Authentication via social networks

Hi! I can't understand how implement authentication via social networks.
I followed all instructions in documentation, but I had stopped at function successCallback, which should contains some code I don't know. At forums I seen many solves, but nothing helped.
Authentication dialog show: "Calling unknown method: dektrium\user\Module::model()" or "Error: redirect_uri_mismatch".
Please help me solve this issue.

You don't need to implement any method yourself. You just need to register applications in needed networks, and then configure authClientCollection application component.
https://github.com/dektrium/yii2-user/blob/master/docs/social-auth.md

Thank you for fast response. Look, in this case, authentication dialog show: Page not found.

Dmitry, please don't leave me with my problem. I fight with social authentication during two days and it not gives me any results.

On which step are you getting "Not found" error? Could you please describe in steps what are you doing before this error occurs?

Of course! At first, I registered web apps at social nets. After, I declared authClientCollection with all clients at config file, as you wrote above. That's all.

I mean, when are you getting error? When you click social network button, or after authenticating in popup window, or on any other moment?

When I click social network button

Could you please provide a screenshot of the error?

http://joxi.ru/LVm6qkwiz1JVrZ

Strange url. Are you sure you are using correct login page? Yii2-user login route is user/security/login, not site/login.

Yes, my used login route is user/security/login, but it route contains login link only. I had to used it somewhere else, didn't I?

It is strange that auth widget redirects you to site/auth, but not to user/security/auth. Are you overriding login page view?

Only for login link

Could you please provide the view file code?

Of course. Here you're.
use yii\helpers\Html;
use yii\widgets\ActiveForm;
use dektrium\user\widgets\Connect;
$this->registerCssFile('@web/css/login.css');
$this->title = Yii::t('user', 'Log in');
$this->params['breadcrumbs'][] = $this->title;
?>
render('/_alert', ['module' => Yii::$app->getModule('user')]) ?>

title) ?>
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text

 'login-form',
                    'enableAjaxValidation'   => true,
                    'enableClientValidation' => false,
                    'validateOnBlur'         => false,
                    'validateOnType'         => false,
                    'validateOnChange'       => false,
                ]) ?>
            <?= $form->field($model, 'login', ['inputOptions' => ['autofocus' => 'autofocus', 'class' => 'form-control', 'tabindex' => '1', 'placeholder' => 'Username']])->label(false) ?>

            <?= $form->field($model, 'password', ['inputOptions' => ['class' => 'form-control', 'tabindex' => '2', 'placeholder' => 'Password']])->passwordInput()->label(false) ?>

                <?= $form->field($model, 'rememberMe')->checkbox(['tabindex' => '4']) ?>

<?= Html::a(Yii::t('user', 'Forgot password?'), ['/user/recovery/request'], ['tabindex' => '5']); ?>

            <?= Html::submitButton(Yii::t('user', 'Sign in'), ['class' => 'btn btn-primary btn-block', 'tabindex' => '3']) ?>

            <?php ActiveForm::end(); ?>

$this->registerCssFile('@web/css/login.css');
$this->title = Yii::t('user', 'Log in');
$this->params['breadcrumbs'][] = $this->title;
?>
render('/_alert', ['module' => Yii::$app->getModule('user')]) ?>
Div site-login contains:
 'login-form',
                    'enableAjaxValidation'   => true,
                    'enableClientValidation' => false,
                    'validateOnBlur'         => false,
                    'validateOnType'         => false,
                    'validateOnChange'       => false,
                ]) ?>
            <?= $form->field($model, 'login', ['inputOptions' => ['autofocus' => 'autofocus', 'class' => 'form-control', 'tabindex' => '1', 'placeholder' => 'Username']])->label(false) ?>

            <?= $form->field($model, 'password', ['inputOptions' => ['class' => 'form-control', 'tabindex' => '2', 'placeholder' => 'Password']])->passwordInput()->label(false) ?>

                <?= $form->field($model, 'rememberMe')->checkbox(['tabindex' => '4']) ?>

<?= Html::a(Yii::t('user', 'Forgot password?'), ['/user/recovery/request'], ['tabindex' => '5']); ?>

            <?= Html::submitButton(Yii::t('user', 'Sign in'), ['class' => 'btn btn-primary btn-block', 'tabindex' => '3']) ?>

            <?php ActiveForm::end(); ?>

I dont see here social buttons widget. Is it view file you are using?

I didn't understood what you want at first time:)) I add this code at layout main:
 ['site/auth']
            ]) ?>

OH!!!!!! I see mistake!!!!

Thank you!!! You are perfect!!!

Dmitry, I have another question:) How can I parse email from social net for authentication form via social net? And for what i should fill out it's field if i can parse email

At the moment, you can do this only by overriding controllers and models and writing all logic yourself. Registration via networks without entering any credentials is on roadmap.

Ok. Thank you for your help!

Dmitry, hi! Do you have work experience in authentication via Google+ or Tumblr? Yesterday I wrote here in first question of this topic about Google error "redirect_uri_mismatch". This problem is not gone still. And added another one with Tumblr (after allowing access to my personal data for application shows an error: "oauth_signature does not match expected value") though I sure it was before. Do you have any ideas how solve it's issues?

I've used only Google API, and I've met the same problem. I've solved it by enabling pretty urls in application, and using http://yoursite.com/user/security/auth?authclient=google. By the way, Google apis settings take some time to be applied, so you should wait 5-10 minutes after changing them.

Dmitry, thank you for your help!!! I'm very inattentive!:(

hi How to access social network attributes?


Composer 2

Upgrade to Composer 2.0
Do not merge until https://github.com/roblib/CrayFits/pull/4 has been merged
Might also wanna hold back on merging this until release pattern is figured out as it could break developers environments if they use the tags latest or 0.0.1.

This will fail to build until roblib/CrayFits#4 has been merged.

Should be good to go now.

Just built this locally and deployed.  Everything looks good.  :rocket:


Choropleth64 layer broken

Choropleth64 layers are broken as of c6b27ce55e365906327fb013c1e2a0747e2fa790
However, removing the type property when adding colors attribute solves the issue.
 --- a/src/layers/fp64/choropleth-layer/choropleth-layer.js
 +++ b/src/layers/fp64/choropleth-layer/choropleth-layer.js
 @@ -61,7 +61,6 @@ export default class ChoroplethLayer64 extends Layer {
        heightsFP64: {size: 2, update: this.calculateHeightsFP64},
        colors: {
          size: 4,
 -        type: GL.UNSIGNED_BYTE,
          update: this.calculateColors
        },
        // Instanced attributes

I'm a bit confused...
@ibgreen do you know how this is happening?

Introduced in https://github.com/uber/deck.gl/pull/161.

Resolved by #172. Closing


Agent verification: if bannergress opened in new tab after leaving to nia suggest go there again. Should show verify button.

Opens in this stage:

Should opens in this stage:

As Niantic closed their forums verification this way is no longer possible. Issue obsolete.


Improve diagnostic to have the ability to format with source code text

For https://github.com/denoland/deno/issues/8529
This would allow taking a Diagnostic and then formatting it showing the position in the source file text the diagnostic occurred for.

Closed by #126


adding datasource need to login but the clickhouse or grafana's username-password both failed

Hi, guys. I met a problem during adding clickhouse datasource .
When I click the "save and test", a confirm form appeared.
Then I tried to using clickhouse profile to fill the username and password input. I get the following error warning:

It is the same as that I input grafana username and password. I search almost answer, but no solution.
Thanks for any reply.

@yishanchuan could share more detail?
could you explain how exactly did you try to add clickhouse data source?
do you use Access: "Browser" or "Server"?
which schema (http, https), host and port  did you use?

by default clickhouse support http:// schema on 8123 port, and https:// schema for 8443 port
also, how do you ensure that you try to use the right username and password?
by default clickhouse allow login with default username without password,  restricted only from localhost (grafana should install to the same server as clickhouse) or inside same docker network if you use docker installation)

@yishanchuan could share more detail?
could you explain how exactly did you try to add clickhouse data source?
do you use Access: "Browser" or "Server"?
which schema (http, https), host and port did you use?

by default clickhouse support http:// schema on 8123 port, and https:// schema for 8443 port
also, how do you ensure that you try to use the right username and password?
by default clickhouse allow login with default username without password, restricted only from localhost (grafana should install to the same server as clickhouse) or inside same docker network if you use docker installation)

yes, I use http://<IP_ADDRESS>:8123 and Server (default)

I use tabix to connect clickhouse , the same username and password can access that.

@yishanchuan how do you install Grafana? is it the same server with the same IP where install clickhouse or is it the separate server with different IP?
did you check Basic auth checkbox?

or do you use Yandex Cloud authorization?

Thanks a lot! It's work!


How to trigger an action such as page navigation after video is finished playing

Is there a way to trigger an action, sucha as navigating to another flutter view, when a video is finished playing?

Hi @sachavieuxroy,
This issue doesn't seem to describe a bug or a feature request. Please see https://flutter.dev/community for resources and asking questions like this.
You may also get some help if you post it on Stack Overflow and if you need help with your code, please see https://www.reddit.com/r/flutterhelp/
Closing, as this isn't an issue with Flutter itself. If you disagree, please write in the comments and I will reopen it.
Thank you


History has undefined state

Version
^5.1.2
Test Case
https://codesandbox.io/s/competent-thunder-ddx49
Steps to reproduce
Line 8 of App.tsx where location state has the typescript definition of PoormansUnknwon stops the code from compiling or ever having location state
Expected Behavior
Location state should have correct typescript definitions
Actual Behavior
https://github.com/DefinitelyTyped/DefinitelyTyped/blob/master/types/history/index.d.ts#L55
This stops code compiling and holding correct state

We don't maintain the types. You should consult the support resources for DefinitelyTyped.


[newsletters/2021/08/04/] grammer nit missing word

working on

This is an amazing special, thanks a bunch!
Sorry for not catching this earlier pre-publishing.

ACK. Thanks Max!


Mention link to creating Azure B2C users programmatically

Although consumer accounts in an Azure AD B2C directory are most commonly created when users sign up to use one of your applications, you can create them programmatically and by using the Azure portal. This article focuses on the Azure portal method of user creation and deletion.
This paragraph is mentioned at the top of the article but no help is given when trying to create multiple B2C users programmatically. This would be more of an Application Developer focused article and will hope to see this in the future as there are almost no other online resources to doing so.
[Enter feedback here]

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

ID: ef6a6152-30d5-3914-843e-e601c036fbaf
Version Independent ID: 470b478d-e537-048a-e516-b473e819eb3d
Content: Create & delete Azure AD B2C consumer user accounts in the Azure portal
Content Source: articles/active-directory-b2c/manage-users-portal.md
Service: active-directory
Sub-service: b2c
GitHub Login: @msmimart
Microsoft Alias: mimart

@eric99r
Thanks for your feedback! We will investigate and update as appropriate.

Thanks! I think this is good feedback and I made a pull request to update the paragraph with the link https://github.com/MicrosoftDocs/azure-docs-pr/pull/124443
CC @msmimart


Add documentation for dot product attention

Description
Add documentation for dot product attention.
Type of change

[x] Documentation change (change only to the documentation, either a fix or a new content)
[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)

Changes

Add documentation, example scripts, benchmarks for dot product attention. Discuss the details of supported backends, their differences, and the nuances of other features such as QKV layouts, mask types, and FP8 attention.

Checklist:

[x ] I have read and followed the contributing guidelines
[x ] The functionality is complete
[x ] I have commented my code, particularly in hard-to-understand areas
[x ] I have made corresponding changes to the documentation
[x ] My changes generate no new warnings
[x ] I have added tests that prove my fix is effective or that my feature works
[x ] New and existing unit tests pass locally with my changes

/te-ci pytorch

/te-ci pytorch

/te-ci pytorch

/te-ci pytorch

/te-ci pytorch

/te-ci pytorch

/te-ci pytorch

/te-ci pytorch


First names not in simple emails

email =<EMAIL_ADDRESS>EmailDecomposer().decompose(data=email, get_host=True)
Out[43]: {'first_name': '', 'last_name': 'Dill', 'host': 'isc.fraunhofer.de'}

email =<EMAIL_ADDRESS>EmailDecomposer().decompose(data=email, get_host=True)
Out[46]: {'first_name': '', 'last_name': 'Papazian', 'host': 'scilifelab.se'}

How come this is neither detecting Katja nor Stefano? I don't believe that neither first name is present in the US Census you use.

Hi @Michael-E-Rose, I checked the US Census data and unfortunately it is not there. See dist.male.first.


[change] Allow passing a specific migration number

In some cases, apps we depend on have data migrations we must depend on which are not included in the initial migration but may be included in the successive migrations.
Depending on latest doesn't fix that and may introduce more harm than good.
In these cases we simply have to depend on the specific migration and recommend anyone wanting to swap that particular app to create a migration with the same name in their swapped models.
I think we should change dependency as follows:
https://github.com/openwisp/django-swappable-models/blob/6698b200fc857a1c147406aa2d0ad8feab017408/swapper/__init__.py#L47-L55

drop latest argument which may do more harm than good
add a version attribute which defaults to None and if present is returned similary to how we return __latest__ now

We should then update the docs about latest and replace those with this concept.
@codesankalp what do you think?
PS: see also https://github.com/openwisp/openwisp-users/pull/300.

I think this was a false alarm, but let me dig deeper and do more testing before closing.
I think latest can work fine if everything is set up correctly.

@codesankalp what do you think?

Yes I also faced this in openwisp-radius. I will add a patch for this.


Use Timeout.timeout for TCP connection

Unfortunately, getting a pure solution to timeouts is essentially impossible without rewriting the entire stack yourself. Which I might actually do for fun later, but for the time being. This is the simplest way of getting a connect timeout :(

@httprb/owners fyi if someone can :+1: quickly

This looks fine to me

:+1: from me as well :D


Is "fsevents" required? It sometimes breaks my build on Modulus, not sure if it relates

Hi, I'm sometimes getting broken builds on Modulus, which complains about "fsevents" not being supported by Linux (OS X specific package). I've found that fsevents is a dependency of this project and wonders if it's really required, or if there is some way to make it an optional/non requirement when on Linux?

Chimpjs uss Chokidar to do file-watching when chimp is used standalone. Chokidar has an optional dep on fsevents
Chimp does work on linux though so this is odd. What flavor of linux is it?

Modulus run applications on Ubuntu 14.04. Which makes this weird, right?

I haven't seen this in a while. Closing it.


2.2.1 blank screen when trying to open document

2.2.1 updated today. Had no issues previously. Upgrades to latest community of docker image and still nothing working... just a blank screen when i go to edit files.
need to know where to get logs to post so i can get a fix going.
don't know how to downgrade the application back to 2.1.7

Hello, @teknoprep, what version Owncloud do you use?

lastest stable version as of July 6th per the updater

@teknoprep, specify the version in numbers please.

We are having the same problem after upgrading to 2.2.1.
owncloud version => <IP_ADDRESS>

For more information

Fixed b429d15aa40b8dac0fe19f3e424d5819a0c32e80

Fixed b429d15

@LinneyS,
Thanks!

great shit... i just git checkout b429d15 and it worked great.. i really appreciate you checking this out and fixing it


Added test for NOMR mertic

Adde the test for NOMR metric that will validate that this metric is calculated properely
Refrences #192

@yegor256 check it out, please

@zaqbez39me thanks!


No template sub-directory with name 'markdown' found in the following path

I get the error below when i try to publish :
Failed to post to Medium
Returned error message below

"ValueError: No template sub-directory with name 'markdown' found in the following paths:
\t/Users/baptistepirault/Library/Jupyter
\t/Users/baptistepirault/Library/Python/3.11/share/jupyter
<EMAIL_ADDRESS>\t/usr/local/share/jupyter
\t/usr/share/jupyter

Traceback (most recent call last):
File \"/opt/homebrew/lib/python3.11/site-packages/traitlets/traitlets.py\", line 656, in get
value = obj._trait_values[self.name]
~~~~~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: 'template_paths'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File \"/opt/homebrew/lib/python3.11/site-packages/jupyter_to_medium/_bundler.py\", line 37, in upload
data = publish(**kwargs)
^^^^^^^^^^^^^^^^^
File \"/opt/homebrew/lib/python3.11/site-packages/jupyter_to_medium/_publish_to_medium.py\", line 300, in publish
p.main()
File \"/opt/homebrew/lib/python3.11/site-packages/jupyter_to_medium/_publish_to_medium.py\", line 218, in main
self.md, self.image_data_dict = self.create_markdown()
^^^^^^^^^^^^^^^^^^^^^^
File \"/opt/homebrew/lib/python3.11/site-packages/jupyter_to_medium/_publish_to_medium.py\", line 127, in create_markdown
me = MarkdownExporter()
^^^^^^^^^^^^^^^^^^
File \"/opt/homebrew/lib/python3.11/site-packages/nbconvert/exporters/templateexporter.py\", line 348, in __init__
super().__init__(config=config, **kw)
File \"/opt/homebrew/lib/python3.11/site-packages/nbconvert/exporters/exporter.py\", line 122, in __init__
self._init_preprocessors()
File \"/opt/homebrew/lib/python3.11/site-packages/nbconvert/exporters/templateexporter.py\", line 528, in _init_preprocessors
conf = self._get_conf()
^^^^^^^^^^^^^^^^
File \"/opt/homebrew/lib/python3.11/site-packages/nbconvert/exporters/templateexporter.py\", line 546, in _get_conf
for path in map(Path, self.template_paths):
^^^^^^^^^^^^^^^^^^^
File \"/opt/homebrew/lib/python3.11/site-packages/traitlets/traitlets.py\", line 703, in __get__
return self.get(obj, cls)
^^^^^^^^^^^^^^^^^^
File \"/opt/homebrew/lib/python3.11/site-packages/traitlets/traitlets.py\", line 659, in get
default = obj.trait_defaults(self.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File \"/opt/homebrew/lib/python3.11/site-packages/traitlets/traitlets.py\", line 1872, in trait_defaults
return self._get_trait_default_generator(names[0])(self)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File \"/opt/homebrew/lib/python3.11/site-packages/traitlets/traitlets.py\", line 1233, in __call__
return self.func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File \"/opt/homebrew/lib/python3.11/site-packages/nbconvert/exporters/templateexporter.py\", line 557, in _template_paths
template_names = self.get_template_names()
^^^^^^^^^^^^^^^^^^^^^^^^^
File \"/opt/homebrew/lib/python3.11/site-packages/nbconvert/exporters/templateexporter.py\", line 642, in get_template_names
raise ValueError(
ValueError: No template sub-directory with name 'markdown' found in the following paths:
\t/Users/baptistepirault/Library/Jupyter
\t/Users/baptistepirault/Library/Python/3.11/share/jupyter
<EMAIL_ADDRESS>\t/usr/local/share/jupyter
\t/usr/share/jupyter
"

Environment used :

mac os monterey
python 3.11
jupyter 6.5.2
jupyter-to-medium 0.2.4

Have exact same error


Update config.yml

Pull request checklist
Use the following template to make sure your PR fits the Quorum Key Manager documentation standard.
Before creating the PR
Make sure that:

[x] You've read the contribution guidelines.
[x] You've previewed your changes locally.

Describe the change

Issue fixed

Impacted parts

For content changes:

[ ] Documentation content
[ ] Documentation page organization

For tool changes:

[ ] CircleCI workflow
[ ] Build and QA tools (for example, lint or vale)
[ ] MkDocs templates
[ ] MkDocs configuration
[ ] Python dependencies
[ ] Node dependencies and JavaScript
[ ] Read the Docs configuration
[ ] GitHub integration

After creating your PR and tests have finished
Make sure that:

[ ] You've fixed any issues raised by the tests.
[ ] You've previewed your changes on Read the Docs
and added a preview link.

Preview

 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.


Incorrect work of tests filter

In some cases filter for tests to be run works incorrectly. For example having two tests: - SomeNamespace.ClassName.Test1 - SomeNamespace.ClassName.Test11
even when I specify filter to be "SomeNamespace.ClassName.Test1" I expect only the first test to be run, but by the fact both tests are run.

done in fa8c3d50ca78


n8n: 1.55.3 -> 1.57.0

Automatic update generated by nixpkgs-update tools. This update was made based on information from passthru.updateScript.
meta.description for n8n is: Free and source-available fair-code licensed workflow automation tool
meta.homepage for n8n is: https://n8n.io
meta.changelog for n8n is<EMAIL_ADDRESS>Updates performed

Ran passthru.UpdateScript

To inspect upstream changes

Release on GitHub

Compare changes on GitHub

Impact
Checks done

built on NixOS

[!CAUTION]
A test defined in passthru.tests did not pass.

found 1.57.0 with grep in /nix/store/wz0qqps5lgn9zbxyi13h0ijd1cxszk7x-n8n-1.57.0
found 1.57.0 in filename of file in /nix/store/wz0qqps5lgn9zbxyi13h0ijd1cxszk7x-n8n-1.57.0

Rebuild report (if merged into master) (click to expand)

2 total rebuild path(s)

2 package rebuild(s)

First fifty rebuilds by attrpath

n8n

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/wz0qqps5lgn9zbxyi13h0ijd1cxszk7x-n8n-1.57.0 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A n8n https://github.com/r-ryantm/nixpkgs/archive/56ba562feb21fa93dd48b4e17864cae98fee7b59.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/56ba562feb21fa93dd48b4e17864cae98fee7b59#n8n

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/wz0qqps5lgn9zbxyi13h0ijd1cxszk7x-n8n-1.57.0
ls -la /nix/store/wz0qqps5lgn9zbxyi13h0ijd1cxszk7x-n8n-1.57.0/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review run on x86_64-linux 1

1 package built:

n8n

Maintainer pings
cc @freezeboy @gepbird @K900 for testing.

[!TIP]
As a maintainer, if your package is located under pkgs/by-name/*, you can comment @NixOS/nixpkgs-merge-bot merge to automatically merge this update using the nixpkgs-merge-bot.

Add a :+1: reaction to pull requests you find important.

Is there any way to view the log of the failing test? It's not in https://r.ryantm.com/log/n8n/2024-09-09.log.
The test passes for me.

vm-test-run-n8n> test script finished in 148.11s

@ofborg build nixosTests.n8n

Most likely unrelated to this PR:

   Failed assertions:
   - Setting virtualisation.diskSize to `auto` is not supported by the current image build or vm runner; use an explicit size.

@NixOS/nixpkgs-merge-bot merge


Create new C++ Boost.Test repository for Test Adapter

Create a new repository which consists of sample Boost.Test use cases for the Boost Unit Test Adapter. The core goal is to create a set of tests which will define the 'Acceptance Criteria' for future Boost Unit Test Adapter releases.
Hint(s):

Consider making use of the examples available in the Boost.Test GitHub repository.
Tests should not consider solely general use, but also use cases which cover the use of '.runsettings' configuration, varying boost versions etc.

Bonus:

Consider automating testing through the use of scripts and vstest.console.exe (if possible).

@netspiri think would be better to contribute directly to the Boost.Test repository and add some command line tests there. This ensures a stable interface before they release a new version. Doing it here we will run typically into the problem that our feedback comes too late.

@netspiri think is a good idea but would do it no more here in this repository. Let's do it in the Microsoft repository for VS2017.


Add translation guide + update repo structure

Triggered by https://github.com/huggingface/huggingface_hub/issues/1601 and private slack thread.
This PR adds:

a docs/source/en/ folder in which all current documentation had been moved
a docs/README.md guide to explain how to write docs (adapted from transformers)
a docs/TRANSLATING.md guide to explain how to start translating to a new language (adapted from transformers)
a .github/ISSUE_TEMPLATE/i18n.md template to create a new translation issue
a new install group (pip install -e ".[docs]")

The goal is to start translating huggingface_hub's docs to other languages like for transformers and diffusers libraries.

Would love to! We'll start as soon as possible. Thank you for the heads up, @LysandreJik !
Much love from Korea,
Won

Thanks for the review @LysandreJik @stevhliu. I'll merge this PR asap so that future PRs are not impacted by it. I'll work on event/promoting it once I'm done with unpiling my notifications after my time off :)


Revert "change debug to info"

Reverts ONSdigital/rm-collection-exercise-service#326
This PR needed to be reverted because I only changed the debugging levels for the purpose of testing things out in preprod, but we don't want these logging statements showing up in prod.
To test, run acceptance tests and check the logs for the pod.

/deploy wilkia


Openbullet - Captcha Tronix

how to use captchatronix on openbullet ??
no have api key ..
just have username , password , domain , port

+1
It'd be nice if we see captchatronix implemented.


"Internal error" with SDK Version 30

I try to show interstitial ad in my app with Plugin version 3.2.0. It works with
compileSdkVersion = 29
targetSdkVersion = 29

But when I set it to 30, I get "Internal error" from function prepareInterstitial. No further details.
I found this thread:
https://stackoverflow.com/questions/38378002/admob-ads-not-loading-failed-to-load-ad-0/63257140#63257140
The user Donovan Phoenix states, that there are bugs with SDK version 30:
https://github.com/googleads/googleads-mobile-android-examples/issues/265
https://issuetracker.google.com/issues/163432178
Is there a workaround for this? Do I have to go back to SDK 29?
Thank you all for your help and for this great plugin!

I think you should go back until a SDK fix is released by Google.

Ok, thank you.
Should we leave this issue open until it is fixed by Google?
Should this not be mentioned in the docs of this plugin as known issue? Took me a few hours to find out, that everything is fine with my code and my AdMob config.

To be honest this is the first time I heard about it. I will let this issue open and pin it until a fix comes. :)

It`s not possible to upload targetSdkVersion = 29 apps to Play Console anymore:

Is there a workaround? AdMob ads are working on Android 12. Android 11 shows "Internal error". Is there a workaround?  I would be suprised then, that I`m the first one submitting this issue. It's a showstopper.

In my app everything is working. But I haven't update it in a while.
Can you reproduce this behavior with the demo project?

@Schwankenson can you create a GitHub repo where this error happens? I tried to reproduce it with the emulator but I was not able to...

I tried it with your demo project. Everything works. Seems to be a problem specific to my configuration. I`m still on Angular 10 and Ionic 5. Could this be the reason? I think you can unpin this task, it does not seem to be a generalist error.
I try to generate a GitHub Repo with this error happening, but it is going to take me some time.

No, I do not think the angular/Ionic version is a problem here.

No idea really. The only way to discover it is looking at the stack trace

@Schwankenson Is this the only plugin you are using? There is a possibility of interference between plugins.
Or you can try to remove android folder and new npx cap add android .
I hope this is helpful to you.

@rdlabo I`m using much more plugins:
implementation project(':capacitor-community-admob')
implementation project(':capacitor-community-fcm')
implementation project(':capacitor-community-firebase-analytics')
implementation project(':capacitor-app')
implementation project(':capacitor-app-launcher')
implementation project(':capacitor-browser')
implementation project(':capacitor-device')
implementation project(':capacitor-push-notifications')
implementation project(':capacitor-splash-screen')
implementation project(':capacitor-status-bar')
implementation "com.android.billingclient:billing:3.0.0"

The regeneration of the app is a good idea. I will try that.


Faster, safer Sets

Basic idea is to make an alternative Set class which bings the Ord at construction time (to keep coherency - hence the safer) and eventually is optimized for membership test if the Ord is a stringOrd / numberOrd via an internal set of keys or maybe a Map (hence to faster).
I'm wondering if that could be part of the lib - or not.
Note: Actually StrMap may be used.

Based on false premises on safety, closing


Scaffold.of() called with a context that does not contain a Scaffold.

Scaffold.of() called with a context that does not contain a Scaffold.

Maybe you can solve this problem by adding ScaffoldStateGlobalKey.

@tenSunFree
Thank you for your advice. That's correct.
But I want to think more about how using Scackbar with Riverpod. So now I don't use the Snackbar this time 🤔


Modify payload formatters according to the LoRaWAN® Codec API specification

See https://resources.lora-alliance.org/technical-specifications/ts013-1-0-0-payload-codec-api
[X] Check existing scripts for standard compliance
[X] Create metadata.json file
[X] Create examples
[ ] Merge uplink_formatter.js and downlink_formatter.js into index.js
[ ] Create npm package

Not sure if and when I will complete this.


allow dispose operations to be carried out with the value in AutoClea…

…redValue.kt before the value is set to null.
This is because onDestroy of the DefaultLifecycleObserver associated with the viewLifeCycle in AutoClearedValue.kt, is called before that of the fragment. Trying to access the auto cleared value in Fragment's onDestroyView will cause an IllegalStateException.
Eg usage:
private var binding: FragmentDeviceVerificationBinding by autoDispose {         //this==FragmentDeviceVerificationBinding         resendCode.cancelTimer()     }
the timer will get cancelled and then the binding will be set to null afterwards.
There's also a safeBind extension that catches the IllegalStateException when accessing binding classes. It's for use in tricky cases where one of the Fragment's lifecycle callbacks doesn't return as expected and you don't want your app to crash.

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@googlebot I signed it!

@JoseAlcerreca @ianhanniballake @dlam @yigit please can you review PR?

You don't need this. Just add your own LifecycleObserver on the viewLifecycleOwner - since Observers are run first in, last out order, it'll run before the AutoCleared clears the object, allowing you to do final clean up.
Please make sure your pull requests serve just a single purpose - safeBind is an independent change that should be its own pull request. However, safeBind is fundamentally flawed and an indication that your design is already causing callbacks to happen after you expect (i.e., you didn't use the coroutineScope associated with the viewLifecycleOwner to cancel your work, etc). Crashing is absolutely what you should be doing all of the time.

Thanks @ianhanniballake

@ianhanniballake I got this issue and tried adding an observer to viewLifecycleOwner to clear viewDataBinding components but viewDataBinding is always null when my observer got notified. Could you give me some advices about it

The autoClearedValue delegate will clear your view binding class in onDestroyView @iTanChi

@Ezike Yes I understand, I use autoClearedValue for my viewDataBinding and it works perfectly but in some cases I need to clear my viewDataBinding's components before viewDataBinding is cleared. From @ianhanniballake suggestion, I add another observer to viewLifeCyclerOwner and clear my viewDataBinding's components when my observer is notified but whenever it's notified, viewDataBinding is null so I can not access to it's components

@iTanChi I was able to write something based on @ianhanniballake 's advice.
fun Fragment.cleanupResources(action: () -> Unit) {     viewLifecycleOwnerLiveData.observe(viewLifecycleOwner) { owner: LifecycleOwner ->         owner.lifecycle.addObserver(             object : DefaultLifecycleObserver {                 override fun onDestroy(owner: LifecycleOwner) {                     action()                 }             })     } }
You can call it like this:
 override fun onViewCreated(view: View, savedInstanceState: Bundle?) {         super.onViewCreated(view, savedInstanceState)         cleanupResources {              // put your cleanup code here             } }

@Ezike weird, I do a similar thing but my viewDataBinding is null so I can't access to it's components

@iTanChi this works for me. Should for you too..
As @ianhanniballake said, the observers are registered first in last out, so while the AutoClearedValue is registered first, it'll be the last to run, which then allows any other observers to run before AutoCleared sets the ViewBinding reference to null.


bug/fetch_first_blocks

First 2242 blocks does not fetch correctly from the gateway: https://github.com/KasarLabs/deoxys/blob/dev/crates/client/deoxys/src/lib.rs#L81
returning this error:
Block processing thread started
[2023-06-13T08:30:47Z INFO  mc_deoxys] Try next block at height #2242
thread 'tests::test_fetch_block' panicked at 'called `Option::unwrap()` on a `None` value', crates/client/deoxys/src/lib.rs:21:94

Merged in dev


Update grub2.rb to add On UEFI Systems, grub.cfg

On UEFI Systems, grub.cfg will be located at: /boot/efi/EFI/distribution/grub.cfg
For example, On RedHat UEFI-based systems, the configuration file is /boot/efi/EFI/redhat/grub.cfg.
/etc/grub2-efi.cfg is a symlink to that EFI File and that's the one I modified to avoid the following error on UEFI RHEL7 Systems and update grub configuration
Could not evaluate: Cannot find grub.cfg location to use with grub-mkconfig

Coverage remained the same at 96.226% when pulling 16e587ff147a8ed0956151fcf279f4e532a2d884 on stivesso:master into 36d078938cc152271e26b30b68c908e5b2b6bc03 on hercules-team:master.

:+1: Looks like a reasonable change to me.


I use UIButton+WebCache, When the button highlighted the image get the wrong  direction

i use UIButton+WebCache, When i touch the button down make the button state turn to highlighted, there is some special image will change the image direction(such as url: http://www.bat360.cn/pics/72af292d-be5f-45f3-95b5-6773abb84550file33672947481238490124)
my button size is (258.0/3.0, 258.0/3.0)
my code at below:
showImageBtn.sd_setBackgroundImageWithURL(NSURL(string: imgPath), forState: .Normal)

i hope you are not using the full image from that url as a background of the button.
That image is 3042x4032  (width x height).

@mythodeia
Thank you for your answer.


Issue with yarn start

start and build function in package.json dont seem to work.

@harrychaklader have you been able to solve your issue? Try to give more context if you can, ie: screenshots, code examples, etc.. There are multiple package.json files in the project repo (it is a monorepo setup), the root package.json just references the others.

It  show this error after i run yarn start

It show this error after i run yarn start

use this cmd
export NODE_OPTIONS=--openssl-legacy-provider

In your package.json go to your "scripts" section and change the start and build commands.
"start": "react-scripts --openssl-legacy-provider start",
"build": "react-scripts --openssl-legacy-provider build"
this should be what you change them to, not sure if running export NODE_OPTIONS=--openssl-legacy-provider will help or not, but I got mine to work by switching the package.json scripts.

In your package.json go to your "scripts" section and change the start and build commands.
"start":` "react-scripts --openssl-legacy-provider start", "build": "react-scripts --openssl-legacy-provider `build"
this should be what you change them to, not sure if running export NODE_OPTIONS=--openssl-legacy-provider will help or not, but I got mine to work by switching the package.json scripts.

yeah this one is a better approach then mine you need to run it every time you restart the terminal window
@mblaw1011 I recommend this


Bugfix: fix url parsing

:warning: Please install the  to ensure uploads and comments are reliably processed by Codecov.
Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 66.98%. Comparing base (be7c018) to head (c5657dc).

:exclamation: Your organization needs to install the Codecov GitHub app to enable full functionality.
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #30      +/-   ##
==========================================
+ Coverage   66.60%   66.98%   +0.38%
==========================================
  Files          14       14
  Lines        1042     1054      +12
==========================================
+ Hits          694      706      +12
  Misses        309      309
  Partials       39       39

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fix: https://github.com/XiaoConstantine/mycli/issues/29


Cannot run bot error

Describe the bug
I made the json file using the html builder and overwrited with the original json file.
But when I run the python file, it shows this error:
File "c-realV2.py", line 403
if not n.isdigit() or (n := int(n) - 1) < 0:
^
helP!!

Can you copy and paste all the error messages? I can't tell what's wrong with these you gave me. And what did you do to get to this bug?


create a digest email for Cecilia with email addresses extracted from the papers and not linked to any person ID

@valearna will match the extracted e-mail address with the e-mail address in WormBase. If different, a report will be sent to Cecilia

not necessary at this point


Fix instantiation of records with multiple parameters

This PR fixes RecordInstantiator, which is calling a record constructor with incorrectly ordered parameters.

Would you mind elaborating a bit on what you think is broken with the current implementation? It feels a bit weird to change the existing tests in combination with the actual implementation, because it means that we can't verify whether the proposed change will still work for the previous test case. Does it make sense to add a new test case instead of changing the current one?

I think it's broken, because sorting record parameters alphabetically and mapping parameters array from Hibernate doesn't mean that parameters will be correctly sorted to pass them to a record constructor.
It's difficult for me to explain it, please modify the current test case on the main branch by adding an age field:
    @Test // #98, #125
    void instantiatesRecord() {

        RecordInstantiator instantiator = new RecordInstantiator(Person.class);

        Object[] values = RecordInstantiator.IS_AFFECTED_HIBERNATE_VERSION
                ? new Object[] { "Matthews", 22, "Dave" }
                : new Object[] { 22, "Dave", "Matthews" };

        ValueAccess access = mock(ValueAccess.class);
        doReturn(values).when(access).getValues();

        assertThat(instantiator.instantiate(access, null))
                .isEqualTo(new Person("Matthews", 22, "Dave"));
    }

    record Person(String lastname, int age, String firstname) {}

The test will fail, as parameters won't be sorted correctly to instantiate a Person record. If you use a RecordInstantiator from my PR, the test will pass.
Sure, I will add my test case as a new one, next to the original test case.

That's been very helpful, thanks. I now understand the issue with the original algorithm. I have a simplified version of your corrected algorithm locally here, which I am going to commit against this ticket.

I'm happy you found a better way to fix it. Thanks!


Remove hack used to disable Predictable Network Interface naming

See related:

https://github.com/geerlingguy/packer-ubuntu-1604/issues/1
https://github.com/mitchellh/vagrant/pull/7241
https://github.com/chef/bento/pull/545

Note: it seems VirtualBox 5.1.2 and Vagrant 1.8.5 with a freshly-built Packer box (not just this one, but all my boxes, with the exact same config that was working with VirtualBox 5.0.24) is resulting in the host-only network/private network interface not being brought up.
Looking at debug level output, it seems the hostonly adapter is brought up correctly:
...
Name:            vboxnet26
GUID:            786f6276-656e-4274-b600-0a002700001a
DHCP:            Disabled
IPAddress:       <IP_ADDRESS>
NetworkMask:     <IP_ADDRESS>
IPV6Address:
IPV6NetworkMaskPrefixLength: 0
HardwareAddress: 0a:00:27:00:00:1a
MediumType:      Ethernet
Status:          Up
VBoxNetworkName: HostInterfaceNetworking-vboxnet26
...
DEBUG subprocess: Waiting for process to exit. Remaining to timeout: 32000
DEBUG subprocess: Exit status: 0
DEBUG network: Adapter configuration: {:adapter=>2, :hostonly=>"vboxnet26", :mac_address=>nil, :nic_type=>nil, :type=>:hostonly}
 INFO network: Enabling adapters...
 INFO interface: output: Preparing network interfaces based on configuration...
 INFO interface: output: ==> ubuntu1604: Preparing network interfaces based on configuration...
==> ubuntu1604: Preparing network interfaces based on configuration...
 INFO interface: detail: Adapter 1: nat
 INFO interface: detail:     ubuntu1604: Adapter 1: nat
    ubuntu1604: Adapter 1: nat
 INFO interface: detail: Adapter 2: hostonly
 INFO interface: detail:     ubuntu1604: Adapter 2: hostonly
    ubuntu1604: Adapter 2: hostonly
 INFO subprocess: Starting process: ["/usr/local/bin/VBoxManage", "modifyvm", "a6adba53-7e78-47c2-8c81-8aa67e3e42ed", "--nic1", "nat", "--nic2", "hostonly", "--hostonlyadapter2", "vboxnet26", "--cableconnected2", "on"]
DEBUG subprocess: Command not in installer, not touching env vars.
 INFO subprocess: Command not in installer, restoring original environment...
DEBUG subprocess: Selecting on IO
DEBUG subprocess: Waiting for process to exit. Remaining to timeout: 32000
DEBUG subprocess: Exit status: 0
 INFO warden: Calling IN action: #<VagrantPlugins::ProviderVirtualBox::Action::NetworkFixIPv6:0x00000102976320>
 INFO warden: Calling IN action: #<VagrantPlugins::ProviderVirtualBox::Action::ForwardPorts:0x00000100e0f898>
 INFO interface: output: Forwarding ports...
 INFO interface: output: ==> ubuntu1604: Forwarding ports...
==> ubuntu1604: Forwarding ports...

The output from the vagrant up command that now fails:
$ vagrant up ubuntu1604 --provider=virtualbox
Bringing machine 'ubuntu1604' up with 'virtualbox' provider...
==> ubuntu1604: Clearing any previously set forwarded ports...
==> ubuntu1604: Pruning invalid NFS exports. Administrator privileges will be required...
==> ubuntu1604: Clearing any previously set network interfaces...
==> ubuntu1604: Preparing network interfaces based on configuration...
    ubuntu1604: Adapter 1: nat
    ubuntu1604: Adapter 2: hostonly
==> ubuntu1604: Forwarding ports...
    ubuntu1604: 22 (guest) => 2222 (host) (adapter 1)
==> ubuntu1604: Running 'pre-boot' VM customizations...
==> ubuntu1604: Booting VM...
==> ubuntu1604: Waiting for machine to boot. This may take a few minutes...
    ubuntu1604: SSH address: <IP_ADDRESS>:2222
    ubuntu1604: SSH username: vagrant
    ubuntu1604: SSH auth method: private key
Timed out while waiting for the machine to boot. This means that
Vagrant was unable to communicate with the guest machine within
the configured ("config.vm.boot_timeout" value) time period.

If you look above, you should be able to see the error(s) that
Vagrant had when attempting to connect to the machine. These errors
are usually good hints as to what may be wrong.

If you're using a custom box, make sure that networking is properly
working and you're able to connect to the machine. It is a common
problem that networking isn't setup properly in these boxes.
Verify that authentication configurations are also setup properly,
as well.

If the box appears to be booting properly, you may want to increase
the timeout ("config.vm.boot_timeout") value.

During boot, if I inspect the VirtualBox console using v.gui = true, then I see the following timeout after 5 minutes:
a start job is running for raise network interfaces

Pictorially:

So something's not getting configured inside the VM correctly.
Glancing at the VM settings inside VirtualBox's GUI, everything seems correct with the 2nd network interface/adapter:

Inside the VM:

ip a returns lo, eth0, and eth1, but none have an IP4 address.
/etc/network/interfaces has an entry for auto eth1 with iface eth1 inet manual

I'm going to bring up a working 16.04 VM with my latest (old) published release and see if I can spot any differences.

I'm going to try to revert the hack from #1 and see if just doing that works with Vagrant 1.8.5... maybe the manual network changes were causing an issue (but it seems they shouldn't be an issue, since the same config worked and still works in the previous build for the same box.

Removing the hack seems to work-ish... but it still doesn't allow SSH to connect.
Tried running sudo ifup enp0s3 but that just looped in the 'waiting for DHCP' segment for a while.
I'm wondering if https://github.com/mitchellh/vagrant/issues/6683 is still not fully resolved :-/
But the weirdest thing is, why is the older box that was generated with VirtualBox 5.0.24 working fine in 5.1.2, but a box with the exact same config generated in 5.1.2 isn't?
I'm also going to switch back to Ubuntu 16.04.0 (I switched to .1) and see if that helps. But it seems like it won't—Vagrant isn't happy connecting to any of my new boxes, CentOS 6/7, Ubuntu 12/14/16, if I build them in 5.1.2.

Just stumbled over the same issue myself (networking broken after updating to Vagrant 1.8.5 and VirtualBox 5.1). I'll downgrade and see what happens.

@Jalle19 - :(
Yeah, after spending about 4 hours on this a couple weeks ago, I haven't had the time to devote to digging deep and finding the exact issue.

Me neither, I downgraded back to Vagrant 1.8.4 and VirtualBox 5.0.22 for now (newer VirtualBox 5.0 releases have the networking bug which can cause provisioning to stall unless you start pinging something from the virtual machine).

Possibly related:

https://github.com/mitchellh/vagrant/pull/7524
https://github.com/mitchellh/vagrant/issues/7610 (but that's likely a different issue)
https://github.com/mitchellh/vagrant/issues/7613
https://github.com/mitchellh/vagrant/issues/7668

Hi @geerlingguy! I'm curious if the problem you're hitting may be resolved by mitchellh/vagrant#7705. If you have a chance to give it a try, I'd be interested to know if it fixes things up. Thanks!

@chrisroberts - Unfortunately with some crazy life events happening right now, I'm going to have to wait to test things out—if there's a new Vagrant release (1.8.6) soon, that could expedite things, but until that happens I am putting updating any of my base boxes on hold, because even if it does solve the issue (it seems like it will), I'd rather not require those using my public boxes have to apply patches to Vagrant to keep working.
For now, the existing versions of my boxes are working, and I've already burned a bit too much time on this issue :P

But THANK YOU for posting that, and for referencing the upstream issue. I think that could be the problem, just looking over the details, what changed, etc.

I had a similar issue where the "Cable connected" checkbox was not checked for the NAT interface, and by generating the box with VirtualBox 5.0.26, it's now working.

The hack was removed in https://github.com/geerlingguy/packer-ubuntu-1604/commit/9455d865a13490e03d7779aee5c04a23d43ec3e5, and I'm going to leave it out; it seems VirtualBox is working fine now, though I'm hitting a snag with VMware Fusion 8.5 builds. So I'll open a separate issue for that.

I confirm that it has been fixed in VirtualBox 5.1.6.

@MiLk - Thanks! I just tested in 5.1.8 and built a new base box, and it seems to be working well now.


vcf_anno fails on exome validation NA12878 when annotating ensemble calls VCF

Hi, I'm trying to run an exome validation workflow on NA12878.  I'm seeing this error:
subprocess.CalledProcessError: Command 'set -o pipefail; gunzip -c /Shared/Bioinformatics/data/mchiment/bcbio_testbed/NA12878_exome_eval/work/gemini/NA12878-1-freebayes.vcf.gz | bcftools view -f 'PASS,.' | vcfallelicprimitives -t DECOMPOSED --keep-geno | sed 's/ID=AD,Number=./ID=AD,Number=R/' | vt decompose -s -  | vt normalize -n -r /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/seq/hg38.fa -  | awk '{ gsub("./-65", "./."); print $0 }' | sed -e 's/Number=A/Number=1/g' | bgzip -c > /Shared/Bioinformatics/data/mchiment/bcbio_testbed/NA12878_exome_eval/work/bcbiotx/tmp0xAqeB/NA12878-1-freebayes-decompose.vcf.gz
The previous logs steps right up to this error look like this:
[2018-06-28T18:15Z] vcfanno.go:241: annotated 147568 variants in 130.62 seconds (1129.8 / second)
[2018-06-28T18:15Z] tabix index NA12878-1-ensemble-nomultiallelic-annotated-gemini.vcf.gz
[2018-06-28T18:15Z] GEMINI: create database with vcf2db
[2018-06-28T18:15Z] skipping 'DP4' because it has Number=4
[2018-06-28T18:15Z] /Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:226: SAWarning: Unicode type received non-unicode bind param value ''. (this warning may be suppressed after 10 occurrences)
[2018-06-28T18:15Z]   (util.ellipses_string(value),))
[2018-06-28T18:15Z] /Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:226: SAWarning: Unicode type received non-unicode bind param value '-9'. (this warning may be suppressed after 10 occurrences)
[2018-06-28T18:15Z]   (util.ellipses_string(value),))
[2018-06-28T18:15Z] /Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:226: SAWarning: Unicode type received non-unicode bind param value '2'. (this warning may be suppressed after 10 occurrences)
[2018-06-28T18:15Z]   (util.ellipses_string(value),))
[2018-06-28T18:15Z] 10000 variant_impacts:69603	effects time: 8.8	chunk time:14.8	675.06 variants/second
[2018-06-28T18:15Z] 20000 variant_impacts:60427	effects time: 7.5	chunk time:12.8	724.85 variants/second
[2018-06-28T18:15Z] 30000 variant_impacts:71424	effects time: 8.7	chunk time:14.4	714.66 variants/second
[2018-06-28T18:16Z] 40000 variant_impacts:66450	effects time: 8.1	chunk time:14.6	706.38 variants/second
[2018-06-28T18:16Z] 50000 variant_impacts:71328	effects time: 8.8	chunk time:14.2	705.81 variants/second
[2018-06-28T18:16Z] 60000 variant_impacts:60540	effects time: 7.6	chunk time:12.7	718.23 variants/second
[2018-06-28T18:16Z] 70000 variant_impacts:65614	effects time: 8.0	chunk time:13.4	722.23 variants/second
[2018-06-28T18:17Z] 80000 variant_impacts:57211	effects time: 7.2	chunk time:12.2	733.14 variants/second
[2018-06-28T18:17Z] 90000 variant_impacts:77636	effects time: 9.4	chunk time:15.2	724.00 variants/second
[2018-06-28T18:17Z] 100000 variant_impacts:67594	effects time: 8.4	chunk time:14.1	722.52 variants/second
[2018-06-28T18:18Z] indexing ... finished in 4.7 seconds...
[2018-06-28T18:18Z] total time: in 216.9 seconds...
[2018-06-28T18:18Z] Multi-allelic to single allele
[2018-06-28T18:18Z] normalize vdecompose v0.50.5
[2018-06-28T18:18Z] options:     input VCF file        options:     input VCF file                                  --
[2018-06-28T18:18Z]          [o] output VCF file                                          [s] smart decomposition   -
[2018-06-28T18:18Z] true         [w] sorting window size                              (experimental)
[2018-06-28T18:18Z]          [o] output VCF file       -
[2018-06-28T18:18Z] 10000
[2018-06-28T18:18Z]          [n] no fail on reference inconsistency for non SNPs true
[2018-06-28T18:18Z]          [q] quiet                                           false
[2018-06-28T18:18Z]          [d] debug                                           false
[2018-06-28T18:18Z]          [r] reference FASTA file                            /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/seq/hg38.fa
[2018-06-28T18:18Z] [variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: 1:761956-761956
[2018-06-28T18:18Z] FAQ: http://genome.sph.umich.edu/wiki/Vt#1._vt_cannot_retrieve_sequences_from_my_reference_sequence_file
[2018-06-28T18:19Z] stats: no. variants                 : 148798
[2018-06-28T18:19Z]        no. biallelic variants       : 148332
[2018-06-28T18:19Z] Uncaught exception occurred

I'm running with this configuration:

upload:
dir: ../final
details:

files: [../input/NA12878_20180111000_S51_L002_R1_001.fastq.gz, ../input/NA12878_20180111000_S51_L002_R2_001.fastq.gz]
description: NA12878-1
metadata:
sex: female
analysis: variant2
genome_build: hg38
algorithm:
aligner: bwa
variantcaller: [freebayes, gatk-haplotype, samtools]
validate: giab-NA12878/truth_small_variants.vcf.gz
validate_regions: giab-NA12878/truth_regions.bed
variant_regions: /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/coverage/coding/ccds.bed.gz
ensemble:
numpass: 2

Any insights are appreciated.  I don't really understand the error or the traceback.  It seems somewhat opaque.

Here is the full traceback and log:

cat exome7.o9530150
[2018-06-28T18:06Z] System YAML configuration: /Dedicated/IIHG-argon/bcbio-1.0.9/galaxy/bcbio_system.yaml
[2018-06-28T18:06Z] Resource requests: bwa, sambamba, samtools; memory: 3.00, 3.00, 3.00; cores: 16, 16, 16
[2018-06-28T18:06Z] Configuring 1 jobs to run, using 16 cores each with 48.1g of memory reserved for each job
[2018-06-28T18:06Z] Timing: organize samples
[2018-06-28T18:06Z] multiprocessing: organize_samples
[2018-06-28T18:06Z] Using input YAML configuration: /Shared/Bioinformatics/data/mchiment/bcbio_testbed/NA12878_exome_eval/config/NA12878-exome-methodcmp.yaml
[2018-06-28T18:06Z] Checking sample YAML configuration: /Shared/Bioinformatics/data/mchiment/bcbio_testbed/NA12878_exome_eval/config/NA12878-exome-methodcmp.yaml
[2018-06-28T18:06Z] Testing minimum versions of installed programs
[2018-06-28T18:06Z] Timing: alignment preparation
[2018-06-28T18:06Z] multiprocessing: prep_align_inputs
[2018-06-28T18:06Z] Skipping trimming of NA12878-1.
[2018-06-28T18:06Z] Resource requests: ; memory: 1.00; cores: 1
[2018-06-28T18:06Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2018-06-28T18:06Z] multiprocessing: disambiguate_split
[2018-06-28T18:06Z] Timing: alignment
[2018-06-28T18:06Z] multiprocessing: process_alignment
[2018-06-28T18:06Z] Aligning lane NA12878-1 with bwa aligner
[2018-06-28T18:06Z] Aligning lane NA12878-1 with bwa aligner
[2018-06-28T18:06Z] Aligning lane NA12878-1 with bwa aligner
[2018-06-28T18:06Z] Aligning lane NA12878-1 with bwa aligner
[2018-06-28T18:06Z] multiprocessing: delayed_bam_merge
[2018-06-28T18:06Z] Timing: callable regions
[2018-06-28T18:06Z] multiprocessing: prep_samples
[2018-06-28T18:06Z] multiprocessing: postprocess_alignment
[2018-06-28T18:06Z] NA12878-1: Assigned coverage as 'regional' with 1.0% genome coverage and 100.0% offtarget coverage
[2018-06-28T18:06Z] multiprocessing: combine_sample_regions
[2018-06-28T18:06Z] Identified 203 parallel analysis blocks
Block sizes:
min: 399526
5%: 8535086.2
25%: 15511990.5
median: 15538080.0
75%: 15639625.5
95%: 16416550.2
99%: 32839507.58
max: 42431749
Between block sizes:
min: 252
5%: 293.8
25%: 1260.0
median: 4933.0
75%: 56240.0
95%: 469126.3
99%: 1409057.62
max: 1561454
[2018-06-28T18:06Z] multiprocessing: calculate_sv_bins
[2018-06-28T18:06Z] multiprocessing: calculate_sv_coverage
[2018-06-28T18:06Z] multiprocessing: normalize_sv_coverage
[2018-06-28T18:06Z] Timing: hla typing
[2018-06-28T18:06Z] Resource requests: freebayes, gatk, gatk-haplotype, picard, samtools; memory: 3.00, 3.50, 3.00, 3.00, 3.00; cores: 16, 1, 16, 16, 16
[2018-06-28T18:06Z] Configuring 28 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2018-06-28T18:06Z] Timing: alignment post-processing
[2018-06-28T18:06Z] multiprocessing: piped_bamprep
mchiment@argon-login-1: work$ cat exome7.o9530150
[2018-06-28T18:06Z] System YAML configuration: /Dedicated/IIHG-argon/bcbio-1.0.9/galaxy/bcbio_system.yaml
[2018-06-28T18:06Z] Resource requests: bwa, sambamba, samtools; memory: 3.00, 3.00, 3.00; cores: 16, 16, 16
[2018-06-28T18:06Z] Configuring 1 jobs to run, using 16 cores each with 48.1g of memory reserved for each job
[2018-06-28T18:06Z] Timing: organize samples
[2018-06-28T18:06Z] multiprocessing: organize_samples
[2018-06-28T18:06Z] Using input YAML configuration: /Shared/Bioinformatics/data/mchiment/bcbio_testbed/NA12878_exome_eval/config/NA12878-exome-methodcmp.yaml
[2018-06-28T18:06Z] Checking sample YAML configuration: /Shared/Bioinformatics/data/mchiment/bcbio_testbed/NA12878_exome_eval/config/NA12878-exome-methodcmp.yaml
[2018-06-28T18:06Z] Testing minimum versions of installed programs
[2018-06-28T18:06Z] Timing: alignment preparation
[2018-06-28T18:06Z] multiprocessing: prep_align_inputs
[2018-06-28T18:06Z] Skipping trimming of NA12878-1.
[2018-06-28T18:06Z] Resource requests: ; memory: 1.00; cores: 1
[2018-06-28T18:06Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2018-06-28T18:06Z] multiprocessing: disambiguate_split
[2018-06-28T18:06Z] Timing: alignment
[2018-06-28T18:06Z] multiprocessing: process_alignment
[2018-06-28T18:06Z] Aligning lane NA12878-1 with bwa aligner
[2018-06-28T18:06Z] Aligning lane NA12878-1 with bwa aligner
[2018-06-28T18:06Z] Aligning lane NA12878-1 with bwa aligner
[2018-06-28T18:06Z] Aligning lane NA12878-1 with bwa aligner
[2018-06-28T18:06Z] multiprocessing: delayed_bam_merge
[2018-06-28T18:06Z] Timing: callable regions
[2018-06-28T18:06Z] multiprocessing: prep_samples
[2018-06-28T18:06Z] multiprocessing: postprocess_alignment
[2018-06-28T18:06Z] NA12878-1: Assigned coverage as 'regional' with 1.0% genome coverage and 100.0% offtarget coverage
[2018-06-28T18:06Z] multiprocessing: combine_sample_regions
[2018-06-28T18:06Z] Identified 203 parallel analysis blocks
Block sizes:
min: 399526
5%: 8535086.2
25%: 15511990.5
median: 15538080.0
75%: 15639625.5
95%: 16416550.2
99%: 32839507.58
max: 42431749
Between block sizes:
min: 252
5%: 293.8
25%: 1260.0
median: 4933.0
75%: 56240.0
95%: 469126.3
99%: 1409057.62
max: 1561454
[2018-06-28T18:06Z] multiprocessing: calculate_sv_bins
[2018-06-28T18:06Z] multiprocessing: calculate_sv_coverage
[2018-06-28T18:06Z] multiprocessing: normalize_sv_coverage
[2018-06-28T18:06Z] Timing: hla typing
[2018-06-28T18:06Z] Resource requests: freebayes, gatk, gatk-haplotype, picard, samtools; memory: 3.00, 3.50, 3.00, 3.00, 3.00; cores: 16, 1, 16, 16, 16
[2018-06-28T18:06Z] Configuring 28 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2018-06-28T18:06Z] Timing: alignment post-processing
[2018-06-28T18:06Z] multiprocessing: piped_bamprep
/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/joblib/externals/loky/process_executor.py:630: UserWarning: A worker timeout while some jobs were given to the executor. You might want to use a longer timeout for the executor.
"the executor.", UserWarning
[2018-06-28T18:12Z] Timing: variant calling
[2018-06-28T18:12Z] multiprocessing: variantcall_sample
[2018-06-28T18:12Z] multiprocessing: concat_variant_files
[2018-06-28T18:12Z] Resource requests: bcbio_variation, fastqc, gatk, gemini, kraken, preseq, qsignature, sambamba, samtools, snpeff; memory: 3.00, 3.00, 3.50, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00; cores: 16, 16, 1, 16, 16, 16, 16, 16, 16, 1
[2018-06-28T18:12Z] Configuring 1 jobs to run, using 16 cores each with 56.1g of memory reserved for each job
[2018-06-28T18:12Z] Timing: joint squaring off/backfilling
[2018-06-28T18:12Z] Timing: variant post-processing
[2018-06-28T18:12Z] multiprocessing: postprocess_variants
[2018-06-28T18:12Z] Finalizing variant calls: NA12878-1, freebayes
[2018-06-28T18:12Z] Calculating variation effects for NA12878-1, freebayes
[2018-06-28T18:12Z] Annotate VCF file: NA12878-1, freebayes
[2018-06-28T18:12Z] Filtering for NA12878-1, freebayes
[2018-06-28T18:12Z] Prioritization for NA12878-1, freebayes
[2018-06-28T18:12Z] Finalizing variant calls: NA12878-1, gatk-haplotype
[2018-06-28T18:12Z] Calculating variation effects for NA12878-1, gatk-haplotype
[2018-06-28T18:12Z] Annotate VCF file: NA12878-1, gatk-haplotype
[2018-06-28T18:12Z] Filtering for NA12878-1, gatk-haplotype
[2018-06-28T18:12Z] Prioritization for NA12878-1, gatk-haplotype
[2018-06-28T18:12Z] Finalizing variant calls: NA12878-1, samtools
[2018-06-28T18:12Z] Calculating variation effects for NA12878-1, samtools
[2018-06-28T18:12Z] Annotate VCF file: NA12878-1, samtools
[2018-06-28T18:12Z] Filtering for NA12878-1, samtools
[2018-06-28T18:12Z] Prioritization for NA12878-1, samtools
[2018-06-28T18:12Z] multiprocessing: split_variants_by_sample
[2018-06-28T18:12Z] Timing: prepped BAM merging
[2018-06-28T18:12Z] Timing: validation
[2018-06-28T18:12Z] multiprocessing: compare_to_rm
[2018-06-28T18:12Z] Timing: ensemble calling
[2018-06-28T18:12Z] multiprocessing: combine_calls
[2018-06-28T18:12Z] Ensemble consensus calls for NA12878-1: freebayes,gatk-haplotype,samtools
[2018-06-28T18:12Z] Timing: validation summary
[2018-06-28T18:12Z] Timing: structural variation precall
[2018-06-28T18:12Z] Timing: structural variation
[2018-06-28T18:12Z] Timing: structural variation
[2018-06-28T18:12Z] Timing: structural variation ensemble
[2018-06-28T18:12Z] Timing: structural variation validation
[2018-06-28T18:12Z] multiprocessing: validate_sv
[2018-06-28T18:12Z] Timing: heterogeneity
[2018-06-28T18:12Z] Timing: population database
[2018-06-28T18:12Z] multiprocessing: prep_gemini_db
[2018-06-28T18:12Z] Annotating /Shared/Bioinformatics/data/mchiment/bcbio_testbed/NA12878_exome_eval/work/gemini/NA12878-1-ensemble-nomultiallelic.vcf.gz with vcfanno, using /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/config/vcfanno/gemini.conf
[2018-06-28T18:12Z] =============================================
[2018-06-28T18:12Z] vcfanno version 0.2.8 [built with go1.8]
[2018-06-28T18:12Z] see: https://github.com/brentp/vcfanno
[2018-06-28T18:12Z] =============================================
[2018-06-28T18:12Z] vcfanno.go:115: found 24 sources from 4 files
[2018-06-28T18:12Z] vcfanno.go:143: using 2 worker threads to decompress query file
[2018-06-28T18:12Z] vcfanno.go:187: Info Error: max_aaf_all not found in INFO >> this error/warning may occur many times. reporting once here...
[2018-06-28T18:12Z] vcfanno.go:187: Info Error: clinvar_sig not found in INFO >> this error/warning may occur many times. reporting once here...
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:14Z] bix.go:200: chromosome 22 not found in /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/variation/esp.vcf.gz
[2018-06-28T18:15Z] vcfanno.go:241: annotated 147568 variants in 130.62 seconds (1129.8 / second)
[2018-06-28T18:15Z] tabix index NA12878-1-ensemble-nomultiallelic-annotated-gemini.vcf.gz
[2018-06-28T18:15Z] GEMINI: create database with vcf2db
[2018-06-28T18:15Z] skipping 'DP4' because it has Number=4
[2018-06-28T18:15Z] /Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:226: SAWarning: Unicode type received non-unicode bind param value ''. (this warning may be suppressed after 10 occurrences)
[2018-06-28T18:15Z]   (util.ellipses_string(value),))
[2018-06-28T18:15Z] /Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:226: SAWarning: Unicode type received non-unicode bind param value '-9'. (this warning may be suppressed after 10 occurrences)
[2018-06-28T18:15Z]   (util.ellipses_string(value),))
[2018-06-28T18:15Z] /Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:226: SAWarning: Unicode type received non-unicode bind param value '2'. (this warning may be suppressed after 10 occurrences)
[2018-06-28T18:15Z]   (util.ellipses_string(value),))
[2018-06-28T18:15Z] 10000 variant_impacts:69603	effects time: 8.8	chunk time:14.8	675.06 variants/second
[2018-06-28T18:15Z] 20000 variant_impacts:60427	effects time: 7.5	chunk time:12.8	724.85 variants/second
[2018-06-28T18:15Z] 30000 variant_impacts:71424	effects time: 8.7	chunk time:14.4	714.66 variants/second
[2018-06-28T18:16Z] 40000 variant_impacts:66450	effects time: 8.1	chunk time:14.6	706.38 variants/second
[2018-06-28T18:16Z] 50000 variant_impacts:71328	effects time: 8.8	chunk time:14.2	705.81 variants/second
[2018-06-28T18:16Z] 60000 variant_impacts:60540	effects time: 7.6	chunk time:12.7	718.23 variants/second
[2018-06-28T18:16Z] 70000 variant_impacts:65614	effects time: 8.0	chunk time:13.4	722.23 variants/second
[2018-06-28T18:17Z] 80000 variant_impacts:57211	effects time: 7.2	chunk time:12.2	733.14 variants/second
[2018-06-28T18:17Z] 90000 variant_impacts:77636	effects time: 9.4	chunk time:15.2	724.00 variants/second
[2018-06-28T18:17Z] 100000 variant_impacts:67594	effects time: 8.4	chunk time:14.1	722.52 variants/second
[2018-06-28T18:18Z] indexing ... finished in 4.7 seconds...
[2018-06-28T18:18Z] total time: in 216.9 seconds...
[2018-06-28T18:18Z] Multi-allelic to single allele
[2018-06-28T18:18Z] normalize vdecompose v0.50.5
[2018-06-28T18:18Z] options:     input VCF file        options:     input VCF file                                  --
[2018-06-28T18:18Z]          [o] output VCF file                                          [s] smart decomposition   -
[2018-06-28T18:18Z] true         [w] sorting window size                              (experimental)
[2018-06-28T18:18Z]          [o] output VCF file       -
[2018-06-28T18:18Z] 10000
[2018-06-28T18:18Z]          [n] no fail on reference inconsistency for non SNPs true
[2018-06-28T18:18Z]          [q] quiet                                           false
[2018-06-28T18:18Z]          [d] debug                                           false
[2018-06-28T18:18Z]          [r] reference FASTA file                            /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/seq/hg38.fa
[2018-06-28T18:18Z] [variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: 1:761956-761956
[2018-06-28T18:18Z] FAQ: http://genome.sph.umich.edu/wiki/Vt#1._vt_cannot_retrieve_sequences_from_my_reference_sequence_file
[2018-06-28T18:19Z] stats: no. variants                 : 148798
[2018-06-28T18:19Z]        no. biallelic variants       : 148332
[2018-06-28T18:19Z] Uncaught exception occurred
Traceback (most recent call last):
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 23, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 103, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; gunzip -c /Shared/Bioinformatics/data/mchiment/bcbio_testbed/NA12878_exome_eval/work/gemini/NA12878-1-freebayes.vcf.gz | bcftools view -f 'PASS,.' | vcfallelicprimitives -t DECOMPOSED --keep-geno | sed 's/ID=AD,Number=./ID=AD,Number=R/' | vt decompose -s -  | vt normalize -n -r /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/seq/hg38.fa -  | awk '{ gsub("./-65", "./."); print $0 }' | sed -e 's/Number=A/Number=1/g' | bgzip -c > /Shared/Bioinformatics/data/mchiment/bcbio_testbed/NA12878_exome_eval/work/bcbiotx/tmp0xAqeB/NA12878-1-freebayes-decompose.vcf.gz
normalize vdecompose v0.50.5
options:     input VCF file        options:     input VCF file                                  --
[o] output VCF file                                          [s] smart decomposition   -
true         [w] sorting window size                              (experimental)
[o] output VCF file       -
10000
[n] no fail on reference inconsistency for non SNPs true
[q] quiet                                           false
[d] debug                                           false
[r] reference FASTA file                            /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/seq/hg38.fa
[variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: 1:761956-761956
FAQ: http://genome.sph.umich.edu/wiki/Vt#1._vt_cannot_retrieve_sequences_from_my_reference_sequence_file
stats: no. variants                 : 148798
no. biallelic variants       : 148332
no. multiallelic variants    : 466
   no. additional biallelics    : 466
   total no. of biallelics      : 149264

Time elapsed: 4.40s
' returned non-zero exit status 1
Traceback (most recent call last):
File "/Dedicated/IIHG-argon/bcbio-1.0.9/bin/bcbio_nextgen.py", line 241, in
main(**kwargs)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/bin/bcbio_nextgen.py", line 46, in main
run_main(**kwargs)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 182, in variant2pipeline
samples = population.prep_db_parallel(samples, run_parallel)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/variation/population.py", line 349, in prep_db_parallel
output = parallel_fn("prep_gemini_db", to_process)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"], batch_size=1)(joblib.delayed(fn)(x) for x in items):
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 952, in call
while self.dispatch_one_batch(iterator):
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 791, in dispatch_one_batch
self._dispatch(tasks)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 748, in _dispatch
job = self._backend.apply_async(batch, callback=cb)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 183, in apply_async
result = ImmediateResult(func)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 543, in init
self.results = batch()
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 224, in call
for func, args, kwargs in self.items]
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 52, in wrapper
return apply(f, *args, **kwargs)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 335, in prep_gemini_db
return population.prep_gemini_db(*args)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/variation/population.py", line 34, in prep_gemini_db
gemini_vcf = normalize.normalize(gemini_vcf, data, passonly=passonly)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/variation/normalize.py", line 70, in normalize
remove_oldeffects=remove_oldeffects)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/variation/normalize.py", line 114, in _normalize
do.run(cmd, "Multi-allelic to single allele")
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 23, in run
_do_run(cmd, checks, log_stdout, env=env)
File "/Dedicated/IIHG-argon/bcbio-1.0.9/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 103, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; gunzip -c /Shared/Bioinformatics/data/mchiment/bcbio_testbed/NA12878_exome_eval/work/gemini/NA12878-1-freebayes.vcf.gz | bcftools view -f 'PASS,.' | vcfallelicprimitives -t DECOMPOSED --keep-geno | sed 's/ID=AD,Number=./ID=AD,Number=R/' | vt decompose -s -  | vt normalize -n -r /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/seq/hg38.fa -  | awk '{ gsub("./-65", "./."); print $0 }' | sed -e 's/Number=A/Number=1/g' | bgzip -c > /Shared/Bioinformatics/data/mchiment/bcbio_testbed/NA12878_exome_eval/work/bcbiotx/tmp0xAqeB/NA12878-1-freebayes-decompose.vcf.gz
normalize vdecompose v0.50.5
options:     input VCF file        options:     input VCF file                                  --
[o] output VCF file                                          [s] smart decomposition   -
true         [w] sorting window size                              (experimental)
[o] output VCF file       -
10000
[n] no fail on reference inconsistency for non SNPs true
[q] quiet                                           false
[d] debug                                           false
[r] reference FASTA file                            /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/seq/hg38.fa
[variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: 1:761956-761956
FAQ: http://genome.sph.umich.edu/wiki/Vt#1._vt_cannot_retrieve_sequences_from_my_reference_sequence_file
stats: no. variants                 : 148798
no. biallelic variants       : 148332
no. multiallelic variants    : 466
   no. additional biallelics    : 466
   total no. of biallelics      : 149264

Time elapsed: 4.40s
' returned non-zero exit status 1

Michael;
Thanks for the detailed report and apologies about the issue. The informative error here is coming from vt normalize where it appears to be having trouble reading the reference from the fasta reference file:
reference FASTA file /Dedicated/IIHG-argon/bcbio-1.0.9/genomes/Hsapiens/hg38/seq/hg38.fa
[2018-06-28T18:18Z] [variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: 1:761956-761956

I have not seen this before but from the vt docs it might indicate some kind of disk access problem or a corrupted/bad index file (hg38.fa.fai).
If you re-run the analysis in place, do you hit this error consistently. If not, this would indicate some temporary issue with the filesystem. If it keeps failing, then it would be worth looking at the fai and fa files to be sure there is nothing problematic about them.
Practically if you need to work around the issue and get the comparison finished you can turn off gemini database creation with tools_off: [gemini] in your configuration.
Thank you for the help debugging and hope these tips help us figure out what is going on.

Hi Brad,
Thanks for your quick reply!  I did hit the error twice, once after restart.  I've taken your suggestion and set "tools_off: [gemini]" in the config yaml.  I will try this first, b/c I just want the pipeline to complete.

Closing this as this is pretty old and is unlikely to still be a problem. Thank you!


Update stable version in repo from 1.7.2 to 1.7.4

Think about update stable version to 1.7.4
Version: stable=1.7.2 (812 days old) => latest=1.7.4 (15 days old)
Installs: stable=7729 (88.41%), latest=537 (6.14%), total=8742
Click to use developer portal
Click to edit
Note: This is an automatically generated message and not personally authored by bluefox!

This issue seems to be outdated.
This issue suggests to update the stable version of this adapter to 1.7.4 but the current stable version is already 1.7.4.
So this issue should be closed.


Graph View: Show Active Date

As the user hovers over the graph, the active date should be displayed somewhere.

I'll add this on Monday.

Added active (hover) date to left panel on graph view.


simple request to download video asks to read secrets in keychain and chrome safe storage on mac

Hi,
I have a very simple piece of code, that when executed seems to escalate to ask to read secrets in chrome safe storage and keychain on mac.
code is:
import pyktok as pyk
pyk.specify_browser('chrome')

def download_trending_videos(tag_val="datascience"):
    pyk.save_tiktok_multi_page(f'https://www.tiktok.com/tag/{tag_val}?lang=en', save_video=True, save_metadata=False)

if __name__ == "__main__":
    download_trending_videos("datascience")

and the dialog box that pops up asking to read secrets is shown in the attached screenshot:

what secrets/password is it asking to read and will it be able to read my critical passwords stored on chrome?
Thanks

I wondered how Pyktok solves authentication and investigated it a little while back: the password is needed to decrypt your chrome cookies, which are needed to authenticate to TikTok. Pyktok uses browser_cookie3 for that. These are the lines which lead to the pop-up:
https://github.com/borisbabic/browser_cookie3/blob/53fa5e30a86216ca2064b129b259fa87509b03dd/browser_cookie3/__init__.py#L101C1-L111C23
My understanding is that the password is needed to decrypt the cookie jar and that this is a relativly secure way to deal with it. If you don't trust  browser_cookie3, you should check the code yourself. Or you can use Firefox instead, which does not encrypt the cookies and hence your password is not read by Python.

@JBGruber is correct, this is a Chrome issue on MacOS, browser_cookie3 needs your password to read the encrypted cookies that let you get the goods. Your options are to give it what it needs or use a different browser that doesn't encrypt its cookies.


Release Versioin 0.1.0

@JuliaRegistrator register()

Registration pull request created: JuliaRegistries/General/81126
After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.
This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:
git tag -a v0.1.0 -m "<description of version>" 9246dd27b79ae69af7cd74e815db8e24fe4041f6
git push origin v0.1.0


linked service token configuration is not right

For section "ADLS Gen2 storage with linked services", if the linked service uses service principal or managed identity, the configuration should be,
spark.conf.set("spark.storage.synapse.linkedServiceName", linked_service_name)
spark.conf.set("fs.azure.account.oauth.provider.type","com.microsoft.azure.synapse.tokenlibrary.LinkedServiceBasedTokenProvider")
instead of
spark.conf.set("spark.storage.synapse.linkedServiceName", "")
spark.conf.set("fs.azure.sas.token.provider.type", "com.microsoft.azure.synapse.tokenlibrary.LinkedServiceBasedTokenProvider")

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

ID: 56d638cd-6592-ce95-90aa-dc8d6e4e90ba
Version Independent ID: 5360961f-6bfc-ecad-cf49-22eee26bd010
Content: Secure access credentials with Linked Services in Apache Spark for Azure Synapse Analytics - Azure Synapse Analytics
Content Source: articles/synapse-analytics/spark/apache-spark-secure-credentials-with-tokenlibrary.md
Service: synapse-analytics
Sub-service: spark
GitHub Login: @mlee3gsd
Microsoft Alias: martinle

@xiopeter3345 Thanks for your feedback! We will investigate and update as appropriate.

@xiopeter3345 The PR for the fix has been created and it will be merged soon. Thanks again for pointing this out, I am closing the issue based on this update, please let us know if there is something else that we can help you with.

Hi @xiopeter3345 ,
I tried both, the code snippet for pyspark in the documentation and your proposed code but both failed:
From the docs:
spark.conf.set("spark.storage.synapse.linkedServiceName", "my_linked_service")
spark.conf.set("fs.azure.sas.token.provider.type", "com.microsoft.azure.synapse.tokenlibrary.LinkedServiceBasedTokenProvider")

df_pmm =<EMAIL_ADDRESS>
df_pmm.show()

After your comment:
spark.conf.set("spark.storage.synapse.linkedServiceName", "my_linked_service")
spark.conf.set("fs.azure.account.oauth.provider.type","com.microsoft.azure.synapse.tokenlibrary.LinkedServiceBasedTokenProvider")
df_pmm =<EMAIL_ADDRESS>
df_pmm.show()

Both returns:
Py4JJavaError: An error occurred while calling o1981.load.
: Operation failed: "This request is not authorized to perform this operation.", 403, HEAD, https://<ACCOUNT>.dfs.core.windows.net/data/?upn=false&action=getAccessControl&timeout=90 ........

I know the linked service is working and the manage identity properly configured, because I can access the same data from a data flow.
Have you collected additional experience on this topics since you summited the issue?

Just new feedback, I had to restart the spark session and now is working in both, scala and pyspark using the configuration suggested by @xiopeter3345


Confirmation dialog on exiting Ignition

Desired behavior
On closing Ignition via the X button in the system title bar, have a dialog pop up to confirm exit.
That behavior can get annoying in development and testing, so an additional checkbox menu item for "ask before exit" would be nice.
Currently, the 3 dot "..." menu button is really close to the Close X button on Ubuntu. It's an easy mistake to close all of Ignition when the user meant to open the menu to inspect something in the middle of a simulation.
Alternatives considered
Hmmmmm alternatives..... tough to think of.
"It's okay, no one wants to keep Ignition open anyway."
"Just let them close it, they can always restart. Who cares."
"Only someone as clumsy as this issue's opener would make a mistake like that." (and I did)
....... None seem acceptable to me, especially the last one.
Implementation suggestion
This PR might help as reference https://github.com/ignitionrobotics/ign-gazebo/pull/609
Additional context
See red box in screenshot below.
The screenshot also illustrates that the problem is exacerbated on HiDPI screens, where the mouse cursor is teeny (common occurrence on HiDPI screens, I'll open another issue for that) and harder to see or control.

I am tackling this on my branch: https://github.com/ignitionrobotics/ign-gui/commit/1589fef6f38209728e465929d8adaeac2abb1747
So far:
https://user-images.githubusercontent.com/53065142/119032527-a8929d80-b982-11eb-8d9e-95053a00bf39.mp4
Actually, I wanted to add this feature from ign-gazebo but given that I had to connect to the closing signal of the AplicationWindow it wasn't that straightforward.
It is true that the request was only for the close button (x), not for the quit option in the sidebar, I could change that if needed.
If this meets what is required I will create the correspondent PR. :+1:

Ooh nice! Thank you for tackling this! Please go ahead and make a PR and we'll review it.

Closed by ignitionrobotics/ign-gui#225 and ignitionrobotics/ign-gazebo#850


use const instead of let in the initial arr definition

You can use const instead of let in the initial example. This clarifies where you get a whole new array (eg. in array.slice), versus when you don't actually mutate arr but just the elements in it (eg. in array.splice).

can't do this because some array methods are mutation methods. thanks though!

Thank you, maybe I missed something.
I've checked the examples, they already consider this by defining another variable where necessary and should work. As long as there is no reassignment to arr, all is fine. You can still do arr.sort() or arr.push(2) on a const arr, and it works. A thing I found confusing when I learned about ES6 const.


Could you please integrate RealEsrgan x4 model also to upscale final output

Thank you very much for wonderful work.

However, better solution to me, should be option to use bsrgan 2x or 4x models.
Please do it if not so hard!
Thanks


Hotfix: Request legacy txn format

Problem: The new version of Solana RPC nodes returns the new transaction v0 format by default, which we do not yet support.
Solution: A workaround explicitly requesting transactions in the 'legacy' format.
Note to Aleph team: Will not immediately fix requests through the HA proxy.

Tried and tested this. Fetched transactions work still fine, as v0 transactions have all the properties of legacy transaction + some info about the lookup tables, which are not being indexed by us. All addresses are listed as expected from "legacy".
txn_v0.txt


fix some docs

I fixed some docs:

docs/contribute/source/plugin/wasi_nn.md

fix misplaced Appendix part for ggml backend

I think the cause is https://github.com/WasmEdge/docs/commit/a2dd6ee153563c8b326d707628aef960e8d26ba1 put the Build WasmEdge with WASI-NN Neural Speed Backend part in the wrong place.

remove duplicate Apple Silicon Model part for ggml backend

The original has two identical Apple Silicon Model parts. One is in the MacOS section after Intel Model part and the other is in the Linux section after General Linux without any acceleration framework part.
I removed the one in the Linux section after General Linux without any acceleration framework part.
I think this duplicate was removed in 26c0689 and wrongly added again in a2dd6ee.

docs/start/install.md

remove extra backtick

Hello, I am a code review bot on flows.network.
It could take a few minutes for me to analyze this PR. Relax, grab a cup of coffee and check back later. Thanks!


Awake system tray icon disappears randomly

Microsoft PowerToys version
0.86.0
Installation method
GitHub
Running as admin
Yes
Area(s) with issue?
Awake
Steps to reproduce
Random occurrence - System tray icon for Awake disappears.
To bring it back, Awake needs to be disabled then re-enabled. Remains OK until the next time.
Could be hours or days until the next time.
Awake still works without the system tray icon being visible.
No other applications experience the same behaviour.
✔ Expected Behavior
No response
❌ Actual Behavior
No response
Other Software
No response

Disable the built-in auto-start, manually add a new startup schedule in Task Scheduler, and set the startup delay to 30 seconds in the trigger, keeping other settings the same as the built-in auto-start.
Work for me


Support Bluetooth Scanner connected over SPP

This is a new feature request to add support for bluetooth scanner connected over SPP.
Would be interesting to be able to demo accessories like RS6000 and DS2278 over SPP with this GenericScanWedge.
This would be a third way to get data on top of ZXing and Google™ Vision API.

Interesting idea! I'll look into it when I have a chance. I don't have either of those devices but I do have an RS5000 that supports SPP.

Like any application with a Bluetooth connection it is difficult to get the connection / disconnection logic 100% bullet proof but the app should now work, at least as a proof of concept.  I've also put a video on YouTube to show ZXing and SPP scanning: https://www.youtube.com/watch?v=OZ9v4kDq8OE .  Hope this is useful.


fix: add support for parameters #69

fix: Add support for parameters in channels placing it in quotation marks
fix: Add missing for the rest of the lines
Fixes issue #69

Sorry forgot to check the tests.
I've fixed them and they are passing now.

@arjungarg07 please have a look

@arjungarg07 any chance you could have a look?

Sure, will check


Check for Unicode chars in PDF files

C:\Users\User\Desktop\python\CouncilAgendaMapper>pdfx --debug agenda.pdf
DEBUG - init - Init with uri: agenda.pdf
Document infos:

Author = blah
CreationDate = D:20151106153359-06'00'
Traceback (most recent call last):
File "C:\Python33\lib\runpy.py", line 160, in _run_module_as_main
"main", fname, loader, pkg_name)
File "C:\Python33\lib\runpy.py", line 73, in run_code
exec(code, run_globals)
File "C:\Python33\Scripts\pdfx.exe_main.py", line 9, in
File "C:\Python33\lib\site-packages\pdfx\cli.py", line 90, in main
print("- %s = %s" % (k, parse_str(v).strip("/")))
File "C:\Python33\lib\encodings\cp437.py", line 19, in encode
return codecs.charmap_encode(input,self.errors,encoding_map)[0]
UnicodeEncodeError: 'charmap' codec can't encode character '\xae' in position 21
: character maps to

Not sure what the correct way to handle encoding errors would be, skip the char?
I usually fix this kind of issue by changing the cmd window encoding, eg.:
cmd> chcp 65001

Thanks for reporting! Can you send me the pdf which produces the error?
On Nov 18, 2015 19:44, "davemcphee"<EMAIL_ADDRESS>wrote:

C:\Users\User\Desktop\python\CouncilAgendaMapper>pdfx --debug agenda.pdf
DEBUG - init - Init with uri: agenda.pdf
Document infos:

Author = blah
CreationDate = D:20151106153359-06'00' Traceback (most recent call
last): File "C:\Python33\lib\runpy.py", line 160, in run_module_as_main
"_main", fname, loader, pkg_name) File "C:\Python33\lib\runpy.py",
line 73, in run_code exec(code, run_globals) File
"C:\Python33\Scripts\pdfx.exe__main_.py", line 9, in File
"C:\Python33\lib\site-packages\pdfx\cli.py", line 90, in main print("- %s =
%s" % (k, parse_str(v).strip("/"))) File
"C:\Python33\lib\encodings\cp437.py", line 19, in encode return
codecs.charmap_encode(input,self.errors,encoding_map)[0]
UnicodeEncodeError: 'charmap' codec can't encode character '\xae' in
position 21 : character maps to

Not sure what the correct way to handle encoding errors would be, skip the
char?
I usually fix this kind of issue by changing the cmd window encoding, eg.:
cmd> chcp 65001
—
Reply to this email directly or view it on GitHub
https://github.com/metachris/pdfx/issues/13.

Hi Chris,
sure thing, I think it was this:
http://www.austintexas.gov/edims/document.cfm?id=242173
I know nothing about PDF encoding, but I do know about parsing HTML from
that source, and it's all generated in MS Word, so expect a horror show
inside that PDF. Good luck :)
On Wed, Nov 18, 2015 at 4:24 PM Chris Hager<EMAIL_ADDRESS>wrote:

Thanks for reporting! Can you send me the pdf which produces the error?
On Nov 18, 2015 19:44, "davemcphee"<EMAIL_ADDRESS>wrote:

C:\Users\User\Desktop\python\CouncilAgendaMapper>pdfx --debug agenda.pdf
DEBUG - init - Init with uri: agenda.pdf
Document infos:

Author = blah
CreationDate = D:20151106153359-06'00' Traceback (most recent call
last): File "C:\Python33\lib\runpy.py", line 160, in run_module_as_main
"_main", fname, loader, pkg_name) File "C:\Python33\lib\runpy.py",
line 73, in run_code exec(code, run_globals) File
"C:\Python33\Scripts\pdfx.exe__main_.py", line 9, in File
"C:\Python33\lib\site-packages\pdfx\cli.py", line 90, in main print("-
%s =
%s" % (k, parse_str(v).strip("/"))) File
"C:\Python33\lib\encodings\cp437.py", line 19, in encode return
codecs.charmap_encode(input,self.errors,encoding_map)[0]
UnicodeEncodeError: 'charmap' codec can't encode character '\xae' in
position 21 : character maps to

Not sure what the correct way to handle encoding errors would be, skip
the
char?
I usually fix this kind of issue by changing the cmd window encoding,
eg.:
cmd> chcp 65001
—
Reply to this email directly or view it on GitHub
https://github.com/metachris/pdfx/issues/13.

—
Reply to this email directly or view it on GitHub
https://github.com/metachris/pdfx/issues/13#issuecomment-157884230.

Just a note: I've found out that this problem is caused by the Windows console not being able to display unicode characters. I'm going to look into a solution.

https://wiki.python.org/moin/PrintFails

Should work now on the Github version. CLI tries to encode contents to console encoding: https://github.com/metachris/pdfx/blob/b52d3a72b18c7331f025b1d9fec67387fc5dd2d1/pdfx/cli.py#L111


Fix migration broken url on changelog

Hi, I just saw that the migration guide link on the changelog is
broken, replaced it with a new one.

Coverage remained the same at 97.063% when pulling 5154f6dfe3b68a17dec16703367b3cd3fd879f05 on iliasmentz:fix_broken_url_on_changelog into bda8e13c90ab00f5a67eab0a3fb050914220308e on Vincit:master.

Thanks!