text:
error on python setup.py install

mbp-dev:gazu-publisher des$ python setup.py install
error in gazupublisher setup command: 'install_requires' must be a string or list of strings containing valid project/version requirement specifiers; Expected version spec in qtazu@git+https://github.com/cgwire/qtazu.git#egg=qtazu at @git+https://github.com/cgwire/qtazu.git#egg=qtazu

Thx for your feedback !
This bug has been fixed, so it shouldn't be a problem anymore. The gazu publisher still remains WIP so let us know if the error persists. If you want to, we've also written a procedure of installation here to make things easier : https://gazu.cg-wire.com/publisher.html

ok! lets move on this one!
os x mojave, 10.14.6
pyside2 installed, pip from python27
mbp-dev:gazu-publisher des$ pip install https://github.com/cgwire/gazu-publisher.git --user
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Collecting https://github.com/cgwire/gazu-publisher.git
Using cached https://github.com/cgwire/gazu-publisher.git
ERROR: Cannot unpack file /private/var/folders/my/nn47_t4d365fr1p3rj6p0r7r0000gn/T/pip-unpack-rrb_dW/gazu-publisher.git (downloaded from /private/var/folders/my/nn47_t4d365fr1p3rj6p0r7r0000gn/T/pip-req-build-ARbn8n, content-type: text/html; charset=utf-8); cannot detect archive format
ERROR: Cannot determine archive format of /private/var/folders/my/nn47_t4d365fr1p3rj6p0r7r0000gn/T/pip-req-build-ARbn8n

Can you try the command pip install git+https://github.com/cgwire/gazu-publisher.git --user, instead of pip install https://github.com/cgwire/gazu-publisher.git --user (add git+ in front of the url) ?
The mistake is in our tutorial, it was corrected but the PR with the fix has not been merged yet, sry for that. Let me know if it worked !

pip install -U setuptools did the trick for me, after the git+https worked just fine in --user mode.
mac mojave 10.14.6, python27, apple python build, no brew

authors: LedruRollin ddesmond

repo: cgwire/gazu-publisher


text:
Serializer Interface

Hey, nice, slim library by the way, will try to use it.
First complain: SerializerInterface should take $context as a second serialize/unserialize parameter.
Otherwise this Interface can have some issues in the future.
Example case i've encoutered:
Made JsonSerializer, json_encode, json_decode method takes additional parameters, which would be impossible to pass.

This is a great suggestion. I'm moving the serializer into my helper library I will definitely consider this change.

Optionally you could construct your JsonSerializer with any options you wanted to use with encoding/decoding.

source: gharchive/issue

authors: arnaspet chadicus

repo: chadicus/psr-cache-redis

license: MIT

license_type: permissive

license_source: github-api


text:
unreliable channels?

Looking through the DataChannel.hpp channel types, there doesn't seem to be an unreliable option. Perhaps I am mis-understanding what webRTC means by unreliable -- is "reliable_unordered" what I am looking for? What I was expecting unreliable to be would be both unordered (of course) but also no guarantee of sending the data, whereas reliable_unordered sounds to me like it would be unordered but data would be re-sent until acknowledged on the other side (which I don't care about).

Here are the explanations from https://tools.ietf.org/html/draft-ietf-rtcweb-data-protocol-08#section-5.1.
I think the "PARTIAL_RELIABLE" ones might be the what you are looking for.
      DATA_CHANNEL_RELIABLE (0x00):  The Data Channel provides a
         reliable in-order bi-directional communication.

      DATA_CHANNEL_RELIABLE_UNORDERED (0x80):  The Data Channel provides
         a reliable unordered bi-directional communication.

      DATA_CHANNEL_PARTIAL_RELIABLE_REXMIT (0x01):  The Data Channel
         provides a partially-reliable in-order bi-directional
         communication.  User messages will not be retransmitted more
         times than specified in the Reliability Parameter.

      DATA_CHANNEL_PARTIAL_RELIABLE_REXMIT_UNORDERED (0x81):  The Data
         Channel provides a partial reliable unordered bi-directional
         communication.  User messages will not be retransmitted more
         times than specified in the Reliability Parameter.

      DATA_CHANNEL_PARTIAL_RELIABLE_TIMED (0x02):  The Data Channel
         provides a partial reliable in-order bi-directional
         communication.  User messages might not be transmitted or
         retransmitted after a specified life-time given in milliseconds
         in the Reliability Parameter.  This life-time starts
         when providing the user message to the protocol stack.

      DATA_CHANNEL_PARTIAL_RELIABLE_TIMED_UNORDERED (0x82):  The Data
         Channel provides a partial reliable unordered bi-directional
         communication.  User messages might not be transmitted or
         retransmitted after a specified life-time given in milli-
         seconds in the Reliability Parameter.  This life-time starts
         when providing the user message to the protocol stack.

Ah. I think you're right.
Still, in the WebRTC documentation and tutorials, typically the behavior of these unreliable channels is controlled by a 'maxRetries' or 'maxTimeout' style parameter. I can't seem to find where such a parameter might be set in librtcdcpp. And in the absence of a such a parameter, what would the behavior PARTIAL_RELIABLE data channels be?
In fact, scanning through the DataChannel.cpp source code, the chan_type parameter seems to be unused.

Still, in the WebRTC documentation and tutorials, typically the behavior of these unreliable channels is controlled by a 'maxRetries' or 'maxTimeout' style parameter. I can't seem to find where such a parameter might be set in librtcdcpp. And in the absence of a such a parameter, what would the behavior PARTIAL_RELIABLE data channels be?

That parameter would be the reliability parameter for which the proper API is not yet implemented in this library.

In fact, scanning through the DataChannel.cpp source code, the chan_type parameter seems to be unused.

The library does not support creating a data channel yet. I have a PR for this, but I hardcoded the RELIABLE chan_type and other params like reliability. Plus it would need more tweaks to actually make it work accordingly at the SCTP layer.

I've added the chan_type and reliability features to the API: https://github.com/chadnickbok/librtcdcpp/pull/30/commits/f20cf66815448f4068a0d00f972e7603c0f133d7

authors: PowerInside an-kumar

repo: chadnickbok/librtcdcpp

license_source: bigquery


text:
[backport] new style rdiv function

Backport of #3615.

jenkins, test this please

LGTM!

source: gharchive/pull-request

authors: kmaehashi takagi

repo: chainer/chainer

license: mit


text:
Use typescript for status actions and statusReducer

This PR aims to use typescript for actions and reducers related to status.

Thank you!

repo: chainer/chainerui


text:
Merge pull request #2 from chakkaphong/main

pull

pr


text:
Set charge state Z0 in AddIon(...)

We should retire PRESCRIBED_FULLY_IONIZED etc and instead allow the shortcut
eqsys.n_i.addIon(name='name', Z=Z, Z0=Z0, iontype=Ions.IONS_PRESCRIBED, n=n)

where Z is the atomic number as usual, but Z0 is now the charge state (= 0 for neutral or = Z for fully ionized).

Sure, but I am not convinced that we should retired IONS_PRESCRIBED_FULLY_IONIZED et al? The notation Z0=... suggests that we are specifying just one charge state (rather than setting all other to zero), while IONS_PRESCRIBED_FULLY_IONIZED is quite verbose.
(Implementing the Z0=... interface should be very simple, though, as the IonSpecies class already has the initialize_XXX_charge_state() method for initializing ions just this way; it's just not exposed to addIon())

For sure, I agree that we should keep the current methods, also for backwards-compatibility.

repo: chalmersplasmatheory/DREAM


text:
Mobile examples are not building

It fails on some missing npm modules like webpack and graphql declared in package.json in subdirectories. It should be buildable out of the box.

if you're referring to relay-mobile-examples then you must need graphQL and webpack because relay uses those to generate/validate relay-graphql queries.

fixed with #17


text:
Snap shot conflict 수정

Summary
https://github.com/channel-io/bezier-react/pull/715 를 머지했으나, https://github.com/channel-io/bezier-react/pull/665 의 변경사항으로 머지 후 돌아간 테스트의 에러 발생, 해당 에러를 수정하는 PR 입니다.
Detail
Snapshot 업데이트 진행

:tada: This PR is included in version 1.0.0-next-v1.93 :tada:
The release is available on:

npm package (@next-v1 dist-tag)
GitHub release

Your semantic-release bot :package::rocket:

authors: ch-builder guswnsxodlf

repo: channel-io/bezier-react


text:
SectionLabel의 help가 Tooltip의 allowHover를 받도록 수정

Summary

SectionLabel 컴포넌트의 help 프롭 타입에 allowTooltipHover: boolean을 추가하여, SectionLabel을 사용할 때 Help tooltip의 allowHover 여부를 정할 수 있게 합니다.
https://user-images.githubusercontent.com/6940439/172295300-46fe61e8-f6d4-4a54-a779-84dc5fc39957.mp4
Details

관련 Desk 이슈: https://github.com/channel-io/ch-desk-web/issues/10023

Help tooltip 내에 Clickable한 요소가 있는 경우 등에는 Tooltip이 호버 가능해야 하며, 이를 SectionLabel.help의 props에 추가하여 해결합니다.
Browser Compatibility
OS / Engine 호환성을 반드시 확인해주세요.
Windows

[ ] Chrome - Blink
[ ] Edge - Blink
[ ] Firefox - Gecko (Option)

macOS

[x] Chrome - Blink
[ ] Edge - Blink
[ ] Safari - WebKit
[ ] Firefox - Gecko (Option)

References

prop 추가가 아니라 기본적으로 allowHover = true로 하는 것은 어떻게 생각하시나요?

반대로 생각했을 때(SectionLabel의 help에 대해 툴팁 allowHover를 원치 않는 경우)가 약간 걸리긴 하지만, 딱히 툴팁 hover를 막아야 할 케이스가 떠오르지 않네요 😅 저는 괜찮을 것 같습니다!

덧붙여, (지금 받는 tooltipContent도 어차피 TooltipProps에 들어가기 때문에) 다음과 같이 tooltipProps를 대신 받아서 이를 spread해주고, tooltipContent를 deprecated 처리하는 방안도 생각해 보았습니다. 사실 위의 논의대로 allowHover를 무조건 true로 주면 해결되는 문제이지만, 이렇게 하면 어떨지 의견 주시면 감사하겠습니다 🙇
As-is:
interface SectionLabelHelpProps extends Partial<IconInfo> {
  iconSize?: IconSize
  tooltipContent: React.ReactNode
}

To-be:
interface SectionLabelHelpProps extends Partial<IconInfo> {
  iconSize?: IconSize
  tooltipProps: Partial<TooltipProps> & Pick<TooltipProps, 'content'>

  /**
   * @deprecated
   */
  tooltipContent: React.ReactNode
}

내부 컴포넌트의 prop을 지정하는 선택지를 늘리고 싶다면, 이를 인터페이스에 추가하기보다는 합성을 통해 해결하는 것이 좋아보입니다.
interface SectionLabelProps {
  ...

  tooltip: { /* preset props for tooltip */ } | React.ReactNode
}

:tada: This PR is included in version 1.0.0-next-v1.148 :tada:
The release is available on:

npm package (@next-v1 dist-tag)
GitHub release

Your semantic-release bot :package::rocket:

authors: Dogdriip ch-builder inhibitor1217


text:
Blueprint middleware interferes with global middleware

Creating some middleware for a blueprint seems to interfere with the main router unexpectedly. E.g.
from sanic import Sanic, Blueprint
from sanic.exceptions import NotFound

app = Sanic(__name__)
key_blueprint = Blueprint('key', url_prefix='/foobar/')

@app.route('/')
async def hello_world(request):
    return "Hello World! Your API is working!"

@key_blueprint.middleware('request')
async def authentication(request):
    raise NotFound("This blueprint is not ready yet!")

app.blueprint(key_blueprint)
app.run()

And then I run
$ curl 127.0.0.1:8000/
Error: This blueprint is not ready yet!%

I would have expected the blueprint 'authentication' not to interfere with an endpoint which is not prefixed /foobar/.

Known issue. A discussion is going on: #37

Going to close this in favor of #37

authors: nasfarley88 seemethere yoloseem

repo: channelcat/sanic


text:
Rewrite v-sanitize into vue3/nuxt3

Closed: #265
Hey!
I started working on the rewrite, couldn't test the directive yet, but the $sanitize function should already work. I ran into issues running sanitize-html under Vite. A possible solution would be to replace sanitize-html with dompurify.
Are you open to that idea, should I prototype up a rewrite with dompurify? You can check it our here https://github.com/cure53/DOMPurify
ToDo

[ ] test directive in vue 3
[ ] write tests
[ ] test / update nuxt implementation for nuxt 3
[ ] add typings extending vue
[ ] fix compatibility issues with Vite and sanitize-html
[ ] add editorconfig or eslint or any other form of keeping codestyle consistent

Also typings not yet finished, specifically declaring the existence of $sanitize under vue instance

Yes, it's nice, let go ahead try that to see if it works fine, we can release it for vue 3 and nuxt 3.

But the another plugin already exist here: https://github.com/LeSuisse/vue-dompurify-html, so better avoid creating the same thing.

@chantouchsek I use the package you linked as a replacement for v-sanitize, 'till I update the implementation :D. The problem with thatone is, that it only implements a directive, there is no sanitize function passed to the context as well as no native nuxt implementation.

@chantouchsek I use the package you linked as a replacement for v-sanitize, 'till I update the implementation :D. The problem with thatone is, that it only implements a directive, there is no sanitize function passed to the context as well as no native nuxt implementation.

Ok, great 👍

@chantouchsek heya! Please could you look into my tsconfig and sanitize.ts file? I am pretty new to TS and I don't know where in the documentation to look for stuff like extending vue or nuxt types so they include $sanitize and stuff like that, so I don't know where to add that in the nuxt3/vue3 version.
I added some basic tests for now and an example environment, where you can run the package in dev mode so you can test it properly without the need of another vue app.
Could you please checkut my version and maybe throw a PR with proper TS settings? After that I'd love to finish writing more tests and giving you the code for PR.
Thanks.

@truesteps what editor/IDE are you using, that seem, you made to lots of files that doesn't related, can you check and revert all of the at first, then i will look up into it again. thanks.

I'm using phpstorm, I added a .editorconfig and reformated the entire project, feel free to modify the .editorconfig to your liking and I'll reformat it again :)

The idea behind that came from the fact, that usually no 2 developers have the same formatting setup, so I added it to ensure all code will look the same in the future

@truesteps no don't use phpstorm to write js or ts, you should use webstorm instead.

@chantouchsek phpstorm is the same like webstorm, except it has support for PHP, nothing else is different. .editorconfig is supported by all editors not just the IntelliJ family of products from jetbrains

@chantouchsek phpstorm is the same like webstorm, except it has support for PHP, nothing else is different. .editorconfig is supported by all editors not just the IntelliJ family of products from jetbrains
anyway, if you want me to rewert the formatting changes, I'll do that :)

No, I don't accept that format.

@chantouchsek phpstorm is the same like webstorm, except it has support for PHP, nothing else is different. .editorconfig is supported by all editors not just the IntelliJ family of products from jetbrains
anyway, if you want me to rewert the formatting changes, I'll do that :)

No, I don't accept that format.

what format do you wish to use? Please define it so I can implement it. Thanks

@chantouchsek phpstorm is the same like webstorm, except it has support for PHP, nothing else is different. .editorconfig is supported by all editors not just the IntelliJ family of products from jetbrains
anyway, if you want me to rewert the formatting changes, I'll do that :)

No, I don't accept that format.

what format do you wish to use? Please define it so I can implement it. Thanks

Thanks, the current format is fine.

authors: chantouchsek truesteps

repo: chantouchsek/v-sanitize


text:
docs: Running list of Eng / Design improvements for 2025

Engineering

[ ] Custom examples of inherited functions #890
[ ] Autogeneration of data model
[ ] Python scripts or notebooks generation for examples and tutorials
[ ] Versioned docs

Improving Design

[ ] Improved API docs styling
[ ] Accordion / admonition styling
[ ] Add ability to link and copy link to specific questions in the doc site faq ( addressing #419)

Effort estimation:
Engineering

Custom examples of inherited functions (1h)
Autogeneration of data model (on hold, waiting for eng suggestions)
Python scripts or notebooks generation for examples and tutorials (10h)
Versioned docs (10h)

Improving Design

Improved API docs styling

I believe this is about the "attributes in table" issue. (10h)

Accordion / admonition styling (5h)
Add ability to link and copy link to specific questions in the doc site faq ( addressing https://github.com/chanzuckerberg/cryoet-data-portal/issues/419) - this may be an engineering issue, waiting on confirmation

authors: dgmccart melissawm

repo: chanzuckerberg/cryoet-data-portal


text:
add support for npe2-enabled features

Summary
We will add support on the napari hub for npe2, inspecting plugins for high priority metadata, presenting the metadata on plugin pages, letting users filter by the plugin metadata, and providing the metadata to napari through the napari hub API.
Outcome
Users will be able to see human-readable plugin names, filter by plugin type, and filter by file extensions that are supported for reading and writing. napari developers will have access to this metadata through the napari hub API. napari plugin developers will be able to preview this metadata on the Plugin Preview Page.
How will it work
When new plugins are detected on PyPI, on the backend we will need to download the Python package and inspect the npe2 manifest file for relevant metadata. For legacy plugins, we will attempt to infer this information using the logic in npe2 convert
Assets

PRD
Designs
Tech Spec

Stories

[x] https://github.com/chanzuckerberg/napari-hub/issues/237
[x] #467
[x] https://github.com/chanzuckerberg/napari-hub/issues/425
[ ] #468

@lauramarcos to QA the following functionality:

Test new npe2 filters on search page: https://staging.napari-hub.org

Test PyPi link on plugin page:

Verify plugin metadata matches what's is being filtered:

repo: chanzuckerberg/napari-hub


text:
Draft relaxed schema compliance

Context
There are emerging requirements for reusing the cellxgene-schema CLIschema+validator for scenarios that are more relaxed than CELLxGENE Discover's current requirements.
Relaxation
The following sections blue-sky possible approaches to documenting relaxed requirements; however, the solution should be driven by concrete scenarios and not theory.
Fine Granularity: Per Schema variant
A limited number of schema variants could be documented such as the "cross modality schema".  schema_reference could be reused for the curator to define the preferred schema for validation.

Fine Granularity: Per Metadata field
For each metadata field, the schema defines separate requirements for strict and relaxed.  Generally, relaxed will indicate that the field MUST NOT be present, but it's also possible to relax other requirements.

uns (Dataset Metadata)
relaxed

Key
relaxed

Annotator
Curator MAY annotate.

Value

list[str]. str values MUST match one or more of the values in the set:

"obs['cell_type_ontology_term_id']"
"obs['development_stage_ontology_term_id']"
...
If present, relaxed validation MUST be performed on the specified metadata field.

Concrete example:  If the assay is silver tier Visium Spatial Gene Expression then assuming that cell_type_ontology_term_id defined its relaxed validation as:

cell_type_ontology_term_id MUST NOT be present in obs
"cell_type_onotlogy_term_id" MUST be annotated in uns['relaxed']

Then the silver tier dataset would simply meet those requirements.

Coarse Granularity: Per Dataset
The schema documents a  relaxed subset of the current required fields. This subset may not include cell_type_ontology_term_id or perhaps development_stage_ontology_term_id.  If a current required field is not included in the relaxed subset, then it MUST NOT be present in the dataset.
Curators annotate whether strict or relaxed validation is desired.

uns (Dataset Metadata)
strict

Key
strict

Annotator
Curator MUST annotate.

Value
bool. This MUST be True for strict validation and MUST be False for relaxed validation.

References

Strict and Relaxed Mode
Categories of AIRR Schema Fields
Compliance with the MiAIRR Data Standard

Compliance to the MiAIRR Data Standard is currently a binary state, i.e., a data either is or is not compliant, there are not “grades” of compliance. However, additional requirements for specific use cases might be defined in the future.

I'd prefer not to overload "relaxed" to mean anything besides "MUST NOT contain". If we want to "relax" in some other way, it should probably be a new schema variant or additional flag.

I like the idea of using a combination of schema_reference to point to variant schemas, and uns.relaxed to point to which requirements to ignore in that given schema reference.
We may have dependent columns that need to be relaxed, like tissue_type and tissue_ontology_term_id. Just wanted to note that we'll have to account for that dependency either by logging an error if tissue_ontology_term_id is relaxed and tissue_type is not, or automatically relaxing dependent columns of relaxed columns.

authors: brianraymor nayib-jose-gloria

repo: chanzuckerberg/single-cell-curation


text:
🛑 de-4 (redglobuli) is down

In 7e53436, de-4 (redglobuli) (https://de-4-mirror.chaotic.cx/no-failover/chaotic-aur/lastupdate) was down:

HTTP code: 503
Response time: 59 ms

Resolved: de-4 (redglobuli) is back up in 659bad6.

repo: chaotic-aur/chaotic-uptimes


text:
🛑 Silky.Network - us-ca is down

In 3de1ce6, Silky.Network - us-ca (https://sjc-us-mirror.silky.network) was down:

HTTP code: 0
Response time: 0 ms

Resolved: Silky.Network - us-ca is back up in c030206 after 2 minutes.


text:
🛑 br (UFSCar Alcateia) is down

In 01370bc, br (UFSCar Alcateia) (mirror.ufscar.br) was down:

HTTP code: 0
Response time: 0 ms

Resolved: br (UFSCar Alcateia) is back up in 5f94546 after 6 minutes.


text:
Specific if jvm_opts sets memory usage per core or per virtual machine

It is not clear to me in the documentation how jvm_opts is passed to the jvm. How should I set this option with respect to my total core and memory availability?
Thank you!
Andrew

Andrew;
The memory specifications are per-core and automatically get scaled to the cores allocated to a process. Sorry this was not more clear -- I added additional documentation on it:
https://bcbio-nextgen.readthedocs.org/en/latest/contents/parallel.html#tuning-core-and-memory-usage
Let us know if you have any other questions and thanks much for the helpful feedback.

repo: chapmanb/bcbio-nextgen


text:
gatk bcbio error

Hi! I'm having problems with the latest dev version of bcbio. The error message is found below. Any ideas?
//Pär
CalledProcessError: Command 'set -o pipefail; export PATH=/home/genetik/bcbio/share/bcbio/anaconda/bin:$PATH && /home/genetik/bcbio/share/bcbio/anaconda/bin/gatk-framework -Xms750m -Xmx2000m -XX:+UseSerialGC -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment realign recal -o /home/genetik/calling/haloplex/160708_M00568_0174_000000000-ARHBP/calling/work/bamprep/16-4623/chr1/tx/tmp0dMrI7/16-4623-sort-chr1_0_25870287-prep-prealign.bam
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.6-24-g59fd391):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid argument value 'realign' at position 6.
##### ERROR Invalid argument value 'recal' at position 7.
##### ERROR ------------------------------------------------------------------------------------------
' returned non-zero exit status 1

I'm pasting a little bit more of the output, if necessary.
 max: 127595531
Between block sizes:
  min: 287
  5%: 344.75
  25%: 1003.25
  median: 2365.5
  75%: 15080.5
  95%: 142929.25
  99%: 24990570.5
  max: 43839113

[2016-08-03T10:00Z] Timing: hla typing
[2016-08-03T10:00Z] Resource requests: freebayes, gatk, gatk-haplotype, picard, platypus, samtools; memory: 2.00, 3.50, 3.50, 3.50, 2.00, 2.00; cores: 16, 1, 1, 1, 16, 16
[2016-08-03T10:00Z] Configuring 16 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2016-08-03T10:00Z] Timing: alignment post-processing
[2016-08-03T10:00Z] multiprocessing: piped_bamprep
[2016-08-03T10:00Z] GATK pre-alignment ('chr1', 0, 25870287) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr1', 25880402, 55505727) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr1', 55509505, 78381828) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr1', 78383240, 116244057) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr1', 116245531, 156085075) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr1', 156095984, 201328393) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr1', 201328740, 218520399) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr1', 218536665, 236850109) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr1', 236881147, 249250621) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr2', 0, 21226216) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr2', 21227130, 105977901) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr2', 105979731, 179392485) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr2', 179392990, 220283772) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr2', 220284806, 243199373) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr3', 30664680, 46899961) : 16-4623
[2016-08-03T10:00Z] GATK pre-alignment ('chr3', 0, 30648479) : 16-4623
[2016-08-03T10:00Z] ##### ERROR ------------------------------------------------------------------------------------------
[2016-08-03T10:00Z] ##### ERROR A USER ERROR has occurred (version 3.6-24-g59fd391):
[2016-08-03T10:00Z] ##### ERROR
[2016-08-03T10:00Z] ##### ERROR This means that one or more arguments or inputs in your command are incorrect.
[2016-08-03T10:00Z] ##### ERROR The error message below tells you what is the problem.
[2016-08-03T10:00Z] ##### ERROR
[2016-08-03T10:00Z] ##### ERROR If the problem is an invalid argument, please check the online documentation guide
[2016-08-03T10:00Z] ##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
[2016-08-03T10:00Z] ##### ERROR
[2016-08-03T10:00Z] ##### ERROR Visit our website and forum for extensive documentation and answers to
[2016-08-03T10:00Z] ##### ERROR commonly asked questions https://www.broadinstitute.org/gatk
[2016-08-03T10:00Z] ##### ERROR
[2016-08-03T10:00Z] ##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
[2016-08-03T10:00Z] ##### ERROR
[2016-08-03T10:00Z] ##### ERROR MESSAGE: Invalid argument value 'realign' at position 6.
[2016-08-03T10:00Z] ##### ERROR Invalid argument value 'recal' at position 7.
[2016-08-03T10:00Z] ##### ERROR ------------------------------------------------------------------------------------------
[2016-08-03T10:00Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
    _do_run(cmd, checks, log_stdout)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; export PATH=/home/genetik/bcbio/share/bcbio/anaconda/bin:$PATH && /home/genetik/bcbio/share/bcbio/anaconda/bin/gatk-framework -Xms750m -Xmx2000m -XX:+UseSerialGC -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment realign recal -o /home/genetik/calling/haloplex/160708_M00568_0174_000000000-ARHBP/calling/work/bamprep/16-4623/chr1/tx/tmpxQ5oLh/16-4623-sort-chr1_25880402_55505727-prep-prealign.bam

Pär;
Sorry about the issue, I'm confused as to what happened here. It looks like the command lines are completely messed up, you're getting realign recal instead of the expected  parameters. I'm not sure what would cause this. Would you be able to run this with a single core (-n 1) so we can see exactly where it fails? Would you also be able to share your configuration so I can try to reproduce here? Thanks much for the help debugging.

Hi!
Please find attached, the complete output from a run using the -n 16 (bcbio_output.txt) and the output from  -n 1. There are gzip: Broken path warnings. I've checked the input fastq files using gzip -t and they seem ok. Also, I upgraded from gatk 3.5 to gatk 3.6, maybe this could have something to do with it?
It appears to me that the error has to do with the realignment step (?) . I do this because I use the alignment when assessing found variants, and using realignment has not been an issue before.
cheers,
Pär
complete -n 16 output:
bcbio_output.txt
-n 1 output:
[2016-08-05T11:12Z] System YAML configuration: /home/genetik/bcbio/share/bcbio/galaxy/bcbio_system.yaml
[2016-08-05T11:12Z] Resource requests: bwa, sambamba, samtools; memory: 2.00, 2.00; cores: 16, 16, 16
[2016-08-05T11:12Z] Configuring 1 jobs to run, using 1 cores each with 2.00g of memory reserved for each job
[2016-08-05T11:12Z] run local -- checkpoint passed: multicore
[2016-08-05T11:12Z] Timing: organize samples
[2016-08-05T11:12Z] multiprocessing: organize_samples
[2016-08-05T11:12Z] Using input YAML configuration: /home/genetik/calling/haloplex/160708_M00568_0174_000000000-ARHBP/calling/config/calling.yaml
[2016-08-05T11:12Z] Checking sample YAML configuration: /home/genetik/calling/haloplex/160708_M00568_0174_000000000-ARHBP/calling/config/calling.yaml
[2016-08-05T11:12Z] Testing minimum versions of installed programs
[2016-08-05T11:13Z] Timing: alignment preparation
[2016-08-05T11:13Z] multiprocessing: prep_align_inputs
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] multiprocessing: disambiguate_split
[2016-08-05T11:13Z] Timing: alignment
[2016-08-05T11:13Z] multiprocessing: process_alignment
[2016-08-05T11:13Z] Aligning lane 16-4623 with bwa aligner
[2016-08-05T11:13Z] Aligning lane 16-4653 with bwa aligner
[2016-08-05T11:13Z] Aligning lane 16-4669 with bwa aligner
[2016-08-05T11:13Z] Aligning lane 16-4670 with bwa aligner
[2016-08-05T11:13Z] Aligning lane 16-4672 with bwa aligner
[2016-08-05T11:13Z] Aligning lane 16-4884 with bwa aligner
[2016-08-05T11:13Z] Timing: callable regions
[2016-08-05T11:13Z] multiprocessing: prep_samples
[2016-08-05T11:13Z] multiprocessing: postprocess_alignment
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] Resource requests: ; memory: 1.00; cores: 1
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-08-05T11:13Z] multiprocessing: combine_sample_regions
[2016-08-05T11:13Z] Identified 66 parallel analysis blocks
Block sizes:
  min: 1661458
  5%: 9448122.5
  25%: 19335508.25
  median: 30527962.0
  75%: 51787653.75
  95%: 97588388.25
  99%: 121930600.3
  max: 127595531
Between block sizes:
  min: 287
  5%: 344.75
  25%: 1003.25
  median: 2365.5
  75%: 15080.5
  95%: 142929.25
  99%: 24990570.5
  max: 43839113

[2016-08-05T11:13Z] Timing: hla typing
[2016-08-05T11:13Z] Resource requests: freebayes, gatk, gatk-haplotype, picard, platypus, samtools; memory: 2.00, 3.50, 3.50, 3.50, 2.00, 2.00; cores: 16, 1, 1, 1, 16, 16
[2016-08-05T11:13Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2016-08-05T11:13Z] Timing: alignment post-processing
[2016-08-05T11:13Z] multiprocessing: piped_bamprep
[2016-08-05T11:13Z] GATK pre-alignment ('chr1', 0, 25870287) : 16-4623
[2016-08-05T11:13Z] ##### ERROR ------------------------------------------------------------------------------------------
[2016-08-05T11:13Z] ##### ERROR A USER ERROR has occurred (version 3.6-24-g59fd391):
[2016-08-05T11:13Z] ##### ERROR
[2016-08-05T11:13Z] ##### ERROR This means that one or more arguments or inputs in your command are incorrect.
[2016-08-05T11:13Z] ##### ERROR The error message below tells you what is the problem.
[2016-08-05T11:13Z] ##### ERROR
[2016-08-05T11:13Z] ##### ERROR If the problem is an invalid argument, please check the online documentation guide
[2016-08-05T11:13Z] ##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
[2016-08-05T11:13Z] ##### ERROR
[2016-08-05T11:13Z] ##### ERROR Visit our website and forum for extensive documentation and answers to
[2016-08-05T11:13Z] ##### ERROR commonly asked questions https://www.broadinstitute.org/gatk
[2016-08-05T11:13Z] ##### ERROR
[2016-08-05T11:13Z] ##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
[2016-08-05T11:13Z] ##### ERROR
[2016-08-05T11:13Z] ##### ERROR MESSAGE: Invalid argument value 'realign' at position 6.
[2016-08-05T11:13Z] ##### ERROR Invalid argument value 'recal' at position 7.
[2016-08-05T11:13Z] ##### ERROR ------------------------------------------------------------------------------------------
[2016-08-05T11:13Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
    _do_run(cmd, checks, log_stdout)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; unset JAVA_HOME && export PATH=/home/genetik/bcbio/share/bcbio/anaconda/bin:$PATH && /home/genetik/bcbio/share/bcbio/anaconda/bin/gatk-framework -Xms750m -Xmx2000m -XX:+UseSerialGC -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment realign recal -o /home/genetik/calling/haloplex/160708_M00568_0174_000000000-ARHBP/calling/work/bamprep/16-4623/chr1/tx/tmp8gCxnZ/16-4623-sort-chr1_0_25870287-prep-prealign.bam
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.6-24-g59fd391):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid argument value 'realign' at position 6.
##### ERROR Invalid argument value 'recal' at position 7.
##### ERROR ------------------------------------------------------------------------------------------
' returned non-zero exit status 1
Traceback (most recent call last):
  File "/home/genetik/bcbio/bin/bcbio_nextgen.py", line 226, in <module>
    main(**kwargs)
  File "/home/genetik/bcbio/bin/bcbio_nextgen.py", line 43, in main
    run_main(**kwargs)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
    fc_dir, run_info_yaml)
  File "/home/genetik/bcbio/share/bcbio/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 "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 148, in variant2pipeline
    samples = region.parallel_prep_region(samples, run_parallel)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/region.py", line 138, in parallel_prep_region
    "piped_bamprep", _add_combine_info, file_key, ["config"])
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/split.py", line 59, in parallel_split_combine
    split_output = parallel_fn(parallel_name, split_args)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 800, in __call__
    while self.dispatch_one_batch(iterator):
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 658, in dispatch_one_batch
    self._dispatch(tasks)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 566, in _dispatch
    job = ImmediateComputeBatch(batch)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 180, in __init__
    self.results = batch()
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in __call__
    return [func(*args, **kwargs) for func, args, kwargs in self.items]
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
    return apply(f, *args, **kwargs)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 120, in piped_bamprep
    return bamprep.piped_bamprep(*args)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/bamprep.py", line 142, in piped_bamprep
    _piped_bamprep_region(data, region, out_file, tmp_dir)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/bamprep.py", line 120, in _piped_bamprep_region
    _piped_bamprep_region_gatk(data, region, prep_params, out_file, tmp_dir)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/bamprep.py", line 89, in _piped_bamprep_region_gatk
    prep_params)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/bamprep.py", line 62, in _piped_realign_gatk
    do.run(cmd, "GATK pre-alignment {0}".format(region), data)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
    _do_run(cmd, checks, log_stdout)
  File "/home/genetik/bcbio/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; unset JAVA_HOME && export PATH=/home/genetik/bcbio/share/bcbio/anaconda/bin:$PATH && /home/genetik/bcbio/share/bcbio/anaconda/bin/gatk-framework -Xms750m -Xmx2000m -XX:+UseSerialGC -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment realign recal -o /home/genetik/calling/haloplex/160708_M00568_0174_000000000-ARHBP/calling/work/bamprep/16-4623/chr1/tx/tmp8gCxnZ/16-4623-sort-chr1_0_25870287-prep-prealign.bam
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.6-24-g59fd391):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid argument value 'realign' at position 6.
##### ERROR Invalid argument value 'recal' at position 7.
##### ERROR ------------------------------------------------------------------------------------------
' returned non-zero exit status 1

Pär -- thanks for the additional details, this helps a lot to identify the bug. This was a problem with the transition to using GATK 3.6 (which has realignment in the freely available version). There was a bug in the code that used realignment but not recalibration. If you update to the latest development version it should work cleanly for you now. Sorry about the problem and thank you for the help tracking it down.

Great, thanks!

authors: chapmanb parlar


text:
Box Characters not showing

When viewing the font "Source Sans Pro" multiple Box Characters such as U+251C are not listed in the Characters Pane. The same Box Characters are verified as present in the font by viewing it in Windows Character Map under Unicode Subrange "Box Characters".
I became aware of the issue because I was using Source Sans Pro in Notepad++ and was able to enter the characters but not able to browse them in Character Map UWP.
I hope this can be resolved because Character Map UWP is infinitely superior to Windows Character Map but it does need to be accurate for me to use it.

Do you know what version of Source Sans Pro you're using? The ones I have installed show fine 🤔

authors: JohnnyWestlake edwinbradford

repo: character-map-uwp/Character-Map-UWP


text:
安卓视频被重命名以后，还是会读到之前的路径，然后拿着这个路径播放的话就会报错

缓存很严重，在相册里将视频删除后 还是会读到路径和缩略图。

缓存很严重，在相册里将视频删除后 还是会读到路径和缩略图。

安卓还是iOS
Caoyunxiao
在2020年10月12日 14:58，Zuozihaonotifications@github.com 写道：
缓存很严重，在相册里将视频删除后 还是会读到路径和缩略图。
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub, or unsubscribe.

安卓还是iOS Caoyunxiao 在2020年10月12日 14:58，Zuozihaonotifications@github.com 写道： 缓存很严重，在相册里将视频删除后 还是会读到路径和缩略图。 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

安卓

authors: Zuozihao charlesYun


text:
Add a basic contributing guide.

Hello @charleskorn,
thanks for your contribution to open source. This tool has made my life easier.
It's not much, but I'd like to start a contributing guide to make it easier for other to collaborate.
Best regards.

Great idea, thanks @pameck!

authors: charleskorn pameck

repo: charleskorn/batect


text:
Preload Language Data Once, then Set in Engine

In my program I am using 10 or so TesseractEngines to work in parallel. One of the issues I am seeing (that could be an enhancement) is that each time you create a new TesseractEngine instance, it has to reload the training data.
It would be great if you could just load it once and "send it into" the engine. The eng language file for v4.0 is ~22MB, but when you make 10 engines, you're then putting ~220MB in memory, way more than you need.
This would be a great improvement for parallelization.

I now realize that it is an issue for the cpp library and not this one, sorry!

repo: charlesw/tesseract


text:
Error on creating TesseractEngine

Hi!
I'm starting with Tesseract and have this code, that runs very well on Windows:
using (var engine = new TesseractEngine("tessdata", "por"))
{
    var image = Pix.LoadFromFile(filePath);

    var page = engine.Process(image);

    text = page.GetText();
}

But I need run this one on Linux, most specifically on Mint distribution, and I use in this form:
using (var engine = new TesseractEngine("./tessdata", "por"))
{
    var image = Pix.LoadFromFile(filePath);

    var page = engine.Process(image);

    text = page.GetText();
}

And I receive this error in the 'new TesseractEngine' line:

Unhandled exception. System.Reflection.TargetInvocationException: Exception has been thrown by the target of an invocation.
---> System.ArgumentNullException: Value cannot be null. (Parameter 'path1')
at System.ArgumentNullException.Throw(String paramName)
at System.IO.Path.Combine(String path1, String path2)
at InteropDotNet.LibraryLoader.InternalLoadLibrary(String baseDirectory, String platformName, String fileName)
at InteropDotNet.LibraryLoader.CheckExecutingAssemblyDomain(String fileName, String platformName)
at InteropDotNet.LibraryLoader.LoadLibrary(String fileName, String platformName)
at InteropRuntimeImplementer.LeptonicaApiSignaturesInstance.LeptonicaApiSignaturesImplementation..ctor(LibraryLoader loader)
at System.RuntimeMethodHandle.InvokeMethod(Object target, Void** arguments, Signature sig, Boolean isConstructor)
at System.Reflection.MethodBaseInvoker.InvokeDirectByRefWithFewArgs(Object obj, Span1 copyOfArgs, BindingFlags invokeAttr)    --- End of inner exception stack trace ---    at System.Reflection.MethodBaseInvoker.InvokeDirectByRefWithFewArgs(Object obj, Span1 copyOfArgs, BindingFlags invokeAttr)
at System.Reflection.MethodBaseInvoker.InvokeWithOneArg(Object obj, BindingFlags invokeAttr, Binder binder, Object[] parameters, CultureInfo culture)
at System.RuntimeType.CreateInstanceImpl(BindingFlags bindingAttr, Binder binder, Object[] args, CultureInfo culture)
at InteropDotNet.InteropRuntimeImplementer.CreateInstanceT
at Tesseract.Interop.LeptonicaApi.Initialize()
at Tesseract.Interop.TessApi.Initialize()
at Tesseract.Interop.TessApi.get_Native()
at Tesseract.TesseractEngine..ctor(String datapath, String language, EngineMode engineMode, IEnumerable1 configFiles, IDictionary2 initialOptions, Boolean setOnlyNonDebugVariables)
at Tesseract.TesseractEngine..ctor(String datapath, String language)
at TesteConversaoPdfParaImagem.Program.ReadImage(String prefix, String filePath, String resultFileName, Boolean isSingleblock) in C:\Users\carlo\source\repos\TesteConversaoPdfParaImagem\TesteConversaoPdfParaImagem\Program.cs:line 127
at TesteConversaoPdfParaImagem.Program.Main(String[] args) in C:\Users\carlo\source\repos\TesteConversaoPdfParaImagem\TesteConversaoPdfParaImagem\Program.cs:line 53

Do you help me with this, please?
Thanks a lot, guys! :)

System.ArgumentNullException: Value cannot be null. (Parameter 'path1')
at System.ArgumentNullException.Throw(String paramName)
at System.IO.Path.Combine(String path1, String path2)

I am not expert but, its definitely about your path :D.
I would Console.WriteLine(filePath); to see what is result of your Path.Combine. Probably you have null there.

Yesterday I discovered the same error on the project that I just started. When I debug from Visual Studio there is no issue. When I publish and run it somewhere else, I get the same error message.

I discovered that I get the error when I enable the checkbox "Produce single file". When it's enabled I get the error. When it's disabled, I don't get the error.
In both situations the tessdata folder is on the same location (on the same level as my console executable). Also in both situations I confirmed my code was pointing to the right location by adding a console message:
string tesseractDataPath = Path.Combine(AppContext.BaseDirectory, "tessdata"); Console.WriteLine($"Tesseract data folder: {tesseractDataPath}"); using var ocrEngine = new TesseractEngine(tesseractDataPath, "nld+eng", EngineMode.Default);

Hi guys!
I found the error. It's happen on the class 'InteropDotNet.LibraryLoader', at the line 86:
var baseDirectory = Path.GetDirectoryName(executingAssembly.Location);
The code executingAssembly.Location return null and it's the cause of the crash. I created a handler class called 'EnvironmentUtils.cs' in 'Tesseract.Internal' with this code:
` using System;
using System.IO;
using System.Reflection;
namespace Tesseract.Internal
{
internal static class EnvironmentUtils
{
public static string AppPath(Assembly assembly)
{
string appPath = Path.GetDirectoryName(Path.GetDirectoryName(assembly?.Location));
        if (!string.IsNullOrWhiteSpace(appPath))
            return appPath;

        return AppPath();
    }

    public static string AppPath()
    {
        string appPath;

        appPath = Directory.GetCurrentDirectory();

        if (!string.IsNullOrWhiteSpace(appPath))
            return appPath;

        appPath = Environment.CurrentDirectory;

        if (!string.IsNullOrWhiteSpace(appPath))
            return appPath;

        appPath = Path.Combine(AppContext.BaseDirectory, "tessdata");

        if (!string.IsNullOrWhiteSpace(appPath))
            return appPath;

        appPath = Path.GetDirectoryName(Path.GetDirectoryName(Assembly.GetEntryAssembly()?.Location));

        if (!string.IsNullOrWhiteSpace(appPath))
            return appPath;

        appPath = AppDomain.CurrentDomain.BaseDirectory;

        if (!string.IsNullOrWhiteSpace(appPath))
            return appPath;

        throw new ArgumentNullException("Application path not found");
    }
}

} `
And the problem has solved. But after this, the error change to this:
Unhandled exception. System.Reflection.TargetInvocationException: Exception has been thrown by the target of an invocation. ---> System.DllNotFoundException: Failed to find library "libleptonica-1.82.0.so" for platform x64.    at InteropDotNet.LibraryLoader.LoadLibrary(String fileName, String platformName) in D:\git\tesseract\src\Tesseract\Internal\InteropDotNet\LibraryLoader.cs:line 57    at InteropRuntimeImplementer.LeptonicaApiSignaturesInstance.LeptonicaApiSignaturesImplementation..ctor(LibraryLoader loader)    at System.RuntimeMethodHandle.InvokeMethod(Object target, Void** arguments, Signature sig, Boolean isConstructor)    at System.Reflection.MethodBaseInvoker.InvokeDirectByRefWithFewArgs(Object obj, Span1 copyOfArgs, BindingFlags invokeAttr)
--- End of inner exception stack trace ---
at System.Reflection.MethodBaseInvoker.InvokeDirectByRefWithFewArgs(Object obj, Span1 copyOfArgs, BindingFlags invokeAttr)    at System.Reflection.MethodBaseInvoker.InvokeWithOneArg(Object obj, BindingFlags invokeAttr, Binder binder, Object[] parameters, CultureInfo culture)    at System.RuntimeType.CreateInstanceImpl(BindingFlags bindingAttr, Binder binder, Object[] args, CultureInfo culture)    at InteropDotNet.InteropRuntimeImplementer.CreateInstance[T]() in D:\git\tesseract\src\Tesseract\Internal\InteropDotNet\InteropRuntimeImplementer.cs:line 45    at Tesseract.Interop.LeptonicaApi.Initialize() in D:\git\tesseract\src\Tesseract\Interop\LeptonicaApi.cs:line 563    at Tesseract.Interop.TessApi.Initialize() in D:\git\tesseract\src\Tesseract\Interop\BaseApi.cs:line 583    at Tesseract.Interop.TessApi.get_Native() in D:\git\tesseract\src\Tesseract\Interop\BaseApi.cs:line 372    at Tesseract.TesseractEngine..ctor(String datapath, String language, EngineMode engineMode, IEnumerable1 configFiles, IDictionary2 initialOptions, Boolean setOnlyNonDebugVariables) in D:\git\tesseract\src\Tesseract\TesseractEngine.cs:line 181    at Tesseract.TesseractEngine..ctor(String datapath, String language) in D:\git\tesseract\src\Tesseract\TesseractEngine.cs:line 37    at TesteConversaoPdfParaImagem.Program.ReadImage(String prefix, String filePath, String resultFileName, Boolean isSingleblock) in C:\Users\carlo\source\repos\TesteConversaoPdfParaImagem\TesteConversaoPdfParaImagem\Program.cs:line 147    at TesteConversaoPdfParaImagem.Program.Extract(String pdfName, String readedFilePath) in C:\Users\carlo\source\repos\TesteConversaoPdfParaImagem\TesteConversaoPdfParaImagem\Program.cs:line 68    at TesteConversaoPdfParaImagem.Program.Main(String[] args) in C:\Users\carlo\source\repos\TesteConversaoPdfParaImagem\TesteConversaoPdfParaImagem\Program.cs:line 14
In the next week I expect return to see this new problem.
Thank's for your help :)

Thanks, I'll see if I can find some time this evening to put in a fix. If I
don't, feel free to create a push request with fix and I'll merge it in.
Sorry haven't been all that active lately, pretty much all my free time is
taken up with home Reno's/repairs.
On Sun, 30 June 2024, 4:53 am Carlos Felippe Vernizze, <
@.***> wrote:

Hi guys!
I found the error. It's happen on the class 'InteropDotNet.LibraryLoader',
at the line 86:
var baseDirectory = Path.GetDirectoryName(executingAssembly.Location);
The code executingAssembly.Location return null and it's the cause of the
crash. I created a handler class called 'EnvironmentUtils.cs' in
'Tesseract.Internal' with this code:
` using System;
using System.IO;
using System.Reflection;
namespace Tesseract.Internal
{
internal static class EnvironmentUtils
{
public static string AppPath(Assembly assembly)
{
string appPath =
Path.GetDirectoryName(Path.GetDirectoryName(assembly?.Location));
    if (!string.IsNullOrWhiteSpace(appPath))
        return appPath;

    return AppPath();
}

public static string AppPath()
{
    string appPath;

    appPath = Directory.GetCurrentDirectory();

    if (!string.IsNullOrWhiteSpace(appPath))
        return appPath;

    appPath = Environment.CurrentDirectory;

    if (!string.IsNullOrWhiteSpace(appPath))
        return appPath;

    appPath = Path.Combine(AppContext.BaseDirectory, "tessdata");

    if (!string.IsNullOrWhiteSpace(appPath))
        return appPath;

    appPath = Path.GetDirectoryName(Path.GetDirectoryName(Assembly.GetEntryAssembly()?.Location));

    if (!string.IsNullOrWhiteSpace(appPath))
        return appPath;

    appPath = AppDomain.CurrentDomain.BaseDirectory;

    if (!string.IsNullOrWhiteSpace(appPath))
        return appPath;

    throw new ArgumentNullException("Application path not found");
}

}
} `
And the problem has solved. But after this, the error change to this:
Unhandled exception. System.Reflection.TargetInvocationException:
Exception has been thrown by the target of an invocation. --->
System.DllNotFoundException: Failed to find library "
libleptonica-1.82.0.so" for platform x64. at
InteropDotNet.LibraryLoader.LoadLibrary(String fileName, String
platformName) in
D:\git\tesseract\src\Tesseract\Internal\InteropDotNet\LibraryLoader.cs:line
57 at
InteropRuntimeImplementer.LeptonicaApiSignaturesInstance.LeptonicaApiSignaturesImplementation..ctor(LibraryLoader
loader) at System.RuntimeMethodHandle.InvokeMethod(Object target, Void**
arguments, Signature sig, Boolean isConstructor) at
System.Reflection.MethodBaseInvoker.InvokeDirectByRefWithFewArgs(Object
obj, Span1 copyOfArgs, BindingFlags invokeAttr)
--- End of inner exception stack trace ---
at System.Reflection.MethodBaseInvoker.InvokeDirectByRefWithFewArgs(Object
obj, Span1 copyOfArgs, BindingFlags invokeAttr) at
System.Reflection.MethodBaseInvoker.InvokeWithOneArg(Object obj,
BindingFlags invokeAttr, Binder binder, Object[] parameters, CultureInfo
culture) at System.RuntimeType.CreateInstanceImpl(BindingFlags bindingAttr,
Binder binder, Object[] args, CultureInfo culture) at
InteropDotNet.InteropRuntimeImplementer.CreateInstanceT in
D:\git\tesseract\src\Tesseract\Internal\InteropDotNet\InteropRuntimeImplementer.cs:line
45 at Tesseract.Interop.LeptonicaApi.Initialize() in
D:\git\tesseract\src\Tesseract\Interop\LeptonicaApi.cs:line 563 at
Tesseract.Interop.TessApi.Initialize() in
D:\git\tesseract\src\Tesseract\Interop\BaseApi.cs:line 583 at
Tesseract.Interop.TessApi.get_Native() in
D:\git\tesseract\src\Tesseract\Interop\BaseApi.cs:line 372 at
Tesseract.TesseractEngine..ctor(String datapath, String language,
EngineMode engineMode, IEnumerable1 configFiles, IDictionary2
initialOptions, Boolean setOnlyNonDebugVariables) in
D:\git\tesseract\src\Tesseract\TesseractEngine.cs:line 181 at
Tesseract.TesseractEngine..ctor(String datapath, String language) in
D:\git\tesseract\src\Tesseract\TesseractEngine.cs:line 37 at
TesteConversaoPdfParaImagem.Program.ReadImage(String prefix, String
filePath, String resultFileName, Boolean isSingleblock) in
C:\Users\carlo\source\repos\TesteConversaoPdfParaImagem\TesteConversaoPdfParaImagem\Program.cs:line
147 at TesteConversaoPdfParaImagem.Program.Extract(String pdfName, String
readedFilePath) in
C:\Users\carlo\source\repos\TesteConversaoPdfParaImagem\TesteConversaoPdfParaImagem\Program.cs:line
68 at TesteConversaoPdfParaImagem.Program.Main(String[] args) in
C:\Users\carlo\source\repos\TesteConversaoPdfParaImagem\TesteConversaoPdfParaImagem\Program.cs:line
14
In the next week I expect return to see this new problem.
Thank's for your help :)
—
Reply to this email directly, view it on GitHub
https://github.com/charlesw/tesseract/issues/673#issuecomment-2198300967,
or unsubscribe
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.
You are receiving this because you are subscribed to this thread.Message
ID: @.***>

authors: Vernizze Yanik39 charlesw mitchuhl


text:
[Feature] Support for non-uint8 and/or non-RGB images

Following up on #15, supporting say uint16 images and say grayscale images would allow more widespread utility of the package.

Support for grayscale and common dtypes added

authors: charliebudd tvercaut

repo: charliebudd/torch-content-area


text:
Modify the log_dir and log_dir_pretrain

What file should to put in the path of log_dir and  log_dir_pretrain

Hi Yao1up, these directories are the parent directories where you store the models, please check the following lines.
https://github.com/charliememory/Disentangled-Person-Image-Generation/blob/e4703860bb1b351050ce50f339985ff0811f1d64/run_market_train.sh#L19
https://github.com/charliememory/Disentangled-Person-Image-Generation/blob/e4703860bb1b351050ce50f339985ff0811f1d64/run_market_train.sh#L48


text:
v0.0.271 pipeline failing on homebrew

Not sure if this belongs here but the pipeline is failing thus my brew and pre-commit versions are out of sync (select = ["ALL"] user here). I have since uninstalled homebrew and installed using pipx. just FYI

It looks like this is because they need to upgrade to the latest version of Rust still https://github.com/Homebrew/homebrew-core/pull/132584

Thank you so much @chenrui333.

authors: ColemanDunn charliermarsh madkinsz

repo: charliermarsh/ruff


text:
Avoid autofixing within nested f-strings

Summary
The permitted grammar within a nested f-string is really hard to work with. For example, there's typically no way to include quotation marks, unless one of the surrounding strings is triple-quoted? Or something like that. So, again, for example, our rule that flags usages of str() can run into problems when it sees f"{f'{str()}'}" -- there's no way to rewrite str() as "" or ''.
I've turned off that specific rule in nested f-strings, but this PR goes one step further, and just avoids attempting to autofix within nested f-strings altogether. This is a pretty bad fix, since we'll still end up using unparse_expr within nested f-strings to format some diagnostics, which means we'll show users code and suggestions that won't quite work. But, our options are pretty limited here.

Would this require that we go through every rule and add a check for ctx.in_nested_f_string(), and use the appropriate applicability method if so?

Would this require that we go through every rule and add a check for ctx.in_nested_f_string(), and use the appropriate applicability method if so?

Hmm yeah. That sounds annoying and very fragile

One note to add here is that most of these will valid syntax with PEP 701 implemented, currently targeted for python 3.12, i.e. we could very ambitiously allow autofixes in f-strings for projects with minimum python version 3.12.
Originally posted by @konstin in https://github.com/charliermarsh/ruff/issues/4324#issuecomment-1540775994

authors: MichaReiser T-256 charliermarsh


text:
spanGaps does not work well

I am using v2.1.6
I tried to create continuous line when there is a null point in the middle.
However, it does not work well in some situations.
For example
  {
    label: "A random label",
    data: [20, 30, 80, 90, 50, null, 30],
    spanGaps: true
  }

    {
      label: "A random label",
      data: [20, 30, 80, 90, null, 20, 30],
      spanGaps: true
    }

@etimberg I would like to work on this issue any recommendations on where to start file wise, if no one else is not working on it already.

Looking a it now this should not be too hard to fix. It only occurs when the line tension is et to something that is not equal to 0 which leads me to believe  it is an issue the way the iff statements are setup in this code.
else if (point._view.tension === 0) {
				ctx.lineTo(point._view.x, point._view.y);
			} else {
				// Line between points
				ctx.bezierCurveTo(
					previousPoint._view.controlPointNextX,
					previousPoint._view.controlPointNextY,
					point._view.controlPointPreviousX,
					point._view.controlPointPreviousY,
					point._view.x,
					point._view.y
				);
			}

I will continue looking it to this and try to fix it :)

@nmac143 feel free to work on this :)

@etimberg Hi, v2.2.0 did not fix this issue. I updated to v2.2.0, but still same.

@eemikula thanks! works well now

authors: Hongbo-Miao etimberg nmac143


text:
options.events property works weird

I want to make my chart static and not to show any tooltips and/or hover highlighting.
So I set options.events = [] for chart. This doesn't work
https://jsfiddle.net/wcfp91bh/
If I set options.events = ["fakeEvent"]. This works better but still provides tooltips for "click" event
https://jsfiddle.net/h7g8hngn/
Idk, but seems it shouldn't work like this.
Any comments?

You can set the global option like this:
Chart.defaults.global.tooltips.enabled = false;
Then it will be work. You can try it.

@rain-js thanks for this tip. I know it.
The problem is not in tooltips but in any event based behavior. I don't want lines and points to be highlighted and hovered as well.
If I do add tooltips.enabled = false to chart's options  you can see that this won't help to achieve what I want. That's better can be seen on Doughnut
https://jsfiddle.net/7ewnxsu6/

I'm not sure why option.events = [] doesn't work properly. As described in doc this assignment should remove any reaction of chart to mouse/touch or other events. Obviously it doesn't which looks like wrong behavior. Also I don't understand why option.events = ["fake"] actually works for some events (mouseover event) but not all (click event).

@demoalex uh, i got it. You also can set the global option like this.
Chart.defaults.global.events = [];
Then it will remove any reaction of chart to mouse/touch or other events.
Try it.

@demoalex You are right.
option,events = [ ]
It won't work. I think it's a bug.@etimberg
but you also can set the global option:
Chart.defaults.global.events = [];
It can solve your problem right now.

Yeah, this looks like a bug. I think it might be in the code that merges properties from the global config to the local config.

authors: demoalex etimberg rain-js


text:
Remove moment from public API

We should remove moment from the public API and just use timestamps and Dates
We should also consider dropping support for Moment entirely since it's purely worse than Luxon. I would especially like to get rid of Moment since it lacks timezone support and is very large

I've been switching everything over to Luxon, but cannot switch web apps that use Chart.js since Chart.js needs Moment anyway. How much of Moment does Chart.js actually use? And could it be replaced with a (much smaller) utility?

@jazoom you may be interested inhttps://github.com/chartjs/Chart.js/pull/5522

@benmccann Thanks for pointing that out. I searched the issues but didn't find that one for some reason.

@benmccann any idea what the hold-up is for accepting #5522 pull request?

The reviewers are all busy and doing this just as a volunteer effort on top of their day jobs

OK, thanks for clarifying, just wondering if there was some deeper refactoring required or if it somehow hinged on a future major release. Looking forward to its acceptance so that moment.js stops bloating production builds!

Hi, I don't know Luxon but you could consider dayjs?
In my app I just did a search and replace moment ->  dayjs and everything worked fine.

@AoDev did the same. It hasn't been a simple search and replace but I was able to migrate the whole app from moment to dayjs within 15minutes (the only issue i encountered: en-gb locale which worked in moment has to be renamed to en in day js).
Now I need to get rid of the moment dependency of chartjs

date-fns would be a good option since you can require/import just the functions you need without bundling the entire library... I am able to get chart.js to work fine using chartjs-plugin-datalabels but I have to add moment as an external in the webpack config to prevent it from getting bunded (because of chart.js). This is more of a nuisance then it sounds since I'm using create-react-app

Perhaps using dayjs, which offers the same functionalities as moment.js, but with a fraction of the bundle size, would be a better option IMHO

authors: AoDev benmccann darkmavis1980 edclement gonzochic jazoom shongololo


text:
JavaScript warnings: reference to undefined property + test for equality misstyped?   (latest release)

WARNINGS:
SyntaxError: test for equality (==) mistyped as assignment (=)?
Chart.bundle.js:1000:37
SyntaxError: test for equality (==) mistyped as assignment (=)?
Chart.bundle.js:1010:38
SyntaxError: test for equality (==) mistyped as assignment (=)?
Chart.bundle.js:1016:37
SyntaxError: test for equality (==) mistyped as assignment (=)?
Chart.bundle.js:1022:41
SyntaxError: test for equality (==) mistyped as assignment (=)?
Chart.bundle.js:1092:34
SyntaxError: test for equality (==) mistyped as assignment (=)?
Chart.bundle.js:1095:33
SyntaxError: test for equality (==) mistyped as assignment (=)?
Chart.bundle.js:1220:44
SyntaxError: test for equality (==) mistyped as assignment (=)?
Chart.bundle.js:1222:43
ReferenceError: reference to undefined property "abbr"
Chart.bundle.js:13692:21

ReferenceError: reference to undefined property "id"
Chart.bundle.js:7197:7
ReferenceError: reference to undefined property "devicePixelRatio"
Chart.bundle.js:8484:3
ReferenceError: reference to undefined property "devicePixelRatio"
Chart.bundle.js:8537:3
ReferenceError: reference to undefined property "xAxes"
Chart.bundle.js:8561:3
ReferenceError: reference to undefined property "bodyFontFamily"
Chart.bundle.js:7523:3
ReferenceError: reference to undefined property "_data"
Chart.bundle.js:3181:7
ReferenceError: reference to undefined property "fontSize"
Chart.bundle.js:2642:14
ReferenceError: reference to undefined property "label"
Chart.bundle.js:4648:5
ReferenceError: reference to undefined property "fontColor"
Chart.bundle.js:18630:20
ReferenceError: reference to undefined property "lineCap"
Chart.bundle.js:18657:5prefixesprefixes

In javascript console of firefox 68.0.2 64bit on Ubuntu 18.04.
Using: https://cdnjs.cloudflare.com/ajax/libs/Chart.js/2.8.0/Chart.bundle.js
See live demo here:
http://community-registry.ff-hamm.de/

Charts are loading, but i can see WARNINGS (22) and DEBUG (1) messages in Firefox JavaScript Console. See screenshot:

Her tested on a private tab in Firefox, to be sure that it is not a Browser plugin that makes trouble...

I can't reproduce the warnings?

Same errors on Firefox 70.0.1 on Windows 10.

These problems do not occure in Chrome 78.0.3904.70 on Windows 10.
Did you tried to reproduce it with a firefox?

@kurkle @benmccann

If I load https://www.chartjs.org/samples/latest/charts/pie.html on Firefox for Linux I do not see any issues in the console

Regarding my earlier comment (https://github.com/chartjs/Chart.js/issues/6488#issuecomment-524934609), Chart.js 2.9.2 will have a fix for the chartjs-color syntax issues.

I am using 2.8.0, i will test 2.9.1.

same issue on 2.9.1, i will wait for 2.9.2

I updated to 2.9.3. And my Firefox is now a 70.0.1.
SyntaxErrors dropped from 8 to 6 entries.
"reference to undefined property" has increased from 12 to 13 entries.
But this do not relate to 2.9.3. With 2.9.1 the numbers are the same.
So your color fix did not fixed that.

I recommend to add "sourceMappingURL" to your minified javascript file and to provide a source map. This makes debugging easyer and would enable your browser to provide real-world line numbers. See: https://developer.mozilla.org/de/docs/Tools/Debugger/How_to/Use_a_source_map for details.
This may help you to fix the "SyntacErrors":
https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Errors/Equal_as_assign
As your script want to be executed in strict mode.
Also recommend to use ESLint to lint your java script source code.

@christian-weiss when I view http://community-registry.ff-hamm.de/ in Firefox 70.0.1 on Linux I do not see any warnings in the console.
Also, when I look at line 7 character 179 I do not see any reference to moment as your screenshot suggests
We do use eslint

Strange is can see it at 3 systems (2x Windows 10, 1x Ubuntu 19.10), always latest Firefox, even weeks later on latest.
I can not reproduce it on 2 other Systems (1x Ubuntu, 1x MacOS). And even not with Ubuntu 19.10 from osboxes.org (Virtualbox).
So i guess it is something system-specific - but it is not related to Plugins (tested on private tabs), not related to Firefox-Profiles (fresh profile), not related to cache - strange.
I close the ticket as i will ignore that warnings now (investigation already took alot of time). If if finde something more, i may re-open the issue in the future.

authors: benmccann christian-weiss kurkle


text:
Bower package for 2.9.4 release is not including dist folder and files

Expected Behavior
Using bower install for 2.9.4 should install distribution package
e.g. include "dist" folder and files
Current Behavior
Package installs the gihub repo code
Steps to Reproduce
Run "bower install" with 2.9.4 release as a dependency
Context
Existing builds fail as the 'dist' folder and expected files are missing

Can this problem be fixed as soon as possible?

bower.json is missing

Hello,
Same problem here.
Our project uses angular-chart.js dependency, and angular-chart.js bower.json is too permissive (version 2.X of Chart.js).
Chart.js version 2.9.3 is OK, but version 2.9.4 fails, so our web application crashs.
Can we help you to solve the problem ?

@f3cp @HereWeR @pblanchardie @fresnault I believe I have fixed this issue by repushing the v2.9.4 tag here on GitHub. I can see the dist folder & bower.json file. Can you confirm that this works for you?

@etimberg It's good for us after clean bower cache. Thank you for fixing this so quickly.

authors: HereWeR etimberg f3cp fresnault pblanchardie


text:
Make moment optional from our UMD builds

Create a rollup plugin altering the UMD header to wrap optional dependencies between try/catch, which allows to load moment only when the dependency is installed.
Since AMD loaders are asynchronous, 'moment' needs to be explicitly loaded before 'chart.js' so when 'chart.js' requires moment, it's already loaded and returns synchronously (at least with requirejs).
require(['moment'], function() {
    require(['chartjs'], function(Chart) {
        new Chart('chart', {
            //...

Still need to write a bit of docs and do more testing.
UMD wrapper in dist/Chart.js:
Before:
(function (global, factory) {
    typeof exports === 'object' && typeof module !== 'undefined' ? module.exports = factory(require('moment')) :
    typeof define === 'function' && define.amd ? define(['moment'], factory) :
    (global.Chart = factory(global.moment));
}(this, (function (moment) { 'use strict';

After:
(function (global, factory) {
    typeof exports === 'object' && typeof module !== 'undefined' ? module.exports = factory(function() { try { return require('moment'); } catch(e) { } }()) :
    typeof define === 'function' && define.amd ? define(['require'], function(require) { return factory(function() { try { return require('moment'); } catch(e) { } }()); }) :
    (global.Chart = factory(global.moment));
}(this, (function (moment) { 'use strict';

Related to #5960
Fixes #4303

Please see the latest docs for details: https://github.com/chartjs/Chart.js/blob/master/docs/getting-started/integration.md

I use chartjs with angular-cli. So I build angular app like ng build --prod. And anguar cli  does not use not webpack nor Rollup. So how can I configure angular project to exclude moment?

look like it is inposible use externals  and angular cli

@lsn793 I'm not familiar with angular / angular-cli, can you share a/your project that uses chart.js?

@lsn793 Can you also try removing the package after install and seeing if complication will succeed in that case? https://github.com/chartjs/Chart.js/pull/5978#issuecomment-453769800

@benmccann  I tried like you advise but got error while build
WARNING in ./node_modules/chart.js/dist/Chart.js
Module not found: Error: Can't resolve 'moment' in 'C:\Users\Serg\dev\calc-weight\node_modules\chart
.js\dist'
And chart is not work

@simonbrunel  https://github.com/lsn793/calc-weight

My workaround for this problem in Angular is to use file replacement. In your angular.json, modify your production environment (and any other environment from which you want to exclude Moment) as follows:
"production": {
  "fileReplacements": [
    {
      "replace": "src/environments/environment.ts",
      "with": "src/environments/environment.prod.ts"
    },
    {
      "replace": "node_modules/moment/moment.js",
      "with": "src/environments/support/moment.js"
    }
  ]

Where src/environments/support/moment.js is an empty module exporting null.
It's a bit of a hack, as file replacements aren't really intended for this, but it seems to be the only way to get it to work.

FWIW I would also propose making a breaking change that changes Moment to a peer dependency, releasing it as v3.0.0, and making v4 the future "big" release.
I understand the desire to make the version numbers correspond to "important" releases with lots of features, but I'm not sure that desire should override making the correct technical solution. In the end, a version number is just a version number.

authors: benmccann jonrimmer lsn793 simonbrunel


text:
Fix docs global fonts property matching current API

This PR refactors example code, documentation in general/fonts.

This is the correct syntax for the current API, what you are trying to make it to is the old V2 syntax, if you look at this fiddle for example you see that the default fontSize is set correctly: https://jsfiddle.net/Leelenaleee/caqxh04t/2/

Thanks for explanation! pardon me.


text:
[BUG]  中文提问 输出中英文混杂

问题描述 / Problem Description
用简洁明了的语言描述这个问题 / Describe the problem in a clear and concise manner.

模型的问题，需要设置好提示词和选择更好的模型

authors: hepengyue zRzRzRzRzRzRzR

repo: chatchat-space/Langchain-Chatchat


text:
⚠ Chatwoot has degraded performance

In bf1ef9a, Chatwoot (https://app.chatwoot.com) experienced degraded performance:

HTTP code: 503
Response time: 3247 ms

Resolved: Chatwoot performance has improved in 1783589.

repo: chatwoot/status


text:
Started getting "savepoint transactional_testing_X does not exist" errors since v1

I'm not quite sure what happened, but exactly the same code throws an error in v1 and doesn't in v0.5.0, using prisma v4.15.0.

Happened in two different projects that use this library.
This is the code that builds the tests:
import { TestingModule, TestingModuleBuilder } from '@nestjs/testing';

import { AuthenticationService } from '../../../src/user/authentication/authentication.service';
import { ConfigService } from '@nestjs/config';
import { PostgreSqlContainer } from 'testcontainers';
import { PrismaService } from '../../../src/prisma/prisma.service';
import { PrismaTestingHelper } from '@chax-at/transactional-prisma-testing';
import { S3Service } from '../../../src/aws/s3/s3.service';
import { getRandomFreePort } from './get-random-free-port';
import { prismaReset } from './prisma-reset';
import { prismaSeed } from './prisma-seed';

export const buildTest = async (
  testID: string,
  testModuleFixture: TestingModuleBuilder,
) => {
  const pgPort = await getRandomFreePort();
  const dbUrl = `postgresql://${testID}:${testID}@localhost:${pgPort}/${testID}?schema=public`;
  const container = await new PostgreSqlContainer()
    .withExposedPorts({ container: 5432, host: pgPort })
    .withName(`${testID}-${pgPort}`)
    .withDatabase(testID)
    .withUsername(testID)
    .withPassword(testID)
    .start();

  await prismaReset(dbUrl);

  let prismaService = new PrismaService({
    datasources: { db: { url: dbUrl } },
  });
  await prismaService.$connect();

  const prismaTestingHelper = new PrismaTestingHelper(prismaService);
  prismaService = prismaTestingHelper.getProxyClient();

  const moduleFixture: TestingModule = await testModuleFixture
    .overrideProvider(ConfigService)
    .useValue({
      get: (value: string) =>
        value === 'DATABASE_URL' ? dbUrl : process.env[value],
    })
    .overrideProvider(PrismaService)
    .useValue(prismaService)
    .compile();

  const app = moduleFixture.createNestApplication();

  prismaService = app.get(PrismaService);

  await Promise.all([app.init(), prismaSeed(dbUrl)]);

  return {
    app,
    prismaService,
    beforeEach: async () => {
      await prismaTestingHelper.startNewTransaction({ timeout: 10000 });
    },
    afterEach: async () => {
      prismaTestingHelper.rollbackCurrentTransaction();
    },
    afterAll: async () => {
      await prismaService.$disconnect();
      await app.close();
      await container.stop();
    },
  };
};

Is it possible that you don't (completely) await all functions that call queries in your test? e.g. something like this
async function firstTest() {
  // ...
  const user = userService.loadUserFromDb(3); // note the missing "await"
}

async function secondTest() {
  // This test will fail now
}

where userService.loadUserFromDb looks like this:
public async loadUSerFromDb(id: number) {
  await this.prismaService.user.findUnique({where: { id }});
}

I did publish a new pre-release version which improves the robustness of savepoint handling and logs a warning if the case mentioned above is detected. You can install it using
npm i -D @chax-at/transactional-prisma-testing@1.0.1-rc.1

This version fixes my own reproduction at least (and logs a warning), please tell me if it's working for you as well (or maybe throws a different error at least).

The fix I mentioned above landed in 1.1.0, if you have time, you can try it out. Otherwise, you can stay on 0.6.0 which doesn't have implicit query transaction/savepoints (in case you don't need it and don't want to deal with debugging).
I'll close the issue for now, assuming it's fixed - but please let me know if you're still encountering any issues with the new version! (I don't know if you can re-open the issue, but just comment here or open another issue in this case if re-opening doesn't work)

authors: DimosthenisK Valerionn

repo: chax-at/transactional-prisma-testing


text:
Allow for alternative color architectures (specifically base16)

Is your feature request related to a problem? Please describe.
I'm a happy user of "cheat" and have found its author to be a super guy, very responsive, and working hard on this great project. One thing I'd personally love to see is for it to use my terminal's current color configuration. Specifically, the excellent Base16 project.
Describe the solution you'd like
Rather than using a "chroma" theme, I'd like that cheat just use the colors currently provided by the shell. Using the base16-shell project, I can easily use a single theme for use in iTerm, Vim or any other CLI. I'd LOVE to be able to view my sheets using this theme as well.
I realize it's probably not a super urgent priority, but it's the ONE thing that keeps me from really enjoying using "cheat" as much as I would like.

Hi, @zeitchef
Thanks for the kind words. I'm glad to hear that you're enjoying cheat!
Regarding your request:
First of all, it's entirely sensible. I'm not afflicted with this personally because I use solarized-dark for everything, but I'd be hugely annoyed if I had your problem.

Rather than using a "chroma" theme, I'd like that cheat just use the colors currently provided by the shell.

Unfortunately, there's some complexity here. There's really no generalized way for cheat to use your shell colors. Rather, each color must be assigned on a per-token basis (keyword, variable, etc) by chroma's parser.
I can think of three possible solutions:
First and best solution
While it would not solve the problem in the general case, you might consider opening a pull-request against chroma which implements a base16 color scheme. Were you to succeed in that, I'd simply need to update cheat's chroma dependency, and then two projects would be improved, rather than one :slightly_smiling_face:
(For what it's worth, I corresponded with chroma's maintainer while refactoring cheat into Go, and can state that he's a pleasure to work with and a wonderful maintainer.)
Second, disgusting solution
bat appears to support the base16 color theme. If you have it installed on your system - and if you're only interested in bash syntax highlighting - you could create a cheat shell function, something like this:
#!/bin/bash
cheat () {
  cheat $1 | bat --theme=base16 --language=bash --style=plain
}

If you were to source that function (perhaps in a .bashrc file or somewhere), cheat would then invoke that function (rather than the executable directly), which would in turn pipe cheat's output through bat.
That's gross, but it might work?
Third solution
It may also be possible for me to provide users with a mechanism for manually passing color values to chroma's parser. This would probably require some work, but it would solve the problem in the most general case. (I'll look into this when I have some time.)
I hope that's helpful. Feel free to share any feedback here.

Hi @chrisallenlane,
I took your advice and submitted a pull request to the chroma project, which was just merged. While this solves my immediate issue, I do love the idea of a more robust way of customizing colors for cheat.
Thanks for your work!

Hi, @zeitchef
That's fantastic. Thanks for making both projects better! :confetti_ball:
I see that your work was merged on Oct 29, but the current latest release of chroma was published on Sept 22. That being the case, your work won't be available in cheat the next version of chroma is released.
The chroma maintainer is excellent, however, so this likely won't be long. Likewise, I have "dependabot" configured on cheat/cheat, so a PR will be submitted automatically once the upstream dependencies are updated.
So, this feature won't be available in cheat yet, but it likely will shortly :slightly_smiling_face:
Thanks!

Tagging as "blocked" while we await the upstream release.

@zeitchef, your changes have been released with cheat@4.2.0:
https://github.com/cheat/cheat/releases/tag/4.2.0
Thanks again!

authors: chrisallenlane zeitchef

repo: cheat/cheat


text:
Restructure Preprocessing Example Analysis

In this PR we restructure the example analysis for preprocessing to have GitHub-contained example data.
This follows the precedents for example analysis set in #8 and #9.
Notes:

For this PR review I have removed the example files. Once the PR review is done I will add them back. They prevent a reviewer from seeing differences.
Some of the input ND2 files were too large to include in this repo, so we will have to come up with a different method to make these accessible to outside users.

@mat10d This is ready for review, let me know if you have any questions!

Yep the goal of this does make sense and I remember seeing in the previous example file that the cell patterns lined up for part of the images (these are the cells that have overlapping data for SBS and PH image iirc).  I am now thinking that maybe this isn't something we need to do here, and instead could be done in the merge/hash step. However, just showing a table of all of the ph and sbs tiles doesn't really make much sense. The goal is to show ones that will align between 10x and 20x, and then essentially display a set of matching ones so that you can see the pattern of cells aligning between the two tiles you selected. Would you recommend we just leave the grid views out of these new examples that don't have that much data? Especially if we want to move this to the merge/hash step? If so I can just remove it from this example analysis eval notebook.

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Yeah, let's just exclude it for now.

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Done in https://github.com/cheeseman-lab/OpticalPooledScreens/pull/12/commits/bef2bd2a5c5a0829458aff49dd878f6f6458a513

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Removed these examples in https://github.com/cheeseman-lab/OpticalPooledScreens/pull/12/commits/bef2bd2a5c5a0829458aff49dd878f6f6458a513

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repo: cheeseman-lab/OpticalPooledScreens