Error doing ABF

Hi,
I am getting the following error that I am not able to understand when using the finemal_loci() function to do ABF
[1] "+ Full UKB LD matrix: 22590 x 22590"
[1] "+ Full UKB LD SNP data.table: 22590 x 5"
[1] "UKB MAF:: Extracting MAF from UKB reference."
[1] "+ CONDA:: Identified axel executable in echoR env."
Error in `[.data.table`(y, x, nomatch = if (all.x) NA else NULL, on = by,  :
  logical error. i is not a data.table, but 'on' argument is provided.
Fine-mapping complete in:
Time difference of 2 mins
Error in `[.data.table`(x, r, vars, with = FALSE) :
  column(s) not found: SNP

This is the function calling:
r$> Maryam_colocFIneMap_Results <- finemap_loci(top_SNPs = top_SNPs,
                                                      results_dir = "/data/kronos/kronos/acarrasco/FOR_MARYAM/results",
                                                      loci = c("locus1"),
                                                      dataset_name = "GWAS_coloc",
                                                      dataset_type = "GWAS",
                                                      force_new_subset = F,
                                                      force_new_LD = T,
                                                      force_new_finemap = T,
                                                      remove_tmps = F,
                                                      fullSS_path = "/data/kronos/kronos/acarrasco/FOR_MARYAM/DLB-vs-Nalls-all_se.txt",
                                                      query_by = "tabix",
                          chrom_col = "CHR", position_col = "POS", snp_col = "SNP", pval_col = "woolf_p",
                          effect_col = "log_woolf_OR", stderr_col = "se", N_cases_col = "NPD", N_controls_col = "NCO",
                          proportion_cases = "prportion_cases",

                          bp_distance = 500000*2,
                          trim_gene_limits = F,

                          finemap_methods = c("ABF"),
                         LD_reference = "UKB",
                             superpopulation = "EUR",
                             download_method = "axel",
                               plot.types=c("fancy"),
                             ## Generate multiple plots of different window sizes;
                             ### all SNPs, 4x zoomed-in, and a 50000bp window
                             plot.zoom = c("all","4x","10x"),
                             ## XGR
                             # plot.XGR_libnames=c("ENCODE_TFBS_ClusteredV3_CellTypes"),
                             ## Roadmap
                             plot.Roadmap = F,
                             plot.Roadmap_query = NULL,
                             # Nott et al. (2019)
                             plot.Nott_epigenome = T,
                             plot.Nott_show_placseq = T,
                             verbose = F )
Also, this is the header of my GWAS
CHR	POS	SNP	A1	A2	NPD	NCO	woolf_p	log_woolf_OR	log_OR1	log_OR2	woolf_p_adjusted	tval	se	prportion_cases
1	798400	chr1:798400	G	A	26035	441778	0.054355312527485	-0.0129364098436779	-0.0937025329495809	-0.0077974327837792	0.149450021680241	1.92408105275612	-0.00672342250091146	0.058932314420365
1	798959	chr1:798959	A	G	26035	441778	0.0624429326097045	-0.0166813371949653	-0.0949059766764264	-0.0116961408205252	0.162749942120059	1.86321743251793	-0.00895297398136848	0.058932314420365
1	1037303	chr1:1037303	C	T	33674	449056	0.413943979264559	-0.0415678483019056	-0.0022959606094905	-0.0436749490486619	0.540481742929293	0.816982901531581	-0.0508797041210767	0.0749884201524977

Of note, the top_SNPs were got by using the import_topSNPs() function after doing a grouping by CHR, and when calling the finemap_loci() function I specify the locus I am interested in through the "loci" flag from the generated top_SNPs datafrmae.
The sessionInfo:
r$> utils::sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS/LAPACK: /home/acarrasco/.conda/envs/echoR/lib/libopenblasp-r0.3.12.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] echolocatoR_0.1.2 data.table_1.14.0 forcats_0.5.1     stringr_1.4.0     dplyr_1.0.5       purrr_0.3.4       readr_1.4.0       tidyr_1.1.3       tibble_3.1.1      ggplot2_3.3.3     tidyverse_1.3.1

loaded via a namespace (and not attached):
  [1] readxl_1.3.1                backports_1.2.1             Hmisc_4.5-0                 BiocFileCache_1.14.0        plyr_1.8.6                  lazyeval_0.2.2              splines_4.0.3
  [8] crosstalk_1.1.1             BiocParallel_1.24.1         GenomeInfoDb_1.26.7         digest_0.6.27               ensembldb_2.14.1            htmltools_<IP_ADDRESS>           fansi_0.4.2
 [15] magrittr_2.0.1              checkmate_2.0.0             memoise_2.0.0               BSgenome_1.58.0             cluster_2.1.1               Biostrings_2.58.0           modelr_0.1.8
 [22] matrixStats_0.58.0          R.utils_2.10.1              ggbio_1.38.0                askpass_1.1                 prettyunits_1.1.1           jpeg_0.1-8.1                colorspace_2.0-0
 [29] rappdirs_0.3.3              blob_1.2.1                  rvest_1.0.0                 haven_2.4.1                 xfun_0.22                   crayon_1.4.1                RCurl_1.98-1.3
 [36] jsonlite_1.7.2              graph_1.68.0                Exact_2.1                   VariantAnnotation_1.36.0    survival_3.2-11             glue_1.4.2                  gtable_0.3.0
 [43] zlibbioc_1.36.0             XVector_0.30.0              DelayedArray_0.16.3         BiocGenerics_0.36.1         scales_1.1.1                mvtnorm_1.1-1               DBI_1.1.1
 [50] GGally_2.1.1                Rcpp_1.0.6                  progress_1.2.2              htmlTable_2.1.0             reticulate_1.19             foreign_0.8-81              bit_4.0.4
 [57] proxy_0.4-25                OrganismDbi_1.32.0          Formula_1.2-4               DT_0.18                     stats4_4.0.3                htmlwidgets_1.5.3           httr_1.4.2
 [64] RColorBrewer_1.1-2          ellipsis_0.3.1              R.methodsS3_1.8.1           pkgconfig_2.0.3             reshape_0.8.8               XML_3.99-0.6                nnet_7.3-15
 [71] dbplyr_2.1.1                utf8_1.2.1                  tidyselect_1.1.0            rlang_0.4.10                reshape2_1.4.4              AnnotationDbi_1.52.0        munsell_0.5.0
 [78] cellranger_1.1.0            tools_4.0.3                 cachem_1.0.4                cli_2.5.0                   generics_0.1.0              RSQLite_2.2.5               broom_0.7.6
 [85] fastmap_1.1.0               knitr_1.33                  bit64_4.0.5                 fs_1.5.0                    AnnotationFilter_1.14.0     rootSolve_<IP_ADDRESS>           RBGL_1.66.0
 [92] R.oo_1.24.0                 xml2_1.3.2                  biomaRt_2.46.3              compiler_4.0.3              rstudioapi_0.13             curl_4.3                    png_0.1-7
 [99] e1071_1.7-6                 reprex_2.0.0                DescTools_0.99.41           stringi_1.5.3               ps_1.6.0                    GenomicFeatures_1.42.3      lattice_0.20-41
[106] ProtGenerics_1.22.0         Matrix_1.3-2                vctrs_0.3.7                 pillar_1.6.0                lifecycle_1.0.0             BiocManager_1.30.12         bitops_1.0-7
[113] lmom_2.8                    rtracklayer_1.50.0          GenomicRanges_1.42.0        R6_2.5.0                    latticeExtra_0.6-29         gridExtra_2.3               IRanges_2.24.1
[120] gld_2.6.2                   dichromat_2.0-0             boot_1.3-27                 MASS_7.3-53.1               assertthat_0.2.1            SummarizedExperiment_1.20.0 openssl_1.4.3
[127] withr_2.4.2                 GenomicAlignments_1.26.0    Rsamtools_2.6.0             S4Vectors_0.28.1            GenomeInfoDbData_1.2.4      expm_0.999-6                parallel_4.0.3
[134] hms_1.0.0                   grid_4.0.3                  rpart_4.1-15                class_7.3-18                MatrixGenerics_1.2.1        biovizBase_1.38.0           Biobase_2.50.0
[141] lubridate_1.7.10            base64enc_0.1-3

Many thanks!,
Alejandro.

I think this is happening bc the "SNP" col in your GWAS has coordinates instead of RSIDs. The step that merges the LD panel with the GWAS sum stats uses the SNP column.

I just changed the the SNP notation from chr:pos to rsIDs, and I am getting the same issue.
[1] "+ Full UKB LD matrix: 20801 x 20801"
[1] "+ Full UKB LD SNP data.table: 20801 x 5"
[1] "UKB MAF:: Extracting MAF from UKB reference."
[1] "+ CONDA:: Identified axel executable in echoR env."
Error in `[.data.table`(y, x, nomatch = if (all.x) NA else NULL, on = by,  :
  logical error. i is not a data.table, but 'on' argument is provided.
Fine-mapping complete in:
Time difference of 2 mins
Error in `[.data.table`(x, r, vars, with = FALSE) :
  column(s) not found: SNP

The GWAS results header after the update:
CHR	POS	A1	A2	NPD	NCO	woolf_p	log_woolf_OR	log_OR1	log_OR2	woolf_p_adjusted	tval	se	prportion_cases	SNP
1	798400	G	A	26035	441778	0.054355312527485	-0.0129364098436779	-0.0937025329495809	-0.0077974327837792	0.149450021680241	1.92408105275612	-0.00672342250091146	0.058932314420365	rs10900604
1	798959	A	G	26035	441778	0.0624429326097045	-0.0166813371949653	-0.0949059766764264	-0.0116961408205252	0.162749942120059	1.86321743251793	-0.00895297398136848	0.058932314420365	rs11240777
1	1037303	C	T	33674	449056	0.413943979264559	-0.0415678483019056	-0.0022959606094905	-0.0436749490486619	0.540481742929293	0.816982901531581	-0.0508797041210767	0.0749884201524977	rs11260592
1	1037313	G	A	33674	449056	0.398505671669803	-0.0420967280143385	-0.00152942739309308	-0.0442746217585758	0.527025397597339	0.844303781275011	-0.049859693806851	0.0749884201524977	rs11260593
Best and many thanks!,
Alejandro.

Did you use  force_new_subset = T to make sure it's not using your old file subset?

Yes. I am actually removing everything under the results file to make sure each command is run from scratch.
There is just one thing I am not sure if it is finr for this tool - I do not have on my GWAS gene and locus info. When getting top SNPs per chromosome, I get a locus name inferred when using import_topSNPs
21:   locus_chr8_rs2513924   locus_chr8_rs2513924   8 103693753   rs2513924 1.234177e-07 -0.061049972
22:   locus_chr9_rs2821150   locus_chr9_rs2821150   9 113520979   rs2821150 2.524724e-06 -0.018425605
                     Locus                   Gene CHR       POS         SNP            P       Effect

Subsequently, the locus name that I pass on the finemap_loci() would be ie locus_chr8_rs2513924. I do not know if this tool is expecting a real locus name? - I deduced this does not really matter as soon as the chromosome and position are correctly passed.
BW and many thanks,
Alejandro.

Maybe it helps If I share the whole code for a locus example
Input GWAS data
CHR	POS	A1	A2	NPD	NCO	woolf_p	log_woolf_OR	log_OR1	log_OR2	woolf_p_adjusted	tval	se	prportion_cases	SNP
1	798400	G	A	26035	441778	0.054355312527485	-0.0129364098436779	-0.0937025329495809	-0.0077974327837792	0.149450021680241	1.92408105275612	-0.00672342250091146	0.058932314420365	rs10900604
1	798959	A	G	26035	441778	0.0624429326097045	-0.0166813371949653	-0.0949059766764264	-0.0116961408205252	0.162749942120059	1.86321743251793	-0.00895297398136848	0.058932314420365	rs11240777
1	1037303	C	T	33674	449056	0.413943979264559	-0.0415678483019056	-0.0022959606094905	-0.0436749490486619	0.540481742929293	0.816982901531581	-0.0508797041210767	0.0749884201524977	rs11260592
1	1037313	G	A	33674	449056	0.398505671669803	-0.0420967280143385	-0.00152942739309308	-0.0442746217585758	0.527025397597339	0.844303781275011	-0.049859693806851	0.0749884201524977	rs11260593
1	1037367	A	G	33674	449056	0.388182072806092	-0.0414481828134772	0	-0.043674956004422	0.517950444263371	0.862930050756748	-0.0480319149589577	0.0749884201524977	rs11260594

The top_SNPs data frame
21:   locus_chr8_rs2513924   locus_chr8_rs2513924   8 103693753   rs2513924 1.234177e-07 -0.061049972
22:   locus_chr9_rs2821150   locus_chr9_rs2821150   9 113520979   rs2821150 2.524724e-06 -0.018425605
                     Locus                   Gene CHR       POS         SNP            P       Effect

The finemap_loci() function and the output
r$> colocFIneMap_Results <- finemap_loci(top_SNPs = top_SNPs,
                                                      results_dir = "/data/kronos/kronos/acarrasco/FOR_MARYAM/results",
                                                      loci = c("locus_chr9_rs2821150"),
                                                      dataset_name = "GWAS_coloc",
                                                      dataset_type = "GWAS",
                                                      force_new_subset = T,
                                                      force_new_LD = T,
                                                      force_new_finemap = T,
                                                      remove_tmps = F,
                                                      fullSS_path = "/data/kronos/kronos/acarrasco/FOR_MARYAM/DLB-vs-Nalls-all.se.rsID_noPoint.txt",
                                                      query_by = "tabix",
                          chrom_col = "CHR", position_col = "POS", snp_col = "SNP", pval_col = "woolf_p",
                          effect_col = "log_woolf_OR", stderr_col = "se", N_cases_col = "NPD", N_controls_col = "NCO",
                          proportion_cases = "prportion_cases",

                         bp_distance = 500000*2,
                          trim_gene_limits = F,

                          finemap_methods = c("ABF"),
                         LD_reference = "UKB",
                             superpopulation = "EUR",
                             download_method = "axel",
                               plot.types=c("fancy"),
                             ## Generate multiple plots of different window sizes;
                             ### all SNPs, 4x zoomed-in, and a 50000bp window
                             plot.zoom = c("all","4x","10x"),
                             ## XGR
                             # plot.XGR_libnames=c("ENCODE_TFBS_ClusteredV3_CellTypes"),
                             ## Roadmap
                             plot.Roadmap = F,
                             plot.Roadmap_query = NULL,
                             # Nott et al. (2019)
                             plot.Nott_epigenome = T,
                             plot.Nott_show_placseq = T,
                             verbose = F )
[1] "+ CONDA:: Activating conda env 'echoR'"
[1] "Checking for tabix installation..."
[1] "Checking for bcftools installation..."

)   )  ) ))))))}}}}}}}} {{{{{{{{{(((((( (  (   (
locus_chr9_rs2821150 (1 / 1)
)   )  ) ))))))}}}}}}}} {{{{{{{{{(((((( (  (   (
[1] "Determining chrom type from file header"
[1] "LD:: Standardizing summary statistics subset."
[1] "++ Preparing Gene col"
[1] "++ Preparing A1,A1 cols"
[1] "++ Preparing MAF,Freq cols"
[1] "++ Could not infer MAF"
[1] "++ Preparing N_cases,N_controls cols"
[1] "++ Preparing `proportion_cases` col"
[1] "++ Preparing N col"
[1] "+ Preparing sample_size (N) column"
[1] "++ Computing effective sample size."
[1] "++ Preparing t-stat col"
[1] "+ Calculating t-statistic from Effect and StdErr..."
[1] "++ Assigning lead SNP"
[1] "++ Ensuring Effect, StdErr, P are numeric"
[1] "++ Ensuring 1 SNP per row"
[1] "++ Removing extra whitespace"
[1] "++ Saving subset ==> /data/kronos/kronos/acarrasco/FOR_MARYAM/results/GWAS/GWAS_coloc/locus_chr9_rs2821150/locus_chr9_rs2821150_GWAS_coloc_subset.tsv.gz"
[1] "LD:: Using UK Biobank LD reference panel."
[1] "+ UKB LD file name: chr9_112000001_115000001"
[1] "+ LD:: Downloading full .gz/.npz UKB files and saving to disk."
[1] "+ Overwriting pre-existing file."
[1] "+ CONDA:: Identified axel executable in echoR env."
[1] "+ Overwriting pre-existing file."
[1] "+ CONDA:: Identified axel executable in echoR env."
[1] "+ LD:: load_ld() python function input: /data/kronos/kronos/acarrasco/FOR_MARYAM/results/GWAS/GWAS_coloc/locus_chr9_rs2821150/LD/chr9_112000001_115000001"
[1] "+ LD:: Reading LD matrix into memory. This could take some time..."
/data/kronos/kronos/acarrasco/FOR_MARYAM/results/GWAS/GWAS_coloc/locus_chr9_rs2821150/LD/chr9_112000001_115000001.gz
/data/kronos/kronos/acarrasco/FOR_MARYAM/results/GWAS/GWAS_coloc/locus_chr9_rs2821150/LD/chr9_112000001_115000001.npz
Processed URL: /data/kronos/kronos/acarrasco/FOR_MARYAM/results/GWAS/GWAS_coloc/locus_chr9_rs2821150/LD/chr9_112000001_115000001
Some other message at the end
[1] "+ Full UKB LD matrix: 22590 x 22590"
[1] "+ Full UKB LD SNP data.table: 22590 x 5"
[1] "UKB MAF:: Extracting MAF from UKB reference."
[1] "+ UKB MAF:: Importing pre-existing file"
Error in `[.data.table`(y, x, nomatch = if (all.x) NA else NULL, on = by,  :
  logical error. i is not a data.table, but 'on' argument is provided.
Fine-mapping complete in:
Time difference of 1.4 mins
Error in `[.data.table`(x, r, vars, with = FALSE) :
  column(s) not found: SNP

Hi @alexMarCar, please accept my sincerest apologies for not following up on this.. I finally have some  time to go back and address these issues, as well as make some changes to echolocatoR to make it more robust.
Locus names
You're correct, locus names are arbitrary. The only thing that matters is that the loci you specify in loci= matches up with the "Locus" column in "top_SNPs". The "Genes" column within "top_SNPs" is optional, as it's only used when a "Locus" column is not given.
Error messages
Given the error above, it's possible there were simply no overlapping RSIDS between your GWAS locus.
Could you tell me how many SNPs are within "/data/kronos/kronos/acarrasco/FOR_MARYAM/results/GWAS/GWAS_coloc/locus_chr9_rs2821150/locus_chr9_rs2821150_GWAS_coloc_subset.tsv.gz"?

Hi,
My apologies this time.
Re. No SNPs overlapping. I see, it makes sense.
The number of SNPs in "data/kronos/kronos/acarrasco/FOR_MARYAM/results/GWAS/GWAS_coloc/locus_chr9_rs2821150/locus_chr9_rs2821150_GWAS_coloc_subset.tsv.gz" is 1367.


chore: release main

:robot: I have created a release beep boop
dev-dependencies-common: 3.2.2
3.2.2 (2024-02-10)
Bug Fixes

bump types and common dependencies (d70f68b)

dev-dependencies-types: 1.1.5
1.1.5 (2024-02-10)
Bug Fixes

bump types and common dependencies (d70f68b)

This PR was generated with Release Please. See documentation.

:robot: Release is at https://github.com/aversini/dev-dependencies/releases/tag/dev-dependencies-common-v3.2.2 :sunflower:

:robot: Release is at https://github.com/aversini/dev-dependencies/releases/tag/dev-dependencies-types-v1.1.5 :sunflower:


feat: support latest-only releases

Changes:

Hard-code v0.0.0-latest as the Kratix chart version (needs to be semver-ish!)
Update the GH Action to set skip_existing to false

TODO:

Investigate how the Helm Chart Releaser deals with a release/tag of the same name (kratix-v0.0.0-latest) already existing
Test that we can deploy this change and see the updated Kratix manifest

It looks like the Helm Chart Releaser generates a new GH release, which creates a new tag of that release name. This was fine when every release name was unique (versioned), but may cause issues when we are always using the same release/tag name.
We might need to delete the old release/tag before regenerating them with the Helm Chart Releaser.

Also check the index.yaml in the gh-pages branch, and whether the created timestamp gets updated when the version doesn't change (suspicion: yes)


docker-setup

docker setup description

Thank you, am traveling on vacation this week, will update the main README with this info once I get back and close it.

Made minor updates to docker-setup.md and linked from main README.md.


Can't execute tests - Executed 0 of 0 ERROR (0.005 secs / 0 secs)

I'am running an unit test with the following comand: ng test --sm=false. 24 hours agor it was working fine and I could see the result on the browser (Chrome) and also on terminal.
After upgrading few npm modules globally and for spesific app, I can't run the test as expected.
I throws following result: Chrome 61.0.3163 (Mac OS X 10.12.6): Executed 0 of 0 ERROR (0.005 secs / 0 secs)
ng --vresion:
node: 8.0.0
os: darwin x64
@angular/animations: 4.4.3
@angular/cdk: 2.0.0-beta.8
@angular/common: 4.4.3
@angular/compiler: 4.4.3
@angular/core: 4.4.3
@angular/flex-layout: 2.0.0-beta.9-0e7d2e0
@angular/forms: 4.4.3
@angular/http: 4.4.3
@angular/material: 2.0.0-beta.8
@angular/platform-browser: 4.4.3
@angular/platform-browser-dynamic: 4.4.3
@angular/platform-server: 4.4.3
@angular/router: 4.4.3
@angular/cli: 1.4.3
@angular/compiler-cli: 4.4.3
typescript: 2.5.2

Here is a part of karma eintries in package.json:
    "karma": "^1.7.1",
    "karma-chrome-launcher": "^2.0.0",
    "karma-cli": "^1.0.1",
    "karma-coverage-istanbul-reporter": "^1.3.0",
    "karma-firefox-launcher": "^1.0.1",
    "karma-jasmine": "^1.0.2",
    "karma-jasmine-html-reporter": "^0.2.2",
    "karma-mocha-reporter": "^2.2.4",
    "karma-remap-istanbul": "^0.6.0",

karma.config.js:
module.exports = function (config) {

    config.set({
        basePath: '',
        frameworks: ['jasmine', '@angular/cli'],
        plugins: [
            require('karma-jasmine'),
            require('karma-chrome-launcher'),
            require('karma-remap-istanbul'),
            require('@angular/cli/plugins/karma')
        ],
        files: [
            { pattern: './src/test.ts', watched: false }
        ],
        preprocessors: {
            './src/test.ts': ['@angular/cli']
        },
        mime: {
            'text/x-typescript': ['ts','tsx']
        },
        remapIstanbulReporter: {
            reports: {
                html: 'coverage',
                lcovonly: './coverage/coverage.lcov'
            }
        },
        angularCli: {
            config: './angular-cli.json',
            environment: 'dev'
        },
        reporters: config.angularCli && config.angularCli.codeCoverage
                  ? ['progress', 'karma-remap-istanbul']
                  : ['progress'],
        port: 9876,
        colors: true,
        logLevel: config.LOG_INFO,
        autoWatch: true,
        browsers: ['Chrome'],
        singleRun: false
    });
};

@bobKasbi check out https://github.com/karma-runner/karma/issues/2711 for getting more information about the error.

Are you experiencing the same issue with the current build from master?

No, not any more. And I found out that it had to do with the wrong path for test file in angular-cli.json Thanks!


orbiton: 2.64.3 -> 2.65.0

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://repology.org/project/orbiton/versions.
meta.description for orbiton is: Config-free text editor and IDE limited to VT100
meta.homepage for orbiton is: https://github.com/xyproto/orbiton
Updates performed

Golang update

To inspect upstream changes

Release on GitHub

Compare changes on GitHub

Impact

Checks done (click to expand)

built on NixOS
The tests defined in passthru.tests, if any, passed
found 2.65.0 with grep in /nix/store/jax36jlfdvl4p7py8hd3lxqy7d2vsw9w-orbiton-2.65.0
found 2.65.0 in filename of file in /nix/store/jax36jlfdvl4p7py8hd3lxqy7d2vsw9w-orbiton-2.65.0

Rebuild report (if merged into master) (click to expand)

1 total rebuild path(s)

1 package rebuild(s)

First fifty rebuilds by attrpath
orbiton

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/jax36jlfdvl4p7py8hd3lxqy7d2vsw9w-orbiton-2.65.0 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A orbiton https://github.com/r-ryantm/nixpkgs/archive/15e29dc46dcf904fde15d5b6e559bf89c0368098.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/15e29dc46dcf904fde15d5b6e559bf89c0368098#orbiton

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/jax36jlfdvl4p7py8hd3lxqy7d2vsw9w-orbiton-2.65.0
ls -la /nix/store/jax36jlfdvl4p7py8hd3lxqy7d2vsw9w-orbiton-2.65.0/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review run on x86_64-linux 1

1 package built:

orbiton

Maintainer pings
cc @sikmir for testing.

Result of nixpkgs-review pr 257374 run on x86_64-darwin 1

1 package built:

orbiton


I was told to report!

Hello! Was just playing around and got a jade item description something along the lines of "HT Tree chop error, plz report" so here it is! I am using the mod with the pyromancer mod which in addition to other things adds two trees to the nether.

Hey, sorry about that. This is the same as #200, so I'm gonna close this and keep that issue open


[React Native] Minimum iOS version requirement does not match with Podspec

I got error related to iOS versions support when trying to validate app bundle for Testflight upload with minimum iOS version set to 12.0:
Invalid Bundle. The bundle AppName.app/Frameworks/aries_askar.framework does not support the minimum OS Version specified
in the Info.plist.

After some investigation I found that minos value in binary is set to 16.2:
aries_askar.framework % vtool -show aries_askar
aries_askar:
Load command 10
      cmd LC_BUILD_VERSION
  cmdsize 32
 platform IOS
    minos 16.2 <---------------
      sdk 16.2
   ntools 1
     tool LD
  version 820.1
Load command 11
      cmd LC_SOURCE_VERSION
  cmdsize 16
  version 0.0

iOS version specified in aries-askar.podspec:
s.platforms    = { :ios => "12.0" }

After I switched app minimum iOS version to 16.2, app bundle validation completes successfully.
This problem is also relevant for indy-vdr and anoncreds RN packages.

@TimoGlastra That's the issue that I mentioned on a AFJ call yesterday.


Remove Map<any, any> constructor overload

⚙ Compilation target
ES2017
⚙ Library
lib.es2015.iterable.d.ts
Missing / Incorrect Definition
This isn't exactly the kind of issue this form (Library issue) seems to be made for, but it looked like the closest match.
The Map constructor has an explicit overload to make new Map() produce a Map<any, any>, rather than safer option of allowing normal type inference to occur. I think the only change that needs to happen is removing the overload. This was already brought up in https://github.com/microsoft/TypeScript/issues/52552, but that was closed because it did not provide a clear usecase, and the focus was on inconsistency between Map and Set.
For me, the usecase is about Map alone - removing a source of silent and infectious anys. noImplicitAny is a recommended setting for good reason, but is undermined by the presence of anys in library types. In fact, I am creating this issue after fixing a bug in my own code that was hidden by this typing.
A fair counterargument is that it may break existing code. My guess - total speculation - is that the override was added in the past when inference was not as effective, and it is no longer necessary in most cases. Where the empty map is meant to conform to a contextual type, it works fine. Toying around with it myself, I find two main cases where it breaks:

Map<any, any> was literally the intent. I'd strongly argue these cases should be explicit.
The Map is constructed without contextual types, but it is meant to conform to them later. As a result, the code in-between those places is unsafe, as in the example below. Though unsafe, this might be a common pattern in practice that the change would break. (Ofc a solution is to explicitly type the Map construction.)

function getWordCounts(text: string): Map<string, number> {
    const m = new Map();
    for (const w of text.split(' ')) {
        m.set(w, (m.get(w) ?? 0) + 1);
    }
    return m;
}

Sample Code
// The problem is that this at-at-glance reasonable function is returning `any`.
function numRudeWords(input: string | null) {
    //   ^? function numRudeWords(input: string | null): any
    const wordCounts = input ? getWordCounts(input) : new Map();
    //    ^? const wordCounts: Map<any, any>
    return (wordCounts.get('meanie') ?? 0) + (wordCounts.get('dangnabit') ?? 0);
}

function getWordCounts(text: string): Map<string, number> {
    const m = new Map<string, number>();
    for (const w of text.split(' ')) {
        m.set(w, (m.get(w) ?? 0) + 1);
    }
    return m;
}

Documentation Link
The MDN doc link is here, though it's not super relevant to this particular question: https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Map/Map

I have a simpler example that bit me recently:
const maybeMap: Map<string, number> | null = null;
const concreteMap = maybeMap ?? new Map(); // concreteMap has type Map<any, any>
declare function functionExpectingDifferentMapType(map: Map<string, Date>): void;

functionExpectingDifferentMapType(concreteMap); // No TypeScript error here! Crash at runtime!💥

Playground: https://www.typescriptlang.org/play/?#code/MYewdgzgLgBAtgQwJ4CMCmBZBAHAXDLbAHmgCcBLMAcwBoYwBXOdUgPhgB96GAbHmALzc+AbgBQoSLEnBSaKJhyD4ydIRgB+DfTQB3AjgAUAShEwA9OZgy5C9QAsEEGFCTY0B4gjBI63pKxiACZowDwIcjAAZgxgwFDk4NGx8YlgAKIAHu6p1AAi5FFRaHJgUIQAKm5ohoh4niRQFNR0eQgKrMb4AG4g5EHiYjFxCeBZOQn5hcWl5ThV7oY28orYphZWAHIgMCWkIKQw9iVoAIRAA
In the real code, we were building up a Map of metadata about various objects, and two parts of the code disagreed about the shape of the metadata. Because ?? new Map() widened the type to Map<any, any>, the mismatch wasn't caught by TypeScript and caused a crash at runtime. Thankfully it was easy to see the mismatched data in the debugger, but this widening was very unexpected.

You can opt into this today with this code:
// Wrap in declare global { if the containing file is a module
interface MapConstructor {
    new(): Map<unknown, unknown>;
}

// m: Map<unknown, unknown>
const m = new Map();

You can opt into this today with this code:

That works, thank you! I will do that. I didn't realize later declarations take precedence over the earlier ones, that is very useful. (The docs do say so, now that I look.)
Note that I will actually be using
interface MapConstructor {
    new<K, V>(): Map<K, V>
}

in order to also allow normal type inference, as in
const foo = (): Map<number, string> => new Map();

which, for me, reduces the false errors that come from the change otherwise.

From https://stackoverflow.com/questions/79061050/why-cant-the-value-of-a-map-be-inferred I see what looks like a desire/expectation for an evolving Map type. I don't know if there's any general desire for that, but I can see why people might expect Map<any, any> to behave that way, since auto-typed things look like "any" to the casual observer, and since new Map() looks like let arr = [].  If new Map() produced something other than Map<any, any> it would possibly help, but it's still potentially confusing because of the existence of other evolving things.


Add RFWSTETH: Respawn Finance Wrapped Staked Ethereum

[x] I understand that token listing is not required to use the Polygon Wallet with a token.

Please provide the following information for your token.
Token Name: Respawn Finance Wrapped Staked Ethereum
Token Symbol: RFWSTETH
Decimals: 18
Polygon Address: 0x716ceb4Dc674FB91C4198c50b837F11f6ef75df0
Ethereum Address: 0x07FA101efde726E0956Edd2c4D5C8d3d1A5E9c53
Logo URI (svg): https://assets.respawn.finance/rfwsteth.svg
Project Name: Respawn Finance
Project Summary: Through respawn crypto economics respawn finance provides the base protocol layer between users and (game) content creators.
Project Contact: https://polygonscan.com/address/0xE2D68336944dC53Ac485413518FE9CDa0F197B7b
Project Website: https://respawn.finance/
Mainnet/Testnet: Mainnet
Additonal Notes: /

Added to AllTokens v2.5.0.


CI and Static Analysis

JET is a static analysis tool - it detects issues currently
AQUA is a linter - it detects issues but I disabled these checks for now
SafeTestsets is a convenient way to ensure variables defined in one test does not affect others. It comes from the SciML ecosystem.
The SciML ecosystem is also suggesting writing test files such that it is trivial to just copy from the file and run a test reported as failing, for ease of interactive development. The SciML styleguide has good suggestions
Doctests are now tested
the macros in runtest are a convenient way to wrap things in SafeTestsets
the CI was somewhat updated

another thing to consider adding is "SnoopPrecompile". See QuantumClifford for examples

Codecov Report

Merging #30 (7a0770e) into main (14a5061) will increase coverage by 39.45%.
The diff coverage is 100.00%.

:exclamation: Current head 7a0770e differs from pull request most recent head 2e4d076. Consider uploading reports for the commit 2e4d076 to get more accurate results

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more
@@             Coverage Diff             @@
##             main      #30       +/-   ##
===========================================
+ Coverage   47.52%   86.97%   +39.45%
===========================================
  Files           9       10        +1
  Lines        1372      975      -397
===========================================
+ Hits          652      848      +196
+ Misses        720      127      -593

Impacted Files
Coverage Δ

src/WaveguideQED.jl
100.00% <100.00%> (ø)

... and 9 files with indirect coverage changes
:mega: We’re building smart automated test selection to slash your CI/CD build times. Learn more

Doctests seem to be disabled in test with your comment "# TODO doctests need fixing
#VERSION == v"1.8" && @doset "doctests""


Bump black version

This PR bumps black version. I only did this atm because I couldn't find out a way on how to modify a github actions workflow file from my own fork (it does make sense that I shouldn't do it 😅).

It's weird that I remember putting pip wheel metadata files to .gitignore yet it still creates and adds them automatically.

I couldn't find out a way on how to modify a github actions workflow file from my own fork

Could you explain what you mean here, I don't get it :D

This PR should also bump the version on the CI, which you can change here: https://github.com/skops-dev/skops/blob/ff5a4e163791199f463ec8b130c05f2933297d60/.github/workflows/build-test.yml#L35
It should also run the new black on the whole codebase and include the changes in a separate commit in this PR (this can also be a separate PR if we want to add it to git ignore revisions)

I wanted to open a PR to that file from my own fork but couldn't figure it out (and it makes sense that you shouldn't be able to modify it from your fork.)

I'm not sure why it wouldn't work. But in the end, do you need your own fork? You can push to this repo directly.

It would work from the fork, please DON'T push to this repo 🙈

It would work from the fork, please DON'T push to this repo see_no_evil

For my better understanding, what is the problem with creating branches on this repo directly and base PRs on those branches?

Got it, thanks for explaining. Maybe we should have a central place to write things like this or our discussion about squashing down?

People at HF aren't on the same page when it comes to these topics, so I rather make it project specific. But I agree we should have this somewhere, in our contributing guidelines.
The work on this project started being much faster once I went on holiday then the conference this week, I haven't had a chance to add documentation or README for these issues :D :P

I'm sorry for being a rookie, I thought forks weren't allowed to modify it. I couldn't see .github because I didn't fetch the upstream on my main, it was added later. I thought it was intentionally made like that. 😅


Fix blinking

Blinking doesn't work. Also, maybe add an "emote" function to player animator so we can combine blinking with the win face?

Blinking is not a high priority right now, might reopen later


ObsListItem media finishing

Right now we're using the same ObsImagePreview component for both ObsListItem and ObsGridItem, but they are slightly different. ObsListItem should follow the Photo-List component in the designs:

The goal here is to get the ObsListItem media to match those designs, so here's a probably incomplete list of todos:

[x] w/ sound + w/o photos should have a centered sound icon, a border, and no background
[ ] w/o sound + w/o photos should have a centered nophotos icon, a border, and no background
[x] w/sound + w/ photo should have sound icon in the lower left
[x] make sure bordered versions are exactly the same width/height as the unbordered ones

Note that Abhas requested that w/o sound + w/o photos continue to use the iconic taxon icon, so that's what I'm going with.

Slowed down a bit by refactoring UI Library so I could preview the different states I was altering, as well as by some back and forth regarding designs that aren't in Figma.


Feature Request

The current version of Meaxure can not deal with 0.5px border, Is there any way to improve this?

What do you mean by can not deal with 0.5px border?

When border width set to 0.5px in Sketch, Meaxur will floor it to 0.

cannot reproduce

This happens when exporting to html.

See this part, it's correct:

As to you part, it's provided by sketch native interface, which I cannot change it's behavior:
https://github.com/qjebbs/sketch-meaxure/blob/e26a618d8553af8f2dd6715357ac51ed4af5db6f/src/sketch/layer/index.ts#L62
But I think Sketch is right, CSS does't support 0.5px borders:
https://stackoverflow.com/questions/13891177/css-border-less-than-1px

Thanks for your patience.
0.5px border is supported in Safari, it may not a good way to achieve this. The problem is in real life when I hand off specs to developers they often missed off border styles... so I guess there is no good solution anyway. 😢


Sync robot-simulator

Sync'ed according to #781. Changes tests heavily in structure, but not in content. So no re-running against existing solutions required.

Spread out test cases to individual test methods
Test only from the interface specified in problem specifications
Still re-design requested in #783

I did find a way to do a re-structuring without altering the interface relied on by existing solutions. There are now no extra methods used, that I think were older than the current instructions property in problem spec.
The exercise is marked as topic: ['oop'] in config.json, which hints on why there were specialised methods to change the internal state. And why our example.php (and an additional test) does method chaining (fluent interface design).
To stay as close to the problem spec as possible, the OOP-isms are seemingly superfluous. A fluent interface design deviates totally from the string style instructions. On the other hand one could transform the string input into the fluent interface while writing the tests, and also allow immutable instances as a more modern approach that way. But still, I think such OOP-isms should only be in additional PHP track exercises.

@fejan-malek I cannot add you as a reviewer, because you are no maintainer yet. Anyways, what do you think about a fluent interface here?

@mk-mxp I agree with using a fluent interface because it helps write clean code, better code readability, and reduces code complexity.
What do you think about the existing solution already submitted in this exercise? Is it gonna affect these changes?

What do you think about the existing solution already submitted in this exercise? Is it gonna affect these changes?

@fejan-malek Not using an implemented method does not invalidate any existing solution.

I've been trying out several variants for a fluent interface. The problem is, that all the benefits of the fluent interface are hidden in the tests. The student experiences nothing but "additional work to return $this".
The exercise becomes rather "boring", with only conditionally adjusting values. "Boring implementation" can be a quality of good design, but is discouraging for students at Exercism. There would be only one challenge left in the exercise. The string splitting and looping disappears.
These two points made me decide: The exercise shall stay as close as possible to problem specifications. Fluent interfaces are a concept to introduce in an extra exercise, most likely a PHP track only exercise.

Note that I didn't took time to take a look yet, I will probably look into this tomorrow.
About fluent interfaces I'm not in favour of having those: https://ocramius.github.io/blog/fluent-interfaces-are-evil/
That said it could be great to introduce them in an exercise just so the students know they can write code like this and understand how to read code like this.


Disable extension update messages

🐛 Describe the bug
Even though quiet sync is enabled, it still pops up a browser window with the changelog after every option
🌴 Visual Studio Code Version: [ 1.27.1 ]
🌴 Code Settings Sync Version: [ 3.1.2 ]
🌴 Operating System : [ Windows 10 1803 ]
🌴 Occurs On: [ Updating the extension ]
🌴 Proxy Enabled: [ No ]
🌴 Gist Id: [ ID_HERE ]
📰 To Reproduce
Steps to reproduce the behavior:

Go to '...'
Click on '....'
Scroll down to '....'
See error

💪 Expected behavior
A clear and concise description of what you expected to happen.
📺 Console Error Log
If applicable, add screenshots or paste the console log from developer console of VSCode.
📺  Additional context
Add any other context about the problem here.

Oh.
It's just a one window that appears on every update.
U want "settings sync" completely quiet :disappointed:  ?

@shanalikhan pretty much, yeah. But you could put the release notes link into the notification that pops up, otherwise this just super disrupts my workflow with auto updates enabled, you are coding on something and suddenly your browser steals pops up :)

@loadbalance-sudachi-kun funded this issue with $256. Visit this issue on Issuehunt

@shanalikhan has submitted output. Visit this issue on Issuehunt

@shanalikhan has rewarded. Visit this issue on Issuehunt

Yeah same, also I seem to get the browser window open when OTHER extensions update sometimes, super weird.

Yeah same, also I seem to get the browser window open when OTHER extensions update sometimes, super weird.

That could be why it's so annoying - must be hooking into a generic event.

@nfour

makes me want to disable it when it pops a browser window up every 30mins smile

Every 30 minutes, can you share the screen shot which extension is showing dialog in every 30mins?

It's not necessarily every 30 minutes but it does pop up multiple times per day. Not sure how I'd diagnose which extension is proccing it.

Okay, when you get dialog, post the screen shot here so i will see.

Not sure how I'd diagnose which extension is proccing it.

My bad, may be Settings Sync is throwing it.
Post the screen shot when you get any.

@shanalikhan

It pops that up when I open a new editor, sometimes. I've looked at that file, write permissions are fine.

{"ignoreUploadFiles":["projects.json","projects_cache_git.json"],"ignoreUploadFolders":["workspaceStorage"],"ignoreExtensions":[],"replaceCodeSettings":{},"gistDescription":"Visual Studio Code Settings Sync Gist","version":322,"token":"<snip>","downloadPublicGist":false,"supportedFileExtensions":["json","code-snippets"],"openTokenLink":true,"disableUpdateMessage":false,"lastUpload":"2018-11-28T00:09:16.218Z","lastDownload":"2018-11-27T06:57:23.209Z","githubEnterpriseUrl":null,"askGistName":false,"customFiles":{},"hostName":null,"useCliBaseInstallation":true}

Haha when I restart vscode it opens a browser with for every single editor I have open with that same tab. This is ridiculous man XD

There is similar issue opened, #706 , and users have auto upload or download on ? If you have either on them enabled - Turn them off and restart code and let me know if it helps.

I have auto upload and download enabled, yea

I think that it would be more supportable if instead of opening a page in the browser, it would just open a page in vscode. Most extensions do that for news/updates information.

It looks like the original feature intent was added with disableUpdateMessage? Might be good to add this flag to the documentation.

I think that it would be more supportable if instead of opening a page in the browser, it would just open a page in vscode. Most extensions do that for news/updates information.

Yes, i will setup a page in the future updates.

disableUpdateMessage is added already.
Will add on documentation


page method conflict between Capybara::DSL and ViewComponent::TestHelpers

I'm getting up and running with the recently-added with_rendered_component_path method (cool!).
I need to write both unit tests and system tests for components, as some require JS and some don't. As such, one spec uses with_rendered_component_path with visit and one uses plain old render_inline.
The testing guide for component system tests doesn't yet include an example for rspec, but I think I'm doing this right.
Steps to reproduce
# rails_helper.rb
RSpec.configure do |config|
  config.when_first_matching_example_defined(type: :component) do
    config.include ViewComponent::TestHelpers, type: :component
    config.include ViewComponent::SystemTestHelpers, type: :component
    config.include Capybara::RSpecMatchers, type: :component
    config.include Capybara::DSL, type: :component # required to use `visit` in the JS spec
  end
end

Write two specs - one using with_rendered_component_path and one without.
RSpec.describe MyJsComponent do
  let(:component) { described_class.new }

  before do
    with_rendered_component_path(render_inline(component), layout: "admin_test") do |path|
      visit path
    end
  end

  scenario "clicking on something does something", :js do
    find("input").click
    expect(page).to have_text "test"
  end
end

RSpec.describe MyComponent do
  let(:component) { described_class.new }

  it "renders some text" do
    render_inline component
    expect(page).to have_text "test"
  end
end

Expected behavior
Both specs pass.
Actual behavior
The MyComponent spec fails.
This is because ViewComponent::TestHelpers AND Capybara::DSL both define page and Capybara's version wins as it's loaded last. This breaks the spec as it needed the one from ViewComponent. Switching to expect(rendered_component) makes it pass, but that method is deprecated.
Is there a way to avoid including Capybara::DSL and access visit another way?
Wondering if @edwinthinks has any thoughts on this?
System configuration
Rails version: 7.0.4
Ruby version: 3.1.2
Gem version: 2.81.0

@edwinthinks might you be up for reviewing this?

@joelhawksley - I think the immediate thinking for handling this is to remove the definition of page in the lib/view_component/system_test_case.rb and make it something that users can include when setting up VC.
Or -- perhaps remove the syntax sugar of being able to call find. Instead, you have to do something like page.find; This seems like a pretty big change that could break it for others, though.
What do you think of these two options?

I've not used with_rendered_component_path myself yet, but shouldn't specs that use with_rendered_component_path be system specs? Then don't include ViewComponent::SystemTestHelpers for component specs. Include it only for system specs. According to the documentation a system tests should inherit from ViewComponent::SystemTestCase, which inherits from ActionDispatch::SystemTestCase:
https://github.com/ViewComponent/view_component/blob/301929fe8f2a5ebaf8257f2dc355785f0d5426e2/lib/view_component/system_test_case.rb#L6
According to the RSpec documentation system specs are wrappers around Rails' system tests, which are inherited from ActionDispatch::SystemTestCase.

Ahh thats a good point @jacob-carlborg-apoex ; Could you try @developius to selectively include:
ViewComponent::SystemTestHelpers

and/or
Capybara::DSL

To be on system or browser type tests and see if that works?

@jacob-carlborg-apoex that is a good point. I was hoping to be able to use both forms of test in the same file, like we can with feature specs with the :js flag. Splitting up the spec into spec/components and spec/features/components feels a little weird, but I understand that one set is running system specs and the other is unit specs. Would be nice if we could configure either setup though.
@edwinthinks  I tried this but it doesn't work, it seems to ignore the js metadata. Maybe I'm not using it correctly?:
config.include ViewComponent::TestHelpers, type: :component, js: false
config.include ViewComponent::SystemTestHelpers, type: :component, js: true
config.include Capybara::DSL, type: :component, js: true
config.include Capybara::RSpecMatchers, type: :component, js: true

I was hoping to be able to use both forms of test in the same file, like we can with feature specs with the :js flag.

Component specs are more similar to view specs than to system specs. Component specs and view specs just contain a string with the rendered content. A system spec consists of some form of browser that supports navigation. You cannot navigate to a page in view or component specs.

I tried this but it doesn't work, it seems to ignore the js metadata. Maybe I'm not using it correctly?

I don't know how config.include works with tags, but when passing multiple tags on the command line it means "or", not "and". Might be the same with config.include.

Thanks for the suggestion @jacob-carlborg-apoex, but unfortunately I can't get that to work either.
Not the end of the world, I don't see a problem with separating the two types of spec in the way we normally do with other kinds of specs. Or, alternatively asserting on the result of render_inline instead of page.
I'm happy to open a PR adding example usage for rspec withwith_rendered_component_path unless you feel better positioned to do that @edwinthinks?

Upon closer inspection, it is caused by https://github.com/ViewComponent/view_component/blame/9c5a9c7727b6186ece8b86fb832e7f6fd969580a/lib/view_component/test_helpers.rb#L11 or at least related to this. The errors I'm seeing are that its trying to call visit on the Capybara::Node::Simple
I want to think about how we can make this work in a more elegant fashion without having to resort to overriding and adding excessive changes. However, here is the approach I was able to use to avoid the issue:
Use a different tag for component tests using JS; in rails helper
  config.include ViewComponent::SystemTestHelpers, type: :component_js

  config.before(:each, type: :component_js) do
    def page
      # Overrides the Capybara overwrite.
      Capybara.current_session
    end
  end

Then in your tests, use the tags system & component_js
Spec.describe ExampleComponent, type: [:system, :component_js] do
  let(:component) { described_class.new }

  before do
    with_rendered_component_path(render_inline(component)) do |path|
      visit path
    end
  end

  scenario "clicking on something does something", :js do
    find("input").click
    expect(page).to have_text "test"
  end
end

Not my ideal way to make this work, I'm curious to know how we can possibly refactor view components to avoid this collision.

While I like the idea of having a single file that mixes multiple test types, I don't think that would align well with standard Rails practices. I don't think the ergonomics of this proposal outweigh that inconsistency, so I'm going to close this issue ❤

Fair enough @joelhawksley, thanks for the consideration.


Document fn executable direct download and setup

Many developers installing Fn don't have root access and can't write to /usr/local/bin.  On some platforms (e.g., DigitalOcean droplets) /usr/local is in a read-only file system and cannot be written to.
The Fn install script should be runnable by a non-root user and support the specification of the installation folder.

Assigned to @treeder for triage.  :)

Can we just tell people to download the bin in these cases?
https://github.com/fnproject/cli/releases

This all sounds good. I'll should be able to work on it in next week.


Remove unnecessary params from rules in Snakemake

Task
Remove unnecessary params from rules in variant_calling Snakemake file. Values can be defined in the wrapper class level.
Rules:

variant_calling_gatk_hc_run
variant_calling_gatk_ug_run

File: snappy_pipeline/workflows/variant_calling/Snakefile

Perhaps also for somatic_variant_calling_varscan_joint_run.
File: snappy_pipeline/workflows/somatic_variant_calling/Snakefile

Conclusion: upon second look it is enough work to make it not worth it. Closing...


01_workOffline.sh:  Incorrect history entry when attaching a file to offlineTransfer.json

Cosmetic change to 01_workOffline.sh
Last action for an attach is displayed as "signed pool registration transaction for '', payment via ''"
at line 153 replace with:
offlineJSON=$( jq ".history += [ { date: "$(date -R)", action: "attached file '${fileToAttach}'" } ]" <<< ${offlineJSON})

:smiley: yeah, thx. have not seen this. typical copy&paste error. i have corrected it for the next version

:smiley: yeah, thx. have not seen this. typical copy&paste error. i have corrected it for the next version


Generate implementsMappers for WinRT Interfaces

Closes #473
Also, I regenerated ApplicationData class and IApplicationData interface as they were a bit outdated.

Nice!


How to match all current items in a certain directory

@kwadrat Is there any way? I want to match all the content under a certain path
有什么办法吗？我希望匹配某一个路径下的所以内容

Sorry, I didn't read the document carefully

@squeaky-pl When I use "router. add_route ("/gh/{path} ", github. getFile)", I cannot match correctly

I am not matching a separate directory, but all the directories below

Additionally, when I call any function or class other than a custom one of 'request', calling 'request. Response' will result in 'SystemError: error return without exception set'

@squeaky-pl

Javac


fix(aws-apigateway-iot and aws-cloudfront-apigateway-lambda): fixed deprecated warnings

Issue #551 , if available:
Description of changes:
-Replaces UsagePlanProp.apiKey with method addApiKey()
-options prop in LambdaRestApi has been deprecated since it now extends RestApiProps, removed options prop in test
By submitting this pull request, I confirm that you can use, modify, copy, and redistribute this contribution, under the terms of your choice.
fixes #551

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Add ability to disable token generation for certain conditions

Why generate a token here: ?
https://github.com/yiisoft/csrf/blob/5f442d47f0c64e07815f2eda0d0194bb1146d9d0/src/CsrfMiddleware.php#L67-L76
If you can generate here:
https://github.com/yiisoft/csrf/blob/5f442d47f0c64e07815f2eda0d0194bb1146d9d0/src/CsrfToken.php#L25-L33
In this case, the token will be generated on the first use, not on the first request.

CsrfToken::getValue() used to get token for send via request. Missing token should throw an exception, not generate a new token.

Why should I throw an exception?

Why should I throw an exception?

For example, exception can show that you not connected middleware.

Why should I throw an exception?

For example, exception can show that you not connected middleware.

For example, I don't want to include this middleware in my API, but I want to generate a token for the Web.
For some other reason, I cannot connect this middleware, but I want to generate a token for the Web.
What should I do?

Why do you need a token if you don't check it?

I need a token because I check it. You have strange statements.

I need a token because I check it. You have strange statements.

You should check and then create/save new token before use token in web.

I need a token because I check it. You have strange statements.

You should check and then create/save new token before use token in web.

Why should I do what you say, and not what the business logic of the application needs?

The simplest example:
On the site for guests, a session is not created, since nothing is stored in it. If the guest performs any specific action, data is placed in the session and session it is automatically created. With this csrf validator, the session will always be created when opening the first page, but this is not necessary.
I do not consider it necessary to continue the discussion further.

We need an ability to enable/disable token generation for certain condition.

We need an ability to enable/disable token generation for certain condition.

It's too complicated.
As I already gave an example, it is possible that the verification of the token should be skipped, but we still need the token.
A token should only be generated when needed.
You don't have to do what is not required.

A token should only be generated when needed.

Is there a certain way to check if token will be needed? For example, it's a GET request and we have a form somewhere in the page. Token should be generated. If it's a GET request and there are no forms at all, it still may be needed for some custom JavaScript that reads token from a meta-tag and does POST request.

A token should only be generated when needed.

Is there a certain way to check if token will be needed? For example, it's a GET request and we have a form somewhere in the page. Token should be generated. If it's a GET request and there are no forms at all, it still may be needed for some custom JavaScript that reads token from a meta-tag and does POST request.

The example is incorrect. JavaScript has nothing to do with middleware.
If JavaScript requires a token, it must be provided in some form on the page. One way to do this is to pass it through the meta tag. In this case, the token will be generated when generating the page template (on request).

https://github.com/yiisoft/csrf/issues/15 should be done first. Then this issue may become obsolete because there will be no sense in not executing the middleware.

#15 should be done first. Then this issue may become obsolete because there will be no sense in not executing the middleware.

Changing the way the token is generated does not solve the 2 aforementioned problems.

Likely not but we'll see.


Hotreloading Type Declerations

Does this support the hotreloading of types mentioned here and if so is there any examples of how to implement it https://module-federation.io/guide/basic/type-prompt.html
Does this have something to do with it not working https://github.com/module-federation/vite/blob/main/src/plugins/pluginMFManifest.ts#L376-L377
react refresh:6 [ dynamic-remote-type-hints-plugin ] err: [object Event] this is also one of the errors on the host side and the remote is using webpack and its manifest has a reference to the .d.ts and zip

Hi @econneely, can you open a PR with a failing scenario in this example pls? With your help we will solve the problem sooner. Thanks

@gioboa that example fails on the host example with this error Failed to resolve entry for package "@module-federation/vite". The package may have incorrect main/module/exports specified in its package.json. [plugin externalize-deps

I ran pnpm install then pnpm run multi-example

I ran pnpm install then pnpm run multi-example

I cloned the repo from scratch and you need to run pnpm run build  after the install

Update the readme with tha that fixed it will get the pr up asap

Update the readme with that, it fixed it will get the pr up asap

Fixed, thanks

Hi any timeframe on this want to know for planning some work with a Vite project thanks

I'm on it, I need few days to figure out a solution.

Thanks much appreciated

The idea is to use the @module-federation/dts-plugin because it's always up to date. I'm trying to feed it with a generic compiler. Let's see


Bump Sentry to recent version, enrich reported events

We recommend you update your SDK from<EMAIL_ADDRESS>to<EMAIL_ADDRESS>(All sentry packages should be updated and their versions should match)

Seems we are using not so latest sentry version.
Recent is 7.0.2 - https://www.npmjs.com/package/@nuxtjs/sentry
https://github.com/kodadot/nft-gallery/blob/main/package.json#L75
https://sentry.nuxtjs.org/guide/migration
Maybe enable lazy-loading?

https://sentry.nuxtjs.org/sentry/lazy-loading

👋


How to copy visual studio debugger to windows 10 iot core os

Unable to Deploy Application visual studio to raspberry pi 3
Error Message :  DEP6957: Failed to connect to device '<IP_ADDRESS>' using Universal Authentication. Please verify the correct remote authentication mode is specified in the project debug settings. COMException - Exception from HRESULT: 0x801C0003 [0x801C0003] IoTServer
i have deployed application from IoT Dashboard success fully but tried from visual above exception is shown,,
i searched many sites finally got this message

F5 driver deployment from Visual Studio does not work on Windows 10 IoT Core. Drivers must be manually copied and registered on the device

How can copy debugger manually to windows 10 IoT Core

Are debugging a driver?
If you are debugging a UWP application F5 should just work.
If you are debugging a console application see these steps: https://docs.microsoft.com/en-us/windows/iot-core/develop-your-app/remotedebugging

@paulmon in Microsoft Docs gives the solution for Debugger is

F5 driver deployment from Visual Studio does not work on Windows 10 IoT Core. Drivers must be manually copied and registered on the device

So, I need to Copy manually (Visual Studio Debugger).

If you building device drivers see this page:
https://docs.microsoft.com/en-us/windows/iot-core/learn-about-hardware/driverdeployment
If you are developing a UWP application see link:
https://docs.microsoft.com/en-us/windows/iot-core/develop-your-app/buildingappsforiotcore
If you are developing a console app see this page:
https://docs.microsoft.com/en-us/windows/iot-core/develop-your-app/remotedebugging


[AST] Make TypeBase::adjustSuperclassMemberDeclType() more robust.

When performing substitutions in this function, allow them to fail
more gracefully by producing error types. Fixes SR-7457 /
rdar://problem/39492060.

@swift-ci please smoke test and merge


Update cloud-deployment-overview.md

Updated the Disaster Recovery section

:x: Organization membership check failed
Members of the MicrosoftDocs organization should use the private repo. Please move your changes to https://github.com/MicrosoftDocs/Dynamics-365-Operations, and close this pull request.

:x: Organization membership check failed
Members of the MicrosoftDocs organization should use the private repo. Please move your changes to https://github.com/MicrosoftDocs/Dynamics-365-Operations, and close this pull request.


Segmentation fault with is_a? and modules

The following code crashes with a segmentation fault (signal 11):
class Super
end
module Mixin
end
class A < Super
  include Mixin
end
class B < Super
  include Mixin
end

a = A.new.as(Super)
if a.is_a? Mixin
  puts a.class
end

It is worth noting that this only happens inside if is_a? Mixin. If it's not inside that, it'll print the expected value (A).
Tested on Crystal 0.19.4+90 7e1afdb.

@zatherz Hey, thank you for reducing this! I'm sure the original code was much bigger :-)

Yeah, it happened in a basic Discord bot. I reduced it to a small size and then @RX14 helped me reduce it even further.


Streaming API output is 3x times larger if streamed into express.response

Hi!
I would appreciate help with optimization of generating and downloading a csv.
Inside an express route I'm converting data to csv with steps as follow:
Option A:

pipe objects from a mongo cursor stream into json2csv
pipe json2csv stream into express response.
The output file downloaded is 36MB.

If I add following steps between 1) and 2) the file will only be 12MB:
Option B:

Same as above
pipe json2csv into fs.createWriteStream
read created file with fs.createReadStream
pipe readStream into express response

Why is that? Is it something with json2csv, my code or some encoding optimizations in the fs module?
(obviously there is an overhead with option B using fs of about 30% more computing time)
lib version: 5.0.6
node version:  14.14.0
code:
Option A (36MB):
onst input = new Readable({ objectMode: true });
  input._read = () => {};

  const opts = { fields, withBOM: true };
  const transformOpts = {objectMode: true};
  const json2csv = new Json2Csv(opts, transformOpts);

  input.pipe(json2csv).pipe(res);  // express response
  while (await cursor.hasNext()) {
    const dataRow = await cursor.next();
    input.push(dataRow));
  }
  input.push(null);

Option B (12MB):
onst input = new Readable({ objectMode: true });
  input._read = () => {};
  const opts = { fields, withBOM: true };
  const transformOpts = {objectMode: true};
  const json2csv = new Json2Csv(opts, transformOpts);
  const write = fs.createWriteStream('./output.csv');
  input.pipe(json2csv).pipe(write);

  while (await cursor.hasNext()) {
    const dataRow = await cursor.next();
    input.push(dataRow));
  }
  input.push(null);

  const read = fs.createReadStream('./output.csv');
  read.pipe(res); // express response

Express server configuration:
const server = express();
server.use(bodyParser.urlencoded({extended: false}));
server.use(bodyParser.json());
server.use(helmet());
server.use(compression());

Don't think it matters but the request to the route is done from browser with a GET request using fetch, converting the response to blob, and using window.URL.createObjectURL(file);
Thanks!

From your example it doesn't seem like you're using the streaming API mentioned here https://github.com/zemirco/json2csv/tree/v5#json2csv-async-parser-streaming-api

Thank you for your comment!
You are correct. I'm using the transform stream from here:
https://github.com/zemirco/json2csv/tree/v5#json2csv-transform-streaming-api
I now tested your reference as well in the following code, and it gives the same result as "Option A":
  const input = new Readable({ objectMode: true });
  input._read = () => {};
  const opts = { fields, withBOM: true };
  const transformOpts = {objectMode: true};
  const asyncParser = new AsyncParser(opts, transformOpts);
  const parsingProcessor = asyncParser.fromInput(input).toOutput(res);

  while (await cursor.hasNext()) {
    const dataRow = await cursor.next();
    input.push(dataRow));
  }
  input.push(null);

If the file is bigger, what's different about the content? Can you do a diff of the two files?

Not sure what you intended, but I tried windows' FC and received:
Comparing files results111.csv and RESULTS222.CSV
Resync Failed.  Files are too different.```

With poorly encoded gibbrish which looks like my data but I can't udnerstand what are the differences.

Also few notes I added in my original post:
1) I edited the sizes. the difference is actualy ~1.5x not 3x.
2) The smaller files outputted with Option B are varying in size from another by 5-10%, while the larger files frm Option A are always the same size exactly.
3) Same data written to file using ExcelJS comes to 50% size of Option B.

If the file is bigger, what's different about the content? Can you do a diff of the two files?

After checking again, it appears content in Option A and Option B are not similiar, and some of the data is not saved to file in Option B.
Not sure why, but since they are the same size if they would have the same data this issue is irrelevant.
Anyway I'm opening a new issue, related, but on another optimization.
@knownasilya thanks!


String right truncation pyodbc.ProgrammingError when using fast_executemany

Environment
To diagnose, we usually need to know the following, including version numbers.  On Windows, be
sure to specify 32-bit Python or 64-bit:

Python: 3.6.3
pyodbc: 4.0.23
OS: Debian Stretch
DB: SQL Server
driver: Microsoft ODBC Driver 17 for SQL Server libmsodbcsql-17.0.so.1.1

Issue
When executing a parameterized "UPDATE" statement with fast_executemany, the following exception is thrown.
ERROR - encoding with 'utf-16le' codec failed (SystemError: <built-in function utf_16_le_encode> returned a result with an error set)
pyodbc.ProgrammingError: ('String data, right truncation: length 666 buffer 510', 'HY000')

The column widths in the target database have more than enough size to hold the data.
This seems equivalent to Issue #337  except that in this case, I'm using 4.0.23 of pyodbc and MS ODBC Driver 17, which fixed the issue in that post but continue to be a problem for me.
I've trimmed down the data to just two rows and can consistently reproduce the problem with just those two rows.
I'm using SQL Alchemy to construct the statements and am using the connection.execute(stmt, [row1, row2]) method to execute.
Turning fast_executemany off fixes the problem, but unacceptably impacts performance.

Some more details:
The column causing the issue is VARCHAR(2000)
After reading #295 , I considered that, even though a TEMP table is not the target of the insert, there is one used in the statement. Changing to a global temp table with ## instead of # fixes in this specific instance, but then the same error happens again on a different table, different column with a different set of data. The TEMP table does not use any varchars, only one integer column, and everywhere in the DB, all columns are varchar, not nvarchar
SET NOCOUNT ON;
BEGIN TRY;
BEGIN TRANSACTION
-- Execute statement here
IF @@ROWCOUNT = '0' THROW 5100, 'FAiled to update or delete record'
COMMIT
END TRY
BEGIN CATCH
ROLLBACK
-- Statement for inserting index of rejected row into temporary table
END CATCH

ColumnEncryption made no difference, unfortunately.

A common thread seems to be the buffer is capped at 510, which is 2 x 255 -- which suggests fast_executemany sometimes assumes a maximum string length of 255 characters (510 bytes)

I've narrowed this down to be a variation of #280
When the SQL statement contains more than one statement (i.e. more complex transactions, try catch blocks, etc...)  and fast_executemany=True,  the SQLDescribeParam call doesn't work and thus VARCHARs are allocated a default buffer size of 510 bytes.
The following code will reproduce the error (notte the "print" statement in the SQL, but this could be TRY/CATCH BLOCKS, etc...
import pyodbc
import sys

print('Python version ' + sys.version)
print('pyodbc version ' + pyodbc.version)

driver = 'ODBC Driver 17 for SQL Server'
server = 'localhost'
database = 'db'
user = 'sa'
password = 'password'

conn_string = f'DRIVER={{{driver}}};' \
                   f'PORT=1433;SERVER={server};' \
                   f'DATABASE={database};' \
                   f'UID={user};' \
                   f'PWD={password};' \
                   f'ColumnEncryption=Enabled;' \
                   f'TrustServerCertificate=yes;'

cnxn = pyodbc.connect(conn_string, autocommit=True)

crsr = cnxn.cursor()

crsr.fast_executemany = True

crsr.execute('DROP TABLE IF EXISTS tmp')
crsr.execute('CREATE TABLE tmp (txt VARCHAR(1024))')

value_to_insert = 'a' * 256

params = [(value_to_insert,), (value_to_insert,)]

sql = """
print 'do nothing';
INSERT INTO tmp (txt) VALUES (?);
"""

crsr.setinputsizes((512,))
crsr.executemany(sql, params)

print(crsr.execute('SELECT txt from tmp').fetchall())

(note that in the actual application, the SQL is significantly more complicated; this is the simplest case that will reproduce the error)
This produces the output with errors:
Python version 3.6.3 (default, Nov  6 2017, 10:55:10)
[GCC 6.3.0 20170516]
pyodbc version 4.0.23
pyodbc.ProgrammingError: ('String data, right truncation: length 512 buffer 510', 'HY000')

The above exception was the direct cause of the following exception:

SystemError: <built-in function utf_16_le_encode> returned a result with an error set

The above exception was the direct cause of the following exception:

SystemError: encoding with 'utf-16le' codec failed (SystemError: <built-in function utf_16_le_encode> returned a result with an error set)

The above exception was the direct cause of the following exception:

SystemError: <built-in function utf_16_le_encode> returned a result with an error set

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "pypirls/memerrortest.py", line 40, in <module>
    crsr.executemany(sql, params)
SystemError: encoding with 'utf-16le' codec failed (SystemError: <built-in function utf_16_le_encode> returned a result with an error set)

However, changing any one of the below will avoid the exception:

Removing the "print" statement from the SQL
Setting the number of 'a' characters in the inserted varchar to 255 (fits in buffer size)
Setting fast_executemany to False

Note that unlike the solution in the wiki, a temporary table is not being used, and ColumnEncryption=Enabled
It's unclear to me why this problem happens when fast_executemany=True but not when False as I would think that SQLDescribeParameter would have the same behaviour in either case, but I'm going to guess it's because in the latter case, a memory array doesn't need to be pre-allocated.
Looking at @v-chojas 's setinputsizes PR -- it looks like that would be a solution to this, but as far as I can tell, it hasn't been released yet?   Any ideas for a workaround?

SQLDescribeParam is not used when not using Fast Executemany, since each cell is bound using only its Python type to determine the binding parameters. When using Fast Executemany, parameters are bound as an array and SQLDescribeParam is used to determine the parameters as well as the size of the array.

Thanks, @v-chojas that clears things up.  The problem with fast_executemany then is when SQLDescribeParam fails due to limitations of when it's supported, the default action (allocate a string of width 255) is not always sufficient.
Options I see:

Use setinputsizes to override (in PR) although this doesn't help set the parameter types
Iterate through all rows of bound parameters to try to infer the Python type of each column. Because a NoneType doesn't confer the type to use, iterating through all rows would be necessary.
At least in my particular case, I could prepare a statement that I know would succeed on SQLDescribeParam, then make some additions to the list of parameters, and pass that parameter list into another statement, although I think this would be very particular for my use case.


Update flye tool

Update Flye up to version 2.9.

@galaxybot test this

@galaxybot test this

@gallardoalba thanks, and I have added you to the list of accounts who can trigger the Jenkins bot, so it should actually respond next time you request a test or deploy. :smile:

@galaxybot deploy this

@gallardoalba thanks, and I have added you to the list of accounts who can trigger the Jenkins bot, so it should actually respond next time you request a test or deploy. :smile:

Thank u!


feat: clvWallet support

Duplicate of #1493 with maintainer changes

@Sophie4140 I'll proceed to merge this PR, but I am seeing issues while QAing the CLV Wallet extension. The isCLVInjected flag seems to fail, or Wagmi does not detect the provider as ready upstream. Please continue to test the wallet against our example deployment here: https://rainbowkit-example-1tl3n12a0-rainbowdotme.vercel.app/


Is this possible to speed up the script?

I have a catalogue of 3000 items and I use pagination, but I have to wait till all the items will be displayed before I get possibility to use pages. Is there any ways to speed up the script?

Generally I wouldn't recommend using MixItUp with a dataset this large. If you are you are reading and looping over these entries from a database in real-time (not cached, not rendered to static files), this will firstly cause a large server-side overhead on page render, let alone issues on the client-side side.
On the client side, you could take this approach to avoid having your browser render/paint 3000 items:
https://demos.kunkalabs.com/mixitup/loading-animation/

Style all mixitup targets as visibility: hidden by default
Initialise your Mixer with filter: 'none'
Once initialised, add a mixitup-ready class to the container, to remove the visibility: hidden style.
Load your first page mixer.filter('all')


chore(wash)!: Replace actor references by component in wash-lib crate

Feature or Problem

Related Issues
#1827
Release Information

Consumer Impact

Testing

Unit Test(s)

Acceptance or Integration

Manual Verification

Hello, thanks for the feedback. I removed the cloud events actor references and applied cargo fmt.


1053 pagination doesnt update on deleting files in a dataset

Now delete will trigger a get request to the backend to update the new list.

I created new redux state (deletedXXXX)
whenever item got deleted this state will change
Upon listening to such change, a request to the backend to fetch the latest list of resources
I also fixed other deletes in the same fashion for API keys, groups, dataset, and metadata definitions.

To test:

Create many files/folders, and delete. The items as well as the pagination should reflect.
Delete datasets
Delete groups. I added a delete button right next to each group
Delete API keys
Delete metadata definition

I think I understand the issue and how you fixed, but I am on main and I can't reproduce :(
If I delete a dataset or a group the list gets updated. In the case of dataset even if it's not on the first page.


[gui error report] Error: Command failed: powershell.exe -NoProfile -NonInteractive -InputF

👉 Please describe what you were doing when this error happened.
Specifications

OS: win32
IPFS Desktop Version: 0.22.0
Electron Version: 19.0.8
Chrome Version: 102.0.5005.148

Error
Error: Command failed: powershell.exe -NoProfile -NonInteractive -InputFormat None -Command Get-AuthenticodeSignature -LiteralPath 'C:\Users\User 1\AppData\Local\ipfs-desktop-updater\pending\temp-IPFS-Desktop-Setup-0.33.0.exe' | ConvertTo-Json -Compress | ForEach-Object { [Convert]::ToBase64String([System.Text.Encoding]::UTF8.GetBytes($_)) }

    at ChildProcess.exithandler (node:child_process:408:12)
    at ChildProcess.emit (node:events:526:28)
    at maybeClose (node:internal/child_process:1092:16)
    at ChildProcess._handle.onexit (node:internal/child_process:302:5)

See workaround in https://github.com/ipfs/ipfs-desktop/issues/2335#issuecomment-2161827010


Pull deeplearning nbs

Creating folder for deeplearning content and adding fashion-mnist project contents

Thanks

@kesmit13 can you merge this pull request? I don't have rights.


Load FXML view file by convention

Followed the PR #20, I would like there is an annotation @FxView  which can attach the FXML file to the controller directly, and no need loading it via FxmlLoader.
@FxView // load MasterView.fxml by default in the same package, or specify the location manually.
// also discover the resources files, css, images etc.
@Dependent
class MasterViewController {}

Thus the codes the codes are similar to the MVC architecture.
Ideally, the controller is a CDI bean to process the business logic, the JavaFX FXML file is used for UI layout, also can access the controller properties/method via EL like Jakarta Faces/Facelets.
I have used JavaFX Weaver core moudle to integrate CDI/Weld with JavaFX in my example project before, https://github.com/hantsy/cargotracker-regapp/blob/master/src/main/java/org/eclipse/cargotrakcer/regapp/ui/HandlingReportController.java#L28, which provides a similar feature.

Hello,
this is indeed a close need of PR #20, except that using annotations makes sense that it belongs in this extension.
I'm working on it, and will propose a PR soon

More simply, make the @FxView includes a specific CustomScope for FXML view. Thus we can remove @Dependent here.

Have a look at branch fx-views if you want to.
And its associated sample (fxviews)
Any feedback appreciated

Hello @hantsy , you reviewed PR #20 but that was not my point.
My proposition is on branch fx-views, no PR yet.
I can create a draft PR if you want.

It looks great for me.
Please create a PR for it, thus other developers will have a chance to discuss on the changes.

It looks great for me.
Please create a PR for it, thus other developers will have a chance to discuss on the changes.

Please have a look at 0.4.0, any feedback appreciated

Marking this as closed / resolved.


TuneIn support, Command line argument changes

TuneIn Support
TuneIn is a internet radio platform hosting thousands of online radio stations. I modified pyradio to search the entered station name on TuneIn and obatin the stream url if it wasnt found in stations.json. This can be disabled with the -d command line option.
Commandline arguments
The station name and volume now are positional arguments. Added -d option.
Updated from urllib2 to requests
I updated pyradio to use the newer requests library instead of the older urllib2 library.
Minor changes
The station list now supports station names of arbitrary length.
The ReadMe was updated to reflect these changes.

I hope I didnt break Linux/OS X support with any of my changes, I dont have a machine to test this right now.

Hey, @sdushantha, sorry if this ping is annoying, but I would be really happy if you could take a look at this.

Sorry for the late response.
I dont really have time to review the code at the moment. (exams... :P)
I trust you that you havent broken anything XD. So I'll just merge this PR now.
Here is cake because you commented your code. 🍰
Thanks for the contribution :D

Sorry... I closed the PR by accident instead of merging it.

Oh god, exams. My condolences.
Anyway, thanks for merging!


display.getAttr() is not a function

At line 132 of file ffcreator/lib/animate/animate.js,
when key in from is not found in to,  display.getAttr() is called.
However, after migrating to InkPaint, display object no longer has getAttr() function.
This causes few animation break, such as moveingInLeft ...
Suggest to either add the function, or just use the following:
to[key] = display[key]

InkPaint DisplayObject has getAttr method


Multiple filters in single step

Hi.
How to add multiple filters in single step?
For example:
ffmpeg.input(path).filter('scale', 1920, 1080).filter('fps', 25)
in command:
[0]scale=1920:1080[s1];[s1]fps=fps=25[s2]
but i need this:
[0]scale=1920:1080,fps=fps=25[s0]
How to put both operation to single step?

anyone found workaround for this?


Type Checker Failure - Unable to generalize a type variable. It is not unranked.

I wasn't sure if this was best for the compiler issues or here. I figured that since it seems to only fail when it should fail that this was the better place to drop it.
The code is obviously incorrect. The interaction seems to be between the a in foo and the List Float in bar. If List is removed or Float or Bool is changed to a type variable or the x parameter omitted, then everything starts working again. I used different definite types to illustrate that they don't seem to matter, but it still fails in the same way even if they are more correct.
foo : a -> Int
foo x =
    bar x

bar : List Float -> Bool
bar x =
    "baz"

elm-make: It looks like something went wrong with the type inference algorithm.
Unable to generalize a type variable. It is not unranked.
Please create a minimal example that triggers this problem and report it to
<https://github.com/elm-lang/elm-compiler/issues>
CallStack (from HasCallStack): error, called at src/Type/Solve.hs:255:3 in elm-compiler-0.18-6b7ElUUnEdQ18JS9q9eLxH:Type.Solve elm-make: thread blocked indefinitely in an MVar operation

I got the same error with this code when the type definition of b was not commented out
valMulti : (a -> Validation e c) -> List a -> Validation e (List c)
valMulti valFunc bs =
    let
        -- go : b -> Validation e (List c) -> Validation e (List c)
        go b acc =
            succeed (::)
                |> andMap (valFunc b)
                |> andMap acc
    in
        L.foldr go (succeed []) bs

I'm gonna track this in https://github.com/elm-lang/elm-compiler/issues/1613 because it is a bug!
Thanks for the very simple SSCCE @gilbertkennen!

Based on commit 4b25980d93ada12236c794f35570e197be82f787, I am now seeing the following error in my development build!

Note: You may see extra qualifiers on types in this error. That is part of the dev build, but should not appear in the final thing.


Fix CrowdStrike typo in CV

I thought you might want to have this fixed ;)

oh yeah! thank you my friend! 👑

but I found having a dedicated cv with it's own styling page is easier - i use this as my primary repo for this
https://github.com/friendlyantz/cv


Update AbstractGraph interface

Add setters/getters to AbstractGraph interface
Implement automatic FeynmanGraph -> Graph conversion
Remove unnecessary parameteric type C for constants in arithmetic operations

Codecov Report
Attention: 120 lines in your changes are missing coverage. Please review.

Comparison is base (9a1cb5f) 64.71% compared to head (c731c69) 62.31%.
Report is 9 commits behind head on computgraph.

:exclamation: Your organization needs to install the Codecov GitHub app to enable full functionality.
Additional details and impacted files
@@               Coverage Diff               @@
##           computgraph     #148      +/-   ##
===============================================
- Coverage        64.71%   62.31%   -2.41%
===============================================
  Files               62       55       -7
  Lines             4328     4134     -194
===============================================
- Hits              2801     2576     -225
- Misses            1527     1558      +31

Files
Coverage Δ

src/FeynmanDiagram.jl
41.66% <ø> (-33.34%)
:arrow_down:

src/quantum_operator/expression.jl
96.22% <100.00%> (-0.33%)
:arrow_down:

src/computational_graph/optimize.jl
87.94% <98.24%> (+1.69%)
:arrow_up:

src/computational_graph/tree_properties.jl
50.00% <85.71%> (+1.31%)
:arrow_up:

src/computational_graph/transform.jl
96.96% <90.69%> (-0.32%)
:arrow_down:

src/computational_graph/conversions.jl
60.00% <60.00%> (ø)

src/computational_graph/feynmangraph.jl
86.15% <74.13%> (-5.03%)
:arrow_down:

src/computational_graph/graph.jl
70.45% <75.00%> (+2.13%)
:arrow_up:

src/backend/static.jl
38.29% <41.17%> (-1.07%)
:arrow_down:

src/computational_graph/io.jl
0.00% <0.00%> (ø)

... and 1 more

... and 50 files with indirect coverage changes

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:loudspeaker: Have feedback on the report? Share it here.


Run out of memory

When I ran train. py with a GPU. It seems that  RAM has run out. My computer has 46G of RAM, including 30G virtual memory.
$ python3 baseline/train.py --max_step=200 --debug --batch_size=96
mkdir: cannot create directory â€˜./modelâ€™: File exists
loaded 10000 images
loaded 20000 images
loaded 30000 images
loaded 40000 images
loaded 50000 images
loaded 60000 images
loaded 70000 images
loaded 80000 images
loaded 90000 images
loaded 100000 images
loaded 110000 images
loaded 120000 images
loaded 130000 images
loaded 140000 images
loaded 150000 images
loaded 160000 images
loaded 170000 images
loaded 180000 images
loaded 190000 images
loaded 200000 images
finish loading data, 197999 training images, 2001 testing images
observation_space (96, 128, 128, 7) action_space 13
/home/rody/xu/npaint/LearningToPaint/baseline/DRL/ddpg.py:157: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
  s0 =torch.tensor(self.state, device='cpu')
/home/rody/xu/npaint/LearningToPaint/baseline/DRL/ddpg.py:163: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
  s1 =torch.tensor(state, device='cpu')
 #0: steps:200 interval_time:9.08 train_time:0.00
 #1: steps:400 interval_time:22.40 train_time:0.00
 #2: steps:600 interval_time:19.66 train_time:6.90
 #3: steps:800 interval_time:20.01 train_time:5.28
 #4: steps:1000 interval_time:20.89 train_time:6.01
 #5: steps:1200 interval_time:20.52 train_time:6.34
 #6: steps:1400 interval_time:18.20 train_time:7.01
Killed

Here's the memory footprint
              total        used        free      shared  buff/cache   available
Mem:          15892       15627         139          11         125          81
Swap:         30273       30273           0

For convenience, I wrote all the images into memory at the beginning. You can try to load fewer images at the beginning and load some new images at regular intervals.

Tanks for your reply.I reduced the number of images  to 20,000, but the memory was still running out quickly.I wonder if there is something wrong with my conda environment.But I configure it according to the instructions in README.m
(py36) rody@rody-System-Product-Name:~/xu/npaint/LearningToPaint$ python3 baseline/train.py --max_step=200 --debug --batch_size=96
mkdir: cannot create directory â€˜./modelâ€™: File exists
loaded 10000 images
loaded 20000 images
finish loading data, 17999 training images, 2001 testing images
observation_space (96, 128, 128, 7) action_space 13
/home/rody/xu/npaint/LearningToPaint/baseline/DRL/ddpg.py:157: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
  s0 =torch.tensor(self.state, device='cpu')
/home/rody/xu/npaint/LearningToPaint/baseline/DRL/ddpg.py:163: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
  s1 =torch.tensor(state, device='cpu')
 #0: steps:200 interval_time:8.38 train_time:0.00
 #1: steps:400 interval_time:7.98 train_time:0.00
 #2: steps:600 interval_time:10.22 train_time:6.51
 #3: steps:800 interval_time:16.51 train_time:5.54
 #4: steps:1000 interval_time:19.01 train_time:5.80
 #5: steps:1200 interval_time:17.32 train_time:7.51
 #6: steps:1400 interval_time:17.48 train_time:6.48
 #7: steps:1600 interval_time:14.97 train_time:6.77
 #8: steps:1800 interval_time:21.19 train_time:6.82
Killed

I see. You set max_step = 200 so that the replay memory need to save more states. I advised setting max_step = 40 or rmsize = 200.

It works ! Thanks a lot !


teleport: 11.2.3 -> 11.3.2

Description of changes
Updates to a new upstream version.
This also changes how we deal with the frontend assets. Previously, gravitational/webassets provided pre-compiled assets. This has been deprecated upstream. Instead, the frontend sources live in the main repo, and we build the assets from this source code (via Yarn/Webpack etc.), as the upstream does.
Things done

Built on platform(s)

[x] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[x] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[x] Tested basic functionality of all binary files (usually in ./result/bin/)
23.05 Release Notes (or backporting 22.11 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module
[ ] (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes

[x] Fits CONTRIBUTING.md.

build is failing on darwin.

$ g-build --config webpack.prod.config.js --progress --bail --output-path=../../../webassets/teleport/app
assets by status 2.82 KiB [cached] 3 assets2mginugin
./src/boot.tsx 1.22 KiB [built] [code generated] [1 error]
WARNING in configuration
The value 'hashed' for option 'optimization.moduleIds' is deprecated. Use 'deterministic' instead.
ERROR in ./src/boot.tsx 41:2
Module parse failed: Unexpected token (41:2)
You may need an appropriate loader to handle this file type, currently no loaders are configured to process this file. See https://webpack.js.org/concepts#loaders
|
| ReactDOM.render(
>   <Teleport history={history.original()} ctx={teleportContext} />,
|   document.getElementById('app')
| );
webpack 5.73.0 compiled with 1 error and 1 warning in 576 ms
✨  Done in 4.03s.
buildPhase completed in 51 seconds
installing
cp: cannot stat 'webassets/.': No such file or director

That's weird. I'm not sure why the loader wouldn't work on Darwin. I'll try to investigate, but I'll have to spin up a VM. If anyone has a real Darwin machine, and is willing to investigate, that would be great.

The loader issue does not occur on:

NixOS (impure build: clone teleport, yarn install, yarn build-ui-oss)
NixOS (derivation)
Darwin (impure build)

The issue is present:

Darwin (derivation)

Still not sure where the problem lies. The tree of node_modules installed by impure yarn install --frozen-lockfile vs the derivation seems identical.

Closed accidentally.

pinging the maintainers to see if they can help: @sigma @tomberek @freezeboy

I have identified the issue. When building on Darwin, the $PWD inside the builder is e.g.: /private/tmp/nix-build-teleport-webassets-11.3.2.drv-1/source
In the Teleport webpack config, there is a line that excludes any file whose full path contains assets or node_modules. Not even a single component of the path (e.g. an exact match), but anything that contains that string.
https://github.com/gravitational/teleport/blob/b1a29ce99a00e1a4d41989d0abdbad5f97fb31c1/web/packages/build/webpack/webpack.base.js#L104
This means that even if a parent (grandparent, etc.) dir is named  "assets", "webassets", "assets-for-build" etc., these files are skipped over in the config.
I'll see if I can get the fix upstream, and if so, will update this PR when the fix is in the v11 branch. Otherwise, we can simply rename the webassets derivation, but that can potentially be a ticking timebomb until someone renames it again :sweat_smile: .

Updated to 11.3.4 which fixes the webpack issue, ofborg passed, should be good to go.

This pull request has been mentioned on NixOS Discourse. There might be relevant details there:
https://discourse.nixos.org/t/trouble-packaging-a-frontend-yarn-with-namespaces/25169/2