mhcflurry-predict errors if input CSV contains bad allele name

This should be more error-tolerant, or have a more informative error message:
(smoking) julia@demeter-csmaz11-19:/data/mhcflurry$ mhcflurry-predict --models /data/mhcflurry/models_fold_0 --out /data/mhcflurry/predictions.fold_0.csv /data/mhcflurry/fold_0.test.csv
Using Theano backend.
Read input CSV with 48387 rows, columns are: allele, peptide, measurement_value, measurement_type, measurement_source, original_allele
Traceback (most recent call last):
  File "/home/julia/Envs/smoking/bin/mhcflurry-predict", line 11, in <module>
    load_entry_point('mhcflurry', 'console_scripts', 'mhcflurry-predict')()
  File "/home/julia/code/mhcflurry/mhcflurry/predict_command.py", line 209, in run
    throw=not args.no_throw)
  File "/home/julia/code/mhcflurry/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py", line 531, in predict_to_dataframe
    mhcnames.normalize_allele_name)
  File "/home/julia/Envs/smoking/local/lib/python2.7/site-packages/pandas/core/series.py", line 2313, in map
    new_values = map_f(values, arg)
  File "pandas/_libs/src/inference.pyx", line 1521, in pandas._libs.lib.map_infer
  File "/home/julia/Envs/smoking/local/lib/python2.7/site-packages/mhcnames/normalization.py", line 72, in normalize_allele_name
    parsed_alleles = parse_classi_or_classii_allele_name(raw_allele)
  File "/home/julia/Envs/smoking/local/lib/python2.7/site-packages/mhcnames/class2.py", line 51, in parse_classi_or_classii_allele_name
    parsed = parse_allele_name(name, species)
  File "/home/julia/Envs/smoking/local/lib/python2.7/site-packages/mhcnames/allele_name.py", line 73, in parse_allele_name
    "species in the name itself: %s, %s, %s" % (species_prefix, species_from_name, original))
ValueError: If a species is passed in, we better not have another species in the name itself

(n this case, the offending allele in the input turned out to be "HLA-SLA01"):
>>> import mhcnames
>>> mhcnames.normalize_allele_name("HLA-SLA01")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/julia/Envs/smoking/local/lib/python2.7/site-packages/mhcnames/normalization.py", line 72, in normalize_allele_name
    parsed_alleles = parse_classi_or_classii_allele_name(raw_allele)
  File "/home/julia/Envs/smoking/local/lib/python2.7/site-packages/mhcnames/class2.py", line 51, in parse_classi_or_classii_allele_name
    parsed = parse_allele_name(name, species)
  File "/home/julia/Envs/smoking/local/lib/python2.7/site-packages/mhcnames/allele_name.py", line 73, in parse_allele_name
    "species in the name itself: %s, %s, %s" % (species_prefix, species_from_name, original))
ValueError: If a species is passed in, we better not have another species in the name itself

I think the issue was that mhcnames 0.1.0 (version used to generate the training data a while ago) had this erroneous behavior:
In [2]: mhcnames.normalize_allele_name("SLA01")
Out[2]: 'HLA-SLA*01:01'

When this output is run through the current version of mhcnames we get the error you see.
It's not clear this error was really fixed though. The current master version of mhcnames gives an error instead of parsing it:
In [4]: mhcnames.normalize_allele_name("SLA-01")
---------------------------------------------------------------------------
AlleleParseError                          Traceback (most recent call last)
<ipython-input-4-39557fbce5ea> in <module>()
----> 1 mhcnames.normalize_allele_name("SLA-01")

/Users/tim/sinai/git/mhcnames/mhcnames/normalization.py in normalize_allele_name(raw_allele, omit_dra1)
     70     if raw_allele in _normalized_allele_cache[omit_dra1]:
     71         return _normalized_allele_cache[omit_dra1][raw_allele]
---> 72     parsed_alleles = parse_classi_or_classii_allele_name(raw_allele)
     73     species = parsed_alleles[0].species
     74     normalized_list = [species]

/Users/tim/sinai/git/mhcnames/mhcnames/class2.py in parse_classi_or_classii_allele_name(name)
     49             "Allele has too many parts: %s" % name)
     50     if len(parts) == 1:
---> 51         parsed = parse_allele_name(name, species)
     52         if parsed.species == "HLA" and parsed.gene.startswith("DRB"):
     53             alpha = AlleleName(

/Users/tim/sinai/git/mhcnames/mhcnames/allele_name.py in parse_allele_name(name, species_prefix)
    118         raise AlleleParseError("No MHC gene name given in %s" % original)
    119     if len(name) == 0:
--> 120         raise AlleleParseError("Malformed MHC type %s" % original)
    121
    122     gene = gene.upper()

AlleleParseError: Malformed MHC type 01

@iskandr is that desired behavior?
If not we should probably open an mhcnames issues

Closing this. SLA-01 is apparently a locus (e.g. HLA-A) not really an allele so I think it's not obviously incorrect for mhcnames to raise an error in this case.


Error on gulp webpack

i have this error running gulp webpack :
sui-seed-webpack/node_modules/babel-core/lib/transformation/file/options/option-manager.js:126
      if (!option) this.log.error("Unknown option: " + alias + "." + key, ReferenceError);
                           ^

TypeError: Cannot read property 'error' of undefined

Which env you are in? I have setup the project in osx without any issues. Few things that you can check, Node version ( I am using 4.2 ). Also you can try to update the babel version to 6.X and see if it solves the issue

I can't reproduce this issue. Since there is no any activity, I probably will close this. @ghernandez81 Please feel free to comment if you think that it should be reopened.

go ahead close it, it work for me now


ring_outlier_filter output is sometimes empty

Checklist

[X] I've read the contribution guidelines.
[X] I've searched other issues and no duplicate issues were found.
[X] I'm convinced that this is not my fault but a bug.

Description
Following the sample sensor kit I have enabled the ring outlier filter on our car.
After that the ndt_scan_matcher started to crash on startup on receiving empty input cloud:

I found ring_outlier_filter is the node responsible for this. On the picture below, I printed on the left the size of ring_outlier_filter output cloud ($ ros2 topic echo /sensing/lidar/top/outlier_filtered/pointcloud --field width) and on the right the size of its input cloud ($ ros2 topic echo /sensing/lidar/top/rectified/pointcloud_ex --field width):

As you can see, the output is sometimes empty.
I could also confirm with Rviz the rectified cloud looks totally normal while the the outlier cloud sometimes "blinks".
Besides the output being empty, I think it is also annoying ndt_scan_matcher crashes because of that.  A small guard could be added to NDTScanMatcher::callback_sensor_points.
Expected behavior
No empty output
Actual behavior
Sometimes empty output
Steps to reproduce
use the outlier filter?
Versions
No response
Possible causes
No response
Additional context
No response

I also observed the similar issue (where the number of points becomes zero occasionally) in the latest awf/autoware with sample rosbag provided in the Autoware tutorial.
@sykwer Do you think the above phenomena is related to this PR? https://github.com/autowarefoundation/autoware.universe/pull/2908/
(Anyway, we need to have some sort of error-catch algorithm in ndt_scan_matcher to accept 0 point inputs)

Thank you for your report!
I also reproduced the problem of the number of point clouds in /sensing/lidar/top/outlier_filtered/pointcloud becomes zero.
But ndt_scan_matcher doesn't crash in my environment (ROS2 galactic).
According to my sources, it seems that the zero division happens in the PCL installed with ROS2 humble.
It seems to be fixed in the latest PCL. https://github.com/PointCloudLibrary/pcl/pull/5113

@YamatoAndo I see. I am not sure how I installed PCL on the car PC, but I think I used autoware setup script. So I guess the PCL people normally have installed on there machine will have this bug, no?

Reverting the above PR https://github.com/autowarefoundation/autoware.universe/pull/2908 solved the problem. Currently @sykwer is trying to investigate and fix the issue for us.

Fixed https://github.com/autowarefoundation/autoware.universe/pull/2992


collaboration does not work for me

many times I want to share with someone my plunker, but I can not pass "Starting stream", I'll collaboration and give a stream with the id generated, but the screen goes Starting stream, and nothing happens, what can happen?

I think this is a duplicate issue with #72


Help !! How to set cross crop to vertical straight crop?

needed straight side of view instead of that triangle !!

can you please response ??
I am waiting for your response.
Please help ! i need it..

@vthakkar66  i need same thing did you find what you were looking for?

@vthakkar66 i need same thing did you find what you were looking for?

Yes i have found this
https://github.com/developer--/before_after_slider


onAttachedToRecyclerView & onDetachedFromRecyclerView not called

My RecyclerViewAdapter used onAttachedToRecyclerView and onDetachedFromRecyclerView Method.
But WrapperAdapter in RecyclerPaginate not called it.

If you are using a loading row (which is set by default) then your source adapter will be wrapped with WrapperAdapter.
The issue that you are mentioning is related to this architectural decision.  Your source adapter is not directly attached and observed by RecyclerView - the WrapperAdapter is.
That leads to immediate attaching and then detaching from RecyclerView which you can see in the logs e.g.:
paginate D/MyAdapter: onAttachedToRecyclerView
paginate D/MyAdapter: onDetachedFromRecyclerView

If you do not use the loading row this won't be the case since your source adapter won't be wrapped.
You can set up like following:
 Paginate.with(recyclerView, this)
            .addLoadingListItem(false)
            .build();

Next, that will be released soon will propagate attach/detach call from WrapperAdapter to the source adapter but this won't completely solve the issue since the adapter will be:

attached
detached and wrapped
attached again

By doing so you will have proper state that the adapter is actually "attached" but this but the glitch could be that you see one iteration od detaching then attaching when Paginate is setup. Depending on what you are doing in these callbacks this might or might not be an issue for you.
In logs you will see something like:
paginate D/MyAdapter: onAttachedToRecyclerView
paginate D/MyAdapter: onDetachedFromRecyclerView
paginate D/MyAdapter: onAttachedToRecyclerView

And when unbind is called, adapter source adapter is swapped back to RecyclerView so calls will be:
paginate D/MyAdapter: onDetachedFromRecyclerView
paginate D/MyAdapter: onAttachedToRecyclerView

The solution mentioned in the comment above has been implemented in the latest release (check release 1.0.0)
I'm closing this issue for now, feel free to reopen it with API suggestion for solving this problem or better yet pull request.


Preserve comments

https://github.com/Microsoft/TypeScript/wiki/Architectural-Overview#trivia

An interface for plugins to insert comments is available in TSTL since February:
https://github.com/TypeScriptToLua/TypeScriptToLua/commit/0fba69b06767811f554f21fa8f3d20cb51d5b25c
Is there anything technical holding back this feature?
I imagine that the end-user could apply "preserveComments: true" to their tsconfig.json, and then:
// This handles improbability
const foo = 42;

-- This handles improbability
local foo = 42

Nothing holding this back, just does not have much priority compared to other stuff I'm working on. If anyone else wants to open a PR for this feel free.

I imagine a feature where the end-user could apply "preserveComments: true" to their tsconfig.json

Just want to point this out, an existing compiler flag/option already exists, removeComments:
https://www.typescriptlang.org/tsconfig#removeComments
So, there is no need to introduce a new option ("preserveComments"), because an existing option could be read instead ("removeComments").

this issue shouldn't be closed, since my PR only gets JSDoc comments

Then you should not have marked your PR as 'fixes #815', I'll reopen


Add support for both width and height in measure

The idea is to make measure more generic. Like sizeThatFits: from iOS.
I'm working on adding a few tests too to go with this. But the Chrome tests interfere - as cannot be tested in Chrome. Also having an issue in the Java tests. The C tests work just fine.

@ColinEberhardt I would like to request some help/suggestions/direction here... What I am trying to do is to make measure more like sizeThatFitsSize: from iOS. Currently measure only takes a width and gives height as output. Hence it can only be used for text.
I would like to use it for images where I would like to maintain an aspect ratio. The way I go about this is to make a custom image module that implements measure. Currently this works in one direction - given a width, the height is maintained as per aspect ratio. But I would like this to work the other way around also.
I started work on this PR towards that direction. But I don't understand the code fully to be able to submit a full-fledged PR with corresponding tests... This is because the new sizeThatFits cannot be tested with the browser testing that is there here. It needs the more basic given this input, expect this output kind of testing.
Please help if you would agree that a more generic sizeThatFits: kind of API would be useful for css-layout. (ref: Apple Docs)

Hi @paramaggarwal sorry but i doubt I will be much help here, I have mostly been responsible for tidying up the JS API and distribution. I don't know enough about the C & Java use cases to be able to determine whether this is a good idea or not.
However, one thought springs to mind, wouldn't a better solution be to expand the CSS vocabulary of this project so that you can create a fixed aspect ratio element via CSS?

@ColinEberhardt Didn't want to extend the CSS vocabulary as it breaks the assumption that the API to this library is CSS itself... This measure based approach allows a generic way to override layout behaviour on a particular node in the layout hierarchy.

Fixed in https://github.com/facebook/css-layout/pull/154.


Regexp have not ProgramSize() function ---(re2)

What version of Go are you using (go version)?
go version go1.14.1 linux/amd64

Does this issue reproduce with the latest release?
Yes, checked https://pkg.go.dev/regexp?tab=doc
What operating system and processor architecture are you using (go env)?
go env amd64
$ go env

What did you do?
Checked https://pkg.go.dev/regexp?tab=doc for ProgramSize() function

What did you expect to see?
Rough estimate of how complex a compiled regex is to evaluate
What did you see instead?
Have not function of  ProgramSize()

I see that in re2 there is a method RE2::ProgramSize.  I assume that this issue is a request for a similar method for regexp.Regexp.  This seems simple enough to implement, though I don't know how meaningful the value is.  Turning this issue into a proposal.

@ianlancetaylor  Yes, this is what I want to say, thank you for your modification to the issue.
In my case, i need rough estimate of how complex a compiled regex is to evaluate.

One potential problem, on a week's reflection, is that today the regexp.Regexp package makes no mention in its API of how the search is implemented. There is always an underlying program today, but in the future maybe certain special cases won't have one. What then?
I wonder if it makes more sense for callers that need to know regexp program size to use regexp/syntax directly.
The original report does not say why this is useful, just that it was expected in the API.
@liangyuanpeng, what use did you have in mind for the program size?

@rsc
Sorry for my late reply.
Just used of regex match and replace in the proxy from http request . and we need checked Regular expression complexity in application started.
One example is the (Envoy)(https://www.envoyproxy.io/docs/envoy/latest/api-v3/type/matcher/v3/regex.proto#envoy-v3-api-msg-type-matcher-v3-regexmatcher) . Envoy use c++ re2 implementation it and we use Golang to do same thing.
If i didn't make it clear, remind me please!

I talked to Envoy folks about this last year. [1][2] I see now that their documentation says "a rough estimate of how complex a compiled regex is to evaluate", which is wrong. The program size is a crude "cost" signal, not a complexity metric. Having it is better than not having it, but one must understand that it's only slightly more informative than the length of the pattern string.

It might make sense to just use regexp/syntax directly to calculate program length. You can do that today, and it avoids adding any specific mention of implementation to package regexp.

Based on the discussion above, especially @junyer's comment, this sounds like a likely decline.
(If the functionality is needed in specific cases, use regexp/syntax directly.)

No change in consensus, so declined.

Forgot to close in July, sorry.


Volume Input Field

A text box to allow for exact input of volume.
Here is an example of what I mean.

Sounds like a nice idea I'll try looking into it


Preloaded image and used on:load for image

Used a new method to load images on application startup to preload the images for Result.
Used on:load property toggle image visibility only after it gets loaded.

Fixed the High-latency for loading Result SVG issue. https://github.com/g-chandran/typo/issues/3


Optimized the code by removing class header-centred #45

What is the purpose of this pull request?
Optimization of code, so even after reducing that there will be no change in the view of the website :)
How is this achieved?
Change a bit of html , by removing class header-centred
Which issue number does this fix?
#45

#54 fixes this and more

Looks like @dvlden has fixed this in #54 as well as much more. Sorry, but I will be closing this PR.

ok , yeah few hours ago he made a pr which had many such changes covering multiple issues @cpdevelops
Anyways thanks


Update examples to use new networking configuration

In #171 we updated the jobset controller to create 1 headless service for the entire jobset, rather than 1 headless service per replicatedJob, and to use the jobset name as the headless service name and subdomain name by default.
However, our examples still use the old paradigm with the subdomain name as the replicated job name, so they will not work with the v0.2.0 release until we update them.

/assign


Serializing Pipelines

We should have some mechanism for serializing pipelines, so we can run them again. This can either be a way to write the whole object to a file or to exactly re-generate it on a subsequent run. We may already be able to accomplish the latter using the __repr__ method; I think this is actually __repr__'s raison d'être

oui, c'est vrai

It turns out that the pipeline.__repr__() output and consistent settings for random.seed and numpy.random.seed are all we need.


[Docbug][Appdesignprocess][1837595]

Bug fix

Docs Build status updates of commit 62e35f6:
:white_check_mark: Validation status: passed

File
Status
Preview URL
Details

msteams-platform/concepts/design/design-teams-app-process.md
:white_check_mark:Succeeded
View

For more details, please refer to the build report.
Note: Broken links written as relative paths are included in the above build report. For broken links written as absolute paths or external URLs, see the broken link report.
For any questions, please:Try searching the docs.microsoft.com contributor guidesPost your question in the Docs support channel

Docs Build status updates of commit b5b9464:
:white_check_mark: Validation status: passed

File
Status
Preview URL
Details

msteams-platform/concepts/design/design-teams-app-process.md
:white_check_mark:Succeeded
View

For more details, please refer to the build report.
Note: Broken links written as relative paths are included in the above build report. For broken links written as absolute paths or external URLs, see the broken link report.
For any questions, please:Try searching the docs.microsoft.com contributor guidesPost your question in the Docs support channel


When to open submission

Hi Tao,
Could you tell me when you plan to open the submission process?
Thanks a lot!
Zecheng

Hi,
Sorry for the delay. We are planning to publish the submission guide by the end of this year.
Tao


Fix frequency string conversion from ts format, add test

Issue #, if available: Fixes #1649
Description of changes:
By submitting this pull request, I confirm that you can use, modify, copy, and redistribute this contribution, under the terms of your choice.
Please tag this pr with at least one of these labels to make our release process faster: BREAKING, new feature, bug fix, other change, dev setup

@borchero could you check whether the problematic cases you've found are covered by the test?

I wonder if we should have a more explicit lookup, ie a mapping from names to pandas frequencies. And then throw an error if we can't find the given input name.

I wonder if we should have a more explicit lookup, ie a mapping from names to pandas frequencies. And then throw an error if we can't find the given input name.

Yeah makes sense, we could do that


Add codecov support

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@0d75e7b). Click here to learn what that means.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master       #4   +/-   ##
=========================================
  Coverage          ?   87.22%
=========================================
  Files             ?       10
  Lines             ?      321
  Branches          ?        0
=========================================
  Hits              ?      280
  Misses            ?       41
  Partials          ?        0

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 0d75e7b...cbd2ffd. Read the comment docs.


adapt bounds of polygon in test

[ ] I added an entry to CHANGELOG.md if knowledge of this change could be valuable to users.

Here is a brief summary of what I did:
i changed the polygon bounds to not wrap into the next tile

 Polygon Raster Join Test mehr robust machen..

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

94 of 94 (100.0%)  changed or added relevant lines in 5 files are covered.
124 unchanged lines in 3 files lost coverage.
Overall coverage increased (+0.1%) to 87.893%

Files with Coverage Reduction
New Missed Lines
%

services/src/pro/users/postgres_userdb.rs
2
95.97%

operators/src/processing/neighborhood_aggregate/aggregate.rs
5
97.55%

operators/src/source/gdal_source/mod.rs
117
92.27%

Totals

Change from base Build<PHONE_NUMBER>:
0.1%

Covered Lines:
86602

Relevant Lines:
98531

💛  - Coveralls

bors merge


One picture mistakenly rejected as a duplicate

From @ToeBee on August 6, 2016 21:5
On some of my uploads I'm seeing the following output from the script:
No sequence file existing
Found 447 pictures to upload
processing G0013736.JPG
skipping - duplicate image
processing G0013738.JPG
Uploaded - 2 of total :447, percentage: 0.45%
processing G0013739.JPG
Uploaded - 3 of total :447, percentage: 0.67%
processing G0013737.JPG
Uploaded - 4 of total :447, percentage: 0.89%
processing G0013741.JPG
Uploaded - 5 of total :447, percentage: 1.12%
processing G0013742.JPG

When this particular upload completed, it only contained 446 images. Here is picture 1 of the sequence: http://openstreetview.com/details/11477/1
If you try to go to picture 0, it forwards to 1.
The first picture is about 20 meters north of the second picture and has a different file name. I'm not sure if this is the upload script or the server responding with an error.
Copied from original issue: openstreetview/uploader#10

From @ToeBee on August 6, 2016 21:14
I added some more print statements in the place where it prints out the duplicate image message. The data variable which I believe contains the response from the server is:
{'status': {'apiMessage': ' You are not allowed to add a duplicate entry (sequenceIndex)', 'httpMessage': 'Bad Request', 'apiCode': '660', 'httpCode': 400}}

But according to the file names in the output, it is uploading different files. So it seems like either there is some kind of off-by-one error in the upload script that causes the same contents to be uploaded twice at the beginning of the sequence or the server is mistakenly flagging images as duplicates somehow.

From @ToeBee on August 6, 2016 22:5
I added more debugging during the upload process. I printed out both the photo and photo_data variables on line 113. Here is the result:
No sequence file existing
Found 522 pictures to upload
photo:  {'photo': ('G0014448.JPG', <_io.BufferedReader name='/G0014448.JPG'>, 'image/jpeg')}
data_photo:  {'sequenceIndex': 0, 'coordinate': '38.65599554001036,-96.48843597000031', 'headers': 59.11930483795209, 'sequenceId': '11489'}
photo:  {'photo': ('G0014449.JPG', <_io.BufferedReader name='/G0014449.JPG'>, 'image/jpeg')}
photo:  {'photo': ('G0014450.JPG', <_io.BufferedReader name='/G0014450.JPG'>, 'image/jpeg')}
photo:  {'photo': ('G0014452.JPG', <_io.BufferedReader name='/G0014452.JPG'>, 'image/jpeg')}
data_photo:  {'sequenceIndex': 3, 'coordinate': '38.656040309998644,-96.48828589000176', 'headers': 92.21664626682987, 'sequenceId': '11489'}
data_photo:  {'sequenceIndex': 1, 'coordinate': '38.656004559988375,-96.48839636003116', 'headers': 67.82361963190183, 'sequenceId': '11489'}
data_photo:  {'sequenceIndex': 2, 'coordinate': '38.656011709996626,-96.48835445003417', 'headers': 71.5006605019815, 'sequenceId': '11489'}
photo:  {'photo': ('G0014453.JPG', <_io.BufferedReader name='/G0014453.JPG'>, 'image/jpeg')}
processing G0014452.JPG
data_photo:  {'sequenceIndex': 4, 'coordinate': '38.6559758199916,-96.48820831999146', 'headers':<PHONE_NUMBER>9733448, 'sequenceId': '11489'}
Uploaded - 1 of total :522, percentage: 0.19%
photo:  {'photo': ('G0014454.JPG', <_io.BufferedReader name='/G0014454.JPG'>, 'image/jpeg')}
processing G0014448.JPG
data_photo:  {'sequenceIndex': 5, 'coordinate': '38.655864060051144,-96.48816235003925', 'headers':<PHONE_NUMBER>1161474, 'sequenceId': '11489'}
data:  {'status': {'httpMessage': 'Bad Request', 'apiMessage': ' You are not allowed to add a duplicate entry (sequenceIndex)', 'httpCode': 400, 'apiCode': '660'}}
name:  G0014448.JPG
skipping - duplicate image

The error message seems to indicate that there is a duplicated sequenceIndex being sent with one of the pictures but I'm not seeing any evidence of this in the output. Maybe there is some threading problem that is changing something being sent across the wire at the last second?
Or what happens on the server if (as in this case) the picture 0 is not the first picture to finish uploading? Could that mess with something?

Can you send me a link with o couple of photos so i can make a test with them.
Thank's for reporting

From @ToeBee on August 6, 2016 22:26
It is looking to me like this is a server-side problem. I just did some packet captures and everything looks to be in order on my end of the wire. All the uploads have a unique sequenceIndex and I can see the file name in the EXIF data being uploaded. The order of the file names matches the expected sequence index number. The server just seems to be incorrectly returning the duplicated error on the first file uploaded.
As I said on the first comment, it isn't happening every time either. But often enough that I was able to reproduce it for my tests.

From @ToeBee on August 8, 2016 15:11
I am now pretty certain that the cause of this error is a picture other than picture 0 being finished uploading before picture 0 finishes. At work I wasn't seeing it happen nearly as much as at home. But now I made a test sequence where the 2nd file is tiny (220 KB instead of 2 MB) and now it happens every time. You can grab this test sequence here: https://dl.dropboxusercontent.com/u/1475575/OSM/test_sequence.zip

From @ToeBee on August 8, 2016 15:30
... Which I suppose means that this issue should actually be moved to the openstreetview.org repository since it seems to be a bug on the server side, not the upload script.

this issue was fixed.


az logic workflow show error

This is autogenerated. Please review and update as needed.
Describe the bug
Command Name
az logic workflow show Extension Name: logic. Version: 0.1.4.
Errors:
Unable to deserialize to object: type, KeyError: 'FlowAccessControlConfiguration'
Traceback (most recent call last):
Temp\pip-unpacked-wheel-k34ct6ah\msrest\serialization.py, ln 1430, in _deserialize
Temp\pip-unpacked-wheel-k34ct6ah\msrest\serialization.py, ln 1588, in deserialize_data
KeyError: 'FlowAccessControlConfiguration'

...

Temp\pip-unpacked-wheel-k34ct6ah\msrest\serialization.py, ln 1430, in _deserialize
Temp\pip-unpacked-wheel-k34ct6ah\msrest\serialization.py, ln 1588, in deserialize_data
msrest.exceptions.DeserializationError: Unable to deserialize to object: type, KeyError: 'FlowAccessControlConfiguration'

To Reproduce:
Steps to reproduce the behavior. Note that argument values have been redacted, as they may contain sensitive information.

Put any pre-requisite steps here...
az logic workflow show --resource-group {} --name {}

Expected Behavior
Environment Summary
Windows-10-10.0.19041-SP0
Python 3.6.8
Installer: MSI

azure-cli 2.15.1 *

Extensions:
logic 0.1.4

Additional Context

route to service team


A comments about adding new gdf_error

Also, added a code to avoid possible mistake that would cause memory bug.

@mtjrider should we mark this as [WIP]?

This seems reasonable to me

This is ready for review and merge.

run tests

Closing and reopening to trigger CI.


Is there a way to exclude an type inheriting a type targeted by an attribute?

I want to exluded all controllers from code coverage.
In runsettings I now have the following
      <!-- Match attributes on any code element: -->
      <Attributes>
          <Exclude>
          <!-- Don't forget "Attribute" at the end of the name -->
              <Attribute>^System\.Diagnostics\.DebuggerHiddenAttribute$</Attribute>
              <Attribute>^System\.Diagnostics\.DebuggerNonUserCodeAttribute$</Attribute>
              <Attribute>^System\.CodeDom\.Compiler\.GeneratedCodeAttribute$</Attribute>
              <Attribute>^System\.Diagnostics\.CodeAnalysis\.ExcludeFromCodeCoverageAttribute$</Attribute>
              <Attribute>^System\.Diagnostics\.CodeAnalysis\.DoesNotReturnAttribute$</Attribute>
              <Attribute>^Microsoft\.EntityFrameworkCore\.Migrations\.MigrationAttribute$</Attribute>
              <Attribute>^Microsoft\.EntityFrameworkCore\.Infrastructure\.DbContextAttribute$</Attribute>
              <Attribute>^System\.ObsoleteAttribute$</Attribute>
              <!-- Controllers shouldn't have to be tested by unit tests. Code that controllers call should. -->
              <Attribute>^Microsoft\.AspNetCore\.Mvc\.ControllerAttribute$</Attribute>
          </Exclude>
      </Attributes>

Unfortunately, despite controllers having the  [Controller] attribute, this attribute is placed on the ControllerBase type. Is it possible to target inheriting types with attributes on the base type?

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

ID: 43dc6fcf-df9f-9d2a-5c6e-8da0f6925afc
Version Independent ID: d0bf2cae-9b59-d537-7acb-7af5f560d8c1
Content: Customizing Code Coverage Analysis - Visual Studio (Windows)
Content Source: docs/test/customizing-code-coverage-analysis.md
Product: visual-studio-windows
Technology: vs-ide-test
GitHub Login: @Mikejo5000
Microsoft Alias: mikejo

@Pentadome -- Wouter, thank you for your thorough question.  Please consider these resources:

Ask a question or find an answer on the Microsoft Q&A page for Visual Studio.
Check the Visual Studio MSDN Forum.
Stack Overflow
Reddit

@Mikejo5000 -- Mike, please look into this issue.


[core] Compilation issues with nested anonymous classes

I would like to report some compilation issues with nested anonymous classes. I tested the following sample with latest git revision 0f00fb9 and openjdk8:
public class JobProcessor {

  public interface Job {
    public void executeJob();
  }

  public void start() {
    runJob(new Job() {
      @Override
      public void executeJob() {
        runJob(new Job() {

          @Override
          public void executeJob() {
            doSomething();
          }
        });
      }

      private void doSomething() {
      }

    });
  }

  public static void runJob(Job job) {
  }
}

Case 1: When I am using this settings
[x] inline anonymous classes
[x] inline methods
the result can't be compiled since "AnonymousClass1" does not exist.
Case 2: When I am using this settings
[ ] inline anonymous classes
[x] inline methods
the result can't be compiled too. Error is "class JobProcessor.AnonymousClass1 is already defined in class JobProcessor".
I'm getting the same result with java-input and java-convert.
This sample can be used in unit tests.

@nitram84 both cases fixed.


added alcohol warning for products with category en:alcoholic-beverages

Description
Added an alcohol warning for products that have the category en:alcoholic-beverages
Related issues and discussion
#2942

Can you provide a screenshot of the change @harshlele ?

A couple of remarks:

I would perhaps extract the category-specific logic to some file named CategorySpecificLogic.java (with the idea that it might grow overtime)
I wouldn't put it in the same line as categories (but possibly at the end of the card)

Something like this?

looks better 👍

@teolemon ive made the changes

@VaiTon storing logic in the translation files sounds a bit dangerous. I only gave a feedback in visual terms, not in code design

You're right. I'll make the string a field and review the entire PR.


logging: upgrade test job

new job that tests if the 'old' logging stack can be upgraded to the 'new' one from a particular PR.
The logic for deploying 'old' logging stack can be controlled with:

ORIGIN_UPGRADE_FROM_PREFIX - prefix/repo for logging images, defaults to 'docker.io/openshift/'
ORIGIN_UPGRADE_FROM_VERSION - version/tag for logging images, defaults to 'latest'
OPENSHIFT_ANSIBLE_UPGRADE_FROM_REF - commit/branch/tag for openshift-ansible, defaults to the branch PR is testing against

The upgrade steps are:

install 'new' origin
build 'new' origin-aggregated-logging images
deploy 'old' logging stack using openshift-ansible
make test-pre-upgrade
store 'test' value to Elasticsearch & query the 'test'
upgrade to 'new' logging stack using ansible and images built in step 2
make test-upgrade
store 'test2' value to Elasticsearch & query both 'test' and 'test2'

@jcantrill @stevekuznetsov  do we still want this? Or is there other way going forward for the EFK upgrade tests

I defer to @stevekuznetsov to whether we should be using alternate infra

stale for too long, closing this in favour of new framework for CI


Bug with JSON columns on >=1.15.0

If a column has this data:
["1", "5", "11155111", "42161", "42170", "43114", "8453", "56", "7700", "42220", "250", "10", "137", "1101", "59144", "1284", "1285", "534352", "7777777"]

And you upgrade to or past 1.15.0
You get this in return instead:
{"0":91,"1":34,"2":49,"3":34,"4":44,"5":32,"6":34,"7":52,"8":50,"9":49,"10":54,"11":49,"12":34,"13":44,"14":32,"15":34,"16":52,"17":50,"18":49,"19":55,"20":48,"21":34,"22":44,"23":32,"24":34,"25":52,"26":51,"27":49,"28":49,"29":52,"30":34,"31":44,"32":32,"33":34,"34":56,"35":52,"36":53,"37":51,"38":34,"39":44,"40":32,"41":34,"42":53,"43":54,"44":34,"45":44,"46":32,"47":34,"48":52,"49":50,"50":50,"51":50,"52":48,"53":34,"54":44,"55":32,"56":34,"57":50,"58":53,"59":48,"60":34,"61":44,"62":32,"63":34,"64":49,"65":48,"66":48,"67":34,"68":44,"69":32,"70":34,"71":49,"72":48,"73":34,"74":44,"75":32,"76":34,"77":49,"78":51,"79":55,"80":34,"81":44,"82":32,"83":34,"84":49,"85":49,"86":48,"87":49,"88":34,"89":44,"90":32,"91":34,"92":53,"93":57,"94":49,"95":52,"96":52,"97":34,"98":44,"99":32,"100":34,"101":49,"102":50,"103":56,"104":52,"105":34,"106":44,"107":32,"108":34,"109":49,"110":50,"111":56,"112":53,"113":34,"114":44,"115":32,"116":34,"117":53,"118":51,"119":52,"120":51,"121":53,"122":50,"123":34,"124":44,"125":32,"126":34,"127":55,"128":55,"129":55,"130":55,"131":55,"132":55,"133":55,"134":34,"135":93}

Possibly introduced in #164 @mattrobenolt @ayrton ?

Can you post the schema? But that serialization you're seeing is just a Uint8Array of the binary data, so something about the schema is causing us to treat it as raw binary.

@mattrobenolt
CREATE TABLE `sample` (
  `address` varchar(66) CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci NOT NULL,
  `chains` json NOT NULL,
  `updated_at` datetime DEFAULT CURRENT_TIMESTAMP,
  PRIMARY KEY (`address`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci;

And I'm guessing the column you're referring to is chains?

That is correct @mattrobenolt

Any updates here? @mattrobenolt
Pretty blocked on upgrading

@ayrton pinned at 1.14 for the time being. Let me know if you need any other information.

@ayrton This is specifically happening when querying this column from a View.

@ayrton It only happens when your view creates the JSON and you query the view. Will try and find time to make a reproducible.

I strongly suspect this was fixed with #174, but if it doesn't, we're in a good position to easily write a test to cover this if we have a query to reproduce exactly.


Submit Reply And Resolve

Hi, When I "Submit reply and change status to Resolved" the reply will be sent but the closed ticket template is not. I was just thinking that this was a bug?
Thanks

I just ran a test against HESK 2.6.2 (without Mods for HESK), and only the reply is sent (this also keeps the customer's inbox slightly cleaner and may also be less confusing). Since the behavior of this is the same with "regular" HESK, I don't plan on changing this anytime soon.


No example for how to load animations by name

How can Bevy's documentation be improved?
The animated_fox example shows how to load animations by path, but not by animation name.
By loading in the Gltf object directly and then debugging it, I was able to determine that I needed the path, not the animation name. However, no example of how I might use the animation name itself was found, despite it being substantially more human-readable.

Assuming "by path" is #Animation0?
The issue is that animations (and every sub asset in a gltf file) is guaranteed to have a path, but labels are optional.
To keep it consistent, labeled assets are always reachable by path, and it's not possible to have the same asset with two labels (#Animation0 and #Animation-Idle).

Assuming "by path" is #Animation0?

Correct, that was what I meant.

I'm working on a name-based GLTF workflow as breaking each individual asset I'm building into individual scenes is a headache.  As a datapoint, with just two sets of wall tiles for a hex world, I'm already over 150 nodes.  There's no easy way for me to figure out which index I want to load at this point.
I'm trying to figure out what are the key barriers to using a name-based asset label (tiles.glb#Node-cell_base_rock) vs index-based (tiles.glb#Node178).

To keep it consistent, labeled assets are always reachable by path, and it's not possible to have the same asset with two labels (#Animation0 and #Animation-Idle).

@mockersf is this a technical limitation of the AssetServer? Or specific to the bevy_gltf crate?
If it's a technical limitation of AssetServer, would there be opposition to a PR that adds a GltfLoaderSettings.by_name field that causes assets to be registered with their name instead of index?  With support for falling back to indexed name if there is no name for the asset.

It's a limitation of how assets work, and adding a setting to the gltf loader could be a good idea 👍

I asked in the discord about how difficult it would be to add LoadContext::add_asset_alias<A<(&mut self, label: String, handle: Handle<A>) and @NthTensor pointed me at this PR #10153 (Extension-less Assets).
I've confirmed that with that PR it's possible to add a second label for an asset.  This is the change I made to verify.  It crashes on the main branch, succeeds on the PR branch.
diff --git a/crates/bevy_gltf/src/loader.rs b/crates/bevy_gltf/src/loader.rs
index dae9cb647..12530e094 100644
--- a/crates/bevy_gltf/src/loader.rs
+++ b/crates/bevy_gltf/src/loader.rs
@@ -500,11 +500,18 @@ async fn load_gltf<'a, 'b, 'c>(
         let handle = load_context.add_labeled_asset(
             mesh_label(&gltf_mesh),
             super::GltfMesh {
-                primitives,
+                primitives: primitives.clone(),
                 extras: get_gltf_extras(gltf_mesh.extras()),
             },
         );
         if let Some(name) = gltf_mesh.name() {
+            load_context.add_labeled_asset(
+                format!("Mesh/{}", name),
+                super::GltfMesh {
+                    primitives,
+                    extras: get_gltf_extras(gltf_mesh.extras()),
+                },
+            );
             named_meshes.insert(name.to_string(), handle.clone());
         }
         meshes.push(handle);

I'm going to hold off on implementing the GltfLoaderSettings option for now.  As the extension-less PR moves forward, I'll open one to add labels for named assets.

I've confirmed that with that PR it's possible to add a second label for an asset. This is the change I made to verify. It crashes on the main branch, succeeds on the PR branch.

It doesn't crash for me on main with that change. What error are you getting?
This change would also be more controversial than adding settings, as it would use a lot more memory as each sub-asset is duplicated

Exception was:
thread 'main' panicked at /Users/dmlary/src/bevy/vendor/bevy/crates/bevy_asset/src/id.rs:219:13:
The target AssetId<bevy_gltf::GltfMesh>'s TypeId does not match the TypeId of this UntypedAssetId

I did also modify the load_gltf example to actually load a Handle<GltfMesh> by name. I can update the diff with that piece tomorrow.
I’ve started a thread in asset-dev talking about the possibility of adding label alias support as a mitigation for the duplication problem.  Initial question:  https://discord.com/channels/691052431525675048/749332104487108618/1193677168216125570
thread:
https://discord.com/channels/691052431525675048/749332104487108618/1193754022721622122
If the alias approach isn’t terribly complicated that would probably be a better solution overall, but honestly I haven’t had much engagement about it in the channel.
If the concept falls into controversial territory, I’ll just fall back to the setting option. Better to have some mechanism to use names now.

Aliases would be good if they don't cost too much performances. I tried before (before asset v2, before pipelined rendering) and it wasn't good, but chances are now it won't be as much costly

Would you be up to talking architecture with me on discord sometime? I poked around and have some ideas on how to approach it in the LoadContext but I don’t have a good view of the larger architecture of AssetServer. Even just a pointer to where the LoadContext::finish() results are ingested by AssetServer would be helpful. I wasn’t able to figure that out quickly on Sunday.

Updated the patch in https://github.com/bevyengine/bevy/issues/10715#issuecomment-1880268103 to include the change made to examples/3d/load_gltf.rs to trigger the crash on main.


Add arm32v7 variant of Stretch images

We want to add ARM32v7 images to fix https://github.com/dotnet/dotnet-docker/issues/223
Based on guidance from Docker folks, we will integrate the new images in our existing dotnet and dotnet-nightly repos. See: https://github.com/moby/moby/issues/33759.
We will make significant use of Docker multi-arch (MA) for dotnet images.
At a later point, we can likely make use of multi-arch for Debian dependencies (when MA shows up for Debian base images).

This PR is not done -- left to do:

[x] Validate correctness of the Dockerfiles
[x] Update README to include arm32 appropriately.
[ ] Generate appropriate MA tags/manifests.

@richlander,
Thanks for having already signed the Contribution License Agreement. Your agreement was validated by .NET Foundation. We will now review your pull request.
Thanks,
.NET Foundation Pull Request Bot

Would it make sense to put the existing Dockerfiles in an architecture directory so that the directory structure is consistent across platforms?
/2.0
/runtime
/stretch
/amd64
/arm32v7

Your formatting got messed up, but I'm pretty sure I know what you meant.
I spent some time looking at our README to see how the GitHub source links would show up per image. Upon further consideration, I like your suggestion better. My suggestion falls a little too much in the "clever" category by compressing the folder structure.

We could add an amd64 directory to the jessie directory for symmetry or leave as-is to keep things simple. Thoughts?

Just tested ASP.NET Core preview 2 within these Docker images on raspbian. The app was dotnet new mvc.

What is left @MichaelSimons? I think we are getting close to landing this PR.

@richlander, my preference would be to add the amd64 dir for Jessie as well in order to have symmetry.

@richlander - Regarding your question about the remaining work.

[ ] Machines to build arm images in official builds.  I have a request out to DDIT on this.
[ ] The image-builder tool used in official builds needs a minor tweak to support ARM builds.  I have the changes locally.
[ ] Once image-builder supports ARM, the new version needs to picked up and then the manifest.json needs to be updated so that official builds will build the MA tags for the ARM images.
[ ] Unit Tests should be updated to cover the new runtime images.

@MichaelSimons I am getting back to this. We should re-up on where we are at. I was looking at the manifest.json. It would be good to get some guidance on how like you'd like to pivot architecture within the format. I can see a couple options.
I just did a git pull --rebase to make this branch current.
Any progress on the work items you mentioned above?

@richlander, I just made https://github.com/dotnet/docker-tools/pull/28 to modify the image-builder tool to support ARM.  In the process of testing my change, I updated the manifest locally.  Once the PR is merged I will check-in my manifest changes.   The blocking issue right now is to get machines to do official builds on.  I will be pushing on this over the next few days to get us unblocked.

Cool. I was wondering how you would model another arch. I haven't thought about it deeply, but that looks good. I could see that the model wasn't quite going to survive as-is. Thanks!
Would be great to get unblocked! Thanks.

@richlander, @dagood I think this PR is ready for review.  I plan on writing a CI test for the ARM images but see that as a separate PR.

If you want to try out the multi-arch arm32 tags, I used the build infrastructure changes within this PR to build and push the images to msimons/dotnet-nightly

LGTM

How close or possible is an SDK image for ARM 32-bit? I saw there is a Runtime - but the source needs to be built too.

@alexellis - The .NET Core SDK does not run on the Linux + ARM32 configuration.  You will need to build your application on X64, copy the binaries to an ARM32 device and then build your Docker image.  Alternatively you can make use of a multi-stage Dockerfile on Window 10 or macOS.  The dotnet-docker-samples include a sample of this flow.  If you have feedback on the sample please feel open an issue in the dotnet-docker-samples repo.

From a workflow/CI perspective this is disappointing. I work with the RPi platform + Docker a lot as a Docker Captain and .NET developer at work.
Is this a temporary stumbling block or a permanent design decision? What about 64-bit ARM? Packet.net for instance have enterprise-grade Cavium servers which are very generously spec'd.

I wrote up the situation here: https://github.com/dotnet/announcements/issues/29.
So, no, not a permanent decision, but also not our highest priority to solve at the moment. The rational given (performance) wouldn't apply to ARM64, so I would expect a different choice there.
Our first focus is reducing the size of the SDK generally. Once we have that in-hand, then making a good experience on ARM32 should be easier.


TypeError: init() takes 2 positional arguments but 3 were given

Hi, I'm trying to use read2tree, but after it finishes making the orthologous genes selection and  allignment it gives me the error I'm attaching. I suspect that it has something to do with this specific line in the Aligner.py script:
SeqRecord(Seq("".join(self._get_translated_seq_list(codon, str(rec.seq))), generic_dna), id=rec.id))
the error is:
TypeError: init() takes 2 positional arguments but 3 were given
maybe I am doing something wrong. I've tried to use it both in single and multi species mode but it crashes in the same place.
Also I'm attaching the print out of the error. Could you help me please? and thanks a lot, it looks like a very promising tool
--- Load OGs with min 0 species from oma OMA/marker_genes - mode = marker_genes ---                                                                                Loading files for pre-filter: 100%|████████████████████████████████████████████| 8047/8047 [00:00<00:00, 10035.98 OGs/s]2023-05-05 14:02:34,049

read2tree.OGSet - INFO - --- Load ogs and find their corresponding DNA seq using the REST api ---                                                                                Loading OGs: 100%|██████████████████████████████████████████████████████████████| 8047/8047 [2:15:21<00:00,  1.01s/ OGs]                                                2023-05-05 16:17:55,512 - read2tree.OGSet
INFO - : Gathering of DNA seq for 8047 OGs took 8121.462993144989.
--- Generating reference for mapping ---
Loading records: 100%█████████████████████████████████████████████████████████████████████████████████████████████████████| 8047/8047 [00:00<00:00, 115837.87 record/s]2023-05-05 16:17:55,583 - read2tree.ReferenceSet - INFO - : Extracted 5 reference species form 8047 ogs took 0.07038140296936035
--- Alignment of 8047 OGs ---                                                                                multiprocessing.pool.RemoteTraceback:                                                                                """                                                                                Traceback (most recent call last):
File "/home/mjuarez/anaconda3/lib/python3.7/multiprocessing/pool.py", line 121, in worker                                                                                result = (True, func(*args, **kwds))
File "/home/mjuarez/anaconda3/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar return list(map(*args))
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/read2tree-0.1.5-py3.7.egg/read2tree/Aligner.py", line 292, in _align_worker align.dna = self._get_translated_alignment(codons, alignment)
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/read2tree-0.1.5-py3.7.egg/read2tree/Aligner.py", line 218, in _get_translated_alignment
SeqRecord(Seq("".join(self._get_translated_seq_list(codon, str(rec.seq))), generic_dna), id=rec.id))
TypeError: init() takes 2 positional arguments but 3 were given                                                                                """

The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/mjuarez/anaconda3/bin/read2tree", line 4, in  import('pkg_resources').run_script('read2tree==0.1.5', 'read2tree')
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 667, in run_script                                                             self.require(requires)[0].run_script(script_name, ns)
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1470, in run_script                                                            exec(script_code, namespace, namespace)
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/read2tree-0.1.5-py3.7.egg/EGG-INFO/scripts/read2tree", line 16, in
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/read2tree-0.1.5-py3.7.egg/read2tree/main.py", line 291, in main
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/read2tree-0.1.5-py3.7.egg/read2tree/Aligner.py", line 51, in init
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/read2tree-0.1.5-py3.7.egg/read2tree/Aligner.py", line 330, in _align                                          File "/home/mjuarez/anaconda3/lib/python3.7/multiprocessing/pool.py", line 268, in map return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/mjuarez/anaconda3/lib/python3.7/multiprocessing/pool.py", line 657, in get raise self._value
TypeError: init() takes 2 positional arguments but 3 were given

Dear @marcejuarez90
Thanks for using read2tree.
I would suggest using python version 3.10.8 (with a fresh environment) instead of python 3.7. I also suggest running  read2tree on the test dataset provided on the github page.
You can run in two steps
read2tree --standalone_path marker_genes --output_path output --reference
read2tree --tree --standalone_path marker_genes --reads sample_1.fastq sample_2.fastq --output_path output

If still you have an issue, please let us how you find the gene markers and the command you run.
Best regards,
Sina

Hello,
I'm also experiencing a similar issue to the one posed in issue #24. I also have the error "TypeError: init() takes 2 positional arguments but 3 were given" and I'm still encountering problems. My python version is 3.10.8. I found the marker genes using the OMA browser and instructions from your GitHub. It could easy be my code because I'm an absolute beginner. The file attached explains how I selected the marker genes, and the code I ran for making the tree:
r2t_2024JAN26.txt
I would be very grateful if you have any advice or can help.
Kind regards,
Alice

Dear Alice @afairnie
Thanks for reaching out.  Could you please send us the mplog.log file?
I had a run with 9 species that you mentioned
wget https://omabrowser.org/media/markers/marker_genes_7887d74f24fe883b16b92fe9f6b0d40b.tgz
tar -cvfz marker_genes_7887d74f24fe883b16b92fe9f6b0d40b.tgz
cat marker_genes/*.fna > dna_ref.fa
read2tree  --reference --standalone_path marker_genes/  --output_path output --dna_reference  dna_ref.fa

Could you please try the same procedure ?
This finished successfully.
--- Load OGs with min 0 species from oma marker_genes - mode = marker_genes ---
Loading files for pre-filter: 100%|█████████████████████████████████████| 400/400 [00:00<00:00, 1002.08 OGs/s]
2024-01-31 11:15:01,262 - read2tree.OGSet - INFO - --- Load ogs and find their corresponding DNA seq from dna_ref.fa ---
2024-01-31 11:15:01,262 - read2tree.OGSet - INFO - Loading dna_ref.fa into memory. This might take a while . . .
Loading OGs: 100%|██████████████████████████████████████████████████████| 400/400 [00:00<00:00, 1117.43 OGs/s]
2024-01-31 11:15:01,676 - read2tree.OGSet - INFO - : Gathering of DNA seq for 400 OGs took 0.3587369918823242.
--- Generating reference for mapping ---
Loading records: 100%|██████████████████████████████████████████████| 400/400 [00:00<00:00, 81880.02 record/s]
2024-01-31 11:15:01,682 - read2tree.ReferenceSet - INFO - : Extracted 9 reference species form 400 ogs took 0.005280256271362305
--- Alignment of 400 OGs ---
/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/r2t_3.10.8b/lib/python3.10/subprocess.py:961: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
  self.stdout = io.open(c2pread, 'rb', bufsize)
/work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/r2t_3.10.8b/lib/python3.10/subprocess.py:966: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
  self.stderr = io.open(errread, 'rb', bufsize)
2024-01-31 11:17:27,686 - read2tree.Aligner - INFO - : Alignment of 400 OGs took<PHONE_NUMBER>2674255.

As I didn't have your sequencing reads, I only run the first step of read2tree by adding  --reference to the command line.  ( and I guess the issue is related to the first step of read2tree)
I'm also wondering what is your Biopython version? mine is 1.81
Best,
Sina


Remove references to terraform vars from README

The variables themselves were removed in 278e081, but this reference to
them was left behind.

Good catch


Unable to write to flash due to "LFS_ERR_NOSPC" which is wrong

I'm using v2.8.1 version of LittleFS. The device is W25Q64JV. Build with STM32 GNU compiler, C++17.  Configs are:
//global context

#define CACHE_SIZE 			256
#define FLASH_READ_SIZE          256
#define FLASH_PROG_SIZE 	256
#define FLASH_SECTOR_SIZE	4096
#define FLASH_SECTOR_COUNT  2048
#define FLASH_SIZE (FLASH_SECTOR_SIZE * FLASH_SECTOR_COUNT)

#define LFS_CACHE_SIZE    CACHE_SIZE
uint8_t readBuffer[LFS_CACHE_SIZE];
uint8_t writeBuffer[LFS_CACHE_SIZE];
uint8_t lookBuffer[LFS_CACHE_SIZE] __attribute__((aligned(32)));

//init function
Database::Database()
{
    // block device operations
    cfg.read  = user_provided_block_device_read;
    cfg.prog  = user_provided_block_device_prog;
    cfg.erase = user_provided_block_device_erase;
    cfg.sync  = user_provided_block_device_sync;

    // block device configuration
    cfg.read_size = FLASH_READ_SIZE;
    cfg.prog_size = FLASH_PROG_SIZE;
    cfg.block_size = FLASH_SECTOR_SIZE;
    cfg.block_count = FLASH_SECTOR_COUNT;
    cfg.block_cycles = 500;
    cfg.metadata_max = 256;
    cfg.name_max = 255;
    cfg.attr_max = 512;
    cfg.file_max = LFS_FILE_MAX;

    cfg.cache_size = LFS_CACHE_SIZE;
    cfg.lookahead_size = LFS_CACHE_SIZE;

    cfg.read_buffer = readBuffer;
    cfg.prog_buffer = writeBuffer;
    cfg.lookahead_buffer = lookBuffer;

//....
}

My write function also could be useful to solve issue:
int Database::writeData(std::string fileName, void *buf, int size, int flags)
{
    lfs_file_t file;
    int status = lfs_file_open(&fs, &file, fileName.c_str(), flags);
    if (status != LFS_ERR_OK)
        return status;
    int sizeWrite = lfs_file_write(&fs, &file, buf, size);
    status = lfs_file_close(&fs, &file);
    if (status != LFS_ERR_OK)
        return status;
    if (sizeWrite != size)
        return -1;
    return sizeWrite;
}

It mounts just fine. I can read and write to flash. I can write 5 files with average file size about 130 bytes and read them. I can rewrite these files as many times as i want. Files content is JSON-strings.
But if i write another file (for example, size: 125, filename length: 26), it returns -28.  Then call lfs_file_close (which returns -28). Call stack is:
1 lfs_dir_commitattr
2 lfs_dir_commit_commit
3 lfs_dir_traverse
4 lfs_dir_relocatingcommit
5 lfs_dir_orphaningcommit
6 lfs_dir_commit
7 lfs_file_rawsync
8 lfs_file_rawclose
9 lfs_file_close

To be exact, lfs.c:1575 returns LFS_ERR_NOSPC while checking condition "commit->off + dsize > commit->end".
commit->off = 256;
commit->end = 248;
dsize = 12;
And for additional context, if i repeat this operation (try to do write operation again with the same file) it will ASSERT on lfs.c:262 (function "", string: LFS_ASSERT(pcache->block == LFS_BLOCK_NULL)), where pcache->block = 955
When i read flash into hex-file i see that there are much more data that i supposed to write and they are repeat each other no matter if i rewrite file or write new. Image viewer show something like this:

So the main question is: how do i solve such issue?
PS: Also write operation could throw "LFS_ERR_NAMETOOLONG" with such filename "/db/c_l/c_10_683642954602", which is not true since the length is only 27.

I managed to make it work downgrading version of littlefs to v2.0.5. I will probably lose some functionality but i actually dont really care.
Issue is still open but not that urgently

Thank you for the reply. It has a good explanation of things which i appreciate. I will try things you suggested and will comment this issue again if something will help

I know it's late, but I found a bug that is probably the cause of this issue: https://github.com/littlefs-project/littlefs/pull/1031
And thanks for reporting, even though it took a while to get to, the more info available the easier it is to root cause bugs like this.

glad to help


How to host on Heroku?

I've been trying to find some example somewhere of how to host an em-websocket app on Heroku and can't seem to find anything anywhere. I'm also new to EventMachine, so that doesn't help.
Can you please add some documentation to the wiki, or Readme that explains how you would go about hosting this on Heroku?
Thanks!

I'm afraid it's not possible to run a websocket server on Heroku - they don't support it. However (shameless plug) you could take a look at pusher.com ;)

Maybe em-websocket needs to be tweaked in order to run on Heroku? I found a blog article that mentioned that they can use Socket.io on node.js because it has some sort of fallback mechanism. em-websocket should be able to do that too. Not sure if it currently supports whatever fallback that is or how easy it is to implement but it would be great if it could do that.

Providing a fallback is outside the scope of em-websocket. As you say socket.io will work by falling back (in which case you're not using websockets, rather defeating the point). You should also take a look at sockjs.
Regardless, if you want efficient push to the browser you'll need to either stop using heroku for that component or use a third party service.

Problem is that Heroku is reseting connection after 40 seconds. Socket.io bypasses it by using long polling and reconnectiong every 40 seconds. That will not work on "real" websocket like em-websocket or any other "pure" server.

Thanks imanel, that makes a lot more sense now. I can see how long polling would be outside the scope of em-websocket. Thanks for the comments!

I would also like an example of a Heroku server running an em-websocket server, if they do indeed support such architectures now.  I will continue investigating on my own and post my results here if successful.


[VL] Enable collect_set, min, max for complex types

What changes were proposed in this pull request?
Follow up for https://github.com/apache/incubator-gluten/pull/5934
How was this patch tested?
UT.

cc @PHILO-HE  and @rui-mo , thanks.


ModernBox not working on Access 2016 x64

Hello Gustav, is it normal your code is not working on Access 2016 x64? I tried correcting function calling adding PtrSafe and replacing function or sub data type with LongPtr instead of Long but nothing.
Thank you, I would really like to use this!

Honestly, I don't know as I never run Office 64-bit. The steps you have taken sounds like those normally needed. Also, the few API calls made should be nothing special.
I will have to fire up an Access 64-bit but I cannot tell when that would happen. It is, however, already on my to-do list; unfortunately, this is very long.

Thank you for replying back, Gustav :)

Hello Gustav, I managed to get it working..... more or less!

First of all I downloaded the one from experts-exchange.com, becaue here on github it's missing the forms.
I then added "ptrsafe" after every declare, literally.

The only problem is, maybe it's related becaue I'm not using English as main language, the MsgMox is completely missing captions inside the buttons.
It writes an empty string inside each buttons I don't know why though...
Any help is appreciated!

That is good news.
First, the forms are there, the *.cls files, but I should make a note, that these must be imported in Access with the command SaveFromText.
Second, adding ptrSafe for all declarations is what I have heard is a must.
Third, the button captions are - as you probably have found out - retrieved by the function FillCaptions as described in the article under the paragraph "Localized captions". It should work for any localization, and User32.dll is the file to call even under 64-bit as discussed here: Invoking user32.dll on a 64 bit system.
You could try to call with other caption ID than FirstCaptionId and LastCaptionId. If no success, please let me know, and I can try to research the issue.
Thanks for your findings.

Hello Gustav, I tried creating a test form with a button that, if pressed, shows the caption corresponding to the index. I tried with some, but it looks like the LoadString call doesn't produce a result.
Yan

Sounds right. I've researched a little on LoadString but found exactly nothing related to issues or different behaviour under 64-bit.
I'll have to get back with this. Thanks for narrowing it down.

Hey again, analyzing deeper with Err.LastDLLError I found that, after the LoadString call it produces either one or the other:

ERROR_RESOURCE_DATA_NOT_FOUND
1812 (0x714)
The specified image file did not contain a resource section.
ERROR_RESOURCE_TYPE_NOT_FOUND
1813 (0x715)
The specified resource type cannot be found in the image file.

I have no explanation for that. But, of course, with those errors, no captions will be retrieved.

Hello Gustav, I finally managed to get it working 100% on 64 bit. I tested it on a 32bit Office 2010 and it seems to work.
Here's all it needs to be done:

Add PtrSafe when you Declare an API function
Change Long to LongPtr in as the LoadLibrary API call data type (and edit the variables and the other related lines of code as well)

It's really cool now!

That is great news. Thank you so much for clearing it up - I don't know when I would have found the time for working with this.
I'll add the changes when I have an Access 64-bit up and running.


Fix ClientBodyBufferSize annotation

replaces https://github.com/kubernetes/ingress/pull/1217

This change is

Coverage increased (+0.02%) to 44.276% when pulling 99193fc2ed98d0a47f8be77a84eb2dcba6ecae7b on aledbf:fix-client-bs into 0c6f15e372c831de52fcc393932540bb3a6d51b5 on kubernetes:master.


remove item

Hi, thanks for your work, it really makes work with caching very frustrating. I have a question. I need to find the cached item and update it, how can I do this?

CachingPlayerItem doesn't do caching, it only provides you with the downloaded data. It's up to you to how to store it


Update Contribution Guide - assign PR to Issue

For preparation to do more and more specification in github itself (up to now published pdf of the specification was the master) we need to have a stringent coupling of issues and PRs. This is the proposal for the update of the current Create Pull Request SubChapter (in the moment it is recommended to prefix with profile name, e.g. BirgitBoss/myNewFeature:
Create Pull Request
Proposals for changes to the content of the repository are managed through Pull Requests (PRs).
To open such a PR, implement the changes in a new feature branch. Each PR must reference an issue and follows the naming schema: -. For a new PR the target branch is the main branch while the source branch is your feature branch The feature branch branch should be developed in a fork of the upstream repository. So before working on your first feature, you need to create such a fork (e.g., by pressing the Fork button in the top right corner of the GitHub page)
When opening a PR please consider the following topics:
- optional: Rebase your development on the branch to which you plan to create the PR.
- Each PR must be linked to an Issue:
    Reference the Issue number in the name of your feature branch and the description of the PR.
    Mention the Issue in one of the commit messages associated to the PR together with a GitHub keyword like closes #IssueNumber or fixes #IssuesNumber. For more details visit the GitHub documentation on linking PR with Issues
- Each PR should only contain changes related to a single work item. If the changes cover more than one work item or feature, then create one PR per work item. You may need to create new more specific Issues to reference if you split up the work into multiple feature branches.
- Commit changes often. A PR may contain one or more commits.

This is not an Issue, but a very good change request. Please feel free to make a commit with s follow-up PR for this particular change.

Every change needs an issue. But this is exactly the scope of the issue to define these rules.


CLOUD-2066. Add CCM client to CB images.

With these changes, the CCM client infrastructure and prerequisites
have been added to the Salt configuration for CB images.

FYI, here is the client package module based on the code that is currently running in Altus. I renamed some of the scripts for consistency and got everything into Salt, but there are no functional changes.
https://github.infra.cloudera.com/thunderhead/thunderhead/tree/master/clients/autossh-adventure


Asynchronous shader warm-up

Internal: b/193584046
It's my understanding that we do shader warm-up synchronously on startup today. We should investigate how much effort it would take to make this asynchronous, so that an app that needs a lot of shaders compiled on startup can still have a fast startup time (time to first frame).

This would be awesome! currently my app is taking 10+ seconds on first start with just a few animations

I'm new to this, so I was wondering what the implications of asynchronous shaders are. A faster startup time, especially for Flutter Web, is killer, but what exactly changes when we do it asynchronously. Are we more likely to see visual glitches because the shaders are still being warmed up or jank?

Tracking: This is being attempted by Jim for Metal on iOS In https://bugs.chromium.org/p/skia/issues/detail?id=12141. More context in go/flutter-skia-async-warmup. Too early to tell what the implications are going to be.

I'm new to this, so I was wondering what the implications of asynchronous shaders are. A faster startup time, especially for Flutter Web, is killer, but what exactly changes when we do it asynchronously. Are we more likely to see visual glitches because the shaders are still being warmed up or jank?
Just to be clear, Flutter Web does not currently perform shader warmup so this will not impact flutter web startup times.

This commit was landed and rolled into the engine after a brief revert. That change relied on the Metal system cache to hold onto the results. I will have to follow up with Jim on whether the other work items in the linked docs are still in progress.

This was committed and landed. customer: money is not willing to benchmark the application with async precompilation so we must benchmark the effects in harnesses that are under construction at the moment.

Closing this as fixed per updates from customer:money.


Remove temp variable [phab:D1075]

Created by salguarnieri at 2016-09-21 22:20:19:

shahms accepted this revision at 2016-09-21 22:25:43

fromberger accepted this revision at 2016-09-21 22:25:44

salguarnieri closed via commit ce5e78f4223e23159a75d626fbb53bd303785e94 at 2016-09-21 22:27:31


Continued issues with publishing modules to vsts package feed and manual nuget source configuration

So I could explain the issues that I have been having with using the publish-module cmdlet to publish modules to a vsts package feed, and about how it was (somewhat) working in powershellget 1.5.0, but you broke it again in the latest version (see this link), and how, even if I were using powershellget version 1.5.0, in order to successfully publish a module to a vsts package feed that does not have the nuget executable which powershellget uses (located at "C:\ProgramData\Microsoft\Windows\PowerShell\PowerShellGet\NuGet.exe") available on the system, we are forced to run publish-module twice (the first time to make the nuget exe available with the expectation the publish operation will fail and the second time after we manually add the source configuration to nuget which actually does publish the module), but why bother when there are numerous, numerous, numerous posts which have already reported this, and many of them quite old (over a year): #234, #133, #61, #101, #199 , #91, and lets go ahead and add this submission to the list.  So that makes a grand total of 7 requests to fix the issues with the powershellget as it pertains to being able to publish powershell modules to vsts feeds, as well as resolving the issues with nuget (having to manually add repo URL to source list), so my question is are there any plans to actually, you know, FIX THE PROBLEM!?!?!?  As I stated previously, around half of the listed issues were posted OVER A YEAR AGO!!!  The fact that this still remains a problem is UNACCEPTABLE!!!  Is there any intention whatsoever to resolve these issues, or are we wasting our time?

@whiggs

Regarding the issue mentioned at link. A parameter cannot be found that matches parameter name 'AllowPrereleaseVersions' error should not happen when you launch a new PowerShell session. More details on this issue can be found at https://github.com/PowerShell/PowerShellGet/issues/208 . If you need to use the newly installed version of PowerShellGet within the current process, you will have to run Import-Module -Name PowerShellGet -Force; Import-PackageProvider -Name PowerShellGet -Force.

Bootstrapping NuGet.exe to "C:\ProgramData\Microsoft\Windows\PowerShell\PowerShellGet\NuGet.exe"

Invoke-RestMethod https://nuget.org/nuget.exe -OutFile "C:\ProgramData\Microsoft\Windows\PowerShell\PowerShellGet\NuGet.exe"

For publishing to a VSTS feed, it is required to register the VSTS feed and credentials with NuGet.exe. NuGet.exe doesn't allow us to specify the credential as a parameter. Let us know if you have any ideas on resolving this.

Apart from the enhancement issues, please let us know what other issues are blocking you from using the VSTS feed with PowerShellGet module. This will help us in prioritization.

@bmanikm : you ask for what are our blocking issues, but have you actually tried using it yourself and got it working? Using PowerShellGet with a VSTS / NuGet repository is still a hot mess.

To start using it, you have to read a series of blogs or articles, all with varying levels or reliability.

I used https://github.com/PowerShell/PowerShell-Docs/issues/1200#issue-227526581

You still have to provide -Credential. Can those credentials not be stored somewhere secure? For example when using Register-Repository, you could use Export-Clixml to store the credential, readable for the current user only.

Having to use -Credential blocks combining multiple repositories, as some need it, and some don't use it.

Find-Module seems to work (somewhat), but Publish-Module fails all the time, and with errors that are not resolvable for a user. How about:

Publish-PSArtifactUtility : Failed to publish module 'My.Module': 'Cannot prompt for input in non-interactive mode.
'.
At C:\Program Files\WindowsPowerShell\Modules\PowerShellGet\1.6.0\PSModule.psm1:1447 char:17
+ ...             Publish-PSArtifactUtility @PublishPSArtifactUtility_Param ...
+                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : InvalidOperation: (:) [Write-Error], WriteErrorException
    + FullyQualifiedErrorId : FailedToPublishTheModule,Publish-PSArtifactUtility

(using Module PowerShellGet 1.6.0, PackageProvider PowerShellGet <IP_ADDRESS>, NuGet <IP_ADDRESS>)

Yes, I have used VSTS repositories. I have also provided the required steps to @jianyunt to add the required documentation https://github.com/PowerShell/PowerShell-Docs/issues/1200.
Regarding credential persistence, please take a look at https://github.com/PowerShell/PowerShellGet/issues/105#issuecomment-369006689.
For publish-module error, did you specified the -Credential parameter for publishing to a VSTS feed as mentioned in https://github.com/PowerShell/PowerShell-Docs/issues/1200#issue-227526581 ?

@bmanikm yes, I am using the credential. See below:
PS C:\Users\My\PowerShell\Release> Get-PSRepository

Name                      InstallationPolicy   SourceLocation
----                      ------------------   --------------
PSGallery                 Untrusted            https://www.powershellgallery.com/api/v2/
company.PowerShell        Trusted              https://company.pkgs.visualstudio.com/_packaging/company.PowerShell/nuget/v2/

PS C:\Users\My\PowerShell\Release> Find-Module -Repository company.PowerShell -Credential $patCred

Version              Name                                Repository           Description
-------              ----                                ----------           -----------
<IP_ADDRESS>              company.PowerShell.Assert           company.PowerShell   company.PowerShell.Assert

PS C:\Users\My\PowerShell\Release> Publish-Module -Path .\company.PowerShell.Assert\ -NuGetApiKey company.PowerShell -Repository Goud
se.PowerShell -Credential $patCred
Publish-PSArtifactUtility : Failed to publish module 'company.PowerShell.Assert': 'Cannot prompt for input in non-interactive mode.
'.
At C:\Program Files\WindowsPowerShell\Modules\PowerShellGet\1.6.0\PSModule.psm1:1447 char:17
+ ...             Publish-PSArtifactUtility @PublishPSArtifactUtility_Param ...
+                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : InvalidOperation: (:) [Write-Error], WriteErrorException
    + FullyQualifiedErrorId : FailedToPublishTheModule,Publish-PSArtifactUtility

PS C:\Users\My\PowerShell\Release> Get-Module PowerShellGet

ModuleType Version    Name                                ExportedCommands
---------- -------    ----                                ----------------
Script     1.6.0      PowerShellGet                       {Find-Command, Find-DscResource, Find-Module, Find-RoleCapability...}

PS C:\Users\My\PowerShell\Release> Get-PackageProvider

Name                     Version          DynamicOptions
----                     -------          --------------
msi                      <IP_ADDRESS>          AdditionalArguments
msu                      <IP_ADDRESS>
NuGet                    <IP_ADDRESS>        Destination, ExcludeVersion, Scope, SkipDependencies, Headers, FilterOnTag, Contains, AllowPrereleaseVersions, ConfigFile, SkipValidate
PowerShellGet            <IP_ADDRESS>          PackageManagementProvider, Type, Scope, AllowClobber, SkipPublisherCheck, InstallUpdate, NoPathUpdate, AllowPrereleaseVersions, Filter, Tag, Inc...
Programs                 <IP_ADDRESS>          IncludeWindowsInstaller, IncludeSystemComponent

As mentioned below at PowerShell/PowerShell-Docs#1200, for publishing to a VSTS feed, please register your source with NuGet.exe.
# Publish modules to your VSTS package management feed using your PAT-base token.
# For publishing, it is required to add your VSTS feed with username and PAT token, so that NuGet.exe uses these credential during push operation.
NuGet.exe sources Add -Name "psgettestfeed" -Source "https://myrepo.pkgs.visualstudio.com/_packaging/psgettestfeed/nuget/v2" -UserName<EMAIL_ADDRESS>-Password $myPatToken

For your VSTS feed, please run below with your user name and PAT as password.
NuGet.exe sources Add -Name "https://company.pkgs.visualstudio.com/_packaging/company.PowerShell/nuget/v2/" -UserName $userName -Password $myPatToken

If NuGet.exe is not available on your machine, please refer to https://github.com/PowerShell/PowerShellGet/issues/245#issuecomment-373525017.


How to project numerical and categorical data?

I want to project the Titanic dataset it contains categorical and numerical data?
I heard in this video (min 48:08), basically says that UMAP can combine multiple data types, so the question is how?
One approach would be to project numerical data only and then categorical data only and finally combine them in the same space. But Is that approach the way to go?
Thank you for your time.

This can be done in theory; in practice I am still working on the code to
do this, so it isn't available in the repository yet. This may not be the
answer you are looking for. As in interim step you can check issue #58
which provides a simple recipe to do this in straightforward cases.
On Sun, Aug 5, 2018 at 1:08 AM romanics<EMAIL_ADDRESS>wrote:

I want to project the Titanic dataset
https://www.kaggle.com/c/titanic/data it contains categorical and
numerical data?
I heard in this video https://www.youtube.com/watch?v=YPJQydzTLwQ (min
48:08), basically says that UMAP can combine multiple data types, so the
question is how?
One approach would be to project numerical data only and then categorical
data only and finally combine them in the same space. But Is that approach
the way to go?
Thank you for your time.
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/lmcinnes/umap/issues/104, or mute the thread
https://github.com/notifications/unsubscribe-auth/ALaKBdRR_uPa94E19J3HWL1wO3R0LbOvks5uNn3EgaJpZM4VvPjc
.

The data with both categorical and numerical data types can be handled using gower-distance metric. You can download the code for gower distance metric from here. It might be available in coming scikit-learn release.

While Gower distance is quite useful it is also somewhat heuristic. I would recommend exploring it as one of the options for handling mixed continuous and categorical data.

Is it possible to create indicator variables from categorical variables.

One approach is pd.get_dummies, but you may also want to look at the dirty-cat library for richer options.


tegra-configs-alsa: install ALSA config files for tegra210

HDMI audio doesn't work with pulseaudio on the Jetson Nano devkit. This adds the missing ALSA configs.

Thanks!


Update storage-blob-event-overview.md

Updating the documentation to enhance the verbiage for one of the practice for consuming events.

@Amrinder-Singh29 : Thanks for your contribution! The author(s) have been notified to review your proposed change.

#sign-off

Thanks, all. Merging in the repo is paused; this PR is in the queue to merge when merging resumes. Thanks.


Local readonly variables not declared correctly

We currently use local readonly to declare local, read-only variables. It turns out that this is not the right way to do it. The proper way is:
local -r var="$1"

For arrays, you need:
local -ar var=(foo bar)

I believe this is resolved in #8.

 This was fixed by https://github.com/gruntwork-io/bash-commons/pull/11. Finally closing :)


Descriptive error for app not found

Exception structure styled under the advice found here: https://stackoverflow.com/questions/5200842/where-to-define-custom-error-types-in-ruby-and-or-rails
Currently, a request for an invalid package raises a NoMethodError on nil. This is pretty hard to catch without potentially catching a bunch of other things.
This PR represents a small departure from the existing style in the spec-file. I'm happy to work to make it uniform with your standards if this is something you'd like for the gem.

@bentheax thanks for the pull requests!

@bentheax the tests fail after merging this request...
........F........................

Failures:

  1) App Updating Quick API not found doesn't raise a generic NoMethodError
     Failure/Error: expect {
     ArgumentError:
       `expect { }.not_to raise_error(SpecificErrorClass)` is not valid, use `expect { }.not_to raise_error` (with no args) instead
     # ./spec/market_bot/android/app_spec.rb:191:in `block (4 levels) in <top (required)>'

I don't have time to dig into the problem at the moment.  Do you have time to send me another pull request to resolve the issue?

@chadrem Sure. I know what the error is, I'm not sure why I didn't encounter it in my own test run :blush:
That's the test I originally wrote in TDD fashion, it's superseded by the "raises a ResponseError" test.The fix here is just to remove it.

@chadrem The issue is due to a deprecation in rspec 3. Since I ran with bundle exec rspec, I got the 2.8 version from Gemfile.lock and it all ran fine.
Since the test adds no value, it can be removed. See: https://github.com/chadrem/market_bot/pull/35

@bentheax Thanks again for the pull requests and fix.  I've just released v0.14.0 with your changes.


Fix gRPC handler unit tests

Mock CSI driver in gRPC request handlers unit tests
Add test case about CSI response error

/assign @carlbraganza

/release-note-none


Tesseract will not load trained data

I installed Tesseract on an iOS11 project and I'm using Xcode 9. I've followed the instructions to a T, but I cannot get Tesseract to see my trained data file.

I imported it as a reference, per the instructions. I've tried with vanilla eng files and best eng files found on Google. Neither works. I get the following error:

Please make sure the TESSDATA_PREFIX environment variable is set to the parent directory of your "tessdata" directory.
Failed loading language 'eng'
Tesseract couldn't load any languages!

Hi
I have checked the build and it did not include my referenced folder (tessdata) unless i added it to the copy bundle resources under build phases. This however only moved the problem to another error
actual_tessdata_num_entries_ <= TESSDATA_NUM_ENTRIES:Error:Assert failed:in file tessdatamanager.cpp, line 53
What did you do with libz.dylib, are you using libz.tbd?!
I have tried, the training data for fast, best and legacy 4.0.0, please comment if you find the solution to this.
Kind regards

Hi,
I have exactly the same problem at the moment :-/

It seems that 4.0.0 isn't yet supported, see #343. I had to download trained files from the 3.04 tree

That works :D thanks alot!

Having the same issue. What's the fix?

Use the Data Files for Version 3.04/3.05.


ouput filename as command line parameter

Looks good for me :) Thank you very much! Sorry for the delay.


HTTPS all the things

Noticed that we still have a bunch of HTTP links, which could present mild MiTM risks that we can totally remove.
One short coming of this was:
cargo/src/etc/_cargo:13 "http://zsh.sourceforge.net/Doc/Release/Completion-System.html#Completion-Functions" of which does not have an HTTPS equivalent yet.

@bors retry

@bors r+

:pushpin: Commit a9480edbc2aeeb4a547a83d0b18c7fa1132bb83e has been approved by dwijnand

:hourglass: Testing commit a9480edbc2aeeb4a547a83d0b18c7fa1132bb83e with merge 770dd2fea698c7fd54a3ed09ab8090739fc71b27...

:broken_heart: Test failed - checks-travis

:umbrella: The latest upstream changes (presumably #6654) made this pull request unmergeable. Please resolve the merge conflicts.

Thanks!
@bors r+

:pushpin: Commit 7185e98fb0c2f7df24fc570287bdfd80e47d40b2 has been approved by ehuss

:hourglass: Testing commit 7185e98fb0c2f7df24fc570287bdfd80e47d40b2 with merge 131823ad4b6f30ff2b67adb7a0ff7214752c1875...

:sunny: Test successful - checks-travis, status-appveyor
Approved by: ehuss
Pushing 131823ad4b6f30ff2b67adb7a0ff7214752c1875 to master...


algorithm for Util.lineSegmentIntersection

In Util.js:
    /*
     * Computes the intersection of two line segments. Algorithm taked from Paul Bourke, 1989:
     * http://astronomy.swin.edu.au/~pbourke/geometry/lineline2d/
     * Ported from MathUtil.java on 9/20/2013 by @samreid
     * line a goes from point 1->2 and line b goes from 3->4
     * @returns a Vector2 of the intersection point, or null if no intersection
     */
    lineSegmentIntersection: function( x1, y1, x2, y2, x3, y3, x4, y4 ) {

The URL is broken, so difficult to determin what "takes from" (sic) means.  Assigning to @jonathanolson to evaluate whether there's a third-party licensing issue here.

@samreid, do you recall the "upgrade piccolo incident"? MathUtil.java was 'created' in that commit, noting "un-deleted all files that were lost in the 'upgrade piccolo incident'".
I can't find history or commit messages for when it was truly added before, but that code's at least 10 years old.

Here's a Bourke reference:
http://paulbourke.net/geometry/pointlineplane/pdb.c
parent page is:
http://paulbourke.net/geometry/pointlineplane/

The "undeleted all files" commit is from Nov 2005, svn revision 5790.  Hunting around online, I found the path for svn revision 5000 to be right here:
https://phet.unfuddle.com/a#/projects/9404/repositories/23262/file?path=%2Ftrunk%2Fphetcommon%2Fsrc%2Fedu%2Fcolorado%2Fphet%2Fcommon%2Fmath%2FMathUtil.java&commit=5000
that is, svn/5000/trunk/phetcommon/src/edu/colorado/phet/common/math/MathUtil.java
r5000 contains bourke algorithms.

@jonathanolson and @pixelzoom is this enough to go on? Should we add it to an upcoming meeting agenda?

I'm not familiar with the algorithm or whether there's a licensing issue here, I only stumbled upon it.  So I'm the wrong person to ask.

I see several algorithms in this file that look like we did not write them ourselves.  Would be good to identify them.  I'll create a separate issue for that (this can be a sub-issue).

I noted this and other potential issues in #31

A problem occurred in one of the sims that was caused by the lineSegmentIntersection algorithm, noted in #53, so I used a small epsilon value instead of zero to check if the intersection exists. This fixes the problem, however, use of the epsilon value may not be a robust way to check for segment segment intersection. I will try to look for a new implementation of lineSegmentIntersection. Also, the error may be introduced by the linelineIntersection algorithm which lineSegmentIntersection uses.

lineSegmentIntersection done. Assigning to @jonathanolson to review.

Ran into issues tonight with this function, will take the time to review here.
Tried running:
dot.Util.lineSegmentIntersection( 30.353261553154365, 16.69400908470202, 72.78826487008264, 73.88814243860902, 72.78826487008264, 73.88814243860902, 89.96204100680747, 97.03505337951492 );

of two lines, essentially:

30.353261553154365, 16.69400908470202 => 72.78826487008264, 73.88814243860902
72.78826487008264, 73.88814243860902 => 89.96204100680747, 97.03505337951492

The current code returns Vector2 {x: 85.33333333333333, y: 85.33333333333333}, while the old code returns the shared endpoint (Vector2 {x: 72.78826487008264, y: 73.88814243860902}).
Investigating and reviewing.

Adding an epsilon for the denominator properly detects this case.

Failing for:
dot.Util.lineSegmentIntersection(<PHONE_NUMBER>302738,<PHONE_NUMBER>440668,<PHONE_NUMBER>431545,<PHONE_NUMBER>4345773,<PHONE_NUMBER>431545,<PHONE_NUMBER>4345773,<PHONE_NUMBER>926097,<PHONE_NUMBER>940025 )

where the true intersection point would be at the shared endpoint (not a point that is 0.0007806235324924636 in distance from the shared endpoint).

Yes adding the epsilon check and also handling the case where it is an exact endpoint overlap does the trick. Closing


Removed debug statement

This pull request is going into the wrong branch for this reason I will close it


[v1.15] Author backport of #32200

Currently, when L7 policies (egress or ingress) are enforced for traffic between Pods, Envoy might change x-forwarded-for related headers because the corresponding Envoy listeners don't trust the downstream headers because XffNumTrustedHops is set to 0.
e.g. x-forwarded-proto header:

Downstream x-forwarded-proto headers will only be trusted if xff_num_trusted_hops is non-zero. If xff_num_trusted_hops is zero, downstream x-forwarded-proto headers and :scheme headers will be set to http or https based on if the downstream connection is TLS or not.

https://www.envoyproxy.io/docs/envoy/latest/configuration/http/http_conn_man/headers#x-forwarded-proto
This might be problematic if L7 policies are used for egress traffic for Pods from a non-Cilium ingress controller (e.g. nginx). If the Ingress Controller is terminating TLS traffic and forwards the protocol via x-forwarded-proto=https, Cilium Envoy Proxy changes this header to x-forwarded-proto=http (if no tls termination itself is used in the policy configuration).
This breaks applications that depend on the forwarded protocol.
Therefore, this commit introduces two new config flags proxy-xff-num-trusted-hops-ingress and proxy-xff-num-trusted-hops-egresss that configures the property XffNumTrustedHops on the respective L7 policy Envoy listeners.
For backwards compabitility and security reasons, the values still default to 0.
Note: It's also possible to configure these values via Helm (envoy.xffNumTrustedHopsL7PolicyIngress & envoy.xffNumTrustedHopsL7PolicyEgress).
Author Backport of #32200 (Config properties not yet in Hive Cell on v1.15)
Once this PR is merged, a GitHub action will update the labels of these PRs:
 32200

l7 policy: add possibility to configure Envoy proxy xff-num-trusted-hops

/test-backport-1.15

Marking manually as ready-to-merge as MLH doesn't seem to do it. (v1.14 backport already merged)


[Bug] After the flink job written to Paimon modifies sink.parallelism, the job will not be able to recover from the checkpoint

Search before asking

[X] I searched in the issues and found nothing similar.

Paimon version
master
Compute Engine
flink
Minimal reproduce step

First set the parallelism degree of 1 to write Paimon

Stop passing the current task

Modify the parallelism to be greater than 1

Restore from the last checkpoint

What doesn't meet your expectations?
The job should be able to resume normally from the last checkpoint or savepoint, even if I change the parallelism of the sink
Anything else?
No response
Are you willing to submit a PR?

[ ] I'm willing to submit a PR!

@huyuanfeng2018 this is a good issue, but a chain committer can reduce resource cost.
maybe we can have an option to control this.

@huyuanfeng2018 this is a good issue, but a chain committer can reduce resource cost.
maybe we can have an option to control this.

+1. Agree


[SUGGESTION] Cross-server messaging

Possibility to link much server tchat with bungee or other methods,

This is something we're looking into currently.


Fix tests affected by changes in HTML

This PR fixes all the test cases affecting by the recent changes in HTML (RHODS v1.18.0).
Fixes:

ODS-1226: fix search in Resources
ODS-1166:  fix restarting a quick start
..
Signed-off-by: bdattoma<EMAIL_ADDRESS>

Jenkins job: 1322: 1 (expected) failure. There is a resource item missing, already asked for a fix


[proposal] merge babel with eslint

eslint use espree parser, built on top of acorn.js.
babel use babylon parser, built on top of acorn.js.
I think, it's will be great if  eslint and babel become a single project - it will be perfect suite for js developing.

Hey @lx93uv! We really appreciate you taking the time to report an issue. The collaborators
on this project attempt to help as many people as possible, but we're a limited number of volunteers,
so it's possible this won't be addressed swiftly.
If you need any help, or just have general Babel or JavaScript questions, we have a vibrant Slack
community that typically always has someone willing to help. You can sign-up here
for an invite.

I think ESLint and Babel are very different projects. AFAIK ESLint basically enforces good habits and checks your code style, and Babel basically transforms your future (and experimental) JavaScript to a functionally equivalent old JavaScript. One can be used without the other (though a lot of people do use them both)
I think this is also why the parsing differs, since it serves different needs. If all this is correct then it'd be really difficult to merge the two projects.
What's your use case here? Did you encounter any problems using Babel and ESLint together? Is it because of efficiency (having to install and configure them separately)?

Personally, I think more smaller projects is much better than one large, bloated, multipurpose project.
Separately, eslint is useful even when not using babel, and not everyone using babel uses eslint.

Thanks for your replies.
As I understand, technically both eslint and babel developers can unite efforts to contributing of acorn. IMHO, if several projects use the same piece of software, they should unify it's interface and contribute to it together together.
From developer point of view, work can be represented as stream from

compiling from es6/7/etc to es5 according to babel-env
linting, static analysis (eslint)
minifying (babili)
so, all tasks can be implemented as acorn plugins, isn't it?

And, @ljharb, management of big "bloated" project is not a problem with proper people.

@lx93uv that having talented people can largely mitigate the inherent flaws in having a large project does not alter that it is inherently flawed.


Utopia

Make a mod so that moves never miss.

I would add that other really annoying things in battles could also be fixed. One that comes to mind is sleeping time; if your Pokemon always woke up immediately that would be wonderful.


guild view return ImportError: cannot import name 'SharedDataMiddleware' from 'werkzeug.wsgi'

When I execute guild view command it returns an errorČ
ImportError: cannot import name 'SharedDataMiddleware' from 'werkzeug.wsgi' (c:\programdata\anaconda3\lib\site-packages\werkzeug\wsgi.py)
I trued to reinstall werkzeug package but didnćt help.

What version of Guild are you running? This should be resolved by upgrading to the latest prerelease.
$ pip install guildai --upgrade --pre

The last version is 0.6.6.?

Yes but the fix for this is in the pre-release of 0.7, which requires upgrading with --pre. If you'd prefer to stick with 0.6.6 you need to downgrade the werkzeug package unfortunately.

It works with --pre version. Thanks