Style attribute out of sync when changing between a css shorthand and specific property like border to border-left

I'm submitting a bug report

Library Version:
1.6.0

Please tell us about your environment:

Operating System:
OSX 10.13.4

Node Version:
8.9.1

NPM Version:
4.6.1

JSPM OR Webpack AND Version
JSPM 0.16.53

Browser:
Chrome 66.0.3359.139 | FF 59.0.2 | all?

Language:
all

Current behavior:
When toggling between a css shorthand property and a specific property like border and border-left in a css/style attribute, the styles get out of sync / don't get applied.
Example gistrun:
https://gist.run/?id=b6dac1c04a230db45afc8825f499edf5
Problem code:
https://github.com/aurelia/binding/blob/master/src/element-observation.js#L124
style.removeProperty('border') will also remove related properties like 'border-left'
also, style.removeProperty('border-width') will also remove 'border-left-width', etc.
Simplest Example:

    Click: border will be removed completely, instead of leaving a left border

Expected/desired behavior:
Actual element styles should always stay in sync with aurelia css/style bindings (while maintaining compatability with other frameworks that mutate styles)

What is the motivation / use case for changing the behavior?

When this happens, it is incredibly mysterious at first, and hard to track down :D

Good find :)! 👍

could we refactor the method to calculate "would be removed properties" and remove them before applying the new ones?

Sadly, it won't be that easy, probably going to have to resort to parsing/setting the style attribute text, as .style.setProperty also tries to be "smart".
ex: this simple binding will cause havoc with style.setProperty:

div = document.createElement('div')
// div =>

div.style.setProperty('border', '4px solid black');
// div =>

div.style.setProperty('border-left', '2px solid black');
// will coerce every other property of border (I think to make style order independent)
// div =>

Most likely have to resort to manipulating with steAttribute('style') getAttribute('style'), because it wont try to outsmart you:
div = document.createElement('div')
// div =>

function addStyle(styleAttrText, style) {
    // parse style text, and add/replace as necessary
    return styleAttrText ? styleAttrText + (!styleAttrText.endsWith(';') ? '; ' : '') + style : style;
}
function removeStyle(styleAttrText, style) {
    // parse style text, and remove as necessary
    return styleAttrText.replace(style, '')
}

div.setAttribute('style', addStyle(div.getAttribute('style'), 'border: 4px solid black;'));
// div =>

div.setAttribute('style', addStyle(div.getAttribute('style'), 'border-left: 2px solid black;'));
// div =>

In my use case, I have resizable dock panels and I need to know the border sizes to ensure docking/pinning behavior accounts for them (border gets thicker when pinning), so setting it all in my js component, instead of having as much coupling with the css seemed good.
Once I figured out the issue, the workaround was easy ... so maybe some documentation warning about mixing shorthand and specific css properties would e sufficient :D

@brantwedel  if you don't use border radius, you might want to use outline or box-shadow.. for visual effects.. they don't affect the layout.. and positioning. so you could rely on constant border-width.
have a look:
https://codepen.io/Alexander-Taran/pen/zjdRgo

Thanmks for the suggestions, shadow as border is is what I had earlier but it would cover the other dock panels docked against since they are outside the box-model which encroaches into the panel to the side, I have tried all the things and am aware of the csss.
I was going to try shadow + margin ... but the docks use flexbox and I didnt want to figure out the right set of proprties to not collapse margins in all browsers ... I'm sure it's possible, but the style tag/border works very well :D
@Alexander-Taran I'll send you a link to my dock-panel git repo if I make it public and you review more 🤣
In any case, with knowlede of this issue, it's quite easy to avoid ... but seemed magically broken initially :D

@brantwedel let's close this (-:


NUH multiple external interfaces on different bridges kvm

Hi,
today Metro only can add a external interface to a single bridge because of the nuh kvm template
It can be easily changed in src/roles/nuh-predeploy/templates/nuh.xml.j2 if the following is changed:
From this:
{% if external_interfaces is defined and external_interfaces|length > 0 %}     <interface type='bridge'>       <source bridge='{{ external_interfaces[0].external_bridge }}'/>       <target dev='vnet2'/>       <model type='virtio'/>       <alias name='net2'/>       <address type='pci' domain='0x0000' bus='0x00' slot='0x07' function='0x0'/>     </interface> {% endif %}
to this:
{% for bridge in external_interfaces %}     <interface type='bridge'>       <source bridge='{{ bridge.external_bridge }}'/>       <model type='virtio'/>     </interface> {% endfor %}

JIRA ticket filed...

This is fixed in dev branch and will be released in MetroAE v4.4.0


Windows Installation

I've been trying to install this on Windows, which I know is not officially supported, but was hoping if I could receive some guidance or advice. I'm somewhat of a beginner but I'd love to help any way I can.
I notice there is currently a branch for Windows development that solved some of the initial issues I was having (namely, not being able to force C++ compilation due to .c extension, etc). I cloned that branch as is and am trying to work from there. I'm currently stuck here:
LINK : fatal error LNK1181: cannot open input file 'realsense.lib'
error: command '"C:\Users\XXXX\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\link.exe"' failed with exit status 1181
librealsense is installed and I verified it is working by going to the bin folder and running the .exe examples.
I've moved the complete librealsense folder (as downloaded and extracted from zip) to C:\RealSense and changed the setup.py file to point to "C:\RealSense\include\librealsense" which contains the .h files.
| Camera Model | R200 |
| Operating System & Version | Windows 10 |
| pyrealsense version |  1.4 |
Thank you very much!

The version of setup.py in the windows branch relies on a couple of environment variables to determine the location of the librealsense files, since they could be almost anywhere on a Windows system. All you should need to do is set a variable called PYRS_INCLUDES to the folder containing the librealsense headers, and another called PYRS_LIBS to the folder containing realsense.lib.
It sounds like you've bypassed the setting of PYRS_INCLUDES by editing setup.py directly, but you will still need to tell it where to find realsense.lib for the compilation to succeed.

Thank you very much and please do pardon the newbie struggle!
Instead of modifying the setup file, I simply added the PYRS_INCLUDES and PYRS_LIBS environment variables, which allowed the setup to complete successfully.
When attempting to run the OpenCV example, I received the error "Unable to invoke 'cpp'.  Make sure its path was passed". This implies that pycparser cannot find cpp.exe.
My first thought was to add this to my PATH, but I believe vcvarsall.bat can be run to set up the various environment variables automatically. This still did not help. I looked into the issue and it seems the Visual Studio C++ compiler command line executable is named cl.exe. I naively created a copy named cpp.exe and am now getting this error:
"cl : Command line warning D9024 : unrecognized source file type 'C:\RealSense\include\librealsense\rs.h', object file assumed"
I also tried compiling with MinGW, with an error related to this line: "rsutilwrapper = ctypes.CDLL(_find_extension_name())" and for some reason not being able to locate rsutilwrapper.pyd.

From a quick look at the pycparser FAQ, I'm not sure VC++ is the best choice as they recommend using other compilers on Windows. It might work but definitely not by simply renaming cl.exe. The parameters it expects will be totally different and you'd probably have to modify the way pyrealsense calls pycparser to fix that issue.
I would suggest that you go back to compiling pyrealsense with VC++ since that was working for you, and then just add the MinGW/bin directory to your PATH. It should contain a valid copy of cpp.exe and so allow things to work as they're supposed to do. This is the setup I have myself and it seems to work fine for me on a Win10 machine.

Finally got it working, thanks for your help!

Some details:
I placed MinGW's bin folder in the PATH and successfully reinstalled the pyrealsense library. That being said, I continued to receive the error when attempting to import the pyrealsense library (or running the OpenCV example).
The error message states the module could not be located, pointing to this line:
rsutilwrapper = ctypes.CDLL(_find_extension_name()))
After some questioning (and cursing!), I ran Process Monitor (https://technet.microsoft.com/en-us/sysinternals/processmonitor.aspx) and realized that the error is caused by Python not being able to locate the previously-compiled realsense libraries. This is odd because the PATH is correctly set.
For now, I placed the compiled libraries in the C:\Python27 folder and all is well.

That does seem strange. If the .pyd file is in the same location as the rest of the pyrealsense source files and the folder containing realsense.dll is on the PATH then everything should just work. But good to hear it's working now anyway, thanks for testing it on Windows!

Camera Model = R200
Operating System = Windows 10
pyrealsense version =1.4
I hope you guys are doing well. when i install pyrealsense using pip install pyrealsense==1.4 having librealsense verison 1.12.1 it generates me following error;
pyrealsense/rsutilwrapper.c(1): fatal error C1083: Cannot open include file: 'rs.h': No such file or directory
but when i install using pip install pyrealsense then it generates following error;
LINK : fatal error LNK1181: cannot open input file 'realsense.lib'
i have set environment variables in users that are PYRS_INCLUDES AND PYRS_LIBS and given the path as shown in the pic below;

I will be very thankful if you guys could help me. Thanks is advance!

Hello,
I have no access to a windows machine right now so won't be able to check solutions.
It might be useful to make sure the terminal you execute the commands from has indeed both variables (PYRS_INCLUDES, PYRS_LIBS) set. You could check with echo %VAR%.
The problem you encounter is clearly a variable issue.

Thanks for replying. i checked the variables using echo and they both outputted the same path as given in environment variable. See the screenshot below;

I think you have a couple of different problems here:

If I remember correctly PYRS_LIBS should be set to the directory containing realsense.lib, not the full path to the file itself
Is there a reason you're trying to use v1.4? That version seems to be too old to have had the Windows workaround with the 2 environment variables in setup.py, that was in the 2.0 release. You can see the v1.4 version here for reference. If you really need to use that specific version you'll have to add the workaround back in yourself and deal with any other problems that crop up
If the installer script is picking up your env vars, you should see that in the compiler output. For example your second screenshot doesn't show a -IF:\FYP\Libraries\librealsense-1.12.1\include\librealsense parameter when calling cl.exe, it should be there if the env var is visible to the setup.py script. Similarly when it tries to link to the .lib file at the next step you should be seeing a /LIBPATH:F:\FYP\Libraries\librealsense-1.12.1\bin\Win32 parameter. In your screenshot they aren't there because of the v1.4 script not checking for the env vars, but if you try a newer release that should allow you to verify they're being detected correctly

Thanks for your response:

Ok now i have changed the path to F:\FYP\Libraries\librealsense-1.12.1\bin\Win32 .
No not really i was just giving it a try.
After changing the path it's now showing both variables path but with new errors. This time i tried pip install pyrealsense --user.

Maybe an x64/x86 mismatch? It looks like you're using 64-bit Python here but the PYRS_LIBS path ends in "bin/Win32" which usually implies 32-bit binaries, so that could be why it's not resolving symbols correctly. If you have a "bin/x64" folder there with a realsense.lib inside I'd try that path instead.

Thank you for the response! Ok i tried rebuilding the solution which created folder x64 in binary folder in which realsense.lib was created with some other .exe files and changed the path to x64 and then tried pip install pyrealsense --user but now it gives following error;

I don't think this is anything to do with pyrealsense at this point. It's successfully compiled and linked the module and is failing for some reason trying to run rc.exe which is the Visual Studio Resource Compiler tool.
From a quick Google you may have hit this bug which was fixed last year... but according to your screenshot you're using a version of pip that's about 3 years old, so you might have other outdated modules too!
If this is a Python 3.6 installation you've been using for a long time you might want to start over with a fresh install of 3.8 or 3.9 to make sure things are properly up to date. At the very least I would try upgrading your versions of pip and setuptools.

I uninstalled python 3.6 and installed the latest python 3.9 and updated pip too but it still shows me this ;

I missed the part that i am using visual studio 2015 update 5 as librealsense 1.12.1 was tested successfully on that. Before that , I tried to run librealsense 1.12.1 on visual studio 2019 but errors occured.
Sorry due to some circumstances i couldn't reply back early.

As I said, I don't think this is a pyrealsense problem. The error is appearing during the compilation + linking of the C++ extension module, and that whole process is handled in a standard way by distutils/Cython. It's clearly picking up your env vars correctly which is the only pyrealsense-specific step in the whole process.
I've just gone through the process of installing pyrealsense on a Win10 system:

Python 3.9.5 x64
VS 2019 (v16.11.3)
Windows SDK v10.0.19041.0
MSVC build tools v142
librealsense-1.12.1

With that configuration it compiled + installed without any trouble. My guess is that there's something wrong with your Visual Studio setup. Have you tried installing any other Python modules that require compilation like this?
If you google that link.exe error code you can see a bunch of people reporting problems with Python modules and VS 2015 (aka 14.0) which is what you're using. If you look into the suggested solutions involving rc.exe and rcdll.dll I think that would be your best bet for fixing this.

Ok so the good news is that pyrealsense-2.2 successfully installed with the help of this solution but the bad news is that when i import pyrealsense it generates following error;

As I said, I don't think this is a pyrealsense problem. The error is appearing during the compilation + linking of the C++ extension module, and that whole process is handled in a standard way by distutils/Cython. It's clearly picking up your env vars correctly which is the only pyrealsense-specific step in the whole process.
I've just gone through the process of installing pyrealsense on a Win10 system:

Python 3.9.5 x64
VS 2019 (v16.11.3)
Windows SDK v10.0.19041.0
MSVC build tools v142
librealsense-1.12.1

With that configuration it compiled + installed without any trouble. My guess is that there's something wrong with your Visual Studio setup. Have you tried installing any other Python modules that require compilation like this?
If you google that link.exe error code you can see a bunch of people reporting problems with Python modules and VS 2015 (aka 14.0) which is what you're using. If you look into the suggested solutions involving rc.exe and rcdll.dll I think that would be your best bet for fixing this.

yep i copy/paste both files into visual studio folder which solved the issue but now the problem is that i cannot import it as shown in the fig above . Thanks for the early reply

It's giving you an extremely clear error message that should have helped you search for solutions. There's even an earlier post in this same issue where that exact problem is mentioned.
Unable to invoke 'cpp' ==> it tried to run a cpp executable and it can't find one.
The exception is obviously coming from the pycparser module which has a README that explains you will need a compatible binary available under Windows.

I will look into it . Thank you for helping me!


Dedicated Server Crashing when using TweakerJs

Describe the bug
When I run my mod on a dedicated server It throws multiple errors.
To Reproduce
I have a script that uses libcd.util.TweakerUtils and lbcd.recipe.RecipeTweaker
I am using the following functions:
getItem() from TweakerUtils
removeRecipesFor() from RecipeTweaker
Expected behavior Optional
I expect it to run the TweakerJS script without error
Screenshots Optional
snippet of crash report
Code Example being run
Version of the (please complete the following information):

Corail Woodcutter Companion Addon
LibCD 2.3.0+1.15.2
Fabric API 0.4.32+build.292-1.15
Minecraft 1.15.2

It looks like the line causing this is if (itemFound.toString().indexOf('air') >= 0). I have no idea why it's causing that, since the error being thrown is that it can't find the TooltipContext class and Item#toString doesn't use TooltipContext, but that seems like the issue. The best thing I could do is add in a way to check if an item ID exists.

It is interesting that it does not throw this error when loading from the client. It only occurs on a dedicated server.
I'll try to write it another way on my end and see if I can also correct it.

That's due to the TooltipContext class being a client-only thing used for building tooltips. It doesn't exist on the server, so it can't be called. I need to figure out why it's looking for TooltipContext on server-side.

ok. I found a workaround for now.


Handle Unknown Permissions as Informational Logs, Not Errors

When calling the get_details_permissions function for unknown permissions, the current behavior logs these cases as errors. However, these are not actual errors but simply permissions that are not recognized by Androguard. Logging them as errors may mislead users and clutter the logs with non-critical information.
I propose changing these log entries from ERROR to INFO to reflect the non-critical nature of these unknown permissions.
System Information

Androguard Version: master
Python Version: 3.12.5
Operating System: macOS 14.6.1

Further Log Files and Output
2024-09-19 21:23:24.468 | ERROR    | androguard.core.apk:get_details_permissions:1346 - Unknown permission com.google.android.gms.permission.AD_ID
2024-09-19 21:23:24.468 | ERROR    | androguard.core.apk:get_details_permissions:1346 - Unknown permission android.permission.DOWNLOAD_WITHOUT_NOTIFICATION
2024-09-19 21:23:24.468 | ERROR    | androguard.core.apk:get_details_permissions:1346 - Unknown permission android.permission.ACCESS_ADSERVICES_ATTRIBUTION
2024-09-19 21:23:24.468 | ERROR    | androguard.core.apk:get_details_permissions:1346 - Unknown permission android.permission.ACCESS_ADSERVICES_AD_ID
2024-09-19 21:23:24.468 | ERROR    | androguard.core.apk:get_details_permissions:1346 - Unknown permission com.google.android.c2dm.permission.RECEIVE
2024-09-19 21:23:24.468 | ERROR    | androguard.core.apk:get_details_permissions:1346 - Unknown permission android.permission.ACCESS_ADSERVICES_TOPICS
2024-09-19 21:23:24.468 | ERROR    | androguard.core.apk:get_details_permissions:1346 - Unknown permission com.samsung.android.providers.context.permission.WRITE_USE_APP_FEATURE_SURVEY
2024-09-19 21:23:24.468 | ERROR    | androguard.core.apk:get_details_permissions:1346 - Unknown permission com.huawei.appmarket.service.commondata.permission.GET_COMMON_DATA
2024-09-19 21:23:24.468 | ERROR    | androguard.core.apk:get_details_permissions:1346 - Unknown permission com.google.android.finsky.permission.BIND_GET_INSTALL_REFERRER_SERVICE

very fair point, thanks @Ch0pin
https://github.com/androguard/androguard/pull/1078/commits/d7b6f6d6fcf9a5ebf1e2c88df46eac58fafa104f


AsyncStreamingClient.delete_rules raises tweepy.errors.BadRequest, when called with a list of StreamRule.

Greetings!
While developing a project I came across a strange error:
tweepy.errors.BadRequest: 400 Bad Request '_tuplegetter(2, 'Alias for field number 2')' is not a valid Long
Investigating with my debugger, I found out this happens because the StreamRule class is used instead of the current StreamRule Tuple Object.
This is the exact place in the code, which should be json["delete"]["ids"].append(str(id.id)) to function properly.
https://github.com/tweepy/tweepy/blob/598ea64d68ab3c27861e0f6dcf9bbce864dc3748/tweepy/asynchronous/streaming.py#L682
Should I open a PR for that, or do you want to do this?
Have a nice day everyone, and don't forget to drink enough! 🥤

Thanks for the bug report! This should be fixed now.


Add context usage docs to README

To help with https://github.com/webpack/webpack.js.org/issues/2289, adding a short description + example of using context.

Thanks


TASK - Organise knowledge transfer sessions

📌 Summary

Mateusz has been the main maintainer of BokehJS for a while; it would be good to have a series of sessions in the spirit of knowledge sharing and upskilling
🔖 Tasks to complete

[ ] Agree on date and time
[ ] Record sessions, identify updates needed to the docs (if any)

🙌🏽 Who: @pavithraes @gabalafou need to be in these sessions

Yes, there is one more session planned on 21st. This will be the 5th session.

We had a total of 7 knowledge shares, recordings for all but one are available in this Google drive folder. Thanks to @mattpap, for being so generous with his time and knowledge. :)
We covered a lot of development details in these sessions, and are comfortable calling this issue complete. We've decided to have ad-hoc meetings to discuss any specific questions as needed in the future.


Invalid Namespace id |Suggestion|

Perhaps we could add something saying that spaces aren't allowed

I'll add a function to check validity of namespace id. It'll show alerts and prevent send button to be activated if invalid.

Nice

also for the max number of character per namespace

Sure ;). Improved in 1.0.10

@fiazk please put in your address


Add the aoc-sre pool to the aoc-sre managedclusterset

Summary of Changes
This PR adds a previously-created pool to the appropriate clusterset

/lgtm


Fix PolygonGeometry per position height extrusion

@mramato
This will also fix the issue of short extruded polygons not extruding, which I'm surprised no one has run into yet.

Thanks!  This also fixes the case where perPositionHeight wouldn't let you extrude up, which I vaguely remember someone asking about on the mailing list.

@hpinkos found an issue with normals when extruding up, but will handle it in a separate issue (since it wasn't a supported feature before anyway).


Support for array dereferencing and class member access on instantiation

When I try to fix a file which contains an array dereferencing and/or a class member access on instantiation I get an empty result. PHP CS Fixer doesn't seem to work with these features.
Using the 1.3 version.

Could you provide a test case for it? Perhaps as PR?

ping @eduardocasas

ping @eduardocasas

Hmm, no feedback, should we close this?

Closing as not suitable


Carousel Cards' sequence getting changed for FB Messenger channel

Issue
We have a bot service running in production which serves multiple channels like directline, FB messenger etc.
We are using botbuilder's NodeJS SDK v3.14.0.
The issue is - The sequence of cards of a carousel is getting changed for FB messenger user. The sequence is retained correctly for directline channel users. This issue is breaking the user experience in production.

Can someone please share where's the issue? All is well with the sequence of cards in a carousel on Skype and Direct Line channels but it changing randomly in FB Not. We are forced to switch off the FB not in production because of this issue :-(
We debugged the code and found the cards sequence correct till they go out but FB Messenger is showing them in a very different and random sequence.
Looking forward for early help.

@bhushanvadgave
@sharmadine
I have just reproduced this issue extensively myself. The Facebook Messenger platform has its own card system called templates that can accessed directly using an activity's channel data. However, the issue persists whether I use a Facebook Messenger payload directly or whether I send a Bot Framework card and let the connector handle it.
It appears to be caused by a change on the Facebook side. There are bug reports that are not limited to the Bot Framework: https://developers.facebook.com/support/bugs/2310937235657679
I am closing this issue because there is nothing we can do from our end, but I hope Facebook fixes this soon.
(Duplicate of https://github.com/Microsoft/BotBuilder-V3/issues/121)

@v-kydela many thanks for your response and guidance. Much appreciated.

@v-kydela Thank you very much for the response! I'm using iOS Facebook Messenger


spatial search map fixes

[x] the map components take a while to load on first page load
[x] the 'expand' control needs a tooltip to say what it's for
[x] when expanding, the map should match the width of and align with the other page elements, which it doesn't do right now
[x] there should not be blank space when the map expands. It should centre on SA or wherever the user has zoomed and continue with map content to the edge of the canvas (like it does after you click the edit icon)
[x] after digitising a rectangle, the apply button overlaps the section below, please polish the placement
[x] the thick blue boundary style doesn't look great
[x] each layer should be mutually exclusive i.e. radio buttons rather than check boxes. Right now it's possible to draw all four layers which gets messy
[x] how does one do a proximity search? (RF04c)

@gubuntu currently my commnet on the first issue is that we are constrained by the deployment and can't modify directly ckan spatial extension, the code first wait for it to load then applies the necessary changes (adding search spatial boundaries, adding buffer for proximity - the last circular button), caching might help to speed load time though

replacing spatial files with lighter versions seeded up the page load, added "search with rectangle bound" as title for the edit button, and "search with circular buffer" for circle edit, added  radio buttons instead of checkbox.

@gubuntu " when expanding, the map should match the width of and align with the other page elements, which it doesn't do right now", this is the default behavior of ckanext-spatial, i've modified it so the map goes edge-to-edge with the content (following screenshot),  if this is not what you mean, please give more clarification.

" there should not be blank space when the map expands. It should centre on SA or wherever ..."  please see https://github.com/kartoza/ckanext-dalrrd-emc-dcpr/pull/383#issue-1465213615

"after digitising a rectangle, the apply button overlaps the section below, please polish the placement"

"the thick blue boundary style doesn't look great" - mock or inspiration please @seabilwe @Jeremy-Prior @ThiashaV
" each layer should be mutually exclusive i.e. radio buttons rather than check boxes. Right now it's possible to draw all four layers which gets messy"
applied with the previous request

"how does one do a proximity search? (RF04c)"
using the circular button which creates a circle buffer for the search

few issues that needs enhancement:

if the rectangle button clicked more than once it doesn't move out the zoomed search and disable the drawer, and even if cancel is clicked the rectangle drawer will still be enabled until the user draws a rectangle then click cancel, this is a default behavior of ckanext-spatial that i spent quite a time to modify without results, unlike previous work so far to enhance the behavior of the extension which is based on adding events after the map is loaded, accessing indefiniter of this exact behavior seems unlikely without adding to ckanext-spatial directly.

adding spatial boundaries while there is an existing rectangle or circle should be disabled, currently even if there is a rectangle or circle the user can still add boundaries.

@seabilwe @Jeremy-Prior @ThiashaV ,  i'm leaving closing this issue and tick off @gubuntu remarks for the result of your test, please examine and close (or tick off) accordingly.

the map components take a while to load on first page load:
The map loads almost simultaneously with the page's first load:

The speed with which the map loads may be affected by internet connection speed because this is with a slower connection:

the 'expand' control needs a tooltip to say what it's for:
Has this been removed? The map automatically expands when a user selects the rectangular search or searches by proximity.

when expanding, the map should match the width of and align with the other page elements, which it doesn't do right now:
The map now matches the width of and aligns with other page elements:

there should not be blank space when the map expands. It should centre on SA or wherever the user has zoomed and continue with map content to the edge of the canvas (like it does after you click the edit icon):
Fixed in PR #383:

after digitising a rectangle, the apply button overlaps the section below, please polish the placement:
Fixed on testing site:

the thick blue boundary style doesn't look great:
Working on mock up / inspiration.

each layer should be mutually exclusive i.e. radio buttons rather than check boxes. Right now it's possible to draw all four layers which gets messy:
Already implemented on the testing site.

how does one do a proximity search? (RF04c):
A user clicks on the circle button, then clicks and drags from a point on the map to make a circular buffer of a desired size.

@Mohab25 potential mock styling:

notice the tooltip over the rectangle (it shows when a user hovers over the rectangle)

the closet color for the previous mock i found appealing is #008000, now implemented, please give a mock if you feel would appear better

Tooltips present on testing site:

@Mohab25 The colour looks good, is it possible to make the border lines thinner? When the map isn't expanded and "Municipal Districts" or "Local Municipalities" are selected the thick lines are a bit overbearing:

Thinner lines implemented, looks great @Mohab25:


OSOE-430: Add support for single-instance NE on Linux

OSOE-430
Fixes #17

We'll open a new PR for this.


Phred score converter

how is it possible to use fastp only for converting phred64 to phred33 score, not any trim or quality control?

add -Q -A -G option to disable quality filtering/trimming, adapter trimming, and polyG trimming

thanks
it worked with a line of code like this:
fastp -A -Q -G --phred64 -i Lib1.fq -I Lib2.fq -o Lib1.fq -O Lib2.fq

Yes, correct.


how to remove rat?

hello
how users can remove the rat?
دانلود تلگرام ایکس

Is /self_destruct not working

Spam; closing


Gh pages additional releases

Additional Javadoc's for subsequent releases since 1.0

Hi @emmetsap, can you please adjust also the index.html, so that the additional versions are listed here: https://corona-warn-app.github.io/cwa-server/

Hi @emmetsap, can you please adjust also the index.html, so that the additional versions are listed here: https://corona-warn-app.github.io/cwa-server/


add a recommended or required plugin - github updater

Apparently this is a WordPress 4 feature, but there are also third party ways to get this functionality.

@idmontie can you find how to do this using WordPress Core? All I can find is methods using https://github.com/TGMPA/TGM-Plugin-Activation

I was just investigating this.

Hmm it looks like that might be it. Not in the core like I thought it was :(

With it not being in core, do you think their solution is worth implementing?

Maybe later? I think it would be useful to recommend Yoast, the HTML Editor, etc. But it still won't install Github Update for us since that is not on the WordPress plugin "store".

The github updater is the main one I would like push for as a required dependency. However we do use a few features from Yoast that would be a good recommendation. I agree we should probably wait until these features get better support.


Please add compatibility with Nextcloud V23

Please add compatibility with Nextcloud V23

Just in case it wasn't noticed - Nextcloud improved policy regarding changes in core to ease app developers in maintaining compatibility with newer Nextcloud versions:
https://help.nextcloud.com/t/new-process-for-documenting-core-code-changes-that-affect-app-developers/149828?u=p-bo


Changed Contributors Page #24

Added github icon to github profile links.
Removed Padding.

#24

@TejasNasre Pls add "hacktoberfest-accepted" label to this pr if you can.

I told you to change card design

@TejasNasre Thanks dude :)


Fix partial apply forwarder emission for coroutines that are methods of structs with type parameters

Simplify the code while here.
This refactors some implementation bits of https://github.com/swiftlang/swift/pull/71653 (and effectively reverts some parts of it). In particular, it implements the coroutine call in terms of CallEmission rather than relying on implementation details of CallEmission.

@swift-ci please test

@asavonic Will you please review?

preset=buildbot,tools=RA,stdlib=RD,test=non_executable
@swift-ci Please test with preset macOS

Thank you! Looks much better now.

@aschwaighofer @rjmccall Will you please take a look?

@rjmccall @eeckstein @aschwaighofer Friendly ping

Another ping. Thanks!

@DougGregor @tkremenek Is there anything that could be done to get this reviewed?

Sorry that got lost. LGTM

@aschwaighofer @drexin Thanks!

@swift-ci please smoke check

@swift-ci please smoke test

@swift-ci please smoke test windows platform


cyan build: -b, --build-dir and -s, --source-dir flags?

Would it be a good idea to add those flags -b, --build-dir and -s, --source-dir flags to cyan build to make it more of a drop-in replacement to tl build? I'm looking forward to removing tl build in the near future and directing users to cyan build instead.

It does make sense to have these options for ease of transitioning from tl build to cyan build and they'd be pretty easy to implement.


De-memoize function?

Hi Chris,
What do you think about adding a function to de-memoize memoized functions?  I'm thinking about using memoize with magit-todos to cache a magit function call, but I'd like to only do that when the minor mode is activated, and then de-memoize it when the mode is deactivated, so as not to permanently interfere with magit.

I suppose the original function could be stashed away in the symbol
plist (e.g. :memoize-original-function). Should be pretty simple.

Yeah, that's what I was thinking.

Sure. Since I don't actually use this library I wasn't intending on
doing anything myself anyway.

LOL, fair enough.


Fixing alignment for "AM" input

I'm not sure I even remember what we're solving here... we should probably rework the dependency graph as we discussed last week. Here's what this looks like after compilation (which was not committed):


RFC: omega as the default decreasing_tactic

Now that we have omega in std, it seems prudent to use it by default for termination checking.
The obvious step is to add
macro_rules | `(tactic| decreasing_trivial) => `(tactic| omega)

after defining omega, but there is more to it (and this is a meta-issue of sorts, keeping track of this):

There are existing tactics that are (hopefully) subsumed by omega:
src/Init/WFTactics.lean:macro_rules | `(tactic| decreasing_trivial) => `(tactic| (simp (config := { arith := true, failIfUnchanged := false })); done)
src/Init/WFTactics.lean:macro_rules | `(tactic| decreasing_trivial) => `(tactic| assumption)
src/Init/WFTactics.lean:macro_rules | `(tactic| decreasing_trivial) => `(tactic| apply Nat.sub_succ_lt_self; assumption) -- a - (i+1) < a - i if i < a
src/Init/WFTactics.lean:macro_rules | `(tactic| decreasing_trivial) => `(tactic| apply Nat.pred_lt'; assumption) -- i-1 < i if j < i
src/Init/WFTactics.lean:macro_rules | `(tactic| decreasing_trivial) => `(tactic| apply Nat.pred_lt; assumption)  -- i-1 < i if i ≠ 0
src/Init/Data/Array/Mem.lean:macro_rules | `(tactic| decreasing_trivial) => `(tactic| array_get_dec)
src/Init/Data/Array/Mem.lean:macro_rules | `(tactic| decreasing_trivial) => `(tactic| array_mem_dec)
src/Init/Data/List/BasicAux.lean:macro_rules | `(tactic| decreasing_trivial) => `(tactic| sizeOf_list_dec)
src/Init/Data/String/Extra.lean:macro_rules | `(tactic| decreasing_trivial) => `(tactic| apply String.Iterator.sizeOf_next_lt_of_hasNext; assumption)
src/Init/Data/String/Extra.lean:macro_rules | `(tactic| decreasing_trivial) => `(tactic| apply String.Iterator.sizeOf_next_lt_of_atEnd; assumption)

Some  of them (simp_arith, apply Nat.…) can hopefully go, making the tactic faster.
Note that ideally, this tactic doesn’t just succeed quickly, but also fails quickly.
Others (array_mem_dec) can maybe be subsumed by extending omega’s frontend.

If we remove them before an empty file imports std users will have a bad experience.
Maybe best to implement this change only when we made it so that an empty file imports a prelude from std that contains omega.

While we are at it, we should revise
macro "simp_wf" : tactic =>
  `(tactic| try simp (config := { unfoldPartialApp := true }) [invImage, InvImage, Prod.lex, sizeOfWFRel, measure, Nat.lt_wfRel, WellFoundedRelation.rel])

used in
macro "decreasing_with " ts:tacticSeq : tactic =>
 `(tactic|
   (simp_wf
    repeat (first | apply Prod.Lex.right | apply Prod.Lex.left)
    repeat (first | apply PSigma.Lex.right | apply PSigma.Lex.left)
    first
    | done
    | $ts
    | fail "failed to prove termination, possible solutions:
  - Use `have`-expressions to prove the remaining goals
  - Use `termination_by` to specify a different well-founded relation
  - Use `decreasing_by` to specify your own tactic for discharging this kind of goal"))

I was expecting simp_wf to really only deal with the listed WF-related technicalities, and otherwise leave the goal completely untouched (to avoid unwanted simplification like here). It should at least be made a simp only.
Or maybe start with something like conv => fun; fun => tactic (or equivalent; we don't have conv => fun yet (https://github.com/leanprover/lean4/issues/3239) and conv is available in WFTactics) so that really only the relation is inferred, but the argument is not touched.
Furthermore, it’s a bit wasteful to run the simplifier here and look deeply into terms, when we only really care about the head of the goal to be brought into the right form. Maybe the tactic can be rewritten to be more targeted without the simplifier.

While we are at it, investigate if the backtracking in
macro "decreasing_tactic" : tactic =>
`(tactic| decreasing_with first | decreasing_trivial | subst_vars; decreasing_trivial)

is beneficial or hurtful. Presumably omega doesn’t need vars to be substituted beforehand – but maybe other tactics do?

Impact
Add :+1: to issues you consider important. If others benefit from the changes in this proposal being added, please ask them to add :+1: to it.

I was giving it a shot, but got stuck because I’d like to use conv => fun; fun => in simp_wf, but Init.Conv depends on Init.Meta and that depends on a lot of things that really use want to use Init.WfTactics.
Is there an easy way out?
I can make Init.Conv depends on Init.Core only, if it was not for this one issue:
macro (name := case) tk:"case " args:sepBy1(caseArg, " | ") arr:" => " s:convSeq : conv =>
  `(conv| tactic' => case%$tk $args|* =>%$arr conv' => ($s); all_goals rfl)

now says
application type mismatch
  args.elemsAndSeps
argument
  args
has type
  Syntax.TSepArray (Name.mkStr4 "Lean" "Parser" "Tactic" "caseArg" :: List.nil) " | " : Type
but is expected to have type
  Syntax.TSepArray (Name.mkStr4 "Lean" "Parser" "Tactic" "caseArg" :: List.nil) "|" : Type

so maybe some coercions are missing?
I can say
macro (name := case) tk:"case " args:sepBy1(caseArg, "|") arr:" => " s:convSeq : conv =>
  `(conv| tactic' => case%$tk $args|* =>%$arr conv' => ($s); all_goals rfl)

to fix this, but this is probably not desirable.

With https://github.com/leanprover/lean4/pull/3503 omega is used for termination. The other refinements described here may or may not happen, but probably not worth keeping this open.


Make the Android support a noop

Due to the OS design, always return an empty array on Android.

The existing implementation is correct and will provide thread stats when /proc is available and an exception when it isn't.


Build failed when $ sudo pyenv install 2.7.9

NAME
patching file ./Lib/site.py
Installing setuptools from https://bootstrap.pypa.io/ez_setup.py...
Installing pip from https://bootstrap.pypa.io/get-pip.py...
curl: (18) transfer closed with 857193 bytes remaining to read
error: failed to install pip via get-pip.py
BUILD FAILED (OS X 10.10.4 using python-build 20150326-498-g5402ce4)
Inspect or clean up the working tree at /tmp/python-build.20150730092617.29954
Results logged to /tmp/python-build.20150730092617.29954.log
Last 10 log lines:
Installing easy_install script to /Users/apple/.pyenv/versions/2.7.9/bin
Installing easy_install-2.7 script to /Users/apple/.pyenv/versions/2.7.9/bin
Installed /Users/apple/.pyenv/versions/2.7.9/lib/python2.7/site-packages/setuptools-18.0.1-py2.7.egg
Processing dependencies for setuptools==18.0.1
Finished processing dependencies for setuptools==18.0.1
File "/tmp/python-build.20150730092617.29954/get-pip.py", line 7048
w#dyy3jdWw9j$g?d@OhQ^E->;%2kfp-gMnA68@}e3=_oGpkE@6Eok@6@n<S&zam#erIB(9cHnVY>Hb
^
SyntaxError: EOF while scanning triple-quoted string literal

---
Want to back this issue? **[Post a bounty on it!](https://www.bountysource.com/issues/25146516-build-failed-when-sudo-pyenv-install-2-7-9?utm_campaign=plugin&utm_content=tracker%2F282009&utm_medium=issues&utm_source=github)** We accept bounties via [Bountysource](https://www.bountysource.com/?utm_campaign=plugin&utm_content=tracker%2F282009&utm_medium=issues&utm_source=github).

Probably you had problem downloading file from https://bootstrap.pypa.io/get-pip.py at that time. I couldn't reproduce this.


Allow pixel-by-pixel filters

Should this be on vectorizer terms or label names? If it were on label names (e.g., [Al/H]) such that any cross terms with [Al/H] would also be zero. Which conceptual filter were you talking about @davidwhogg: label names or terms or both?

label names!

excited about this closure!

It was fun to put in! I can explain the implementation details next time we chat, but they are user-friendly.

I will try to call today. Also, my nucleosynthesis code works completely now!


the 'download count' is not incremented after packge install

After installing a package it's download count is not increment right away (need to click 'refresh')
might be misleading concerning if a package install was successful or not

@RichiCoder1 I'd just say we incremented the displayed value by 1 after the package install is successful - might not be totally correct on the community feed with a lot of concurrent installs - but it definitely would be an improvement

but I'm not sure how I feel about that
me neither - drop it / working as intended?

it just came up because we're using Chocolatey GUI in a small environment with just 100+ Packages (a change in download-count is noticeable if a lot of packages have only 30+ downloads 🤣 )

I'm going to say it's an interesting idea, but veto for now.  Puts things in an inconsistent state, and our package state management in GUI is already a bit weird :P

For what it is worth, I agree with this decision.  I prefer the concept of a single source of truth.  ChocolateyGUI is not the source of truth in this instance, so I think we should leave it as is.


Search result broken on some titles Grabber 4.0.5 (zerochan.net)

What steps will reproduce the problem?

Searching "Atelier escha & logy" Or "Atelier Escha and Logy"
clicking next page

What is the expected output? What do you see instead?
i expect to see 20 images per page but it only displayed 8 and when i go to the next page the pictures are the same with the first page also when i click get all and download the images it only generated 8 links and downloaded just that 8 links.
What version of the product are you using? On what operating system?
Grabber 4.0.5
Please provide any additional information below if necessary.
Other title such as "blood lad" don't have the same problem
The result shows page 1 of 11 (8 of 83) but only generates 8 picture
My search is set on zerochan.net
Image per page is set to 20 and number of columns is set to 1 (default configuration) tried changing it but problem persist
sources is set to RSS>XML>JSON>Regex

Original issue reported on code.google.com by<EMAIL_ADDRESS>on 15 Jan 2015 at 1:22

This is due to Zerochan returning an invalid RSS feed for this search, because of the & character in the tag. Unfortunately, there is little I can do about this.
As you can see here:
https://validator.w3.org/feed/check.cgi?url=http%3A%2F%2Fwww.zerochan.net%2FAtelier%2520Escha%2520%2526%2520Logy%3Fs%3Did%26xml%26p%3D1
This feed does not validate.
line 4, column 24: XML parsing error: <unknown>:4:24: not well-formed (invalid token)

<title>Atelier Escha & Logy - Zerochan Anime Image Board</title>
                     ^


feat(viewports): Add support for custom pixel densities

This diff adds support for changing deviceScaleFactor for individual viewports. To set this value for a viewport, add an @ with the desired scale to the viewport string. For example, to simulate a Retina display (2x), you can invoke html-sketchapp like so:
html-sketchapp --viewports.Retina 1024x768@2 --url example.com

This also accepts floating point values. If no @ is provided, then the scale factor defaults to 1.
Note: even without this diff, you can change deviceScaleFactor globally by passing a flag to the browser instance via puppeteer. The difference here is that this change allows different scales for individual viewports, which may be useful. That said, if you'd prefer to just rely on the browser flag for this behavior, I understand completely 😄 Let me know what you think, I'm happy to update the README if you do want to move forward with this change.

This looks great. Would you also be able to add a simple test for this to viewports.test.js?

Thanks! Done 😄

Just published as v0.3.0. Thanks so much for this addition, with such a simple API and perfect documentation too 👏👏


RDKit learns how to filter PAINS/BRENK/ZINC/NIH via FilterCatalog

FilterCatalogs give RDKit the ability to screen out or reject
undesirable molecules based on various criteria.  Supplied
with RDKIt are the following filter sets:

PAINS - Pan assay interference patterns.
These are separated into three sets PAINS_A, PAINS_B and PAINS_C.
Reference: Baell JB, Holloway GA. New Substructure Filters for
Removal of Pan Assay Interference Compounds (PAINS)
from Screening Libraries and for Their Exclusion in
Bioassays.
J Med Chem 53 (2010) 2719Ð40. doi:10.1021/jm901137j.

BRENK - filters unwanted functionality due to potential tox reasons
or unfavorable pharmacokinetics.
Reference: Brenk R et al. Lessons Learnt from Assembling Screening
Libraries for Drug Discovery for Neglected Diseases.
ChemMedChem 3 (2008) 435-444. doi:10.1002/cmdc.200700139.

NIH - annotated compounds with problematic functional groups
Reference: Doveston R, et al. A Unified Lead-oriented Synthesis of
over Fifty Molecular Scaffolds. Org Biomol Chem 13
(2014) 859Ð65.
doi:10.1039/C4OB02287D.
Reference: Jadhav A, et al. Quantitative Analyses of Aggregation,
Autofluorescence, and Reactivity Artifacts in a Screen
for Inhibitors of a Thiol Protease.
J Med Chem 53 (2009) 37Ð51. doi:10.1021/jm901070c.

ZINC - Filtering based on drug-likeness and unwanted functional
groups
Reference: http://blaster.docking.org/filtering/

The following is C++ and Python examples of how to filter molecules.
[C++]
#include <GraphMol/FilterCatalog.h>
using namespace RDKit;
SmilesMolSupplier suppl(…);

// setup the desired catalogs
FilterCatalogParams params;
params.addCatalog(FilterCatalogParams::PAINS_A);
params.addCatalog(FilterCatalogParams::PAINS_B);
params.addCatalog(FilterCatalogParams::PAINS_C);

// create the catalog
FilterCatalog catalog(params);

unique_ptr<ROMol> mol; // automatically cleans up after us
int count = 0;
while(!suppl.atEnd()){
  mol.reset(suppl.next());
  TEST_ASSERT(mol.get());

  // Does a PAINS filter hit?
  if (catalog.hasMatch(*mol)) {
    std::cerr << "Warning: molecule failed filter " << std::endl;
  }

  // More detailed data by retrieving the catalog entry
  const FilterCatalogEntry *entry = catalog.getFirstMatch(*mol);
  if (entry) {
    std::cerr << "Warning: molecule failed filter: reason " <<
      entry->getDescription() << std::endl;

    // get the matched substructure atoms for visualization
    std::vector<FilterMatch> matches;
    if (entry->getFilterMatches(*mol, matches)) {
      for(std::vector<FilterMatch>::const_iterator it = matches.begin();
          it != matches.end(); ++it) {
        // Get the SmartsMatcherBase that matched
        const FilterMatch & fm = (*it);
        boost::shared_ptr<SmartsMatcherBase> matchingFilter = \
          fm.filterMatch;

        // Get the matching atom indices
        const MatchVectType &vect = fm.atomPairs;
        for (MatchVectType::const_iterator it=vect.begin();
             it != vect.end(); ++it) {
             int atomIdx = it->second;
        }

      }
    }
  }
  count ++;
} // end while

Python API
import sys
from rdkit.Chem import FilterCatalog
params = FilterCatalog.FilterCatalogParams()
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_A)
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_B)
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_C)
catalog = FilterCatalog.FilterCatalog(params)
...
for mol in mols:
if catalog.HasMatch(mol):
print("Warning: molecule failed filter", file=sys.stderr)
# more detailed
entry = catalog.GetFirstMatch(mol)
if entry:
print("Warning: molecule failed filter: reason %s"%(
entry.GetDescription()), file=sys.stderr)
     # get to the atoms involved in the substructure
     #  there ma be many matching filters here...
     for filterMatch in entry.getFilterMatches(mol):
         filter = filterMatch.filterMatch
         # get a description of the matching filter
         print(filter)
         for queryAtomIdx, atomIdx in filterMatch.atomPairs:
             # do something with the substructure matches

Advanced
FilterCatalogs are fully serializable and can be stored for later use.
To serialize a catalog, use the catalog.Serialize() method.
std::string pickle = catalog.Serialize();
To unserialize, send the resulting string into the constructor
FilterCatalog catalog(pickle);
The underlying matchers can be arbitrarily complicated and new
ones with more complicated semantics can be created.  The default
matching objects are:
SmartsMatcher - match a smarts pattern or query molecule with a minimum
and maximum count
ExclusionList - returns false if any of the supplied matches exist
And - combine two matchers
Or  - true if any of two matchers are true
Not - invert the match (note that this can have confusing semantics
when dealing with substructure matches)
Entries can be added at any time to a catalog:
ExclusionList excludedList;
excludedList.addPattern(SmartsMatcher("Pattern 1", smarts));
excludedList.addPattern(SmartsMatcher("Pattern 2", smarts2));

A FilterCatalog supports a few different types of matching.  One is
a traditional rejection filter where if a substructure exists in
the target molecule, the molecule is rejected.
These types of queries can indicate the substructure that triggered
the rejection through the FilterCatalogEntry::GetMatch(mol)
function.
The FilterCatalog also supports acceptance filters, that are
designed to indicate which molecules are ok.  These have
to be transformed into rejection filters or simply wrapped in a
Not( acceptanceFilter ) when entered into the catalog.  For example,
from Zinc:
carbons [#6] 40

means that we have a maximum of 40 carbon atoms.  We can write this by
converting the max count to a min count (i.e. the pattern is triggered
when the molecule has mincount atoms);
const unsigned int minCount = 40+1;
SmartsMatcher( "Too many carbons", "[#6"], minCount );

This can be properly substructure searched.
Or we can wrap this in a not:
const unsigned int minCount = 0;
const unsigned int maxCount = 40;
Not( SmartsMatcher( "ok number of carbons", "[#6]", minCount, maxCount) );

Note: Wrapping in a Not loses the ability to highlight the rejecting
pattern when visualizing the molecule.

@bp-kelley : I think you forgot to include $RDBASE/rdkit/Chem/FilterCatalog in the PR

You are correct, it's in my tree but not in the pull request!

Brian Kelley

On Jul 14, 2015, at 11:27 AM, Greg Landrum<EMAIL_ADDRESS>wrote:
@bp-kelley : I think you forgot to include $RDBASE/rdkit/Chem/FilterCatalog in the PR
—
Reply to this email directly or view it on GitHub.

This filter set is a very interesting addition to the RDKit, esp. the PAINS filters, thanks a lot.
I have tried the original Smarts filters from the KNIME implementation of the filters (Simon Saubern, Rajarshi Guha and Jonathan B. Baell; KNIME Workflow to Assess PAINS Filters in SMARTS Format. Comparison of RDKit and Indigo Cheminformatics Libraries; Mol. Inf. 2011, 30 (10), 847-850) and could increase their compound hit count with RDKit/Python in their example data set of10k compounds from 329 to 799, when adding hydrogens to the molecules. However, this is still less than what PPilot finds (858) and what the original SLN filters found (861).
My question is:
Is anyone aware of a reference compound set that covers all (480, I think) Smarts filters of the PAINS set?
I have just run the whole ChEMBL20 with them and found that only 322 filters (out of 480) were hitting (with PPilot).
I could of course go on and try other open databases and hope to hit more, but for such a prominent filter set like the PAINS, it would be really great to have a reference compound set.
Kind regards,
Axel

Axel,
Thanks for the comments.  One of the reference datasets (used in the original paper) is MDDR 2008 that we could use to generate a reference set, but I don't know the hit rate count. I believe Chembl may also be a good reference, but I will have to look at that.
Practically,  we have found that a lot of differences are actually caused by aromaticity perception of the underlying chemistry engine, however this is just a guess at this point (and doesn't take into account the SLN->Smarts conversion).  I know of a few alternate implementations of PAINS that perhaps could be used in generating a proper reference set which (based on your analysis) seems like the right thing to do at this point just for validation purposes.
Cheers,
Brian

Given that Brian and I are both sitting in the same room with Rajarshi Guha for the next couple days, I think we should be able to come up with something here. :-)

That sounds just great!!
Kind regards,
Axel

I just did a bit of experimentation.
I was going to suggest that Axel shouldn't need to add Hs to make the queries work. The "mergeHs" argument to MolFromSmarts() should really prevent that. However... while testing I found a bug, #544, which is relevant to this discussion.

I don't know, Greg, just using mergeHs does not work for me, here is an example:
In [26]:
# Filter indol_3yl_alk(461) from the PAINS set:
smarts = 'n:1(c(c(c:2:c:1:c:c:c:c:2-[#1])-[#6;X4]-[#1])-[$([#6](-[#1])-[#1]),$([#6]=,:[!#6&!#1]),$([#6](-[#1])-[#7]),$([#6](-[#1])(-[#6](-[#1])-[#1])-[#6](-[#1])(-[#1])-[#7](-[#1])-[#6](-[#1])-[#1])])-[$([#1]),$([#6](-[#1])-[#1])]'
mol = Chem.MolFromSmiles("Cc1ccc(NC(=O)Cc2c(C(=O)O)[nH]c3ccccc23)c(Br)c1")

In [27]:
smarts_mol = Chem.MolFromSmarts(smarts)
mol.HasSubstructMatch(smarts_mol)

Out[27]:
False

In [28]:
smarts_mol = Chem.MolFromSmarts(smarts, mergeHs=True)
mol.HasSubstructMatch(smarts_mol)

Out[28]:
False

In [29]:
mol_h = Chem.AddHs(mol)
smarts_mol = Chem.MolFromSmarts(smarts)
mol_h.HasSubstructMatch(smarts_mol)

Out[29]:
True

Kind regards,
Axel

Hi Axel,
There are (at least) two problems there:

a problem in the way Hs are merged in recursive SMARTS : #544. I have made some progress on this
there is one piece of the SMARTS: '[$(#1)]' that isn't currently well handled (and will be difficult to handle)

Thanks a lot, Greg.
Sorry for opening this can of worms....

@apahl and @bp-kelley ,
Here's where this stands: Yesterday I checked in a few more code changes along with a bunch of edits of the SMARTS from the KNIME workflow. These edits are mainly intended to remove explicit Hs appearing in the SMARTS that the H merging code will not be able to handle. A lot of these are explicit Hs in an atom or list; these need to be merged by hand. An example of this, I convert things like C-[#1,#6,#7] to [C;!H0,$(C-[#6,#7])]
I tested using the 10000 WEHI molecules that were part of the KNIME workflow.
The test code looks like this:
smas = [x[0] for x in csv.reader(file('./wehi_pains.csv'))]
osmas = [x[0] for x in csv.reader(file('./wehi_pains.orig.csv'))]
if len(sys.argv)>1:
    keep = int(sys.argv[1])
    smas = [smas[keep]]
    osmas = [osmas[keep]]
opatts = [Chem.MolFromSmarts(x,mergeHs=False) for x in smas]
patts = [Chem.MolFromSmarts(x,mergeHs=True) for x in smas]
print("   reading mols")
smis = [x[0] for x in csv.reader(file('./test_data/wehi_mols.csv'))]
ms = [Chem.MolFromSmiles(x) for x in smis]
mhs = [Chem.AddHs(x) for x in ms]

print("   filtering")
matches=[]
found=0
for i,(m,mh) in enumerate(zip(ms,mhs)):
    for j,(patt,opatt) in enumerate(zip(patts,opatts)):
        t1 = m.HasSubstructMatch(patt)
        t2 = mh.HasSubstructMatch(opatt)
        if t1:
            found+=1
        if t1^t2:
            matches.append((i,j,smis[i],smas[j]))
            print(i,j,smis[i],smas[j])
    if not (i+1)%100:
        print("    Done: ",i+1," matches: ",len(matches)," found: ",found)

I'm running something similar across CHEMBL20 now. This will take a while and is certainly going to turn up additional problems.
Along the way I am keeping track of how many times each pattern occurs; would be good to make sure that we have at least one example for each pattern.

Ok, the ChEMBL experiment is done and I fixed a couple more SMARTS.
The SMARTS in https://github.com/rdkit/rdkit/blob/3af7aeaaea348ef25e974056ad1b593efa4e7f8d/Data/Pains/wehi_pains.csv
now work on deprotonated molecules (as long as you use the mergeHs=True argument to Chem.MolFromSmarts()).
This has been tested against all 10K molecules in the WEHI set that was used in the original KNIME workflow (only has matches for 144 of the PAINS) and the 1.4M molecules in ChEMBL20 (only has matches for 293 of the PAINS).
I will try to find a dataset (likely going to be pubchem... shudder!) to find matches for the remaining ~200 PAINS so that we have at least one matching molecule for each of them to use in a test set.

Greg, thanks a lot again for all the work you put into this.
Do you think it is possible that a lot of the remaining filters in the PAINS set don't code for "real" molecules (although RDKit can generate mols from them)?

That is certainly a possibility, I'm not convinced that the SLN -> SMARTS translation went flawlessly.
The supplementary material for the "PAINS in KNIME" paper (http://onlinelibrary.wiley.com/store/10.1002/minf.201100076/asset/supinfo/minf_201100076_sm_miscellaneous_information.pdf?v=1&s=5e9531fd6b228e4f1d4db17b31bc31b254d23558) includes a set of examples that did have matches in those 10K molecules from SLN but that do not from SMARTS. I'm going to spot-check some of those to see if I can figure out why.
Going to have to brush up on on my SLN first though... :-)

This morning I ran the remaining unmatched queries (for some reason now I only have 81) against pubchem. This gave me an additional 62 matches (only 18 left without matches) and allowed me to do some more testing/tweaking of the SMARTS. The differences were mainly due to different aromaticity models (primarily to do with the impact of exocyclic double bonds). At this point most of the pubchem matches also match with the RDKit code.
The changes are all checked in, as are a set of tests that have one matching molecule per SMARTS. This isn't optimal, but going much beyond that would be pretty onerous.
@bp-kelley : apologies, but the FilterCatalog is going to need to be updated again. I think I'm done tweaking these things for now though.

No worries, I have a script that does the conversion, so it is fairly trivial.
I'll also incorporate your test into the filter catalog suite when I have a moment.

Brian Kelley

On Aug 6, 2015, at 7:42 AM, Greg Landrum<EMAIL_ADDRESS>wrote:
This morning I ran the remaining unmatched queries (for some reason now I only have 81) against pubchem. This gave me an additional 62 matches (only 18 left without matches) and allowed me to do some more testing/tweaking of the SMARTS. The differences were mainly due to different aromaticity models (primarily to do with the impact of exocyclic double bonds). At this point most of the pubchem matches also match with the RDKit code.
The changes are all checked in, as are a set of tests that have one matching molecule per SMARTS. This isn't optimal, but going much beyond that would be pretty onerous.
@bp-kelley : apologies, but the FilterCatalog is going to need to be updated again. I think I'm done tweaking these things for now though.
—
Reply to this email directly or view it on GitHub.

Thank you for the PAINS SMARTS curation, Greg. We were making progress on
our own effort to curate them, and it was real slog!  We appreciate this
very much, along with so much else you do in RDKit!
John
On Thu, Aug 6, 2015 at 4:42 AM, Greg Landrum<EMAIL_ADDRESS>wrote:

This morning I ran the remaining unmatched queries (for some reason now I
only have 81) against pubchem. This gave me an additional 62 matches (only
18 left without matches) and allowed me to do some more testing/tweaking of
the SMARTS. The differences were mainly due to different aromaticity models
(primarily to do with the impact of exocyclic double bonds). At this point
most of the pubchem matches also match with the RDKit code.
The changes are all checked in, as are a set of tests that have one
matching molecule per SMARTS. This isn't optimal, but going much beyond
that would be pretty onerous.
@bp-kelley https://github.com/bp-kelley : apologies, but the
FilterCatalog is going to need to be updated again. I think I'm done
tweaking these things for now though.
—
Reply to this email directly or view it on GitHub
https://github.com/rdkit/rdkit/pull/536#issuecomment-128337930.

Thanks for the positive feedback John! It's always great to hear that the work is appreciated.
The cleanup that's been done so far was, indeed, something of a slog. Enough of one that I haven't yet tried to figure out why I'm not finding matches for the 18 PAINS I still haven't found examples for. I'm guessing that something got seriously borked in the conversion from SLN to SMARTS, but haven't drilled into it yet.
This will show up in a blog post at some point (hopefully soon), but here are the missing SMARTS as well as the name of the corresponding PAINS in case anyone has the time/desire to investigate further:
"[#8]-[#6](=[#8])-[#6](-[#1])(-[#1])-[#16;X2]-[#6](=[#7]-[#6]#[#7])-[#7](-[#1])-c:1:c:c:c:c:c:1","<regId=cyanamide_A(1)>"
"c:1-3:c(:c:c:c:c:1)-[#16]-[#6](=[#7]-[#7]=[#6]-2-[#6]=[#6]-[#6]=[#6]-[#6]=[#6]-2)-[#7]-3-[#6](-[#1])-[#1]","<regId=colchicine_het(1)>"
"c:1(:c(:c:2:c(:n:c:1-[#7](-[#1])-[#1]):c:c:c(:c:2-[#7](-[#1])-[#1])-[#6]#[#7])-[#6]#[#7])-[#6]#[#7]","<regId=cyano_amino_het_A(1)>"
"[#6](-[#1])-[#6]:2:[#7]:[#7](-c:1:c:c:c:c:c:1):[#16]:3:[!#6&!#1]:[!#1]:[#6]:[#6]:2:3","<regId=het_thio_N_55(5)>"
"[#6]-2(=[#16])-[#7]-1-[#6]:[#6]-[#7]=[#7]-[#6]-1=[#7]-[#7]-2-[#1]","<regId=thio_urea_K(2)>"
"[#7](-[#1])(-[#1])-c:1:c(:c(:c(:c(:c:1-[#7](-[#1])-[#16](=[#8])=[#8])-[#1])-[#7](-[#1])-[#6](-[#1])-[#1])-[F,Cl,Br,I])-[#1]","<regId=anil_NH_no_alk_B(1)>"
"[#7]-4(-c:1:c:c:c:c:c:1)-[#6](=[#7+](-c:2:c:c:c:c:c:2)-[#6](=[#7]-c:3:c:c:c:c:c:3)-[#7]-4)-[#1]","<regId=het_5_inium(1)>"
"c:1:3:c(:c:c:c:c:1)-[#7]-2-[#6](=[#8])-[#6](=[#6](-[F,Cl,Br,I])-[#6]-2=[#8])-[#7](-[#1])-[#6]:[#6]:[#6]:[#6](-[#8]-[#6](-[#1])-[#1]):[#6]:[#6]:3","<regId=anil_OC_alk_B(3)>"
"[#6]-1(=[#6](-!@[#6]=[#7])-[#16]-[#6](-[#7]-1)=[#8])-[$([F,Cl,Br,I]),$([#7+](:[#6]):[#6])]","<regId=thiaz_ene_C(11)>"
"s:1:c(:c(-[#1]):c(:c:1-[#6]-3=[#7]-c:2:c:c:c:c:c:2-[#6](=[#7]-[#7]-3-[#1])-c:4:c:c:n:c:c:4)-[#1])-[#1]","<regId=het_76_A(1)>"
"[#7]=[#6]-1-[#7](-[#1])-[#6](=[#6](-[#7]-[#1])-[#7]=[#7]-1)-[#7]-[#1]","<regId=het_6_imidate_A(4)>"
"[#6]-2(=[#7]-c1c(c(nn1-[#6](-[#6]-2(-[#1])-[#1])=[#8])-[#7](-[#1])-[#1])-[#7](-[#1])-[#1])-[#6]","<regId=het_65_G(1)>"
"c:1:2(:c(:c(:c(:o:1)-[#6])-[#1])-[#1])-[#6](=[#8])-[#7](-[#1])-[#6]:[#6](-[#1]):[#6](-[#1]):[#6](-[#1]):[#6](-[#1]):[#6]:2-[#6](=[#8])-[#8]-[#1]","<regId=anthranil_acid_I(1)>"
"[#6](-[#1])(-c:1:c(:c(:c(:c(:c:1-[#1])-[#1])-[Cl])-[#1])-[#1])(-c:2:c(:c(:c(:c(:c:2-[#1])-[#1])-[Cl])-[#1])-[#1])-[#8]-[#6](-[#1])(-[#1])-[#6](-[#1])(-[#1])-[#6](-[#1])(-[#1])-c3nc(c(n3-[#6](-[#1])(-[#1])-[#1])-[#1])-[#1]","<regId=misc_imidazole(1)>"
"c2(c-1n(-[#6](-[#6]=[#6]-[#7]-1)=[#8])nc2-c3cccn3)-[#6]#[#7]","<regId=het_65_H(1)>"
"[#7](-[#1])(-c:1:c(:c(:c(:c(:c:1-[#1])-[#1])-[#1])-[#1])-[#8]-[#1])-[#6]-2=[#6](-[#8]-[#6](-[#7]=[#7]-2)=[#7])-[#7](-[#1])-[#1]","<regId=het_6_imidate_B(1)>"
"[#8]=[#6]-3-c:1:c(:c:c:c:c:1)-[#6]-2=[#6](-[#8]-[#1])-[#6](=[#8])-[#7]-c:4:c-2:c-3:c:c:c:4","<regId=quinone_C(2)>"
"c:1:c:c-2:c(:c:c:1)-[#7](-[#6](-[#8]-[#6]-2)(-[#6](=[#8])-[#8]-[#1])-[#6](-[#1])-[#1])-[#6](=[#8])-[#6](-[#1])-[#1]","<regId=misc_aminal_acid(1)>"


Disable install of recommended packages

In order tio resolve bsc#975726 also for our openSUSE images I have
applied the same changes to disable the installation of recommended
packages within the zypper configuration.

lgtm


Roadmap tracker?

Hi, Do you have any place where you have documented the roadmap for this kit? For e.g we could do something like this https://github.com/reactql/cli/issues/10 and track the upcoming features. It would make it easy for the contributors to work on this kit too.

Hi @mairh Great idea! I've added issue for Roadmap, feel free to post ideas there:
https://github.com/sysgears/apollo-fullstack-starter-kit/issues/176


New Frontend Resource - CSS In JS

Fixes Issue : Closes #610

Changes proposed

Added a new Frontend Subcategory: Css In Js libraries
Added emotion and styled-components.

Screenshots

Note to reviewers

@rupali-codes I added the required changes and rebased the PR with the main branch. Thanks!


Cloud users download the Visio file of architecture?

[Enter feedback here]

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

ID: dff802a9-6ee1-3875-5f0b-7261f6dc4724
Version Independent ID: 2bd75318-e74f-3b09-4a1d-c6d4d7fad9b9
Content: Architecture: Migrate to Azure Virtual WAN
Content Source: articles/virtual-wan/migrate-from-hub-spoke-topology.md
Service: virtual-wan
GitHub Login: @cherylmc
Microsoft Alias: cherylmc

@jiankefu , could you please provide some more details on your query? Is your query related to the below doc?
https://docs.microsoft.com/en-us/azure/virtual-wan/migrate-from-hub-spoke-topology
If yes, could you please elaborate it a little for further discussion?

Hi, I am very glad to hear from you, as a reader, I have seen a lot of
network topologies in your documents, and I want to download and edit these
topologies, so cloud you upload the original files of these topologies in
the documents? Thanks very much.
Gitarani Sharma @.***> 于2022年8月25日周四 18:29写道：

@jiankefu https://github.com/jiankefu , could you please provide some
more details on your query? Is your query related to the below doc?
https://docs.microsoft.com/en-us/azure/virtual-wan/migrate-from-hub-spoke-topology
If yes, could you please elaborate it a little for further discussion?
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@jiankefu , We have assigned this to the content owner/author for review.
@cherylmc , is there a way for the users to download the network topologies from our documents?

Unfortunately, there isn't a way to do this. They are just flat files, not editable.

#please-close


<SRC FILE> not provided with default options

❯ mkdir pre-commit-test
❯ cd pre-commit-test
❯ git init
Initialized empty Git repository in /Users/mz/workspace/pre-commit-test/.git/
❯ echo "anyio" > "requirements.in"
❯ git add requirements.in
❯ pre-commit try-repo https://github.com/astral-sh/uv-pre-commit
[INFO] Initializing environment for https://github.com/astral-sh/uv-pre-commit.
===============================================================================
Using config:
===============================================================================
repos:
-   repo: https://github.com/astral-sh/uv-pre-commit
    rev: 8830f06b90d5d856ee2d058a33ded4b6820ab925
    hooks:
    -   id: pip-compile
===============================================================================
[INFO] Installing environment for https://github.com/astral-sh/uv-pre-commit.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
pip-compile..............................................................Failed
- hook id: pip-compile
- exit code: 2

error: the following required arguments were not provided:
  <SRC_FILE>...

Usage: uv pip compile <SRC_FILE>...

For more information, try '--help'.

Default args would have to be provided. I guess it would make sense to have to at least handle the most common use case. And then require users to manually change it for their use case.
https://github.com/astral-sh/uv-pre-commit/blob/8830f06b90d5d856ee2d058a33ded4b6820ab925/.pre-commit-hooks.yaml#L7
could become
args: [requirements.in]

I think it would also be fine to leave the README as is. Since ideally, the user will always just set up the args how they need it.

I'll leave this issue here for discoverability for people that encounter this error, but let's discuss defaults in #3.


Bump commons-lang3 version to 3.13.0

Description
Fixed jarhell errors related to update of commons-lang library, we're seeing those errors in neural-search CI for main branch. Update version to 3.13.0 to match same in core
Check List

[X] All tests pass
[X] Commits are signed per the DCO using --signoff

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.
For more information on following Developer Certificate of Origin and signing off your commits, please check here.

Closed due to duplicate in #1288


Failed assertion: line 459 pos 7: '_ticker != null': AnimationController.forward() called after AnimationController.dispose()

I get the same error when the ripple is on, only when it's on.
Unhandled Exception: 'package:flutter/src/animation/animation_controller.dart': Failed assertion: line 453 pos 7: '_ticker != null': AnimationController.forward() called after AnimationController.dispose()
AnimationController methods should not be used after calling dispose.
#0      _AssertionError._doThrowNew (dart:core-patch/errors_patch.dart:51:61)
#1      _AssertionError._throwNew (dart:core-patch/errors_patch.dart:40:5)
#2      AnimationController.forward (package:flutter/src/animation/animation_controller.dart:453:7)
#3      AnilocationTaskImpl._rippleStatusListener. (package:flutter_animarker/infrastructure/anilocation_task_impl.dart:226:44)
#4      new Future.delayed. (dart:async/future.dart:427:39)
#5      Timer._createTimer. (dart:async-patch/timer_patch.dart:18:15)
#6      _Timer._runTimers (dart:isolate-patch/timer_impl.dart:398:19)
#7      _Timer._handleMessage (dart:isolate-patch/<…>


I think I've done a types??

Copied from https://github.com/DefinitelyTyped/DefinitelyTyped/tree/master/types/fetch-mock, and hopefully integrated successfully

Coverage remained the same at 97.072% when pulling 62847f89fb7f3cd1359ab228ddedc8b1ae7ce85e on types into 0f0137c7830c6b800ff86581d22179251529d444 on v8.

@berstend does this look good to you? Does v8.0.0-alpha.9 work ok with typescript?


Auto-created topics partitions incorrect / divide by zero

PyKafka version: 2.8.0
Kafka version: 2.2.0
When producing to an auto-created topic a divide by zero exception can occur.
Traceback (most recent call last):
  File "/opt/system/project/usr/share/signal_generator.py", line 464, in emit
    producer.produce(j.encode())
  File "/usr/local/lib/python3.7/site-packages/pykafka/producer.py", line 385, in produce
    partition_id = self._partitioner(partitions, partition_key).id
  File "/usr/local/lib/python3.7/site-packages/pykafka/partitioners.py", line 47, in __call__
    self.idx = (self.idx + 1) % len(partitions)
ZeroDivisionError: integer division or modulo by zero

My thought is that the partition list may be incomplete when a message is produced.  (eg. Kafka hasn't fully created the partition list or pyKafka hasn't updated it yet.)

@emmett9001 Hi Emmett, Could you have a look at this one?  I'm not sure what the best course of action is here.  Thanks.

Assuming your topic is actually being created with the proper number of partitions, a workaround could be to initialize a producer with a preexisting topic name instead of relying on autocreation.

So I found a retry and update_cluster does work.  These topics are low volume, single partition.
    retry = 0
    topic = self.kafka.topics[mytopic]
    while retry < self.retry_topic_partitions_found:
        if len(topic.partitions):
            break
        logging.warning("No partitions found on retry %d for %s" % (
            retry, mytopic))
        retry += 1
        time.sleep(.25)
        self.kafka.update_cluster()
        topic = self.kafka.topics[mytopic]

    if len(topic.partitions) == 0:
        logging.error("No partitions found after retries for %s" % (
            mytopic))

    self.producer = topic.get_producer()

For this, I've only ever seen a single retry.


wrong index when adjusting z-wise

In function ' coarse2fine_localization', for adjusting z-wise only, I think we use cam_maps_3d[:, :, :, :, 0], not [:, :, :, :, 2] because self.coordmap_3d is the result of concatenate (Z_map, Y_map, X_map).
        center_maps_3d = self.center_map_refiner(center_maps_3d.unsqueeze(1)).squeeze(1)
        cam_maps_3d = self.coordmap_3d + cam_maps_offset.unsqueeze(-1).transpose(4,1).contiguous()
        cam_maps_3d[:,:,:,:,2] = cam_maps_3d[:,:,:,:,2] + cam_maps_offset_bv.unsqueeze(2).contiguous()

Hi, MJ Shin @170928
Thanks a lot for pointing out this error! I will fix it in the next version.

@Arthur151 Is it already fixed? 🙂

Yes.


refactor lavague into lavague-core

This PR probably does too many things at once, but it is what it is.
Main goals:

Improve our ability to receive meaningfull contributions by having an integration-oriented architecture (integrations folder) in which contributors can derive base components to customize (and improve) the pipeline.
Split lavague into lavague (lavague-core folder), lavague-vscode, lavague-cli, lavague-gradio, to enable pushing quickly on core without having to care for compatibility with the tools because we fix the version of the lavague-core dependency in the others packages.
Refactor the config structure into a context because the recent retrievers are needing the drivers and it would quickly become a mess of references otherwise.

TODOs:

[ ] adapt the tools to the new architecture
[ ] put telemetry directly in ActionEngine
[ ] test and review everything, these are BIG (but needed) changes, and we don't want to merge them carelessly.
[ ] redo the documentation :smiling_face_with_tear: sorry @lyie28

@dhuynh95 @JoFrost

from lavague.integrations.contexts.playwright import PlaywrightContext
from lavague import ActionEngine

selenium_context = PlaywrightContext.from_defaults()
action_engine = ActionEngine.from_context(selenium_context)
action = action_engine.get_action("Enter hop inside the search bar and then press enter", "https://news.ycombinator.com")
print(action)

This is what it looks like with the new implementation. You can customize the context as you want to add your own llms, retrievers ...


Vidoe is not showing, but audio is playing

Hello sir,
I am trying to use this library(10.0.5) in android app it doesn't showing video,
and i also this library version(7.0.1) in tv app here it works well but on android is not work
i also try on real device but video is not showing
can you help me?
i also try by creating another project and it works perfectly but in my project not working in any activity

Hello, can you explain shortly, how you solved this problem?

Are you using a device or an emulator? this is a common issue on emulators.

Yeah, it is android emulator, but I found out that, in real device it is
working.
пн, 6 мар. 2023 г., 20:42 Pierfrancesco Soffritti @.***

:

Are you using a device or an emulator? this is a common issue on emulators.
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Cleanup fhs-chrootenv's environment and workaround Steam's sound issues

This adds locale support in FHS chrootenv, reworks environment, unifies and refactors /etc and finally workarounds Steam and its games' PulseAudio sound issues.
One controversial thing this uses is storing absolute symlinks like "/host-etc/passwd" in Nix store; this allows to greatly unify code between fhs-chrootenv and fhs-userenv.
Also this makes FHS chroot less NixOS-specific; if someone has used it in just Nix, they should have less issues now.
cc @jagajaga

Seems pretty nice.
Have you built it locally? There is a travis error, but it's not connected with subject.

Yes, it fixed my sound issues at least at expense of ld.so errors spam (it's a shame we don't have LD_PRELOAD_32/LD_PRELOAD_64).


Fix: Consistently indent YML files with 2 spaces

This PR

[x] consistently indents .travis.yml with 2 spaces

💁♂ Probably not needed when we decide to go with #1826.

Please see #1851

Closing in favour of #1847.


bug: React Dev Tools causes an error on console

Provide environment information
System:
OS: Windows 10 10.0.19044
CPU: (24) x64 AMD Ryzen 9 5900X 12-Core Processor
Memory: 5.65 GB / 15.93 GB
Binaries:
Node: 16.16.0 - C:\Program Files\nodejs\node.EXE
npm: 8.19.1 - C:\Program Files\nodejs\npm.CMD
"ct3aMetadata": {
"initVersion": "6.3.0"
}
Describe the bug
When I define const utils = trpc.useContext(); and <Head></Head>  tags inside component browser throws an error on console something like contextMap[utilName] is not a function.

To reproduce
When I turn off React Developer Tools it no longer crashes or gives error.
Additional information

I can't reproduce this using the latest version of React Devtools.

Either way this is is not something we could even fix as creators of an init tool - you're probably better off opening a bug on tRPC or React Devtools.


How to install prometheus vuls exporter send metric to grafana

Hi All
I deployment vuls and grafana below:
Server A (Grafana/Prometheus server) <----> Server B (Vuls server)
I have question: With such architecture. How can I send metric to Prometheus server.
On Vuls server:
$ export REPORTS_DIR=/root/results
$ export VULS_DIR=/root/vulsctl
[root@VULS prometheus-vuls-exporter]# pwd
/root/prometheus-vuls-exporter
[root@VULS prometheus-vuls-exporter]# ./example/run_exporter.sh
Running exporter with Go
src/metrics/createMetrics.go:6:2: cannot find package "github.com/prometheus/client_golang/prometheus" in any of:
/usr/local/go/src/github.com/prometheus/client_golang/prometheus (from $GOROOT)
/root/go/src/github.com/prometheus/client_golang/prometheus (from $GOPATH)
src/metrics/createMetrics.go:7:2: cannot find package "github.com/prometheus/client_golang/prometheus/promauto" in any of:
/usr/local/go/src/github.com/prometheus/client_golang/prometheus/promauto (from $GOROOT)
/root/go/src/github.com/prometheus/client_golang/prometheus/promauto (from $GOPATH)
src/main.go:12:2: cannot find package "github.com/prometheus/client_golang/prometheus/promhttp" in any of:
/usr/local/go/src/github.com/prometheus/client_golang/prometheus/promhttp (from $GOROOT)
/root/go/src/github.com/prometheus/client_golang/prometheus/promhttp (from $GOPATH)
src/main.go:13:2: cannot find package "github.com/spf13/pflag" in any of:
/usr/local/go/src/github.com/spf13/pflag (from $GOROOT)
/root/go/src/github.com/spf13/pflag (from $GOPATH)
src/main.go:14:2: cannot find package "github.com/spf13/viper" in any of:
/usr/local/go/src/github.com/spf13/viper (from $GOROOT)
/root/go/src/github.com/spf13/viper (from $GOPATH)
src/metrics/parseReport.go:9:2: cannot find package "github.com/tidwall/gjson" in any of:
/usr/local/go/src/github.com/tidwall/gjson (from $GOROOT)
/root/go/src/github.com/tidwall/gjson (from $GOPATH)
[root@VULS prometheus-vuls-exporter]#
Hope my question is not too silly
Thank so much

Hi Daniel.
If you're running examples from source and not the pre-built binary, you need to install Go dependencies.  This will install/update all packages that it finds.
Alternatively, you can replace the go ./src (or whatever command I'm using in the example) with prometheus-vuls-exporter binary - you can get it on the Releases page.
Hope this helps!

Thank so much @iakovmarkov
It seems I have adjusted properly.
[root@VULS tmp]# ls /root/results/
2020-08-02T23:00:00+07:00  2020-08-03T23:00:00+07:00 current

[root@VULS tmp]# prometheus-vuls-exporter
2020/08/04 16:15:48 prometheus-vuls-exporter Warning! HTTP Basic Auth disabled, your vulnerability metrics are readable by anyone!
2020/08/04 16:15:48 prometheus-vuls-exporter Reports folder configured: /root/results
2020/08/04 16:15:48 prometheus-vuls-exporter listening on :8080

But when I configured data source to fetch data from Vuls server is defective.I make sure firewall allow port 8080 from grafana

Do you have ideal for check metric on vuls server?
Thank you!!!

The exporter doesn't do much by itself - it collects reports from Vuls and exposes metrics over HTTP in Prometheus-friendly format. You need a running Prometheus instance, and you need to configure it to scrape the metrics from this exporter. The Prometheus configuration is really similar to any other exporter like BlackboxExporter or NodeExporter.
On Grafana side, you need to point it to Prometheus instance - that's where the data is stored, not on the Exporter side. Also, http://10.*.*.*:8080 cannot be a correct URL. If you're running on Grafana and Prometheus on the same host, you can use http://localhost there; otherwise you need Prometheus instance hostname/port combo.

@iakovmarkov
Really thank you for the suggestion. My system was running smoothly.
I was confused about how Prometheus works.
One more thing. In Installation Guide.
Curl-Lo Prometheus-vuls-exporter https://github.com/iakovmarkov/prometheus-vuls-exporter/releases/latest/prometheus-vuls-exporter-linux-386--> Not work
We need change to:
https://github.com/iakovmarkov/prometheus-vuls-exporter/releases/tag/0.1.3/prometheus-vuls-exporter-linux-386
Thank so much friend

Glad it worked out for you :+1:
Thanks for letting me know about README, I thought that the latest thing worked at some point... I'll update the README.


Invalid property 'dynamoDBMapperConfig' of bean class [org.socialsignin.spring.data.dynamodb.repository.support.DynamoDBRepositoryFactoryBean] - Release 5.1.1

Many users still have this issue: (see #230 #237)
Caused by: org.springframework.beans.NotWritablePropertyException: Invalid property 'dynamoDBMapperConfig' of bean class [org.socialsignin.spring.data.dynamodb.repository.support.DynamoDBRepositoryFactoryBean]: Bean property 'dynamoDBMapperConfig' is not writable or has an invalid setter method. Does the parameter type of the setter match the return type of the getter?
	at org.springframework.beans.BeanWrapperImpl.createNotWritablePropertyException(BeanWrapperImpl.java:243)
	at org.springframework.beans.AbstractNestablePropertyAccessor.processLocalProperty(AbstractNestablePropertyAccessor.java:426)
	at org.springframework.beans.AbstractNestablePropertyAccessor.setPropertyValue(AbstractNestablePropertyAccessor.java:278)
	at org.springframework.beans.AbstractNestablePropertyAccessor.setPropertyValue(AbstractNestablePropertyAccessor.java:266)
	at org.springframework.beans.AbstractPropertyAccessor.setPropertyValues(AbstractPropertyAccessor.java:97)
	at org.springframework.beans.AbstractPropertyAccessor.setPropertyValues(AbstractPropertyAccessor.java:77)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1714)
	... 31 common frames omitted

I read in your comment in issue #235 (https://github.com/derjust/spring-data-dynamodb/issues/235#issuecomment-471334275_) that its fixed in master and is part of 5.1.1
Please some maintainer, please release 5.1.1 because many of us are blocked and need this fix.
Also see Pullrequest https://github.com/derjust/spring-data-dynamodb/pull/238

This one is fixed in master and will be part of 5.1.1
Originally posted by @derjust in https://github.com/derjust/spring-data-dynamodb/issues/235#issuecomment-471334275

https://github.com/derjust/spring-data-dynamodb/wiki/Access-to-releases
Go grab the snapshot, that's what I am running

Thanks for that hint

@boostchicken  I have my Gradle build set with the snapshot URL.
repositories {
	mavenCentral()
	maven(url = "https://oss.sonatype.org/content/repositories/snapshots")
}

Now my dilemma is how should I define the dependency (version wise )?  I have tried the below but it is not working:
dependencies {
        ...
	implementation("com.github.derjust:spring-data-dynamodb:5.1.1-SNAPSHOT")
}

Unable to resolve. How is it identified on the snapshots repo?

not sure mine giving a weird error (below) when I start using the snapshot
`FAILURE: Build failed with an exception.

What went wrong:
java.lang.ArrayIndexOutOfBoundsException (no error message)`

api  group: 'io.github.boostchicken', name: 'spring-data-dynamodb', version: '5.2.1'
On maven central now

@boostchicken  is the repo transitioning to your repo from now on ?

I have PRs sent, but I have not heard from derjust lately.  I would like to not fork it but unless we see movement here it might be the best idea

I have tried @boostchicken's 5.2.1 and that did indeed resolve the issue.
Still don't see a 5.1.1 on the "derjust/spring-data-dynamodb" project ? Any progress with this ?

I used @boostchicken  5.2.1 and "@Primary" on "dynamoDBMapper" and "dynamoDBMapperConfig" and solved the issue


New training: genome-wide alternative splicing analysis

Also you may be interested in generating a data-library.yaml so users can access data through the data library.

Also you may be interested in generating a data-library.yaml so users can access data through the data library.

Yes, I just included it :)

Great tutorial. I suggest to use the variable zenodo_link which makes updates easier. Also I am wondering if it could be interesting to generate a coverage at the mapping step (available in the last STAR wrapper see https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html#mapping) and then generate a picture for RGMB with pyGenomeTracks (if you are interested I can write this part).

Could you open a different PR for that? I think it will be great, but I would like to include it for Smorgasbord and I'm a bit in a hurry I think :yellow_circle:

Sorry I pushed my corrections directly on your branch (but they are only bug fixed).

I am testing the tutorial and I found some mistakes. I am writting you a PR. Also, it seems to me that it is more work to build 2 collections and run each tool twice rather than building a single collection and then using the Filter dataset from collection to split between the health and cancer. Also, for the fastQC in the reference-based tutorial we use a different trick which is to use 'Flatten'. This presents the advantage of not taking computational time. What do you think?

Both suggestions are great I think :D

I am testing the tutorial and I found some mistakes. I am writting you a PR. Also, it seems to me that it is more work to build 2 collections and run each tool twice rather than building a single collection and then using the Filter dataset from collection to split between the health and cancer. Also, for the fastQC in the reference-based tutorial we use a different trick which is to use 'Flatten'. This presents the advantage of not taking computational time. What do you think?

Both suggestions are great I think :D

Should I integrate that into my PR?

I started the PR but not done yet. https://github.com/gallardoalba/training-material/pull/1

Still running some analysis. The last two steps are failing. I sent a bug report.

Thank you so much for the review @pavanvidem! This error was caused by a mistake in the training.

ach i shouldn't've merged the linting, that merge is annoying, but done now.

The linting error is actually on the test file, it seems. the yaml was very broken.

The linting error is actually on the test file, it seems. the yaml was very broken e456cbf

Ah sorry, that I modified manually. Thanks a lot!


Rosettacode: Create HTML tables

Signed-off-by: Mehdi<EMAIL_ADDRESS>

+1

ping @privat

+1

closed by 305f372e18dee0b8ddf0d3df2c28c1f2c127977a


The secrets operation is treating an ssh warning as an error and aborting

(SystemCall:) Making call:
    rsync --archive --verbose /Use  ...
building file list ... done
./
.gitignore
ngrok_token.txt
s3_auth.json

sent 4858 bytes  received 280 bytes  2055.20 bytes/sec
total size is 4600  speedup is 0.90
ERR>> Warning: Permanently added the ECDSA host key for IP address '[<IP_ADDRESS>]:13573' to the list of known hosts.
barnserv_alpha1]

Repeating the command works without problems, as a workaround.

The 'adding key' warning occurs if the LOCAL machine doesn't have the remote url in its ~/.ssh/known_hosts file.
Actually, what is happening, the call is succeeding, it is just that the warning is being sent to stderr, so it looks like there was an error ('ERR>>').
It would be better to look at the stderr output, and if the system call succeeded, change all ERR>> prefixes to something else, e.g. HEY>>.

I addressed this in java-core.


Auth module

Codecov Report

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:exclamation: Current head 1794e37 differs from pull request most recent head 03b93b0. Consider uploading reports for the commit 03b93b0 to get more accurate results

@@            Coverage Diff             @@
##             modular     #301   +/-   ##
==========================================
  Coverage           ?   60.96%
  Complexity         ?     1513
==========================================
  Files              ?      169
  Lines              ?     6601
  Branches           ?      374
==========================================
  Hits               ?     4024
  Misses             ?     2412
  Partials           ?      165

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unclosed bracket error, but works on pgadmin

migration sample code:
raw(`
CREATE MATERIALIZED VIEW view_papers AS
 SELECT papers.created_at,
    papers.updated_at,
    papers.id,
    papers.name,
    (   setweight(to_tsvector(papers.name::text), 'A'::"char") ||
        setweight(to_tsvector(papers.author_name), 'B'::"char")
    ) || setweight(to_tsvector(papers.description), 'C'::"char")
    AS paper_vector
   FROM
   ( SELECT papers.id, string_agg(categories.code, ',') as categories
    FROM papers
    LEFT JOIN paper_categories ON paper_categories.paper_id=papers.id LEFT JOIN (select * from categories order by weight asc) categories ON categories.id=paper_categories.category_id
    GROUP BY papers.id
   ) a
   LEFT JOIN papers on a.id=papers.id
  WHERE (papers.doc_status = ANY (ARRAY[1, 3])) AND papers.status = 1
WITH DATA
`)

got this error:
...view_papers.up.fizz: line 9: expected next token to be ), got IDENT instead
line 23: no prefix parse function for ) found
line 50: expected next token to be ), got IDENT instead
line 65: no prefix parse function for ) found

i think it has something todo with plush script runner

i found the work around, replace all " with "
but i think plush should by default be able to handle single " when we use ` in fizz


VSTS REST API List Iterations does not accept 'past' or 'current' values for $timeframe

The feedback is from https://github.com/MicrosoftDocs/feedback/issues/445
Using the VSTS REST api version 4.1 AND 5.0 preview 1, making a GET request to list iterations using the $timeframe query parameter works when supplying 'current' as a timeframe value, but does not work when using 'past' or 'future' as per the documentation.
To Reproduce
Make a get request using the following URL (fill in appropriate values):
https://{CompanyName}.visualstudio.com/{ProjectName}/_apis/work/teamsettings/iterations?$timeframe=past&api-version=4.1
This returns:
{
    "$id": "1",
    "innerException": null,
    "message": "Specified argument was out of the range of valid values.\r\nParameter name: timeframe",
    "typeName": "System.ArgumentOutOfRangeException, mscorlib",
    "typeKey": "ArgumentOutOfRangeException",
    "errorCode": 0,
    "eventId": 0
}

Using either $timeframe=past or $timeframe=future reproduces the fault.
Using $timeframe=current works fine.
Expected behaviour
Using 'past' and 'future' as defined in the documentation here https://docs.microsoft.com/en-us/rest/api/vsts/work/iterations/list?view=vsts-rest-4.1 and https://docs.microsoft.com/en-us/rest/api/vsts/work/iterations/list?view=vsts-rest-5.0 should return a list of past and future iterations.
Desktop (please complete the following information):
n/a.
Smartphone (please complete the following information):
n/a
Additional context
Reproduced in Postman and C#, .Net framework 4.7.2 console application using NuGet package RestSharp v106.2.2.

Hello @stuntbeaver. Thank you for reporting the issue. We've updated the documentation to mention that only $timeframe=current is supported.

@hellosnow this issue has been resolved. The descriptions has been updated to show only current is supported.

@wnjenkin thanks for the quick fix!

I'm getting the incorrect value returned when using current option. See attached image.

The same here. Only "current" is accepted but the timeframe attribute return is "past".

@lealcrf are you still seeing this? This looks like it was resolved in July and I am not able to reproduce it myself. If you are still seeing this it might be related to how your iterations are configured. Are you able to provide some more information on the request and response you are seeing and what you expect to see based on the current configuration you are seeing in the browser?


Testmyapp v0.0.69

Checklist for Pull Requests

[x] Have you signed the Contributor License Agreement?
[ ] Is there a linked Issue?

Manifests

[x] Have you checked that there aren't other open pull requests for the same manifest update/change?
[x] This PR only modifies one (1) manifest
[x] Have you validated your manifest locally with winget validate --manifest <path>?

[x] Does your manifest conform to the 1.6 schema?

Note: <path> is the name of the directory containing the manifest you're submitting.

Microsoft Reviewers: Open in CodeFlow

@stephengillie happening again even though the diff is just those three commits from master 🤷

Thanks @mdanish-kh!
That happened after moved the release of winget to the windows actions which has messed up the path separator.
Closing this and will create another one.


Adding a watermark

I think it is not possible yet to add another picture with an watermark on top of an image.
Are you considering that?
Thank you.

What ImageMagick command are you trying to use?

I was thinking composite.

You could try something like https://github.com/route/mogrify/issues/39#issuecomment-287486610
image_operator(image, "convert -size:  1200x1200 #{image_path} \ #{image_to_combine_path}  -geometry  +0+10  -composite")
|> create(in_place: true)

Thank you!
Maybe if you would put this in README you wouldn't be bothered anymore by someone asking for composite feature... :)

Well, after a few attempts I wasn't able to make any image_operatorwork. For example, image = open(Path.absname("priv/static/uploads/45992.png"))
image_operator(image, "convert -resize:  50% ")
|> create(in_place: true)`
doesn't output nothing although I get no errors...