Ability to create tags with a capital letter in the middle of the name

Subj.

@rultor merge

@rultor merge

@kniazkov OK, I'll try to merge now. You can check the progress of the merge here

@rultor merge

@kniazkov Done! FYI, the full log is here (took me 6min)

@rultor release, tag is 0.2.17

@rultor release, tag is 0.2.17

@kniazkov Done! FYI, the full log is here (took me 7min)


Extension issue

Issue Type: Bug
Extension Name: LiveServer
Extension Version: 5.6.1
OS Version: Windows_NT x64 10.0.17763
VSCode version: 1.50.1

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Q
A

Is bugfix?
✔/❌

New feature?
✔/❌

Breaks BC?
✔/❌

Fixed issues
comma-separated list of tickets # fixed by the PR, if any

👍


How to provide more context to AI and AIEdit

Hello,
My goal is to provide context to the model when doing a call to :AI or :AIEdit.
My first try was to pass the whole file to AIEdit, but then I have to wait for the model to write the same file again and it takes time.
" custom command adding filetype to the instruction
function! AIEditSyntaxFn(...) range

  if a:firstline < a:lastline
    let l:firstline = a:firstline
    let l:lastline  = a:lastline
  else
    " Whole file
    let l:firstline = 0
    let l:lastline  = line('$')
  endif

  let l:instruction = "programming language is " . &filetype
  if a:0
    echomsg "a:1" . a:1
    let l:instruction = l:instruction . " - " . a:1
  endif
  exe l:firstline . ',' . l:lastline . 'call vim_ai#AIEditRun(g:vim_ai_edit, l:instruction)'
endfunction
command! -range -nargs=? AISEdit <line1>,<line2>call AIEditSyntaxFn(<f-args>)

I wish I could select the line I want the model to edit, and pass the whole buffer as context only. Even better, I wish I could pass all the open buffers as context.
I read the documentation that says that you can include files using the >>>> include syntax. However, I don’t understand where to input this.
Did you already try something similar ?
Best,

I just quickly prototyped, this custom command should send content of the file as a system message:
let g:initial_file_prompt_prefix =<< trim END
>>> system
You are a code assistant.
Answer shortly, consisely and only what you are asked.
Do not provide any explanantion or comments if not requested.
If you answer in a code, do not wrap it in markdown code block.
Below is the code context to the questions:
END

function! AIAskFileFn(...) range
  let l:instruction = a:0 > 0 ? a:1 : ""
  let l:selection = a:0 > 1 ? a:2 : 0
  let l:buf_nr = bufnr("%")
  let l:buf_content = join(getbufline(l:buf_nr, 1, '$'), "\n")
  let l:initial_prompt_prefix = join(g:initial_file_prompt_prefix, "\n")
  let l:initial_prompt = l:initial_prompt_prefix . "\n######\n" . l:buf_content . "\n######"
  let l:config = {
  \  "options": {
  \    "initial_prompt": l:initial_prompt,
  \  },
  \}
  exe a:firstline.",".a:lastline . "call vim_ai#AIEditRun(l:config, l:instruction, l:selection)"
endfunction
command! -range -nargs=? -complete=customlist,vim_ai#RoleCompletion AIAskFile <line1>,<line2>call AIAskFileFn(<q-args>)

It should be easy to extend it with multiple buffers or >>> include syntax.
Please let me know if this or similar command actually improved your AI workflow.

Injecting in the initial prompt is a much better idea! I tested real quick with qwen2.5-coder and it is behaving much like what I would expect.
I guess being able to pour all open buffers into AIAskFile would be fantastic: I could just query with AIAskFile and whenever I realize that some context is missing, I open that other file in another tab for example and run the same query again.
But what you just did is already very good I think.  I would need to continue using it in a real working situation for sometimes first.

You can also share files solely with an initial prompt, for example see this "codebase" role:
[codebase]
[codebase.options]
initial_prompt =
  >>> system
  You are a code assistant.
  Answer shortly, consisely and only what you are asked.
  Do not provide any explanantion or comments if not requested.
  If you answer in a code, do not wrap it in markdown code block.
  I will share sorce code that you use as a context to provide better answers.
  >>> include
  /home/user/myproject/requirements.txt
  /home/user/myproject/**/*.py

This will however send content of any matching file (not only open buffers).
Anyway, you probably want to make sure not to share any sensitive files, such as secrets.

Right, there was a breaking change, now you need to pass range as first parameter. See custom commands


Fix TLSv1.3 session issues

This PR does two main things:

Don't remove sessions from the cache during PHA in TLSv1.3

If we issue new tickets due to post-handshake authentication there is no reason to remove previous tickets from the cache. The code that did that only removed the last session anyway - so if more than one ticket got issued then those other tickets are still valid.

Always issue new tickets when using TLSv1.3 stateful tickets

Previously we were failing to issue new tickets if a resumption attempt failed.
This also improves the testing of this area.
Fixes #6654.

Pushed. Thanks.


Implement method to create a referrer record

Need to pass next arguments:

referrer
referral
expire
percent
breakout

#368


Version Packages

This PR was opened by the Changesets release GitHub action. When you're ready to do a release, you can merge this and publish to npm yourself or setup this action to publish automatically. If you're not ready to do a release yet, that's fine, whenever you add more changesets to main, this PR will be updated.
Releases
<EMAIL_ADDRESS>Minor Changes

7f8bb2b: Initial release of Backstage GraphQL Plugin

<EMAIL_ADDRESS>Patch Changes

Updated dependencies [7f8bb2b]

<EMAIL_ADDRESS>

The following preview packages were published:

Name
Version
Install Command

@frontside/backstage-plugin-graphql
0.2.1-changeset-release-main.0
yarn add @frontside/backstage-plugin-graphql@changeset-release-main

Generated by @thefrontside/actions


Feat: global statusline should still displays for all filetypes, including ignored_filetypes

Requested feature
When global statusline is used, statusline should works for all buffer, including those in disabled_filetypes tables.
Motivation
disabled_filetypes is used to prevent rendering a crammed statusline in overly small windows, this doesn't apply with global statusline.

One option is just to not disabled any filetypes, but that means winbar (if it is ever officially supported #736 ) will not ignore some filetypes with small windows either.
Another option is to have separate options, i.e statusline_disabled_filetypes and winbar_disabled_filetypes (again if it's ever supported)
Or just ignore ignored_filetypes altogether when using global statusline.

I think I'll just let users specify which filetypes are to be ignored for winbar. That gives more control to user.


i18n(ja): Add media.mdx

Description (required)
Add media.mdx.
Related issues & labels (optional)

Suggested label: i18n

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guides/media.mdx
Localization added, will be marked as complete.

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@morinokami
ありがとうございます、  nav.ts の変更取り込み & このコミットでの変更の削除を行いました！ 👍


Need help on elastalert config

I have setup an ELK such as installed filebeat on target hosts and configured 1 centralised logstash server. Created an Elastic search domain and given the domain url in logstash conf file. Also I have setup an Elastalert in same logstash server to send me mail when certain error text is matched. Below is elastalert conf file

# (Required)
# Index to search, wildcard supported
index: logstash-*

# (Required, frequency specific)
# Alert when this many documents matching the query occur within a timeframe
num_events: 1

# (Required, frequency specific)
# num_events must occur within this amount of time to trigger an alert
timeframe:
  hours: 4
# A list of elasticsearch filters used for find events
# These filters are joined with AND and nested in a filtered query
# For more info: http://www.elasticsearch.org/guide/en/elasticsearch/reference/current/query-dsl.html

alert_text_type: alert_text_only

filter:
- query:
    query_string:
      query: "Invalid Password"

# (Required)
# The alert is use when a match is found
alert:
- "email"

alert_text: |
    ElastAlert has detected suspicious activity for {0}.
    At {1}, an {2} error occured under {3} path. {4}. Do something about it!

alert_text_args:
  - email
  - host
  - type
  - source
  - message
# (required, email specific)
# a list of email addresses to send alerts to
email:
-<EMAIL_ADDRESS>

the issue it the email I am getting has other irrelevant info in it. Below is email

# (Required)
# Index to search, wildcard supported
index: logstash-*

# (Required, frequency specific)
# Alert when this many documents matching the query occur within a timeframe
num_events: 1

# (Required, frequency specific)
# num_events must occur within this amount of time to trigger an alert
timeframe:
  hours: 4
# A list of elasticsearch filters used for find events
# These filters are joined with AND and nested in a filtered query
# For more info: http://www.elasticsearch.org/guide/en/elasticsearch/reference/current/query-dsl.html

alert_text_type: alert_text_only

filter:
- query:
    query_string:
      query: "Invalid Password"

# (Required)
# The alert is use when a match is found
alert:
- "email"

alert_text: |
    ElastAlert has detected suspicious activity for {0}.
    At {1}, an {2} error occured under {3} path. {4}. Do something about it!

alert_text_args:
  - email
  - host
  - type
  - source
  - message
# (required, email specific)
# a list of email addresses to send alerts to
email:
-<EMAIL_ADDRESS>-<EMAIL_ADDRESS>

Please let me know how would I remove the irrelevant data from mail.

What do you mean by irrelevant data? Do you mean the example ElastAlert has detected suspicious activity for ... Do something about it! text? If so, just remove that section.

No, not that text. I mean the "message" alert_txt_args with {4} is pulling all not needed text apart from actual message. In kibana the actual message is below
[17/May/2016:05:05:00 -0400] SEARCH REQ conn=101665 op=107836 msgID=107837 base="ou=people,dc=recall,dc=com" scope=wholeSubtree filter="(&(uid=BackbasePortal)(objectclass=inetorgperson))" attrs="uid"
But the what I get in my mail is huge irrelevant data with above data

You need to parse this in Logstash if you want better control of what's in the message, either using grok or perhaps the key/value filter. Elastalert is not adding extra things to the message, I think you are just looking at the wrong one in Kibana. All it does is put the message field into the alert.


Speedup PriorityQueue a little

Saving some field accesses results in small but visible savings:
                            TaskQPS baseline      StdDevQPS my_modified_version      StdDev                Pct diff p-value
                         LowTerm      617.46      (8.2%)      615.47      (7.4%)   -0.3% ( -14% -   16%) 0.855
                    OrHighNotLow      488.90      (9.5%)      491.20      (7.8%)    0.5% ( -15% -   19%) 0.808
                    OrHighNotMed      384.07      (7.9%)      386.54      (6.4%)    0.6% ( -12% -   16%) 0.688
                       OrHighMed      269.60      (4.9%)      271.50      (4.5%)    0.7% (  -8% -   10%) 0.504
                         Prefix3      397.59      (7.4%)      401.40      (6.8%)    1.0% ( -12% -   16%) 0.546
                      AndHighMed      156.59      (4.2%)      158.14      (4.2%)    1.0% (  -7% -    9%) 0.290
                      AndHighLow     1711.42      (7.5%)     1729.95      (6.7%)    1.1% ( -12% -   16%) 0.496
                       OrHighLow      564.40      (4.6%)      570.66      (5.3%)    1.1% (  -8% -   11%) 0.315
             LowIntervalsOrdered      255.12      (5.7%)      258.02      (7.6%)    1.1% ( -11% -   15%) 0.448
                        HighTerm      688.93      (6.5%)      697.31      (6.4%)    1.2% ( -10% -   15%) 0.400
                        PKLookup      242.28      (1.5%)      245.33      (2.5%)    1.3% (  -2% -    5%) 0.006
            HighTermTitleBDVSort       37.87      (3.3%)       38.37      (3.3%)    1.3% (  -5% -    8%) 0.073
             MedIntervalsOrdered       48.08      (5.5%)       48.72      (6.7%)    1.3% ( -10% -   14%) 0.335
                   OrHighNotHigh      419.24      (6.8%)      424.98      (6.3%)    1.4% ( -10% -   15%) 0.350
                         MedTerm      668.97      (7.0%)      678.42      (5.4%)    1.4% ( -10% -   14%) 0.311
               HighTermTitleSort       76.23      (6.0%)       77.32      (5.0%)    1.4% (  -9% -   13%) 0.254
                    OrNotHighLow      993.21      (7.3%)     1007.93      (5.6%)    1.5% ( -10% -   15%) 0.310
                      TermDTSort      207.44      (3.7%)      210.59      (4.2%)    1.5% (  -6% -    9%) 0.086
                          IntNRQ      216.19      (6.9%)      219.48      (7.3%)    1.5% ( -11% -   16%) 0.340
                          Fuzzy1       98.73      (2.1%)      100.28      (2.7%)    1.6% (  -3% -    6%) 0.004
            BrowseDateTaxoFacets        5.31      (8.6%)        5.40      (7.8%)    1.7% ( -13% -   19%) 0.368
            MedTermDayTaxoFacets       34.37      (4.4%)       34.94      (4.2%)    1.7% (  -6% -   10%) 0.086
       BrowseDayOfYearTaxoFacets        5.39      (8.4%)        5.48      (7.9%)    1.7% ( -13% -   19%) 0.343
                      OrHighHigh       79.75      (7.3%)       81.16      (5.7%)    1.8% ( -10% -   15%) 0.227
                   OrNotHighHigh      355.03      (6.4%)      361.39      (5.8%)    1.8% (  -9% -   14%) 0.188
                    OrNotHighMed      384.05      (6.4%)      391.18      (7.6%)    1.9% ( -11% -   16%) 0.237
            HighIntervalsOrdered       34.09      (4.9%)       34.76      (6.3%)    2.0% (  -8% -   13%) 0.118
               HighTermMonthSort     1504.80      (6.1%)     1537.64      (6.1%)    2.2% (  -9% -   15%) 0.111
                       LowPhrase      144.85      (4.6%)      148.15      (4.7%)    2.3% (  -6% -   12%) 0.029
           HighTermDayOfYearSort      359.83      (6.6%)      368.10      (6.9%)    2.3% ( -10% -   16%) 0.127
         AndHighMedDayTaxoFacets       22.54      (3.7%)       23.08      (4.0%)    2.4% (  -5% -   10%) 0.006
     BrowseRandomLabelTaxoFacets        4.41      (3.4%)        4.52      (3.8%)    2.4% (  -4% -    9%) 0.003
                HighSloppyPhrase       27.97      (5.9%)       28.70      (6.2%)    2.6% (  -9% -   15%) 0.055
                     LowSpanNear       18.23      (7.2%)       18.71      (8.1%)    2.7% ( -11% -   19%) 0.120
                      HighPhrase      279.12      (7.9%)      286.62      (7.2%)    2.7% ( -11% -   19%) 0.112
                 MedSloppyPhrase        5.58      (4.1%)        5.73      (4.9%)    2.7% (  -6% -   12%) 0.007
                     AndHighHigh       61.57      (4.6%)       63.31      (4.2%)    2.8% (  -5% -   12%) 0.004
           BrowseMonthTaxoFacets       12.23     (28.7%)       12.58     (31.2%)    2.8% ( -44% -   88%) 0.672
                        Wildcard       84.87      (3.2%)       87.37      (3.0%)    2.9% (  -3% -    9%) 0.000
                         Respell       56.85      (1.9%)       58.60      (2.4%)    3.1% (  -1% -    7%) 0.000
            BrowseDateSSDVFacets        1.24      (6.0%)        1.28      (6.4%)    3.2% (  -8% -   16%) 0.020
                          Fuzzy2       69.18      (3.5%)       71.42      (3.4%)    3.2% (  -3% -   10%) 0.000
                    HighSpanNear       18.56      (6.8%)       19.19      (6.9%)    3.4% (  -9% -   18%) 0.028
          OrHighMedDayTaxoFacets        8.58      (7.4%)        8.88      (7.0%)    3.5% ( -10% -   19%) 0.031
                 LowSloppyPhrase       20.16      (8.0%)       20.88      (9.9%)    3.5% ( -13% -   23%) 0.079
                     MedSpanNear       30.28      (2.6%)       31.46      (4.4%)    3.9% (  -3% -   11%) 0.000
        AndHighHighDayTaxoFacets        8.28      (5.8%)        8.60      (5.9%)    3.9% (  -7% -   16%) 0.003
           BrowseMonthSSDVFacets        4.48      (9.6%)        4.66      (9.1%)    4.1% ( -13% -   25%) 0.048
                       MedPhrase       32.89      (4.5%)       34.28      (6.1%)    4.3% (  -6% -   15%) 0.000
     BrowseRandomLabelSSDVFacets        3.29      (3.8%)        3.43      (5.4%)    4.4% (  -4% -   14%) 0.000
       BrowseDayOfYearSSDVFacets        4.41      (4.2%)        4.65      (6.5%)    5.5% (  -5% -   16%) 0.000

This results in a lot more code complexity, which makes maintenance difficult. Maybe the version of java you are testing with has a bug in its register allocator or something?
seriously? I think we should take a step back before making all of our code more complex for a 1% benefit which might just be an upstream compiler bug.

I think the queue methods changed here  in isolation get a far bigger improvement than 1% in many cases. Plus making methods like the ones adjusted here smaller and easier on the CPU cache tends to help the performance of "neighboring" code as well in many case (hence the across the board speedup in the luceneutil run).
I don't think this is the result of a JVM bug, it's just something that is hard to optimize by the compiler with Java so dynamic. It's a combination of two things.

Current JIT implementations don't really take advantage of final fields in normal objects https://openjdk.org/jeps/8132243, https://bugs.openjdk.org/browse/JDK-8058164 and so on. That's what makes caching stuff like size or the heap array so helpful.
Field loads simple result in larger methods when measuring byte code size than caching in a local variable. Unless JIT implementations become more sophisticated (looking at e.g. https://mail.openjdk.org/pipermail/core-libs-dev/2023-July/109461.html it doesn't look like that's happening anytime soon), avoiding field access tends to result in deeper inlining here and there.


Loss of coverage after adding a new unit test

Environment:

JaCoCo version: 0.8.8
Operating system: ubuntu
Tool integration: Maven
Pull request: https://github.com/nbauma109/jd-core-v0/pull/65

Steps:

Create a new branch from master
Commit and push a new unit test to the new branch
Create a new pull request
Read codecov report

Expected behaviour

Global code coverage increases or remains the same
None of the classes may have decreased coverage

Actual behaviour
A loss of coverage is observed but this is due to wrong initial coverage.
The native jacoco reports do not show any coverage loss (the version before also has the same uncovered pieces).

@nbauma109 can you open a topic in our community boards for this?


Add TCP tunnel integration test

Scenario is a tunnel with mutual TLS between egressgateway and ingressgateway.
This integration test is not working due to issue #9659.

Could we have a 'ok-to-test' label for this PR? (@nmittler could you do us that favour?)

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At the moment the e2e test fails because the ingress complains about certificates that actually belong to egress. As mentioned in Issue #9659 we opened a PR to solve the problem for envoy.

not stale

/ok-to-test

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prow/istio-pilot-multicluster-e2e.sh
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/test istio-pilot-multicluster-e2e

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prow/e2e-simpleTests-cni.sh
74d699c89c9618dd3441f6112f7ee8f9ea3aba52
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74d699c89c9618dd3441f6112f7ee8f9ea3aba52
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5701e1d848e93d21f190bbf6cabbc2f7069d4e39
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prow/istio-pilot-multicluster-e2e.sh
5701e1d848e93d21f190bbf6cabbc2f7069d4e39
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prow/e2e-simpleTests-cni.sh
0120f2dc99f689b94348897cebc23f39c88d7d15
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/test e2e-simpleTests-cni

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prow/istio-pilot-multicluster-e2e.sh
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[APPROVALNOTIFIER] This PR is NOT APPROVED
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/test istio-integ-k8s-tests

prow/istio-pilot-multicluster-e2e.sh
0120f2dc99f689b94348897cebc23f39c88d7d15
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/test istio-pilot-multicluster-e2e

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prow/istio-pilot-multicluster-e2e.sh
0120f2dc99f689b94348897cebc23f39c88d7d15
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/test istio-pilot-multicluster-e2e

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/test e2e-simpleTests-cni

prow/istio-pilot-multicluster-e2e.sh
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prow/istio-pilot-multicluster-e2e.sh
ce8b0cb0649d1747f212e7a0cd17e096ebbef2bd
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/test istio-pilot-multicluster-e2e

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[APPROVALNOTIFIER] This PR is NOT APPROVED
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/test e2e-simpleTests-cni

prow/istio-pilot-multicluster-e2e.sh
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/retest

/retest

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prow/istio-pilot-multicluster-e2e.sh
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prow/istio-pilot-multicluster-e2e.sh
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prow/istio-integ-k8s-tests.sh
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@nmittler, could you have a look at this PR again. We have tried to incorporate all your suggestions.

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/test istio-integ-k8s-tests

prow/istio-pilot-multicluster-e2e.sh
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[APPROVALNOTIFIER] This PR is NOT APPROVED
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/test istio-pilot-multicluster-e2e

prow/istio-integ-k8s-tests.sh
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prow/istio-integ-k8s-tests.sh
9d9073147bb1407beb6929b34a47e8fbec6afb59
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/test istio-integ-k8s-tests

prow/istio-integ-local-tests.sh
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/test istio-integ-k8s-tests

prow/istio-integ-local-tests.sh
4f8261eabd4f387e17cbe2a02f6234b30624b910
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/test istio-integ-local-tests

prow/istio-pilot-multicluster-e2e.sh
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prow/istio-integ-local-tests.sh
4f8261eabd4f387e17cbe2a02f6234b30624b910
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/test istio-integ-local-tests

prow/istio-pilot-multicluster-e2e.sh
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prow/istio-pilot-multicluster-e2e.sh
4f8261eabd4f387e17cbe2a02f6234b30624b910
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/test istio-pilot-multicluster-e2e

prow/istio-integ-k8s-tests.sh
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prow/istio-pilot-multicluster-e2e.sh
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/test istio-pilot-multicluster-e2e

prow/istio-integ-k8s-tests.sh
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prow/istio-pilot-multicluster-e2e.sh
12d291a371b256226d13dcd2678ee1a68ca36c13
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12d291a371b256226d13dcd2678ee1a68ca36c13
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@kramerul: PR needs rebase.

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link
/test istio-pilot-multicluster-e2e

prow/istio-integ-k8s-tests.sh
12d291a371b256226d13dcd2678ee1a68ca36c13
link
/test istio-integ-k8s-tests

prow/istio-integ-local-tests.sh
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/test istio-pilot-multicluster-e2e

prow/istio-integ-k8s-tests.sh
12d291a371b256226d13dcd2678ee1a68ca36c13
link
/test istio-integ-k8s-tests

prow/istio-integ-local-tests.sh
4681cc1a2045aeaf0e8fb9a5c9c051ea5e5c4676
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/test istio-integ-local-tests

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prow/istio-integ-k8s-tests.sh
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/test istio-integ-k8s-tests

prow/istio-integ-local-tests.sh
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/test istio-integ-local-tests

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prow/istio-pilot-multicluster-e2e.sh
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prow/istio-integ-k8s-tests.sh
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/notstale

@kramerul: PR needs rebase.

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Oh no! Now it needs a rebase again. We did that already a few times, do you think it makes sense to keep it up to date or should we give up on this additional test?
@costinm : I had the impression you were asking in the last environments working group meeting specifically for more tests to be written. Perhaps speeding up the merge of already existing PRs that try to add tests could also improve the situation?

Just discussed this in our team. We're giving up now. It has become too much effort to keep this pr properly rebased and there seems to be no interest from the community to get it merged anyway.


QUESTION: Is there no Python v3 lib for all the v3 routes?

https://api.flutterwave.com/v3/

Hello @rocktimsaikia,
We are working on a library that uses the v3 endpoints. We'll provide updates on our development as we reach certain milestones.

Thanks for the update. In the meantime, we will be using the v3 API endpoints directly.


vim-plug and Nixos?

Hello!
I really, really like vim-plug, but at the moment I am installing Nixos on all my systems, and it's a bit of a hassle to get vim-plug to be my prefered plugin manager, because I haven't figured out how to get vim-plug to start, without putting plug.vim in the corret autoload folder, but I have no idea how to do that with Nixos configuration files.
I have a vim.nix file where I override neovim, and ask it to start with vim-plug, but that doesn't seem to work. Anyone have any ideas?
with import <nixpkgs> {};

neovim.override {
  configure = {
    customRC = builtins.readFile "/home/peterstorm/.config/nvim/init.vim";
    packages.myVimPackage = with pkgs.vimPlugins; {
      start = [ vim-plug ];
    };
  };
}

Did you check https://github.com/NixOS/nixpkgs/issues/56338?

Did you check NixOS/nixpkgs#56338?

I did skim it, but reading it again, I'm not sure there is anything in there that can help me :(
I just want to autoload vim-plug through my configuration file, without having to manually install vim-plug and then copy it from the store to the autoload dir.

This is not something we can answer. Please use the issue tracker of NixOS.
FWIW, you can set up your Vim configuration file to automatically download vim-plug.

https://github.com/junegunn/vim-plug/wiki/tips#automatic-installation

I'm working on my test vim configuration in a Nixos project. vim-plug  almost works for me, with the following configuration
  {
   # ...
    plugvim = pkgs.vim_configurable.customize {
      name = "plugvim";

      vimrcConfig.packages.myVimPackage = with pkgs.vimPlugins; {
        start = [
          vim-plug
          # Below is an example of how to modify the plugin before installation.
          # This particular modification doesn't work for me.
          # (vim-plug.overrideAttrs (old: {
          #   postInstall = ''
          #    mkdir -pv $target/autoload
          #     ln -s $target/plug.vim $target/autoload
          #   '';
          # }))
        ];
      };
      vimrcConfig.customRC = ''

        runtime! plug.vim

        call plug#begin($HOME.'/_vim')
        Plug 'https://github.com/grwlf/litrepl.vim' , { 'rtp': 'vim' }
        call plug#end()
      '';
    };
  # ...
  }

The expression defines a barebone Vim with a single vim-plug plugin. It could be built with nix-build -A plugvim and run with ./result/bin/plugvim.
The only problem I see is probably a Vim-related one. The runtime! line of the config line returns successfully, but plug#* functions don't appear on this run of the config, so vim issues errors. If I re-type the commands manually or source the config (by looking its absolute path) then everything start to work.
Do you have an idea why


create RIO command-line tool

Trying to load https://permid.org/sfiles/bulkDownload/OpenPermID-bulk-organization-20180805_070415.ttl.gz to GraphDB (need free registration at permid.org to obtain this file).
I get this exception:
[ERROR] 2018-08-08 12:02:17,230 [import-task-permid-1 | c.o.f.i.FileImportRunnableTask] Could not import file
java.lang.StringIndexOutOfBoundsException: String index out of range: 21
at java.lang.String.codePointAt(String.java:687)
at org.eclipse.rdf4j.common.net.ParsedIRI.error(ParsedIRI.java:1139)
at org.eclipse.rdf4j.common.net.ParsedIRI.parseHost(ParsedIRI.java:997)
at org.eclipse.rdf4j.common.net.ParsedIRI.parse(ParsedIRI.java:858)

Ok, so I'll use jena riot to validate it.
Please create an rdf4j rio command-line utility like RIOT, so I can validate with RIO.

Sounds like an issue for https://github.com/eclipse/rdf4j-tools subproject.
There is a verify command in the console tool, but what is really missing (IMHO)  is a way to run a command/script from the command line (e.g. Console -x verify ) and exit with an exit code (so it could be used in a batch script, instead of interactively)

@barthanssens you can kinda do that though:
$ echo verify test.ttl | ./console.sh

but I agree command line switches would be useful.

We're kinda conflating issues here though. I'll keep this issue to focus on the parser bug reported, I'll add a separate feature ticket to the tools project for command line switches to do actions like verification.

I can reproduce this issue in the latest milestone.

I didn't know about console verify, thanks! Does it say the line number?
Riot reports about 50 malformed web URLs (see graphdb jira), I fixed them with a perl script but no cigar

The problem is specific to an IRI with in IP address, but no path: http://<IP_ADDRESS> . There is a bug in ParsedIRI that expects either a port number or a path behind this. I'm working on a fix.

Btw the line on which this first occurs in this file is 6360967. Unfortunately the console also doesn't report this, due to a related error.

PR up for a fix. I have verified that with this fix in place, the file parses without issues (it doesn't even require disable URI checking).


Case Insensitive Filtering on client side

Problem Description
Currently the built in filter-system works great but can we configure react-table to support additional facilities like: Case Insensitive Filtering and Substring Matching While Filtering.
caseInsensitiveFiltering = {true}
subStringFiltering = {true}
P.S. I am a fan of react-table :)

Glad it is working for you.
You have full control over how the filter is rendered as well as how the filtering works for each column.
See the Filtering section of the readme for more information:
https://github.com/tannerlinsley/react-table#filtering
Also take a look at the Custom Filtering demo:
https://react-table.js.org/#/story/custom-filtering
If you have more implementation questions the Slack channel is a great place to get answers:
https://react-chat-signup.herokuapp.com/

For case insensitive filtering - with help from a previous issue:
function filterCaseInsensitive(filter, row) {
	const id = filter.pivotId || filter.id;
	return (
		row[id] !== undefined ?
			String(row[id].toLowerCase()).startsWith(filter.value.toLowerCase())
		:
			true
	);
}

<ReactTable
	data={data}
	columns={columns}
	filterable
	defaultFilterMethod={filterCaseInsensitive}
/>

@ashtarcommunications I can't seem to get that function working that way. Where do you put the filterCaseInsensitive in the scope? In render? I've tried both in render, as well as the outside scope(main React class), but to no avast. Thanks :)

Arh, I rewrote it ES6-style and has some better luck. It even worked for a nested table. Here's what I wrote in render():
`
const filterCaseInsensitive = (filter, row) => {
const id = filter.pivotId || filter.id;
return (
row[id] !== undefined ?
String(row[id].toLowerCase()).startsWith(filter.value.toLowerCase())
:
true
);
};

And called as such:

return(

<ReactTable
showFilters={true}
className='-striped -highlight'
defaultPageSize={10}
defaultFilterMethod={filterCaseInsensitive}
pageSizeOptions={[5, 10, 15]}
data={tableArr}
columns={columns}
noDataText="No assets detected on network"
SubComponent={(row) => {
return (

)
}}
/>

return(

<ReactTable
showFilters={true}
className='-striped -highlight'
defaultPageSize={10}
defaultFilterMethod={filterCaseInsensitive}
pageSizeOptions={[5, 10, 15]}
data={tableArr}
columns={columns}
noDataText="No assets detected on network"
SubComponent={(row) => {
return (

)
}}
/>

Not sure what I did wrong the first time, but works for me like this!

Here's a fix to handle case insensitive filtering of rows that include empty cells:
        const filterCaseInsensitive = (filter, row) => {
            const id = filter.pivotId || filter.id;
            if (row[id] !== null){
                return (
                    row[id] !== undefined ?
                        String(row[id].toLowerCase()).startsWith(filter.value.toLowerCase())
                        :
                        true
                );
            }
        };

In my case, I have the filter in a separate module and am just importing it at the top of the file, e.g.:
import { filterCaseInsensitive } from './filters';
The files where I'm using the filter are all stateless functional components though, not ES6 classes, so there's no render function.
Good call on the null values. Also worth keeping an eye out for how the custom filtering interacts with custom accessor functions, Cell render functions, or higher order components that wrap ReactTable and accidentally mutate the table state - I've run into a couple weird but easily worked around edge cases.

Use the endsWith String function. If you need to support IE then you will need to also add a polyfill for the endsWith function.

thankyou @gary-menzel , in my case i tried to make a case insensitive filtering, and can be filtered from the start or the end of the string. and also can be filtered if the field contains the word i typed. here is my code:
const defaultFiltering = (filter, rows) =>
matchSorter(rows, filter.value, {
keys: [filter.id]
});
return (
<LayoutContentWrapper style={{ height: "100vh" }}>

<ReactTable
data={result}
filterable
defaultFilterMethod={defaultFiltering}
columns={columns}
loading = {this.state.loadingState}
style={{
height: "600px"
}}
className = "-striped -highlight"
/>

);
sorry if my english is bad

Hi, everyone.
Please let me know kindly about my issue.
I am using custom dropdown for reacttable filtering.(every colum has own filter method.)
All are working correctly, but not working to show original column list with setting "all" item in select.
I was set as like following.

colume setting
{
Header: translations['cocom'],
accessor: 'cocom',
Filter: ({ filter, onChange }) =>
<FilterDropdown dropdownData={(value)=>
{onChange({filterValue:value}); console.log(value);}} value={this.state.filterValue}/>
},
- FilterDorpdown
renderItems() {
return this.state.dropdownItems.map(function(data, key){
if(data.label == "All"){
return ( {data.label}) ;
} else {
return ({data.label} );
}
})
}

handleChange = (e) => {
    const { name, value } = e.target;
    const { selectedDropDownValue } = this.state;
    this.setState({
        selectedDropDownValue: value
    }, () =>{
        this.props.dropdownData(this.state.selectedDropDownValue);
    });
}

render() {
    let key = this.props.id || 0;
    return (

            <select name={key} onChange={this.handleChange}>
                {this.renderItems()}
            </select>

    );
}

But in this https://react-table.js.org/#/story/custom-filtering, I was setting as like following attached image
http://prntscr.com/jk03y4
Mean's to set filter value with "", then working to show original list.
What is my fault using this?
Hope to get kindly teaching.
Regards.

Just in case anyone has columns with numbers, this will filter both string types and numbers without throwing an error.
const filterCaseInsensitive = (filter, row) => {
            const id = filter.pivotId || filter.id;
            if (row[id] !== null && typeof row[id] === 'string'){
                return (
                    row[id] !== undefined ?
                        String(row[id].toLowerCase()).startsWith(filter.value.toLowerCase()) : true
                )
            }
        }

How can we achieve case insensitive string, case insensitive substring, and number (Integer) filter?

Use your favorite method to check for a substring instead of startsWith. Depending on your environment and your particular use case, you can use string.includes, string.contains, string.indexOf, etc.
function filterCaseInsensitive(filter, row) {
    const id = filter.pivotId || filter.id;
    if (row[id] !== null) {
        return (
            row[id] !== undefined ?
                String(row[id].toString().toLowerCase())
                    .includes(filter.value.toString().toLowerCase())
            :
                true
        );
    }
}

Here’s ours 😉
const filterCaseInsensitive = ({ id, value }, row) =>
  row[id] ? row[id].toLowerCase().includes(value.toLowerCase()) : true

this does not work for number. what if I have number in my table too!!

@okothomondi please read all comments. @brianhankins wrote the solution for that case

Solutions above didn't solve my needs, as i have number and null values as well. However great starting point, kudos to all who provide the answers. Below my 5 cents ;)
const filterCaseInsensitive = (filter, row) => {   const id = filter.pivotId || filter.id;   if(row[id] !== null && typeof row[id] === 'string') {     return (       row[id] !== undefined ?           String(row[id].toLowerCase()).startsWith(filter.value.toLowerCase()) : true     )   }else if(row[id] !== null) {     let re = new RegExp("^" + filter.value, "i");     let match = (String(row[id]).match(re) === null) ? false : true;     return match;   }else{     return false;   } }

Solutions above didn't solve my needs, as i have number and null values as well. However great starting point, kudos to all who provided the answers. Below my 5 cents ;)
const filterCaseInsensitive = (filter, row) => {
  const id = filter.pivotId || filter.id;
  if(row[id] !== null && typeof row[id] === 'string') {
    return (
      row[id] !== undefined ?
          String(row[id].toLowerCase()).startsWith(filter.value.toLowerCase()) : true
    )
  }else if(row[id] !== null) {
    let re = new RegExp("^" + filter.value, "i");
    let match = (String(row[id]).match(re) === null) ? false : true;
    return match;
  }else{
    return false;
  }
}

Thanks ! That helped me with my boolean field columns


fmt: document the behaviour of %p on slices

I was surprised by the following program's output:
package main

import (
	"fmt"
)

func main() {
	foo := make([]int, 0, 1)
	fmt.Printf("same: %p\n", foo)

	foo = append(foo, 0)
	fmt.Printf("same: %p\n", foo)

	foo = append(foo, 0)
	fmt.Printf("different: %p\n", foo)
}

Example output:
same: 0xc420018060
same: 0xc420018060
different: 0xc420018070

I was expecting an error because there is no documentation regarding %p with slices in https://golang.org/pkg/fmt/ but it works fine.
I was surprised by the output as the printed address changed when the underlying array of the slice was modified. This is the expected behaviour because fmt is using the reflect package's Pointer() method on the slice, which will return the address of the first element of the slice. See https://github.com/golang/go/blob/38c561cb2caa8019e44059e2be71c909ceef30a6/src/reflect/value.go#L1267-L1269
There should be some documentation regarding this behaviour because it is unexpected imo.

PR #24600 seeks to address this issue, by documenting that %p on a slice prints the address of its first element (rather than the address of the slice descriptor).


Updating MySQL versions and adding features

MySQL and MariaDB drivers have diverged a bit and require separate drivers for MySQL storage type
Added a Condition for queries to allow specification for a general prismatic region (API)
Moved "ApplierCommand" logic to a separate named function (API)

Can you see why this build is failing?

It's failing because of gradle issues: ./gradlew: Permission denied
https://travis-ci.org/github/prism/Prism/jobs/666203178?utm_medium=notification&utm_source=github_status

Alright, permissions fixed and SSL qualifier was removed. I don't think a config setting is really necessary for the SSL specification and my local database works fine with just the new drivers.

Looks fine now, ready for me to squash and merge?

ready


[SPARK-43374][INFRA] Move protobuf-java to BSD 3-clause group and update the license copy

What changes were proposed in this pull request?

protobuf-java is licensed under the BSD 3-clause, not the 2 we claimed.
And the copy should be updated via https://github.com/protocolbuffers/protobuf/commit/9e080f7ac007b75dacbd233b214e5c0cb2e48e0f
Why are the changes needed?

fix license issue
Does this PR introduce any user-facing change?

no
How was this patch tested?

Existing tests.

thanks @dongjoon-hyun


Group - Users with an external domain are displayed as Hidden in the group list

If you haven’t already, check out our contributing guidelines for onboarding and email<EMAIL_ADDRESS>to request to join our Slack channel!

Version Number: 9.0.27-0
Reproducible in staging?: Y
Reproducible in production?: Y
If this was caught during regression testing, add the test name, ID and link from TestRail: https://expensify.testrail.io/index.php?/tests/view/4909728
Email or phone of affected tester (no customers<EMAIL_ADDRESS>Issue reported by: Applause - Internal Team
Action Performed:

Open NewExpensify app
Log in to the new HT account
Create a group chat with two users<EMAIL_ADDRESS>and<EMAIL_ADDRESS>Open the list of members of the created group

Expected Result:
Users with an external domain should be displayed by email or name in a group list
Actual Result:
Users with an external domain are displayed as Hidden in the group list
Workaround:
Unknown
Platforms:

Which of our officially supported platforms is this issue occurring on?

[ ] Android: Native
[ ] Android: mWeb Chrome
[x] iOS: Native
[ ] iOS: mWeb Safari
[ ] MacOS: Chrome / Safari
[ ] MacOS: Desktop

Screenshots/Videos
Add any screenshot/video evidence

https://github.com/user-attachments/assets/52a75928-874e-4436-9e93-c634b093af07
View all open jobs on GitHub

@Christinadobrzyn  FYI I haven't added the External label as I wasn't 100% sure about this issue. Please take a look and add the label if you agree it's a bug and can be handled by external contributors

Proposal
Please re-state the problem that we are trying to solve in this issue.
Users with an external domain should be displayed by email or name in a group list
What is the root cause of that problem?
The problem is here. If a participant does not have a displayName it defaults to the text "Hidden".
What changes do you think we should make in order to solve the problem?
We can simply check if the participant has either a displayName or an email ( eg: login ).
The new version will be :
let displayName = passedPersonalDetails?.displayName ?? passedPersonalDetails?.login ?? '';

What alternative solutions did you explore? (Optional)
Result:

I can reproduce this. This Hidden user has been going on for a while. I don't know if we have another GH related to resolving this - I don't see one. I'm assuming this is a BE fix but adding external for a C+ review first.

Side note: I'm going to be ooo 9/4-9/10. Adding a BZ teammate to monitor this - @abekkala this is brand new and I'm not sure if this needs to be external or internal so I first added a C+ to review. TY!

Thanks for the proposal @brad-isbell!
Unfortunately I don't think this will entirely solve the issue here as I think for some reason the BE clears out certain emails from personalDetailsList, so there would be no value for passedPersonalDetails?.login. I see this, for example, if I log out and back in, the list of group members changes so that Bob & Alice are both Hidden with no email at all in their profiles. Weirdly if I invite a new user to the group chat and sign in with that user, I see all the emails displaying normally.

Proposal
Please re-state the problem that we are trying to solve in this issue.
Users with an external domain are displayed as Hidden in the group list
What is the root cause of that problem?
The hidden is displayed as expected because the personal detail has no login and displayName fields and firstName, lastName are empty strings. But we have a bug in the video of OP that is report participant detail page doesn't display Hidden as we did in ReportParticipantPage
The problem is here we only use details.displayName without falling back to Hidden as we do in here
https://github.com/Expensify/App/blob/562d7b48226247253625b9ac1fd45266cb53eda8/src/pages/ReportParticipantDetailsPage.tsx#L56
What changes do you think we should make in order to solve the problem?
We should use getDisplayNameOrDefault function as we do in ReportParticipantsPage and also use displayName as the condition to check whether we should show the display name or not. Or we can remove this condition because we always fallback into hidden
const displayName = PersonalDetailsUtils.getDisplayNameOrDefault(details);
{!!(displayName ?? '') && (
    <Text
        style={[styles.textHeadline, styles.pre, styles.mb6, styles.w100, styles.textAlignCenter]}
        numberOfLines={1}
    >
        {displayName}
    </Text>
)}

https://github.com/Expensify/App/blob/562d7b48226247253625b9ac1fd45266cb53eda8/src/pages/ReportParticipantDetailsPage.tsx#L94
What alternative solutions did you explore? (Optional)

@nkdengineer Do you see these users as hidden immediately? I only see it after signing out and back in, otherwise I see hidden and the email address.

Weirdly if I invite a new user to the group chat and sign in with that user, I see all the emails displaying normally.

I'd also like to see this explained. I'm leaning towards this being a BE issue, as I don't see why these emails specifically should be hidden for the user who added them to the group.

@nkdengineer Thanks, I see what you mean now! I agree the participant detail page should be fixed so that it doesn't show an empty string, but I think the BE is also incorrectly removing the email in these cases so I think that needs to be sorted too.
Let's go with @nkdengineer's proposal to fix up the empty name on the participant details page. We also need a potential BE fix if these emails are not supposed to be Hidden.
:ribbon::eyes::ribbon: C+ reviewed

monitoring the PR - https://github.com/Expensify/App/pull/48681

PR merged 4 days ago so adding a payment due date to this GH. https://github.com/Expensify/App/pull/48681
Payouts due:

[ ] Contributor: $250 @nkdengineer (Upwork - https://www.upwork.com/nx/wm/workroom/38330876/overview)
[ ] Contributor+: $250 @jjcoffee (Upwork - https://www.upwork.com/nx/wm/workroom/38275996/overview)

The PR that introduced the bug has been identified. Link to the PR: https://github.com/Expensify/App/pull/39639
The offending PR has been commented on, pointing out the bug it caused and why, so the author and reviewers can learn from the mistake. Link to comment: https://github.com/Expensify/App/commit/9dba74f24da04664948197aaca3681c85a236216#r146817794
A discussion in #expensify-bugs has been started about whether any other steps should be taken (e.g. updating the PR review checklist) in order to catch this type of bug sooner. Link to discussion: N/A - this type of thing would be hard to catch in standard PR testing imo
Determine if we should create a regression test for this bug. Yes
If we decide to create a regression test for the bug, please propose the regression test steps to ensure the same bug will not reach production again.

Regression Test Proposal

Create a group chat with two users<EMAIL_ADDRESS>and<EMAIL_ADDRESS>Open the list of members of the created group
Tap on one of the added users to open the participant details page
Verify that either the user's name, email or Hidden is displayed below the avatar (not an empty space)

Do we agree 👍 or 👎

Ah thanks for the nudge @jjcoffee!
Regression test - https://github.com/Expensify/Expensify/issues/429387
Payment is initiated in Upwork based on this summary - https://github.com/Expensify/App/issues/48464#issuecomment-2354023086
Closing!


Worker timeout when posting between handlers

I got a worker timeout when trying to do http from one handler to another in the same app. This was due to starting with only one worker, so it has be resolved.

This sounds like an issue with your WSGI server configuration. How are you hosting your Falcon App? Gunicorn, uWSGI, wsgiref, something else?

I used Gunicorn when this issue appeared, but I could reconfigure and resolve the issue. You may close this issue because I have no more problem. Thanks


Sweep private keys fails with empty address

When opening the sweep private keys window, there should be an address displayed. In some cases, that address is not displayed and it is not possible to continue. This seems to be the case when the user already has an unconfirmed sweep in progress.
Clicking on the address button displays an error in the console.
Traceback
File gui/qt/util.py, lin 313, in func
i = address.index(str(address_e.text())) + 1
ValueError: '' in not in list

"This seems to be the case when the user already has an unconfirmed sweep in progress."
I am thinking that is how it is supposed to work.

I tried to reproduce this but can't.
no problem doing 2 sweep operations after one another. The address input field will be filled with 2 fresh address on 2nd sweep while 1st sweep tx is still uncomfirmed

I also can not reliably reproduce this, but it still is occurring frequently. It does not appear to be caused by there being multiple sweep operations, as sometimes it occurs immediately after loading the program.

I also tried creating a new wallet by import priv keys, and encounter the same issue. Next button is grayed out, as if it thinks the priv keys I am pasting are not valid, but they are.


Feature: stable tag for docker images

Gitea version (or commit ref):
Git version:
Operating system: containers / docker

Description
Hi everybody,
it would be awesome, to see a tag "stable" in the docker registry, pointing to the latest stable release.  As a user, this may ensure using the stable version, which is easily identifiable. This tag can also be used for several documentation, currently using outdated version numbers or latest as reference.
Background
At the moment, the "latest" tag seems to point to the latest build, some release candidates are present, etc. As far as I can see, there is already a tag "1", pointing to the latest stable release, adding a tag "stable" should be easily doable.

I can add one more reason for the importance of the "stable" tag. Currently, according to the documentation: For a stable release you can use :1
However, tag :1 is published with every v.1.* release. This has lead to a regression between tags v1.11.7, v1.12.0 and v1.11.8. What has happened is the following:

Until 3 days ago, tag :1 was still referring to v1.11.7
3 days ago, with the publication of v1.12.0, tag :1 became v1.12.0
Today tag v1.11.8 got published and therefore docker tag :1 has been updated to point to v1.11.8.

This behaviour is not ideal, but most importantly can lead to big issues for CI systems relying in tag :1 to be stable. If after updating gitea to v1.12.0, the CI catches the "new" :1 tag and gitea is "updated" from v1.12.0 to v1.11.8, it is expected that gitea will break due to new features and breaking changes introduced in v1.12.0

So we need a version comparable for :1 on drone configuration but not a new tag stable? Two tags will make people confusing.

I personally would recommend to use the following tags:

latest for the latest stable version of Gitea, in a monotonic fashion (i.e. without downgrades)
dev or development for the latest commited version (what is currently "latest")
1 for the latest stable version og Gitea 1.x, in a monotonic fashion. And later 2 when Gitea 2.x is released.

I agree with @hweidner. That seems like a more standard docker tag naming convention.

For me what is important is that the corresponding documented stable tag (as :1 is currently marked in the documentation) never jumps backwards as it happened yesterday. Any implemented solution should be fine

But as I know many fellows like to use latest to try the newest version of gitea but not dev. They don't use :1 which documented as a stable version.

Or we can follow the tags to keep compitable as before.

latest keep compitable as now to follow the master
stable point to 1 or 2 when gitea upgraded to 2.x
1 gitea 1.x stable version.
2 gitea 2.x stable version.

For me, all of the suggested options would be fine. As long as I can point to a tag and will get the latest stable image for deployments in production environment :)

Stable seems redundant as I don't see 2 coming anytime soon and most probably it will be breaking enough to require changing label to :2 manually. We just need to figure way how to make drone not to override :1 tag when publishing minor release for previous major verion

@lafriks Yes, that's the first step we need to do. I think we have to contribute to https://github.com/drone-plugins/drone-docker or create a fork.

Glad to see this. Just popped in because I found out about the new release, and remembered I hadn't yet looked into the footer saying it was version 1.13 dev.
Fixed that now.

see https://github.com/drone-plugins/drone-docker/issues/287

IMHO :latest = master branch and :1 = latest stable for v1.x.x and :2 = latest stable for v2.x.x would be the best. Having a :stable which gets updated from v1.x.x to a breaking change v2.x.x (otherwise it wouldn't be a major version change) will lead to a lot trouble.
For the docker plugin you can just generate a .tags file within a step before the docker plugin which got a better logic to decide the tags that got to be pushed. The 1.11 release branch can just drop :1 from the tags file while 1.12 release branch can keep :1 until 1.13 gets released, or you could even query the releases API to check if there are more current minor versions.

As a user that only wants a the most recent stable release. I should be able to just point to the stable docker image tag and automatically pickup the latest stable version. Whenever 2.0 is officially released the stable tag will point to it. I don't think a user should have to constantly investigate if it's "safe" or stable to update 1.x to 2.0. It should be up to the maintainers to determine that.
I understand the issue that @tboerger brings up, that there may be breaking changes migrating from 1.x to 2.0 but hopefully those issues would be thoroughly tested and mostly ironed out before 2.0 is marked stable.

:1 is our stable tag, however we've had a few releases of 1.11.x that happen at the same time as our 1.12.x releases, we've tried our hardest to ensure that they happen right before we make a tag for a newer version, however occasionally it doesn't always happen that we tag them in the correct order.
I'm going to keep this open as we can add some protections to our CI to prevent overwriting newer versions with older versions (using @tboerger suggestion), however adding a new specific "stable" tag is something that has been discussed previously and for various reasons decided against.
I will lock this to maintainers as there is much discussion on this, however changing how tag names would be a massive breaking change with little to no added benefit (especially since we already offer a tag for latest stable version).


Packet Optimization

Use ctypes library for enhanced performance.
Performance gain of ~100% (i.e. twice as fast) on a data transfer from CxlHost to mem.bin via CXL.mem packets. I believe we can do even better, but given the time constraint, pushing for now.
Known regressions / TODOs:

Random tags. Will be addressed shortly
"Truly" dynamic fields (currently a hard select between 4-byte and 8-byte packet types), not a high priority
Further gains via removing unnecessary mem copies.
Further ctypes changes to additional files (e.g. events.py)

All above issues will be given GitHub Issues.

I believe using ctype structure is a right direction for performance improvement when it's used with packet definitions. However for debugging, we should maintain the feature that allows inspecting the packet in human readable way.

Certainly. I will implement get_pretty_string()-similar mechanism.


negative run error

Description of the bug
i try a lot and always meet the same error message when run negative data
Command used and terminal output
Command error:
  Adding neutral: ---------- Adduct -----------------
  Charge: 0
  Amount: 1
  MassSingle: -18.0106
  Formula: H-2O-1
  log P: -2.99573

  Adding neutral: ---------- Adduct -----------------
  Charge: 0
  Amount: 1
  MassSingle: 46.0055
  Formula: C1H2O2
  log P: -0.693147

  MassExplainer table size: 4
  Error: Unexpected internal error (WARNING!!! implicit number of default adduct is negative!!! left:-1 right: -1
  )
  Generating Masses with threshold: -2.99573 ...
  done

Relevant files
No response
System information
No response

i setting skip_adduct_detection=true to skip the adduct work and finish the nextflow pipeline.

i setting skip_adduct_detection=true and finish the nextflow pipeline.
but  my SIRIUS results have a lot of positive adduct, it seems unbelievable.
i find that Linked_data_part1.mgf and Linked_data_part1.ms have different CHARGE in NFCORE_METABOIGNITER:METABOIGNITER:IDENTIFICATION:PYOPENMS_GENERATESEARCHPARAMS
$ grep CHARGE Linked_data_part1.mgf |head
CHARGE=1-
CHARGE=1-
CHARGE=1-
CHARGE=1-
CHARGE=1-
CHARGE=1-
CHARGE=1-
CHARGE=1-
CHARGE=1-
$ grep charge Linked_data_part1.ms |head

charge 1
charge 1
charge 1
charge 1
charge 1
charge -1
charge 1
charge 1
charge 1
charge 1

the parameters is same as full_test. only polarity set  "negative".
identification= false
polarity="negative"
ms2_collection_model="separate"
run_sirius = true
sirius_split = true
mgf_splitmgf_pyopenms = 100
run_ms2query = true
requantification = true

Thanks. Found the problem. working on a fix for it. should be in the dev branch very soon.

https://github.com/nf-core/metaboigniter/blob/master/bin/generate_ms_params.py#L406
I think it have some error
if charge == 1 and polarity == "negative".  charge_f  will output  1

yes. exactly. this must be replaced with
charge_f = (1 if polarity == "positive" else -1) * (1 if charge_f == 0 else abs(charge_f))

regarding
Command error:
  Adding neutral: ---------- Adduct -----------------
  Charge: 0
  Amount: 1
  MassSingle: -18.0106
  Formula: H-2O-1
  log P: -2.99573

  Adding neutral: ---------- Adduct -----------------
  Charge: 0
  Amount: 1
  MassSingle: 46.0055
  Formula: C1H2O2
  log P: -0.693147

  MassExplainer table size: 4
  Error: Unexpected internal error (WARNING!!! implicit number of default adduct is negative!!! left:-1 right: -1
  )
  Generating Masses with threshold: -2.99573 ...
  done

you can set the adducts_neg to something like "H-1:-:0.8 H-3O-1:-:0.2". We will later change the defaults.

Thanks.  i try it

hi metaboigniter teams,
i meet a new problem. when i input a lot of mzML, it report
`
cat <<-END_VERSIONS > versions.yml
"NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPALIGNERPOSECLUSTERINGMZML":
openms: $(OpenMSInfo | awk '/OpenMS Version/{getline; getline; print $3}')
END_VERSIONS
Command exit status:
134
Command output:
Picking a reference (by size) ... done
Progress of 'Aligning input maps':
2.44 %
4.88 %
7.32 %
9.76 %
12.20 %

FATAL: uncaught exception!
last entry in the exception handler:
exception of type IllegalArgument occurred in line 74, function OpenMS::TransformationModelLinear::TransformationModelLinear(const OpenMS::TransformationModel::DataPoints&, const OpenMS::Param&) of /opt/conda/conda-bld/openms-meta_1689839222968/work/src/openms/source/ANALYSIS/MAPMATCHING/TransformationModelLinear.cpp
error message: no data points for 'linear' model
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Picking a reference (by size) ... done
Progress of 'Aligning input maps':
2.44 %
4.88 %
7.32 %
9.76 %
12.20 %

FATAL: uncaught exception!
last entry in the exception handler:
exception of type IllegalArgument occurred in line 74, function OpenMS::TransformationModelLinear::TransformationModelLinear(const OpenMS::TransformationModel::DataPoints&, const OpenMS::Param&) of /opt/conda/conda-bld/openms-meta_1689839222968/work/src/openms/source/ANALYSIS/MAPMATCHING/TransformationModelLinear.cpp
error message: no data points for 'linear' model
---------------------------------------------------`
same sample in metaboigniter:1.0.1 can run

hi metaboigniter team,
i meet a new problem. i input more than 40 mzML files (it can run in metaboigniter:1.0.1) , it report this `
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Picking a reference (by size) ... done
Progress of Aligning input maps:
2.44 %
4.88 %
7.32 %
9.76 %
12.20 %

FATAL: uncaught exception!
last entry in the exception handler:
exception of type IllegalArgument occurred in line 74, function OpenMS::TransformationModelLinear::TransformationModelLinear(const OpenMS::TransformationModel::DataPoints&, const OpenMS::Param&) of /opt/conda/conda-bld/openms-meta_1689839222968/work/src/openms/source/ANALYSIS/MAPMATCHING/TransformationModelLinear.cpp
error message: no data points for 'linear' model
---------------------------------------------------`

hi metaboigniter team,
i find that it will have long path name when we run a lot of sample (such as test data)
ls results/alignment_mzml/
'[X2_Rep1, X3_Rep1, X6_Rep1, Pilot_MS_Control_2_peakpicked, Pilot_MS_Pool_2_peakpicked]'

https://github.com/nf-core/metaboigniter/blob/master/conf/modules.config#L175

Thanks. I will be addressed.

hi metaboigniter team,
i try 41 MS12 sample and met a new question
[14/854763] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_FEATUREFINDERMETABO (N29_neg_IS)          [100%] 41 of 41 ✔ [26/a88e18] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPALIGNERPOSECLUSTERING (Multiple files) [100%] 1 of 1, cached: 1 ✔ [da/4f406d] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPRTTRANSFORMER (G27_neg_IS)             [100%] 39 of 39 ✔
i find it OPENMS_MAPRTTRANSFORMER  only run 39 sample
i resume twice ,OPENMS_MAPRTTRANSFORMER restart with different  sample num
[82/02db78] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_FEATUREFINDERMETABO (N69_neg_IS)          [100%] 41 of 41, cached: 41 ✔ [26/a88e18] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPALIGNERPOSECLUSTERING (Multiple files) [100%] 1 of 1, cached: 1 ✔ [d2/4b2173] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPRTTRANSFORMER (N60_neg_IS)             [100%] 35 of 35, cached: 35 ✔
[33/ee8d44] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_FEATUREFINDERMETABO (G38_neg_IS)          [100%] 41 of 41 ✔ [26/a88e18] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPALIGNERPOSECLUSTERING (Multiple files) [100%] 1 of 1, cached: 1 ✔ [bd/cb9a38] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPRTTRANSFORMER (N14_neg_IS)             [100%] 36 of 36 ✔

hi metaboigniter team,
i try 41 MS12 sample and met a new question
[14/854763] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_FEATUREFINDERMETABO (N29_neg_IS)          [100%] 41 of 41, cached: 41 ✔
[26/a88e18] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPALIGNERPOSECLUSTERING (Multiple files) [100%] 1 of 1, cached: 1 ✔
[da/4f406d] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPRTTRANSFORMER (G27_neg_IS)             [100%] 39 of 39, cached: 37 ✔

i find it OPENMS_MAPRTTRANSFORMER only run 39 sample
i resume twice ,OPENMS_MAPRTTRANSFORMER restart with different sample num
[82/02db78] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_FEATUREFINDERMETABO (N69_neg_IS)          [100%] 41 of 41, cached: 41 ✔
[26/a88e18] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPALIGNERPOSECLUSTERING (Multiple files) [100%] 1 of 1, cached: 1 ✔
[d2/4b2173] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPRTTRANSFORMER (N60_neg_IS)             [100%] 35 of 35, cached: 35 ✔

[33/ee8d44] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_FEATUREFINDERMETABO (G38_neg_IS)          [100%] 41 of 41, cached: 41 ✔
[26/a88e18] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPALIGNERPOSECLUSTERING (Multiple files) [100%] 1 of 1, cached: 1 ✔
[bd/cb9a38] process > NFCORE_METABOIGNITER:METABOIGNITER:QUANTIFICATION:OPENMS_MAPRTTRANSFORMER (N14_neg_IS)             [100%] 36 of 36, cached: 35 ✔

Thanks a lot for finding this bug.
https://github.com/nf-core/metaboigniter/blob/2f8f077d38fcacd2caef9590dc557ddcc17c78c6/subworkflows/local/quantification.nf#L61-L72
These have to be replaced by
 combined_data =quantified_features.map{meta,featurexml->
   tuple(featurexml.baseName, meta)}
    .join(OPENMS_MAPALIGNERPOSECLUSTERING.out.featurexml.map{it[1]}.flatten().map{featurexml ->
    tuple(featurexml.baseName, featurexml)})
     .join(OPENMS_MAPALIGNERPOSECLUSTERING.out.trafoxml.map{it[1]}.flatten().map{trafoxml ->
    tuple(trafoxml.baseName, trafoxml)})
    .join(quantificaiton_data.map{meta,mzml->
 tuple(mzml.baseName, mzml)}).map{it[1..4]}

I will have to check if there are other places that we should replace the grouping.

in NFCORE_METABOIGNITER:METABOIGNITER:IDENTIFICATION:PYOPENMS_MSMAPPING pipeline ,  sometime my neg mzML cant map with linked_data. （ I not sure that the charge data in my mzML is 1 , linked_data is -1 , so it cant map success )
can i add below to the code https://github.com/nf-core/metaboigniter/blob/master/bin/extract_mapping.py#L42
parameters.setValue("ignore_charge", "true")

and i find that my test link_data mz and rt value change site
example:
<groupedElementList>
        <element map="0" id="1846111275860413" rt="540.393717669934404" mz="341.923878832888192" it="3.075653e04" charge="1"/>
        <element map="1" id="9952900658436292523" rt="548.849116174641267" mz="341.923931444177526" it="1.836938e05" charge="1"/>
        <element map="2" id="2972814306089124318" rt="540.956951552158557" mz="341.923878832888192" it="4.02439e05" charge="1"/>
</groupedElementList>
<PeptideIdentification identification_run_ref="PI_0" score_type="" higher_score_better="true" significance_threshold="0" MZ="540.393717669934" RT="341.923878832888" >
        <UserParam type="stringList" name="masstrace_intensity" value="[]"/>
        <UserParam type="stringList" name="masstrace_centroid_mz" value="[]"/>
        <UserParam type="floatList" name="isotope_calcdist_mz" value="[341.9241943359375]"/>
        <UserParam type="floatList" name="isotope_calcdist_int" value="[2613.7314453125]"/>
        <UserParam type="float" name="feature_quality" value="1.164749979972839"/>
        <UserParam type="float" name="normalized_intensity" value="8.045819655895059e-07"/>
        <UserParam type="int" name="map_index" value="0"/>

another question , if i run MS12 ,the mzml will use raw instead of rt correct  one.
thanks for your reply

and i find that my test link_data mz and rt value change site example:
<groupedElementList>
        <element map="0" id="1846111275860413" rt="540.393717669934404" mz="341.923878832888192" it="3.075653e04" charge="1"/>
        <element map="1" id="9952900658436292523" rt="548.849116174641267" mz="341.923931444177526" it="1.836938e05" charge="1"/>
        <element map="2" id="2972814306089124318" rt="540.956951552158557" mz="341.923878832888192" it="4.02439e05" charge="1"/>
</groupedElementList>
<PeptideIdentification identification_run_ref="PI_0" score_type="" higher_score_better="true" significance_threshold="0" MZ="540.393717669934" RT="341.923878832888" >
        <UserParam type="stringList" name="masstrace_intensity" value="[]"/>
        <UserParam type="stringList" name="masstrace_centroid_mz" value="[]"/>
        <UserParam type="floatList" name="isotope_calcdist_mz" value="[341.9241943359375]"/>
        <UserParam type="floatList" name="isotope_calcdist_int" value="[2613.7314453125]"/>
        <UserParam type="float" name="feature_quality" value="1.164749979972839"/>
        <UserParam type="float" name="normalized_intensity" value="8.045819655895059e-07"/>
        <UserParam type="int" name="map_index" value="0"/>

another question , if i run MS12 ,the mzml will use raw instead of rt correct one.
thanks for your reply

If you choose to perform the alignment the adjusted RT will be used. however, if you are running MS12 in separate mode, the alignment is based on raw spectra, in the paired mode the alignment is based on features.
Thanks for reporting the inconsistencies. I have now fixed it.

these should have been fixed now. I'm closing the issue.


Early break the inner loop in MmapAllocator::SizeClass::allocateFromMappdFree

Description
At the end of each iteration in the inner loop in MmapAllocator::SizeClass::allocateFromMappdFree, if allUsed is true for the current iteration, it will look ahead and check next iteration, as follows:
      if (allUsed) {
        if (index == group + kWidth ||
            isAllZero(mappedFreeBits(index + kWidth))) {
          bits::setBit(mappedFreeLookup_.data(), group / kWordsPerGroup, false);
        }
      }

Consider the case when index == group + kWidth is false and isAllZero(mappedFreeBits(index + kWidth)) is true, we can break the inner loop after setBit to avoid step into next iteration and do duplicated mappedFreeBits().
cc @mbasmanova please take a look, I'm opening a PR.

CC: @xiaoxmeng


Notebooks headings are bold and H1

Hello,
I was going through this notebook: https://www.tensorflow.org/addons/tutorials/networks_seq2seq_nmt and noticed that all the headings are bold and H1.
Can you please make it not bold and H2 heading?
# **Setup** becomes ## Setup

Related pr #1216 is merged, so it can be closed.

Thanks a lot @us !