Questions on ReSeq

Hi,
Thanks for the excellent tool to simulate NGS data.

When I was generating the "my_mappings.bam" using bowtie2 with the following commands,

bowtie2-build my_reference.fa my_reference bowtie2 -p 32 -X 2000 -x my_reference -1 my_data_1.fq -2 my_data_2.fq | samtools sort -m 10G -@ 4 -T _tmp -o my_mappings.bam -
I got the following errors,
Saw ASCII character 10 but expected 33-based Phred qual. terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT)
This error seems like a known bug of bowtie2 [(https://github.com/BenLangmead/bowtie2/issues/218)]. Could you please give me some suggestions?

Alternatively, I am considering applying errors and qualities directly to sequences using the following provided commands
reseq seqToIllumina -j2 -i my_sequences.fa -o my_simulated_reads.fq -s my_stats_profile.reseq
so, in the above example, is the fie file my_sequences.fa the ground truth file compared with the simulated data my_simulated_reads.fq?

and is there any function that can generate the required my_refeence.fa directly? By calling the commands reseq illuminaPE -r my_reference.fa -s my_stats_profile.reseq --stopAfterEstimation --writeSysError my_systematic_errors.fq, reseq can produce my_systematic_errors.fq, but I am confused about how to integrate the my_systematic_errors.fq into my_sequences.fa or use it with the commands reseq seqToIllumina. I really appreciate it if you could give me more detailed instructions.
Best regards,
Jappy

For bowtie2 I would recommend to look into the following parameter:
  --int-quals        qualities encoded as space-delimited integers

What is your encoding if it is not phred33 or phred64? This does not sound like Illumina data?
Alternatively, you can also align with bwa in case it helps.
reseq seqToIllumina -j2 -i my_sequences.fa -o my_simulated_reads.fq -s my_stats_profile.reseq

You can use to simulate data without a reference, but you still need a profile, which needs a bam file and a reference in fasta.

For bowtie2 I would recommend to look into the following parameter:
  --int-quals     qualities encoded as space-delimited integers

What is your encoding if it is not phred33 or phred64? This does not sound like Illumina data?
Alternatively, you can also align with bwa in case it helps.

It was really wired, there should be some unproper settings during my test because I was using the real datasets (e.g. SRR490124) used in your paper for alignment. I will try to use the above recommendations. Thanks so much for your help.

reseq seqToIllumina -j2 -i my_sequences.fa -o my_simulated_reads.fq -s my_stats_profile.reseq

You can use to simulate data without a reference, but you still need a profile, which needs a bam file and a reference in fasta.

This alternative function seems great, but it is a little confusing.

" You can use to simulate data without a reference," do you mean this reference is a genome reference?

"but you still need a profile, which needs a bam file and a reference in fasta." What does this reference mean?

"but you still need a profile, which needs a bam file and a reference in fasta."
The required bam file has to be generated from aligning real sequencing data to the genome reference, in this case, alignment is a mandatory step. Am I understanding right? Thanks so much for your time and efforts in explaining.

SRR490124 does not have ASCII character 10 as quality score. So you are right, something else is wrong. Was there an issue during the download that the file is not complete or has some errors? You can verify with an md5sum, they are normally stated for the downloaded files.
Or is the file compressed? That sometimes causes problems and interpreting binary data as ascii leads to all sorts of normally not expected characters.
The simulation has two steps. First, the reads are randomly selected from the provided reference following some previously learned distributions. Second, quality scores and errors are added to the reads based on previously learned distributions. Using the seqToIllumina command you skip part one and only use part two. Thus, you do not provide a reference, but directly the reads. This you can use when the selection from the reference does not fit your use case or you want to change something before. I consider this advanced use and so far the users have been other developers.
Independently, on how you generated the reads for adding qualities and errors you need to learn the distributions beforehand (the profile) and for this you need the alignment, so yes it is a mandatory step. The only alternative is to use a previously created profile, like for example one from here:
https://github.com/schmeing/ReSeq-profiles


How can I reduce the measurement interval?

How can I reduce the measurement interval?
I changed the baud rate from 9600 to 115200, but it was useless.
Can I also increase the effective number of measured values?
thank you. sir.

This PZEM version has fixed baud rate and measurement interval of ~1 sec.


Enable SDS to plug your own certificate for Egress Gateway as a client

Describe the feature request
Currently we have an option to include a node-agent container in the ingress-gateway pods to enable SDS as the communication channel to manage the external-facing certificates. We should have a similar mechanism for egress gateway.
Describe alternatives you've considered
Without a node-agent, loading new certificates requires a process restart.
Additional context
Ingress and Egress gateways are symmetrical concepts to provide edge-traffic management capabilities via Istio. The use-cases for adding egress gateway to a service mesh are listed at https://istio.io/docs/examples/advanced-gateways/egress-gateway/. We can maintain symmetry and enable SDS at the egress gateway by including a node-agent.

@JimmyCYJ @myidpt @costinm: Would this make sense? Any complexities apart from adding the required sections in the helm chart for gateways?

Can you elaborate what identity you want to use for what connection?
Are you using your own certificate with DNS SAN or you're using Citadel issued certificate? Is the connection between workload in the mesh and egress gateway or gateway and public internet?
@Monkeyanator is working on something related, https://github.com/istio/istio/issues/15485, FYI.

Can you elaborate what identity you want to use for what connection?

I am not sure what you mean by identity. So i probably dont have a good answer for that, sorry :/

Are you using your own certificate with DNS SAN or you're using Citadel issued certificate?
We will  be using our own certificate for this.

Is the connection between workload in the mesh and egress gateway or gateway and public internet?
Neither of the two. This will be from Gateway to Gateway. We will be using mTLS between an Egress Gateway in namespace A talking to the Ingress Gateway in namespace B.

Something like
{//NS-A ... [worload->sidecar]->[egress GW] //end NS-A}->{ //NS-B [ingress GW]->[sidecar->workload] ... //end NS-B}

@nitishm Okay, I see. So you want the connection between egress gateway to ingress gateway in mutual TLS. So given both them are Istio workloads, it's okay and possible to use Citadel issued workload certificates with "SPIFFE" SAN? Or you're looking for having control what certificates to use in egress as well?

We most definitely need to control the certificates. We will use citadel for inter-workload comms but namespace to namespace will need our own certificates (client and server)

I think what @nitishm asked for is to create k8s secret which has (1) CA cert of ingress GW B when B is TLS gateway, or (2) CA cert of ingress GW B and client key/cert when B is mTLS gateway. So that egress gateway agent could watch this k8s secret, extract key/cert/ca cert and push to egress GW A.

I should add that we want the management to be symmetric to the ingress gateway. Using the sds agent like the ingress gateway, for the egress gateway.

I think what @nitishm asked for is to create k8s secret which has (1) CA cert of ingress GW B when B is TLS gateway, or (2) CA cert of ingress GW B and client key/cert when B is mTLS gateway. So that egress gateway agent could watch this k8s secret, extract key/cert/ca cert and push to egress GW A.

Yea that seems to capture the requirements pretty well. Thanks @JimmyCYJ

I am working on PKI reliability. Once the ingress SDS is stable and we have better monitoring and test coverage. I will enable SDS on egress gateway. Please let us know if you have any concerns. @myidpt

@nitishm Okay, I see. So you want the connection between egress gateway to ingress gateway in mutual TLS. For the first question, let me ask in another way, given both them are Istio workloads, it's okay and possible to use Citadel issued workload certificates with "SPIFFE" SAN? Or you're looking for having control what certificates to use in egress as well?

I also should've added that we provision and manage our certificates using cert-manager.
As for now SDS is the right choice by watching the secret generated by cert-manager, but if there are any proposals to support cert-manager directly through the agen, rather than a secretFetcher that would be ideal.
Let me know what you think about this enhancement @JimmyCYJ @incfly

We do have a plan to let gateway agent fetch secret directly from cert-manager or let's encrypt. https://github.com/istio/istio/issues/12132.
But we need to make the SDS feature reliable before we move forward.
The short term solution would be using cert-manager with gateway agent to provision key/cert via SDS.

The short term solution would be using cert-manager with gateway agent to provision key/cert via SDS.

Just to add more information, for everybody else reading though this issue, the Secret generated by Cert Manager is only good for mode: SIMPLE and will not work for mode: MUTUAL TLS since the secretFetcher in SDS agent is not capable of reading ca-certificates from the type/tls Secret type.
It is however possible to read the ca certificates from a separate Secret (manually/programatically generated) that contains only the certificate based on the changes merged by @JimmyCYJ in this PR https://github.com/istio/istio/pull/15496

Yes, there is still a requirement for this; as well as (arguably) to support SDS for sidecar egress, e.g for direct TLS and mTLS origination to external services from sidecars. Currently you have to use the sidecar.istio.io/userVolumeMount annotation approach.

for direct TLS and mTLS origination to external services from sidecar

I think our DestinationRule API already covers that with full TLS configuration knobs. Along with the annotations you mentioned, they should be able to achieve what you want.
Reopening for the sake of SDS... I doubt the full built-in or extensible SDS support for bring your own identity can be satified in the near feature, but open this as I believe it's a legit feature request.

Hi @incfly - thanks for the reply! Are you able to point us to where the documentation/example is to say how to get a sidecar to mount TLS/mTLS secrets via SDS rather than direct userVolumeMounts and how to configure the DestinationRule as such? We looked for it, but could only find examples which rely on volume mounts. :'(

Sorry maybe I confused you. By that, I don't mean the SDS works. We don't offer a mechansim to extend SDS for certificate for the workloads. I'm just saying that the DestinationRule can be used to configure client TLS after the cert/key are mounted.

@incfly OK thanks for the clarification. In a general sense it'd be great to have SDS support everywhere, based on the magic secret discovery used for ingress.
It's rather messy at the moment having to use a mixture of SDS and volume mount support across the mesh for various purposes (ingress gateway - SDS, inter-workload - SDS, egress gateway - mounts, workload egress - mounts); and automating the config generation for mounting secrets and server certs into workloads and gateways is a bit painful for use cases where you might be calling multiple external services (/clusters) outside the mesh.

Can this be prioritized in any way? Egress Gateway should be symmtric to the Ingress Gateway. Would love to see this added to the roadmap for a future release.

What's the roadmap for SDS vs volume mount support in later releases of Istio 1.4.x and Istio 1.5 and beyond ?
I'd like to adopt SDS but encounter issues like  not being able to install egress-gateway if using SDS on the ingress-gateway.

Assuming we still don't have this, what are the ways we can achieve configuring multiple certs, key dynamically possibly w/o restarting envoy. As I understand current we would have to:

Use the cert, key provided to generate secret.
Mount this at egress gw.
To handle any dynamic addition of #1 or revocation, generate new secrets and restart envoy.
@chadlwilson

@JimmyCYJ @myidpt can we have this feature for 1.7 still?

Yes we do. We have an intern to work on this.

@nschhina is working on this, but I cannot find his id in the assignee list.

Do I need to be a part of Istio organization first? If so I'll request membership now

Do I need to be a part of Istio organization first? If so I'll request membership now

After you left the comment, your ID shows up in the assignee list now :)

Design Doc for this feature is now in review. Please take a look if interested, feature is scheduled to be out in Istio 1.7

I change the title. Since this is already causing some confusion when we think about egress gateway as server, receiving traffic from sdiecar within the mesh.
That SDS && ISTIO_MUTUAL is already supported.

@incfly thanks for point that out- I think the title I changed to is more explicit for this issue. Feel free to change it back if you think the older title described the issue better


add nginx variables for .env configuration

We have a pretty big database and need to adjust the timeouts up from 60 seconds for some things. I had hardcoded these at one point, but they should really be variables.

Sure.


DPoP: refactor interface

Coverage: 82.53% (-0.5%) from 82.984% when pulling 0c385cb7775c604702ba01ef0de83a8f1b26c1ad on dissoupov into 14dac410c611a204b36e485a55e56a2dec55eecc on main.


adding type/type_id to datastore class

Related Issue:
Description of changes:
Adding the following to the base datastore activity class
	"type": {
		"caption": "Type",
		"description": "The datastore resource type (e.g. database, datastore, or table).",
		"requirement": "optional"
	},
	"type_id": {
		"caption": "Datastore Type ID",
		"description": "The normalized datastore resource type identifier.",
		"enum": {
			"99": {
				"caption": "Other",
				"description": "The datastore resource type is not mapped."
			},
			"0": {
				"caption": "Unknown",
				"description": "The datastore resource type is unknown."
			},
			"1": {
				"caption": "Database"
			},
			"2": {
				"caption": "Databucket"
			},
			"3": {
				"caption": "Table"
			}
		},
		"requirement": "recommended"
	},

Looks good! It might have been my mistake but the constraint should be just_one not at_least_one as the activity and the type apply to only one at a time. I suppose there is an argument that the event would include more than one, and if so, let me know and we can resolve this comment.

The reasoning behind keeping at least one was that I can imagine a scenario where a database and table both have information present in the log. This doesn't apply to datastore however.


Fix intergrating hyper-parameters

Integrating hyper-parameters didn't work with multi-output models or acquisitions without gradients.
By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

Codecov Report

Merging #237 into master will decrease coverage by 0.25%.
The diff coverage is 45.45%.

@@            Coverage Diff             @@
##           master     #237      +/-   ##
==========================================
- Coverage   89.34%   89.09%   -0.26%
==========================================
  Files         113      113
  Lines        3267     3283      +16
  Branches      353      354       +1
==========================================
+ Hits         2919     2925       +6
- Misses        278      288      +10
  Partials       70       70

Impacted Files
Coverage Δ

emukit/model_wrappers/gpy_model_wrappers.py
77.88% <16.66%> (-7.99%)
:arrow_down:

emukit/core/acquisition/integrated_acquisition.py
88.88% <80%> (-1.74%)
:arrow_down:

...ization/acquisitions/probability_of_improvement.py
100% <0%> (+3.33%)
:arrow_up:

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This got broken after #241, and I've submitted a PR with a fix already: #244


CI test run on the new Node LTS version

Is your feature request related to a problem? Please describe.
At present, only tests in Node 12.x and 14.x are being conducted.
The operation verification in the recent Node version is insufficient.

fixed on c882d90


Update version: Wasmer.Wasmer version 4.2.3

Pull request has been created with WinGet Automation :rocket:
Microsoft Reviewers: Open in CodeFlow

@wingetbot waivers Add Validation-Executable-Error


Updated Pagarme::API service

handling PagarMe::RequestError raised when a juntos' model which represents a pagarme resource has a nil model_code.

@jonatasrancan, you're right, I didn't make tests because I am already treating the ResourceNotFound error. But I must have sure that the PagarMe::RequestError will raises that error. Thanks.


Set FieldGroups on base tables

Hi,
Please add FieldGroups to standard tables Archive tables
T5107 - Sales Header Archive, T5109 - Purchase Header Archive and all related tables - T5108 - Sales Line Archive, T5110 - Purchase Line Archive
We need to add fieldgroups and brick on all Documents Archived tables, so that users will be able to clearly identify the document displayed on the tiles of the page lists. This is needed so that users can use the BC inside Outlook and on the go, using BC application on Android and iOS.
And, it must be supported that fieldgroups, and bricks can be added to the base tables via the tableextension objects. My customers do not understand when I say to them, that sorry, it's not possible.
Thank you
BR Damjan

Please specify which fields do you need per each table

Hi

Please specify which fields do you need per each table

Please see below:
T5107 - Sales Header Archive -> "No.","Version No.","Sell-to Customer Name"
T5108 - Sales Line Archive -> "Document No.","Line No.","Version No.","Sell-to Customer No."
T5109 - Purchase Header Archive -> "No.","Buy From Vendor Name","Version No."
T5110 - Purchase Line Archive -> "Document No.","Line No.","Version No.","Buy From Vendor No."
Thank you
BR Damjan

Thanks for reporting this. We agree, and we’ll publish a fix asap, either in an update for the current version or in the next major release. Please do not reply to this, as we do not monitor closed issues. If you have follow-up questions or requests, please create a new issue where you reference this one.


Property border-radius does not work in Android

In iOS, border-radius is perfectly working. In Android however, the property seems to be completely ignored and all images appear as rectangles.

Hi @moritzvieli i believe this is actually an issue with NativeScript, not the plugin -- https://github.com/NativeScript/NativeScript/issues/540

Hi @moritzvieli , you can use radius property to make radius work on android, or rounded property to make it rounded. Just updated the docs https://github.com/yezarela/nativescript-image-cache#usage


Fix NPE if value is null

This is a FIX suggestion for a NPE when a value is null on a POJO.

Thank you for the PR. Since we are getting the value by calling a getter method, we can use the return type of that getter to get the sql type instead of the value's class, something like:
-- Object value = propertyDescriptor.getReadMethod().invoke(record);
-- Integer sqlType = javaTypesToSqlTypes.get(value.getClass());
++ Method readMethod = propertyDescriptor.getReadMethod();
++ Integer sqlType = javaTypesToSqlTypes.get(readMethod.getReturnType());
++ Object value = readMethod.invoke(record);

The getter method should be there (by definition of a javabean). This approach avoids an additional check in the prepareStatement method which starts to become a bit complex already..
Do you agree? If you agree, please update the PR accordingly and it will be good to merge.

I've changed per your suggestion.
Now I have a problem because my Use Case is a little bit "akward". I generate my beans at runtime an don't know the type of the objects my field will have so all my field have the type java.lang.Object. The way I had it, the SQL type would be inferred by the value of the object and that would work. This way it won't (for my use case) recognize the SQL type. Maybe I'll have to stick with a forked version after all...

For my side I would always have to re-implement the prepareStatement method. Would it be okay to move private properties to protected, so I could extend this class, instead of having to make a copy of it to change the method prepareStatement?

LGTM. Rebased, squashed and merged as 0babc6ff643d0fd1ee495ce524520170f1983476.
If you need to fork the project (or one of its classes), that means there is something wrong with Easy Batch! The BeanPropertiesPreparedStatementProvider is designed for regular JavaBeans. Your use case is very specific, so I would keep the implementation targeted at the majority of use cases, and make it possible to extend the default behaviour for specific cases (I made all fields protected as you suggested, see 5e541f8ba550a441da35fd15e63c54d0699c9116).
You can already try that in 6.1.0-SNAPSHOT.
Thank you for your PR!


Add initial k8s service discovery

Add KuberenetesDiscoveryClient
If spring:cloud:kubernetes:discovery is configured, services.AddDiscoveryClient(Configuration); will add a KubernetesDiscoveryClient

 Thank you for your submission, we really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.:x: tscrypter sign nowYou have signed the CLA already but the status is still pending? Let us recheck it.

/azp run

Hey, sorry I haven't looked at this yet, I am fully expecting to spend time with it tomorrow!
Changes from this PR and #378 will need to merge with each other very soon, so as you're looking at this space your thoughts on that PR might be interesting as well if you're interested in taking a look.

No problem, I got pulled back into some work. I am planning on finishing resolving my config error and will try to resolve the failed checks.

The code generally looks good and I had at least partial success using it, but I had local environment issues trying to test it out today (likely not related) so I can't say I've completely tested through it all yet

The specific issue I'm still working through is setting kubernetes discovery options via appsettings. When attempting to override the namespace, the values for the options are the class defaults.


Sorting results

Is there anyway to sort ag's result by the most recent date? That would be very helpful!
Thanks!

There isn't, and doing so would require extensive changes and ruin ag's performance. It would have to wait until the entire search was finished before it could print out any results. You should probably use find for these sorts of searches.


test C# on .NET core by default too

.NET core has become the default platform for .NET, but on some platforms we were only running tests on net45.

Known failures:
https://github.com/grpc/grpc/issues/18637


RestoreNature features

I'm looking for feedback on how you would like RestoreNature implemented. Currently, I am able to restore the entire chunk but would like to know exactly how you all would want to use these features.
So for example, if an admin wants to restore a chunk they currently enter /rn or /restorenature command with a golden shovel equipped. This will switch the player to RestoreNature mode which allows for restores. For restoring an entire chunk, what kind of actions would you want to take with the shovel? Should there even be a click with shovel when restoring chunks? another command? etc...
Please take the above example and list out exactly how you would want each submodule of RestoreNature to work. So the current features I have in mind are

Restore 1 or more blocks
a. If 2D mode, all chunks within selection would be restored
b. If 3D mode, only the blocks within selection would be restored.

Would be nice to have a way to only restore the terrain, or restore + decorate (trees, grass, etc).
Also, if the admin is inside a claim, /restorenatureclaim or /rnc could restore nature only in the claim he is standing on.

Would be nice to have a separate command for restoring chunks and have it set you to 3D claim mode where you would select the region to reset with the normal /restorenature command.

Would be nice to auto restore claims which expired to keep the map clean.
We use mods like Real World Terrain Generation, will that cause issues?


chore: remove superfluous intros

!bench

FYI, the awaiting-review label was recently removed: you can simply omit it now. (See zulip for details.)

No performance effect - if you fix the nit, this is ready to be merged.

Thanks again for your contribution!
maintainer merge

Thanks :tada:
bors merge


Issue 154

Integrate pre-fetching plan and phase from 25e2669115561213d10e970d974460a20cc8b9c8
after_save callback for answer model with tests. #154
rake task to update completed plans. #154
statistics#completed_plans action done. #154
HTML view for completed plans and tweaks to JS file associated. #154

Note this commit requires to run at ruby level:
rake db: migrate
rake bugfix:set_plan_complete

and at JS leve:
npm install

This PR does not include the "Download CSV" functionality @stephaniesimms and @sjDCC. I would create a new issue to address that separately.


Add field for network:wikidata

See #168

see https://github.com/openstreetmap/id-tagging-schema/pull/769#issuecomment-1411862885


cannot install rexray from bintray file downloads

here are my steps to recreate
wget
Download the file using wget, tar, move, +x, install
$ wget https://bintray.com/artifact/download/akutz/generic/rexray-linux_amd64-0.2.0-rc2%2B18.tar.gz
$ tar xzfv rexray-linux_amd64-0.2.0-rc2+18.tar.gz
$ sudo mv rexray /bin/rexray
$ sudo chmod +x /bin/rexray
$ sudo rexray service install
update-rc.d: /etc/init.d/rexray: file does not exist
FATA[0000] installation error exit status 1

curl
Download the file using wget, tar, move, +x, install
$ curl -LOk https://bintray.com/artifact/download/akutz/generic/rexray-linux_amd64-0.2.0-rc2%2B18.tar.gz
$ tar xzfv rexray-linux_amd64-0.2.0-rc2+18.tar.gz
$ sudo mv rexray /bin/rexray
$ sudo chmod +x /bin/rexray
$ sudo rexray service install
ERRO[0000] error reading configuration file(s) from default path(s)  error=open : no such file or directory global=/etc/rexray/config.yaml user=/root/.rexray/config.yaml
ERRO[0000] error reading configuration file(s) from default path(s)  error=open : no such file or directory global=/etc/rexray/config.yaml user=/root/.rexray/config.yaml
ERRO[0000] error reading configuration file(s) from default path(s)  error=open : no such file or directory global=/etc/rexray/config.yaml user=/root/.rexray/config.yaml
panic: open /root/.rexray/usage.template: permission denied

goroutine 1 [running]:
github.com/emccode/rexray/rexray/commands.initUsageTemplates()
	/home/travis/gopath/src/github.com/emccode/rexray/rexray/commands/usage.go:25 +0x38e
github.com/emccode/rexray/rexray/commands.init.1()
	/home/travis/gopath/src/github.com/emccode/rexray/rexray/commands/rexraycli.go:113 +0x40
github.com/emccode/rexray/rexray/commands.init()
	/home/travis/gopath/src/github.com/emccode/rexray/rexray/commands/usage.go:139 +0x4c9
main.init()
	/home/travis/gopath/src/github.com/emccode/rexray/rexray/rexray.go:28 +0x40

goroutine 17 [syscall, locked to thread]:
runtime.goexit()
	/usr/local/go/src/runtime/asm_amd64.s:1696 +0x1

goroutine 6 [runnable]:
os/signal.loop()
	/usr/local/go/src/os/signal/signal_unix.go:20
created by os/signal.init.1
	/usr/local/go/src/os/signal/signal_unix.go:28 +0x37

@kacole2 what is the linux distro and version?

Ubuntu 14.04

@kacole2 Your system is FUBAR. Works fine here on same distro.
[0]akutz@ubuntu:~$ /bin/rexray version
SemVer: 0.2.0-rc2+20
Binary: linux_amd64
Branch: master
Commit: f23b8217b38e9461cf795e97463c4b006182aa5c
Formed: Mon, 14 Sep 2015 23:59:27 CDT

[0]akutz@ubuntu:~$ uname -a
Linux ubuntu 3.19.0-25-generic #26~14.04.1-Ubuntu SMP Fri Jul 24 21:16:20 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

[0]akutz@ubuntu:~$

Here's the process I used:
[0]akutz@ubuntu:~$ wget https://bintray.com/artifact/download/akutz/generic/rexray-linux_amd64-0.2.0-rc2%2B20.tar.gz
--2015-09-15 00:02:47--  https://bintray.com/artifact/download/akutz/generic/rexray-linux_amd64-0.2.0-rc2%2B20.tar.gz
Resolving bintray.com (bintray.com)... <IP_ADDRESS>, <IP_ADDRESS>
Connecting to bintray.com (bintray.com)|<IP_ADDRESS>|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://dl.bintray.com/akutz/generic/rexray-linux_amd64-0.2.0-rc2+20.tar.gz [following]
--2015-09-15 00:02:47--  https://dl.bintray.com/akutz/generic/rexray-linux_amd64-0.2.0-rc2+20.tar.gz
Resolving dl.bintray.com (dl.bintray.com)... <IP_ADDRESS>, <IP_ADDRESS>
Connecting to dl.bintray.com (dl.bintray.com)|<IP_ADDRESS>|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 4096707 (3.9M) [application/x-gzip]
Saving to: ‘rexray-linux_amd64-0.2.0-rc2+20.tar.gz’

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Last-modified header invalid -- time-stamp ignored.
2015-09-15 00:02:48 (5.36 MB/s) - ‘rexray-linux_amd64-0.2.0-rc2+20.tar.gz’ saved [4096707/4096707]

[0]akutz@ubuntu:~$ tar xzf rexray-linux_amd64-0.2.0-rc2+20.tar.gz
[0]akutz@ubuntu:~$ ls
total 18M
drwxr-xr-x 4 akutz 4.0K Sep 15 00:02 ./
drwxr-xr-x 3 root  4.0K Aug 12 17:31 ../
-rw------- 1 akutz  25K Aug 18 12:46 .bash_history
-rw-r--r-- 1 akutz  220 Aug 12 17:31 .bash_logout
-rw-r--r-- 1 akutz 3.6K Aug 12 17:31 .bashrc.dist
drwx------ 2 akutz 4.0K Aug 12 17:41 .cache/
lrwxrwxrwx 1 akutz   13 Aug 12 17:47 go -> /media/psf/go/
-rw------- 1 akutz   42 Aug 12 19:16 .lesshst
-rw-r--r-- 1 akutz 1.2K Aug 12 18:19 .profile
-rwxr-xr-x 1 akutz  14M Sep 14 23:59 rexray*
-rw-rw-r-- 1 akutz 4.0M Sep 15 00:02 rexray-linux_amd64-0.2.0-rc2+20.tar.gz
drwx------ 2 akutz 4.0K Aug 12 17:53 .ssh/
-rw------- 1 akutz 4.7K Aug 17 12:57 .viminfo
[0]akutz@ubuntu:~$

[0]akutz@ubuntu:~$ sudo mv rexray /bin/
[sudo] password for akutz:
[0]akutz@ubuntu:~$ sudo rexray service install
update-rc.d: warning: /etc/init.d/rexray missing LSB information
update-rc.d: see <http://wiki.debian.org/LSBInitScripts>
 System start/stop links for /etc/init.d/rexray already exist.
REX-Ray is now installed. Before starting it please check http://github.com/emccode/rexray for instructions on how to configure it.

 Once configured the REX-Ray service can be started with the command 'sudo /etc/init.d/rexray start'.

[0]akutz@ubuntu:~$ sudo /etc/init.d/rexray start
Oops, an error occured!

  no storage drivers initialized

To correct the error please review:

  - Debug output by using the flag -l debug
  - The REX-ray website at https://github.com/emccode/rexray
  - The on↓ine he↓p be↓ow

Start the service

Usage:
  rexray service start [flags]

Flags:
      --client="": Socket the daemon uses to communicate to the client
  -f, --foreground[=false]: Starts the service in the foreground

Global Flags:
  -c, --config="/root/.rexray/config.yaml": The REX-Ray configuration file
  -?, --help[=false]: Help for start
  -h, --host="tcp://:7979": The REX-Ray service address
  -l, --logLevel="info": The log level (panic, fatal, error, warn, info, debug)
  -v, --verbose[=false]: Print verbose help information

[0]akutz@ubuntu:~$

Hi @kacole2,
Your system likely has SELinux or some other security restrictions enabled on top of ACLs. That or the VM is provisioned with increased lockdowns in place. Your logs make zero sense unless you're specifically trying to break the program. If that's the case, bully for you, but let me know so I can put some guard in place. I'm not being sarcastic. I traced the logs, and one place it checks for the existence of a debug file, and if it exists it tries to read it. Well, you're in the inner logic, but that means the debug file would have to exist! On your system! That's nuts!
I don't know what's going on with it, but you'll have to do digging to figure it out.

Hi @kacole2,
By the way, I did some digging of my own and verified that the REX-Ray function for checking if a file exists does not check a user's permission to read it, but that should be okay, because here's the thing. If the files /etc/rexray/config.yaml or $HOME/.rexray/config.yaml exist your user should absolutely be able to read them. The same for $HOME/.rexray/usage.template. First of all, why on earth you'd have that file in place is beyond me, but what's more likely is somehow you've got a system with screwed up permissions and you can't read $HOME/.rexray and it's throwing a permissions error. Here's the code FWIW:
func FileExists(filePath string) bool {
	if _, err := os.Stat(filePath); !os.IsNotExist(err) {
		return true
	}
	return false
}

The above will return a false-positive for files that don't exist at locations that you're prohibited from reading, but that's okay as it's not used for anything for which you shouldn't have read perms such as /etc/rexray and $HOME/.rexray.

Hi @kacole2,
I've pushed a patch to handle the panics you're seeing. It institutes an access check as well as the existence check, but this is more about failing gracefully than solving the problem. The issue is that your system has permission restrictions that will keep REX-ray from ever working at all. You need to figure out why that is. I know you've had it running before, so did something happen to the system? Have you reprovisioned it lately? Any updates?

Hey @akutz, your error is showing that it tried to check if the /etc/init.d/rexray file was installed or not.  This isn't not the same test from @kacole2.  Try and remove that file and run the same command.
I have the same problem.. Found a fix..
If /etc/init.d/rexray doesn't exist you can put a /bin/ prefix before rexray to make it work in the short term.  It looks like the path being linked to is based from the relative path of the process executing.
root@test14:~# sudo rexray service install
update-rc.d: /etc/init.d/rexray: file does not exist
FATA[0000] installation error exit status 1
root@test14:~# sudo /bin/rexray service install
update-rc.d: /etc/init.d/rexray: file does not exist
FATA[0000] installation error exit status 1
root@test14:~# ls /etc/init.d/rexray
/etc/init.d/rexray
root@test14:~# ls /etc/init.d/rexray -laF
lrwxrwxrwx 1 root root 12 Sep 15 01:52 /etc/init.d/rexray -> /root/rexray
root@test14:~# rm /etc/init.d/rexray
root@test14:~# sudo /bin/rexray service install

Hi @clintonskitson,
I pasted the wrong log, but I removed that file as well and it still worked. Oh ye of little faith, I don't assert blindly :)

I have no idea what you mean about the /bin prefix, but that's the directory to which he copied the file and it's perfectly the valid. The problem is his system has FUBAR permissions.

Look at my steps more clearly.. The system he is using is from the same
build as mine.  The /bin prefix makes it work correctly.
On Monday, September 14, 2015, Schley Andrew Kutz<EMAIL_ADDRESS>wrote:

Hi @clintonskitson https://github.com/clintonskitson,
I pasted the wrong log, but I removed that file as well and it still
worked. Oh ye of little faith, I don't assert blindly :)
[image: image]
https://cloud.githubusercontent.com/assets/101085/9869025/05a77d4e-5b45-11e5-8edc-41b08831322b.png
I have no idea what you mean about the /bin prefix, but that's the
directory to which he copied the file and it's perfectly the valid. The
problem is his system has FUBAR permissions.
—
Reply to this email directly or view it on GitHub
https://github.com/emccode/rexray/issues/55#issuecomment-140289229.

There is a link that gets created at first po bring to /root which makes no
sense since it does not exist there.
On Monday, September 14, 2015, Clinton Kitson<EMAIL_ADDRESS>wrote:

Look at my steps more clearly.. The system he is using is from the same
build as mine.  The /bin prefix makes it work correctly.
On Monday, September 14, 2015, Schley Andrew Kutz <
<EMAIL_ADDRESS><javascript:_e(%7B%7D,'cvml','notifications@github.com');>> wrote:

Hi @clintonskitson https://github.com/clintonskitson,
I pasted the wrong log, but I removed that file as well and it still
worked. Oh ye of little faith, I don't assert blindly :)
[image: image]
https://cloud.githubusercontent.com/assets/101085/9869025/05a77d4e-5b45-11e5-8edc-41b08831322b.png
I have no idea what you mean about the /bin prefix, but that's the
directory to which he copied the file and it's perfectly the valid. The
problem is his system has FUBAR permissions.
—
Reply to this email directly or view it on GitHub
https://github.com/emccode/rexray/issues/55#issuecomment-140289229.

Sorry for typo, pointing to..
On Monday, September 14, 2015, Clinton Kitson<EMAIL_ADDRESS>wrote:

There is a link that gets created at first po bring to /root which makes
no sense since it does not exist there.
On Monday, September 14, 2015, Clinton Kitson<EMAIL_ADDRESS><javascript:_e(%7B%7D,'cvml','clintonskitson@gmail.com');>> wrote:

Look at my steps more clearly.. The system he is using is from the same
build as mine.  The /bin prefix makes it work correctly.
On Monday, September 14, 2015, Schley Andrew Kutz <
<EMAIL_ADDRESS>wrote:

Hi @clintonskitson https://github.com/clintonskitson,
I pasted the wrong log, but I removed that file as well and it still
worked. Oh ye of little faith, I don't assert blindly :)
[image: image]
https://cloud.githubusercontent.com/assets/101085/9869025/05a77d4e-5b45-11e5-8edc-41b08831322b.png
I have no idea what you mean about the /bin prefix, but that's the
directory to which he copied the file and it's perfectly the valid. The
problem is his system has FUBAR permissions.
—
Reply to this email directly or view it on GitHub
https://github.com/emccode/rexray/issues/55#issuecomment-140289229.

Hi @clintonskitson,
I see what you mean, but I would have said something like:
When creating a symlink to a file, if the file itself creates the symlink by taking its own execution path, then the full path must be given at time of execution else the file's execution path will be invalid as it could represent a relative path, or a path that expects to exist in the PATH variable scope which is what happened in this instance.
This is easy enough to fix. I just released 0.2.0-rc2, so file an issue and I'll fix it for rc3. I don't want this to be the issue itself unless we can dismiss the rest of @kacole2's concerns.

Hi @clintonskitson,
That's does not appear to be the issue as I double-checked, and I already get the abspath for the executing binary. See the following example with debug logging enable. Note I'm installing the service using a relative path:
[0]akutz@ubuntu:rexray$ sudo .bin/linux_amd64/rexray service install -l debug
DEBU[0000] updated log level                             logLevel=debug
DEBU[0000] creating symlink                              exeFile=/media/psf/go/src/github.com/emccode/rexray/.bin/linux_amd64/rexray initFile=/etc/init.d/rexray
update-rc.d: warning: /etc/init.d/rexray missing LSB information
update-rc.d: see <http://wiki.debian.org/LSBInitScripts>
 System start/stop links for /etc/init.d/rexray already exist.
REX-Ray is now installed. Before starting it please check http://github.com/emccode/rexray for instructions on how to configure it.

 Once configured the REX-Ray service can be started with the command 'sudo /etc/init.d/rexray start'.

[0]akutz@ubuntu:rexray$ ls /etc/init.d | grep rexray
lrwxrwxrwx  1 root   67 Sep 15 01:22 rexray -> /media/psf/go/src/github.com/emccode/rexray/.bin/linux_amd64/rexray*
[0]akutz@ubuntu:rexray$

If you'd like to look at the code, you can back track it from (here)[https://github.com/emccode/rexray/blob/master/rexray/commands/service.go#L383].

Hi @clintonskitson,
Scratch that. It works as long as you give it any anchored path, relative or not. If however you rely on a path that is in the PATH variable it seems to simply take the parent directory and append "rexray" as the suffix.
Found the (issue)[http://golang.org/pkg/path/filepath/#Abs]:
Abs returns an absolute representation of path. If the path is not absolute it will be joined with the current working directory to turn it into an absolute path. The absolute path name for a given file is not guaranteed to be unique.

The above is the stupidest thing I ever heard. Why join it with the current WD to turn it into an abs path when the nature of the function is to get the ABS PATH! DON'T GUESS! GET THE ABS PATH! sigh
Okay, I'll fix this bug.

Hi @clintonskitson / @kacole2,
Thank you both for identifying and tracking down this bug. PR #56 is building for it right now, and I'll merge it as soon as the build succeeds.

Hi @kacole2,
0.2.0-rc3+3 has the patch.

:+1:
thanks. all working
Using SSH client type: external
About to run SSH command:
sudo rexray service start
&{/usr/bin/ssh [/usr/bin/ssh -o PasswordAuthentication=no -o IdentitiesOnly=yes -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -o LogLevel=quiet -o ConnectionAttempts=3 -o ConnectTimeout=10 -o ControlMaster=no -o ControlPath=no -i /Users/kcoleman/.docker/machine/machines/fun21/id_rsa -p 22<EMAIL_ADDRESS>sudo rexray service start] []  <nil> <nil> <nil> [] <nil> <nil> <nil> <nil> false [] [] [] [] <nil>}
SSH cmd err, output: <nil>: Starting REX-Ray...SUCESS!

  The REX-Ray daemon is now running at PID 30433. To
  shutdown the daemon execute the following command:

    sudo /bin/rexray stop


TypeError: function missing 1 required positional arguments

After running the execfile('webcam.py') I received this error message:

execfile('webcam.py')
Traceback (most recent call last):
File "", line 1, in
File "webcam.py", line 126, in
TypeError: function missing 1 required positional arguments

I found solution to this bug in the webcam.py camera initialize step. The camera.init() was missing the 3 require parameters. I replaced the camera.init() with the follow:
#cam = camera.init()
cam = camera.init(0, format=camera.JPEG, fb_location=camera.PSRAM)

I'm sure you're using a firmware that's not from my repository. The camera.init() method does not take a parameter. I'm sure you're using a firmware provided by other developers from another repository.
The firmwares I have provided have a "kaki5" tag attached to them, for example:
>>>
MPY: soft reboot
MicroPython v1.20.0-206-g33b403dfb-kaki5 on 2024-01-19; ESP32 AIT OV2640 (KAKI5) with ESP32

If the script "webcam.py" is a copy from my repository and used on MicroPython firmware from another repository, you will get some errors like the one you mentioned.
Please note that MicroPython firmware supporting the camera module is not the official version of MicroPython, developers may choose different implementations.
I am glad that you have found a solution to your problem.


Hi, I'm interested in this TastyIgniter

Hi, I want to be one of contributors.. Thanks

Sounds great and looking to get you on board.


allow scheduler to schedule all pending tasks

Switched the return to a continue so that any pending, run-once tasks can be sent to the broker in one shot.
This is particularly handy if there's a large amount of run-once tasks that are scheduled in the past and need to be caught up.

Current coverage is 90.82%

Merging #165 into master will decrease coverage by -5.80% as of b64fbcf

@@            master    #165   diff @@
======================================
  Files           40      40
  Stmts         2724    2725     +1
  Branches         0       0
  Methods          0       0
======================================
- Hit           2632    2475   -157
  Partial          0       0
- Missed          92     250   +158

Review entire Coverage Diff as of b64fbcf

Powered by Codecov. Updated on successful CI builds.

Nice one


[ci skip] adding user @kujaku11

Hi! This is the friendly automated conda-forge-webservice.
I've added user @kujaku11 as instructed in #4.
Merge this PR to add the user. Please do not rerender this PR or change it in any way. It has [ci skip] in the commit message to avoid pushing a new build and so the build configuration in the feedstock should not be changed.
Please contact conda-forge/core to have this PR merged, if the maintainer is unresponsive.
Fixes #4

Done in PR ( https://github.com/conda-forge/mth5-feedstock/pull/6 )


[FEATURE]imroving the navbar

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
i will improve the nav var and make it more attractive
Describe the solution you'd like
A clear and concise description of what you want to happen.
Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Hey @arpitghura , assign this issue to me

@arpitghura  please assign me under kwoc

What Improvements can be made in navBar? Can you please describe?

@arpitghura can you please assign this issue to me?

i Make it more attractive.
On Tue, Dec 20, 2022, 17:12 Arpit Ghura @.***> wrote:

What Improvements can be made in navBar? Can you please describe?
—
Reply to this email directly, view it on GitHub
https://github.com/arpitghura/typing-test/issues/75#issuecomment-1359238200,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AVJXF2MRTBOQY6ZLXZBH4PDWOGLUFANCNFSM6AAAAAATARYBUM
.
You are receiving this because you authored the thread.Message ID:
@.***>


Error back

I created this PR to address #32 enhancement.
My previous code from the #37 is also here, so, sorry for the long commit.
I'd suggest taking a look at https://github.com/stepstone-tech/android-material-stepper/commit/2c33eaf626368a40ecda9ec4947dec71262eb61f for code only of the #32 issue.
I managed the issue addressed by @zawadz88 :

When we go to the previous step? If so, when we then go back to the failed step the regular state should be shown instead of the error state?

Adding a showErrorStateOnBack flag, so the user can choose whether or not to clean the error from the current step when moving back.
The main point I'd like to discuss is when we get an error on "complete" state, do all the necessary steps to get it right and press "complete" again. Currently the callback is correctly fired, but the "error" state is never cleared. Not sure if this should be treated, as most of the cases the user will move forward to another screen.
What are your thoughts on that ?
Thanks!

Hi @leonardo2204,
Thanks for the PR!
I have a few comments:

According to the material doc (https://material.io/guidelines/components/steppers.html#steppers-types-of-steps) the tab title should also change to red on error.
Regarding:

Not sure if this should be treated, as most of the cases the user will move forward to another screen.
I guess it should get cleared as well in this scenario.

Showing an error in the tabs should be optional and disabled by default. Enabling this should be probably done via a custom attribute from StepperLayout. The reason for this is that we wouldn't want to change the default behavior for ppl already using this library.
It might be worth adding an option to override the default color of the warning with styles in a similar way you can change the color of the selected tab.

About your points:

You got it, I really forgot it.
Sure, totally agree.
Agreed also.
Ok, no problem !

Thanks

Hi @leonardo2204,
Could you rebase your commits on top of master as a 2.0.0 version was released?
Also, I noticed that ShowErrorOnBackTabActivity does not show the errors - I suppose setShowErrorState should be called?
Could you add a sample where an attribute is used + custom color + maybe a different one were setShowErrorStateOnBack is set to false & setShowErrorState is set to true. The samples are so that we can test this with each update :)
I've also noticed that point 2. from my previous comment is still not covered?

Hi @leonardo2204,
Thanks for the PR! I have no further comments and I have to say it's looking good :)

Hey @zawadz88 Cool, thank you !


taxonomy convertkb not mapping

Expected Behavior
Attempting to run to convert annotation mapping file
mmseqs convertkb uniprot_sprot_trembl.dat.gz targetDB.mapping --kb-columns OX --mapping-file targetDB.lookup
Current Behavior
Can not find accession in mapping:
Could not find accession Q6P378 in mapping!
Could not find accession P34974 in mapping!
Could not find accession Q9Z1S9 in mapping!
Steps to Reproduce (for bugs)
Please make sure to execute the reproduction steps with newly recreated and empty tmp folders.

Downloaded all viral proteins from UniProtKB
Created target DB with UniProtKB entries

mmseqs createdb target.fasta targetDB

Confirmed targetBD.lookup format
0	H8YHR3
1	A0A0E3HJU1
2	A0A0M3M679
3	A0A142IHD3
4	A0A1D8Q0G9
5	I3XPF8
6	Q66N09
7	D5XLT2
8	D9IRE9
9	Q50BU6

Downloaded and concatenated uniprot_sprot_trembl.dat.gz

Ran:
mmseqs convertkb uniprot_sprot_trembl.dat.gz targetDB.mapping --kb-columns OX --mapping-file targetDB.lookup

MMseqs Output (for bugs)
Please make sure to also post the complete output of MMseqs. You can use gist.github.com for large output.
Context
Providing context helps us come up with a solution and improve our documentation for the future.
Your Environment
Include as many relevant details about the environment you experienced the bug in.

Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters):
Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.):
For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation:
Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
Operating system and version:

Thanks for reporting this issue. I have reworked the taxonomy. I will adjust the documentation tomorrow.

I have updated the wiki. Sorry for the delay. I will build a more convenient way to create taxonomical databases soon.

I have added a createtaxdb tool which should help to add taxonomical information to a sequence database. I have also added it the documentation. Please let me know if you encounter any problems. https://github.com/soedinglab/MMseqs2/wiki#taxonomy-assignment-using-mmseqs-taxonomy


[feature] CONTRASTIVE REPRESENTATION DISTILLATION with dataset wrapper

Thanks for your contribution and we appreciate it a lot. The following instructions would make your pull request more healthy and more easily get feedback. If you do not understand some items, don't worry, just make the pull request and seek help from maintainers.
Motivation
Update CRD dataset building method
Modification
Update CRD datasets as wrapper
BC-breaking (Optional)
Does the modification introduce changes that break the backward compatibility of the downstream repositories?
If so, please describe how it breaks the compatibility and how the downstream projects should modify their code to keep compatibility with this PR.
Use cases (Optional)
If this PR introduces a new feature, it is better to list some use cases here and update the documentation.
Checklist
Before PR:

[ ] Pre-commit or other linting tools are used to fix the potential lint issues.
[ ] Bug fixes are fully covered by unit tests, the case that causes the bug should be added in the unit tests.
[ ] The modification is covered by complete unit tests. If not, please add more unit tests to ensure the correctness.
[ ] The documentation has been modified accordingly, like docstring or example tutorials.

After PR:

[ ] If the modification has potential influence on downstream or other related projects, this PR should be tested with those projects, like MMDet or MMSeg.
[ ] CLA has been signed and all committers have signed the CLA in this PR.

It‘s ok to me


JSONPreview decorator didSet func crash

JSONPreview decorator didSet func crash：

Can you provide me with the json you previewed so I can try to reproduce the issue.

Not mandatory

close with #10


Scaphandre does not run on Debian 12

Bug description

When trying to run the debian package provided in the 1.0.0 release on a Debian 12 server, the following error happens ;
➜  ~ scaphandre
scaphandre: error while loading shared libraries: libssl.so.1.1: cannot open shared object file: No such file or directory

To Reproduce
Steps to reproduce the behavior. Something like:

Go to the relase page
Click on the debian package
Install it on a debian 12 up to date computer
See error

The bug was not caught because the CI is buggy too. It sais "Run scaphandre for 10 seconds, but it only outputs the Scaphandre version.
I've tried running the same commands as the CI to reproduce by bugs, but I indeed do have all the dependencies, and all is well on the APT side, but I still can't run scaphandre.
See :  https://github.com/hubblo-org/scaphandre/actions/runs/7652515152/workflow#L104
 steps:
      - name: Install dependencies
        run: |
          apt update
          apt install -y curl
      - name: Download Debian 12 scaphandre package
        run: |
          curl -O https://s3.fr-par.scw.cloud/scaphandre/x86_64/${{ env.DEB12PKG }}
      - name: Install and run scaphandre Stdout exporter for 10 seconds
        run: |
          apt install -y ./${{ env.DEB12PKG }}
          scaphandre -V

Expected behavior

Scaphandre should run.
Environment

Linux distribution version :

No LSB modules are available.
Distributor ID:	Debian
Description:	Debian GNU/Linux 12 (bookworm)
Release:	12
Codename:	bookworm

Kernel version (output of uname -r) [e.g. 5.4.0-54-generic]

6.1.0-13-amd64

The bug was not caught because the CI is buggy too. It sais "Run scaphandre for 10 seconds", but it only outputs the Scaphandre version.

This changed for the last release. I thought maybe something wrong was up with that ( and they could be a single line with timeout 10s scaphandre --stdout to make sure everything runs ). So the CI is not buggy, but maybe had a regression in testing ?
I can provide a pull request to implement that little change, if need be.

I continued digging to find where the bug could come from. I thought maybe the docker image stayed on debian 11 ( that indeed has libssl1.0 ) and not debian 12, that switched to libssl3.0, but the CI does indeed use   /usr/bin/docker pull debian:bookworm-slim, so no good on that side.
I've looked into https://github.com/hubblo-org/scaphandre/actions/runs/7872701050 and nothing seems weird on my side, it looks like I've followed all the steps and that I have all the good packages etc...

I tried installing Rust bindings to the libssl librairies, maybe that was missing, but no chance on that side either.
My best guest now would be to build scaphandre against the libssl3.0 lib and not the libssl1.1. But that's out of my capacities :(

Hello @N07070 !
I think the problem is that, presently, the Debian installer available for download on the release page was built for Debian 11. Could you try installing Scaphandre with the installer available with the following link : Debian 12 installer ?
I just tried it on a quick Debian 12 Docker container and I didn’t get your error. I think we just have to link the Debian 12 installer to the release page.

Indeed, I missed the part that said : deb11_amd64.deb. Derp.
It works perfectly with the link you provided.
For the futur, are the releases of the .deb planned to be build for Bookworm, Debian 12 directly ? I'm asking because I'm writing an Ansible role for Scaphandre and I would find it nice to have the deb file downloaded directly in the role, until the day it's added to Debian's repo :crossed_fingers: .

On a side note, it there anything I can do to update the installer's deb link on the release page ? I gather it's done by the maintainers, but maybe a pull request for the CI could be useful ?

On a side note, it there anything I can do to update the installer's deb link on the release page ? I gather it's done by the maintainers, but maybe a pull request for the CI could be useful ?

Avec plaisir très chère !
Bon courage :)

Merci !
Added the Debian 12 package to release, so I will close this issue now.


scikit-xray vs xray

FYI: it's likely there will be confusion in the future.
https://github.com/scikit-xray

Yep, we've been considering renaming this package, though nothing has been decided yet. It's possibly worth adding an entry to the FAQ in the meanwhile.

we've been considering renaming this package

so I guess you should rename before it's too late. :P

Too late for what? :)

To rename. :p


Add GitHub template for GitHub issues

Hello @alanyee , I would like to take this up

Sounds good to me

Are you looking for any specific sections? Fields to includes as such? or a simple one would do?

Something like https://github.com/alanyee/rsa-keygen/pull/11 is fine. A description section at the very least, but up to you for which sections you think are important.

Thank you! 💯


Did you mean Pi Zero WH?

I think the BOM should specify the Pi Zero WH (wireless + header) or specify that you have to solder on the header if you have a Pi Zero W.

Good catch, fixed in latest commit.


Can't manage to get the extension running in VSCode with WSL2

I'm pretty sure that opening a github issue is not the proper way to get support but I'm trying to run this extension inside of VSCode using WSL2 with latest Ubuntu with no luck, I made sure that I installed all the requirements in my ubuntu wsl and even made an alias in zsh so bat is batcat. I sourced my zsh config and made sure it updated. batcat works from the terminal.
When I try to pres control + shift + j I get the following message:
Failed to activate plugin: bat not found on your PATH
.
Make sure you have the required command line tools installed as outlined in the README.

Is it trying to read my windows terminal or something like that? If so, why is that the case if I'm running VSCode withing a WSL folder and the plugin is installed in my WSL.

If there is a Discord for this extension I'm more than happy to join and ask for support there.

I can replicate this, seems to be related to the renaming of bat to batcat and the supplied fix, at least thats my first guess

I only renamed it because it didnt get it by default, I googled and it said that bat is ran as batcat in ubuntu, so I added an alias for it

@Jaizu Can you please run which bat in the Ubuntu console and send the result of that in here?

~/decomp/recharged-yellow master !7 ?2 ❯ which bat                                                                                13:43:04
bat: aliased to batcat
~/decomp/recharged-yellow master !7 ?2 ❯ which batcat                                                                                13:51:15
/usr/bin/batcat

That seems to fuck it up, can you try installing bat via the .deb file in the release?
For this you first need to comment out your alias, then download the newest bat release via wget (or whatever else you wanna use) wget https://github.com/sharkdp/bat/releases/download/v0.24.0/bat-musl_0.24.0_amd64.deb, then install it sudo dpkg -i bat-musl_0.24.0_amd64.deb

Just as a quick info, I tried it on my own WSL installation and using the .deb file, everything worked.
This is more of a temporary workaround tho

Hi, installing the .deb one worked. I didn't have an alias when I tried this the first time, I only added it because WSL couldn't run bat and only batcat after doing sudo apt-get install bat

Because I am sadly not a big linux user, I did more digging. The preflight check script runs doesnt run in your "session", so it doesn't load the alias's from the .bashrc

I was getting similar issues ("fzf not found on your PATH") despite having fzf on the path. Simple fix was settings ->Find-it-faster -> Disable Startup Checks

@Jaizu Do you still have this issue or could you close it maybe?

sudo dpkg -i bat-musl_0.24.0_amd64.deb

it's worked in ubuntu also


Development Freeze, Today at 6:00 PM CST to December 26th

I will not be working on Catalyst Today at 6PM CST, to December 26th as I will not be available during this period (Christmas).
Feel free to make PRs and issues and discuss features with other developers during this period, I will merge and confirm ideas afternoon December 26th.

Merry Christmas!

The period of the development freeze has ended, development will continue.

Well, it didn't really freeze, I was working on bookmarks


Trigger official documentation build when documentation is updated here

Codecov Report

Merging #1147 (f68b443) into master (978258e) will not change coverage.
 Consider uploading reports for the commit 11117e3 to get more accurate results

@@           Coverage Diff           @@
##           master    #1147   +/-   ##
=======================================
  Coverage   97.28%   97.28%
=======================================
  Files          67       67
  Lines        4235     4235
=======================================
  Hits         4120     4120
  Misses        115      115

Continue to review full report at Codecov.

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question: setTemplate doesn't know env function

Hello @mumoshu,
I've been playing around with relatively new features and bumped into that that during the second pass I get this failure, is this expected behavior?
second-pass rendering result of "80-identity.yaml.part.0":
11:     setTemplate:
12:     - name: config.logging\.json.logLevel
13:       value: "{{ env "LOG_LEVEL"  }}"

err: failed to read 80-identity.yaml: reading document at index 1: yaml: line 13: did not find expected key

I've checked other functions like upper and default they do work. Could you please shortly explain why this is so or maybe it's a bug?

@dennybaa Sorry I'm overwhelmed by the sea of github notifications. This seems like due to some mistake in your helmfile template. The second-pass rendering result should be a valid YAML, where value: "{{ env "LOG_LEVEL"  }}" in your result isn't a valid YAML snippet. Perhaps there was something wrong in go template comments that resulted in rendering value: "{{ env "LOG_LEVEL"  }}".

@mumoshu No worries and thank you. I totally understand, that's why I closed the issue since it was definitely an error...


Adding tgb for alias & removed lowercase only cl searching

Description:

made it so when you search on the cl, and you start with a capital letter it will register it. ex: Halloween instead of halloween both will now work.
added tgb for alias to tester gift box

Changes:

Other checks:

[ ] I have tested all my changes thoroughly.

I'm not sure what you did here, but you merged in changes from master, including my most recent PR, so it seems like the way you updated your PR wasn't right.


Use string values in DateFilter null-management constants

Do we also want to export these class constants as container parameters?
So that instead of writing
    resource.book.date_filter:
        parent: api.doctrine.orm.date_filter
        arguments:
          - datePublished: 0 # Dunglas\ApiBundle\Doctrine\Orm\Filter\DateFilter::EXCLUDE_NULL

I can just write
    resource.book.date_filter:
        parent: api.doctrine.orm.date_filter
        arguments:
          - datePublished: api.doctrine.orm.date_filter.exclude_null

IMO it's better to have string values in DateFilter constants.

:+1: for string values in DateFilter constants

Are we good?

I'm okay with that. But as there's a BC break, I'm waiting another maintainer's :+1:.

:+1: it's the good time to break things (before 1.0).
Can you also update the changelog please?

Added a line in changelog

Thank you @teohhanhui ! :+1:


MSID: 86687 Version: 1 DOI: 2<IP_ADDRESS>9215

"msas": "Evolutionary Biology", "Genetics and Genomics"
"msid": "86687"
"version": "1"
"preprintDoi": "10.1101/2<IP_ADDRESS>9215"
"articleType": "Reviewed Preprint"
"status": "Published from the original preprint after peer review and assessment by eLife."
"Reviewed Preprint posted": "2023-05-30"
"Sent for peer review": "2023-02-20"
"Posted to bioRxiv": "2023-02-21" (link: "Go to bioRxiv": "https://www.biorxiv.org/content/10.1101/2<IP_ADDRESS>9215v1")
[PLACE PDF URL HERE WHEN AVAILABLE] See step 7
Step 1. Inform bioRxiv
Who can help: @QueenKraken, @nlisgo, @scottaubrey

[x] Manuscript is in data hub index (https://data-hub-api.elifesciences.org/enhanced-preprints/docmaps/v1/by-publisher/elife/get-by-manuscript-id?manuscript_id=86687)

Step 2. Create preview of manuscript
Who can help: @fred-atherden, @nlisgo, @scottaubrey

[ ] Manuscript is available for preview (https://prod--epp.elifesciences.org/preview/86687/v1)

[ ] Trigger import for staging: https://prod--epp.elifesciences.org/import
[ ] Sync data folder with s3://prod-elife-epp-data/data
[ ] Trigger import for staging: https://staging--epp.elifesciences.org/import
[ ] Sync data folder with s3://staging-elife-epp-data/data
[ ] Pull request created to enhanced-preprint-data
[ ] Post link to pull request below

Pull request: https://github.com/elifesciences/enhanced-preprints-data/pull/90
Detailed instructions: https://github.com/elifesciences/enhanced-preprints-data#add-a-manuscript
Step 3: Awaiting public reviews
Who can help: Editorial team

[x] Public reviews available on sciety (https://sciety.org/articles/activity/10.1101/2<IP_ADDRESS>9215)
[x] Manuscript and editor details at the top of this issue (Supplied by Editorial team)
[ ] Reviews returned by EPP - https://prod--epp.elifesciences.org/api/reviewed-preprints/86687/v1/reviews

Example
"msas": "Genetics and Genomics", "Neuroscience"
"msid": "84628"
"version": "1"
"preprintDoi": "10.1101/2<IP_ADDRESS>4241"
"articleType": "Reviewed Preprint"
"status": "Published from the original preprint after peer review and assessment by eLife."

"Reviewed Preprint posted": "2023-01-02"
"Sent for peer review": "2022-10-28"
"Posted to bioRxiv": "2022-11-21" (link: "Go to bioRxiv": "https://www.biorxiv.org/content/10.1101/2<IP_ADDRESS>4241v1")

Editors:
Reviewing Editor
Michael B Eisen
University of California, Berkeley, United States
Senior Editor
Michael B Eisen
University of California, Berkeley, United States

Step 4: Modify manuscripts.json (no PDF)

[ ] Reviewed preprint is published to EPP (https://elifesciences.org/reviewed-preprints/86687)

[ ] Pull request created to enhanced-preprint-client
[ ] Pull request switched to "Ready for review"
[ ] Post link to pull request below

[ ] Request that a doi be registered

[ ] Post link to #enhanced-preprint comment below

Pull request: [PLACE LINK TO PULL REQUEST HERE]
#enhanced-preprint comment thread: [PLACE LINK TO COMMENT HERE]

Instructions to modify manuscripts.json

Visit: https://github.com/elifesciences/enhanced-preprints-client/actions/workflows/publish-manuscript.yaml
Click: Run workflow
Complete the form and click "Run workflow"
A successful run should result in a new pull request at https://github.com/elifesciences/enhanced-preprints-client/pulls
Open the pull request and click the "Ready for review" button to trigger tests
Once the tests pass and you are happy with the changes the PR can be merged

Example pull request: https://github.com/elifesciences/enhanced-preprints-client/pull/334/files
Once the pull request is merged in it should be available a few minutes later.

Request that a doi
Post the following in #enhanced-preprint:
@Fred can you register a doi for https://elifesciences.org/reviewed-preprints/86687

Step 5: Awaiting search reindex

[ ] Reviewed preprint is avaliable on journal homepage (https://elifesciences.org)

The search reindex is triggered once an hour. We need the reviewed preprint to be indexed as the search application serves the journal homepage.

Additional info
If needed, the jenkins pipeline to reindex search can be triggered sooner.
https://alfred.elifesciences.org/job/process/job/process-reindex-reviewed-preprints/

Step 6: Published! Request PDF generation

[ ] Post the link to the PDF url at the top of the issue

[ ] Post link to #enhanced-preprint comment below

#enhanced-preprint comment thread: [PLACE LINK TO COMMENT HERE]
Post the following to the #enhanced-preprint on slack:
@Ryan Dix-Peek please can you generate a PDF for https://elifesciences.org/reviewed-preprints/86687

Step 7: Introduce PDF to data folder and git repo

[ ] PDF is avaliable at https://github.com/elifesciences/enhanced-preprints-data/raw/master/data/86687/v1/86687-v1.pdf

Detailed instructions: https://github.com/elifesciences/enhanced-preprints-data#add-a-pdf
Step 8: Add PDF url to manuscripts.json

[ ] Reviewed preprint PDF is available for download (https://prod--epp.elifesciences.org/reviewed-preprints/86687)

[ ] Pull request created to enhanced-preprint-client
[ ] Pull request switched to "Ready for review"
[ ] Post link to pull request below

[PLACE LINK TO PULL REQUEST HERE]

Instructions to add PDF url to manuscripts.json

Visit: https://github.com/elifesciences/enhanced-preprints-client/actions/workflows/add-pdf-url-to-manuscript.yaml
Click: Run workflow
Complete the form and click "Run workflow"
A successful run should result in a new pull request at https://github.com/elifesciences/enhanced-preprints-client/pulls
Open the pull request and click the "Ready for review" button to trigger tests
Once the tests pass and you are happy with the changes the PR can be merged

Example pull request: https://github.com/elifesciences/enhanced-preprints-client/pull/397/files
Once the pull request is merged in it should be available a few minutes later.

Step 9: Done!

[ ] Kettle is on!

Hi Andy,
I'm assuming this because the response is not present in the docmap (for some reason):
https://data-hub-api.elifesciences.org/enhanced-preprints/docmaps/v1/by-publisher/elife/get-by-manuscript-id?manuscript_id=86687

JSON
"_:b2": {
      "actions": [
        {
          "participants": [
            {
              "actor": { "name": "anonymous", "type": "person" },
              "role": "peer-reviewer"
            }
          ],
          "outputs": [
            {
              "type": "review-article",
              "published": "2023-05-26 08:47:32.174911+00:00",
              "doi": "10.7554/eLife.86687.1.sa1",
              "license": "http://creativecommons.org/licenses/by/4.0/",
              "url": "https://doi.org/10.7554/eLife.86687.1.sa1",
              "content": [
                {
                  "type": "web-page",
                  "url": "https://hypothes.is/a/9BmMEPuhEe2-8pNsuN5NiQ"
                },
                {
                  "type": "web-page",
                  "url": "https://sciety.org/articles/activity/10.1101/2<IP_ADDRESS>9215#hypothesis:9BmMEPuhEe2-8pNsuN5NiQ"
                },
                {
                  "type": "web-page",
                  "url": "https://sciety.org/evaluations/hypothesis:9BmMEPuhEe2-8pNsuN5NiQ/content"
                }
              ]
            }
          ]
        },
        {
          "participants": [
            {
              "actor": { "name": "anonymous", "type": "person" },
              "role": "peer-reviewer"
            }
          ],
          "outputs": [
            {
              "type": "review-article",
              "published": "2023-05-26 08:47:32.940771+00:00",
              "doi": "10.7554/eLife.86687.1.sa2",
              "license": "http://creativecommons.org/licenses/by/4.0/",
              "url": "https://doi.org/10.7554/eLife.86687.1.sa2",
              "content": [
                {
                  "type": "web-page",
                  "url": "https://hypothes.is/a/9I5F5vuhEe2YEH87ouOu7w"
                },
                {
                  "type": "web-page",
                  "url": "https://sciety.org/articles/activity/10.1101/2<IP_ADDRESS>9215#hypothesis:9I5F5vuhEe2YEH87ouOu7w"
                },
                {
                  "type": "web-page",
                  "url": "https://sciety.org/evaluations/hypothesis:9I5F5vuhEe2YEH87ouOu7w/content"
                }
              ]
            }
          ]
        },
        {
          "participants": [
            {
              "actor": {
                "name": "Christian Landry",
                "type": "person",
                "_relatesToOrganization": "Université Laval, Canada"
              },
              "role": "editor"
            },
            {
              "actor": {
                "name": "Christian Landry",
                "type": "person",
                "_relatesToOrganization": "Université Laval, Canada"
              },
              "role": "senior-editor"
            }
          ],
          "outputs": [
            {
              "type": "evaluation-summary",
              "published": "2023-05-26 08:47:33.933968+00:00",
              "doi": "10.7554/eLife.86687.1.sa3",
              "license": "http://creativecommons.org/licenses/by/4.0/",
              "url": "https://doi.org/10.7554/eLife.86687.1.sa3",
              "content": [
                {
                  "type": "web-page",
                  "url": "https://hypothes.is/a/9SXyLvuhEe2PzKcqK2YCdQ"
                },
                {
                  "type": "web-page",
                  "url": "https://sciety.org/articles/activity/10.1101/2<IP_ADDRESS>9215#hypothesis:9SXyLvuhEe2PzKcqK2YCdQ"
                },
                {
                  "type": "web-page",
                  "url": "https://sciety.org/evaluations/hypothesis:9SXyLvuhEe2PzKcqK2YCdQ/content"
                }
              ]
            }
          ]
        }
      ],
      "assertions": [
        {
          "item": {
            "type": "preprint",
            "doi": "10.1101/2<IP_ADDRESS>9215",
            "versionIdentifier": "1"
          },
          "status": "peer-reviewed"
        }
      ],
      "inputs": [
        {
          "type": "preprint",
          "doi": "10.1101/2<IP_ADDRESS>9215",
          "url": "https://www.biorxiv.org/content/10.1101/2<IP_ADDRESS>9215v1",
          "versionIdentifier": "1"
        }
      ],
      "previous-step": "_:b1"
    }

Maybe this is something for @hazalCiplak can help with?

Hi @fred-atherden and @acollings ,
Thank you for bringing this to our attention.
The reason seems like the tags hasn’t been defined in hypothesis. Please find the related screenshot below. In the DocMaps API we are using tags for differentiate summary, review or author response. If a tag is null we are not able to import it into DocMaps result. Once the tags are updated, this information should properly appear in the results.
Could you please let me know who we should contact to address this update?

Thanks Hazal!
I'm not sure. @acollings do you know? Is this something to check with Paul about? Is it an issue with Kotahi?

Thanks @fred-atherden and @HazalCiplak: that would have been human error (Sue's away this week so someone else is posting author responses). Now I've fixed it, should this pull in automatically?

Thanks Andy.
@HazalCiplak can confirm, but I'd expect dataHub to update later today, and then the RP to be updated next subsequent time data is loaded/the app is deployed.

Thank you. I can confirm tags has been updated in Data Hub, so in DocMaps API result it should be updated soon. Please note that there is a small delay between DocMaps API result and Data Hub because of cashing the query.


Remove unnecessary css

There is css directory for setting up styles.
But these are no longer needed since material-ui overwrites more appropriate style values.
I want to remove them.

Thank you for review!


[FEATURE] React-Native Roadmap is not available

Description
There is a roadmap of android development that is totally in Java & XML. React-Native is a JS framework for mobile app development.
Screenshots

This roadmap should be added under a new section "React-native development" or this should be added under "Android development"
Additional information
No

because react native comes under WebDev


Fix missing basestring on python3

python3 lacks the 'basestring' class, instead all strings are unicode and of type 'str'.
this patch makes easywebdav py3-able

Just insert at the beginning of the code (after import statements):
try:
    unicode = unicode
except NameError:
    # 'unicode' is undefined, must be Python 3
    str = str
    unicode = str
    bytes = bytes
    basestring = (str,bytes)
else:
    # 'unicode' exists, must be Python 2
    str = str
    unicode = unicode
    bytes = str
    basestring = basestring


Fix config not passed to setup_audio_service

This change fixes a problem with setup_audio_service not having the right config dictionary when initializing ovos-audio plugins. If no config is passed, setup_audio_service uses Configuration(), which is the whole configuration object, not the  audio-specific config. This resulted in no audio service being loaded, making ovos unable to speak.
https://github.com/OpenVoiceOS/ovos-plugin-manager/blob/dev/ovos_plugin_manager/audio.py#L53C39-L53C39
This line may also need to be fixed, but because I'm not familiar with the codebase, I wasn't sure which method would be the best to use here.

@inkybutton @Ramblurr's PR got merged first for the same fix.
Thanks :+1:


Use an organization variable for the Python testing matrix entries

Changes introduced with this PR
This change replaces the hard-coded list of Python versions in the test matrix with a reference to the Arcalot organization variable, ARCALOT_PYTHON_SUPPORTED_VERSIONS.
This PR is waiting for the fix in https://github.com/arcalot/arcaflow-plugin-sdk-python/pull/135 to be released.

By contributing to this repository, I agree to the contribution guidelines.

I agree it seems good to go once the new release is created for the python sdk.


[citrix-ingress-controller] feat(extraVolumes): Addition

Adds extraVolume/Mounts to the Chart
this allows us to deploy cic with additional volumemounts to implemente CSI Secret Provider Classes for holding the nslogin secret.

Signed-off-by: Toni Tauro<EMAIL_ADDRESS>

hi @eyenx,
Thanks for your enhancement, we will review and validate. And also we need to take care of other files as well, we will consider this as an enhancement.

any update?

bump

hi @eyenx , with the extraVolumeMounts, this will only create extra mounts inside CIC, but you will still need to create the secret as CIC looks for environment variables NS_USER and NS_PASSWORD which picks the values from secret.
        - name: "NS_USER"
          valueFrom:
            secretKeyRef:
              name: {{ .Values.adcCredentialSecret }}
              key: username
        - name: "NS_PASSWORD"
          valueFrom:
            secretKeyRef:
              name: {{ .Values.adcCredentialSecret }}
              key: password

hi @eyenx
we have added this feature to have extra volume mounts and the same can be found in values.yaml
extraVolumeMounts: []
  # We usually recommend not to specify default resources and to leave this as a conscious
  # choice for the user.
  #- name: github-key
  #  mountPath: /etc/config/keys/
  #  readOnly: true
  #- name: agent-init-scripts
  #  mountPath: /docker-entrypoint.d/

extraVolumes: []
  # We usually recommend not to specify default resources and to leave this as a conscious
  # choice for the user.
  #- name: agent-init-scripts
  #  configMap:
  #     name: agent-init-scripts
  #     defaultMode: 0755
  #- name: github-key
  #  secret:
  #    secretName: github-key
  #    defaultMode: 0744


Streaming Enhancement: Alternate way to add feeds

Pretty self explanatory, I would like to see an alternate way to display streamers like with yt feed but instead you would input a twitch id.

Some things I found about the APIs:
https://dev.twitch.tv/docs/api/reference#get-streams
https://discuss.dev.twitch.tv/t/client-id-requirement-faqs/6108


N@TM Individual Review

Video: https://drive.google.com/file/d/1WqF-G02QAHNMW8MfoRlQ9doerc4gdX2O/view?usp=sharing
Blog: https://aditi99b.github.io/notebook//2024/02/26/indireview_IPYNB_2_.html

0.96/1
You did a great job making sure you covered all the requirements and had everything you needed. Your implementation of the create() method within the Pulse class stands out. It nicely adds new database records and is very important for the project to function. Next time, try to make your descriptions more detailed so someone new can easily follow along. Great work

Your Blog was well organized, and I liked how you explained how your code matched College Board requirements. The styling of the whole webpage was consistent, and I liked the concept of fitness.
Glows:

Styling of CSS and HTML was engaging
Code explanations were concise and clear
The details on the page that give more information about heart rate based on the user input was interesting
I liked how you organized the key commits
Grows:
Video could be less fuzzy in the beginning, maybe cut the first few seconds
Could have been more creative with the user input
Could have displayed the backend database in the video

Overall: 0.97/1.0


Thanks from the community for the huge help

We are a community that helps others, for free, thank you so much for the amazing video

We are a community that helps others, for free, thank you so much for the amazing video


Update env.md

Proposed changes

Unreleased project version (optional)

Related issues (optional)

Gotta love the Oxford comma :)


Amazon Lex ASR/STT support

Closes issue #330

Tested successfully only thing I am not sure about is the contentType I'm passing, but I am getting results back so it might be right? Also needs to be adjusted if we want to support another sample rate.

Actually the Pull Request title should be "Amazon Lex ASR support", not "Amazon Lex TTS support", since TTS means "Text to Speech", but you perform Speech Recognition, not Speech Synthesis.

You are correct. I am great at mixing up the terminology.
On Fri, Mar 2, 2018, 12:20 AM Josef Hölzl<EMAIL_ADDRESS>wrote:

Actually the Pull Request title should be "Amazon Lex ASR support", not
"Amazon Lex TTS support", since TTS means "Text to Speech", but you perform
Speech Recognition, not Speech Synthesis.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/Uberi/speech_recognition/pull/331#issuecomment-369853265,
or mute the thread
https://github.com/notifications/unsubscribe-auth/ACbIG74ym99GEj1YinVHJuxzqIsVUDzuks5taQDegaJpZM4SZCdZ
.

--
Thank you,
Patrick Artounian

Why did you abandon this? Does the Amazon service not work as expected?

Why did you abandon this? Does the Amazon service not work as expected?

It did work, but was never merged in, and eventually I just closed it. Also moved things internal for the company I was working for at the time.
If it is of any help, Google performed better than the rest on average. Also, the quality of audio you input is very important. There are times when I would not get a read on the text, and lowering the quality helped (8khz). If STT is a core feature, not only test against other services/data sets, but also 8/16khz and with/without audio filtering for background noise.  Some services (Google) like to filter out background themselves.

Yeah, I understand. This project appears to be borderline dead. I submitted a fix for their IBM API, and that's been ignored too. I've actually found Houndify and Bing to be pretty good, even a little better than Google in my own benchmarking.

I wonder what is etiquette to "adopt" a project like this. That's interesting that Houndify had better results. You made me recall that I tested IBM for a short period after the rest, and it is indeed really good.

I think the etiquette is to just fork the project and develop it in parallel.
Which reminds me, I just noticed you implemented an interface to Amazon's Lex bot service, not their transcription service. Did you ever test Transcribe? I just wrote up a rough implementation and found it has one of the better accuracy rates. Unfortunately, it's one of the more obnoxious APIs since it requires you to separately upload to and manage your data in S3, and the actual transcribe job is incredibly slow, but it looks like it could be sped up through launching jobs in parallel.


Simulate ADT

You may be interested in https://github.com/sviperll/adt4j and a recent design discussion of the project: https://github.com/sviperll/adt4j/issues/20

This is great!
We should take this into account when designing the collections. List and Stream are there, Map (#170) and Set (#214) are in the pipeline. I'm currently investigating which form of binary search tree to take in order to create efficient Map and Set implementations. Not only time complexity is important but also space complexity, particularly for HashMaps. There are important balanced tree impls, AVL and RedBlack. Scala uses binary encoded Tries in order to fail fast if a key/hash is not present. I'm into it - a very exiting topic!

@sirinath Could you please provide some details, what to implement?
I think if it is a Java equivalent of Scala case classes, like adt4j project does, @jbgi mentioned above, it is out of scope for Javaslang. There already exists a great project that exactly does that!

What would be nice is having some way that the two projects could intersect in user-land, which is in part the discussion @jbgi linked to - awhile ago I was thinking "it would be nice if these ADT4j classes were monads..."

I'm against baking this annotation trickery into Javaslang. With JEP 169 there is already an official project to add Value Objects to Java. Beside that I don't like annotations very well.

@talios I think the Monad operations on one ADT can be expressed in multiple ways. It is likewise with Monoids (String concatenation, String multiplication, etc). It is better to express this explicitly.

@danieldietrich True, altho going FooMonad.map(foo, foo2 -> .... ); is kinda arse.

@talios Yes, right...

Also https://github.com/talios/javagadt/

And now also https://github.com/derive4j/derive4j
(no special support for javaslang... yet!)

Nice!

In order to add special support for javaslang into derive4J, what I would need is a none and a some static factory method in the Option interface. the methods should return an Option (not a Some or a None). Same for Either, with left and right constructors.

Can't this be declared as some sort of mapping file within derive4J? From the API perspective this does not scale very well. I mean, why isn't it possible to declare within derive4J which class is Option and how to create a None and a Some?

The main problem is type inference. Derive4J use invariant generics: using explicit subtyping (new Some() / None.instance()) will probably breaks generated code.

I did some tests, it complicate things a little bit but should be doable.
From a user point a view still thinks that having some/none constructors in Option that return Option is a good thing. Sub-typing complicate usage of parametric polymorphism a lot and I find the later far more useful for FP than the former.

Great, this sound like the right direction!

Too many ADT projects in Java land. We will wait for official Java support by oracle...


YOSYS_HOME to override process path

To be able to use and check pyosys builds without installing yosys itself (for CI) we need to override main process location, since in this case it points out to python executable location itself.

Related to #2417, and I think these two should be fixed in the same way (but I'm not yet sure which). I'll try to come up with something.

This should also resolve same issue as #2417 but also those covered by #2416 but with providing one environment. Think #2416 should stay as well, since it gives more fine grain setup.

Agreed, I mainly merged #2416 because it may be useful to override abc location for local testing or such, and it's using an utterly standard way of doing so.

in this case it points out to python executable location itself.

Thinking more about this case: shouldn't configuration in this case happen through Python? If pyosys is a native extension I would expect to be able to make it relocatable without messing with the environment of the process, i.e. through some kind of pyosys.yosys_data_dir hook or something. Basically, I would probably want to be able to build pyosys as a redistributable binary wheel.

Yeah, good point. In that case exposing abc location would be needed as well (since we need to be able to execute that one as well).

In that case exposing abc location would be needed as well (since we need to be able to execute that one as well).

Agreed. Seems like they could go in two globals, initialized with the current method by default, but overridable?

well ABC can be overwritten only if ABCEXTERNAL is set on compile that means that we would need to have global keeping "calculated" location that can be over written by python code. And also another global for "proc_share_dirname".
Other way would be just exposing "proc_self_dirname" able to be overwritten since ABC location is deduced from it.

that means that we would need to have global keeping "calculated" location that can be over written by python code. And also another global for "proc_share_dirname".

Yup, I think that would be a reasonable way to do it.

Created new branch for this https://github.com/YosysHQ/yosys/tree/paths_as_globals, works fine but makes python tests bit more complicated (setup fixtures), will see what I can do to improve that, using environment made test code not aware of paths.

Created new branch for this https://github.com/YosysHQ/yosys/tree/paths_as_globals,

Looks reasonable to me, there are a few minor cleanups I'll ask you to do, but we can leave that until PR review.

will see what I can do to improve that, using environment made test code not aware of paths.

I think you can still use environment in the testsuite, I am only concerned about two things:

To a greater degree, the fact that you currently cannot ship a pyosys wheel;
To a lesser degree, Yosys changing its behavior based on obscure environment variables.


Update iot.md

Fixed a small typo:
Changed the line
DeviceAuthenticationWithRegistrySymmetricKeyvar deviceAuthentication = new DeviceAuthenticationWithRegistrySymmetricKey(deviceId, deviceKey);
to
var deviceAuthentication = new DeviceAuthenticationWithRegistrySymmetricKey(deviceId, deviceKey);

:white_check_mark: Validation status: passed

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@olivierbloch @CamSoper can you please review this?


C# build failing for unclear reason

https://source.cloud.google.com/results/invocations/afc994a2-46fb-4a02-87e9-377c0c657f3d/targets
End of relevant log output:

Build succeeded.
    0 Warning(s)
    0 Error(s)
Time Elapsed 00:00:15.38
2019-05-15 17:03:47,245 FAILED: tools/run_tests/helper_scripts/build_csharp.sh [ret=134, pid=7043, time=16.1sec]
2019-05-15 17:03:47,245 FAILED: Some tests failed
  adding: reports/ (stored 0%)
+ DOCKER_EXIT_CODE=1
++ mktemp
+ TEMP_REPORTS_ZIP=/tmpfs/tmp/tmp.4SzwJ3J9Mx
+ docker cp run_tests_ce16a783-f198-49a1-be8c-4291e7191955:/var/local/git/grpc/reports.zip /tmpfs/tmp/tmp.4SzwJ3J9Mx
+ unzip -o /tmpfs/tmp/tmp.4SzwJ3J9Mx -d /tmpfs/src/github/grpc
Archive:  /tmpfs/tmp/tmp.4SzwJ3J9Mx
   creating: /tmpfs/src/github/grpc/reports/
+ rm -f /tmpfs/tmp/tmp.4SzwJ3J9Mx
+ docker rm -f run_tests_ce16a783-f198-49a1-be8c-4291e7191955
run_tests_ce16a783-f198-49a1-be8c-4291e7191955
+ exit 1
Traceback (most recent call last):
  File "tools/run_tests/run_tests.py", line 1540, in <module>
    env=env)
  File "/usr/lib/python2.7/subprocess.py", line 540, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'tools/run_tests/dockerize/build_docker_and_run_tests.sh' returned non-zero exit status 1
2019-05-15 10:03:50,457 FAILED: run_tests_csharp_linux_opt_native [ret=1, pid=8980, time=147.7sec]

Seems transient. Closing.


Add support for imblearn's Pipeline and Samplers.

I'm using dask-ml to parallelized my sklearn pipeline, which consist of imblearn pipeline. I hack the code to make it work with it.
This would be extremely useful for people that are using both libraries.

cc @glemaitre, if you have any thoughts on how this should be supported.

Basically, we just inherit from Pipeline and allow to call fit_resample during fit of the Pipeline.
Actually, it would be interesting to have some supported resamplers in dask: random under- and over-sampling. The rest of the sampler would not make so much sense with large dataset and not sure that you can generate sample without a full view on the dataset. However, random sampler could be handy to resample on each node maybe.

Would this PR close #317? It seems certainly is related.

@xKHUNx can you include a test with these changes (will need to include imblearn in the environment file)? It'd be helpful to have an example to play with.

Would this PR close #317? It seems certainly is related.

Yes

@xKHUNx are you able to provide a simple test / example using this. That'd help me with reviewing.

@xKHUNx are you able to add tests here?

I have not test it myself, but this should do:
import numpy as np
from sklearn.compose import ColumnTransformer
from imblearn.pipeline import Pipeline
from sklearn.impute import SimpleImputer
from sklearn.preprocessing import StandardScaler, OneHotEncoder
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import train_test_split, GridSearchCV
from imblearn.over_sampling import SMOTE
from dask_ml.model_selection import RandomizedSearchCV

np.random.seed(0)

# Read data from Titanic dataset.
titanic_url = ('https://raw.githubusercontent.com/amueller/'
               'scipy-2017-sklearn/091d371/notebooks/datasets/titanic3.csv')
data = pd.read_csv(titanic_url)

# We create the preprocessing pipelines for both numeric and categorical data.
numeric_features = ['age', 'fare']
numeric_transformer = Pipeline(steps=[
    ('imputer', SimpleImputer(strategy='median')),
    ('scaler', StandardScaler())])

categorical_features = ['embarked', 'sex', 'pclass']
categorical_transformer = Pipeline(steps=[
    ('imputer', SimpleImputer(strategy='constant', fill_value='missing')),
    ('onehot', OneHotEncoder(handle_unknown='ignore'))])

preprocessor = ColumnTransformer(
    transformers=[
        ('num', numeric_transformer, numeric_features),
        ('cat', categorical_transformer, categorical_features)])

# Append classifier to preprocessing pipeline.
# Now we have a full prediction pipeline.
clf = Pipeline(steps=[('preprocessor', preprocessor),
                      ('smote', SMOTE(sampling_strategy='all')),
                      ('classifier', LogisticRegression(solver='lbfgs'))])

X = data.drop('survived', axis=1)
y = data['survived']

params = {
    'classifier__C': loguniform(0.001, 1)
}

X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2)

final_clf = RandomizedSearchCV(final_clf, n_iter=10, param_distributions=params, cv=3, n_jobs=-1, refit=True)
print("model score: %.3f" % clf.score(X_test, y_test))

I won't have time, unfortunately. Are you interested in working on this PR still?

Are you interested in working on this PR still?

This PR is good enough for my personal use case, I don't see the need to improve it for the near future.

OK. We would need to add a tests, clean up a few things, and clarify a couple changes before this will be merged. Let me know if you want to pick it up again.


@sqfmi Hmm.. Reset didn't work for me - the LED on the ESP8266 blinks when reset - but nothing. In fact, I get absolutely nothing happenng now :( sketches won't upload and the currently loaded sketch (weather) won't refresh :,( Oh, and the circled component is scortching hot -

Originally posted by @ibuildrockets in https://github.com/sqfmi/badgy/issues/20#issuecomment-430591985

Left on with websocketDraw example and I'm having the same problem. This is very hot and nothing is working now. It was left on for 2 days. Will not reset. The CH340C is still in-place, unmodified board.

I've tested the hot component. Ambient is 25ºC (77ºF) and the component is at 89ºC (192.5ºF)
Again, no life in the badge :(

The inductor shouldn't be that hot ♨ ! Please try replacing it with an equivalent 68uH 1210 inductor, or reach out to us with your order number and we'll send you a replacement board.

@ibuildrockets they should both be the same, just different packaging. Closing this issue now.


Productionize claims_hosp

Description
Adds the necessary Ansible bits and scripts to deploy claims_hosp like an indicator while keeping intact its current automation routines.
Changelog

Adds additonal directory structure and current automation scripts.
Gives Ansible the ability to place a templated secrets.py file into an indicator's root directory.
Updates vars and vault with new secrets.

Start from Jingjing

All the pipeline required code are moved to delphi_claims_hosp.
HospClaims could be dropped. But didn't do that currently just for a backup.
Switch from print() to logger
Add pulling steps from shell scripts to run.py
Pulled files are downloaded and stored in ./retrieve_files. All the raw files will be deleted after a production run
refactor secrets into params.json
Check the validation results. The type of hrr geo_ids are preferred to be string. However, if I change it to zero-filled strings, it does not match the history which generates more problems. So, switched back.

Fixes
Fixes #1623

@mariajahja Can you take a quick pass through this, maybe check out those comment-cleanup questions?

Please address remaining comments from my previous review -- switch to structured logging is still incomplete; outdated paths are still present; etc.
Happy to review again once those are fixed or otherwise resolved.

All the things required for the pipeline are moved to delphi_claims_hosp. The problems that you mentioned in HospClaims/automate are

either solved in delphi_claims_hosp, eg. switch from print() to logger
or ignored, eg.
- hard coded links: that shell scrip won't be used any more.
- import logging: we switch to validator for checks.

In that case, please remove all unused code.

In that case, please remove all unused code.

./HospClaims is removed.

I'll fix the vault; we had an update to the safegraph secrets while this PR was in flight

@krivard Looks reasonable. As best I can tell we won't need any prep, but imo best path is to merge and test 👍