Add NCBI taxonomy IDs to the rowData

Is your feature request related to a problem? Please describe.
cMD 3.0 serves TreeSummarizedExperiments based on Metaphlan clade names. For integration purposes with other data resources such as microbe signatures from BugSigDB, it is typically helpful to have them mapped to NCBI taxonomy IDs.
Describe the solution you'd like
A convenient solution from a user's perspective would be to have a column in the rowData that stores the NCBI taxonomy ID for each species. That is very similar to what we eg have in curatedOvarianData where datasets are based on gene symbols but mapping to NCBI Entrez Gene IDs is available in the fData of each dataset.
Describe alternatives you've considered
There are arguments to leave annotation  to the user. One could just point the user to the corresponding metaphlan mapping file or packages for ID conversion such as taxize. Especially less experienced users will however appreciate a way to easily map without taking those steps.
Additional context
Happy to help with this + can provide code / pull request if pointed to the place where the TreeSummarizedExperiments are assembled and additional annotations can be made.

Thanks @lgeistlinger! I think you are right, there is no reason to leave annotation to the user. Let's get it fixed by adding the mapping file from metaphlan – do you know where it is? Or do we need to create mapping annotations using taxize? Either way, could you take a look at data-raw/sysdata.R and add some lines there to read and save the file as an R object?

Yes we have metaphlan2.0 and metaphlan3.0 mapping files from Francesco, let me dig them up and take a look at data-raw/sysdata.R. Will report back.

Here's the NCBI taxid --> taxonomy map. This consider only the NCBI taxonomy ID of the species, let me know if you want the full taxonomy with the IDs for all the ranks
mpa_v30_taxonomy.txt

Thanks Francesco, yep the full file would be helpful as I currently think that we want to mirror the existing rowData columns
> se <- curatedMetagenomicData("AsnicarF_2017.relative_abundance", dryrun = FALSE)
> colnames(rowData(se[[1]]))
[1] "Kingdom" "Phylum"  "Class"   "Order"   "Family"  "Genus"   "Species"

storing taxonomic names for each taxonomic rank with the corresponding NCBI IDs for each taxonomic rank.

I have this file - so if this hasn't changed I have everything I need, Francesco: https://github.com/seandavi/MungeCuratedMGS/blob/master/inst/extdata/mpa_v30_CHOCOPhlAn_201901_taxonomy.txt.gz

> se <- curatedMetagenomicData("AsnicarF_2017.relative_abundance", dryrun = FALSE)
> colnames(rowData(se[[1]]))
[1] "Kingdom" "Phylum"  "Class"   "Order"   "Family"  "Genus"   "Species"

Note though that AFAIK cMD 3.0 only has rows corresponding to species, so the other columns refer only to ancestors and not to the species in the row itself (in other words, species is never missing, it is always the terminal node).

I think you do, having aggregation operations like those implemented by mia::splitByRanks in mind. You'd like to eg easily aggregate species counts to genus level, and intersect genus level NCBI IDs for the genus level with other data sources of interest (such as genus level signatures from BugSigDB using NCBI IDs).

Just checked checked back in here and will add a bit of clarification. Yes, only the species level clades remain in the object that is served to users. This would mean we could just do those mappings and depend on aggregate by rank to do the right thing as it moved up the taxonomy. (We should check that it modifies rowData as needed). Otherwise, we would need all levels (Class, Order, etc.) as stated by @lgeistlinger. If the files are handy, just import both and then we can check the behavior of aggregate by rank.

Hi. Just coming back to this. @schifferl: if I understand you correctly you just want to add
map.df <- readr::read_tsv("https://raw.githubusercontent.com/seandavi/MungeCuratedMGS/master/inst/extdata/mpa_v30_CHOCOPhlAn_201901_taxonomy.txt.gz", col_names = c("metaphlan", "ncbi"), col_types = "cc")

to data-raw/sysdata.R and take it on yourself from there. Any other input from my side needed?
Take a look at:
> head(map.df)
# A tibble: 6 x 2
  metaphlan                                            ncbi
  <chr>                                                <chr>
1 k__Bacteria|p__Proteobacteria|c__Deltaproteobacteri… 2|1224|28221||||1797814
2 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteri… 2|1224|28211|204458|7689…
3 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacill… 2|1239|91061|186826|3395…
4 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteri… 2|1224|28211|204457|4129…
5 k__Viruses|p__Viruses_unclassified|c__Viruses_uncla… 10239|||28883|10699|1299…
6 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__… 2|201174|1760|85007|1762…

My idea would have been to extract rank-level mapping from and and then map the existing cMD rowData columns (storing taxonomic names at each rank for each of the rows/species included in the dataset).
Not sure whether the mapping in the file is complete for all levels (but we could supplement that) and whether MungeCuratedMGS is really the right repo for hosting and pulling this file from (I had hoped for a central metaphlan data repo hosting this file @fbeghini).

After some discussion at the coordination meeting, this feature will be added by providing an additional argument to the curatedMetagenomicData method as follows.
Current:
curatedMetagenomicData(pattern, dryrun = TRUE, counts = FALSE)

Future:
curatedMetagenomicData(pattern, dryrun = TRUE, counts = FALSE, rownames = c("long", "short", "NCBI")

The rownames (long, short, and NCBI) will come from the MetaPhlAn tree file, which will be parsed into a mapping file (probably a data.frame). This design will allow users to choose rownames to suit their needs and will not interfere with mia:: splitByRanks or the command line interface. If there are any objections (@lgeistlinger, since you've asked for the feature), let me know; otherwise, I'll move ahead with the stated implementation shortly.

It sounds great. I'll be interested to see how mia::splitByRanks will work out, when choosing NCBI Ids as rownames. AFAIK that means for a species-level CMD dataset, that you will also need to have the NCBI IDs for the other ranks in the rowData (?) in order to get a genus-level dataset on NCBI IDs from altExps.

Hmm, this is a good point... Even with rownames = "NCBI" I guess the row name would come out as the "short" taxonomic clade (e.g. Bacteroidetes)  when running mia:: splitByRanks and then need to be mapped again. (The elements of the rowData table are always the names of clades in my scenario; only the row names change per the rownames argument). I would have to test this, but if it is the case, it would be better to provide users with a method to map the row names (as many times as needed). The method could then be integrated into the curatedMetagenomicData method or used independently. I'll experiment and report back.

@lgeistlinger this feature now exist in the rownames branch and is ready to be tried out. The implementation is as described above. For example to get the NCBI taxonomy IDs as the rownames for the AsnicarF_2017 relative_abundance data set, do the folllowing:
curatedMetagenomicData("AsnicarF_2017.relative_abundance", dryrun = FALSE, rownames = "NCBI")

The other choices for the rownames argument are "long" (the default) and "short" (the species name). Just needs to be tried out (@lgeistlinger) and documented/unit-tested (@schifferl) before merging into main.
FYI @lwaldron and @fbeghini too, since you were members of the converstation.
Also, this exposed what I think is a bug in TreeSummarizedExperiment because changing the rownames was not a simple rownames() <- and rather required the following.
base::rownames(tree_summarized_experiment) <-
    new_names

base::rownames(tree_summarized_experiment@rowLinks) <-
    new_names

If not fixed in TreeSummarizedExperiment it will make it difficult for users to update the rownames of any relative_abundance data type.
Finally, as to the previous comment – mia::splitByRanks still works as expected with rownames = "NCBI". The list of experiments returned changes the rownames to taxa and that seems like the correct behavior. If users wanted to map those to NCBI taxonomy, they would have to do so on their own using taxize. It's not such a big ask though because the rowData already contains the valid taxonomic names from NCBI (i.e. I didn't just split the names from the taxonomic tree; I mapped the entire hierarchy down the species-level). Anyway, please try this out and report back.

Maybe only my perspective, but it seems as if we are stopping halfway and end up a bit in a mixed state. I'd think it would be cool / very useful if somebody decides s/he likes to work on NCBI IDs that agglomeration options downstream would consistently return NCBI IDs too. For that to work, taxonomy rank columns in the rowData would need to be the corresponding NCBI IDs too. If the argument is users can use taxize for ID mapping, then there seems to be no rationale for including an option to return NCBI rownames. What do you think?

I’ll add that taxonomy names are a bit analogous to gene symbols, and NCBI
IDs are more analogous to Entrez IDs. Species names can change or be
re-assigned to other parts of the taxonomy, but IDs are much more stable.
These particular IDs are valuable if they are taken from MetaPhlAn
output, because they guarantee knowing exactly what was meant by that name.
If you look up names with taxize, there is no such future guarantee. So
it’s valuable to maintain the NCBI IDs from the MetaPhlAn data files
somewhere, but less valuable to provide taxize IDs.
The MetaPhlAn  output provides only species IDs, but looking up the rest of
the taxonomy from those IDs should be reliable. I tend to agree that if
rownames are IDs, it may be surprising / undesirable for those using them
to see reversion to (potentially aliased, moved, outdated) names after
splitByRank, and full use of IDs would be more consistent. But that’s only
an inconvenience, not providing the original MetaPhlAn NCBI IDs anywhere in
the package is information loss that could necessitate future sleuthing to
recover. (sub-note, I guess this must not be a huge deal though, since
previous versions of MetaPhlAn didn’t include NCBI IDs in the data files).
--
Levi Waldron
Associate Professor
Department of Epidemiology and Biostatistics
CUNY Graduate School of Public Health and Health Policy
Institute for Implementation Science in Population Health
55 W 125th St, New York NY 10035
https://waldronlab.io
Join the microbiome Virtual International Forum: https://microbiome-vif.org

Just to be extra clear, this is the way rowData is currently returned per the implementation, given rownames argument.

rownames = "long"

superkingdom
...
species

k__Bacteria|p__Spirochaetes...
Bacteria
...
Treponema lecithinolyticum

...
...
...
...

k__Bacteria|p__Spirochaetes...
Bacteria
...
Treponema bryantii

rownames = "short"

superkingdom
...
species

Treponema lecithinolyticum
Bacteria
...
Treponema lecithinolyticum

...
...
...
...

Treponema bryantii
Bacteria
...
Treponema bryantii

rownames = "NCBI"

superkingdom
...
species

53418
Bacteria
...

Treponema bryantii

The suggestion is that for rownames = "NCBI" the rowData should look like this instead.
rownames = "NCBI"

superkingdom
...
species

53418
2
...
53418

...
...
...
...

163
2
...
163

I don't know that I'm convinced of this design yet, and it doesn't really coincide with the rownames argument to be certain. To achieve the desired result without completely removing the clade names from the rowData, a data.frame of mappings could be exposed to users. In my mind, it would look like this:

txid
level
name

2
superkingdom
Bacteria

163
species
Treponema bryantii

53418
species
Treponema lecithinolyticum

This data.frame would come from @fbeghini's mappings above:

Here's the NCBI taxid --> taxonomy map. This consider only the NCBI taxonomy ID of the species, let me know if you want the full taxonomy with the IDs for all the ranks
mpa_v30_taxonomy.txt

Just that I wonder about the provenance of this file and think the MetaPhlAn repo might be a better place for it, so it's maintained long-term and we don't receive issues that our taxonomy is out of date. If it were there, I would just download and process it into the mapping data.frame, which would be used to provide the rowData per the current implementation and allow users to do mappings of their own after mia::splitByRanks.
If the file is there, like the phylogenetic tree is, most of the programming is already done and we can do updates easily in the future.

The suggestion is that for rownames = "NCBI" the rowData should look like this instead.

Exactly. I am noting that there would be alternatives to completely stripping off the clade names from the rowData, and rather just add ".NCBI" columns such as "species.NCBI", "genus.NCBI". Those ".NCBI" columns could then be registered by modifying taxonomyRanks of the TreeSE when rownames = NCBI is chosen.

Just that I wonder about the provenance of this file and think the MetaPhlAn repo might be a better place for it, so it's maintained long-term and we don't receive issues that our taxonomy is out of date

Fully with you on this one.

I couldn't believe that the NCBI taxonomy hasn't been wrapped in one way or another into Bioconductor annotation resources. After a bit of search, I think mapping from GenomeInfoDbData comes close to what we are looking for.
library(GenomeInfoDbData)
data(specData)
> head(specData)
  tax_id        genus     species
1      1          all        <NA>
2      1         root        <NA>
3      2     Bacteria        <NA>
4      6 Azorhizobium        <NA>
5      7 Azorhizobium caulinodans
6      9     Buchnera  aphidicola
> dim(specData)
[1] 2521271       3
> subset(specData, c(genus == "Escherichia" & species ==" coli"))$tax_id
[1] 562

They only include genus and species in a somewhat simplified/incorrect way in that table (eg bacteria = genus), but there is a
script that extracts this table from the full dump of the NCBI Taxonomy, that we could extend via a pull request to pull out also the other taxonomic ranks. Do we think that this is worth a try, or are we better off having a file laying around somewhere? My hope with a Bioconductor annotation package such as GenomeInfoDbData would be that it comes with provenance and regular updates that we need.

That sounds like a great idea @lgeistlinger, having the full and correct NCBI taxonomy seems like an obvious omission and correcting it would have value for us and others. I'll post a question on bioc-devel about whether to update or add.

Hi all, just chiming in because while in MetaPhlAn 2 we provide in the
output only the species-level NCBI IDs, we do have all the internal IDs and
in MetaPhlAn version >2 we report them as well in the output. For MetaPhlAn
2 we can provide all the IDs. Because of the problems Ludwig was observing
in the NCBI hierarchical taxonomy, in all MetaPhlAn versions we edited the
taxonomy to derive a hierarchy with a fixed number of levels (from phyla
p__ to species s__) and to fill in the missing ones. Having a fixed number
of levels is important otherwise when summing up abundances at levels
higher than the species it becomes difficult to interpret. I would thus
suggest getting all the NCBI taxonomy from MetaPhlAn, it is going to be
super easy for version >2 (and doable for version 2)
Nicola
On Sun, Aug 8, 2021 at 8:00 PM Levi Waldron @.***>
wrote:

That sounds like a great idea @lgeistlinger
https://github.com/lgeistlinger, having the full and correct NCBI
taxonomy seems like an obvious omission and correcting it would have value
for us and others. I'll post a question on bioc-devel about whether to
update or add.
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Thanks @nsegata! I agree that for curatedMetagenomicData, this cleanup indicates we should be using a map from MetaPhlAn. Would you mind publicly posting this file along with versions indicating which versions of MetaPhlAn it should be used with?
@lgeistlinger having the full NCBI taxonomy in Bioconductor may still be useful for bugsigdb, which is full of modifiers that aren't relevant for MetaPhlAn ("Unclassified" genera and family, sp., species missing a genus, etc).

Sure, @Francesco Beghini @.> and @Aitor Blanco
@.> should have the whole taxonomic tree to
provide for MetaPhlAn 3 and >3 respectively. For MetaPhlAn 2 maybe @Paolo
Manghi @.> or @@.
@.***> can locate it?
On Tue, Aug 10, 2021 at 10:30 AM Levi Waldron @.***>
wrote:

Thanks @nsegata https://github.com/nsegata! I agree that for
curatedMetagenomicData, this cleanup indicates we should be using a map
from MetaPhlAn. Would you mind publicly posting this file along with
versions indicating which versions of MetaPhlAn it should be used with?
@lgeistlinger https://github.com/lgeistlinger having the full NCBI
taxonomy in Bioconductor may still be useful for bugsigdb, which is full of
modifiers that aren't relevant for MetaPhlAn ("Unclassified" genera and
family, sp., species missing a genus, etc).
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@fbeghini @paolinomanghi see above, I think your handles got munged.

Thank you all for all the comments, it's pretty clear on my end how to handle this now. If @fbeghini puts the mpa_v30_taxonomy.txt file into the MetaPhlAn repo, I can take it from there and get this finished.
And just to clarify on @lgeistlinger's comment about annotation resources:

Do we think that this is worth a try, or are we better off having a file laying around somewhere? My hope with a Bioconductor annotation package such as GenomeInfoDbData would be that it comes with provenance and regular updates that we need.

Both, because I want the exact mapping from MetaPhlAn and something to check them against too.

Sorry, one more comment. We can keep that file, mpa_v30_taxonomy.txt, in our repo if we really need too. Just that @fbeghini (or someone else who knows how to update it) would have to maintain it for us.

Sorry, one more comment. We can keep that file, mpa_v30_taxonomy.txt, in our repo if we really need too. Just that @fbeghini (or someone else who knows how to update it) would have to maintain it for us.

@schifferl, no problem, there should not be any updates for this release, so the IDs will not change. The file can be easily generated by loading the pkl file and inspecting the ['taxonomy'] field.

Both, because I want the exact mapping from MetaPhlAn and something to check them against too.

Hi @schifferl: I agree that the metaphlan3 file from Franceso is the reference point (likely with edge cases resolved), but here is a script that maps metaphlan3 taxonomic clades to NCBI taxonomy IDs and returns a 3-column data.frame (txid, level, name) as per your specification. Can pull request if that's convenient, but you might want to work it into the repo in a way that you see fit best. Hope that helps.

Awesome @schiffer!!

If you notice any issues, just let me know; otherwise, I'll close the issue in the next day or so. If you care about the specifics of the implementation, you can study the files in the data-raw directory. Finally, the feature brought to my attention one other change I'd like to suggest for MetaPhlAn3: the Newick tree file should be stored with the other CHOCOPhlAn files on Zenodo. Essentially, I'd like the second line of phylogeneticTree.R and rowData.R coming from the same place, just for consistency. Let me know if that's possible @fbeghini and I'll make the changes to cMD once it's done. Anyway, hope you're all happy with the feature and let me know if there's anything else.

@schifferl  I updated the Zenodo record with the Newick tree, here's the new link https://zenodo.org/record/5668382

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I suppose that I got this message by mistake.
Best regards,
J.Schiffer
----- Ursprüngliche Nachricht -----
Von: Francesco Beghini @.>
Datum: 10.11.2021 17:20
An: waldronlab/curatedMetagenomicData @.>
Kopie: schiffer @.>, Mention @.>
Betreff: Re: [waldronlab/curatedMetagenomicData] add NCBI taxonomy IDs to the rowData (#245)

If you notice any issues, just let me know; otherwise, I'll close the issue in the next day or so. If you care about the specifics of the implementation, you can study the files in the data-raw directory. Finally, the feature brought to my attention one other change I'd like to suggest for MetaPhlAn3: the Newick tree file should be stored with the other CHOCOPhlAn files on Zenodo. Essentially, I'd like the second line of phylogeneticTree.R and rowData.R coming from the same place, just for consistency. Let me know if that's possible @fbeghini and I'll make the changes to cMD once it's done. Anyway, hope you're all happy with the feature and let me know if there's anything else.
@schifferl I updated the Zenodo record with the Newick tree, here's the new link https://zenodo.org/record/5668382
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Publish mc-build-rs crate

[x] Add unit tests for Environment

[x] https://github.com/mobilecoinfoundation/build-rs/pull/10

https://crates.io/crates/mc-build-rs


support tsvector columns for Postgres fulltext search

Problem
See https://github.com/prisma/prisma/issues/8950#issuecomment-1067395682 a search runs 1,000x faster with a tsvector column with an index, when compared to the "TEXT" field with an GIN index approach you currently recommend (which does not use the index due to the bug linked)
Suggested solution
Support tsvector columns
Alternatives
None
Additional context
n/a

That's actually one of my proposed solution, using a tsvector stored generated column from one or more column + index
https://github.com/prisma/prisma/issues/8950#issuecomment-982915628

I know, @janpio  told me to open a new feature request and they view this as different issue, but I see it as same issue. Prisma is slow is the only issue from my perspective. I do not care how it gets solved as long as it is no longer slow :)

As I added onto https://github.com/prisma/prisma/issues/5027#issuecomment-1067422323, it appears the suggested workaround does not work either.

Here's the workaround I used for now:
-- AlterTable
ALTER TABLE "products" ADD COLUMN     "indexed_name" tsvector DEFAULT ''::tsvector;
CREATE INDEX products_indexed_name ON products USING GIN indexed_name);

const myQuery = 'foo':*
const query = `SELECT id from products where indexed_name @@ to_tsquery(${myQuery})`; // important, do not select indexed_name!
const res = await prisma.$queryRawUnsafe(query);
// use Prisma to hydrate the IDs

Hello everyone 👋
We are starting design work to improve Prisma's support for Full Text Search (FTS)!
If you would like to help, please help us learn about your needs via a short FTS user research survey.
Thank you!

Hello @joshribakoff-sm,
I just read the solution you are proposing which seems interesting.
I have a model with multi language field title.
I need to enable full text search based on user language cookie.
If the cookie has spanish, and the user types a spanish keyword, i need to point Prisma to use the Spanish FTS index and Use Ts_vector spanish.
Can you help with the implementation ?
I opened a full issue about this on #14749

Has anyone here succesfully managed to coax Prisma into working efficiently with PG full text search, even if the actual tfvector column  /index is hand added to a migration?
If I could manually add a stored generated tfvector column and have prisma treat it like a string that can be fulltext searched with search in a query that would be good enough to unblock me for now without having to handwrite queries


[Bug]: JSeditor : Prettify for given code is not working properly

Is there an existing issue for this?

[X] I have searched the existing issues

Description
For below code snippet prettify code does not work properly
Recording - https://www.loom.com/share/19017c4971a649c988c4e5fb951958f4
simplify :()=> {
return Api2.run()
.then(async ()=>{
await showAlert('test1'),
await console.log('test2'),
await console.log('test3')})
},
}
[Environment - https://app.appsmith.com/app
Browser - Chrome ]
Steps To Reproduce

Navigate to JSeditor
Write below code snippet
Use Prettify code option for the code

simplify :()=> {
return Api2.run()
.then(async ()=>{
await showAlert('test1'),
await console.log('test2'),
await console.log('test3')})
},
}
Expected:
simplify: () => {
return Api2.run()
.then(async () => {
await showAlert('test1'),
await console.log('test2'),
await console.log('test3')
})
},
}
Public Sample App
https://app.appsmith.com/app
Version
cloud

works ok now


Not utilizing multiple GPU's even when batch size is changed.

Hi, I've changed my batch size to 128, 256, 512, 1024, 2048 (I get an OOM above 1000) none of them seem to utilize any but one of the GPU's. Tensorflow see's the other GPU's and so does Nvidia-SMI. I'm using 4x Nvidia Tesla P100's.
Nvidia-SMI:

Is this an issue on my part or something else?

Hi, @dr-mccoy
You are right. That's expected behavior: the implementation utilizes the compute ability of only the first GPU, with the memories from all GPUs. The original implementation supported model parallelism, but in a two-GPU case, it was even slower to train. In your case with 4 GPUs, you can probably try data parallelism. If you have a solution for that, please share with us.

Ah okay, thought I was going crazy. I'm going to stay with one GPU for the moment in that case. Will look into data parallelism on a later date.


Crawlab Pro task logs are stuck after certain time even if underlying task keeps executing.

Describe the bug
Task logs stop updating after certain amount of time even though underlying task keeps executing correctly and docker logs show steady output of them.
To Reproduce
Steps to reproduce the behavior:

Run task that executes for long time
Wait for several hours
Task stops outputting logs despite still running correctly without any errors

Expected behavior
Task keeps outputting logs for as long as task is being executed.

Is there any error in the docker logs?

There are no errors in docker logs for either worker or master node. The only logs are about the task starting and constant output of what is shown on the screenshot in main post until the task ends with log "task finished successfully".

前端一直显示日志是否可以有个阀值，clear 旧的日志信息


dataurl not updated when leaving drawing area

If you use the demo in Google Chrome and start drawing in de canvas but leave the canvas area while still holding the mouse down, the dataurl is not updated so when you click the "sign" button the image is empty. Any solutions for this?

same for me

I can't reproduce it. I mean at some point I need to release mouse button to actually click the "Save" button.


HttpInputStream -> ArgumentNullException

Hi there,
i getting an error while passing an HttpInputStream to the ExcelReaderFactory.CreateOpenXmlReader(Stream) method.
The file comes from an Mvc application which posts a file to a System.Web.HttpInputStream (canread/canseek = true)
=> https://msdn.microsoft.com/en-us/library/system.web.httppostedfile.inputstream(v=vs.110).aspx
Stack:
bei Excel.Core.OpenXmlFormat.XlsxWorkbook..ctor(Stream workbookStream, Stream relsStream, Stream sharedStringsStream, Stream stylesStream) in c:\development\ExcelDataReader\Excel\Core\OpenXmlFormat\XlsxWorkbook.cs:Zeile 30.
bei Excel.ExcelOpenXmlReader.ReadGlobals() in c:\development\ExcelDataReader\Excel\ExcelOpenXmlReader.cs:Zeile 58.
bei Excel.ExcelOpenXmlReader.Initialize(Stream fileStream) in c:\development\ExcelDataReader\Excel\ExcelOpenXmlReader.cs:Zeile 345.
bei Excel.ExcelReaderFactory.CreateOpenXmlReader(Stream fileStream) in c:\development\ExcelDataReader\Excel\ExcelReaderFactory.cs:Zeile 74.
bei *.Shared.ExcelManager.GetReaderForFile(Stream stream, String filename) in
[...]
Lib from NuGet V. <IP_ADDRESS>, runtime version v4.0.30319 (packages\ExcelDataReader.<IP_ADDRESS>\lib\net45\Excel.dll)
Do you have any idea, why this error occurs?
If i open that file with a manual instantiated System.IO.Stream the method works properly and i am getting the correct output.
So there is maybe an error while working with the HttpInputStream.
Thanks in advance for any idea to solve the problem.
Kind regards.
MS

I'm fairly sure HttpInputStream is canseek = false. So the best bet is to copy it to a memory stream first.


Little Bug - only comparing first char

Hi Amrani,
thanks for your project - I love it!
I think I found a little bug: Because of the [0] this function compares only the first char of each string - so two table names with equal first letters would return true.
private function check(array $request)     {         return $request['table1'][0] == $request['table2'][0] ? true : false;     }
it should be:
private function check(array $request)     {         return $request['table1'] == $request['table2'] ? true : false;     }
https://github.com/amranidev/scaffold-interface/blob/master/src/Http/Controllers/GuiController.php#L275

@osthafen
Fixed in (v1.7.1)
Thank you so much for your request, I really appreciate it.
cheers!!


nixos/modules/services/hardware/u2f: init

Motivation for this change
Yubikeys requires special hidraw device permissions to be usable in eg Chrome.
Things done

[x] Tested using sandboxing (nix.useSandbox on NixOS, or option build-use-sandbox in nix.conf on non-NixOS)
Built on platform(s)

[x] NixOS
[ ] macOS
[ ] other Linux distributions

[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
[ ] Tested execution of all binary files (usually in ./result/bin/)
[x] Fits CONTRIBUTING.md.

Thanks @bjornfor, tested again and everything seems to work after unplugging and replugging the device.

Thank you! I've been wondering how to get my yubikey working for ages. I didn't know about services.udev.packages. Having this option will be great to improve discoverability.

Applied to master (5a5325d11f3ed8373b6abbecbe8b4cebf91a9390). Thanks!


How do I convert a curve point into a public key?

If I have an x25519 curve point (say, returned from hashToCurve from "npm:@noble/curves/ed25519"), how do I convert it into a corresponding ed25519 public key? Does curvePoint.toRawBytes() yield the public key, or something else? I cannot find any documentation on what exactly toRawBytes actually returns.

x25519 (curve25519) is a different curve from ed25519. they are used for different cases
“Does curvePoint.toRawBytes() yield the public key, or something else?” - nope. It simply returns the encoded point.
hashToCurve does not really “encode to public key”. it encodes to point

can you clarify what’s your use case?

Thank you both for your replies 💜
@nflatrea Yes, if this is not implemented by noble, we'll just have to implement that part of the ed25519 spec ourselves. I was simply hoping to get around that.
@paulmillr Good point asking for clarification, We might not actually need this.
TLDR: We need to somehow transmit curve points over the wire, and converting them into public keys seems like a well-specified and widely-implemented choice.
There are two independent use-cases: We want to use curve25519 for a multiset-homomorphic hash function, and we want to use curve25519 to implement private equality testing.
For the homomorphic hash function, the underlying idea is simple: to hash a set of items, hash every individual item into the curve (via curve25519XMD:SHA-512_ELL2_RO, i.e., hashToCurve), then add the curve points together to obtain the hash of the set. But then, as a final step, we need to transmit the result over the wire. To do so, we need to encode the curve point into a sequence of bytes. My impression was that converting it into a public key would be a convenient choice of encoding, since that conversion would be part of the curve25519 spec, and hence widely implemented.
In principle, we could also just use noble's toRawBytes, but we would need to specify the exact behavior, not just refer to a javascript function that does not precisely specify what it does - this is for writing a specification (draft state), not just for hacking on a codebase.
For the privat equality testing part, two peers need to exchange curve points and perform scalar multiplication on them, which again requires encoding them over the wire. Since crypto libraries often implement scalar multiplication functions that take an encoded public key as input (or at least, some raw byte array and not a curve point struct, compare, e.g., libsodium scalar_mult), it again seemed sensible to simply exchange public keys over the wire. But before we can do that, we must first hash the items for which we want to test for set intersection into the curve. Which is again a job for RFC9380, but leaves us with a curve point that we now need to encode into a public key to send to the other peer.
Here again, we don't necessarily need to use public keys. We could also specify our own encoding of curve points, send that over the wire, and the other peer could decode and do scalar multiplication (with APIs that operate on actual curve points and scalars, not keys).

well, all ed25519 pubkeys are encoded in a way that is specified in toRawBytes. so it is a “public key”. it’s just that a concept of public key is different from a concept of point. public key has a specific private key
but again you need curve25519, not ed25519


Improve multi-class model reloading

Loading a multi-class model requires you to know the label dict and preset the classes, this is cumbersome.
If you use main.save_model and are loading a multi_class model, it requires you to create a new object, since main.deepforest() instantiates a deepforest single class model by default.
TRAINED_MODEL = "/blue/ewhite/everglades/Zooniverse/20211215_112228/species_model.pl"
train = pd.read_csv("/blue/ewhite/everglades/Zooniverse/parsed_images/species_train.csv")
label_dict = {key:value for value, key in enumerate(train.label.unique())}
m = main.deepforest(num_classes=len(label_dict), label_dict=label_dict)
m.load_state_dict(torch.load(TRAINED_MODEL, map_location="cpu")["state_dict"])

In the mean time the docs need to be clearer.

:+1: I've been running into this issue as well.

Added to docs.
Loading a multi_class model which was saved using main.save_model is currently somewhat cumbersome (see https://github.com/weecology/DeepForest/issues/287).
The easiest way is to create a new deepforest object and preset the number of classes and label dict, just as you did during training.
import pandas as pd

TRAINED_MODEL = "/blue/ewhite/everglades/Zooniverse/20211215_112228/species_model.pl"
train = pd.read_csv("/blue/ewhite/everglades/Zooniverse/parsed_images/species_train.csv")
label_dict = {key:value for value, key in enumerate(train.label.unique())}
m = main.deepforest(num_classes=len(label_dict), label_dict=label_dict)
m.load_state_dict(torch.load(TRAINED_MODEL, map_location="cpu")["state_dict"])

Yeah, I had done what you did, just echoing that I think making it easier is important.

https://pytorch-lightning.readthedocs.io/en/latest/common/hyperparameters.html is somewhere in the right direction.


how can I get the kubeconfig file without Rancher Auth-proxy?

often we create a k8s cluster by using Rancher UI, that's easy. And we can also download the kubeconfig file on the cluster level easily.
but my question is, the kubeconfig file on Rancher UI we can get is a Rancher Auth-Proxy kubeconfig file, that means, if the rancher server is down, we can not control our k8s cluster anymore.
I know that we can get the kubecfg-kube-admin.yaml file in the path /etc/kubernetes/ssl or /etc/kubernetes/.tmp of the rancher-node-agent pod, but acturally, not every time the yaml file is exists there. that makes me very confused. cuz if my Rancher Server is down, I recreate a rancher server, but without the original kubeconfig file, I can not reimport the k8s cluster to the new rancher server again.
is there any convinent way to get the orignal kubeconfig file directly connected to the k8s apiserver without rancher-auth-proxy?
or can you add a new button on Rancher UI for us to download such a file easier? thanks.
@loganhz

@satomic "Make clusters reachable without master" feature will be available in rancher 2.2. Here is the ticket for the ref:
https://github.com/rancher/rancher/issues/13698

@alena1108 cool, thanks! can not wait for the 2.2 GA anymore

@satomic np! Closing the issue as a duplicate of 13698


Esp-Idf examples

Hi,
Do you have examples of using this with esp-idf.  All the examples look to be .ino (arduino).
I am not familiar with Arduino so having trouble getting SensorQMI8658 working.
Thanks,

Please ignore this - just found https://github.com/lewisxhe/SensorLib/tree/master/examples/ESP_IDF_TouchDrv_Example/main


ERROR CODE: Subscription Not Registered exception

Expected Behavior
azqr should not failed if provider for a service is not registered.
Actual Behavior
azqr fails with exception: ERROR CODE: Subscription Not Registered exception

Closed by #59


yargs-parser vulnerability

gulp > gulp-cli > yargs > yargs-parser
gulp-nodemon > gulp > gulp-cli > yargs > yargs-parser
https://www.npmjs.com/advisories/1500
Overview
Affected versions of yargs-parser are vulnerable to prototype pollution. Arguments are not properly sanitized, allowing an attacker to modify the prototype of Object, causing the addition or modification of an existing property that will exist on all objects.
Parsing the argument --foo.__proto__.bar baz' adds a bar property with value baz to all objects. This is only exploitable if attackers have control over the arguments being passed to yargs-parser.

Remediation
Upgrade to versions 13.1.2, 15.0.1, 18.1.1 or later.

That's a breaking change. We are currently working towards an update.

@phated Could you please reopen the issue so that we can track the progress, or maybe guide us to other issue/PR!


User credentials in login should be used to launch pre-populated Tray login

I realized that I have to enter the same login and password twice with the launcher. Once with the launcher, and afterward with the tray. Perhaps launcher can automatically launch the tray in the end and enter user parameters.

Duplicate of #222, which is invalid and can't be implemented


Remove unused counter visits from workload detail templates

visits counter in the workload detail template is neither used for calculating performance metrics nor is it exported. It can be removed to enhance the performance of workload detail metrics collection.

Verified on 24.05.0 commit 74dcf38a


feat: add overwrite confirmation when genesis file is existed

Overview

This PR add support for displaying cover confirmation prompt to user when genesis file is existed

New Features

Addition of displaying overwrite confirmation prompt to user when genesis file is existed
Addition of a new bool flag yes, used to Skip overwrite confirmation prompt when genesis.json is existed(in order to compatible with some old scripts)

Screenshots

Thanks for the contribution! Is this feature something you want or has someone else requested it?
Is it possible to refactor the implementation to reduce the amount of indentation?

I ran celestia-appd download-genesis for testing, and found
celestia-appd download-genesis celestia or
celestia-appd download-genesis mocha-4 or
celestia-appd download-genesis  arabica-10
will use the same path ~/.celestia-app/config/genesis.json. So I think it would be better to prompt user for this confirmation.

@rootulp Hi sir, just tried and didn't find the way to reduce the amount of indentation, like check file stat _, err := os.Stat(outputFile) no matter --yes is provided, but this will lead to extra io.
Could u please give me some suggestions😀

Going to close this based on Evan's last comment.
Note in response to @Halimao's https://github.com/celestiaorg/celestia-app/pull/2967#issuecomment-1870836008, I think a user could work around this by specifying a home directory:
$ celestia-appd download-genesis mocha-4 --home ~/.celestia-app-mocha
Downloading genesis file for mocha-4 to /Users/rootulp/.celestia-app-mocha/config/genesis.json
Downloaded genesis file for mocha-4 to /Users/rootulp/.celestia-app-mocha/config/genesis.json
SHA-256 hash verified for mocha-4

$ celestia-appd download-genesis arabica-10 --home ~/.celestia-app-arabica
Downloading genesis file for arabica-10 to /Users/rootulp/.celestia-app-arabica/config/genesis.json
Downloaded genesis file for arabica-10 to /Users/rootulp/.celestia-app-arabica/config/genesis.json
SHA-256 hash verified for arabica-10


vendor: updated jwt-go to 3.0.0. Also fixed a few go vet issues.

This is in reply to #229.
WIP: This uses the current HEAD ref in .glide for Fosite. This MUST be changed to a semantic version of Fosite prior to accepting this PR.
NOTE: Untested

ah right, the error is because the client does not have the privilege to access the warden api which was previously possible due to my mistake which @faxal solved here: https://github.com/ory-am/fosite/commit/7faee6bbd53ee762ddfe194fb2ea5e7d0205e46d
this is now #232


[tool_crash] RangeError: RangeError (index): Invalid value: Valid value range is empty: 0

Command
flutter --no-color pub get

Steps to Reproduce

...
...
...

Logs
RangeError: RangeError (index): Invalid value: Valid value range is empty: 0
#0      _StringBase.[] (dart:core-patch/string_patch.dart:260:41)
#1      LocalizationsGenerator._isValidGetterAndMethodName (package:flutter_tools/src/localizations/gen_l10n.dart:1048:13)
#2      LocalizationsGenerator.loadResources (package:flutter_tools/src/localizations/gen_l10n.dart:1073:12)
#3      generateLocalizations (package:flutter_tools/src/localizations/gen_l10n.dart:68:9)
#4      GenerateLocalizationsTarget.build (package:flutter_tools/src/build_system/targets/localizations.dart:56:5)
#5      _BuildInstance._invokeInternal (package:flutter_tools/src/build_system/build_system.dart:839:27)
<asynchronous suspension>
#6      FlutterBuildSystem.build (package:flutter_tools/src/build_system/build_system.dart:606:16)
<asynchronous suspension>
#7      generateLocalizationsSyntheticPackage (package:flutter_tools/src/dart/generate_synthetic_packages.dart:58:30)
<asynchronous suspension>
#8      PackagesGetCommand._runPubGet (package:flutter_tools/src/commands/packages.dart:133:7)
<asynchronous suspension>
#9      PackagesGetCommand.runCommand (package:flutter_tools/src/commands/packages.dart:176:5)
<asynchronous suspension>
#10     FlutterCommand.run.<anonymous closure> (package:flutter_tools/src/runner/flutter_command.dart:1165:27)
<asynchronous suspension>
#11     AppContext.run.<anonymous closure> (package:flutter_tools/src/base/context.dart:150:19)
<asynchronous suspension>
#12     CommandRunner.runCommand (package:args/command_runner.dart:209:13)
<asynchronous suspension>
#13     FlutterCommandRunner.runCommand.<anonymous closure> (package:flutter_tools/src/runner/flutter_command_runner.dart:281:9)
<asynchronous suspension>
#14     AppContext.run.<anonymous closure> (package:flutter_tools/src/base/context.dart:150:19)
<asynchronous suspension>

[✓] Flutter (Channel beta, 2.11.0-0.1.pre, on Microsoft Windows [Version 10.0.19043.1526], locale en-IN)
    • Flutter version 2.11.0-0.1.pre at C:\flut\flutter
    • Upstream repository https://github.com/flutter/flutter.git
    • Framework revision b101bfe32f (3 weeks ago), 2022-02-16 07:36:54 -0800
    • Engine revision e355993572
    • Dart version 2.17.0 (build 2.17.0-69.2.beta)
    • DevTools version 2.10.0-dev.1

[✓] Android toolchain - develop for Android devices (Android SDK version 29.0.2)
    • Android SDK at C:\Users\HP\AppData\Local\Android\sdk
    • Platform android-31, build-tools 29.0.2
    • Java binary at: C:\Program Files\Android\Android Studio\jre\bin\java
    • Java version OpenJDK Runtime Environment (build 11.0.10+0-b96-7249189)
    • All Android licenses accepted.

[✓] Chrome - develop for the web
    • Chrome at C:\Program Files\Google\Chrome\Application\chrome.exe

[!] Visual Studio - develop for Windows (Visual Studio Build Tools 2019 16.11.5)
    • Visual Studio at C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools
    • Visual Studio Build Tools 2019 version 16.11.31729.503
    ✗ The current Visual Studio installation is incomplete. Please reinstall Visual Studio.

[✓] Android Studio (version 2020.3)
    • Android Studio at C:\Program Files\Android\Android Studio
    • Flutter plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/9212-flutter
    • Dart plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/6351-dart
    • Java version OpenJDK Runtime Environment (build 11.0.10+0-b96-7249189)

[✓] VS Code (version 1.64.2)
    • VS Code at C:\Users\HP\AppData\Local\Programs\Microsoft VS Code
    • Flutter extension version 3.34.0

[✓] Connected device (3 available)
    • Windows (desktop) • windows • windows-x64    • Microsoft Windows [Version 10.0.19043.1526]
    • Chrome (web)      • chrome  • web-javascript • Google Chrome 98.0.4758.102
    • Edge (web)        • edge    • web-javascript • Microsoft Edge 99.0.1150.30

[☠] HTTP Host Availability (the doctor check crashed)
    ✗ Due to an error, the doctor check did not complete. If the error message below is not helpful, please let us know about this issue at https://github.com/flutter/flutter/issues.
    ✗ HandshakeException: Connection terminated during handshake
    •

! Doctor found issues in 2 categories.

Flutter Application Metadata
Type: malformed
Version: 1.0.0+5
Material: true
Android X: false
Module: false
Plugin: false
Android package: null
iOS bundle identifier: null
Creation channel: null
Creation framework version: null
Plugins
audio_session-0.1.6+1
device_info-2.0.3
file_picker-4.2.7
firebase_core-1.10.5
firebase_core_web-1.5.2
firebase_messaging-10.0.9
firebase_messaging_web-2.2.4
flutter_local_notifications-8.2.0
flutter_plugin_android_lifecycle-2.0.5
fluttertoast-8.0.8
geocoding-2.0.1
geolocator-7.7.1
geolocator_android-2.1.0
geolocator_apple-1.2.2
geolocator_web-2.0.6
google_maps_flutter-2.1.1
image_picker-0.8.4+4
image_picker_for_web-2.1.4
just_audio-0.7.5
just_audio_web-0.3.2
location-4.3.0
location_web-3.1.1
open_file-3.2.1
path_provider-2.0.8
path_provider_android-2.0.9
path_provider_ios-2.0.7
path_provider_linux-2.1.4
path_provider_macos-2.0.4
path_provider_windows-2.0.4
permission_handler-8.3.0
record-3.0.2
record_web-0.2.1
shared_preferences-2.0.11
shared_preferences_android-2.0.9
shared_preferences_ios-2.0.8
shared_preferences_linux-2.0.3
shared_preferences_macos-2.0.2
shared_preferences_web-2.0.2
shared_preferences_windows-2.0.3
url_launcher-6.0.17
url_launcher_android-6.0.13
url_launcher_ios-6.0.13
url_launcher_linux-2.0.2
url_launcher_macos-2.0.2
url_launcher_web-2.0.5
url_launcher_windows-2.0.2

Fixed it by prepending @ to the key for .arb key.
{
"@mykey":"somevalue"
}
Author -- https://github.com/Stinox22


Provide eclipse.classpath.outputBaseDir

Gradle uses separate output folders for each source folder since 4.4. They are all located under the bin directory by default. Changing that base dir is rather cumbersome:
classpath {
   file.whenMerged {
       entries.each { entry ->
            if (entry instanceof org.gradle.plugins.ide.eclipse.model.Output) {
               entry.path = entry.path.replace('bin', 'build/eclipse')
            }
       }
   }
}

It would be great if there was an outputBaseDir instead that users can change:
classpath {
   outputBaseDir = 'build/eclipse'
}

This is a follow-up to #3825

@jereh16 this would be a good candidate for a pull request

Your example in the description:
classpath {
   file.whenMerged {
       entries.each { entry ->
            if (entry instanceof org.gradle.plugins.ide.eclipse.model.Output) {
               entry.output = entry.output.replace('bin', 'build/eclipse')
            }
       }
   }
}

Gives the following error:
<backtrace lines here>
Caused by: groovy.lang.MissingPropertyException: No such property: output for class: org.gradle.plugins.ide.eclipse.model.Output

When I look at Output.java, I see a get/set Path but no output field; what am I missing?

I meant path, changed the example above.

BTW it would be nice to have a way to restore 4.3. behavior, i.e. to have a possibility to put all the compiled classes to the single output folder.

You can use the code I showed above and adjust it to remove the output folder attribute instead.

I tried this, and it didn't work.  Specifically, I put this in build.gradle for one project in a multi-project build:
   eclipse { 	classpath { 	   file.whenMerged { 	       entries.each { entry -> 	            if (entry instanceof org.gradle.plugins.ide.eclipse.model.Output) { 	               entry.path = entry.path.replace('bin', 'build/classes/')     			} 		 	} 		} 	}   }
After refreshing the project, I found that the default output directory has been updated as expected, but the output folders for each source file have not been updated. For example:
<classpath> 	<classpathentry kind="output" path="build/classes//default"/> 	<classpathentry output="bin/main" kind="src" path="src/main/java"> 		<attributes> 			<attribute name="gradle_scope" value="main"/> 			<attribute name="gradle_used_by_scope" value="main,test"/> 		</attributes> 	</classpathentry> 	<classpathentry output="bin/main" kind="src" path="src/main/resources"> 		<attributes> 			<attribute name="gradle_scope" value="main"/> 			<attribute name="gradle_used_by_scope" value="main,test"/> 		</attributes> 	</classpathentry>
Also, I tried this in the root project, like this:
subprojects {   eclipse { 	classpath { 	   file.whenMerged { 	       entries.each { entry -> 	            if (entry instanceof org.gradle.plugins.ide.eclipse.model.Output) { 	               entry.path = entry.path.replace('bin', 'build/classes/')     			} 		 	} 		} 	}   } }
... and I got this error on the "file.whenMerged" line:
Cannot invoke method whenMerged() on null object

What the EclipsePlugin is doing:

defying intuitive Eclipse standard by using: DEFAULT_PROJECT_OUTPUT_PATH = "bin/default";
defying intuitive Eclipse standard by specifying an output dir per source folder: 	<classpathentry kind="src" output="bin/main" path="src">
adding clutter like to .classpath: <attribute name="gradle_scope" value="main"/>			<attribute name="gradle_used_by_scope" value="main,test"/>
making it straight up cumbersome, ugly and error-prone to fix this insanity

I played through ever interpretation of how this absolutely unexpected behavior of EclipsePlugin could have come to live. Even the most positive reading (incompetence and a complete lack of understanding of what Eclipse users expect) doesn't seem plausible. It all doesn't make sense.
Help me out here. What's the plan?

The thing is, one can already customize the defaultOutputPath and I expected it to be the baseDir for all other output paths, but it is not:
eclipse {
    classpath {
        defaultOutputDir = file('build') // this should be enough
        file {
            whenMerged { // but we still need to adjust the outputs for src paths
                cp -> cp.getEntries().forEach{
                    cpEntry -> if(cpEntry.kind=='src') {
                        cpEntry.output = cpEntry.output.replace('bin/', 'build/')
                    }
                }
            }
        }
    }
}

and even this defaultOutputDir is not set to 'build' but 'build-default'.

All Gradle-Eclipse-Defaults should be identical to Eclipse-Defaults when you create a project. Since ALL (src, per source-folder outputdir, default output dir, etc.) the Eclipse-Defaults are ignored by the Gradle-Eclipse plugin one wonders if this is deliberate? The IDEA plugin respects all of IDEA's defaults. Does this all make sense now?

It is sad and unfortunate one has to clutter the build scripts with explicit eclipse plugin customizations.  It could just use the default Eclipse output-dir as baseOutputDir instead of hard-coding it to bin/.


⚠ Bofrost.de has degraded performance

In 658957b, Bofrost.de (https://www.bofrost.de) experienced degraded performance:

HTTP code: 200
Response time: 1435 ms

Resolved: Bofrost.de performance has improved in 060eeba after 6 minutes.


Get the list of global classes in scripting language

Godot version:
master branch
OS/device including version:
Ubuntu 19.04
Just wanted to know how to get the list of global classes registered by class_name, My guess is you can only get the list from ScriptServer which is not exposed for scripting, Is there a way to expose methods related to global classes,

My proposal is to add get_global_class_list, global_class_exists to the _ClassDB and expose that to the scripting, and isn't ClassDB suppose to have all the class info, why global_classes are inside ScriptServer in the first place,

Ok, It seems we can get global_class_list from ProjectSettings, but doing so looks kinda ugly.

Maybe I should just create a PR and hope it gets accepted

Closing in favor of https://github.com/godotengine/godot-proposals/issues/5444, as feature proposals are now tracked on the Godot proposals repository.


Timecode rate is ignored

Fix: #606
This addresses the issue as written... but because having an implicit rescale in to_timecode seems iffy, I'm also proposing another PR that drops the rate argument from to_timecode entirely in favor of explicitly calling rescale_to in calling code.  Thoughts?

Codecov Report

Merging #612 into master will increase coverage by <.01%.
The diff coverage is 100%.

@@            Coverage Diff            @@
##           master    #612      +/-   ##
=========================================
+ Coverage   81.69%   81.7%   +<.01%
=========================================
  Files          72      72
  Lines        2732    2733       +1
=========================================
+ Hits         2232    2233       +1
  Misses        500     500

Flag
Coverage Δ

#py27
81.68% <100%> (ø)
:arrow_up:

#py36
81.68% <100%> (ø)
:arrow_up:

#py37
?

Impacted Files
Coverage Δ

src/opentime/rationalTime.cpp
86% <100%> (+0.14%)
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Gemma support

Add support for gemma model type:
Should run with:
python -m mlx_lm.generate --model google/gemma-7b-it --prompt "Write a quick sort in C++"

Can we already qlora it with mlx?

Oh yea that should work fine! I just added it to the allowed LoRA models.

I'm impress, this landed minutes after the official release.
Right now I'm working with the examples/lora but there's also mlx-llm.
Both dir have specific conf for llama, phi, etc but I cannot see update for gemma.
What's is the up to date way to train? is lora deprecated?
Thank you!

awesome!

@Solido
The lora/ example is not deprecated. It's just not being extended to be more fully featured. It is mostly used as an educational example and/or starting point for someone wanting to extend.
To use all the bells and whistles, use mlx_lm.lora : https://github.com/ml-explore/mlx-examples/blob/main/llms/mlx_lm/LORA.md

@awni I'm on master, last commit, running
python3 -m mlx_lm.lora --model google/gemma-2b-it --train --iters 200 --resume-adapter-file ./adapters.npz
ValueError: Model type gemma not supported.

Sorry I might have messed that up, let me check!

@Solido it works find for me:
python -m mlx_lm.lora --model google/gemma-7b-it --train --data ../lora/data
Loading pretrained model
Fetching 11 files: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████| 11/11 [00:00<00:00, 45862.17it/s]
Total parameters 8539.516M
Trainable parameters 1.835M
Loading datasets
Training
Starting training..., iters: 1000
Iter 1: Val loss 9.731, Val took 15.371s
Iter 10: Train loss 8.709, Learning Rate 1.000e-05, It/sec 0.734, Tokens/sec 272.181, Trained Tokens 3708

Maybe you need to uninstall mlx_lm and reinstall (or force update):
pip install -U mlx-lm

This was it! thank you very much for mlx, even dev like me can be on track with such a tool!

This was fast...and crazy. I got this up and running on my Mac. Amazing!

Has anyone had any success instruction tuning the base gemma models via the mlx_lm lora? Curious if it's worth trying.

@awni I am having same problem @Solido bash ValueError: Model type gemma not supported.

What are you running? Share the command?

python3 lora.py \
  --train \
  --model google/gemma-2b-it \
  --data ~/Fine-tuning/data \
  --adapter-file ~Fine-tuning/adapters_file \
  --batch-size 2 \
  --lora-layers 4 \
  --iters 200```

Ah you should use the mlx LM Lora https://github.com/ml-explore/mlx-examples/blob/main/llms/mlx_lm/LORA.md

Thanks for the response,  it's working now.

@awni I think the code used for generating from the fine-tuned model using adapters.npz is missing from the doc?
https://github.com/ml-explore/mlx-examples/blob/main/llms/mlx_lm/LORA.md#Generate
and i am not sure how to do it.

Would you mind filling an issue or asking in a discussion? I am happy to help but I will lose track if it’s in this PR

Sure, i will create an issue.


PHP error in Hpp.php

In my magento log there is this line:
[31-May-2017 08:36:04] PHP Parse error:  syntax error, unexpected '[' in app/code/community/Adyen/Payment/Model/Adyen/Hpp.php on line 176
[31-May-2017 08:36:04] PHP Fatal error:  Some transactions have not been committed or rolled back in lib/Varien/Db/Adapter/Pdo/Mysql.php on line 4039
Can you help me?

Hi @cpieroni
Seems that you are using PHP < 5.4.0 that doesn't support short array syntax.
I would suggest to upgrade to one that is actively supported (5.6.0 or higher).
Regards,
Giorgos
Adyen


Prevent metric dtype conversion when metric is part of LightningModule

What does this PR do?
Fixes #1561
Added a simple check to prevent applying .half() and .float() calls that are passed on the LightningModule to metric states and defaults. Instead, users will have to use set_dtype(), as proposed in #493.

Before submitting

[ ] Was this discussed/agreed via a Github issue? (no need for typos and docs improvements)
[X] Did you read the contributor guideline, Pull Request section?
[X] Did you make sure to update the docs?
[X] Did you write any new necessary tests?

PR review
Anyone in the community is free to review the PR once the tests have passed.
If we didn't discuss your PR in Github issues there's a high chance it will not be merged.

Did you have fun?
Make sure you had fun coding 🙃

seems that the GPU tests are hanging... :thinking:


Email address for acceptance testing

Acceptance testing creates a lot of team invitations.  Currently they're all going to my gmail account.  This is not ideal because it makes the testing infrastructure dependent on a resource that belongs to me not to Rollbar.
@coryvirok Can we get a rollbar.com email address for use with acceptance testing?
It would be super awesome if we could figure out a way to have some of those invitations programmatically accepted, so we can do automated testing on the full user lifecycle.

Ideally we want a forwarding address.  Something like<EMAIL_ADDRESS>that forwards to me and anyone else involved with maintaining the provider.

I created a group and added you to it. The address is<EMAIL_ADDRESS>

The new address is not working.
I received the response below to a test message sent from Protonmail.   However I received no response (and no forwarded message) when sending from my Gmail account.

Hello<EMAIL_ADDRESS>We're writing to let you know that the group you tried to contact (terraform-provider-test) may not exist, or you may not have permission to post messages to the group. A few more details on why you weren't able to post:

You might have spelled or formatted the group name incorrectly.
The owner of the group may have removed this group.
You may need to join the group before receiving permission to post.
This group may not be open to posting.

If you have questions related to this or any other Google Group, visit the Help Center at https://support.google.com/a/rollbar.com/bin/topic.py?topic=25838.
Thanks,
rollbar.com admins

Code is updated to use new email address in branch update-email-to-rollbar-address.
However that branch cannot pass acceptance tests until I register<EMAIL_ADDRESS>as a Rollbar user.  That can't happen until the new address is able to forward message to me.

Please forward messages to<EMAIL_ADDRESS>not to my Protonmail.


main

Created a branch, created a file and made a commit, and opened a pull request

changes

test

Created a branch, created a file and made a commit, and opened a pull request

Created a branch, created a file and made a commit, and opened a pull request

###Test


'digger unlock' command should work even if branch has been deleted

at the moment pipeline fails at checkout stage because branch doesn't exist and it makes it impossible to unlock project 'normal' way

I believe this was first raised by @fleroux514 initially. Adding "user-reported" label to track


Needs not working as expected

Hello there,
With the below helmfile, I expect the test-tenant release to be released after gatekeeper, reverseproxy and tos-database when executing:
helmfile --environment local sync
It is however released in the second batch of releases, before gatekeeper (or reverseproxy) have been released. In debug logging I see:
GROUP RELEASES
1     default/passlayer-proxy, default/tos-database
2     minikube/default/passlayer-session, minikube/default/reverseproxy, default/test-tenant
3     minikube/default/passlayer-pks
4     minikube/default/gatekeeper

When executing  helmfile --environment local -l name=test-tenant sync --include-needs, I get this error:
panic: bug: unexpectedly failed to get releases for id "default/gatekeeper": [default/test-tenant default/tos-database]

goroutine 1 [running]:
github.com/roboll/helmfile/pkg/state.GroupReleasesByDependency
....

Any ideas what could be the issue?
helmfile.yaml
environments:
  local:
    values:
    - kubeContextBase: minikube

helmDefaults:
  createNamespace: false
  timeout: 120
  wait: true
commonLabels:

releases:
  - name: gatekeeper
    chart: bitnami/nginx
    atomic: true
    kubeContext: minikube
    namespace: default
    needs:
      - passlayer-pks
  - name: passlayer-pks
    chart: bitnami/nginx
    atomic: true
    kubeContext: minikube
    namespace: default
    needs:
      - passlayer-session
  - name: passlayer-session
    chart: bitnami/nginx
    atomic: true
    kubeContext: minikube
    namespace: default
    set:
      - name: fullnameOverride
        value: passlayer-session
    needs:
      - passlayer-proxy
  - name: reverseproxy
    chart: bitnami/nginx
    atomic: true
    kubeContext: minikube
    namespace: default
    needs:
      - passlayer-proxy
  - name: passlayer-proxy
    chart: stable/mssql-linux
    namespace: default
    set:
      - name: image.repository
        value: mcr.microsoft.com/mssql/server
      - name: image.tag
        value: 2019-latest
      - name: acceptEula.value
        value: "Y"
  - name: tos-database
    chart: stable/mssql-linux
    namespace: default
    set:
      - name: image.repository
        value: mcr.microsoft.com/mssql/server
      - name: image.tag
        value: 2019-latest
      - name: acceptEula.value
        value: "Y"
    needs:
  - name: test-tenant
    chart: stable/mssql-linux
    namespace: default
    set:
      - name: image.repository
        value: mcr.microsoft.com/mssql/server
      - name: image.tag
        value: 2019-latest
      - name: acceptEula.value
        value: "Y"
    needs:
      - reverseproxy
      - gatekeeper
      - tos-database

never worked for me either

What if you added the namespace to every needs entry? What's your helmfile version?

hm, I swear I tried it before and it didn't work, but now in my current helmfile if I add:
needs:
- istio-system/base

it works, thanks!

I did try the namespace before, but now I realized that helmfile also groups according to the kubeContext. So all services must have a matching namespace and kubeContext for groups depending on needs to be setup.
Thanks for the help!


Use a descriptive name instead of raw 4096 constant for database path buffer size

…h buffer size
Description
Use a descriptive name instead of raw 4096 constant for database path buffer size
Fixes # (issue)
Type of change
Readability improvement
How Has This Been Tested?
Nothing to test for the change.
Test Configuration:

Firmware version:
Hardware:

Checklist:

[x] My code follows the style guidelines of this project
[x] I have performed a self-review of my own code
[x] I have commented my code, particularly in hard-to-understand areas
[x] I have made corresponding changes to the documentation
[x] My changes generate no new warnings
[x] I have added tests that prove my fix is effective or that my feature works
[x] New and existing unit tests pass locally with my changes
[x] Any dependent changes have been merged and published in downstream modules

Closing this for now, as not sure if this single buffer is still used


Add uninstall playbook

Closes #1297

@lulf playbook works fin, but one note we should make note in doc about this playbook and how it run (inventory/extra vars)

@lulf another note: when I install enmasse, and create an address space and then run uninstall playbook, it stuck in delete project phase and project is marked for deletion but it isn't deleted.


The neighbour DNS address is replaced by the IP address

With some of my neighbors I could see that the DNS address I entered was replaced by the IP address. This change has also been made automatically in the peering.json.
To Reproduce
I have no idea when or why this is happening. In my case, it did not affect all of the neighbors, only some.
Expected behavior
It would be great if the entered values were retained. If the error occurs, the neighbor will no longer be recognized when the IP is changed. (gossipUnknownPeersLimit -> 0)
Environment information:
Hetzner CPX21 and Hetzner CPX31. (It happened on both nodes.)
Ubuntu 20.04.2 LTS / Node 1.01

This bug has not happened in a long time. I think it can be closed.


Secret_frames bug still happening on latest version

Hey - Still experiencing the secret_frames bug on the latest version

Resolved the issue was an issue with my assets folder :)


Reset doesn't work if start is pressed twice

if you press start twice or more, reset doesn't stop the timer

Great Catch


chore: use semantic-release cross-formula standard structure

Automated using ssf-formula (v0.1.0-rc.1)

@myii merged it

@aboe76 Thanks.

:tada: This PR is included in version 0.12.3 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


Merge Adapters and Bottleneck models

Refactor so that pretrained encoders/decoders can be used in combination with any bottleneck.

Update: This should already be done for the SequenceEncoder, it just needs adding to SequenceDecoder. PretrainedAdapterModel then becomes redundant.

Should be fixed by 7ccc7bfb1faae924deada5ccdf8fbecf314e26c1


[style]: Changing the layout of the home page

What's the style idea?
We need to improve  the layout of the page to vertical which is in Horizontal and add a NavBar
please assign me this issue I want to enhance the style of the webpage
Add the labels hactoberfest-accepted, Gssoc -ext24, Level 1/2/3
Best Regards
Sanjeev
Contributor
Add screenshots

Code of Conduct

[X] I agree to follow this project's Code of Conduct

@omkarvashistha
Assign me this Issue

@omkarvashistha Assign me this Issue

@sanjeev0304  I don't have required permissions to assign this issue , could you please check with someone who has the proper permissons

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[1.9.4] Electric Bow gets destroyed after shooting an arrow

Electric Bow disappears (or gets destroyed) after shooting an arrow.
https://youtu.be/NwIEa2HyNwE

Fixed!


Update Diff Settings

This changes the 'Diff settings' text to the settings icon and removes
the whitespace options if diff-view-without-whitespace-options is
enabled.
Example URL:
https://github.com/sindresorhus/refined-github/pull/1146/files
Closes #1292

The readme still has this image 😬

Or... 1-click

Do the icon make kind of sense?
https://octicons.github.com/icon/book/
https://octicons.github.com/icon/diff/

Did all the feedback, thanks! Except for the delegate or separate buttons, I can see both working, what do others like? Same for the readme update, I'll save that till we decide on the dropdown or buttons.

Or... 1-click

I like the one-click icons @bfred-it suggested.

Tested on:

PR files: https://github.com/sindresorhus/refined-github/pull/1799/files
PR files (single commit): #1799@67be67a

Forgot about this, thanks for finishing it up, looks good to me.

🎉


remote config for kill-switch

r @Raynos @jcorbin  @kriskowal

Needs more work.
We need to rely on deltas and do things #coolstory

lgtm.


Extra column which shows date of 1st reported case.

This feature will help people to get information that may be important sometimes as the date of first reported case shows the level of danger in the particular state/district. This will also help doctors, analysts, and other people to take important decisions if required.
Simply add one column in the table which shows the date of first reported case in each state as well as in each district.
Look on this website https://www.worldometers.info/coronavirus/ which also have a same column which I'm talking about.

@JunaidBabu I would like to work on this issue

I'd like to take this up

@JunaidBabu Is this issue still open?

Can someone work on API for this? Data that is to be populated in the column isn't present in the current API and it is not possible to calculate the same.

Can someone work on API for this? Data that is to be populated in the column isn't present in the current API and it is not possible to calculate the same.

@pk1997 yeah I would like work on the API for this issue. Let distribute the work and Integrate this feature.

@strikertanmay Sure. Let me know once you are done with API. BTW do we have slack channel or something for communication

@strikertanmay Sure. Let me know once you are done with API. BTW do we have slack channel or something for communication

@pk1997 Please tell me the response structure which u needed to populate the table. I will modify the api response on that basis.

@strikertanmay In API response of 'https://api.covid19india.org/data.json', In statewise array, send a field saying first_reported with date in it.
Ex of json data in statewise array
{
"active":"183",
"confirmed":"215",
"deaths":"7",
"delta":{
"active":12,
"confirmed":12,
"deaths":0,
"recovered":0
},
"lastupdatedtime":"30/03/2020 10:02:25",
"recovered":"25",
"state":"Maharashtra"
"first_reported":"30 jan 2020"
}
Hope this helps

@strikertanmay In API response of 'https://api.covid19india.org/data.json', In statewise array, send a field saying first_reported with date in it.
Ex of json data in statewise array
{
"active":"183",
"confirmed":"215",
"deaths":"7",
"delta":{
"active":12,
"confirmed":12,
"deaths":0,
"recovered":0
},
"lastupdatedtime":"30/03/2020 10:02:25",
"recovered":"25",
"state":"Maharashtra"
"first_reported":"30 jan 2020"
}
Hope this helps

Okay I get it. If I change in state_district_wise.json (https://api.covid19india.org/state_district_wise.json)as this will cover both district and state, it will worked for you ?
"Goa": {
"districtData": {
"North Goa": {
"confirmed": 3,
"lastupdatedtime": "",
"firstReported" : "30/01/2020"
},
"Unknown": {
"confirmed": 2,
"lastupdatedtime": ""
}
}
"firstReported" : "30/01/2020"
},

Sure

@strikertanmay Even though yours is a good idea to cover both, I feel its bad design to involve state data in district wise data. Add first reported for the state in https://api.covid19india.org/data.json API and first reported of the district in https://api.covid19india.org/state_district_wise.json API so that it will be a clean code

@strikertanmay Even though yours is a good idea to cover both, I feel its bad design to involve state data in district wise data. Add first reported for the state in https://api.covid19india.org/data.json API and first reported of the district in https://api.covid19india.org/state_district_wise.json API so that it will be a clean code
Hope you understand my concern here

I'm also not truly satisfied with my idea and your concern is totally valid. Actually I explored but not found any way to update the data.json just like there is a way for state_district_wise.json. We can do one more thing as all states have first_reported cases and there is no update in this field so you can also hardcoded it for the state. And for district_wise I will update the API and it will populate through API response

Sure lets do that

Sure lets do that

https://github.com/covid19india/api/pull/36

Sure lets do that

https://github.com/covid19india/api/pull/38

Can you help me curate an object contains ifo first reported case of each and every state.
Ex: right now we are getting district wise info of the first reported case. But doing it statewise requires creating const object with values in it.
const firstReported = {
'Goa' : '12th feb',
'Karnataka': 1st Mar',....
}
Can you help me create this constant object ?

Can you help me curate an object contains ifo first reported case of each and every state.
Ex: right now we are getting district wise info of the first reported case. But doing it statewise requires creating const object with values in it.
const firstReported = {
'Goa' : '12th feb',
'Karnataka': 1st Mar',....
}
Can you help me create this constant object ?

Yeah sure..
I will make a separate json object and make a PR for it. Does it work?

Sure Thanks

Sure Thanks

@pk1997 Please view the PR and suggest if any change required.

PR link please ?

Gotcha. That should have been done in frontend repo. Anyway thanks for the help I got what I needed

Gotcha. That should have been done in frontend repo. Anyway thanks for the help I got what I needed

U can directly fetch data by requesting api/state_wise_first_reported.json. According to me this will be good to fetched all data from api.

Got it.

Will do that once your pr is up and running

Hey there @strikertanmay I respect your work but can you change date format, US uses months first so lets keep it like this. I will give you JSON please paste the same
{   'Andaman and Nicobar Islands': '26th March',   'Andhra Pradesh': '12th March',   Bihar: '22th March',   Chandigarh: '23th March',   Chhattisgarh: '19th March',   Delhi: '02th March',   Goa: '25th March',   Gujarat: '19th March',   Haryana: '04th March',   'Himachal Pradesh': '20th March',   'Jammu and Kashmir': '09th March',   Karnataka: '09th March',   Kerala: '30th January',   Ladakh: '07th March',   'Madhya Pradesh': '20th March',   Maharashtra: '09th March',   Manipur: '24th March',   Mizoram: '25th March',   Odisha: '16th March',   Puducherry: '17th March',   Punjab: '09th March',   Rajasthan: '03th March',   'Tamil Nadu': '07th March',   Telangana: '02th March',   'Uttar Pradesh': '04th March',   Uttarakhand: '15th March',   'West Bengal': '17th March', };
This will look good too on the actual table

Hey there @strikertanmay I respect your work but can you change date format, US uses months first so lets keep it like this. I will give you JSON please paste the same
{ 'Andaman and Nicobar Islands': '26th March', 'Andhra Pradesh': '12th March', Bihar: '22th March', Chandigarh: '23th March', Chhattisgarh: '19th March', Delhi: '02th March', Goa: '25th March', Gujarat: '19th March', Haryana: '04th March', 'Himachal Pradesh': '20th March', 'Jammu and Kashmir': '09th March', Karnataka: '09th March', Kerala: '30th January', Ladakh: '07th March', 'Madhya Pradesh': '20th March', Maharashtra: '09th March', Manipur: '24th March', Mizoram: '25th March', Odisha: '16th March', Puducherry: '17th March', Punjab: '09th March', Rajasthan: '03th March', 'Tamil Nadu': '07th March', Telangana: '02th March', 'Uttar Pradesh': '04th March', Uttarakhand: '15th March', 'West Bengal': '17th March', };
This will look good too on the actual table

Okay, I will change for the state data. But For district data, will u change the format during populating or I will have to change in JSON itself?

Closed in favor of #1496


Dataset download from Google Drive

Hi,
I downloaded TNCR dataset from Google drive and checked contents (all 5 parts).
The 1st part of them contains 6,621 images and annotations, and I think it means all data of TNCR are included in the 1st part.
Could you give more information about each part of them?
Best regards 👍

Thank you for your reply.
Honestly speaking, I didn't understand decompression method correctly.
Now, I got correct images and annotations from Google Drive.


Fixed Merge Issue: Added TodoItem Model

I have fixed the merge conflicts.

Thanks for the feedback.. can u please check if everything is fine now that i have changed the requested changes.
✨


dataset duck typing for dataloader

removing knowledge of dataset and everything else outside the Tags and dispatch from dataloader package.

Not that I have any problem with this kind of change, but is there a motivating issue or explanation of the rational here?

@rjzamora I think this is related to wanting to move the dataloaders into the new models library without that library needing to depend on NVTabular. From talking to @jperez999 earlier, it sounds like allowing the dataloaders to operate on a plain ddf makes it easier to cleanly separate datasets (in NVT) from dataloaders (in the models library in a way that lets them be used either together or separately.

Sounds good @karlhigley !  This does make sense to me. However, since I occasionally find myself tracking down performance regressions in NVTabular, I like there to be a linked issue or motivation described in any PR touching the IO interface.


App: Demonstrate lidar sensor streaming with HoloViz

Adds an operator and application to demonstrate streaming from the Velodyne VLP-16 3D lidar sensor to display with HoloViz.
Change:

Implements C++ VelodyneLidarOp for processing VLP-16 packets on GPU, informed by the NVIDIA DeepMap SDK
Implements C++ VelodyneLidarApp demonstration pipeline to receive VLP-16 packets over IP/UDP, process them into a Cartesian point cloud on GPU, and then pass them to HoloViz for display.

Portions of CUDA VLP-16 processing code are contributed by the NVIDIA nvMap team via the NVIDIA DeepMap SDK. Collaborators are credited in metadata files.

Thanks @jjomier! Will leave this PR open a little longer to allow others to review.

Thanks @AndreasHeumann ! Updated to address your review comments.


Local Execution Engine RFC

Current WIP: https://www.notion.so/minaprotocol/Local-Testing-Framework-RFC-WIP-c7cc3d551b294590b2b9442157fea380

See here for current RFC issue: https://github.com/MinaProtocol/mina/issues/8890


„Alt character codes“ (e.g., – and the quotes) open various tool windows – instead of typing a character. Windows 10

Hello,
while using Archi, I have run into the afore- and below mentioned issue with special characters. It is a bit frustrating, though not a breaking issue. Since we use Archi to create or edit official government documents, we would prefer to use proper characters, e.g., – instead of - , „ and “ instead of so called "quotes" (actually inch sign) and so forth.
I really enjoy using Archi at work (and have actually supported it financially in the recent past), so this „quality of life improvement“ would be very much welcome. Note: I am a programmer, so if this fix were simple to implement, I am open to help.
Version of Archi
5.0.2 ,  [The current latest version]
Archi Plug-ins
None installed
Operating System
Windows 10
Expected Behaviour
A character by given code should be placed in the currently focused text field or area (e.g., element's name or documentation field), e.g., alt + 0150 to – , alt + 0147 to “ , alt + 0132 to „ , and so on.
Actual Behaviour
The text field loses focus and tool windows are open depending on pressed alt combinations. E.g., alt + 0132 toggles Models (alt + 1), Outline (alt + 3), and Properties (alt + 2) windows (open or close depending on their current state).
Steps to Reproduce the Behaviour

Add any element, for example Application Component
Double-click this element to edit it
Click the Documentation field to focus it
Input the alt + 0132 code in an attempt to write the „ sign.
Watch the world burn Observe a loss of focus and Models, Outline and Properties windows toggle (as described above)

Note: I have no error log for this as the program does not crash or „think“ it is broken – so none are provided.

Summary - Alt key shortcuts for different views (Alt 1, Alt 2, etc) conflict with character combinations like Alt + 0132 when inputting in a text field.
You can re-assign these key combinations in Preferences -> System -> Keys.
I might change the defaults to Alt + Shift

I'll close this one now because:

You can re-assign these key combinations in Preferences -> System -> Keys.
You can use the numeric keypad if you have one.
I've set the shortcut keys to "Alt+Shift+num" in the next version

@Phillipus Thank you very much for such a quick resolution!
For your info, I am already using the numeric keypad („Num lock-ed keys“). But the tip about rebinding window shortcuts in configuration is a solid workaround for now. Thank you.
But: although setting the defaults to alt + shift will fully solve the problem, I think it may be better for Archi to ignore the num pad number for the window shortcuts (as you have suggested should already work). Would it not be worth looking at? I expect that to be a simple change, but I am not familiar with Eclipse development, so I do not want to force any solution upon you.

Why would it not work if the key bindings for the windows are not set to Alt + num?


Performance assignment poll

* why an admin login is required for assignment voting? (e.g. performance votes -a 100 --interreupt -i 42 -d example.com -u admin -p admin) -> works without admin login for motion poll.

On assignment-votes the client needs the option-ids. Therefore a read request before the votes is required. I changed the code to use "dummy1" for this read request.

* YNA election does not work, only Y election works

Currently only "Y" elections are supported. Do you think it is necessary for the performance tool to test different votes? Do you think this makes a difference in performance?

* I prefere to use "--motion" when we introduce "--assignment"

I changed it as arguments. Now you have to run:
performance votes motion ...
performance votees assignment ...

The arguments m and a do also work.

* Can you add short flags for --answer (e.g. -c for 'choice') --assignment (-a), --motion (-m) and --amount (-n)

done

I retested your performance script. Works good! Two minor documentation issues:

The votes  flags motion and assignment are not listed in the help (performance votes --help). Maybe an example command would be helpful.
The help text sentence with "old_url" is outdated and can removed, right?

@ostcar ping for the last changes ;-)

Pong

I fixed the help text. I don't know how to automatically add the arguments to the help text by the cli-lib that I am using. I hope, the examples in the help text is enough.


raftstore: fix panic when building snapshot after being deleted

Hi,
This PR tries to fix the issue #1852. It adds existence checking in build() to make sure proper initialization is done for the race case.
PTAL @BusyJay @siddontang @zhangjinpeng1987

PTAL @BusyJay

It's a better way to solve the read/write race case to impl the snapshot manager using reference count and make the deletion only happen by calling snapshot manager interface when GCing snapshots.
A new PR will be raised. This PR will be obsolete.


Adding typst-slides to the offical packages repository

Typst has added support for packages through a Github repository, so it's probably a good idea to add this template as an official package.

In fact, there's another fontawesome package which is based on unicode in the official repository. However, this repo is dependent on local svg. The dependency is kind of heavy, and does not fit for the online app, so I wonder if it can be accepted by the official repo.
I will try to make a PR recently.
Thanks for your interest.

I tried to make a PR, but this package doesn't suit the official repo.
https://github.com/typst/packages/pull/310


UI: Unreadable tables

https://en.wikipedia.org/wiki/Amateur_radio_call_signs#Formation_of_an_amateur_radio_call_sign

Thanks, will fix immediately

Also here: https://en.wikipedia.org/wiki/Piano_key_frequencies

Good catch - I have fixed now and will upload later, please let me know if you find more tables.
The issue with tables is that they have td elements and I cannot override all td elements to dark because that would mess up some other tables, for example this one here would be completely dark: https://es.wikipedia.org/wiki/King_Crimson#Miembros_pasados and also temperature tables with colors would be replaced with dark.

Sure, I'll gladly complain about anything that isn't as perfect as it should be! lol
Thanks for the effort and I commend your taste in music too if you like King Crimson.

It should be fixed now, included in the latest update. Haha actually I don't listen to King Crimson - I just remember some user linking me it when I messed up the table colors ;)

I have found something similar, not exactly tables but same problem:
[https://en.wikipedia.org/wiki/Emperor_Monmu]

[https://en.wikipedia.org/wiki/Mineral_(nutrient)]

Another occurrence in another particular case implying special characters (phonological):
https://en.wikipedia.org/wiki/Affricate

As you can (not) see some characters are black on black thus not showing.

Yeah I noticed that too, seems like some changes became overridden. Will look into this soon!

Thanks

List of other tables I found (adding them here to keep an eye of them)
https://en.wikipedia.org/wiki/The_Economist_Democracy_Index#By_region
https://en.wikipedia.org/wiki/2024_United_States_presidential_election#Forecasts
https://en.wikipedia.org/wiki/London#Climate

Before using the extension:

After using the extension:

https://en.wikipedia.org/wiki/XCOM#Released
Dark Mode for Wikipedia 4.5.7 (July 7, 2024)
Mozilla Firefox 129.0b1 (64-bit)


:GoLint, causes asyncmake.lua  Invalid %( in format string

When I tried to run:
:GoLint

I just got this:
stack traceback:
^I[C]: in function 'setqflist'
^I...nvim/site/pack/packer/start/go.nvim/lua/go/asyncmake.lua:104: in function <...nvim/site/pack/packer/start/go.nvim/lua/go/asyncmake.
lua:77> function: builtin#18 Vim:E377: Invalid %( in format string

Any ideas what might be causing this?

I don't know how to reproduce this,
but I ran :GoLint in a repository that
did not have an updated go.mod / go.sum file.
When I updated go.mod / go.sum in my tree, this problem went away and I was able to successfully run :GoLint.
Any idea how the code in go.nvim could be made more robust and display a more helpful error message?

Thanks.
It was caused by the error message of 'go mod not found'
I updated the code so it will handle those messages.

Thanks I verified the fix.  Now I got a more useful error message after running :GoLint:
| Running error: context loading failed: failed to load packages: failed to load with go/packages: err: exit status 1: stderr: go<EMAIL_ADDRESS>missing go.sum entry; to add it:\n\tgo mod download myrepo\ngo<EMAIL_ADDRESS>missing go.sum entry; to add it:\n\tgo mod download myrepo\n

Great!

@ray-x I started some new Go development, and using go.nvim, my experience is excellent.
I have all the functionality I had with https://github.com/fatih/vim-go , but the experience is better with neovim, treesitter, etc.
Thanks for the great work!

I am glad you enjoy the plugin!


Change migration format

I've been having issues with this package when I use autoloading of migrations from domain paths in my project that uses DDD, in specific this package: lunarstorm/laravel-ddd.
I get error like Cannot declare class CreateUsersIndex, because the name is already in use because the file is loaded multiple times which makes the class names clash. That DDD package autoloads several types of files which scans the Domain directory and creates this problem.
While this could be fixed in that package as well, but I think it would be better if this migration format is updated to be the same as the Laravel format with anonymous classes.
I.e:
return new class implements MigrationInterface
Instead of:
final class CreateVehiclesIndex implements MigrationInterface
The file names are not changed.
This change is made to be backwards compatible with the current format.
I have added some tests, but some more tests could probably be added to to test this format further.

Hey @pelmered, thank you for the PR! Could you please resolve the conflicts and look at the comment I left?

Could you please also adjust the code so that all checks would be green?


Selection frame is displayed improperly for overlapped images

Steps to Reproduce

Click on "Add Image"
Select the image and add the first image to the canvas
Click on "Add Image" again and add the second image to canvas to overlap the first image
Select the second image

Actual behavior
The second image is on the top layer, but only part of the selection frame (or mouse over frame) is displayed

Expected behavior
The second image is on the top layer and the selection frame (or mouse over frame) is fully displayed
Desktop:

OS: Windows 11 Enterprise
Browser: Chrome 126.0.6478.127 (Official Build) (64-bit)

Ketcher version: Nightly 4902 [Version 2.23.0-rc.1] Build at 2024-07-12; 10:06:35.
Additional Context:

It also looks not proper when image and element are intersected:

Found during preview testing of https://github.com/epam/ketcher/issues/4897

Discussed with DM - no plans to fix in 2.24.0-rc.1, added to Refined Backlog

Verified.

Ketcher Version 2.26.0-rc.2 Build at 2024-10-14; 19:59:03
Indigo Toolkit Version 1.25.0-rc.2.0-g867ae250b-wasm32-wasm-clang-19.0.0
Chrome Version 129.0.6668.101 (Official Build) (64-bit)
Win10


Regarding the usage of Robotic Arm in Docker Setup

As specified on the [README.md] of the main page, we should ideally be able to run the same code from either a source installation, or from a docker setup, and obtain the same result. We observed a simple problem when trying to spawn a Robotic arm-equipped USV:
ros2 launch mbzirc_ign spawn.launch.py name:=usv world:=coast model:=usv x:=-1462 y:=-16.5 z:=0.3 R:=0 P:=0 Y:=0 arm:=mbzirc_oberon7_arm gripper:=mbzirc_oberon7_gripper

When we run this code on a source installation of the sim environment, it spawns a USV with robotic arm at the start gate coordinates
When we run this code using the docker (using the latest docker image version), no USV  is spawned
Strangely, when we run in docker, but removing the flags for the robotic arm (i.e as per the bottom of this issue), it successfully spawns the USV, but of course, without a robotic arm, which we need

We checked the docker side of things, using 2 completely different machines, and observed the same behaviour
Could you kindly check from your end to see if this issue of spawning a robotic arm with above mentioned command is reproduced?
Warm regards,
ros2 launch mbzirc_ign spawn.launch.py name:=usv world:=coast model:=usv x:=-1462 y:=-16.5 z:=0.3 R:=0 P:=0 Y:=0

hi, I tested the latest docker image from dockerhub but I'm not able to reproduce the issue. Maybe try removing the docker images you have locally and pull from dockerhub again? In my testing, I removed any old docker images from the osrf/mbzirc repo (docker rmi -f <image>) before pulling the latest version from dockerhub. I ran the command you have for spawning the USV and the arm and I was able to see the USV.


*: use built-in etcdclt in tests

PTAL @huachaohuang @siddontang @qiuyesuifeng
Address comment https://github.com/pingcap/pd/pull/311/commits/33e5784113e8024de0da602c5dedf234a02b4a9d#diff-d5666a18e51cbff4c4f482faa6f9f449R191

CI failed.

LGTM
PTAL @huachaohuang

LGTM


Markdown guide for publishing design system releases?

During the experience of publishing a previous release tag, I found that it would have been helpful if there is a markdown guide in the repo to share a few tips / gotchas about publishing logistics with topics such as:

npmrc tool to ensure publish npm registry (v.s. private enterprise npm registry)
a check list of required npm account, authentication 2FA security and org access to support npm publishing
a set of standardized npm scripts
release note process after publishing
anything any WG member can think off to add to the discussion of this issue.

What do the WG members think of this proposal of writing such guide to ensure the ease & success of any future pcln-design-system publisher?

This issue was discussed in a previous WG session. The guideline of publishing could explore other inner-source document space. Closing this issue now. Can re-open if needed.


Embed mixpanel into an sdk

Integration Method: CocoaPods or Manual
Xcode Version:  9.0
Library Version:  latest
Platform: iOS
Language: Swift  or Objective-C
Description:  I cant integrate mixpanel into my sdk. when I build it it creates a separate folder for mixpanel. i want it to be embedded
Expected Behavior: demo app should find mixpanel famework

@masaldana2 I wonder if there's an Xcode project setting you need to change. Maybe you have to add the Mixpanel library to the "Embedded Binaries" section? As far as I know there's nothing special about the Mixpanel library that forces it to be separate.

Closing this. @masaldana2 feel free to reopen or create new issues if you have further questions.