been Tested?:
Calico pods in cluster:
  Type     Reason     Age   From               Message
  ----     ------     ----  ----               -------
  Normal   Pulling    64s   kubelet            Pulling image "quay.io/calico/cni:v3.22.0"

Quickstart e2e:
LABEL_FILTERS="prblocker" make test-e2e-calico

Ran 1 of 21 Specs in 820.216 seconds
SUCCESS! -- 1 Passed | 0 Failed | 0 Pending | 20 Skipped
PASS

Special notes for your reviewer:
N/A
Release note:
None

Minimal trivial change, so merging without additional review.


new instance expression in the ast

Hi. The NewInstance instruction is interpreted in the ast as the following:
if isinstance(op, instruction.InvokeInstruction):
        base = op.var_map[op.base]
        params = [op.var_map[arg] for arg in op.args]
        params = list(map(visit_expr, params))
        if op.name == '<init>':
            if isinstance(base, instruction.ThisParam):
                keyword = 'this' if base.type[1:-1] == op.triple[0] else 'super'
                return method_invocation(op.triple, keyword, None, params)
            elif isinstance(base, instruction.NewInstance):
                return ['ClassInstanceCreation', params,
                        parse_descriptor(base.type)]
            else:
                assert (isinstance(base, instruction.Variable))
                # fallthrough to create dummy <init> call

See also https://github.com/androguard/androguard/blob/master/androguard/decompiler/dad/dast.py#L332
Here is a sample ast I got:
['ClassInstanceCreation', [['Local', 'this'], ['Literal', ['TypeName', ('tests/sample/MainActivity', 0)], ('java/lang/Class', 0)]], ['TypeName', ('android/content/Intent', 0)]]]

It reflects a simple instance creation of an Intent.
My question is why the triple is not put in NewInstance expression as it is in the MethodInvocation. Constructors are also polymorphic like normal methods. To uniquely identify a constructor, we need the whole signature instead of a type.
In my example, only knowing the instance is an android/content/Intent is not enough because Intent has several constructors. I need to know which one is being called.
Can we also add a triple to NewInstance expression? Thanks.

unfortunately, I have really no idea :(
If you think it would be a good idea, can you implement it?

Hi @reox . I simply add the 'triple' in the 'ClassInstanceCreation' node. Can you review this?
https://github.com/androguard/androguard/pull/675


⚠ Bofrost.be has degraded performance

In 6085c07, Bofrost.be (https://www.bofrost.be) experienced degraded performance:

HTTP code: 200
Response time: 1781 ms

Resolved: Bofrost.be performance has improved in b502695 after 6 minutes.


[Impeller]

我在iOS真机(iOS14.7的系统)测试，并且设置了impeller(FLTEnableImpeller)为true。然后显示系统表情出现灰白色图片。系统表情是采用String.fromCharCode方式呈现的，如这个表情："unicode": 128513。并且滑动时整个画面还出现闪烁的情况。
[✓] Flutter (Channel stable, 3.3.7, on macOS 11.6.4 20G417 darwin-x64, locale zh-Hans-CN)
Checking Android licenses is taking an unexpectedly long time...
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Impeller should only be tested on the master channel. In this particular case, we fixed emojis in https://github.com/flutter/engine/pull/36161


Ollama Linux seg fault with GPU on Ubuntu 22.04

Ran into seg faults trying to run Ollama on Ubuntu 22.04. This is with an Intel Arc A750 card.
A few searches showed a similar finigerprint in https://github.com/intel/compute-runtime/issues/710. Reporting this as similar workaround of:
export NEOReadDebugKeys=1
export OverrideGpuAddressSpace=48
does the trick to get things working. Did a:
pip install --pre --upgrade ipex-llm[cpp]
just today, still not getting versions that have this fixed, so maybe coming soon, but wanted to raise failure fingerprint and workaround.

Hi @doucej , could you please provide more information from the ollama server side (like the ollama server log)? This would be helpful for us in addressing the issue and fixing it.

hi @doucej, this issue is due to oneAPI not being installed correctly. You may run ollama with following steps:

Please run sycl-ls to check your sycl devices. The expected output should be as below:
[opencl:acc:0] Intel(R) FPGA Emulation Platform for OpenCL(TM), Intel(R) FPGA Emulation Device OpenCL 1.2
[2<IP_ADDRESS>.12_195853.xmain-hotfix]
[opencl:cpu:1] Intel(R) OpenCL, Intel(R) Core(TM) Ultra 5 125H OpenCL 3.0 (Build 0) [2<IP_ADDRESS>.12_195853.xmain-hotfix]
[opencl:gpu:2] Intel(R) OpenCL Graphics, Intel(R) Arc(TM) Graphics OpenCL 3.0 NEO  [24.09.28717.12]
[ext_oneapi_level_zero:gpu:0] Intel(R) Level-Zero, Intel(R) Arc(TM) Graphics 1.3 [1.3.28717]

If [ext_oneapi_level_zero:gpu] is not present, please proceed to step 2.

You may follow our guide to reinstall oneAPI: https://ipex-llm.readthedocs.io/en/latest/doc/LLM/Overview/install_gpu.html#id1.

Thanks -- yes, I do have my GPU listed:
(base) doucej@kryten:~$ source /opt/intel/oneapi/setvars.sh

:: initializing oneAPI environment ...
   bash: BASH_VERSION = 5.2.21(1)-release
   args: Using "$@" for setvars.sh arguments:
:: advisor -- latest
:: ccl -- latest
:: compiler -- latest
:: dal -- latest
:: debugger -- latest
:: dev-utilities -- latest
:: dnnl -- latest
:: dpcpp-ct -- latest
:: dpl -- latest
:: ipp -- latest
:: ippcp -- latest
:: mkl -- latest
:: mpi -- latest
:: tbb -- latest
:: vtune -- latest
:: oneAPI environment initialized ::

(base) doucej@kryten:~$ sycl-ls
[opencl:acc:0] Intel(R) FPGA Emulation Platform for OpenCL(TM), Intel(R) FPGA Emulation Device OpenCL 1.2  [2<IP_ADDRESS>.08_160000]
[opencl:cpu:1] Intel(R) OpenCL, Intel(R) Xeon(R) CPU E5-2696 v4 @ 2.20GHz OpenCL 3.0 (Build 0) [2<IP_ADDRESS>.08_160000]
[opencl:gpu:2] Intel(R) OpenCL Graphics, Intel(R) Arc(TM) A750 Graphics OpenCL 3.0 NEO  [23.43.027642]
(base) doucej@kryten:~$

I did try creating a new conda environment today through:
conda create -n llm-cpp python=3.11
conda activate llm-cpp
pip install --pre --upgrade ipex-llm[cpp]

And followed through with deleting the old ollama binary and an init-ollama.
Back to the same point, need those extra environment variables for it to see/utilize the GPU without crashing.
When installing as above, do I also need to go through and install/update the oneapi packages through apt, or is above PIP getting that set up for me? I could try that if this still seems like a setup/installation issue.
Thanks!

Hi @doucej , this failure of Ollama to run is because you haven't correctly installed OneAPI. If you have installed OneAPI correctly, [ext_oneapi_level_zero:gpu] should be present as expected in the output of sycl-ls.
To fix this issue, you may follow our guide to reinstall oneAPI: https://ipex-llm.readthedocs.io/en/latest/doc/LLM/Overview/install_gpu.html#id1.
Also, would you mind running https://github.com/intel-analytics/ipex-llm/tree/main/python/llm/scripts to check system environment and reply us the output?

Some notes below. I did go through and try to reinstall oneAPI, looks like indeed I had an old version on there from previous rev ubuntu most likely.
Some notes:
Before touching anything, after activating llm-cpp conda, source /opt/intel/oneapi/setvars.sh:
(llm-cpp) doucej@kryten:~$ ~/Downloads/env-check.sh
-----------------------------------------------------------------
PYTHON_VERSION=3.11.9
-----------------------------------------------------------------
transformers=4.41.2
-----------------------------------------------------------------
torch=2.2.0+cu121
-----------------------------------------------------------------
ipex-llm Version: 2.1.0b20240620
-----------------------------------------------------------------
IPEX is not installed.
-----------------------------------------------------------------
CPU Information:
Architecture:                         x86_64
CPU op-mode(s):                       32-bit, 64-bit
Address sizes:                        46 bits physical, 48 bits virtual
Byte Order:                           Little Endian
CPU(s):                               44
On-line CPU(s) list:                  0-43
Vendor ID:                            GenuineIntel
Model name:                           Intel(R) Xeon(R) CPU E5-2696 v4 @ 2.20GHz
CPU family:                           6
Model:                                79
Thread(s) per core:                   2
Core(s) per socket:                   22
Socket(s):                            1
Stepping:                             1
CPU(s) scaling MHz:                   55%
CPU max MHz:                          3700.0000
CPU min MHz:                          1200.0000
-----------------------------------------------------------------
Total CPU Memory: 39.0826 GB
-----------------------------------------------------------------
Operating System:
Ubuntu 24.04 LTS \n \l

-----------------------------------------------------------------
Linux kryten 6.8.0-35-generic #35-Ubuntu SMP PREEMPT_DYNAMIC Mon May 20 15:51:52 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
-----------------------------------------------------------------
/home/doucej/Downloads/env-check.sh: line 148: xpu-smi: command not found
-----------------------------------------------------------------
/home/doucej/Downloads/env-check.sh: line 154: clinfo: command not found
-----------------------------------------------------------------
Driver related package version:
rc  intel-fw-gpu                                    2022.47.1+190                            all          Firmware package for Intel integrated and discrete GPUs
ii  intel-level-zero-gpu                            1.3.26241.33-647~22.04                   amd64        Intel(R) Graphics Compute Runtime for oneAPI Level Zero.
-----------------------------------------------------------------
igpu not detected
-----------------------------------------------------------------
xpu-smi is not installed. Please install xpu-smi according to README.md
(llm-cpp) doucej@kryten:~$

after:
wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
sudo apt update
sudo apt install intel-oneapi-common-vars=2024.0.0-49406
intel-oneapi-common-oneapi-vars=2024.0.0-49406
intel-oneapi-diagnostics-utility=2024.0.0-49093
intel-oneapi-compiler-dpcpp-cpp=2024.0.2-49895
intel-oneapi-dpcpp-ct=2024.0.0-49381
intel-oneapi-mkl=2024.0.0-49656
intel-oneapi-mkl-devel=2024.0.0-49656
intel-oneapi-mpi=2021.11.0-49493
intel-oneapi-mpi-devel=2021.11.0-49493
intel-oneapi-dal=2024.0.1-25
intel-oneapi-dal-devel=2024.0.1-25
intel-oneapi-ippcp=2021.9.1-5
intel-oneapi-ippcp-devel=2021.9.1-5
intel-oneapi-ipp=2021.10.1-13
intel-oneapi-ipp-devel=2021.10.1-13
intel-oneapi-tlt=2024.0.0-352
intel-oneapi-ccl=2021.11.2-5
intel-oneapi-ccl-devel=2021.11.2-5
intel-oneapi-dnnl-devel=2024.0.0-49521
intel-oneapi-dnnl=2024.0.0-49521
intel-oneapi-tcm-1.0=1.0.0-435
Let apt upgrade a bunch of intel-oneapi packages after initial install & reboot for good measure:
(ollama) doucej@kryten:~$ ~/Downloads/env-check.sh
-----------------------------------------------------------------
PYTHON_VERSION=3.11.9
-----------------------------------------------------------------
transformers=4.41.2
-----------------------------------------------------------------
torch=2.2.0+cu121
-----------------------------------------------------------------
ipex-llm Version: 2.1.0b20240624
-----------------------------------------------------------------
IPEX is not installed.
-----------------------------------------------------------------
CPU Information:
Architecture:                         x86_64
CPU op-mode(s):                       32-bit, 64-bit
Address sizes:                        46 bits physical, 48 bits virtual
Byte Order:                           Little Endian
CPU(s):                               44
On-line CPU(s) list:                  0-43
Vendor ID:                            GenuineIntel
Model name:                           Intel(R) Xeon(R) CPU E5-2696 v4 @ 2.20GHz
CPU family:                           6
Model:                                79
Thread(s) per core:                   2
Core(s) per socket:                   22
Socket(s):                            1
Stepping:                             1
CPU(s) scaling MHz:                   55%
CPU max MHz:                          3700.0000
CPU min MHz:                          1200.0000
-----------------------------------------------------------------
Total CPU Memory: 39.0826 GB
-----------------------------------------------------------------
Operating System:
Ubuntu 24.04 LTS \n \l

-----------------------------------------------------------------
Linux kryten 6.8.0-35-generic #35-Ubuntu SMP PREEMPT_DYNAMIC Mon May 20 15:51:52 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
-----------------------------------------------------------------
/home/doucej/Downloads/env-check.sh: line 148: xpu-smi: command not found
-----------------------------------------------------------------
/home/doucej/Downloads/env-check.sh: line 154: clinfo: command not found
-----------------------------------------------------------------
Driver related package version:
rc  intel-fw-gpu                                    2022.47.1+190                            all          Firmware package for Intel integrated and discrete GPUs
ii  intel-level-zero-gpu                            1.3.26241.33-647~22.04                   amd64        Intel(R) Graphics Compute Runtime for oneAPI Level Zero.
-----------------------------------------------------------------
igpu not detected
-----------------------------------------------------------------
xpu-smi is not installed. Please install xpu-smi according to README.md
(ollama) doucej@kryten:~$ sycl-ls
[opencl:cpu][opencl:0] Intel(R) OpenCL, Intel(R) Xeon(R) CPU E5-2696 v4 @ 2.20GHz OpenCL 3.0 (Build 0) [2<IP_ADDRESS>.02_160000]
[opencl:gpu][opencl:1] Intel(R) OpenCL Graphics, Intel(R) Arc(TM) A750 Graphics OpenCL 3.0 NEO  [23.43.027642]
(ollama) doucej@kryten:~$

Now even the setenvs I was doing to workaround before aren't helping, just seg faults trying to start up. Will take another look at my oneapi install, I'm guessing something's messed up there. Odd that it wanted to update a bunch of those immediately after installation, not sure if that's expected.

Realized the title was off, working with Ubuntu 24.04. I've still not been able to get a good OneAPI installation even after a clean reinstall. I was able to get Ollama running with Vulkan with the the changes in https://github.com/ollama/ollama/pull/5059#. So maybe operator error here, nonetheless, I'm up and running, so this issue is moot for me for now.


Debug camera perception in VS code

System information

**OS Platform and DistributionLinux Ubuntu 18.04
**Apollo installed from source :
**Apollo version 5.0

I have few questions

I would like to know how the images from camera (which is being published on /apollo/sensor/camera/front_6mm/image etc by the camera driver) are being subscribed by perception module.
How do I debug perception module in VS code within the docker container. I am running a pre-recorded record file which has the cyber_topics needed for perception and I am using this for gdb server command in tasks.json file " bash docker/scripts/dev_start_gdb_server.sh perception 1111", but not able to attach to perception process. I could do so successfully for control and camera modules.

thanks for your help

Appreciate any comment on this. thank you

Appreciate any comment on this. thank you


num_read_fastp

I couldn't identify when num_read_fastp is added to the metadata table, and its lack caused an error in the curate step. Am I missing something?

This column seems to be used in cstmm too, so should be generated before that.

I just double checked the data I've been downloading recently and it's missing there as well. I remember num_read_fastp got added in the metadata.tsv output that is produced for each SRR ID, not the full table produced by amalgkit metadata.
It's missing there as well, though.
In curate num_read_fastp is used for mapping rate calculation, but it should not be part of cstmm.

OK, I thought cross_species.R is a part of cstmm, but it's not actually.
We need mapping rates, num_read_fastp, and other related info to be reported as a part of metadata table. We shouldn't overwrite the input metadata, so a new tsv should be created. The new table should also store other per-SRR stats that can only be calculated after processing fastq, e.g., TMM normalization factors, updated exclusion column (e.g., low mapping rate), and so on. Would you be able to work on this?

Having briefly looked through the code, num_read_fastp should be saved somewhere in the variable/dataframe seq_summary, but isn't actually properly dumped into the new metadata.tsv.
I will investigate this.

OK, I thought cross_species.R is a part of cstmm, but it's not actually.
We need mapping rates, num_read_fastp, and other related info to be reported as a part of metadata table. We shouldn't overwrite the input metadata, so a new tsv should be created. The new table should also store other per-SRR stats that can only be calculated after processing fastq, e.g., TMM normalization factors, updated exclusion column (e.g., low mapping rate), and so on. Would you be able to work on this?

cross_species.R is an obsolete debugging file, I will remove this file in the next update.
Since the user has the option to not use fastp during quant, we should also account for that possibilty as well. And the mapping rate is calculated with the original metadata stats.

Since the user has the option to not use fastp during quant, we should also account for that possibilty as well.
The first half is right. You can pick num_read_XXX depending on its presence.

And the mapping rate is calculated with the original metadata stats.
This is not correct. The read numbers should be obtained from actual fastq. This is because there is no guarantee that all the reads have been extracted.

Turns out it was a very straight forward solution. I can add any other fastp and fastq statistics as well, like dumped, rejected and written reads. Should I just add them all?
Also I would change curate to take the fastq_dump written reads for mapping rate calculation, if num_read_fastp isn't available, correct?

Another thing: My current solution is to use the already implemented flag --save_metadata and output the statistics within a single-row metadata.tsv
But since this table contains statistics necessary for curate, even if fastp was turned off, I'd remove the argument --save_metadata entirely and just always output the single-row metadata.tsv. We can keep the option, of course and leave it on as default, but I can't think of any reason why someone would not need this output.

Turns out it was a very straight forward solution. I can add any other fastp and fastq statistics as well, like dumped, rejected and written reads. Should I just add them all?
Yes, let's keep as many info as possible.

Also I would change curate to take the fastq_dump written reads for mapping rate calculation, if num_read_fastp isn't available, correct?
Yes, you are right.

But since this table contains statistics necessary for curate, even if fastp was turned off, I'd remove the argument --save_metadata entirely and just always output the single-row metadata.tsv. We can keep the option, of course and leave it on as default, but I can't think of any reason why someone would not need this output.
Please obsolete the option as it becomes a mandatory feature.

I need one last clarification:
num_read_unfiltered in curatewould be equivalent to the number of fastq dumped reads in getfastq, or something else entirely?

Should be the same. I annotated this as num_read_unfiltered because there was another "filtering" step in the NC paper (filtering out reads mapped to mitochondria genomes), which is not present in amalgkit because of its limited effectiveness. You can rename the column.

Changes
getfastq
getfastq output now looks like this:

The metadata.tsv is a single line (plus header) for that particular ID.
New statistics added to the metadata.tsv:

num_read_fastq_dumped (formerly num_read_unfiltered)
num_read_fastq_written
num_read_fastq_rejected
num_read_fastp
num_read_fastp_input

curate

num_read_unfiltered is now num_read_fastq_dumped

affects: fraction_lost_fastp
new: fraction_lost_fastq (if num_read_fastp` is unavailable)

mapping rate is calculated with num_read_fastq_written ifnum_read_fastp is unavailable

If these changes are OK, I'll push the update.

Idea to maybe add tomerge or another subfunctionality (maybe amalgkit gather), to collect and merge all the metadata.tsv`s from the getfastq output into a single file.

I'm wondering where we should put the metadata single-row tsv files. These files will be accessed/updated by different subcommands, so wouldn't it make more sense to put them in a new, dedicated sub-directory under outdir/metadata/ rather than under outdir/getfastq/?
I'm thinking something like this:
outdir
 |
 +--metadata
      |
      +--metadata
      +--pivot_tables
      +--temp
      +--updated_metadata (<-THIS!)
            |
            +--metadata_SRR0000000.tsv
            +--metadata_SRR0000001.tsv
            +--metadata_SRR0000002.tsv

yeah, that makes a lot of sense. And then the merge of all these .tsvs is just a cataway to be used forcurate` too.

curate should change the metadata, because there may be some excluded SRRs, which should be noted in the exclusion column. Merging all single-row tsv should be done in the very final step after curate, maybe amalgkit summary.

In that case I'll need to also adjust curate to take the updated_metadata folder as additional input to get the num_read_fastp info.

Why does curate need num_read_fastp?

for mapping rate calculation

and calculation of lost read %

Yes, multiple subcommands including curate should share and use a function to load it into DataFrame. I guess it wouldn't take time even when 1000s rows should be concatenated.

CHANGES
amalgkit getfastq

amalgkit getfastq will now output metadata.tsv's with updated fastp/fastq statistics into a folder structure like this:

work_dir
 |
 +--metadata
      |
      +--metadata
      +--pivot_tables
      +--temp
      +--updated_metadata (<-THIS!)
            |
            +--metadata_SRR0000000.tsv
            +--metadata_SRR0000001.tsv
            +--metadata_SRR0000002.tsv

amalgkit curate

amalgkit curate now requires --updated_metadata_directory (kind of a long name, maybe truncating this in the future) as input
amalgkit curate reads out fastp and fastq statistics from all runs, where exclusion==no and calculates

mapping_rate
fraction_lost_fastp OR
fration_lost_fastq, depending on availability

This join would be confusing. --updated_metadata_dir should receive a valid path, not a truncated path that is valid only when joined with args.work_dir. Same applies to https://github.com/kfuku52/amalgkit/issues/24.

updated_metadata_dir = os.path.join(args.work_dir, args.updated_metadata_dir)

Also, please change to required=False. You can set arbitrary default value such as "infer" and detect it later to replace it with as.path.join(args.work_dir, 'metadata/updated_metadata/'). Please see --iqtree_treefile in csubst for example.
pcu.add_argument('--updated_metadata_dir', metavar='PATH', default='./metadata/updated_metadata/', type=str, required=True, action='store',
help='default=%(default)s: Directory containing metadata.tsv files as put out by amalgkit getfastq.')

Just FYI, some quick testing make it seem that os.path.join(args.work_dir, args.updated_metadata) is smart enough to resolve the correct path:
Here, I give absolute paths to all input files:
amalgkit curate --work_dir /Users/s229181/MSN --metadata /Users/s229181/MSN/metadata/Metadata_all_2.tsv --infile /Users/s229181/MSN/counts/Citrullus_lanatus_est_counts.tsv --eff_len_file /Users/s229181/MSN/eff_length/Citrullus_lanatus_eff_length.tsv --tissues 'root,flower,leaf' --norm fpkm --cleanup 1 --updated_metadata_dir /Users/s229181/MSN/metadata/updated_metadata/
the R-script reports (ommiting some other input parameters):
working_directory = /Users/s229181/MSN/
metadata:  /Users/s229181/MSN/metadata/Metadata_all_2.tsv
infile:  /Users/s229181/MSN/counts/Citrullus_lanatus_est_counts.tsv
gene length file:  /Users/s229181/MSN/eff_length/Citrullus_lanatus_eff_length.tsv
updated metadata directory:  /Users/s229181/MSN/metadata/updated_metadata

The same code, but I only give the truncated paths, starting from the working directory:
amalgkit curate --work_dir /Users/s229181/MSN/ --metadata metadata/Metadata_all_2.tsv --infile counts/Citrullus_lanatus_est_counts.tsv --eff_len_file eff_length/Citrullus_lanatus_eff_length.tsv --tissues 'root,flower,leaf' --norm fpkm --cleanup 1 --updated_metadata_dir metadata/updated_metadata/
Rscript reports:
working directory:  /Users/s229181/MSN
metadata:  /Users/s229181/MSN/metadata/Metadata_all_2.tsv
infile:  /Users/s229181/MSN/counts/Citrullus_lanatus_est_counts.tsv
gene length file:  /Users/s229181/MSN/eff_length/Citrullus_lanatus_eff_length.tsv
updated metadata directory:  /Users/s229181/MSN/metadata/updated_metadata

I do concede that it might be confusing, but whatever the user decides should still working as intended.

The coding should be done in a way that prevents possible errors in the future. Please imagine the cases like this, in which os.path.join() failed to handle nested directories with the same name.
https://stackoverflow.com/questions/44022916/combine-two-paths-with-common-folder

Ah, yes, that makes sense. I did not consider this. Will adjust the code accordingly!

Changed the pathing default to "inferred". If inferred, path is set to workdir/metadata/updated_metadata/, otherwise the full path the user provided.
I pushed the update to master, so the updated_metadata input from getfastq is now required. For testing, I split my large metadata table from metadata into single line metadata files with:
 awk -F$'\t' {print>$1;close($1)} metadata.tsv
 rename 's/$/\.tsv' .*

then you have to add the header of the original metadata.tsv to all the small ones with:
sed -i '1 i\copy_and_paste_header_here' ./*.tsv

Thank you. Please close the issue if everything looks fine.

fixed the rest of the input files as well. All curate inputs require the full path (instead of work_dir + truncated path)

The above awk command wasn't valid on my mac. It worked when {...} was single-quoted, but the result looks not correct. Files were generated per-species, not per-run. Could you share a couple of single-line metadata files? I need to know how it should look like, especially in file names.

ah yeah, sorry!  The number behind the $ need to match the run column number. In a metadata sheet put out by metadata it should be $16, I think? I rearranged the run column to the front in my original file.
Here is for reference, they look like the big, original file, but have just a single entry:
updated_metadata.zip

also, rename (brew install rename)has to be installed via brew and sed -i does not work with mac either (mac sed does not have sed -i for some reason. I installed GNU sed on my mac via brew: brew install gnu-sed)

Thank you. The rename command wasn't valid too but it seems you've corrected already. Good! So the last thing to fix is the sed command.
header="`cat run.tsv`"
gsed -i '1i '"${header}" ./*.tsv
rm run.tsv

ah yeah, that's a lot cleaner than what I did.
I manually copied the header line from the original metadata, changed the tab seperator to ;;; and used sed to change it back to tab once the header was in the target file. :D

It seems that I didn't tell you enough about the "inferred" option. This is not right:
    if args.updated_metadata_dir == "inferred":
        updated_metadata_dir = os.path.join(args.work_dir, args.updated_metadata_dir)
    else:
        updated_metadata_dir = os.path.realpath(args.updated_metadata_dir)

Because it produces a PATH like /path/to/gfe_data/inferred, which doesn't make sense. And this is what we wanted:
    if args.updated_metadata_dir == "inferred":
        updated_metadata_dir = os.path.join(args.work_dir, 'metadata/updated_metadata')
    else:
        updated_metadata_dir = os.path.realpath(args.updated_metadata_dir)

Do you have a test dataset to quickly confirm whether your changes work well? I'm wondering how you test new functionalities.

fixed in https://github.com/kfuku52/amalgkit/commit/b8bed6f1deccdda7c4f2e9e1c4d38e37bb9b7a69

I usually use a dataset I'm currently working with to test these. Sometimes I have to create an artificial one, like I did as described a few comments above (where I split the large metadata sheet into hundreds of artificial updated_metadata.tsv's).
During the last week, I could successfully test this with actual updated_metadata from ~3000 SRA samples (out of which ~2500 made it into curate). Updated metadata was properly created by getfastq and were read by curate and processed without issue.

At some point, we should find a minimal dataset only for testing. Continued here https://github.com/kfuku52/amalgkit/issues/41


Not showing on LAN (PS4)

So I think I did everything right.

I downloaded phantom-windows.exe and phantom-0.5.1.zip
I launched cmd, dragged the .exe into there and added this server: RushNation.NET:19132
It loaded and it wrote this: (https://user-images.githubusercontent.com/67229391/85225767-c30b7200-b3d3-11ea-84b5-b74bcebad103.PNG)

I am using windows 10, phantom-0.5.1 and I am on my ps4

That looks correct, have you allowed phantom through the firewall when prompted during the first run?

Are you using phantom 0.5.1? Because I used it and it didn't work either.

I am also on PS4

Although now you can't use any phantom, because of 1.16.
I thried and 1.16 breaks it.

Although now you can't use any phantom, because of 1.16.
I tried and 1.16 breaks it.

I have been able to connect to a 1.16 server hosted from my win 10 computer from my phone.

For me it is broken, and it has been ever since 1.16

So I think I did everything right.

I downloaded phantom-windows.exe and phantom-0.5.1.zip
I launched cmd, dragged the .exe into there and added this server: RushNation.NET:19132
It loaded and it wrote this: (https://user-images.githubusercontent.com/67229391/85225767-c30b7200-b3d3-11ea-84b5-b74bcebad103.PNG)

I am using windows 10, phantom-0.5.1 and I am on my ps4

Have you tried letting it through firewall?

Do this: how to join servers on minecraft ps4 1.16

So I think I did everything right.

I downloaded phantom-windows.exe and phantom-0.5.1.zip
I launched cmd, dragged the .exe into there and added this server: RushNation.NET:19132
It loaded and it wrote this: (https://user-images.githubusercontent.com/67229391/85225767-c30b7200-b3d3-11ea-84b5-b74bcebad103.PNG)

I am using windows 10, phantom-0.5.1 and I am on my ps4

I think I found the problem: both your pc and ps4 have to be connected to LAN.
I hac the exact same problem until I did this.

Hey @Mineaxe, sorry for the delay! Along with the above suggestions, please make sure this setting is also enabled on your server, otherwise it won't show up in the list when phantom is running.

Hey @Mineaxe, sorry for the delay! Along with the above suggestions, please make sure this setting is also enabled on your server, otherwise it won't show up in the list when phantom is running.


RoBERTa - Separator Discrepancy

In the sentence prediction task, there's the following behavior:

For a single sentence, a separator token is not used
For a pair of sentences, a single separator token is used between them

This is the code that is used in the fine-tuning examples, for example GLUE as specified in https://github.com/pytorch/fairseq/blob/7e4c1a4b6a40d0c6cde638dc2c7f2eeb459bc7fb/examples/roberta/README.glue.md:
https://github.com/pytorch/fairseq/blob/7e4c1a4b6a40d0c6cde638dc2c7f2eeb459bc7fb/fairseq/tasks/sentence_prediction.py#L130-L136
However, RoBERTa's hub interface is used for inference (https://github.com/pytorch/fairseq/blob/7e4c1a4b6a40d0c6cde638dc2c7f2eeb459bc7fb/examples/roberta/README.glue.md#inference-on-glue-task).
In the hub interface, there's the following behavior:

For a single sentence, a separator token is added at the end of it
For a pair of sentences, two separator tokens are used between them, and another at the end of the second

https://github.com/pytorch/fairseq/blob/7e4c1a4b6a40d0c6cde638dc2c7f2eeb459bc7fb/fairseq/models/roberta/hub_interface.py#L57-L60
My questions are:

What is the reason for the discrepancy in separator usage?
Was roberta.large.mnli fine-tuned using the hub interface separator style, or was it trained exactly as specified in https://github.com/pytorch/fairseq/blob/7e4c1a4b6a40d0c6cde638dc2c7f2eeb459bc7fb/examples/roberta/README.glue.md#finetuning-roberta-on-glue-tasks, hence with a single separator?

By default :
https://github.com/pytorch/fairseq/blob/7e4c1a4b6a40d0c6cde638dc2c7f2eeb459bc7fb/fairseq/models/roberta/hub_interface.py#L36
no_separator=False
Therefore there is only one separator.

But I'm also curious why would anyone use no_separator=True ?

By default :
https://github.com/pytorch/fairseq/blob/7e4c1a4b6a40d0c6cde638dc2c7f2eeb459bc7fb/fairseq/models/roberta/hub_interface.py#L36
no_separator=False
Therefore there is only one separator.
But I'm also curious why would anyone use no_separator=True ?

The default behavior of the hub interface results in two separators between sentences. If the glad

Oups sorry, my bad, I was looking at BART implementation of Hub interface :
https://github.com/pytorch/fairseq/blob/7e4c1a4b6a40d0c6cde638dc2c7f2eeb459bc7fb/fairseq/models/bart/hub_interface.py#L44

Does this comment explain things: https://github.com/pytorch/fairseq/blob/7e4c1a4b6a40d0c6cde638dc2c7f2eeb459bc7fb/fairseq/models/roberta/hub_interface.py#L40
Basically we use the same symbol for end of sentence (EOS) and separator. So for a single sentence task there’s a single EOS at the end, and for sentence pairs we have two EOS between sentences and one at the end.

Thanks! I wasn't aware of the insertion of the EOS token by the dataloader.
For anyone else who wondered where it happens:
https://github.com/pytorch/fairseq/blob/7e4c1a4b6a40d0c6cde638dc2c7f2eeb459bc7fb/preprocess.py#L303-L304
which eventually gets to
https://github.com/pytorch/fairseq/blob/7e4c1a4b6a40d0c6cde638dc2c7f2eeb459bc7fb/fairseq/data/dictionary.py#L284-L285
in encode_line.


Replace .tsx React icon with TypeScript icon

How to replace .tsx React icon with TypeScript icon? Thanks.

Well... switching back to Material Icons...
https://github.com/tal7aouy/vscode-icons/issues/46


Request: add yargs to support command line arguments for the CLI

The arguments should support at the very least the config options we have with gigsboat.json
Initial MVP to add support here, would be:

--help / -h flag for showing the standard help CLI output
--config / -c for pointing out the config file location (right now the code looks for a default location of the same directory it was running from

In the future, a follow up PR can then add more:

--debug / -d to add debug output (along with adding various debug() points across the codebase using the debug dep)
--json / -j to process the output as json
--outfile / -o to save the output to a specific filename/path (whether it is a README.md file or the json output)

I would like to work on this issue.

That would be awesome, thank you @marquicodes 🙏


Change {title: "Hello"} to {title: "Home Page"}

Change {title: "Hello"} to {title: "Home Page"} so that "Advanced Node and Express - Create New Middleware" later in the Curriculm passes. This change is discussed in issue #17618
Issues: #38882 and #17618
Checklist:

[x] I have read freeCodeCamp's contribution guidelines.
[x] My pull request has a descriptive title (not a vague title like Update index.md)
[x] My pull request targets the master branch of freeCodeCamp.
[x] All the files I changed are in the same world language, for example: only English changes, or only Chinese changes, etc.

Closes #17618

Hey @Sky020, I haven't looked at your PR for the upgrade of this section - is this PR still relevant? I don't see the issue this closes in the list of issues on your PR.

@moT01 This is a partial fix to one of the problems still relevant, and could serve as a stand-by, until my PR is merged.

I don't see the issue this closes in the list of issues on your PR.

My PR closes all current issues relating to the Advanced Node and Express section. I probably missed adding the issue to the list. The mentioned issue this PR closes does not appear to be related to this fix. There are many separate issues mentioned within that issue. The OP issue was likely CORS related, but that is just a guess.
I will take a closer look, tomorrow, at my PR, as well as all of the current issues, and do a thorough search for which issues it will close.

@ajm896 Thank you for opening this pull request.
This is a standard message notifying you that we’ve reviewed your pull request and have decided not to merge it. We have decided to move forward with changes in another PR.
We still would welcome future pull requests from you.
Thank you and happy coding.


Resource Types: Add White Paper in Text Resources Group

Still need to source definition. Per DIWG Metadata Subcommittee meeting, 2019/11/19.

COAR has "other type of report" that includes "white paper". However, "other type of report" is under "report". Can Report cover White Paper for us?

I'd be in favor of that. We can put that suggestion in the agenda for our next metadata subcommittee meeting. Thanks for finding this!


Trailing whitespaces after / causes parser to fail

Given the BAI2 file below:
01,123456,123456,220310,0022,1,,,2/
02,,123456,1,220309,,USD,2/
03,654321,USD,010,10372793,,,015,11384293,,/
16,195,1011500,,20220681582200,Test Transaction/
49,22768586,3/
98,22768586,1,5/
99,22768586,1,7/

Which should be valid, when trying to parse it I am given the following error:
~/.asdf/installs/python/3.9.13/lib/python3.9/site-packages/bai2/parsers.py in _parse_field_from_config(self, field_config, raw_value)
    141
    142         field_name, parser = field_config
--> 143         field_value = parser(raw_value) if raw_value else None
    144         return field_name, field_value
    145

ValueError: invalid literal for int() with base 10: '2/                                             '

A simple solution is to just strip the strings on https://github.com/ministryofjustice/bai2/blob/main/bai2/bai2.py#L13 .

@Isaben – are you content with this fix and do you want to close the issue?

@ushkarev yes, thank you!


Remove the need to enter \n to return EXIT_FAILURE

Change exception handling to always return EXIT_FAILURE, when handling exception.
Before EXIT_FAILURE was only returned if one enters '\n' after an exception catch

Change std::cout << "Press enter to exit." << std::endl; to std::cout << "Press a key to exit." << std::endl;

Change std::cout << "Press enter to exit." << std::endl; to std::cout << "Press a key to exit." << std::endl;

Not needed since it will exit on pressing enter with no character input.


Fix make {update|verify}[-codegen]

First:
verify-codegen.sh was a thin wrapper around update-codegen.sh that
passed a --verify-only flag to the generators. But generators wasn't
the only thing in update-codegen.sh, which led to inconsistencies.
This commit changes the strategy entirely:
We're getting rid of the verify-codegen.sh wrapper. Instead
verify-codegen will run update-codegen and then check if anything
changed. (This is similar to how verify-vendor works.)
Second:
Apparently the generators invoked by update-codegen.sh used to put the
generated files under vendor/, so we had an extra line to copy them back
to the non-vendor/ side. At some point this seems to have changed such
that the generators put the files in non-vendor/. So that copy was
actually undoing what the generators had just done.
We're getting rid of that copy-back entirely. So now, make update-codegen shouldn't touch the vendor/ directory; and verify will
catch discrepancies here (i.e. you forgot to run make vendor) via
verify-vendor rather than in verify-codegen itself (which wasn't
working anyway).
Third:
make update-codegen wouldn't fail if something in it went wrong. Add
-e to update-codegen.sh so it does. (This is almost totally
unrelated to the rest of what's going on here.)
Finally:
Check in the changed files that are now properly generated.

In putting this together, I made the first commit, then ran make verify to prove that it would fail. Checked in the files changed thereby -- which were just the non-vendor/ ones! -- and ran make verify again to prove that it would still fail. Ran make vendor to get them all copied down to vendor/, checked those in, and then make verify ran cleanly.

/assign @suhanime

/lgtm


Owl DateTime Picker Not Opening in MatDialog in Angular 18

Description
The Owl DateTime Picker works correctly in a standard component but fails to open within an Angular Material MatDialog. This results in a TypeError: Cannot read properties of null (reading 'deserialize'). Not only this error, but there are also other null errors like this.dateTimeAdapter is null
.localservice@runtime.d3acb9e1.js:26
ERROR TypeError: Cannot read properties of null (reading ‘deserialize’)
at set pickerMoment (@danielmoncada_angul…?v=8c276e69:8932:34)
at applyValueToInputField (chunk-HQF6UBNU.js?v=8c276e69:7400:27)
at writeToDirectiveInput (chunk-HQF6UBNU.js?v=8c276e69:11710:7)
at setInputsForProperty (chunk-HQF6UBNU.js?v=8c276e69:12569:5)
at elementPropertyInternal (chunk-HQF6UBNU.js?v=8c276e69:12111:5)
at ɵɵtwoWayProperty (chunk-HQF6UBNU.js?v=8c276e69:21084:5)
at OwlDateTimeContainerComponent_owl_date_time_calendar_1_Template (@danielmoncada_angul…s?v=8c276e69:6777:5)
at executeTemplate (chunk-HQF6UBNU.js?v=8c276e69:11833:5)
at refreshView (chunk-HQF6UBNU.js?v=12880:7)
at detectChangesInView (chunk-HQF6UBNU.js?v=13044:5)

Steps to Reproduce

Add the Owl DateTime Picker to a standard Angular component that's built in Angular 18. Verify it works as expected.
Add the same DateTime Picker to a component loaded within an Angular Material MatDialog.
Open the dialog and attempt to interact with the DateTime Picker.
Observe the error and the picker failing to open.

Expected Behavior
The Owl DateTime Picker should open and function correctly within an Angular Material MatDialog, as it does in a standard Angular component.

Actual Behavior
The picker fails to open when used inside the MatDialog, logging a runtime error as shown above.

Reproducible Example
Please provide a minimal reproducible example:

A GitHub repository or StackBlitz link that demonstrates the issue.
Alternatively, include a small code snippet to showcase the problem.

Environment Details

Angular Version: 18.x
Owl DateTime Picker Version:"@danielmoncada/angular-datetime-picker": "18.1.0",

Stackblitz reproducible link here
Errored modal

Turns out. You must import [MatDialogModule] and required modules in the parent component to show the date time picker in the dialog.


Error during installing ZeroClipboard assets.

Hi there! I tried to use your zeroclipboard library wrapper, and it isn't bad, but I had some errors.
First of all, documentation doesn't have any information about cURL library. AssetsInstallCommand.php file uses Curl\Curl. I installed php-curl-class https://github.com/php-curl-class/php-curl-class. After that I had another problem: when curl response returned, it's not a string, but already array, so you mustn't use json_decode anymore (AssetsInstallCommand.php file, line 110). And the last is - it will be very useful to see simple example how to use it (I had spent some time before everything worked). My little example:
/* Template */

Copy link
/* End template */
/* main.js /
/ Copy to clipboard */
ZeroClipboard.setMoviePath("/bundles/zeroclipboard-assets/ZeroClipboard.swf");
var client = new ZeroClipboard.Client(),
copiedText = $("#my-input").attr('value');
client.setText( copiedText );
/* Listener for succeed copy */
client.addEventListener('complete', function (client, text) {
        alert("Copied text to clipboard." );
    });

client.glue('copy-link');

/* end main.js */
Best wishes, Ruslan

Hi, let me know how you are using ZeroclipboardBundle (wrapper) . Do you installed it by composer or by downloading it?

Yes, you are right. I missed in documentation to talk about Curl library, or to add it in Composer.json.
I am not using https://github.com/php-curl-class/php-curl-class this is why it doesn't work for you. I am using https://github.com/php-mod/curl another curl wrapper.

Yes, I installed it by composer: sudo composer require "symfony-bundle/zeroclipboard-bundle".
Now it's clear to me, thanks

Thank you for this issue, and for your example. I will update the composer.json and the documentation to avoid the same issue for the other users.


Replace 'BQL' by 'MML' in quickstart output

The output of quickstart is returning BQL instead of MML

As I understand it -- though the three-letter acronym 'MML' and other related three-letter acronyms are consistently nebulous --, 'MML' refers only to the little language inside CREATE GENERATOR where you specify a hypothesis space for a generator, and maybe also ANALYZE where you could conceivably specify an inference program except it's currently very limited.

584719c. Nevermind, didn't see Riastradh's response. Rolled back.
Yeah, BQL is pretty well defined. Will leave it for now.


Human Gene Reports show RGD as primary source

Would this be a frontend or backend bug? The web address looks good (HGNC:132), so is it something in the React code?

Ah, it's probably the dataProvider field in metaData from the JSON. I will look and report back shortly.

Yep, OK, so the dataProvider is flagged as RGD, which is technically correct. Perhaps some logic to make this a Human Gene Report when the taxonid is 9606?
  "dataProvider": "RGD"
 "dateProduced": "2017-02-21T15:01:04-06:00"

Yeah, I was just talking to @sierra-moxon about this yesterday. There are probably a collection of little, weird things caused by the fact that the gene record's dataProvider is not one-to-one with species. So, yeah, we could special case it in the front-end code, especially for now. Maybe that's the best we can do, or maybe there's a better back-end solution. Not sure.

A front-end solution would be fantastic, if you could pull if off for the imminent 0.3.0 internal release.
It's an interesting point about dataProvider vs species. Moving forward, there are cases such as UniProt, EMBL, etc which we have as dataProviders but they aren't tied to a single species. It's probably best to go by species id (unless we have cases where multiple species are grouped into a single MOD). That's my humble opinion on the matter.

@christabone I agree. Although we included a "dataProvider" stanza in the JSON, I (at least) regarded this as internal tracking data, and not for display on the website.
For the website, it's more appropriate to have an "authoritative source", probably at the per-species level. And since we are using HGNC id as primary for human genes, HGNC would be the de facto authoritative source for the human gene entries.


Created the help command that lists all available commands

Created the help command.

Requested changes have been made


Param type fix for inspect_all()

inspect_all() simply goes over an iterable param and passes values to inspect() which accepts only PromiseInterface instances.

Looks good! 👍

I just did a quick test. PHPStorm do recognise iterable but it does not understand iterable<PromiseInterface>. But PHPStan/Psalm will find that for users.


Fix: use estimations v2 endpoint for tx nonce

What it solves
Resolves #3190
How this PR fixes it
Uses the estimations endpoint v2 to fetch the next recommended txNonce
A Cancel transaction is used if we are only interested in fetching the recommendedNonce
POST body:
{
    "to": "0xc1e55e565a40BB76686C94E0688be8F00cbE9d60",
    "value": "0",
    "data": "0x",
    "operation": 0
}

Waiting for the safe-react-gateway-sdk to publish a new version.

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

2 of 5 (40.0%)  changed or added relevant lines in 3 files are covered.
1 unchanged line in 1 file lost coverage.
Overall coverage decreased (-0.003%) to 32.378%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

src/routes/safe/container/hooks/useTransactionParameters.ts
1
2
50.0%

src/logic/safe/transactions/gas.ts
0
2
0.0%

Files with Coverage Reduction
New Missed Lines
%

src/routes/safe/container/hooks/useTransactionParameters.ts
1
75.51%

Totals

Change from base Build<PHONE_NUMBER>:
-0.003%

Covered Lines:
3085

Relevant Lines:
8478

💛  - Coveralls

I'll merge this to dev because it's broken after Safe Apps were moved to the SDK. This new version fixes it.


Backdrop style

Is your feature request related to a problem?
Consistency with the search behavior in Starlight base
Describe the solution you'd like
Give 2 options. Current, and blurred backdrop.
Blur with search:

Solid color with image-zoom plugin:

Describe alternatives you've considered
Option to use the blurred backdrop with theme color like in Starlight search menu. Currently it uses a 100% opacity with the base color.
Additional Context
No response

Thanks for your report :raised_hands:
v0.2.0 now includes a new --starlight-image-zoom-backdrop-bg CSS custom property that can be used to customize the backdrop background color.


GPIO12 causes ESP boot issue

Using GPIO12 for the sensing LED interferes with the boot process as it is a strapping pin.
The compilation process also warns about this:

This caused an issue for me where the device would boot only intermittently with GPIO12 connected. When I switched to GPIO13, the issue device booted (and worked) correctly.
I suggest changing the default yaml config file and related documentation to use GPIO13

Seems like a good plan, I have no idea whether GPIO13 is better, but that something needs to be changed, that's one thing for sure.

For me GPIO12 caused the OTA update to fail. I switched to GPIO5 which resolved the issue. It would be good to change the default to something else.

FYI GPIO15 was also a strapping pin on my board. GPIO16 was not, however.


Add fuzzing for parsing based on JSON schema

Use a fuzzing library to generate different JSON input and pass it through the parser. Make sure to use a fixed seed.

Some research shows that this is not so simple as there is no pypi-installable json schema based fuzzer that I could find.


fix test failure due to my own lint

@bors r+

:pushpin: Commit 94cd0ce734db8f760b5a8de877684f917d0a9d90 has been approved by RalfJung

:hourglass: Testing commit 94cd0ce734db8f760b5a8de877684f917d0a9d90 with merge 285a585fd0e2bfd4e2c4b4e2ee95bb14cb1b26ed...

:sunny: Test successful - checks-travis, status-appveyor
Approved by: RalfJung
Pushing 285a585fd0e2bfd4e2c4b4e2ee95bb14cb1b26ed to master...


Add misc Danish wordlists

Proposing adding a couple of lists from my repo danish-wordlists.
These include all legally valid Danish names and last names (Nov 2021), fullform corpus from DDO (The Danish Dictionary), all Danish street and city/town names and a collection of words from the old and new testament in Danish.

Thank you!


fix: Fix expected names for releases

Summary

Use proper names for build artifacts on release workflow
Ticket Link

Checklist

[ ] Added or updated unit tests (required for all new features)
[ ] Has UI changes
[ ] Includes text changes and localization file updates
[ ] Have tested against the 5 core themes to ensure consistency between them.

Device Information
This PR was tested on:
Screenshots

Release Note

Cherry pick is scheduled.


hooks not being called

hots.sh is set up as per template but never executed.
This seems to be because in the config-file from dehydrated, HOOKS is undefined.
When I define the variable, I can see the hook being executed.
Since these hooks are certificate-specific whiel dehydrated does not support that, there is a need for some  translation mechanism - maybe a script that calls the right hook.sh.

The solution would be to add a file config to the cert directory with the content
HOOK=hook.sh

tried it, that works.


add Arabic source named :نادي الروايات

Source name
نادي الروايات
Source link
https://rewayat.club/
Language
Arabic
Other details
No response
Acknowledgements

[X] I have searched the existing issues and this is a new ticket, NOT a duplicate or related to another open issue.
[X] I have written a title with source name.
[X] I have checked that the extension does not already exist by searching the GitHub repository and verified it does not appear in the code base.
[X] I will fill out all of the requested information in this form.

Duplicate of #78


Design Visualisation Style

Designers create a unified visualisation style for how the graphs should look. What labels, ticks, colours should be used for maximum effect.

I will create several (rough)layoust tomorrow. @notconfusing you could tell if you like it or not.

Hi Komal,
As I'm the owner of this task, I'd like if you review them with me first
tomorrow. Please email your rough layouts to<EMAIL_ADDRESS>Thanks,
Frances
On Wed, May 6, 2015 at 9:45 AM, Komal Patel<EMAIL_ADDRESS>wrote:

I will create several (rough)layoust tomorrow. @notconfusing
https://github.com/notconfusing you could tell if you like it or not.
—
Reply to this email directly or view it on GitHub
https://github.com/notconfusing/WIGI/issues/10#issuecomment-99533889.

--
Frances Soong
Visual UX Designer
(908) 635-1534
francessoong.com http://www.francessoong.com/
LinkedIn https://www.linkedin.com/in/francessoong | Twitter
https://www.linkedin.com/in/francessoong

REMINDER: one of the "interactions" we need to design for is socializing the data.

Expecting next set of inputs from Beta release.


Correct handling of offset in fetch & install

cc @bergzand

Ack, full A/B image update works now. Both from A→B and from B→A. Thanks for the quick fix!


Micronaut platform pom file generates duplicate versions of some modules

Issue description
The pom file https://central.sonatype.com/artifact/io.micronaut.platform/micronaut-platform contains entries like this:
...
<micronaut.mongo.version>5.4.0</micronaut.mongo.version>
<micronaut.mongodb.version>5.4.0</micronaut.mongodb.version>
...
<micronaut.oracle.cloud.version>4.2.0</micronaut.oracle.cloud.version>
<micronaut.oraclecloud.version>4.2.0</micronaut.oraclecloud.version>
...
<micronaut.problem.json.version>3.5.0</micronaut.problem.json.version>
<micronaut.problem.version>3.5.0</micronaut.problem.version>
...

This can cause issues when importing micronaut boms since not sure which version will be used by the platform.

@melix could this be caused by the inlining of other BOMs?

Yes, I think it's because of inlining. Ideally such situations shouldn't happen: either one module should be driving the version and the other module should use its catalog, or one module is using the same dependencies but shouldn't manage them. There are actually warnings during the platform generation, but we ignore them. However, it's probably a bug that there are duplicate dependencies, this should issue a warning and no duplication.

It is also in the dependency management block, e.g. for the Kafka versions:
      <dependency>
        <groupId>org.apache.kafka</groupId>
        <artifactId>kafka-clients</artifactId>
        <version>${kafka.compat.version}</version>
      </dependency>
      <dependency>
        <groupId>org.apache.kafka</groupId>
        <artifactId>kafka-clients</artifactId>
        <version>${kafka.version}</version>
      </dependency>

This generates warnings in my build, although I only refer to micronaut-kafka.

I find Kafka deps particularly confusing:
      <dependency>
        <groupId>org.apache.kafka</groupId>
        <artifactId>kafka-streams</artifactId>
        <version>${kafka.version}</version>
      </dependency>
      <dependency>
        <groupId>io.micronaut.kafka</groupId>
        <artifactId>micronaut-kafka</artifactId>
        <version>${micronaut.kafka.version}</version>
      </dependency>
      <dependency>
        <groupId>org.apache.kafka</groupId>
        <artifactId>kafka-clients</artifactId>
        <version>${kafka.compat.version}</version>
      </dependency>
      <dependency>
        <groupId>org.apache.kafka</groupId>
        <artifactId>kafka-clients</artifactId>
        <version>${kafka.version}</version>
      </dependency>
      <dependency>
        <groupId>io.micronaut.kafka</groupId>
        <artifactId>micronaut-kafka-bom</artifactId>
        <version>${micronaut.kafka.version}</version>
      </dependency>
      <dependency>
        <groupId>io.micronaut.kafka</groupId>
        <artifactId>micronaut-kafka-streams</artifactId>
        <version>${micronaut.kafka.version}</version>
      </dependency>

where the properties are defined as
<kafka.compat.version>3.8.0</kafka.compat.version>
<kafka.version>3.7.0</kafka.version>
<micronaut.kafka.version>5.6.0</micronaut.kafka.version>

Here you can see that kafka-clients is mentioned twice, with different versions.

@melix how can we fix this?

There are 2 different problems here. First, in micronaut-kafka, we define:
managed-kafka-compat = "3.7.0"
...
# Duplicated to keep catalog compatibility with 3.4.x.  Can be removed for 4.0.0
managed-kafka = { module = 'org.apache.kafka:kafka-clients', version.ref = 'managed-kafka-compat' }

Fun fact, Micronaut Kafka is already 5.x, so this should have been removed in micronaut-kafka long ago.
Second, this shows that it's possible for an inlined module to conflict with an upstream definition. Currently the BOM generator doesn't capture this, and there's, as far as I can see, no way to workaround. So the easiest for this particular Kafka issue is probably to remove the aliases in Micronaut Kafka, since they were deprecated (and probably document that in major releases we should review the module catalog for deprecation removals).
Then the next step would be to implement some mechanism to detect duplicates in the BOM generator. I have this on my todo list, not sure how complicated it is yet. If such a thing happens, we're not in a good situation though, since basically it means there are 2 properties which can be used to declare a version for a single module, one coming from us, the other from the upstream project, and who knows which takes precedence when order of imported BOMs change.


max_template_date for running Alphafold

Hi,
I am new to this, and trying to set up Alphafold on my server. I tried to run the following command and got an error message
python3 docker/run_docker.py --fasta_paths=../protein_seq/sam_orig.fasta  --preset=reduced_dbs
FATAL Flags parsing error: flag --max_template_date=None: Flag --max_template_date must have a value other than None.
Pass --helpshort or --helpfull to see help on flags.
So, I added the flag but still not able to run: python3 docker/run_docker.py --fasta_paths=../protein_seq/sam_orig.fasta --max_template_date=2021-05-14 --preset=reduced_dbs
I0915 18:02:01.947087<PHONE_NUMBER>14784 run_docker.py:119] Mounting /home/dw524/Documents/protein_seq -> /mnt/fasta_path_0
I0915 18:02:01.947247<PHONE_NUMBER>14784 run_docker.py:119] Mounting /home/dw524/Documents/alphafold/~/dw524/Documents/alphafold/reduced_db/uniref90 -> /mnt/uniref90_database_path
I0915 18:02:01.947338<PHONE_NUMBER>14784 run_docker.py:119] Mounting /home/dw524/Documents/alphafold/~/dw524/Documents/alphafold/reduced_db/mgnify -> /mnt/mgnify_database_path
I0915 18:02:01.947427<PHONE_NUMBER>14784 run_docker.py:119] Mounting /home/dw524/Documents/alphafold/~/dw524/Documents/alphafold/reduced_db/pdb70 -> /mnt/pdb70_database_path
I0915 18:02:01.947496<PHONE_NUMBER>14784 run_docker.py:119] Mounting /home/dw524/Documents/alphafold -> /mnt/data_dir
I0915 18:02:01.947571<PHONE_NUMBER>14784 run_docker.py:119] Mounting /home/dw524/Documents/alphafold/~/dw524/Documents/alphafold/reduced_db/pdb_mmcif -> /mnt/template_mmcif_dir
I0915 18:02:01.947643<PHONE_NUMBER>14784 run_docker.py:119] Mounting /home/dw524/Documents/alphafold/~/dw524/Documents/alphafold/reduced_db/pdb_mmcif -> /mnt/obsolete_pdbs_path
I0915 18:02:01.947713<PHONE_NUMBER>14784 run_docker.py:119] Mounting /home/dw524/Documents/alphafold/~/dw524/Documents/alphafold/reduced_db/small_bfd -> /mnt/small_bfd_database_path
Traceback (most recent call last):
File "/home/dw524/.local/lib/python3.8/site-packages/docker/api/client.py", line 268, in _raise_for_status
response.raise_for_status()
File "/usr/lib/python3/dist-packages/requests/models.py", line 940, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 400 Client Error: Bad Request for url: http+docker://localhost/v1.41/containers/create
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "docker/run_docker.py", line 201, in
app.run(main)
File "/home/dw524/.local/lib/python3.8/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/home/dw524/.local/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
File "docker/run_docker.py", line 173, in main
container = client.containers.run(
File "/home/dw524/.local/lib/python3.8/site-packages/docker/models/containers.py", line 811, in run
container = self.create(image=image, command=command,
File "/home/dw524/.local/lib/python3.8/site-packages/docker/models/containers.py", line 870, in create
resp = self.client.api.create_container(**create_kwargs)
File "/home/dw524/.local/lib/python3.8/site-packages/docker/api/container.py", line 430, in create_container
return self.create_container_from_config(config, name)
File "/home/dw524/.local/lib/python3.8/site-packages/docker/api/container.py", line 441, in create_container_from_config
return self._result(res, True)
File "/home/dw524/.local/lib/python3.8/site-packages/docker/api/client.py", line 274, in _result
self._raise_for_status(response)
File "/home/dw524/.local/lib/python3.8/site-packages/docker/api/client.py", line 270, in _raise_for_status
raise create_api_error_from_http_exception(e)
File "/home/dw524/.local/lib/python3.8/site-packages/docker/errors.py", line 31, in create_api_error_from_http_exception
raise cls(e, response=response, explanation=explanation)
docker.errors.APIError: 400 Client Error for http+docker://localhost/v1.41/containers/create: Bad Request ("invalid mount config for type "bind": bind source path does not exist: /home/dw524/Documents/alphafold/~/dw524/Documents/alphafold/reduced_db/uniref90")
Could anyone help me with this please? I am just using the reduced database, and not sure how I should set the max_template_date. Thanks!

Hi, you are setting the max_template_data correctly and the error is unrelated to that. I believe the problem is with the uniref90 path since the error says:
Bad Request ("invalid mount config for type "bind": bind source path does not exist: /home/dw524/Documents/alphafold/~/dw524/Documents/alphafold/reduced_db/uniref90")

Could you check that directory exists and Docker is able to access it?

Hi, you are setting the max_template_data correctly and the error is unrelated to that. I believe the problem is with the uniref90 path since the error says:
Bad Request ("invalid mount config for type "bind": bind source path does not exist: /home/dw524/Documents/alphafold/~/dw524/Documents/alphafold/reduced_db/uniref90")

Could you check that directory exists and Docker is able to access it?

Ah, ok. I checked the path and uniref90 folder does not exist. I was following the instructions on Github and installed only the reduced dataset. How should I install uniref90? I just tried 'scripts/download_all_data.sh reduced_db/ uniref90', and it does not work. Thank you!

You will have run the following:
scripts/download_uniref90.sh <full path to the directory where you have other databases>

i.e.
scripts/download_uniref90.sh /home/dw524/Documents/alphafold/~/dw524/Documents/alphafold/reduced_db/

Make also sure you have enough space on your disk to download UniRef90 (58 GB unpacked, 29.7 GB when downloaded as tar.gz) – that might have been the reason it failed to download before.


ion-label floating cursor in very odd position

Ionic version:  (check one with "x")
(For Ionic 1.x issues, please use https://github.com/ionic-team/ionic-v1)
[ ] 2.x
[x ] 3.x
[ ] 4.x
I'm submitting a ...  (check one with "x")
[ x] bug report
[ ] feature request
Current behavior:
When using  in the most vanilla way with ios 11 on Iphone 6 the cursor when the keyboard appears is a bad location.  This did not appear in ios 10.

Expected behavior:
Expect see cursor inline with inserted text.
Related code:

<ion-item>
  <ion-label floating>Username</ion-label>
  <ion-input type="text"></ion-input>
</ion-item>

<ion-item>
  <ion-label floating>Password</ion-label>
  <ion-input type="password"></ion-input>
</ion-item>

Ionic info:

cli packages: (/Users/pbrack/.nvm/versions/node/v8.5.0/lib/node_modules)

    @ionic/cli-utils  : 1.12.0
    ionic (Ionic CLI) : 3.12.0

global packages:

    cordova (Cordova CLI) : 7.0.1

local packages:

    @ionic/app-scripts : 2.1.4
    Cordova Platforms  : ios 4.4.0
    Ionic Framework    : ionic-angular 3.6.1

System:

    ios-deploy : 1.9.2
    ios-sim    : 5.0.8
    Node       : v8.5.0
    npm        : 5.3.0
    OS         : macOS Sierra
    Xcode      : Xcode 9.0 Build version 9A235

Misc:

    backend : legacy

github sample project uploaded.  ionic cordova build ios and run on device will mainfest issue.  FYI this is simply the blank starter project using the prescribed floating label example.

+1. Issue seems to have popped up after upgrading to iOS 11.

I cannot duplicate this with your sample project. I tried on an iPhone 7 running iOS 11 and on an iPhone 6 simulator also running iOS 11.

You know what...  In playing with my sample this afternoon, it appears to only happen sometimes when I click on the label itself.  Never seems to happen if I click toward the right of the screen.

I took my app where I discovered this initially and remove the viewport-fit=cover in the meta tag for my index.html.
<meta name="viewport"         content="width=device-width, initial-scale=1.0, minimum-scale=1.0, maximum-scale=1.0, user-scalable=no">
After this change the cursor shows up in the correct place when I interact with the inputs and the keyboard.
However it did something weird to the status bar.

I fixed my issue.  with the following-

ionic cordova plugin add cordova-plugin-ionic-webview --save
ionic cordova platform update ios
rm -rf ./plugins
ionic cordova prepare
ionic cordova build ios

for some reason before when I installed the cordova-plugin-ionic-webview it wasn't saved.


feat: purity computer

Summary of Changes
Add a new service that infers whether a call or callable is pure or has side effects.

@WinPlay02 services.purity.PurityComputer adds the methods you need to implement the remainder of #542. Let me know if something is missing.

:tada: This PR is included in version 0.4.0 :tada:
The release is available on:

npm package (@latest dist-tag)
npm package (@latest dist-tag)
v0.4.0
GitHub release

Your semantic-release bot :package::rocket:


Prevent redeferral of FunctionBody's that are being processed when GC happens.

Fix a class of bugs involving redeferral of functions that are being accessed by some runtime method that allocates memory, triggering GC and possibly redeferral. When a GC that will result in redeferral scans the stack, mark any FunctionBody's we find as having active references. Do this by for now adding a method to FinalizableObject and overriding it in FunctionBody. We'll replace this with a new object info bit if and when bits become available.

@curtisman , @rajatd
Thanks.

LGTM. You can also get rid of the AutoDisableRedeferral class and its objects, or defer it until we are certain of stability of this change, upto you.


An error occurs when IE11 is running  vue2+cli-service5

I want to know if this plugin supports IE11?

Hi @shihaohaoshiwo,
Can you confirm that this is issue is IE11 specific (i.e. not reproducible in other browsers)? If so, could you try logging loading-failed and rendering-failed?

Hi @shihaohaoshiwo,
Feel free to reopen the issue with more details. Answering your previous question, this library supports IE11 in versions 1.x when used with Vue 2.


Splash screen is missing on Android

I am not seeing a splash screen on Android. It shows a blank, purple screen.
Note: I do see a splash screen on iOS

@dharding We're aware of this. I've been sent the following link: https://android.jlelse.eu/the-complete-android-splash-screen-guide-c7db82bce565, but we have yet to choose and implement a solution.
Things to figure out: how do we want to approach it? Is it worth it at this point the time investment against other issues (given it might be a lengthier task... for me at least :)  )

Since https://github.com/project-vagabond/covid-green-app/pull/152 we show this during app load on Android:

It's technically not a splash screen and there is a second or so of flat purple before the branding overlays, but as a long time Android user I'd say this is within ordinary user expectations. All sorts of apps, from the built-in Samsung phone and messages apps to Facebook Messenger on my Note 8 show a second of flat colour initially on loading up from being closed just like this.
Just going through apps now, the only ones I can find that don't start up with a second of flat colour before showing their own branding or initial screen are Google's own in built apps (which generally show an enlarged app icon overlaid over a flat colour initially).

FYI. Today, on Lenovo P2. I see a flat purple screen for 1 s. then the screen above from Alan loads then the page loads.

I believe this can be closed in favor of https://github.com/project-vagabond/covid-green-app/issues/141
@dharding pls confirm.


Testcafe hangs if global eval function is overriden

I want to use testcafe in an electron app and managed to configure it so that it loads the start page of the app.
When I now try to run a simple test I see the loading of the fixture but then nothing happens...
No error, the app just stays loaded. (see log attached)
If I remove the script which loads the bundled code of the react app the tests run through, the results are shown and the app is closed again. (see log attached)
These are my tests: https://github.com/deltachat/deltachat-desktop/blob/testcafe/test/testcafe/test.js
This is the test page: https://github.com/deltachat/deltachat-desktop/blob/testcafe/static/test.html
I added a clientScript which is correct loaded once the app is ready.
Is there anything special to consider if testing an electron/react app ?
For tests or reproducing the problem: https://github.com/deltachat/deltachat-desktop/pull/1363
test-hangs-log.txt
without-react-log.txt

The solution (hammerhead.nativeMethods.eval(fnCode)) suggested previously will not work if ClientFunction has dependencies.
Our code uses eval in local scope (local function arguments available in eval context). If we change the code to  hammerhead.nativeMethods.eval(fnCode) the eval scope becomes global.