Several GP Tools requiring Spatial Analyst failing on Pro 2.1

Find Local Peaks and Line Of Sight are failing on Pro 2.1
Tested on Pro 2.1.10044

ERROR: 2017-11-10 09:16:45,744 ERRORS ==================================================
ERROR: 2017-11-10 09:16:45,746 test_findLocalPeaks (visibility_tests.VisibilityUtilitiesTestCase.VisibilityUtilitiesTestCase)
ERROR: 2017-11-10 09:16:45,747 Traceback (most recent call last):
ERROR: 2017-11-10 09:16:45,748   File "C:\Users\chri0020\Documents\Github\military-tools-geoprocessing-toolbox-csm\utils\test\visibility_tests\VisibilityUtilitiesTestCase.py", line 360, in test_findLocalPeaks
ERROR: 2017-11-10 09:16:45,748     self.assertTrue(arcpy.Exists(resultPoints), "Output features do not exist or were not created")
ERROR: 2017-11-10 09:16:45,749   File "C:\Program Files\ArcGIS\Pro\Resources\ArcPy\arcpy\__init__.py", line 836, in Exists
ERROR: 2017-11-10 09:16:45,751     return gp.exists(dataset)
ERROR: 2017-11-10 09:16:45,755   File "C:\Program Files\ArcGIS\Pro\Resources\ArcPy\arcpy\geoprocessing\_base.py", line 303, in exists
ERROR: 2017-11-10 09:16:45,756     self._gp.Exists(*gp_fixargs(args, True)))
ERROR: 2017-11-10 09:16:45,756 AttributeError: Object: Error in parsing arguments for Exists
ERROR: 2017-11-10 09:16:45,757 test_find_local_peaks (visibility_tests.FindLocalPeaksTestCase.FindLocalPeaksTestCase)
ERROR: 2017-11-10 09:16:45,758 Traceback (most recent call last):
ERROR: 2017-11-10 09:16:45,758   File "C:\Users\chri0020\Documents\Github\military-tools-geoprocessing-toolbox-csm\utils\test\visibility_tests\FindLocalPeaksTestCase.py", line 92, in test_find_local_peaks
ERROR: 2017-11-10 09:16:45,759     arcpy.FindLocalPeaks_mt(self.inputArea, 10, self.inputSurface, self.outputPoints)
ERROR: 2017-11-10 09:16:45,760   File "C:\Users\chri0020\Documents\Github\military-tools-geoprocessing-toolbox-csm\toolboxes\Military_Tools_pro.tbx", line 644, in FindLocalPeaks
ERROR: 2017-11-10 09:16:45,760     8M/Aev8Axf8AGM3xS+Jc39oajd7TZWbRlIY4lJMaRxkny4U3HYmSSSzsWZmZvoSkVQqhVGAOABS1
ERROR: 2017-11-10 09:16:45,761   File "C:\Users\chri0020\Documents\Github\military-tools-geoprocessing-toolbox-csm\toolboxes\Military_Tools_pro.tbx", line 641, in FindLocalPeaks
ERROR: 2017-11-10 09:16:45,762     UUAFFFFABRRRQAV5t+0B8ctK/Z/+H0niTUbSfUrmadbHTtOgypurpkd0RpMERJtjdmdgcKh2h3Ko
ERROR: 2017-11-10 09:16:45,762   File "C:\Program Files\ArcGIS\Pro\Resources\ArcPy\arcpy\geoprocessing\_base.py", line 506, in <lambda>
ERROR: 2017-11-10 09:16:45,763     return lambda *args: val(*gp_fixargs(args, True))
ERROR: 2017-11-10 09:16:45,764 arcgisscripting.ExecuteError: Start Time: Friday, November 10, 2017 9:13:13 AM
ERROR: 2017-11-10 09:16:45,768 Failed to execute. Parameters are not valid.
ERROR: 2017-11-10 09:16:45,768 ERROR 000824: The tool is not licensed.
ERROR: 2017-11-10 09:16:45,769 Failed to execute (FeatureToPoint).
ERROR: 2017-11-10 09:16:45,770 Failed at Friday, November 10, 2017 9:13:13 AM (Elapsed Time: 0.00 seconds)
ERROR: 2017-11-10 09:16:45,770 Failed to execute (FindLocalPeaks).
ERROR: 2017-11-10 09:16:45,771 test_linear_line_of_sight (visibility_tests.LinearLineOfSightTestCase.LinearLineOfSightTestCase)
ERROR: 2017-11-10 09:16:45,772 Traceback (most recent call last):
ERROR: 2017-11-10 09:16:45,772   File "C:\Users\chri0020\Documents\Github\military-tools-geoprocessing-toolbox-csm\utils\test\visibility_tests\LinearLineOfSightTestCase.py", line 113, in test_linear_line_of_sight
ERROR: 2017-11-10 09:16:45,773     self.outputTargets)
ERROR: 2017-11-10 09:16:45,773   File "C:\Users\chri0020\Documents\Github\military-tools-geoprocessing-toolbox-csm\toolboxes\Military_Tools_pro.tbx", line 722, in LinearLineOfSight
ERROR: 2017-11-10 09:16:45,775     7MpNSV0FFFFSMKKKKACs3V/DWla8m3UdOt7wdMyxgkfQ9RWlRTUnF3Qmk9Geaan8BdDlm+0aVc3m
ERROR: 2017-11-10 09:16:45,776   File "C:\Users\chri0020\Documents\Github\military-tools-geoprocessing-toolbox-csm\toolboxes\Military_Tools_pro.tbx", line 719, in LinearLineOfSight
ERROR: 2017-11-10 09:16:45,781     3g/miH8zntXTWdnBp9rHb20SQQRjakcYwqj2FS0USlzaLRBGNtXuFFFFZlhRRRQAUUUUARXlpDf2
ERROR: 2017-11-10 09:16:45,782   File "C:\Program Files\ArcGIS\Pro\Resources\ArcPy\arcpy\geoprocessing\_base.py", line 506, in <lambda>
ERROR: 2017-11-10 09:16:45,783     return lambda *args: val(*gp_fixargs(args, True))
ERROR: 2017-11-10 09:16:45,784 arcgisscripting.ExecuteError: Start Time: Friday, November 10, 2017 9:15:00 AM
ERROR: 2017-11-10 09:16:45,785 Failed to execute. Parameters are not valid.
ERROR: 2017-11-10 09:16:45,786 ERROR 000824: The tool is not licensed.
ERROR: 2017-11-10 09:16:45,787 Failed to execute (FeatureVerticesToPoints).
ERROR: 2017-11-10 09:16:45,788 Failed at Friday, November 10, 2017 9:15:00 AM (Elapsed Time: 0.00 seconds)
ERROR: 2017-11-10 09:16:45,792 Failed to execute (LinearLineOfSight).
INFO: 2017-11-10 09:16:45,793 END OF TEST =========================================

@csmoore can you dig into this more and give an explanation for the failure/errors?

I do see the problem here at Pro 2.1, the raster outputs of the Spatial Analyst calls no longer have the attribute tables built - so the next step ("CountRows") fails..
Since every other version of the product until Pro 2.1 (ArcMap, < Pro 2.1) did do this - this may be an issue we should report - and not intended behavior.
If we can't fix this in Pro 2.1, we will have to call "Build Attribute Table" GP Tool separately. Ex:
Add: if Pro version >= 2.1 gp.BuildRasterAttributeTable calls to any SA-dependent tools that require an attribute table.
FYI: @BobBooth @mfunk @adgiles - just in case I am missing anything

This is still an issue as of 2.1.10195

Just a cursory glance at this issue now...
So the ERROR 000824: The tool is not licensed. was not an error in the recent builds?
W.r.t the raster attribute tables, if that is the problem you should not have any issue adding BuildRasterAttribute table as it was supported back at 10.3 and probably earlier. Also the "OVERWRITE" option should be in all caps for backwards support for Desktop. The framework used to be really picky about stuff like this. Not sure if Pro will accept any form of it or not. Just a thought.


Create a repository and grant admin access to ak/devs team

Created new repo and added aramakuni/devs team as admin.


Adds support for expanding templates before rules check

Signed-off-by: Harkishen Singh<EMAIL_ADDRESS>Fixes: #6467

Explanatory gif:

Output before the patch:
Checking test.yml
  FAILED:
../../test.yml: yaml: line 11: could not find expected ':'

test.yml
groups:
    - name: test
      rules:
      - alert: Test Alert
        expr:  up == 0
        annotations:
          description: This is a test alert that should always fire
        labels:
          severity: warning
        {{define "test-macro"}}
            expr:  time() > {{.arg0}}
        {{end}}

@Harkishen-Singh I think there was some misunderstanding unfortunately - this looks like it's adding templating functionality to the top-level file, before YAML is even parsed. The creator of the linked issue https://github.com/prometheus/prometheus/issues/6467 apparently assumed that this was functionality that was supposed to work and that we want to have, but so far we've decided pretty explicitly against having general templating functionality in the top-level of the YAML. And for the specific fields where templating is supported, we already check the template parsing when the file is loaded. So I believe there is nothing to actually do there, as indicated by https://github.com/prometheus/prometheus/issues/6467#issuecomment-589329945.

Ah indeed, this is not something that should work.

@juliusv @brian-brazil I get your point. Thank you for explaining the issue. Can we close the issue if it points to something we do not need?

I have closed it. Thanks however to look into it. Sorry you did not see my comment in time.


Support default custom output path

pull request for #817

updated test, init, new commands to support --output-path
added build and serve command
new, init, build, serve, test, deploy commands support default output path value from angular-cli.json
removed test and deploy commands hard-coded output path value

@filipesilva @hansl
for build, test, serve commands unit testing them doesn't feel appropriate due to having to have a proper project initialised to test and will slow down the acceptance tests a lot I think. I can do it as e2e tests, would prefer me to add it to the existing basic workflow e2e or create new e2e tests?

Heya @JonCubed, we ended up implementing this in other PRs. I'm sorry we didn't take yours in, but thank you for the work you put into it.

@filipesilva no worries


Unable to reset the Rancher admin password

Could you please tell me how we can change the Rancher password in Elemental OS?

You don't. 😉
Elemental is not supposed to make changes to the configuration of a deployed node.
Instead, you change (the root password in) the machineRegistry and redeploy.

Link to rancher docs: https://ranchermanager.docs.rancher.com/faq/technical-items#how-can-i-reset-the-administrator-password
Nothing to do with Elemental OS as we dont install rancher ourselves :)

@Itxaka I already tried with this link, but it's reset the password and provided a random one. I want to change it with some specific one.
I'm using an Elemental airgap OS and Rancher is pre-installed & have an admin.yaml file which store the password in encrypted form, and this is the same password which I'm using for the login. I guess if we change the password in this file it'll work. But I don't know which Encryption algorithm it is using. I tried few but no luck.
File - /usr/local/.state/var-lib-rancher.bind/k3s/server/manifests/iqem/rancher-settings/admin.yaml
---
apiVersion: management.cattle.io/v3
kind: User
metadata:
  name: admin
  labels:
    created-by: test
    authz.management.cattle.io/bootstrapping: admin-user
username: admin
password: "$2a$12$.DyyasORiWTxwooS2oNUX.kEchlw99v/2EsW.v1.A0.z.XQ1HEx/K"
displayName: "Default Admin"
mustChangePassword: false
enabled: true

It would be great if you could tell me which Encryption algorithm it's using?

@Itxaka I already tried with this link, but it's reset the password and provided a random one. I want to change it with some specific one.
I'm using an Elemental airgap OS and Rancher is pre-installed & have an admin.yaml file which store the password in encrypted form, and this is the same password which I'm using for the login. I guess if we change the password in this file it'll work. But I don't know which Encryption algorithm it is using. I tried few but no luck.
File - /usr/local/.state/var-lib-rancher.bind/k3s/server/manifests/iqem/rancher-settings/admin.yaml
---
apiVersion: management.cattle.io/v3
kind: User
metadata:
  name: admin
  labels:
    created-by: test
    authz.management.cattle.io/bootstrapping: admin-user
username: admin
password: "$2a$12$.DyyasORiWTxwooS2oNUX.kEchlw99v/2EsW.v1.A0.z.XQ1HEx/K"
displayName: "Default Admin"
mustChangePassword: false
enabled: true

It would be great if you could tell me which Encryption algorithm it's using?

I think you are mistaken here. This is elemental OS, your question is related to rancher. I gave you a link to the rancher docs as I had it handy but ultimately you need to go through the rancher channels for rancher related questions.

Okay, Thanks. Let me check with them.


Run some integration tests on a private network RPC during CI

Some CLI scripts like deploy/__main__.py or utils/mint_tokens.py are better tested on RPC on an Ethereum client running on a private network.  This issue keeps track of setting up such an environment.
Currently, many tests run on Web3 instances that uses EthereumTesterProvider.
Alternatively, if we can see the RPC endpoint from an Web3 instance, that might also work.  Or, if EthereumTestProvider exposes an RPC endpoint, that might also work.

https://web3py.readthedocs.io/en/stable/providers.html#web3.providers.eth_tester.TestRPCProvider

This provider will be slower than the EthereumTesterProvider since it uses an HTTP server for RPC interactions with.

https://pypi.org/project/eth-tester-rpc/ might be useful.


Disambiguate call to LinalgTransformationFilter constructor.

This should fix the build failure reported at https://github.com/google/iree/pull/7662#discussion_r761391994
(Logs: https://buildkite.com/iree/iree-build-configurations/builds/1496#91c054cd-df7a-4758-84bd-91a621668581)

Nice, thanks Scott!


Fixes docker issues

This upgrades docker to v20.10.7, fixes an issue that prevented pulling images and adds support for building image from Dockerfile on demand.
This upgrades docker, requiring that a few of our uses had to change accordingly due to API changes in docker's SDK.
This also adds support for building a new image if the requested image isn't locally available and cannot be pulled from docker.io.
Also fixes pulling images from docker that was previously broken, probably due to changes in docker's SDK.
Also upgrades uber/zap to v1.17 and adds support for logger in the docker client and provides a new log.Zap function to create quickfeed-specific logger.
Fixes #400.
Fixes #287.

Note to self: docker.go:Run() method is now quite long (106 lines). Break into smaller pieces and add more tests.


Quick manual inspection of the tracks

Figure out (roughly) how often these things happen:

false negatives (aka missing detections)
false positive (aka something is tracked but it's not a crab)
how often (roughly) do we have ID switches/swaps (a crab swaps ID with another crab)?
how often a crab is re-IDed (a fresh ID)?
are there many short tracks? how many of them are actually crabs?
how many crabs could we interpolate the trajectories of?

Potentially plotting the trajectories of the bboxes is useful.

Consider Sanna's comments from labelling (see #132) and try to check how we could programmatically improve the tracks before/after manual labelling

Have a quick look and have some plot to shows some of the point, but need further investigation based on Sanna  feedback as well


Question: possible false positive for sol.sfc.keio.ac.jp?

Hi, seems like there may be a false positive for sol.sfc.keio.ac.jp.  It's being flagged as CNAME cloaking for Adobe Experience Cloud according to:
https://github.com/AdguardTeam/cname-trackers/blob/39cd5f7250ea99bb537973c229bcca598437a617/trackers/adobe-experience-cloud-(formerly-omniture).json#L4177
However, the site is a set of A/AAAA records that both resolve to IP addresses.  (The site itself is a learning management system in use at my university hosted on Canvas LMS, which as far as I know doesn't use any internal tracking either).

Definitely a false positive.
We've got some yesterday, the situation should normalize when we rebuild the list.

Great, thanks for the quick clarification!


Blank screens on Safari

Problem
The extension KV store, ExtensionKVStore, is causing a full app crash (blank screen) on Safari (mobile and desktop).
TypeError: undefined is not an object (evaluating 'browser.storage.local')
extension.ts:
import { BaseKVStore } from "./base";
import { KVStoreProvider } from "./interface";

const ExtensionKVStoreProvider: KVStoreProvider = {
  get:
    typeof browser !== "undefined" <=====err
      ? browser.storage.local.get
      : (undefined as any),
  set:
    typeof browser !== "undefined" <=====err
      ? browser.storage.local.set
      : (undefined as any),
};

export class ExtensionKVStore extends BaseKVStore {
  constructor(prefix: string) {
    super(ExtensionKVStoreProvider, prefix);
  }
}

This seems to have recently surfaced, as I remember accessing the app from Safari on mobile and desktop not too long ago. Interestingly, it still works in the embedded Keplr wallet browser (WebKit). This affects deployments from frontier, master, and refactor.
Proposed Solution
From my brief investigation, it appears some extension-only KV logic is running in the web apps. The check for browser functions as expected on Chrome where browser is undefined, however on Safari browser is defined yet has no member storage. We should add an additional check at this level, or at a higher level prevent any ExtensionKV logic from running within the window.

The browser is used as a polyfill to support both chromium and firefox. (Nevertheless, firefox is not supported.) I thought that there would be no browser in safari, but it seems to exist regardless of extension api. This is a problem on @keplr-wallet/* libraries. We will fix it in the next version.

Closing due to bug in Keplr

https://github.com/chainapsis/keplr-wallet/issues/378
Keplr tracks & fixes here ^


Make sure we have action mailer set up for https

This is where plum does it. https://github.com/pulibrary/plum/blob/AT11/config/environments/staging.rb

Added options to application.rb using config parameters from scholarsphere.yml


Xamarin Forms - gaps between tiles when rotating map

Mapsui Version 4.0
Mapsui Platform Android (monodroid10)
Device Various phones and tablets. (Google Pixel 3a/6a, Samsung S10/S2x, Samsung Galaxy Tab A6, A8 and others)
Describe the bug
When the map is zoomed to circa zoom level 18, the map tiles have a noticeable grid effect when rotated. This seems to happen with OSM, but also other map tile providers.
To Reproduce
Steps to reproduce the behavior:

Create a mobile app with a map
Set the map provider to be OSM (or any other online tile provider of XYZ tiles)
Zoom the map to the maximum zoom level
rotate the map (this currently only works in one direction due to other bugs in 4.0)

Your map will now have gaps between the tiles. These seem to lessen and often vanish when the map is rotated back to north.
Expected behavior
A clear and concise description of what you expected to happen.
The map should cleanly rotate and the map tiles should not have spaces between them. The spaces are actually offsetting the geographical points and skewing the map rendering.
Screenshots
If applicable, add screenshots to help explain your problem.

Additional context
Add any other context about the problem here.

I'm experiencing this too. Would be great to see if this can get fixed.

Thanks for you clear bug report. It was easy to reproduce it on WPF, rotate and zoom maximally. I've seen this before in other situations and often choose to ignore it but this is more noticeable.

A PR was created an merged. This should be fixed in 4.1.0


Using Sortable.js Options

More of a question than an issue...
Is there a way to utilise Sortable.js' options? Would be nice to add some animations or similar to the draggable states.

@cjmellor I made PR for u.
https://github.com/nextapps-be/livewire-sortablejs/pull/11/files
CDN:


BUG-Text Visual Element does not support break lines

Description
I can not find a way to break lines in a text visual element
I expected one of those two to work:
<|{"a\nb"}|text|>
<|{"a
b"}|text|>
But unfortunately, it just shows
 as text and ignores and hides \n
Expected behavior
\n should break lines in a text visual element
Runtime environment

OS: Windows 11
Browser: Chrome

DUplicate for taipy-Gui #420

I don't think this should be closed. Text visual element still does not support break lines

it should be closed
mode=pre


ring: Append Ketama nodes, not panic on small rings

The Ketama hash may not assign points to servers that are particularly
small compared to the total storage. This makes some sense -- they can't
cover much. However, this causes errors, and we need to return a full
permutation, so simply append the small ones as "overflow". Fixes #246.
Rings can also declare their replication factor as being higher than the
number of nodes they contain. This causes panics. Raise a warning when
such a ring is detected, but continue operation. Fixes #219.

Merging Sua Sponte


.NET Core SDK for Windows installer doesn't honor custom location

Download and run DotNetCore.1.0.0.RC2-SDK.Preview1-x64.exe
Click options and enter the path for e.g. c:.NetCoreSDK-1.0.0-RC2
Click Install and installer will put files under c:\program files\dotnet and NOT in c:.NetCoreSDK-1.0.0-RC2

@zorbasolutions does this repro with the RTM installers you can download from https://dot.net/core?

Yes, same results. From the page you sent me, I downloaded https://go.microsoft.com/fwlink/?LinkID=809122 which is version Preview 2. I clicked on options and changed the directory to C:\mydotnet
Installer ran just fine but after install is complete my c:\mydotnet is still Empty.
Thanks,
On Thu, 14 Jul 2016 18:58:43 -0700
Zlatko Knezevic<EMAIL_ADDRESS>wrote:

@zorbasolutions does this repro with the RTM installers you can download from https://dot.net/core?

You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub:
https://github.com/dotnet/core/issues/118#issuecomment-232841446

I remember seeing this issue reported before and the answer was that custom paths would be disabled in the future but can't remember where I saw this. @ericstj do you know anything about this?

Just use the ZIP if you want this.  https://github.com/dotnet/cli/issues/3568

Fine, Zip can work but please remove the option from the installer msi. It is confusing to any user if it doesn't work.
On Fri, 15 Jul 2016 07:57:45 -0700
Eric StJohn<EMAIL_ADDRESS>wrote:

Just use the ZIP if you want this.  https://github.com/dotnet/cli/issues/3568

You are receiving this because you were mentioned.
Reply to this email directly or view it on GitHub:
https://github.com/dotnet/core/issues/118#issuecomment-232974742

Yep, I believe the linked issue is tracking the removal.

Closing this issue as its tracked in the repo where the fix needs to be.


Hint: you might have seenlazy being used when configuring styles in the angular.json. It has been deprecated in favor of inject however, as the latter better expresses the actual meaning.

Source:
https://juristr.com/blog/2019/08/dynamically-load-css-angular-cli/

Angular docs about inject:
https://angular.io/guide/workspace-config#styles-and-scripts-configuration


Unable to clear MagicCodeInput

If you haven’t already, check out our contributing guidelines for onboarding and email<EMAIL_ADDRESS>to request to join our Slack channel!

Action Performed:

Open signin page
write email and continue
type some numbers om
try to clear the input by clicking the x on keyboard

Expected Result:
The input will be cleared step by step
Actual Result:
the input is not cleared
Workaround:
Can the user still use Expensify without this being fixed? Have you informed them of the workaround?
Platforms:

Which of our officially supported platforms is this issue occurring on?

[ ] Android / native
[x] Android / Chrome
[ ] iOS / native
[ ] iOS / Safari
[ ] MacOS / Chrome / Safari
[ ] MacOS / Desktop

Version Number:
Reproducible in staging?: needs reproduction
Reproducible in production?: needs reproduction
If this was caught during regression testing, add the test name, ID and link from TestRail:
Email or phone of affected tester (no customers):
Logs: https://stackoverflow.com/c/expensify/questions/4856
Notes/Photos/Videos: Any additional supporting documentation
https://github.com/Expensify/App/assets/43996225/9fbc25cf-8c9c-43a7-8937-aa3eddf98d79
Expensify/Expensify Issue URL:
Issue reported by: @getusha
Slack conversation: https://expensify.slack.com/archives/C049HHMV9SM/p1686598483616689
View all open jobs on GitHub

I've run into this issue as well on Chrome/Android, but only when not using the default keyboard.

Can someone test on real device ? I think I saw a comment in the code about a keyboard probelm on emulators

Thanks @ShogunFire, I can't replicate on an actual android.
https://github.com/Expensify/App/assets/42940078/d496c274-aaf7-48e8-a40c-dee2023662b1


filterLanguagesByRules prevents correct language to be detected

As far as I can see, filterLanguagesByRules in LanguageDetector is used to narrow down the search space of candidate languages. It tries to find "typical" characters found only in certain languages, e.g. the character "ö" in ESTONIAN, FINNISH, GERMAN, HUNGARIAN, ICELANDIC, SWEDISH, TURKISH. However, given large English text containing only one such character makes it impossible to correctly detect the languages's text.
Is this the expected behaviour?
Thanks

Hi @rotzbouw, thank you for evaluating my library. Can you please give me a concrete example where language detection fails for you? Then I can help you better.
Also, please check out the current development branch v0.6.0-dev and try your input with that version. It may be that your problems are fixed there already. Unfortunately, I do not have much free time at the moment to finish this version. It still takes a little while.

I'm using the latest release and I don't see changes in the relevant classes and methods. Anyway, here's a minimal example illustrating the problem:
        LanguageDetector languageDetector = LanguageDetectorBuilder.fromAllBuiltInLanguages().build();
        String language = languageDetector.detectLanguageOf("Über (German pronunciation: [ˈyːbɐ] (About this soundlisten), sometimes written uber /ˈuːbər/[1] in English-language publications) is a German language word meaning \"over\", \"above\" or \"across\".").getIsoCode();

        assertThat(language).isEqualTo("en");

This test fails due to the diacritic in 'Über' excluding english as candidate language.
Let me know if you need more info.
Cheers

@rotzbouw Sorry for the late response. You are right with everything you said. There is a bug in the algorithm of filterLanguagesByRules that prevents the correct language to be detected. The problem is that the umlaut is in the first word of the input string. If it occurs later in the string instead, English is returned as the correct language.
I'm labeling this issue as a bug now and I'm going to fix it soon. Thank you for letting me know about this.

Hi @rotzbouw, with the last commit I applied some changes to the algorithm that filters the languages. Your problems with sentences like the one above should be gone now. I was able to slightly improve the overall sentence detection accuracy as well. Can you please try again and verify my statement? Thank you.

Hi @pemistahl, yes, that works, thanks a lot!


change license to MIT instead of it showing both BSD and GPL

the project showed BSD license on Pip and GPL on github, switching both to MIT.

Can you comment your approval of this PR and license change @hansen-m ?

License change has my approval. Thank you for continuing to support this project @jgstew.


Add support branch for 4.2.1 Irrigation code

@bartnijssen  has asked that we add a support branch for @hydrotian's VIC 4.2.1 Irrigation work (https://github.com/hydrotian/VIC_4.2.1_irrigation).  We have a few questions to answer before we can create the branch.

The irrigation code is not on a branch that came from the main git repository (only 2 commits in history). So, do we want to maintain the history or should I just copy the code over to an empty branch?
Was the original root of this repository actually 4.2.1 or did @hydrotian just copy over some pieces of the 4.2.1 repo? This is important for describing what the support branch really is.

For question 2. My impression is that the original root of this repository was VIC 4.2. Ted Bohn and Ingjerd Haddeland incorporated the irrigation scheme into the model and named it 4.2.1.

All I know about this is that I sent my private code (based on 4.2) to
Ingjerd, who might have used some portion of my irrigation code in her
version (but I would not blame her if she didn't use my irrigation code -
it was pretty messy).  But presumably the branch point would be 4.2.
Ted
On Wed, Oct 14, 2015 at 10:29 PM, Tian Zhou<EMAIL_ADDRESS>wrote:

For question 2. My impression is that the original root of this repository
was VIC 4.2. Ted Bohn and Ingjerd Haddeland incorporated the irrigation
scheme into the model and named it 4.2.1.
—
Reply to this email directly or view it on GitHub
https://github.com/UW-Hydro/VIC/issues/300#issuecomment-148285826.

Okay, but the directory and file structure in https://github.com/hydrotian/VIC_4.2.1_irrigation looks nothing like 4.2 so I'm not sure how to proceed.

@Tbohn: Was there a specific reason to send your private version of the code? We are using git to establish a trail for source code modifications. It's an important step in ensuring reproducibility and thus a part of the scientific process. Sending people your private version of the code subverts this and is something I frankly find extremely frustrating.
@hydrotian and @tbohn : Please sort out between the two of you what the provenance of this code is. This is not for @jhamman or me to sort out. And PLEASE start using git the way it is supposed to. Your shortcuts are simply creating more work for others and I think it is a dangerous path to be on if you want to publish papers.

@hydrotian: This is not optional. This code needs to be as a support branch on our github repo since it has been used as part of a paper. In the future I will no longer allow people in my group to submit a manuscript unless their code is under version control on our github site.

@hydrotian: I just looked at your repo. The readme and the way you just plopped this into github as a "first commit" are wholly inadequate. Please take this serious, this is not a joke.

I think I should clarify: I only gave my code to Ingjerd to show her what
I'd done, in case she wanted to use anything I'd written.  I was not part
of Ingjerd and Tian's project and I was not directly involved in their code
development.  It's their business how they present their code for inclusion
in the repo.
Ted
On Thu, Oct 15, 2015 at 8:39 AM, Bart Nijssen<EMAIL_ADDRESS>wrote:

@hydrotian https://github.com/hydrotian: I just looked at your repo.
The readme and the way you just plopped this into github as a "first
commit" are wholly inadequate. Please take this serious, this is not a joke.
—
Reply to this email directly or view it on GitHub
https://github.com/UW-Hydro/VIC/issues/300#issuecomment-148427074.

@tbohn: Did you point her to your github repo or did you email her a tar file of code (or point her to your directory on disk)?
@hydrotian: Please figure out with Ingjerd where your code comes from. This needs to happen now as we may need to correct the proofs of the paper with regards to the model version.

I created my private code outside of git.  I believe I sent her a tar file.
Now that I know better, I will use git for these purposes in the future.
Sorry if this has caused any problems.
Ted
On Thu, Oct 15, 2015 at 9:50 AM, Bart Nijssen<EMAIL_ADDRESS>wrote:

@tbohn https://github.com/tbohn: Did you point her to your github repo
or did you email her a tar file of code (or point her to your directory on
disk)?
@hydrotian https://github.com/hydrotian: Please figure out with Ingjerd
where your code comes from. This needs to happen now as we may need to
correct the proofs of the paper with regards to the model version.
—
Reply to this email directly or view it on GitHub
https://github.com/UW-Hydro/VIC/issues/300#issuecomment-148452757.

So please provide Tian with the provenance of your code: At what point did you split off from what version?

Hi all,
The code I handed to Ingjerd and Tian was based on 4.1.2.k.  However, this
code included the veg_hist code that I later ported to 4.2.  So, it is
somewhat intermediate between 4.1.2.k and 4.2.
I apologize for any confusion this might have caused.  From now on, I will
use GIT to develop and share code.
Regards,
Ted
On Thu, Oct 15, 2015 at 10:01 AM, Bart Nijssen<EMAIL_ADDRESS>wrote:

So please provide Tian with the provenance of your code: At what point did
you split off from what version?
—
Reply to this email directly or view it on GitHub
https://github.com/UW-Hydro/VIC/issues/300#issuecomment-148457410.

@bartnijssen @tbohn I apologize for this chaotic situation I created here. First of all, The VIC irrigation model used for the JHM paper was based on VIC 4.0.6, developed by Ingjerd about 10 years ago and it has been added to our VIC repo as a supporting branch about 2 years ago (https://github.com/UW-Hydro/VIC/tree/support/VIC.4.0.6.irrigation). Second, for the ISI-MIP project, Ingjerd modified Ted's private code earlier this year because it has the varying land cover feature in it, which is required by ISI-MIP project. The model was transferred as tar files through emails.

If it's helpful to piecing this together, as I worked on my private code, I
ported fixes from 4.1.2 and 4.2 into my private code until I froze my code
and ported veg_hist into 4.2.  So, I think you'll find that the diff
between the source code of Ingjerd/Tian's code and the 4.2/src directory is
not super big - should primarily consist of the irrigation stuff plus
possibly a few of the later fixes to 4.2.
Ted
On Thu, Oct 15, 2015 at 11:07 AM, Tian Zhou<EMAIL_ADDRESS>wrote:

@bartnijssen https://github.com/bartnijssen @tbohn
https://github.com/tbohn I apologize for this chaotic situation I
created here. First of all, The VIC irrigation model used for the JHM paper
was based on VIC 4.0.6, developed by Ingjerd about 10 years ago and it has
been added to our VIC repo as a supporting branch about 2 years ago (
https://github.com/UW-Hydro/VIC/tree/support/VIC.4.0.6.irrigation).
Second, for the ISI-MIP project, Ingjerd modified Ted's private code
earlier this year because it has the varying land cover feature in it,
which is required by ISI-MIP project. The model was transferred as tar
files through emails.
—
Reply to this email directly or view it on GitHub
https://github.com/UW-Hydro/VIC/issues/300#issuecomment-148475721.

@hydrotian : What dis we say was the VIC version in the JHM manuscript? Did we make is clear that that was 4.0.6. That would alleviate my immediate concern.

@hydrotian - Since there is not really any history in your git repository, I recommend updating the src/ directory in the support/VIC.4.2.a.irrigation branch that I just created and opening a pull request from your fork.
Please do not include any temporary files (e.g. #get_global_param.c#) or Make file objects (e.g. .depend).
Also in that PR, we should have:

a thorough commit message describing the changes made, versions, etc.
an update to the readme file.  Probably just add in the header that this is a support branch and you can cite your paper there.

Once that PR is open, we should have @tbohn and Ingjerd give things a review to make sure everything looks right.  It would be helpful if we could actually see the diff between these two sets of code.
Lastly, we may want to run a few short simulations with the updated branch to show that we can reproduce the results from your paper.

@hydrotian : Please keep moving this forward, so we can close this asap.

closed via #301


RequestAsBrowserOptions TS type is missing options useInsecureHttpParser & ignoreSslErrors

TS type declarations of RequestAsBrowserOptions are missing options mentioned in https://sdk.apify.com/docs/api/utils#utilsrequestasbrowseroptions and if you look in the code, the options are cleary consumed and handled, but they're missing in the type declarations.

IMPORTANT: This function uses an insecure version of HTTP parser by default and also ignores SSL/TLS errors. This is very useful in scraping, because it allows bypassing certain anti-scraping walls, but it also exposes some vulnerability. For other than scraping scenarios, please set useInsecureHttpParser: false and ignoreSslErrors: false.

System information:

OS: Ubuntu 18.04.4 LTS
Node.js version v10.22.0
Apify SDK version 0.21.3, yarn.lock.txt

code:
import Apify from "apify";
import * as cheerio from "cheerio";

export async function test() {
    const {body} = await Apify.utils.requestAsBrowser({
        url: 'https://www.google.cz',
        useInsecureHttpParser: false,
        ignoreSslErrors: false
    });

    const $ = cheerio.load(body);
}

tsc output:
src/reproducer.ts:7:9 - error TS2345: Argument of type '{ url: string; useInsecureHttpParser: boolean; ignoreSslErrors: boolean; }' is not assignable to parameter of type 'RequestAsBrowserOptions'.
  Object literal may only specify known properties, and 'useInsecureHttpParser' does not exist in type 'RequestAsBrowserOptions'.

7         useInsecureHttpParser: false,
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~

@pocesar could you please take a look? requestAsBrowser uses http-request options, even though all JSDocs are correctly specified. Thanks!

Thanks :clap:


Automatically select the desired vehicle on pairing

Hi
Would it be possible to add an anchor like #VIN_NUMBER (or vehicle id) at the end of https://tesla.com/_ak/example.com to automatically select the desired vehicle and do the pairing?
Regards;

Plus one for this. The current workflow is not very user friendly, eg:

in our app, show instructions, something like:
if you have multiple vehicles, switch to the Tesla app, select the correct vehicle
switch back to this app
click the pairing link, which will open the Tesla app
accept the pairing request

+1 to this. The current required flow results in a very frustrating UX for vehicle owners with multiple vehicles, and also adds complexity (as described well by @jbanyer).
I have had multiple vehicle owners with 6-12 vehicles express their displeasure, which would be mostly resolved by defining a vehicle ID or VIN to the URL to direct the Tesla App to the desired vehicle.

Hi, any progress/workaround for this?


Add travis build for different platforms

Any plan to add travis build for different platforms? Right now mxnet/cpp_package on windows are broken(according to #14343, it is broken since 2 years ago), there are too many bugs when try to build/deploy. If there are travis build for different platforms, there are many bugs should be able to avoid when develop, unless the users could have more insight which platform they are able to build the mxnet with cpp_package.

@mxnet-label-bot Add [Feature Request, Build]

@marcoabreu Is this something we plan to do with Travis ? Or are the Jenkins CI testing out various platform sufficient for now ?

Or are the Jenkins CI testing out various platform sufficient for now ?

I hope it is enough too, but it is not, there are many bugs when you try to build mxnet on windows, especially when you try to build with intel mkl, please check issues #14343, #14364


Asm.js SIMD.js : Clean up : Disable SIMD.js opcodes not specified in spec

Hi @Krovatkin, I'm your friendly neighborhood Microsoft Pull Request Bot (You can call me MSBOT). Thanks for your contribution!
You've already signed the contribution license agreement. Thanks!
The agreement was validated by Microsoft and real humans are currently evaluating your PR.
TTYL, MSBOT;

@nmostafa  @arunetm this PR is for issue #907

@abchatra @nmostafa put float64x2 under a config flag

:+1:

@dilijev Fixed trailing whitespaces and extra blank lines. Please take a look when you have a mnt and let us now if this PR is approved.

Please merge this. Looks good.

Sign off please.

@dilijev, we had to rebase because of conflicts. Can you sign off again please ? I will merge it.


Drop down field value not found breaks import

Hi,
I am running an import routine which has a drop down field in it.
My import data has 'WA' as the text value but the value of the drop down field in the CMS is actually 'wa'. Because of this, when I run the import, it breaks without explanation/logs and the task fails to get beyond the first step. So something in the DropdownFeedMeFieldType::prepFieldData() method is not quite right (perhaps that $preppedData is initialised as an array?)
How I got around the problem was to change the source code for the drop down field to match on the label if it can't find a value.
So the code becomes:
        // find matching option label
        foreach ($options as $option) {
            if ($data == $option['value']) {
                $preppedData = $option['value'];
                break;
            }
            else if ($data == $option['label']) {
                $preppedData = $option['value'];
                break;
            }
        }

This might be a worthwhile change you could implement. However, it solves the problem in my case because I have a 'WA' label that matches my textual import value of 'WA', so the bug no longer gets triggered. But this might not actually be the real fix for the bug.

To be fair, value matching should be case sensitive. What if you had several options (values) in your dropdown field for WA, Wa, wA, wa, you wouldn't want Feed Me to match against the incorrect one. I would suggest either changing the Dropdown value, or the value in your feed (if either is possible.
I'm hesitant to adding that code to match against the label, purely from a simplicity standpoint. In the unlikely case you have WA as the label for one option, and WA as the value for another, Feed Me doesn't know which one is the 'correct' option.
If anything, I think the solution would be to choose what your data is coming in as, something like the below:

I see your point and agree that your proposed solution is much better.
Hope it gets into the next build.

I'm having a similar issue, had the following Dropdown (label | value):
Signed by the Author | signedByTheAuthor
Signed & Lined | signedLined

When the imported field had the value unsigned which was missing from the dropdown, the following error would be logged in craft.log, and the takes would get stale.
Stacktrace of the error:
...
2017/03/11 00:11:21 [info] [application] [Forced] Starting step 5 of 10 total steps.
2017/03/11 00:11:21 [info] [application] [Forced] Starting step 6 of 10 total steps.
2017/03/11 00:11:21 [info] [application] [Forced] Starting step 7 of 10 total steps.
2017/03/11 00:11:21 [info] [application] [Forced] Starting step 8 of 10 total steps.
2017/03/11 00:11:21 [error] [php] Array to string conversion (/PROJECT/craft/app/fieldtypes/OptionData.php:58)
Stack trace:
#0 /PROJECT/craft/app/fieldtypes/BaseFieldType.php(182): arrayToString()
#1 /PROJECT/craft/app/services/ContentService.php(403): Craft\DropdownFieldType->getSearchKeywords()
#2 /PROJECT/craft/app/services/ContentService.php(154): Craft\ContentService->_updateSearchIndexes()
#3 /PROJECT/craft/app/services/ElementsService.php(1416): Craft\ContentService->saveContent()
#4 /PROJECT/craft/plugins/commerce/services/Commerce_ProductsService.php(171): Craft\ElementsService->saveElement()
#5 /PROJECT/craft/plugins/feedme/FeedMe/ElementTypes/Commerce_ProductFeedMeElementType.php(164): Craft\Commerce_ProductsService->saveProduct()
#6 /PROJECT/craft/plugins/feedme/services/FeedMe_ProcessService.php(166): Craft\Commerce_ProductFeedMeElementType->save()
#7 /PROJECT/craft/plugins/feedme/tasks/FeedMeTask.php(68): Craft\FeedMe_ProcessService->processFeed()
#8 /PROJECT/craft/app/services/TasksService.php(239): Craft\FeedMeTask->runStep()
#9 /PROJECT/craft/app/services/TasksService.php(200): Craft\TasksService->runTask()
#10 /PROJECT/craft/app/controllers/TasksController.php(63): Craft\TasksService->runPendingTasks()
#11 /PROJECT/craft/app/framework/web/actions/CInlineAction.php(49): Craft\TasksController->actionRunPendingTasks()
#12 /PROJECT/craft/app/framework/web/CController.php(308): CInlineAction->runWithParams()
#13 /PROJECT/craft/app/framework/web/CController.php(286): Craft\TasksController->runAction()
#14 /PROJECT/craft/app/framework/web/CController.php(265): Craft\TasksController->runActionWithFilters()
#15 /PROJECT/craft/app/framework/web/CWebApplication.php(282): Craft\TasksController->run()
#16 /PROJECT/craft/app/etc/web/WebApp.php(817): Craft\WebApp->runController()
#17 /PROJECT/craft/app/etc/web/WebApp.php(287): Craft\WebApp->_processActionRequest()
#18 /PROJECT/craft/app/framework/base/CApplication.php(185): Craft\WebApp->processRequest()
#19 /PROJECT/craft/app/index.php(62): Craft\WebApp->run()
#20 /PROJECT/craft/index.php(8): require_once()
REQUEST_URI=/index.php?p=manager/actions/tasks/runPendingTasks
2017/03/11 00:11:21 [error] [application] Encountered an error running task 156 (FeedMe), step 8 of 10: Array to string conversion on line 58 of /PROJECT/craft/app/fieldtypes/OptionData.php

@ugin This should be fixed in the latest master.


Code review - Apply best practices

[ ] #6
https://github.com/limavfabio/todo-list/blob/eebef4508cd818b1ee1978cc16457419f0319b42/src/index.html#L15

[ ] The file src/assets/plus-solid.SVG is never used in the project, consider removing it as to keep the file tree cleaner.

[ ] The constant  "text" in src/modules/add.js line 6 should be declared in the beginning of the file as to adhere to Javascript best practices
https://github.com/limavfabio/todo-list/blob/eebef4508cd818b1ee1978cc16457419f0319b42/src/modules/add.js#L6


Derivation of big case class

Derivation of big case class finish by a could not find implicit value for parameter e: io.circe.Encoder[A]and could not find implicit value for parameter e: io.circe.Decoder[A]
Here a gist that show the problem

I am facing the same issue with way smaller case classes that are, however, deeply nested (like 5-6 levels deep). Gradually commenting some of the fields out, then compiling, and finally reenabling commented lines to compile again will eventually lead to a working build, but a clean build always fails with the missing Encoder/Decoder error. This issue keeps me from actually using circe.

FYI, the example in the gist above is fine with argonaut-shapeless. There has to be a way to have this working here...


feat: auto hide or show editor

feat: #594

hide the editor when scrolling down fast enough.
show the editor when scrolling up fast enough.

https://user-images.githubusercontent.com/17293034/205955671-3e8511d9-283d-43dc-b1cf-68828edc3e74.mov

#697

Thanks for the PR. I removed the sticky style for editor in https://github.com/usememos/memos/pull/752. It's scrollable and will not hide the content as same as Twitter.


volatile GPU-Util 0%

Hi dyelax,
I really appreciate for your work.
I tried to modified your code to Wgan and trained on AWS. But it seems like training pretty slow, it only trained 4000 iterations a day. Also it has high GPU Memory-Usage but zero volatile cpu-util. Do you have any idea why does this happening?
(tensorflow) ubuntu@ip-172-31-8-95:~$ nvidia-smi
Sun Apr 23 19:53:29 2017
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 375.51                 Driver Version: 375.51                    |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|===============================+======================+======================|
|   0  Tesla K80           Off  | 0000:00:1E.0     Off |                    0 |
| N/A   40C    P0    71W / 149W |  10941MiB / 11439MiB |      0%      Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|    0     20379    C   python                                       10937MiB |
+-----------------------------------------------------------------------------+
Thank you!

Sorry for the delay on this. Are you getting the same results if you try running this code without your WGAN edits?


Logged in users with an application should not be able to Apply again

[ @nickaddy and @warrensearle to discuss ]
When a logged in user, with an existing application, is viewing the vacancy details page they are still presented with the Apply button and upon pressing it are directed through the Eligibility Check and GDPR pages (which they will have already completed).
It makes more sense to replace the Apply button with a View Application button which takes the user directly to their started, or completed, application.

It would be great to gain clarification that candidate can only apply once for each vacancy, I'm presuming that is the case


fix: multiple issues the odin project

fix: multiple issues
fix: show expand collaps button
fix: make variable instead

Checklist:

[ ] I have read freeCodeCamp's contribution guidelines.
[ ] My pull request has a descriptive title (not a vague title like Update index.md)
[ ] My pull request targets the main branch of freeCodeCamp.
[ ] I have tested these changes either locally on my machine, or GitPod.

Closes #XXXXX

LGTM 👍
I hope, one day soon, we can refactor odin/Show.tsx as it is so similar to video/Show.tsx. Also, the keyboard a11y of the odin stuff is not fun.

Thanks Shaun, that was the original plan, but Oliver suggested to keep them separate.


Fixed pom versioning

mvn build fails because of pom setting, version mismatch.

dev-ops is 0.1.1-SNAPSHOT but specified 0.1.0-SNAPSHOT in pom.xml
ilp-annotations  is 0.1.1-SNAPSHOT but specified 0.1.0-SNAPSHOT in pom.xml and ilp-annotations/pom.xml

Codecov Report

Merging #131 into master will decrease coverage by 0.04%.
The diff coverage is n/a.

@@             Coverage Diff              @@
##             master     #131      +/-   ##
============================================
- Coverage     76.33%   76.29%   -0.05%
+ Complexity      413      401      -12
============================================
  Files            91       91
  Lines          2092     2080      -12
  Branches        200      200
============================================
- Hits           1597     1587      -10
+ Misses          399      397       -2
  Partials         96       96

Impacted Files
Coverage Δ
Complexity Δ

...org/interledger/core/InterledgerAddressParser.java
90.69% <0%> (-2.96%)
15% <0%> (-14%)

.../java/org/interledger/core/InterledgerAddress.java
100% <0%> (+4.76%)
21% <0%> (+2%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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Let's align the versioning of all the modules so we don't encounter this issue in the future. To do that, we'll need to do the following:

Update the parent pom.xml to have version 0.11.0-SNAPSHOT.
In each of ilp-core, ilp-annotations, dev-ops, and codec-framework, remove the <group-id> and the <version> tags so that each module simply inherits these from the parent pom.

For example, ilp-core would look like this:
  <parent>
    <groupId>org.interledger</groupId>
    <artifactId>quilt-parent</artifactId>
    <version>0.1.0-SNAPSHOT</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>

  <artifactId>ilp-core</artifactId>

  <name>Interledger Core</name>

Finally, in the <dependencyManagement> section in the parent pom, we will need to update the versions to be as follows:
 <dependency>
        <groupId>${project.groupId}</groupId>
        <artifactId>ilp-annotations</artifactId>
        <version>${project.version}</version>
      </dependency>

      <dependency>
        <groupId>${project.groupId}</groupId>
        <artifactId>codec-framework</artifactId>
        <version>${project.version}</version>
      </dependency>

      <dependency>
        <groupId>${project.groupId}</groupId>
        <artifactId>ilp-core</artifactId>
        <version>${project.version}</version>
      </dependency>

      <dependency>
        <groupId>${project.groupId}</groupId>
        <artifactId>ilp-dev-ops</artifactId>
        <version>${project.version}</version>
      </dependency>

Note two things:

We'll need to update the dev-ops project to inherit from quilt-parent.
Let's not touch anything related to the crypto-conditions modules -- I'm working on a PR to extract these from the project into https://github.com/hyperledger/quilt-crypto-conditions.

Should we move crypto-conditions into it's own project first?

Should we move crypto-conditions into it's own project first?

CryptoConditions is pretty independent as far as versioning is concerned - we could leave that along, and just update everything else.

I've fixed this in #138
All submodules inherit from the parent per Maven convention
Also added the versions plugin to help with managing versions: http://www.mojohaus.org/versions-maven-plugin/

Thanks @dora-gt for pushing this along


Option to COVER the previous menu?

Is there an option to not show a glimpse of the previous menu behind the active menu group? I want to just have the selected menu cover all the rest - the more deeper you go into the menu - it just gets more crowded. I just want to show one group of menu.
Thanks

Set levelSpacing option to zero.


Cannot Generate .cache file

Hi there. After following some guides from other posts, I have gotten to the part where you need to let the Spotipy program have access to my Spotify account. After loading up a VNC and going to the localhost:8080 site, and allowing it access to my account, it takes me to a site that Midori cannot load. I was told to paste this into the console, but there is no prompt to do so, and nothing happens when I do. Any leads? Here is a screenshot of after I authorize it through spotify:

Hi, does the promt appear if you start spotifypod.py  instead? It has been a while since I performed these steps but I don’t think I did use another script to authenticate

That worked! However, now I am stuck with the openbox default desktop, instead of the spotifypod.py program. I checked the autostart paths and it should work, and trying to run the program manually via the terminal emulator in openbox resulted in this line of errors...

I have the client IDs, and redirect URI in the /etc/xdg/openbox/environment file, so this is odd.

I added the variables to:
/etc/environment
I also have a copy of them in .bashrc in the home directory of my user.
Not sure which one makes it work. but it works 🤷
but it only works after it boots and not from rc.local.
I ended up making spotifypod a service and set environment variables there.
Not sure if it works on boot though. I don't think it does.
but maybe you'll have more luck with one of the options I suggested.


jaxopt.LBFGS is 2x slower than jax.scipy.optimize.minimize

I am in the process of translating an implementation that used jax.scipy.optimize.minimize to jaxopt.LBFGS as it seems that the former is becoming deprecated (or at least unsupported) in favor of the latter.
I have noticed that jaxopt.LBFGS is slower than jax.scipy.optimize.minimize, roughly 2x both on CPU and on GPU (although I have to say that I did not spend a lot of time making sure I was correctly using GPU acceleration, it was just faster).
I have a colab illustrating the issue where I install jaxopt from my own fork/branch because it solves an issue with the current jaxopt LBFGS implementation described here (I have a PR for it here).
Here is the example to be run in a notebook using my fork on branch line-search-failed-breaks-lbfgs of jaxopt:

import jax.numpy as jnp
from jax.scipy.optimize import minimize
from jax.config import config

# config.update('jax_disable_jit', True)

from jaxopt import LBFGS
from jaxopt import objective
from jaxopt._src import test_util

from sklearn import datasets

X, y = datasets.make_classification(n_samples=100, n_features=50,
                                        n_classes=3, n_informative=3,
                                        random_state=0)
data = (X, y)
fun = objective.multiclass_logreg

W_init = jnp.zeros((X.shape[1], 3))
pytree_init = W_init

#######################
%%timeit
lbfgs = LBFGS(fun=fun, tol=1e-3, maxiter=500, use_gamma=True,
                linesearch='zoom', allow_line_search_fail=True)
# Test with positional argument.
pytree_fit, info = lbfgs.run(pytree_init, data)
#######################

#######################
%%timeit
def logreg_1d(w, data):
    w_reshaped = w.reshape(W_init.shape)
    return fun(w_reshaped, data)

soln_jaxminimize = minimize(
    logreg_1d,
    pytree_init.ravel(),
    args=(data,),
    method="l-bfgs-experimental-do-not-rely-on-this",
    options={"gtol": 1e-3, "maxiter": 500, "maxls": 15},
)
x_jax_minimize = soln_jaxminimize.x.reshape(W_init.shape)
#######################

#######################
%%timeit
# this last one serves purely to show that the fact that we are using 1d in jax.scipy does not make
# a big difference in jaxopt
def logreg_1d(w, data):
    w_reshaped = w.reshape(W_init.shape)
    return fun(w_reshaped, data)

lbfgs = LBFGS(fun=logreg_1d, tol=1e-3, maxiter=500, use_gamma=True,
                linesearch='zoom', allow_line_search_fail=True)
# Test with positional argument.
pytree_fit, info = lbfgs.run(pytree_init.ravel(), data)
pytree_fit = pytree_fit.reshape(W_init.shape)
#######################

test_util.JaxoptTestCase().assertArraysAllClose(pytree_fit, x_jax_minimize, atol=1e-3)

I will try to profile the 2 codes to see where the slowness might be coming from but I thought it would be nice to have an issue open to track the progress and potentially have some feedback on how best to tackle the problem.

This problem disappears entirely when jitting the minimization functions so I am going to close this.

Just making sure that my ccls are clear : jitting corrects the issue in runtime, but this is after I applied my fix for the number of iterations. So #323 is still needed to correct the overall discrepancy.


GPR curation for Transport reactions (15)

Current behavior:

50 genes are discovered to be uncorrelated with their corresponding reactions in Transport reactions.

Gene
UniProtID
Reaction
GPR
Correlation
Manually check

ENSG00000102743
Q9Y619
MAR06314: H+ + histidine + ornithine --> H+ + histidine + ornithine
ENSG00000102743 or ENSG00000120329
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000102743 encodes a mitochondrial ornithine-citrulline antiporter which facilitates the exchange of ornithine and other amino acids like citrulline, arginine, and lysine along with protons (H+), critical for the urea cycle. However, the reaction provided involves H+ with histidine and ornithine, which is not mentioned among the catalytic activities or functions of the gene as specified in the annotations. Therefore, the gene is not related to the provided reaction.
No

ENSG00000125454
Q9HC21
MAR07827: dTDP + dUTP --> dTDP + dUTP
ENSG00000125454
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000125454 encodes a mitochondrial transporter that mediates the uptake of thiamine diphosphate into mitochondria, with its catalytic activity involving the exchange of thiamine diphosphate and thiamine phosphate. However, the reaction provided involves the conversion of dTDP and dUTP, which are different substrates unrelated to thiamine metabolism, indicating that the gene and the reaction are not related.
No

ENSG00000125454
Q9HC21
MAR07836: dTDP + dTTP --> dTDP + dTTP
ENSG00000125454
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000125454 encodes a mitochondrial transporter responsible for the uptake of thiamine diphosphate into mitochondria, and it exhibits a specific catalytic activity related to the exchange of thiamine diphosphate and thiamine phosphate. The reaction provided, "dTDP + dTTP --> dTDP + dTTP," does not involve these compounds or the described function of the gene, indicating no relevance between the two.
No

ENSG00000125454
Q9HC21
MAR07844: dADP + dCTP --> dADP + dCTP
ENSG00000125454
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000125454 encodes a mitochondrial transporter that mediates the uptake of thiamine diphosphate into mitochondria and facilitates an antiporter activity involving thiamine diphosphate and thiamine phosphate. The catalytic action described involves thiamine diphosphate and thiamine phosphate, while the reaction provided involves dADP and dCTP, which are unrelated to thiamine metabolism. Therefore, there is no connection between the gene's annotated function and the reaction given.
No

ENSG00000184343
Q9UPE1
MAR03008: ATP + H2O + propanoyl-CoA --> ADP + H+ + Pi + propanoyl-CoA
ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000184343 codes for a serine/arginine-rich protein-specific kinase, which phosphorylates serine and threonine residues in protein substrates. However, the reaction provided involves the conversion of ATP, H2O, and propanoyl-CoA to ADP, H+, Pi, and propanoyl-CoA, which is not related to the described kinase activity of phosphorylating protein serine/threonine residues. Therefore, the noted phosphorylation activity of the gene product does not align with the biochemical transformation described in the reaction.
No

ENSG00000130821
P48029
MAR03014: arachidonyl-CoA + ATP + H2O --> ADP + arachidonyl-CoA + H+ + Pi
ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000130821 encodes for a creatine:sodium symporter involved in the uptake of creatine and its transport across the blood-brain barrier. The catalytic activity of this gene involves the transport of chloride, creatine, and sodium ions. The reaction provided involves the conversion of arachidonyl-CoA, ATP, and water to ADP, arachidonyl-CoA, proton, and phosphate, which is unrelated to the function of the creatine:sodium symporter produced by this gene.
No

ENSG00000120253
Q8NFH3
MAR07796: UTP <=> UTP
(ENSG00000030066 and ENSG00000069248 and ENSG00000075188 and ENSG00000110713 and ENSG00000111581 and ENSG00000120253 and ENSG00000125450) or ENSG00000093000 or ENSG00000095319 or ENSG00000102900 or ENSG00000108559 or ENSG00000113569 or ENSG00000124789 or ENSG00000126883 or ENSG00000132182 or ENSG00000136243 or ENSG00000138750 or ENSG00000139496 or ENSG00000143552 or ENSG00000153201 or ENSG00000155561 or ENSG00000163002 or ENSG00000198088 or ENSG00000213024
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000120253 encodes a component of the Nup107-160 subcomplex of the nuclear pore complex (NPC), which is involved in NPC assembly, kinetochore microtubule attachment, mitotic progression, and chromosome segregation. It does not have any documented catalytic activity or any direct involvement in the reaction UTP <=> UTP.
No

ENSG00000205060
Q969S0
MAR04125: UDP-xylose + UMP <=> UDP-xylose + UMP
ENSG00000205060
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000205060 encodes an antiporter that transports nucleotide sugars across the endoplasmic reticulum membrane, specifically involved in exchanging UDP-alpha-D-glucuronate (UDP-GlcA) with UDP-N-acetyl-alpha-D-glucosamine (UDP-GlcNAc) or UDP-alpha-D-xylose (UDP-Xyl). The reactions catalyzed by this gene involve these specific nucleotide sugars. However, the reaction provided (UDP-xylose + UMP <=> UDP-xylose + UMP) does not involve the transport or exchange of nucleotide sugars across the ER membrane but rather a simple equilibrium reaction involving UDP-xylose and UMP, which is unrelated to the gene's described functions and catalytic activities.
No

ENSG00000205060
Q969S0
MAR08857: UDP-glucose + UMP <=> UDP-glucose + UMP
ENSG00000117620 or ENSG00000130958 or ENSG00000205060
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000205060 encodes an antiporter that transports nucleotide sugars across the endoplasmic reticulum (ER) membrane, specifically exchanging UDP-alpha-D-glucuronate and UDP-N-acetyl-alpha-D-glucosamine or UDP-alpha-D-xylose. In contrast, the reaction provided involves UDP-glucose and UMP, which are not substrates for the antiporter encoded by this gene. Therefore, the gene's function does not align with the reaction's substrates or mechanism.
No

ENSG00000163295
P09923
MAR08969: FMN + H2O --> Pi + riboflavin
ENSG00000163295
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000163295 encodes an enzyme responsible for alkaline phosphatase activity, which hydrolyzes phosphate monoesters to produce an alcohol and phosphate. The provided reaction, however, involves the hydrolysis of FMN (flavin mononucleotide) to produce phosphate (Pi) and riboflavin, which does not involve a phosphate monoester and does not align with the annotated function of the gene.
Not sure, keep it now.

ENSG00000023839
Q92887
MAR09882: ATP + folate + H2O --> ADP + folate + H+ + Pi
ENSG00000005471 or ENSG00000023839 or ENSG00000103222 or ENSG00000114770 or ENSG00000118777 or ENSG00000121270 or ENSG00000125257
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. According to the provided annotation for the gene ENSG00000023839, its function pertains to ATP-dependent transport of a wide variety of conjugated organic anions, drugs, and toxicants across cell membranes. It specifically mediates the excretion of mono- and bis-glucuronidated bilirubin, 17beta-estradiol glucuronide, leukotriene C4, and other substrates, but it does not mention any involvement with folate. Moreover, the reaction provided involves the catalysis of ATP and folate, which falls outside the documented activities of the gene. Therefore, the gene is not relevant to the ATP + folate reaction.
Not sure, keep it now.

ENSG00000073734
O95342
MAR11380: 5beta-cholestane-3alpha,7alpha,26-triol + ATP + H2O --> 5beta-cholestane-3alpha,7alpha,26-triol + ADP + H+ + Pi
ENSG00000073734 or ENSG00000108846 or ENSG00000121270
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000073734 encodes a protein that catalyzes the ATP-dependent transport of bile salts and other compounds across the canalicular membrane of hepatocytes, playing a role in bile acid and lipid homeostasis. The reaction provided (5beta-cholestane-3alpha,7alpha,26-triol + ATP + H2O --> 5beta-cholestane-3alpha,7alpha,26-triol + ADP + H+ + Pi) does not involve the transport of bile salts or related compounds, nor does it align with the known catalytic activities associated with the gene's protein function as described.
Yes

ENSG00000100170
P13866
MAR11410: galactose + 2.0 H+ <=> galactose + 2.0 H+
ENSG00000100170
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000100170 encodes for a Na(+)-coupled sugar symporter, which actively transports D-glucose and D-galactose along with Na(+) ions across the plasma membrane, driven by the Na(+) electrochemical gradient. The catalytic activities involve the transport of D-glucose or D-galactose coupled with Na(+), unlike the provided reaction, which involves a galactose and proton (H+) exchange. Thus, the gene's function does not align with the given reaction's description involving H+ ions.
No

ENSG00000165970
Q9Y345
MAR11456: chloride + isovalerylglycine + 3.0 Na+ <=> chloride + isovalerylglycine + 3.0 Na+
ENSG00000165970
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000165970 codes for a sodium- and chloride-dependent glycine transporter involved in the reuptake of glycine for terminating neurotransmission at glycinergic synapses. The provided reaction involves the molecule isovalerylglycine and does not pertain to the reuptake or transport of glycine as outlined by the gene's function. Therefore, the gene's annotated function does not match the provided reaction.
No

ENSG00000173638
P41440
MAR11647: 20alpha-hydroxy-4-pregnen-3-one + hydroxide <=> 20alpha-hydroxy-4-pregnen-3-one + hydroxide
ENSG00000173638
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000173638 encodes an antiporter that imports reduced folates or a subset of cyclic dinucleotides and exports organic anions. The catalytic activities described for the antiporter include reactions involving folates and cyclic dinucleotides like 2',3'-cGAMP and 3',3'-cGAMP. However, the provided reaction involves "20alpha-hydroxy-4-pregnen-3-one" and hydroxide, which are not substrates of the antiporter encoded by this gene. Therefore, the gene and the reaction are not related.
No

ENSG00000142583
P22732
MAR11779: D-glucarate <=> D-glucarate
ENSG00000142583
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000142583 encodes a protein functioning as a fructose transporter with specific reference to its activity in transporting D-fructose across the cell membrane. The annotated catalytic activity explicitly states the reaction D-fructose(out) = D-fructose(in). However, the given reaction involving D-glucarate <=> D-glucarate does not involve fructose transport and falls outside the functional range of the gene. Therefore, the gene and the reaction are not related.
No

ENSG00000112759
Q99808
MAR11801: quinonoid dihydrobiopterin <=> quinonoid dihydrobiopterin
ENSG00000112759 or ENSG00000174669
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000112759 functions as a Na(+)-independent transporter involved in the transport of nucleosides and nucleobases, such as adenosine, guanosine, inosine, uridine, thymidine, and cytidine. This includes transporting purine and pyrimidine nucleobases across cellular membranes, maintaining cellular homeostasis, and regulating extracellular inosine levels. The reactions catalyzed by this gene involve the exchange of specific nucleosides and nucleobases in and out of cells. However, the reaction provided involves quinonoid dihydrobiopterin, which is unrelated to the transport activities of nucleosides and nucleobases facilitated by the gene. Therefore, the gene and the reaction are not related.
No

ENSG00000131686
P23280
MAR00190: ATP + H2O + lauric acid --> ADP + H+ + lauric acid + Pi
ENSG00000074410 or ENSG00000104267 or ENSG00000107159 or ENSG00000118298 or ENSG00000131686 or ENSG00000133742 or ENSG00000159593 or ENSG00000164879 or ENSG00000165029 or ENSG00000166747 or ENSG00000167434 or ENSG00000168748 or ENSG00000169239 or ENSG00000174990 or ENSG00000185015
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000131686 encodes for an enzyme that catalyzes the reversible hydration of carbon dioxide, as indicated in its function and catalytic activity. This enzyme's activity involves the conversion of H(+) and hydrogencarbonate to CO2 and H2O. In contrast, the reaction provided involves the conversion of ATP, H2O, and lauric acid to ADP, H+, lauric acid, and Pi. These two reactions involve entirely different substrates and products, indicating that the gene product does not participate in or influence the provided reaction.
No

ENSG00000165029
O95477
MAR00215: ATP + H2O + pentadecylic acid --> ADP + H+ + pentadecylic acid + Pi
ENSG00000165029
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000165029 encodes a protein that catalyzes the translocation of specific phospholipids, such as phosphatidylcholine and phosphatidylserine, as well as sphingomyelin and cholesterol across membranes, using ATP hydrolysis. However, the reaction provided involves ATP, H2O, and pentadecylic acid, which is not a substrate mentioned in the gene's known catalytic activities. Therefore, the gene's function does not align with the provided reaction.
No

ENSG00000165029
O95477
MAR00231: ATP + H2O + palmitolate --> ADP + H+ + palmitolate + Pi
ENSG00000165029
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000165029 encodes a protein that catalyzes the translocation of specific phospholipids such as phosphatidylcholine, phosphatidylserine, sphingomyelin, and cholesterol across membranes, coupled with the hydrolysis of ATP. The described reactions involve transferring these phospholipids and cholesterol between intracellular and extracellular spaces. However, the reaction provided (ATP + H2O + palmitolate --> ADP + H+ + palmitolate + Pi) involves palmitolate, which is not mentioned among the substrates handled by this gene product. Therefore, the gene does not match the specific reaction involving palmitolate.
No

ENSG00000165029
O95477
MAR00239: ATP + H2O + margaric acid --> ADP + H+ + margaric acid + Pi
ENSG00000165029
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000165029 encodes a protein that specifically catalyzes the translocation of phospholipids (such as phosphatidylcholine and phosphatidylserine) and cholesterol across the membrane utilizing ATP. However, the reaction provided involves the conversion of ATP and H2O with margaric acid (a type of fatty acid) to produce ADP, H+, margaric acid, and Pi. This reaction does not involve the translocation of phospholipids or cholesterol, which are the primary substrates for the gene product, indicating the gene is not relevant to the given reaction.
No

ENSG00000165029
O95477
MAR00269: ATP + elaidate + H2O --> ADP + elaidate + H+ + Pi
ENSG00000165029
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000165029 is involved in the translocation of specific phospholipids, such as phosphatidylcholine, phosphatidylserine, sphingomyelin, and cholesterol, coupled with ATP hydrolysis. It plays a role in forming nascent high-density lipoproteins (HDLs) and phospholipid transfer to apolipoproteins. The reaction provided involves ATP, elaidate, and water to produce ADP, elaidate, H+, and phosphate, which does not correspond to the specific phospholipid translocation activity described for this gene. Therefore, the gene's function does not match the reaction.
No

ENSG00000165029
O95477
MAR00277: (6Z,9Z)-octadecadienoic acid + ATP + H2O --> (6Z,9Z)-octadecadienoic acid + ADP + H+ + Pi
ENSG00000165029
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000165029 encodes a protein that catalyzes the translocation of specific phospholipids and cholesterol across membranes utilizing ATP, specifically involving phosphatidylcholine, phosphatidylserine, sphingomyelin, and cholesterol. The provided reaction involves (6Z,9Z)-octadecadienoic acid, which is a type of fatty acid and not a phospholipid, hence the gene's function does not encompass the given reaction.
No

ENSG00000165029
O95477
MAR00287: ATP + eicosanoate + H2O --> ADP + eicosanoate + H+ + Pi
ENSG00000165029
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000165029 encodes for a protein that is involved in the translocation of specific phospholipids and cholesterol from one leaflet of the membrane to the other, utilizing ATP hydrolysis. The gene products catalyze reactions involving phosphatidylcholine, phosphatidylserine, sphingomyelin, and cholesterol, but there is no evidence or annotation indicating its involvement in the translocation of eicosanoates. Therefore, the reaction involving ATP, eicosanoate, and H2O resulting in ADP, eicosanoate, H+, and Pi is not related to the gene's annotated functions.
No

ENSG00000165029
O95477
MAR00351: ATP + H2O + linolenate --> ADP + H+ + linolenate + Pi
ENSG00000165029
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000165029 functions as a catalyst for the translocation of specific phospholipids, such as phosphatidylcholine, phosphatidylserine, sphingomyelin, and cholesterol, from the cytoplasmic to the extracellular/lumenal leaflet of membranes coupled to ATP hydrolysis. The provided reaction pertains to the conversion of ATP and linolenate to ADP, H+, linolenate, and Pi, which does not involve the translocation of phospholipids or cholesterol. Therefore, the gene's function is unrelated to the reaction given.
No

ENSG00000021488
P82251
MAR01902: HCO3- + serotonin + S-glutathionyl-2-4-dinitrobenzene <=> HCO3- + serotonin + S-glutathionyl-2-4-dinitrobenzene
ENSG00000021488 or ENSG00000084453 or ENSG00000111700
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000021488 functions as a transporter complex that mediates the exchange of cationic and neutral amino acids. It specifically catalyzes reactions involving various amino acids like L-arginine, L-leucine, L-histidine, L-phenylalanine, L-cysteine, L-cystine, and L-lysine. However, the provided reaction involves HCO3-, serotonin, and S-glutathionyl-2-4-dinitrobenzene, which are not substrates or products in any of the reactions catalyzed by the transporter associated with this gene. Therefore, there is no direct relevance between the gene and the provided reaction.
No

ENSG00000021488
P82251
MAR01904: acetylcholine + glutathionyl-leukotriene C4 + HCO3- <=> acetylcholine + glutathionyl-leukotriene C4 + HCO3-
ENSG00000021488 or ENSG00000084453 or ENSG00000111700
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000021488 encodes a protein that forms a transporter complex responsible for the electrogenic exchange of cationic and neutral amino acids, such as L-arginine, L-leucine, L-histidine, L-phenylalanine, L-cysteine, and L-cystine. However, the reaction involves molecules like acetylcholine, glutathionyl-leukotriene C4, and bicarbonate ion (HCO3-), which are unrelated to the amino acid transport facilitated by the gene's protein product. Therefore, there is no functional link between the gene and the given reaction.
No

ENSG00000108932
O15403
MAR04935: acetate + H+ --> acetate + H+
ENSG00000100156 or ENSG00000108932 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000108932 encodes for a monocarboxylate transporter that is selective for taurine, facilitating its transport across the plasma membrane. The annotated reaction involves taurine transport, while the provided reaction describes the conversion of acetate and H+, which does not involve taurine and falls outside the gene's functional scope.
No

ENSG00000141526
O15427
MAR04935: acetate + H+ --> acetate + H+
ENSG00000100156 or ENSG00000108932 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000141526 encodes a proton-dependent transporter of monocarboxylates, facilitating the transport of L-lactate and pyruvate. The described reactions involve transporting (S)-lactate and pyruvate across the membrane. However, the provided reaction involves acetate and H+, which is not the same as the substrates L-lactate or pyruvate. Thus, the gene's function does not align with the provided acetate reaction.
Yes, acetate belongs to monocarboxylates which can be transported by this transporter.

ENSG00000163581
P11168
MAR04973: mannose <=> mannose
ENSG00000059804 or ENSG00000117394 or ENSG00000163581
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000163581 encodes a facilitative hexose transporter that mediates the transport of glucose, fructose, galactose, and dehydroascorbate, but it is not involved in the transport or catalysis of mannose, as indicated in the reaction provided. Therefore, this gene is not relevant to the mannose reaction.
Yes, mannose belongs to hexose which can be transported by this transporter.

ENSG00000100156
O95907
MAR05018: (R)-3-hydroxybutanoate + H+ --> (R)-3-hydroxybutanoate + H+
ENSG00000100156 or ENSG00000108932 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000100156 is annotated to be involved in the transport of (S)-lactate and H+ across the retinal pigment epithelium, playing a role in pH and ion homeostasis of the outer retina. The reaction provided, however, involves (R)-3-hydroxybutanoate and H+, which is different from (S)-lactate. Therefore, the gene's function does not relate to the reaction specified.
No

ENSG00000167703
Q8N370
MAR05070: histidine <=> histidine
(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000167703 encodes a uniporter that specifically mediates the transport of L-phenylalanine, L-methionine, and L-branched-chain amino acids such as L-leucine and L-isoleucine, using facilitated diffusion. However, the provided reaction involves the transport of histidine, which is not one of the amino acids mentioned in the gene's described function or catalytic activities. Therefore, based on the annotation, the gene and the reaction are not related.
No

ENSG00000139514
P30825
MAR05070: histidine <=> histidine
(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000139514 encodes a high-affinity, low-capacity permease involved in the transport of the cationic amino acids arginine, lysine, and ornithine in non-hepatic tissues. It facilitates the inward and outward transport of L-arginine, L-lysine, L-ornithine, and L-homoarginine. However, it does not facilitate the transport of histidine, which is the reaction mentioned. Therefore, the gene is not relevant to the histidine transport reaction.
No

ENSG00000165349
Q8WY07
MAR05074: tyrosine <=> tyrosine
(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000112394 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: ENSG00000165349 gene mediates the uptake of cationic L-amino acids such as L-arginine, L-lysine, and L-ornithine but does not catalyze the conversion or transportation of tyrosine. The reactions associated with the gene specifically involve L-arginine, L-lysine, and L-ornithine, as evidenced by the cited references. Therefore, it does not have any functional or catalytic role related to the reaction involving tyrosine.
No

ENSG00000139514
P30825
MAR05074: tyrosine <=> tyrosine
(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000112394 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000139514 encodes a high-affinity, low-capacity permease involved in the transport of specific cationic amino acids, including arginine, lysine, ornithine, and homoarginine, as evidenced by various PubMed sources. The annotated catalytic activities of this gene product do not include any reaction involving tyrosine. Therefore, the gene and the provided tyrosine reaction are not related.
No

ENSG00000165349
Q8WY07
MAR05076: glycine --> glycine
(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000164363 or ENSG00000165349 or ENSG00000167703
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000165349 encodes a protein that functions as a uniporter responsible for the uptake of cationic L-amino acids such as L-arginine, L-lysine, and L-ornithine, through a sodium ions- and pH-independent mechanism involving passive diffusion. It facilitates the translocation of these specific amino acids across the membrane, as evidenced by the cited study. However, the reaction provided involves only glycine, which is not one of the substrates mentioned in the gene's functional or catalytic activity description. Therefore, the gene's function does not align with the given reaction involving glycine.
No

ENSG00000165349
Q8WY07
MAR05078: glutamine <=> glutamine
(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000165349 encodes for a uniporter that specifically mediates the uptake of cationic L-amino acids such as L-arginine, L-lysine, and L-ornithine. The catalytic activities annotated for this gene involve the transport of these specific amino acids and are not related to the reaction involving glutamine. Therefore, based on the annotation of the gene, it does not participate in the reaction converting glutamine.
No

ENSG00000003989
P52569
MAR05078: glutamine <=> glutamine
(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000003989 is a permease involved in the transport of cationic amino acids such as L-arginine, L-lysine, L-ornithine, and L-homoarginine. The catalytic activities described for the gene involve the transport of these specific amino acids across cellular membranes. However, the reaction provided is related to the transport of glutamine, which is not mentioned as a substrate for the permease function of this gene. Therefore, the gene does not participate in the glutamine transport reaction.
No

ENSG00000149150
O75387
MAR05080: tryptophan <=> tryptophan
(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000112394 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000149150 mediates the transport of specific neutral amino acids such as L-leucine, L-isoleucine, L-valine, and L-phenylalanine, as indicated by its function and multiple catalytic activities. The annotated catalytic activities do not include the transport or reaction involving tryptophan. Therefore, the gene does not relate to the reaction involving tryptophan.
Yes, tryptophan is a neutral amino acid.

ENSG00000165349
Q8WY07
MAR05088: asparagine --> asparagine
(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000165349 is involved in mediating the uptake of cationic L-amino acids such as L-arginine, L-lysine, and L-ornithine through passive diffusion, as evidenced by catalytic activities documented in various publications. However, the provided reaction involves asparagine, which is not a cationic L-amino acid and falls outside the transport activities mediated by the gene ENSG00000165349. Therefore, the gene does not influence the asparagine reaction.
No

ENSG00000149150
O75387
MAR05088: asparagine --> asparagine
(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000149150 encodes a protein that transports neutral amino acids such as L-leucine, L-isoleucine, L-valine, and L-phenylalanine. Its transport activity is sodium ions-independent and electroneutral, mediated by facilitated diffusion. The catalytic activities listed involve the transport of L-leucine, L-isoleucine, L-methionine, L-phenylalanine, and L-valine. However, the reaction provided involves the conversion of asparagine to asparagine, which is unrelated to the function and catalytic activities of the gene ENSG00000149150. Therefore, the gene is not relevant to the reaction provided.
Yes, asparagine is a neutral amino acid.

ENSG00000149150
O75387
MAR05091: threonine --> threonine
(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000130876 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000149150 encodes a transporter protein that facilitates the transport of neutral amino acids such as L-leucine, L-isoleucine, L-valine, L-phenylalanine, and L-methionine, among others, across cell membranes. The specific reactions mentioned in the annotation involve the transport of these amino acids. However, the provided reaction involves threonine, which is not listed among the substrates transported by the protein encoded by the gene ENSG00000149150. Therefore, the gene is not relevant to the reaction involving threonine.
Yes

ENSG00000139209
Q969I6
MAR05315: leucine + Na+ --> leucine + Na+
ENSG00000003989 or ENSG00000072041 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000168003 or ENSG00000174358
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000139209 encodes a symporter involved in the transport of neutral amino acids and sodium ions across the cell membrane. It specifically transports smaller amino acids such as glycine, L-alanine, L-serine, L-asparagine, L-threonine, L-cysteine, L-histidine, L-proline, L-glutamine, and L-methionine. The reaction provided involves leucine and Na+, which is not listed among the substrates that the symporter encoded by the gene ENSG00000139209 transports. Therefore, the gene is not relevant to the reaction involving leucine and Na+.
Yes

ENSG00000111371
Q9H2H9
MAR05319: Na+ + phenylalanine --> Na+ + phenylalanine
ENSG00000003989 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000174358
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000111371 encodes a symporter that cotransports short-chain neutral amino acids and sodium ions across the cell membrane. It shows catalytic activity in the transport of amino acids like L-glutamine, L-alanine, L-asparagine, L-histidine, L-serine, L-cysteine, L-methionine, glycine, L-threonine, and L-proline in the presence of Na+. However, the reaction Na+ + phenylalanine --> Na+ + phenylalanine does not correspond to the catalytic activities described for this gene because phenylalanine is not listed among the amino acids transported by this symporter.
No

ENSG00000154025
A0PJK1
MAR05450: glucose + Na+ --> glucose + Na+
ENSG00000117834 or ENSG00000140675 or ENSG00000148942 or ENSG00000154025 or ENSG00000158865
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000154025 encodes for a Na+-coupled sugar symporter that specifically transports D-mannose and D-fructose, with no mention of glucose transport activity. The specified reactions involve D-mannose and D-fructopyranose, whereas the provided reaction involves glucose, indicating that the transport activity of the gene product does not relate to the transport of glucose and Na+.
Not sure, keep it now.

ENSG00000103257
Q01650
MAR05467: glycine + proline <=> glycine + proline
ENSG00000103257
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000103257 encodes for a protein that functions primarily as a high-affinity transporter mediating the uptake and exchange of large neutral amino acids, thyroid hormones, and other selective substances across membranes. It does not have any known catalytic activity related to the reaction involving glycine and proline. The described functions and catalytic activities of the gene do not include any involvement with glycine and proline, thereby making it not relevant to the given reaction.
No

ENSG00000165029
O95477
MAR05540: homoserine + phenylalanine <=> homoserine + phenylalanine
ENSG00000103257 or ENSG00000165029
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000165029 encodes a protein that functions in the translocation of specific phospholipids and cholesterol across cellular membranes using ATP hydrolysis. Its annotated catalytic activities involve reactions with phospholipids (such as phosphatidylcholine, phosphatidylserine, and sphingomyelin) and cholesterol. However, the reaction provided is a simple exchange reaction involving homoserine and phenylalanine, which is unrelated to the lipid translocation or ATP-dependent activities carried out by the gene's protein product. Therefore, the gene does not participate in the given reaction.
No

ENSG00000103257
Q01650
MAR05575: homoserine + threonine <=> homoserine + threonine
ENSG00000103257
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000103257 encodes a protein that functions as a sodium-independent, high-affinity transporter mediating the uptake and exchange of large neutral amino acids, thyroid hormones, and certain toxins across cell membranes. The specific reactions facilitated by this gene involve amino acids such as phenylalanine, tryptophan, histidine, leucine, isoleucine, valine, tyrosine, methionine, and alanine, as well as thyroid hormones. However, the provided reaction involves homoserine and threonine, which are not substrates associated with the transport activities of the protein encoded by this gene. Therefore, the gene is not relevant to the reaction involving homoserine and threonine.
No

ENSG00000103257
Q01650
MAR05588: glutamine + glycine + Na+ --> glutamine + glycine + Na+
ENSG00000103064 or ENSG00000103257
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000103257 encodes a protein that functions primarily as a transporter of large neutral amino acids and thyroid hormones across cell membranes in a sodium-independent manner. The reaction provided involves the transfer of glutamine and glycine along with sodium ions, which falls under the category of sodium-dependent transport processes. Therefore, based on its annotated function, the gene ENSG00000103257 does not relate to the reaction described.
No

ENSG00000103064
Q92536
MAR05606: alanine + Na+ + tryptophan --> alanine + Na+ + tryptophan
ENSG00000103064 or ENSG00000103257
Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000103064 encodes a protein functioning as an antiporter primarily involved in the exchange of cationic and neutral amino acids such as L-arginine, L-lysine, L-leucine, L-glutamine, and others, often coupled with sodium ions. The given reaction (alanine + Na+ + tryptophan --> alanine + Na+ + tryptophan) does not involve these amino acids and does not describe an antiport exchange mechanism, indicating the gene's products do not participate in this reaction.
No

keep gene ENSG00000163295 for MAR08969: FMN + H2O --> Pi + riboflavin, encoded protein P09923 has catalytic activity(a phosphate monoester + H2O = an alcohol + phosphate).
for MAR11410, the gene ENSG00000100170 encodes a transporter that facilitates the movement of galactose using sodium ions (Na+) instead of hydrogen ions (H+), thereby it seems to modify the reaction.

Aha, It looks like we got some same opinions about ENSG00000163295 for MAR08969 and ENSG00000100170 for MAR11410, which both checked in last column of the table. Do you have any other disagreements?

Others seem fine to me.


Sending test mails to mail-tester.com

When I try to send a message to a mail-tester.com address from postal panel, I see an error as No SMTP servers were available for mail-tester.com. Tried mail-tester.com on delivery report with a "SOFT FAIL" status. What can be the problem?

Could be a DNS issue.
What does
dig -t MX mail-tester.com
give you?

 One possibility here is that your server (or your ISP) has a firewall that is preventing connections out on port 25. You can test connectivity with telnet:
telnet mail-tester.com 25

I had once the same error. It is Mail-Tester related. Just try another tool for that test. It seems like https://www.emailchecky.com is an interesting alternative.


ERROR: Could not find a version that satisfies the requirement torchaudio (from versions: none) ERROR: No matching distribution found for torchaudio

🐛 Describe the bug
ERROR: Could not find a version that satisfies the requirement torchaudio>=0.5.0 (from asteroid) (from versions: none)
ERROR: No matching distribution found for torchaudio>=0.5.0 (from asteroid)
21:40:18-root@Desktop:/pr/Neural/voicefixer_main# pip3 install torchaudio
Versions
python collect_env.py
Traceback (most recent call last):
File "/media/sd/Projects/Neural/voicefixer_main/collect_env.py", line 16, in
import torch
File "/home/plab/.local/lib/python3.9/site-packages/torch/init.py", line 196, in
from torch._C import *
RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd
21:45:45-root@Desktop:/pr/Neural/voicefixer_main# pip3 install numpy
Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (1.19.5)
Please fix torchaudio to install.  Thanks!

Hi @clort81
This looks like there is something wrong with the installation of PyTorch itself.
What version did you install, and how?
Also torchaudio does not have binary distribution for Aarch64, so the installation failure is expected.
Is it possible for you to switch to conda, install PyTorch core and build torchaudio manually?

Thanks for pointing me to the problem.  I'll wait for aarch64 support.

Closing as build on aarch64 has been fixed a while ago, and there are aarch64 distributions since PT 2.0