0.15.1: build fails with implicit declaration of function ‘s2n_cleanup_final’

Describe the bug
Build fails with implicit declaration of function ‘s2n_cleanup_final’.
Regression Issue

[ ] Select this option if this issue appears to be a regression.

Expected Behavior
Build shuld not fail.
Current Behavior
/usr/bin/gcc -DAWS_CAL_USE_IMPORT_EXPORT -DAWS_COMMON_USE_IMPORT_EXPORT -DAWS_IO_EXPORTS -DAWS_IO_USE_IMPORT_EXPORT -DAWS_USE_EPOLL -DHAVE_SYSCONF -DINTEL_NO_ITTNOTIFY_API -DUSE_S2N -Daws_c
_io_EXPORTS -I/home/tkloczko/rpmbuild/BUILD/aws-c-io-0.15.1/include -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -g -grecord-gcc-switches -p
ipe -mtls-dialect=gnu2 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fdata-sections -ffunction-sections -fstack-protector-strong -specs
=/usr/lib/rpm/redhat/redhat-hardened-cc1 -flto=auto -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -Wall -Werror=format-security -O2 -g -DNDEBUG -std=gnu99 -fPIC -fvisi
bility=hidden -Wall -Wstrict-prototypes -fno-omit-frame-pointer -Wextra -pedantic -Wno-long-long -fPIC -MD -MT CMakeFiles/aws-c-io.dir/source/tls_channel_handler.c.o -MF CMakeFiles/aws-c-io
.dir/source/tls_channel_handler.c.o.d -o CMakeFiles/aws-c-io.dir/source/tls_channel_handler.c.o -c /home/tkloczko/rpmbuild/BUILD/aws-c-io-0.15.1/source/tls_channel_handler.c
/home/tkloczko/rpmbuild/BUILD/aws-c-io-0.15.1/source/s2n/s2n_tls_channel_handler.c: In function ‘aws_tls_clean_up_static_state’:
/home/tkloczko/rpmbuild/BUILD/aws-c-io-0.15.1/source/s2n/s2n_tls_channel_handler.c:258:9: error: implicit declaration of function ‘s2n_cleanup_final’; did you mean ‘s2n_cleanup_thread’? [-W
implicit-function-declaration]
  258 |         s2n_cleanup_final();
      |         ^~~~~~~~~~~~~~~~~
      |         s2n_cleanup_thread
gmake[2]: *** [CMakeFiles/aws-c-io.dir/build.make:345: CMakeFiles/aws-c-io.dir/source/s2n/s2n_tls_channel_handler.c.o] Error 1
gmake[2]: *** Waiting for unfinished jobs....

s2n-tls 1.5.6.
Reproduction Steps
Try to build with s2n-tls 1.5.6.
Possible Solution
No response
Additional Information/Context
No response
aws-c-io version used
0.15.1
Compiler and version used
gcc 14
Operating System and version
Linux x86/64
### Tasks

s2n_cleanup_final was added recently to s2n-tls very recently: https://github.com/aws/s2n-tls/commit/9819ac0e2e028e3b761855fc4f2f8134008d3f4b. You can use that specific commit of s2n-tls, or their main branch, until they make another release (likely within a week). Or you can hold back updating aws-c-io to
Sorry, this was a case of bad timing. The s2n-tls team asked us to use this function, and we didn't realize it wasn't available yet in a tagged release (aws-c-io's tests build against the main branch of s2n-tls). I've asked the s2n-tls team to do their next release ASAP, but I don't know what rigamarole they might go through before each release.
I'll post more when I have updates...

Don't worry about me. I can wait until next release 😄
Thank you for confirmation that it is real issue 👍

Ok, fix if you use the latest S2N-TLS release: v1.5.7

Just tested and all looks good now 👍
Thank you.


[ENH] Kotsu application to sktime

Reference Issues/PRs

Solution to Issue #2804. See also Issue #2777
What does this implement/fix? Explain your changes.

Demonstration in notebook showing the kotsu could be implemented with sktime.
This this notebook the evaluate method was used as CV splitter method.
Does your contribution introduce a new dependency? If yes, which one?

Yes, kotsu
What should a reviewer concentrate their feedback on?

Performance, design and viability of implementing kotsu in sktime
Any other comments?

PR checklist

For all contributions

[x] I've added myself to the list of contributors.
[ ] Optionally, I've updated sktime's CODEOWNERS to receive notifications about future changes to these files.
[x] I've added unit tests and made sure they pass locally.
[x] The PR title starts with either [ENH], [MNT], [DOC], or [BUG] indicating whether the PR topic is related to enhancement, maintenance, documentation, or bug.

For new estimators

[ ] I've added the estimator to the online documentation.
[ ] I've updated the existing example notebooks or provided a new one to showcase how my estimator works.

This issue is closed and moved to #2977


[PE-D][Tester B] Some text in the UI appears really small on the webpage

As a potential user, it may be distracting to have to zoom in to view the details of the UI elements.
The text fields like Employee ID, phone number etc in each person card is almost illegible.

Labels: type.DocumentationBug severity.Low
original: bokung/ped#2

to be discussed


This window pops up when loading futbin. How can this be fixed?

here is the error code

here is the error code


Debug issue in bam_to_h5.R when running Edward's new S.cerevisiae FASTA and GFF

On 23rd April, noticed riboviz error when running new transcriptome annotations for S. cereviseae, new FASTA and GFF files. Was testing with full-size files from Brar et al 2012 (B-Sc_2012).

vignette runs fine
dry run is fine (6 samples, 0 failed)
full run (6 samples) FAILS:  6 samples, 6 failed:

# 23 Apr 2020
# B-Sc_2012, FULL RUN, 6 samples, updated .gff, updated .fasta (these pass check_fasta_gff.py)
# develop branch, last commit: 6324166
# 23 Apr 2020, started: 1636, ended:
(base) flic@circe:~/riboviz$ time python -m riboviz.tools.prep_riboviz -c B-Sc_2012/B-Sc_2012_config.yaml
Running under Python: 3.7.3 (default, Mar 27 2019, 22:11:17)
[GCC 7.3.0]
Created by: RiboViz Date: 2020-04-23 16:36:29.836118 Command-line tool: /home/flic/riboviz/riboviz/tools/prep_riboviz.py File: /home/flic/riboviz/riboviz/tools/prep_riboviz.py Version: commit 63241663f2cf91fdac18a6ba1d5a80e3f47101dd date 2020-04-23 16:30:48+01:00
Configuration file: B-Sc_2012/B-Sc_2012_config.yaml
Command file: run_riboviz_B-Sc_2012.sh
Number of processes: 8
Build indices for alignment, if necessary/requested
Build indices for alignment (B-Sc_2012/input/yeast_rRNA_R64-1-1.fa). Log: B-Sc_2012/logs/20200423-163629/hisat2_build_r_rna.log
Build indices for alignment (B-Sc_2012/input/verifiedORF_abundant_full-ORF_ypd_plus_other_fixed_UTR_length_transcripts_nointrons_issues_removed.fasta). Log: B-Sc_2012/logs/20200423-163629/hisat2_build_orf.log
Processing samples
Processing sample: PRE_ENTRY_1
Processing file: B-Sc_2012/input/SRR387873_GSM843749_footprints_for_the_A_timepoint_of_the_traditional_timecourse_premeiotic_Saccharomyces_cerevisiae_RNA-Seq.fastq.gz
Cut out sequencing library adapters. Log: B-Sc_2012/logs/20200423-163629/PRE_ENTRY_1/01_cutadapt.log
Remove rRNA or other contaminating reads by alignment to rRNA index files. Log: B-Sc_2012/logs/20200423-163629/PRE_ENTRY_1/02_hisat2_rrna.log
Align remaining reads to ORFs index files using hisat2. Log: B-Sc_2012/logs/20200423-163629/PRE_ENTRY_1/03_hisat2_orf.log
Trim 5' mismatches from reads and remove reads with more than 2 mismatches. Log: B-Sc_2012/logs/20200423-163629/PRE_ENTRY_1/04_trim_5p_mismatch.log
Convert SAM to BAM and sort on genome. Log: B-Sc_2012/logs/20200423-163629/PRE_ENTRY_1/05_samtools_view_sort.log
Index BAM file. Log: B-Sc_2012/logs/20200423-163629/PRE_ENTRY_1/06_samtools_index.log
Calculate transcriptome coverage for + strand and save as a bedgraph. Log: B-Sc_2012/logs/20200423-163629/PRE_ENTRY_1/07_bedtools_genome_cov_plus.log
Calculate transcriptome coverage for - strand and save as a bedgraph. Log: B-Sc_2012/logs/20200423-163629/PRE_ENTRY_1/08_bedtools_genome_cov_minus.log
Make length-sensitive alignments in H5 format. Log: B-Sc_2012/logs/20200423-163629/PRE_ENTRY_1/09_bam_to_h5.log
Problem processing sample: PRE_ENTRY_1
AssertionError
Traceback (most recent call last):
  File "/home/flic/riboviz/riboviz/tools/prep_riboviz.py", line 515, in process_samples
    sample_logs_dir, run_config)
  File "/home/flic/riboviz/riboviz/tools/prep_riboviz.py", line 430, in process_sample
    orf_gff_file, config, log_file, run_config)
  File "/home/flic/riboviz/riboviz/workflow.py", line 533, in bam_to_h5
    run_config.is_dry_run)
  File "/home/flic/riboviz/riboviz/process_utils.py", line 130, in run_logged_command
    run_command(cmd, f, f)
  File "/home/flic/riboviz/riboviz/process_utils.py", line 22, in run_command
    assert exit_code == 0, "%s failed with exit code %d" % (cmd, exit_code)
AssertionError: ['Rscript', '--vanilla', '/home/flic/riboviz/rscripts/bam_to_h5.R', '--num-processes=8', '--min-read-length=10', '--max-read-length=50', '--buffer=250', '--primary-id=Name', '--secondary-id=NULL', '--dataset=B-Sc_2012', '--bam-file=B-Sc_2012/output/PRE_ENTRY_1/PRE_ENTRY_1.bam', '--hd-file=B-Sc_2012/output/PRE_ENTRY_1/PRE_ENTRY_1.h5', '--orf-gff-file=B-Sc_2012/input/transcriptcentric_abundant_full-ORF_ypd_plus_other_fixed_UTR_length_transcripts_issues_removed.gff', '--is-riboviz-gff=True', '--stop-in-cds=False'] failed with exit code 1
Processing sample: PRE_ENTRY_2
# ... same error messages for other samples...
Make length-sensitive alignments in H5 format. Log: B-Sc_2012/logs/20200423-163629/META_II_2/09_bam_to_h5.log
Problem processing sample: META_II_2
AssertionError
Traceback (most recent call last):
  File "/home/flic/riboviz/riboviz/tools/prep_riboviz.py", line 515, in process_samples
    sample_logs_dir, run_config)
  File "/home/flic/riboviz/riboviz/tools/prep_riboviz.py", line 430, in process_sample
    orf_gff_file, config, log_file, run_config)
  File "/home/flic/riboviz/riboviz/workflow.py", line 533, in bam_to_h5
    run_config.is_dry_run)
  File "/home/flic/riboviz/riboviz/process_utils.py", line 130, in run_logged_command
    run_command(cmd, f, f)
  File "/home/flic/riboviz/riboviz/process_utils.py", line 22, in run_command
    assert exit_code == 0, "%s failed with exit code %d" % (cmd, exit_code)
AssertionError: ['Rscript', '--vanilla', '/home/flic/riboviz/rscripts/bam_to_h5.R', '--num-processes=8', '--min-read-length=10', '--max-read-length=50', '--buffer=250', '--primary-id=Name', '--secondary-id=NULL', '--dataset=B-Sc_2012', '--bam-file=B-Sc_2012/output/META_II_2/META_II_2.bam', '--hd-file=B-Sc_2012/output/META_II_2/META_II_2.h5', '--orf-gff-file=B-Sc_2012/input/transcriptcentric_abundant_full-ORF_ypd_plus_other_fixed_UTR_length_transcripts_issues_removed.gff', '--is-riboviz-gff=True', '--stop-in-cds=False'] failed with exit code 1
Finished processing 6 samples, 6 failed
Processing error: B-Sc_2012/B-Sc_2012_config.yaml
Exception
Traceback (most recent call last):
  File "/home/flic/riboviz/riboviz/tools/prep_riboviz.py", line 823, in prep_riboviz
    run_workflow(config_file, is_dry_run)
  File "/home/flic/riboviz/riboviz/tools/prep_riboviz.py", line 702, in run_workflow
    raise Exception("No samples were processed successfully")
Exception: No samples were processed successfully

real	13m22.078s
user	72m34.655s
sys	33m48.946s
# FAIL!

Error for one sample:
# error for 1 sample from riboviz*.log
2020-04-23 16:38:45,280:riboviz.workflow:INFO: Make length-sensitive alignments in H5 format. Log: B-Sc_2012/logs/20200423-163629/PRE_ENTRY_1/09_bam_to_h5.log
2020-04-23 16:38:49,770:__main__:ERROR: Problem processing sample: PRE_ENTRY_1
2020-04-23 16:38:49,770:__main__:ERROR: AssertionError
Traceback (most recent call last):
  File "/home/flic/riboviz/riboviz/tools/prep_riboviz.py", line 515, in process_samples
    sample_logs_dir, run_config)
  File "/home/flic/riboviz/riboviz/tools/prep_riboviz.py", line 430, in process_sample
    orf_gff_file, config, log_file, run_config)
  File "/home/flic/riboviz/riboviz/workflow.py", line 533, in bam_to_h5
    run_config.is_dry_run)
  File "/home/flic/riboviz/riboviz/process_utils.py", line 130, in run_logged_command
    run_command(cmd, f, f)
  File "/home/flic/riboviz/riboviz/process_utils.py", line 22, in run_command
    assert exit_code == 0, "%s failed with exit code %d" % (cmd, exit_code)
AssertionError: ['Rscript', '--vanilla', '/home/flic/riboviz/rscripts/bam_to_h5.R', '--num-processes=8', '--min-read-length=10', '--max-read-length=50', '--buffer=250', '--primary-id=Name', '--secondary-id=NULL', '--dataset=B-Sc_2012', '--bam-file=B-Sc_2012/output/PRE_ENTRY_1/PRE_ENTRY_1.bam', '--hd-file=B-Sc_2012/output/PRE_ENTRY_1/PRE_ENTRY_1.h5', '--orf-gff-file=B-Sc_2012/input/transcriptcentric_abundant_full-ORF_ypd_plus_other_fixed_UTR_length_transcripts_issues_removed.gff', '--is-riboviz-gff=True', '--stop-in-cds=False'] failed with exit code 1

Investigation into bam_to_h5.R, since that's where the error happens:
NOTE: to debug this, it currently requires you to add the fix for interactive debugging #147 that we added to generate_stats_figs.R but which I don't think was added to bam_to_h5.R...
# threw in the interactive fix from regen-stats-32:

(base) flic@circe:~/riboviz$ R --vanilla --args --num-processes=8 --min-read-length=10 --max-read-length=50 --buffer=250 --primary-id=Name --secondary-id=NULL --dataset=B-Sc_2012 --bam-file=B-Sc_2012/output/PRE_ENTRY_1/PRE_ENTRY_1.bam --hd-file=B-Sc_2012/output/PRE_ENTRY_1/PRE_ENTRY_1.h5 --orf-gff-file=B-Sc_2012/input/transcriptcentric_abundant_full-ORF_ypd_plus_other_fixed_UTR_length_transcripts_issues_removed.gff --is-riboviz-gff=True --stop-in-cds=False

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
 # ...other R startup chat...

> source("/home/flic/riboviz/rscripts/bam_to_h5.R")
[1] "Created by: RiboViz"
[1] "Date: 2020-04-23 17:17:17"
[1] "File: /home/flic/riboviz/rscripts/bam_to_h5.R"
[1] "Version: commit 63241663f2cf91fdac18a6ba1d5a80e3f47101dd date 2020-04-23 15:30:48"
The following object is masked _by_ .GlobalEnv:
    secondary_id
[1] "bam_to_h5.R running with parameters:"
Error: subscript contains invalid names

> traceback()
14: stop(wmsg(...), call. = FALSE)
13: .subscript_error("subscript contains invalid ", what)
12: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,
        allow.NAs = allow.NAs)
11: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,
        allow.NAs = allow.NAs)
10: normalizeSingleBracketSubscript(i, xstub)
9: extractCOLS(x, j)
8: extractCOLS(x, j)
7: mcols(gff)[primary_id]
6: mcols(gff)[primary_id]
5: unique(mcols(gff)[primary_id][, 1]) at bam_to_h5.R#218
4: eval(ei, envir)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("/home/flic/riboviz/rscripts/bam_to_h5.R")

So it's in there somewhere.. I tried running lines through separately to see if I could identify what was the problem in the script.
> reads_to_list <- function(gene_location, bam_file, read_range, left_flank,right_flank, mult_exon=TRUE)
+ {
+   # Computes matrix of read counts with starting position and read length
+   # on a signle gene whose co-ordinates are supplied as arguments
+   #
+   # Args:
+   #   gene_location: (list) gff line containing gene co-ordinates
+   #   bam_file: (string) name of bam_file with reads in it
+   #   read_range: (int) vector of integer read lengths, e.g. 15:50
+   #   flank: (int) width of flanking region to include outside gene body/CDS
+   #   mult_exon: If TRUE, uses only the first supplied exon for gene co-ordinates
+   #
+   # Returns:
+   #   output: matrix of integer counts for each row/start position and column/read length
+   #
+
+   if(!mult_exon)
+     # If the gene is a single exon gene but multiple GRanges specified,
+     # use the first GRange
+   { gene_location <- gene_location[1]
+   }
+
+   # Number of read length categories
+   read_range_len <- length(read_range)
+
+   # Specify output matrix to store read data
+   gene_length = sum(sum(coverage(gene_location)))
+   output <- matrix(0,nrow=read_range_len,ncol=(gene_length + left_flank + right_flank))
+
+ # If CDS is on negative strand
+   if(as.character(strand(gene_location)[1])=="-"){
+     tmp <- left_flank
+     left_flank <- right_flank
+     right_flank <- tmp
+   }
+
+   # Expand genomic locations to include flanking region positions
+   if(length(gene_location)==1)
+   {# For single exon genes
+     start(gene_location) <- start(gene_location) - left_flank
+     end(gene_location) <- end(gene_location) + right_flank
+   }else{
+     # For multiple exon genes
+     start(gene_location)[start(gene_location)==min(start(gene_location))] <-
+         start(gene_location)[start(gene_location)==min(start(gene_location))] - left_flank
+     end(gene_location)[end(gene_location)==max(end(gene_location))] <-
+         end(gene_location)[end(gene_location)==max(end(gene_location))] + right_flank
+   }
+
+   # Specify variables to read in and create a parameter file for bam data
+   bam_what <- c("strand", "pos", "qwidth")
+   bam_param <- ScanBamParam(which = gene_location, what = bam_what)
+
+   # Read in bam data
+   bam_data <- scanBam(bam_file, param=bam_param)
+
+   # Subset reads that are on the same strand at the genomic location
+   read_strand <- unlist(lapply(bam_data,function(x) x$strand ))
+   read_location <- unlist(lapply(bam_data,function(x) x$pos ))[read_strand==as.factor(strand(gene_location)[1])]
+   read_width <- unlist(lapply(bam_data,function(x) x$qwid ))[read_strand==as.factor(strand(gene_location)[1])]
+
+   # Column numbers based on genomic position
+   nucleotide_pos <- unlist(which(coverage(gene_location)[seqnames(gene_location)[1]]==1))
+
+   # If the specified flanking regions of a gene end up outside the chromosome locations (<0)
+   # add pseudo columns with negative numbers
+   if(min(start(gene_location))<min(nucleotide_pos))
+   { nucleotide_pos <- c(min(start(gene_location)):0,nucleotide_pos)
+   }
+
+   # Count reads whose 5' ends map to each nucleotide and save them in output matrix
+   if(all(strand(gene_location)=="+")){
+     # For genes on positive strands
+     j <- 1 # counter for output row
+     for(i in read_range){
+       read_loc_len_i <- read_location[read_width==i] # subset reads of a particular length
+       count_reads_len_i <- table(factor(read_loc_len_i,levels=nucleotide_pos)) # count reads of a particular length
+       output[j,] <- c(count_reads_len_i)
+       j <- j+1
+     }
+   }
+
+   if(all(strand(gene_location)=="-")){
+     # For genes on negative strands
+     j <- 1 # counter for output row
+     for(i in read_range){
+       read_loc_len_i <- read_width[read_width==i]+read_location[read_width==i]-1 # subset reads of a particular length
+       count_reads_len_i <- table(factor(read_loc_len_i,levels=nucleotide_pos)) # count reads of a particular length
+       output[j,] <- c(rev(count_reads_len_i))
+       j <- j+1
+     }
+   }
+
+   # Return the output matrix
+   return(output);
+ }
>
> print_provenance(path_to_this_script)
[1] "Created by: RiboViz"
[1] "Date: 2020-04-23 17:29:40"
[1] "File: /home/flic/riboviz/rscripts/bam_to_h5.R"
[1] "Version: commit 63241663f2cf91fdac18a6ba1d5a80e3f47101dd date 2020-04-23 15:30:48"
> if (opt$secondary_id == "NULL") {
+   # unquote NULL option in secondary_id
+   secondary_id <- NULL
+ }
>
> attach(opt)
The following object is masked _by_ .GlobalEnv:

    secondary_id

The following objects are masked from opt (pos = 3):

    bam_file, buffer, dataset, hd_file, help, is_riboviz_gff,
    is_test_run, max_read_length, min_read_length, num_processes,
    orf_gff_file, primary_id, secondary_id, stop_in_cds

>
> print("bam_to_h5.R running with parameters:")
[1] "bam_to_h5.R running with parameters:"
> opt
$num_processes
[1] 8

$min_read_length
[1] 10

$max_read_length
[1] 50

$buffer
[1] 250

$primary_id
[1] "Name"

$secondary_id
[1] "NULL"

$bam_file
[1] "B-Sc_2012/output/PRE_ENTRY_1/PRE_ENTRY_1.bam"

$hd_file
[1] "B-Sc_2012/output/PRE_ENTRY_1/PRE_ENTRY_1.h5"

$orf_gff_file
[1] "B-Sc_2012/input/transcriptcentric_abundant_full-ORF_ypd_plus_other_fixed_UTR_length_transcripts_issues_removed.gff"

$dataset
[1] "B-Sc_2012"

$stop_in_cds
[1] FALSE

$is_riboviz_gff
[1] TRUE

$is_test_run
[1] FALSE

$help
[1] FALSE

>
> # Range of read lengths
> read_range <- min_read_length:max_read_length
>
> # Read in the positions of all exons/genes in GFF format and subset CDS locations
> gff <- readGFFAsGRanges(orf_gff_file)
>
> if(!is_riboviz_gff){
+   gff <- gff[gff$type=="CDS"]
+ }
>
> # Read in the list of genes
> genes <- unique(mcols(gff)[primary_id][,1])
Error: subscript contains invalid names

# HERE.

So the issue is in the line genes <- unique(mcols(gff)[primary_id][,1]). at LINE 202.
Investigated some of the relevant-seeming variables:
> primary_id
[1] "Name"

> str(gff)
Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..@ seqnames       :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. ..@ values         : Factor w/ 5086 levels "YAL001C_tx0",..: 1 2 3 4 5 6 7 8 9 10 ...
  .. .. ..@ lengths        : int [1:5086] 3 3 3 3 3 3 3 3 3 3 ...
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ ranges         :Formal class 'IRanges' [package "IRanges"] with 6 slots
  .. .. ..@ start          : int [1:15258] 1 26 3509 1 26 3851 1 22 643 1 ...
  .. .. ..@ width          : int [1:15258] 25 3483 125 25 3825 125 21 621 221 62 ...
  .. .. ..@   If ‘use.names=TRUE’ and the metadata
          columns are not ‘NULL’, then the names of ‘x’ are propagated
          as the row names of the returned DataTable object.  When
          setting the metadata columns, the supplied value must be
          ‘NULL’ or a DataTable object holding element-wise metadata.

Does it have anything to do with the bit of code here in bam_to_h5.R about secondary_id?
if (opt$secondary_id == "NULL") {
  # unquote NULL option in secondary_id
  secondary_id <- NULL
}

What is different when this script is running on the USUAL GFF/FASTA?
In the 09_bam_to_h5.logs it's not clear what's different since the code isn't particularly helpful.
Both have:
$primary_id [1] "Name"
$secondary_id [1] "NULL"
I realised why the "The following object is masked by .GlobalEnv: secondary_id" bit happens - it's because the script is referring to opt$secondary_id and doing stuff to it, BEFORE it does the attach, I think. Don't think that's relevant to this issue but might be nice to fix, especially if I'm removing attach() in #32 refactoring...
# Read in commandline arguments
opt <- parse_args(OptionParser(option_list=option_list),
                  convert_hyphens_to_underscores=TRUE)

if (opt$secondary_id == "NULL") {          # <<<<<<<< THIS BIT HERE
  # unquote NULL option in secondary_id
  secondary_id <- NULL
}
attach(opt)                                # BEFORE THIS

print("bam_to_h5.R running with parameters:")
opt                                        # AND DEFINITELY BEFORE THIS

So I'm going to have to do a step-through of the normal-gff/fasta data to compare what it gives before the break point with the new gff/fasta.
Perhaps the issue is that the GFF attribute the line genes <- unique(mcols(gff)[primary_id][,1]) is looking for (ie primary_id) ISN'T "Name" in this particular new-GFF file? Is it perhaps something different?
That's the next step of investigating, I think? Check out differences between attributes in GFFs?
Advice welcome!

This is possibly something I can advance in combination with (or more reasonably after!) resolving some of the GFF/FASTA format issues with example-datasets/#10 Drosophila dataset, since that'll involve me getting a better working knowledge of examining GFFs and what riboviz expects.
Also worth checking if I actually did remove attach() in the refactoring in #184 ... :cold_sweat:

Commit 84cf1a1 of refactor-bam-to-h5-61 has refactored bam_to_h5.R to avoid the attach. It now does:
opt <- parse_args(OptionParser(option_list = option_list),
                  convert_hyphens_to_underscores = TRUE)
...
if (opt$secondary_id  ==  "NULL") {
  # Unquote NULL option.
  secondary_id <- NULL
}
BamToH5(opt$bam_file, opt$orf_gff_file, opt$feature,
        opt$min_read_length, opt$max_read_length,
        opt$buffer, opt$primary_id, secondary_id, opt$dataset,
        opt$stop_in_cds, opt$is_riboviz_gff, opt$hd_file,
        opt$num_processes)

This ensures that secondary_id is NULL and not "NULL".

Perhaps the issue is that the GFF attribute the line genes <- unique(mcols(gff)[primary_id][,1]) is looking for (ie primary_id) ISN'T "Name" in this particular new-GFF file? Is it perhaps something different?

During #61 I also ran into
Error: subscript contains invalid names

and you're right. Consider the bam_to_h5.R test data in refactor-bam-to-h5-61:
$ cat data/Mok-tinysim-gffsam/tiny_2genes_20utrs.gff3
##gff-version 3
##ewallace -<EMAIL_ADDRESS>##date 2021-01-13
MAT	ewallace	UTR5	1	20	.	+	.	Name=MAT
MAT	ewallace	CDS	21	32	.	+	.	Name=MAT
MAT	ewallace	UTR3	33	52	.	+	.	Name=MAT
MIKE	ewallace	UTR5	1	20	.	+	.	Name=MIKE
MIKE	ewallace	CDS	21	35	.	+	.	Name=MIKE
MIKE	ewallace	UTR3	36	55	.	+	.	Name=MIKE

Run bam_to_h5.R:
$ samtools view -S -b data/Mok-tinysim-gffsam/A.sam > A.bam
$ samtools index A.bam
$ Rscript --vanilla rscripts/bam_to_h5.R --num-processes=1 \
  --min-read-length=10 --max-read-length=50 --buffer=20 \
  --primary-id=Name --secondary-id=NULL --dataset=Mok-tinysim \
  --bam-file=A.bam --hd-file=A.h5 \
  --orf-gff-file=data/Mok-tinysim-gffsam/tiny_2genes_20utrs.gff3 \
  --is-riboviz-gff=true --stop-in-cds=false
...
$primary_id
[1] "Name"

$secondary_id
[1] "NULL"
...
[1] "Saving mapped reads in a H5 file"
[1] "bam_to_h5.R done"
$ rm A.h5

Set primary_id to XXX and rerun:
$ Rscript --vanilla rscripts/bam_to_h5.R --num-processes=1 \
  --min-read-length=10 --max-read-length=50 --buffer=20 \
  --primary-id=XXX --secondary-id=NULL --dataset=Mok-tinysim \
  --bam-file=A.bam --hd-file=A.h5 \
  --orf-gff-file=data/Mok-tinysim-gffsam/tiny_2genes_20utrs.gff3 \
  --is-riboviz-gff=true --stop-in-cds=false
...
$primary_id
[1] "XXX"

$secondary_id
[1] "NULL"
...
Error: subscript contains invalid names
Execution halted

Copy GFF file:
$ cp data/Mok-tinysim-gffsam/tiny_2genes_20utrs.gff3  xxx.gff3

Replace Name with XXX in xxx.gff3:
$ cat xxx.gff3
##gff-version 3
##ewallace -<EMAIL_ADDRESS>##date 2021-01-13
MAT	ewallace	UTR5	1	20	.	+	.	XXX=MAT
MAT	ewallace	CDS	21	32	.	+	.	XXX=MAT
MAT	ewallace	UTR3	33	52	.	+	.	XXX=MAT
MIKE	ewallace	UTR5	1	20	.	+	.	XXX=MIKE
MIKE	ewallace	CDS	21	35	.	+	.	XXX=MIKE
MIKE	ewallace	UTR3	36	55	.	+	.	XXX=MIKE

Run:
$ Rscript --vanilla rscripts/bam_to_h5.R --num-processes=1 \
  --min-read-length=10 --max-read-length=50 --buffer=20 \
  --primary-id=XXX --secondary-id=NULL --dataset=Mok-tinysim \
  --bam-file=A.bam --hd-file=A.h5 \
  --orf-gff-file=xxx.gff3 \
  --is-riboviz-gff=true --stop-in-cds=false
...
$primary_id
[1] "XXX"

$secondary_id
[1] "NULL"
...
[1] "Saving mapped reads in a H5 file"
[1] "bam_to_h5.R done"

Success!


Bs1770gainsupport-tests

first proposal for tests of the bs1770gain replaygain support

This looks right to me! I don't have bs1770gain installed currently, and it looks like it will be nontrivial to get it running on Travis, so this is a little bit of a leap of faith. But it should do just fine for now. Thank you!


Cannot run/test Kata

I attempted 2 different kata today and every time I attempt to run the sample tests I receive the following error:
"This error was caused due to an issue processing the web request, not because of an issue executing your code. You can retry the request."
I retried several times with the same results.

Same here :( Doesn't matter which language I choose, I always end up with this message :(

Same here :(

+1

Duplicate of #1057. Sad~ No kata can be trained.


Example fails to be built.

wasm-on-jvm/examples/hello-world$ gradle compileJava
Starting a Gradle Daemon (subsequent builds will be faster)
Download https://plugins.gradle.org/m2/gradle/plugin/com/athaydes/wasm/wasm-gradle-plugin/1.0/wasm-gradle-plugin-1.0.pom
Download https://plugins.gradle.org/m2/com/github/cretz/asmble/asmble-compiler/0.3.0/asmble-compiler-0.3.0.pom
Download https://plugins.gradle.org/m2/org/jetbrains/kotlin/kotlin-stdlib/1.2.51/kotlin-stdlib-1.2.51.pom.pom
Download https://plugins.gradle.org/m2/org/jetbrains/kotlin/kotlin-reflect/1.2.51/kotlin-reflect-1.2.51.pom
Download https://plugins.gradle.org/m2/org/ow2/asm/asm-util/5.2/asm-util-5.2.pom
Download https://plugins.gradle.org/m2/org/ow2/asm/asm-tree/5.2/asm-tree-5.2.pom
Download https://plugins.gradle.org/m2/com/github/cretz/asmble/asmble-annotations/0.3.0/asmble-annotations-0.3.0.pom
Download https://plugins.gradle.org/m2/org/ow2/asm/asm-parent/5.2/asm-parent-5.2.pom
Download https://plugins.gradle.org/m2/org/jetbrains/kotlin/kotlin-stdlib-common/1.2.51/kotlin-stdlib-common-1.2.51.pom
Download https://plugins.gradle.org/m2/org/ow2/asm/asm/5.2/asm-5.2.pom
Download https://plugins.gradle.org/m2/org/jetbrains/kotlin/kotlin-stdlib/1.2.51/kotlin-stdlib-1.2.51.jar
Download https://plugins.gradle.org/m2/org/ow2/asm/asm-util/5.2/asm-util-5.2.jar
Download https://plugins.gradle.org/m2/org/ow2/asm/asm/5.2/asm-5.2.jar
Download https://plugins.gradle.org/m2/gradle/plugin/com/athaydes/wasm/wasm-gradle-plugin/1.0/wasm-gradle-plugin-1.0.jar
Download https://plugins.gradle.org/m2/org/jetbrains/kotlin/kotlin-stdlib-common/1.2.51/kotlin-stdlib-common-1.2.51.jar
Download https://plugins.gradle.org/m2/org/jetbrains/kotlin/kotlin-reflect/1.2.51/kotlin-reflect-1.2.51.jar
Download https://plugins.gradle.org/m2/org/ow2/asm/asm-tree/5.2/asm-tree-5.2.jar
Download https://plugins.gradle.org/m2/com/github/cretz/asmble/asmble-compiler/0.3.0/asmble-compiler-0.3.0.jar
Download https://plugins.gradle.org/m2/com/github/cretz/asmble/asmble-annotations/0.3.0/asmble-annotations-0.3.0.jar

FAILURE: Build failed with an exception.

* Where:
Build file '/mnt/bkel/vi/src/wasm-on-jvm/examples/configured-c-to-wasm/build.gradle' line: 17

* What went wrong:
A problem occurred evaluating project ':configured-c-to-wasm'.
> Failed to apply plugin [id 'com.athaydes.wasm']
   > Extension of type 'SourceSetContainer' does not exist. Currently registered extension types: [ExtraPropertiesExtension, DefaultArtifactPublicationSet, ReportingExtension, WasmExtension]

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 11s

$ gradle --version

------------------------------------------------------------
Gradle 4.4.1

Why are you using such old Gradle version?
As you can see in gradle.properties this project uses Gradle 5.2.1 (which is also old, but should work with Gradle 6 and maybe even 7).
Gradle 4 is very old and the upgrade to Gradle 5 broke lots of stuff.
To make sure the project works, don't use gradle, use ./gradlew.

Indeed, using gradle wrapper make complication successful:
$ ../../gradlew compileJava
Downloading https://services.gradle.org/distributions/gradle-5.2.1-all.zip
..............................................................................................................................

Welcome to Gradle 5.2.1!

Here are the highlights of this release:
 - Define sets of dependencies that work together with Java Platform plugin
 - New C++ plugins with dependency management built-in
 - New C++ project types for gradle init
 - Service injection into plugins and project extensions

For more details see https://docs.gradle.org/5.2.1/release-notes.html

Starting a Gradle Daemon (subsequent builds will be faster)

> Task :hello-world:compileWasm
Compiling wasm file /mnt/bkel/vi/src/wasm-on-jvm/examples/hello-world/src/main/wasm/HelloWasm.wast to class HelloWasm

> Task :hello-world:compileJava
warning: unknown enum constant WasmExternalKind.FUNCTION
  reason: class file for asmble.annotation.WasmExternalKind not found
1 warning

BUILD SUCCESSFUL in 40s
2 actionable tasks: 2 executed
$ java -cp build/classes/java/main:build/classes/wasm/main Hello
WASM says 42

Maybe hello-world's README should mention ../../gradlew instead of just gradle, so that it would be clear that there is specific Gradle version?
4.4.1 is gradle version in current's Debian stable.


[USDU-199] Delete GameObjects when updating USD Instancers to avoid duplication.

Purpose of this PR
Ticket/Jira #: USDU-199
When refreshing a USD asset, Point Instancers were generating a new set of instances without cleaning up the previous ones, resulting in duplication. This change destroys the old instances first to avoid the duplication.
Performance wise this isn't perfect, as destroying GameObjects has a cost. However (I don't think) we have a way of knowing whether the prototype has changed, so this seems like the safest way for now.
I've also added a fix for the error ApplicationException: USD ERROR: /instancer -- all sample times in times and baseTime must either all be numeric or all be default that was occurring on refresh of any PointInstancer. I've based the fix on the docs:

If your application does not care about off-sample interpolation, it can supply the same value for baseTime that it does for time.

I'm assuming for the time being that we do not care about this.
Testing
Functional Testing status:
Tested against original asset (linked in Jira), confirmed no more duplication.
Performance Testing status:
Measured the performance of previous vs new with Superluminal- for 100 instances, before = 17ms, after = 22ms. Average of 0.05ms extra per instance.
Overall Product Risks

Complexity: Low

Halo Effect: Low

Additional information
Note to reviewers:

Reminder:

[x] Add entry in CHANGELOG.md (if applicable)

LGTM!


Adding Test App not showing in Workspace

Should adding a Test app update the workspace?  It does not for me, wondering if this is intentional.

It should add it to the workspace, yes.
Will check

I see you noted you can't reproduce.  Here is the steps I did for this repo.
Created the repo from the AL-GO-PTE repo template
Added a new APP, changing the WorkSpace from "." to PTEFLOW as I wanted to test multiple apps (using the sample code).
after trying to add new app without the "PTEFLOW" workspace name, I added a new Test App (without the sample code).
The test app does not show in the workspace.
Happy to add you to the repo if that would assist you in your investigation.

yes, this field

Yep - that results in a multi-project repo, which really is intended for having totally unrelated (or maybe even conflicting) apps in the same repository - basically every project ships seperatly.
If the apps have inter-dependencies - you should keep the . and have all apps in the same root project,
I will check the issue


Package flutter_test based on async 2.6.1 dependence

Please, upgrade async dependence to 2.7.0 version.

Updated on dev channel, need to wait for release on stable channel


Sending mail with attachment

How to send a email with attachment using gmail api?
am able to send mail successfully without an attachment,but am not getting how to attach a file and send the  mail...can anyone please help me on this .
following is the snippet am using for sending a mail with out attachment
function sendMessage(auth) {
    var gmail =google.gmail('v1');

    var email_lines =[];
    email_lines.push("From: abc@gmail.com");
<EMAIL_ADDRESS>");
    email_lines.push('Content-type: text/html;charset=iso-8859-1');
    email_lines.push('MIME-Version: 1.0');
    email_lines.push("Subject: Testing ");
    email_lines.push("");
    email_lines.push("hai");
    email_lines.push("<b>And henge naavu</b>");

    var email =email_lines.join("\r\n").trim();

    var base64EncodedEmail = new Buffer(email).toString('base64');

  base64EncodedEmail= base64EncodedEmail.replace(/\//g,'_').replace(/\+/g,'-');

  gmail.users.messages.send({
     auth:auth,
    'userId': 'me',

 'resource': {
        'raw': base64EncodedEmail
      }

  },function(err, response) {
    if (err) {
      console.log('The API returned an error: ' + err);
      return;
    }
 console.log(response);
});

Thanks in advance

please anyone can help me on this

You could try to form a Content-Type: multipart/mixed email, this allows to send attachments and text in parts. https://tools.ietf.org/html/rfc2183

@Chethandsagar what do i need to send in auth parameter.

@Chethandsagar  did you get the solution for this problem? I am trying to send attachment in the mail. Not getting much help anywhere.

@ishwarrimal Does this page help?

(Closing this issue for now - @ishwarrimal @Chethandsagar feel free to reopen if this is still an issue for you. Thanks!)

Here is the solution that worked for me,
function makeBody(subject, message) {
var boundary = "myapp";
var nl = "\n";
var attach = new Buffer(fs.readFileSync(__dirname + "/../"+fileName)) .toString("base64");
// console.dir(attach);
var str = [
        "MIME-Version: 1.0",
        "Content-Transfer-Encoding: 7bit",
        "to: " + receiverId,
        "subject: " + subject,
        "Content-Type: multipart/alternate; boundary=" + boundary + nl,
        "--" + boundary,
        "Content-Type: text/plain; charset=UTF-8",
        "Content-Transfer-Encoding: 7bit" + nl,
        message+ nl,
        "--" + boundary,
        "--" + boundary,
        "Content-Type: Application/pdf; name=myPdf.pdf",
        'Content-Disposition: attachment; filename=myPdf.pdf',
        "Content-Transfer-Encoding: base64" + nl,
        attach,
        "--" + boundary + "--"

    ].join("\n");

    var encodedMail = new Buffer(str).toString("base64").replace(/\+/g, '-').replace(/\//g, '_');
    return encodedMail;
}

@ishwarrimal please help as the solution given by you is not working. Everything is going as a text in the mail.

Why isn't there an example of such basic functionality anywhere? I've been spending 4 hours trying to send a mail with an attachment. Impossible.

Hi!
I would advise building the MIME message with mail-composer from nodemailer const MailComposer = require('nodemailer/lib/mail-composer'); this will help you to create the MIME requests with ease including the attachment components.
Furthermore it will help you understand, by reverse engineering, how the MIME spec works which i my opinion is the biggest road block in this topic.

Here is the solution that worked for me,
function makeBody(subject, message) {
var boundary = "__myapp__";
var nl = "\n";
var attach = new Buffer(fs.readFileSync(__dirname + "/../"+fileName)) .toString("base64");
// console.dir(attach);
var str = [
        "MIME-Version: 1.0",
        "Content-Transfer-Encoding: 7bit",
        "to: " + receiverId,
        "subject: " + subject,
        "Content-Type: multipart/alternate; boundary=" + boundary + nl,
        "--" + boundary,
        "Content-Type: text/plain; charset=UTF-8",
        "Content-Transfer-Encoding: 7bit" + nl,
        message+ nl,
        "--" + boundary,
        "--" + boundary,
        "Content-Type: Application/pdf; name=myPdf.pdf",
        'Content-Disposition: attachment; filename=myPdf.pdf',
        "Content-Transfer-Encoding: base64" + nl,
        attach,
        "--" + boundary + "--"

    ].join("\n");

    var encodedMail = new Buffer(str).toString("base64").replace(/\+/g, '-').replace(/\//g, '_');
    return encodedMail;
}

what is "my_app" here? is it an arbitrary value?

@ved1995 it is the variable that @ishwarrimal uses as the boundary variable. It can be any random string.

Maybe this helps people with the same problem.
https://stackoverflow.com/a/52310846/5099642


[WIP] testing Shiva's branch for multi-arch build

test-path: prow gpu-operator publish_master_bundle
/hold

/test ?

/test test-commit

/uncc @mkowalski
/uncc @osherdp

/test test-commit

/test test-commit

/test test-commit

/test test-commit

/test test-commit

/test test-commit

/retest
/test test-commit

/test test-commit

/test test-commit

/test 4.10-nvidia-gpu-operator-e2e
/test 4.6-nvidia-gpu-operator-e2e

/unhold
/cc @fabiendupont
/cc @kpouget

seems good,
you may want to hold until they merge the PR in the GPU Operator?

@kpouget, Its merged into master already. AFAIK we build from master (or a commit). correct?

oh indeed  https://gitlab.com/nvidia/kubernetes/gpu-operator/-/merge_requests/396
looks good them!

/lgtm
/approve


create a static reference to interior mutable const

this is the result of the following clippy lint which i have blindly followed
https://rust-lang.github.io/rust-clippy/master/#declare_interior_mutable_const
I can't see any statistically significant difference in the benches on my machine.

Huh, that's an odd one.

This really looks like a false positive on clippy's part. This method call doesn't mutate the constant...
Looking at the surrounding code, I think this log may be wrong! It should be logging the header value that was just removed.

https://github.com/rust-lang/rust-clippy/issues/3825


Add new concept exercise : errors

This fixes #949
This PR is replacing the PR in the v3 repo => https://github.com/exercism/v3/pull/2545

Hiya! Can you rebase?

Ohhhh yeaaaaah


Revert "Remove Spanner Entity Framework Core provider source"

Reverts googleapis/google-cloud-dotnet#3703

I'm going to close this PR, as we definitely don't want that source code live in this repo. You're welcome to revert the change in your own fork, of course, but it's not code we intend to maintain within this team.


target/idl/tic_tac_toe.json doesn't exist

⚠ Don't use issues for support questions ("How does x feature work in Anchor? How to do x in Anchor?"). Use the discord instead https://discord.gg/NHHGSXAnXk (but don't ping maintainers). ⚠
Cannot run anchor test.

Your program is named tic_toc_toe instead of tic_tac_toe. Change the program module name:
- mod tic_toc_toe
+ mod tic_tac_toe


Test jobs always fails to pull code

May I know when did this happen? We recently added cleanWs() for every clone retry https://github.com/adoptium/aqa-tests/pull/4061

re:https://github.com/adoptium/aqa-tests/issues/4075#issuecomment-1288981919 based on the related PR, this issue relates to buildenv/jenkins/testJobTemplate rather than openjdk_tests & Jenkinsfilebase groovy scripts.

May I know when did this happen? We recently added cleanWs() for every clone retry #4061

If the current repo has no relevant history with the original repo with the same name, it will occur when the master node pulls the script code.I've read the merge request https://github.com/adoptium/aqa-tests/pull/4061,I'm sorry it cannot solve above problem.


[WIP] PR: Put section header rows in the file switcher at item level

Description of Changes

[ ] Wrote at least one-line docstrings (for any new functions)
[ ] Added unit test(s) covering the changes (if testable)
[x] Included a screenshot (if affecting the UI)

Remove section header rows in the file switcher and add them to the left of the file name in blue.
Issue(s) Resolved

Fixes Item 6 of Issue #8580
Affirmation
By submitting this Pull Request or typing my (user)name below,
I affirm the Developer Certificate of Origin
with respect to all commits and content included in this PR,
and understand I am releasing the same under Spyder's MIT (Expat) license.

I certify the above statement is true and correct:
Juanis2112

Hello @juanis2112! Thanks for submitting the PR.

In the file spyder/widgets/fileswitcher.py, following are the PEP8 issues :

Line 684:21: E265 block comment should start with '# '
Line 707:21: E265 block comment should start with '# '

@juanis2112, please update your screenshot above to let's see your latest changes.
Also, please merge with master to get the fix I pushed a couple of days ago for Python 3.5/CircleCI.

Besides Editor, what other possible section headers are there?

@juanis2112 and @dalthviz thanks for taking a look at this. I suggest we continue the integration of the new switcher (https://github.com/spyder-ide/spyder/pull/9133) which already makes this functionality much simpler, generic and decoupled from the actual process (of selecting files in this case)

That's not going to be ready for beta2, so let's allow Juanita to finish this one.

(@ccordoba12 feels like duplicated effort.)
@juanis2112 this is how I accomplished it https://github.com/spyder-ide/spyder/pull/9133/files#diff-48bee778d0036aea166212d1e04c5ad0R195

feels like duplicated effort.

I know, but @juanis2112 has worked hard to implement this, so I'd like her fix to be part of beta2.


Enum-Tuple-Variant with single element should not be a sequence

#[Deserialize]
enum A {
    B(i32),
    C(Vec<i32>),
}

The json for this requires additional square brackets for another array layer.
{"C":[[5, 6, 7]]}

or

{"B":[42]}

Unit variants are already handles specially. I propose to also handle single element variants specially, so the following would be legal:
{"C":[5, 6, 7]}

or

{"B":42}

Anyone that wishes to have the previous behavior, could use an explicit tuple.
#[Deserialize]
enum A {
    B((i32,)),
    C((Vec<i32>,)),
}

Alternatively deserialization might accept both, but that might be more of a mess than it's worth

The use-case is the pandoc ast
http://hackage.haskell.org/package/pandoc-types-<IP_ADDRESS>/docs/Text-Pandoc-Definition.html

That is interesting, because "normal" single element variants serialize directly as their inner type.

O_o, i need to investigate further then... maybe a newtype might come to my rescue

My claim isn't true, it was in a faulty version I wrote some time ago. Sorry for the rush.

That's an interesting idea. Way back in the early days of rustc-serialize, we used to serialize unit variants as a string, but someone from mozilla (maybe @pcwalton?) mentioned that JIT engines working with an array of enums really prefer those serialized enums to be of the same "shape". So this:
["a", {"b":[1]}, , {"c":[1, 2]}]

Is slower to work with than this:
[{"a": []}, {"b":[1]}, , {"c":[1, 2]}]

I wonder if the speed is worth it. @pcwalton: do you have an opinion on this?

That would be the obvious conclusion of my simplification. Serde could trivially deserialize from old-style unit enum variants in it's current setup, so both could be allowed. Serialization is a different issue though...

I guess that's true, but I wouldn't contort serde's JSON output to try to be JS JIT-friendly.


BeatTogether on ModAssistant

I know that not a real issue, but since an update for 1.18.X came out, can you update it on ModAssistant ?

This is not being added to ModAssistant at this time until we can guarantee better stability.  Use the manual install method if you want to install the mod for now.


explicit use tls12 when downloading nuget during dotnetsdk image build

Description
Local container build of dotnetsdk fails when calling Invoke-WebRequest since powershell on dotnet framework sdk image does not explicitly use tls1.2 by default.
This "fix" explicitly set tls version before calling invoke-webrequest
I also bumped up the nuget version to 5.8.0 for no particular reason, other than it makes sense.
Motivation
It makes the build run locally.
How Has This Been Tested?
The container build completed successful, while it did not without the change.
Types of changes

[x] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to change)
[ ] Documentation update (non-breaking change; modified files are limited to the /docs directory)

Checklist:

[x] I have read the Contributing guide.
[x] My code follows the code style of this project.
[ ] My code/comments/docs fully adhere to the Code of Conduct.
[ ] My change is a code change and it requires an update to the documentation.
[ ] My change is a documentation change and it requires an update to the navigation.

This PR doesn't really address the root issue. The reason TLS 1.2 is not enabled by default is, because an LTSC2016 image is being pulled in as base rather than the expected LTSC2019.
It happens here: https://github.com/Sitecore/MVP-Site/blob/5bfafc85d17d35ebfc79588a232a14443e493cc1/.env#L50
This line needs to be changed to
SOLUTION_BUILD_IMAGE=mcr.microsoft.com/dotnet/framework/sdk:4.8-ltsc2019
Which will then in turn mean that the correct base OS is applied and the workaround in this PR is no longer required. I say this with certainty since I did exactly this yesteday to solve the same problem.
I believe this approach to be the correct one. While this PR does work around it and enforce TLS 1.2 - that is just one problem in a list of potentially many problems that could arise, from basing the build on 2016 when everywhere else we use 2019.

@cassidydotdk I completely agree. I did not notice the tag on the sdk 4.8 image in the env file. I'll change my PR to this asap.


Beta runtime not supported note

Added a note about the lack of Swagger auto-generate support in the beta runtime.

@msimecek : Thanks for your contribution! The author, @alexkarcher-msft, has been notified to review your proposed change.

Sorry @msimecek, I just transferred ownership of this topic and forgot to pass along this PR. @ggailey777 -- can you confirm this change and sign off. Thanks.

This looks good to me.
#sign-off


Enable ssl

Enable SSL connections to the database
Add an ssl object based on ISSLConfig
interface
Allow for null geometry and srid
ESRI Feature Services can support tables, which have no geometry. This
change keeps the provider from erroring when reading postgres tables
that have no geometry but can still be served as a Feature Layer

Thanks @saltaverde, do you have an example of some data to test against?

Thanks @saltaverde, do you have an example of some data to test against?

@doneill It could be pretty much any table that doesn't have a column of type geometry or geography in it.
For example
create table test_data as (select (random() * 1000 + 1)::integer as id, substr(md5(random()::text), 1, 25) as name from generate_series(0, 9));

@saltaverde Can you change the base branch to develop?  I updated the error handling around tables w/o geometry columns.  Let me know if that addresses your issue.

@saltaverde not sure if this is still relevant, but v1.0.9 generates an empty json object when geometry column not available on the table.  Not sure if that is what you would expect, but the provider doesn't error out now.


[Search for a journey]  Wrong design of the "CONFIRM" button.

Reproducible: always
Build found:  1.0.99
Preconditions
The "Car" app is opened.
The user is logged in.
Steps to reproduce

Go to the 'Search for a journey' page
Click on non requested journey
Tap the "Request to driver" button.
Observe the result

Actual result
The "CONFIRM" button label and frame are colored grey.
Expected result
The "CONFIRM" button label and frame must be black.
Labels to be added
"Bug" ("bug"), Priority ("pri: ")


The Long Katex formula would overflow the document page.

Have you read the Contributing Guidelines on issues?

[X] I have read the Contributing Guidelines on issues.

Prerequisites

[X] I'm using the latest version of Docusaurus.
[X] I have tried the npm run clear or yarn clear command.
[X] I have tried rm -rf node_modules yarn.lock package-lock.json and re-installing packages.
[X] I have tried creating a repro with https://new.docusaurus.io.
[X] I have read the console error message carefully (if applicable).

Description
When the inserted Katex formula is very long, the formula range will overflow the page.
This breaks the responsive look and feel of the page

Reproducible demo
https://leetcode.terminels.com/docs/notes/algorithm/recursion/fast-pow
Steps to reproduce

Open an page and insert the long formula,such as

$$
\text{power}(x, n) = \begin{cases}
1 & \text{if } n = 0 \\
\text{power}(x, \frac{n}{2}) \cdot \text{power}(x, \frac{n}{2}) & \text{if } n > 0 \text{ and } n \text{ is even} \\
x \cdot \text{power}(x, \frac{{n-1}}{2}) \cdot \text{power}(x, \frac{{n-1}}{2}) & \text{if } n > 0 \text{ and } n \text{ is odd}
\end{cases}
$$

Expected behavior
It would be better to add scroll bars to the formula block instead of overflowing content and destroying the page.
Actual behavior

Your environment
No response
Self-service

[X] I'd be willing to fix this bug myself.

Hi! KaTeX is entirely delegated to third party plugins and we implemented none of its logic. It's only included in our docs for your convenience. To implement other designs, you can add custom CSS yourself.

couldn't we put the formula in a overflow-x auto container?
This should be easy to do and probably be considered a good workaround?


Add env id to filters in normal and advanced views

Checklist:

[X] Have you successfully deployed to an AWS account with your changes?
[X] Have you successfully tested with your changes locally?

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

Reviewed in office hours, Nov 29, 2023.


⚠ AsianCinema has degraded performance

In b96febb, AsianCinema ($ACM) experienced degraded performance:

HTTP code: 200
Response time: 17677 ms

Resolved: AsianCinema performance has improved in 929b7f0 after 10 minutes.


feat: import package ot-simian from AUR

Note: before merging I want to address the issues marked with FIXME: in the PKGBUILD.

CI check currently fails because the build is not reproducible. I have found no indication that the ldc2 compiler is actually capable of making reproducible builds or whether it supports the SOURCE_DATE_EPOCH env var.
The dmd compiler supports it, but using dmd for building Dplug plugin on linux is not supported :disappointed:
How should we handle that?

Another question: is it worth packaging dplug-build separately?

@SpotlightKid if there's no easy way to make it reproducible for now, I'd leave it like that and open an issue here and/or upstream to tackle that.
Btw, new release came out today 🎉

Upstream has no issue tracker :disappointed:
Time fire up the email client...

Right. If it's a Dplug issue however we could report it there.

To<EMAIL_ADDRESS>Subject: OneTrick Simian reproducible builds?

Hello there,

great plugin and thanks for releasing it under the GPL!

I have created an Arch user repository package for OneTrick SIMIAN, to help users compile it as an LV2 or VST3 format plugin for Arch Linux:

https://aur.archlinux.org/packages/ot-simian

We also want to provide binary packages for Arch Liux users via our third-party binary package repository at https://arch.osamc.de.

We noticed that the produced binaries are not reproducible (as in https://reproducible-builds.org/). On Linux only the ldc2 compiler is supported for compiling Dplug plugins and I could not find out how to make reproducible builds with it.

Do you know whether its is possible to make reproducible builds with Dplug on Linux and, if so, how?

Might I also suggest that you also offer the LV2 version for Linux for sale? As far as I have tested, it works well.

Christopher Arndt

Dplug issue: https://github.com/AuburnSounds/Dplug/issues/715

Hello, I'm not sure it's worth it to make a dplug-build package.
Note that you can often use a dplug-build from a different Dplug version than strictly used to build a plugin, though using the same Dplug to build a plugin and dplug-build itself is safest.
Dplug follows Semver, so in this case the latest dplug-build from Dplug v12 tag will be able to build any plugin using Dplug v12 even from an earlier version.
dplug-build is also not strictly necessary on Linux, you can extract the DUB commands you are interested in with dplug-build -v flag.

dplug-build is also not strictly necessary on Linux, you can extract the DUB commands you are interested in with dplug-build -v flag.

Good to know, thanks!

dplug-build is also not strictly necessary on Linux, you can extract the DUB commands you are interested in with dplug-build -v flag.

Good to know, thanks!

It doesn't show the commands to generate the LV2 manifest.ttl file, though.

@SpotlightKid I've been imprecise, dplug-build is necessary to build the VST2

The code that does this is:

Nice. I converted this into Python:
https://github.com/osam-cologne/archlinux-proaudio/blob/feat/package-ot-simian/packages/ot-simian/generate-manifest-ttl.py


[main, macOS] post-5432 (VispyCanvas), canvas.background isn't initialized properly

🐛 Bug
#5432 (love git bisect) has introduced a bug where a new viewer made with Light theme gets a black canvas background. However, toggling to light sets the background correctly to white.
To Reproduce
Steps to reproduce the behavior:

Set light theme in Preferences.
Open a new viewer in light theme
make empty labels layer -> see black canvas in light viewer

If you toggle the theme to dark/system and back to light using viewer.theme = 'light' it will show correct white canvas.
Expected behavior
The canvas of new viewer should respect theme settings.
Environment
napari: 0.5.0a2.dev188+gefa55a5b
Platform: macOS-13.3.1-arm64-arm-64bit
System: MacOS 13.3.1
Python: 3.10.10 | packaged by conda-forge | (main, Mar 24 2023, 20:12:31) [Clang 14.0.6 ]
Qt: 5.15.6
PyQt5: 5.15.7
NumPy: 1.24.3
SciPy: 1.10.1
Dask: 2023.4.1
VisPy: 0.13.0
magicgui: 0.7.2
superqt: unknown
in-n-out: 0.1.7
app-model: 0.1.4
npe2: 0.7.1.dev2+gb33bc09

OpenGL:
- GL version: 2.1 Metal - 83.1
- MAX_TEXTURE_SIZE: 16384

Screens:
- screen 1: resolution 1680x1050, scale 2.0

Settings path:
- /Users/piotrsobolewski/Library/Application Support/napari/napari-dev_a1eb8b76ba95fa16ad06e26097b46b8455dfbf0b/settings.yaml

Additional context
this is on macOS, happens with system during the day too. Sorry I missed it!

I will pick it up

Looks like in the init of VispyCanvas self.bgcolor isn't set to anything.
Adding:
self.bgcolor = transform_color(
            get_theme(self.viewer.theme, False).canvas.as_hex()
        )[0]

(and the import) fixes the issue on my end.
I can make a PR if you think that's fine.


Periodic targets IPTT: When a program has no targets set up, don't include it in the program menu

Applies to the following two places:

IPTT landing page
Filter panel for the periodic targets version of the IPTT report.

Acceptance criteria
IPTT landing page

[x] When a program has no targets set up for any indicator, it does not show up in the Program menu.
[x] It's not necessary for all indicators in the program to have targets set up; there just needs to be at least one indicator with targets.

Filter panel of the periodic targets IPTT

[x] When a program has no targets set up, it does not show up in the Program menu.
[x] It's not necessary for all indicators in the program to have targets set up; there just needs to be at least one indicator with targets.

Context: Why are we bothering?
We have a number of older programs in the system that have no targets set up -- usually because they're older and have missing field values that prevented us from automatically giving them a target value of LoP-only. Right now, all programs show up in the Periodic Targets program menu, but I get no Target Periods options when there are no periodic targets set for that program. This is correct behavior from a technical standpoint. However, if I'm a regional desk officer not familiar with every program in the region, I won't understand why I'm not seeing any options for some programs. Instead of displaying error messages, it would be best to simply remove those options from the program menu.

@mahmoodkhan I think we do need to exclude programs that do not have reporting start and end dates, because otherwise it'll generate an error message for the Actuals-only report. And if we're excluding from one, we may as well exclude from both.

@mahmoodkhan I am not able to generate Actuals-only reports for many of the programs. I think it may only be permitting me to see reports when ALL indicators have targets set up. We need it to still work even if some of the indicators don't yet have targets.


Add 'allowsBackForwardNavigationGestures' property to the iOS WKWebview

Fixes issue for the WKWebView.

Add 'allowsBackForwardNavigationGestures' property to the iOS WKWebview

Ouch I did break cocoapods when setting up semantic release then :( . Can you split your PR for more visibility ? I'll merge ASAP

Hello, I updated master so that semantic release is now publish the version to package.json. Were you using a git url to pull the code by the way instead of npm registry ? Else I don't understand how you got that bug 🤔

I needed this feature so I was using forked git url. If this commit merged and package is published, we will fix it and you can ignore that errors.

Okay this is why you had no version inside package.json. It makes sense now :)

:tada: This PR is included in version 2.5.0 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


Merge codebase

I want to merge the login page to be up to date in the git version control.

LGTM!! Merge!


About github page of lobor is down

Trying getting into the link provided in the repo, lobor.github.io/crossed/ but I think is down.

Yes the repo has been transfer and url have been changed
th e new url is paymium.github.io/crossed/


Fix #4: Update requirements to websockets 7.0

Fixes websockets build errors by updating required version to 7.0.
I just picked the newest version and didn't check to see which exact version started building successfully. Feel free to lower requirement.
Also feel free to double-check that source changes aren't necessary. I don't have an extensive Python environment on my machine.

Thanks for taking the time to update this.


Update Fortran dense linear algebra optimize integral sample

Existing Sample Changes
Description

Update sample to work with ifx
Formatting updates
Minor editorial updates

Type of change

[X] Bug fix (non-breaking change which fixes an issue)

@krisdale The sample.json needs to be updated to remove darwin and add in linux and windows just like PR#1797.

Thanks for the review @jimmytwei  - updates applied.

@krisdale Approved. Sample works with the latest (7/31/23) 2024.0 BaseKit and HPCKit. Merging into development branch.


Change repository location for sl_SI language pack

Hello, this patch fixes the location for the Slovenian translation since it has been renamed.

Thank you!


Fix git hook

Coverage remained the same at 100.0% when pulling f269a896f7f67ba55ad6ec52b5e7e665e5d35cab on fix_git_hook into de4db65b20115b09ede7635021acac0a73e62356 on master.

Ended up changing the way we consume these hooks back to the standard way as I thought that was the issue. In reality it was an import error for the version that was preventing this hook from working.

After fixing this we are working again, will keep the doc changes though as its more in line with how other projects will use git hooks.


[Bug]: Custom Image Selector not identifing photo location

Summary
The "custom picture selector" is not recognizing the locations from my photo's EXIF data.  If I upload a photo using the regular file selctor, the app is able to identify the location of the photo from EXIF data.  If I select the same photo with the custom selector, I get a "no location found" dialog box.
By "regular selector," I am referring to the button highlighted by a green box in the image below.  "Custom selector" is in the red box.

(Not totally sure I have the name correct, but this is the feature I am referring to: https://github.com/commons-app/apps-android-commons/issues/4764)
Steps to reproduce

Select a photo known to have associated location data using the "regular selector".  Note whether the app is able to idenfiy the image's location.
Select the same photo using the "custom selector".
The app indicates that no location is found.

Expected behaviour
Expected to identify location from EXIF data.
Actual behaviour
App indicates no location is found for the photo.
Device name
Google Pixel 4a
Android version
Android 12
Commons app version
4.0.1
Device logs
I didn't capture logs but can reproduce if they would be helpful.
Screen-shots
Image selected with custom picker does not identify location:

The same photo via the regular image selector identifies a location:

Would you like to work on the issue?
Prefer not

Thanks for reporting!
I have experienced a rather similar problem, always on Pixel 4, and never with my old Samsung somehow. If you have access to other phones, would you mind trying?
Does sharing from Google Photos work? And what about from a third-party gallery app? Thanks!

I don't have another phone easily available but I'll see what I can dig up.
Sharing from Google Photos works without issue, but sharing from a third-party image gallery (Solid Explorer's "SE Image Viewer" in my case) has the same problem identifying image location.

@sivaraam , would you mind trying to reproduce this issue on your OnePlus Nord?
Checking whether image locations are identified when sharing photos from a third-party image gallery and/or using the Custom Photo Selector.

From third-party gallery (Simple Gallery, by Simple Mobile Tools), I share to:

EXIF Viewer: It shows coordinates
Commons app: It tells me "no location found"

Screencast: https://youtu.be/-azE7U-lGgA
Pixel 4, picture taken using stock camera

Apologies. I somehow happened to miss the ping here.

@sivaraam , would you mind trying to reproduce this issue on your OnePlus Nord?
Checking whether image locations are identified when sharing photos from a third-party image gallery and/or using the Custom Photo Selector.

Sure. I tried to check but I'm facing a somewhat weird situation. The app doesn't seem to be considering the location information in any of the images I try to upload i.e., I get the "No location found" pop-up in all cases though the image has location information in it. I tried to use regular upload option / custom image selector and sharing to the app from gallery app. All have consistent results.
Not sure why this is happening. I don't remember it being like this before. I'm using v4.0.3.~23c474b06 on OnePlus Nord that runs Android 12. I've checked that the "Location" checkbox is turned on in the "Manage EXIF" setting.

I would like to mention that I am also experiencing this issue on my Moto G50 running Android 12. Location works as expected on the "regular" selector but not the custom selector.

I did some experiments using a picture that has location (proved by ExifViewer app).
At presenter.receiveImage(uploadableFile, place) in UploadMediaDetailFragment.java, uploadableFile's file points to /data/user/0/fr.free.nrw.commons/cache/CommonsContributions/9886dd0c-bf3f-41bb-83a6-9aa5eaff20d3.jpg (or similar) which contains 0,0 as EXIF location (downloaded via Device File Explorer then analyzed with exif command line tool)
Using the "normal" picker, at the same breakpoint, uploadableFile's file points to a jpg which contains a real (non-zero) EXIF location.
Both normal picker and custom picker go via receiveInternalSharedItems
The intent is sent by methods called from onPictureReturnedFromCustomSelector whose data argument contains an Image object whose path is /storage/emulated/0/DCIM/Camera/PXL_20220921_005652237.jpg which has correct EXIF coordinates (even for custom picker) as seen by the EXIF tool after download using Android Studio's Device File Explorer.
Anyone willing to help: It could be interesting to check what happened in older versions of the app, in both custom and not (and maybe also in Android 8 where I did not observe this issue).

https://commonsware.com/Q/pages/chap-location-002.html :
"in Android 10, access to [EXIF location] is much more restricted than it had been."
"only option appears to be to get the Uri for each individual image and use ExifInterface"

On branch https://github.com/commons-app/apps-android-commons/tree/location-loss I did an experiment following https://developer.android.com/training/data-storage/shared/media#media-location-permission
I added the ACCESS_MEDIA_LOCATION permission to the manifest. I also requested the permission at runtime as it is also required but no permission dialog is shown, apparently it is normal: https://stackoverflow.com/a/74288314/226958.
Then in FilePicker.getFilesFromGalleryPictures I got Intent.getClipData().getItemAt(0).getUri() and passed it to ExifInterface.getLatLong(), unfortunately the result is null.
Any idea what I might be missing?

Any idea what I might be missing?

I'm not absolutely sure but maybe you missed the following point mentioned in the article ?

Your app needs to call MediaStore.setRequireOriginal(), supplying the Uri for which you would like the location — this method then returns a decorated Uri that can be used with openInputStream()

Oops sorry that error was my fault, specific to my dev branch.

oops again wrong issue...

@Keerthivardhan1 Thanks for the investigation! Feel free to modify the source code and try. i assign you to the issue, please let us know about your progress every few days. 🙂

Thanks a lot @nicolas-raoul . I will give my best to solve this issue.

I tried to setup the project locally its  done but when i tried to run the app via USB (connected to my phone )
while I am logging in I am getting this error

So I skipped the process .
after entering into the app it was showing
error occurred :
2023-03-06 17:58:36.185 8995-8995/fr.free.nrw.commons.beta D/ExploreMapFragment: Map projection bounds are null
2023-03-06 17:58:36.199 8995-8995/fr.free.nrw.commons.beta D/ExploreMapFragment: java.lang.NullPointerException: Attempt to read from null array
at fr.free.nrw.commons.explore.map.ExploreMapPresenter.getLatLngBounds(ExploreMapPresenter.java:223)
at fr.free.nrw.commons.explore.map.ExploreMapPresenter.updateMapMarkers(ExploreMapPresenter.java:193)
at fr.free.nrw.commons.explore.map.ExploreMapFragment.updateMapMarkers(ExploreMapFragment.java:393)
at fr.free.nrw.commons.explore.map.ExploreMapFragment.lambda$populatePlaces$5$ExploreMapFragment(ExploreMapFragment.java:373)
at fr.free.nrw.commons.explore.map.-$$Lambda$ExploreMapFragment$roHh3jxKNXZ05whErtypW_DhcmQ.accept(Unknown Source:6)
at io.reactivex.internal.observers.LambdaObserver.onNext(LambdaObserver.java:63)

so I started  debugging .. these are the following takeaways .

in ---> private LatLngBounds getLatLngBounds(LatLng[] boundaries) ....
boundaries array is pointing to null

These is the reason why its generating null pointer exception

this is called at
exploreMapFragmentView.setMapBoundaries(CameraUpdateFactory.newLatLngBounds(- - -getLatLngBounds(explorePlacesInfo.boundaryCoordinates), 50)- - --);

that means : - > explorePlacesInfo.boundaryCoordinates  is null
it is failed to update .

right now I am unable to find where it should get updated ? but I will try to find it out . are there any suggestions ?
Your suggestions matters a lot . it will be very helpful .
please let me know if I am wrong .  Thank you

@Keerthivardhan1 Make sure the device has internet access. And maybe try to use the prodDebug flavor.

when we try to upload By "regular selector,"
exif data has the information of location

but we try to uppload the img from custom selector
there is no geo location

Hear :-
exif object == red color
latitude value == blue color
because
exif object is pointing to null ..
so there will be no values of latitude and longitude.
in the path of the normal img selector the imagecoordinates class  it is  getting the exif object with all the information . so
it is successfully assigning the value of the cordinaties (location ) to latitude and longitude  .
Can you please tell me what is the path followed when user clicks the " custom selector "  ??? ( even a rough idea or explanation could help me a lot ).
same as that of normal selector or different ?
so that I can know what makes the uploading process of custom selector different from that of normal one . and by this we can know the reason for this issue or exif object to become null .
thank you .

@Keerthivardhan1 Custom selector is highlighted in red in the issue description. To know how the execution paths differ, you will need to execute both in your Android IDE's debugger, and compare.

Ok , Thanks a lot for giving me this idea  @nicolas-raoul

@nicolas-raoul I have quite some experience in building android apps with Kotlin/XML & Kotlin/Compose. I do know java but haven't worked with java on an android project. I'm yet to go through the code but first wanted to test the app as a user. I'm in need of images with EXIF data containing location to test & observe the app's behavior.
In the developer workflow guide the 5th point states that anyone can contact the mailing list to obtain good pictures. But I'm new to 'mailing lists and not sure how to do so. Can you provide me with forward guidance? How do I contact others via the mailing list?
Or please send the pictures via email to<EMAIL_ADDRESS>

@nicolas-raoul Can you review my PR?

GSoC applicants: While this issue was the most representative location loss issue, I suggest working on these ones instead: https://github.com/commons-app/apps-android-commons/labels/location-loss


Add inlang to make the contribution of translations easier

Added as suggested in https://github.com/blakeblackshear/frigate-hass-integration/pull/478#issuecomment-1518792669
Description
This pull request adds the possibility for contributors and translators to manage translations in a UI instead of files with no overhead for the maintainers.
To get a UI for translations contained in this repository, an inlang.config.js has been created at the root of the repository.
Note: This link should be changed to point to dermotduffy instead of NiklasBuchfink after this PR has been merged.
Preview
The changes of this PR and a live instance of the editor can be previewed with the following link https://inlang.com/editor/github.com/NiklasBuchfink/frigate-hass-card.
Limitations
Certain actions are slow
inlang is running entirely on git, giving tremendous CI/CD and contribution power to localization. That means that the whole frigate-hass-card repo is cloned into the browser which makes certain actions like the initial load and pushing changes slow. Those limitations will be fixed with future releases and require no input from frigate-hass-card.

@dermotduffy At the moment there are 26 translations missing for it and pt-BR and unfortunately I don`t speak any of the languages. But I could still add a machine translation for the missing strings via the editor if you want.
I added the information above because it may be useful if someone comes back to this PR at a later date.

@NiklasBuchfink -- there are other contributors that occasionally provide other translations, and the code falls back to English when a translation is not available. The sense I got from them was that this was preferred than relying on machine translation, hence I avoided providing machine translations when I added those strings. So, in short: don't worry about it! (But German obviously very welcome if you speak it natively).

Oh, would you mind putting it into the dev branch?

@dermotduffy I understand, that makes sense.
Translating the 342 strings in German would definitely take a bit more time. I hope it's ok if I don't do it immediately.

Thanks @NiklasBuchfink . No worries I know it's not a trivial exercise, appreciate the consideration & contribution!


setup-cpp step fails in Node 12

The latest version appears to have a syntax error somewhere, leading to a very noisy error log. I suspect this is caused by a change within a8d76c6b538f9bc09243b13387cc83478537cde1.
SyntaxError: Unexpected token '?'
    at wrapSafe (internal/modules/cjs/loader.js:915:16)
    at Module._compile (internal/modules/cjs/loader.js:963:[27](https://github.com/SK83RJOSH/nifly-utils/actions/runs/3079336898/jobs/4975505857#step:5:28))
    at Object.Module._extensions..js (internal/modules/cjs/loader.js:1027:10)
    at Module.load (internal/modules/cjs/loader.js:863:32)
    at Function.Module._load (internal/modules/cjs/loader.js:708:14)
    at Function.executeUserEntryPoint [as runMain] (internal/modules/run_main.js:60:12)
    at internal/main/run_main_module.js:17:47

I cannot reproduce this in the CI:
https://github.com/aminya/setup-cpp/actions/runs/3076474508

The issue seems to be Node 12 installed in the GitHub images. Not sure why the Parcel compilation is not generating proper code for Node 12

This is a bug in Parcel that is triggered when the optimizations are enabled. I am disabling the optimizations for now.

The actual reason was the terser config. I have enabled optimizations back!


[CT-1899] [Bug] exceptions.warn does not actually give model WARN status

Is this a new bug in dbt-core?

[X] I believe this is a new bug in dbt-core
[X] I have searched the existing issues, and I could not find an existing issue for this bug

Current Behavior
When using exceptions.warn in either a model, or a macro called by a model, in both cases the warning message is written to the log but the model itself runs as a SUCCESS (counts as a PASS in the summary).
Expected Behavior
When a model, or a macro called within a model, raises a warning via exceptions.warn this should log the message as it currently does, but also complete the model with a WARN status.
Steps To Reproduce

Create a new project with a valid profile
Create a macro called raise_a_warning.sql  {% macro raise_a_warning() %}
  {% if execute %}
      {% do exceptions.warn("Alert, alert, warning warning!") %}
  {% endif %}
  {% endmacro %}

Create a model called warn_test.sql (adjust the dummy table query as needed for your warehouse)  {{ raise_a_warning() }}
  {% if execute %}
      {% do exceptions.warn("Warning, warning, alert, alert!") %}
  {% endif %}

  select 1 as x

Call dbt run - observe warning messages but model registers as SUCCESS/PASS
Call dbt --warn-error run - model now errors as expected

Relevant log output
09:18:01  Running with dbt=1.3.2
09:18:01  Found 1 model, 0 tests, 0 snapshots, 0 analyses, 304 macros, 0 operations, 0 seed files, 0 sources, 0 exposures, 0 metrics
09:18:01
09:18:03  Concurrency: 1 threads (target='dev')
09:18:03
09:18:03  1 of 1 START sql view model dbt_ryan.warn_test ................................. [RUN]
09:18:03  Alert, alert, warning warning!
09:18:03  Warning, warning, alert, alert!
09:18:03  1 of 1 OK created sql view model dbt_ryan.warn_test ............................ [SUCCESS 1 in 0.79s]
09:18:03
09:18:03  Finished running 1 view model in 0 hours 0 minutes and 2.28 seconds (2.28s).
09:18:03
09:18:03  Completed successfully
09:18:03
09:18:03  Done. PASS=1 WARN=0 ERROR=0 SKIP=0 TOTAL=1

Environment
- OS: Mac OS
- Python: 3.9.13
- dbt: 1.32

Which database adapter are you using with dbt?
No response
Additional Context
Exceptions docs: https://docs.getdbt.com/reference/dbt-jinja-functions/exceptions

Thanks for opening @rlh1994! I'm not convinced that this is the expected behavior, since the warning message raised does not actually stop the model from proceeding to build (either successfully or unsuccessfully).
I do see it as expected behavior that {{ exceptions.warn() }} yields a WARN-level event, which appears in logs and can be observed/parsed/reacted to accordingly, including by means of --warn-error.
Currently, model result statuses can be only Success, Error, or Skipped:
https://github.com/dbt-labs/dbt-core/blob/cbb9117ab997289062cd5bacaf4cfd4466ab9b1e/core/dbt/contracts/results.py#L91-L94
Whereas tests and source freshness checks can indeed return Warn as a result status.
There's an issue from last year proposing a more thorough review of result statuses: https://github.com/dbt-labs/dbt-core/issues/5276. If we're going to change this, I would want it to be part of a more-holistic review, rather than adding Warn to the set of possible model result statuses in a vacuum.


Support mpm (move package manager)

The move package manager has released version v1.10.0-rc.1, and the move command is no longer supported.

Use mpm to replace move command, and adapter mpm package and mpm release command.
Support new spectests.

The move package manager documents is at https://github.com/starcoinorg/guide-to-move-package-manager

pick!


/cdns/capacity returning wrong json keys

What does this PR (Pull Request) do?

[x] This PR fixes #REPLACE_ME OR is not related to any Issue

Which Traffic Control components are affected by this PR?

Traffic Ops

What is the best way to verify this PR?

Make a request to cdns/capacity with change and the json should have the keys
{
    response: {
        availablePercent: 99.9695,
        unavailablePercent: 0,
        utilizedPercent: 0.0305,
        maintenancePercent: 0
    }
}

instead of
{
    response: {
        availablePercent: 99.9695,
        unavailablePercent: 0,
        UtilizedPercent: 0.0305,
        MaintenancePercent: 0
    }
}

If this is a bug fix, what versions of Traffic Control are affected?

The following criteria are ALL met by this PR

[x] This PR includes tests OR I have explained why tests are unnecessary
[x] This PR includes documentation OR I have explained why documentation is unnecessary
[x] This PR includes an update to CHANGELOG.md OR such an update is not necessary
[x] This PR includes any and all required license headers
[x] This PR ensures that database migration sequence is correct OR this PR does not include a database migration
[x] This PR DOES NOT FIX A SERIOUS SECURITY VULNERABILITY (see the Apache Software Foundation's security guidelines for details)

Additional Information

Refer to this link for build results (access rights to CI server needed):
https://builds.apache.org/job/trafficcontrol-PR/4874/


Images have spaces between in less

Issue summary
When you render images in less there are black spaces between. The height of single slice is 13px
Expected behavior
Images should render seamlessly
Actual behavior
The're black spaces between slices.
Steps to reproduce

Open https://codepen.io/jcubic/pen/BaoegLZ
Image is not correct

Works fine on Linux/Chrome. To be tested.

Also works fine on Windows/Chrome. I cannot reproduce this issue anymore.


Guides - getting started

Related with https://github.com/CartoDB/carto-vl/issues/966 https://github.com/CartoDB/carto-vl/issues/950 and https://github.com/CartoDB/carto-vl/issues/949

It LGTM, there is just a constant to add at basic-setup.html instead of the url for the style. but the PR looks pretty good! 👍

After that I think we can merge it!

Hi @VictorVelarde, I updated the examples to step-1 and step-2 to follow the convention :) However, I think that dealing with numbers helps us to know the guides order when looking at the code immediately. It is true that if we do that, then we would have to change it if we want to include one guide in between other two, but I do not think it is going to happen very often once we release the public version, and if so there is no problem with renaming the files in my opinion.

Ok. Then I'll rename mine, adding the '02-' preffix in this very same PR, fix the link from 01-getting-started, and then merge to master


Somebody knows whan we can start using this tool?

When i get paid for development, i don't have time for those toys when i'm broke

Duplicate of #11


Add script to align event dates and action rules

Motivation and Context

Currently action rule trigger dates and event dates do not match
in various environments. This script updates all action rules and
events.
What has changed

python script added
How to test?

Install the single additional dependency for the script
pip install python-dateutil
and then run this against your local docker dev environment:
python3 align_events_and_rules.py \ http://<IP_ADDRESS>:8145/collectionexercises/{id}/events/{tag} \ http://<IP_ADDRESS>:8145/collectionexercises \ admin \ secret
Check all events (except events for CE that are ready for live or live) have been updated and action rules in the database has been updated.
Links

 UI for adding and updating remaining optional dates


Using Sheen node

Hey guys,
Is it possible to make model-viewer to enable/support Sheen.
This node is must-have for PBR fabric material
It is already supported for gLTF files and three.js:
https://threejs.org/examples/?q=sheen#webgl_materials_physical_sheen

In general we intend to support whatever Three.js supports regarding glTF. Three.js gains support for glTF PBR via updates to its GLTFLoader. Whatever the GLTFLoader produces,<model-viewer> will use.
Has sheen been specified and accepted for glTF? cc @donmccurdy

Sheen is not specified in glTF yet, but it's coming.
Of the new material parameters planned for glTF, I think Clear Coat will be first.

Great, thank you, guys!


Update zpreztorc

Make a .zpreztorc.local that are not versioned in order to make update on prezto easier to update.
This PR is a discuss proposal related to https://github.com/sorin-ionescu/prezto/pull/1344
This must not be merged.
How can we manage the other files in runcoms?

@Yoshyn I think work doing the same with the other files that may be used to setup the user environment, namely:

zlogin
zlogout
zprestorc
zprofile
zshrenv
zshrc

Does it make sense?

I'm not sure about that.
For exemple zshenv source ~/.zprofile so I think that we don't have to manage it.
What should be great is avoid to define ours rules but take the rules of others projects that have already reflect on it.
For exemple concerning the naming : .zpreztorc.local is pretty ugly (at least for me)
Maybe .zpreztorc-profile would be better (probably cause i thought to bash-profile)

That makes sense! =)

As far as I know, .local is fairly standard. It may make sense to add these to most of the runcoms. I personally haven't run into this because I don't actually use any of the runcoms (shh, don't tell anyone ;)) and I load modules with antigen.
.bash-profile was intended to be .profile (something from sh) for bash, so it's not quite the same thing. If we move forward with this, I'd prefer .local.
Also thanks for the idea! This solves some of my long running complaints with the runcoms.

@Yoshyn if you want to look at my other PR https://github.com/sorin-ionescu/prezto/pull/1352 I don't know if we would want to have those variables stored inside the .local file? though I'd assume we'd want that run afterwards? Wanted to know what you think. Though personally I think this thing is best handled with hand merges but that may not work for people who don't know git very well. So I'm at a loss for how to handle zpreztorc and zpreztorc.local, since things that load in zpreztorc need the data available beforehand, and .local is usually loaded afterward?

if you want to look at my other PR #1352 I don't know if we would want to have those variables stored inside the .local file? though I'd assume we'd want that run afterwards? Wanted to know what you think.
=> I do not understand the advantage of storing theses value into an array. It's not a bad think but i do not see how it help for the current concern.

I think this thing is best handled with hand merges but that may not work for people who don't know git very well.
=> Exactly my point.

So I'm at a loss for how to handle zpreztorc and zpreztorc, since things that load in zpreztorc need the data available beforehand, and .local is usually loaded afterward?
=> For me zpreztorc should load zpreztorc.local at the end of the file and override value thank to zstyle but maybe i did not well understand the purpose of zstyle.

@Yoshyn about what should be done with the .local, what if there is a 'default' behavior on the zprestorc file that the user does not want (load a module, for example)? That should be a problem right, since that the zprestorc.local will not unload the already loaded module.
Being so, may be the zprestorc should check for each variable on the zprestorc.local file before taking any action?

what if there is a 'default' behavior on the zprestorc file that the user does not want (load a module, for example)? That should be a problem right, since that the zprestorc.local will not unload the already loaded module.

zpreztorc doesn't actually do any of the loading, so if you override the zstyle setting, it will be fine. The actual loading happens in init.zsh after zpreztorc has been loaded.
The rest of this is mostly a mind dump with what I'd like to see happen to the runcoms. Suggestions and comments are welcome.
The way I see it, there are a few ways of "solving" this issue which I'll do my best to outline below:

Add .local files for all the runcoms. This lets us change defaults and add new options easily but some defaults will be missed because they would be silently overridden in the .local files.
Stop recommending that runcoms should be symlinked. This raises some problems about how to change defaults or let people know new options have been added.
Leave it as is.
Rework the runcoms so most of them just bootstrap into prezto (removing the random fortune calls and what not) and zpreztorc is used for all settings.

The problems with the runcoms I would like to see solved:

Make it easier for people who don't understand git and merging to use prezto (without sacrificing the flexibility we currently have for power users)
Make it possible to change defaults without breaking and (maybe) inform the user
Make it possible to add options without breaking (maybe) and inform the user
The changes cannot be extremely inconvenient or annoying... I don't want to get issues filed because people are super annoyed with how verbose it gets. I'd like to avoid another issue like the controversial oh-my-zsh auto-updater.

The solutions I listed above don't solve all these problems. At most, they solve one or two. Are there any suggestions (or variations on the above solutions) which aim to solve as many of these as possible without sacrificing too much?

zpreztorc doesn't actually do any of the loading, so if you override the zstyle setting, it will be fine. The actual loading happens in init.zsh after zpreztorc has been loaded.

ok, no problem with that so! =)

Make it possible to change defaults without breaking and (maybe) inform the user
Make it possible to add options without breaking (maybe) and inform the user

Just trying to understand... what do  you mean by 'without breaking' here? I mean, how would these problems occur? Any examples so we can try to think on solutions?
I'm not a so much advanced user on how zsh/prezto works under the hood, that's why I'm asking ;)

As an example, there was a push to change the default alias of rm (and similar tools) to remove -i by default. However, I don't like changing defaults in a way that could break people. It would be nice if there was a way to notify people of the change without them having to check the commit log.
Note that the list above is more of a wish list... I realize we probably can't fix all of them, but I'd like a solution which solves as much as possible.

@belak we could maybe add a hook into zprezto-update that would give certain notifications? Or even like zprezto-news or something which could show them whenever they wanted to find out, but also show them when they update with zprezto the notification?
Or we could have a folder in $ZPREZTODIR/news which would contain text files that are news entries and if there are files in that folder we could show a notification of unread messages. That would allow people to either use our yet to be made interface for reading news or just clearing the folder.

I remember that I read at somewhere a discussion about defining some release-rules for prezto. Considering this, I think it would be nice to have a CHANGELOG file in order to keep track of the changes.
If we have this CHANGELOG file, after a zpresto update then we can just print the changelog diff on the screen (or a formatted version of this "diff").
To ease the tracking of versions we can store the 'current commit hash' on a '.current_hash' file. When the users start a new zpresto term, then we compare the latests commit hash (from git log) to this '.current_hash'. If they are different, then we show the CHANGELOG diff (formatted) and update the '.current_hash' file with the latest commit hash.
This file would be ignored on .gitignore.

Hey all, any new ideas over here?
I've seem some discussions going around some issues/PRs that would benefit from some changes proposed on this PR. =)

I second the question @diraol I kind of like the .local idea because it seems like every time i update there is a good number of changes.

I'm in favor of a .local, however, I'm against giving users notifications as a default. That needs to be an opt-in feature as we don't want to be sending data across the network without the user explicitly saying it's ok to do so. In terms of a news/changelog, that needs to be discussed in a different issue otherwise this is going to off the rails with features.

@johnpneumann The notifications which were described above would be local only and would happen when they pull. There would be no network traffic. I would also like to avoid the oh-my-zsh auto-update controversy if possible.
One thing that comes to mind... if we have a zpreztorc.local, what is the zpreztorc going to be used for? It seems entirely superfluous. Would it be better to remove zpreztorc entirely (because it's all commented out default settings) and/or have users copy it?

@johnpneumann as @belak said, there wouldn't be any network traffic for the notifications to go on. After an active request by the user to update its own prezto, the update would be handled by git versioned information.
@belak about the zprestorc vs zpreztorc.local, I've taken the idea of a .local from vim-spf13. Over there, the .vimrc file is used to store the default configs (not commented versions of it). It can be seen here.
One advantage of keep using zprestorc is to join all defaults at the same place. This would make the life of prezto uses easier because they do not need to look for defaults they didn't even know the existence for all the files around.
Another point I would like to bring is that I wouldn't leave the defaults commented out on the zprestrc file. Sometimes it can be confusing for the user to understand if the commented version is the default or one option that can be used if uncommented.

Just adding one more info regarding #1354.
By using zprestorc and setting there all the 'defaults', it would also make it easier to document the differences between two releases, in terms of settings/options. We will only need to diff between the previous stable release and the 'current one being released'.

Does this remove the need for the unit function where the runcomms version of the files are then pre populated so you can do a dif?
Sent from my iPhone

On Aug 8, 2017, at 8:52 PM, Diego Rabatone Oliveira<EMAIL_ADDRESS>wrote:
Just adding one more info regarding #1354.
By using zprestorc and setting there all the 'defaults', it would also make it easier to document the differences between two releases, in terms of settings/options. We will only need to diff between the previous stable release and the 'current one being released'.
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Good suggestions, @diraol. I think adding all the defaults to the zpreztorc and suggesting that users use zpreztorc.local would be a good option.
Still not sure what to do with the other runcoms, but this should be a good starting point.

About the other runcoms, I would keep them just if they are "executed" on distinct moments and they need to be executed at that moments. Otherwise, I would merge them with zprestorc (maybe splitted by "sections" [just comments to organize the content]).

What about removing some of the oddities from the runcoms? The calls to fortune and printing messages (in zlogin and zlogout respectively) seem a bit strange to put into a config framework.

Also, thinking about it... setting all the values in the zpreztorc will make it harder for people using plugin managers (as normally you set values in your zshrc then load prezto).

@belak, I do not use plugin managers, so can you give some examples why the proposal can be problematic with this tools?

Quick question: I decided to drop zgen and use prezto directly, and I am not sure where to put my existing prezto customization. Should I directly edit the runcoms, specifically, .zpreztorc? I have no issues managing git conflicts.
If yes, can we update the root level README.md to instruct new users to directly edit the runcoms while we make progress on this PR?

Hi all, any news about this issue? What do we need to move forward here? Can I help with something? =)


Accept payment for BackupMinder in app

Wouldn't hurt to put a donate link in it... either paypal, like we already have, or a Stripe one. Suggested value of $15, but any amount should be accepted.
If it works out to put a series of values with an "other" button, do the following:
10
15*
25
50
Other

Definitely doable. Would this be say just in the About? Or maybe a one time pop up sometime after the first launch (like maybe the third?).

No pop ups please, anything static would be fine.
I like the idea of the way how carbon copy cloner used to do it, where there was a checkbox somebody could click that said "I paid". There is no validation of this box, just something that would remove any nag.
Conversely, we could just sell a branded version of this.

A banner at the bottom? How obvious do you want it to be?

This would remove "brought to you by Watchman Monitoring".
There would be a donate button much like what's shown on https://backupminder.org
In app's Preferences, there's be a box that said "I Paid" and it would remove the Donate from the main page.
Here's the code:

https://www.paypal.com/cgi-bin/webscr?cmd=_s-xclick&hosted_button_id=44XW83JDM7SL6

or
<form action="https://www.paypal.com/cgi-bin/webscr" method="post" target="_top">
<input type="hidden" name="cmd" value="_s-xclick">
<input type="hidden" name="hosted_button_id" value="44XW83JDM7SL6">
<input type="image" src="https://www.paypalobjects.com/en_US/i/btn/btn_donateCC_LG.gif" border="0" name="submit" alt="PayPal - The safer, easier way to pay online!">
<img alt="" border="0" src="https://www.paypalobjects.com/en_US/i/scr/pixel.gif" width="1" height="1">
</form>


[Twitch] Streamlink bugfix

Description
Bugfix for an issue when using Streamlink with the Twitch extension. Extension is now fully functional but still needs attention to address other files using deprecated methods. Closes #1554.
Checklist

[x] I read the extension guidelines
[x] I read the documentation about publishing
[x] I ran npm run build and tested this distribution build in Raycast
[x] I checked that files in the assets folder are used by the extension itself
[x] I checked that assets used by the README are placed outside of the metadata folder

Thanks for the quick look, I missed the icons! A link icon seems appropriate for Streamlink.
First day using the app and I'm already super impressed!