Add optional arguments to functions besides model_ds

Many functions have model_ds (a model dataset) as an argument. In these functions data arrays and attributes from the model dataset are used. When you call this function it is very unclear which data arrays or attributes are necessary to run the function. We should change these functions to include all the data variables and/or attributes as function arguments. Then each function can be called using model_ds or by providing all the other function arguments.
Current function ghb_from_model_ds in nlmod.mfpackages.mfpackages
def ghb_from_model_ds(model_ds, gwf, da_name):
    """get general head boundary from model dataset.

    Parameters
    ----------
    model_ds : xarray.Dataset
        dataset with model data.
    gwf : flopy ModflowGwf
        groundwaterflow object.
    da_name : str
        name of the ghb files in the model dataset.

Proposal for new function
def ghb_from_model_ds(gwf,
                      model_ds=None,
                      ghb_cond=None,
                      ghb_stage=None,
                      gridtype=None,
                      only_first_active_layer=True,
                      first_active_layer=None,
                      only_active_cells=False,
                      idomain=None):
    """get general head boundary from model dataset.

    Parameters
    ----------
    gwf : flopy ModflowGwf
        groundwaterflow object.
    model_ds : xarray.Dataset or None, optional
        dataset with model data. If model_ds is None the function arguments
        ghb_cond, ghb_peil and gridtype should be defined. Default is None
    ghb_cond : xarray.DataArray or None, optional
        dataarray with the conductivity of the ghb. All non-zero cells are used
        as ghb cells. If None the function argument model_ds should be defined.
        Default is None
    ghb_stage : xarray.DataArray or None, optional
        dataarray with the stage of the ghb. If None the function argument
        model_ds should be defined. Default is None
    gridtype : str or None, optional
        can be 'structured' or 'vertex'. If None the function argument model_ds
        should be defined. Default is None
    only_first_active_layer : bool, optional
        if True only the ghb is only added to the first active layer in the
        model. Default is True
    first_active_layer : xarray.DataArray or None, optional
        dataarray with for each cell the first active layer. Only necesarry
        when use_first_active_layer is True. Default is None
    only_active_cells : bool, optional
        if True ghb cells are only to cells with an idomain of 1. Default is
        False.
    idomain : xarray.DataArray or None, optional
        dataarray with the idomain. Only necesarry
        when only_active_cells is True. Default is None

I have a suggestion for an alternative approach, which might even co-exist and might not be mutual excusive.
What about that every function that makes use of model_ds starts with a list that contains which data_vars and coords it uses from model_ds. More or less similar to what __slots__ is to modules, which announces which methods are available from the module/class. Right after defining this list, we call a checking function that has model_ds and the list as arguments. That function checks if all vars are already part of model_ds or, if not, provides hints for which functions/example notebooks can be used to generate those vars. I see two advantages over your suggestion:

We can centralize the hints in a single function.
I think we should stick close to the model_ds for generating the packages, and put as much in model_ds as is needed to generate those packages. Your approach allows for flexibility, but is that flexibility needed/desired?

The parameter descriptions you just gave, are great to put in the attrs of each corresponding data_vars, and of cours in the hints of the checking function.
What is your take on this?

I'm not entirely sure, but isn't there a way to document it slightly different?
def ghb_from_model_ds(model_ds, gwf, da_name):
    """get general head boundary from model dataset.

    Parameters
    ----------
    model_ds : xarray.Dataset
        dataset with model data.
    gwf : flopy ModflowGwf
        groundwaterflow object.
    da_name : str
        name of the ghb files in the model dataset.

    Model_ds data_vars
    -----------
    ghb_cond : xarray.DataArray or None, optional
        dataarray with the conductivity of the ghb. All non-zero cells are used
        as ghb cells. If None the function argument model_ds should be defined.
        Default is None
    ghb_stage : xarray.DataArray or None, optional
        dataarray with the stage of the ghb. If None the function argument
        model_ds should be defined. Default is None
    gridtype : str or None, optional
        can be 'structured' or 'vertex'. If None the function argument model_ds
        should be defined. Default is None
    only_first_active_layer : bool, optional
        if True only the ghb is only added to the first active layer in the
        model. Default is True
    first_active_layer : xarray.DataArray or None, optional
        dataarray with for each cell the first active layer. Only necesarry
        when use_first_active_layer is True. Default is None
    only_active_cells : bool, optional
        if True ghb cells are only to cells with an idomain of 1. Default is
        False.
    idomain : xarray.DataArray or None, optional
        dataarray with the idomain. Only necesarry
        when only_active_cells is True. Default is None

    Returns
    -------
    ....

Would something like that be allowed in the documentation standard we're using?

I like your solution a lot and I think this the way to go.
When I tried to implement my original plan I didn't like all the function arguments with the default None value. I think it makes the function less readable.

Use DataArray source attribute to indicate source of data and maybe log (DEBUG level) when writing MF6 packages where data is coming from.
Linked to #48

Solved by PR #188


"Indoor" radio button not displaying as checked.

Challenge Check Radio Buttons and Checkboxes by Default has an issue.
User Agent is: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/57.0.2987.133 Safari/537.36.
Please describe how to reproduce this issue, and include links to screenshots if possible.
My code:

<link href="https://fonts.googleapis.com/css?family=Lobster" rel="stylesheet" type="text/css">

CatPhotoApp

Click here for cat photos.

Things cats love:

cat nip

laser pointers

lasagna

Top 3 things cats hate:

flea treatment

thunder

other cats

<form action="/submit-cat-photo">
<input type="radio" name="indoor-outdoor" checked> Indoor
  <input type="radio" name="indoor-outdoor" checked> Outdoor
  <input type="checkbox" name="personality" checked> Loving
  <input type="checkbox" name="personality" checked> Lazy
  <input type="checkbox" name="personality" checked> Energetic
  <input type="text" placeholder="cat photo URL" required>
  <button type="submit">Submit</button>
</form>

I'm able to get all the other buttons to display as checked.  Yet for some reason the "Indoor" button won't displayed checked.

I am having the exact same issue.

I have just ran into the same issue, indoor starts as checked once coded but loses it as the rest follow

Yes, it has a problem there, but you can actually move forward by only type in the first one  type radio and  then you pass to de checkboxes en put them in check which complete the task of the exercise.


Fix permission denied

I build my docker image follow the instruction in README.md, but when I run the image, permission denied error appeared.

Thanks @persevereVon ! 👍

Thanks @persevereVon ! 👍


SKU Search Blogpost

Submission for the Coveo tech blog.  The subject matter is searching by partial SKU/part ID in commerce and complex manufacturing.

Here is the rendered link, by the way: https://khancoveo.github.io/source.coveo.com/2021/06/21/partial-sku-search/
Instead of using extensions, people could just push the data to the Push API pre-decomposed, right? Should it be mentioned that it could be done by whatever service is pushing the data as well? :sweat_smile:


1.2 - GEOMESA-1448 Fixing explain logger configs

Signed-off-by: Emilio Lahr-Vivaz<EMAIL_ADDRESS>

@elahrvivaz, @anthonyccri would note that he has some scripts which assume that commit titles are GEOMESA-####.  It is silly, but mind moving the '1.2' to the end of the line (or removing it)?

@jnh5y the commit message doesn't have the 1.2, just the title of the PR.

@elahrvivaz Ah!  Excellent!

Does this change need to be backported to the 1.2.6 docs?

@mdzimmerman do you mean to update the web site? that would be great!


Do not call ShapeHelper Compute functions within assert

ShapeHelper's Compute functions such as ONNXOpShapeHelper::Compute
and ONNXOpBroadcastedShapeHelper::Compute have side-effects.
They cannot be placed within an ``assert'' macro, which becomes a
no-op in the release build. Consequently, we would end up with not
calling these functions at all and hitting subsequent failures.

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.

Can one of the admins verify this patch?

Can one of the admins verify this patch?

Hi @yangchen-MS thanks for the patch, I believe this has already been addressed in another patch from Microsoft by @NathanielMcVicar :
https://github.com/onnx/onnx-mlir/pull/459 .

Hi @yangchen-MS thanks for the patch, I believe this has already been addressed in another patch from Microsoft by @NathanielMcVicar :
https://github.com/onnx/onnx-mlir/pull/459 .

Hi @yangchen-MS thanks for the patch, I believe this has already been addressed in another patch from Microsoft by @NathanielMcVicar :
#459 .

@tjingrant Thank you for pointing it out. I wasn't aware of that. Closing the PR since it has been taken care of. Thanks for reviewing the code, Tian.

Hi @yangchen-MS thanks for the patch, I believe this has already been addressed in another patch from Microsoft by @NathanielMcVicar :
#459 .

@tjingrant Thank you for pointing it out. I wasn't aware of that. Closing the PR since it has been taken care of. Thanks for reviewing the code, Tian.

Should we separate the bug fix from LLVM updates?

Should we separate the bug fix from LLVM updates?

@KeDengMS I agree it's ideal to have each patch address a distinct issue; it's not strictly enforced only because some collaborators point out that their PR submission requires a lengthy internal review (not sure whether it's the case for #459).
Furthermore, due to the way our CI is set up (with LLVM as a base docker image), it'll be a complicated process to merge any patch before #459 goes in, because the new LLVM base image has been pushed to Dockerhub, and any patch based on the current master will fail our Docker-based CI. Thus it's worth considering that breaking up the patch won't expedite things.
With such understanding, if you have a compelling reason to break up the patch, it'll probably be best to chat with @NathanielMcVicar .

@KeDengMS I agree it's ideal to have each patch address a distinct issue; it's not strictly enforced only because some collaborators point out that their PR submission requires a lengthy internal review (not sure whether it's the case for #459).
Furthermore, due to the way our CI is set up (with LLVM as a base docker image), it'll be a complicated process to merge any patch before #459 goes in, because the new LLVM base image has been pushed to Dockerhub, and any patch based on the current master will fail our Docker-based CI. Thus it's worth considering that breaking up the patch won't expedite things.
With such understanding, if you have a compelling reason to break up the patch, it'll probably be best to chat with @NathanielMcVicar .

@KeDengMS I did it as part of the LLVM patch because it was causing our internal builds that I was using to verify the correctness of that patch to fail. If you would prefer it separately I don't have any objections to that, but I will second the note that the CI system makes that cumbersome (same reason for splitting the loop lowering tests, even though it's probably not correct from a software engineering perspective).

@KeDengMS I did it as part of the LLVM patch because it was causing our internal builds that I was using to verify the correctness of that patch to fail. If you would prefer it separately I don't have any objections to that, but I will second the note that the CI system makes that cumbersome (same reason for splitting the loop lowering tests, even though it's probably not correct from a software engineering perspective).

@tjingrant @NathanielMcVicar thanks for the explanation. I didn't realize that other PRs are blocked by #459 because of the CI setup cannot select LLVM base docker image. Please go ahead with #459 as one patch then.

@tjingrant @NathanielMcVicar thanks for the explanation. I didn't realize that other PRs are blocked by #459 because of the CI setup cannot select LLVM base docker image. Please go ahead with #459 as one patch then.


"error CS0104: 'Vector3Parameter' is an ambiguous reference" After importing

Here is the different error codes i get right after importing
Unity version : 2022.3.22.f1 (Latest VRC SDK)
Assets\BakedVolumetrics\Runtime\Scripts\PostProcessing\V1\BakedVolumetricsV1.cs(34,10): error CS0104: 'Vector3Parameter' is an ambiguous reference between 'UnityEngine.Rendering.PostProcessing.Vector3Parameter' and 'UnityEngine.Rendering.Vector3Parameter
Assets\BakedVolumetrics\Runtime\Scripts\PostProcessing\V3\BakedVolumetricsV3.cs(15,16): error CS0104: 'TextureParameter' is an ambiguous reference between 'UnityEngine.Rendering.PostProcessing.TextureParameter' and 'UnityEngine.Rendering.TextureParameter'
Assets\BakedVolumetrics\Runtime\Scripts\PostProcessing\V2\BakedVolumetricsV2.cs(31,10): error CS0104: 'TextureParameter' is an ambiguous reference between 'UnityEngine.Rendering.PostProcessing.TextureParameter' and 'UnityEngine.Rendering.TextureParameter'
Assets\BakedVolumetrics\Runtime\Scripts\PostProcessing\V4\BakedVolumetricsV4.cs(14,16): error CS0104: 'TextureParameter' is an ambiguous reference between 'UnityEngine.Rendering.PostProcessing.TextureParameter' and 'UnityEngine.Rendering.TextureParameter'

If you are using this only for VRC then to fix those errors you just simply delete the post processing scripts folder.
Those errors are appearing because the post processing package is not installed in your project (or the API might have changed) but for usage in VRC the post process versions don't get used, only the "Scene Object" version gets used since VRChat does not support custom post process effects.

Yeah, I started toying with the project in another Unity project, and figured this might be a conflict issue with some of the modifications the SDK does.
Thanks for the answer !


Mount /var/cache/amd-sev/ into the GHA runner; use sevctl to cache the certificate chain there before AND after all CI jobs

This machine is a CI machine and a developer machine. The CI invalidates any cached certificate chains. For this to scale beyond 1 developer, we need the CI to leave the system in the same state that it found it in.

Update the sev tests to iterate through all the paths until it finds one that exists, rather than defaulting to the home dir cache. (code)
Mount /var/cache/amd-sev/:/var/cache/amd-sev into the GHA runner container
Before any tests run, sevctl export --full /var/cache/amd-sev/chain
After all tests have run: sevctl export --full /var/cache/amd-sev/chain

After this is fixed, developers should remove their home-dir cached chain: rm ~/.cache/amd-sev/chain and in most cases, can stop caching it there manually entirely.
Ultimately the goal here is to start caching it in a system-wide location rather than expecting developers to manually cache this in their home dir.
edit: we might also want to consider adding a sevctl export --full /var/cache/amd-sev/chain as part of the enarx kickstart as well.

So, here is my thought of a user experience:
search:

iterate through the paths, until it finds one that exist
check if that cache is valid
if not, report to the log/user, that there is an invalide cache file and goto search

if no cache file was found, perform the expensive operation and create one, where the app has permissions to do so.

I'm worried that re-entering the search would only encourage users to leav redundant certificate chains on the system.
I think if we only leave a certificate chain in /var/amd-sev/chain by convention, the certificate chain management will be entirely transparent to developers and CI.


Cross-account replication fix

what

Add missing replication policy permissions

why

Without this permission cross-account replication is not possible

references

https://github.com/cloudposse/terraform-aws-s3-bucket/issues/68
closes #68

/test all

/test all


How to prepare ImageNet-1K?

May I ask who can tell me why I cannot directly access the ImageNet-1k dataset through the code provided below?
from dinov2.data.datasets import ImageNet
for split in ImageNet.Split:
dataset = ImageNet(split=split, root="", extra="")
dataset.dump_extra()

RuntimeError: can not read labels file "/labels.txt"


<StatsGl /> broken in 3.7.0

Describe the bug
While upgrading all the packages in my starter I noticed that <StatsGl /> doesn't work and triggers the following error:

Reproduction
https://stackblitz.com/github/kekkorider/vue-tres-starter/tree/feat/cientos-3.7.0
Steps to reproduce
If you remove the <StatsGl /> component In src/App.vue the error is gone.
System Info
System:
    OS: macOS 14.2.1
    CPU: (8) arm64 Apple M1
    Memory: 485.48 MB / 16.00 GB
    Shell: 5.9 - /bin/zsh
  Binaries:
    Node: 18.17.1 - ~/.nvm/versions/node/v18.17.1/bin/node
    Yarn: 1.22.19 - ~/.yarn/bin/yarn
    npm: 9.6.7 - ~/.nvm/versions/node/v18.17.1/bin/npm
    pnpm: 8.10.5 - /opt/homebrew/bin/pnpm
  Browsers:
    Chrome: 120.0.6099.234
    Safari: 17.2.1
  npmPackages:
    @tresjs/cientos: ^3.7.0 => 3.7.0
    @tresjs/core: ^3.6.1 => 3.6.1
    vite: ^5.0.12 => 5.0.12

Used Package Manager
pnpm
Code of Conduct

[X] I agree to follow this project's Code of Conduct
[X] Read the Contributing Guidelines.
[X] Read the docs.
[X] Check that there isn't already an issue that reports the same bug to avoid creating a duplicate.
[X] The provided reproduction is a minimal reproducible example of the bug.

Hi, @RenaudRohlinger quick question about this one, debugging a little seems like the problem is that StatsGl his version still uses StatsGl.Container

That is a photo in my local with all dependencies updated.
In the Cientos Playground works fine with StatsGl.dom. The fix is easy, just check if StatsGl.dom is empty, to use StatsGl.Container.
But I'm curious about why this happened. Do you have any Idea?

It's super odd, I just checked the source published on npm and everything points to .dom and there is a fallback available:
  get container() {
    console.warn("Stats: Deprecated! this.container as been replaced to this.dom ");
    return this.dom;
  }

For example if using the source code from the pnpm-lock file in the example:
https://registry.npmjs.org/stats-gl/-/stats-gl-2.0.1.tgz
To be honest I have no idea for the solution except the patch proposed on cientos side.

@RenaudRohlinger thanks for answer so fast, and no problem the solution is not difficult.
I just wanted to know why could happen, :) have a nice day


Added new extension to get ST node from reference position

Purpose

Describe the problems, issues, or needs driving this feature/fix and include links to related issues.

Fixes #39118
Approach

Describe how you are implementing the solutions along with the design details.

Samples

Provide high-level details about the samples related to this feature.

Remarks

List any other known issues, related PRs, TODO items, or any other notes related to the PR.

Check List

[ ] Read the Contributing Guide
[ ] Updated Change Log
[ ] Checked Tooling Support (#)
[ ] Added necessary tests

[x] Unit Tests
[ ] Spec Conformance Tests
[ ] Integration Tests
[ ] Ballerina By Example Tests

[ ] Increased Test Coverage
[ ] Added necessary documentation

[ ] API documentation
[ ] Module documentation in Module.md files
[ ] Ballerina By Examples

Refactor issue created: https://github.com/ballerina-platform/ballerina-lang/issues/39220


fetch-ubuntu fails for versions 12 and 19

What did you do? (required. The issue will be closed when not provided.)
There are two issues with the fetch-ubuntu functionality. The first is that version 12 is no longer supported, and so the download fails. The second is that the config is storing an old release name for 19.
# checked help doc for ubuntu
goval-dictionary fetch-ubuntu --help

# ran suggested command from help doc
goval-dictionary 12 14 16 18 19 20

What did you expect to happen?
I expected all of them to be downloaded correctly
What happened instead?
Installation for 12 and 19 failed.
12 failed because it's no longer supported
19 failed because the release name in the config file is no longer accurate

Current Output

Please re-run the command using -debug and provide the output below.
➜  goval-dictionary git:(update-fetch-versions) ./goval-dictionary fetch-ubuntu 12 -debug
EROR[06-11|01:17:18] Failed to create log directory           err="mkdir /var/log/vuls: permission denied"
WARN[06-11|01:17:18] Skip unknown ubuntu.                     version=-debug
INFO[06-11|01:17:18] Fetching...                              URL=https://people.canonical.com/~ubuntu-security/oval/com.ubuntu.precise.cve.oval.xml.bz2
INFO[06-11|01:17:19] Finished fetching OVAL definitions
EROR[06-11|01:17:19] Failed to fetch files                    err="Failed to fetch. err: [aborting: could not write to output stream: Expected HTTP Status 200, received: \"404 Not Found\"]"

➜  goval-dictionary git:(update-fetch-versions) ./goval-dictionary fetch-ubuntu 19 -debug
EROR[06-11|01:17:24] Failed to create log directory           err="mkdir /var/log/vuls: permission denied"
WARN[06-11|01:17:24] Skip unknown ubuntu.                     version=-debug
INFO[06-11|01:17:24] Fetching...                              URL=https://people.canonical.com/~ubuntu-security/oval/com.ubuntu.disco.cve.oval.xml.bz2
INFO[06-11|01:17:24] Finished fetching OVAL definitions
EROR[06-11|01:17:24] Failed to fetch files                    err="Failed to fetch. err: [aborting: could not write to output stream: Expected HTTP Status 200, received: \"404 Not Found\"]"
➜  goval-dictionary git:(update-fetch-versions)

Steps to reproduce the behaviour
git clone git@github.com:kotakanbe/goval-dictionary.git
make build
./goval-dictionary fetch-ubuntu 12 19

Configuration (MUST fill this out):
n/a

Go version (go version):

go version go1.14.4 darwin/amd64

Go environment (go env):

GO111MODULE=""
GOARCH="amd64"
GOBIN=""
GOCACHE="/Users/redacted/Library/Caches/go-build"
GOENV="/Users/redacted/Library/Application Support/go/env"
GOEXE=""
GOFLAGS=""
GOHOSTARCH="amd64"
GOHOSTOS="darwin"
GOINSECURE=""
GONOPROXY=""
GONOSUMDB=""
GOOS="darwin"
GOPATH="/Users/redacted/go"
GOPRIVATE=""
GOPROXY="https://proxy.golang.org,direct"
GOROOT="/usr/local/go"
GOSUMDB="sum.golang.org"
GOTMPDIR=""
GOTOOLDIR="/usr/local/go/pkg/tool/darwin_amd64"
GCCGO="gccgo"
AR="ar"
CC="clang"
CXX="clang++"
CGO_ENABLED="1"
GOMOD=""
CGO_CFLAGS="-g -O2"
CGO_CPPFLAGS=""
CGO_CXXFLAGS="-g -O2"
CGO_FFLAGS="-g -O2"
CGO_LDFLAGS="-g -O2"
PKG_CONFIG="pkg-config"
GOGCCFLAGS="-fPIC -m64 -pthread -fno-caret-diagnostics -Qunused-arguments -fmessage-length=0 -fdebug-prefix-map=/var/folders/96/8g5pq9753glcvlyk5jcy0rk00000gq/T/go-build168065861=/tmp/go-build -gno-record-gcc-switches -fno-common"
➜  test git:(init) ✗

I've tested a fix locally, I can open a PR if you'd like:

https://github.com/kotakanbe/goval-dictionary/compare/master...ahulab:update-fetch-versions

@ahulab
Very appreciated if you open a PR :)

@ahulab Thank you for your support.
I made a pull request on your behalf using your souce code.
https://github.com/kotakanbe/goval-dictionary/pull/96/files
Thank you very much.


Add recognition for contributions

Entity: @archithdwij
Contributions:

review
eventOrganizing

@all-contributors kindly add @archithdwij for review and eventOrganizing.


Merge prTesting_201910011252 branch to master branch

Docs Build status updates of commit aa23425:
:warning: Validation status: warnings

File
Status
Preview URL
Details

split/updateTestRef.md
:warning:Warning

Details

split/updateTestRef.md

[Warning] Missing attribute: author. Add the current author's GitHub ID.
[Warning] Missing attribute: title. Add a title string to show in search engine results.

For more details, please refer to the build report.
Note: If you changed an existing file name or deleted a file, broken links in other files to the deleted or renamed file are listed only in the full build report.


Further improve interpolation

Some improvements to the new interpolation method (see #75):

Make sure the from.. methods of the Obs class always return an Obs object (and not a dictionary).
move the logic for interpolation from the observation module to the io_knmi module

Other changes:

make xy a single function argument instead of separate x and y.
remove some caching logic, we should make a general caching method and not add this to single functions
improve notebook for merging observations

@martinvonk, I made some changes to the recently added interpolation functions. I think the functions are as fast as they used to be. Can you check if you agree with the changes?


Send FirstFrame event after reassemble

@Hixie
Fixes https://github.com/flutter/flutter/issues/5245


Support array without position?

bring this to
{
  items[0]: 'item1',
  items[1]: 'item2'
}

{
  items: ['item1', 'item2']
}

this one
{
  items[]: 'item1',
  items[]: 'item2'
}

{
  items: ['item1', 'item2']
}

Objects in JSON/JavaScript do not have guaranteed order in their properties, thats why it's is required to define a position, otherwise order would not be guaranteed in the array.


module spams errors in mm log

Hi,
thanks for the module. great Work!
It works for me on the surface, but.. :)
I have configured two stations like this:
 modules: [{
                module: "mvgmunich",
                position: "bottom_left",
                header: "Harras",
                config: {
                        haltestelle: "Harras",
                        maxEntries: 10, // 10 items on screen
                        updateInterval: 30000, // 30 s
                        showIcons: true, // Show transport type icon
                        transportTypesToShow: {
                                "ubahn": true, // show ubahn route
                                "sbahn": true, // show sbahn route
                                "bus": false, // show bus route
                                "tram": false // show tram route
                        },
                        ignoreStations: [], // destination not to be shown
                        timeToWalk: 10, // 10 min walking time to station. Default is 0
                        showWalkingTime: true, // if the walking time should be included and the starting time is displayed
                        showTrainDepartureTime: true, // show tran departure time
                        trainDepartureTimeFormat: "relative", // format of the train departure time
                        walkingTimeFormat: "relative", // format of the walking time
                }
        },
        {
                module: "mvgmunich",
                position: "bottom_right",
                header: "Johann-Clanze-Straße",
                config: {
                        haltestelle: "Johann-Clanze-Straße",
                        maxEntries: 10, // 10 items on screen
                        updateInterval: 30000, // 30 s
                        showIcons: true, // Show transport type icon
                        transportTypesToShow: {
                                "ubahn": false, // show ubahn route
                                "sbahn": false, // show sbahn route
                                "bus": true, // show bus route
                                "tram": false // show tram route
                        },
                        ignoreStations: [], // destination not to be shown
                        timeToWalk: 5, // 10 min walking time to station. Default is 0
                        showWalkingTime: true, // if the walking time should be included and the starting time is displayed
                        showTrainDepartureTime: true, // show tran departure time
                        trainDepartureTimeFormat: "relative", // format of the train departure time
                        walkingTimeFormat: "relative", // format of the walking time
                }
        }]

This results in tons of the same error in the log
SyntaxError: Unexpected end of JSON input
    at JSON.parse (<anonymous>)
    at Request._callback (/home/pi/MagicMirror/modules/mvgmunich/node_helper.js:56:27)
    at Request.self.callback (/home/pi/MagicMirror/node_modules/request/request.js:185:22)
    at Request.emit (events.js:182:13)
    at Request.<anonymous> (/home/pi/MagicMirror/node_modules/request/request.js:1161:10)
    at Request.emit (events.js:182:13)
    at IncomingMessage.<anonymous> (/home/pi/MagicMirror/node_modules/request/request.js:1083:12)
    at Object.onceWrapper (events.js:273:13)
    at IncomingMessage.emit (events.js:187:15)
    at endReadableNT (_stream_readable.js:1090:12)
SyntaxError: Unexpected end of JSON input
    at JSON.parse (<anonymous>)
    at Request._callback (/home/pi/MagicMirror/modules/mvgmunich/node_helper.js:56:27)
    at Request.self.callback (/home/pi/MagicMirror/node_modules/request/request.js:185:22)
    at Request.emit (events.js:182:13)
    at Request.<anonymous> (/home/pi/MagicMirror/node_modules/request/request.js:1161:10)
    at Request.emit (events.js:182:13)
    at IncomingMessage.<anonymous> (/home/pi/MagicMirror/node_modules/request/request.js:1083:12)
    at Object.onceWrapper (events.js:273:13)
    at IncomingMessage.emit (events.js:187:15)
    at endReadableNT (_stream_readable.js:1090:12)

Maybe it makes sense to create a catch here or to fix the issue.
Thanks for any help

Ho @motey,
I just fix something similar in this branch 'showing_2_stations'. Would be possible to check it if it's working for you?
I will try to create a new version asap I will get confirmation that this is working also for someone else not only for me and on my computer.

that was quick :)
looks good at first glance. Will leave it running until tomorow and give you another feedback.
cheers

Still got some errors in the log (definitive less errors), but this time in combination with an out of memory error. will investigate if its maybe node.js + raspi issue. maybe its not the modules fault.

@motey would be possible to past errors here if they are related to this module?

@mrVragec Maybe, did not found the time yesterday to investigate. will do the next days

Could not pinpoint the memoryleak yet, but assuming that this is the cause for my issues. Closing this issue for now. Thanks for the help and the module in general :heart:


chore: configure changests pr titles

What kind of change does this PR introduce?
Bug fix, feature, docs update, ...
What is the current behaviour?
You can also link to an open issue here.
What is the new behaviour?
...
Does this PR introduce a breaking change?
What changes might users need to make in their application due to this PR?
Other information:
Please check if the PR fulfills these requirements:

[ ] Tests for the changes have been added
[ ] Docs have been added / updated
[ ] Relevant Changeset has been added

coverage: 0.0%. remained the same
when pulling 19d48454a40a3122c358f1194ad8c4009bc776dd on changesets-title
into 2ef84284a7f32233f5698ae64fd19e022e6360a3 on master.


Fullscreen switch problem on Linux after glfwWindowHint(GLFW_RESIZABLE, GL_FALSE)

When I add a line 'glfwWindowHint(GLFW_RESIZABLE, GL_FALSE);' before 'window = glfwCreateWindow' in 'examples/boing.c' (line 630).
On Windows, it works well when switch back from fullscreen to windowed. (get 400*400 window).
On Linux, the window become windowed but remain the screen size. (get 1366*768 window on my laptop).
http://pastebin.ubuntu.com/15805342/
The only difference i made is the 'glfwWindowHint(GLFW_RESIZABLE, GL_FALSE);'  in line 630.
My system is ubuntu14.04 and my X server version is 1.17.1.

@linkmauve This affects Wayland as well?


Reorder organizations that appear in dropdown menu in step 10 of MFB

Suggestions for reordering orgs that appear in referrer dropdown menu in Step 10 of MFB:

Move Denver Human Services up. It's a significant partner that should generate good numbers when it launches the MFB button and trains its staff.
Village Exchange, VITA/Tax Help, and Denver Human Services are all below Test/Prospective Partner. Would like to move all of these up in the list. Suggestion: Place specific orgs above generic items like Social Media, Google or other search Engine, Test/Prospective Partner, and Other.
Move Other to the bottom of the list.

Updates to ticket: Delete these orgs from referrer dropdown:

Let's Get Set
Community Economic Defense Project (CEDP)
Village Exchange
Tax Assistance Site (VITA/Tax Help Colorado)


RuntimeWarning: Mean of empty slice

Hello,
I am trying to use JACKS and running into following issues:
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File.tab --sgrna_hdr=sgrna --gene
_hdr=Gene --ctrl_sample_hdr=Sample  --outprefix JACKS
[2021-11-09 18:05:01,363] jacks: INFO     Loading sample specification
[2021-11-09 18:05:01,363] jacks: INFO     Loading gene mappings
[2021-11-09 18:05:01,365] jacks: INFO     Loading data and pre-processing
[2021-11-09 18:05:01,424] jacks: INFO     Applying median normalisation
[2021-11-09 18:05:01,471] jacks: INFO     Collating 0 samples
[2021-11-09 18:05:01,487] jacks: INFO     Running JACKS inference
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice
  return fun(*args, **kwargs)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice.
  LOG.debug("After init, mean absolute error=%.3f, <x>=%.1f <w>=%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice.
  LOG.debug("After W update, <w>=%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean()))
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice.
  LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x1**2)**0.5), w1.mean(), SP.median((w2-w1**2)**0.5), x1.mean()*w1.mean()))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
[2021-11-09 18:05:01,801] jacks: INFO     Writing JACKS results
/gpfs/fs1/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice
  ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice
  ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]

Here are snippets of how various files look:
head -n +4 Count_Matrix.tab
sgRNA   P23H1   P23H2   Control1        Control2        Control3
Amfr_sgRNA1     150     44      602     530     302
Amfr_sgRNA2     141     24      380     350     162
Amfr_sgRNA3     203     21      443     435     303

head Exp_Summary_JACKS.tab
Replicate       Sample
P23H1   P23H
P23H2   P23H
Control1        CTRL
Control2        CTRL
Control3        CTRL

head -n +3 sgRNA_Mapping_File.tab
sgrna   Gene
Sec24d_sgRNA2   Sec24d
Gm30534_sgRNA3  Gm30534

Not exactly sure why any array slice will produce a mean of <0( assuming that is the error). The counts is tab separated and so are the other files as well. I do see a  Collating 0 samples could this be the issue?
Any help will be much appreciated.
Thanks,
D

Hmm, there seems to be a problem earlier, "collating 0 samples" feels like
an item of concern. I'm not sure if it is a potential mismatch in column
headings for the sgRNA in Count_Matrix.tab vs sgrna [all lower case] in
sgRNA_Mapping_File , or ability to identify the sample from sample file.
The way in which the replicate and sample are specified has been improved
over the years, so I am not completely sure what the right encoding is, but
I would think it to potentially be the main culprit. Let me know if this
does not help rapidly resolve,
Leo
On Tue, Nov 9, 2021 at 11:24 PM sum732 @.***> wrote:

Hello,
I am trying to use JACKS and running into following issues:
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File.tab --sgrna_hdr=sgrna --gene
_hdr=Gene --ctrl_sample_hdr=Sample  --outprefix JACKS
[2021-11-09 18:05:01,363] jacks: INFO     Loading sample specification
[2021-11-09 18:05:01,363] jacks: INFO     Loading gene mappings
[2021-11-09 18:05:01,365] jacks: INFO     Loading data and pre-processing
[2021-11-09 18:05:01,424] jacks: INFO     Applying median normalisation
[2021-11-09 18:05:01,471] jacks: INFO     Collating 0 samples
[2021-11-09 18:05:01,487] jacks: INFO     Running JACKS inference
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice
return fun(*args, kwargs)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice.
LOG.debug("After init, mean absolute error=%.3f, =%.1f =%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice.
LOG.debug("After W update, =%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean()))
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice.
LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x12)0.5), w1.mean(), SP.median((w2-w12)**0.5), x1.mean()*w1.mean()))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
[2021-11-09 18:05:01,801] jacks: INFO     Writing JACKS results
/gpfs/fs1/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
Here are snippets of how various files look:
head -n +4 Count_Matrix.tab
sgRNA   P23H1   P23H2   Control1        Control2        Control3
Amfr_sgRNA1     150     44      602     530     302
Amfr_sgRNA2     141     24      380     350     162
Amfr_sgRNA3     203     21      443     435     303
head Exp_Summary_JACKS.tab
Replicate       Sample
P23H1   P23H
P23H2   P23H
Control1        CTRL
Control2        CTRL
Control3        CTRL
head -n +3 sgRNA_Mapping_File.tab
sgrna   Gene
Sec24d_sgRNA2   Sec24d
Gm30534_sgRNA3  Gm30534
Not exactly why any array slice will produce a mean of <0( assuming that
is the error). The counts is tab separated and so are the other files as
well.
Any help will be much appreciated.
Thanks,
D
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Hi Leo,
Thank you for responding and for the suggestion.
I had tried setting things correctly
head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab
==> Count_Matrix-Fixed.tab <==
sgrna   Gene    P23H_rep1       P23H_rep2       Control_rep1    Control_rep2    Control_rep3

==> sgRNA_Mapping_File-Fixed.tab <==
sgrna   Gene

Got this error
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgrna --gene_h
dr=Gene --ctrl_sample_hdr=Sample  --outprefix JACKS
[2021-11-11 17:39:54,074] jacks: INFO     Loading sample specification
[2021-11-11 17:39:54,075] jacks: INFO     Loading gene mappings
[2021-11-11 17:39:54,078] jacks: INFO     Loading data and pre-processing
[2021-11-11 17:39:54,136] jacks: INFO     Applying median normalisation
[2021-11-11 17:39:54,184] jacks: INFO     Collating 0 samples
[2021-11-11 17:39:54,200] jacks: INFO     Running JACKS inference
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice
  return fun(*args, **kwargs)
/homes/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice.
  LOG.debug("After init, mean absolute error=%.3f, <x>=%.1f <w>=%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound))
/gpfs/fs1/home/mehrotras/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice.
  LOG.debug("After W update, <w>=%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean()))
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice.
  LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x1**2)**0.5), w1.mean(), SP.median((w2-w1**2)**0.5), x1.mean()*w1.mean()))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
[2021-11-11 17:39:54,511] jacks: INFO     Writing JACKS results
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice
  ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice
  ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
(jacksenv) mehrotras@login01:$/JACKS>head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab

Changed to Match
head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab
==> Count_Matrix-Fixed.tab <==
sgRNA   Gene    P23H_rep1       P23H_rep2       Control_rep1    Control_rep2    Control_rep3

==> sgRNA_Mapping_File-Fixed.tab <==
sgRNA   Gene

Error
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgRNA --gene_hdr=Gene --ctrl_sample_hdr=Sample  --outprefix JACKS
[2021-11-11 17:42:37,162] jacks: INFO     Loading sample specification
[2021-11-11 17:42:37,162] jacks: INFO     Loading gene mappings
[2021-11-11 17:42:37,164] jacks: INFO     Loading data and pre-processing
[2021-11-11 17:42:37,223] jacks: INFO     Applying median normalisation
[2021-11-11 17:42:37,272] jacks: INFO     Collating 0 samples
[2021-11-11 17:42:37,288] jacks: INFO     Running JACKS inference
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice
  return fun(*args, **kwargs)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice.
  LOG.debug("After init, mean absolute error=%.3f, <x>=%.1f <w>=%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice.
  LOG.debug("After W update, <w>=%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean()))
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice.
  LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x1**2)**0.5), w1.mean(), SP.median((w2-w1**2)**0.5), x1.mean()*w1.mean()))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
[2021-11-11 17:42:37,602] jacks: INFO     Writing JACKS results
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice
  ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice
  ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]

Here is Expsummary
cat Exp_Summary_JACKS.tab
Replicate       Sample
P23H_rep1       P23H
P23H_rep2       P23H
Control_rep1    CTRL
Control_rep2    CTRL
Control_rep3    CTRL

These all are tab separated, I reconfirmed this.

Just to triple check - did you use the latest version, and have you tried
explicitly setting
--rep_hdr=Replicate --sample_hdr=Sample
? The --ctrl-sample-hdr is for the third header, I worry if the defaults
for first two match what you use.
https://github.com/felicityallen/JACKS/tree/master/jacks has the example
On Thu, Nov 11, 2021 at 10:50 PM sum732 @.***> wrote:

Hi Leo,
Thank you for responding and for the suggestion.
I had tried setting things correctly
head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab
==> Count_Matrix-Fixed.tab <==
sgrna   Gene    P23H_rep1       P23H_rep2       Control_rep1    Control_rep2    Control_rep3
==> sgRNA_Mapping_File-Fixed.tab <==
sgrna   Gene
Got this error
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgrna --gene_h
dr=Gene --ctrl_sample_hdr=Sample  --outprefix JACKS
[2021-11-11 17:39:54,074] jacks: INFO     Loading sample specification
[2021-11-11 17:39:54,075] jacks: INFO     Loading gene mappings
[2021-11-11 17:39:54,078] jacks: INFO     Loading data and pre-processing
[2021-11-11 17:39:54,136] jacks: INFO     Applying median normalisation
[2021-11-11 17:39:54,184] jacks: INFO     Collating 0 samples
[2021-11-11 17:39:54,200] jacks: INFO     Running JACKS inference
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice
return fun(*args, kwargs)
/homes/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice.
LOG.debug("After init, mean absolute error=%.3f, =%.1f =%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound))
/gpfs/fs1/home/mehrotras/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice.
LOG.debug("After W update, =%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean()))
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice.
LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x12)0.5), w1.mean(), SP.median((w2-w12)0.5), x1.mean()w1.mean()))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
[2021-11-11 17:39:54,511] jacks: INFO     Writing JACKS results
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
(jacksenv) @.:$/JACKS>head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab
Changed to Match
head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab
==> Count_Matrix-Fixed.tab <==
sgRNA   Gene    P23H_rep1       P23H_rep2       Control_rep1    Control_rep2    Control_rep3
==> sgRNA_Mapping_File-Fixed.tab <==
sgRNA   Gene
Error
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgRNA --gene_hdr=Gene --ctrl_sample_hdr=Sample  --outprefix JACKS
[2021-11-11 17:42:37,162] jacks: INFO     Loading sample specification
[2021-11-11 17:42:37,162] jacks: INFO     Loading gene mappings
[2021-11-11 17:42:37,164] jacks: INFO     Loading data and pre-processing
[2021-11-11 17:42:37,223] jacks: INFO     Applying median normalisation
[2021-11-11 17:42:37,272] jacks: INFO     Collating 0 samples
[2021-11-11 17:42:37,288] jacks: INFO     Running JACKS inference
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice
return fun(*args, kwargs)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice.
LOG.debug("After init, mean absolute error=%.3f, =%.1f =%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice.
LOG.debug("After W update, =%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean()))
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice.
LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x12)0.5), w1.mean(), SP.median((w2-w12)**0.5), x1.mean()*w1.mean()))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
[2021-11-11 17:42:37,602] jacks: INFO     Writing JACKS results
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
Here is Expsummary
cat Exp_Summary_JACKS.tab
Replicate       Sample
P23H_rep1       P23H
P23H_rep2       P23H
Control_rep1    CTRL
Control_rep2    CTRL
Control_rep3    CTRL
These all are tab separated, I reconfirmed this.
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Hi Leo,
I cannot say about the version, as there is none to show. I had done a recent pull ( last commit shown is Oct 2, 2020).
There are different versions of examples to setup the experiment design, here and  here, that i have tried to follow.
I think you are right and that it could be the Exp design file is not set correctly. The issues is I am not sure which is right one?
Based on your suggestion I made this change:
cat Exp_Summary_JACKS.tab
Replicate       Sample  CONTROL
P23H_rep1       P23H
P23H_rep2       P23H
Control_rep1    Control1        Control_rep1
Control_rep2    Control2        Control_rep2
Control_rep3    Control3        Control_rep3

python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgRNA --gene_hdr=Gene --
rep_hdr=Replicate  --sample_hdr=Sample --ctrl_sample_hdr=CONTROL --outprefix JACKS

I am getting
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgRNA --gene_hdr=Gene --
rep_hdr=Replicate  --sample_hdr=Sample --ctrl_sample_hdr=CONTROL --outprefix JACKS
[2021-11-15 11:32:53,381] jacks: INFO     Loading sample specification
[2021-11-15 11:32:53,382] jacks: INFO     Loading gene mappings
[2021-11-15 11:32:53,384] jacks: INFO     Loading data and pre-processing
[2021-11-15 11:32:53,443] jacks: INFO     Applying median normalisation
[2021-11-15 11:32:53,468] jacks: WARNING  Undefined variances in sample Control1, set --ctrl_genes input to JACKS to infer variances from control genes
[2021-11-15 11:32:53,471] jacks: WARNING  Undefined variances in sample Control2, set --ctrl_genes input to JACKS to infer variances from control genes
[2021-11-15 11:32:53,473] jacks: WARNING  Undefined variances in sample Control3, set --ctrl_genes input to JACKS to infer variances from control genes
[2021-11-15 11:32:53,478] jacks: INFO     Collating 4 samples
Traceback (most recent call last):
  ...........
......
...
ValueError: 'Control_rep1' is not in list

So it seems that I need the third column. However, I am not sure how set this correctly. I have 3 WT/Controls and 2 muts/treatments.
Making this change
cat Exp_Summary_JACKS.tab
Replicate       Sample  CONTROL
P23H_rep1       P23H
P23H_rep2       P23H
Control_rep1    Control1        Control1
Control_rep2    Control2        Control2
Control_rep3    Control3        Control3

shows following error
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgRNA --gene_hdr=Gene --rep_hdr=Replicate  --sample_hdr=Sample --ctrl_sample_hdr=CONTROL --outprefix JACKS
[2021-11-15 11:35:40,198] jacks: INFO     Loading sample specification
[2021-11-15 11:35:40,199] jacks: INFO     Loading gene mappings
[2021-11-15 11:35:40,201] jacks: INFO     Loading data and pre-processing
[2021-11-15 11:35:40,259] jacks: INFO     Applying median normalisation
[2021-11-15 11:35:40,294] jacks: INFO     Collating 1 samples
Traceback (most recent call last):
 ...
.......
ValueError: None is not in list


ADS table Contextual menu options do nothing after a while

Azure Data Studio Version:
Version: 1.27.0 (system setup)
Commit: 765c7064d46253d88393e0e1ff78874b6fe8fa64
Date: 2021-03-16T21:24:59.168Z
VS Code: 1.51.0
Electron: 9.4.3
Chrome: 83.0.4103.122
Node.js: 12.14.1
V8: <IP_ADDRESS>-electron.0
OS: Windows_NT x64 10.0.17763

Steps to Reproduce:

Open ADS
Use it (Or not) and leave it open for a while
At some point, the contextual menu on a table (Select Top 1000, Edit Data) become unresponsive

The only way I found to fix the issue is a restart of ADS. I'm not exactly what the cause is but I do use these function quite a lot and I have to restart ADS pretty often. Where it is installed or fresh installation changes nothing. (I have it on my personal computer, my work one and on a VM in Azure. All of them do that.)
New Query on the database seems to continue working (Probably since it does nothing except a new tab). Tab that are already opened continue to work normally so I doubt it is just disconnected.
Regards,

For the table you are trying to query, is this a local DB or one in Azure?

These are DB in an elastic pool on Azure. I have 12 of them in two different pool and this does the same thing for all.

Additional Information: This seems to affect only the DBs that were used during the session. The other works flawlessly when I switch to them but does the same thing over time.
Please see the GIF for the steps.
Suggestions: Open a TAB no matter what with the appropriate query and return an error message or a loading. That should at least covers the "User experience" portion of the issue where the user is left without any clues as to what's the problem. being connected or not to a particular DB should not affect if a tab will open or not. It should work with what it has available already. If I can see the list of columns in a table, it should have no issues building the query, opening a tab with it and then executing (Or at least try).

When you try to run Select Top 1000, do you get any error messages in the Developer Tools? (you can open developer tools using Help -> Toggle Developer Tools)

Yes. I do:
ERR Scripting failed. error: An error occurred while scripting the objects. Failed to connect to server xxxxxxxxxxx.database.windows.net,1433.
With the exact same pattern and DB used in the GIF above:

The first message is from the first "Select Top 1000" in the "not used for a while DB". The remaining one are from the "never used DB", still a "Select Top 1000".
we can see the first one failing whatever script it is suposed to. And the second one clearly just reconnecting if it has been lost in the meantime. I supose somewhere in the script, it doesn't properly reconnect.
It isn't a configuration issue as this issue doesn't exist in SSMS and I can run for days (or until I'm required to re-authenticate MFA).

Today, when working. Since it seems to be a connection issue, When I saw the same issue again, I tried the "Refresh" option on the database object. It seem to work but when I expanded the table folder, it gave me this:

Microsoft.SqlServer.Management.Common.ConnectionFailureException: Failed to connect to server xxxxxxx.database.windows.net,1433.
---> Microsoft.Data.SqlClient.SqlException (0x80131904): Login failed for user ''. Token is expired.
at Microsoft.Data.SqlClient.SqlInternalConnection.OnError(SqlException exception, Boolean breakConnection, Action1 wrapCloseInAction) at Microsoft.Data.SqlClient.TdsParser.ThrowExceptionAndWarning(TdsParserStateObject stateObj, Boolean callerHasConnectionLock, Boolean asyncClose) at Microsoft.Data.SqlClient.TdsParser.TryRun(RunBehavior runBehavior, SqlCommand cmdHandler, SqlDataReader dataStream, BulkCopySimpleResultSet bulkCopyHandler, TdsParserStateObject stateObj, Boolean& dataReady) at Microsoft.Data.SqlClient.TdsParser.Run(RunBehavior runBehavior, SqlCommand cmdHandler, SqlDataReader dataStream, BulkCopySimpleResultSet bulkCopyHandler, TdsParserStateObject stateObj) at Microsoft.Data.SqlClient.SqlInternalConnectionTds.CompleteLogin(Boolean enlistOK) at Microsoft.Data.SqlClient.SqlInternalConnectionTds.AttemptOneLogin(ServerInfo serverInfo, String newPassword, SecureString newSecurePassword, Boolean ignoreSniOpenTimeout, TimeoutTimer timeout, Boolean withFailover) at Microsoft.Data.SqlClient.SqlInternalConnectionTds.LoginNoFailover(ServerInfo serverInfo, String newPassword, SecureString newSecurePassword, Boolean redirectedUserInstance, SqlConnectionString connectionOptions, SqlCredential credential, TimeoutTimer timeout) at Microsoft.Data.SqlClient.SqlInternalConnectionTds.OpenLoginEnlist(TimeoutTimer timeout, SqlConnectionString connectionOptions, SqlCredential credential, String newPassword, SecureString newSecurePassword, Boolean redirectedUserInstance) at Microsoft.Data.SqlClient.SqlInternalConnectionTds..ctor(DbConnectionPoolIdentity identity, SqlConnectionString connectionOptions, SqlCredential credential, Object providerInfo, String newPassword, SecureString newSecurePassword, Boolean redirectedUserInstance, SqlConnectionString userConnectionOptions, SessionData reconnectSessionData, Boolean applyTransientFaultHandling, String accessToken, DbConnectionPool pool) at Microsoft.Data.SqlClient.SqlConnectionFactory.CreateConnection(DbConnectionOptions options, DbConnectionPoolKey poolKey, Object poolGroupProviderInfo, DbConnectionPool pool, DbConnection owningConnection, DbConnectionOptions userOptions) at Microsoft.Data.ProviderBase.DbConnectionFactory.CreateNonPooledConnection(DbConnection owningConnection, DbConnectionPoolGroup poolGroup, DbConnectionOptions userOptions) at Microsoft.Data.ProviderBase.DbConnectionFactory.TryGetConnection(DbConnection owningConnection, TaskCompletionSource1 retry, DbConnectionOptions userOptions, DbConnectionInternal oldConnection, DbConnectionInternal& connection)
at Microsoft.Data.ProviderBase.DbConnectionInternal.TryOpenConnectionInternal(DbConnection outerConnection, DbConnectionFactory connectionFactory, TaskCompletionSource1 retry, DbConnectionOptions userOptions) at Microsoft.Data.SqlClient.SqlConnection.TryOpen(TaskCompletionSource1 retry, SqlConnectionOverrides overrides)
at Microsoft.Data.SqlClient.SqlConnection.Open(SqlConnectionOverrides overrides)
at Microsoft.SqlServer.Management.Common.ConnectionManager.InternalConnectImpl()
at Microsoft.SqlServer.Management.Common.ConnectionManager.InternalConnect()
at Microsoft.SqlServer.Management.Common.ConnectionManager.Connect()
ClientConnectionId:xxxxx-e719e586bd8f
Error Number:18456,State:233,Class:14
ClientConnectionId before routing:xxxxx-7ffe36f3ce06
Routing Destination:xxxxx.worker.database.windows.net,11156
--- End of inner exception stack trace ---
at Microsoft.SqlServer.Management.Common.ConnectionManager.Connect()
at Microsoft.SqlServer.Management.Common.ConnectionManager.PoolConnect()
at Microsoft.SqlServer.Management.Common.ConnectionManager.get_IsContainedAuthentication()
at Microsoft.SqlServer.Management.Sdk.Sfc.ConnectionHelpers.UpdateConnectionInfoIfContainedAuthentication(Object& connectionInfo, Urn urn)
at Microsoft.SqlServer.Management.Sdk.Sfc.Enumerator.GetData(Object connectionInfo, Request request)
at Microsoft.SqlServer.Management.Smo.ExecutionManager.GetEnumeratorDataReader(Request req)
at Microsoft.SqlServer.Management.Smo.SqlSmoObject.GetInitDataReader(String[] fields, OrderBy[] orderby)
at Microsoft.SqlServer.Management.Smo.SqlSmoObject.ImplInitialize(String[] fields, OrderBy[] orderby)
at Microsoft.SqlServer.Management.Smo.SqlSmoObject.Initialize(Boolean allProperties)
at Microsoft.SqlServer.Management.Smo.SqlSmoObject.OnPropertyMissing(String propname, Boolean useDefaultValue)
at Microsoft.SqlServer.Management.Smo.PropertyCollection.RetrieveProperty(Int32 index, Boolean useDefaultOnMissingValue)
at Microsoft.SqlServer.Management.Smo.PropertyCollection.GetValueWithNullReplacement(String propertyName)
at Microsoft.SqlServer.Management.Smo.Database.get_IsSqlDw()
at Microsoft.SqlTools.ServiceLayer.ObjectExplorer.SmoModel.DatabaseTreeNode.EnsureContextInitialized() in D:\a\1\s\src\Microsoft.SqlTools.ServiceLayer\ObjectExplorer\SmoModel\DatabaseTreeNode.cs:line 51
at Microsoft.SqlTools.ServiceLayer.ObjectExplorer.SmoModel.SmoTreeNode.GetContext() in D:\a\1\s\src\Microsoft.SqlTools.ServiceLayer\ObjectExplorer\SmoModel\SmoTreeNode.cs:line 98
at Microsoft.SqlTools.ServiceLayer.ObjectExplorer.Nodes.TreeNode.GetContextAsT in D:\a\1\s\src\Microsoft.SqlTools.ServiceLayer\ObjectExplorer\Nodes\TreeNode.cs:line 310
at Microsoft.SqlTools.ServiceLayer.ObjectExplorer.SmoModel.DatabaseTreeNode.PopulateChildren(Boolean refresh, String name, CancellationToken cancellationToken) in D:\a\1\s\src\Microsoft.SqlTools.ServiceLayer\ObjectExplorer\SmoModel\DatabaseTreeNode.cs:line 55
at Microsoft.SqlTools.ServiceLayer.ObjectExplorer.Nodes.TreeNode.Expand(String name, CancellationToken cancellationToken) in D:\a\1\s\src\Microsoft.SqlTools.ServiceLayer\ObjectExplorer\Nodes\TreeNode.cs:line 248
at Microsoft.SqlTools.ServiceLayer.ObjectExplorer.Nodes.TreeNode.Expand(CancellationToken cancellationToken) in D:\a\1\s\src\Microsoft.SqlTools.ServiceLayer\ObjectExplorer\Nodes\TreeNode.cs:line 257
at Microsoft.SqlTools.ServiceLayer.ObjectExplorer.ObjectExplorerService.<>c__DisplayClass35_0.b__0(IBindingContext bindingContext, CancellationToken cancelToken) in D:\a\1\s\src\Microsoft.SqlTools.ServiceLayer\ObjectExplorer\ObjectExplorerService.cs:line 431
at Microsoft.SqlTools.ServiceLayer.LanguageServices.BindingQueue1.<>c__DisplayClass34_1.<ProcessQueue>b__1() in D:\a\1\s\src\Microsoft.SqlTools.ServiceLayer\LanguageServices\BindingQueue.cs:line 381


ePON config V2801F

Hello!
For the past two weeks, I've been unable to configure the ePON connection on the V2801F module. The native provider's ONU is the C-Data FD511G-E (listed in OMCICLI as EchoLife HG8010H GPON Terminal), and I have full access to the native ONU.
My network setup is Keneetic Peak + Vsol V2801F. The router isn't receiving an IP address from the provider, even though I can see that the ePON connection is active. Additionally, I'm concerned that the native ONU has the same MAC address on all interfaces, while the V2801F has different MAC addresses for the optical and wired interfaces.
If anyone has any thoughts on this, I would appreciate it.

anyone here have use EPON would help


Restore group membership when undeleted?

I've noticed that when a user is undeleted, they're not re-added to any groups they used to be in.
Is it possible to fully restore their account including group memberships, or is this data completely lost when they were deleted?

Can this be done?

Probably not possible without adding more code that tracks which groups they were a member of.
When a user is deleted they are removed from all groups  https://github.com/NodeBB/NodeBB/blob/master/src/user/delete.js#L151


Update or deprecate quickstart guide

The README.md quickstart points to fuels-ts quickstart docs.
Following this guide strictly results in error=enough coins could not be found when attempting to call the increment function.
Update or deprecate the docs to fix this issue.
One suggestion is to reflect the updated way of creating a wallet and running a node, as in The Fuel Book's Developer Quickstart, that is:

Using forc-wallet and
Running a testnet node with forc deploy --url https://node-beta-1.fuel.network/graphql --gas-price 1

instead of what is suggested in the current fuels-ts quickstart guide, that is:

Setting initial_state in the chainConfig.json file
Running a local node with fuel-core run --ip <IP_ADDRESS> --port 4000 --chain ./chainConfig.json

The quickstart is focused on local development, did you try to deploy or connect in a different network? Folowing the steps here looks to be working correctly.

@QuinnLee or @camsjams can you also try the quickstart locally to see if it works as expected?

@luizstacio are you able to call the incerement function without getting insufficient coins error?


feat: add new textspliter option: lenfunc

I want to add a new parameter to the textspliter struct,lenfunc, to represent a custom length function. In this way, sentences can be splited according to lenfuc, for example,   utf8.RuneCountInString can be passed to split Chinese characters.
Also aligned with the python code https://github.com/langchain-ai/langchain/blob/00a09e1b7117f3bde14a44748510fcccc95f9de5/libs/langchain/langchain/text_splitter.py.
For me, it's a must-have feature.

Also satisfy issue #231

ping @tmc

Hmm, it might be best to just default to RuneCount/RuneCountInString to treat content more naturally, thoughts?
I think I prefer this over erroneously using len() on strings.

This is better, but I can't help but think we shouldn't even make this configurable and just use utf8.RuneCountInString -- thoughts?

Hmm, I don't think so.
Some scenarios require custom length functions.
Let's say I want to have the same number of words, not characters  in each chunk.
I can simply set the LenFunc:
func countWords(s string) int {
    words := strings.Fields(s)
    return len(words)
}

Or the number of tokens divided by other word dividers.


Policy CSP DDF File Missing ADMX-Backed Policies?

The ADMX-backed policies are listed on another page but not included in the downloadable Policy CSP DDF XML file. (I checked the 2004 and 20H2 versions.) Is that page the definitive list of ADMX-backed policies? Is there a way to know which ones are supported by each version of Windows 10?

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

ID: 051c376e-e9dd-368d-0af7-ac0d997226c2
Version Independent ID: e49d31fa-4ba6-2140-54ee-f9564f59371b
Content: Policy DDF file - Windows Client Management
Content Source: windows/client-management/mdm/policy-ddf-file.md
Product: w10
Technology: windows
GitHub Login: @Dansimp
Microsoft Alias: dansimp

@eppsilon . Answering your question is too difficult to me, only author of this article can give correct  solutions

Hello @eppsilon ,
Is that page the definitive list of ADMX-backed policies? - yes, according to its history, the article is being updated regularly
Is there a way to know which ones are supported by each version of Windows 10? - as far as I can see, it is not shown anywhere in Microsoft Docs. You can use ADMX file information for this purpose. As you will need to download ADMX file to use ADMX-backed policies, the settings will apply to all versions that support this ADMX.
Thank you


New install defaults to Internal Console tab

A new install defaults to Internal Console tab instead of IPython. This means that when a script is run, there are lots of errors. Default tab should be IPython console. I am sure this confuses a lot of people. Must be fixed in next release if not sooner.

This is most certainly an issue with updated Spyder causing problem with older settings. It should not cause problems on new users but I will look into solving it in the next release.

I can try installing it on a clean machine to see how it goes.
H
On Thu, Aug 6, 2015 at 5:08 PM, Kiri Choi<EMAIL_ADDRESS>wrote:

This is most certainly an issue with updated Spyder causing problem with
older settings. It should not cause problems on new users but I will look
into solving it in the next release.
—
Reply to this email directly or view it on GitHub
https://github.com/sys-bio/tellurium/issues/35#issuecomment-128543258.

Not reproducible in Tellurium 1.2.3


clearTimeout and clearInterval could accept undefined

I suspect this issue is in a wrong place. Forgive me if I missed where I can raise it for it to be more appropriate.
clearTimeout and clearInterval are currently typed as (handle: number) => void. I’d like that to change to accept undefined: (handle?: number) => void).
The WHATWG spec says anything goes as a handle:

If handle does not identify an entry in the list of active timers of the WindowOrWorkerGlobalScope object on which the method was invoked, the method does nothing.

In practice passing in an obviously invalid value (like Hello) is an error we’d like to catch, but passing in undefined is a common enough event:
let myTimer;

sometimeInTheFuture(function(){
  myTimer = window.setTimeout(...);
});

sometimeInTheFuture(function(){
  window.clearTimeout(myTimer);
});

Obviously the latter can be guarded with a conditional, but in practice, given that browsers ignore clearTimeout with undefined, an unguarded version is used in many codebases I have seen.

Some programmers use myTimer: number | null.

This has been fixed 🎉


crash on 32 bit systems

This problem was viewed in version 0.11.1, I think. I am currently not able to test it with the current version but the corresponding source code did not change in 0.12.1 thus I think it is still a problem.
I am using mitmdump as transparent proxy. After changing the system mitmdump was running on, it crashes after some time with
  File "/usr/local/lib/python2.7/dist-packages/libmproxy/protocol/http.py", line 813, in _refresh_cookie
    i["expires"] = formatdate(d)
  File "/usr/lib/python2.7/email/utils.py", line 161, in formatdate
    now = time.gmtime(timeval)
ValueError: timestamp out of range for platform time_t

After some time I realised that the problem occurs after the change from 64 bit to 32 bit and disappeared after another change to 64 bit again.
Looking at libmproxy/protocol/http.py:810 or in 0.12.1 at libmproxy/protocol/http.py:842
            d = parsedate_tz(i["expires"])
                if d:
                    d = mktime_tz(d) + delta
                    i["expires"] = formatdate(d)

The documentation for email.utils.formatdate mentioned for the first parameter Optional timeval if given is a floating point time value as accepted by time.gmtime() and time.localtime(), otherwise the current time is used.
Internally time.gmtime is used. The documentation for time mentioned The functions in this module do not handle dates and times before the epoch or far in the future. The cut-off point in the future is determined by the C library; for Unix, it is typically in 2038.
Under 32 bit Ubuntu python crashes with time.gmtime(sys.maxint+1) but with time.gmtime(sys.maxint) you will get 2038-01-19 and some hours.
Thus under 32 bit this code will only work with expiration dates previous to 2038-01-19. But unfortunately there are site setting cookies with expiration dates far in the future. Different advertiser set it 30 years in future thus in 2045. But I also see dates after year 2080.

I'm rarely convinced by bug reports from old versions, but this sounds like a very good find. I'd be super happy if someone could step up and provide a fix + test case!

This problem is known as the Year 2038 Problem (similar to the infamous Y2K problem). IMO this is not an bug with mitmproxy but rather Python and the  time.gmtime() function specifically. You could submit a bug report with them. One suggestion would be for Python to not use POSIX time.h but rather build and use an external version into their project, such as time64.h (from here).

I am not sure if this is correctly marked as a "good first contribution". It's more of an upstream issue. :smile:

The used library documented the internal used structures and the documentation of these structures mentioned that it can "typically" only handle dates up to 2038. This is good enough for many python programs. But it seems it is not for use of uncontrolled data of third party.
You can say it is a bug of python. You can say it's an upstream issue. But you could also say that an unsuitable library is used. It's your decision to call it unfixable, a third party issue, to revoke the use of mitmproxy under 32 bit or to fix it, e.g. by writing the necessary code or using another library. But I am not able to tell you a better one, sorry.

We are using the Python standard library in many places - if this already fails to handle timestamps (far) in the future, then we have a more general problem anyway.
I'm closing this for now, since there is very little we can do - and eventually going to 64bit will solve this by itself.

apparently there is no x86 version available, is it because of this issue?


Tabs don't switch with hotkeys sometimes

Can't switch Hyper tabs with Shift-Command-[ and Shift-Command-] hotkeys sometimes. It starts to work again after switching with mouse.

Hyper 1.1.0
Electron 1.4.7
darwin x64 16.3.0

@karevn could you confirm if this happens only after you switch back from a new tab?

you have only one open tab
cmd+t
switch to the other tab
the hotkeys will not work (you will not be able to type anything)
you switch with the mouse to the other tab OR you click anywhere
the shortcuts works again

@matheuss yes, it works exactly like that.

Seems to be a duplicate of #1273
Fixed in master and will be shiped in next release

@karevn then it's indeed a duplicate of #1273, @karevn. We'll ship it ASAP. Thanks for reporting 🙆


Vulnerability roundup 79: aspell-<IP_ADDRESS>: 1 advisory

search, files

[ ] CVE-2019-17544 CVSSv3=9.1 (nixos-19.03)

Scanned versions: nixos-19.03: d1dff0bcd9f. May contain false positives.

See also: #73616


Ability to avoid using JS import in production for non-recent browsers ("Legacy" support for ES2015)

Describe the problem
Following my question in StackOverflow, I'm asking for support for ES2015 target, i.e. that the production output for the client will be able to be with no import keywords nor JavaScript modules, only bundled JS.
Describe the proposed solution
Vite compiler does support ES2015, so I think Svelte should be able to support it as well with no too much effort(again, only for production).
Probably Svelte output code should be modified to support no JavaScript modules in production, but I don't know for how much.
Alternatives considered
No response
Importance
i cannot use SvelteKit without it
Additional Information
No response

Duplicate of #12 . This isn't supported yet, but is on the roadmap post-1.0


Suport for WMS with Time parameter

How can I implement this plugin with support to a wms service with the parameter time? The structure of the time parameter is like this example 2005-01-01

I think that it should be straightforward. You can call the wms through your custom changeMap function and use the resulting data to attach to a leaflet object that can then be added to the map. In the demo, for example, this code would be in the getDataAddMarkers function.


[WB-4340] Type interface/interface.py

https://wandb.atlassian.net/browse/WB-4340
Description
Add type annotations to interface.py
Testing
mypy, pytest, flake

refactor the to_json methods to support different targets (simple, Run, Artifact, etc...)

Added a ticket for this in our Code quality epic:
https://wandb.atlassian.net/browse/WB-4642


Training the model for a different language

Hello @jxzhanggg,
First of all, thank you for your helpful replies to the previous issues I posted.
I would like to adapt this voice conversion model to European Portuguese. The thing is, I do not have a data set as large as VCTK in terms of nr. of utterances per speaker. I do have enough training data for at least 5-6 speakers (more than 500 utterances per speaker), sampled at 16 kHz. I tried several configurations, with batch sizes 8, 16 and 32 for pre-training but never managed to generate intelligible speech (decoder alignments did not converge). I changed the phonemizer backend in extract_features.py from Festival to Espeak, so that I could obtain phoneme transcriptions in Portuguese. I noticed that the total number of different phonemes increased substantially, from 41 (in English) to 66 (in Portuguese). I assume this makes the decoding task more difficult. Also, I experimented with the fine-tune model and the results improved a little bit (sometimes one or two words are intelligible, but still unintelligible utterances overall).
My questions are the following:

Should I try to use the pre-train model, even with only 5-6 speakers, or should I use only the fine-tune model instead?
What would you suggest in order to solve the decoder alignment problem?

Thank you very much

Should I try to use the pre-train model, even with only 5-6 speakers, or should I use only the fine-tune model instead?
I think more data is always favorable for training the model. So it should be useful to pretrain on more data.
What would you suggest in order to solve the decoder alignment problem?
I found the alignment converagence can be tricky, here're some of my experience:

Try to use shorter utterances, you can cut long utterances into smaller pieces if possible.
Also you can gradually increase the maximum length of utterances, it's kind like curriculum learning. At the begining, only use short utterances to train the model to make alignment easy to learn.
If alignment collapse during training, try to decease the learning rate or enlarge batch size.


Docs: Refine and review workflow files

linked to #33

Ensure that deployed site only show for PR(merge) to main. Use this as an example during refinement and review of workflow files.

To review on 23rd of Aug to decide whether we do this the following week.


Add Container Image Support

AWS supports packaging and deploying Lambdas as container images, however this plugin only supports traditional deployment based on S3. Supporting container images would allow this plugin to be used regardless of the type of packaging used.

@cjlpowers supporting container images is on the roadmap. We are working towards making the plugin production ready in the first phase and will look into supporting container images next. Needless to say that PRs on proposed enhancements are always welcome.

@nimakaviani would you be able to shed some light on the timeline here?

@a7i no immediate plans for adding the feature just yet.

Nearly two later, it this still on the project's roadmap?


Move the showView method to AbstractFxmlView

The responsibility of an AbstractFxmlView to be shown should recall on its own, and not on AbstractJavaFxApplicationSupport via a static call.
To show a view, now you have to do it this way
Main.showView(FirstView.class);

This makes code hardly testable.
This gives the control of showing a class to the Main class (that is nothing special, just the entry point of the application), but an AbstractFxmlView should have the ability to be requested to be shown, and how.

The solution should provide showView methods to AbstractFxmlView so that:

There are separation of concerns
Code is testable since is easier to mock an instance of a class rather than an static method
There are methods that provides ways to show a view, I. e. under which Window, with which Modality, and if the Window should be shown as show or showAndWait

I totally agree!
Looking forward to a pull request...
Thanks so far!

I already raised the Pull Request, but it decreases the code coverage.
I will add tests soon and push the changes, in the meantime any reviews are appreciated.


Environ

Problems with the environ package when doing
cookiecutter https://github.com/pydanny/cookiecutter-django
project_name [Project Name]: cookeddjango
project_slug [cookeddjango]:
author_name [Daniel Roy Greenfeld]: D R G
email<EMAIL_ADDRESS><EMAIL_ADDRESS>description [A short description of the project.]: Cookie django for poodle
domain_name [example.com]: umlv.fr
version [0.1.0]:
timezone [UTC]: CTE
use_whitenoise [y]: y
use_celery [n]:
use_mailhog [n]:
use_sentry_for_error_reporting [y]:
use_opbeat [n]:
use_pycharm [n]:
windows [n]:
use_python3 [y]:
use_docker [y]: n
use_heroku [n]:
use_elasticbeanstalk_experimental [n]:
use_compressor [n]:
Select postgresql_version:
1 - 9.6
2 - 9.5
3 - 9.4
4 - 9.3
5 - 9.2
Choose from 1, 2, 3, 4, 5 [1]: 2
Select js_task_runner:
1 - Gulp
2 - Grunt
3 - None
Choose from 1, 2, 3 [1]: 1
use_lets_encrypt [n]:
Select open_source_license:
1 - MIT
2 - BSD
3 - GPLv3
4 - Apache Software License 2.0
5 - Not open source
Choose from 1, 2, 3, 4, 5 [1]: 1
(env) MBPdeDominique3:cookeddjango dr$ python manage.py test
Traceback (most recent call last):
File "manage.py", line 23, in
execute_from_command_line(sys.argv)
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/django/core/management/init.py", line 367, in execute_from_command_line
utility.execute()
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/django/core/management/init.py", line 316, in execute
settings.INSTALLED_APPS
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/django/conf/init.py", line 53, in getattr
self._setup(name)
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/django/conf/init.py", line 41, in _setup
self._wrapped = Settings(settings_module)
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/django/conf/init.py", line 97, in init
mod = importlib.import_module(self.SETTINGS_MODULE)
File "/Users/dr/.pyenv/versions/3.5.2/lib/python3.5/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 986, in _gcd_import
File "", line 969, in _find_and_load
File "", line 958, in _find_and_load_unlocked
File "", line 673, in _load_unlocked
File "", line 665, in exec_module
File "", line 222, in _call_with_frames_removed
File "/Users/dr/POODLE/SANDBOX/cookeddjango/config/settings/local.py", line 15, in
from .common import *  # noqa
File "/Users/dr/POODLE/SANDBOX/cookeddjango/config/settings/common.py", line 13, in
import environ
ImportError: No module named 'environ'
(env) MBPdeDominique3:cookeddjango dr$ pip install environ
Collecting environ
Installing collected packages: environ
Successfully installed environ-1.0
(env) MBPdeDominique3:cookeddjango dr$ python manage.py test
Traceback (most recent call last):
File "manage.py", line 23, in
execute_from_command_line(sys.argv)
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/django/core/management/init.py", line 367, in execute_from_command_line
utility.execute()
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/django/core/management/init.py", line 316, in execute
settings.INSTALLED_APPS
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/django/conf/init.py", line 53, in getattr
self._setup(name)
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/django/conf/init.py", line 41, in _setup
self._wrapped = Settings(settings_module)
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/django/conf/init.py", line 97, in init
mod = importlib.import_module(self.SETTINGS_MODULE)
File "/Users/dr/.pyenv/versions/3.5.2/lib/python3.5/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 986, in _gcd_import
File "", line 969, in _find_and_load
File "", line 958, in _find_and_load_unlocked
File "", line 673, in _load_unlocked
File "", line 665, in exec_module
File "", line 222, in _call_with_frames_removed
File "/Users/dr/POODLE/SANDBOX/cookeddjango/config/settings/local.py", line 15, in
from .common import *  # noqa
File "/Users/dr/POODLE/SANDBOX/cookeddjango/config/settings/common.py", line 13, in
import environ
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/environ.py", line 114
raise ValueError, "No frame marked with %s." % fname
^
SyntaxError: invalid syntax

I think that you probably install a wrong package.
Since, python does not force the package name to be the same as the python
module name, do not rely on the functionality of the IDE's to automatically
install the packages.
Load your virtualenv and run:
pip uninstall environ
pip install django-environ -U
All other packages are listed on requirements folder. Install all packages
on your virtualenv
If this solve the problem, please, close this issue
Em 30/12/2016 09:36, "plgitlogin"<EMAIL_ADDRESS>escreveu:

Problems with the environ package when doing
cookiecutter https://github.com/pydanny/cookiecutter-django
project_name [Project Name]: cookeddjango
project_slug [cookeddjango]:
author_name [Daniel Roy Greenfeld]: D R G
email<EMAIL_ADDRESS><EMAIL_ADDRESS>description [A short description of the project.]: Cookie django for poodle
domain_name [example.com]: umlv.fr
version [0.1.0]:
timezone [UTC]: CTE
use_whitenoise [y]: y
use_celery [n]:
use_mailhog [n]:
use_sentry_for_error_reporting [y]:
use_opbeat [n]:
use_pycharm [n]:
windows [n]:
use_python3 [y]:
use_docker [y]: n
use_heroku [n]:
use_elasticbeanstalk_experimental [n]:
use_compressor [n]:
Select postgresql_version:
1 - 9.6
2 - 9.5
3 - 9.4
4 - 9.3
5 - 9.2
Choose from 1, 2, 3, 4, 5 [1]: 2
Select js_task_runner:
1 - Gulp
2 - Grunt
3 - None
Choose from 1, 2, 3 [1]: 1
use_lets_encrypt [n]:
Select open_source_license:
1 - MIT
2 - BSD
3 - GPLv3
4 - Apache Software License 2.0
5 - Not open source
Choose from 1, 2, 3, 4, 5 [1]: 1
(env) MBPdeDominique3:cookeddjango dr$ python manage.py test
Traceback (most recent call last):
File "manage.py", line 23, in
execute_from_command_line(sys.argv)
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/
django/core/management/init.py", line 367, in execute_from_command_line
utility.execute()
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/
django/core/management/init.py", line 316, in execute
settings.INSTALLED_APPS
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/
django/conf/init.py", line 53, in getattr
self._setup(name)
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/
django/conf/init.py", line 41, in _setup
self._wrapped = Settings(settings_module)
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/
django/conf/init.py", line 97, in init
mod = importlib.import_module(self.SETTINGS_MODULE)
File "/Users/dr/.pyenv/versions/3.5.2/lib/python3.5/importlib/init.py",
line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 986, in _gcd_import
File "", line 969, in _find_and_load
File "", line 958, in _find_and_load_unlocked
File "", line 673, in _load_unlocked
File "", line 665, in exec_module
File "", line 222, in _call_with_frames_removed
File "/Users/dr/POODLE/SANDBOX/cookeddjango/config/settings/local.py",
line 15, in
from .common import * # noqa
File "/Users/dr/POODLE/SANDBOX/cookeddjango/config/settings/common.py",
line 13, in
import environ
ImportError: No module named 'environ'
(env) MBPdeDominique3:cookeddjango dr$ pip install environ
Collecting environ
Installing collected packages: environ
Successfully installed environ-1.0
(env) MBPdeDominique3:cookeddjango dr$ python manage.py test
Traceback (most recent call last):
File "manage.py", line 23, in
execute_from_command_line(sys.argv)
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/
django/core/management/init.py", line 367, in execute_from_command_line
utility.execute()
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/
django/core/management/init.py", line 316, in execute
settings.INSTALLED_APPS
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/
django/conf/init.py", line 53, in getattr
self._setup(name)
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/
django/conf/init.py", line 41, in _setup
self._wrapped = Settings(settings_module)
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/
django/conf/init.py", line 97, in init
mod = importlib.import_module(self.SETTINGS_MODULE)
File "/Users/dr/.pyenv/versions/3.5.2/lib/python3.5/importlib/init.py",
line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 986, in _gcd_import
File "", line 969, in _find_and_load
File "", line 958, in _find_and_load_unlocked
File "", line 673, in _load_unlocked
File "", line 665, in exec_module
File "", line 222, in _call_with_frames_removed
File "/Users/dr/POODLE/SANDBOX/cookeddjango/config/settings/local.py",
line 15, in
from .common import * # noqa
File "/Users/dr/POODLE/SANDBOX/cookeddjango/config/settings/common.py",
line 13, in
import environ
File "/Users/dr/POODLE/SANDBOX/env/lib/python3.5/site-packages/environ.py",
line 114
raise ValueError, "No frame marked with %s." % fname
^
SyntaxError: invalid syntax
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/pydanny/cookiecutter-django/issues/965, or mute the
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.

Ok
thanks


Issue with playback video size

Issue as seen by user

Problem
I have a normal 1080p landscape monitor and I am observing large black borders above and below the actual video content.
Other extensions
None
Chrome Version
Version 93.0.4577.63 (Official Build) (64-bit)
Thanks for building the extension btw...

I don't know much about html and css, but when I changed the following code I was able to get a more usable player.
<div id="vjs_video_3" style="width: 100%; outline: none; ...

<div id="vjs_video_3" style="width: 100%; outline: none; height: 800px;...

Obviously this is very hacky, but I'm not much of a front end dev.

Thank you very much for resolving the issue!


syncthing_exporter: init at 0.3.0

Motivation for this change
Things done

[ ] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
Built on platform(s)

[x] NixOS
[ ] macOS
[ ] other Linux distributions

[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
[x] Tested execution of all binary files (usually in ./result/bin/)
[ ] Determined the impact on package closure size (by running nix path-info -S before and after)
[ ] Ensured that relevant documentation is up to date
[ ] Fits CONTRIBUTING.md.

Also, all prometheus exporters have a common naming scheme in nixpkgs, namely prometheus-<name>-exporter for packages.

Also, all prometheus exporters have a common naming scheme in nixpkgs, namely prometheus-<name>-exporter for packages.

Thanks! I noticed that after pushing. I made the changes locally but haven't had time to test yet. Will update probably by weekend.

Any progress on this?

Hi, sorry I’ve been pccupied with other aspects of life, and cannot tell when I can get back to fixing the comments. We can abandon this one.


parser issue: a <!-- style comment inside javadoc causes "is not print idempotent" parsing error

What version of OpenRewrite are you using?
I am using

Maven plugin 5.36.0

How are you running OpenRewrite?
I am using the Maven plugin, and my project is a multi-module project.
Please see https://github.com/valters/test-openrewrite for repro case: https://github.com/valters/test-openrewrite/blob/main/source-problems/src/main/java/ch/vingolds/testopenrewrite/FailsToParse.java
What is the smallest, simplest way to reproduce the problem?
I happen to have a java file with auto-generated javadoc comment like this:
/**
 *  <!--
 Does this html-style comment cause a "is not print idempotent" parsing problem?
 -->
 */
public class FailsToParse {
}

What did you expect to see?
The file should be processed normally as it does not have anything of note in it.
What did you see instead?
(...)
[WARNING] There were problems parsing some source files
[WARNING] There were problems parsing source-problems/src/main/java/ch/vingolds/testopenrewrite/FailsToParse.java
[WARNING] java.lang.IllegalStateException: source-problems/src/main/java/ch/vingolds/testopenrewrite/FailsToParse.java is not print idempotent.
diff --git a//Users/valters.vingolds/_sandbox/test-openrewrite/source-problems/src/main/java/ch/vingolds/testopenrewrite/FailsToParse.java b//Users/valters.vingolds/_sandbox/test-openrewrite/source-problems/src/main/java/ch/vingolds/testopenrewrite/FailsToParse.java
index 8442fdd..0733a49 100644
--- a//Users/valters.vingolds/_sandbox/test-openrewrite/source-problems/src/main/java/ch/vingolds/testopenrewrite/FailsToParse.java
+++ b//Users/valters.vingolds/_sandbox/test-openrewrite/source-problems/src/main/java/ch/vingolds/testopenrewrite/FailsToParse.java
@@ -4,6 +4,8 @@
  *  <!--
  Does this html-style comment cause a "is not print idempotent" parsing problem?
  -->
+
+
  */
 public class FailsToParse {
 }

  org.openrewrite.Parser.requirePrintEqualsInput(Parser.java:52)
[INFO] Project [parent-test-openrewrite] Parsing source files
(...)

What is the full stack trace of any errors you encountered?
No error, just unexpected parsing weakness.

Very similar to #4248 bug report

Thanks for the detailed report, and finding that similar issue. While the question there was originally to skip parsing JavaDocs, I've renamed that issue to more closely match this one. As that other issue already has a unit test associated with it I propose we close this one and continue to track on.

https://github.com/openrewrite/rewrite/issues/4248


Android walletconnect stuck when opening wc: deeplink

On android open a dapp
choose walletconnect (then hit connect)
choose goodwallet from available wallets
wallet stuck on splash or on walletconnect screen

hotfixed 8ec403f941ad3af65c8da0fe51075ec0f66051cb

verified on prod