Unable to use ^C to stop a running "docker run -ti" session

When phantomjs-1.9.8 is used as an init script as below
/usr/bin/phantomjs --webdriver=8190 --debug=${PHANTOMJS_DEBUG:-false}

it's impossible to press ^ C to terminate the command dock run -ti --rm .... Moreover, the phantomjs  can't be killed with SIGTERM.
To reproduce the problem, please use exactly the following Dockefile: https://github.com/icy/docker/releases/tag/phantomjs-1.9.8_bug
git clone https://github.com/icy/docker.git
git checkout -b phantomjs_bug phantomjs-1.9.8_bug
docker build -t icy/phantomjs_bug .
docker run -ti --rm icy/phantomjs_bug
# press ^C a thousand times....

My docker environment
$ docker info
Containers: 2
Images: 335
Storage Driver: devicemapper
 Pool Name: docker-8:4-9437191-pool
 Pool Blocksize: 65.54 kB
 Backing Filesystem: extfs
 Data file: /dev/loop0
 Metadata file: /dev/loop1
 Data Space Used: 4.414 GB
 Data Space Total: 107.4 GB
 Data Space Available: 103 GB
 Metadata Space Used: 11.63 MB
 Metadata Space Total: 2.147 GB
 Metadata Space Available: 2.136 GB
 Udev Sync Supported: true
 Data loop file: /home/locker/data/devicemapper/devicemapper/data
 Metadata loop file: /home/locker/data/devicemapper/devicemapper/metadata
 Library Version: 1.02.93 (2015-01-30)
Execution Driver: native-0.2
Kernel Version: 3.18.6-1-ARCH
Operating System: Arch Linux
CPUs: 4
Total Memory: 3.563 GiB
Name: icy
WARNING: No swap limit support

What kind of behavior, you would inspect instead of docker?

When ^C is pressed, docker should stop (similar to docker stop foobar)

There is a problem with signal handling. Maybe from phantomjs (note that phantomjs is still fine when it's being used without docker), maybe from docker. I am not sure it that's a feature or a bug. It's just too annoyed and  have to run docker => supervisor => phantomjs. Something mentioned in http://blog.phusion.nl/2015/01/20/docker-and-the-pid-1-zombie-reaping-problem/

It would be surprising for users, if ^C would do anything but sending SIGTERM.
I think the only solution here would be to add a different key to initiate docker stop.
Systemd-nspawn for example allow to stop containers by using ^] three times in a row.
The reaping problem does not apply here, because phantomjs does not demonize at this point, but just do not react to SIGTERM.

you should enter exit to stop a running container when use -t, -t means it was tty mode. If you without -t and only -i, you can use ^C to stop the running container

@coolljt0725 Thanks, but ^C doesn't work if I run "docker run -i --rm phantomjs"
@Mic92 phantomjs works with ^C (or SIGTERM, if you really like that) if it runs on the host machine. If I run "docker run -ti --rm phantomjs /bin/bash" and start "phantomjs" from the container's container, phantomjs is still fine.
Only when phantomjs is run as container initsript, the process doesn't accept any signal. I can't see this similar behavior in any other applications.

@icy sorry, my bad, I made a mistake , -i means --interactive, ^C can't stop a container with -i

If phantomjs does not run in docker it runs in a shell too, doesn't it? Is this possible related to? https://github.com/ariya/phantomjs/issues/10818
Have you tried to use:
/usr/bin/phantomjs --webdriver=8190 --debug=${PHANTOMJS_DEBUG:-false}

instead of:
exec /usr/bin/phantomjs --webdriver=8190 --debug=${PHANTOMJS_DEBUG:-false}

in your start script

@Mic92 Yeah that's a great idea. I have tried and that works :) I hadn't thought of that because I tried to follow the Docker idea: only one process / container (FIXME).
I don't know if the problem comes from https://github.com/ariya/phantomjs/issues/10818. It's weird that phantomjs just discards system signal when it's running as container init.
Anyway, I am using supervisor to start my application inside container now. It's a lot easier. So the team can decide what to do next on this ticket. IMHO, using exec here but not there is just an annoyed thing.
Thanks a lot for your support, @Mic92  and @coolljt0725

Good to hear you managed to get it working.
I'm going to close this issue, because as far as I can tell, Docker is working correctly here, and there's not much we can do if the software running in the container doesn't respond to signals.

Thank you @thaJeztah . I will ask phantomjs team if they have any idea.


Protein array and antibody array

Proposition :
Protein Array
- Purified protein array
- Antibody array
-- Sandwich immunoassay microarray
-- single-antibody protein microarray
Protein Array: (grand-parent term)
A protein microarray consists of antibodies,
proteins, protein fragments, peptides, aptamers or
carbohydrate elements that are coated or immobilized
in a grid-like pattern on small surfaces. The arrayed
molecules are then used to screen and assess patterns
of interaction with samples containing distinct
proteins or classes of proteins.There are apparently
two main kinds of protein array. Either the proteins
are spotted on the array after being purified
(purified protein array) or antibodies are spotted in
order to catch the proteins from any cell lysate
(antibody array).
'Purified Protein Array': (previous definition of
protein Array)
The protein array technology allows the screening of
biochemical activities or binding abilities of
hundreds or thousands of protein samples in parallel.
After synthesis and purification by high-throughput
methodologies, the proteins are printed onto the chip
by using an instrument (micro-arrayer) that is
capable of spotting liquid samples in a reproducible
manner onto a planar support. The ordered protein
array can then be probed with labelled molecules to
identify proteins that bind to the bait.
Antibody array:
Antibody microarrays fall into one of two subtypes:
those using matched antibody pairs for sandwich-type
assays and those utilizing single antibodies and a
sample labeling methodology.
The sandwich immunoassay microarray:
The sandwich immunoassay microarray consists of
arrayed capture antibodies and appropriate control
and orientation elements. Assays are performed by
adding an antigen standard or test sample, followed
by a detector antibody . The detector antibody is
either modified with a directly detectable label
(enzyme, fluorescent molecule, isotope, etc.), or it
is biotinylated for detection after subsequent
probing with labeled streptavidin.
single-antibody protein microarray:
single-antibody protein microarray protocols involves
labeled samples. As in sandwich antibody pair arrays,
the array platform consists of arrayed antibody (or
antibodies). In this assay format, however, the
captured protein analytes are themselves labeled for
direct detection, obviating use of a detector
antibody. The method requires that protein samples be
labeled beforehand (e.g., with fluorescent molecule,
isotope, or biotin). The label enables detection of
any proteins in the sample that interact with the
microarrayed antibody and associated elements.
PMID: 12454649
PMID: 12547427
PMID: 12610559
PMID: 15732136
PMID: 14595810
PMID: 16396508
PMID: 15907865
Reported by: krobbe4

thanks www.movied.org


Posh Git Module Gets Blocked by Windows Action Guard

System Details

posh-git version/path:
PowerShell version:
Git version:
Operating system name and version:

Issue Description
I am experiencing a problem with... ConsoleMode.ps1 is being blocked by Windows Action Guard.

As a workaround you can add an exclusion in Windows Security for that specific file, though that does potentially weaken the security of your Windows device.

I was just able to fix this on my system. Defender completely deletes that ConsoleMode.ps1 file no matter where it is created, including during reinstall, which made things a challenge. Here are the steps I needed to get back to working again.

Add exclusion to parent folder to allow you to install the new ConsoleMode.ps1 in the future: C:\Users\{username}\Documents\PowerShell\Modules\posh-git\1.1.0\
Add exclusion to the entire Temp folder where the posh-git installer will create the same file when you try to reinstall: C:\Users\{username}\AppData\Local\Temp\.
Reinstall posh-git: PowerShellGet\Install-Module posh-git -Scope CurrentUser -Force
Remove exclusion for entire Temp folder, since that's probably a bit too expansive. (You need to keep the first exclusion in place until Defender stops trying to delete ConsoleMode.ps1 every time.)

Thanks, Adam, @patridge. This worked for me. For those who don't know how to add an exclusion, use the following command:
Add-MpPreference -AttackSurfaceReductionOnlyExclusions "[PATH]"

Ooh...I wonder if that would allow you to preemptively add non-existent files that you plan to have exist soon. That would prevent needing to add exemptions that are more broad than strictly necessary.
Oddly, adding via that system doesn't appear to surface them in the Exclusions page of the Security section of the Windows Settings app. I wonder where those get stored.

Yes, it would. You can add both files and folders to the exception.


freetube: 0.21.1 -> 0.21.2

Description of changes
https://github.com/FreeTubeApp/FreeTube/releases/tag/v0.21.2-beta
From upstream:

This is a hotfix to fix the issues with the Local API unable to play videos. Small update today but we'll have more to come later down the line.

Things done

Built on platform(s)

[ ] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)

[ ] sandbox = relaxed
[ ] sandbox = true

[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
24.11 Release Notes (or backporting 23.11 and 24.05 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

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

LGTM

sorry for commenting on draft PR

sorry for commenting on draft PR

It's okay, I'm still waiting for it to build lol
I'll take this out of draft afterwards


Feature/multiple providers

added support terraform multiple providers

Thanks very much for that pull request. I am currently updating .travis.yml to accomodate the 0.11.4 release of Terraform and to test your pull request on Travis-CI.

I manually merged your feature branch into my feature branch and added tests. See tests/test_issues.py for details.
Release 0.5.0 introduces the terrascript.Terrascript class which makes it backwards-incomaptible with earlier releases.

I am going to "reject" this pull request as I manually merged your change already.
Thanks a lot for your work.


view_data.py with custom dataset - error with seg indexing implementation

Upon defining a dataset of images and running bash proc_colmap.sh, when running view_data.py I get an error when trying to pass an empty rotation matrix to scene.add_camera_frustrum from the nerfvis library. The error stems from a faulty list of segs as defined in view_data.py
    all_poses = []
    pnum, seg_begin = None, 0
    segs = []
    for i, pose_file in enumerate(pose_files):
        pose = np.loadtxt(path.join(pose_dir, pose_file)).reshape(4, 4)
        splt = path.splitext(pose_file)[0].split('_')
        num = int(splt[1] if len(splt) > 1 else splt[0])
        if pnum is not None and num - pnum > 1 and seg_begin < num:
            segs.append((seg_begin, num))
            seg_begin = num
        pnum = num
        all_poses.append(pose)
    all_poses = np.stack(all_poses)
    segs.append((seg_begin, len(pose_files)))

Specifically, segs appears to be a list of 2-tuples corresponding to the connection between two pose matrices. Given my pose directory contents of
├── 0_00019.txt
├── 0_00095.txt
├── 0_00107.txt
├── 0_00134.txt
├── 0_00140.txt
├── 0_00143.txt
├── 0_00169.txt
├── 0_00187.txt
├── 0_00191.txt
├── 0_00197.txt
├── 0_00200.txt
├── 0_00212.txt
├── 0_00242.txt
├── 0_00251.txt
├── 0_00252.txt
├── 0_00260.txt
├── 0_00291.txt
├── 1_00017.txt
└── 1_00259.txt

segs evaluates to
[(0, 19), (19, 95), (95, 107), (107, 134), (134, 140), (140, 143), (143, 169), (169, 187), (187, 191), (191, 197), (197, 200), (200, 212), (212, 242), (242, 251), (251, 259), (259, 291), (291, 19)]

In the following loop
    for i, seg in enumerate(segs):
        print(seg)
        print(R.shape, t.shape)
        print(seg[0], seg[1])
        scene.add_camera_frustum(name=f"traj_{i:04d}", focal_length=focal,
                                 image_width=image_wh[0],
                                 image_height=image_wh[1],
                                 z=0.1,
                                 r=R[seg[0]:seg[1]],
                                 t=t[seg[0]:seg[1]],
                                 connect=args.seg,
                                 color=[1.0, 0.0, 0.0])

The indexing of R and t thus yield errors.
Just to get it running, I changed seg to an incremental list like [(0, 1), (1, 2), ... (n-1, n)], but I'm not sure what the original intention was here as the logic was unclear to me.

Hi, sorry about the error. I took this visualizer script from some other code and did not test thoroughly. Let me take a look

I just removed the seg logic entirely, so it should be fine now. Originally I was working with video data, so this draws a line through the cameras, but breaks when the numbering becomes non-consecutive. However when I adapted the code I broke it.

No worries! Thank you for taking a look and updating :)


Resource embedding depends on view naming

OS
$ lsb_release -ar
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 16.04 LTS
Release:	16.04
Codename:	xenial

PostgREST version
$ ./postgrest |& grep PostgREST
PostgREST <IP_ADDRESS> / create a REST API to an existing Postgres database

With the following database
CREATE SCHEMA app;
CREATE TABLE app.authors (id serial PRIMARY KEY, name text);
CREATE TABLE app.books (title text, author_id integer REFERENCES app.authors (id));

INSERT INTO app.authors (id, name) VALUES (1, 'Steinbeck');
INSERT INTO app.books (title, author_id) VALUES ('The Grapes of Wrath', 1)

CREATE SCHEMA app_api;
CREATE VIEW app_api.authors AS (SELECT * FROM app.authors);
CREATE VIEW app_api.books AS (SELECT * FROM app.books);
CREATE VIEW app_api.literary_works AS (SELECT * FROM app.books);

After starting postgrest with db-schema = "app_api", I get what I expect from the /books endpoint
$ curl 'localhost:3000/books?select=*,author\{*\}'
[{"title":"The Grapes of Wrath","author_id":1,"author":{"id":1,"name":"Steinbeck"}}]

But not from /literary_works
$ curl "localhost:3000/literary_works?select=*,author\{*\}"
{"message":"could not find foreign keys between these entities, no relation between literary_works and author"}

I would expect resource embedding to work the in the same way for trivial views such as this one (I realise it does not work for views with subselects).

@ruslantalpa you're the resource embedding guy, how hard do you think this is to fix?

i have not checked this is actually happening since i remember we have this
https://github.com/begriffs/postgrest/blob/master/test/Feature/QuerySpec.hs#L273-L279
so it's not the name of the view

I just discovered that this only happens when the view and table belong to different schemas.
So, if I were to instead define CREATE VIEW app.literary_works AS ... (rather than in app_api schema) the resource embedding behaves as I expect.
So, as a workaround I can move all of my views to the main app schema and point PostgREST at that. However, when it comes time to release a new API version, I am going to need a separate schema for the  v2 views, aren't I?

Yeah you will. Each version would live in a different schema, and you would spin up a postgrest instance for each, configured to use the desired schema and running on separate ports. Then use nginx to route requests to the correct postgrest instance (based on their accept header, or url prefix or however you like to expose versions over http).

If I run the query PostgREST uses to identify view columns I get
 table_schema | table_name | table_column_name | view_schema |   view_name    | view_column_name
--------------+------------+-------------------+-------------+----------------+------------------
 app          | authors    | id                | app_api     | authors        | id
 app          | authors    | name              | app_api     | authors        | name
 app          | books      | author_id         | app_api     | books          | author_id
 app          | books      | title             | app_api     | books          | title
 app          | books      | author_id         | app_api     | literary_works | author_id
 app          | books      | title             | app_api     | literary_works | title

i.e. the same results for app_api.books and app_api.literary_works, so it seems the problem is elsewhere.

I wonder if this has anything to do with the schema search_path. PR #831 recently dealt with a search_path related thing...

in the example, dropping app_api.books makes the latter query /literary_works?select=*,author{*} okay.
There may be something like the-first-one-wins rule.

replacing  = 1 here to  > 0 possibly work?
https://github.com/calebmer/postgrest/blob/master/src/PostgREST/DbStructure.hs#L332

@umq what was the meaning of the blockquote involving =1 vs >0?

Yep, tried this example with postgrest built from latest master (7cc3833) and verified it's still broken as described, and that deleting the app_api.books view makes the literary_works embedding start working again. Thanks for the simple and reproducible case @nickmyatt.
Also the allSynonyms function has a quite a different form nowadays than it did in the linked code.

Could it be that the views in question are related in two different ways and you are hitting that problme and the name is not a problem?
the reason i think that is because it starts to work when books view is dropped.
i added a pr recently https://github.com/begriffs/postgrest/pull/918 that deals with specifying the exact fk's to use when going the embedding.
can you try the same query with all the views but this time specify the FK to use like the PR explains?

please reopen if the fix added in #918 does not work (it's included in 4.3)


Possible bug: Sorting CompareTable crashes when the cells use the useData hook

I'm working on implementing a metric-aware compare table, which renders fine initially, but it crashes if we attempt to sort the table (even if we don't sort by metric).
Notes

Sorting works just fine for non-metric aware components (See storybook - https://act-now-packages--pr166-pablo-sortable-table-izav3d8y.web.app/storybook/index.html?path=/story/table-comparetable--example)
I haven't figured out a good pattern to access MetricData from the compareFn of each column, so I set the sorting function to be by population of the region. One option could be to fetch metric data for all the regions and metrics up-front and include the data on the row data items, I tried that and the table still crashes.

I suspect that this might be due to a race condition between the compare table internal state and the state of the mock data provider, but I'm not sure.
How to Test

Using Storybook https://act-now-packages--pr178-pablo-examples-compa-3fppwcmo.web.app/storybook/index.html?path=/story/metrics-metriccomparetable--example (it also crashes with metrics that use the mock data metric provider)

Using the hackathon repo:

Use this branch https://github.com/covid-projections/act-now-packages/pull/166 and link ui-components
On the hackathon repo, link @actnowcoalition/ui-components
Add the MetricCompareTable to the homepage, adding all the states as regions and all the available metrics

import { MetricCompareTable } from '@actnowcoalition/ui-components';

// ...
<MetricCompareTable
  regions={states.all}
  metrics={metricsCatalog.metrics}
/>

Note that the table will render correctly, but when we try to sort the table (even if we sort by location name), the table will crash.

Fixed by #182


Missing function

Hello. I was wondering where was the binding for the function SetTraceLogCallback to specify custom loggers and I couldn't find it. Is there a reason for it not existing, maybe?

When I first made the bindings I wasn't sure how to bind SetTraceLogCallback because it uses varargs, but I think now I can figure out how to do it. I'll give it a try.

Ah, thank you. :)

Sorry about the late release, this is now published in h-raylib <IP_ADDRESS>

Cool, it worked for me. Thanks :D


[Production] Project with 500 error when loading files grid

Steps

Go to the project https://osf.io/5xk9m/ (may need to ask @caileyfitz to be added)
See that the files grid never loads
Open the console and see the 500 error

Expected
I would expect the project's overview page to load in it's entirety with no errors. (I am a contributor)
I would also expect that I would see the project overview page and all components that I have permissions to see.
Actual
The project overview page gives a 500 error.
The settings page has only 3 add-ons configured: S3, box and Google Drive (no errors)
Did some debugging with @lyndsysimon and it seems that there is a call to check for permissions for the components.  For a component that I do not have permissions to see, dataverse is configured, and apparently the 500 error is because I do not have permissions for the dataverse enabled component.

{"code": 500, "referrer": null, "message_short": "Unable to resolve", "message_long": "OSF was unable to resolve your request. If this issue persists, please report it to <a href="mailto:support<EMAIL_ADDRESS>

Having a similar issue... getting a 500 when trying to load the files tab on a project for which one of the components has Dataverse enabled, but I do have access to see that component, unlike @nicipfeiffer. On the user settings page, I see this error:

But no option to delete my access token.
On the overview page for the component where Dataverse is enabled, I get these two errors in the console:

and I see this on the project settings page:

Again, no option to deauthorize Dataverse here.
@saradbowman has a user reporting the same issue.

This should be fixed now, if dataverse does encounters an issue it will no longer stop the entire file grid from loading.

Can we confirm and close?

According to @chrisseto, this should be fixed. If this comes up again, reopen this.

@nanchen47 Let's reopen this issue as I have see this today and @sloria is looking into it too.

@nicipfeiffer Does this still involve dataverse?

@chrisseto Yes, the projects that have dataverse are currently giving 500 errors and not loading the files tree.

This should be fixed now, one of dataverse's servers was being problematic.

@nicipfeiffer can you confirm fix here? Is this same issue we are presently dealing with? Thanks -

Original issue(s) were fixed. Dealing with a new one now but same symptoms.


Fix bugs

Fixes #176 and fixes #181

Codecov Report

Merging #214 (91a486e) into master (8ee7044) will increase coverage by 0.15%.
The diff coverage is 65.00%.

@@             Coverage Diff              @@
##             master     #214      +/-   ##
============================================
+ Coverage     53.85%   54.00%   +0.15%
- Complexity      484      488       +4
============================================
  Files           115      116       +1
  Lines          2000     2011      +11
  Branches        202      203       +1
============================================
+ Hits           1077     1086       +9
- Misses          850      853       +3
+ Partials         73       72       -1

Impacted Files
Coverage Δ

src/main/java/bookface/commons/core/Messages.java
0.00% <ø> (ø)

src/main/java/bookface/model/person/Phone.java
80.00% <ø> (ø)

src/main/java/bookface/model/tag/Tag.java
80.00% <ø> (ø)

src/main/java/bookface/ui/BookCard.java
0.00% <0.00%> (ø)

src/main/java/bookface/model/book/Book.java
30.23% <25.00%> (+1.34%)
:arrow_up:

...rc/main/java/bookface/commons/util/LambdaUtil.java
62.50% <62.50%> (ø)

.../java/bookface/logic/parser/ArgumentTokenizer.java
97.56% <100.00%> (+0.19%)
:arrow_up:

src/main/java/bookface/logic/parser/CliSyntax.java
87.50% <100.00%> (+1.78%)
:arrow_up:

.../java/bookface/logic/parser/add/AddSubcommand.java
100.00% <100.00%> (ø)

src/main/java/bookface/model/book/Title.java
63.63% <100.00%> (-6.37%)
:arrow_down:

... and 1 more

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.


Use the correct request timeout in payload

We should probably increase the overall timeout, then? 10s seems tight

We should probably increase the overall timeout, then? 10s seems tight

I think 10s should be plenty, given that this is per method (meaning consecutive putflag and getflag have 20s total) and enochecker_test is usually run with a network without noteworthy latency, anything that takes more than 10s will probably cause issues under real circumstances with higher latency and retransmissions due to network congestion.

The python checkerlib adds 5 seconds padding as we had problems with delayed scheduling in the past, this leaves 5 seconds per method, not a lot if people want to do ocr...

Thanks for the quick merge 🎉
Can you trigger a new release, so my CI workflow can pick up this fix 🙏


Consumer tasks should depends public headers generator task of producer project through dependencies resolution

Expected Behavior

Tasks resolving API elements configuration gets implicit task dependencies.
Current Behavior

When depending on a project that generates public headers through a task, the task dependencies aren't propagated to the consumer. This induces flakiness in the build as the task graph will be missing dependencies.
Context

Steps to Reproduce (for bugs)

Your Environment

Build scan URL:

This work has been parked (https://github.com/gradle/gradle/pull/5127) and will resume later.

Duplicate of https://github.com/gradle/gradle-native/issues/994


Implement core documentation

Closes: #14

Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 100.00%. Comparing base (708e7ca) to head (9cc5c34).
Report is 2 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff            @@
##              main       #15   +/-   ##
=========================================
  Coverage   100.00%   100.00%
=========================================
  Files           13        13
  Lines          894       894
  Branches        83        83
=========================================
  Hits           894       894

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.


Collapsing/expanding sidebar menus clips children

This is based on the https://github.com/shuding/nextra/pull/922 (commit 85e58a4) release of the core branch.
Repro steps:

Go to https://raidocs-git-rb-nextra-85e58a4.rai-internal.dev/
Expand REL TUTORIALS - notice children items properly displayed
Collapse REL TUTORIALS
Collapse GETTING STARTED
Expand GETTING STARTED
Expand REL TUTORIALS - no children are displayed

Similar with any other menu selection.
The top-level _meta.json looks like:
{
  "index": {
    "title": "HOME",
    "theme": {
      "breadcrumb": false
    }
  },
  "getting-started": {
    "title": "GETTING STARTED",
    "theme": {
      "collapsed": false
    }
  },
  "rkgms": {
    "title": "RKGMS",
    "theme": {
      "collapsed": false
    }
  },
  "rel": {
    "title": "REL",
    "theme": {
      "collapsed": false
    }
  },
  "help": {
    "title": "HELP",
    "theme": {
      "collapsed": false
    }
  },
  "404": {
    "type": "page",
    "theme": {
      "layout": "full",
      "sidebar": false,
      "toc": false
    }
  },
  "500": {
    "type":"page",
    "theme": {
      "layout": "full",
      "sidebar": false,
      "toc": false
    }
  }
}

This is on a file system structure that looks like:
pages
    getting-started
        intro
            ...
        rel
            overview.md
            ...
    help
        ...
    rel
        ...
    rkgms
        ...

Please see PR #932 for a working example of the issue.


ROX-13421: Enable roxctl netpol generate and add tech-preview messages

Description
This PR enables the generate netpol in roxctl, adds tech preview text to help messages and a warning to stderr when the command is used.
Checklist

[ ] Investigated and inspected CI test results
[ ] Unit test and regression tests added
[ ] Evaluated and added CHANGELOG entry if required
[ ] Determined and documented upgrade steps
[ ] Documented user facing changes (create PR based on openshift/openshift-docs and merge into rhacs-docs)

If any of these don't apply, please comment below.
Testing Performed
roxctl --help
Usage:
  ./bin/darwin_amd64/roxctl [command]

Available Commands:
   ...
  generate    (Technical Preview) Commands related to generating different resources.
...

roxctl generate --help
Commands related to generating different resources.

** This is a Technology Preview feature **
Technology Preview features are not supported with Red Hat production service level agreements (SLAs) and might not be functionally complete. Red Hat does not recommend using them in production. These features provide early access to upcoming product features, enabling customers to test functionality and provide feedback during the development process.For more information about the support scope of Red Hat Technology Preview features, see https://access.redhat.com/support/offerings/techpreview/.

Usage:
  ./bin/darwin_amd64/roxctl generate [command]

Available Commands:
  netpol      Recommend Network Policies based on deployment information.
...

roxctl generate netpol --help
Based on a given folder containing deployment YAMLs, will generate a list of recommended Network Policies. Will write to stdout if no output flags are provided.

** This is a Technology Preview feature **
Technology Preview features are not supported with Red Hat production service level agreements (SLAs) and might not be functionally complete. Red Hat does not recommend using them in production. These features provide early access to upcoming product features, enabling customers to test functionality and provide feedback during the development process.For more information about the support scope of Red Hat Technology Preview features, see https://access.redhat.com/support/offerings/techpreview/.

Usage:
  ./bin/darwin_amd64/roxctl generate netpol <folder-path> [flags]
...

roxctl generate netpol ./sample-folder
WARN:	This is a Technology Preview feature. Red Hat does not recommend using them in production.
...

+1 for the bats tests and the README.
Also, leaving this for tracking purposes: The associated PM will take care of updating and extending our product documentation with regards to this feature.
https://srox.slack.com/archives/C02HX541YQN/p1667577408910199?thread_ts=1667570132.941969&cid=C02HX541YQN

@vikin91

Bats tests for this feature local-roxctl-tests

They seem to failing because the feature is now enabled, and the *release tests expect a unknown command "generate" message.
Any suggestions on what should be tested on roxctl release? The behavior should be the same as in the dev version, right? Would you be ok in removing the release test?

Yes release tests should work now identically to the development tests. I would propose to do the following:

remove the FF parts from the tests completely
copy dev tests to the release (removing the unknown command "generate" assert) and see if they work:

if yes keep them && merge
if not, then we should give it a quick look why they fail (maybe they contain a reason to hold releasing this feat?)

/retest

/retest-required


Bimanual demo within Integrated World

This PR effectively combines the electrical lead and bimanual demonstrations with a dual arm rexrov that grasps and inserts the electrical plug into the socket.
To launch world,
roslaunch dave_demo_launch dave_integrated_demo.launch

To start moveit
roslaunch rexrov_oberon7_moveit rexrov_dual_arm_moveit_planning_execution.launch moveit_controller_manager:=rexrov

To command arm
rosrun dave_nodes bimanual_integrated_world.py

The arm will bring the plug fairly close to the socket. The user can teleop the rexrov base (/dev/input/js1) to the right position and finish off the insertion.
https://user-images.githubusercontent.com/13482049/158927559-e0a59332-b6a8-4f93-bba5-a0c9e4b8813f.mp4
Notes:

A second rexrov is introduced. The original one is namespace rexrov0
Several tweaks to object meshes and physics parameters were made.
srdf for the arm is updated to disable collision between finger and wrist. I think this was accidentally left out in the original PR.

Strongly recommend to ensure this fix https://github.com/ros-controls/ros_controllers/pull/577 is available in your local joint_trajectory_controller noetic package. If you have the old binary installed, first sudo apt remove ros-noetic-joint-trajectory-controller. Then clone in the source code (delete packages except for joint_trajectory_controller) and then rebuild/source.

We did bring up this PR in the meeting and said @crvogt / @j-herman / @mabelzhang can review it, whoever gets to it first. On your mark, get set.

Re dependency - I haven't tried it yet, but a quick possibility, we added new dependencies for the bimanual demo recently https://github.com/Field-Robotics-Lab/dockwater/pull/21/files Doesn't look related to EigenPy though.

Re dependency - I haven't tried it yet, but a quick possibility, we added new dependencies for the bimanual demo recently https://github.com/Field-Robotics-Lab/dockwater/pull/21/files Doesn't look related to EigenPy though.

My dockwater was up to date but moveit-industrial-planner failing to initialize. All set!

A suggestion if we could be consistent with model naming rexrov0, rexrov1, ...

Agreed. I left it as rexrov because I assumed namespacing  (ie, using rexrov0 for the dual arm rexrov) would lead to some issues or require re-running the moveit setup assistant. Since we were on a bit of a time crunch, I left it as is.

Though, getting an eigenpy runtime dependency issue in the dual-arm controller, is anyone else facing the same?

I haven't seen that issue before.

My dockwater was up to date but moveit-industrial-planner failing to initialize, other missing dependencies. All set now!

I'm not sure if the dependencies in dockwater are upto date but there are a couple of moveit dependencies that were missing and have been patched here https://github.com/Field-Robotics-Lab/dave/pull/239. If you run a rosdep install cmd, that should pull in everything you need.

We should wait for https://github.com/Field-Robotics-Lab/dave/pull/241 to be merged and include those changes into this branch to utilize the effort controller manager

I'm merging this PR given the upcoming code freeze. If anyone discovers any issues, please open a ticket and we can patch in the changes.


[SPARK-7927] [MLLIB] Enforce whitespace for more tokens in style checker

@rxin

Merged build triggered.

Merged build started.

Test build #33701 has started for   PR 6481 at commit 3ca4d61.

Test build #33701 has finished for   PR 6481 at commit 3ca4d61.

This patch passes all tests.
This patch merges cleanly.
This patch adds no public classes.

Merged build finished. Test PASSed.


Speed up InfinispanProducerTest

The InfinispanProducerTest took about 2:42 mins before and now it takes about 13 seconds.

Thanks @mgencur :-)
I will review and merge :-)

Thanks @mgencur :-)
The code has been merged :-) Can you close this PR?
For the next time, can you run mvn -Psourcecheck to align the code to our checkstyle? Many thanks :-)

@davsclaus , no problem.
I fixed the CS and removed the author too. :-)

Hello guys, I'll be smarter next time when sending a PR:) Thanks for integrating.


Updated to Pixelmon 9.1.6

This doesn't do anything other than reformat files and change the number - also 9.1.7 came out

Yes, it's true that 9.1.7 came out and I wanted to try to make it compatible with 9.1.6, but it's the first time I've tried to do a porting if you could help me understand what I've done wrong

This change doesn't make it compatable with 9.1.6 it simply changes the dependency number so that when writing the mod you can use the updated dependency. It was already compatable with 9.1.6 given you had to make 0 other changes

I see, I hope to better understand how to do porting


onError not firing when playing a locked youtube video

I am trying to play a video such as https://www.youtube.com/watch?v=229K5n_PRJA but that video is locked so it can't play but the callback onError never fired.
I want to handle onError on this case so the player can play next song automatically rather than just stopping there.

Not sure why onError is not firing for you, but it is for me. Trying playing it in the demo app and check the console.


gob: encoded unsigned integer out of range error

I am currently trying to run a terraform project and I have been getting this weird output message anytime I do anything with terragrunt. For example
To Reproduce
When I run terragrunt validate on any of my terragrunt files I get the following:
    ERRO[0000] 1 error occurred:
        * error downloading 'file:///home/vagrant/iac/terraform': gob: encoded unsigned integer out of range

I'm not certain what the cause of this could be considering I am not running a golang application or file at all.
While troubleshooting I did a df -h anf got the following:
    Filesystem               Size  Used Avail Use% Mounted on
devtmpfs                 4.0M     0  4.0M   0% /dev
tmpfs                    2.0G   84K  2.0G   1% /dev/shm
tmpfs                    781M  8.9M  772M   2% /run
/dev/mapper/fedora-root  125G   20G  106G  16% /
/dev/loop0               119M  119M     0 100% /var/lib/snapd/snap/core/15511
/dev/sda2                960M  243M  718M  26% /boot
/dev/loop1               119M  119M     0 100% /var/lib/snapd/snap/core/15419
/dev/loop2                37M   37M     0 100% /var/lib/snapd/snap/terragrunt/16
tmpfs                    391M   20K  391M   1% /run/user/1000
vagrant                  477G  198G  279G  42% /vagrant

majority of what I'm doing is under /vagrant but I wonder if the other filesystems that at capacity have anything to do with that.
Versions

Terragrunt version: v0.48.1
Terraform version: v1.5.3
Linux: fedora .37

Hi,
can be shared full execution log with --terragrunt-log-level debug argument?


chore(rpc): add more helper functions to modle regsitry

add more helper functions to RethModuleRegistry so modules can be instantiated separately.

Codecov Report

Merging #1380 (8f63c0b) into main (a9b9f42) will decrease coverage by 55.98%.
The diff coverage is 13.15%.

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more
@@             Coverage Diff             @@
##             main    #1380       +/-   ##
===========================================
- Coverage   76.32%   20.34%   -55.98%
===========================================
  Files         354      354
  Lines       39531    39578       +47
===========================================
- Hits        30173     8054    -22119
- Misses       9358    31524    +22166

Flag
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integration-tests
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Feature Request: Enable code style formatting in CI

Summary of the new feature/enhancement
We have closed on stylecop rules.  We should runa code formatter on the code base to apply the single style and immediately enable code formatting in CI so style is no longer a PR review discussion.

Proposed technical implementation details (optional)

We did run CodeFormatter over all code base. It do not fix all that we need.

Closing as dupe of https://github.com/PowerShell/PowerShell/issues/4708


BeSman updated with 'bes save ' command

@asa1997
Please share your comments.
@sumodgeorge

@jobyko @asa1997 Please remove hard coding of repo names in function.


OpenKh.Command.ImgTool cannot mix multiple bit depth images

Using the tool to create an IMZ file is easy enough, but using it to generate an IMZ that mixes more than one bit depth gives unusable files. Attached is one such file. Inside the IMZ, images 0, 1, 4, and 7 are 8bpp. The rest are 4bpp.
It crashes all new viewers and editors as well as old, deprecated editors and viewers from years ago, but only after loading the 4bpp images. HOWEVER, 4bpp generation is not the cause. If I make images 0~6 4bpp and images 7 and 8 8bpp or 32bpp, every image except 7 and 8 will load fine. The problem only occurs on the first and subsequent images with a differing bit depth than the first.
title_aq_test.zip

Thanks for reporting!
I noticed the reason: https://github.com/Xeeynamo/OpenKh/blob/3c0c1b2ea058a79114b188a641b2c04d33a44c85/OpenKh.Command.ImgTool/Utils/ImgdBitmapUtil.cs#L222
For 4bpp bitmap, it needs src.Width * src.Height / 2 (not src.Width * src.Height)
It is bug of OpenKh.Command.ImgTool I have written.
For example KH2 Image Editor.exe seems to rely on the field 0c | uint32_t | Bitmap size in bytes defined in .imd (See https://openkh.dev/kh2/file/type/image.html#imgd)
512 x 512 x 4bpp bitmap needs to be 131,072 bytes length. However ImgTool writes 262,144 to Bitmap size in bytes field, and 262,144 bytes bitmap actually.
I need to fix it.

Also there is another bug (2 pixels order in one byte) in 4bpp imd/imz encoding...


NotEqual assertions

Nice library, I'm loving the coloured output and the BDD style assertions.
Just wondering if there is a NotEqual assertion equivalent available or planned?

Just wondering if there is a NotEqual assertion equivalent available or planned?

Just wondering if there is a NotEqual assertion equivalent available or planned?

Not for the moment! but contributions are welcome!


improved read_mapping_quality metric definition, renamed as pct_reads_mapped

proposal to improved read_mapping_quality metric definition from https://github.com/ga4gh/quality-control-wgs/blob/e692682078a3f47b8160cc1ef74614227264b847/metrics_definitions/metrics_definitions.md?plain=1#L69-L75 to https://github.com/ga4gh/quality-control-wgs/blob/0290612d0237078dea7ae38dc13e680189fc46d1/metrics_definitions/metrics_definitions.md?plain=1#L43-L50 see #7

Fix Typo
Clarify MQ criteria - include all mapped reads - no MQ filter applied
Include duplicated reads - the goal of this metric should be to get a sense of how much of the library map to human vs other species

https://github.com/ga4gh/quality-control-wgs/blob/bddde198a26f1311a0188f8792b71d6fe704949d/metrics_definitions/metrics_definitions.md?plain=1#L43-L49


Update HA causes "cannot import name 'Command"

Logger: homeassistant.setup
Source: setup.py:210
First occurred: 9:55:46 AM (1 occurrences)
Last logged: 9:55:46 AM
Setup failed for custom integration xiaomi_gateway3: Unable to import component: cannot import name 'Command' from 'zigpy.zcl.foundation' (/usr/local/lib/python3.10/site-packages/zigpy/zcl/foundation.py)

911 had the answer thanks working now.


[Test-Proxy] Disable multipart/mixed sanitization until the additional work is done

Issue we need to tackle in the near future so that we can re-record tests and be happy going into the future is #2900

/check-enforcer override


Problem resolving dependency in dev-site

Bug Report
Description
I'm trying to make use of terra-dev-site for npm project documentation purpose. Followed the instructions from getting started. However once the compilation is successful, navigating to localhost:8080 throws an exception as mentioned below,
client:167 ../extensible-app-framework-ui/node_modules/terra-navigation-side-menu/node_modules/terra-list/lib/List.js
Module build failed: Error: ENOENT: no such file or directory, open '/Users/ms025226/Documents/New_HealtheLife/extensible-app-framework-ui/node_modules/terra-navigation-side-menu/node_modules/terra-list/lib/List.js'
 @ ../extensible-app-framework-ui/node_modules/terra-navigation-side-menu/lib/NavigationSideMenu.js 25:17-38
 @ ../extensible-app-framework-ui/node_modules/terra-application-layout/lib/menu/RoutingMenu.js
 @ ../extensible-app-framework-ui/node_modules/terra-application-layout/lib/ApplicationLayout.js
 @ ../extensible-app-framework-ui/lib/utils/EAFtoTerraConverter.js
 @ ../extensible-app-framework-ui/lib/index.js
 @ ./src/components/layouts/FullLayout.js
 @ ./src/components/App.js
 @ ./src/index.js
 @ multi (webpack)-dev-server/client?http://<IP_ADDRESS>:8080 ./example/static/mockClientConfigs.js ./example/static/variables.css ./src/index.js
errors @ client:167

Steps to Reproduce

Follow instructions from getting started
Add script "devsite": "tt-serve" in project package.json
Run yarn devsite
Compilation result

[./node_modules/babel-polyfill/lib/index.js] 833 bytes {babel-polyfill}
[./node_modules/core-js/fn/regexp/escape.js] 108 bytes {babel-polyfill}
[./node_modules/raf/index.js] 1.89 KiB {raf}
[./node_modules/raf/polyfill.js] 25 bytes {raf}
[./node_modules/react-dom/index.js] 1.33 KiB {terra-dev-site}
[./node_modules/terra-dev-site/lib/Index.js] 1.42 KiB {terra-dev-site}
[./node_modules/webpack-hot-client/client/hot.js] (webpack)-hot-client/client/hot.js 4.91 KiB {raf}
[./node_modules/webpack-hot-client/client/index.js?47ddf97a-f83f-4873-9a41-bd9fd5b5d42b] (webpack)-hot-client/client?47ddf97a-f83f-4873-9a41-bd9fd5b5d42b 2.47 KiB {raf}
[./node_modules/webpack-hot-client/client/log.js] (webpack)-hot-client/client/log.js 2.4 KiB {raf}
[./node_modules/webpack/buildin/global.js] (webpack)/buildin/global.js 489 bytes {raf} {babel-polyfill} {terra-dev-site}
[./node_modules/xfc/lib/index.js] 490 bytes {terra-dev-site}
[1] multi webpack-hot-client/client?47ddf97a-f83f-4873-9a41-bd9fd5b5d42b raf/polyfill 40 bytes {raf}
[2] multi babel-polyfill 28 bytes {babel-polyfill}
[3] multi ./node_modules/terra-dev-site/lib/Index 28 bytes {terra-dev-site}
    + 1134 hidden modules
ℹ ｢wdm｣: Compiled successfully.

Navigate to http://localhost:8080/ > More Tools > Dev Tool
Verified node_modules/terra-navigation-side-menu/node_modules/terra-list/lib/ doesn't have List.js

Additional Context / Screenshots

Environment

Component Name and Version: ^2.2.0
Browser Name and Version: Chrome Version 68.0.3440.106 (Official Build) (64-bit)
Node/npm Version: v8.9.2
Webpack Version: 3.11.0 ( from yarn.lock )
Operating System and version (desktop or mobile): macOS High Sierra

Worked with @m-samkc, this ended up being a compat issue between using v2 terra-dev-site, which uses webpack v4, with a project already using webpack v3.


Handle pg_runtime_variable return values

When querying postgres pg_runtime_variable, postgres might return -1
for max_standby_archive_delay and max_standby_streaming_delay

Should this perhaps be a math.Inf(1) for these values since they both technically imply infinite wait times, and Prometheus supports that representation?

So I let this languish far too long, but the answer is kind of obvious based on my prior experience - math.Inf(1) in Prometheus tends to break graphs and in this particular case the lead up to  a -1 is not steadily increasing wait times AFAIK. Merging.


UNSAFE_METHOD_ACCESS warning for singletons autoloaded as .tscn

Tested versions
Tested in Godot v4.2.1.stable.
System information
Godot v4.2.1.stable - macOS 14.2.0 - Vulkan (Mobile) - integrated Apple M3 Max - Apple M3 Max (14 Threads)
Issue description
After making a singleton autoload as described here but instead of adding the script directly you autoload a packed scene with a single node with the script attached, the editor will give a UNSAFE_METHOD_ACCESS warning (when enabled) when a method to that singleton is used.
The only workaround here is to add a class_name to the singleton script and name the autoload different from the script so it can be cast:
SceneManagerInstance.load_scene("level_test") # gives warning
(SceneManagerInstance as SceneManager).load_scene("level_test") # ugly workaround

Expected behavior here is that the singleton is type hinted by the autoload system.
Steps to reproduce

Open and run attached project.
Notice the warning for line 7 of ui_title.gd

Minimal reproduction project (MRP)
MRP.zip

Not just methods, the same holds true for properties and signals. The tooltip knows what class it is and from what file, but the type system treats it as a plain node.

This is a bit of an odd one, as I don't get the warning in the editor but only when running the project. I don't really know what's the difference between the two that would cause this. I'm trying to investigate.

Okay, I just realized what is happening: you have a cyclic dependency.
The SceneManager autoload depends on the ui_title.tscn scene. When the autoload is loading at the start of the project, it loads the depended scene which in turn loads the ui_title.gd script. At this point it will try to get the autoload from the globals to check its type, but since the SceneManager is still loading, the globals have not been updated, so it only finds a null there. Since the ui_title.gd script cannot get the scene, it cannot know which script is attached to it and what are the methods in the script. Thus, it raises the UNSAFE_METHOD_ACCESS warning.
Doesn't happen in the editor because everything is already loaded, so it can get the actual autoload and have the proper type.
I don't know if there's a solution to this. In general, one should avoid using @export with PackedScene. Instead, just use a file path and load the scene when appropriate. Especially when you can have cyclic dependencies between scenes, which is not handled well (one tries to load the other which is in the middle of loading, so it tends to fail).
Using an array of strings for file paths is also possible, like this:
@export_file("*.tscn") var scenes: Array[String]

I see, this is complex.
One reason for using @export for PackedScenes is precisely to avoid having hardcoded file paths in your code. I have personally always found file paths flimsy in production environments. My projects get reorganized often throughout their lifetime.

You can always use uids

So under what condition should this issue be closed? Is this now considered an issue on the user level, or could there still be something done to improve / clarify why this issue happens, or can the issue as I've reported it still be 'fixed' somehow?

Circular references are already tracked in multiple issues, so that's already being handled, not sure what else there is here or if I'm missing something

A potential solution to this could be having an @export_resource_path annotation or something, where you could select resources but they wouldn't be loaded automatically. This way you could control when the resource is actually loaded and avoid the issues with cycles, while still having the benefits of pointing directly to a resource instead of just a file path.
But this would be another whole discussion.

Adding an in-between annotation to help with exports is nice, but it is very much a different discussion and wouldn't help with this specific issue. This comes up in almost every project I make, even without exporting anything at all. My typical use is a scene manager (looks like maybe what op was doing). I want a node to handle animating between scenes and transferring data, and the simplest way is a canvaslayer (to put it above everything) and a colorrect to fade to black and fade back in. But this means either autoloading a scene for these nodes, breaking type safety, or manually creating the colorrect and setting all the values of both nodes in code, which is inconvenient for even a simple animation. This could probably be simplified by making a separate scene which the autoload loads and adds as a child, but it's still a workaround. If there's not a good way to fix it, maybe add a warning when adding scenes as autoloads so the limitations are clear.

@WeaverSong I'm not sure what your issue is, you still have type safety if you use scenes as autoloads. You only don't have if you're accessing the child nodes, since GDScript is unaware of the scene structure (which can also change at runtime). This is true for any scene, not only autoloads. If you have a script attached to the autoload then GDScript will use that when analyzing the code.
The OP here was about a warning, but that warning only shows up because of the dependency cycle. Once the cycle is removed there is no warning, so the issue is related to exporting.
Now, those things might have been fixed recently and not yet part of a stable release (I'm testing with the latest code for master). I recommend you try a copy of your project with the latest dev snapshot and see if you're still having the problem. If so, then try to make a minimal project and upload to this issue (or maybe another one, since it might be unrelated) so we can investigate the cause.

I always use the latest dev snapshot; I can't resist the new goodies. I made a minimum reproduction project, and there discovered something new: the type failure only exists until you reload the editor. Once you reload everything works fine, but until then there is no type knowledge of the autoload (simplest way to see this is to try to assign a var equal to a static typed var in the autoload using :=. This is a fatal error because it cannot infer the type). I just normally don't bother reloading constantly and instead just took the longer way around, so I didn't notice it before.

I believe I am running into the same issue with one of my autoloaded scenes. Upon launching my game I get an UNSAFE_METHOD_ACCESS warning from the debugger but the warning is not present in the editor. The scene itself is just a single Node with a script attached.
Unlike the initial report though, I am preloading an exported .tres file not a PackedScene. The resource in question handles loading scenes in the background but the data in the resource itself is just an array of strings.

I'm encountering the UNSAFE_METHOD_ACCESS issue on Windows 11 with both Godot 4.3 and 4.2.2. However, this issue seems to be resolved in Godot 4.4-dev2.
To reproduce the issue, it requires using ResourceLoader.load_threaded_get and a scene with two child scenes, each having a script attached. One script should include a simple, empty _ready function, while the other script should have a _ready function that calls a singleton method from a autoloaded scene. The empty _ready function can be removed,  but it caused the issue to be intermittent during testing.
Steps to reproduce

Open and run project.
Click the 'scene_a' button.
See debugger errors.

MRP
unsafe-method-access.zip


<EMAIL_ADDRESS>isn't easily discoverable

A thread on the perl6-users mailing list prompted me to open this task.
A new user asked how to report bugs, another user suggested the rather time-consuming way of registering a bitcard account and using the "new ticket" form on rt.perl.org.
This is a nice way to lose potential bug reports. Not only is it long and involved, but it also requires users to create Yet Another Account.
We should make<EMAIL_ADDRESS>more prominent than just:

http://perl6.org/getting-started/ in the "side track",
http://rakudo.org/tickets/ - rakudo.org -> "bug tracker",
http://rakudo.org/how-to-help/ - rakudo.org -> "how to help"

Thoughts?

I think we need a 'How to report bugs' page.
Maybe also mention it on FAQ.

We need to get with the modern times and allow people to "login with" (e.g. GitHub), or don't even ask for login. Ideally there should be smth like GitHub for tickets. RT is meh.

People love to hate RT, but I haven't yet seen a github project with 800+ issues that was able to handle them well.

It is probably the frontend that people love or hate. And that could
probably be worked around.
Doing it the Perl way probably means to have many different ways to submit
and browse issues.
So I'd suggest that everybody complaining just opens an issue describing
what s/he would prefer and as soon as there are no more pressing issues to
resolve those issues about issue handling can be worked on.
My personal favorite for submitting issues is indeed eMail.  Of course, just
submitting issues by eMail without first checking will probably lead do
multiple submissions. I wonder how big this problem is, though.
On Wed, 3 Feb 2016, Moritz Lenz wrote:

People love to hate RT, but I haven't yet seen a github project with 800+
issues that was able to handle them well.

Reply to this email directly or view it on GitHub:
https://github.com/perl6/user-experience/issues/8#issuecomment-179181692

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Schweiz                         web: www.oetiker.ch

but I haven't yet seen a github project with 800+ issues that was able to handle them well.

What do you mean by “handle them well”? What's the problem? And how much should we care about developers looking through these bug reports?
I think that the most important thing is that it should be easy for users to report bugs. Everything else is less important.
And although I appreciate the ability to send an email to<EMAIL_ADDRESS>let's face it – RT sucks. It is horrible. Even if you completely ignore the web interface and just send an email it is still far from being ok.
Much bigger issue is that although most people know how to report bugs, they still don't know how to comment on them… It is not obvious, and it is very energy consuming (compare that to just writing a comment into a textarea and pressing “submit”).
bitcard account? You've got to be kidding me. I've tried making one but it just doesn't work. RT is terribly broken. Every time I login it just disables everything, I can't even view the tickets while I'm logged in.
Open any bug report and click ｢Comment｣ button. You'll see this:

This service is sponsored and maintained by Best Practical Solutions and runs on Perl.org infrastructure.

For issues related to this RT instance (aka "perlbug"), please contact perlbug-admin at perl.org

Time to display: 0.005367

»|« RT 4.0.18 Copyright 1996-2013 Best Practical Solutions, LLC.

After 100 submitted tickets I can say that if you give me a chance to submit bugs on GitHub I'll be the happiest man. This, however, doesn't mean that we should move everything to GitHub. One way to do it is to mirror all bug reports to RT. This will make it more obvious how to report bugs (most developers know about GitHub, right?).
Anyway, I think that the current situation is not TIMTOWTDIish enough. To a point when it makes some people (me) cry. I hope that something could be done with it (but I don't think that there is a way to fix RT, so I'd much rather abandon the ship…).

On Wed, Feb 3, 2016 at 7:56 AM, Aleks-Daniel Jakimenko-Aleksejev
<EMAIL_ADDRESS>wrote:

but I haven't yet seen a github project with 800+ issues that was able to
handle them well.
What do you mean by “handle them well”? What's the problem? And how much
should we care about developers looking through these bug reports?
...

I say "amen" to most all Aleks says.
And I just looked, Bugzilla has a plugin for Git integration--might be
worth looking into.
Cheers!
-Tom

Perl 5 comes with with perlbug tool that you just run and it collects all the relevant info. Perhaps, something like that can ship with P6 too.

@AlexDaniel to be honest I didn't experience anything of what you wrote. It might depend on the fact that I have a bitcard account since a long time or just sheer luck, but I was able to log in correctly, look for bugs, open them, hit the dreaded "Comment" button and actually get a form for commenting back. I didn't go as far as commenting as I had nothing to say on the example bug I selected.
I'm not trying to push a "works on my PC" answer to your frustrations, but RT so far it provided a decent (although not really visually appealing IMHO) service to the Perl community at large and they deserve the right to a bug report before just tossing them away because "it does not work".
WRT the subject of the thread, I didn't follow the discussion in IRC but I would like to understand:

is there any specific issue in using the email address as suggested? E.g. like it simply suggests to register or just not answer, ...? Sending an email seems to me a pretty low barrier, and I like @zoffixznet's idea very much
regarding visibility, rakudo.org seems in pretty good shape to me as there's a main menu item "Bug tracker". Maybe we might:

add a "Bugs" or "Issues" link in the main menu for perl6.org, pointing to a page with the relevant bug reporting facility chosen by each Perl 6 compiler
add pointers to the bug reporting in the Compilers page

Couldn't we create a form on rakudo.org or perl6.org that submits the email for you?  The form could even search issues based on your subject line and then if you decide to continue as a comment, it would just plug the required RT# into the subject line of the email.  It could either send it for you from the server or just open a mailto link with the details filled in from the form.

I agree that RT really doesn't provide a great user experience. Email isn't a great user experience for most folks either. They expect something pointy and clicky. GitHub isn't perfect, but it's pervasive, which is nice.

What do you mean by “handle them well”? What's the problem? And how much should we care about developers looking through these bug reports?

I say "amen" to most all Aleks says.

I'm not sure what you mean by that. To clarify, Perl 6 has always been about “torture the implementor on behalf of the user” kind of thing. So if we are looking for a balance between “the users are frustrated with the ticket system” and “the developers are frustrated with the ticket system” we should probably move as much pain as we can from the user side.

On Wed, Feb 3, 2016 at 8:31 AM, Flavio Poletti<EMAIL_ADDRESS>wrote:

@AlexDaniel to be honest I didn't experience anything of what you wrote. It
might depend on the fact that I have a bitcard account since a long time or
just sheer luck, but I was able to log in correctly, look for bugs, open

Him Flavio.  Good comments, but it may be the OS and browser.  I meant
to ask about that earlier.
I, too, have been a long-time RT account holder (with a bitcard
account) but I don't remeber ever having any luck.
I have always tried to use RT on Linux (Debian for the past eight
years or so) with either the Chrome or Firefox browser.
I still have problems with RT as others have had.  When I login with
my account I see NOTHING about Perl 5 or Perl 6 or help.  I do notice
words saying that this is a perlbug instance.
And, again, I have attempted to ask for help with the problem through
the e-mail address shown there and have yet to receive a reply.  I
have gone to the RT site and haven't found any help with the initial
user interface.
I vaguely remember the reason I joined years ago was for Perl 5
issues, but I think I had the same type problems then
Just my experience so far.
Best,
-Tom
P.S. With a new language, perhaps its time for a new bug tracker.  And
GCC seems to function very well with it and has for many years.

@tbrowder I've uses RT for some time as a CPAN Author and it mostly did its job but again, "works for me" is no excuse. My consideration was about providing feedback on issues to the devs of RT instead of just ditching it away for those very issues.
I'm anyway curious of the alternatives if we want to select something different, e.g. more in line with Perl 6 approach ("torture the implementor on behalf of the user") and what a casual user might expect ("... something pointy and clicky" as opposed to email). I have to admit I didn't understand the reference to GCC though.

Does RT provide something that github’s issue tracking does not?  The experience from a reporter/reporting perspective is kind of nice and you can attribute bugs/enhancements to milestones (or releases) and you get feedback on bugs you’ve filed or are interested in; RT seems to turn into a black hole but that could just be me not using it well.
To @moritz’s point, it doesn’t handle huge volumes of data well out of the box.  I have private repos that have had 300-500 issues on them that are manageable but require administrative work to keep things organized, filed, and assigned to milestones/people.  Essentially it requires someone to do the administrative side of a project manager.
Those things said, RT is pretty decent as far as bug tracking systems go.  Github’s is nice from a “pointy clicky” perspective.  Both require management and reporter/maintainer tooling knowledge or training.

Some points:

If a new user finds a potential bug, and they're willing to file it, they're going to look at perl6.org for instructions. Specifically, a relevant heading in the green headings at the top of the page ("maybe under Community?"). I'd expect to find a "Contributing" or "Development" heading, but don't see those. Linking to rakudo.org after that would be fine.

They'll need a link and quick instructions for how to search existing bugs, to avoid duplication.

New users won't understand that they can submit a bug report by simply sending an email. That should be explained explicitly --- that the bug tracking system will create a ticket automatically when it receives their email (or however the system works).

Some users may prefer to file bug reports at the respective project's github page. http://rakudo.org/tickets/ suggests you can do that already for moarvm and nqp. Seems like this would lead to bug duplication.

I'm not familiar with perlbug. From the first few paragraphs of its man page, I'm not sure what it's supposed to do. My guess is that folks won't use it unless there are some explicit and simple instructions for what they're supposed to do with it.

I'm not familiar with perlbug. From the first few paragraphs of its man page, I'm not sure what it's supposed to do. My guess is that folks won't use it unless there are some explicit and simple instructions for what they're supposed to do with it.

You run it and it asks you a few questions about the bug you're reporting, as well as prepares some info about your environment (OS, perl version, etc). Then, as I recall, it attempts to email the report and if that fails, it gives you what to mail and where to mail it and you just email it yourself.
I don't think that last part is too usable; maybe we could make it so if it fails to send email, it'd attempt to use the web API to create it, first.

I don't think "torture the implementors on behalf of the user" applies here – we've already got enough bugs in Perl 6 for doing that, without also having to fight with the (non-Perl 6) tool used to track them. Everyone's a user in this context (and the implementors insufficiently tortured, IMHO).

Here's my first draft at an issue submitter design. I think the search results will accordion out between the subject field and version dropdowns. It will then fold back in if you click any of the textarea boxes. Each search result item will have a linked title of the issue on rt.perl.org and a button to "Change to Comment" or something that will prepend the RT# at the beginning of your subject. (Or should it replace the whole subject line?) I could also add a "miscellaneous" textarea but I feel that if you're really going to write it your way, then just use an email (agree?). All that these sections will do is provide some structure to the resultant email message.

perlbug: what if I have a problem installing Perl? How do I use perlbug then?
RT: It was good. But now we have better. Let's not be romantic about it. It's time to move on. The most widely used ticket system now is GitHub. It's also not perfect. But almost every developer has an account. If they don't, I'm sure GitHub made it VERY straightforward to onboard. After all, it's a business and they probably optimized the on boarding funnel to the max. There is code highlighting, you can link to images. Email notifications out of the box.

perlbug: what if I have a problem installing Perl? How do I use perlbug then?

You email to<EMAIL_ADDRESS>assuming, of course, you don't have problems with your email :stuck_out_tongue_closed_eyes:

RT: It was good.

Was it? It seems ridiculously.. RIDICULOUSLY.. over-engineered to the point where you can't even link to the Perl 6 queue directly because of CSRF protection and you are presented with more than a dozen of search fields to do a search. I'm glad sanity prevailed and they stopped before adding such silly things as editing.

But almost every developer has an account

I know quite a few people without one, due to concerns over GitHub's terms of service.

I'm sure GitHub made it VERY straightforward to onboard

Yeah, many services offer a one-click subscription if you have, say, a Facebook account, but why the hell would I want to get "onboard" of some service I never intend to use? Multiple services get hacked yearly with all the emails and personal info leaked. Why would I want to increase my risk just so some group of people could fix their software? Each hoop your users have to jump through to report a bug filters out a portion of reporters unwilling to jump through it... which brings me back on topic:

Here's my first draft at an issue submitter design.

The one obvious thing I see missing is spam protection, like reCAPTCHA.
Also, to me, that form looks daunting. If a compiler implements a particular language version, why do I need to specify the langauge version as well? I've no idea what compiler version I'm using, how do I find it? Actually, all I'm reporting is a typo in the docs, do I need to fill all of that stuff out?
I'd go with the simplest form, like in the screenshot below, as the primary form and maybe have all of the fields you propose available in the "advanced" version of the form.

@AlexDaniel

What do you mean by “handle them well”? What's the problem? And how much should we care about developers looking through these bug reports?

What's the use of bug reports if developers don't look through them, find the most relevant, and fix them?

@zoffixznet maybe the default should be the advanced form.  Otherwise, no one will ever use it.  "Path of least clicks" and all.  The language drop down has no other available option, I could remove it but it's just there for future-proofing (and I think it's healthy to remind users of the distinction between language and compiler).
Also in regards to a simple form, perhaps what I could do is include a category dropdown and it would subsequently show different fields for each. For documentation it would just show "Is there a typo or missing information?", for articles it'd show "Is there an out-of-date article/blog that you're aware of?", and so on (some other categories could be "repl", "module usage", "module creation", "syntax error" "unexpected result", "crashes", "perl6.org", etc.).  This could even be plugged into the subject line as an added way to filter bugs.

@tony-o

Does RT provide something that github’s issue tracking does not?

For me, the things that RT provides are dashboards for organizing issues and attachments.  I have a dashboard for issues I've filed (which GH provides), but also for issues I've starred in RT, which I find interesting and have maybe considered fixing myself.  As far as I know, the only way to "star" issues is to watch them for updates, assign yourself, or label it.  Watching for updates gets you updates on the issue, but I can't ask the top level issues view to just "show me issues I'm watching".  Assigning an issue to myself would communicate the wrong message (plus, can you have more than one assignee, if multiple people want to star an issue?), and labelling would just make labels noisy for everyone.
Regarding attachments, I know GH issues supports image attachments, but I thought that it doesn't allow arbitrary text files (although that may have changed).  I make heavy use of RT's attachments to attach example code that demonstrates a bug.  Granted, you can put that in the issue in fenced code blocks, but to me that's LTA.
@moltar

RT: It was good. But now we have better.

Which ways in particular make GH issues better than RT?

But almost every developer has an account. If they don't, I'm sure GitHub made it VERY straightforward to onboard. After all, it's a business and they probably optimized the on boarding funnel to the max.

True, but as @zoffixznet points out, not everyone wants to have a GH account.

here is code highlighting

I'll concede that.

you can link to images.

You can still attach images in RT.  Granted, I don't think it will display them inline, which is definitely LTA.

Email notifications out of the box.

Doesn't RT do this too?
Other advantages others have pointed out:

More pervasive
Point and clicky, which some people prefer
GH is where Rakudo development happens already

I'm definitely coming at this from the perspective of a veteran RT user, but I don't know if we should uproot our entire issues system for a handful of advantages.  I have no love for RT, but to me, GH issues just feels like a minimalistic issue system for projects to use until they get off the ground - until they need to migrate to a "serious" issue tracker.  The recent "Open Letter to GitHub" seems to confirm that.

On Thu, 4 Feb 2016, Jake Russo wrote:

@zoffixznet maybe the default should be the advanced form.  Otherwise, no
one will ever use it.  "Path of least clicks" and all.  The language drop
down has no other available option, I could remove it but it's just there
for future-proofing (and I think it's healthy to remind users of the
distinction between language and compiler).

I think the distinction between language and compiler is better left to the
developers (or queue maintainers) to decide.  I think I finally got it by
now, but especially new users will not always be able to tell if the want to
report a language issue or compiler bug.

Also in regards to a simple form, perhaps what I could do is include a
category dropdown and it would subsequently show different fields for
each.  For documentation it would just show "Is there a typo or missing
information?", for articles it'd show "Is there an out-of-date
article/blog that you're aware of?", and so on (some other categories
could be "repl", "module usage", "module creation", "syntax error"
"unexpected result", "crashes", "perl6.org", etc.).  This could even be
plugged into the subject line as an added way to filter bugs.

Oh my god ...
If I want to report a typo, I'd rather just have a text field to enter
s/string with bug/string without bug
I could even put that into the subject line of my eMail.
I certainly don't want to find my way through a myriade of selections in a
drop down. And even less so, have initially selected the wrong one, entered
my info into some field, and then correct my mistake with the entry field
disappearing and other (empty ones) appearing.
I am all for submitting useful bug reports, but I'd suggest to rather err on
the side of getting too little information (without asking back) than not
getting any report because of asking to much.
Cheers,
Fritz
--
Oetiker+Partner AG              tel: +41 62 775 9903 (direct)
Fritz Zaucker                        +41 62 775 9900 (switch board)
Aarweg 15                            +41 79 675 0630 (mobile)
CH-4600 Olten                   fax: +41 62 775 9905
Schweiz                         web: www.oetiker.ch

I certainly don't want to find my way through a myriade of selections in a drop down.

Right. I think what @MadcapJake is saying is that he can javascript it up so the form starts simple (just a drop-down "what type of problem are you reporting"), and then the form only gets more detailed if the user goes in that direction. For example, if the user says it's a doc bug, then they just type in the box, prove they're not a bot, and click submit. If the user says it's a something more technical, then the form can expand to ask which implementation, version, etc.
As for explanation of the form's fields, I've usually found hover tooltips to be excellent. For example, the tooltip over a "compiler version" field a might contain something like "Run perl6 --version and look for ...".

can javascript it up so the form starts simple [...] then the form only gets more detailed

:+1: on a dynamic form that asks extra questions, providing the user can just short-circuit it and submit the form if they "had enough"

@uvtc right! and that's a great idea for the tooltips!
I think I've come up with a plan that should alleviate some of the fears of complexity.
Instead of changing the html of the fields, the issue category would just change the placeholder text. This way the user can just skip the category and get a blank form and do their thang, but if they want to get some direction on how to fill it out, then selecting a category will add some general questions into the body to be filled out (or removed).

What @zoffixznet posted is perfect. The form should not force you into some strict structure, but it should give you some good ideas (just like it does on the image, great!). Yes, yes and yes! Just think about it, if that thing submits a bug to RT just like we do now, then we're not loosing anything but at the same time it is much, MUCH more easier to submit bugs (I don't even have to type that this bug should go to rakudobug@perl.org!).
That being said, it should also link to other places to submit bug reports. E.g. documentation bugs should go to https://github.com/perl6/doc/issues/new (notice how it points directly to the submit form).
Also, it is missing a Title field.
@moritz

What do you mean by “handle them well”? What's the problem? And how much should we care about developers looking through these bug reports?

What's the use of bug reports if developers don't look through them, find the most relevant, and fix them?

I'm not saying that bug reports should go down the sink. I'm saying that it should be easier for users to submit bugs, but it's OK if it will be a bit harder for developers to view these bugs. I think that developers will do it anyway, but most users will just say “screw it” if it's too tedious.
@hoelzro

Email notifications out of the box.

Doesn't RT do this too?

Uhm, not really. Often I find activity on my bug reports that I haven't seen in my email. Non-comment changes are not emailed for sure, but I think that sometimes comments are left unnoticed too. Also, in the past I emailed comments to the wrong address (there are different email addresses!) so every time I do something on RT I just go and hit F5 until it actually appears, otherwise I have no idea if it actually succeeded and if everything is correct.
Unless someone can guide me through getting my bitcard account to work I don't think that I'll ever feel at home when using RT. Too much pain. Sure enough, a pretty form on perl6.org is not going to solve most of these problems (so I'm still voting to switch to something else), but at least it may hide some of them.
Now comes a good question: if we're going to have a form on perl6.org, is it possible to get a link to the bug report once it is submitted?

On Thu, 4 Feb 2016, Aleks-Daniel Jakimenko-Aleksejev wrote:

Email notifications out of the box.

Doesn't RT do this too?

Uhm, not really.  Often I find activity on my bug reports that I haven't
seen in my email.  Non-comment changes are not emailed for sure, but I
think that sometimes comments are left unnoticed too.

I think this is just a matter of configuration
--
Oetiker+Partner AG              tel: +41 62 775 9903 (direct)
Fritz Zaucker                        +41 62 775 9900 (switch board)
Aarweg 15                            +41 79 675 0630 (mobile)
CH-4600 Olten                   fax: +41 62 775 9905
Schweiz                         web: www.oetiker.ch

I think this is just a matter of configuration

Configuration of what? I can't get my bitcard account to work, so I cannot fix that myself.

On Thu, 4 Feb 2016, Aleks-Daniel Jakimenko-Aleksejev wrote:

I think this is just a matter of configuration

Configuration of what? I can't get my bitcard account to work, so I cannot fix that myself.

Of what is sent out by eMail. But I don't know out of my head what and
where. I just know that the RT instance we run here at our company sends me
(more than) enough eMails. But we might just have a simpler use case, I
didn't really look into the Perl RT setup(s).
--
Oetiker+Partner AG              tel: +41 62 775 9903 (direct)
Fritz Zaucker                        +41 62 775 9900 (switch board)
Aarweg 15                            +41 79 675 0630 (mobile)
CH-4600 Olten                   fax: +41 62 775 9905
Schweiz                         web: www.oetiker.ch

On Wed, Feb 3, 2016 at 8:04 AM, Tom Browder<EMAIL_ADDRESS>wrote:

On Wed, Feb 3, 2016 at 7:56 AM, Aleks-Daniel Jakimenko-Aleksejev
<EMAIL_ADDRESS>wrote:

but I haven't yet seen a github project with 800+ issues that was able to
handle them well.
What do you mean by “handle them well”? What's the problem? And how much
should we care about developers looking through these bug reports?
...

I say "amen" to most all Aleks says.
And I just looked, Bugzilla has a plugin for Git integration--might be
worth looking into.

I would be willing to donate exclusive use of one of my leased server
for a Perl (or just Perl 6) Bugzilla installation:
Intel Core 2 Quad - Pre-built Server - dedi3
Primary Hard Drive: 500GB Hard Drive (Default)
Memory: 4GB DDR2 RAM (Default)
IP Allocation: 1 Usable IPv4 (Default)
Bandwidth: 100Mbit 95th Percentile
Operating System: Debian 7 64-bit
Control Panel: No Control Panel (Default)
Server Management: None (Default)
It's not been touched yet.
-Tom

If we are going to go with self hosted form, then we can do the following:
Page 1: Name, Email, Textarea (bug report)
Once user submits that, the ticket is already saved, but on page 2, user has an option to add more info. There we can ask additional questions about versions and all that.
Worst case, we have the info already from page 1 and we can talk to the user to find out more, if necessary.
If we look at a bug report as a form of conversion, then it should ask the bare minimum of questions. Arguable it doesn't even need to ask for user's name. Just an email and description of the problem.

On Thu, Feb 4, 2016 at 10:26 AM, Aleks-Daniel Jakimenko-Aleksejev
<EMAIL_ADDRESS>wrote:

I think this is just a matter of configuration
Configuration of what? I can't get my bitcard account to work, so I cannot
fix that myself.

Aleks, I finally got a response to my plea for rt help at
<EMAIL_ADDRESS>and I can get a better display after logging
in.  I'm sure, if you can't get help with the bitcard people, you
might be able to get help from the Perl RT people.
In spite of the better view on RT now, I'll put my money would on
making a plan to move to Bugzilla.
Cheers to all!
-Tom

I'm not sure moving from one fairly hard to use piece of software (RT) to another (Bugzilla) would help much. Both of these tools are great for organizations that need a lot of complex logic around bug reporting. These tools provide a lot of power for people who spend a lot of time using them.
However, the most important use case here is "casual/first time Perl 6 user finds a bug and wants to report it". From that standpoint, GitHub is a huge win. A custom form on the perl6.org site is better than what we have now. Bugzilla is really not any better than RT for that use case.

On Sun, Feb 7, 2016 at 12:47 PM, Dave Rolsky<EMAIL_ADDRESS>wrote:

I'm not sure moving from one fairly hard to use piece of software (RT) to
another (Bugzilla) would help much. Both of these tools are great for
...
However, the most important use case here is "casual/first time Perl 6 user
finds a bug and wants to report it". From that standpoint, GitHub is a huge
win. A custom form on the perl6.org site is better than what we have now.
Bugzilla is really not any better than RT for that use case.

Dave, I do agree with you.  What I failed to remember was the
awkwardness of my initial Bugzilla uses (and some aspects still "bug"
me).
Best,
-Tom

Aleks, I finally got a response to my plea for rt help at<EMAIL_ADDRESS>and I can get a better display after logging in.

Yeah, I also wrote an email to the same address and they fixed my account too (it took two days). Perhaps this should be mentioned somewhere.

Somewhat relevant: https://github.com/blog/2111-issue-and-pull-request-templates

Ok, my issue submitter is making progress, you can check it out here.  I still need input on issue templates, please submit a PR (place them in templates), issue, or message me on IRC/slack/email with your suggestions. I'm thinking markdown at first and then I'll translate into html when sending the email.

I think this issue may be largely moot now given perl6/perl6.org#96 (Rakudo bugs are now using GitHub issues).
Also, see duplicate of this bug at perl6/perl6.org#61.

This is indeed an old thread that can be closed now that Github Issues are also used.


Added a ScmIntegration for Gerrit

Signed-off-by: Niklas Aronsson<EMAIL_ADDRESS>Hey, I just made a Pull Request!
A new ScmIntegration has been added for gits hosted by Gerrit. The UrlReader implementation will be done in an upcoming patch.  This is the first part of #9896.
The Gerrit configuration supports the following values:

host (required) : The host of the gerrit instance to use.
apiBaseUrl (required): The base url of the gerrit api.
username (optional): The username to use during authentication.
password (optional): The password or http token to use for
authentication.

:heavy_check_mark: Checklist

[ ] A changeset describing the change and affected packages. (more info)
[ ] Added or updated documentation
[ ] Tests for new functionality and regression tests for bug fixes
[ ] All your commits have a Signed-off-by line in the message. (more info)

Thanks for your contribution @anicke 🙌 Please let me know if you’d like some help to contribute further.


GAMINGSHOP

1. Why is this change necessary?
2. What does this change do, exactly?
3. Describe each step to reproduce the issue or behaviour.
4. Please link to the relevant issues (if any).
5. Which documentation changes (if any) need to be made because of this PR?
6. Checklist

[x] I have written tests and verified that they fail without my change
[x] I have squashed any insignificant commits
[x] This change has comments for package types, values, functions, and non-obvious lines of code
[x] I have read the contribution requirements and fulfil them.

sorry, but it seems, that you messed something up here :blush:
There are only commits of @janbuecker
I will close this PR for now, feel free to create a new clean PR again :wink: :+1:


[SMALLFIX] Enable Findbugs checking for uses of potentially uninitialized fields

https://tachyon.atlassian.net/browse/TACHYON-1197

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Same comment as Calvin's, otherwise LGTM

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I just had a minor question. Thanks!

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LGTM


Bad imagens on .md/.pdf - linux and windows

OS:
Arch linux 64x - gnome  firefox
Windows Pro 64x - firefox
In the .pdf  and .md ALL images  with VS Code with light theme is bad.
It is almost impossible to read,
You can see page 17  has a image with great quality, but page 21 has a bad one.
Page 17:

Page 21

where can I get the clear images? because the zip folder have the same images and they are compiled in LATEX.

Resolved by #233 - will be available in next PDF release


rad.json

After I compile the AL against the sandbox, I noticed there is additional file called rad.json created, I don't documentation about this. I heard it's something to do with incremental publish but is there official document from Microsoft for how to use it?

AL Extension Version:
3.0.115791

Server Version:
13.4 (29682)

You can find a documentation here:
https://docs.microsoft.com/en-us/dynamics365/business-central/dev-itpro/developer/devenv-rad-publishing

Hi @jeffgit, thanks for filing this issue. As @JulienDecottignies kindly commented, you can read more about this in our official documentation. I'll go ahead and close this issue now, thanks.


Peptide Genomic Coordinate issue while applying GalaxyP proteogenomics Tutorial3

Galaxy server : usegalaxy.eu
History link: https://usegalaxy.eu/u/_luisfr/h/peptidegenomiccoordinateissue
Tool version : Galaxy Version 0.1.1
While executing Peptide Genomic Coordinate (following this Galaxy-P hands-on tutorial : [Tutorial3 : Novel peptides](https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html). See also Tutorial 1 : Database creation and Tutorial 2 : Database search), with our dataset (human species), the “Peptide Genomic Coordinate” tool  returned an empty file.
I went through the source code; executing it locally in a « Debug » mode, I noticed that it didn’t enter in the « if » condition (in line  47), i.e. « coordinates » variable is empty at each iteration. However if I change line 41 : « acc = each[1] » for « acc = each[1].strip() » (trimming the spaces) it works. I noticed that, sometimes, proteins accession number (Ensembl ENSP) in the mz_to_sqlite input file, comes with a  char at the end e.g.  'ENSP00000267884_A82P,P124A '. When, in line 44 (line when we do the query to fill « coordinates » variable), we did the matching with another tool’s input « Peptide_Genomic_Coordinate.sqlite »,  it does not work well because in this file, protein accessions do not contain this space e.g.  'ENSP00000267884_A82P,P124A'.
To help, I uploaded in the history the input files (data #1, #5 and #7) to execute Peptide Genomic Coordinate and the empty file, resulting from the execution on Galaxy of this tool (data #8). Also, I have uploaded the  customized database (data #3) and the output file produced when I executed the tool locally with the modifications commented above (data #9 ).
Thank you for your help.

@luisfdez94  @subinamehta   Luis, can you share the Database creation history?   I want to figure out why there is a SPACE character after the protein ID from the CustomProDB workflow output.

generic|ENSP00000355265 |5239.2894|ENST00000361851|ENSG00000228253|MT-ATP8|mitochondrially encoded ATP synthase 8 [Source:HGNC Symbol;Acc:HGNC:7415]

Should have been:

generic|ENSP00000355265|5239.2894|ENST00000361851|ENSG00000228253|MT-ATP8|mitochondrially encoded ATP synthase 8 [Source:HGNC Symbol;Acc:HGNC:7415]

Thank you for your fast answer.

Luis, can you share the Database creation history? I want to figure out why there is a SPACE character after the protein ID from the CustomProDB workflow output.
There it goes: https://usegalaxy.eu/u/_luisfr/h/peptidegenomiccoordinateissuedbcreation
As you can see at item #30, I also use the tool Regex Find And Replace to add generic| before each sequence in the customized DB (item #28): e.g. >ENSP00000355265 to >generic|ENSP00000355265 . I do this in order, SearchGui works.

@luisfdez94 @subinamehta The protein IDs from customProDB as a SPACE character at the end of the ID.  I'm asking @chambm if that seems correct.  Most steps in these workflows do not handle an ID ending with a SPACE.  We could add a steps after customProDB using regex tools to remove the SPACE.

@jj :I think the workflow already takes care of that
On Mon, Nov 30, 2020 at 10:32 AM Jim Johnson<EMAIL_ADDRESS>wrote:

@luisfdez94 https://github.com/luisfdez94 @subinamehta
https://github.com/subinamehta The protein IDs from customProDB as a
SPACE character at the end of the ID. I'm asking @chambm
https://github.com/chambm if that seems correct. Most steps in these
workflows do not handle an ID ending with a SPACE. We could add a steps
after customProDB using regex tools to remove the SPACE.
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Thanks to @jj-umn and Galaxy-P team help, I have been able to solve this issue. I had to do some modifications to the headers of every sequence of the customized DB (fasta) obtained at the end of  Galaxy-P Tutorial 1 : Database creation. For that purpose I have used Regex Find And Replace v1.0.0 tool with the parameters shown at the end of the message.

Delete spaces at the end of each protein's accession ID (for Ensembl-PRO and STRG database)[see checks 3 and 5 at the end of the message]
Indel and snv reformatting (coming from CustomProDB) [checks 1 and 2] This is also done in Galaxy-P Tutorial 1 : Database creation section Genomic mapping database In this way our genomic mapping is consistent with our protein database.
Add generic| prefix at the beginning of each header coming from Ensembl-PRO and STRG database (not standard format for SearchGUI). See http://compomics.github.io/projects/searchgui/wiki/DatabaseHelp [checks 1, 3, 4 and 5]

Another important point if you follow Galaxy-P hands on tutorials is to input this modified Custom DB to mz_to_sqlite tool at Tutorial 2: DB search! I was inputting the original custom DB.
Regex Find And Replace v1.0.0

check: from ">ENSP00000360709_1123:GAT>CAAT " to ">generic|ENSP00000360709_1123:GAT_CAAT"

“Find Regex”: >(ENS.*_\d+:)([ACGTacgt]+)>([ACGTacgt]+)\s*
"Replacement": >generic|\1\2_\3

check: from ">ENSP00000457107_D77*,L258P,L264P,S457G " to ">ENSP00000457107_D77*.L258P.L264P.S457G "

“Find Regex”: ([A-Z,*][0-9]+[A-Z,*]),
"Replacement”: \1.

check: delete the final espace at the end of a protein accession ID (Ensembl DB). Also add the prefix "generic". From "ENSP00000360709 " to ">generic|ENSP00000360709"

“Find Regex”: >ENS[A-Z]*(.*)\s\|
"Replacement”: >generic|ENSP\1|

check: from ">STRG00000058243|" to ">generic|STRG00000058243|"

“Find Regex”: >STRG(\S*)\|
"Replacement”: >generic|STRG\1|

check: from ">STRG00000058243 |" to ">generic|STRG00000058243|"

“Find Regex”: >STRG(.*)\s\|
"Replacement”: >generic|STRG\1|


MIT License?

Hi, can you release this under MIT As well?

Done.

Thanks!I was going to sit down and build a flexbox / sass progress wizard and through the magic of google found your perfect solution! I am allergic to bootstrap positioning classes and yours is perfecto. Thanks!

I'm glad to hear it, that's great!


FITS image doesn't updated on Fits tab of Aux Monitor

The first FITS image is loaded when the tab is selected, but it never updates to a different one.

Surprising. Just to be specific:

[ ] You manually select FITS tab, before the end of the exposure.
[ ] when the first exposure is finished, fits image is refreshed.
[ ] with each next exposure the fits image is NOT refreshed

what happens when You don't touch fits tab ? (the tab should be brought up automatically after exposure is ready)

fixed by magic

fixed by magic