AttributeError: type object 'opentimelineio._opentime.TimeRange' has no attribute 'range_from_start_end_time_inclusive'

C:\Users\Chad>python -m pip install git+https://github.com/PixarAnimationStudios/OpenTimelineIO.git
Collecting git+https://github.com/PixarAnimationStudios/OpenTimelineIO.git
  Cloning https://github.com/PixarAnimationStudios/OpenTimelineIO.git to c:\users\chad\appdata\local\temp\pip-req-build-g9jqi4a1
  Running command git clone -q https://github.com/PixarAnimationStudios/OpenTimelineIO.git 'C:\Users\Chad\AppData\Local\Temp\pip-req-build-g9jqi4a1'
  Running command git submodule update --init --recursive -q
Requirement already satisfied: pyaaf2~=1.4.0 in c:\users\chad\appdata\local\programs\python\python37\lib\site-packages (from OpenTimelineIO==0.14.0.dev1) (1.4.0)
Installing collected packages: OpenTimelineIO
  Found existing installation: OpenTimelineIO 0.13.0
    Uninstalling OpenTimelineIO-0.13.0:
      Successfully uninstalled OpenTimelineIO-0.13.0
  Running setup.py install for OpenTimelineIO ... done
Successfully installed OpenTimelineIO-0.14.0.dev1
WARNING: You are using pip version 19.2.3, however version 21.1 is available.
You should consider upgrading via the 'python -m pip install --upgrade pip' command.

C:\Users\Chad>python
Python 3.7.7 (tags/v3.7.7:d7c567b08f, Mar 10 2020, 10:41:24) [MSC v.1900 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import opentimelineio as otio
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\Chad\AppData\Local\Programs\Python\Python37\lib\site-packages\opentimelineio\__init__.py", line 35, in <module>
    from . import (
  File "C:\Users\Chad\AppData\Local\Programs\Python\Python37\lib\site-packages\opentimelineio\opentime.py", line 13, in <module>
    range_from_start_end_time_inclusive = TimeRange.range_from_start_end_time_inclusive
AttributeError: type object 'opentimelineio._opentime.TimeRange' has no attribute 'range_from_start_end_time_inclusive'

This is a function in the opentime namespace, not a method on the TimeRange class:
>>> import opentimelineio as otio
>>> otio.opentime.range_from_start_end_time_inclusive(...)

Or maybe I'm misunderstanding this bug report.  Is that just happening on import?  On windows w/ python 3.7?
It looks like our CI is passing so is there more context on this?
https://github.com/PixarAnimationStudios/OpenTimelineIO/runs/2422614364?check_suite_focus=true

What you see above is all that I've done, in it's entirety. I just stumbled upon this project today, and went to try it out and this is what happened.
To answer your question; no more context, this is the full context. Just a Windows 10 machine, using Python 3.7.7

Can you try installing from pypi instead of from the GitHub HEAD?
python -m pip install opentimelineio
We've been tinkering with the build system so I'm curious to track this down.
Thanks!

Already tried that (that's why it says "Found existing installation: OpenTimelineIO 0.13.0"). That version doesn't work either, but it has a different error (more serious error; missing libraries).

This is from pypi
C:\Users\Chad>python -m pip install opentimelineio
Collecting opentimelineio
  Downloading https://files.pythonhosted.org/packages/9e/bb/a3b1f7c94b42f20a59a0d5dbc693ebfeb7623f0f86953f0d946595e2b03d/OpenTimelineIO-0.13.0.tar.gz (2.0MB)
     |████████████████████████████████| 2.0MB 3.3MB/s
Collecting pyaaf2==1.4.0 (from opentimelineio)
  Downloading https://files.pythonhosted.org/packages/69/0a/64f466f1517c9e5d63f8d65545aca085a2dfa47d5c0332d5dafea25d7785/pyaaf2-1.4.0.tar.gz (88kB)
     |████████████████████████████████| 92kB ...
Installing collected packages: pyaaf2, opentimelineio
  Running setup.py install for pyaaf2 ... done
  Running setup.py install for opentimelineio ... done
Successfully installed opentimelineio-0.13.0 pyaaf2-1.4.0
WARNING: You are using pip version 19.2.3, however version 21.1 is available.
You should consider upgrading via the 'python -m pip install --upgrade pip' command.

C:\Users\Chad>python
Python 3.7.7 (tags/v3.7.7:d7c567b08f, Mar 10 2020, 10:41:24) [MSC v.1900 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import opentimelineio as otio
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\Chad\AppData\Local\Programs\Python\Python37\lib\site-packages\opentimelineio\__init__.py", line 35, in <module>
    from . import (
  File "C:\Users\Chad\AppData\Local\Programs\Python\Python37\lib\site-packages\opentimelineio\opentime.py", line 1, in <module>
    from . _opentime import ( # noqa
ImportError: DLL load failed: The specified module could not be found.


importing a modular component from github

Coverage remained the same at 48.702% when pulling c24f6731d3edb77a897ff2e992bb759c91b7f3f3 on integrate-modular-component into 2ec70526324ccce5f6a6235ff37ea11eb67488c3 on master.

I’m definitely thinking about making this more generic and configurable, but for now I’m gonna follow PEP-20 and favor the explicit over the implicit.


tmpfiles.sh : doesn't support tmpfiles.d   v option

tmpfiles: ignoring invalid entry on line 11 of /usr/lib/tmpfiles.d//tmp.conf' tmpfiles: ignoring invalid entry on line 12 of /usr/lib/tmpfiles.d//tmp.conf'
tmpfiles: ignoring invalid entry on line 21 of `/usr/lib/tmpfiles.d//var.conf'
these are the 3 lines that gives this message :
v /tmp 1777 root root 10d
v /var/tmp 1777 root root 30d
v /var/lib/machines 0700 - - -
from man timpfiles.d :
v
Create a subvolume if the path does not exist yet and the file system supports this (btrfs). Otherwise  create a normal directory, in the same way as d.
Note : archlinux, booting openrc 0.16.4 with systemd 219 (used for udev)

This has since been fixed


Beautify bookmark stars

Actual Behaviour
Currently the bookmarks look like this:
0. Grey and black

I experimented with some alternative styles for the bookmarks, which you can see below.

I felt the grey and black were somewhat similar. When I am on a page where I can only see grey bookmarks, I sometimes get confused: am I looking at all bookmarked or no bookmarked sessions?

I felt the star was crowding the right hand side of the box. So I added some more spacing around it, and moved it out of the corner.

(Bonus.) FOSSAsia 2018 had a lot of sessions in one time period. Often I could not fit all the sessions for one time period together on the screen. I reduced the padding inside each session, and reduced the margins between sessions in the same time period. That way I could fit more sessions onto one screen. This is the same for all the screenshots below.

1. Opaque grey and black (flat design)

It is difficult to see the unbookmarked stars against the dark background. Scheme 3 is the best solution for that. (An alternative would be to use only medium/light shades for the track colours, rather than a mix of light and dark colours.)
2. Open and closed stars (flat design)

3. Sunken holes and white border (high contrast)

4. Sunken and raised yellow star

5. Like 4 but with depth inverted
This invites the user to tap by raising the unbookmarked stars and depressing the selected stars.

Do you like any of these designs, or perhaps a combination? If you do, I would be happy to implement one.
(As a start, a refactored some of the code, without making any visual changes, in #1799)

@geekyd what do you think would appear good?


Slashing should reduce registered amount that is bonded

The account 5F7BJL6Z4m8RLtK7nXEqqpEqhBbd535Z3CZeYF6ccvaQAY6N has more DOTs bonded than available in free_balance. Also it has no vesting and no reserved balance.
staking.ledger from its controller:
{
    "stash": "5F7BJL6Z4m8RLtK7nXEqqpEqhBbd535Z3CZeYF6ccvaQAY6N",
    "total": "0x00000000000000000023829049fb9940",
    "active": "0x00000000000000000023829049fb9940",
    "unlocking": []
}

which is ~9,9951×10¹⁵
balances.freeBalance: ~9,9946x10¹⁵

@Tbaut any other strange behavior regarding this? Now, reading the discussion again, I think the original offset was simply because of paying fees.

It's not about the fee, it's about the registered amount (this this comment) and the new title of this issue.

This is fixed already, as we do call update-ledger now with the new amount bonded after the slash.
https://github.com/paritytech/substrate/blob/9467f562ddb9c85ff78fca69d08137950b948019/frame/staking/src/slashing.rs#L599-L606


add key tool

in addition to the *key tools, a more mnemonic version of the tools would be nice, so one can call
jose key new -u sig -R -s 2048
jose key add -j keystore
jose key ls -j keystore
jose key rm -j keystore
jose key find -j keystore some_kid
jose key publish -j keystore

This requires the sanitizer to check more than one arguments.
Maybe it even makes sense to split the tools as such:
jwt info
jwk new
jwks new
jwks add
jwks ls | jwks list
jwks rm
jwks find
jwks publish
jwe encrypt
jwe decrypt
jws sign
jws verify

Decision: The key tool is ok, tool shorthands are not.


TabBar indicator color is not displaying one particular color

Steps to Reproduce

After giving TabBar indicatorColor: Color(0xffCF2C29), color wont show. But if i change at least one character (lets say number 9 to 8) suddenly i can see the color.
Expected results: Red indicator color under tabbar
Actual results:

could provide some more code

Maybe help you
TabBar(
indicatorColor: Colors.white,
labelColor: Colors.white,
labelStyle: Get.textTheme.subtitle2,
indicatorSize: TabBarIndicatorSize.label,
tabs: [
Tab(child: Text('Home Page'),),
Tab(child: Text('View All'),),
],
),


Chemical Substances - Gene HGNC:4593 GRM1 (Spinocerebellar ataxia)

This query has been created to address https://github.com/NCATSTranslator/testing/issues/62. This query returned 72 results earlier but it does not return any results as TRAPI 1.1 query.

Replaced HGNC id in the original query as follows:
{
    "message": {
        "query_graph": {
            "edges": {
                "e01": {
                    "object": "n0",
                    "subject": "n1"
                }
            },
            "nodes": {
                "n0": {
                    "categories": [
                        "biolink:ChemicalSubstance"
                    ]
                },
                "n1": {
                    "categories": [
                        "biolink:Gene"
                    ],
                    "ids": [
                        "NCBIGene:2911"
                    ]
                }
            }
        }
    }
}

Got several results.

Followed up: https://github.com/NCATSTranslator/testing/issues/62#issuecomment-894362803


Running quickstart_spark. Error [DATA_SOURCE_NOT_FOUND]

I am having some troubles trying to run the python example: delta-sharing/examples/python/quickstart_spark.py and I am getting this error:
Py4JJavaError: An error occurred while calling o61.load.
: org.apache.spark.SparkClassNotFoundException: [DATA_SOURCE_NOT_FOUND] Failed to find the data source: deltaSharing. Please find packages at `[https://spark.apache.org/third-party-projects.html`](https://spark.apache.org/third-party-projects.html%60).
	at org.apache.spark.sql.errors.QueryExecutionErrors$.dataSourceNotFoundError(QueryExecutionErrors.scala:724)

I tried to follow instructions adding pyspark --packages io.delta:delta-sharing-spark_2.12:3.1.0 and I get that error and also by adding Hadoop
spark = (SparkSession .builder .config('spark.jars.packages', 'org.apache.hadoop:hadoop-azure:3.3.1,io.delta:delta-core_2.12:2.2.0,io.delta:delta-sharing-spark_2.12:0.6.2') .config('spark.sql.extensions', 'io.delta.sql.DeltaSparkSessionExtension') .config('spark.sql.catalog.spark_catalog', 'org.apache.spark.sql.delta.catalog.DeltaCatalog') .getOrCreate() )   as some other user suggest in another Issue.
So, it would be great if anyone could help me here. Thanks!

Hi @pepinho14 ,
my first guess would be that delta-sharing-spark_2.12:0.6.2 may be a bit outdated.
You could try utilizing this:
spark = (SparkSession
         .builder
         .config('spark.jars.packages', 'io.delta:delta-sharing-spark_2.12:3.1.0')
         .config('spark.sql.extensions', 'io.delta.sql.DeltaSparkSessionExtension')
         .config('spark.sql.catalog.spark_catalog', 'org.apache.spark.sql.delta.catalog.DeltaCatalog')
         .getOrCreate()
         )


No render on iOS when loading a file

Hi,
I'm loading CKEditor (from a file) inside your Webview, it's working great on Android but not on iOS (with no error).
I tried with the latest dependencies and xcode 16 + iOS18.
The project in the zipped file.
CKEditorApp fail.zip
Thanks

I found the issue https://github.com/KevinnZou/compose-webview-multiplatform/blob/ef536008cc645d19fb80b4b65c9a9b751709f2d9/webview/src/iosMain/kotlin/com/multiplatform/webview/web/IOSWebView.kt#L87-L91
For loadFileURL, the first parameter is the file to load and the second one is the folder assets only!


erlang_check_file.erl: Add support for Erlang.mk

Now, it first determines the compilation "profile" (are we building tests or the program itself?) and the build tool. Once it found it - either rebar when there is a rebar.config file, or Erlang.mk when there is a
erlang.mk file - it calls the appropriate function to query ERL_LIBS paths and compiler options.
The Erlang.mk function uses the show-ERL_LIBS, show-ERLC_OPTS and show-TEST_ERLC_OPTS Make targets to query those informations.
Signed-off-by: Gerhard Lazu<EMAIL_ADDRESS>

Merged, thank you.


Implement skeleton codes for Notification APIs

This is an initial implementation to provide notification APIs to client app.
The APIs always return false right now and we can implement them later.

It's hard to understand because the notification API is not friendly with me.

@romandev It was fixed :)


NO LOGIN, Unable to connect to ssl://localhost:993 (Connection refused)

I always get the error: "NO LOGIN". I updated my firewall to open port 993. Can't seem to make it work. The e-mail address that i'm trying to connect to does allow "IMAP" connections.
$client = Client::make([
      'host' => 'outlook.office365.com',
      'port' => 993,
      'encryption' => 'ssl',
      'validate_cert' => false, //Just for testing, otherwise true.
      'username' => 'USERNAME,
      'password' => 'PASSWORD,
      'protocol' => 'imap'
  ]);

dd($client->connect());

Could anyone point me in the right direction?

I'm also Facing similiar issues, Any help?

I'm also facing a similar issue. Anyone find the solution?


update: add badge

![](https://img.shields.io/badge/made%20for-Nervos%20AppChain-blue.svg)

Updated Badge Color and set link to AppChain @Mine77


Support for bootstrap snippets?

Very great project,
have been looking for something like this.
Would it be possible to create support for bootstrap components?
Carousel , etc?

Thank you!  I do use the Bootstrap Carousel for the slideshow plugin in Respond.  You could use that as a starting point for custom implementations.
https://github.com/madoublet/respond/blob/master/public/themes/bootstrap/plugins/slideshow.html
I have tried to make it really easy to create new plugins in Respond.  You can read the docs here:
https://respondcms.com/documentation/creating-plugins
If you have suggestions for specific plugins, let me know.  I am hesitant to re-create the whole Bootstrap framework though.  I tend to just build plugins as I need them.


Area2D colliding with StaticBody2D - No Event

Hi, this is really cool and the physics seem 'better' than the default Godot 2D.
I am having an issue with getting any signals i.e. _on_body_entered() when an Area2D collides with a StaticBody2D.
It works fine with the Godot 2D Physics, but not with Box2D.  Not sure if I am doing something wrong or this is a bug, or just the way Box2D works.
Thanks,

Thanks for reporting it. Will look into it.

Disregard previous comment. Doesn't seem to be related.
Can you upload a project where you can reproduce this specific case? That would help a lot.(I have stumbled another issue I am trying to fix, but area and staticbody2d works for me).

Thanks for your response.  It may be related to the fact that I am moving the Area2D with position * delta * speed, however, it does work with the default & GodotPhysics2D modules.  I am always sensitive to the fact that I am doing something wrong. ;-)
Here is a simple example project.  The Area2D is being moved manually using the transform position and when it collides with the StaticBody2D, no signals are being emitted.  Using the built-in physics modules, it reports a body_entered signal.
Thank you for taking the time to look at this situation!
Box2D_Area2D_StaticBody2D.zip

I tested with https://github.com/godot-box2d/godot-box2d/pull/20 and it seems to have fixed it. Will make a release and let you know when you can test.

Ughuuu, that seems to have fixed it!!!  Thank you very much for your help.  I have to say, the physics with Box2D are just much better in certain circumstances.  I have some RigidBody2Ds falling to the ground (StaticBody2D) and the collisions when they bump into each other and bounce around are far better with Box2D.  Thank you again.


remove unused $this->_csrf_hash assignment in Security::CSRFVerify()

property never used

Coverage decreased (-0.005%) to 62.268% when pulling 66d52e32f94755586fa54e1eb13b1541354321fe on samsonasik:security-csrf into 0b387c71aa8717d54d62436a814da1d519f4636f on bcit-ci:develop.


Update GLVis Spack package

We should update the Spack package for GLVis to support version 4.0+

@tomstitt, are you still interested in working on this?

I still have more testing to do but I have started this here and have tested on os x

merged: https://github.com/spack/spack/pull/25045

thanks @tomstitt 🙏


[WIP] Jaeger Support

@kim just wanted to say thanks for all your effort so far! I've been playing with using this library with jaeger and even in it it's experimental state its been so far so good (one exception being jaeger seems crash when I through a lot of traffic at it, could be just the all-in-one container running out of mem). I had to make a tweak to pass in the Process/Service name but it looks like you've got a solution for that. Keep up the good work and let me know if you need any help testing/bouncing ideas back and forth. Your changes in #5 really cleaned stuff up!

Hey @mjrussell, thanks for the thanks :) Good to hear people find this useful.
If you have ideas around automating integration tests with the various backends, or have some working setup already, please let me know! A lot of details are encoded not in the spec, but in the implementations, so having something in place will be a prerequisite for an actual release.

@kim I downloaded the Jaeger all in one image and was using master with a minor tweak. But I was getting traces to appear in their UI which was awesome. One thing I did notice was if I sent enough UDP messages at it, I'd wind up with the following crash message:
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x10 pc=0x8d88c6]

goroutine 36 [running]:
github.com/jaegertracing/jaeger/cmd/agent/app/reporter/tchannel.(*Reporter).EmitBatch(0xc420176c40, 0x0, 0x0, 0x0)
    /home/travis/gopath/src/github.com/jaegertracing/jaeger/cmd/agent/app/reporter/tchannel/reporter.go:119 +0x86
github.com/jaegertracing/jaeger/thrift-gen/jaeger.(*agentProcessorEmitBatch).Process(0xc420224a30, 0xc400000000, 0xfe3ec0, 0xc420342780, 0xfe3ec0, 0xc420342780, 0xc420256200, 0x89fa18, 0xc420224a70)
    /home/travis/gopath/src/github.com/jaegertracing/jaeger/thrift-gen/jaeger/agent.go:137 +0xc9
github.com/jaegertracing/jaeger/thrift-gen/jaeger.(*AgentProcessor).Process(0xc42023c360, 0xfe3ec0, 0xc420342780, 0xfe3ec0, 0xc420342780, 0x0, 0x0, 0x0)
    /home/travis/gopath/src/github.com/jaegertracing/jaeger/thrift-gen/jaeger/agent.go:111 +0x302
github.com/jaegertracing/jaeger/cmd/agent/app/processors.(*ThriftProcessor).processBuffer(0xc4202265a0)
    /home/travis/gopath/src/github.com/jaegertracing/jaeger/cmd/agent/app/processors/thrift_processor.go:110 +0x179
created by github.com/jaegertracing/jaeger/cmd/agent/app/processors.(*ThriftProcessor).Serve
    /home/travis/gopath/src/github.com/jaegertracing/jaeger/cmd/agent/app/processors/thrift_processor.go:82 +0x62

Not yet sure if thats just because the all in one ran out of memory (it stores traces in-memory) or there is an issue with the messages sent by this library. I was gong to setup their recommendation production setup and see if the problem persisted. Happy to take a swing at this PR though and add it into my project and see if its working.
I'd also like to hear more about your plan for propagation (can discuss in a separate issue). I say the new types but Im not yet sure how they fit it and how to potentially make a custom propagator (we use websockets instead of HTTP  so headers won't work but I can pass along ids inside the messages)

the following crash message

Aww, this looks bad - like the jaeger agent deserializes an incomplete thrift message off the wire, and then segfaults when trying to access its fields. Not sure how this can happen. Would you mind sharing some code which demonstrates the issue?

plan for propagation

Well, I think most other language implementations just go through TextMap for any kind of not-HTTP propagation. For WebSockets, it would be rather application-dependent as it depends on the message format. A simple solution would be to encode the TextMap as JSON (which you get for free as it's just a HashMap Text Text) and embed that in your message.
The spec also demands an opaque "binary" carrier format, which I've held off supporting until now as it isn't clear what the benefits are when the structure is not specified -- apart from a potential de/serialisation speedup compared to going through a TextMap, at the expense of potential runtime failure because of incompatible de/serialisers at either end. Since it can also not be defined generically, I'm not sure how to encode it -- the only choice I see is that some concrete Prism' ByteString SpanContext would have to be supplied by the user when constructing Propagations.
Note, however, that you're not obliged to use traceInject/traceExtract from the library in your instrumentation code -- you just need to get hold of a SpanContext by whatever means suits your use case.

Aww, this looks bad - like the jaeger agent deserializes an incomplete thrift message off the wire, and then segfaults when trying to access its fields. Not sure how this can happen. Would you mind sharing some code which demonstrates the issue?

Yeah let me try to setup a minimal example to work through. Strange that the auto generated Thrift message would have an issue. Also that it only happens when we send many messages. I wonder if its related to how the ThriftReporter packs up the messages and flushes them over UDP.
Thanks for the notes on propagation, I think I need to dive into that a bit more and will let you know if I run into any issues threading it along my set of services.

@mjrussell I was able to reproduce your issue by running some traced actions concurrently.
3c00cd4 fixes is by using a Handle as the thrift Transport, which provides safe concurrent access. Note, however, that this only works as long as we leave the Handle in unbuffered mode (ie. flush after each and every Span being emitted). This is most likely not the fastest solution, but I'll leave a more elaborate implementation to when someone actually needs it.

Sorry I don't know how I missed the response to this but thanks so much for finding the issue and fixing it! We've been focused on a few other tasks lately but we definitely still plan to use your library in our production apps with Jaeger. Appreciate all the hard work and will send any issues/feedback/PRs as we find them.


Re-adding TFModels run_id logging

Accidentally left run_id logging commented out while testing in previous push - fixed it here.

Codecov Report

Merging #64 into master will increase coverage by <.01%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master      #64      +/-   ##
==========================================
+ Coverage    77.2%   77.21%   +<.01%
==========================================
  Files          45       45
  Lines        2610     2611       +1
==========================================
+ Hits         2015     2016       +1
  Misses        595      595

Impacted Files
Coverage Δ

mlflow/tensorflow.py
98% <100%> (+0.04%)
:arrow_up:

Continue to review full report at Codecov.

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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Use HTTPs for aerial map tiles

Fixes issue where aerial tiles do not load because of CSP problems because the scheme was http

Trivial, merging


Displays error when open

Description
What steps will reproduce the problem?

Installed with conda in miniconda environment, ubuntu 16.04.5.
Run spyder in terminal, conda environment.
Traceback
  File "/home/pedro/dev/conda-python/envs/qutip-env/lib/python3.6/site-packages/spyder/app/mainwindow.py", line 1961, in valid_project
    if bool(self.projects.get_active_project_path()):
AttributeError: 'NoneType' object has no attribute 'get_active_project_path'

Versions

Spyder version: 3.3.0
Python version: 3.6.6
Qt version: 5.9.6
PyQt5 version: 5.9.2
Operating System: Linux 4.15.0-30-generic

Dependencies
pyflakes >=0.6.0  :  2.0.0 (OK)
pycodestyle >=2.3 :  2.4.0 (OK)
pygments >=2.0    :  2.2.0 (OK)
sphinx >=0.6.6    :  1.7.6 (OK)
rope >=0.9.4      :  0.11.0 (OK)
jedi >=0.9.0      :  0.12.1 (OK)
psutil >=0.3      :  5.4.6 (OK)
nbconvert >=4.0   :  5.3.1 (OK)
pandas >=0.13.1   :  None (NOK)
numpy >=1.7       :  1.15.0 (OK)
sympy >=0.7.3     :  1.2.1.dev (OK)
cython >=0.21     :  0.28.5 (OK)
qtconsole >=4.2.0 :  4.3.1 (OK)
IPython >=4.0     :  6.5.0 (OK)
matplotlib >=2.0.0:  2.2.2 (OK)
pylint >=0.25     :  2.1.1 (OK)

This is a duplicate of issue #7403 and it was fixed in our 3.3.1 release. If you're using Anaconda, please be patient, new conda packages for that version should be available shortly.

Thanks for the update!
On Tue, 14 Aug 2018, 14:57 Carlos Cordoba<EMAIL_ADDRESS>wrote:

This is a duplicate of issue #7403
https://github.com/spyder-ide/spyder/issues/7403 and it was fixed in
our 3.3.1 release. If you're using Anaconda, please be patient, new conda
packages for that version should be available shortly.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/spyder-ide/spyder/issues/7683#issuecomment-412880807,
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Running tinyMediaManager.sh doesn't start the app, but copy/pasting the command does

What TMM version are you using?
Freshly built tmm_2.9.7-SNAPSHOT_a1c3c7a_linux using Maven 3.3.9
What is the actual behaviour?
Running tinyMediaManager.sh opens a new terminal widow and briefly flashes the TMM splash before closing.
java -jar tmm.jar results in the following error
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.NoClassDefFoundError: ch/qos/logback/core/filter/Filter
	at java.lang.Class.getDeclaredMethods0(Native Method)
	at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
	at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
	at java.lang.Class.getMethod0(Class.java:3018)
	at java.lang.Class.getMethod(Class.java:1784)
	at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
	at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
Caused by: java.lang.ClassNotFoundException: ch.qos.logback.core.filter.Filter
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 7 more

Additional
OS Name: Linux
OS Arch: amd64
OS Vers: 4.9.0-4-amd64
Java Vers: 1.8.0_151
Java Home: /usr/lib/jvm/java-8-openjdk-amd64/jre

I copy pasted the command found in tinyMediaManager.sh
java -Djava.net.preferIPv4Stack=true -Dappbase=http://www.tinymediamanager.org/ -jar getdown.jar . and ran it manually in the terminal and now it starts properly

Building the jar and simply starting it with java -jar tmm.jar does not work.
Reason is, that you do not have the required libraries in correct place.
You need at least specify -cp lib/*
Unfortunately, we cannot fixate this in manifest, because when we dynamically extent this via getdown, it is not adhered.
So we always call our getdown.jar updater first, which then calls TMM correctly (and w/o actually updateing it)
Where did you find this shell script? the ones i checked, do not call TMM directly....

The real question here is how you unpacked tge tmm? Cause it seems it should run properly

Where did you find this shell script? the ones i checked, do not call TMM directly...

First I thought the way to start tMM was by running tmm.jar but then I looked in the sh file what it was doing. So this was simply a wrong assumption on my part.
Double clicking the sh file opens a terminal window and flashes the tMM splash before closing again without starting, but I just ran the command sh tinyMediaManager.sh and now it does start properly.
edit: I also just figured out there is difference between choosing Run in Terminal and Run when double clicking an executable sh file.

The real question here is how you unpacked tge tmm? Cause it seems it should run properly

I simply extracted the tmm_2.9.7-SNAPSHOT_a1c3c7a_linux.tar.gz created in the dist folder.

I'm new to this whole linux thing and tmm is also the first piece of software I didn't just apt install
So, thank you both for the quick replies but I think the only real issue here is on my part.

You can do the following
chmod +x tinyMediaManager.sh

and run it exactly like this
./tinyMediaManager.sh

It already has the execute permission and running the script from the terminal works fine.
The only problem I had was double clicking prompted me for using the terminal or not and doing so doesn't start tMM, I just had to select run
I'm using Gnome as DE and want tMM in my favourites (I use it quite a lot), so I can create a custom icon which launches the .sh file from my launcher.
Anywhere I can find a somewhat high res version of your logo?


Docs: changed instructions for running unit tests

I simplified the instructions for running all the unit tests, and added some links in an "Aside", so that curious people can easily find out more about pytest and pytest-runner.

Current coverage is 83.31%

Merging #178 into master will not affect coverage as of 5414f17

@@            master    #178   diff @@
======================================
  Files           19      19
  Stmts          923     923
  Branches         0       0
  Methods          0       0
======================================
  Hit            769     769
  Partial          0       0
  Missed         154     154

Review entire Coverage Diff as of 5414f17

Powered by Codecov. Updated on successful CI builds.

I guess this is the simplest way of running the tests.
:+1:

++
merging now

As a note: using setup.py to run the tests is somewhat impractical when one needs to pass parameters to pytest, as it needs to be done via --addopts and is not as straightforward as simply using py.test.

@sbellem That section of the documentation is aimed at people who just want some way to make sure that BigchainDB is working properly (by running all unit tests), but they don't intend to do any developing.
@vrde You were going to add some notes to CONTRIBUTING.md to help developers get set up for developing / contributing to BigchainDB. Maybe add a note about there about using py.test -v or python -m pytest -v if they want to do more sophisticated things with pytest?

@vrde Never mind - I see you already submitted PR #180. I'll make some minor edits to that branch and add the suggested comments on pytest at the same time.

@ttmc ok! :+1: Just wanted to share the information, as I had tried both.


lib: add groupBy

Motivation for this change
Add groupBy function inspired by Scala lib
Basically it just a partiton function which is not limited to 2 groups
(partition could be simplified to partition = pred: groupBy (x: if pred x then "right" else "wrong"))
Example use case #37690: generating bash case-expression without duplicates

rebased merge conflict


Using llama-cpp-python logits escapes RegEx constraints. Negative Regex Charset Matches don't work?

I'm using patterns such as ([^"][^\n]+[^"]) and ([^"]([^>/;:\n]+)( > [^>/;:\n]+)+[^"]) which contain negated character matches, but I'm still getting the unwanted characters?
Is this a bug or does not the regex library support negative matches? I looked at the regex library site, and it was unclear to me what it supports or does not support.

Example getting unwanted commas and there are no matching semicolons?
Pattern: - Keywords: [^;:,/\n\r]+; [^;:,/\n\r]+; [^;:,/\n\r]+; [^;:,/\n\r]+; [^;:,/\n\r]+
LLM Output: - Keywords: intranasal vaccine, long-lasting immunity, mucosal antibody response, T cells, adjuvants, IgG antibodies

Attached is an example jupyter notebook which exhibits the LLM escaping the regex. I've also attached the python environment.yml for the test.
This is for the Llama-cpp-python GGUF Mixtral-8x7b-Instruct-0.1. The code assumes at 24GB GPU. See function load_mixtral_8x7b_Q4 to adjust. (variables offload_kqv and layers). You also might need to adjust the parameter n_threads.
bug_reproduce.ipynb.tar.gz
environment.yml.tar.gz

Anyone looking into this?

I have limited time to work on LMFE, and the last release was focused around TensorRT-LLM. I hope to get to this for the next release.


Bad server whith region set to FR (France)

When I use my FR (France) ewelink account with the ewelink-api (3.0.0), I get an http error because the API is looking for the server "fr-api.coolkit.cc" instead of the good one wich seems to be "eu-api.coolkit.cc" for european countries.

Hello @lbenech
Whats happens when you run this: https://github.com/skydiver/ewelink-api/blob/master/docs/available-methods/getregion.md ?


Song title is wrong when downloaded

System OS
MacOS
Python Version
3.10 (CPython)
Install Source
pip / PyPi
Install version / commit hash
4.0.0rc3
Expected Behavior vs Actual Behavior
Expected
Downloaded file should have the corect name from Spotify
Actual
name in download directory is: file?file=Daft Punk - Around the World.mp3&client_id=3deacd0b-022a-45f2-b308-cfd1cb177fd9 with no extension

Steps to reproduce - Ensure to include actual links!

start web interface
search for song or add from spotify
click on download
no errors

Traceback
INFO:     <IP_ADDRESS>:61050 - "GET /api/song/url?url=https:%2F%2Fopen.spotify.com%2Ftrack%2F1pKYYY0dkg23sQQXi0Q5zN%3Fsi%3D0f3a7d0879564927 HTTP/1.1" 200 OK
INFO:     <IP_ADDRESS>:61050 - "POST /api/download/url?url=https:%2F%2Fopen.spotify.com%2Ftrack%2F1pKYYY0dkg23sQQXi0Q5zN&client_id=3deacd0b-022a-45f2-b308-cfd1cb177fd9 HTTP/1.1" 200 OK
INFO:     <IP_ADDRESS>:61050 - "GET /api/download/file?file=Daft%20Punk%20-%20Around%20the%20World.mp3&client_id=3deacd0b-022a-45f2-b308-cfd1cb177fd9 HTTP/1.1" 200 OK

Other details
No response

Can I work on this?

Can I work on this?

Go ahead

I can't reproduce this on v4.0.1. If anyone still has this issue feel free to reopen this issue.


Preset option for errors & warnings only

I've noticed that I often need just see warnings and errors since during rapid development I don't really need to see the modules stats. So I tend to write the same code every time and it would be nice to be able to just provide an "errors-warnings" preset to save space and improve readability.
What kind of change does this PR introduce?
Extension to the existing stats preset.
Did you add tests for your changes?
Tests added.
Does this PR introduce a breaking change?
No, this is a just an extension which will not break anything
What needs to be documented once your changes are merged?
The following page will need to be updated with additional stats preset option: https://webpack.js.org/configuration/stats/

Thanks


Update silver__near_github_repos.csv

added additional repos from near.toml file

@WHYTEWYLL - could I get a review on this PR for adding to tracking of NEAR electric capital repos?


Decide on sort order of releases

Common Changelog currently contradicts itself. In the introduction it says:

A changelog is a file which contains a curated, chronologically ordered list of notable changes

Then later it says:

Releases must be sorted latest-first according to Semantic Versioning rules.

It's tricky to decide which order is best (and whether we should enforce it at all) because there are conflicting concerns. Consider these use cases:

As a maintainer, having multiple release lines or hotfixes (maintained in git branches).

Side note: is there a "canonical" changelog?

As a consumer, wanting to find the changes of the semver-last release. You're on 2.x and don't care about a 1.x release.
As a consumer, upgrading from several versions back (e.g. from 1.x to 3.x) and wanting to read the changelog in semver-order
As a maintainer, migrating from Keep a Changelog (which sorts chronologically) to Common Changelog

What use cases are there for wanting to see chronologically ordered releases?

I don't really see why you would want everything to be chronologically sorted. Say I'm on 1.x and not ready to upgrade to 2.x, but still want e.g. patches for bug fixes etc. Then it would be handy for me to look at the top and see updates to 1.x, but that use case is not the most common one, so if I'm on 1.x and want to see release notes for an update to 1.x I might as well have to scroll down to the 1.x-line and pick the latest there. So maybe sort chronologically per server major?

So maybe sort chronologically per server major?

The same problem exists on "minor release lines" - when you release a hotfix for say 1.2.x and 1.3.x - though this is less common. We might as well sort all by semver, because typically that's effectively the same order as chronologically per server major.


fix entrypoint.sh print error msg when use shell commands

fix 'docker run CMD', print '2018/11/22 09:12:03 command sh not found' error msg

@sqos can you details the issue you're trying to fix here please?
As for today, we have this:
docker run traefik:v1.7.12-alpine version
Version:      v1.7.12
Codename:     maroilles
Go version:   go1.11.10
Built:        2019-05-29_07:35:02PM
OS/Arch:      linux/amd64

=> There is no error here?


String URL not returned.

The plugin works perfect. Just to point out, the return is no more String Url. it returns the json response. Please fix that
then((String url) {
// Get your uploaded Image file link from ImageKit.io
//then save it anywhere you want. For Example- Firebase, MongoDB etc.
if (kDebugMode) {
print(url); // your Uploaded Image/Video Link From Imagekit
}

Upgrade to imagekit_io: ^0.0.3


Cant Able to print the am/pm

Hello Sir,
I cant able to print the am/pm when time is selected from the TimePickerDialog please find code
TimePickerDialog catertimedialog= TimePickerDialog.newInstance(new TimePickerDialog.OnTimeSetListener() {
           @Override
           public void onTimeSet(TimePickerDialog view, int hourOfDay, int minute, int second) {
               catering_time.setText(hourOfDay+":"+minute);
           }
       },false);
       catertimedialog.show(getActivity().getFragmentManager(),"Timepicker");

The callback always returns time in 24 hour format, you are responsible for figuring out whether it's AM or PM


feat(FTL-8509): add info about active and default project

:tada: This PR is included in version 1.10.0 :tada:
The release is available on:

Visual Studio Marketplace
GitHub release

Your semantic-release bot :package::rocket:


fix(TDI-47178):[Jenkins][TCOMPv0] Need to make sure jenkins build deploy  jars automaticly

What is the current behavior? (You can also link to an open issue here)
https://jira.talendforge.org/browse/TDI-47178
What is the new behavior?
Please check if the PR fulfills these requirements

[ ] The commit message follows Talend standard
[ ] Tests for the changes have been added (for bug fixes / features)
[ ] Docs have been added / updated (for bug fixes / features) ?
[ ] The code coverage on new code >75%
[ ] The new code does not introduce new technical issues (sonar / eslint)

What kind of change does this PR introduce?

[ ] Bugfix
[ ] Feature
[ ] Code style update (formatting, local variables)
[ ] Refactoring (no functional changes, no api changes)
[ ] Build / CI related changes
[ ] Other... Please describe:

Does this PR introduce a breaking change?

[ ] Yes
[ ] No

If this PR contains a breaking change, please describe the impact and migration path for existing applications: ...
Other information:

Pull request test result: failure :x:

Pull request test result: failure :x:


Adding portable pre-built versions for Mac aarch64 and x86 to the release

Hello, friends in the fselect community,
Will fselect add portable pre-built versions for Mac aarch64 and x86 to the release? We are developing x-cmd and want to add fselect to our pkg: https://www.x-cmd.com/pkg/fselect
We can compile fselect according to the README, but we usually prefer to use the official release to avoid any possible inconsistencies introduced by our team.
Take trdsql as an example: https://www.x-cmd.com/pkg/trdsql

Can this support ARM64 orch?


DOCS-2633: Add documentation for distributed XGBoost on Modin

Signed-off-by: Alexey Prutskov<EMAIL_ADDRESS>
What do these changes do?
This changes add documentation for distributed XGBoost on Modin

[ ] commit message follows format outlined here
[ ] passes flake8 modin
[ ] passes black --check modin
[ ] signed commit with git commit -s
[ ] Resolves #2633 ?
[ ] tests added and passing

@YarShev , @devin-petersohn I'll add screуnshots of new doc pages after #2659 is merged

@YarShev , @devin-petersohn I'll add screуnshots of new doc pages after #2659 is merged

@devin-petersohn Are you talking about docstrings in functions? If yes, this was added in those files (DMatrix, train, predict). Part of generated docs are presented below. Is your question about it?

Thanks @prutskov, that is what I was talking about.


feat: Support for documents + embeddings

Hello! Great work!
It would be great to have OllamaSpring support documents and Ollama's embeddings' endpoint.

coming soon


telomerase difference

I'm checking a community submission related to telomerase.
I don't understand the difference between these 2 terms:
GO:0003720 telomerase activity
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence.
telomerase RNA reverse transcriptase activity
Catalysis of the extension of the 3' end of a DNA strand by one deoxynucleotide at a time. Cannot initiate a chain de novo; uses the RNA subunit of the telomerase enzyme complex as its template.

GO:0032203	telomere formation via telomerase
A cellular process that results in the formation of a telomere at a non-telomeric double-stranded DNA end that involves the activity of a telomerase enzyme.
So, I presume this is describing elongation (although I am a little confused by the  meaning of the 'telomere assembly' term?
I expected to see a relationship here

Hi Val, Nancy is back in October, do you mind waiting for her input?
Ruth

@NancyCampbell

No hurry,  the session is curated using
"positive regulation of telomere maintenance via telomerase"
https://curation.pombase.org/pombe/curs/be9521cb5c4791ae
but the parentage doesn't seem to encapsulate the process of DNA biosynthesis in any way as it stands.
@mah11  may also have input as she has been curating in this area, and may have some knowledge of the current arrangement. No hurry though.

I don't understand the difference between these 2 terms:

Telomerase activity (GO:0003720) has two parts: the reverse transcriptase activity (GO:0003721) and the RNA template "activity" (GO:0000332). Being a template isn't as graceful a fit with GO MF's "molecular activity" scope as your typical catalytic activity, but it is what the telomerase RNA is there for, and people have wanted to annotate its role at the molecular level. If it's done at all, GO is doing it as best it can.

GO:0032203 telomere formation via telomerase
[should it link to GO:0022616 DNA strand elongation?]

There isn't a link, and it looks like there should be, but it will have to be has_part (telomere formation via telomerase has_part DNA strand elongation). I think QuickGO doesn't show has_part links, so its display would look the same with the link in the ontology.

My question is then, which term to use for "telomere elongation by telomerase"

I would say GO:0032203 for the process, and GO:0003720 if you're actually annotating the telomerase itself.

Hmm, making the has_part link won't really prevent annotation inconsistence though...

On telomerase catalytic subunit, the same process can be correctly described in 2 ways, either as 'telomere maintenance',  or as 'DNA elongation'

I don't understand why the process
"telomere maintenance by telomerase"
can't be equally called
"DNA synthesis by telomerase" (or exact synonym) as this is what telomerase is doing
and as telomerase activity is defined as
"Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence."
The term "telomere maintenance by telomerase/DNA synthesis by telomerase" could be "part_of" the broader telomere maintenance term

@NancyCampbell :  back in September, Ruth mentioned that you'd be  back in October, do you mind waiting for her input?"  Could you please have a look at this issue?  Thanks.

My two pennies' worth:
Telomerase is an enzyme formed of two parts TERT(protein) and TERC (RNA template). So neither can have/perform telomerase activity without the other,
Therefore I would expect to see:
TERT contributes_to Telomerase activity GO:0003720
TERC contributes_to Telomerase activity GO:0003720
Then
TERT-TERC complex annotated directly (no contribues_to) to Telomerase activity GO:0003720
Furthermore,
TERC annotated to telomerase RNA reverse transcriptase activity GO:0003721
Having said that:
That is not how the annotations on QuickGO currently stand. Depending on what is agreed here, some work might need to be done. I can do ours to make sure they are standardised. Any comments?

and definitely Val ...then the definitions will need some adjusting! I agree they are not very clear as they stand now!

The links may possibly go further down the tree to the children?!

@NancyCampbell
could you summarize the reationships to be added?
(I.e what the red lines represent...I'm not sure what needs to be added.
Val
(I have another question...isn't DNA strand elongation always a DNA biosynthetic process?)

Hi @ValWood
How does the following sound:
telomerase RNA reverse transcriptase activity part_of telomeric 3' overhang formation part_of telomere formation via telomerase.
What do the editors @tberardini think about this? should this type of relationship at this granular level be relfected in the ontology tree itself? - the curator can add it as part of the annotation itself in the AE field?!
Val, I am surprised though that telomere formation via telomerase has no children?? What am i missing?
As to the question: (I have another question...isn't DNA strand elongation always a DNA biosynthetic process?)
I think it is!! the definitions on QuickGO below are in agreement too! But it is not reflected in the tree (below)!!!
DNA biosynthetic process: GO:0071897 The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
DNA strand elongation: GO:0022616 The DNA metabolic process in which a DNA strand is synthesized by adding nucleotides to the 3' end of an existing DNA stand.
The parent of both of the terms above is  GO:0006259 DNA metabolic process: Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides

Various comments, which I hope don't add to the confusion ...
Annotations:

TERT-TERC complex annotated directly (no contribues_to) to Telomerase activity GO:0003720
TERC annotated to telomerase RNA reverse transcriptase activity GO:0003721

Should the second annotations say TERT (not TERC)? If so, these both look fine. Furthermore, annotating TERT to GO:0003721 makes it unnecessary to include this one explicitly:

TERT contributes_to Telomerase activity GO:0003720

... because the ontology has GO:0003721 part_of GO:0003720. Similarly, 'template for synthesis of G-rich strand of telomere DNA activity' GO:0000332 is also part_of GO:0003720, so if TERC is annotated to GO:0000332 it doesn't need to be annotated to GO:0003720 as well.
Ontology:
I'm no expert on telomere biology, so I don't know whether what GO has is exactly as it should be, especially in BP.

telomerase RNA reverse transcriptase activity part_of telomeric 3' overhang formation (GO:0031860)

Does telomerase only synthesize the 3' overhang? That's what this link would imply (i.e. the part_of link won't always be correct if telomerase also synthesizes any of the telomere other than the overhang).

telomeric 3' overhang formation part_of telomere formation via telomerase

This may well be true - it's one of the things I don't know so well. In any case, the GO:0031860 definition could probably stand to be improved, to say more explicitly what it entails (its current shortcomings are probably my fault; the term dates back to before any of us were so careful about beginnings, ends, and MF parts of processes).

I don't understand why the process "telomere maintenance by telomerase" can't be equally called "DNA synthesis by telomerase"

Again, not sure but it may just be to make the "telomere maintenance" term names match nicely.
I seem to recall people (Eurie and Rob? guessing from def dbxrefs) saying that telomeres could be maintained either by synthesis or by recombination, which accounts for GO:0007004, GO:0032201 and GO:0000722. I also wonder if GO:0032201 should be is_a  telomere maintenance via telomere lengthening GO:0010833?

isn't DNA strand elongation always a DNA biosynthetic process?

I think the strand elongation defs in GO are a bit simplistic; I would say that strand elongation is a process that always has DNA biosynthesis as a part, but not necessarily the only part. Certainly in the context of replication, lagging strand elongation involves primer synthesis (i.e. an RNA biosynthetic process) as well as DNA synthesis, and for both strands helicase and ligase activities are necessary, and not obviously covered by the GO:0022616 def. I would adjust the elongation defs to include the other activities, and then say elongation has_part synthesis.

Great discussion. When it all settles down, please enumerate the changes you would like to see and I will implement.
@NancyCampbell : Can you explain this one please,

"telomerase RNA reverse transcriptase activity part_of telomeric 3' overhang formation part_of telomere formation via telomerase."?

Does this mean:
telomere formation via telomerase.
--[p] telomeric 3' overhang formation
---[p] telomerase RNA reverse transcriptase activity

should this type of relationship at this granular level be relfected in the ontology tree itself?

Sure, if that's a true capture of the biology.

Comments in italics below (I hope it works)
Various comments, which I hope don't add to the confusion ...
On the contrary, clear. Thank you
Annotations:
TERT-TERC complex annotated directly (no contribues_to) to Telomerase activity GO:0003720
TERC annotated to telomerase RNA reverse transcriptase activity GO:0003721

Should the second annotations say TERT (not TERC)? If so, these both look fine. Furthermore, annotating TERT to GO:0003721 makes it unnecessary to include this one explicitly:
Yes (typo- sorry!)
TERT annotated to telomerase RNA reverse transcriptase activity GO:0003721
&
TERC annotated to template for synthesis of G-rich strand of telomere DNA activity GO:0000332 (which you mention/allude to in the next point - unless I am mistaken)
TERT contributes_to Telomerase activity GO:0003720

... because the ontology has GO:0003721 part_of GO:0003720. Similarly, 'template for synthesis of G-rich strand of telomere DNA activity' GO:0000332 is also part_of GO:0003720, so if TERC is annotated to GO:0000332 it doesn't need to be annotated to GO:0003720 as well.
_ yes
so is this what the annotation looks like (?):
TERT annotated to telomerase RNA reverse transcriptase activity GO:0003721
TERC annotated to template for synthesis of G-rich strand of telomere DNA activity GO:0000332
TERT-TERC complex annotated to Telomerase activity GO:0003720
if yes, and since GO:0003721 & GO:0000332 are children of GO:0003720 and consequently do not need to be annotated explicitly to GO:0003720 (which is the sensible/usual thing to do as suggested), then my question would be:
how can one indicate that both components are needed together for telomerase activity and neither of them can perform the activity alone, in context of annotating an exisiting complex term?
suggestion 1: an automatic mechanism that will inherit/cascade this annotation to the components of the complex from the annotation of TERT-TERC complex to telomerase activity GO:0003720, does this even exist? (I feel it was one of the options in discussion amongst other alternatives on how to deal with this in the past but I am not aware of the outcome - was a decision made and implemented? And in the meantime how do we deal with it?)
Suggestion 2:
TERT contributes_to Telomerase activity GO:0003720
TERC contributes_to Telomerase activity GO:0003720
The emphasis above is on using the qualifier contributes_to
_
Ontology:
I'm no expert on telomere biology, so I don't know whether what GO has is exactly as it should be, especially in BP.
telomerase RNA reverse transcriptase activity part_of telomeric 3' overhang formation (GO:0031860)

Does telomerase only synthesize the 3' overhang? That's what this link would imply (i.e. the part_of link won't always be correct if telomerase also synthesizes any of the telomere other than the overhang).
_so if telomerase has other functions, for example some are TERC-independent i.e. TERT binds with RMRP and the TERT-RMRP complex has TERC-INDEPENDENT RNA-DEPENDENT RNA POLYMERASE ACTIVITY PMID 23061047 (figure 1 below) (review), the link can't be made, correct?

_
telomeric 3' overhang formation part_of telomere formation via telomerase

This may well be true - it's one of the things I don't know so well. In any case, the GO:0031860 definition could probably stand to be improved, to say more explicitly what it entails (its current shortcomings are probably my fault; the term dates back to before any of us were so careful about beginnings, ends, and MF parts of processes).
I don't understand why the process "telomere maintenance by telomerase" can't be equally called "DNA synthesis by telomerase"

Again, not sure but it may just be to make the "telomere maintenance" term names match nicely.
I seem to recall people (Eurie and Rob? guessing from def dbxrefs) saying that telomeres could be maintained either by synthesis or by recombination, which accounts for GO:0007004, GO:0032201 and GO:0000722. I also wonder if GO:0032201 should be is_a telomere maintenance via telomere lengthening GO:0010833?
_We have struggled to find evidence in human/mammalian non-cancer cells to support Alternative Lengthening of Telomeres (ALT) (which is a telomerase independent mechanism involving homologous recombination-mediated DNA replication). I am assuming that ALT is what this term GO:0032201 means/alludes to/is understood to mean or maybe is a more general term that includes ALT? (GO:0032201 telomere maintenance via semi-conservative replication: The process in which telomeric DNA is synthesized semi-conservatively by the conventional replication machinery and telomeric accessory factors as part of cell cycle DNA replication).
Wouldn't is_a mean that they are the same? - which they are not. Consequently, the two terms GO:0032201 telomere maintenance via semi-conservative replication &  and GO:0010833  telomere maintenance via telomere lengthening are fine as they stand.
GO:0010833  telomere maintenance via telomere lengthening: Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins and lengthening the telomeric DNA._
isn't DNA strand elongation always a DNA biosynthetic process?

I think the strand elongation defs in GO are a bit simplistic; I would say that strand elongation is a process that always has DNA biosynthesis as a part, but not necessarily the only part. Certainly in the context of replication, lagging strand elongation involves primer synthesis (i.e. an RNA biosynthetic process) as well as DNA synthesis, and for both strands helicase and ligase activities are necessary, and not obviously covered by the GO:0022616 def. I would adjust the elongation defs to include the other activities, and then say elongation has_part synthesis.
agree

@tberardini
sorry it was not clear.
I meant
telomeric 3' overhang formation part_of telomere formation via telomerase
and a separate statement
telomerase RNA reverse transcriptase activity part_of telomeric 3' overhang formation (GO:0031860)
However, @mah11 commented on these. Ongoing discussion is in the post immediately prior to this.

Responses to just a few parts of Nancy's latest contribution ...

how can one indicate that both components are needed together for telomerase activity and neither of them can perform the activity alone, in context of annotating an exisiting complex term?

In the case of telomerase, this could be done at the level of the ontology, by adding has_part links:
telomerase activity GO:0003720 has_part GO:0000332 [template]
and
telomerase activity GO:0003720 has_part GO:0003721 [reverse transcriptase]

More generally, I'm not sure we have a reliable way of distinguishing at the level of annotation when a gene product makes an essential as opposed to dispensable contribution to an activity. Even using contributes_to doesn't quite say the contribution is essential, just that it makes a detectable difference.
I wonder if there's anything relevant in LEGO?

so if telomerase has other functions, for example some are TERC-independent i.e. TERT binds with RMRP and the TERT-RMRP complex has TERC-INDEPENDENT RNA-DEPENDENT RNA POLYMERASE ACTIVITY PMID 23061047 (figure 1 below) (review), the link can't be made, correct?

Not sure about this example, although at a quick glance it does seem inconsistent with making the link.
What I actually had in mind is that making the link would logically imply that the telomerase RT activity synthesizes only the 3' overhang. So if telomerase RT actually synthesizes more of the telomere than just the part that ends up as the 3' overhang, the link can't be made.

We have struggled to find evidence in human/mammalian non-cancer cells to support Alternative Lengthening of Telomeres (ALT) (which is a telomerase independent mechanism involving homologous recombination-mediated DNA replication). I am assuming that ALT is what this term GO:0032201 means/alludes to/is understood to mean or maybe is a more general term that includes ALT?

That's another thing I don't know. (Judging from the ID I must have added the term years ago, but I think I did so using information from someone else, possibly Eurie and/or Rob.) But from your description ALT sounds more like GO:0000722, 'telomere maintenance via recombination'.

Wouldn't is_a mean that they are the same?

No, it would mean that one is more specific than the other, and that the more specific thing has all of the features of the less specific thing, plus one or more additional distinguishing features. If they were the same there would only need to be one term.
I thought from the part of the GO:0032201 definition that says "telomeric DNA is synthesized semi-conservatively by the conventional replication machinery" that it sounds an awful lot like a way of, well, lengthening a telomere.

Re:
I seem to recall people (Eurie and Rob? guessing from def dbxrefs) saying that telomeres could be maintained either by synthesis or by recombination, which accounts for GO:0007004, GO:0032201 and GO:0000722. I also wonder if GO:0032201 should be is_a telomere maintenance via telomere lengthening GO:0010833?
We have struggled to find evidence in human/mammalian non-cancer cells to support Alternative Lengthening of Telomeres (ALT) (which is a telomerase independent mechanism involving homologous recombination-mediated DNA replication).
===
I might be responsible for the term originally. I think you are correct and this is not a "normal" process. For sure, if you mutate telomerase, there are rare survivors where the chromosomes are circularized via recombination (which is usually prevented by the telomere proteins). I don't think that these mutants can survive long term.
This would help the clean up. Would require input from SGD

and for sure, this is not replication. The telomeres are maintained only because the chromosome
circularization prevents degradation.

Reiterating my earlier comment: Great discussion. When it all settles down, please enumerate the changes you would like to see and I will implement.

I don't think I know enough nitty-gritty telomere biology to help more than I already have there (if it's been helpful at all). I do have some suggestions for DNA strand elongation:
GO:0022616 DNA strand elongation
new def: The DNA metabolic process in which an existing DNA strand is extended by activities including the addition of nucleotides to the 3' end of the strand. [GOC:mah, GOC:isa_complete]
add link has_part GO:0071897 DNA biosynthetic process
GO:0006271 DNA strand elongation involved in DNA replication
new def: The process in which an existing DNA strand is extended by activities including the addition of nucleotides to the 3' end of the strand, complementary to an existing template, as part of DNA replication. [GOC:mah, ISBN:071673706X, ISBN:0815316194]
add link has_part GO:0090592 DNA synthesis involved in DNA replication
GO:0006272 leading strand elongation
new def: The process in which an existing DNA strand is extended continuously in a 5' to 3' direction by activities including the addition of nucleotides to the 3' end of the strand, complementary to an existing template, as part of DNA replication. Leading strand elongation proceeds in the same direction as the replication fork. [GOC:mah, ISBN:071673706X, ISBN:0815316194]
add link has_part GO:0043137 DNA replication, removal of RNA primer
(keep existing link has_part GO:0006269 DNA replication, synthesis of RNA primer)
GO:0006273 lagging strand elongation
new def: The process in which an existing DNA strand is extended in a net 3' to 5' direction by activities including the addition of nucleotides to the 3' end of the strand, complementary to an existing template, as part of DNA replication. Lagging strand DNA elongation proceeds by discontinuous synthesis of short stretches of DNA, known as Okazaki fragments, from RNA primers; these fragments are then joined by DNA ligase. Although each segment of nascent DNA is synthesized in the 5' to 3' direction, the overall direction of lagging strand synthesis is 3' to 5', mirroring the progress of the replication fork. [GOC:mah, ISBN:071673706X, ISBN:0815316194]
add link has_part GO:0043137 DNA replication, removal of RNA primer
(keep existing link has_part GO:0006269 DNA replication, synthesis of RNA primer)
Also adjust text defs of regulation terms as needed to match.
Note: GO:0043137 should not be part_of GO:0006273, because each leading strand also has one primer that must be removed.
These have defs that don't really need changing, because they're just 'generic part involved in specific whole' without any of the bumf explaining what the part is:

GO:1902296 DNA strand elongation involved in cell cycle DNA replication (but can add link has_part GO:1904860 DNA biosynthetic process involved in mitotic DNA replication)
GO:1903459 mitotic DNA replication lagging strand elongation
GO:1903460 mitotic DNA replication leading strand elongation

Hi @mah11
This was a while ago. Can you confirm that your suggestions in the last comment are what needs to be done ? Thanks :)
Pascale

I'm happy to confirm that the changes in the "strand elongation" area can be made. I'm less sure that sorts out everything about telomeres from earlier in the ticket, but I think at this point people can open new tickets for anything outstanding.

[ ]  GO:0060382 regulation of DNA strand elongation
[ ]  GO:0060383 positive regulation of DNA strand elongation

There are no regulation for lagging strand elongation, leading strand elongation, and DNA strand elongation involved in DNA replication.


Pod error will appear when creating vm, which should not appear under normal circumstances

Is your feature request related to a problem? Please describe.
The vm status may change to pod err, and it will be normal after a while
expect
There is no need to display this pod err, unless it is really wrong

duplicate of https://github.com/rancher/harvester/issues/662


V3.2.1

This was on Anaconda Recipes but no submodule had been created.

Linter check found the following problems:
The following problems have been found:
WARNING: /tmp/abs_ec4e_wrso1/clone/recipe/meta.yaml:57: missing_license_url: The recipe is missing a license_url
WARNING: /tmp/abs_ec4e_wrso1/clone/recipe/meta.yaml:57: missing_doc_source_url: The recipe is missing a doc_source_url
Warnings were found


Sphinx documentation

#13 Implement Sphinx to automatically generate documentation

Documentation can be built locally (provided Sphinx is installed) with cd doc && make html
Documentation is built (as a test) using Travis
Any commits to master will automatically rebuild documentation on readthedocs: http://improver.readthedocs.io/

I just noticed that the RTD hosted documentation has an "Edit on Github" link which results in a 404 error on most pages - this is because they link to the *.rst files in the repo, which are not present because they are instead generated at build time.
Note: Local builds use the Sphinx default theme (rather than the RTD theme), and so this won't be a problem.
Apparently, we can fix this problem by copying one of the template files from the RTD theme to our repo:
https://stackoverflow.com/questions/36019670/removing-the-edit-on-github-link-when-using-read-the-docs-sphinx-with-readthed
...I think that this fix is quite messy though. Including a single file to fix something which is not actually a part of the repo doesn't seem like an elegant solution.

Two comments, otherwise fine apart from the Travis failure - try a rebase?

@benfitzpatrick, merged in the changes from master and still couldn't figure out why Travis was failing - it turned out that I'd not updated all of the BATS tests for improver-tests (I added a reference to documentation in the script usage string).
...Hopefully that should fix things.

Raised #89 for addressing these Sphinx warnings by altering the docstrings

Could we make sure it is either IMPROVER (project) or improver (codebase), and include the following blurb somewhere noticeable:
IMPROVER is a library of algorithms for meteorological post-processing and verification.
Otherwise good.

@benfitzpatrick How's that?

I think the 'edit on GitHub' bit is probably unnecessary to fix right now, let's leave it.

@gavinevans: Following a conversation with @benfitzpatrick, the Makefile has been updated to make it clear that it was automatically generated by Sphinx (as the other files already do). This makes it absolutely clear that we are not attempting to relicense any part of/any files generated by Sphinx.


Connection issue with latest version of Fishnet (v4.5.4hf0R Pro)

Just try to connect as a server and client and you should see the issues popping up. When you then disconnect you will see errors as well.

Fixed in version 1.2.0


private-cli to record dnadiff comparisons in the DB

This PR proposes changes related to #131, expanding the private CLI to allow logging a single dandify comparison, following the pattern used for methods like ANIm and ANIb.

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

Action Checklist

[X] Work on a single issue/concept (if there are multiple separate issues to address, please use a separate pull request for each)
[X] Fork the pyani-plus repository under your own account (please allow write access for repository maintainers)
[X] Set up an appropriate development environment (please see CONTRIBUTING.md for this repository)
[X] Create a new branch with a short, descriptive name
[X] Work on this branch

[X] style guidelines have been followed (please see CONTRIBUTING.md for this repository)
[X] new code is commented, especially in hard-to-understand areas
[ ] corresponding changes to documentation have been made
[X] tests for the change have been added that demonstrate the fix or feature works

[X] Test locally with pytest-plus -v non-passing code will not be merged
[X] Rebase against origin/master
[X] Check changes with linting/formatting tools before submission (please see CONTRIBUTING.md for this repository)
[X] Commit branch
[X] Submit pull request, describing the content and intent of the pull request
[X] Request a code review
[X] Continue the discussion at Pull requests section in the pyan-plus repository

That looks good - just minor remarks about the comment lines.

 If you happy with it, we can merge and I will start woriking on removing the unwanted code mentioned in #133.

Sure - talk again tomorrow.

I marked it as approved, so once the tests finished take that as a green-light to merge


[bug] Codeunit "Item Jnl.-Post Line" - using boolean OnRun return

var
    JnlLine: Record "Item Journal Line";
    JnlLinePost: Codeunit "Item Jnl.-Post Line";
begin
        JnlLine.Init();
        ...
        Validate needed fields in here...
        ...
            if JnlLinePost.Run(JnlLine) then begin
                ...
            end;
 end;

This 'if JnlLinePost.Run(JnlLine) then'  kind of code was working fine until last friday but suddenly, the same extension in the same environment started to throw this error:
"Form.RunModal is not allowed in write transactions."
It is still working fine in a Sandbox copied from the productive environment.
The call is inside a repeat-until loop, but a commit is done after each loop, and I repeat, it was working fine until last friday
Thanks in advance!

Please create support ticket if you need this addressed. This is wrong place for this kind of requests.


feat(aggregator): Aggregator Retry improvements

Retry interface improvements:
closes #1401 #1414 #1391
Description
Description of the pull request changes and motivation.
Type of change
Please delete options that are not relevant.

[x] Refactor

Checklist

[x] Linked to Github Issue

DefaultRetryConfig may be confusing. We should use the same names as in the batcher, to split the chain and non chain constants

The Batcher uses the following naming scheme for the constants:

/// Ethereum calls retry constants
pub const ETHEREUM_CALL_MIN_RETRY_DELAY: u64 = 500; // milliseconds
pub const ETHEREUM_CALL_MAX_RETRIES: usize = 5;
pub const ETHEREUM_CALL_BACKOFF_FACTOR: f32 = 2.0;
pub const ETHEREUM_CALL_MAX_RETRY_DELAY: u64 = 3600; // seconds

/// Ethereum transaction retry constants
pub const BUMP_MIN_RETRY_DELAY: u64 = 500; // milliseconds
pub const BUMP_MAX_RETRIES: usize = 33; // ~ 1 day
pub const BUMP_BACKOFF_FACTOR: f32 = 2.0;
pub const BUMP_MAX_RETRY_DELAY: u64 = 3600; // seconds

Which indicate the parameters for performing an eth call vs eth transaction. In the operator/aggregator we are differentiating between on-chain vs not on-chain.  @MauroToscano I'm not sure if there is overlap as the eth tx retry factors in bumping the tx fee. @avilagaston9 would welcome your thoughts.

DefaultRetryConfig may be confusing. We should use the same names as in the batcher, to split the chain and non chain constants

The Batcher uses the following naming scheme for the constants:
/// Ethereum calls retry constants
pub const ETHEREUM_CALL_MIN_RETRY_DELAY: u64 = 500; // milliseconds
pub const ETHEREUM_CALL_MAX_RETRIES: usize = 5;
pub const ETHEREUM_CALL_BACKOFF_FACTOR: f32 = 2.0;
pub const ETHEREUM_CALL_MAX_RETRY_DELAY: u64 = 3600; // seconds

/// Ethereum transaction retry constants
pub const BUMP_MIN_RETRY_DELAY: u64 = 500; // milliseconds
pub const BUMP_MAX_RETRIES: usize = 33; // ~ 1 day
pub const BUMP_BACKOFF_FACTOR: f32 = 2.0;
pub const BUMP_MAX_RETRY_DELAY: u64 = 3600; // seconds

Which indicate the parameters for performing an eth call vs eth transaction. In the operator/aggregator we are differentiating between on-chain vs not on-chain. @MauroToscano I'm not sure if there is overlap as the eth tx retry factors into bumping the tx fee. @avilagaston9 would welcome your thoughts.

We can use ETHEREUM_CALL as name for consistency if we don't have the other ones.
Default is the strangest one, It's not clear what a default is or why we need it

We will re do this PR in parts


Style changes not reflected on Netlify build

Sometimes changes on style aren't reflected on Netlify build probably due to cache.
Important to keep that in mind when we implement it on our build.

this problem only happens on netlify, it is not happening anymore, so I am closing this issue.


logstash can not connect to localhost_9200

logstash     | [WARN ] 2020-10-21 21:04:11.839 [Ruby-0-Thread-12: /usr/share/logstash/vendor/bundle/jruby/2.5.0/gems/logstash-output-elasticsearch-10.6.2-java/lib/logstash/outputs/elasticsearch/http_client/pool.rb:241] elasticsearch - Attempted to resurrect connection to dead ES instance, but got an error. {:url=>"http://localhost:9200/", :error_type=>LogStash::Outputs::ElasticSearch::HttpClient::Pool::HostUnreachableError, :error=>"Elasticsearch Unreachable: [http://localhost:9200/][Manticore::SocketException] Connection refused (Connection refused)"}

@hcwwadmin - I apologize for the inconvenience.  I failed to properly update the 50-outputs.conf file.  The host should have been http://elastic:9200 and not http://localhost:9200
Additionally, I found that both the 35-ruels-desc.conf and 36-ports-desc.conf files resulted in logstash crashing.
Please give it another try with the revised files.  I've tested without issue.

the error is gone
thanks for your help

Running into same issue as this.
logstash    | [INFO ] 2022-01-27 21:19:12.147 [[pfelk]-pipeline-manager] elasticsearch - New Elasticsearch output {:class=>"LogStash::Outputs::ElasticSearch", :hosts=>["http://localhost:9200"]}
logstash    | [INFO ] 2022-01-27 21:19:12.157 [[pfelk]-pipeline-manager] elasticsearch - Elasticsearch pool URLs updated {:changes=>{:removed=>[], :added=>[http://localhost:9200/]}}
logstash    | [WARN ] 2022-01-27 21:19:12.168 [[pfelk]-pipeline-manager] elasticsearch - Attempted to resurrect connection to dead ES instance, but got an error {:url=>"http://localhost:9200/", :exception=>LogStash::Outputs::ElasticSearch::HttpClient::Pool::HostUnreachableError, :message=>"Elasticsearch Unreachable: [http://localhost:9200/][Manticore::SocketException] Connect to localhost:9200 [localhost/<IP_ADDRESS>] failed: Connection refused (Connection refused)"}
logstash    | [WARN ] 2022-01-27 21:19:12.974 [[pfelk]-pipeline-manager] grok - Relying on default value of pipeline.ecs_compatibility, which may change in a future major release of Logstash. To avoid unexpected changes when upgrading Logstash, please explicitly declare your desired ECS Compatibility mode.

@kk0201 - thanks! The issue was just fixed...had a typo where http://localhost:9200 should have been http://es01:9200

Thanks for fixing it so quickly.


subsys: usb: class: hid: Allow control of USB poll interval

This closes issue #10807
Signed-off-by: Pawel Dunaj<EMAIL_ADDRESS>

Codecov Report

Merging #10808 into master will not change coverage.
The diff coverage is n/a.

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=======================================
  Files         215      215
  Lines       25820    25820
  Branches     5692     5692
=======================================
  Hits        13748    13748
  Misses       9756     9756
  Partials     2316     2316

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This looks like a good idea to make this configurable, and it looks like the correct way to do that. That said, I think the name and the description of the option are wrong. The bInterval field corresponds to a period in number of frames, and not to a frequency in Hz. In full speed mode, there is one frame per millisecond, so this corresponds to the number of milliseconds between two polls.
I guess the option should be changed to USB_HID_POLL_INTERVAL_MS and the help text to Polling interval in ms selected by the USB HID Device.

@aurel32 , thanks for spotting this - text was obviously wrong.

hi @carlescufi , can you merge this?


Error in variable explorer for dicts with mixed-type keys

Description of your problem
What steps will reproduce the problem?

Create a dict with str and int keys: d = {'1': 1, 2: 2}
Open it in the variable explorer
Click ok to close the window: error pops-out

  File "...\spyder\widgets\variableexplorer\collectionseditor.py", line 527, in <lambda>
    lambda eid=id(editor): self.editor_accepted(eid))
  File "...\spyder\widgets\variableexplorer\collectionseditor.py", line 549, in editor_accepted
    self.set_value(index, conv_func(value))
  File "...\spyder\widgets\variableexplorer\collectionseditor.py", line 1370, in set_value
    self.set_value_func(name, value)
  File "...\spyder\widgets\variableexplorer\namespacebrowser.py", line 304, in set_value
    value = serialize_object(value)
  File "...\ipykernel\serialize.py", line 85, in serialize_object
    for k in sorted(obj):
TypeError: '<' not supported between instances of 'int' and 'str'

Versions and main components

Spyder Version: 3.2.3
Python Version: 3.6

Dependencies
IPython >=4.0    :  5.3.0 (OK)
cython >=0.21    :  0.25.2 (OK)
jedi >=0.9.0     :  0.10.2 (OK)
nbconvert >=4.0  :  5.1.1 (OK)
numpy >=1.7      :  1.12.1 (OK)
pandas >=0.13.1  :  0.20.1 (OK)
pycodestyle >=2.3:  2.3.1 (OK)
pyflakes >=0.6.0 :  1.5.0 (OK)
pygments >=2.0   :  2.2.0 (OK)
pylint >=0.25    :  1.6.4 (OK)
qtconsole >=4.2.0:  4.3.0 (OK)
rope >=0.9.4     :  0.9.4-1 (OK)
sphinx >=0.6.6   :  1.5.6 (OK)
sympy >=0.7.3    :  1.0 (OK)

Actually I think the error comes from ipykernel. I do not think there is something we can do within spyder. I will open an issue  there.

@Prikers, we need to deal with this error in our side because it's a failure to serialize an object so that it can be saved by Spyder to the current namespace.

@ccordoba12, ok noted! How can we handle that?

@5341 trades the use of IPython-parallel's protocol extensions for an equivalent Spyder-controlled extension, and in doing so using cloudpickle for serialization, which should fix this particular bug.

@Prikers, Min's PR is a great improvement for Spyder 4. For now, we should simply catch the error and skip setting a new value for the dict.


Create InfixToPrefix.cpp

provide a detailed description of your commit

do i need to add explanation? or the steps ?

you need to add some description of your commit, do not leave it blank

ok

I am unable to commit changes now, can u help

Done


OP-14834: Added missing import statement

https://devopsmx.atlassian.net/browse/OP-14834

This PR  triggered this build in this execution, please merge to v3.9 branch only if this succeeds:  https://spin.prod.opsmx.com/#/applications/isd39/executions/details/01G3XC845T1XH9491KH7HR7G8P

This PR  triggered this build in this execution, please wait for it  and child pipelines to succeed before merging:  https://isd.prod.opsmx.net/deck/#/applications/gcp-gitprtrigger/executions/details/01G3XC7E316S3TX5WKVTV00QPA


Build break when updating to v2.1.0

If I update from v 1.0.1 to 2.1.0, I'll get the following exception during build.
`extract-text-webpack-plugin/index.js:267
var shouldExtract = !!(options.allChunks || chunk.isInitial());
^
TypeError: chunk.isInitial is not a function
at /Users/Christian/dev/portal/node_modules/extract-text-webpack-plugin/index.js:267:55
at /Users/Christian/dev/portal/node_modules/extract-text-webpack-plugin/node_modules/async/dist/async.js:3025:16
at eachOfArrayLike (...)`

There were a lot of breaking changes from v1 to v2. I'm not sure if the function still exists.

Actually I am not using webpack 2. I was updating this plugin while sticking to webpack 1.

Can you post your webpack config, please?

v2.1.0 won't work with webpack1, this breaking change has been added quite a while ago https://github.com/webpack-contrib/extract-text-webpack-plugin/commit/ba0a71dcc72dd298f602f96906e2042a08cbe039
I would recommend updating to webpack 2 or sticking with v1.0.1

@orangecoding See @kostasmanionis's comment


Upgrade Gu packages to TS 5.1

There needs to be a integration tests to ensure that the generated declaration files are valid.
With #659 we got invalid directives like /// <reference types="x">


Don't render tooltips when they are disabled

When hovering over a point tooltips are displayed/animated, but this can be skipped when tooltips have been disabled in the chart options.
This was causing multiple unnecessary redraws as the user moves the mouse over the chart.

Oops, I think I was getting confused with tooltips.enabled when I wrote hover.enabled, it is not an existing option.
Not sure if you are happy to add the option or not. It makes sense for me as it avoids extra chart rendering, but I don't know if that's enough for you to feel it's worth adding.

I think we already support tooltips: false|object, tooltips.enabled: boolean and hover: false|object, so it makes sense to also support hover.enabled: boolean.

@teroman have you had a chance to address @simonbrunel's comments?

Hi, sorry, I lost track of this!
I think the check for hoverOptions.enabled makes sense because me.active is set by getElementsAtEventForMode(), and stepping into that options.enabled isn't checked (e.g. in indexMode() or nearest() )
I didn't want to add more checks into each function, one place seemed simpler to my mind.
As Simon is happy to have .enabled added to the hover options, does the default need to be set somewhere? Currently it is undefined and so just defaults to true, but I don't know if is expected to be set more explicitly.

@teroman no, you don't need to explicitly set the default, but please add it to the documentation.
As a side note, you can find examples of explicitly setting defaults by looking for defaults._set. For example:
defaults._set('bar', {
	hover: {
		mode: 'label'
	},

.
.
.

defaults._set('horizontalBar', {
	hover: {
		mode: 'index',
		axis: 'y'
	},

I don't think you probably need to do this however.

@teroman would you be able to give this PR another look?

@teroman just a reminder about this PR

@teroman if you can give this PR another look, we'd love to get it merged

@teroman I'm closing this PR as inactive for now. Please feel free to reopen at any point when you get a chance to address the comments


Flagged as Trojan after compiling

I'm not sure why this would be flagged as a Trojan but it is on carbon black which is what my corp uses. Ran it through virustotal.com And it's flagged as Trojan as well and a couple different scanners.
The original executable that's already compiled and released is perfectly fine. Does it have something to do with signing or lack thereof?
Any ideas?

Yeah, not sure why you're getting that. The latest release is here:
https://github.com/MouseUnSnag/MouseUnSnag/releases/tag/V2.2
And the actual .exe is here:
https://github.com/MouseUnSnag/MouseUnSnag/releases/download/V2.2/MouseUnSnag.exe
And if you plop that .exe URL into VirusTotal, this is what comes out:
https://www.virustotal.com/gui/url/6b5df0bc4a3c9f40680c2b5ae02c0301f3800498875b6ca32eaa3703404e4a58
Can you link to your VirusTotal result? Maybe the version you provided did have some kind of trojan in it, maybe (although not from the source here on Github, but possibly added later).

p.s. That said, I do know that some corps are pretty locked down (rightfully so) and this does hook into and manipulate mouse movement a bit. So, that could be considered suspicious maybe. Carbon Black (which my company also uses, I have Carbon Black Cloud installed right now) is unfortunately not listed on Virus Total and the Mouse Unsnag version I'm using right now is the same one I linked you to.

Hi,
I'm not sure how the results are different, i literally downloaded the v2.2 executable, uploaded it and it shows trojan
https://www.virustotal.com/gui/file/026eea82a460dbcf8e059abcf74737aac887de11a3b48f6d77d6e99a35040aa6
I see the difference is you are linking github but I actually downloaded the exe to my desktop and uploaded it that way. Try it my way and you will see what I see.

confirmed, downloaded again on a clean VM, same result
https://www.virustotal.com/gui/file/026eea82a460dbcf8e059abcf74737aac887de11a3b48f6d77d6e99a35040aa6

That's weird that the same exact file (which has the same SHA 256 body hash as the URL version) on one report shows that it's clean (without downloading) vs. the downloaded and uploaded version showing a totally different result. I don't really use that site but I assume it's because they have different uses/functions. Odd (or at least unintuitive).
Anyway yeah that said, I just got the same result you did after reuploading it. Not sure what to tell you except that @GrantMoyer built this version last year, maybe he knows more. I don't work much in native code, I'm a web developer and I ended up being a contributor since I tinker a little bit in C# (and happened to be very adamant about fixing the issue in Windows that this app fixes). So, I really hope it doesn't have a trojan.
Also, FWIW, what's funny is now that I know is clean that I built and uploaded myself on this very computer a few years ago (at https://github.com/patricknelson/MouseUnSnag/releases) does get blocked by Carbon Black. 😅 I'm guessing these apps are using heuristics. It's a binary that hasn't been seen before, it hooks into the mouse, etc. 🤷♂ All conjecture here.

@GrantMoyer any ideas? You might know more about this than I do.

Thanks for confirming, yea I'm perplexed why it behaves this way too. Could it be lack of signature bc it makes no sense for this to be a Trojan after looking at the code.

Since I'm not well versed in this (and thankfully this is open source) and you happen to have the ability, feel free to clone the code and compile it yourself I'm fairly certain it's safe, which is why I'm not too concerned. I don't know what it'd take to get it removed from those databases.
p.s. After some thought (it's been a while), I don't know for sure, but there's a possibility that in the past year or two, I convinced my IT to allow this app. So, it may just be explicitly listed which might be why "it works on my machine" with Carbon Black.

I have compiled it and it got flagged originally so I took the executable and same results. It makes no sense, I'm just curious what could be causing it to get flagged than anything really

Thanks for the report @decodering22. Unfortunately, I'm not sure why it's being flagged, although I'm certain it's a false positive. I am not the original author of the code in this repo, but at some point, I've looked through it all, and there's nothing malicious. Supply chain attack on my compiler is also exceedingly unlikely, since I built the executable in question on Linux using my distribution's mono packages, which are cryptographically verified.
Like, @patricknelson says though, MouseUnSnag's main function (changing the position of the cursor) is something that malware often does, so that could be part of the reason. I'll see if I can report the false positives to the relevant anti-malware vendors.

No worries, I know it's not malicious but trying to convince others in a corp when they are not technical will be a challenge. I didn't see anything I could strip that would make it better so I figured why not ask here

I've submitted false positive reports to the three vendors reporting malware on VirtusTotal: Fortinet, SecureAge, and MaxSecure. However, I'm unable to find any support contact for VMWare Carbon black, since I don't have a subscription to VMWare's service. Carbon Black's knowledge base article How to report Malware False Positives to VMware Carbon Black describes how to report a false positive, but I'm unable to register an account to open a support ticket as described.

Appreciate it.

I'd be happy to close it for now, sure. Thanks for the reminder @mbomb007.


WIP: TEAMNADO-1993 - Fix to update side panels SCA status

In the scenario in which the side panel is open, and then a user clicks the SCA toggle switch, this PR fixes the UI so that the side panel's SCA status is also updated.

Codecov Report

Merging #22 (c87361b) into main (25f6f4d) will increase coverage by 0.02%.
The diff coverage is 83.33%.

:exclamation: Current head c87361b differs from pull request most recent head 2daaf08. Consider uploading reports for the commit 2daaf08 to get more accurate results

@@            Coverage Diff             @@
##             main      #22      +/-   ##
==========================================
+ Coverage   73.20%   73.23%   +0.02%
==========================================
  Files          43       43
  Lines         515      523       +8
  Branches       95       96       +1
==========================================
+ Hits          377      383       +6
- Misses        137      139       +2
  Partials        1        1

Impacted Files
Coverage Δ

src/hooks/useUpdateManifestSCAStatus.ts
94.87% <83.33%> (-5.13%)
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[Question] Inconsistency in Model Weight Precision during Conversion and Initialization

Hello,
I am currently writing an article about your project, and while examining the source code of the faster_whisper engine, I've noticed an intriguing detail in the model_converter function as well as during the initialization stage of the WhisperModel.
In brief, the model conversion is carried out to a precision of float16. However, the model is initialized in float32 mode. If both the conversion and initialization were done with the same weight precision, the VRAM memory usage would decrease by as much as half.
Could you please provide some insight into the reason behind this discrepancy?
Thank you for your time and consideration.

Apologies for the slow response on this issue and your PR. Will have time this week for this.

Closed with release of v1.2.


Extension issue

Issue Type: Bug
Extension Name: LiveServer
Extension Version: 5.6.1
OS Version: Windows_NT x64 10.0.19042
VS Code version: 1.56.1

:warning: We have written the needed data into your clipboard. Please paste! :warning:

Done


feat(spark): support materialized view for spark sql

Support Materialized View for Spark (#258)

+1


embed tag

in the indexing and when you search there's nothing actually about  tag , it will be great to actually have the compatibility status of  and most of its types such application/pdf.
thank you very much.

Now available at https://caniuse.com/#feat=mdn-html_elements_embed


Build fails in create-react-app

Hi there, thanks for this amazing library. It helped me a lot. I'm new to all this, So excuse me if this isn't something I should create an issue for. But this is whats happening:
I've installed the library using npm and it works flawlessly. But when I try to create a production build of my app using npm run build it fails with the following error.

The link mentioned leads to a section of react-react-app repo where the say:

Sounds like they suggest that you transpile your code to ES5 code. Could you please look into it? Also, do you have any idea how I might ignore this so I can keep developing while it's being fixed?
Thanks for the hard work again! 😄

Hello @faahim
Thanks a lot, for the information. I'll fix it. Anyway my suggestion is you wait a few hours, or I can show you a way to fix this temporary.
see ya

Hi there! I managed to fix my problem by just extracting the index.js file in my /src folder.
I thought I'd need some of the other files also, but it works just fine. 😃
Thanks again! 😄

Wow, nice dude. I happy for help you. Anyway can count on me.
Close #2
see ya


Add fluctuations

Some small tweaks to the ULDM halo function from a while back
Added realization extension for quantum fluctuations
Added test for the fluctuation extension

Yes please

On Jan 19, 2022, at 2:29 PM, AlexLaroche7 @.***> wrote:
@AlexLaroche7 commented on this pull request.
In pyHalo/realization_extensions.py https://github.com/dangilman/pyHalo/pull/20#discussion_r788030024:

args_fluc=[{'amp': amps[i], 'sigma': sigs[i], 'center_x': xs[i], 'center_y': ys[i]} for i in range(len(amps))]
fluctuations = [Gaussian(5*sigs[i], xs[i], ys[i], None, None, realization._zlens, None, realization.lens_cosmo,args_fluc[i],np.random.rand()) for i in range(len(amps))]
That was a bug, it should have been:

masses=[GaussianKappa().mass_3d_lens(5*arg_fluc['sigma'],arg_fluc['amp'],arg_fluc['sigma']) for arg_fluc in args_fluc]
and then I use those masses instead of 5*sigs[i]. Do you want me to implement this mass definition in the Gaussian class?
—
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Forgot to change the corresponding tests after modifying the free parameters in the fluctuations realization extension, will do that soon


apt-get update needs to happen before apt-install

👍

@gurugv can you sign our CLA?
http://druid.io/community/cla.html

Closing as this appears to be abandoned.