Allow dynamic creation of LDAPErrors for client-search operations

The docs for Client.prototype.search say

Note that the error event will only be for client/TCP errors, not LDAP error codes like the other APIs. You'll want to check the LDAP status code (likely for 0) on the end event to assert success. LDAP search results can give you a lot of status codes, such as time or size exceeded, busy, inappropriate matching, etc., which is why this method doesn't try to wrap up the code matching.

Which means when there was an LDAP error, there will be no error event with an error object, even though ldapjs has all the LDAP errors implemented as classes. But these errors need to be handled. I therefor tried the following code to construct an LDAPError myself:
request.on('end', () => {
  if (request.status === 0) {
    resolve(entries)
  } else {
    const error = new ldap.LDAPError(request.errorMessage)
    error.code = request.status
    error.name = _.capitalize(_.camelCase(_.findKey(ldapErrorCodes, code => code === request.status)))
    reject(error)
  }
})

(with ldapErrorCodes being a require('ldapjs/lib/errors/codes')). But this fails with an error, "Cannot set property code of Error which has only a getter". This is because LDAPError, for whatever reason, defines code as a non-configurable property with only a getter. I don't get why it does this instead of simply setting the value? Now, in 1.0.0 the LDAPError actually has a code parameter. But in dcce6ebe1ebadb962bb712b78769b71d12dedbf3, this parameter has been removed, so I don't really want to rely on it. It is therefor impossible to create LDAPErrors for use in search requests from the client, even though the documentation says the user is expected to do so.
Please implement the LDAPError class so that it is possible to create LDAPErrors like this:
request.on('end', () => {
  if (request.status === 0) {
    resolve(entries)
  } else {
    const error = new ldap.LDAPError(request.errorMessage, request.status)
    reject(error)
  }
})

Where error.name and error.code would be set automatically.
I would submit a PR if you dont have any objections.

Or, as that would be a breaking change (just like dcce6eb is atm), maybe just export a different createLdapError function that chooses the right error class dynamically?

Basically this algorithm, which I'm using now:
const errorName = _.capitalize(_.camelCase(_.findKey(ldapErrorCodes, ldapAnfrage.status).substr('LDAP_'.length))) + 'Error'
const error = new ldap[errorName](ldapAnfrage.errorMessage)
reject(error)

I believe you should be able to pass the result to ldap.getError in order to general a suitably constructed LDAPError object.  It's designed to consume result.status and result.errorMessage when generating an error.

@pfmooney Thanks for the quick answer. What do you mean by result, the eventemitter in the callback or the return value of search()?
I think this functions should be documented in Client.prototype.search and under Error API.
Btw, why do you pass a new eventemitter in the callpack instead of just using the return value of searc h as an EventEmitter?

Never mind, found it out.

⚠ This issue has been locked due to age. If you have encountered a recent
problem that seems to be covered by this issue, please open a new issue.
Please include a minimal reproducible example
when opening a new issue.


Use Modal initially to get User Name

CHAKRA to get name...do we need this? as we scrapping the Leaderbord Modal is not needed ...this is open to discussion

Agreed this is going to be a future improvement once the Game will allow multiple players and have  a Leader board


end to end tests failing in at_client SDK

Describe the bug
The end2end tests are failing in at_client sdk and following are the observations

The Hive keystore and commit log keystore are being removed and the end of test and being re-initialized for every test. As a result the initial sync happens before all the tests in a given file (in some cases before each test). which is time consuming and also blocking the server.

The empty batch requests are being sent to secondary server: https://github.com/atsign-foundation/at_client_sdk/issues/731

Temporary workaround:
Added skip for the failing tests. A permanent fix would be to refactor the tests.

Spend 5 SP for the analysis in PR 46

[ ] Refactor tests such that sync and creation encryption keys happens at the beginning of all tests and clears at the end of all tests

Refactored the tests and push to the refactor_tests

Half of the tests have been refactored, and the remaining tests must be refactored. I spent 5SP in this sprint. Moving it to PR49

Refactoring tests are done, The tests are failing in the GitHub actions that need to be looked at.
Draft PR - (#774 )

There is a change in the workflow file that's a part of the PR. But the GitHub actions is considering the workflow file of the trunk branch instead of my local branch. Hence the tests are failing

@purnimavenkatasubbu That is not why the tests are failing, the GitHub actions is using the workflow file of your working branch


Consider caching and/or lazy-init of DateTimeFormat instances in intl.mjs

#7 and #8 showed that new DateTimeFormat() is astoundingly expensive in time and memory. Big perf wins come from caching these instances.
The constructor for DateTimeFormat in this polyfill (which is called in every toLocaleString call) calls the builtin Intl.DateTimeFormat constructor 8 times. This will be slooooooooooow.
All those instances are probably unnecessary. At a minimum, we should lazy-init these instances so they're only constructed when needed. Given that users typically re-use the same options over and over, we could also consider caching  DateTimeFormat instances too.

Fixed by #7. Closing.


new custom menu: menuwheel

"Wheel Menus" was the best name I could come up with, I'd be happy to take better suggestions ;-)
(The idea being that you are looking at a wheel with menu items on it's side)

Nice - thanks! Yes, we definitely needed a different menu.
Nice idea searching for < Back as well! I was trying to think of a nice backward-compatible way of doing that but I think right now it's probably the best solution


feat: Introduce EphemeralStorage

Introduce EphemeralStorage trait, allowing storages to shard off usage for an EphemeralStore.
Sled/Rocks/IndexedDb implementations of EphemeralStorage with tests. Sled uses ephemeral trees, and rocks/indexeddb shard a shared ephemeral store. Ephemeral stores are cleared from the provider on Drop, and again on startup for shared ephemeral stores in the event cleanups are missed (e.g. force quit)
A few friends from #633:

OpenStorage for unified paths over other trait operators
NonPersistentStorage for tests
IterableStore for testing internal details of store ensuring ephemeral storage is cleared (now also implemented for Rocks, with tests)

IndexedDb migration tests (for the new ephemeral store).

This stack overflow  in multiplayer::orb_can_render_peers_in_the_sphere_address_book may not be an intermittent in the rocksdb build
#[ignore] doesn't not run the IndexedDb migration test, timing out

This stack overflow  in multiplayer::orb_can_render_peers_in_the_sphere_address_book may not be an intermittent in the rocksdb build

#[ignore] doesn't not run the IndexedDb migration test, timing out

The RocksDB build would consistently stack overflow on orb sphere render in  multiplayer::orb_can_render_peers_in_the_sphere_address_book, introduced by SphereDb<S> owning a Storage:
--- a/rust/noosphere-storage/src/db.rs
+++ b/rust/noosphere-storage/src/db.rs
@@ -40,6 +40,7 @@ where
     link_store: S::KeyValueStore,
     version_store: S::KeyValueStore,
     metadata_store: S::KeyValueStore,
+    storage: S,
 }

 impl<S> SphereDb<S>
@@ -52,6 +53,7 @@ where
             link_store: storage.get_key_value_store(LINK_STORE).await?,
             version_store: storage.get_key_value_store(VERSION_STORE).await?,
             metadata_store: storage.get_key_value_store(METADATA_STORE).await?,
+            storage: storage.to_owned(),
         })
     }

Changing RocksDbStore to hold an Arc<String> instead of String no longer causes a stack overflow:
--- a/rust/noosphere-storage/src/implementation/rocks_db.rs
+++ b/rust/noosphere-storage/src/implementation/rocks_db.rs
@@ -85,13 +85,13 @@ impl Storage for RocksDbStorage {

 #[derive(Clone)]
 pub struct RocksDbStore {
-    name: String,
+    name: Arc<String>,
     db: Arc<DbInner>,
 }

 impl RocksDbStore {
     pub fn new(db: Arc<DbInner>, name: String) -> Result<Self> {
-        Ok(RocksDbStore { db, name })
+        Ok(RocksDbStore { db, name: Arc::new(name) })
     }

RocksDB's !Sync cf_handle would be preferable here. Adding any other field to RocksDbStore causes the overflow again. While we make heavy use of cloning stores in the workflows, we "only" have less than 100 stores at once.

Filed https://github.com/subconsciousnetwork/noosphere/issues/675 for further work on figuring out the rocksdb stress test issue
This PR configured such to avoid the issue, though we can recreate when needed for further work on #675

This is consistently causing a stack overflow on Windows:

2023-10-19T23:42:07.2354734Z thread 'multiplayer::orb_can_render_peers_in_the_sphere_address_book' has overflowed its stack
2023-10-19T23:42:09.8418064Z error: test failed, to rerun pass -p noosphere --test distributed_stress
2023-10-19T23:42:09.8419281Z
2023-10-19T23:42:09.8419673Z Caused by:
2023-10-19T23:42:09.8421990Z   process didn't exit successfully: D:\a\noosphere\noosphere\target\debug\deps\distributed_stress-6752626ddf09eb78.exe (exit code: 0xc00000fd, STATUS_STACK_OVERFLOW)
2023-10-19T23:42:09.8424887Z note: test exited abnormally; to see the full output pass --nocapture to the harness.
2023-10-19T23:42:11.2052981Z ##[error]Process completed with exit code 1.

This is consistently causing a stack overflow on Windows:

2023-10-19T23:42:07.2354734Z thread 'multiplayer::orb_can_render_peers_in_the_sphere_address_book' has overflowed its stack
2023-10-19T23:42:09.8418064Z error: test failed, to rerun pass -p noosphere --test distributed_stress
2023-10-19T23:42:09.8419281Z
2023-10-19T23:42:09.8419673Z Caused by:
2023-10-19T23:42:09.8421990Z   process didn't exit successfully: D:\a\noosphere\noosphere\target\debug\deps\distributed_stress-6752626ddf09eb78.exe (exit code: 0xc00000fd, STATUS_STACK_OVERFLOW)
2023-10-19T23:42:09.8424887Z note: test exited abnormally; to see the full output pass --nocapture to the harness.
2023-10-19T23:42:11.2052981Z ##[error]Process completed with exit code 1.

Fixed by increasing thread stack size on Windows.
Separately, rerunning the failed builds resulted in a successful rocksdb test run

rebased on #685


Manta async work

This PR adds Manta support and the tomo scan plan with ophyd-async.

The changes look good to me, but I'd like to have another pair of eyes on that.
@jwlodek, do you mind checking/merging?

I suggest to merge this PR #6 first, then #5, and keep #4 open for now until we use the released version of ophyd-async with the fixes.


Expand input/ouput attributes

Add optional min and max partial shapes that can be used do dynamic shape execution planning, and inferred versions for use by a dynamic shape reduction pass.
Add a connected output element type and shape information cache to inputs. This is to be used when doing sub-graph replacement to optionally verify that the replacement element type and shape match the original.

Superseded by #4466


BPMN

Would it be possible to add BPMN as an initialism?

You can create your own set of recognized initialisms by doing the following:
ini := snaker.NewDefaultInitialisms()
if err := ini.Add("BPMN"); err != nil {
    panic(err)
}


Swict to be selected by default

Hello,
Thank you for this swicth. I am using it in my application.
Just wondering of tehre was a way to ensure that the swicth is turned on (selected) by default.
Thanks in advance.

There is no way right now. But it is not hard to implement that feature so i will add it and let you know.

Hey, in the meantime, I used this approach to click the switch automatically upon load
from PyQt5.QtTest import QTest
from PyQt5.QtCore import Qt
the swict should be in combined mode by default
Click the button
QTest.mouseClick(switch, Qt.LeftButton)

There you go. I've just finished that feature and you can use below:
`isChecked()`
`setChecked(f: bool)`

You can use it as in example on README.

Thank you so much.
I have used this feature in my QGIS Geoprivacy plugin, with a 5-minute video on YouTube: https://www.youtube.com/watch?v=gq4wX3kMTfE
The plugin can be downloaded from GitHub https://github.com/sharmapn/MapSafe-QGIS-plugin
Help guide here: https://sharmapn.github.io/MapSafeQGISGeoPrivPlugin/

It's great that you find my widget useful ! Your application looks great ! I can't imagine your huge effort to make it.
I've just liked your video and subscribed as well.

Thank you so much Jung!
Is there a way to control the X and Y coordinates of the switch?
It would be nice to vertically align the switch with the rest of the controls under it.

You want to set the x and y coordinates of the switch(inner circle to me) rather than resizing it inside (which can be done by setCircleDiameter)? I can do that, but i want to do it in a different sort of way.
It would be nice to add the feature to set margin or padding than add the feature which absolutely changing the coordinates.


Include prerequisites in README install instructions.

This is a small change to README.md that makes mention of how to install node and use npm to install bower globally. These are required to complete the first npm install step of the installation instructions.
Since on most machines this will already be done, and is not specific to black-screen, I created a prerequistes section in the README so most people can just skip over it.

Bower is in dependencies already so it must be installed with npm install command.

Also I like compact model, like this one.

@xtoddx, I agree with @G07cha. We do expect some level of knowledge from our users (prerequisites, huh?). I think it's hard to find a developer who doesn't know how to install node.js.

Maybe we were racing each other :racehorse:  #89 landed after my fork, it fixes the use of bower in a preinstall script.

@xtoddx that's true. Thank you for help in any case.


[KV] KV View - Node & Bucket improvements

Update panels to use the timeseries type. The old "graph" type is deprecated and shows a warning.

Add the mutation_mem_ratio/threshold to the memory usage graph

Add descriptions of the important memory thresholds

Make the thresholds use dashed lines and no fill, to visually distinguish them from the other metrics (reduces clutter)

Before

After

Very nice! Thanks for the patch.


FootBall Club Website

Project title
FootBall Club Website
Project Description
A front-end website for MAnchester United FootBall Club
Stack:
And in order to tick the check box just but x inside them for example - [x] like this. Please delete options that are not relevant.

[x] Html
[x] CSS

https://leafy-crumble-33f5b9.netlify.app/

/assign


DRILL-7456: Batch count fixes for 12 operators

Enables batch validation for 12 additional operators:

MergingRecordBatch
OrderedPartitionRecordBatch
RangePartitionRecordBatch
TraceRecordBatch
UnionAllRecordBatch
UnorderedReceiverBatch
UnpivotMapsRecordBatch
WindowFrameRecordBatch
TopNBatch
HashJoinBatch
ExternalSortBatch
WriterRecordBatch

Fixes issues found with those checks so that this set of
operators passes all checks.
Includes code cleanup in many files touched during this
work.

@arina-ielchiieva, thanks much for the review. Addressed comments. Reverted (most) changes to header files. Have disabled automatic import organization in my IDE; will deal with maintaining imports manually until we decide on a standard order.

+1, LGTM


Feature: Allow layered Parameter definitions for Path Parameters

Description
Controller.parameters does not allow to "pre-declare" path arguments
MCVE
from __future__ import annotations

import json

from litestar import get, Controller
from litestar.app import Litestar
from litestar.params import Parameter

class UserController(Controller):
    path = "/users/{path_item:str}"
    parameters = {
        "path_item": Parameter(description="Lorem ipsum"),  # this breaks it
        "query_item": Parameter(description="Lorem ipsum"),
        "header_item": Parameter(header="header-item", description="Lorem ipsum"),
        "cookie_item": Parameter(cookie="cookie_item", description="Lorem ipsum"),
    }

    @get()
    async def get(self, path_item: str, query_item: str, header_item: str, cookie_item: str) -> str:
        return "hello"

app = Litestar(
    [UserController],
    debug=True,
)

print(json.dumps(app.openapi_schema.to_schema(), indent=4))

Steps to reproduce
Above leads to:
Traceback (most recent call last):
  File "/home/mtvx/Projects/myproject/api/litestar_testapp.py", line 24, in <module>
    app = Litestar(
  File "/home/mtvx/.cache/pypoetry/virtualenvs/oura-1LPe1lTf-py3.10/lib/python3.10/site-packages/litestar/app.py", line 470, in __init__
    self.register(route_handler)
  File "/home/mtvx/.cache/pypoetry/virtualenvs/oura-1LPe1lTf-py3.10/lib/python3.10/site-packages/litestar/app.py", line 657, in register
    route.create_handler_map()
  File "/home/mtvx/.cache/pypoetry/virtualenvs/oura-1LPe1lTf-py3.10/lib/python3.10/site-packages/litestar/routes/http.py", line 99, in create_handler_map
    kwargs_model = self.create_handler_kwargs_model(route_handler=route_handler)
  File "/home/mtvx/.cache/pypoetry/virtualenvs/oura-1LPe1lTf-py3.10/lib/python3.10/site-packages/litestar/routes/base.py", line 135, in create_handler_kwargs_model
    return KwargsModel.create_for_signature_model(
  File "/home/mtvx/.cache/pypoetry/virtualenvs/oura-1LPe1lTf-py3.10/lib/python3.10/site-packages/litestar/_kwargs/kwargs_model.py", line 282, in create_for_signature_model
    cls._validate_raw_kwargs(
  File "/home/mtvx/.cache/pypoetry/virtualenvs/oura-1LPe1lTf-py3.10/lib/python3.10/site-packages/litestar/_kwargs/kwargs_model.py", line 466, in _validate_raw_kwargs
    raise ImproperlyConfiguredException(
litestar.exceptions.http_exceptions.ImproperlyConfiguredException: 500: Kwarg resolution ambiguity detected for the following keys: p, a, t, h, _, i, t, e, m. Make sure to use distinct keys for your dependencies, path parameters and aliased parameters.

If you comment out the path_item from parameters, then it works (but "Lorem ipsum" is not set for the path item).
Litestar Version
2.7.0
Platform

[X] Linux
[ ] Mac
[ ] Windows
[ ] Other (Please specify in the description above)

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Thanks for reporting, could you include the full traceback please?

Added to the description.

Aah we're not ignoring ParameterKwarg for path parameters that are included in the layered parameters here.
Also, it seems there's a small error in the error message since it's displaying each letter instead of all the duplicate names.

This is documented behavior:

Aww crap, indeed I didn't see that 🙈

Also, it seems there's a small error in the error message since it's displaying each letter instead of all the duplicate names.

Yeah, maybe the error message could be polished if not anything else.
Does it still stand that it would be complicated to implement this, or have things changed...?

I'm thinking if we should even allow this. I can't think of a good use case for this actually. Since you can, due to their nature, only define paths locally, it makes sense that their parameters should be declared as close as possible as well.

I'm thinking if we should even allow this. I can't think of a good use case for this actually. Since you can, due to their nature, only define paths locally, it makes sense that their parameters should be declared as close as possible as well.
@litestar-org/maintainers?

I don't think this is something we should support either. As shown here, there would be some ambiguity and while we can deal with it, there would still be room for a lot of confusion.


Uncaught AssertionError in fun.py line 210

Aider version: 0.55.0
Python version: 3.11.5
Platform: Windows-10-10.0.22631-SP0
Python implementation: CPython
Virtual environment: No
OS: Windows 10 (64bit)
Git version: git version 2.43.0.windows.1
An uncaught exception occurred:
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "__main__.py", line 7, in <module>
    sys.exit(main())
             ^^^^^^
  File "main.py", line 551, in main
    if not sanity_check_repo(repo, io):
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "main.py", line 302, in sanity_check_repo
    repo.get_tracked_files()
  File "repo.py", line 274, in get_tracked_files
    staged_files = [path for path, _ in index.entries.keys()]
                                        ^^^^^^^^^^^^^
  File "util.py", line 253, in __getattr__
    self._set_cache_(attr)
  File "base.py", line 168, in _set_cache_
    self._deserialize(stream)
  File "base.py", line 197, in _deserialize
    self.version, self.entries, self._extension_data, _conten_sha = read_cache(stream)
                                                                    ^^^^^^^^^^^^^^^^^^
  File "fun.py", line 252, in read_cache
    version, num_entries = read_header(stream)
                           ^^^^^^^^^^^^^^^^^^^
  File "fun.py", line 210, in read_header
    assert version in (1, 2)
           ^^^^^^^^^^^^^^^^^
AssertionError

Thanks for trying aider and filing this issue.
The fix is available in the main branch. You can get it by installing the latest version from github:
aider --install-main-branch

# or...

python -m pip install --upgrade git+https://github.com/paul-gauthier/aider.git

If you have a chance to try it, let me know if it works better for you.


Destination Collection Error returns Acceptable Destinations in extended_headers rather than status_detail

Version 1.1 of the TAXII Services Specification states that additional information relating to Status Messages should be provided in the Status Detail field, but in the OpenTAXII response to an Inbox Message containing no collection names when one or more is required, the Acceptable Destination values are returned in the extended_headers attribute instead.
You can see the block of code here which is causing the problem.  It looks like StatusMessageException will happily take a status_details attribute, so it seems like it just needs to be switched over.

awesome point, @danielsamuels. made a pull request

@danielsamuels merged. I'm closing this ticket


Update SPF records

It might be useful update SPF records that contain IP addresses.

Just use the a mechanism.


Do not use OZ test helpers

Recognize, cite, and incorporate best practices in:

https://hardhat.org/config
https://github.com/ProjectOpenSea/seaport/blob/a9552b9c89bbeeee49392ab4947d4ed93c565fbc/test/basic.spec.ts

They are not using contract(), just using plain describe() / it().
Let's do that, it is less dependencies.
Also they are using a simpler Hardhat config. Let's do that.

fixed at https://github.com/fulldecent/solidity-template/commit/9af875778a56de72ab4d9859c0896f44ef6da9b6


Uncaught Error: Cannot read property 'object' of undefinedTypeError: Cannot read property 'objec...

[Enter steps to reproduce below:]

...
...

Atom Version: 1.10.2
Electron Version: 0.37.8
System: Mac OS X 10.11.6
Thrown From: Atom Core
Stack Trace
Uncaught Error: Cannot read property 'object' of undefined
TypeError: Cannot read property 'object' of undefined
at ObjectsRegistry.get (/Applications/Atom.app/Contents/Resources/electron.asar/browser/objects-registry.js:44:28)
at EventEmitter. (/Applications/Atom.app/Contents/Resources/electron.asar/browser/rpc-server.js:309:31)
at emitMany (events.js:121:13)
at EventEmitter.emit (events.js:195:7)
at EventEmitter. (/Applications/Atom.app/Contents/Resources/electron.asar/browser/api/web-contents.js:141:25)
at emitTwo (events.js:100:13)
at EventEmitter.emit (events.js:185:7)
At /Applications/Atom.app/Contents/Resources/electron.asar/renderer/api/remote.js:178

Error: Cannot read property 'object' of undefined
TypeError: Cannot read property 'object' of undefined
    at ObjectsRegistry.get (/Applications/Atom.app/Contents/Resources/electron.asar/browser/objects-registry.js:44:28)
    at EventEmitter.<anonymous> (/Applications/Atom.app/Contents/Resources/electron.asar/browser/rpc-server.js:309:31)
    at emitMany (events.js:121:13)
    at EventEmitter.emit (events.js:195:7)
    at EventEmitter.<anonymous> (/Applications/Atom.app/Contents/Resources/electron.asar/browser/api/web-contents.js:141:25)
    at emitTwo (events.js:100:13)
    at EventEmitter.emit (events.js:185:7)
  at metaToValue (/Applications/Atom.app/Contents/Resources/electron.asar/renderer/api/remote.js:178:13)
  at undefined.remoteMemberFunction (/Applications/Atom.app/Contents/Resources/electron.asar/renderer/api/remote.js:112:18)
  at AtomEnvironment.module.exports.AtomEnvironment.getWindowDimensions (/Applications/Atom.app/Contents/Resources/app.asar/src/atom-environment.js:636:29)
  at AtomEnvironment.module.exports.AtomEnvironment.storeWindowDimensions (/Applications/Atom.app/Contents/Resources/app.asar/src/atom-environment.js:670:36)
  at WindowEventHandler.module.exports.WindowEventHandler.handleWindowBlur (/Applications/Atom.app/Contents/Resources/app.asar/src/window-event-handler.js:182:35)
  at /Applications/Atom.app/Contents/Resources/app.asar/src/window-event-handler.js:3:61

Commands

Config
{
  "core": {
    "customFileTypes": {
      "source.ini": [
        ".buckconfig",
        ".flowconfig"
      ],
      "source.json": [
        ".arcconfig",
        "BUCK.autodeps"
      ],
      "source.python": [
        "BUCK"
      ]
    },
    "disabledPackages": [
      "tree-view"
    ]
  },
  "editor": {
    "fontSize": 25
  }
}

Installed Packages
# User
atom-prettify, v0.1.3 (inactive)
atom-ternjs, v0.15.0 (active)
autocomplete-python, v1.8.6 (active)
base64, v0.3.0 (inactive)
docblockr, v0.8.2 (active)
emmet, v2.4.3 (active)
nuclide, v0.159.0 (active)
pretty-json, v1.5.1 (active)
react, v0.15.0 (active)
remote-sync, v4.1.2 (active)
script, v3.9.0 (inactive)
atom-dark-syntax, v0.27.0 (inactive)
atom-dark-ui, v0.52.0 (inactive)
atom-light-syntax, v0.28.0 (inactive)
atom-light-ui, v0.44.0 (inactive)
base16-tomorrow-dark-theme, v1.1.0 (inactive)
base16-tomorrow-light-theme, v1.1.1 (inactive)
one-dark-ui, v1.5.0 (active)
one-light-ui, v1.5.0 (inactive)
one-dark-syntax, v1.3.0 (active)
one-light-syntax, v1.3.0 (inactive)
solarized-dark-syntax, v1.0.2 (inactive)
solarized-light-syntax, v1.0.2 (inactive)
about, v1.5.3 (active)
archive-view, v0.61.1 (active)
autocomplete-atom-api, v0.10.0 (active)
autocomplete-css, v0.11.2 (active)
autocomplete-html, v0.7.2 (active)
autocomplete-plus, v2.31.1 (active)
autocomplete-snippets, v1.11.0 (active)
autoflow, v0.27.0 (inactive)
autosave, v0.23.1 (active)
background-tips, v0.26.1 (active)
bookmarks, v0.41.0 (active)
bracket-matcher, v0.82.1 (active)
command-palette, v0.38.0 (inactive)
deprecation-cop, v0.54.1 (active)
dev-live-reload, v0.47.0 (active)
encoding-selector, v0.22.0 (active)
exception-reporting, v0.39.0 (active)
find-and-replace, v0.201.0 (active)
fuzzy-finder, v1.3.0 (active)
git-diff, v1.1.0 (active)
go-to-line, v0.31.0 (inactive)
grammar-selector, v0.48.1 (active)
image-view, v0.58.2 (active)
incompatible-packages, v0.26.1 (active)
keybinding-resolver, v0.35.0 (active)
line-ending-selector, v0.5.0 (active)
link, v0.31.1 (inactive)
markdown-preview, v0.158.0 (active)
metrics, v0.53.1 (active)
notifications, v0.65.0 (active)
open-on-github, v1.2.0 (inactive)
package-generator, v1.0.0 (inactive)
settings-view, v0.242.2 (active)
snippets, v1.0.2 (active)
spell-check, v0.67.1 (active)
status-bar, v1.4.1 (active)
styleguide, v0.47.0 (active)
symbols-view, v0.113.0 (inactive)
tabs, v0.100.2 (active)
timecop, v0.33.2 (active)
tree-view, v0.208.2 (inactive)
update-package-dependencies, v0.10.0 (active)
welcome, v0.34.0 (active)
whitespace, v0.33.0 (active)
wrap-guide, v0.38.1 (active)
language-c, v0.52.1 (active)
language-clojure, v0.21.0 (active)
language-coffee-script, v0.47.2 (active)
language-csharp, v0.12.1 (active)
language-css, v0.37.1 (active)
language-gfm, v0.88.0 (active)
language-git, v0.15.0 (active)
language-go, v0.42.1 (active)
language-html, v0.45.1 (active)
language-hyperlink, v0.16.0 (active)
language-java, v0.23.0 (active)
language-javascript, v0.119.0 (active)
language-json, v0.18.2 (active)
language-less, v0.29.5 (active)
language-make, v0.22.2 (active)
language-mustache, v0.13.0 (active)
language-objective-c, v0.15.1 (active)
language-perl, v0.35.0 (active)
language-php, v0.37.2 (active)
language-property-list, v0.8.0 (active)
language-python, v0.45.0 (active)
language-ruby, v0.69.0 (active)
language-ruby-on-rails, v0.25.0 (active)
language-sass, v0.56.0 (active)
language-shellscript, v0.22.4 (active)
language-source, v0.9.0 (active)
language-sql, v0.23.0 (active)
language-text, v0.7.1 (active)
language-todo, v0.28.0 (active)
language-toml, v0.18.0 (active)
language-xml, v0.34.9 (active)
language-yaml, v0.26.0 (active)

# Dev
No dev packages

This is a duplicate of #11692 - feel free to subscribe there for updates.


maybe update portal to fetch the src and if the status is a 200 then add as the srcdoc of the child itself

also add helpers for:

https://developer.mozilla.org/en-US/docs/Web/HTML/Element/iframe#attr-referrerpolicy
https://developer.mozilla.org/en-US/docs/Web/HTML/Element/iframe#attr-sandbox

add a centered error_icon attribute callback to an optional image to show if srcdoc fails


Setting Google Play package name for intent

I've added setting Google Play package name for rate intent (if available). This will allow to avoid the 'Complete Action by using (Play, Chrome, Web Browser)' dialog

Sorry for the delay.
I reviewed your contribution:)

Hi @hotchemi !
Also sorry for the delay. I have fixed that you asked for.
getInstalledApplications(0) returns full list of installed application packages.

Thx! Perfect!


Remove containerd v1 runtime jobs

The v1 runtimes have been deprecated within containerd. Removing jobs related to the v1 runtimes as they will no longer be supported in contianerd.

/ok-to-test


AutoSave pastes file(s) with changes into the pane with the focus, on top of the code already there.

 Wait for, or trigger autoSave. (I have reinstalled vscode, restarted, and tried all the autosave options multiple ways. Issue started after I updated my computer. I'm on the Windows Insiders fast ring. Issue has persisted for more than two weeks.) These screenshots show original saved files, edited text, focus change/save, and then another focus change/save.

Copied from original issue: Microsoft/vscode#22552

From @1nsomniac on March 13, 2017 17:20
Ummm, so I resolved this issue. JS-CSS-HTML Formatter (sic) by lonefy instigates the issue. When it's off it doesn't happen.

It is possible that this issue is caused by an installed extension. Can you try to run VS Code without extensions? From the command line, execute: code --disable-extensions and try your steps again to see if it reproduces. If you see it is an issue with the extension, please file it against the extension repository itself.

From @1nsomniac on March 13, 2017 17:23
Thanks :)

I will move this issue to the https://marketplace.visualstudio.com/items?itemName=lonefy.vscode-JS-CSS-HTML-formatter
You can find the repository yourself o the Marketplace.


improve StringUtil impl and add test

Pull request type
improvement

Please check the type of change your PR introduces:

[ x] Bugfix
[ ] Feature
[ ] Code style update (formatting, renaming)
[ ] Refactoring (no functional changes, no api changes)
[ ] Build related changes
[ ] Documentation content changes
[ ] Other (please describe):

What is the current behavior?

Issue Number: N/A
What is the new behavior?

Other information

Please @djy0 rename String.move to StringUtil.move in the new PR.


ParameterObject::WriteParameterFiles does not write the first map!

It appears that ParameterObject::WriteParameterFiles skips the first map from the specified parameterMapVector: https://github.com/SuperElastix/elastix/blob/81324cf0158256ae48a14762514ce60e786ac485/Core/Main/elxParameterObject.cxx#L379-L401
The bug appears introduced with pull request #50 commit 9ba16836e1a0642ecd2006a70ce3886b1fa4720e "ENH: Add convenience methods for writing parameter files", merged on March 20, 2018, when the member function became as follows: https://github.com/SuperElastix/elastix/blob/9ba16836e1a0642ecd2006a70ce3886b1fa4720e/Core/Main/elxParameterObject.cxx#L256-L280
FYI @kaspermarstal

I also encountered this issue:
https://github.com/InsightSoftwareConsortium/ITKElastix/blob/29ce6866414070136bb5bc2f70129eafcdde7040/wasm/write-parameter-files.cxx#L74-L76

@dzenanz @thewtex Please check:

https://github.com/SuperElastix/elastix/pull/967

I also encountered this issue:
https://github.com/InsightSoftwareConsortium/ITKElastix/blob/29ce6866414070136bb5bc2f70129eafcdde7040/wasm/write-parameter-files.cxx#L74-L76

@thewtex Thanks Matt! Please remember that these two lines should be removed, once ITKElastix has been updated to include elastix PR #967 (commit a57470b0ccfcab925e101f6e6577abaf2074574a):
// The initial is not written by WriteParameterFiles
ITK_WASM_CATCH_EXCEPTION(pipeline, elastix::ParameterObject::WriteParameterFile(parameterMaps[0], parameterFiles[0]));


Any examples of Nucleus in use?

I've gone over the examples and read a bit through the source, but would also like to see it used in real projects. I'm currently just setting up an RxPresenter with my NucleusFragments/Activities and just interacting with the presenter through public methods, but would like to try some more advanced features. Does anyone know of any examples of using Nucleus in a full project?

Hi, just serach github for info.android15.nucleus


Update CRD configuration docs and fix the CDP build

Update CRD configuration docs

Coverage remained the same at 23.766% when pulling 6c5c5859ce76c8ba0bcea0d649171c9f935849d8 on improve-crd-docs into f25351c36a4e62e18f2af6704d9aace38b7539d6 on master.

:+1:


Package board-automation scripts

Description of changes
This PR packages the build_automation scripts into their own package.
Testing
Basic functionality for boardctl and nvtopo.py were tested against an Orin AGX developer kit and confirmed to work.

Tested working on Orin AGX. There's some documentation for using this package here:
https://docs.nvidia.com/jetson/archives/r35.2.1/DeveloperGuide/text/AT/BoardAutomation.html


Bug in plot_nodal_values

Before submitting the issue

[X] I have visited the Troubleshooting section.
[X] I have searched among the existing issues.
[X] I am using a Python virtual environment.
[X] I have a fully updated virtual environment (i.e. pip install --upgrade --upgrade-strategy eager ansys-mapdl-core)

Description of the bug
Calling PostProcessing.plot_nodal_values results in an Error, which is produced by the function call self.nodal_values.
The "comp"-parameter in the function call self.nodal_values is always an empty string and is not set to the right value
https://github.com/pyansys/pymapdl/blob/71d326fd31cfd80c858f6d9996944bbd86809213/src/ansys/mapdl/core/post.py#L509
Steps To Reproduce
Steps:

First I did...
...

And I ran the following code:

from ansys.mapdl.core import launch_mapdl
mapdl = launch_mapdl()

# Insert your code here
mapdl.post1()
mapdl.post_processing.plot_nodal_values("B", "X")

Which Operating System are you using?
Windows
Which Python version are you using?
3.10
PyMAPDL Report

Show the Report!

# PASTE HERE THE OUTPUT OF `python -c "from ansys.mapdl import core as pymapdl; print(pymapdl.Report())"` here

Installed packages

Show the installed packages!

# PASTE HERE THE OUTPUT OF `python -m pip freeze` here

Logger output file

Show the logger output file.

# PASTE HERE THE CONTENT OF THE LOGGER OUTPUT FILE.

@Jrek98 Hi, this is not a bug.  The results have not been read into the MAPDL database yet for post processing.  Try this instead:
mapdl.post1()
mapdl.set('last')
mapdl.post_processing.plot_nodal_values("B", "X")

Mike

@mikerife Hey, thanks for your reply. Unfortunately this does not solve the problem.
You are right, I missed the reading, but when you have a look at the mentioned line the comp(onent) will always be set to ""
This is the error that occurs after executing the code:

TypeError                                 Traceback (most recent call last)
Cell In[4], line 3
1 mapdl.post1()
2 mapdl.set('last')
----> 3 mapdl.post_processing.plot_nodal_values("B", "X")
File [c:\Python310\lib\site-packages\ansys\mapdl\core\post.py:509](file:///C:/Python310/lib/site-packages/ansys/mapdl/core/post.py:509), in PostProcessing.plot_nodal_values(self, item, comp, show_node_numbering, **kwargs)
458 def plot_nodal_values(self, item, comp, show_node_numbering=False, **kwargs):
459     """Plot nodal values
460
461     Displays solution results as continuous element contours.
(...)
506     ... )
507     """
--> 509     values = self.nodal_values(self, item, comp="")
510     kwargs.setdefault(
511         "scalar_bar_args", {"title": f"item: {item}\nComponent: {comp}"}
512     )
513     return self._plot_point_scalars(
514         values, show_node_numbering=show_node_numbering, **kwargs
515     )
TypeError: PostProcessing.nodal_values() got multiple values for argument 'comp'

Hi @Jrek98 @germa89
Adding germa89 for visibility as it does seem to be a bug.  Jrek98: we can element plot Bx, or create native (mapdl) png files of nodal Bx plots; or dump the data and the grid out and use PyVista to plot the result.
The 'Normal' Power Graphics MAPDL PLNSOL plot will not average across the material boundaries so any non-MAPDL plot is kind of hard to replicate since the method used to retrieve the nodal values returns an average (of all attached elements of the node) value.
Mike
BFluxPlot.zip

Hi @Jrek98 @germa89
Jrek98 attached is a cleaned up version with a better PyVista plot of the Bx result for the model.  By the way the model is not an verification manual model; rather is is the example from the Ansys MAPDL Help -> Low Frequency Electromagnetic Analysis Guide -> Section 2.5.1 Example: Basic 2D Static Magnetic Analysis.
To compare results first the following is done to create a Power Graphics, reversed video (white background, black element edges and text), Bx plot:
mapdl.graphics('power')
mapdl.rgb('INDEX',100,100,100, 0)
mapdl.rgb('INDEX', 80, 80, 80,13)
mapdl.rgb('INDEX', 60, 60, 60,14)
mapdl.rgb('INDEX', 0, 0, 0,15)

mapdl.edge(1,1)
mapdl.show('png')
mapdl.plnsol('b','x')
mapdl.show('')

Which results in this plot:

Next we take advantage of both PyMAPDL mesh.grid and post_processing respecting element and node selections to gather the results on a body-by-body basis.  Bodies here defined as element groups that share material ID numbers.  We can get a list of unique material IDs (having imported numpy as np) and loop over each set gathering the mesh.grid and result for each element group:
elem_mats = mapdl.mesh.material_type
grids = []
scalars = []
for mat in np.unique(elem_mats):
    mapdl.esel('s','mat','',mat)
    mapdl.nsle()
    grids.append(mapdl.mesh.grid)
    scalars.append(mapdl.post_processing.nodal_values('b','x'))
mapdl.allsel()

I'm still learning PyVista (and am not a developer) so this may not be the best approach.  But we can then loop over each element group in the grid list and add them to a PyVista plotter, along with some plot controls, to recreate the above plot.  Matplotlib is imported as mpl and PyVista as pv.
cmap1 = (mpl.colors.ListedColormap(['blue','royalblue', 'cyan', '#00FA9A','#7CFC00', '#ADFF2F','yellow', 'orange','red'])
        .with_extremes())

plotter = pv.Plotter()

for i in range(0,4):
    _ = plotter.add_mesh(grids[i],scalars=scalars[i], show_edges = True, cmap=cmap1,n_colors=9,scalar_bar_args = {
    "color": "black",
    "title": "B Flux X",
    "vertical": False,
    "n_labels": 10,})

_ = plotter.set_background(color='white')
_ = plotter.camera_position = 'xy'
_ = plotter.color_map = 'jet'
plotter.show()

Which results in this plot...pretty close!

Mike
BFluxPlot-Version2.zip

Hey Mike, thanks for the very good example. It does exactly what I wanted to achieve. Maybe this can be included in the documentation to show how to plot results that are not directly available. So that some more people can profit from your work/example.

Hey Mike, thanks for the very good example. It does exactly what I wanted to achieve. Maybe this can be included in the documentation to show how to plot results that are not directly available. So that some more people can profit from your work/example.

I think this is a good idea. If @mikerife can do a first approach to the example (like give it a title, objectives, document the sections, etc), I can work on it to upload it to the example database :)


Code First: Consider going "all-in" on nested closure

Several folks expressed usability concerns re our current "dual" mode fluent API patterns. The main problem is that it is natural (for some users at least) to want method chaining for sibling configuration; not for child configuration. E.g.You can't currently easily do this:
modelBuilder
    .Entity<Foo>()
    .Entity<Bar>()

@anpete
The more usable thing that is missing is moving from one child configuration to another.
e.g. changing the column type of two columns with one chain.
NHiberante has it, though if not designed right, it can cause people to use invalid configurations.

Related to #4960

We decided not to do it.


[Feature]: Burn time

Describe the Feature
Simple suggestion, allow more time until camp fire goes out. I would like to make mine go for 45 minutes
Current limit 10000 ticks

There is a config option "campfireLitTime" where you can configure the time a campfire burns.
There is a defaultconfig directory, where you can find the config file. If you change something there it has only an effect on new savegames. For existing savegames you need to go to the serverconfig directory of the savegame.

Did you read what I wrote?
I know there's a configurados file, but you have set a limit of 10000 ticks. What I was asking is to remove that limit and allow for it to burn for more time

Sorry, I seem to have misunderstood your request. :)

The max limit of the following configurations was increased to 2.000.000: campfireLitTime, campfireRainUnlitTime, soulCampfireLitTime, soulCampfireRainUnlitTime
The change is included in the mod versions: 1.18.1-<IP_ADDRESS> & 1.19-<IP_ADDRESS>


Invalid handling of parameter values starting with double quotes ("), e.g. --order-by='"quoted" value'

Information

OS: Linux, Ubuntu 18.04 LTS
Version: 0.44
Terminal: xterm-256color, zsh

Describe the bug
Parameter values cannot start with double quotes ("), they are either replaced or handled completely wrong. Additionally, parameter values are TRIMMED (remove leading spaces), so adding a space to workaround this is not possible.
The following example even cuts off the parameter value and treats everything after the space as EXTRA argument, in the following case value is handled as positional argument and not part of --order-by:
cli-tester test --order-by '"quoted" value' input.mp3

This may be a security flaw under specific circumstances.
More examples of invalid handling:
# `quoted` instead of `"quoted" value` and cut off handling as positional argument
cli-tester test --order-by '"quoted" value' input.mp3
cli-tester test --order-by='"quoted" value' input.mp3

# `quoted` instead of `"quoted"`
cli-tester test --order-by '"quoted"' input.mp3

# `quoted` instead of ` "quoted"`
cli-tester test --order-by ' "quoted"' input.mp3

The following examples work like expected, if not starting with double quotes or single quotes are used
# `value "quoted" like expected
cli-tester test --order-by 'value "quoted"' input.mp3

# `'quoted' value` like expected
cli-tester test --order-by "'quoted' value" input.mp3

# `\"quoted" value' value` like expected
cli-tester test --order-by='\"quoted" value' input.mp3

To Reproduce

Compile https://github.com/sandreas/tone/tree/main/cli-tester
Run the above examples

Expected behavior
I would expect double quotes (") and spaces ( )  CAN be a valid part of a parameter value and should not be replaced or parsed out in any way.

Unfortunately, this is out of our hands. We are just parsing the args that .NET gets from its command line handler. In fact, on Windows I get different results from you with different examples.
David Deley has a nice resource keeping track of all the nuisances.
I'm gonna go ahead and close this because as you can tell from David's doc there are just so many possible combinations of behaviors there really isn't anyway we'd be able to rework this in a logical way so we'll continue relying on the OS and framework's behaviors.

Unfortunately, this is out of our hands. We are just parsing the args that .NET gets from its command line handler. In fact, on Windows I get different results from you with different examples.

Thank you for your response, but I still think, that it IS a problem in spectre.console. On Windows, single quotes (') CANNOT be used to enclose arguments, so on Windows this problem might not be reproducible, because only double quotes (") are supported for enclosure.
On POSIX you can either use double quotes or single quotes (" or ') to enclose an argument - the difference is, that in double quotes shell variables are evaluated (e.g. echo --path="$HOME" => --path="/home/sandreas", while echo --path='$HOME' => --path=$HOME)
It would be a HUGE problem in dotnet to not parse command line args correctly on macOS and Linux, so I tried the code example below with the according shell command to verify it is NOT a dotnet problem (maybe I'm still wrong, but my example works correctly without using spectre.console and FAILS when I try to integrate it):
// Program.cs, dotnet 6
    Console.WriteLine("== Environment.CommandLine ==");
    Console.WriteLine(Environment.CommandLine);
    Console.WriteLine("");

    Console.WriteLine("==  Environment.GetCommandLineArgs() ==");
    foreach(var a in Environment.GetCommandLineArgs()){
        Console.WriteLine(a);
    }
    Console.WriteLine("");

    Console.WriteLine("== args ==");
    foreach(var b in args){
        Console.WriteLine(b);
    }
    return 0;

Output:
./dist/cli-tester test --order-by '"quoted" value' input.mp3
== Environment.CommandLine ==
/home/sandreas/projects/tone/cli-tester/dist/cli-tester.dll test --order-by "\"quoted\" value" input.mp3

==  Environment.GetCommandLineArgs() ==
/home/sandreas/projects/tone/cli-tester/dist/cli-tester.dll
test
--order-by
"quoted" value
input.mp3

== args ==
test
--order-by
"quoted" value
input.mp3

Side note: If you don't really compile and run the binary, but try with the debugger / IDE, it might reorganize the command arguments you are running and break the args string WITHIN the IDE - this happened to me in JetBrains Rider and resulted in:
== Environment.CommandLine ==
/home/sandreas/projects/tone/cli-tester/bin/Debug/net6.0/cli-tester.dll test --order-by 'quoted value' input.mp3

==  Environment.GetCommandLineArgs() ==
/home/sandreas/projects/tone/cli-tester/bin/Debug/net6.0/cli-tester.dll
test
--order-by
'quoted
value'
input.mp3

== args ==
test
--order-by
'quoted
value'
input.mp3

So looking at the args dump for a real compiled program, which I use in my example, the "quoted" value is definitely preserved as I would expect. That makes me think something happens with args in CommandApp.RunAsync(args)

I'm gonna go ahead and close this

Could you please verify my results from above with a real compiled program on a POSIX system? That would be awesome.


Commenting use_label_encoder - xgboost

Why are these changes needed?
use_label_encoder is deprecated since 1.7.0. (xgboost), yet it is still currently provided as part of the hyperparameter for xgboost

Related issue number
https://github.com/microsoft/FLAML/issues/1120

Checks

[ ] I've included any doc changes needed for https://microsoft.github.io/FLAML/. See https://microsoft.github.io/FLAML/docs/Contribute#documentation to build and test documentation locally.
[ ] I've added tests (if relevant) corresponding to the changes introduced in this PR.
[ ] I've made sure all auto checks have passed.

@qingyun-wu Check benchmark option.

@minghao51, thank you for the contribution. We have some installation option that requires xgboost version earlier than 1.7.0.  Can you please first check the version of xgboost and only comment the line only when the version number is larger than or equal to 1.7.0? This ensure the code still works fine even when an earlier version of xgboost is used.
Thank you!

Sure

Updated the PR


mmseq2 vs. blastp

Recently I came across the tool you have developed: MMseqs2 and I have tested for the protein search. It is very fast comparing to blastp. However, I noticed the number of hit is about 1/3 of the blastp hit if I use the most sensitive parameter -s 7.5 and the same evalue cutoff 0.01. The target database is about 2M sequence and the query is 10K sequence. I noticed a lot of warning message was printed "Sequence 131 produces too many hits. Results might be truncated”. I have tried to change other parameters, such as —max-accept, but the situation does not change. It would be great if you could provide some information about how to produce all the hits as close as possible to blastp (with the same evalue cutoff), but much faster. Thanks.

Could you please explain how you compare blastp and MMseqs2? Could you please provide the hits that you can not find?
We do not produce exactly the same hits than blast since we do use a different compositional bias correction.
The warning "Sequence XXX produces too many hits. Results might be truncated" indicates that their are too many high scoring diagonal (> target database size / 2). So we can not order them perfectly. How often does this message occur?

My taget database contains about 2M sequence (from ~120 species) and my query database contains about 10K sequence (one species)
For blastp, I use blastp command with evalue cutoff 0.01 as following:

blastp -db $db_blastp/AllDB -query $spe_fasta -out $spe_id.blastp.txt -evalue 0.01 -outfmt 6 -num_threads $num_cores

For mmseq2, I use

mmseqs search $mmseq_db_dir/$spe_id $mmseq_db_dir/AllDB $search_dir/$spe_id $tmp_dir --threads $num_cores -s 7.5 -e 0.01
Then I convert them to outfmt6,
mmseqs convertalis $mmseq_db_dir/$spe_id $mmseq_db_dir/AllDB $search_dir/$spe_id $outfmt6/$spe_id.mmseq.txt

Then I count the number of lines of the two output files. I noticed that blastp has about 3 times hits than mmseqs.
The message “…too many hits” occurs very frequently and therefore I wondered mmseqs could identify the hits, but the results may be truncated.

We only report the top 300 hits as default. You need to increase --max-seqs. Also the e-value of 0.01 corresponds to an e-value of '0.1' in MMseqs2.

In total I have 2.2M sequences in the target DB and I set --max-seqs=3000000. It still prints the message "...too many hits". What else am I missing?

--max-seqs= should not work and give an error. You have to leave out the equal sign.

Yes, I mean --max-seqs 3000000

Did the --max-seqs reduce the difference between blastp and MMseqs2 a lot?
Did you also use the '-e 0.1'?
Could you give us some examples of sequences that can not be found please?

MMseqs (max-seqs=target DB size, evalue=0.1) produce more hits than blastp (max_target_seqs=target DB size, evalue=0.01). blastp has about 1% not found by MMseqs and MMseqs has about 5% not found by blastp. I think the difference was due to the cutoff sensitivity as most of hits not found by each other has the bitscore is around 50.  For my case, it takes about 5hours using 64 cores for MMseqs and 8 hours for blastp. The speed is not much faster than blastp.
However, about 5% of the sequences still prints a lot of warning "sequence ... too many hits" even if I set max-seqs to the size of target DB for MMseqs. Do you know why? I think if all the hits are printed out, then it would find more hits.
I noticed that MMseqs also produced more than HSPs. How could I limit to the best HSP? is this parameter --alt-ali for number of output HSP?
One example, the pair was identified by blastp (evalue 0.01), not by MMSeqs (evalue 0.1): https://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId=emboss_needle-I20180724-094628-0802-32011448-p2m&context=protein&analysis=alignment

In my experience, MMseqs could be more faster if you index (mmseqs createindex) the database before the searches, like more than 10 times faster.

@acpguedes I do not think the indexing should take too much time in the case of @yiming-gcm. Because he uses sequence/sequence searches.
@acpguedes Since you perform iterative search the index has to be  rebuild every iteration. Building the index several times and searching a small query sets leads to a high overhead.

@martin-steinegger Thanks for providing the help.
What I am looking for is: I have 2M sequences containing from ~100 species. For each of 2M sequence, I want to find out ALL the hits/similar sequences within the given threshold, such as evalue 0.01, NOT the best hit.
I tested the following approach:
First I build the targetDB using 2M sequence. Then I created the index. Then for each query species (~20K sequence), I created the queryDB, then I use MMseqs search with the parameters --max-seqs num_DB_Seq, -s 7.5 -e 0.01
The program call is:
~/db_mmseqs/10141 ~/db_mmseqs/AllDB ~/db_mmseqs/tmp/8799019798690856849/pref_7.5 --sub-mat blosum62.out -k 0 --k-score<PHONE_NUMBER> --alph-size 21 --max-seq-len 65535 --max-seqs 2264996 --offset-result 0 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --cov-mode 0 --comp-bias-corr 1 --diag-score 1 --exact-kmer-matching 0 --mask 1
--min-ungapped-score 15 --spaced-kmer-mode 1 --pca 1 --pcb 1.5 --threads 64 -v 3 -s 7.5
How long do you think it takes for 64 cores to get the results for 2M vs. 2M sequences with all the possible hits?

Could you also provide the log please?  The --max-seqs num_DB_Seq slows down the search.

Is the following what you need?
Program call:
~/seq_data/fasta/10141.fasta ~/seq_data/db_mmseqs/10141
MMseqs Version:      	a6fadb4b083af4575e9117d4b405128051468c1e
Max. sequence length 	65535
Split Seq. by len    	true
Offset of numeric ids	0
Verbosity            	3
.Time for merging files: 0h 0m 0s 4ms
Time for merging files: 0h 0m 0s 5ms
Time for merging files: 0h 0m 0s 6ms
Time for merging files: 0h 0m 0s 3ms
Time for processing: 0h 0m 0s 225ms
Program call:
~/seq_data/db_mmseqs/10141 ~/seq_data/db_mmseqs/AllDB ~/seq_data/search/10141 ~/seq_da
ta/db_mmseqs/tmp --threads 64 --max-seqs 2264996 -s 7.5 -e 0.1
MMseqs Version:                    	a6fadb4b083af4575e9117d4b405128051468c1e
Sub Matrix                         	blosum62.out
Add backtrace                      	false
Alignment mode                     	2
E-value threshold                  	0.1
Seq. Id Threshold                  	0
Seq. Id. Mode                      	0
Alternative alignments             	0
Coverage threshold                 	0
Coverage Mode                      	0
Max. sequence length               	65535
Max. results per query             	2264996
Compositional bias                 	1
Realign hit                        	false
Max Reject<PHONE_NUMBER>
Max Accept<PHONE_NUMBER>
Include identical Seq. Id.         	false
No preload                         	false
Early exit                         	false
Pseudo count a                     	1
Pseudo count b                     	1.5
Score bias                         	0
Threads                            	64
Verbosity                          	3
Sensitivity                        	7.5
K-mer size                         	0
K-score<PHONE_NUMBER>
Alphabet size                      	21
Offset result                      	0
Split DB                           	0
Split mode                         	2
Split Memory Limit                 	0
Diagonal Scoring                   	1
Exact k-mer matching               	0
Mask Residues                      	1
Minimum Diagonal score             	15
Spaced Kmer                        	1
Mask profile                       	1
Profile e-value threshold          	0.001
Use global sequence weighting      	false
Filter MSA                         	1
Maximum sequence identity threshold	0.9
Minimum seq. id.                   	0
Minimum score per column           	-20
Minimum coverage                   	0
Select n most diverse seqs         	1000
Omit Consensus                     	false
Min codons in orf                  	30
Max codons in length               	32734
Max orf gaps<PHONE_NUMBER>
Contig start mode                  	2
Contig end mode                    	2
Orf start mode                     	0
Forward Frames                     	1,2,3
Reverse Frames                     	1,2,3
Translation Table                  	1
Use all table starts               	false
Offset of numeric ids              	0
Add Orf Stop                       	false
Number search iterations           	1
Start sensitivity                  	4
Search steps                       	1
Sets the MPI runner
Remove Temporary Files             	false
Program call:
~/seq_data/db_mmseqs/10141 ~/seq_data/db_mmseqs/AllDB ~/seq_data/db_mmseqs/tmp/8799019798690856849/pref_7.5 --sub-mat blosum
62.out -k 0 --k-score<PHONE_NUMBER> --alph-size 21 --max-seq-len 65535 --max-seqs 2264996 --offset-result 0 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --cov-mode 0 --comp-bias-corr 1 --diag-score 1 --exact-kmer-matching 0 --mask 1
--min-ungapped-score 15 --spaced-kmer-mode 1 --pca 1 --pcb 1.5 --threads 64 -v 3 -s 7.5
MMseqs Version:           	a6fadb4b083af4575e9117d4b405128051468c1e
Sub Matrix                	blosum62.out
Sensitivity               	7.5
K-mer size                	0
K-score<PHONE_NUMBER>
Alphabet size             	21
Max. sequence length      	65535
Max. results per query    	2264996
Offset result             	0
Split DB                  	0
Split mode                	2
Split Memory Limit        	0
Coverage threshold        	0
Coverage Mode             	0
Compositional bias        	1
Diagonal Scoring          	1
Exact k-mer matching      	0
Mask Residues             	1
Minimum Diagonal score    	15
Include identical Seq. Id.	false
Spaced Kmer               	1
No preload                	false
Early exit                	false
Pseudo count a            	1
Pseudo count b            	1.5
Threads                   	64
Verbosity                 	3
Initialising data structures...
Using 64 threads.
Use index  ~/seq_data/db_mmseqs/AllDB.sk6
Index version: 7
Generated by:  a6fadb4b083af4575e9117d4b405128051468c1e
KmerSize:     6
AlphabetSize: 21
Type:         1
Spaced:       1
KmerScore:    0
SequenceType: 0
Headers:      0
ScoreMatrix:  blosum62.out
Substitution matrices...
Use kmer size 6 and split 1 using Target split mode.
Needed memory<PHONE_NUMBER>5 byte) of total memory<PHONE_NUMBER>64 byte)
Target database: ~/seq_data/db_mmseqs/AllDB(Size: 2264995)
Query database type: Aminoacid
Target database type: Aminoacid
Time for init: 0h 0m 3s 994ms
Query database: ~/seq_data/db_mmseqs/10141(size=18106)
Process prefiltering step 1 of 1
k-mer similarity threshold: 73
k-mer match probability: 0
Starting prefiltering scores calculation (step 1 of 1)
Query db start  1 to 18106
Target db start  1 to 2264995

Yes, could you please upload the whole log as file. I need to see the exact runtimes of the prefilter and alignment in order to reason about it.

mmseqs.log

Thanks a lot for the log!
The prefilter takes 15 minutes, while the alignment runs for 4.5 hours. I think your --max-seqs is way to high since in average only 4000 hits are accepted by the alignment. You could reduce --max-seqs to 100.000 without losing many, if any at all, hits.
Another tweak is using the property of the prefilter results, that they are already well sorted and distinguish well between homologs and non-homologs. It is possible to reduce the run time without losing many, if any, hits of the alignment by using the --max-rejected parameter. It stops aligning after N consecutive rejected alignments (alignments that do not fulfill the alignment criteria). You could try --max-rejected 10.
Another tweak would be to increase the --min-ungapped-score. I have never really optimized this parameter. It could lead to a huge gains in speed for the alignment by rejecting prefilter hits more strictly. Try --min-ungapped-score 30.
You mentioned in an email that you also tested DIAMOND and it was less sensitive. Could you please give us your comparison results?

DIAMOND missed about 1/3 of blastp hits, but it takes about 10 mins, while for blastp, it takes 8 hours to generate the blastp hits. For MMseqs with -s 5.7, it takes about 1 hours to generate the results and it missed about 15% of blastp and gain 5% more hits than blastp. For MMseq with -s 7.5, it takes about 5 hours, it missed about 3% of blastp hits and gain 10% more hits than blastp.

For iterative searches, 3 iterations at least, it's seems that mmseqs retrieve more sequences than psi-blast. Anyway you can see some differences that could be explained by bias composition, that's why I include Jackhmmer in comparision, since Jackhmmer use HMM instead PSSM and have diferent bias composition.

mmseqs search example.db /databases/mmseqs/all.mmseqs example_found.db tmp/ --e-profile 0.001 -k 7 -s 7 -a -e 10 --threads  --max-seqs 17702628 --alignment-mode 3 --num-iterations 3
time psiblast -query  -db /databases/fadb/freeze/all.fa -evalue 10  -num_iterations 3 -num_alignments 17702628 -num_descriptions 17702628 -inclusion_ethresh 0.001  -num_threads
time jackhmmer --cpu  -N 3 -E 10 --incE   /databases/fadb/freeze/all.fa

The number of alignments was:

mmseqs = 155565
psi-blast = 162250
jackhmmer = 965722
but the number of sequences was:
mmseqs = 155565
psi-blast = 147355
jackhmmer = 231779

The query was a multi domain proteins that could lead to higher number of hits.
Sample_size_1_Report_size_17702628_e-value_10.pdf

@yiming-gcm were you able to test any of my recommendations to improve the speed of mmseqs?

sorry to the late response. it did improve the speed. Thanks.

We only report the top 300 hits as default. You need to increase --max-seqs. Also the e-value of 0.01 corresponds to an e-value of '0.1' in MMseqs2.

@martin-steinegger
Hi, could you give me some advice for the following questions?
I used the  MMseqs2 Version: 24f6b52a38cd8cf66d10ce00bf37dc815fef986e-MPI
I would like to get the same or more sensitive result than PSI-blast, the commond I used for PSI-blast is :
psiblast -query query.faa -db database -evalue 0.001 -outfmt 6 -out psiblast.out
So how could I set the parameter of MMseqs2:
(1) evalue 0.001 of PSI-blast corresponds to evalue 0.01 of MMseqs2, right?
(2) the default -num_iterations of PSI-blast is 1, that corrsponds to 2 in MMseqs2? more this parameter, more sensititive ?
(3) default -max_target_seqs is 500 for PSI-blast, the --max-seqs of MMseqs2 is [0.000], that means output all hits? the --max-seqs is the number of different subjects or just the HSP for each query?
Thanks in advance.


add container name and image to pod detail

#1211

I changed the tab padding on purpose because in edit tabs with backgrounds like yaml editors its weird, but will quibble with lauren outside of this.


How to build section of Aura README file need instructions for Mac

The existing instructions in the Aura README file 'How to build' section are for PC users only.  We need to have corresponding instructions for Mac users.

Fixed by Pull Request #14


Failing to restore RectifiedAdam optimizer from checkpoint

System information

OS Platform and Distribution (e.g., Linux Ubuntu 16.04): Linux Ubuntu 18.04
TensorFlow version and how it was installed (source or binary): source, nightly
TensorFlow-Addons version and how it was installed (source or binary): source, nightly
Python version: 3.6.7
Is GPU used? (yes/no): yes

Describe the bug
When restoring the RectifiedAdam optimizer from a checkpoint, restoring fails with the following error message:
ValueError: Tensor conversion requested dtype float32 for Tensor with dtype int32: <tf.Tensor: shape=(), dtype=int32, numpy=0>
The reason is that RectifiedAdam stores total_steps as an integer hyper-parameter:
https://github.com/tensorflow/addons/blob/master/tensorflow_addons/optimizers/rectified_adam.py#L134
OptimizerV2 however creates variables by calling add_weight without a dtype in _create_hypers. In other words, it assumes that all hyper-parameters are floating point parameters.
Storing the total_steps parameter as float fixes the problem for me.

https://github.com/olesalscheider/addons/commit/cceaa69a5b04dcd73344fc236e46ee2f4df1181e seems to fix it for me, but I am not sure if this is the intended way.

https://github.com/olesalscheider/addons/commit/cceaa69a5b04dcd73344fc236e46ee2f4df1181e seems to fix it for me, but I am not sure if this is the intended way.

Can you open a PR?

Can you open a PR?


Add Array.fromAsync

Hi!
This is currently being proposed: https://github.com/tc39/proposal-array-from-async
It is already in some Stack Overflow answers mentioned as a proposed solution.
I think pretty soon if not already more people than just me will attempt to look this up on CanIUse.
Please consider adding this to the database.
Thanks!

Available via MDN now: https://caniuse.com/mdn-javascript_builtins_array_fromasync


Test Explorer: What's the sidebar called?

Testing #119545
I think we typically call it the "Test Explorer" internally, but it's called "Test" when right clicking the icon and the header is "Testing":

Test is a verb and a "call to action" much like Run and Debug, but it being a noun makes it sound more confusing. I still vote for Test rather than Test Explorer

I went with Testing


Upgrade Code Syntax Highlighting for CopyCode

This PR updates Code Copy to have syntax highlighting. It appears not to have been working. We also customized it to Buzz's specifications (roughly)
We had a component called highlight, but it was only being used by CodeCopy, to simplify things, I removed it.
cc: @digitaldesigner

Pull Request Test Coverage Report for Build 2586

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 100.0%

Totals

Change from base Build 2581:
0.0%

Covered Lines:
21

Relevant Lines:
21

💛  - Coveralls

Mate this is perfect, really nice work! One tiny thing, can you remove 10px padding from the top and 10px from the bottom — just to reduce the leading and trailing whitespace. So pumped :)


Payload CMS 3.0

Migrate CMS to Payload
Tools being used:
[Payload CMS](https://payloadcms.com/docs/getting-started/what-is-payload l)
[Supabase] (https://supabase.com/docs)

Set up payload
Setup supabase postgres account
Create relationships between data
Configure admin, read,write, permissions
Set up relationships
Refactor all firebase code

Created Supabase account, msg Syed for login


es plugin thread leak problem

Please answer these questions before submitting your issue.

Why do you submit this issue?
[ ] Question or discussion
[x] Bug
[ ] Requirement
[ ] Feature or performance improvement

Question

What do you want to know?
How to fix it？ I need some suggestions and solutions.

Bug

Which version of SkyWalking, OS, and JRE?
skywaling : 8.1
java version "1.8.0_45"
Java(TM) SE Runtime Environment (build 1.8.0_45-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)
Plugin name: apm-elasticsearch-6.x-plugin
ES version used: elasticsearch-rest-high-level-client-6.8.4.jar
apache.pool version: commons-pool2-2.4.3

Which company or project?

What happened?
If possible, provide a way to reproduce the error. e.g. demo application, component version.
Problem description: We built an es connection pool based on apache.pool, and thread leaks occurred when using the skywalking plugin
Cause investigation:
In the es plug-in, a connection will be built here, causing the es client to fail to release the connection, and the thread cannot be released and continues to rise.

Requirement or improvement

Please describe your requirements or improvement suggestions.

I think we should close this client after get nodeList. Could you try to submit a pull request to fix this?

I think we should close this client after get nodeList. Could you try to submit a pull request to fix this?

I did try to do this, but I found that if you call the close method directly, the connection cannot be closed. The phenomenon is that the number of threads will be reduced by 10 after the connection is closed, but it will be created back, which does not solve the problem. The specific reason I suspect is to use HttpAsyncCloseableHttpAsyncClientBase will judge the link status when closing the link, causing the closing to fail. I haven't found any further reasons~

I did try to do this, but I found that if you call the close method directly, the connection cannot be closed. The phenomenon is that the number of threads will be reduced by 10 after the connection is closed, but it will be created back, which does not solve the problem. The specific reason I suspect is to use HttpAsyncCloseableHttpAsyncClientBase will judge the link status when closing the link, causing the closing to fail. I haven't found any further reasons~

Then, the other direction is, do you have any other way to get the node list? It is important for the topology.

Then, the other direction is, do you have any other way to get the node list? It is important for the topology.

I tested it again, it is effective to close the connection manually, and I will submit the change to fix this problem

I tested it again, it is effective to close the connection manually, and I will submit the change to fix this problem

Please go ahead.

Please go ahead.


please provide the dataset

Hello,
your work is very interesting. However, dataset access form is not publically available. Can you please provide the access to the dataset?
waiting for your response.
Thanks a lot

https://opendatalab.com/OpenDataLab/SensatUrban/cli/main

Thanks a  lot, but can you provide these commands in english please?

Thanks a lot. These  point clouds are split into tiles. Can you provide the point clouds by any chance which are holistic and are not split into the tiiles? I mean the pre-tiled version of the point clouds?
Thanks a lot

You can try signing in with your GitHub account.

b

I am still not able to download. As secret key is causing issues I geuess. Please help.

I think, I have successfully entered both the keys and logged in, but still I am getting this error at this step.
openxlab dataset get --dataset-repo OpenDataLab/SensatUrban

Thanks a lot. These point clouds are split into tiles. Can you provide the point clouds by any chance which are holistic and are not split into the tiiles? I mean the pre-tiled version of the point clouds? Thanks a lot

Thanks a lot.  I am able to download the dataset now. However, if you can please reply about this.

You can refer to the following repository: https://github.com/zouzhenhong98/SensatUrban-BEV-Seg3D.

Thank you for the repo. But it didn't serve my purpose. I was trying to say that can I get a complet point cloud instead of a tiled one, just like this?

The points in the dataset use absolute coordinates, and you can directly concatenate the point clouds to obtain the entire scene.


PUMI Mesh with Multiple Materials

Currently, the PUMI mesh reader for ParPumiMesh does not support multiple materials. Instead of reading the tag/material number, the reader in MFEM fixes the value to 1. This can be seen in the line below.
https://github.com/mfem/mfem/blob/8a565cad67b456bedc4b6c906226c66c2eddb79d/mesh/pumi.cpp#L523
It looks like we need a function call to getTag(ent) but I am not familiar enough with PUMI to know the function syntax/signature.
This was originally found and reported in the SCOREC (PUMI) repo after support for Gmsh meshes with multiple materials was added to PUMI. Original issue here.

Thanks for reporting this @wcdawn.
@cwsmith, do you think you can help?

@tzanio Certainly.  I'll talk with @mortezah and we'll put something in place.

@wcdawn @cwsmith @tzanio I usually update the attributes in my application code right after I create my MFEM mesh from a PUMI mesh (see the example code below, which updates the attributes for boundary faces and volume regions)
   ParMesh *mesh = new ParPumiMesh(PCU_Get_Comm(), pumi_mesh);

   //Add attributes based on reverse classification
   //Boundary faces
   int dim = mesh->Dimension();
   apf::MeshIterator* itr = pumi_mesh->begin(dim-1);
   apf::MeshEntity* ent ;
   int ent_cnt = 0;
   while ((ent = pumi_mesh->iterate(itr)))
   {
      apf::ModelEntity *me = pumi_mesh->toModel(ent);
      if (pumi_mesh->getModelType(me) == (dim-1))
      {
         //Get tag from model by  reverse classification
         int tag = pumi_mesh->getModelTag(me);
         (mesh->GetBdrElement(ent_cnt))->SetAttribute(tag);
         ent_cnt++;
      }
   }
   pumi_mesh->end(itr);

   //Volume Regions
   itr = pumi_mesh->begin(dim);
   ent_cnt = 0;
   while ((ent = pumi_mesh->iterate(itr)))
   {
       apf::ModelEntity *me = pumi_mesh->toModel(ent);
       int tag = pumi_mesh->getModelTag(me);
       mesh->SetAttribute(ent_cnt, tag);
       ent_cnt++;
   }
   pumi_mesh->end(itr);

   //Apply the attributes
   mesh->SetAttributes();

I was not part of the orginal developers of the ParPumiMesh calss and I don't know what was the logic (if any) to not include the above code in that class. That is certainly a possibility, and by having a quick look at the code, I don't see any reason why that cannot be done.

Thank you @mortezah.
If we consider the GMesh 'physical_type' tags being transferred here as model classification then the conversion becomes cleaner.  I'll revisit that part of the pumi code and see what I can do.

@wcdawn The pumi branch (cws/gmshTags) has been updated and when used with the cws/pumi-gmsh-phys-ents branch will set the element attribute from the gmsh 'physical entity'.  A screenshot from a quick sanity check with glvis and pumi_ex1 is below:

@wcdawn can you confirm if @cwsmith's fixes work for you?

Sorry for the delay. The fixes from @cwsmith do, in fact allow attributes to be read, but only for PumiMesh, not for ParPumiMesh. In PumiMesh, the mesh is loaded with PumiMesh::ReadSCORECMesh() but in ParPumiMesh, the mesh is simply loaded in the constructor ParPumiMesh::ParPumiMesh().
Similar changes need to be made to the ParPumiMesh constructor to allow this to be used with parallel mesh objects. This can be tested with examples/pumi/ex1p.

@wcdawn This commit (followed by a cleanup commit) enables attribute transfer from gmsh for the partitioned meshes.  Running ./glvis -m /path/to/parallel/mfem/mesh -np 8 -a on an eight part mesh produced by pumi/ex1p.cpp (which loads an eight part pumi mesh) results in the following figure.

Thanks @cwsmith! I've been able to replicate your results and use PUMI to pre-partition a mesh in my own MFEM based program.

@wcdawn You're welcome.  I'm glad that worked.
The PUMI changes should be merged into PUMI master tomorrow morning.  Once that goes through I'll submit a PR to merge the MFEM changes.

thanks @cwsmith !

Discussion continued in #2782.


Why not having Keyboard.None to show no keyboard at all?

There are plenty cases where this would be useful

I am making my own keyboard and I dont want the softkeyboard to pop up when Entry is focused
I am scanning into this field and I dont want softkeyboard to show

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Microsoft Alias: dotnetcontent

@dinobu The idea may have merits, but this isn't the right repo to open the issue. You probably want to post this in https://github.com/xamarin/Xamarin.Forms/issues.

Microsoft support for Xamarin will end on May 1, 2024 for all Xamarin SDKs including Xamarin.Forms. In preparation for this, all issues and PRs in this repository are being closed.
.NET MAUI is the replacement for Xamarin.Forms, and its API docs are built from /// in the dotnet/maui repository. Therefore, any issues with the .NET MAUI API docs should be opened in that repository.


(node:45413) [DEP0018] Deprecation

Steps to reproduce
Tell us about your environment:

ndb version:
Platform / OS version:
Node.js version:

What steps will reproduce the problem?
Please include code that reproduces the issue.

What is the expected result?
What happens instead?

Please, fill the template next time when you file an issue. :)


TBC Module Configuration

Hi,
I'm training my own model and have everything good to go up until I get to this step:
fairseq preprocess -sourcelang de -targetlang en \   -trainpref $TEXT/train -validpref $TEXT/valid -testpref $TEXT/test \   -thresholdsrc 3 -thresholdtgt 3 -destdir data-bin/iwslt14.tokenized.de-en
I get the following error:
THCudaCheck FAIL file=/home/dpechi/torch/extra/cutorch/lib/THC/THCGeneral.c line=70 error=30 : unknown error not found: TemporalConvolutionTBC_updateOutput_Cuda not found: TemporalConvolutionTBC_updateGradInput_Cuda not found: TemporalConvolutionTBC_accGradParameters_Cuda not found: TemporalConvolutionTBC_updateOutput_CudaDouble not found: TemporalConvolutionTBC_updateGradInput_CudaDouble not found: TemporalConvolutionTBC_accGradParameters_CudaDouble
That line in the THCGeneral.c is as follows:
THCudaCheck(cudaGetDeviceCount(&numDevices));
I made sure I had the TBC rock downloaded, but am otherwise uncertain of how to proceed. Upon checking the TBC github, I found that there were functions such as accGradParameters and updateGradInput, however I didn't see anything specific for Cuda or CudaDouble. Is there a separate TBC build I should be using or other way to configure this module with fairseq?

Please try to rebuild the TBC convolution and then check that you can create a nn.TemporalConvolutionTBC in a REPL.

This looks like it has been resolved. Please re-open if necessary.


Accessor methods return locale identifier

When I use the api.contentful.com to retrieve an entry, it loads the following dict into _fields:
{'en-US': {'title': "{'en-US': 'Prepare the Big Wall Estimation (1)'}", 'moderated': True, 'image': {'en-US': {'sys': {'type': 'Link', 'linkType': 'Asset', 'id': '6jIWlcxic8IAA0qYqAqymI'}}}, 'description': "{'en-US': 'This preparation allows you to do a the Big Wall Estimation with your team.'}", 'tags': ['en-US'], 'steps': ['en-US'], 'creator': {'en-US': {'sys': {'type': 'Link', 'linkType': 'Entry', 'id': '5oGDjpcUNymKUuIqkko0aQ'}}}, 'practice': {'en-US': {'sys': {'type': 'Link', 'linkType': 'Entry', 'id': 'LWRx0vUZYk6EU2imIAuI8'}}}}}

The locale is used as a key in the main dictionary as well as for each field.
In the Python wrapper, this means that I cannot use the accessor methods. E.g. entry.title returns  "{'en-US': 'Prepare the Big Wall Estimation (1)'}" where I'd expect it to return simply the string 'Prepare the Big Wall Estimation (1)'.
I'm not sure if this is a bug or if I'm doing something wrong.
I'm using version 1.4.3 of contentful.py.

api.contentful.com is actually for the Contentful Management API. This SDK is for the Content Delivery API which can be found at cdn.contentful.com.
There is another python SDK specifically for the management API here: https://github.com/contentful/contentful-management.py

Ah, @Roblinde thanks for the swift response, I missed that.
Maybe you could consider raising a warning of some kind when creating a client using
    client = Client(SPACE_ID, ACCESS_TOKEN, api_url='api.contentful.com'')

Now a lot of functionality just works, but we run into strange behavior like described in this issue.

That's a great suggestion. I'll look into that!
Thanks!


upgrade video.js to 7.13.3

Video.js has updates

Package.json should also be updated, and yarn file?

yarn.lock is there, but package.json is not. also rebase pls.


why not source? prolly dual hooked or a logger itself

give source bro prolly dual hooking kid

def a logger lol


use list collect for household members?

instead of do you have another?
pro: consistent with income loops
con: we may want to change away from list collect
maybe ask how many?

Duplicate of #31, IMO.


[Android] - Can't open url: intent://

Bug description:
I have a webview, inside the webview there is a QR Code, with this QR code used to open another application on the store (Google Play, AppStore)

On the browser -> When clicking, it will redirect to the application if available
When using the library -> When clicking, there is a message:

"Can't open url: intent://"

To Reproduce:

Expected behavior: edirect to the application if available

Screenshots/Videos:

Environment:

OS: Android
OS version:
react-native version:"react-native-webview": "13.2.2",
react-native-webview version:

Going by this section of the docs. It seems likely that you may have to handle this manually via library or with your own code. Similar issue here  + here here


Upgrade buildings

Create available commands for the different upgrades. Bescods peculiarities have been managed.
I decided to create two different academy building, because they have different behaviours.
Still missing: payCosts, check if the mine is isolated, check if the planet is in the range

@coyotte508 I tried, please have a look at the result. I definitely need a tutorial to understand how to deal with upstream / origin / brand and pull requests

@rzulian  One of the new tests is failing.
Regarding handling multiple remotes, you should have the origin remote pointing to your own repository.
You can add a main remote pointing to this repository: git remote add main https://github.com/donkeytech/gaia-engine.
Then you have two possibilities:

To fetch new changes, do git pull main master
If you already committed locally, you can do git pull main master --rebase. If will unwind your local commits, apply the commits from the main remote, and then apply the local commits. If there are conflicts, the rebase will stop, you can edit the conflicting files and continue the rebase.

You can also edit an existing commit with git commit --amend, and forcefully overwrite commits with git push force.
Here is a cheat sheet: https://www.git-tower.com/blog/git-cheat-sheet/


Invoice and payment relationships guide

Go over:

Pure payment APIs use-cases
Pure invoice APIs use-cases (external charges, credits, ...)
Relationship between

Invoices and Payment
Subscription and Invoices

fyi: I had already added some explanation on our a api doc, but we should discuss what exactly.


Extracting (x,y) positions of cell centers

Hi,
I like the work you have done, your model seems to work well for the task I need. I am trying to use your code in a pipeline for cell clustering. Is there a way to get the x,y position of the center of each of the cells.
Thanks!

Agree! Altought imagepy (a ImageJ-liked python-based package) integrate cellpose and probably can do such things, but I found many issues when I use cellpose as a plugin in imagepy. So, if cellpose can provide a basic function to get the x,y position of the center of each mask/cell. That will be very helpful.

The output of cellpose includes pixel masks for every cell, in the npy file. Therefore to get the centers, all you have to do is average those coordinates (or take the median).

Thanks, I ended up using the unique cell  using the method here to find the center. If anyone is interested.
https://www.learnopencv.com/find-center-of-blob-centroid-using-opencv-cpp-python/
After getting the mask object given by cellpose I did the following.
def get_centroid(img):
    img[img>0]=1
    img =np.array(img,dtype=np.uint8)
    gray_image = cv2.cvtColor(cv2.cvtColor(img, cv2.COLOR_GRAY2BGR), cv2.COLOR_BGR2GRAY)
    # calculate moments of binary image
    M = cv2.moments(gray_image)

    # calculate x,y coordinate of center
    cX = int(M["m10"] / M["m00"])
    cY = int(M["m01"] / M["m00"])

    return (cY,cX)

coords =[]
for idx in range(len(masks)):
    maski = masks[idx]

    # get the number of cells we found
    num = np.unique(maski)[-1]
    print(f'num: {num}')

    for i in range(num):
        if i == 0:
            # 0 means nothing there 1 is the first cell
            continue
        m = maski.copy()
        m[m!= i] = 0
        coords.append(get_centroid(m))


The gopherjs install for https://github.com/visualfc/gopherjs

Hi,
You meant 1.12, 1.13 and 1.14?

The gopherjs install for https://github.com/visualfc/gopherjs

The official GopherJS still supports only Go 1.12, right?

The GopherJS server success for Go 1.2 1.3 1.4, and wasmserve fails on Go 1.14.

Please use precise version numbers. 1.12, 1.13, 1.14, right?

The gopherjs install for https://github.com/visualfc/gopherjs

The official GopherJS still supports only Go 1.12, right?

Please use precise version numbers. 1.12, 1.13, 1.14, right?

go version go1.14beta1 darwin/amd64

Yes, https://github.com/gopherjs/gopherjs supports only Go 1.12

Thanks. Then, I think it is too early to merge your PR. It is OK to keep this PR open until the original GopherJS accepts newer Go.

The GopherJS server success for Go 1.2 1.3 1.4, and wasmserve fails on Go 1.14.

Please use precise version numbers. 1.12, 1.13, 1.14, right?

go version go1.14beta1 darwin/amd64

I mean, you are saying 1.2 instead of 1.12, and 1.3 instead of 1.13.

The GopherJS server success for Go 1.2 1.3 1.4, and wasmserve fails on Go 1.14.

Please use precise version numbers. 1.12, 1.13, 1.14, right?

go version go1.14beta1 darwin/amd64

I mean, you are saying 1.2 instead of 1.12, and 1.3 instead of 1.13.

Yes, sorry. this is Go 1.12 1.13 and 1.14

It is OK to keep this PR open until the original GopherJS accepts newer Go.

I said the above, but it looks like there has been no update in GopherJS recently. Let me close this once.