Could not install an example package - mice

Greetings,
   I am getting below error.   Might you know what may be going wrong?   Please note the weird "{checkbox} Successfully loaded .Rprofile.site" errors in the g++ errors.   Is there something going on with the .Rprofile?   Many thanks,

              Toshi

install.packages("mice")
Installing package into ‘/yakdata/site-library/R/4.1.3’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/all/2022-02-15+Y3JhbiwyOjQ1MjYyMTU7REM3MzYwMUI/src/contrib/mice_3.14.0.tar.gz'
Content type 'binary/octet-stream' length 790161 bytes (771 KB)
==================================================
downloaded 771 KB

✅ Successfully loaded .Rprofile.site
🎉 Welcome to YakData SmartDesktop with RStudio Desktop
📕 Learn more at: https://yakdata.com/smart

installing source package ‘mice’ ...
** package ‘mice’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/cpp11/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/cpp11/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c legendre.cpp -o legendre.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/cpp11/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match.cpp -o match.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/cpp11/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matchindex.cpp -o matchindex.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o mice.so RcppExports.o legendre.o match.o matchindex.o ✅ Successfully loaded .Rprofile.site 🎉 Welcome to YakData SmartDesktop with RStudio Desktop 📕 Learn more at: https://yakdata.com/smart -L/usr/local/lib/R/lib -lR
g++: error: ✅: No such file or directory
g++: error: Successfully: No such file or directory
g++: error: loaded: No such file or directory
g++: error: .Rprofile.site: No such file or directory
g++: error: 🎉: No such file or directory
g++: error: Welcome: No such file or directory
g++: error: to: No such file or directory
g++: error: YakData: No such file or directory
g++: error: SmartDesktop: No such file or directory
g++: error: with: No such file or directory
g++: error: RStudio: No such file or directory
g++: error: Desktop: No such file or directory
g++: error: 📕: No such file or directory
g++: error: Learn: No such file or directory
g++: error: more: No such file or directory
g++: error: at:: No such file or directory
g++: error: https://yakdata.com/smart: No such file or directory
make: *** [/usr/local/lib/R/share/make/shlib.mk:10: mice.so] Error 1
ERROR: compilation failed for package ‘mice’
removing ‘/yakdata/site-library/R/4.1.3/mice’
Warning in install.packages :
installation of package ‘mice’ had non-zero exit status

The downloaded source packages are in
‘/tmp/RtmpzOBz9R/downloaded_packages’

P.S. This is on MacOS Monterey 12.3.1.   Many thanks!

Hi,
I also received a similar error.
Here is a fix:

Go to your command line and enter the running container:
docker exec -it rstudio-4.1.3 /bin/bash

Start R with the "vanilla" option from the command prompt within the container:
R --vanilla

Install the package:
install.packages("mice")

This will prompt you for a CRAN mirror, I selected option
1

Quit the R session once installation completes.
q()

Exit the session.
exit

Refresh the Packages pane from RStudio web interface. Click the mice package. The following code executes:
library(mice, lib.loc = "/usr/local/lib/R/site-library")

Run some test code:
require(rpart)
imp <- mice(nhanes2, meth = "cart", minbucket = 4)
plot(imp)

I see this:


Lab 14 Task 2 Step 3-6 UI Difference

Module: 4
Lab/Demo: 14
Task: 2
Step: 3 -6
UI Difference
#3 Click Secure Score and Click View Recommendations
#4 scroll down and look for Install endpoint protection solution on virtual machine and click it
#5 Select Install on 1VMs
#6 Select Microsoft Antimalware and click Create and then OK

updated


test: test server error stack

[!WARNING]
This pull request is not mergeable via GitHub because a downstack PR is open. Once all requirements are satisfied, merge this PR as a stack on Graphite.
Learn more

#107  👈
#106
#105
main

This stack of pull requests is managed by Graphite. Learn more about stacking.

Join @hi-ogawa and the rest of your teammates on  Graphite


New analysis rule: strict_named_imports

While working on a project, dependency injection in Angular Dart was not working.
I spend few 3-4 hours debugging this issue at the end I found that:
dart:html and http package export class Client and they were colliding with each other and DI was not able to provide the right class.
I was developing in a rush and did not pay attention to this.
Many other users were having similar issues:
https://github.com/dart-lang/angular/issues/1847
https://github.com/dart-lang/angular/issues/1851
https://stackoverflow.com/questions/57420313/import-darthtml-in-service-got-exception-no-provider-found-for-dynamic
It might be a good idea to add a new rule in the analyzer plugin strict_named_imports, similar to how Golang does its imports with 0 name collisions.
I would like to keep this rule enabled by default on all of my projects so that name collision issues can be avoided.
This is just a suggestion.

have been there too.


Pass through Run ID Explicitly

@hinthornw
May I ask that when these changes will be release?
I saw the release of langchain 0.1.20 but didn't found the fix in that.
There isn't any release notes, it is difficult.

@hinthornw
I found it on 0.2.0rc.
I guess it may take time.


FeatureRequest: Add the "h:sender" parameter to message.

Using the REST api directly it is possible to specify the sender using: "h:sender".
Would it be possible to add this parameter to com.mailgun.model.message.Message ?

You can use the from field for this.
.from(custom value)
or
.from(EmailUtil.nameWithEmail(USER_NAME, EMAIL_FROM))

Alright, thank you for your help.

Using this mailgun-java library on my project I faced the issue similar to previously described on stackoverflow and explained at Mailgun Help page.
In a nutshell, the "On Behalf Of" notation is displaying as a From address in case of the mismatch between the domain used in the Sender field (mail.foo.com) and the domain used in the From field (foo.com):
<EMAIL_ADDRESS><EMAIL_ADDRESS>on behalf of; John Smith<EMAIL_ADDRESS>To solve the issue described above we need to set the sender property in the email header to the from address.
Using the from field: .from(custom value) or .from(EmailUtil.nameWithEmail(USER_NAME, EMAIL_FROM)) is not the equivalent of setting h:sender parameter, as it only sets the From address.
So, adding the possibility to specify the h:sender parameter directly does make sense, at least to solve the "On Behalf Of" issue. Also, more general approach can be considered to add additional sending options/parameters by implementing .addParameter(String name, Object value) and/or .addParameters(Map<String, Object> parameters) methods within com.mailgun.model.message.Message.MessageBuilder to create corresponding com.mailgun.model.message.Message.
@szagr, would it be possible to extend mailgun-java library with additional sending options/parameters in the nearest release? It's quite crucial for my project, as we can keep using this handy mailgun-java library. Otherwise, having this limitation, we will have to search some alternative solutions.


Method for distinguishing PCR-induced errors from sequencing errors

For families of reads where the consensus base does not match our reference, we should check to see what fraction of the reads supported that incorrect base. I expect to see errors scattered throughout the reads, but only piling up in PCR or other chemistry-related events.
This will also get us a clearer/better idea as to how effective BMFTools is at eliminating sequencing errors by separating chemical from optical errors.

We might get around to this at some point, but juice is likely not worth the squeeze.


Provide way of displaying, selecting and possibly aggregating data from groups of devices

It would be advantageous for users to be able to select groups of devices in a system where there may be 100's or 10000's of devices. This should be handled by adding a group select option and then restricting the devices. Once selected it should be possible to average the devices where the measurement is the same to provide a single composite set of data points.
Additionally we might provide a method for showing outliers from the data set and other manipulations allowing easy visual display of useful data.

we have now added group selection and aggregation (sum/average)


v1.2.3 not in PSGallery

As per the title, please can you publish the new release to the PSGallery.
Thank-you

bump!


[bug] readability of text in dark mode

When I switch to dark mode some elements are hardly not readable.

(this bug report is based on the version on https://lnkd.in/d_-9zhux, not sure if it has been fixed in the meanwhile)

For now, the issue is fixed with PR https://github.com/JankariTech/web-app-presentation-viewer/pull/25


[feature] Add collections endpoint to API v2

Purpose
Create endpoint for collections due to restricted feature set
This closes #3047, #3167 and complies with the changes made in #3118
Changes
Create api/collections directory similar to that of api/nodes but with stricter serialization.
Create, update, and delete for both folders as well as their pointers
Cannot update your Dashboard
Smart folders for all my projects and all my registrations are viewable in collections/dashboard/children as well as in /collections/~amp/ and /collections/~amr/ respectively
Update url routes to all have trailing slashes
View tests for this end point are based on API_BASE
Routes
/collections/  - List of all collections:

GET
POST

/collections/dashboard/ - Only lists the user's dashboard:

GET
POST

/collections/dashboard/children - Lists all child collections of the dashboard. Alias for /collections/{dash_id}/children

GET

/collections/{pk}/ - Detailed view of the one collection:

GET
PUT
PATCH
DELETE

/collections/{pk}/children/ - All children collections of the parent:

GET

/collections/{pk}/pointers/ - All pointer collections of the parent:

GET
POST

/collections/{collection_pk}/pointers/{pointer_pk}/ - Detailed view of the pointer

GET
DELETE

Okay, there was one more kind of big thing that I've just noticed, sorry. As things stand, there is no such thing as a public collection, and collections can currently only be owned by a single person. The second is more likely to change in the near future than the first.
In general terms, what this means is that the default query should look for nodes that are owned by the current user, and that the permission classes should not expect public folders or any sort of read-only access. If you want, I can go through and point out some things that will change based on this, or you can do a pass first and let me look through after.
I will try to see if there are any more differences between normal nodes and collections during this pass. Hopefully no.

Be sure to start by modifying your tests first, then change the code.

Looks like we'll need tests for smart folders, as well. Ensure that they are getting what we expect.

Addressed the above issues. We will need to discuss how we want to test smart folders based on where we want to display their information (i.e. in Dashboard Detail vs say a Collection List or Detail). The Travis failure looks like a problem with invoke and requirements rather than my code but I could be so I will leave that to be reviewed. Other than that, ready for another pass!

Could you pull from develop? That should fix the build issue with Travis.

Pass done. :penguin: Some small things, implementation of Smart Collections, and tests.

The unused FolderFactory import is breaking travis.

I saw, shame on me! Will be removed in the next commit

@brianjgeiger this is ready for another pass

Pass done. :penguin: Some little things, a general cleaning of tests, and smart folder detail tests.

Oh, and it looks like your "be cool with a ~ in the pk" regex fix has some side effects, so you might need to fix it in a different way.

It occurs to me that the node id for the smart folders in v2 doesn't have to match the node id for smart folders in v1.  After that's done, hopefully he can finish up on this.

@sloria @brianjgeiger Correct, IIRC test coverage is the main thing left on this

@brianjgeiger trying to get this knocked out, 2 tests for pointer collections are failing thought. It seems like validated_data isn't getting passed to the serializer #create. Any idea what could be going on here?
Also, I assume I will need to make some changes to the response format; ping @pattisdr on this. From what I understand this will include a new relationships LinkField containing children. Are pointers a relationship or do they stay in links?

Pointers have had their name changed, so that could be what's causing that trouble. Don't worry about the changes based on @pattisdr's stuff yet, but it will be hitting in the next week-ish I would imagine. Hopefully it won't be too many changes to handle that.

In my opinion, pointers are a relationship.


step 4 issue

hello,
when I ran splitseqdemultiplex, I find that the step 4 takes a long time.
it seems that the step4 has been running 1 day:
Beginning STEP4: Extracting UMIs. Current time : 2021-05-03 06:45:57.
Do you think it is fine?

Hi, I don't think so. I have been using this pipeline for a long time and for me the step 4 never took 24 hours !!!!! For a input data of around  80GB ( R1 and R2 ), it takes around 12/15 hours ( slower version ) for all the steps to finish completely. I feel that your input sequence file has some kind of problem ....

the R1/2 is about 100G, respectively.

Even if for input file of around 100G and 130G respectively, the STEP4 must not take 1 day or more. The step 4 is not the most computational intensive step of this pipeline. Only if, in the case your machine has not enough memory and CPUs. Please check whether your machine has enough memory and CPUs cores ....

OK.
the barcodes I used are correct, right?

The barcode in the paper are correct. But, You must check whether the barcode in the paper really correspond with the barcode of your input fastq file. If not, then there is problem with your input fastq file.

Hi Biohubx,
Hi Biohubx, I have observed similar challenges with step 4 runtime for some datasets.  One setting change that will help a lot is to use a higher minimum read threshold like -m 200 instead of -m 10 That way the program wont have to spend time extracting the UMIs from reads assigned to low detection cells that will later be discarded anyway.
There is actually an even better solution available which is to use the latest version of the software which has eliminated the UMI extraction step completely.  This version is accessible in the "python_only_tool" directory.  The input arguments are slightly different but quite similar.  The executable file is called python_only_tool/splitseqdemultiplex_0.2.2.py.
The long runtime for UMI finding does not mean that there is a problem with the tool or your input... but it will be faster to use the python only tool

Yes, i agree with @paulranum11

@paulranum11
python_only_tool/splitseqdemultiplex_0.2.2.py does not generate expression matrix, right?
if I set m to a very high value, such as 20, does it will impact downstream results?

python_only_tool/splitseqdemultiplex_0.2.2.py does generate the expression matrix.  You have to think of the -m argument in the context of your downstream analysis in Seurat.  If in Seurat you do filtering to exclude cells.  Often you will set parameters to retain cells with between 100 and 10,000 genes.  A cell with 90 genes detected may have 150 unique UMIs (some UMIs may map to the same gene) detected but it will ultimately be eliminated form the analysis.  This is why i recommend setting a -m threshold to 200 (to drop any cells with fewer than 200 unique UMIs).  This speeds up the analysis and does not have a major impact on the results of the single-cell analysis.

@paulranum11
thanks，I am trying to run splitseqdemultiplex_0.2.2.py. I also set m and b to 200 and 100000, respectively.

@biohubx
That sounds like it should perform well.  Also please remember to enter the actual length of your input fastqR file for the -l parameter.  To get this number you can run wc -l path/to/your/fastqR.fastq

thanks.
I set -l to<PHONE_NUMBER>

Hi @biohubx Biohubx,
I believe @dumaatravaie and I will both be curious to know if this completed successfully.  Can you let us know if it worked for you?
Thanks,
Paul

hi @paulranum11 , as i have been reading all the issues posted by @biohubx , i am also as curious as you.
First @biohubx said he had 4/5 barcodes, then he said the gene/cell_barcode matrix or gene expression matrix is empty. Then he opened the issue about the problem with Step 4. But, I do not know whether he is talking about the same input files for all these issues or not ?
Also, at least he should tell us the average length of his sequences in both of his R1 and R2 file, if he does not want to give you a small sample of his sequences !
I have great confidence on this pipeline. Even last week i ran it for the input sequences of a different species other then human/mouse. The pipeline worked as expected without any issue.

@paulranum11
yes, when I set m to 200, the entire analysis was done whtin 15h.
However, I made some changes to your codes.
When I ran the main shell script, some python scripts can't be found. So I add the absolute path to these scripts.
And you set result to the default output in your main shell script, but when I ran the main shell script, I set o to another output name, the main shell script reported an error" the result output file cannot find it. "

hi @paulranum11 , as i have been reading all the issues posted by @biohubx , i am also as curious as you.
First @biohubx said he had 4/5 barcodes, then he said the gene/cell_barcode matrix or gene expression matrix is empty. Then he opened the issue about the problem with Step 4. But, I do not know whether he is talking about the same input files for all these issues or not ?
Also, at least he should tell us the average length of his sequences in both of his R1 and R2 file as it seems he does not want ( or may be he has some kind of constraints ) to give you a small sample of his sequences to test !
I have great confidence on this pipeline. Even last week i ran it for the input sequences of a different species other then human/mouse. The pipeline worked as expected without any issue.


Optimize output: group_by

Separated from #971. Possibly for output: group_by = N a better implementation is to translate it to _index based syntax under the hood so that for every input group only the relevant output files are checked for signature. That is, make output: group_by a wrapper to fancy a _index theme.

Not much can be done here... try to avoid this option is the key.


Update README.md

Price mentioned.
also for all other If deadlines column will be more useful,just a suggestion.

update DLRL fee

Thanks a lot. I'm not sure as to what you are suggesting. Could you please clarify?

looks like already mentioned.My bad.


Suggestion: Better Paramedic/Doctor Bot

Would it be possible to have a better yet more expensive paramedic? I often use transhumanist idealogy with my mech lords, and augmenting a solo mechlord with implants is not possible with the paramedic's base 10 doctoring skill.

It's actually complete on my local build. I just need to test it when I get off work and I'll push it here and on steam. Level 20 with increased speed, but will have a high cost due to it being a perfect doctor.
After that I plan to look into upgrading the militor.


pass missing initializeDatabase property to WasmProbeResult.open

WasmDatabase.open takes an initializeDatabase argument, but this is never passed to WasmProbeResult.open so it's never actually called.

Actually I managed to resolve that (I think, anyway?), I suspect there was an old file in the VFS IndexedDB cache from when I was manually experimenting with files.

Could there be a similar cause in your app?
The tests are passing for me as well, so I'll merge this and release a patch to pub.dev soon.

I managed to track down the source of the problem in my app - it's unrelated to this PR, so will open a separate issue.
I was waiting until I was certain they were unrelated before pushing the tests but looks like you beat me to it!


internal/grpc: adds SDS and registers xds for sds

Addresses the first high-level design bullet point, creatign a gRPC
server for SDS by adding an SDS cache interface, implementing
FetchSecrets and StreamSecrets, and registering the server as an SDS
handler.
Updates #898

I've left the block to register the resource type out until the second bullet point on the high-level design
				secretType: &SDS{
					Cache: cacheMap[secretType],
				},

once cacheMap carries a secretType

@stevesloka rebased and ready :)


Wrong aspect ratio

I recently ran across a video file which shows with a wrong aspect ratio when using our lib. It is supposed to be 4:3, but we display it at 16:9. The pixel resolution truly is 4:3, but when we open the file, it reports sample_aspect_ratio 4:3. This means that it does not have square pixel but wide pixels (4:3). We correctly forward this, so the output gets stretched from 4:3 to 16:9 (4/3 * 4/3 = 16/9). The question is, why does this file report non-square pixels, when in fact the pixels must be shown as square 1:1 pixels. And why do other players show it correctly.
Interesting output from ffprobe:
Stream #0:0: Video: h264 (High), yuv420p(progressive), 1440x1080 [SAR 4:3 DAR 16:9], SAR 1:1 DAR 4:3, 23.98 fps, 23.98 tbr, 1k tbn, 47.95 tbc (default)
So it shows both [SAR 4:3 DAR 16:9] and SAR 1:1 DAR 4:3. Why are there two different sample aspect ratio and display aspect ratio values? Where can we get the "true" aspect ratio? We must forward SAR, otherwise a lot of other files will be incorrectly stretched. But we must forward the "right" SAR value, whatever that means. Currently, we use the first set, which results in wrong output. We must find the other set. But I have not found any other SAR on the codec context.
Sample file

I will take a look next week. If i understand correctly, the second set of metadata is the correct one?

I checked a few videos from various sources with ffprobe, and this sample is the only file that has 2 sets.
All others just show something along the lines of this
yuv420p10le(tv), 3840x2160 [SAR 1:1 DAR 16:9]
I am going to hazard a guess and we should use the 2nd pair every time it exists.
The sample aspect ratio in AVStream is {num=1 den=1 }
However, the sample aspect ratio in avStream->codecpar->sample_aspect_ratio = {num=4 den=3 }
some other files I tried have matching values there.
So I guess if values do not match, we should use the one from AVStream.
No idea how yet.

Thanks for the hint, I did not see that AVStream has a SAR as well. I tested lots of non-square SAR files today and none of them had SAR on AVStream level. This is the only file that has it. And all players give AVStream SAR preference over codec SAR, so this is what we should do as well. I will make a PR for this.

Cool. I was going to hack something together but didn't have the time. Nice work.


Capture the relevant error in test retry loop.

Previously we would always return the context cancellation.

actually it looks like we used to do the right thing, but a refactor clobbered the error


dependencies note

I'm installing now in a conda environment and had a couple of notes for the install.
It took me a minute to figure out einverted is part of emboss
conda install -c bioconda emboss

Not mentioned but phava complained if I didn't install pysam as a dependency
conda install -c bioconda pysam

That along with the mentioned
pip install biopython
conda install -c bioconda minimap2

and it shows the usage screen without errors

Thanks for the helpful note, I updated the readme to be more clear on the dependencies


Cannot locate datasets for some recipes

Hi,
I installed ESMValtool using miniforge, and have ESMValCore version 2.11.1, ESMValTool version 2.11.0.
I am unable to run some recipes (e.g. recipe_tebaldi21esd.yml) due to missing datasets.
I can run the example recipe examples/recipe_python.yml and it works perfectly, the relevant datasets are downloaded in the configured data directory. However, when I run esmvaltool run recipe_tebaldi21esd.yml --search_esgf=always, the job fails due to missing datasets, even though the relevant datasets are available on ESGF.
Here are some relevant snippets from main_log_debug.txt (the full file is too large to attach):
2024-12-04 06:24:19,972 UTC [386794] DEBUG   esmvalcore.local:439 Looking for files matching:
/data/esmvaltool/climate_data/cmip5/output1/CCCma/CanESM2/historical/mon/atmos/Amon/r5i1p1/*/tas_Amon_CanESM2_historical_r5i1p1*.nc
/data/esmvaltool/climate_data/cmip5/output2/CCCma/CanESM2/historical/mon/atmos/Amon/r5i1p1/*/tas_Amon_CanESM2_historical_r5i1p1*.nc
2024-12-04 06:24:19,973 UTC [386794] DEBUG   esmvalcore.esgf._search:116 Searching https://esgf.ceda.ac.uk/esg-search for datasets using facets={'project': 'CMIP5', 'model': 'CanESM2', 'ensemble': 'r5i1p1', 'experiment': 'historical', 'time_frequency': 'mon', 'institute': 'CCCma', 'cmor_table': 'Amon', 'product': 'output1,output2', 'variable': 'tas'}
2024-12-04 06:24:19,973 UTC [386794] DEBUG   requests_cache.backends:66 Initializing backend: None /home/ubuntu/.esmvaltool/cache/pyesgf-search-results
2024-12-04 06:24:19,973 UTC [386794] DEBUG   requests_cache.backends.base:322 Initialized SQLiteDict with serializer: SerializerPipeline(name=pickle, n_stages=2)
2024-12-04 06:24:19,973 UTC [386794] DEBUG   requests_cache.backends.sqlite:252 Opening connection to /home/ubuntu/.esmvaltool/cache/pyesgf-search-results.sqlite:responses
2024-12-04 06:24:19,974 UTC [386794] DEBUG   requests_cache.backends.base:322 Initialized SQLiteDict with serializer: None
2024-12-04 06:24:19,974 UTC [386794] DEBUG   requests_cache.backends.sqlite:252 Opening connection to /home/ubuntu/.esmvaltool/cache/pyesgf-search-results.sqlite:redirects
2024-12-04 06:24:19,976 UTC [386794] DEBUG   requests_cache.policy.actions:103 Cache directives from request headers: CacheDirectives()
2024-12-04 06:24:19,977 UTC [386794] DEBUG   requests_cache.policy.actions:368 Pre-read cache checks: Passed
2024-12-04 06:24:19,977 UTC [386794] DEBUG   requests_cache.policy.actions:217 Post-read cache actions: CacheActions(expire_after=86400, resend_request=True)
2024-12-04 06:24:19,977 UTC [386794] DEBUG   requests_cache.session:284 Stale response; attempting to re-send request
2024-12-04 06:24:19,978 UTC [386794] DEBUG   urllib3.connectionpool:1051 Starting new HTTPS connection (1): esgf.ceda.ac.uk:443
2024-12-04 06:24:20,441 UTC [386794] DEBUG   urllib3.connectionpool:546 https://esgf.ceda.ac.uk:443 "GET /esg-search/search?format=application%2Fsolr%2Bjson&limit=500&distrib=true&offset=0&type=File&project=CMIP5&model=CanESM2&ensemble=r5i1p1&experiment=historical&time_frequency=mon&institute=CCCma&cmor_table=Amon&product=output1%2Coutput2&variable=tas HTTP/11" 200 1273
2024-12-04 06:24:20,442 UTC [386794] DEBUG   requests_cache.policy.actions:368 Pre-write cache checks: Passed
2024-12-04 06:24:20,446 UTC [386794] DEBUG   requests_cache.backends.base:115 Closing backend connections
2024-12-04 06:24:20,446 UTC [386794] DEBUG   esmvalcore.esgf._search:154 Found the following files matching facets {'project': 'CMIP5', 'model': 'CanESM2', 'ensemble': 'r5i1p1', 'experiment': 'historical', 'time_frequency': 'mon', 'institute': 'CCCma', 'cmor_table': 'Amon', 'product': 'output1,output2', 'variable': 'tas'}: none
2024-12-04 06:24:20,447 UTC [386794] DEBUG   esmvalcore.esgf._search:364 Selected files:

2024-12-04 06:24:20,447 UTC [386794] ERROR   esmvalcore._recipe.check:131 No input files found for Dataset:
{'diagnostic': 'fig3b',
 'variable_group': 'tas',
 'dataset': 'CanESM2',
 'project': 'CMIP5',
 'mip': 'Amon',
 'short_name': 'tas',
 'alias': 'CanESM2_historical',
 'ensemble': 'r5i1p1',
 'exp': 'historical',
 'frequency': 'mon',
 'institute': 'CCCma',
 'long_name': 'Near-Surface Air Temperature',
 'modeling_realm': ['atmos'],
 'original_short_name': 'tas',
 'preprocessor': 'preproc_map',
 'product': ['output1', 'output2'],
 'recipe_dataset_index': 17,
 'standard_name': 'air_temperature',
 'timerange': '1986/2005',
 'units': 'K'}
session: 'recipe_tebaldi21esd_20241204_061245'
2024-12-04 06:24:20,451 UTC [386794] ERROR   esmvalcore._recipe.check:137 Looked for files matching
/data/esmvaltool/climate_data/cmip5/output1/CCCma/CanESM2/historical/mon/atmos/Amon/r5i1p1/*/tas_Amon_CanESM2_historical_r5i1p1*.nc
/data/esmvaltool/climate_data/cmip5/output2/CCCma/CanESM2/historical/mon/atmos/Amon/r5i1p1/*/tas_Amon_CanESM2_historical_r5i1p1*.nc
2024-12-04 06:24:20,452 UTC [386794] ERROR   esmvalcore._recipe.check:138 Set 'log_level' to 'debug' to get more information

Any help on fixing this issue would be much appreciated! Thanks in advance!

hi @VSumanth99 those files are available at the CEDA ESGF node, see https://esgf.ceda.ac.uk/thredds/catalog/esg_dataroot/cmip5/output1/CCCma/CanESM2/historical/mon/atmos/Amon/r5i1p1/latest/tas/catalog.html so ESMValTool can download them, make sure you have set:
search_esgf: when_missing
download_dir: ~/climate_data

in your .esmvaltool/config-user.yml configuration file.
Also ping @bouweandela or @schlunma - they run the Tool a lot more frequently than myself :beer:

Hi @valeriupredoi, thanks a lot of the response! I would like to confirm that those settings are already set in the config-user.yml file.  Here is the relevant snippet:
search_esgf: when_missing
download_dir: /data/esmvaltool/climate_data/

It still does not work as expected.
I would also like to add that some datasets are "found" from ESGF but others are not. The file I indicated was one of several that were not found by ESMValTool.
Here is the full list of datasets not found:
2024-12-04 06:50:06,140 UTC [391825] ERROR   esmvalcore._recipe.recipe:747 Could not create all tasks
2024-12-04 06:50:06,140 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor fig3b/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,140 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor fig3b/pr:
- Missing data for Dataset: pr, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,141 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor fig3a/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,141 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor fig3d/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,141 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor fig3d/pr:
- Missing data for Dataset: pr, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,141 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor fig3c/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,141 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor fig4d/pr:
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,141 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor fig4b/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,141 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor figA5b/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,141 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor figA5b/pr:
- Missing data for Dataset: pr, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,141 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor figA5a/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,141 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor figA5f/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,141 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor figA5f/pr:
- Missing data for Dataset: pr, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,141 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor figA5e/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,142 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor figA5d/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,142 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor figA5d/pr:
- Missing data for Dataset: pr, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,142 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor figA5c/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanCM4, historical, r9i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,142 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor tableA6_pr_cmip5/pr:
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: pr, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,142 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor tableA6_tas_cmip5/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r5i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r5i1p1
2024-12-04 06:50:06,142 UTC [391825] ERROR   esmvalcore._recipe.recipe:749 Missing data for preprocessor tableA8_cmip5/tas:
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, historical, r1i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp26, r1i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp45, r1i1p1
- Missing data for Dataset: tas, Amon, CMIP5, CanESM2, rcp85, r1i1p1
2024-12-04 06:50:06,430 UTC [391825] INFO    esmvalcore._task:128 Maximum memory used (estimate): 0.6 GB
2024-12-04 06:50:06,431 UTC [391825] INFO    esmvalcore._task:130 Sampled every second. It may be inaccurate if short but high spikes in memory consumption occur.
2024-12-04 06:50:06,432 UTC [391825] ERROR   esmvalcore._main:538 Could not create all tasks
2024-12-04 06:50:06,432 UTC [391825] DEBUG   esmvalcore._main:539 Stack trace for debugging:
Traceback (most recent call last):
  File "/home/ubuntu/miniforge3/envs/esmvaltool/lib/python3.11/site-packages/esmvalcore/_main.py", line 533, in run
    fire.Fire(ESMValTool())
  File "/home/ubuntu/miniforge3/envs/esmvaltool/lib/python3.11/site-packages/fire/core.py", line 135, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/miniforge3/envs/esmvaltool/lib/python3.11/site-packages/fire/core.py", line 468, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
                                ^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/miniforge3/envs/esmvaltool/lib/python3.11/site-packages/fire/core.py", line 684, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
                ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/miniforge3/envs/esmvaltool/lib/python3.11/site-packages/esmvalcore/_main.py", line 413, in run
    self._run(recipe, session)
  File "/home/ubuntu/miniforge3/envs/esmvaltool/lib/python3.11/site-packages/esmvalcore/_main.py", line 455, in _run
    process_recipe(recipe_file=recipe, session=session)
  File "/home/ubuntu/miniforge3/envs/esmvaltool/lib/python3.11/site-packages/esmvalcore/_main.py", line 127, in process_recipe
    recipe = read_recipe_file(recipe_file, session)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/miniforge3/envs/esmvaltool/lib/python3.11/site-packages/esmvalcore/_recipe/recipe.py", line 73, in read_recipe_file
    return Recipe(raw_recipe, session, recipe_file=filename)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/miniforge3/envs/esmvaltool/lib/python3.11/site-packages/esmvalcore/_recipe/recipe.py", line 740, in __init__
    self.tasks = self.initialize_tasks()
                 ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/miniforge3/envs/esmvaltool/lib/python3.11/site-packages/esmvalcore/_recipe/recipe.py", line 1066, in initialize_tasks
    tasks = self._create_tasks()
            ^^^^^^^^^^^^^^^^^^^^
  File "/home/ubuntu/miniforge3/envs/esmvaltool/lib/python3.11/site-packages/esmvalcore/_recipe/recipe.py", line 1054, in _create_tasks
    raise recipe_error
esmvalcore.exceptions.RecipeError: Could not create all tasks

Pinging @bouweandela, @schlunma for visibility.
Thanks again for your help!

We've seen something similar with other CMIP5 data (CESM1): https://github.com/ESMValGroup/ESMValTool/issues/3693. @ehogan was this every resolved? I don't think we found the root problem there.

Can you try searching for the data with the ESGF REST API? The data may still be available on the storage site, but if it got removed from the index it will no longer be findable.
You could also try using a different index node for searching, sometimes index nodes are in a bad state and only return a fraction of the available data. The index node that ESMValCore uses to search for data can be configured as described here.

We've seen something similar with other CMIP5 data (CESM1): #3693. @ehogan was this ever resolved? I don't think we found the root problem there.

I thought the problem was that the data were removed from ESGF, we just didn't know why? 🙁

Hi,
Thanks for the pointers!
Running the query https://esgf-node.llnl.gov/esg-search/search?type=Dataset&project=CMIP5&model=CanESM2&format=application%2Fsolr%2Bjson seems to give very few datasets, and certainly doesn't include the dataset that is needed by the recipe [recipe_tebaldi21esd.yml](https://docs.esmvaltool.org/en/latest/recipes/recipe_tebaldi21esd.html). So it seems like the ESGF index might not contain all the datasets.
Any suggestions on next steps? Thanks!

Hi, thanks again for the suggestions! I tried other index nodes (with distrib=true) and still couldn't find the datasets. So it certainly seems like an issue with the index nodes.
I also tried manually downloading the datasets from the catalog, and it works fine! So (1) the dataset is not missing from the ESGF servers, (2) there are no firewall issues.
I shall try sending an email to the ESGF support mailing list about the missing datasets. Feel free to close the issue if needed. Thank you!


TTD-327: mm-gql: sorting and filtering not updating

https://tractiontools.atlassian.net/browse/TTD-327

Few problems I fixed in this PR that I found on the side nav use case;

Undefined filters and sorting are included that's why it messes up the results.
Filter doesn't work well with single node queries.


Datacapture, add material date picker to datacapture module.

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 [...]
Currently, datacapture module provide date type widget with default platform DatePickerDialog, and as of now it does not uses MaterialDatePicker, we can refer DatePickerFragment class in datacapture.
If it is required to make changes as per figma design, then datacapture must start including material date picker.
Material date picker looks as below.

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.
Additional context
Add any other context or screenshots about the feature request here.
Would you like to work on the issue?
Please state if this issue should be assigned to you or who you think could help to solve this issue.

#1108

#1045


WorkerPool cannot have additional protocol conformance

Context:
Just learning about swift-distributed actor and system. I tried to make WorkerPool to adapt ClusterSingleton protocol to use it as single instance.
extension WorkerPool: ClusterSingleton {}
Then Xcode compiler fails with following message:
/Users/pbk/Documents/XcodeWorkSpace/ToyWorkSpace/DemoToycraft/DistributedActors.WorkerPool:3:16: Property 'actorSystem' cannot be defined explicitly, as it conflicts with distributed actor synthesized stored property
/Users/pbk/Documents/XcodeWorkSpace/ToyWorkSpace/DemoToycraft/DistributedActors.WorkerPool:2:16: Property 'id' cannot be defined explicitly, as it conflicts with distributed actor synthesized stored property
Also WorkerPool cannot conform to empty protocol.
protocol EmptyProtocol {}
extension WorkerPool: EmptyProtocol {}

Commit hash: 811d2e88a12db8477a0edde6311c1299102314d3 ( 1.0.0-beta.2 )
Environment:
IDE and tool chain : Xcode 14.0 RC, Xcode 14 RC tool chain
My application targets iOS 16.0 iphone 8  simulator
$ swift --version
swift-driver version: 1.45.2 Apple Swift version 5.6.1 (swiftlang-<IP_ADDRESS>3.66 clang-13<IP_ADDRESS>)
Target: x86_64-apple-macosx12.0
Operating system: macOS Monterey 12.5.1
$ uname -a
Darwin iquest1127ui-MacBookPro.local 21.6.0 Darwin Kernel Version 21.6.0: Wed Aug 10 14:25:27 PDT 2022; root:xnu-8020.141.5~2/RELEASE_X86_64 x86_64
My system has IPv6 enabled.

Hmm, thanks for the report, I wonder if that's a language issue actually... Will look into it soon.

Having that said, it is a bit weird to make a worker pool a singleton -- are you sure that's what you'd need, usually you'd reach for one or the other?

Having that said, it is a bit weird to make a worker pool a singleton -- are you sure that's what you'd need? usually you'd reach for one or the other.

I thought it would be appropriate to have one Worker Pool instance per WorkerPoolSetting.Selector in actorSystem, so I tried the above approach. I don't have specific goal or need for this. Just working around learning new features of swift 5.7.
If you can afford it, could you explain why it's weird or where the reference or url about it?

This issue is not related to singleton. WorkerPool can't adapt any additional protocol. It can't adapt even empty protocol. If I do same compiler fail occurs.


Add Python nightly (3.7) on Travis without container.

To follow latest development Python easily.

Considering non-rpm environment, the test became complicated.
As I do not have a non-rpm environment on local, I have to test it on Travis.
That is very cost.
We should not assume non-rpm environment as one of the testing environment.
Close it right now.


Do not stop on first JSP containing a compile error

Solves this issue for Tomcat7 only.
https://github.com/Jasig/jspc-maven-plugin/issues/17
Uses the workaround proposed by Lynorics. except that copying JspC to plugin directory does not seem to work. I had to rename it.

Hey @akram , thanks for the pull request!
Unfortunately are merge conflicts that have cropped up that are blocking these changes from being merged.
I'm going to close this PR, feel free to re-open it if you have time to resolve the merge conflicts.


Link #set is broken in spec.md

Added in 4b7dd59. It seems sets are not supported in bazel ?

No. I've removed it from the table of contents.


adjust XL Fortran OMP flag; fixes #232

Can you please look over this @robertodr?

Hmm. Yes, that would be even better. Thanks. One thing that starts to bother me a bit is the diffuse versioning in Autocmake but that is a separate issue. We need to think about it.

One problem that I see with this is that FindOpenMP.cmake potentially pulls in other modules (I haven't tested this but see this happening with FindMPI.cmake. I think we should merge this since it's better than before but I think that offloading to FindOpenMP.cmake is not so trivial.

Agreed that this is better than nothing.
On Wed, Mar 7, 2018, 12:36 Radovan Bast<EMAIL_ADDRESS>wrote:

One problem that I see with this is that FindOpenMP.cmake potentially
pulls in other modules (I haven't tested this but see this happening with
FindMPI.cmake. I think we should merge this since it's better than before
but I think that offloading to FindOpenMP.cmake is not so trivial.
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Remove debug code

slog example is not working.
Removed debug code and uncommented correct code.

Thanks for the contrib ☺


Write exp.asm test program

Pseudo-code:
// y must be non-negative
int exp(int x, int y) {
	int result = 1;
	while (y != 0) {
		if (y & 1 == 1)
			result *= x;
		x = x*x;
		y >>= 1;
	}
	return result;
}

Please add a bigger testcase as an addition to the current program. For example 7^11.

Fixed.


Add support for including specific tables

add option --include, type array.
include tables in the query
example:  dexter mydb --include users

Thanks @stevelacy 👍  Here's what I ended up merging (some cleanup and tests): https://github.com/ankane/dexter/commit/1b46f20522f0d4b2d8dce2f639c3e950706bcbe8


in_keys() not evaluated even when it's present in term constraint

#lookupMemory implementation:
    syntax Int ::= #lookupMemory  ( Map , Int ) [function, functional, smtlib(lookupMemory)]

    rule [#lookupMemory.some]:   #lookupMemory( (KEY |-> VAL:Int) _M, KEY ) => VAL modInt 256
    rule [#lookupMemory.none]:   #lookupMemory(                    M, KEY ) => 0                 requires notBool KEY in_keys(M)
    //Impossible case, for completeness
    rule [#lookupMemory.notInt]: #lookupMemory( (KEY |-> VAL    ) _M, KEY ) => 0                 requires notBool isInt(VAL)

Test:
rule <k> runLemma ( #lookupMemory((KEY |-> 33), KEY') ) => doneLemma ( 0 ) ... </k> requires notBool KEY' in_keys(KEY |-> 33)

Result:
  #Not ( {
    #lookupMemory ( KEY |-> 33 , KEY' )
  #Equals
    0
  } )
#And
  #Not ( {
    KEY
  #Equals
    KEY':Int
  } )
#And
  <kevm>
    <k>
      doneLemma ( #lookupMemory ( KEY |-> 33 , KEY' ) ) ~> DotVar2 ~> .
    </k>
...

Code: https://github.com/kframework/evm-semantics/pull/855

domains.k has a rule for symbolically evaluating in_keys. Please run this example with --debug-equation to find out why it is not applied.

The rules from domains.k are for Java, not Haskell:
module MAP-JAVA-SYMBOLIC [kast, symbolic]
...
  rule K1 in_keys(M K2 |-> _) => true          requires K1  ==K K2 orBool K1 in_keys(M) [simplification]
  rule K1 in_keys(M K2 |-> _) => K1 in_keys(M) requires K1 =/=K K2 [simplification]

  rule K1 in_keys(M [ K2 <- _ ]) => true          requires K1  ==K K2 orBool K1 in_keys(M) [simplification]
  rule K1 in_keys(M [ K2 <- _ ]) => K1 in_keys(M) requires K1 =/=K K2 [simplification]
endmodule

I debugged the failing test with full --log-level debug. Something rewrites in_keys expression into
        \equals{SortKItem{}, R}(
            /* Fl Fn D Sfa */ VarKEY:SortKItem{},
            /* Fl Fn D Sfc */
            /* Inj: */ inj{SortInt{}, SortKItem{}}(
                /* Fl Fn D Sfa */ VarKEY'Apos':SortInt{}
            )

but that piece of logic is not logged.
There's this piece also which looks strange:
kore-exec: [2020-07-10 21:23:48.1551454] Debug (DebugEvaluateCondition):
    (DebugAttemptEquation) while applying equation at /mnt/d/evm-semantics/evm-types.md:664:34-664:129:
    evaluating predicate:
        /* Sfc */
        \not{R}(
            /* Sfc */
            \not{R}(
                /* Spc */
                \equals{SortKItem{}, R}(
                    /* Fl Fn D Sfa */ VarKEY:SortKItem{},
                    /* Fl Fn D Sfc */
                    /* Inj: */ inj{SortInt{}, SortKItem{}}(
                        /* Fl Fn D Sfa */ VarKEY'Apos':SortInt{}
                    )
                )
            )
        )
    with side condition:
        \and{_PREDICATE{}}(
            /* Sfc */
            \not{_PREDICATE{}}(
                /* Spc */
                \equals{SortKItem{}, _PREDICATE{}}(
                    /* Fl Fn D Sfa */ VarKEY:SortKItem{},
                    /* Fl Fn D Sfc */
                    /* Inj: */ inj{SortInt{}, SortKItem{}}(
                        /* Fl Fn D Sfa */ VarKEY'Apos':SortInt{}
                    )
                )
            ),

The rule it refers to is:
rule [#lookup.none]:         #lookup( M, KEY ) => 0    requires notBool KEY in_keys(M)

Questions:

Should we enable in_keys lemmas for Haskell?
Why the predicate above has double negation (\not{R}( \not{R}(...)? It seems to be generated incorrectly.

There are rules for the backend which evaluate in_keys.
This predicate:
            \not{R}(
                /* Spc */
                \equals{SortKItem{}, R}(
                    /* Fl Fn D Sfa */ VarKEY:SortKItem{},
                    /* Fl Fn D Sfc */
                    /* Inj: */ inj{SortInt{}, SortKItem{}}(
                        /* Fl Fn D Sfa */ VarKEY'Apos':SortInt{}
                    )
                )
            )

comes from checking that a symbolic Map is defined. This would be a condition required to match some rule, probably the rule for #lookup you mentioned. The double negation appears because we are evaluating \not(\implies(sideCondition, required)); if that predicate is unsatisfiable, then the equation is applied.

Fixed by #2147.


FileSaveDialog fails to open with UTF8String as value

Describe the bug
Evaluate in a workspace:
FileSaveDialog showModalOn: 'Camión'
This works ok:
FileSaveDialog showModalOn: 'Camión' asUtf16String
One coworker solved this implementing in FileDialog
value: aString
    super value: aString asUtf16String

I'm not sure if it's correct or enough in all cases.

Yes, it hasn't updated correctly for Unicode. It's copying the supplied string into the buffer using a string block copy operation, (replaceFrom:to:with:startingAt:) which doesn't work between different encodings because the number of code units to represent the same string could be different - i.e. the range will be wrong. It needs to be converted to UTF-16 as your co-worker has done, although I would put it in prepareStruct method because that is closer to the external interfacing that requires it. It looks like the file type filters are already handled correctly.


Added and edited colors

Docs design uses gray-700 which is a new color so I've added that along with other new color changes while I'm at it

no primary-gradient-2 isn't used anywhere i've check all projects


Docker builds do not store SCM information

Describe the bug
The buildnumber-maven-plugin tries to retrieve SCM information that is used to display when printing out ./dspace version
Until recently the plugin wasn't configured to gracefully handle not finding any version control initiated #6772. This was fixed with PR 9016.
However, I found out that docker builds invariably displayed the fallback value: "UNKNOWN_REVISION".
Running a docker compose build with standard output like so:
$ docker compose -f docker-compose.yml -f docker-compose-cli.yml build --no-cache --progress plain

(with --progress plain to show everything in the usual standard out way)
shows:
#39 13.54 [INFO] --- buildnumber-maven-plugin:3.2.0:create (default) @ dspace-api ---
#39 13.74 [INFO] Executing: /bin/sh -c cd '/app/dspace-api' && 'git' 'rev-parse' '--verify' 'HEAD'
#39 13.74 [INFO] Working directory: /app/dspace-api
#39 13.75 [INFO] Storing buildNumber: null at timestamp:<PHONE_NUMBER>925
#39 13.76 [INFO] Executing: /bin/sh -c cd '/app/dspace-api' && 'git' 'symbolic-ref' 'HEAD'
#39 13.76 [INFO] Working directory: /app/dspace-api
#39 13.76 [WARNING] Cannot get the branch information from the git repository:
#39 13.76 Detecting the current branch failed: fatal: not a git repository (or any of the parent directories): .git
#39 13.76
#39 13.76 [INFO] Executing: /bin/sh -c cd '/app/dspace-api' && 'git' 'rev-parse' '--verify' 'HEAD'
#39 13.76 [INFO] Working directory: /app/dspace-api
#39 13.77 [INFO] Storing scmBranch: UNKNOWN_BRANCH

whereas:
#39 11.38 [INFO] --- buildnumber-maven-plugin:3.2.0:create (default) @ dspace-api ---
#39 11.52 [INFO] Executing: /bin/sh -c cd '/app/dspace-api' && 'git' 'rev-parse' '--verify' 'HEAD'
#39 11.52 [INFO] Working directory: /app/dspace-api
#39 11.53 [INFO] Storing buildNumber: UNKNOWN_REVISION at timestamp:<PHONE_NUMBER>418
#39 11.53 [INFO] Executing: /bin/sh -c cd '/app/dspace-api' && 'git' 'symbolic-ref' 'HEAD'
#39 11.53 [INFO] Working directory: /app/dspace-api
#39 11.53 [WARNING] Cannot get the branch information from the git repository:
#39 11.53 Detecting the current branch failed: fatal: not a git repository (or any of the parent directories): .git
#39 11.53
#39 11.53 [INFO] Executing: /bin/sh -c cd '/app/dspace-api' && 'git' 'rev-parse' '--verify' 'HEAD'
#39 11.53 [INFO] Working directory: /app/dspace-api
#39 11.54 [INFO] Storing scmBranch: UNKNOWN_BRANCH

This means that the PR that fixed requiring git as a build dependency worked as intended. However, the docker builds build commands are not being executed in git repos, or otherwise the revision number would be successfully retrieved.
I'm not certain this is a problem. It is however not how the build is intended to work.
Git is explicitly installed in Dockerfile.dependencies in order to retrieve the version control revision number.
https://github.com/DSpace/DSpace/blob/main/Dockerfile.dependencies#L18C1-L22
Note
I'm not sure why this would cause non-Docker builds to fail but Docker builds can recover from.
To Reproduce
Steps to reproduce the behavior:
Try running docker compose -f docker-compose.yml -f docker-compose-cli.yml build --no-cache --progress plain  observing the API output with out without the lines 120-122 in pom.xml for dspace-api.
Expected behavior
Currently non Docker builds should successfully store revision information. Perhaps that is enough. But a bit of diggging in the Docker build sequence should establish why this is broken and then Docker builds can again store build revision information.
Related work
#6772

I'll admit, I'm not sure if this is a concern either.  I will note though that the ./dspace version command does return the accurate DSpace Version even in Docker.  So, for example, I see this in a Docker instance running from main:
# ./dspace version
DSpace version:  8.0-SNAPSHOT
  SCM revision:  UNKNOWN_REVISION
    SCM branch:  UNKNOWN_BRANCH
            OS:  Linux(amd64) version <IP_ADDRESS>-microsoft-standard-WSL2
  Applications:
     Discovery:  enabled.
           JRE:  Eclipse Adoptium version <IP_ADDRESS>
   Ant version:  null
 Maven version:  3.8.6
   DSpace home:  /dspace

This also means that our Demo Site and Sandbox Site backends report the correct version:

https://demo.dspace.org/server/ -> Reports "dspaceVersion": "DSpace 7.6.1-SNAPSHOT"
https://sandbox.dspace.org/server/ -> Reports "dspaceVersion": "DSpace 8.0-SNAPSHOT"

So, the basics of reporting the version of DSpace that is running does work.  But, I can verify that the SCM information is lost in Docker instances.
For now, I'm leaving this as low priority & needs volunteer.  We can update the priority if we find that this has a greater impact than currently known.

thanks  @tdonohue
I did not mean to suggest that version information wasn't been stored
I just wanted to point out that the reason git was added as a build dependency was to store VCS information, the branch and the commit hash.
As can be seen from the log excerpts I posted, the build directory  '/app/dspace-api' is not a git repository as expected
I can think of three options:

this should be fixed by having the git repository in the docker build container
git should be removed as a build dependency for docker
possibly, if it is desirable to have branch or commit hash as part of version information, it could be passed into the container as an environment variable

When building in a git repository output will be similar to:
[INFO] --- buildnumber-maven-plugin:3.2.0:create (default) @ dspace-api ---
[INFO] Executing: /bin/sh -c cd '/home/jabbi/IdeaProjects/DSpace/dspace-api' && 'git' 'rev-parse' '--verify' 'HEAD'
[INFO] Working directory: /home/jabbi/IdeaProjects/DSpace/dspace-api
[INFO] Storing buildNumber: 1d4c441cea315281f3691a0240584790cc907847 at timestamp:<PHONE_NUMBER>811
[INFO] Executing: /bin/sh -c cd '/home/jabbi/IdeaProjects/DSpace/dspace-api' && 'git' 'symbolic-ref' 'HEAD'
[INFO] Working directory: /home/jabbi/IdeaProjects/DSpace/dspace-api
[INFO] Storing scmBranch: feature/all_config_endpoint


"Colți" is listed in the drop-down menu

Description:
"Colți" is listed in the drop-down menu alongside its corresponding county and commune, according to the law
Precondition:
The website is up an running.

Step 1
Type "Colți" in the search bar.

Expected results
The location is listed in the drop-down menu as "Colți, Buzău".


[RFC]: add findLast method to array/fixed-endian-factory

Description
This RFC proposes adding support for a findLast method to @stdlib/array/fixed-endian-factory.
This method is the equivalent of the TypedArray.prototype.findLast method, but for fixed-endian typed arrays.
When adding support, the following tasks should be completed:

The ./lib/main.js file should be updated with the added method.
A new test file should be created which includes unit tests testing against expected behavior.
Two benchmark files should be added: one measuring baseline performance and another measuring performance as the array length increases.
The README should be updated to include documentation for the added method.

To provide a concrete example of what a PR adding the desired method should contain, see https://github.com/stdlib-js/stdlib/commit/956a4624c788689b1bca285856b987ea3aa32eb6, which is a commit adding forEach support. This should provide an idea of what is expected.
For an example of specialized typed arrays having customized methods, see

@stdlib/array/bool
@stdlib/array/complex128
@stdlib/array/complex64

While the method proposed in this RFC will likely not match the implementations found in the above packages, those packages should provide a conceptual idea of what is desired. Do not simply copy-paste the code found in those packages.
Notes

If you are interested in contributing a PR which addresses this RFC and are a first-time contributor or not yet familiar with our project conventions, please do not submit LLM-generated code. Please consult our contributing guidelines and the associated development guide. Failure to respect project conventions will result in your PR being rejected without review. Thank you for understanding!

Checklist

[X] I have read and understood the Code of Conduct.
[X] Searched for existing issues and pull requests.
[X] The issue name begins with [RFC]:.

working on this
48h


First pass of the CDC Indicator

Description
First pass on the CDC Indicator with tests

Missing HI and TX data by county.

The changes requested have been made. We should talk about the two open issues still - the unknown states/counties and the megacounty thread.

@krivard @dshemetov , do we need to do anything else for this indicator?

@Ananya-Joshi just the Nancodes annotation in the thread above and it should be good to go 👍

@Ananya-Joshi just the Nancodes annotation in the thread above and it should be good to go 👍
As far as I can see on my local, they're changed! Is this not the case for what you can see?

Oh, now we're missing the actual "se" and "sample_size" columns. I will make a commit with what I mean.


Gridfield custom fragments

Created an API for defining custom fragments.

See also: http://open.silverstripe.org/ticket/6911

Very elegant solution for the problem! I'll wait for Stig's feedback before merging, good to go from my perspective.

I like the solution, flexible.

Cool, I'll rebase and merge directly.

@Ingo we definitely need it merge into big_O master and further to the integration branch before demo

@chillu @normann I'd suggest that you do your demo on the main version.


IDT Error: [RunTests_task] ERROR: Private key not found

Describe the bug
IDT Error: [RunTests_task] ERROR: Private key not found
System information

Hardware board: company private board with WIFI module
IDE used: Cmake
Operating System: FreeRTOS on board
Project/Demo: All AWS IDT test cases for coreMQTT_Integration_AWS_IoT_Compatible and other cases which need the TLS feature

Expected behavior
The private key is auto-created by IDT, so i think the key should always ready.
Screenshots or console output
This the mbedtls log:
Private key not found
ERROR: The handshake failed and it is likely due to a failure in PKCS #11. Consider enabling
Steps to reproduce bug
Sometimes run the cases, the issue will happen, it's intermittent.

Issue was fixed , thanks


multiple raw/mzML files from one sample

Hi,
when there are multiple raw/mzML files from one sample, how does the match-between-run mode work?
Will moFF consider each mzML file as one sample?  or how do i tell moFF to consider these multiple mzML files are from one sample. I did n't find in the Readme for this situation.

Hi,
I am not talking about technical replicates.
when peptide pre-fractionation methods are used, one sample usually consists of multiple raw files from different fractions collected in pre-fractionation step.  Say we collect 6 fractions for each sample and it will produce 6 raw files after LC-MS/MS analysis.
For 10 samples, there will be 10x6 = 60 raw files generated. In maxQuant, it allows users to set the 6 different fractions as 1 experiement and the output will output quantiative values for 10 experiments (corresponding to 10 samples).
If I use moFF, how does it output MS1 quant values? one for each raw file ?

Hi,
In moFF , you cannot  set all the 6 different  fraction as one experiments. The mbr works for all the comparison between the input sample, so in your case (fractionated samples 6 fractions, 10 samples ) for all the 60 raws  it won 't works. I couldtry to implement this this features in the updates.
But you can try to run moFF with mbr for each fraction for all the sample (10 file at time for 6 times). In this case the mbr will work because across samples the same fraction should have enough shared peptides to train the model. I never tried but it should work.


Downloads list should be unique by outpoint/key, not claimid

The Issue
You get the below console warning if two downloads have the same claim id (which is normal if a claim is updated with a new file). Currently, both claims will show the same content as it is pulled up by the claimid, but it should really use the outpoint or key from file_list. This may be somewhat related to https://github.com/lbryio/lbry-app/issues/1203
 C:\Users\SoloDolo\Desktop\new3\lbry-app\node_modules\fbjs\lib\warning.js:33 Warning: Encountered two children with the same key, `lbry://one#008401a48cecef2a13cf5376b696169bb36b18c6`. Keys should be unique so that components maintain their identity across updates. Non-unique keys may cause children to be duplicated and/or omitted — the behavior is unsupported and could change in a future version.
    in div (created by FileList)
    in section (created by FileList)
    in FileList (created by Connect(FileList))
    in Connect(FileList) (created by FileListDownloaded)
    in main (created by Page)
    in Page (created by Connect(Page))
    in Connect(Page) (created by FileListDownloaded)
    in FileListDownloaded (created by Connect(FileListDownloaded))
    in Connect(FileListDownloaded) (created by Router)
    in Router (created by Connect(Router))
    in Connect(Router) (created by App)
    in div (created by App)
    in main (created by App)
    in div (created by App)
    in App (created by Connect(App))
    in Connect(App)
    in div
    in Provider

Steps to Reproduce

Download a claim
Update claim with new data
Download the claim again

Expected Behaviour
Should be able to access both files in the LBRY downloads
Actual Behaviour
Can only access by claim id, which leads to a single file.
Suggested Solutions
Use the outpoint/key
System Configuration

LBRY Daemon version:
LBRY App version:
LBRY Installation ID:
Operating system:

Anything Else

Screenshots

The long-term fix here is not straightforward, though switching to outpoint as a unique key might be an acceptable short term change .
If claim id stays the same, it is supposed to be the publisher saying this is the same piece of content. If the claim id stays the same but the outpoint changes, the user should not have to re-pay a key fee and instead should be prompted to update to the latest version of the content.
Part of the problem is probably that all edits keep the claim id the same, when instead we should ask the creator if the edit is actually a new publish against the same name. And in that case, change the claim id.

Even if the file does change on edit, isn't it normal behavior to have the old and the new file? I'm sure we can make this an option in the future where the user chooses to overwrite the existing file or keep it (both on the physical download and on the LBRY downloads list).

Got rid of the console errors in #1724 but we can keep this open for now for more discussion around claim id behavior on edits vs new publishes

While I agree the user should have access to the old file and should know what's up, I feel very strongly that the ideal solution is not two distinct listings.
Instead, multiple outpoints for the same claim id should be treated/displayed as two different versions of the same content.

^ If above is unclear I can elaborate


OSM regression tests starting to fail due to external API change

E.g. http://clinker.cartodb.net/jenkins/job/CartoDB-PR-testing/2155/console :
...
18:21:18
18:21:18   1) OSM regression tests displays a specific error message for too many nodes requested
18:21:18      Failure/Error: result.error_code.should eq 1007
18:21:18
18:21:18        expected: 1007
18:21:18             got: 1001
18:21:18
18:21:18        (compared using ==)
18:21:18      # ./services/importer/spec/acceptance/osm_spec.rb:43:in `block (2 levels) in <top (required)>'
18:21:18
18:21:18 Finished in 2 minutes 4.68 seconds
18:21:18 255 examples, 1 failure, 2 pending
18:21:18
18:21:18 Failed examples:
18:21:18
18:21:18 rspec ./services/importer/spec/acceptance/osm_spec.rb:31 # OSM regression tests displays a specific error message for too many nodes requested
18:21:19 make: *** [check-3] Error 1
18:21:19 Build step 'Execute shell' marked build as failure
18:21:19 Sending e-mails to<EMAIL_ADDRESS>18:21:19 Slack Notifications is waiting for a checkpoint on CartoDB-PR-testing #2154
18:22:52 Finished: FAILURE

As nacho pointed out, no tests should depend on external data as a general rule.
Will disable the offending test for now.

@juanignaciosl @rafatower @Kartones I guess someone of you should look into this? for now I've disabled the test in https://github.com/CartoDB/cartodb/pull/2678 to have clinker pass again, as per @juanignaciosl's comment

As OSM is external to properly remove the external dependency the test should mock the call and response... feel free to move it to me but at minimum will be for next sprint

Ok, I'll do that! For me there's no rush. Thanks!

There has been no activity on this issue for more several months. We are closing it. If you think this still needs to be addressed please open a new issue.


Prevent a player's mob from being controlled through the control mob verb

Fixes #1266
If a player's mob is supposed to be controllable then close this PR.

I'd definitely rather have it that the crash is fixed. Controlling an already-controlled mob (as long as it boots the person inside to ghost or whatever sanely) should totally be possible.


Prevent search icon focus on close

Fixes issue where closing via keydown causes the icon to become focused, which is confusing behavior

Coverage decreased (-0.01%) to 76.426% when pulling 3505fcb0c2b94143e584abf7af10e4c2d532b503 on bugfix/fix-search-close-focus into 4f836096a56be93ee1322f3c98cbaca485f0b064 on master.


Added a mutli-stage Dockerfile

How about a lighter-weight base image, like quay.io/prometheus/busybox.
See the Prometheus Dockerfile

Not a bad idea - gains 2MB :)

Hey could we resume this ?  It would be nice to have public docker images following the releases

I've been thinking about what to do about this fork. I'd like there to be one official pgbouncer exporter. I was hoping to get some comments in https://github.com/larseen/pgbouncer_exporter/issues/13 about either resuming upstream work or hard-forking things over to prometheus-community.

FYI, I've filed https://github.com/prometheus-community/community/issues/21. I'm intending to do a hard fork, so that the code here would become the canonical source.

We've completed the move to prometheus-community. I've added our standard multi-arch Dockerfile.
It's now available on prometheuscommunity/pgbouncer-exporter.


Fixes nesting default/flex grids within a container

In the flex grid there were 2 issues:

The use of & & on line 158
.row & on line 194

The issues on the standard grid were almost the same
Fixes #9225
--

Thanks, I never thought to it when I was working on grids.
You just forgot an empty line at the end of scss/grid/_flex-grid.scss
@kball It can be merged now in develop. But the nesting often causes problems (arbitrary higher specificity), so I think it should be removed it later (it's a breaking change).

@ncoden Thanks for pointing that out, fixed 😄


Refactor/divide common.rs into smaller files

Reasons / Why

common.rs is ~2600 lines long, it's pretty huge.
It takes roughly 3 thousand light years 10+ seconds for rust-analyzer to recompile it at every change (Ctrl+S)... on my average laptop.
Another reason for refactoring is the fact that common name is too... common.

I was trying to make a simple patch into common.rs, and clippy recompilation delays made it quite challenging.
Thanks :)

@fadeevab common.rs is a pile of ugly hacks that we have to decouple into dedicated crates. We have started to work on it here: https://github.com/akorchyn/near-api


danb27/sar_single_node_improvements: allow for getting most frequent …

Description

Bug fix: The documentation says that self.item_frequencies should contain the frequencies of every item, but in fact, it currently shows a different value, generated by using the diagonal of the response from self.compute_cooccurrence_matrix, which is not actually equal to item frequencies when there are duplicates in the dataframe. The test we had written before (test_get_popularity_based_topk) was only passing because the test it has no duplicates. If you add any duplicates to the test, it will fail, and nothing in the fit() method will stop you or warn you that you are using the object incorrectly. Many of the tests we have written do include duplicates also.
Improvement: Allow users to get similar users using the new method, self.get_user_based_topk, similarly to how users are currently able to get similar items using self.get_item_based_topk
Improvement: Allow users to use the self.get_popularity_based_topk method with items=False to get the most popular users rather than the most popular items. The parameter defaults to True (return items, not users) for backwards compatibility
Add tests for 1-3

Checklist:

[x] I have followed the contribution guidelines and code style for this project.
[x] I have added tests covering my contributions.
[x] I have updated the documentation accordingly.
[x] This PR is being made to staging branch and not to main branch.

Looking forward to your feedback!

the issue (I'm no longer sure that it is a bug) with the frequencies was introduced here: #https://github.com/microsoft/recommenders/pull/1588
The problem happens when there are duplicate user-item pairs in the dataset. A note was added to the docstring telling the user not to provide duplicates, but there is no warning or error thrown if duplicates are present. If there were an error thrown, then a lot of our current tests would fail also.
Without any warning or without dropping duplicates, you can get weird results like this:

I added a warning if there are duplicates found in the dataset, but I think we can still improve by changing how we calculate frequency to be unrelated to the cooccurrence matrix (just count occurrences in the user provided dataframe).
Any thoughts?

Codecov Report

Merging #1666 (bf7c730) into staging (afd0597) will decrease coverage by 34.42%.
The diff coverage is 86.66%.

@@             Coverage Diff              @@
##           staging    #1666       +/-   ##
============================================
- Coverage    57.97%   23.54%   -34.43%
============================================
  Files           88       88
  Lines         9096     9153       +57
============================================
- Hits          5273     2155     -3118
- Misses        3823     6998     +3175

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Coverage Δ

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23.54% <86.66%> (-34.43%)
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Impacted Files
Coverage Δ

recommenders/models/lightfm/lightfm_utils.py
62.50% <ø> (ø)

recommenders/models/sar/sar_singlenode.py
92.89% <85.29%> (-3.99%)
:arrow_down:

recommenders/datasets/spark_splitters.py
87.27% <100.00%> (+1.55%)
:arrow_up:

...enders/models/deeprec/models/sequential/sli_rec.py
0.00% <0.00%> (-100.00%)
:arrow_down:

...ders/models/deeprec/models/sequential/nextitnet.py
0.00% <0.00%> (-100.00%)
:arrow_down:

...commenders/models/deeprec/models/sequential/sum.py
0.00% <0.00%> (-96.50%)
:arrow_down:

recommenders/models/ncf/ncf_singlenode.py
2.29% <0.00%> (-96.19%)
:arrow_down:

recommenders/models/newsrec/models/npa.py
0.00% <0.00%> (-95.59%)
:arrow_down:

recommenders/models/wide_deep/wide_deep_utils.py
0.00% <0.00%> (-93.55%)
:arrow_down:

recommenders/models/newsrec/models/naml.py
0.00% <0.00%> (-92.44%)
:arrow_down:

... and 35 more

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@miguelgfierro Sorry for the back and forth, but your comments made me realize a much simpler + better way to achieve what I was trying to do. Here is a summary of what the PR does now:

change how we calculate user + item frequencies to come directly from the user's data
remove need for user to drop duplicates ahead of calling .fit(). The issue was when we calculated item cooccurrences and there were duplicates, but we can instead just temporarily drop any duplicates in the user dataframe before calculating cooccurrences. this ensures that our unit tests are still working AND our cooccurrences are accurate
allow someone to retrieve the most frequent users, the same way we can already retrieve the most popular items
allow someone to retrieve the k most similar users based on our user affinity matrix. This allows ratings to be factored into the results of grabbing the most similar users and also avoids the weird situation I had created where we needed to calculate user cooccurrences if we wanted to call a specific method.

I think these changes are a lot better and hopefully make the PR more palatable.
What do you think?
Is there any reason we should still tell users to not include duplicates? I am assuming that if our unit test dataset has duplicates, then we should also be accepting duplicates, but I don't know where this test data comes from.

@anargyri Thank you for your clarification on point 1. This is very helpful. I will think about if I can adapt my code or if I should just change those parts back to how they were before.

Of course this could be misused if you are leaking information to other users. But I believe there are legitimate use cases also. For example, you want to make sure that your model has some overlap in the recommendations for similar users, but that similar users are not getting the exact same recommendations. Please note that this sort of functionality is featured within recommenders for LightFM, see the LightFM notebook and the code

You might want to look at how your model performs for users with a lot of data points vs. very few to understand your model biases and at what number of datapoints you know enough about a user to make good recommendations.

So given Andreas' comment on the frequencies, I went back to the old way of calculating item_frequencies, without using value_counts, and also rewrote how we calculate user_frequencies to not use the dataframe directly.
I think there are two remaining questions:

do we want to have some sort of warning / error if a data scientist does provide duplicates?
are we okay with providing these methods for grabbing the most frequent users and grabbing similar users, similar to the functionality provided in the LightFM code? Of course these could be misused, but I think there are legitimate uses for them as well.

If the answer to both is no, then we can probably just close this PR.
@miguelgfierro @anargyri Please let me know how to proceed when you get a chance.

@danb27 sorry for not answering earlier. Answering your questions:

do we want to have some sort of warning / error if a data scientist does provide duplicates?

I think we should throw an error if there are duplicates, see details of faster implementations in this comment

are we okay with providing these methods for grabbing the most frequent users and grabbing similar users, similar to the functionality provided in the LightFM code? Of course these could be misused, but I think there are legitimate uses for them as well.

I think this is ok.
Any other perspective @anargyri?


TestPeerConnection_Renegotiation_AddTrack_Rename failure on CI

=== RUN   TestPeerConnection_Renegotiation_AddTrack_Rename
    TestPeerConnection_Renegotiation_AddTrack_Rename: peerconnection_renegotiation_test.go:242:
        	Error Trace:	peerconnection_renegotiation_test.go:242
        	Error:      	Should be true
        	Test:       	TestPeerConnection_Renegotiation_AddTrack_Rename

Is this still valid? I haven't seen this error. Any idea how to reproduce?

Closed for https://github.com/pion/webrtc/issues/1466


Upgraded the Module to work with Current accounts and to be more pythonic

I came across this module yesterday and thought it was a great start to making a Python wrapper of the Monzo API.
I've taken the original repo and given it a bit of love.
Changes Include:

Created a class to map JSON responses to Python Class with Attributes
Created classes for each object Monzo API currently supports. Utilising a simple, re-usable approach that simply maps JSON key/values to Python class attribute/values
Added some Current account specific features
Added support for Pots (Working on adding support for deposits/withdrawal), Watch this space.

Thanks
Neil

Thanks for the PR. I’ll check this out soon and get back to you with a proper review 🙂

@nmyster this looks pretty good to me :+1: — there are some tests that need to be fixed, and I'm happy to approve and merge.


Run tests on release

I am trying to package fortranformat for fedora, however I cannot run the tests for the pypi archives, as the Makefile is not included.
Also, there are no tags or releases on github, thus I cannot simply take a tarball from here.
Could you please tag your versions or provide some other mechanism to get releases with the bits for testing?

Hi, thanks for maintaining the package, ite's really appreciated.
I put source release in the dist folder. Do they need to be explicitly tagged? Do you need a .whl binary release as well?

A tag would be super useful :-)
https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository
I do not need anything in the dist/ folder (I have never seen that folder being tracked by git), just a tag for the version that ends up being released. https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository is a documentation on how to add tags.

Hi @dschwoerer I've included tags now. Please beware that running tests for older versions might not be easy or even possible. I had taken an approach where I wrote a script to auto-generate python test files for, frankly, too many variations of FORTRAN edit descriptors. This got a bit unwieldy and often the test suite wouldn't complete. If I remember correctly I was able to use nose (or maybe another tool?) to run the tests in batches however doing the whole suite in one go didn't work well.
More recent versions having a make runminimaltests command which are more targeted and written by hand. I would recommend running that where available.

Thanks :100:
That resolves my issue.
I will open a different issue about the failing tests.
The minimal / hand written tests all pass, thus I guess that is sufficient.
I do not intend to run the old tests or on old version, but mostly to ensure that fortranformat works well with the packages in fedora.


Fix link to shared Makefile source

The link to the shared Makefile source is broken.

Work for this was done in #20, but that was closed and I can't reopen it.

See 9161331cde3ac14491fd16439af83afaf664af68


make sure using the always tag for os-specific includes makes sense

wont the included tasks always be executed? or do they need tags as well?

adjusted with d6415ac


Remove references to liblog

In https://github.com/BrighterCommand/Docs/blob/master/contents/Logging.md we talk about liblog which was removed in V9

Killed the logging section, so that we can rewrite from scratch


Add public_asset_host method

This returns the GOVUK_ASSET_HOST, which is suitable for public
consumption. This will resolve to
https://assets.digital.cabinet-office.gov.uk in production.
This is mostly needed for Publishing apps like Whitehall to
differentiate between the Rails-style asset root used to serve JS and
CSS for Admin interfaces, versus the public CDN that they should
reference in content that is pushed to publishing-api.

Comments addressed, all up to date.


[FR] White labeling

Problem
A lot of companies do not want it to be known which software they use. Either for not letting their competitor know what they use or for security reasons.
Suggested solution
Removing all tags and graphics that identify InvenTree would be a great option.
Also hiding normal debug and version info from users should be an option.
Describe alternatives you've considered
This is nice to have.
Examples of other systems
Most 'big vendor' solutions come with a very reduced custom login page (that they charge for like they invented HTML). That should be enough.
Do you want to develop this?
Yes

Fair enough as a run-time configuration option!

Fair enough as a run-time configuration option!

I would phase it sometime after 0.7 - could you maybe add a 1.0 milestone for that? There is a ton to do before that gets important.

@SchrodingersGat I would start working on an option to remove any and every mention of inventree and all logos if that is ok with you. Should I go ahead for 0.7.0 or is this better for later?

0.7.0 would be fine for this


Update how-to-view-associated-resources-for-an-identity.md

Corrected code sample

Docs Build status updates of commit 92beb46:
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Details

articles/active-directory/managed-identities-azure-resources/how-to-view-associated-resources-for-an-identity.md
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For more details, please refer to the build report.
Note: Broken links written as relative paths are included in the above build report. For broken links written as absolute paths or external URLs, see the broken link report.
For any questions, please:Try searching the docs.microsoft.com contributor guidesPost your question in the Docs support channel

#sign-off


[Bug Report] menu or text inside Nav Menu Vertical not break into new line if character length more than wrapper width

Element UI version
2.9.1
OS/Browsers version
Google Chrome
Vue version
2.6.10
Reproduction Link
https://codepen.io/michaelchandrag/pen/MMbxVd?&editable=true
Steps to reproduce
Hi,
I create a Nav Menu Vertically using Element UI following this link https://element.eleme.io/#/en-US/component/menu.
However, when i have like a long-text menu, it didnt automatically break into new line or break-word
What is Expected?
If there are more character on the menu, then it should be break into new line or auto width based on the wrapper content
What is actually happening?
The word isnt break to a new line, but continously write as inline text

You can set CSS. Long text is not recommended.


2023.9.1: Add mode 5 for day, to the center, without leading 0

At @malinovsku request.

Why floating point operation?
Can you change this
if (mode == 5 && (d / 10 % 10) == 0) to
if (mode == 5 && (d < 10))?

Why floating point operation?

Sorry :) copy - paste :(

Can you change this

Changed :)


SSL certificates page lists some certificates as expired

Describe the bug
Just upgraded docker image from 2.7.1 to the latest (docker-compose pull; docker-compose down; docker-compose up -d).
When logging in I notice the SSL certificates page lists a number of certificates as expired, with an expiry date in the past. However, running certbot renew inside the image shows that the certificates are not due for renewal, and I have confirmed that the sites proxied have valid certificates that expire in the future.
Nginx Proxy Manager Version
2.9.3
To Reproduce
Steps to reproduce the behavior:

Go to SSL Certificates page
See certificates listed as expired
Run "docker exec -it nginx-proxy-manager_app_1 certbot renew"
See output processing all npm-N.conf files and indicating that the certificates are not due for renewal yet

Expected behavior
SSL Certificates page should match certbot renew command
Screenshots

Operating System
Ubuntu 18.04.5 LTS
Additional context
$  docker version
Client: Docker Engine - Community
Version:           19.03.13
API version:       1.40
Go version:        go1.13.15
Git commit:        4484c46d9d
Built:             Wed Sep 16 17:02:59 2020
OS/Arch:           linux/amd64
Experimental:      false
docker-compose.yml file:
version: "3"
services:
app:
image: 'jc21/nginx-proxy-manager:latest'
restart: always
ports:
# Public HTTP Port:
- '80:80'
# Public HTTPS Port:
- '443:443'
# Admin Web Port:
- '81:81'
environment:
# These are the settings to access your db
# DB_MYSQL_HOST: "db"
# DB_MYSQL_PORT: 3306
# DB_MYSQL_USER: "npm"
# DB_MYSQL_PASSWORD: "npm"
# DB_MYSQL_NAME: "npm"
# If you would rather use Sqlite uncomment this
# and remove all DB_MYSQL_* lines above
DB_SQLITE_FILE: "/data/database.sqlite"
# Uncomment this if IPv6 is not enabled on your host
# DISABLE_IPV6: 'true'
volumes:
- ./data:/data
- ./letsencrypt:/etc/letsencrypt
networks:
- reverseproxy-nw
networks:
reverseproxy-nw:
external: true

Duplicate of https://github.com/jc21/nginx-proxy-manager/issues/792


Do not wait for PVC to reach bound state

We currently wait until the associated PVC is bound before proceeding with further Glance component deployment.  This is a problem for WaitForFirstConsumer storage classes, however, as the consumer of the PVC is the PV that is created for the Glance pod -- but that PV won't be created until the pod is being created, and we're blocking that creation by waiting for the PVC to bind.  We should just create the PVC and move on instead, allowing the native k8s PVC/PV/Pod reconciliations to work themselves out.

I tested this PR and I no longer hit the problem I mentioned in the following with it. LGTM. Thanks.
https://github.com/openstack-k8s-operators/install_yamls/pull/23


Reconstructor fbp fdk

Reconstructor class extended for FBP, and cone-beam renamed to FDK.
CIL FBP is Filtering in C++ backend (with IPP) , back-projection with TIGRE
CIL FBP of 1800 1024x1024 radiographs and reconstruction volume 1024x1024x1024
time (s): 22.619497128063813
TIGRE FBP of 1800 1024x1024 radiographs and reconstruction volume 1024x1024x1024
time (s):<PHONE_NUMBER>780511
ASTRA FBP of 1024 1800x1024 radiographs and reconstruction volume 1024x1024x1024
time (s): 58.41945098794531
closes #1037

There is definitely overlap between it all. I think issue #926 (Slicer, Binner and Padder functionality could be method of DataContainer)  is a good idea. Maybe masker should be added to this, the mask could live alongside the dataset. It seems that anything that can act on any data-container could be a method and act in-place by default (which would also go some way to solving the CIL issue of many versions of the data in memory at once).
If we pull them out I think that just leaves acquisition specific processors: transmission-absorption, CofR and normalisation. I'm not sure it's necessary for them to be methods. Do something that acts on AcquisitionData and returns an AcquisitionData could be a preprocessor. I'm not sure that leaves any postprocessors, but maybe that's denoising processors similar to the reconstructors but act on AcquistionData.
Which means I think I'm arguing for processors to contain preprocessors (preprocessing?), reconstructors/recon and postprocessing/postprocessors.

Most of this is my fault. Initially I thought of the processors as a pipeline that has an origin, e.g. a reader, which ends with some result. The pipeline can be assembled by chaining processors in a way that one could run the whole pipeline as VTK does. In practice we've never done it this way and the complication added has always made the DataProcessor class a bit of a pain, really.
At any rate, currently we've got:

Processor
Role
Proposed organisation
notes

Binner
generic data manipulation
method of AcquisitionData

Slicer
generic data manipulation
method of AcquisitionData

Padder
generic data manipulation
method of AcquisitionData

MaskGenerator
outliers detection
method of AcquisitionData ??

Masker
outlier removal
method of AcquisitionData ??

Normaliser
Tomography pre-process
processor.preprocessing

TransmissionAbsorptionConverter
Tomography pre-process
processor.preprocessing
name is unclear to me

AbsorptionTransmissionConverter
Tomography pre-process
processor.preprocessing
name is unclear to me

CentreOfRotationCorrector
Tomography pre-process
processor.preprocessing
modifies metadata (inline)

RingRemover
Tomography pre/post processor
processor.preprocessing ???
Can be applied to ImageData and AcquisitionData

Reconstructor
Tomography reconstruction
processors.reconstruction
takes AcquisitionData and returns ImageData

However, after 4 years of development, I think we are currently seeing the potential use of the DataProcessor chaining, for instance in the GUI that we are developing. There you would experiment with some settings, and potentially one could export the pre-processing chain up to the reconstructor, I would say. The chain can be applied to different dataset.
If the processors would be able to operate inline, we would save memory resources, spending a bit of compute.

After discussing with @epapoutsellis @lauramurgatroyd @jakobsj we agreed that the following is a nice structure for forthcoming CIL with the reconstructor class being in the recon module.
In the future we will move the processors to other modules: prep and filters. The postprocessing module is not in the current plan as we don't have it in the code, but we could add it in the future.

from cil.recon import FDK, FBP, TV

from cil.prep import CentreOfRotationCorrector
from cil.prep import Normaliser
from cil.prep import TransmissionAbsorptionConverter
from cil.prep import AbsorptionTransmissionConverter

from cil.filters import Masker, MaskGenerator
from cil.filters import StripeRemover # currently is RingRemover
from cil.filters import Binner, Slicer, Padder # possibly be methods of DataContainer

Consensus achieved on not bloating DataContainer and/or ImageData, AcquisitionData with additional pre-processing specfic methods:
data.normalise()
data.find_center()

The actual name TV is to be decided, after #1030 and decision on the iterative reconstructor class #990 #430.

Added reset() method as discussed.

@jakobsj , @paskino This is ready to review when you get a chance


vCenter snapshots and tm_mad

Description
vCenter driver is not working like always when snapshots are used.
We need to make a solution when Vms are using snapshots and vCenter (tm_mad related: persistency, templates, terminate ...)
To Reproduce
Import a template, instantiate, make snapshots, terminate
import a template, instantiate as persistent, make snapshots, terminate...
import template, instantiate, add managed disk, make snapshot, detach managed disk
....
Details

Affected Component: TM_MAD vCenter
Hypervisor: vCenter
Version: development

Additional context
Add any other context about the problem here.

Progress Status

[ ] Branch created
[ ] Code committed to development branch
[ ] Testing - QA
[ ] Documentation
[ ] Release notes - resolved issues, compatibility, known issues
[ ] Code committed to upstream release/hotfix branches
[ ] Documentation committed to upstream release/hotfix branches

add to 5.8 known issues