Hammerdin-update-new

Update to trav tele and walking pather to better clear trav. Also implemented the update on pindal based on information from Alternating#1115 & https://github.com/aeon0/botty/pull/473. Tested on both Tele and Walking Hammerdin and solving the issue from pathing instead.

Did pressure test this PR 75 runs vs 0.6.4
This PR:
1:40 avg by run &
32 items over 75 runs
0 fails
0 MD
(2h 05min runtime)
0.25 items/min
versus Botty 0.6.4:
1:21 avg by run &
20 items over 75 runs
0 fails
0 MD
(1h 40 runtime)
0.24 items/min
Whilst items/min is almost useless parameter for these durations tested, it seems a good idea to merge this PR to master with regard to TRAV.
Didn't test pindle though- not a fan of hammerdin pindle ;)

I personally ran and reviewed this and do not like either of the scripts. hammerdin could use a couple small tweaks but this script is not it. The PIndle script is pointless. I would heavily advise on not merging pindle and having the attack sequence cut down on trav theres a lot of excess sequences that are not needed and poorly positioned. A good tweak will require offsetting nodes. I would not merge either of these.

I'm not very persuaded by the comments that the changes are helpful. Please make any needed adjustments and provide some comparison pre-vs-post run statistics (time spent per run, chicken percent, death percent, run fail percent, etc.) for both TP hammerdin and walking hammerdin. Closing for now while you work on those changes and provide the data--let me know when you've done so and we can reopen.


Implement best practices for grafana-agent app

Coming from here.
The goal of this issue is to have the App eventually adhere to standard cloud-native best-practices. The points below are to be considered non-exhaustive. Feel free to add some that make sense and remove some that don't. If this issue does not make sense (e.g. is a duplicate or covers a deprecated app) please close it.
Expected outcome:

[ ] the app has properly set PDBs (as percentages)
[ ] the app can scale horizontally based on Custom Metrics (if it makes sense)
[ ] the app runs with more than 1 replica by default (if it needs HA)
[ ] the app does not use emptyDir volumes if not strictly necessary

Running more than 1 replica (HA setup) requires to externalize the Grafana database (from sqlite to mysql or postgresql). See Set up Grafana for high availability.
horizontal scalability requires more than 1 replica
PDBs require more than 1 replica

So the first step for this issue is to run grafana with a "real" database and HA.
It's not only a change of architecture, but also changes how we operate grafana: this will add persistence to custom-imported dashboards and datasources.

This is not really feasible for us and will be closed out of scope for now.
we are adressing any stability issues of the grafana agent app by improving the resource usage. Closing it for now.


Integrate KUDO test harness into kudoctl

The test harness should be integrated into kudoctl:

It can be run by KUDO users to validate KUDO and framework installation.
It lowers the barrier to entry for writing to Frameworks to just kudoctl, rather than kudoctl and Go.

First, I will do the getting started guide #340 and #353. This can come later.


support non-x86_64 targets

It would be useful to support fuzzing non-x86_64 targets on existing Azure VMs.
For fully self-contained targets, such as AARCH64-based libfuzzer targets, we can get away with running within qemu-user.
Fully-featured QEMU VMs would be required for anything more complex.

We're moving forwards with qemu-user for now.  If users have a need for fully featured qemu based fuzzing, we can revisit this.


[Program]: Write a Haskell program to print inverted pyramid pattern

Description
Write a Haskell program to print inverted pyramid pattern
Input   : 5

Output :
1 2 3 4 5
1 2 3 4
1 2 3
1 2
1

Contributed by - @PraaneshSelvaraj

How to contribute

Save the solution in program/program/print-inverted-pyramid-pattern/print_inverted_pyramid_pattern.hs file

!assign


Create devcontainer.jsonhttps://github.com/matomo-org/matomo-sdk-andr…

…oid.git

Please enlighten me: what's the purpose of this ?

@dependabot rebase

Spam PR, imho. Amateur GitHub user or a bot.

Spam PR, imho. Amateur GitHub user or a bot.

I'm new to all of this I'm trying to learn


feat(stack): request dedicated stack form

Looks great! Found 1 small bug:
After stack form submission, the support form also shows a success banner, not a big deal though.

I'll follow up with that one


ci: disable unstable test

This test seems to be unstable when running in CI on a Windows machine.

coverage: 80.751%. remained the same when pulling 3f1860ff838e983d310ef19a2377bf4155859705 on disable-test into 3d178a0801524667fc411663c8eab657aa2582a3 on master.


Add more data types

Describe what the PR does:
This PR adds additional data types that the Ecowitt device can read.
Does this fix a specific issue?
Fixes https://github.com/bachya/ecowitt2mqtt/issues/15
Checklist:

[ ] Update README.md with any new documentation.
[ ] Add yourself to AUTHORS.md.

Please view the other MR#17 before this one is approved.


updated the syncdb command with migrate

since syncdb is deprecated from Django 1.7 maybe it is time to update it.

Closing in favor of PR #164, which is updated version of this PR, based on the above feedback of @solarissmoke.


Make specifying project ID optional for PubSub Topic

Currently, creating a topic requires knowing the project ID. However, the client libraries have a way of automatically figuring out what the project ID is based on the environment. It should fall back to that if project ID is not specified.

Our current recommendation is for users to call ServiceOptions.getDefaultProjectId() and pass that in.
There is a circular problem with having generated code depend on types in google-cloud-java, so we have decided not to make this automatic for the time being.

garrettjonesgoogle Do you have any java tutorial link where it's explain this object change notification with code?

@yasikmondal , could you elaborate? I don't quite understand.

@garrettjonesgoogle  - I have created a servlet project to do image transform on google app engine. I will take the image from cloud bucket and will convert and will store it back to the another cloud bucket. Now I want to do it automatically like if anyone is updating or changing any object to any cloud bucket, our application should automatically get triggered (object change notification) and should do all those stuff (conversion).
Now I need to implement this feature object change notification as I am running my application on cloud app engine.
Do you have any demo or tutorial in java so that I can check.

@yasikmondal your request seems to be unrelated to the present issue. I recommend filing an issue at https://github.com/GoogleCloudPlatform/java-docs-samples . Thanks!

This has been added to our feature backlog: https://github.com/GoogleCloudPlatform/google-cloud-java/wiki/Feature-backlog. This issue will be closed but is linked in the backlog and can continue to be used for comment and discussion.


fix: Node/Image Component bug fixes

Description
Fixes the following Jiras:
ROX-11649
ROX-11650
ROX-11651
ROX-11652
ROX-11720
ROX-11721
ROX-11722
ROX-11723
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)

Testing Performed

/retest

/retest


[BUG] Reproducible failure in SearchCancellationIT.testMSearchChildReqCancellationWithHybridTimeout

#986 introduced test failures; indicating the feature was likely merged prematurely.
REPRODUCE WITH: ./gradlew ':server:internalClusterTest' --tests "org.opensearch.search.SearchCancellationIT.testMSearchChildReqCancellationWithHybridTimeout" -Dtests.seed=596A2CDAD4EE2410 -Dtests.security.manager=true -Dtests.jvm.argline="-XX:TieredStopAtLevel=1" -Dtests.locale=he -Dtests.timezone=America/Halifax -Druntime.java=15

First and third queries are expected to be cancelled. But only the first query is cancelled. Expanding the clusterCancellationTimeout has no effect (possibly ruling out a race condition) so there is a separate issue going on here.
org.opensearch.search.SearchCancellationIT > testMSearchChildReqCancellationWithHybridTimeout FAILED
    java.lang.AssertionError: Actual child request with cancellation failure is different that expected expected:<[0, 2]> but was:<[0]>
        at __randomizedtesting.SeedInfo.seed([596A2CDAD4EE2410:A60B6D246603635E]:0)
        at org.junit.Assert.fail(Assert.java:88)
        at org.junit.Assert.failNotEquals(Assert.java:834)
        at org.junit.Assert.assertEquals(Assert.java:118)
        at org.opensearch.search.SearchCancellationIT.ensureMSearchWasCancelled(SearchCancellationIT.java:195)
        at org.opensearch.search.SearchCancellationIT.testMSearchChildReqCancellationWithHybridTimeout(SearchCancellationIT.java:566)

/cc @sohami This failure is occurring frequently on main branch.

Thanks for sharing this, will open a PR with the fix

The fix has been backported.


specs

Author name
chubbyducky
About your game
This game is about trying to give your friend their glasses while they blindly search for them.

How do you play your game?
Press WASD to move.
Code
Check off the items that are true.

[x] The game was made using the Sprig editor.
[x] The game is placed in the in the /games directory.
[x] The code is significantly different from all other games in the Sprig gallery (except for games labeled "demo").
[x] The game runs without errors.
[x] The name of the file/game contains only alphanumeric characters, -s, or _s.
[x] The game name is not the same as the others from gallery

Image (If an image is used)

[ ] The image is in the /games/img directory.
[ ] The name of the image matches the name of your file.

Thanks for your PR!

Closing this PR as it is quite old and hasn't moved in some time.  Feel free to reopen this if you want to advocate for its merge.


fixing a namespace issue in error message validation

Critical Changes
Changes
Issues Closed
New Metadata
Deleted Metadata

@sgovindankutty Configure Advanced Mapping is a button on Data Imports Advanced Mapping page. Yes Advanced Mapping is being enabled at org level. Org should come with it being disabled and then a user should enable it and test stuff


Separate stores/caches

how do we create separate state "stores" (is that the word?) - think of separate modules each needing one of these

closing as dupe


Using vue template in custom plugin

Hi! I'm thinking to move from vue CKeditor to Toast UI Editor, but I need to be sure that custom plugins can be developed by using Vue js template.
Basically, I need to create a custom button that when it's clicked a bootstrap vue modal is opened. The purpose of this button/modal is to search uploaded media from server or upload a new file and insert it in content.
I've taken a look at the documentation and everything seems to point that plugins can be created just by js.
Any guidance will be appreciated.

@lucianobosco What I understand is that there is logic to create button/modal within a custom plugin, and I think you asked if you can use Vue template at this time. First of all, there is currently no way to use Vue template in the Editor. And whether or not to support templates is difficult because of the internal structure. If the Editor supports it, it will be possible after the next major version update. (Support is difficult in v2)


Fix aggressive application of search filter to submissions

Fix aggressive application of search filter to submissions
Summary: Addresses #896 by modifying the filter bar to apply the search filter to datagrid submissions only on certain user actions.
Changelog

Edit handleFilterChange to no longer apply the filter when invoked - it now only updates the local state of the Grading component with the new filterValue
Edit the filter bar <InputGroup> to only apply the filter when the user presses the ENTER key (whilst in focus) or clicks away from the filter bar (loses focus)

Last updated 25 Aug 2019, 05:00AM

Pull Request Test Coverage Report for Build 3271

0 of 5 (0.0%)  changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.03%) to 36.882%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

src/components/academy/grading/index.tsx
0
5
0.0%

Totals

Change from base Build 3254:
-0.03%

Covered Lines:
2671

Relevant Lines:
6488

💛  - Coveralls


multiple item selected

Thank you for your awesome package.
Can we add a multiple config to selected multiple options?

I would like that too!


[tibs] Extend error types to include process output

When there is a failure, include the stdout + stderr if they can be
decoded. This should help track down some failures we're seeing
sporadically in CI.

@swift-ci please test


Hide Checked Items

Is your feature request related to a problem?
I would like to use this as an alternative to Google Keep, but the one feature that is missing for me is the ability to hide checked items which is really useful when using a memo as a shopping list.
Describe the solution you'd like
As stated, add an option to hide checked items.
Additional context
No response

Hey, what do you mean about "hide"? Can you show me a example?
I guess it can be solved by additional css.

Here as an example how Google Keep does it - but I don't care about the actual implementation, i.e. moving checked items to the bottom, just hiding them completely, as long as there is a way to only see items that are not yet checked.

.todo-block.done{color:#c8c6c4;}
.todo-block.done+span{text-decoration:line-through;color:#c8c6c4;}

Hey @Froghut, perhaps this additional CSS can help you in some way. However, it is worth noting that currently we do not sort the todo items, i.e. moving the completed items to the bottom as shown in the above image.
This may be an interesting idea, but I am not sure if it will be implemented.


Rename Value::{ListValue, ObjectValue, EnumValue}

I guess the name of the enum comes from http://facebook.github.io/graphql/October2016/#Value but I didn't see why those 3 still had the Value suffix., which creates the unfortunate Value::ListValue repetition when using the AST.
Any reason those were kept?

Yes, you're right. No good reason. I tried to stick to the grammar when prototyping and had no chance to review it yet.


[Color 4] Add JS type definitions and docs for CSS Color Level 4.

https://github.com/sass/sass/blob/main/proposal/color-4-new-spaces-js.d.ts.md
https://github.com/oddbird/dart-sass/pull/1
https://github.com/oddbird/sass-spec/pull/13

 I want JS users to have access to new color spaces.

@nex3 Thanks! I think this is ready for another round of review.

Closing in favor of upstream PR.


Update dependencies to latest available version

test this

Codecov Report

Merging #538 into master will increase coverage by 0.38%.

@@            Coverage Diff             @@
##           master     #538      +/-   ##
==========================================
+ Coverage   82.36%   82.74%   +0.38%
==========================================
  Files          25       25
  Lines        2370     2498     +128
  Branches      212      212
==========================================
+ Hits         1952     2067     +115
- Misses        418      431      +13

Impacted Files
Coverage Δ

browser/services/platform.js
87.9% <ø> (-1.58%)
:x:

browser/directives/breadcrumb.js
10% <ø> (-1.12%)
:x:

browser/services/request.js
20% <ø> (-0.84%)
:x:

browser/services/data.js
98.97% <ø> (-0.47%)
:x:

browser/directives/pathValidator.js
82.97% <ø> (-0.36%)
:x:

browser/model/cdk.js
67.77% <ø> (-0.04%)
:x:

browser/pages/start/controller.js
44.79% <ø> (-0.04%)
:x:

browser/model/helpers/hash.js
100% <ø> (ø)
:white_check_mark:

browser/pages/location/controller.js
100% <ø> (ø)
:white_check_mark:

browser/model/jbds-autoinstall.js
100% <ø> (ø)
:white_check_mark:

... and 13 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update cf97172...a64b3fa. Read the comment docs.


Enter "workingman with hand so hairy-sturdy"

https://github.com/palewire/cummings.ee/blob/master/_data/poems/is-5/one-iv.yaml
https://archive.org/details/is-5-ee-cummings/page/n21/mode/2up

Sure. There's a contribution guide here: https://github.com/palewire/cummings.ee/blob/main/CONTRIBUTING.md
And a fuller tutorial of how to do a pull request, using this repository as the fodder, here: https://bit.ly/first-pr


composer 无法安装 tymon/jwt-auth

Your requirements could not be resolved to an installable set of packages.

  Problem 1
    - tymon/jwt-auth 0.5.4 requires namshi/jose 5.0.* -> satisfiable by namshi/jose[5.0.0, 5.0.1, 5.0.2].
    - tymon/jwt-auth 0.5.5 requires namshi/jose 5.0.* -> satisfiable by namshi/jose[5.0.0, 5.0.1, 5.0.2].
    - tymon/jwt-auth 0.5.6 requires namshi/jose 5.0.* -> satisfiable by namshi/jose[5.0.0, 5.0.1, 5.0.2].
    - tymon/jwt-auth 0.5.7 requires namshi/jose 5.0.* -> satisfiable by namshi/jose[5.0.0, 5.0.1, 5.0.2].
    - tymon/jwt-auth 0.5.8 requires namshi/jose 5.0.* -> satisfiable by namshi/jose[5.0.0, 5.0.1, 5.0.2].
    - tymon/jwt-auth 0.5.9 requires namshi/jose 5.0.* -> satisfiable by namshi/jose[5.0.0, 5.0.1, 5.0.2].
    - tymon/jwt-auth 0.5.1 requires namshi/jose 2.2.* -> satisfiable by namshi/jose[2.2.0, 2.2.1, 2.2.2].
    - tymon/jwt-auth 0.5.2 requires namshi/jose 2.2.* -> satisfiable by namshi/jose[2.2.0, 2.2.1, 2.2.2].
    - tymon/jwt-auth 0.5.3 requires namshi/jose 2.2.* -> satisfiable by namshi/jose[2.2.0, 2.2.1, 2.2.2].
    - tymon/jwt-auth 0.5.0 requires namshi/jose 2.0.* -> satisfiable by namshi/jose[2.0.0, 2.0.1, 2.0.2, 2.0.3].
    - namshi/jose 5.0.2 requires lib-openssl * -> the requested linked library openssl has the wrong version installed or is missing from your system, make sure to have the extension providing it.
    - namshi/jose 5.0.1 requires lib-openssl * -> the requested linked library openssl has the wrong version installed or is missing from your system, make sure to have the extension providing it.
    - namshi/jose 5.0.0 requires lib-openssl * -> the requested linked library openssl has the wrong version installed or is missing from your system, make sure to have the extension providing it.
    - namshi/jose 2.2.2 requires lib-openssl * -> the requested linked library openssl has the wrong version installed or is missing from your system, make sure to have the extension providing it.
    - namshi/jose 2.2.1 requires lib-openssl * -> the requested linked library openssl has the wrong version installed or is missing from your system, make sure to have the extension providing it.
    - namshi/jose 2.2.0 requires lib-openssl * -> the requested linked library openssl has the wrong version installed or is missing from your system, make sure to have the extension providing it.
    - namshi/jose 2.0.3 requires lib-openssl * -> the requested linked library openssl has the wrong version installed or is missing from your system, make sure to have the extension providing it.
    - namshi/jose 2.0.2 requires lib-openssl * -> the requested linked library openssl has the wrong version installed or is missing from your system, make sure to have the extension providing it.
    - namshi/jose 2.0.1 requires lib-openssl * -> the requested linked library openssl has the wrong version installed or is missing from your system, make sure to have the extension providing it.
    - namshi/jose 2.0.0 requires lib-openssl * -> the requested linked library openssl has the wrong version installed or is missing from your system, make sure to have the extension providing it.
    - Installation request for tymon/jwt-auth 0.5.* -> satisfiable by tymon/jwt-auth[0.5.0, 0.5.1, 0.5.2, 0.5.3, 0.5.4, 0.5.5, 0.5.6, 0.5.7, 0.5.8, 0.5.9].

找到问题了。。
tymon/jwt-auth 0.5.4 requires namshi/jose 5.0.*
namshi/jose 5.0.* requires lib-openssl *
composer show --platform

并没有 lib-openssl
composer-plugin-api 1.0.0     The Composer Plugin API
ext-bcmath          7.0.14    The bcmath PHP extension
ext-bz2             7.0.14    The bz2 PHP extension
ext-calendar        7.0.14    The calendar PHP extension
ext-ctype           7.0.14    The ctype PHP extension
ext-curl            7.0.14    The curl PHP extension
ext-date            7.0.14    The date PHP extension
ext-dom             20031129  The dom PHP extension
ext-exif            0         The exif PHP extension
ext-fileinfo        1.0.5     The fileinfo PHP extension
ext-filter          7.0.14    The filter PHP extension
ext-gd              7.0.14    The gd PHP extension
ext-hash            1.0       The hash PHP extension
ext-iconv           7.0.14    The iconv PHP extension
ext-imap            7.0.14    The imap PHP extension
ext-json            1.4.0     The json PHP extension
ext-ldap            7.0.14    The ldap PHP extension
ext-libxml          7.0.14    The libxml PHP extension
ext-mbstring        7.0.14    The mbstring PHP extension
ext-mcrypt          7.0.14    The mcrypt PHP extension
ext-mysqli          7.0.14    The mysqli PHP extension
ext-openssl         7.0.14    The openssl PHP extension
ext-pcre            7.0.14    The pcre PHP extension
ext-PDO             7.0.14    The PDO PHP extension
ext-pdo_mysql       7.0.14    The pdo_mysql PHP extension
ext-Phar            2.0.2     The Phar PHP extension
ext-posix           7.0.14    The posix PHP extension
ext-readline        7.0.14    The readline PHP extension
ext-redis           3.0.0-rc1 The redis PHP extension
ext-Reflection      7.0.14    The Reflection PHP extension
ext-session         7.0.14    The session PHP extension
ext-SimpleXML       7.0.14    The SimpleXML PHP extension
ext-soap            7.0.14    The soap PHP extension
ext-sockets         7.0.14    The sockets PHP extension
ext-SPL             7.0.14    The SPL PHP extension
ext-sqlite3         0.7-dev   The sqlite3 PHP extension
ext-tokenizer       7.0.14    The tokenizer PHP extension
ext-xdebug          2.5.0     The xdebug PHP extension
ext-xml             7.0.14    The xml PHP extension
ext-xmlwriter       7.0.14    The xmlwriter PHP extension
ext-xsl             7.0.14    The xsl PHP extension
ext-Zend-OPcache    7.0.14    The Zend OPcache PHP extension
ext-zip             1.13.5    The zip PHP extension
ext-zlib            7.0.14    The zlib PHP extension
lib-curl            7.52.1    The curl PHP library
lib-libxml          2.9.4     The libxml PHP library
lib-pcre            8.38      The pcre PHP library
lib-xsl             1.1.29    The xsl PHP library
php                 7.0.14    The PHP interpreter
php-64bit           7.0.14    The PHP interpreter, 64bit


Stuck on trying to install torchvision

Have tried many times to install torchvision (which is installed) but after looking through the errors it tries to download it through piware (i think) and there is no windows version so it can't download. any help?

I double checked the error is actually about torch which I've tried using pip but it doesn't even exist

Update when trying "pip install deep_daze" it is stuck on this error:


Retrieve every possible temperature sensor

This feature will help to detect the temperature of server components (CPU, GPU, inner box...) and detect component overheat.
Linked to disk drive health check this would potentially allow to determine an index of server health.

In the following folder, you have access to temperature sensors, without the help of other applications.
/sys/class/hwmon/hwmon0/

device/           temp1_crit_alarm  temp2_crit_alarm  temp3_crit_alarm
name              temp1_input       temp2_input       temp3_input
power/            temp1_label       temp2_label       temp3_label
subsystem/        temp1_max         temp2_max         temp3_max
temp1_crit        temp2_crit        temp3_crit        uevent

Looks like we can get these values there: cat /sys/class/thermal/thermal_zone*


feat: added dbFlow to save response of apply for loan section

Fixes #25
Please Add Screenshots If there are any UI changes.

Please make sure these boxes are checked before submitting your pull request - thanks!

[x] Run the unit tests with ./gradlew check to make sure you didn't break anything

[x] If you have multiple commits please combine them into one commit by squashing them.

@therajanmaurya  I have created the db and it is so far it is saving the db. Can you please tell me how to link list of accountAssignment with the loan account table.I was unable to guess the foreign key.


UI: Navigating the complex data inside of a transaction receipt

What would you like to be added?
The experience for "picking" a sub-transaction in an Atomic (4) one needs to give you some insight into which are which without picking one
Is the whole State Receipt available yes/no?
The Domain
Why is this needed?
Make the UX easier to navigate through and more effective.

Proposal: replace the dropdown control in the upper section of the transaction details dialog box with a table where each entry has a radio control and represents a transaction, indicating its id (in short format), domain and whether it has a receipt or not. Mockup:

@peterbroadhurst do you think the design above would provide a good UX?

Regarding the yes/no - on Receipt let me give some examples of the actual complexity we're trying to navigate as humans when we're clicking this list:

The transaction was submitted by me, I have:

A transaction object
A receipt object
A state receipt
A domain receipt
The domain is pente

The transaction was submitted by me, and I only have:

A transaction object
Debug information about what's happening with the transaction
... because the transaction is still going through

The transaction was submitted by someone else, but I am included fully so I have:

A receipt object
A state receipt
A domain receipt
The domain is pente

The transaction was submitted by someone else, and I'm not included so I have:

A state receipt that is incomplete

This certainly isn't a complete list of possibilities, but it hopefully illustrates the enum style situation we're in here, and why I'm not sure it's a yes/no on one english word (particularly "receipt" which is very loaded).

Adding the exact same information above, but in table format to see if it might make it easier to collaborate on a design for that portion of the UX:


Phytec PhyVerso BSP driver

Describe your changes
This is a BSP driver for phytec's phyverso controller board.
Issue ticket number and link
Checklist before requesting a review

[X] I have performed a self-review of my code
[ ] I have made corresponding changes to the documentation
[X] I read the contribution documentation and made sure that my changes meet its requirements

@SirVer this is our latest version of the driver. Do you have modifications as well? If yes feel free to push to this branch

@corneliusclaussen Thanks!
@golovasteek @dorezyuk Can you please take over the code review & the communication here.

I'll fix the clang format later

I'll fix the clang format later

done


feat: GATK utils for common IO files

Utilities for bam/vcf indexes, for argument file(s) and MD5 files.

Thanks for the contribution!
I was just wondering if it would make more sense to have the defaults to True or False? I know the others (e.g. samtools) default to True, but it might make more sense to always default to False` so that the parsing of the option is specifically activated. What do you think?

It just feels a bit safer to have everything disabled by default so that each wrapper has to specifically activate the options it needs.
But do not have a strong opinion, so up to you! :smile:


Disabled expressions are not detected as empty expressions

Here the text block "Hallo" is disabled and the generated code is not compilable.
For disabled expressions it is important, that they are handled as empty expressions and an error message is returned:

Tested successfully on dev server with the following program:
NEPOprog EV3Issue#1449.xml.txt


[pGlyco]  File E:\G-test32\eclipse\IgG\process1\pGlycoDB-GP-FDR-Pro.txt does not exist!

最近在使用之前下载的pGlyco3,发现会报如下错误，以前可以正常搜库。重新下载了最近版本使用后还是会报错，具体报错如截图，最终结果如截图，日志见附件，辛苦您抽空帮忙看下，十分感谢。
[pGlyco] Starting task ...
Process ID=59104: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>rem ***************************************************
Process ID=59104: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>parse_raw.exe "E:\G-test32\eclipse\M-G-HCD\1\process1\pGlyco.cfg"
Process ID=59104: [pGlyco]  Processing 1 raw files.

Process ID=59104: [pGlyco] 2920 glycan structures
Process ID=59104: [pGlyco] Ion Indexing ...
Process ID=59104: [pGlyco] Ion Indexing done
Process ID=59104: [pGlyco] Glycan grouping ...
Process ID=59104: [pGlyco] Glycan grouping done.
Process ID=59104: [pGlyco] Loading protein sequences ...
Process ID=59104: [pGlyco] 490420 peptide sequences ...
Process ID=59104: [pGlyco] Preparing spectra ...
Process ID=59104: [pGlyco] E:\G-test32\eclipse\M-G-HCD\G_Test_32-M-G1-en-glyco-HCD-1_HCDFT.mgf
Process ID=59104: [I.D.] 100.0% [==================================================]Process ID=59104:
Process ID=59104: [pGlyco] E:\G-test32\eclipse\M-G-HCD\G_Test_32-M-G1-en-glyco-HCD-1_HCDFT.mgf finished!
Process ID=59104: [I.D.] 100.0% [==================================================]Process ID=59104: Timing: 2074.97 seconds
Process ID=59104: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>gpPercolator.exe -p "E:\G-test32\eclipse\M-G-HCD\1\process1\pGlyco.cfg"
Process ID=59104: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoFDR.exe -p "E:\G-test32\eclipse\M-G-HCD\1\process1\pGlyco.cfg"
Process ID=59104: TDA_fmm.py:194: RuntimeWarning: invalid value encountered in divide
Process ID=59104: TDA_fmm.py:94: RuntimeWarning: divide by zero encountered in log
Process ID=59104: E:\G-test32\eclipse\M-G-HCD\1\process1\pGlycoDB-GP-Raw1-FDR.txt
Process ID=59104: [pGlycoFDR] 27969 GPSMs at 100.0% FDR
Process ID=59104: E:\G-test32\eclipse\M-G-HCD\1\process1\pGlycoDB-GP-Raw1-FDR-noFiltered.txt
Process ID=59104: [pGlycoFDR] 27969 GPSMs at 100.0% FDR
Process ID=59104: merge into E:\G-test32\eclipse\M-G-HCD\1\process1\pGlycoDB-GP-FDR.txt
Process ID=59104: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoProInfer.exe -p "E:\G-test32\eclipse\M-G-HCD\1\process1\pGlyco.cfg"
Process ID=59104: 'pGlycoProInfer.exe' is not recognized as an internal or external command,
Process ID=59104: operable program or batch file.
Process ID=59104: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>XIC.exe -p "E:\G-test32\eclipse\M-G-HCD\1\process1\pGlyco.cfg"
Process ID=59104: Traceback (most recent call last):
Process ID=59104:   File "XIC.py", line 471, in
Process ID=59104:   File "XIC.py", line 195, in PeakArea
Process ID=59104:   File "pGlycoReader.py", line 97, in ReadAllGPSMs
Process ID=59104: FileNotFoundError: [Errno 2] No such file or directory: 'E:\G-test32\eclipse\M-G-HCD\1\process1\pGlycoDB-GP-FDR-Pro.txt'
Process ID=59104: [60364] Failed to execute script 'XIC' due to unhandled exception!
Process ID=59104: [XIC] Smoothing window = 21
Process ID=59104: [XIC] Smoothing method = savgol_filter
Process ID=59104: [XIC] Loading pGlyco results ...
Process ID=59104: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoSite.exe "E:\G-test32\eclipse\M-G-HCD\1\process1\pGlyco.cfg"
Process ID=59104: Already registered!
Process ID=59104: Unhandled Exception: System.Collections.Generic.KeyNotFoundException: The given key was not present in the dictionary.
Process ID=59104:    at System.ThrowHelper.ThrowKeyNotFoundException()
Process ID=59104:    at System.Collections.Generic.Dictionary2.get_Item(TKey key) Process ID=59104:    at GPSMReader.pGlycoReader.GetEachGlycan(List1 items)
Process ID=59104:    at pGlycoSite.pGlycoSite.FindEachMaxGlyco()
Process ID=59104:    at pGlycoSite.pGlycoSite..ctor(String cfg)
Process ID=59104:    at pGlycoSite.Program.Main(String[] args)
[pGlyco]  File E:\G-test32\eclipse\M-G-HCD\1\process1\pGlycoDB-GP-FDR-Pro.txt does not exist!
[pGlyco]  File E:\G-test32\eclipse\M-G-HCD\1\process1\pGlycoDB-GP-FDR-Pro-Quant.txt does not exist!
[pGlyco]  File E:\G-test32\eclipse\M-G-HCD\1\process1\pGlycoDB-GP-FDR-Pro-Quant-Site.txt does not exist!
[pGlyco] All results are merged!
[pGlyco] Running time = 35.2 minutes.
[pGlyco] Task completed!
[pGlyco] Task completed.
Process 1 has been killed
[pGlyco] User terminated.
[pGlyco] Starting task ...

Process ID=60656: [pGlyco]  6.52%Process ID=44820: [pGlyco]  Processing 1 raw files.
Process ID=44820: [pGlyco]  6.46%Process ID=59976: [pGlyco]  Processing 1 raw files.
Process ID=59976: [pGlyco]  100%Process ID=44820: 	  *********************************************
Process ID=44820: 	 /       pParse2.2 (x64) from pFind Studio
Process ID=44820: 	/        Email<EMAIL_ADDRESS>Process ID=44820: 	\        Website:  http://pfind.ict.ac.cn       /
Process ID=44820: 	  *********************************************
Process ID=44820: The license will expire in 2100-1-1
Process ID=44820: [pParse]  - pParse writes logs in E:\G-test32\eclipse\IgG\pParsePlusLog.txt
Process ID=44820: [pParse]  - --------- BEGIN PARAMETERS -----------
Process ID=44820: [pParse]  - 01: check_activationcenter = 1
Process ID=44820: [pParse]  - 02: co-elute = 1
Process ID=44820: [pParse]  - 03: cut_similiar_mono = 1
Process ID=44820: [pParse]  - 04: datanum = 1
Process ID=44820: [pParse]  - 05: datapath1 = E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.ms1
Process ID=44820: [pParse]  - 06: delete_msn = 0
Process ID=44820: [pParse]  - 07: dia_mode = 0
Process ID=44820: [pParse]  - 08: dia_mode_to_filter_by_selectedMS2ScanNoSet = 1
Process ID=44820: [pParse]  - 09: input_format = ms1
Process ID=44820: [pParse]  - 10: intensity = 1
Process ID=44820: [pParse]  - 11: ipv_file = IPV.txt
Process ID=44820: [pParse]  - 12: isolation_width = 2.000000
Process ID=44820: [pParse]  - 13: logfilepath = E:\G-test32\eclipse\IgG
Process ID=44820: [pParse]  - 14: m/z = 5
Process ID=44820: [pParse]  - 15: mars_model = 4
Process ID=44820: [pParse]  - 16: mars_threshold = -0.500000
Process ID=44820: [pParse]  - 17: mstol = 20.000000
Process ID=44820: [pParse]  - 18: mstolppm = 1
Process ID=44820: [pParse]  - 19: output_mgf = 1
Process ID=44820: [pParse]  - 20: output_pf = 1
Process ID=44820: [pParse]  - 21: outputpath =
Process ID=44820: [pParse]  - 22: recalibrate_window = 7.000000
Process ID=44820: [pParse]  - 23: rewrite_files = 0
Process ID=44820: [pParse]  - --------- END PARAMETERS -------------
Process ID=44820: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.ms1
Process ID=44820: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.ms2
Process ID=44820: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.pf1
Process ID=44820: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3_HCDFT.pf2
Process ID=44820: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3_HCDFT.mgf
Process ID=60656: 	  *********************************************
Process ID=60656: 	 /       pParse2.2 (x64) from pFind Studio
Process ID=60656: 	/        Email<EMAIL_ADDRESS>Process ID=60656: 	\        Website:  http://pfind.ict.ac.cn       /
Process ID=60656: 	  *********************************************
Process ID=60656: The license will expire in 2100-1-1
Process ID=60656: [pParse]  - pParse writes logs in E:\G-test32\eclipse\IgG\pParsePlusLog.txt
Process ID=60656: [pParse]  - --------- BEGIN PARAMETERS -----------
Process ID=60656: [pParse]  - 01: check_activationcenter = 1
Process ID=60656: [pParse]  - 02: co-elute = 1
Process ID=60656: [pParse]  - 03: cut_similiar_mono = 1
Process ID=60656: [pParse]  - 04: datanum = 1
Process ID=60656: [pParse]  - 05: datapath1 = E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.ms1
Process ID=60656: [pParse]  - 06: delete_msn = 0
Process ID=60656: [pParse]  - 07: dia_mode = 0
Process ID=60656: [pParse]  - 08: dia_mode_to_filter_by_selectedMS2ScanNoSet = 1
Process ID=60656: [pParse]  - 09: input_format = ms1
Process ID=60656: [pParse]  - 10: intensity = 1
Process ID=60656: [pParse]  - 11: ipv_file = IPV.txt
Process ID=60656: [pParse]  - 12: isolation_width = 2.000000
Process ID=60656: [pParse]  - 13: logfilepath = E:\G-test32\eclipse\IgG
Process ID=60656: [pParse]  - 14: m/z = 5
Process ID=60656: [pParse]  - 15: mars_model = 4
Process ID=60656: [pParse]  - 16: mars_threshold = -0.500000
Process ID=60656: [pParse]  - 17: mstol = 20.000000
Process ID=60656: [pParse]  - 18: mstolppm = 1
Process ID=60656: [pParse]  - 19: output_mgf = 1
Process ID=60656: [pParse]  - 20: output_pf = 1
Process ID=60656: [pParse]  - 21: outputpath =
Process ID=60656: [pParse]  - 22: recalibrate_window = 7.000000
Process ID=60656: [pParse]  - 23: rewrite_files = 0
Process ID=60656: [pParse]  - --------- END PARAMETERS -------------
Process ID=60656: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.ms1
Process ID=60656: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.ms2
Process ID=59976: 	  *********************************************
Process ID=59976: 	 /       pParse2.2 (x64) from pFind Studio
Process ID=59976: 	/        Email<EMAIL_ADDRESS>Process ID=59976: 	\        Website:  http://pfind.ict.ac.cn       /
Process ID=59976: 	  *********************************************
Process ID=59976: The license will expire in 2100-1-1
Process ID=59976: [pParse]  - pParse writes logs in E:\G-test32\eclipse\IgG\pParsePlusLog.txt
Process ID=59976: [pParse]  - --------- BEGIN PARAMETERS -----------
Process ID=59976: [pParse]  - 01: check_activationcenter = 1
Process ID=59976: [pParse]  - 02: co-elute = 1
Process ID=59976: [pParse]  - 03: cut_similiar_mono = 1
Process ID=59976: [pParse]  - 04: datanum = 1
Process ID=59976: [pParse]  - 05: datapath1 = E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.ms1
Process ID=59976: [pParse]  - 06: delete_msn = 0
Process ID=59976: [pParse]  - 07: dia_mode = 0
Process ID=59976: [pParse]  - 08: dia_mode_to_filter_by_selectedMS2ScanNoSet = 1
Process ID=59976: [pParse]  - 09: input_format = ms1
Process ID=59976: [pParse]  - 10: intensity = 1
Process ID=59976: [pParse]  - 11: ipv_file = IPV.txt
Process ID=59976: [pParse]  - 12: isolation_width = 2.000000
Process ID=59976: [pParse]  - 13: logfilepath = E:\G-test32\eclipse\IgG
Process ID=59976: [pParse]  - 14: m/z = 5
Process ID=59976: [pParse]  - 15: mars_model = 4
Process ID=59976: [pParse]  - 16: mars_threshold = -0.500000
Process ID=59976: [pParse]  - 17: mstol = 20.000000
Process ID=59976: [pParse]  - 18: mstolppm = 1
Process ID=59976: [pParse]  - 19: output_mgf = 1
Process ID=59976: [pParse]  - 20: output_pf = 1
Process ID=59976: [pParse]  - 21: outputpath =
Process ID=59976: [pParse]  - 22: recalibrate_window = 7.000000
Process ID=59976: [pParse]  - 23: rewrite_files = 0
Process ID=59976: [pParse]  - --------- END PARAMETERS -------------
Process ID=60656: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.pf1
Process ID=59976: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.ms1
Process ID=60656: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2_HCDFT.pf2
Process ID=59976: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.ms2
Process ID=60656: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2_HCDFT.mgf
Process ID=59976: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.pf1
Process ID=59976: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1_HCDFT.pf2
Process ID=59976: [pParse]  - Start to process E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1_HCDFT.mgf
Process ID=59976: [pParse]  - Extracting MS2, Scan Num = 1000
Process ID=44820: [pParse]  - Extracting MS2, Scan Num = 1000
Process ID=60656: [pParse]  - Extracting MS2, Scan Num = 1000
Process ID=44820: [pParse]  - Extracting MS2, Scan Num = 2000
Process ID=59976: [pParse]  - Extracting MS2, Scan Num = 2000
Process ID=60656: [pParse]  - Extracting MS2, Scan Num = 2000
Process ID=44820: [pParse]  - Extracting MS1, Scan Num = 1000
Process ID=60656: [pParse]  - Extracting MS1, Scan Num = 1000
Process ID=59976: [pParse]  - Extracting MS1, Scan Num = 1000
Process ID=44820: [pParse]  - Extracting MS2, Scan Num = 3000
Process ID=59976: [pParse]  - Extracting MS2, Scan Num = 3000
Process ID=60656: [pParse]  - Extracting MS2, Scan Num = 3000
Process ID=44820: [pParse]  - Extracting MS2, Scan Num = 4000
Process ID=59976: [pParse]  - Extracting MS2, Scan Num = 4000
Process ID=60656: [pParse]  - Extracting MS2, Scan Num = 4000
Process ID=44820: [pParse]  - Extracting MS2, Scan Num = 5000
Process ID=59976: [pParse]  - Extracting MS2, Scan Num = 5000
Process ID=60656: [pParse]  - Extracting MS2, Scan Num = 5000
Process ID=59976: [pParse]  - Extracting MS2, Scan Num = 6000
Process ID=44820: [pParse]  - Extracting MS2, Scan Num = 6000
Process ID=60656: [pParse]  - Extracting MS2, Scan Num = 6000
Process ID=44820: [pParse]  - Extracting MS2, Scan Num = 7000
Process ID=59976: [pParse]  - Extracting MS2, Scan Num = 7000
Process ID=60656: [pParse]  - Extracting MS2, Scan Num = 7000
Process ID=60656: [pParse]  - Extracting MS1, Scan Num = 2000
Process ID=59976: [pParse]  - Extracting MS2, Scan Num = 8000
Process ID=60656: [pParse]  - Extracting MS2, Scan Num = 8000
Process ID=44820: [pParse]  - Extracting MS2, Scan Num = 8000
Process ID=59976: [pParse]  - Extracting MS1, Scan Num = 2000
Process ID=44820: [pParse]  - Extracting MS1, Scan Num = 2000
Process ID=59976: [pParse]  - Extracting MS2, Scan Num = 9000
Process ID=44820: [pParse]  - Extracting MS2, Scan Num = 9000
Process ID=60656: [pParse]  - Extracting MS2, Scan Num = 9000
Process ID=59976: [pParse]  - Extracting MS2, Scan Num = 10000
Process ID=60656: [pParse]  - Extracting MS2, Scan Num = 10000
Process ID=44820: [pParse]  - Extracting MS2, Scan Num = 10000
Process ID=59976: [pParse]  - Extracting MS2, Scan Num = 11000
Process ID=60656: [pParse]  - Extracting MS2, Scan Num = 11000
Process ID=44820: [pParse]  - Extracting MS2, Scan Num = 11000
Process ID=59976: [pParse]  - Extracting MS2, Scan Num = 12000
Process ID=60656: [pParse]  - Extracting MS2, Scan Num = 12000
Process ID=44820: [pParse]  - Extracting MS2, Scan Num = 12000
Process ID=60656: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.ms1
Process ID=60656: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.ms1
Process ID=60656: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.ms1: 2583
Process ID=60656: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.pf1
Process ID=60656: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.pf1
Process ID=60656: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.pf1: 2583
Process ID=60656: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.ms2
Process ID=60656: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.ms2
Process ID=60656: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.ms2: 12744
Process ID=60656: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2_HCDFT.pf2
Process ID=60656: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2_HCDFT.pf2
Process ID=60656: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2_HCDFT.pf2: 12739
Process ID=60656: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2_HCDFT.mgf
Process ID=60656: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2_HCDFT.mgf
Process ID=60656: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2_HCDFT.mgf: 12739
Process ID=60656: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.csv
Process ID=60656: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.csv
Process ID=60656: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.csv: 12739
Process ID=60656: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.precurosr.csv
Process ID=60656: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.precurosr.csv
Process ID=60656: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2.precurosr.csv: 12739
Process ID=60656: [pParse]  -  == == == Time elapsed: 233 secondss. == == == =
Process ID=60656: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoDB.exe "E:\G-test32\eclipse\IgG\process1\pGlyco.cfg"
Process ID=59976: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.ms1
Process ID=59976: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.ms1
Process ID=59976: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.ms1: 2556
Process ID=59976: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.pf1
Process ID=59976: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.pf1
Process ID=59976: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.pf1: 2556
Process ID=59976: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.ms2
Process ID=59976: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.ms2
Process ID=59976: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.ms2: 12927
Process ID=59976: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1_HCDFT.pf2
Process ID=59976: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1_HCDFT.pf2
Process ID=59976: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1_HCDFT.pf2: 12917
Process ID=59976: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1_HCDFT.mgf
Process ID=59976: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1_HCDFT.mgf
Process ID=59976: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1_HCDFT.mgf: 12917
Process ID=59976: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.csv
Process ID=59976: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.csv
Process ID=59976: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.csv: 12917
Process ID=59976: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.precurosr.csv
Process ID=59976: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.precurosr.csv
Process ID=59976: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1.precurosr.csv: 12917
Process ID=59976: [pParse]  -  == == == Time elapsed: 235 secondss. == == == =
Process ID=59976: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoDB.exe "E:\G-test32\eclipse\IgG\process3\pGlyco.cfg"
Process ID=60656: *****************************************************
Process ID=60656: *                                                   *
Process ID=60656: *              * Welcome to pGlyco3 *               *
Process ID=60656: *                                                   *
Process ID=60656: *               *<EMAIL_ADDRESS>*                *
Process ID=60656: *                                                   *
Process ID=60656: *****************************************************
Process ID=60656: [pGlyco] pGlyco software will be expired in 2027/01/01
Process ID=60656: [pGlyco] top_n_peaks=300
Process ID=60656: [pGlyco] output_top_n=5
Process ID=60656: [pGlyco] --. [key-config]
Process ID=60656: [pGlyco]  1. aaini=aa.ini
Process ID=60656: [pGlyco]  2. glycoini=glyco.ini
Process ID=60656: [pGlyco]  3. modini=modification.ini
Process ID=60656: [pGlyco] --. [glycan]
Process ID=60656: [pGlyco]  4. glycan_type=N-glycan
Process ID=60656: [pGlyco]  5. glycosylation_sites=J
Process ID=60656: [pGlyco]  6. glycan_core=N(1),N(2),N(2)H(1),N(2)H(2),N(2)H(3),N(1)F(1),N(2)F(1)
Process ID=60656: [pGlyco]  7. glycan_db=pGlyco-N-Human.gdb
Process ID=60656: [pGlyco]  8. glycan_fix_mod=
Process ID=60656: [pGlyco]  9. glycan_var_mod=
Process ID=60656: [pGlyco] 10. max_var_mod_on_glycan=1
Process ID=60656: [pGlyco] 11. max_glycan_db_size=100000
Process ID=60656: [pGlyco] 12. gp_marker_glyco=N
Process ID=60656: [pGlyco] --. [protein]
Process ID=60656: [pGlyco] 13. fasta=E:\G-test32\eclipse\IgG\IgG-human.fasta.N2J
Process ID=60656: [pGlyco] 14. enzyme=Trypsin Nterm _ _ Cterm KR _
Process ID=60656: [pGlyco] 15. max_miss_cleave=3
Process ID=60656: [pGlyco] 16. protein_fix_mod=Carbamidomethyl[C]
Process ID=60656: [pGlyco] 17. protein_var_mod=Oxidation[M]
Process ID=60656: [pGlyco] 18. max_var_mod_on_peptide=2
Process ID=60656: [pGlyco] --. [search]
Process ID=60656: [pGlyco] 19. fragmentation_type=HCD
Process ID=60656: [pGlyco] 20. precursor_tolerance=10 ppm
Process ID=60656: [pGlyco] 21. fragment_tolerance=20 ppm
Process ID=60656: [pGlyco] 22. output_dir=E:/G-test32/eclipse/IgG/process1/
Process ID=60656: [pGlyco] Loading glycan database ...
Process ID=60656: [pGlyco] 2920 glycan structures
Process ID=60656: [pGlyco] Ion Indexing ...
Process ID=44820: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.ms1
Process ID=44820: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.ms1
Process ID=44820: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.ms1: 2562
Process ID=44820: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.pf1
Process ID=44820: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.pf1
Process ID=44820: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.pf1: 2562
Process ID=44820: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.ms2
Process ID=44820: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.ms2
Process ID=44820: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.ms2: 12924
Process ID=44820: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3_HCDFT.pf2
Process ID=44820: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3_HCDFT.pf2
Process ID=44820: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3_HCDFT.pf2: 12916
Process ID=44820: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3_HCDFT.mgf
Process ID=44820: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3_HCDFT.mgf
Process ID=44820: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3_HCDFT.mgf: 12916
Process ID=44820: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.csv
Process ID=44820: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.csv
Process ID=44820: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.csv: 12916
Process ID=44820: [pParse]  - Closed E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.precurosr.csv
Process ID=44820: [pParse]  - Finished Operations on E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.precurosr.csv
Process ID=44820: [pParse]  - Scan Number in E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3.precurosr.csv: 12916
Process ID=44820: [pParse]  -  == == == Time elapsed: 237 secondss. == == == =
Process ID=60656: [pGlyco] Ion Indexing done
Process ID=60656: [pGlyco] Glycan grouping ...
Process ID=60656: [pGlyco] Glycan grouping done.
Process ID=60656: [pGlyco] Loading protein sequences ...
Process ID=60656: [pGlyco] 94 peptide sequences ...
Process ID=60656: [pGlyco] Preparing spectra ...

Process ID=60656: [pGlyco] E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2_HCDFT.mgf
Process ID=59976: [pGlyco] 2920 glycan structures
Process ID=59976: [pGlyco] Ion Indexing ...
Process ID=60656: [I.D.] 0.7% [                                                  ]Process ID=59976: [pGlyco] Ion Indexing done
Process ID=60656: [I.D.] 1.0% [                                                  ]Process ID=59976: [pGlyco] Glycan grouping ...
Process ID=59976: [pGlyco] Glycan grouping done.
Process ID=59976: [pGlyco] Loading protein sequences ...
Process ID=60656: [I.D.] 1.4% [                                                  ]Process ID=59976: [pGlyco] 94 peptide sequences ...
Process ID=59976: [pGlyco] Preparing spectra ...

Process ID=59976: [I.D.] 0.3% [                                                  ]Process ID=44820: [pGlyco] 2920 glycan structures
Process ID=44820: [pGlyco] Ion Indexing ...
Process ID=59976: [I.D.] 1.0% [                                                  ]Process ID=44820: [pGlyco] Ion Indexing done
Process ID=59976: [I.D.] 1.4% [                                                  ]Process ID=44820: [pGlyco] Glycan grouping ...
Process ID=44820: [pGlyco] Glycan grouping done.
Process ID=44820: [pGlyco] Loading protein sequences ...
Process ID=59976: [I.D.] 1.7% [                                                  ]Process ID=44820: [pGlyco] 94 peptide sequences ...
Process ID=44820: [pGlyco] Preparing spectra ...
Process ID=60656: [I.D.] 3.8% [=                                                 ]Process ID=44820: [pGlyco] E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3_HCDFT.mgf
Process ID=60656: [I.D.] 100.0% [==================================================]Process ID=60656:
Process ID=60656: [pGlyco] E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-2_HCDFT.mgf finished!
Process ID=44820: [I.D.] 92.9% [==============================================    ]Process ID=60656: Timing: 105.232 seconds
Process ID=60656: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>gpPercolator.exe -p "E:\G-test32\eclipse\IgG\process1\pGlyco.cfg"
Process ID=60656: 'gpPercolator.exe' is not recognized as an internal or external command,
Process ID=60656: operable program or batch file.
Process ID=60656: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoFDR.exe -p "E:\G-test32\eclipse\IgG\process1\pGlyco.cfg"
Process ID=59976: [I.D.] 97.6% [================================================  ]Process ID=60656: E:\G-test32\eclipse\IgG\process1\pGlycoDB-GP-Raw1-FDR.txt
Process ID=60656: [pGlycoFDR] 775 GPSMs at 100.0% FDR
Process ID=60656: E:\G-test32\eclipse\IgG\process1\pGlycoDB-GP-Raw1-FDR-noFiltered.txt
Process ID=60656: [pGlycoFDR] 775 GPSMs at 100.0% FDR
Process ID=60656: merge into E:\G-test32\eclipse\IgG\process1\pGlycoDB-GP-FDR.txt
Process ID=59976: [I.D.] 97.9% [================================================  ]Process ID=60656: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoProInfer.exe -p "E:\G-test32\eclipse\IgG\process1\pGlyco.cfg"
Process ID=60656: 'pGlycoProInfer.exe' is not recognized as an internal or external command,
Process ID=60656: operable program or batch file.
Process ID=60656: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>XIC.exe -p "E:\G-test32\eclipse\IgG\process1\pGlyco.cfg"
Process ID=44820: [I.D.] 96.3% [================================================  ]Process ID=60656: Traceback (most recent call last):
Process ID=60656:   File "XIC.py", line 471, in
Process ID=60656:   File "XIC.py", line 195, in PeakArea
Process ID=60656:   File "pGlycoReader.py", line 97, in ReadAllGPSMs
Process ID=60656: FileNotFoundError: [Errno 2] No such file or directory: 'E:\G-test32\eclipse\IgG\process1\pGlycoDB-GP-FDR-Pro.txt'
Process ID=60656: [48364] Failed to execute script 'XIC' due to unhandled exception!
Process ID=60656: [XIC] Smoothing window = 21
Process ID=60656: [XIC] Smoothing method = savgol_filter
Process ID=60656: [XIC] Loading pGlyco results ...
Process ID=59976: [I.D.] 100.0% [==================================================]Process ID=59976:
Process ID=59976: [pGlyco] E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-1_HCDFT.mgf finished!
Process ID=44820: [I.D.] 96.6% [================================================  ]Process ID=59976: Timing: 106.844 seconds
Process ID=59976: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>gpPercolator.exe -p "E:\G-test32\eclipse\IgG\process3\pGlyco.cfg"
Process ID=59976: 'gpPercolator.exe' is not recognized as an internal or external command,
Process ID=59976: operable program or batch file.
Process ID=59976: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoFDR.exe -p "E:\G-test32\eclipse\IgG\process3\pGlyco.cfg"
Process ID=44820: [I.D.] 97.7% [================================================  ]Process ID=60656: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoSite.exe "E:\G-test32\eclipse\IgG\process1\pGlyco.cfg"
Process ID=44820: [I.D.] 98.0% [================================================  ]Process ID=59976: E:\G-test32\eclipse\IgG\process3\pGlycoDB-GP-Raw1-FDR.txt
Process ID=59976: [pGlycoFDR] 734 GPSMs at 100.0% FDR
Process ID=59976: E:\G-test32\eclipse\IgG\process3\pGlycoDB-GP-Raw1-FDR-noFiltered.txt
Process ID=59976: [pGlycoFDR] 734 GPSMs at 100.0% FDR
Process ID=59976: merge into E:\G-test32\eclipse\IgG\process3\pGlycoDB-GP-FDR.txt
Process ID=44820: [I.D.] 98.3% [================================================= ]Process ID=59976: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoProInfer.exe -p "E:\G-test32\eclipse\IgG\process3\pGlyco.cfg"
Process ID=59976: 'pGlycoProInfer.exe' is not recognized as an internal or external command,
Process ID=59976: operable program or batch file.
Process ID=59976: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>XIC.exe -p "E:\G-test32\eclipse\IgG\process3\pGlyco.cfg"
Process ID=44820: [I.D.] 100.0% [==================================================]Process ID=44820:
Process ID=44820: [pGlyco] E:\G-test32\eclipse\IgG\23-8-31-IgG-HCD-3_HCDFT.mgf finished!
Process ID=44820: [I.D.] 100.0% [==================================================]Process ID=44820: Timing: 107.637 seconds
Process ID=44820: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>gpPercolator.exe -p "E:\G-test32\eclipse\IgG\process2\pGlyco.cfg"
Process ID=44820: 'gpPercolator.exe' is not recognized as an internal or external command,
Process ID=44820: operable program or batch file.
Process ID=44820: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoFDR.exe -p "E:\G-test32\eclipse\IgG\process2\pGlyco.cfg"
Process ID=59976: Traceback (most recent call last):
Process ID=59976:   File "XIC.py", line 471, in
Process ID=59976:   File "XIC.py", line 195, in PeakArea
Process ID=59976:   File "pGlycoReader.py", line 97, in ReadAllGPSMs
Process ID=59976: FileNotFoundError: [Errno 2] No such file or directory: 'E:\G-test32\eclipse\IgG\process3\pGlycoDB-GP-FDR-Pro.txt'
Process ID=59976: [60856] Failed to execute script 'XIC' due to unhandled exception!
Process ID=59976: [XIC] Smoothing window = 21
Process ID=59976: [XIC] Smoothing method = savgol_filter
Process ID=59976: [XIC] Loading pGlyco results ...
Process ID=60656: Already registered!
Process ID=60656: Unhandled Exception: System.Collections.Generic.KeyNotFoundException: The given key was not present in the dictionary.
Process ID=60656:    at System.ThrowHelper.ThrowKeyNotFoundException()
Process ID=60656:    at System.Collections.Generic.Dictionary2.get_Item(TKey key) Process ID=60656:    at GPSMReader.pGlycoReader.GetEachGlycan(List1 items)
Process ID=60656:    at pGlycoSite.pGlycoSite.FindEachMaxGlyco()
Process ID=60656:    at pGlycoSite.pGlycoSite..ctor(String cfg)
Process ID=60656:    at pGlycoSite.Program.Main(String[] args)
Process ID=59976: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoSite.exe "E:\G-test32\eclipse\IgG\process3\pGlyco.cfg"
Process ID=44820: E:\G-test32\eclipse\IgG\process2\pGlycoDB-GP-Raw1-FDR.txt
Process ID=44820: [pGlycoFDR] 785 GPSMs at 100.0% FDR
Process ID=44820: E:\G-test32\eclipse\IgG\process2\pGlycoDB-GP-Raw1-FDR-noFiltered.txt
Process ID=44820: [pGlycoFDR] 785 GPSMs at 100.0% FDR
Process ID=44820: merge into E:\G-test32\eclipse\IgG\process2\pGlycoDB-GP-FDR.txt
Process ID=44820: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoProInfer.exe -p "E:\G-test32\eclipse\IgG\process2\pGlyco.cfg"
Process ID=44820: 'pGlycoProInfer.exe' is not recognized as an internal or external command,
Process ID=44820: operable program or batch file.
Process ID=44820: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>XIC.exe -p "E:\G-test32\eclipse\IgG\process2\pGlyco.cfg"
Process ID=59976: Already registered!
Process ID=59976: Unhandled Exception: System.Collections.Generic.KeyNotFoundException: The given key was not present in the dictionary.
Process ID=59976:    at System.ThrowHelper.ThrowKeyNotFoundException()
Process ID=59976:    at System.Collections.Generic.Dictionary2.get_Item(TKey key) Process ID=59976:    at GPSMReader.pGlycoReader.GetEachGlycan(List1 items)
Process ID=59976:    at pGlycoSite.pGlycoSite.FindEachMaxGlyco()
Process ID=59976:    at pGlycoSite.pGlycoSite..ctor(String cfg)
Process ID=59976:    at pGlycoSite.Program.Main(String[] args)
Process ID=44820: Traceback (most recent call last):
Process ID=44820:   File "XIC.py", line 471, in
Process ID=44820:   File "XIC.py", line 195, in PeakArea
Process ID=44820:   File "pGlycoReader.py", line 97, in ReadAllGPSMs
Process ID=44820: FileNotFoundError: [Errno 2] No such file or directory: 'E:\G-test32\eclipse\IgG\process2\pGlycoDB-GP-FDR-Pro.txt'
Process ID=44820: [52412] Failed to execute script 'XIC' due to unhandled exception!
Process ID=44820: [XIC] Smoothing window = 21
Process ID=44820: [XIC] Smoothing method = savgol_filter
Process ID=44820: [XIC] Loading pGlyco results ...
Process ID=44820: E:\G-test32\eclipse\pGlyco3.1_build20231220\pGlyco3.1_build20231220\bin>pGlycoSite.exe "E:\G-test32\eclipse\IgG\process2\pGlyco.cfg"
Process ID=44820: Already registered!
Process ID=44820: Unhandled Exception: System.Collections.Generic.KeyNotFoundException: The given key was not present in the dictionary.
Process ID=44820:    at System.ThrowHelper.ThrowKeyNotFoundException()
Process ID=44820:    at System.Collections.Generic.Dictionary2.get_Item(TKey key) Process ID=44820:    at GPSMReader.pGlycoReader.GetEachGlycan(List1 items)
Process ID=44820:    at pGlycoSite.pGlycoSite.FindEachMaxGlyco()
Process ID=44820:    at pGlycoSite.pGlycoSite..ctor(String cfg)
Process ID=44820:    at pGlycoSite.Program.Main(String[] args)
[pGlyco]  File E:\G-test32\eclipse\IgG\process1\pGlycoDB-GP-FDR-Pro.txt does not exist!
[pGlyco]  File E:\G-test32\eclipse\IgG\process2\pGlycoDB-GP-FDR-Pro.txt does not exist!
[pGlyco]  File E:\G-test32\eclipse\IgG\process3\pGlycoDB-GP-FDR-Pro.txt does not exist!
[pGlyco] Task completed.

同样报错pGlycoDB-GP-FDR.txt does not exist! 请问您解决了吗？

同样报错pGlycoDB-GP-FDR.txt does not exist! 请问您解决了吗？

一样原因的报错！！！！
pGlycosite.exe运行到80%时突然停止，
Unhandled Exception: System.Collections.Generic.KeyNotFoundException
导致最后无法输出pGlycoDB-GP-FDR-Pro-Quant-Site文件
请问解决了吗，谢谢！

@jalew188 麻烦曾老师帮忙看一下pGlycosite的bug吧 谢谢！


Unicode character, hyperlink, image embed support

This library has very less overhead for PDF generation.
Are you planning  to support unicode character, hyperlink, image embed feature in near future?

Hi,
This is a PDF viewer AngularJS directive based on PDF.js. It's not a PDF generation lib.
As far as I can tell, all the features you mention are supported (except from hyperlinks inside the document itself, which should be handled by the application using the directive).
Check TCPDF examples using the demo application. Download the PDF from TCPDF's page and select it in the demo using the Choose File button at the top toolbar.


CLN: Fix compile time warnings

[x] passes git diff upstream/master | flake8 --diff

This commit suppresses these warnings
warning: comparison of constant -1 with expression
of type 'PANDAS_DATETIMEUNIT' is always true
[-Wtautological-constant-out-of-range-compare]

can u run all tests on Windows and report (if u can) otherwise I will

Sorry I can not setup Windows environments soonly 😢

[Current coverage][cc-pull] is 84.31%

Merging [#13607][cc-pull] into [master][cc-base-branch] will increase coverage by <.01%

@@             master     #13607   diff @@
==========================================
  Files           138        138
  Lines         51157      51157
  Methods           0          0
  Messages          0          0
  Branches          0          0
==========================================
+ Hits          43131      43132     +1
+ Misses         8026       8025     -1
  Partials          0          0

Powered by Codecov. Last updated by [5701c69...6df8c9b][cc-compare]
[cc-base-branch]: https://codecov.io/gh/pydata/pandas/branch/master?src=pr
[cc-compare]: https://codecov.io/gh/pydata/pandas/compare/5701c69369264f3aa6f571384602ceec1133dabc...6df8c9b4c53ca0c2ed2c85f77372409f0fd95d35?src=pr
[cc-pull]: https://codecov.io/gh/pydata/pandas/pull/13607?src=pr

ok @yui-knk this lgtm. and tests out on windows. (the warning only seems to appear on linux/osx), but that's ok!
pls add a whatsnew entry in bug fix for 0.19.0, reference this PR. ping when green.

@jreback I added a whatsnew entry :)

thanks @yui-knk

No problem 😄


Bird Nests

I'm curious to know how you look at the birds at all.
Should they be similar to bees? Have own nests and fly around them, or be ambient creatures like now?

I plan on adding nests for birds, as well as behaviours for them building nests, laying eggs, and incubating them. These nests will also naturally generate on trees. I'm not sure how long it will be until I implement this, but I will probably begin development on it shortly.
Currently, the songbirds spawn randomly and act as mostly ambient creatures. The pigeon has some unique interactions, as well as the penguin, although they are a bit unrefined as of now.

So promising! I definitely will follow the development! Keep going!


adding scRNAseq galaxy howto

Adding in the scRNAseq workflows too. Sorry, probably a manual merge with the shotgun metagenomics workflow, happy to add a new PR later if that's easier.

Thanks @swbioinf
Made a suggestion above


OSX: Add app packing tooling - tweaks and polish

Continuation of work started in https://github.com/jwilm/alacritty/pull/301 by @cema-sp which seems to be stalled at the moment. I've just followed all the suggestions in that PR until the code worked for me.
Instructions for building an app bundle:

cargo build --release
make app
cp -r target/release/os/Alacritty.app /Applications/Alacritty.app

For me, this allows me to run Alacritty from the Dock.

Thanks for trying to move this along! The only reason I haven't landed this yet is because the instance of Alacritty opened from this launcher is broken for me. The shell launches with PWD=/, and programs like vim are horribly broken (probably PATH and vimrc/config related).
Any thoughts on that?

@brycefisher Not sure if something's broken on my end but after following the instructions I still get the LSOpenURLsWithRole() failed with error -10810 for the file /Applications/Alacritty.app. error
@jwilm if I open this with ./target/release/osx/Alacritty.app/Contents/MacOS/launcher my pwd is ~, happy to help fix the bug if I can reproduce it first!

If you install the launcher to your /Applications folder and run it from the launcher, you should see the problem.

er, install Alacritty.app to the /Applications folder

When I start alacritty with this mac launcher, I see no unicode special characters inside a tmux session (but all works fine without the tmux session). This does not happen when I run the binary via shell.

Any ideas what could cause that? Here's my current config

I was able to launch it @brycefisher !
And @jwilm I just opened directly through /Applications/Alacritty.app and... PWD is home. Maybe this actually helped fix that problem: https://github.com/jwilm/alacritty/pull/462/commits/018beee8b65e2c69f0145d33dc7dc50db5aac4cf
Are you still getting that behavior in this branch?

Ah that does seem to be fixed on this branch. The other problem I'm seeing is that the LANG and LC_CTYPE environment variables aren't being set appropriately from Alacritty.app.
After running
export LANG=en_US.UTF-8
export LC_CTYPE=en_US.UTF-8

Everything works as expected.

@jwilm I can confirm that the language settings were also the root of the problem I described above. 👍

It looks like iTerm gets around this by actually using the OS APIs to read the system locale.

Glad the lang issue resolved themselves before I was even aware of what they were!
@jwilm do I need
export LANG=en_US.UTF-8
export LC_CTYPE=en_US.UTF-8

to launcher.sh?

@brycefisher unfortunately no. We need to actually query NSLocale.

@jwilm should that work happen inside this PR?

You can also get it with AppleScript, something along osascript -e "return user locale of (get system info)".

I've incorporated @casimir's feedback into this PR, but I'm not sure of all the edge cases that need to be covered here (ex: if AppleScript doesn't return a locale under some conditions, or what versions of OSX support that AppleScript snippet, or if I should not be hardcoding UTF-8).

@jwilm any other issues I should address in this PR?

@brycefisher I don't think so, thanks for driving this home! (I'll merge later)
It would be really nice if we had a config Action for running arbitrary commands. Then on macOS we could add a Cmd+N binding for launching more Alacritty instances. Otherwise, the launcher is only good for one instance.
Fancy tackling that in another PR? :D

🎉 !
@jwilm I'd like to help routing shortcuts to the OS like Cmd+Q for closing, but honestly have no idea on where to start. With a bit of direction I can get it started.

@jwilm hooray! So excited to have this this excellent work from @cema-sp land in master.
I'd love to see that work for MacOS shortcuts happen, but I'd happily leave it to @mondras since I too have no idea where to start.

Thanks again for pushing this forward and fixing the outstanding issues. Happy to include this finally :grin:

This is fantastic! Thanks for the great work guys!


ci: set up team as codeowner

Description
Use the QCM team as code-owner instead of single members. Allows our Bot to automatically confirm pull requests.

:tada: This PR is included in version 3.0.8 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


[FLINK-6532] [checkpoints] Ensure proper classloading for user-defined checkpoint hooks

This also adds a test that validates that the correct class loader is passed.
Note the neat trick via CommonTestUtils.createObjectForClassNotInClassPath(classLoader) to conjure up an object that is not in the test's class path.

The title should refer to FLINK-6531


.db-zabbix/log/log.go:299 Error()] [E] Error while executing script: sql: Scan error on column index 0: unsupported Scan, storing driver.Value type  into type *string

Hi
I don't really know why but at the first load I get this error.

More information, the issue seems to occur on history_uint for now.
I've tried the sql query on a psql and it's working fine.
Do you have any ideas ?

Hi,
it is strange because the table history_uint has not any nullable column.
Could you please double check the table definition ?

Hi
That's correct the history_uint table have not null on all fields.
By the way, my setup is using history and trend partionning using partition inheritance but it shouldn't have any effect (it worked for trend).
Any chance to put more debug option ?

Hi,
Do you have any idea why it's failing ?
I tried to find a reason, but the data structure seems good to me....
By googling the error message I got, I can find some related issues but referencing the mysql or sqllite driver.
By the way I encounter this issue with history_uint and trend_uint not the others.
But executing the history_uint manually give me some results

Ok I made some progress on my issue.
The issue is not related to the table structure at all.
In fact from what I see if I put a limit to 10000 records data is correctly transfered in influxdb.
Digging around the data itself made me focus on the item name formatting in the query.
First issue I see is when using $3 parameter in the item name, it's not being replaced
example :
TCP count SRC 636 $3 --> net.tcp.count[636,,ESTABLISHED]

Another issue but I don't know if it can have an impact is all the "various" characters such as :

/
"
(
)
special characters such as accents : é à ....

I don't know yet where to find the $3 value in the db but I'm afraid the query will be bigger and bigger and cpu consuming on the db.
What do you think ?

Ok for the table definition.
As shown in the log, the program stops here:
if err := ****(&result); err != nil {
return err
}
The issue comes from the rows.Scan operation.
You can add a counter inside the loop to identify the row that seems to be NULL...
I will check how to replace the $3 value.

Hi,
Ok I've found the issue, in the output I get some blank lines which make the fetch failing.
I think by security it would be best to skip those lines.
I have fixed the issue by modifying the Scan if statement like the following (quick and dirty I know...)
for rows.Next() {
  var result string
  if err := rows.Scan(&result); err != nil {
      counter += 1
      // blank line skipping
    } else {
      resultTmp = append(resultTmp, result)
    }
}

and for the sql query with missing $3 arguments I've done the following :
WHEN (position('$3' in ite.name) > 0)
       THEN replace(ite.name, '$3', split_part(substring(ite.key_ FROM '\[(.+)\]'), ',', 3))
   WHEN (position('$1' in ite.name) > 0) AND (position('$3' in ite.name) > 0)
     THEN replace(replace(ite.name, '$1', split_part(substring(ite.key_ FROM '\[(.+)\]'), ',', 1)), '$3', split_part(substring(ite.key_ FROM '\[(.+)\]'), ',', 3))

If you are ok I can push a pull request for that (even if I don't like the if statement

And the real issue is that your query is based on the fact that all items belong to an application.
Which is not mandatory in zabbix

I will bring the modification this week.

solved


are there anyway to retieve chatper pages?

i read the docs.
and i guess there is no way to retieve a chapter's pages urls.
is there anyway i can do it?

You maybe did not read the documentation carefully.
Here’s the page about MD@H, it has examples on how to retrieve download links and what you should do after downloading them.
You can also take a look at the downloader.py file:
https://github.com/Proxymiity/MangaDex.py/blob/7f3e95248500b733409b44544c17eab9de49c3d4/MangaDexPy/downloader.py#L23-L46


Question: Change stroke color of existing HanziWriter

Is there any way to change the color of a HanziWriter that already exists in the DOM without messing with its internal variables?
Looks like I could make it work by hacking on hw._canvas.svg / hw._renderState.state.character.main.strokeColor, but that doesn't seem like a great idea 😈
Alternatively, looks like I might be able to use CSS to colour the paths instead of relying on a JS way..
svg g g:nth-child(2) path {
  stroke: hotpink;
}

Not sure if there's a better way :)

There's currently not a method to do this, but it should be relatively easy to add. Just need to add a mutation in characterActions.js which changes some of the color variables and then add a method to HanziWriter.js to initiate it. I'll see if I can get a PR together implementing this.

After taking a look at the options and given my use case I'm thinking that colouring the characters with CSS would actually be for the best - assuming it works in enough browsers (probably 'sorry IE users' kinda moment).
Basically, I'm trying to have characters coloured according to tone, with users able to select their choice of tone colours from a set list of common colouring schemes/define their own and have them updated without a page refresh as part of a Vue-based 'single-page' app deely - similar to the Hanping dictionary.
Turns out using CSS I can just swap out class names on the <body /> or some other wrapper, ie tone-coloring-<scheme> and it'll take care of things across the board - plain text & the SVGs from HanziWriter...
For anyone else who finds this, I think I've settled on something like the following using, the tone colors mentioned by Albert Wolfe.
.tone-colors.tone-colors-dummit.color-char .char.t1 svg g g:nth-child(2) path {
  stroke: #f41d2f;
}

Using CSS like you described should work. I also went ahead and adding a PR to do this via a method on the HanziWriter instance in #88, since this seems like a reasonable feature to expect should exist. It turned out to be slightly trickier than I thought originally since tweening colors requires parsing color strings and turning them into corresponding color values, but it wasn't too bad. I'll get this merged soon.

writer.updateColor(colorName, colorVal) is now live in v1.1.0


Extremely High Risk of Password Leakage on Private Repositories

At the moment, password management for private repositories is far too primitive, and causes the username and password to be exposed in far too many places. Every place the private repository URL is used, the username and password must also be included. This means the following places require a copy of the username and password:
On a client:

requirements.yaml
requirements.lock
helm repo list command shows username/password
~/.helm/repository/repositories.yaml

On a server:

htaccess file
index.yaml

Failure to place the username/password in the repository URL in any of these places will cause a failure.
Having the username/password duplicated in this many places, and especially if you're keeping the requirements files in a git repository, creates an extremely high risk of accidental password leakage. The only places where the username/password should be required are in ~/.helm/repository/repositories.yaml and htaccess

I agree the security situation needs improvement but since it is functioning "as designed" right now I labeled this issue as Feature.

@jascott1 Makes sense to me.

/remove-lifecycle stale

Helm has provided support for repository shorthand in requirements.yaml, which helps with this problem, but doesn't fully solve it.
EG, if you have a repository with the name "stable" you can use "@stable" in your requirements.yaml, rather than the full URL as previously required.
However, the other problem areas remain:
On a client:

helm repo list command shows username/password

On a server:

index.yaml requires username/password

helm repo list command shows username/password

See #3206 for that

I think we can close this entire issue out with #3206 actually.

@bacongobbler Just a couple of things of note

This should probably be linked to #3206 and be closed when that PR is merged rather than just closed immediately.
It's not clear if #3206 will fix the index.yaml problem.

I believe that was fixed when relative path support was introduced in https://github.com/kubernetes/helm/pull/3065 in v2.7.1. Can you describe how you're generating your index.yaml files?

closed via #3206