Files from tumor specimen are associated with normal specimen, and vice versa

Description
In the response received from cda-python, proteomics files derived from tumor are associated with the normal sample, Files derived from the normal are associated with the tumor.
To Reproduce
See  09CO022 Example-CDA v2 notebook for full details including the results. The following code isolates the specific problem:
q1 = Q('ResearchSubject.id = "c5421e34-e5c7-4ba5-aed9-146a5575fd8d"')
r = q1.run(limit=2)
print(r)
j = json.dumps(r[0], indent=3)
with open('query_results/09CO022.json', 'w') as f:
    f.write(j)

subject2 = r[0]['ResearchSubject'][1]
for s2 in subject2['Specimen']:
    if s2['specimen_type'] == 'sample':
        for k, v in s2.items():
            if v.__class__.__name__ == 'list':
                if len(v) < 2:
                    print(k, v)
                else:
                    if k == 'File':
                        for f in v:
                            print(f['label'])
                    else:
                        print ('{} has {} items'.format(k, len(v)))
            else:
                print ('{} : {}'.format(k, v))

        print('_'*80)

Expected behavior
See the notebook for the step that associates the files with the correct aliquot.
The preferable result is that the files are listed once - only at the aliquot level.

PDC were asked "could you let me know if a file can contain data from both tumor and normal in the testing scenario described here? https://github.com/ianfore/cdatest/blob/main/v2tests/09CO022 Example - CDA v2.ipynb"
They responded as follows:

My first thought is that this is expected because the PNNL study is TMT where the VU study is label-free.  During TMT analysis samples are mixed (i.e., multiplexed) giving a one to many relationship between files and aliquots.  So both tumor and normal aliquots are present in those files.  Maybe ask him to verify that the extra files are coming only from the PNNL query?  I'd note that label-free represents less than 10% of the data in the PDC and is not currently being performed outside of a few newer DIA studies.  Happy to discuss.

Response

It looks like the extra files come from both PNNL and VU when query is performed at the sample level.  We have a known issue of files existing in multiple locations in the CDA schema so this may be another cause for this issue.  CDA is working on removing duplicate files and if this issue remains after that, multiplexing certainly would explain this as samples have one to many relationships.  I will let Ian know and confirm that he sees the extra files in both VU and PNNL queries.

PDC

Cases/samples shared across studies and the multiplexing within studies certainly complicate the PDC queries that are deemed straight forward with GDC. It is always good stratify the outputs at lowest level (aliquot, study) when performing higher level queries (case, sample).

The information provided essentially supports the issue as originally raised. . It does raise one other issue.

The basic confirmation is that the listing, at the sample level, includes files which do not derive from the sample. This is true for both VU and PNNL, though in the case of PNNL issue 2 confounds things.
This occurs where the files are listed at the sample level. At the aliquot level the listing in CDA appears to be correct reflection of what PDC says.

One confirmation would be useful. PDC put it that the VU study was label free. MS was done on the tumor sample without the corresponding normal. It would be good to confirm that VU did not use the normal sample at all. I did look at PDC directly (see the notenook) and that’s what it seemed to suggest.

Why are there two files for each PNNL tumor/normal pair rather than one for the plex?
This new issue comes from the point made by PDC that PNNL used the TMT platform i.e. multiplexed samples
There are many other studies in PDC of multiplexing. What you see in those studies that the file is listed under each of the specimens in the plex.
That’s not what we see for this PNNL study
Here’s an example pair of files
13CPTAC_COprospective_P_PNNL_20170215_B4S1_f01.mzid.gz
16CPTAC_COprospective_P_PNNL_20170215_B4S4_f01.mzid.gz
PDC associates the first one with the normal and the second with the tumor. The question is why are there no multiplex files for this study.

This is not directly a CDA issue though. CDA (at the aliquot level) simply repeats what is in PDC.

One possibility is that the aliquot was run twice, i.e. in replication.
This happens in several studies.
Also note that you are querying files across multiple studies, typically
split by enrichment type.
File names containing P indicate phosphoproteomics and W indicate
whole proteomics.  So the aliquots commonly generate two sets of files
across the PDC.  This is of course on top of the fact that data for
multiple aliquots 4-11 are in all iTRAQ/TMT study.  For "label-free"
studies, each .raw, .mzml, .psm file contains data for only a single
aliquot.  This would be the case for the VU colon study.
Maybe send me the pair of aliquot identifiers and I can look into it more
specifically?  I think I lost track of the issue/question.
On Wed, Jan 12, 2022 at 2:52 PM Ian Fore @.***> wrote:

The information provided essentially supports the issue as originally
raised. . It does raise one other issue.

The basic confirmation is that the listing, at the sample level,
includes files which do not derive from the sample. This is true for both
VU and PNNL, though in the case of PNNL issue 2 confounds things.
This occurs where the files are listed at the sample level. At the
aliquot level the listing in CDA appears to be correct reflection of what
PDC says.

One confirmation would be useful. PDC put it that the VU study was label
free. MS was done on the tumor sample without the corresponding normal. It
would be good to confirm that VU did not use the normal sample at all. I
did look at PDC directly (see the notenook) and that’s what it seemed to
suggest.

Why are there two files for each PNNL tumor/normal pair rather than
one for the plex?
This new issue comes from the point made by PDC that PNNL used the TMT
platform i.e. multiplexed samples
There are many other studies in PDC of multiplexing. What you see in
those studies that the file is listed under each of the specimens in the
plex.
That’s not what we see for this PNNL study
Here’s an example pair of files
13CPTAC_COprospective_P_PNNL_20170215_B4S1_f01.mzid.gz
16CPTAC_COprospective_P_PNNL_20170215_B4S4_f01.mzid.gz
PDC associates the first one with the normal and the second with the
tumor. The question is why are there no multiplex files for this study.

This is not directly a CDA issue though. CDA (at the aliquot level) simply
repeats what is in PDC.
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Thanks Paul - that helps.
All the details of aliquot ids etc. are in the notebook linked from this GitHub issue.
To summarize for PNNL :
Each of the normal and tumor aliquots has 70 (different) files which break down as follows

Phosphoproteome - 24 files

6 fractions - 4 files per fraction as follows

Peptide Spectral Matches - .psm and .mzid.gz
Processed Mass Spec - .mzML.gz
Raw Mass Spectra-  .raw

Whole Proteome - 46 files
* 12 fractions -mostly 4 files per fraction
* in the same pattern as above
* There appear to be two files randomly missing from the pattern for both tumor and normal - hence 46 not 48.

The set of 70 files for the tumor is a completely different set of files than for the normal. If this is multiplexed one would expect to see files that derive from both. Any light you can throw on that would be helpful.
If you want to see the digging behind that summary see this notebook. I reorganized it based on the info you provided. Unfortunately GitHub mucks up the html table formatting a bit - so it loses some clarity (working on how to fix that).

The other thing that emerges from Paul's input is that in PDC, and perhaps in the "real world" (i.e. CPTAC), the two proteomes are considered different studies. PDC000116 for the whole proteome and PDC000117 for the phosphoproteome. This has some implications for CDA but it would cloud the current issue to get into that here. Thought it might need a new issue but it's essentially part of what was raised in #105, so will pick that aspect up there.
This issue should continue with its original focus.

Thanks Ian.
I'll figure out why those 2 files are missing.  We should consistently
distribute 4 files per MS run, with the other 3 derived from the primary
.raw file (1 per fraction.)
One note to your comment: Not all studies are paired tumor/normal.  In
fact, the earlier TCGA studies were all tumor + a (pooled )control
channel.  So that paradigm may only exist within certain studies.  In
addition, there is no requirement that the tumor and "normal" sample
(paired or not) be run within the sample plex.  In cases of paired normal,
it makes the most sense to include them together.  But in cases of
unassociated normal tissue being included, these may be spread around or
even randomized.  I will need to dig deeper for these aliquots as well to
see if they are indeed associated with the same case.  Did you make that
association through the PDC data?
On Thu, Jan 13, 2022 at 5:54 AM Ian Fore @.***> wrote:

Thanks Paul - that helps.
All the details of aliquot ids etc. are in the notebook
https://github.com/ianfore/cdatest/blob/main/v2tests/09CO022 Example - CDA v2.ipynb
linked from this GitHub issue.
To summarize for PNNL :
Each of the normal and tumor aliquots has 70 (different) files which break
down as follows

Phosphoproteome - 24 files

6 fractions - 4 files per fraction as follows

Peptide Spectral Matches - .psm and .mzid.gz
Processed Mass Spec - .mzML.gz
Raw Mass Spectra- .raw

Whole Proteome - 46 files

12 fractions -mostly 4 files per fraction
in the same pattern as above
There appear to be two files randomly missing from the pattern for
both tumor and normal - hence 46 not 48.

The set of 70 files for the tumor is a completely different set of files
than for the normal. If this is multiplexed one would expect to see files
that derive from both. Any light you can throw on that would be helpful.
If you want to see the digging behind that summary see this notebook
https://github.com/ianfore/cdatest/blob/main/v2tests/09CO022 Proteomic Files on v2.ipynb.
I reorganized it based on the info you provided. Unfortunately GitHub mucks
up the html table formatting a bit - so it loses some clarity (working on
how to fix that).
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@.***>

Above: "In addition, there is no requirement that the tumor and "normal" sample
(paired or not) be run within the sample plex."
Should read:  "In addition, there is no requirement that the tumor and "normal" sample
(paired or not) be run within the same plex."

It's actually 4 files in total.

For the tumor:

for fraction f03 the raw.cap.psm file is missing (or at least is not associated with the specimen (aliquot)
for fraction f10 .raw - ditto

For the normal:

fraction f01 .mzML.gz - ditto
fraction f02 .raw - ditto

These are my predicted names of the files that seem to be missing:

16CPTAC_COprospective_W_PNNL_20170123_B4S4_f03.raw.cap.psm
16CPTAC_COprospective_W_PNNL_20170123_B4S4_f10.raw
13CPTAC_COprospective_W_PNNL_20170123_B4S1_f01.mzML.gz
13CPTAC_COprospective_W_PNNL_20170123_B4S1_f02.raw

I will need to dig deeper for these aliquots as well to
see if they are indeed associated with the same case.  Did you make that
association through the PDC data?

I used the PDC API to do cross-checks in some of my tests. I've also looked at the studies in the PDC UI. I didn't see anything unexpected in the subject-sample-aliquot relationships - but I don't think I tested them in a rigorous sense.

I looked a bit more closely at the file_ids within the two samples in case_id "459e3b69-63d6-11e8-bcf1-0a2705229b82". After getting all file_id's associated with each sample, I found NO overlap of file_id's between the samples, so no files are shared between the tumor and normal samples. I do find it odd that each sample has files that are not associated with their aliquots though. A bit more searching could determine which aliquot or samples those extra files are from.

Is this helpful?  I queried this table out of the PDC dB.
From this I would conclude that only PNNL ran the normal tissue.
PNNL ran the normal for both phospho and whole proteome analyses both in plex 13.
PNNL also analyzed the tumor for both phospho and whole proteome both in plex 16.
VU only ran the tumor, and since they ran it label free, it was run as sample 87.

Limited bandwidth here too, but I did revisit the files and came up with the same answer as I did previously.

I do find it odd that each sample has files that are not associated with their aliquots though.

I think that cuts to the chase. If you follow the curiosity you expressed there I believe you will get to the truth of it.
It's best if you do that yourself, but what I suspect is happening is as follows. In the process of denormalization of the file content up to higher level specimens, files seem are being copied across to samples to which they do not apply. That is why I would question "our extraction process is not altering the data given to us by PDC in an any unexpected way". At the aliquot level your representation of the PDC seems accurate. It is at the higher levels of specimen that it goes off.
For reference, the content returned for this Subject is here
As an independent confirmation of my original test I copied the entire content of the tumor "sample" and the normal "sample" into two separate files and did the following diff. The only difference is in the ids and the source_material_type. The file content is the same for both.
diff 09CO022_normal_sample.json 09CO022_tumor_sample.json
2c2
<                "id": "f4af3e4d-641b-11e8-bcf1-0a2705229b82",
---
>                "id": "f6cce507-641b-11e8-bcf1-0a2705229b82",
6c6
<                      "value": "f4af3e4d-641b-11e8-bcf1-0a2705229b82"
---
>                      "value": "f6cce507-641b-11e8-bcf1-0a2705229b82"
13c13
<                "source_material_type": "Solid Tissue Normal",
---
>                "source_material_type": "Primary Tumor",

To confirm: this is on the second ResearchSubject within the Subject - the PDC Subject. It may be different for the GDC ResearchSubject, but I don't have time to check, and it's not of primary relevance.

So, yeah, the tumor and normal tissue for this case were run in separate plexes by PNNL.  I'm not really sure why they would do that.  Also, the files that Ian predicted absent do appear on this list.  Not sure where the mismatch is happening.

Thanks @rudnickp. Our efforts crossed. This does help - partly in following this specific issue through, also in highlighting a couple of others that we might want to fork off.
We have a couple of sideshows to the main event. The main event for issue #99 is the incorrect association of certain files with certain samples.
Sideshow 1 - missing files
Yes, the missing files are in the list you shared above. I did some quick pivot tables on the spreadsheet and it seems to have the full deck of 72 PNNL files for each of tumor and normal. CDA only returns 70 for each (see above), but I don't think it's a CDA issue. It's my recollection (documented above and in the notebooks) that the missing files are not visible in the PDC via its UI or its API. It would be good to have independent confirmation of that. We may to create a PDC issue.
Sideshow 2 - why VU and PNNL ran the samples and plexes they did

From this I would conclude that only PNNL ran the normal tissue.

i.e. VU only ran the tumor - not the normal. That's certainly how it seemed 3+ years ago. Thanks for digging in and providing an independent check.

the tumor and normal tissue for this case were run in separate plexes by PNNL. I'm not really sure why they would do that

I can't say 'nor am I'. I don't even have the specific proteomics knowledge to ask the question. In terms of data aggregation the fact that someone doesn't have the knowledge is actually important.
In order to keep focus am not going to dig in further on this here. Creating separate issue.
** Not a Sideshow - what samples and plexes VU and PNNL ran and what files correspond to them**
That was originally my title for sideshow 2 - but then I realized it was key to what a data aggregator has to do. CDA currently misrepresents what the files relate to.


rename sem_summary

After consulting with @Maximilian-Stefan-Ernst  and @aaronpeikert, I suggest renaming sem_summary(...) with details(...).

in a similar spirit sem_fit() to fit?


ARROW-17455: [Go] Function and Kernel execution architecture

In addition to implementing the function execution architecture, this also shifts some files around for better package naming and scoping. A new package exec is created inside of compute/internal/ to make it easier to scope other internal-only methods / functionality such as the kernel implementations themselves.
This is a fairly large change because so much is interconnected, but it also includes extensive tests covering ~85% of the internal/exec package and nearly 80% of the entire compute package. More tests will be added as functionality is added.

@cyb70289 you can see some simple kernels in the tests which are used to test the infrastructure :smile:

@cyb70289 also following this I'm already starting to implement kernels for various functions, so aside from the tests there'll also be lots of implemented kernels to use for examples.


Version bump for rebuild

Update docs for missing parameters
Use postgresql v16 because postgresql contrib is uninstalling v15 after installing

approving for build


Installer msi not updated

It is good to see to have frequent updates, but I really miss the up-to-date installer, because the official site offers HTTP only download option.
Installer should be included in the further releases, so we can download it from github over HTTPS. The official DL link also could have HTTPS enabled.
Thank you! :)

@gridcoin Any chance we could get HTTPS/SSL enabled for the MSI download? I can't change this on the web server.

Could we serve the MSI over HTTPS?

@gridcoin Stupid question: Why is the MSI hosted on Gridcoin.us and not on GitHub? Wouldn't it be possible to attach the MSI to Github releases along with the sources? This way the download would be available via HTTPS as well.

Oh I see the problem: the download subdomain isnt part of the https settings.  I can fix that on the server - we have a 5 site HTTPS license.
Adding it to github adds more work to the deploy process; Id rather fix the HTTPS problem first.


SVG not rendering properly on canvas

On chrome (Version 50.0.2661.86 (64-bit)) or Safari some svgs are not properly rendered on a canvas whereas other svgs render fine.
Open the following html page to reproduce the issue. The bottom svg is the svg rendered by html2canvas on a canvas :
test.html.zip
Used version of html2canvas is 0.5.0-alpha1. You can replace the src attribute to use a local file of the library such as the v0.5.0-beta4 or the dist version from the sources, but the issue remains.

Duplicate of https://github.com/niklasvh/html2canvas/issues/871

and https://github.com/niklasvh/html2canvas/issues/846

Is this still an issue with v1.0.0? If so, could you please share an example on jsfiddle.


helm install command for cert-manager is missing name parameter for helm2

Following the instructions here for upgrading cert-manager
https://staging.rancher.com/docs/rancher/v2.x/en/installation/options/upgrading-cert-manager/
I tried copy/pasting the following command (Step 4 install the new version of cert-manager):
$ helm install \
  cert-manager jetstack/cert-manager \
  --namespace cert-manager \
  --version v0.12.0

What kind of request is this (question/bug/enhancement/feature request):
Bug
Steps to reproduce (least amount of steps as possible):
Follow the steps in the documentation using helm version 2
Result:
$ helm install \
  cert-manager jetstack/cert-manager \
  --namespace cert-manager \
  --version v0.12.0
Error: This command needs 1 argument: chart name

Other details that may be helpful:
I was able to do the install with the following command parameters:
$ helm install \
  --name cert-manager \
  --namespace cert-manager \
  --version v0.12.0 \
  jetstack/cert-manager

helm version
Client: &version.Version{SemVer:"v2.16.1", GitCommit:"bbdfe5e7803a12bbdf97e94cd847859890cf4050", GitTreeState:"clean"}
Server: &version.Version{SemVer:"v2.16.1", GitCommit:"bbdfe5e7803a12bbdf97e94cd847859890cf4050", GitTreeState:"clean"}

Environment information

Rancher version (rancher/rancher/rancher/server image tag or shown bottom left in the UI): 2.2.9
Installation option (single install/HA): HA

Cluster information

Cluster type (Hosted/Infrastructure Provider/Custom/Imported):  HA in AWS
Machine type (cloud/VM/metal) and specifications (CPU/memory): cloud
Kubernetes version (use kubectl version):

 v1.15.5

I've opened an issue in rancher/docs instead: https://github.com/rancher/docs/issues/2116

my helm version is 2.14.3, kubectl version is 1.15.5,   when i follow the doc guide run
helm install \
  --name cert-manager \
  --namespace cert-manager \
  --version v0.13.1 \
  jetstack/cert-manager

It break for Error: This command needs 1 argument: chart name
But I don't know why it's wrong?


Keycloak self-managed documentation

Issue: #568
First draft

Alright thank you Christian!
Seems like we should have gone for more of a complete guide!

Alright thank you Christian!
Seems like we should have gone for more of a complete guide!

@Mlundm I think it's good that you asked for early feedback. Why bother with a complete guide if you are not 100% sure you are on the right track. :smile:


Approvals and checks api - List approvals

From this documentation: https://docs.microsoft.com/en-us/rest/api/azure/devops/approvalsandchecks/approvals/query?view=azure-devops-rest-7.1
Is it possible to list all approvals?  It looks like you can only query/filter on approvalIds.  How do you find those Ids?

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

ID: 34deb54c-8078-eb28-4e13-05ddd2b95d65
Version Independent ID: d8065284-dd42-736a-400b-2262a6cf0657
Content: Approvals - REST API (Azure DevOps Approvals And Checks)
Content Source: docs-ref-autogen/7.1/approvalsAndChecks/Approvals.yml
Product: devops
Technology: devops-ref
GitHub Login: @wnjenkin
Microsoft Alias: whjenkin

Hey @safari137 ,Do you think using this will be helpful for you?
https://learn.microsoft.com/en-us/rest/api/azure/devops/approvalsandchecks/approvals/query?view=azure-devops-rest-7.1&tabs=HTTP

the following sample from that url:
GET https://dev.azure.com/{organization}/{project}/_apis/pipelines/approvals?api-version=7.1-preview.1
results in this error response:
{"$id":"1","innerException":null,"message":"Query for approvals failed. A minimum of one query parameter is required.\r\nParameter name: queryParameters","typeName":"System.ArgumentException, mscorlib","typeKey":"ArgumentException","errorCode":0,"eventId":0}
this is the url I'm using with a fake organization and project name
https://dev.azure.com/my-org/my-proj/_apis/pipelines/approvals?api-version=7.1-preview.1

Do we have any update on this? I'm still needing it :)

I believe you need to query a checks object first in order to get the related approvals. In the checks result you will find approval objects with guids. That can be probably be used somehow. But when I query for these guids I get an exception back. I will share my findings when I have any success.


Support Nitro servers

It would be very nice if there was some documentation for deploying Nitro servers.
This could be very helpful both for Nuxt and Solid users.
Cross-reference: https://github.com/unjs/nitro/issues/2236

@ryansolid just messaged me about this - i'm going to take a look this week to get solid-start working

Curious if solid start is supported? I see it referenced in the docs but haven't been able to successfully deploy. Thanks!

Now that SolidStart is supported on AWS, is Cloudflare support planned for nitro-based apps?


Convert search parameters to form inputs when using data-turbo-stream

Fixes a problem pointed out recently on #612 by @seanabrahams and @kevinmcconnell.
Links with data-turbo-stream are converted to forms, and forms with method="GET" don't submit the query string part of their action. This can be circumvented by iterating through any query string parameters and adding them to the generated form as hidden inputs.
Note: MDN refers to what we usually call "query string parameters" as "search parameters". This is a bit confusing, but it's the correct terminology I guess :)

I've been looking at a different approach to this problem as well. Originally it seemed like submitting data-turbo-stream links as forms would be a straightforward & safe way to do this (especially as we already have data-turbo-method doing something similar), but seeing that issue with parameters come up it's making me doubt that approach.
I've got a branch going where I'm trying a different tack -- rather than submit these stream links as GET forms, the navigation code can simply add the stream MIME type to its usual request if the link has data-turbo-stream (in much the way way as the FormSubmission adds it according to its own logic). I think that will actually be a less invasive change, and less likely to introduce any unexpected behaviour, since the only change to the request will be that extra item in the Accept header.
I think it would be worth looking at that approach before we settle on the right fix. I'll try to get a PR open as soon as I can (but it will probably be a few days, sorry; busy week at work!)
@seanpdoyle does that sound reasonable to you?

@kevinmcconnell I'm in favor of that change.

I'll try to get a PR open as soon as I can (but it will probably be a few days, sorry; busy week at work!)

I could draft something up today, if that's OK with you.
@LVMBDV could you create a test or two exercising the implementation change in this pull request? If you're able to add them here, I'll make sure to get them passing on the alternative PR.

I could draft something up today, if that's OK with you.

Absolutely, that would be great 👍
FWIW, the approach I was looking at is to add an acceptsStreamResponse option to VisitOptions, which Visit can refer to in a prepareHeadersForRequest. That way, the Session can set that option appropriately when handling clicks. Seems to work pretty well, and is a less intrusive change. The part I hadn't tackled yet is that the FrameController will (I think) also want something similar, for the cases where it's issuing the request. That's where I ran out of time :)
Of course you may have an entirely different approach in mind; just wanted to mention where I'd reached, in case it saves you any time.

Hi, I needed this for a specific use case I stopped pursuing to allocate more time to releasing an MVP. If the other approaches don't work out, I can refine this PR i.e. add tests and documentation but let's shelve this one until that's decided.

Solved via https://github.com/hotwired/turbo/pull/647 instead.


[dvsim] Initial verible lint integration

This allows us to call Verible through dvsim and produce a dashboard similar to the one that we produce for Ascentlint. The report parsing script has been largely reused from the Ascentlint flow.
See here for a sneak preview of the dashboard. I am going to add this to my lint cronjob once this PR is merged.
Note that this flow still produces many warnings, since we do not yet make use of the new configurability features that have been added to Verible (#229). For that we have to make sure we can pass the configuration file to Verible through Fusesoc by extending the Edalize backend:
https://github.com/olofk/edalize/blob/63d9512f29dc552099492f10cc45ae0df1490a9f/edalize/veriblelint.py#L64
The "run-in-bash" wrapper is currently needed in order to write the tool output to a logfile. If there would be another way to write such an output file that would of course be great. We mainly have two options to achieve this: we could either add that functionality to Verible or the Fusesoc command wrapper (I tend to prefer the former if that is possible).
For reference, Ascentlint generates two output files that are of interest to us:

a .log file with general tool errors/warnings, including messages from syntax checking.
a .rpt file with lint-rule-specific messages with different severities (info, warning, error)

Example of Ascentlint invocation in the Edalize backend:
https://github.com/olofk/edalize/blob/63d9512f29dc552099492f10cc45ae0df1490a9f/edalize/templates/ascentlint/Makefile.j2#L7-L8
CC @hzeller @mithro @fangism
Signed-off-by: Michael Schaffner<EMAIL_ADDRESS>

See here for a sneak preview of the dashboard.

Can you make sure this is listed as either verible lint or style lint
to distinguish from the RTL lint?

Thanks for the comments! I'll update this PR once #1749 has made it in, since I will need features that have been added there.

Please file an issue with Verible to get this functionality added, add big TODOs with the upstream issue number to the current code, and file a follow-up issue here in OT to get that workaround removed once upstream adds this functionality. Ideally, they directly add structured reporting as well to save us from fragile text file parsing.
If we'd want to keep that longer than a couple weeks, I'd at least change the sim.mk file to get this functionality in there, and avoid the need for a wrapper script.

Thanks for giving this a look. I had a discussion about this with @sriyerg, and it appears that we need some sort of tee functionality, since we found that also other tools do not have this functionality built in. For instance, while Synopsys DC can write a command log and all sorts of report files, it looks like there is no way to write a complete DC shell log.
Hence, we decided to add this functionality to the corresponding {flow}.mk file, and this allows to get rid of this ugly workaround I have used here. The functionality is already in place as I have added that in one of the synthesis-related PRs last week (#1749).
I have heard that we may eventually get some sort of structured result output from Verible, which will make the result parsing script superfluous. I'll check again with the authors (also regarding common log files) in the next meeting that we have with them. In the meantime, I have added a tracking item to https://github.com/lowRISC/opentitan/issues/1727 for structured tool output support.

Thanks @imphil for the review! Waiting for @sriyerg's final approval before merging in.

Thanks @sriyerg, updated.


nearest neighbour queries in ES

we can run cosineSimilarity script queries
we can run regular match queries on LSH encoded vectors
can we run both for fast and accurate nearest neighbours?

query = {
    "query": {
        "bool": {
            "should": [{
                "script_score": {
                    "query": {"match_all": {}},
                    "script": {
                        "source": "cosineSimilarity(params.query_vector, 'features') + 1.0",
                        "params": {
                            "query_vector": QUERY_VECTOR
                        }
                    }
                }            }],
            "filter": [{
                "terms_set": {
                    "lsh_features": {
                        "terms": QUERY_LSH,
                        "minimum_should_match_script": {"source": "15"}
                    }
                }
            }]
        }
    },
    "stored_fields": [],
    "size": 100
}

this is working nice and fast thanks to the terms_set filter, across a wide range of dataset sizes. yet to do any real calculations for how this might scale to 40,000,000 vectors
still to do:

would still be desirable to switch the filter to a more_like_this query. this would allow us to swap out that minimum_should_match_script for a more easily interpreted threshold. seems very doable.
less doable, to somehow pass that more_like_this context to the script_score query so that we only make one request to the es index. Currently, the QUERY_VECTOR and QUERY_LSH come from a previous es.get() call by id, and are passed into the above secondary query. A more_like_this should allow us to do this in one step
an approximation of the request time for a query of this style run on 40,000,000 documents


Exceptions

Is it expected that I should get the ff. exception messages while running the train script?
Exception: need more than 3 values to unpack
Exception: a must be non-empty
Setup
Python = 2.7.13
TF version = 1.2.1

It seems like the Exception: need more than 3 values to unpack is caused by line

X2, Y1, Y2, IouS = roi_helpers.calc_iou(R, img_data, C, class_mapping)

of the training script. Is the IouS variable needed? I seems it's not use anywhere in the script.

I deleted the IouS, since it appear it was for debugging purposes. I trained and everything seems to be working fine. So my advice is to delete it.

ok, everything seems after removing the IouS. Thank you.


Fix for nightly dependancy workflow

Description
Fixes workflow deployed in #291.
Issue reference
Fixes #290
Review
Before you mark your PR as ready for review, please ensure that you've considered the following:

Updated the CHANGELOG.md in reverse chronological order (newest at the top) with a concise description of the changes, including the PR number.
Noted any breaking changes, including details on how it might impact existing functionality.

Type of change

[ ] New Feature: A non-breaking change that adds new functionality.
[ ] Optimization: A code change that improves performance.
[ ] Examples: A change to existing or additional examples.
[ ] Bug Fix: A non-breaking change that addresses an issue.
[ ] Documentation: Updates to documentation or new documentation for new features.
[ ] Refactoring: Non-functional changes that improve the codebase.
[ ] Style: Non-functional changes related to code style (formatting, naming, etc).
[ ] Testing: Additional tests to improve coverage or confirm functionality.
[ ] Other: (Insert description of change)

Key checklist:

[ ] No style issues: $ pre-commit run (or $ nox -s pre-commit) (see CONTRIBUTING.md for how to set this up to run automatically when committing locally, in just two lines of code)
[ ] All unit tests pass: $ nox -s tests
[ ] The documentation builds: $ nox -s doctest

You can run integration tests, unit tests, and doctests together at once, using $ nox -s quick.
Further checks:

[ ] Code is well-commented, especially in complex or unclear areas.
[ ] Added tests that prove my fix is effective or that my feature works.
[ ] Checked that coverage remains or improves, and added tests if necessary to maintain or increase coverage.

Thank you for contributing to our project! Your efforts help us to deliver great software.

Should we add the automated issue action in a separate PR? I thought that you were going to do it in the same PR, but you merged it :) We can also do it later when PyBaMM gets ready with the nightlies.

Fair shout, I'm happy for it to be added here and we can update the PR (or create a new one). I wanted to get the workflow in before travelling next week so pushed it through. At least now something is in a develop. Apologies for the quick trigger!

No worries! I think we can merge this one – I'll create a new PR and add it there.


DDB Importer | ERR > TypeError: Cannot read properties of null (reading 'includes')

I am receiving the following errors when importing monsters and it seems to stop the monster import on "Updating Zuggtmoy: Madness of Zuggtmoy". I checked my Monster Actor folder, and there is no updating going on in the background.
logger.js:62
       DDB Importer | ERR > TypeError: Cannot read properties of null (reading 'includes')
log @ logger.js:62
error @ logger.js:82
parseCritters @ ddb.js:266

logger.js:62
       DDB Importer | ERR > TypeError: Cannot read properties of null (reading 'includes')
    at getLanguages (https://assets.forge-vtt.com/bazaar/modules/ddb-importer/2.8.9/dist/main.js:9386:29)
    at parseMonster (https://assets.forge-vtt.com/bazaar/modules/ddb-importer/2.8.9/dist/main.js:11707:40)
    at https://assets.forge-vtt.com/bazaar/modules/ddb-importer/2.8.9/dist/main.js:11821:28
    at Array.forEach (<anonymous>)
    at parseMonsters (https://assets.forge-vtt.com/bazaar/modules/ddb-importer/2.8.9/dist/main.js:11819:15)
    at https://assets.forge-vtt.com/bazaar/modules/ddb-importer/2.8.9/dist/main.js:21262:64
log @ logger.js:62
error @ logger.js:82
parseCritters @ ddb.js:267

edit: It seems to be getting stuck at the end of item table creation

Fixed in v2.8.10. Hopefully.


Remove unused function in Traffic Portal

What does this PR (Pull Request) do?
Remove an unused Traffic Portal function.

[x] This PR is not related to any Issue

Which Traffic Control components are affected by this PR?

Traffic Portal

What is the best way to verify this PR?

Double-check the TP codebase for any actual usage of getParamUnassignedProfiles
Maybe overkill, but you could run the end_to_end TP tests to verify (I did this via CIAB and everything passed)

The following criteria are ALL met by this PR

[x] Removes unused code, no new tests necessary
[x] Removes unused code, no docs necessary
[x] Removes unused code, no changelog necessary
[x] This PR includes any and all required license headers
[x] This PR ensures that database migration sequence is correct OR this PR does not include a database migration
[x] This PR DOES NOT FIX A SERIOUS SECURITY VULNERABILITY (see the Apache Software Foundation's security guidelines for details)

Refer to this link for build results (access rights to CI server needed):
https://builds.apache.org/job/trafficcontrol-PR/4400/


Streamline CI

As a follow-up to the previous PR, this one adds two new CI workflows for the bytecode version on Windows and the corresponding badges. It also removes some remaining mentions of rc1, drops the alpha opam repository (which is no longer necessary with the release of OCaml 5) and logs the opam repositories from which dependencies are pulled (to make sure the multiple opam repositories are indeed providing exactly the packages they are expected to provide, and not conflicting with the main default one).

PR looks great - thanks!
I'll let the CI run finish and then merge. The early macOS failure looks like a temporary network hiccup.

This looks a lot greener! :smiley:  ... but it does include a Win bytecode crash! :grimacing:
If nothing else, this looks relatively easy to trigger consistently? :thinking:

Indeed, I see many many deadlocks, maybe the bytecode version is the right one to try and finally corner that bug (if it’s indeed #203 since PR11846 seems to fix-or-hide it in native)

OK, so we have

a windows bytecode crash
a windows threadomain timeout

We cannot blame the PR for any of these though.
Do you agree to merge and then investigate these in parallel @shym?

Indeed, I think we can merge it! :+1:


Regularization methods: Why no LASSO ?

Hello,
Thank you very much for this library. I am loving using it for my current project.
I was wondering why there is no L1 regularization proposed in the methods ? Since it is "simpler" than the other methods, is there any rationale no to have in the library ? Could it be possible to have it ?
Thank you in advance.

Hi @mamadyonline,
Thank you very much for your attention on this library! I will look into adding this feature and keep you posted.
Best regards,
Jin

Hi @powerfulbean,
That would be super nice. Thank you for your quick reaction. And I am looking forward.
Best regards,
Mamady


it is not possible to run

hello  . I download your project and i want to run on emulator but i got this error :
`Build file '/mnt/Projects/Projects/Practices/gitProject/flutter-cleanarch-weight-management-app/android/app/build.gradle' line: 60

What went wrong:
A problem occurred evaluating project ':app'.

path may not be null or empty string. path='null'`

How can i run ?

Hi,
Try the patch file I have sent. It is happening because of the Flutter
version updates and library I used have updated. Try to apply the patch and
tell me if it doesn't work.
Regards,
Mayank Rai
On Wed, Feb 5, 2020 at 5:25 AM tazik561<EMAIL_ADDRESS>wrote:

hello . I download your project and i want to run on emulator but i got
this error :
`Build file
'/mnt/Projects/Projects/Practices/gitProject/flutter-cleanarch-weight-management-app/android/app/build.gradle'
line: 60

What went wrong:
A problem occurred evaluating project ':app'.

path may not be null or empty string. path='null'`
How can i run ?
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
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or unsubscribe
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.


Problem when starting Anaconda

Description
What steps will reproduce the problem?

What is the expected output? What do you see instead?
Please provide any additional information below
File "C:\Users\hamdi\Anaconda3\lib\site-packages\traitlets\traitlets.py", line 528, in get
value = obj._trait_values[self.name]
KeyError: 'session'
Traceback (most recent call last):
File "C:\Users\hamdi\Anaconda3\lib\site-packages\jupyter_client\session.py", line 522, in _check_packers
packed = pack(msg)
File "C:\Users\hamdi\Anaconda3\lib\site-packages\jupyter_client\session.py", line 103, in
ensure_ascii=False, allow_nan=False,
File "C:\Users\hamdi\Anaconda3\lib\site-packages\zmq\utils\jsonapi.py", line 43, in dumps
s = s.encode('utf8, udc92')
LookupError: unknown encoding: utf8, udc92
Traceback (most recent call last):
File "C:\Users\hamdi\Anaconda3\lib\site-packages\spyder\plugins_init_.py", line 511, in
toggled=lambda checked: self.toggle_view(checked),
File "C:\Users\hamdi\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole.py", line 725, in toggle_view
self.create_new_client(give_focus=False)
File "C:\Users\hamdi\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole.py", line 1033, in create_new_client
self.connect_client_to_kernel(client)
File "C:\Users\hamdi\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole.py", line 1059, in connect_client_to_kernel
stderr_file)
File "C:\Users\hamdi\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole.py", line 1485, in create_kernel_manager_and_kernel_client
kernel_manager.start_kernel(stderr=stderr)
File "C:\Users\hamdi\Anaconda3\lib\site-packages\jupyter_client\manager.py", line 239, in start_kernel
self.write_connection_file()
File "C:\Users\hamdi\Anaconda3\lib\site-packages\jupyter_client\connect.py", line 467, in write_connection_file
transport=self.transport, ip=self.ip, key=self.session.key,
File "C:\Users\hamdi\Anaconda3\lib\site-packages\traitlets\traitlets.py", line 556, in get
return self.get(obj, cls)
File "C:\Users\hamdi\Anaconda3\lib\site-packages\traitlets\traitlets.py", line 535, in get
value = self._validate(obj, dynamic_default())
File "C:\Users\hamdi\Anaconda3\lib\site-packages\jupyter_client\connect.py", line 354, in _session_default
return Session(parent=self)
File "C:\Users\hamdi\Anaconda3\lib\site-packages\jupyter_client\session.py", line 482, in init
self._check_packers()
File "C:\Users\hamdi\Anaconda3\lib\site-packages\jupyter_client\session.py", line 530, in _check_packers
msg.format(packer=self.packer, e=e, jsonmsg=jsonmsg)
ValueError: zmq.utils.jsonapi.jsonmod = <module 'json' from 'C:\Users\hamdi\Anaconda3\lib\json\init.py'>
Version and main components

Spyder Version: 3.2.6
Python Version: 3.6.4
Qt Versions: 5.6.2, PyQt5 5.6 on Windows

Dependencies
pyflakes >=0.6.0 :  1.6.0 (OK)
pycodestyle >=2.3:  2.3.1 (OK)
pygments >=2.0   :  2.2.0 (OK)
pandas >=0.13.1  :  0.22.0 (OK)
numpy >=1.7      :  1.14.2 (OK)
sphinx >=0.6.6   :  1.6.6 (OK)
rope >=0.9.4     :  0.10.7 (OK)
jedi >=0.9.0     :  0.11.1 (OK)
nbconvert >=4.0  :  5.3.1 (OK)
sympy >=0.7.3    :  1.1.1 (OK)
cython >=0.21    :  0.27.3 (OK)
qtconsole >=4.2.0:  4.3.1 (OK)
IPython >=4.0    :  6.2.1 (OK)
pylint >=0.25    :  1.8.2 (OK)

Thanks for reporting. Looks similar to #7093 , and a likely installation issue. Please try the steps listed in the Spyder Troubleshooting Guide, specifically the Basic First Aid and Emergency CPR sections, which resolve the great majority of Spyder installation issues. Also, are you using any non-standard file encodings for anything? Also, try conda update --all in the Anaconda prompt.
If it still isn't working, please describe in detail the circumstances in which the error occurred, and post the information listed in relevant subsection of the Calling for Help section as a comment to this issue, and we'll try to help if we can. Otherwise, your issue will likely have to be closed after one week (7 days). Thanks, and best of luck!

Closed due to lack of response. If you can provide more information, please re-open and do so. Thanks.


Unsupported file type png

Hi,
I extended standard collection by adding new trait types with PNG images made in Adobe Photoshop. It seems like my files are unsupported by canvas. I get 'Error: Unsupported image type' at drawImage (/cryptopunk-nft-generator/index.js:101:27), .
I compared files that I made with the standard ones and saw some differences that can be the reason. I am mostly concerned about Resolution, Print size and Units. I also wonder what is the reason for such significant size difference between these 2 files. Did you encounter such issues before?
My png file:
Image:
Filename: ciggareteclassic.png
Format: PNG (Portable Network Graphics)
Mime type: image/png
Class: DirectClass
Geometry: 24x24+0+0
Resolution: 37.8x37.8
Print size: 0.634921x0.634921
Units: PixelsPerCentimeter
Colorspace: sRGB
Type: PaletteAlpha
Base type: Undefined
Endianness: Undefined
Depth: 8-bit
Channel depth:
Red: 8-bit
Green: 8-bit
Blue: 8-bit
Alpha: 8-bit
Channel statistics:
Pixels: 576
Red:
min: 143  (0.560784)
max: 255 (1)
mean: 253.554 (0.994329)
median: 255 (1)
standard deviation: 11.3377 (0.0444615)
kurtosis: 78.998
skewness: -8.75387
entropy: 0.0884987
Green:
min: 0  (0)
max: 255 (1)
mean: 252.684 (0.990918)
median: 255 (1)
standard deviation: 17.058 (0.066894)
kurtosis: 104.779
skewness: -9.37562
entropy: 0.0884427
Blue:
min: 0  (0)
max: 255 (1)
mean: 252.226 (0.98912)
median: 255 (1)
standard deviation: 21.4986 (0.0843082)
kurtosis: 101.709
skewness: -9.64306
entropy: 0.0964019
Alpha:
min: 0  (0)
max: 255 (1)
mean: 4.55208 (0.0178513)
median: 0 (0)
standard deviation: 30.6758 (0.120297)
kurtosis: 53.678
skewness: 7.26621
entropy: 0.0727769
Image statistics:
Overall:
min: 0  (0)
max: 255 (1)
mean: 190.754 (0.748055)
median: 191.25 (0.75)
standard deviation: 20.1425 (0.0789902)
kurtosis: -0.661727
skewness: -1.1472
entropy: 0.0865301
Alpha: srgba(255,255,255,0)   #FFFFFF00
Colors: 15
Histogram:
4: (143,143,143,0) #8F8F8F00 srgba(143,143,143,0)
1: (143,143,143,68) #8F8F8F44 srgba(143,143,143,0.266667)
1: (191,191,191,0) #BFBFBF00 srgba(191,191,191,0)
1: (191,191,191,94) #BFBFBF5E srgba(191,191,191,0.368627)
1: (226,226,226,135) #E2E2E287 srgba(226,226,226,0.529412)
1: (226,226,226,0) #E2E2E200 srgba(226,226,226,0)
1: (226,226,226,147) #E2E2E293 srgba(226,226,226,0.576471)
1: (226,226,226,123) #E2E2E27B srgba(226,226,226,0.482353)
1: (226,226,226,139) #E2E2E28B srgba(226,226,226,0.545098)
1: (255,0,0,255) #FF0000FF red
2: (255,132,0,255) #FF8400FF srgba(255,132,0,1)
555: (255,255,255,0) #FFFFFF00 srgba(255,255,255,0)
4: (255,255,255,255) #FFFFFFFF white
1: (255,255,255,93) #FFFFFF5D srgba(255,255,255,0.364706)
1: (255,255,255,38) #FFFFFF26 srgba(255,255,255,0.14902)
Rendering intent: Perceptual
Gamma: 0.454545
Chromaticity:
red primary: (0.64,0.33)
green primary: (0.3,0.6)
blue primary: (0.15,0.06)
white point: (0.3127,0.329)
Matte color: grey74
Background color: white
Border color: srgb(223,223,223)
Transparent color: none
Interlace: None
Intensity: Undefined
Compose: Over
Page geometry: 24x24+0+0
Dispose: Undefined
Iterations: 0
Compression: Zip
Orientation: Undefined
Properties:
date:create: 2021-11-02T21:50:37+00:00
date:modify: 2021-11-02T14:13:12+00:00
png:IHDR.bit-depth-orig: 8
png:IHDR.bit_depth: 8
png:IHDR.color-type-orig: 6
png:IHDR.color_type: 6 (RGBA)
png:IHDR.interlace_method: 0 (Not interlaced)
png:IHDR.width,height: 24, 24
png:pHYs: x_res=3780, y_res=3780, units=1
png:sRGB: intent=0 (Perceptual Intent)
signature: e7f965c05ce79f960e3a19b1b71fd2ac9989c68f833839aca98584edee46431c
Artifacts:
verbose: true
Tainted: False
Filesize: 204B
Number pixels: 576
Pixels per second: 554041P
User time: 0.000u
Elapsed time: 0:01.001
Version: ImageMagick 7.1.0-12 Q16-HDRI x86_64 2021-10-25 https://imagemagick.org
Standard png file:
Image:
Filename: cigarette.png
Format: PNG (Portable Network Graphics)
Mime type: image/png
Class: DirectClass
Geometry: 24x24+0+0
Resolution: 28.35x28.35
Print size: 0.846561x0.846561
Units: PixelsPerInch
Colorspace: sRGB
Type: PaletteAlpha
Base type: Undefined
Endianness: Undefined
Depth: 8-bit
Channel depth:
Red: 8-bit
Green: 8-bit
Blue: 8-bit
Alpha: 8-bit
Channel statistics:
Pixels: 576
Red:
min: 0  (0)
max: 255 (1)
mean: 248.345 (0.973904)
median: 255 (1)
standard deviation: 38.3086 (0.15023)
kurtosis: 36.8919
skewness: -6.16777
entropy: 0.141537
Green:
min: 0  (0)
max: 255 (1)
mean: 248.111 (0.972985)
median: 255 (1)
standard deviation: 38.8546 (0.152371)
kurtosis: 35.0178
skewness: -6.00828
entropy: 0.141537
Blue:
min: 0  (0)
max: 255 (1)
mean: 248.019 (0.972624)
median: 255 (1)
standard deviation: 39.2877 (0.154069)
kurtosis: 34.2894
skewness: -5.9593
entropy: 0.141537
Alpha:
min: 0  (0)
max: 255 (1)
mean: 9.74479 (0.0382149)
median: 0 (0)
standard deviation: 47.1645 (0.184959)
kurtosis: 21.5315
skewness: 4.79385
entropy: 0.184351
Image statistics:
Overall:
min: 0  (0)
max: 255 (1)
mean: 188.555 (0.739432)
median: 191.25 (0.75)
standard deviation: 40.9038 (0.160407)
kurtosis: -0.781766
skewness: -1.09773
entropy: 0.152241
Alpha: srgba(255,255,255,0)   #FFFFFF00
Colors: 5
Histogram:
13: (0,0,0,255) #000000FF black
5: (198,198,198,255) #C6C6C6FF srgba(198,198,198,1)
6: (221,221,221,128) #DDDDDD80 srgba(221,221,221,0.501961)
1: (226,91,38,255) #E25B26FF srgba(226,91,38,1)
551: (255,255,255,0) #FFFFFF00 srgba(255,255,255,0)
Rendering intent: Perceptual
Gamma: 0.454545
Chromaticity:
red primary: (0.63999,0.33001)
green primary: (0.3,0.6)
blue primary: (0.15,0.05999)
white point: (0.31269,0.32899)
Matte color: grey74
Background color: white
Border color: srgb(223,223,223)
Transparent color: none
Interlace: None
Intensity: Undefined
Compose: Over
Page geometry: 24x24+0+0
Dispose: Undefined
Iterations: 0
Compression: Zip
Orientation: TopLeft
Profiles:
Profile-xmp: 14350 bytes
Properties:
date:create: 2021-11-02T21:41:48+00:00
date:modify: 2021-11-02T13:30:13+00:00
dc:format: image/png
photoshop:ColorMode: 3
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png:pHYs: x_res=2835, y_res=2835, units=1
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xmp:ColorSpace: 65535
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xmp:PixelXDimension: 24
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xmpMM:InstanceID: xmp.iid:360514aa-4c57-8447-8597-b6adb1bda980
xmpMM:OriginalDocumentID: xmp.did:360514aa-4c57-8447-8597-b6adb1bda980
Artifacts:
verbose: true
Tainted: False
Filesize: 14578B
Number pixels: 576
Pixels per second: 320577P
User time: 0.010u
Elapsed time: 0:01.001
Version: ImageMagick 7.1.0-12 Q16-HDRI x86_64 2021-10-25 https://imagemagick.org

actually it was the reason, if you want to extend traits library remember to resample them all to one size and resolution. Resampling the standard files to the same parameters as my new ones solved the issue.


Grow the resource_version monotonically when watching

See https://github.com/kubernetes-client/python/issues/819 for the explanation of the problem, dilemma, and examples.
With this proposal, the remembered resource_version grows monotonically, i.e. never decreasing.
Specifically, after the list...() operation is finished, it will remember the maximum of all the resource_versions of all currently existing objects. In case of disconnection and reconnection, it will continue from the last seen state of all objects — as expected.

I signed it

Codecov Report

Merging #131 into master will increase coverage by 0.12%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #131      +/-   ##
==========================================
+ Coverage   92.84%   92.97%   +0.12%
==========================================
  Files          13       13
  Lines        1328     1352      +24
==========================================
+ Hits         1233     1257      +24
  Misses         95       95

Impacted Files
Coverage Δ

watch/watch_test.py
98.85% <100%> (+0.15%)
:arrow_up:

watch/watch.py
100% <100%> (ø)
:arrow_up:

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Moved the detailed description to https://github.com/kubernetes-client/python/issues/819 for discussion of the possible ways to solve the problem (it is not so straightforward).

This PR looks reasonable and at worst does not do anything. But if order is not really assured, then much more than just this change should probably be done, no? I mean, that assumption is all around the codebase.

Closing this PR as the implementation is not correct. The proper way to get list the resources normally, get a resourceVersion of the list itself (not of its items!), and use that resourceVersion as a starting point for watching. And only then the latest seen resourceVersion of the items should be used to restarting watching. In either case, the resourceVersion should not be interpreted in any way, and should not be assumed to be sortable or monotonically growing. See kubernetes-client/python#819 for discussion.

Closing this PR as the implementation is not correct. The proper way to get list the resources normally, get a resourceVersion of the list itself (not of its items!), and use that resourceVersion as a starting point for watching. And only then the latest seen resourceVersion of the items should be used to restarting watching. In either case, the resourceVersion should not be interpreted in any way, and should not be assumed to be sortable or monotonically growing. See kubernetes-client/python#819 for discussion.


PMID:23615450

abolished protein localization to medial cortical node in interphase
normal protein localization to medial cortical node in interphase

abolished protein localization to medial cortical node in interphase

can you use FYPO:0007115, or do you need the version that doesn't have the "mislocalized to cytoplasm" part? (you mentioned this paper in #3540)

hmm, it seems to hang around the nucleus and nuclear envelope (The nucleus is its interphase location too)

um, is that "need the new term" or "can use FYPO:0007115"?
adding the "normal" term in the meantime ...

Yes I need the term,
chdeers

normal protein localization to medial cortical node during mitotic interphase FYPO:0007133
edit file: f623968cf338deb197a749ed344b11922bde331f
release: 22a37036cb982537b07873689c6932f2397082a6

hi, I still need
abolished protein localization to medial cortical node in interphase
too

Thx for clarifying - I kinda figured that from your last comment y'day, but then had to troubleshoot the release (PATO update; details boring) so didn't have time to get back to this until now.
abolished protein localization to medial cortical node during mitotic interphase FYPO:0007139
edit file: 7cdfb70ef7bb837e093e54eeef43a32367d31e6a
release: 9e424b104963eb8c58bb7613b2607baefef6f9b9


I want to open application from background when I have received invite message.

Hello,
I'm very excited to use this library and resolved my real world problems.
but I'm stuck when my application is in background and someone want to call me.
I have received invite message but unable to open mobile application.
I don't want to integrate notifications because I want to build apps like WhatsApp.
so please help me.

I don' this there are many alternatives rather than using PUSH messages and Google FCM

@97loser Take android as an example, if you do receive an invite in the background, just add the following code to the native part to wake up the app UI.
https://github.com/flutter-webrtc/callkeep/blob/master/android/src/main/java/io/wazo/callkeep/CallKeepModule.java#L545
If you are on iOS, you must use PushKit + CallKit in callkeep to wake up your app, and you must pass RFC8599 to complete the standard process.
This is a complicated process that must work together through the server, dart-sip-ua and the client's native push function

I know this is difficult. For other IP PBX, you must upgrade the server accordingly.
But if you want to try to run the complete RFC8599 function, you can use my other b2bua open-source project to test, this project can use FCM+APNS and dart-sip-ua to run together, and realize the background state, or the app is killed The process of being awakened to answer the call.


Add Barplot, Visualizer and Event Table as NPM package

Add Barplot, Visualizer and Event Table as NPM package
https://github.com/inab/Scientific_Barplot
https://github.com/inab/OpenEBench_scientific_visualizer
https://github.com/inab/bench_event_table

https://www.npmjs.com/package/@inb/oeb-classification-table
https://www.npmjs.com/package/@inb/oeb-chart-scatter
https://www.npmjs.com/package/@inb/oeb-chart-barplot
Added packages to npm, included in the codebase


The face mesh v2 model download link used in face blendshape

Issue Type
Support
OS
Ubuntu, Other
OS architecture
aarch64
Programming Language
C++
Framework
TensorFlowLite
Model name and Weights/Checkpoints URL
https://github.com/PINTO0309/facemesh_onnx_tensorrt/issues/4
Description
A demo video is attached in readme. md.  I wonder if is it achieved by the model using blendshape.tflite  and corresponding face mesh v2 model in the repository or just recording using mediapipe web demo?  For now, I cannot download the corresponding face mesh v2 model mentioned in face blendshape model card which outputs 478 landmarks. Only face mesh with 468 landmarks is what I can find now.
Relevant Log Output
No response
URL or source code for simple inference testing code
No response

https://github.com/PINTO0309/PINTO_model_zoo/tree/main/410_FaceMeshV2


Update cats-effect, cats-effect-laws to 3.3.13

Updates

org.typelevel:cats-effect
org.typelevel:cats-effect-laws

from 3.2.9 to 3.3.13.
GitHub Release Notes - Version Diff
I'll automatically update this PR to resolve conflicts as long as you don't change it yourself.
If you'd like to skip this version, you can just close this PR. If you have any feedback, just mention me in the comments below.
Configure Scala Steward for your repository with a .scala-steward.conf file.
Have a fantastic day writing Scala!

Applied Scalafix Migrations

org.typelevel:{cats-effect,cats-effect-laws}:3.3.0 (created no change)

github:typelevel/cats-effect/v3_3_0?sha=series/3.x

Adjust future updates
Add this to your .scala-steward.conf file to ignore future updates of this dependency:
updates.ignore = [ { groupId = "org.typelevel" } ]

Or, add this to slow down future updates of this dependency:
dependencyOverrides = [{
  pullRequests = { frequency = "@monthly" },
  dependency = { groupId = "org.typelevel" }
}]

labels: library-update, early-semver-minor, semver-spec-minor, scalafix-migrations, commit-count:1

Codecov Report

Merging #615 (9d01e08) into main (2a51408) will decrease coverage by 0.39%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main     #615      +/-   ##
==========================================
- Coverage   90.23%   89.84%   -0.40%
==========================================
  Files          15       15
  Lines         758      758
  Branches       40       43       +3
==========================================
- Hits          684      681       -3
- Misses         74       77       +3

Impacted Files
Coverage Δ

core/src/main/scala/io/iteratee/Enumeratee.scala
98.71% <0.00%> (-1.29%)
:arrow_down:

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Superseded by #616.


remove a useless if found in the method GameObjectDecoder

Hello,
I found a redundant if in the method so i remove it.
Thanks

Looks good, needs rebasing though

I rebase my branch
Thanks

Hi there,
Merging master into your fork isn't exactly what I had in mind, because it pollutes the commit history (you can see that your PR now includes code committed by another user). A rebase reverts all of your commits, adds the latest changes other users have made, and applies all of your commits again on top of the changes other people made. The git book has a very good guide on doing this (and some more information about rebasing), which you can find here.
Feel free to ask in IRC if you need any help with doing this

I close this PR by removing my commit, i din't know why.
Sorry about that, i will create a new branch for this PR.


Feature: modular addon design for packages

First, I'd like to make rename public packages so that they reference the target platform in the title.
For instance how we have pixeloven-node-logger
Next -tasks should be renamed to webpack since it's primary function is for webpack based development.
in a similar fashion I'd like to make it so we only have a single CLI entry point pixeloven-cli. that way -tasks, -docs, -generators become addons.

Blocked by: https://github.com/pixeloven/pixeloven/issues/42


Update types.md

This is reflected in 8407ff664d2481b78e18cbe516cc3392a217bb78, which unfortunately did not get marked as a merge due to tooling hiccup. Sorry about that.
Thank you for the contribution.


Fix error of version_info.cc not being generated on windows

If tensorflow_BUILD_PYTHON_BINDINGS is disabled in CMake, the Python interpreter is never resolved in CMake, but it is needed in tf_core_framework.cmake for generating the version_info.cc file with the script tensorflow/tools/git/gen_git_source.py. This seems to only be a problem on windows, resulting in a failed build complaining about version_info.cc missing. This is not an issue on linux, probably because of the shebang #!/usr/bin/env python in the script.
I suggest moving the part in tf_python.cmake that sets up the python interpreter to the CMakeLists.txt as done in this PR so that it is always executed.

Can one of the admins verify this patch?

@smistad it helps to let us know when the code is ready to review again -- let us know!

Ok, the commit is updated and ready for review

@tensorflow-jenkins test this please


Idr fix

What problem is the PR solving / What's new?
see #319

I didn't start from branch develop, so now it seems more is changed than actually is. Only the changes in call_peak.smk are relevant. And they are quite irrelevant :angel:


Unknown Initialize API framework Error

Getting the following error on the "Initialize API framework" step after successfully creating a session.

The session info is logged in the console after the "Create a session" step but nothing logged when I run the "Initialize API framework" step. Thought it had something to do with the DDE base url being https://eu-gb.dynamic-dashboard-embedded.cloud.ibm.com instead of  https://dde-us-south.analytics.ibm.com for my Congnos Dashboard Embedded service. However, after setting the DDE_BASE_URL environment variable I was still getting the same error.
I'm also seeing the same error message in the official demo https://ibm-cognos-dashboard-demo.ng.bluemix.net/

Turns out this issue is specific to Firefox, works fine in chrome


Automatically roll karpenter deployment on logging or global settings configuration change

Tell us about your request
Use Helm sha256 trick to automatically roll the karpenter controller pods when any of its config changes.
Tell us about the problem you're trying to solve. What are you trying to do, and why is it hard?
Currently you would need to manually restart Karpenter on certain configuration changes.
Are you currently working around this issue?
Manually.
Additional Context
https://helm.sh/docs/howto/charts_tips_and_tricks/#automatically-roll-deployments
Attachments
No response
Community Note

Please vote on this issue by adding a 👍 reaction to the original issue to help the community and maintainers prioritize this request
Please do not leave "+1" or "me too" comments, they generate extra noise for issue followers and do not help prioritize the request
If you are interested in working on this issue or have submitted a pull request, please leave a comment

Thanks for the feature request!  We recently moved away from dynamic reload of the configmap to statically loading it. https://github.com/aws/karpenter-core/pull/174
This seems like a good idea to do this type of thing in our helm deploy to make sure configmap changes are applied properly on an update.

This change already exists for the karpenter-global-settings here. I'm confused by the ask. Are you not observing correct behavior or are you looking for the same change to be applied to the logging config?

but when I changed logging settings it had not rolled.

Yeah, we expected that logging settings would be changed more frequently, so we decided to dynamically update those at runtime as opposed to restarting the deployment and causing unnecessary disruptions. Did you observe any issues when you updated the logging config with it updating dynamically?

but when I changed logging settings it had not rolled.

Yeah, we expected that logging settings would be changed more frequently, so we decided to dynamically update those at runtime as opposed to restarting the deployment and causing unnecessary disruptions. Did you observe any issues when you updated the logging config with it updating dynamically?

I didn't notice it change after updating, but had also read you guys had changed this behavior for settings in ~0.24/5 so I did not think it dynamically updated.
I generally have disliked any dynamic config update processes I have used. It throws out the deployment rolling update features of Kubernetes and introduces many failure modes that are not obvious to users like:

The dynamic config system needs to handle incorrect settings/not use the new settings. Usually this means the signal that the deployment was wrong can be totally lost
scaling/rescheduling can fail to run since any new pods will not have an old config to fall back on
Time to new config can be unpredictable

The dynamic config system needs to handle incorrect settings/not use the new settings. Usually this means the signal that the deployment was wrong can be totally lost
scaling/rescheduling can fail to run since any new pods will not have an old config to fall back on
Time to new config can be unpredictable

I think the last two here are critical, particularly #2. Do you find that you often get the logging config wrong when you make changes?

I've run into problem 2 before in other apps that rely on dynamic config reloading + fallback to working config. Then when new pods that don't have the old config loaded run they just crash.

We've deprecated the configmap from v1beta1 APIs as part of v0.32+. You can now use environment variables for settings, where the configmap support will be removed as part of v1. More information about the environment variables here.


⚠ ClamAV has degraded performance

In 18544b1, ClamAV (https://spamassassin.apache.org/) experienced degraded performance:

HTTP code: 200
Response time: 445 ms

Resolved: ClamAV performance has improved in e18313d.


Add support for command aliases to bash completion of docker volume

When bash completion for docker volume was created, there were no command aliases.
This PR adds support for the aliases docker volume list and docker volume remove.
Like in the other command families this means that the aliases are not completed at command level (docker volume <tab>). They are, however, considered if the user types a command alias manually (e.g. docker volume list --<tab>).
Related: #31190

@mlaventure Would you like to take a look at this PR? - Thanks!

@mlaventure Thanks!


Classic BT Peering algorithm when setting io cap to display only (IDFGH-5626)

Environment

Development Kit:      ESP32-Wrover

Kit version 1.1

Module or chip used:  ESP32-WROOM

IDF version 4.3

Build System:         idf.py

Compiler version xtensa-esp32-elf-gcc (crosstool-NG esp-2020r3) 8.4.0

Operating System:     Windows

Using an IDE?: Eclipse

Power Supply:        USB

Problem Description
I'm writing an application for classic bluetooth to demo pairing algorithms.  I will document both scenarios (Laptop &  Smartphone).
In both cases I set io cap to display only.
Expected Behavior
Passkey display on both devices
Actual Behavior
Laptop : Displays a pin to compare to but ESP doesn't display anything.
Android phone : Connects directly (Just Works)
Steps to reproduce

set  esp_bt_io_cap_t iocap = ESP_BT_IO_CAP_OUT; //Display only
Connect to esp from a laptop/android phone

@BetterJincheng  Hi, Peter
Thanks for your reply :)
Actually the screenshot is taken from 4.2 Core specs, this is page 323  on the specs :

I already demonstrated it with other configuration. I'm interested though if the other device have io cap set as "Display Keyboard". Unfortunately, I don't have another ESP board in hand to test this scenario, Do you suggest anything?
Also, I Think laptop has the setting already as "Display Keyboard" because it's already asking for a pin number. So, I highly doubt that this is a bug.
Another thing that might be irrelevant, What if the other device sets its configuration on purpose to force Just Works pairing algorithm, I can see any event that let's me decide if I accept of the reject the connection. Is there any other option?

Hi, @mohannadmaklad!
The table of  IO capability I mentioned is on page 323 in Vol 3, Part 3. It demonstrated all the settings and corresponding behaviors.
In ESP-IDF v4.3, we only provided four options listed as ESP_BT_IO_CAP_OUT (DisplayOnly), ESP_BT_IO_CAP_IO (DisplayYesNo), ESP_BT_IO_CAP_IN (KeyboardOnly) and ESP_BT_IO_CAP_NONE (NoInputNoOutput). We just follow the Core Spec.

Hi, @mohannadmaklad
The table of IO capability I mentioned is on page 323 in Vol 3, Part 3.
It does look a little weird. I will do some checking and reply to you as soon as possible.

This is the correct one :

BR/EDR v4.2 Doesn't have display + Keyboard input?
Anyway, Do you know how can I force authentication process?

As the IO cap of Initiator (laptop or android phone) is unknown, you can just set the Responder (esp32) with esp_bt_io_cap_t iocap = ESP_BT_IO_CAP_IN;  //Keyboard Only to force the authentication process. Then the PIN will show on your phone or laptop, input it into the terminal to establish the connection. (To do this, an input method is needed. r.f. /esp-idf/examples/bluetooth/bluedroid/classic_bt/bt_spp_initiator/)

Thanks for reporting, feel free to reopen.


⚠ Bofrost.lu has degraded performance

In 21064d3, Bofrost.lu (https://www.bofrost.lu) experienced degraded performance:

HTTP code: 200
Response time: 2025 ms

Resolved: Bofrost.lu performance has improved in 3ea2ce8 after 41 minutes.


Path /var/lib/kubelet is mounted on / but it is not a shared mount.

Describe your issue here
centos7 , Docker version 1.12.6
[workerPlane] Failed to bring up Worker Plane: Failed to start [kubelet] container on host [<IP_ADDRESS>]: Error response from daemon: linux mounts: Path /var/lib/kubelet is mounted on / but it is not a shared mount.
and I have edit /etc/systemd/system/multi-user.target.wants/docker.service and set MountFlags= (no value) , I still have the same issue.

Useful
Info

Versions
Rancher v2.0.0-alpha21 UI: v2.0.25

Access
local admin

Route
global-admin.clusters.index

Can you try setting MountFlags=shared?

The simplest way to test this is to run Rancher 2.0 and use b2d as a custom host.

@HuiAz  Have you solved the problem? I got the same issue

When I tried to bring up a rhel 7.5 cluster with native docker and selinux enabled , I get the same error
``[workerPlane] Failed to bring up Worker Plane: Failed to start [kubelet] container on host [<IP_ADDRESS>]: Error response from daemon: linux mounts: Path /var/lib/rancher is mounted on / but it is not a shared mount.```

Tested with latest build from master
rancher/server      master              1e1b97f08975        2 hours ago         785 MB
Tried to  bring up a rhel 7.5 cluster with native docker and selinux enabled , I get the same error:
2018/04/20 00:51:20 [INFO] cluster [c-h6x7x] provisioning: [workerPlane] Failed to bring up Worker Plane: Failed to start [kubelet] container on host [<IP_ADDRESS>]: Error response from daemon: linux mounts: Path /var/lib/kubelet is mounted on / but it is not a shared mount.

Tested with latest builf from master
Tried to bring up a rhel 7.5 cluster with native docker and selinux enabled , I get the following error now

https://github.com/rancher/rancher/issues/12953

I made only slight progress since I muttered about this issue over in #12384--I'm still facing the shared-mount issue. My setup (now):

vSphere provider (using vSphere 6.0.0 and ESXi 5.1.0, with hope to upgrade soon)
rancher/server:master with hash a80ca3ea4ad3 (extended by custom Dockerfile to add internal CA certificates via update-ca-certificates)
boot2docker.iso from url https://github.com/boot2docker/boot2docker/releases/download/v17.03.2-ce/boot2docker.iso
Kubernetes version v1.10.1-rancher1
Network Provider: Canal

Now, I'm getting:
[workerPlane] Failed to bring up Worker Plane: Failed to start [kubelet] container on host [<IP_ADDRESS>]: Error response from daemon: linux mounts: Path /mnt/sda1/var/lib/docker is mounted on /mnt/sda1 but it is not a shared or slave mount.

Which is technically a different error message from this issue, but it smells deeply like the same issue.
Substituting Kubernetes version 1.9.7-rancher1 does not work around the issue, but using https://github.com/gaui/boot2docker-rootfs-mount-fix/releases/download/17.03.2-ce/boot2docker.iso as an alternate b2d URL does work around the issue.

Tested with v2.0.0-beta4-rc2.
Create a custom cluster with rhel 7.5 hosts with native docker (1.13) with selinux enabled having following configuration:
1 control node
1 etcd node
3 woker nodes
Cluster gets to "Active" state. All nodes in the cluster get to "active" state.
Able to deploy workloads and ingress successfully in the clusters.

anyone tell me how to resolve this issue? I have run into the same issue when using the rancher 2.0

anyone could help?

@nrh387 is this using the latest beta4? I used to have this issue but it's been fixed in the last beta.

Yes, i used the sudo docker run -d --restart=unless-stopped -p 80:80 -p 443:443 rancher/server:preview to get it yesterday. So i think this is the latest version for rancher 2.0.

If you still experience issues, please make sure you are testing on v2.0.0-rc3 shown in the bottom left of the UI.
If you are using that and still see the error, please file an issue with the following info:

OS used (cat /etc/os-release and uname -r)
Docker used (docker info and docker version)

@superseb I checked the version is v.2.0.0-rc3

OS is 3.13.0-86-generic
Here is the docker info
Containers: 1
Running: 1
Paused: 0
Stopped: 0
Images: 15
Server Version: 17.03.2-ce
Storage Driver: aufs
Root Dir: /var/lib/docker/aufs
Backing Filesystem: extfs
Dirs: 83
Dirperm1 Supported: false
Logging Driver: json-file
Cgroup Driver: cgroupfs
Plugins:
Volume: local
Network: bridge host macvlan null overlay
Swarm: inactive
Runtimes: runc
Default Runtime: runc
Init Binary: docker-init
containerd version: 4ab9917febca54791c5f071a9d1f404867857fcc
runc version: 54296cf40ad8143b62dbcaa1d90e520a2136ddfe
init version: 949e6fa
Security Options:
apparmor
Kernel Version: 3.13.0-86-generic
Operating System: Ubuntu 14.04.4 LTS
OSType: linux
Architecture: x86_64
CPUs: 2
Total Memory: 3.861 GiB
Name: iZ947ei2rr7Z
ID: YDG7:CKNZ:SEUJ:XHKY:N6CT:5HQF:NOPL:KSL7:PQSC:BL24:N6VF:ZNQP
Docker Root Dir: /var/lib/docker
Debug Mode (client): false
Debug Mode (server): false
Registry: https://index.docker.io/v1/
Experimental: false
Insecure Registries:
<IP_ADDRESS>/8
Registry Mirrors:
https://20bh91iy.mirror.aliyuncs.com
Live Restore Enabled: false
Here is docker version
Client:
Version:      17.03.2-ce
API version:  1.27
Go version:   go1.7.5
Git commit:   f5ec1e2
Built:        Tue Jun 27 03:11:13 2017
OS/Arch:      linux/amd64
Server:
Version:      17.03.2-ce
API version:  1.27 (minimum version 1.12)
Go version:   go1.7.5
Git commit:   f5ec1e2
Built:        Tue Jun 27 03:11:13 2017
OS/Arch:      linux/amd64
Experimental: false

here is more information of OS info
NAME="Ubuntu"
VERSION="14.04.4 LTS, Trusty Tahr"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 14.04.4 LTS"
VERSION_ID="14.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"

@nrh387 Quick workaround is running mount --make-rshared / on the host, and then docker start kubelet should work.
Rest of the info is partly here https://github.com/moby/moby/issues/19625 and here https://github.com/kubernetes/kubernetes/issues/61058. As far as I could find it's because it's not using systemd, so setting the flags there won't help.

@superseb Hello, it looks the mount shared problem have been skipped, and the host is suspending on the status "Waiting to register with Kubernetes" and here is the docker logs on the rancher server
2018/05/02 01:40:40 [ERROR] error updating ns default status: Operation cannot be fulfilled on namespaces "default": the object has been modified; please apply your changes to the latest version and try again
E0502 01:40:40.362725       1 generic_controller.go:204] ClusterRoleTemplateBindingController c-76wdh/user-khzht-admin [cluster-crtb-sync] failed with : couldn't ensure roles: couldn't create role cluster-owner: clusterroles.rbac.authorization.k8s.io "cluster-owner" already exists
2018/05/02 01:40:40 [INFO] namespaceHandler: addProjectIDLabelToNamespace: adding label field.cattle.io/projectId=project-zdqz4 to namespace=default
2018/05/02 01:40:40 [INFO] projectSyncer: createDefaultNetworkPolicy: successfully created default network policy for project: project-zdqz4
2018/05/02 01:40:41 [ERROR] error updating ns cattle-system status: Operation cannot be fulfilled on namespaces "cattle-system": the object has been modified; # please apply your changes to the latest version and try again
2018/05/02 01:41:14 [INFO] Handling backend connection request [c-76wdh]
2018-05-02 01:45:55.619766 I | mvcc: store.index: compact 412734
2018-05-02 01:45:55.623947 I | mvcc: finished scheduled compaction at 412734 (took 3.662457ms)

The problem still exists on Rancher 2.0.2 on Ubuntu 18.04+Docker 18.05.0-ce

It should be a different error, caused by https://github.com/moby/moby/issues/37032. You shouldn't use Docker 18.05 because of this bug. Other versions should be fine. Track Ubuntu 18.04 support here: https://github.com/rancher/rancher/issues/13888

Oh thanks for the message~

Facing the same issue on Rancher 2.0.2 + Ubuntu 16.04 + Docker 17.03.2

Please create a new issue with the information requested in the template (OS, kernel, docker info)


pecl-event incompatible with Laravel

Bug ? Notice ?
pecl-event registers class Event::class
laravel has own "Facade" system and register Event as Illuminate\Support\Facades\Event::class
but can not, pecl-event has already done this
Laravel's Event::dispatch(something) ends with error.

Hi @TKr, sorry for the issue. Can you help me reproduce? Can you please write which libraries are you installing and their versions? Maybe try attaching your composer.json redacting anything that you don't want to share…?


Support for the time-varying neural network model constraints modelling

Hi @Tim-Salzmann ,
I'm trying to model an NN constraint while the NN constraint is time-varying, a static example will be like the provided Nerf optimization example. There are some parameters related to the output of the NN model, more than the state of the robot.
The current code I used is     learned_cons = l4c.L4CasADi(NNModel(), batched=False, scripting=True). I try to update the parameters within the class public properties of NNModel() so that when learned_cons is called, it can return correct values so as to model the time-varying constraint. However, after I update the parameters of NNModel, it doesn't affect the evaluation of the constraint.
Then I put the update function into the forward() function of the neural network. I found that this function is only called several times, and the model will be updated within these calls but later forward() is not used.
The neural network model will be like
class NNModel(nn.Module):
    def __init__(self):
        super(NNModel, self).__init__()
        (parameters used to update)
    def forward(self, x):
        self.updateParameters()
        (other computations)
        return values
    def updateParameters(self):
        (computations)

Is there a way to resolve this issue? I don't know if this is the correct way to model the time-varying constraint, please let me know if I was wrong.
best,
Xuemin

Hi,
I am not entirely following. What about adding time to the state and passing it to the model explicitly?
Best
Tim

Hi,
I am not entirely following. What about adding time to the state and passing it to the model explicitly?
Best Tim

Hi, thanks for the advice, and let me clarify the question with an example. For a given SDF circle model
class sdfCircle(nn.Module):
    def__init__(self):
        super(sdfCircle, self).__init__();
        self.center = None;
        self.radius = None;
    def forward(self, x):
        dist = torch.norm(x - self.center) - self.radius;
        return dist.reshape(-1,1)

To model a moving circle SDF, the center needs to update according to the time and the velocity, like x=x+dt * v. Could you provide some insights about how to implement this with l4casadi? Thanks.
Best,
Xuemin

How about something like this
def forward(self, inp):
   x = inp[0]
   t = inp[1]
   center = self.center_function(t)
   radius = self.radius_function(t)
   dist = torch.norm(x - center) - radius;
   return dist.reshape(-1,1)

How about something like this
def forward(self, inp):
   x = inp[0]
   t = inp[1]
   center = self.center_function(t)
   radius = self.radius_function(t)
   dist = torch.norm(x - center) - radius;
   return dist.reshape(-1,1)

Thank you so much for the quick feedback. I have tried this. I found that the way to make this forward function work correctly is to set mutable = True and update the model online. If I don't turn on the mutable, even though I put the time into the forward function, it still doesn't work. However, the update operation consumes a lot of time. Could you explain a bit about this? Thanks!

even though I put the time into the forward function, it still doesn't work.

Can you explain exactly what does not work? If you can calculate the center and radius given the time then I am not sure why this would not work..
Best
Tim

even though I put the time into the forward function, it still doesn't work.

Can you explain exactly what does not work? If you can calculate the center and radius given the time then I am not sure why this would not work..
Best Tim

I added an output to the forward function to check if the circle updates correctly. print(center), but after the code started running, it only printed 5 times. Then there was no print from the forward function and the circle center also stopped updating by checking the distance while the solver kept running. Is this normal?
def forward(self, inp):
   x = inp[0]
   t = inp[1]
   center = self.center_function(t)
   radius = self.radius_function(t)
   dist = torch.norm(x - center) - radius;
   print('center is : ', center)
   return dist.reshape(-1,1)

It is expected that the print out is not happening when the optimization is running. This does not mean it does not work.
The model is exported and compiled to C / C++ where the Python print statement is not included.

Let me know if you have any more open questions. Otherwise feel free to close this issue.


Pokemon appeared as Gym

Has anybody else experienced this issue? I just noticed it for the first time.
A Pokemon appeared as a gym and then the image disappeared but the timer stayed there. I provided images.

Are you using the IPA version of the app ?

No

@blackhattristar Can you test with the latest version of the project plz ?

@istornz Version 2.0.1 or should I test the master?

Test the master