Start index must be 1 or larger; GFF is 1-based

Hi,
I appreciate you to distribute such a nice tool.
I have a problem with viewing the GFF file produced by AGOUTI.
To check gene structure on IGV, I have first made sorted GFF.
$ igvtools sort platanus_k35.sorted.cleaned.nsorted.k3.agouti.gff platanus_k35.sorted.cleaned.nsorted.k3.agouti.sorted.gff

then, indexed
$ igvtools index platanus_k35.sorted.cleaned.nsorted.k3.agouti.sorted.gff

and got error
ERROR [2016-01-19 20:03:26,381]  [IgvTools.java:250] [main]  Failed to parse line -1:
	platanus_k35.sorted.cleaned.nsorted.k3_scaf_12	AGOUTI	gene	-2	1679	.	.	.	ID=AGOUTI_Merged_gene_14;MERGE_FROM_GENES=scaffold361749_cov106_AGOUTI_fake_0,scaffold305397_cov53_AGOUTI_fake_0;MERGE_FROM_CONTIGS=scaffold361749_cov106,scaffold305397_cov53

  Start index must be 1 or larger; GFF is 1-based
org.broad.igv.exceptions.ParserException: Failed to parse line -1:
	platanus_k35.sorted.cleaned.nsorted.k3_scaf_12	AGOUTI	gene	-2	1679	.	.	.	ID=AGOUTI_Merged_gene_14;MERGE_FROM_GENES=scaffold361749_cov106_AGOUTI_fake_0,scaffold305397_cov53_AGOUTI_fake_0;MERGE_FROM_CONTIGS=scaffold361749_cov106,scaffold305397_cov53

  Start index must be 1 or larger; GFF is 1-based
	at org.broad.igv.feature.tribble.GFFCodec.decode(GFFCodec.java:241)
	at org.broad.igv.feature.tribble.GFFCodec.decode(GFFCodec.java:67)
	at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79)
	at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41)
	at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:43)
	at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:502)
	at htsjdk.tribble.index.IndexFactory$FeatureIterator.next(IndexFactory.java:464)
	at htsjdk.tribble.index.IndexFactory.createIndex(IndexFactory.java:338)
	at htsjdk.tribble.index.IndexFactory.createLinearIndex(IndexFactory.java:223)
	at org.broad.igv.tools.IgvTools.createTribbleIndex(IgvTools.java:1016)
	at org.broad.igv.tools.IgvTools.doIndex(IgvTools.java:968)
	at org.broad.igv.tools.IgvTools.run(IgvTools.java:379)
	at org.broad.igv.tools.IgvTools.main(IgvTools.java:245)
Failed to parse line -1:
	platanus_k35.sorted.cleaned.nsorted.k3_scaf_12	AGOUTI	gene	-2	1679	.	.	.	ID=AGOUTI_Merged_gene_14;MERGE_FROM_GENES=scaffold361749_cov106_AGOUTI_fake_0,scaffold305397_cov53_AGOUTI_fake_0;MERGE_FROM_CONTIGS=scaffold361749_cov106,scaffold305397_cov53

  Start index must be 1 or larger; GFF is 1-based
org.broad.igv.exceptions.ParserException: Failed to parse line -1:
	platanus_k35.sorted.cleaned.nsorted.k3_scaf_12	AGOUTI	gene	-2	1679	.	.	.	ID=AGOUTI_Merged_gene_14;MERGE_FROM_GENES=scaffold361749_cov106_AGOUTI_fake_0,scaffold305397_cov53_AGOUTI_fake_0;MERGE_FROM_CONTIGS=scaffold361749_cov106,scaffold305397_cov53

  Start index must be 1 or larger; GFF is 1-based
	at org.broad.igv.feature.tribble.GFFCodec.decode(GFFCodec.java:241)
	at org.broad.igv.feature.tribble.GFFCodec.decode(GFFCodec.java:67)
	at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79)
	at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41)
	at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:43)
	at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:502)
	at htsjdk.tribble.index.IndexFactory$FeatureIterator.next(IndexFactory.java:464)
	at htsjdk.tribble.index.IndexFactory.createIndex(IndexFactory.java:338)
	at htsjdk.tribble.index.IndexFactory.createLinearIndex(IndexFactory.java:223)
	at org.broad.igv.tools.IgvTools.createTribbleIndex(IgvTools.java:1016)
	at org.broad.igv.tools.IgvTools.doIndex(IgvTools.java:968)
	at org.broad.igv.tools.IgvTools.run(IgvTools.java:379)
	at org.broad.igv.tools.IgvTools.main(IgvTools.java:245)

According to error message, I checked my GFF and found a lot of '-2'.
Could you tell me how can I fix this problem?
Thank you for your kind helps.
Takashi

Hi Takashi,
Thanks for using AGOUTI.
It looks like there is a bug when gene models got merged. The coordinates were not updated in a right way. I have some idea where it might go wrong. Please give me a bit time to look into this.
Thanks,
Simo

Hi Simo,
Thank you for your reply.
OK. This is quite nice tool. Please let me know if you fix this problem.
Thanks,
Takashi

Hi Takashi,
You are very welcome!
I think I figured out why. Let me try to explain using an example. Let's say the leftmost positions of a read is mapped to 5261 on a contig of length 5330, and the alignment length is 70. The rightmost position can then be derived as 5261+70-1=5330. I coded this wrong as 5261+70=5331, which is one base pair beyond the length of this contig. Also The leftmost position in SAM is 1-based, which I treated as 0-based (because I thought I read directly from BAM...). Together this gives two base pairs beyond the boundary of the contig, which in turn gave you gene models starting at -2.
I released a new version: v0.3.1. Could you please pull out this version and try again? And please keep me post it on whether it works out.
Thank you for reporting this bug :)
Simo

Hi Simo,
Thank you for fixing the bug quickly.
It works fine with my data and I think the problem is fixed.
But I found other problems.

The fasta file agouti produced has header in which scaffold name, length and original scaffold names are separated by '|'. IGV can't seem to recognize this as separator and so the produced header names do not match with the name in gff.
I could replace '|' with space by sed command but I think it would be helpful if you change separator.

IGV does not display exon-intron structure from gff agouti produced. Unfortunately I am not familiar with gff format and I cannot figure out what is problem. For your information, I will show you a part of my gff from agouti and augustus respectively.

gff from agouti
##gff-version3
# This output was generated with AGOUTI (version 0.1)
# start gene g23520
platanus_k35.sorted.cleaned.nsorted.k3_scaf_1	AGOUTI	gene	1	1294	.	.	.	ID=AGOUTI_Merged_gene_1;MERGE_FROM_GENES=scaffold145281_cov18_AGOUTI_fake_0;MERGE_FROM_CONTIGS=scaffold145281_cov18,scaffold289495_cov27
platanus_k35.sorted.cleaned.nsorted.k3_scaf_1	AGOUTI	exon	1	100	.	.	.	ID=AGOUTI_Merged_gene_1.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_1	AGOUTI	exon	1101	1294	.	.	.	ID=AGOUTI_Merged_gene_1.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	gene	15092	15468	.	+	.	ID=g86
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	15092	15196	.	+	.	ID=g86.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	15346	15468	.	+	.	ID=g86.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	gene	26142	27833	.	-	.	ID=g85
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	26142	27833	.	-	.	ID=g85.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	gene	33928	34485	.	+	.	ID=g84
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	33928	33942	.	+	.	ID=g84.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	34194	34350	.	+	.	ID=g84.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	34412	34485	.	+	.	ID=g84.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	gene	42606	43230	.	+	.	ID=g83
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	42606	42652	.	+	.	ID=g83.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	42751	42866	.	+	.	ID=g83.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	43178	43230	.	+	.	ID=g83.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	gene	49425	52344	.	-	.	ID=g82
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	49425	49586	.	-	.	ID=g82.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	51640	51735	.	-	.	ID=g82.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	52303	52344	.	-	.	ID=g82.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	gene	53978	56782	.	-	.	ID=g81
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	53978	54076	.	-	.	ID=g81.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	55235	55399	.	-	.	ID=g81.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	56243	56275	.	-	.	ID=g81.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	56747	56782	.	-	.	ID=g81.exon
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	gene	74542	76766	.	-	.	ID=g80
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2	AUGUSTUS	exon	74542	75306	.	-	.	ID=g80.exon

gff from augustus
##gff-version 3
# This output was generated with AUGUSTUS (version 3.2.1).
# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
# O. Keller, S. KÃ¶nig, L. Gerischer and L. Romoth.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters using config directory /home/samba/public/software/augustus-3.2.1/config/ ...
# yellowtail_bycegma version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like platanus_k35_gapClosed.substituted.fixfasta.fasta.masked.masked is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 1154345, name = SquSD_finalassembly150907) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
scaffold2_cov39	AUGUSTUS	gene	1420	2935	0.84	+	.	ID=g31458
scaffold2_cov39	AUGUSTUS	transcript	1420	2935	0.84	+	.	ID=g31458.t1;Parent=g31458
scaffold2_cov39	AUGUSTUS	start_codon	1420	1422	.	+	0	Parent=g31458.t1
scaffold2_cov39	AUGUSTUS	CDS	1420	1492	0.94	+	0	ID=g31458.t1.cds;Parent=g31458.t1
scaffold2_cov39	AUGUSTUS	intron	1493	2409	0.94	+	.	Parent=g31458.t1
scaffold2_cov39	AUGUSTUS	CDS	2410	2596	0.97	+	2	ID=g31458.t1.cds;Parent=g31458.t1
scaffold2_cov39	AUGUSTUS	intron	2597	2847	0.9	+	.	Parent=g31458.t1
scaffold2_cov39	AUGUSTUS	CDS	2848	2935	0.9	+	1	ID=g31458.t1.cds;Parent=g31458.t1
scaffold2_cov39	AUGUSTUS	stop_codon	2933	2935	.	+	0	Parent=g31458.t1
scaffold3_cov51	AUGUSTUS	gene	14898	15140	0.78	+	.	ID=g11991
scaffold3_cov51	AUGUSTUS	transcript	14898	15140	0.78	+	.	ID=g11991.t1;Parent=g11991
scaffold3_cov51	AUGUSTUS	start_codon	14898	14900	.	+	0	Parent=g11991.t1
scaffold3_cov51	AUGUSTUS	CDS	14898	15140	0.78	+	0	ID=g11991.t1.cds;Parent=g11991.t1
scaffold3_cov51	AUGUSTUS	stop_codon	15138	15140	.	+	0	Parent=g11991.t1
scaffold3_cov51	AUGUSTUS	gene	26107	34467	0.48	-	.	ID=g11992
scaffold3_cov51	AUGUSTUS	transcript	26107	34467	0.48	-	.	ID=g11992.t1;Parent=g11992
scaffold3_cov51	AUGUSTUS	stop_codon	26107	26109	.	-	0	Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	CDS	26107	26133	0.82	-	0	ID=g11992.t1.cds;Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	intron	26134	26250	0.82	-	.	Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	CDS	26251	26425	0.92	-	1	ID=g11992.t1.cds;Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	intron	26426	26782	0.99	-	.	Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	CDS	26783	26995	0.99	-	1	ID=g11992.t1.cds;Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	intron	26996	30476	0.96	-	.	Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	CDS	30477	30613	0.99	-	0	ID=g11992.t1.cds;Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	intron	30614	31339	1	-	.	Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	CDS	31340	31460	1	-	1	ID=g11992.t1.cds;Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	intron	31461	32544	0.99	-	.	Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	CDS	32545	32791	1	-	2	ID=g11992.t1.cds;Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	intron	32792	34439	0.68	-	.	Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	CDS	34440	34467	0.68	-	0	ID=g11992.t1.cds;Parent=g11992.t1
scaffold3_cov51	AUGUSTUS	start_codon	34465	34467	.	-	0	Parent=g11992.t1
scaffold11_cov44	AUGUSTUS	gene	12889	15307	0.99	-	.	ID=g14783

I really appreciate all of your helps.
Takashi

Hi Simo,
I have found another problem.
If I execute agouti with '-k 3', agouti works fine. But if with '-k 2', igvtools index produced error.
The error message below still find start position with '-'.
$ igvtools index platanus_k35.sorted.cleaned.nsorted.k2.agouti.sorted.gff
ERROR [2016-01-21 15:27:40,271]  [IgvTools.java:250] [main]  Failed to parse line -1:
	platanus_k35.sorted.cleaned.nsorted.k2_scaf_3551	AGOUTI	exon	-13239	-13144	.	-	.	ID=AGOUTI_Merged_gene_4067.exon

  Start index must be 1 or larger; GFF is 1-based
org.broad.igv.exceptions.ParserException: Failed to parse line -1:
	platanus_k35.sorted.cleaned.nsorted.k2_scaf_3551	AGOUTI	exon	-13239	-13144	.	-	.	ID=AGOUTI_Merged_gene_4067.exon

  Start index must be 1 or larger; GFF is 1-based
	at org.broad.igv.feature.tribble.GFFCodec.decode(GFFCodec.java:241)
	at org.broad.igv.feature.tribble.GFFCodec.decode(GFFCodec.java:67)
	at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79)
	at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41)
	at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:43)
	at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:502)
	at htsjdk.tribble.index.IndexFactory$FeatureIterator.next(IndexFactory.java:464)
	at htsjdk.tribble.index.IndexFactory.createIndex(IndexFactory.java:338)
	at htsjdk.tribble.index.IndexFactory.createLinearIndex(IndexFactory.java:223)
	at org.broad.igv.tools.IgvTools.createTribbleIndex(IgvTools.java:1016)
	at org.broad.igv.tools.IgvTools.doIndex(IgvTools.java:968)
	at org.broad.igv.tools.IgvTools.run(IgvTools.java:379)
	at org.broad.igv.tools.IgvTools.main(IgvTools.java:245)
Failed to parse line -1:
	platanus_k35.sorted.cleaned.nsorted.k2_scaf_3551	AGOUTI	exon	-13239	-13144	.	-	.	ID=AGOUTI_Merged_gene_4067.exon

  Start index must be 1 or larger; GFF is 1-based
org.broad.igv.exceptions.ParserException: Failed to parse line -1:
	platanus_k35.sorted.cleaned.nsorted.k2_scaf_3551	AGOUTI	exon	-13239	-13144	.	-	.	ID=AGOUTI_Merged_gene_4067.exon

  Start index must be 1 or larger; GFF is 1-based
	at org.broad.igv.feature.tribble.GFFCodec.decode(GFFCodec.java:241)
	at org.broad.igv.feature.tribble.GFFCodec.decode(GFFCodec.java:67)
	at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:79)
	at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:41)
	at htsjdk.tribble.AbstractFeatureCodec.decodeLoc(AbstractFeatureCodec.java:43)
	at htsjdk.tribble.index.IndexFactory$FeatureIterator.readNextFeature(IndexFactory.java:502)
	at htsjdk.tribble.index.IndexFactory$FeatureIterator.next(IndexFactory.java:464)
	at htsjdk.tribble.index.IndexFactory.createIndex(IndexFactory.java:338)
	at htsjdk.tribble.index.IndexFactory.createLinearIndex(IndexFactory.java:223)
	at org.broad.igv.tools.IgvTools.createTribbleIndex(IgvTools.java:1016)
	at org.broad.igv.tools.IgvTools.doIndex(IgvTools.java:968)
	at org.broad.igv.tools.IgvTools.run(IgvTools.java:379)
	at org.broad.igv.tools.IgvTools.main(IgvTools.java:245)

Thanks,
Takashi

For your first question:
The fasta file agouti produced has header in which scaffold name, length and original scaffold names are separated by '|'. IGV can't seem to recognize this as separator and so the produced header names do not match with the name in gff.
I could replace '|' with space by sed command but I think it would be helpful if you change separator.
Could you please give me an example both the seq name generated by AGOUTI and how IGV interpreted that. And also what did you replaced with that IGV recognized.
Thanks!

I made a new patch (I have not yet released a new version; you can use git pull to get the patch I believe) with the following fixes:

added an extra space before |: >80k.run10.n2_scaf_1 |21038bp |IV_664,IV_665,IV_666. IGV now should load the sequences correctly.
reformatted the final GFF file to be more standard. IGV now should be able to show the exon/intron boundaries. I ran igvtools sort on my GFF files before feeding them to IGV.
fixed a bug that did not update the coordinates of gene models correctly. But I am not sure if this can help with the last error (i.e. negative starting position) you saw. If not, could you please send all the debug files generated by AGOUTI to<EMAIL_ADDRESS>We then go from there. To generate debug files, simply specify -debug option.

Thanks again for your patience and help!

Hi, Simo

The sequence name is now correctly loaded by IGV. Thanks!
IGV still do not display exon-intron structure from revised gff. For example, gene structure of g73 in the revised gff is as below.

platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        gene    187581  195864  .       +       .       ID=g73
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        mRNA    187581  195864  .       +       .       ID=g73.mRNA;Parent=g73
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        exon    187581  187704  .       +       .       ID=g73.exon.1;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        exon    188885  189037  .       +       .       ID=g73.exon.2;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        exon    189898  190099  .       +       .       ID=g73.exon.3;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        exon    191122  191262  .       +       .       ID=g73.exon.4;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        exon    191617  191722  .       +       .       ID=g73.exon.5;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        exon    192345  192442  .       +       .       ID=g73.exon.6;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        exon    193056  193176  .       +       .       ID=g73.exon.7;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        exon    194353  194582  .       +       .       ID=g73.exon.8;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        exon    195825  195864  .       +       .       ID=g73.exon.9;Parent=g73.mRNA

And IGV display attached view.

However, if I changed 'exon' in the revised gff to 'CDS' as below,
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        gene    187581  195864  .       +       .       ID=g73
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        mRNA    187581  195864  .       +       .       ID=g73.mRNA;Parent=g73
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        CDS     187581  187704  .       +       .       ID=g73.exon.1;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        CDS     188885  189037  .       +       .       ID=g73.exon.2;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        CDS     189898  190099  .       +       .       ID=g73.exon.3;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        CDS     191122  191262  .       +       .       ID=g73.exon.4;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        CDS     191617  191722  .       +       .       ID=g73.exon.5;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        CDS     192345  192442  .       +       .       ID=g73.exon.6;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        CDS     193056  193176  .       +       .       ID=g73.exon.7;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        CDS     194353  194582  .       +       .       ID=g73.exon.8;Parent=g73.mRNA
platanus_k35.sorted.cleaned.nsorted.k3_scaf_2   AUGUSTUS        CDS     195825  195864  .       +       .       ID=g73.exon.9;Parent=g73.mRNA

IGV display gene structure correctly:)

So, could you change 'exon' in the script to 'CDS'?

I still have error if I execute agouti.py with '-k 2'. I will send my debug files. I usually use hotmail. If you have not received my mail, please check spam mail directory.

Thank you for your kind helps!
Takashi

Can I ask you what version of IGV you were using. I tested on the lastest 2.3. This version does not show exon/intron structures automatically. You need to specify Expanded view from the pop-up menu by right-clicking your track.  Here is a screenshot of my GFF in the IGV using exon as feature with Expanded view.

Without Expanded, it looks like this:

Could you please give this a try? If still not working, let me think about using CDS instead of exon, because some exons are additional evidences from RNA-seq mapping. In other words, they are not necessarily part of coding frames.
Thank your for bearing with me here a bit longer.

Hi Simo,
Ah, I didn't know that. I finally got exon-intron view! Thanks!

Takashi

WooHoooo! Great!

Hi Simo,
I tried the revised version of AGOUTI.
I found one syntax error.
Traceback (most recent call last):
  File "/home/koyama/Downloads/AGOUTI/agouti.py", line 20, in <module>
    from src import agouti_scaffolding as agSCAFF
  File "/home/koyama/Downloads/AGOUTI/src/agouti_scaffolding.py", line 408
    elif preSensePair == "++" and curSensePair == "--" or curSensePair == "-+"):
                                                                              ^

So I changed
elif preSensePair == "++" and curSensePair == "--" or curSensePair == "-+"):

to
elif preSensePair == "++" and (curSensePair == "--" or curSensePair == "-+"):

And AGOUTI produced gff which can be perfectly parsed by igvtools!
Yeah! You are amazing!!
Thank you so much!
Takashi

Aha, missing parenthesis... Thanks!
Just fixed!
I am gonna close this issue now. Any further problems you have, please go ahead create a new thread.
Simo


get_namespace fix.

Get namespace now looks at the bottom of the stack for the correct file, and breaks the while loop early to avoid prepending Modules_.

The last commit (e5544f6) could cause big issues if the user has an @ somewhere above the CommandCenter folder. Whether this is better or worse than ignoring<EMAIL_ADDRESS>cases (which currently do not exist) is up the the Pull Request Approver.

A better fix might have knowledge of the CC path, but that means that CC would have to be loaded and there would have to be yet another case for running drivers independently (without this knowledge).

The only path info that is necessary is whatever MATLAB's path is. A better use of the builtin what does precisely this from what I understand. We don't need to choose between two edge cases - this should be solvable with just a bit more work.

As discussed in slack, but for sake of a record - we realized this is impossible due to the ambiguity of the stack. Inheritance vs calling a member of a class is impossible to differentiate. I will change to provide the full classname as an input using either class(obj) or mfilename('class') for static methods.


Disallow double slash in basepath

basePath: //api should be forbidden

Do you refer to the schema?

yes

Then that's not really an issue. If the user chooses to input a value that doesn't make sense, it's their problem. We've decided to not include complex regex to validate fields that may catch a few user errors. Just like in mime types, user can input whatever they want and it would still work, not really a concern.

👍 works for me!

Cool. There's just a limit to what we can and should check.
That said, the tools around it should be robust enough to deal with malformed values.


Can't connect to the back end

Can't connect to the back end

number 1... your using socket.io not websockets. number 2 please go more into depth about this error


Fix #2

Codecov Report

Merging #4 into master will increase coverage by 0.11%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master       #4      +/-   ##
==========================================
+ Coverage   85.97%   86.09%   +0.11%
==========================================
  Files          18       18
  Lines         278      266      -12
  Branches        9        9
==========================================
- Hits          239      229      -10
+ Misses         39       37       -2

Impacted Files
Coverage Δ

.../io/circe/generic/extras/ConfiguredJsonCodec.scala
100% <ø> (+14.28%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
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Python version(s)?

What version(s) of Python should this work with? Trying on Chromebook, with

pip install -r requirements.txt

(which runs fine) and then

python main.py

With Python 3.8 I get
Traceback (most recent call last):   File "src/main.py", line 4, in <module>     import gui   File "/home/danbri/ ... /evogym-design-tool/src/gui.py", line 3, in <module>     from ttkbootstrap import Style   File "/opt/miniconda3/lib/python3.8/site-packages/ttkbootstrap/__init__.py", line 3, in <module>     from ttkbootstrap.widgets import *   File "/opt/miniconda3/lib/python3.8/site-packages/ttkbootstrap/widgets.py", line 13, in <module>     from ttkbootstrap.dialogs import Querybox   File "/opt/miniconda3/lib/python3.8/site-packages/ttkbootstrap/dialogs.py", line 15, in <module>     from tkinter import _get_default_root ImportError: cannot import name '_get_default_root' from 'tkinter' (/opt/miniconda3/lib/python3.8/tkinter/__init__.py)

If I comment out the tkinter import in /opt/miniconda3/lib/python3.8/site-packages/ttkbootstrap/dialogs.py
i.e.

#from tkinter import _get_default_root

It seems to run

According to  __ pycache __ , it seems to use Python 3.7. @danbri

Hello! Thanks for your interest in EvoGym. If you haven't resolved the issue yet, I think there might be a problem with conflicting package versions.
I've added package versions to requirements.txt and also added a environment.yml file from which you can create a conda environment -- see the README for installation instructions.
Please let me know if this resolves your issue!

thanks! I have not had a chance to test this, but I have no ongoing problems so please close the issue if you like.


Include the godot_plugin_jni.cpp file into the platform/android/SCsub file

This should resolve https://github.com/godotengine/godot/issues/57209

I didn't test, but most likely this is needed to fix the build:
diff --git a/platform/android/plugin/godot_plugin_jni.cpp b/platform/android/plugin/godot_plugin_jni.cpp
index 2207eec18d..48aeb3d070 100644
--- a/platform/android/plugin/godot_plugin_jni.cpp
+++ b/platform/android/plugin/godot_plugin_jni.cpp
@@ -126,7 +126,7 @@ JNIEXPORT void JNICALL Java_org_godotengine_godot_plugin_GodotPlugin_nativeEmitS
 		env->DeleteLocalRef(j_param);
 	};

-	singleton->emit_signal(SNAME(signal_name), args, count);
+	singleton->emit_signal(StringName(signal_name), args, count);
 }

 JNIEXPORT void JNICALL Java_org_godotengine_godot_plugin_GodotPlugin_nativeRegisterGDNativeLibraries(JNIEnv *env, jclass clazz, jobjectArray gdnlib_paths) {

SNAME() only works on string literals / const char * to create a static stringname. Here this is evaluated at runtime so it should be a plain old StringName() constructor.

The fix was validated in https://github.com/godotengine/godot/issues/57209#issuecomment-1022789804!


Adding a JIRA username to GitHub username converter and finishing moving necessary fields

I still need to move the reporter, assignee, and comment fields from JIRA to GitHub.

Issue #18 is an example of an issue with all currently migrated JIRA fields in a GitHub issue. The spacing is inconsistent for the comments because the body of each comment is HTML, so depending on the contents, it might have 1 or 2 spaces below the creator and date line.


Unreal Engine pipeline start with config and a rs2::net_device results in start exception

Required Info

Camera Model
D455

Firmware Version
<IP_ADDRESS>

Operating System & Version
Windows 10 / Raspberry Pi (Raspbian 10.6)

Kernel Version (Linux Only)
5.4.51

Platform
PC/Raspberry Pi/

SDK Version
2.39

Language
UE4 c++

Segment
Realtime Interactivity

Starting the rs2 pipeline results in a device not connected error even though the network device exists
I'm using the realsense2 UE4 plugin to get depth frames from the camera. We need it to work over the network from a Raspberry Pi and it works without fail in the RealSense viewer, but fails when we try to start the pipeline in the RealsenseInspector in the plugin. The network device is properly enumerated and everything, we can pull the serial number but when it comes to starting the pipeline with the config, it fails and says the device is not connected.
I've double checked the proper net module is built and working with all source we're using, but it just doesn't seem to want to work unfortunately. Any help would be appreciated.

Hi @elliotstronge  Is your network-connected D455 camera correctly identifying as a D455 in BP_RealSenseInspector above the serial number, please?

Also, can you confirm please that the serial number is appearing correctly in BP_RealSenseInspector in the Unreal wrapper on the central host computer please?  In other words, that it is retrieving the serial number through an ethernet cable that has a Pi with a D455 camera on the end of it.

Hi Marty,
It does when I add these lines to ARealsenseInspector::Start()
rs2::net_device device("<IP_ADDRESS>");
rs2::context_ref RsContext(Context->GetHandle());
device.add_to(RsContext);
This is what I get:

Which is the correct serial number according to Realsense Viewer. It's worth noting that when I play in editor from here, it seems to grab one frame and then time out with a bunch of messages that look like this:

If I try the other method in URealsenseContext::QueryDevices(), i.e. this
rs2::net_device device("<IP_ADDRESS>");
Devices.Add(NewDevice(device.get().get(), TEXT("RealSenseIPDevice")));
It doesn't show up in the inspector, and also fails to find any connected devices even though the device exists in the URealsenseContext::Devices TArray.

Investigating further today has lead me to the root of the issue. I made a small C++ program to test different ways to enable the net device and what isn't working seems to be this line:
RsConfig.enable_device(std::string(TCHAR_TO_ANSI(*ActiveDevice->Serial)));
in ARealSenseInspector::Start(); If I change that to:
rs2_context* ctx = Context->GetHandle();
rs2_device* dev = ActiveDevice->GetHandle();
rs2_context_add_software_device(ctx, dev, nullptr);
I get frames coming through from the Raspberry Pi on the network again in the editor. It seems like a real hack, but good to find the issue and good to get something working.

Thanks so much for sharing your workaround with the RealSense community @elliotstronge     :)

You're welcome. Worth adding to the bug tracker I reckon.

I will refer your fix to Intel for consideration.  Thanks again!

Hi again @elliotstronge   Would you consider contributing your workaround code as a pull request for merging into the RealSense SDK?  Doing so is completely optional though.  Thanks!
https://github.com/IntelRealSense/librealsense/pulls

I'd be happy to when I can find some time to wrangle one together that works well enough.

@elliotstronge  Thanks very much!


python312Packages.lmcloud: 1.1.13 -> 1.2.1

Diff: https://github.com/zweckj/lmcloud/compare/refs/tags/v1.1.13...v1.2.1
Changelog: https://github.com/zweckj/lmcloud/releases/tag/v1.2.1
Description of changes

Things done

Built on platform(s)

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

For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)

[ ] sandbox = relaxed
[ ] sandbox = true

[ ] 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
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
24.11 Release Notes (or backporting 23.11 and 24.05 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

[ ] Fits CONTRIBUTING.md.

Add a :+1: reaction to pull requests you find important.

Result of nixpkgs-review pr 338348 run on x86_64-linux 1

5 packages built:

home-assistant-component-tests.lamarzocco
python311Packages.lmcloud
python311Packages.lmcloud.dist
python312Packages.lmcloud
python312Packages.lmcloud.dist


cdylib and C bindings for enso-parser

Pull Request Description
Provide a C dynamic-library interface to enso_parser for use via Java FFI.
Important Notes

The library can be built with: cargo build -p enso-parser-cdylib. I'm not sure how best to integrate this with the build process. The Java code will have a runtime dependency on the built dynamic library; I don't know how we will be using the C headers.
When the library is built, the generated C header file will be placed at: target/enso_parser_headers/enso_parser.h
The API documentation is in the rustdocs, and also emitted in the generated C headers.

Checklist
Please include the following checklist in your PR:

[x] The documentation has been updated if necessary.
[x] All code conforms to the
Scala,
Java,
and
Rust
style guides.
All code has been tested:

[x] Unit tests have been written where possible.
[x] If GUI codebase was changed: Enso GUI was tested when built using BOTH
./run ide dist and ./run ide watch.

[ci no changelog needed]

The binary to load seems to be available at target/rust/debug/libenso_parser.so.

FYI: https://docs.rs/jni/latest/jni/ - do we need the C interface for anything? We need Java interface, right? That'd be JNI.


use-flag cannot be wired; comes from satdb

Description
Use flag settings were wired ... these need to come from sat-db (mksi)
Dependencies
None
Impact
Correct use of data in general way - for now this is correct since in the test cases the choice wired was consistent w/ satdb, but not in general. This removes the wiring.

Would this require UFO test changes?

Would this require UFO test changes?

It didn't, merging.


user16217248: Watch abortion clinic

user16217248 requests the watch of the watch_keyword abortion clinic. See the MS search here and the Stack Exchange search in text, in URLs, and in code.

Rejected by cocomac in Charcoal HQ. Reason: 'Too many FPs. Also use [\W_]+ instead of spaces in regex unless there’s a good reason to not. For this spam, watching/blacklisting the phone number might be a better choice. Also Abortion[\W_]+clinic[\W_]*+in is one FP/39 TP which I’d be much more comfortable watching or blacklisting'


ARROW-4886: [Rust] Cast to list with offset

The initial problem with casting a primitive array to a list array (with 1 primitive per list slot) where the primitive had an offset, is now solved.
This PR just enables such casting, as it was previously disabled.

Hi @andygrove @paddyhoran @liurenjie1024 may I please have a concurring review when you get a chance


Optionally return minimal overlapping subset of tile and asset

ref #167; ref https://github.com/developmentseed/cogeo-mosaic-tiler/issues/4
Loading a local file on my own laptop doesn't improve performance as much as I'd like. 😢 With the example below, reading 7% of the pixels still takes 70% of the time.
Example
import os
from rio_tiler.io.cogeo import tile

os.environ['AWS_REQUEST_PAYER'] ="requester"
address = 's3://naip-visualization/ca/2018/60cm/rgb/34118/m_3411861_ne_11_060_20180723_20190208.tif'
x = 701
y = 1635
z = 12
tilesize = 256
data, mask, pixel_bounds = tile(address, x, y, z, tilesize, minimal_subset=True)

Data shape
> data.shape
(3, 101, 48)
> mask.shape
(101, 48)
> pixel_bounds
[0, 155, 48, 256]

> data
array([[[102, 116, 112, ..., 106, 121,   0],
        [100,  97, 101, ..., 108, 128,   0],
        [107, 113, 116, ..., 107, 127,   0],
        ...,
        [135, 134, 115, ..., 114, 115, 110],
        [144, 137, 111, ...,   0,   0,   0],
        [  0,   0,   0, ...,   0,   0,   0]],

       [[110, 124, 118, ..., 110, 121,   0],
        [108, 105, 107, ..., 110, 123,   0],
        [115, 121, 122, ..., 110, 126,   0],
        ...,
        [139, 138, 119, ..., 122, 122, 114],
        [148, 141, 115, ...,   0,   0,   0],
        [  0,   0,   0, ...,   0,   0,   0]],

       [[112, 126, 120, ..., 115, 121,   0],
        [111, 107, 110, ..., 114, 121,   0],
        [118, 123, 125, ..., 114, 126,   0],
        ...,
        [140, 139, 120, ..., 124, 126, 123],
        [149, 142, 116, ...,   0,   0,   0],
        [  0,   0,   0, ...,   0,   0,   0]]], dtype=uint8)

> mask
array([[255, 255, 255, ..., 255, 255,   0],
       [255, 255, 255, ..., 255, 255,   0],
       [255, 255, 255, ..., 255, 255,   0],
       ...,
       [255, 255, 255, ..., 255, 255, 255],
       [255, 255, 255, ...,   0,   0,   0],
       [  0,   0,   0, ...,   0,   0,   0]], dtype=uint8)

Benchmark
aws s3 cp s3://naip-visualization/ca/2018/60cm/rgb/34118/m_3411861_ne_11_060_20180723_20190208.tif ./ --request-payer

address = 'm_3411861_ne_11_060_20180723_20190208.tif'
tilesize = 512

%timeit tile(address, x, y, z, tilesize)
26.8 ms ± 975 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)

%timeit tile(address, x, y, z, tilesize, minimal_subset=True)
19 ms ± 920 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)

thanks @kylebarron, please see my comment in https://github.com/developmentseed/cogeo-mosaic-tiler/issues/4#issuecomment-603008465 about benchmark result between full and partial tiles

@kylebarron should we close ?

Yeah, I think closing is fine.


configure Coveralls to reduce noise

Mailed support:

Greetings! We recently started using Coveralls again (after our configuration went stale for a while due to a repo rename). Now we're once again getting Coveralls comments on PRs. However, we're finding these notifications to be too noisy. I find on the notifications page of the Coveralls.io dashboard that I can configure percentage thresholds for certain kinds of notifications (email, hipchat, campfire, webhook). How do I configure thresholds for the GitHub comments? Thanks! :-)
chad

IRC one two

Closing. I don't remember how or when but obviously the problem got solved.


GroverOperator doesn't work properly in 'ibmq_qasm_simulator'

When running the Grover operator in the simulator we get the following error:
dev = qml.device('qiskit.ibmq', wires=6, backend='ibmq_qasm_simulator')

@qml.qnode(dev)
def circuit():

    qml.GroverOperator(wires = range(6))

    return qml.probs(wires = range(6))

circuit()

WireError: Did not find some of the wires <Wires = [3, 5, None]> on device with wires <Wires = [0, 1, 2, 3, 4, 5]>.

In default.qubit it works correctly.
Tested with version 0.32

Thanks @KetpuntoG! We should definitely get this fixed. Is it blocking any work you are doing now?

It is not blocking me @trbromley
but that error is not something that the user can solve right? @albi3ro

@KetpuntoG
GroverOperator(wires(0,1,2,3), work_wires="aux")


Pin versions on linters for tests

The linters really need to specify an exact version, because when
either flake8 or pylint release a new version, a whole lot of new
issues are caught, causing failures on the code unrelated to the
patches being pushed.
Pinning is a best practice for linters. This allows patches which move
forward the linter version to happen with any code fixes required for
it to pass.

Merging this to get tests running again for new contributors. Please feel free to modify later if we want something less strict than this.

Thanks


You can replace water blocks with water blocks forever

This is probably a fairly simple case of "abusing" the system where you can place blocks in water to make the water go away. If you do so with actual water - you can place "new" water blocks over and over and over until you run out of blocks ;-)
If a block is replaceable like that it probably shouldn't be replaceable by its own kin (exact block, block family, or what not)

You probably should NOT be able to obtain water in block form, so I would ignore this problem.

Eh, that's sort of aside the point :-)
Some mode will end up allowing it, and it probably affects similar situations (lava maybe?)
I have a vague recollection that you used to be able to replace billboard plants with blocks without first breaking the plant, but that doesn't seem to work anymore. Had wondered if you'd be able to replace tall grass with tall grass forever too

I would suggest to close this and have an note in a related issue on water/fluid overhaul. Water replacement is just special because water blocks are special, but it is not really tailored towards liquids in general.

That's fair. But interestingly ... we don't have an issue for an entire overhaul, looks like :D
We just collectively know of it, more or less, along with various forum mentions of turning liquids into "something else" that yeah would probably obsolete this issue.
If we go that route one day I imagine actual liquid "blocks" being acquirable would probably also truly go away. Thought I'm not sure (creative mode)
@skaldarnar whenever you post a fresh liquid module thread in the forum (no rush!) feel free to just include a bullet point for this then close it :-)

Closing as fixed by #2225!


Frame drop in CupertinoApp while using CupertinoPageRoute

Details

Frame drop in CupertinoApp while using CupertinoPageRoute navigation,
Video recording while flutter run --release command

https://user-images.githubusercontent.com/63861163/232711117-3574b9ca-abc6-48f1-bd45-c17c2ddf729e.MP4

Target Platform: iOS
Target OS version/browser: 15.7.3 (iPhone SE 1st generation) , 16.4
Devices: iPhone SE (1st generation), iPhone SE 3rd Generation (Simulator)
Logs

Logs

Analyzing frawla...
No issues found! (ran in 2.8s)

[✓] Flutter (Channel stable, 3.7.11, on macOS 13.3.1 22E261 darwin-arm64, locale en-IN)
    • Flutter version 3.7.11 on channel stable at /Users/akshayn/project/flutter
    • Upstream repository https://github.com/flutter/flutter.git
    • Framework revision f72efea43c (7 days ago), 2023-04-11 11:57:21 -0700
    • Engine revision 1a65d409c7
    • Dart version 2.19.6
    • DevTools version 2.20.1

[✓] Android toolchain - develop for Android devices (Android SDK version 33.0.1)
    • Android SDK at /Users/akshayn/Library/Android/sdk
    • Platform android-33, build-tools 33.0.1
    • Java binary at: /Applications/Android Studio.app/Contents/jbr/Contents/Home/bin/java
    • Java version OpenJDK Runtime Environment (build 11.0.15+0-b2043.56-8887301)
    • All Android licenses accepted.

[✓] Xcode - develop for iOS and macOS (Xcode 14.3)
    • Xcode at /Applications/Xcode.app/Contents/Developer
    • Build 14E222b
    • CocoaPods version 1.12.0

[✓] Chrome - develop for the web
    • Chrome at /Applications/Google Chrome.app/Contents/MacOS/Google Chrome

[✓] Android Studio (version 2022.1)
    • Android Studio at /Applications/Android Studio.app/Contents
    • Flutter plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/9212-flutter
    • Dart plugin can be installed from:
      🔨 https://plugins.jetbrains.com/plugin/6351-dart
    • Java version OpenJDK Runtime Environment (build 11.0.15+0-b2043.56-8887301)

[✓] VS Code (version 1.77.3)
    • VS Code at /Applications/Visual Studio Code.app/Contents
    • Flutter extension version 3.62.0

[✓] Connected device (3 available)
    • iPhone SE (3rd generation) (mobile) • 3397BC41-96B7-49A0-AD4E-586489E7453A • iOS            •
      com.apple.CoreSimulator.SimRuntime.iOS-16-4 (simulator)
    • macOS (desktop)                     • macos                                • darwin-arm64   • macOS
      13.3.1 22E261 darwin-arm64
    • Chrome (web)                        • chrome                               • web-javascript •
      Google Chrome 109.0.5414.119

[✓] HTTP Host Availability
    • All required HTTP hosts are available

• No issues found!

Hi @akshaynjarangal
This looks similar to https://github.com/flutter/flutter/issues/88668. Can you try removing all texts on the destination page to see if the issue still persists?

Hi @huycozy
yes, issue persist

Please provide a completed and minimal reproducible code sample that doesn’t include 3rd party plugins or complex production code so that we may verify this.
And please run it in profile mode and attach the timeline trace JSON file as well. You can find the instructions for it in this issue https://github.com/flutter/flutter/issues/74833.
Thank you!

When creating a sample project, it's not facing any issue , when going increase contents in the pages and increase the screens , the issue will begin.
import 'package:flutter/cupertino.dart';

void main() {
  runApp(const MyApp());
}

class MyApp extends StatelessWidget {
  const MyApp({super.key});

  // This widget is the root of your application.
  @override
  Widget build(BuildContext context) {
    return const CupertinoApp(
      title: 'Flutter Demo',

      home: MyHomePage(title: 'Flutter Demo Home Page'),
    );
  }
}

class MyHomePage extends StatefulWidget {
  const MyHomePage({super.key, required this.title});

  // This widget is the home page of your application. It is stateful, meaning
  // that it has a State object (defined below) that contains fields that affect
  // how it looks.

  // This class is the configuration for the state. It holds the values (in this
  // case the title) provided by the parent (in this case the App widget) and
  // used by the build method of the State. Fields in a Widget subclass are
  // always marked "final".

  final String title;

  @override
  State<MyHomePage> createState() => _MyHomePageState();
}

class _MyHomePageState extends State<MyHomePage> {

  @override
  Widget build(BuildContext context) {
    // This method is rerun every time setState is called, for instance as done
    // by the _incrementCounter method above.
    //
    // The Flutter framework has been optimized to make rerunning build methods
    // fast, so that you can just rebuild anything that needs updating rather
    // than having to individually change instances of widgets.
    return  CupertinoPageScaffold(
      navigationBar: const CupertinoNavigationBar(
        middle: Text('Test Rendering'),
      ),
      child: Center(
        child: Column(
          mainAxisAlignment: MainAxisAlignment.center,
          crossAxisAlignment: CrossAxisAlignment.center,
          children: [
            const Text('HEllo Graphic Test'),
            SizedBox(height: 10),
            CupertinoButton.filled(

              child: const Text('Hello'), onPressed: (){
              Navigator.of(context).push(CupertinoPageRoute(builder: (context)=>const MyWidget()));
            })
          ],
        ),
      ),
    );
  }
}

class MyWidget extends StatelessWidget {
  const MyWidget({super.key});

  @override
  Widget build(BuildContext context) {
    return const CupertinoPageScaffold(
      navigationBar: CupertinoNavigationBar(
      middle: Text('Hello'),
      ),
      child:Center(
        child: Text('hELLOOOOOO'),
      ) );
  }
}

When checking this with more texts on the destination page, switching pages back and forth, I see frames drop clearly. This is not clear to see when there are only a few texts on the screen.
So I will close this issue in favor of https://github.com/flutter/flutter/issues/88668 for better tracking. Please follow up on it for further updates. You can leave there your comment and react an upvote to the original comment will help to raise the issue. Thanks!


[FP]: CVE-2023-42794 (OSSINDEX) is tripped on Tomcat 10.1.15

Package URl
<EMAIL_ADDRESS>CPE
cpe:2.3:a:apache:tomcat:10.1.15:::::::*
CVE
CVE-2023-42794
ODC Integration
{"label"=>"CLI"}
ODC Version
8.4.0
Description
The details for CVE-2023-42794 ( https://nvd.nist.gov/vuln/detail/CVE-2023-42794 ) indicate an issue in 8.5 & 9.0.  Apache Tomcat 10.x builds are not listed and I'm assuming are not affected.
However, the ODC CLI is tripping on this issue when run against an Apache Tomcat 10.1.5 package.

We are facing the same issue, but Sonatype found out that 10.x and 11.x branches are vulnerable.

Advisory Deviation Notice:
The Sonatype Security Research team discovered that this vulnerability is also present and remains unfixed in the 10.x and 11.x branches of Apache Tomcat.


Run existing DP tests against a production SAS

When FCC certs are issued for domain proxy, we should run all our existing code and tests against the production SAS to verify the passive mode implementation, which was mostly based on "Spectrum Access System (SAS) - Citizens Broadband Radio Service Device (CBSD) Interface Technical Specification Document" WINNF-TS-0016 and a Fake SAS implementation.
It is likely that we will need some code adjustments based on the result of this exercise.

Tests were run but Production SAS will not allow registration and further SAS flow from test dummy data (like user "John Doe").
Task postponed until we have a working real radio with real SAS params, and fully operational Active Mode for this support.

WONT FIX.
Passive mode is no longer supported and does not fall into the scope of certification.
Certification will only be done on eNBs via TR069 (enodebd)


Add custom data to redux store

I'm not able to add custom keys to the redux store. Is there something special I need to do?
import { combineReducers } from 'redux'
import createStore from 'phenomic/lib/redux/createStore'
import * as phenomicReducers from 'phenomic/lib/redux/modules'

window.__INITIAL_STATE__ = {
  test: 'please add to redux store'
}
const store = createStore(
  combineReducers(phenomicReducers),
  { ...(typeof window !== 'undefined') && window.__INITIAL_STATE__ }
)

export default store

I'm getting this error when trying to add my own custom keys
"warning.js?07c3:14Unexpected key "test" found in initialState argument passed to createStore. Expected to find one of the known reducer keys instead: "pages". Unexpected keys will be ignored."

Any ideas?

window.INITIAL_STATE doesn't expect to be alter by hand.
Please read this section about how to add custom redux reducer (along with your own initialState) here
https://phenomic.io/docs/advanced/redux/

Thanks for the quick response! I saw those docs. Do you have any live examples I can checkout?
I was just trying to combine the initial state, with some custom stuff to start. I was going to hook up the reducers for them later.
import { combineReducers } from 'redux'
import createStore from 'phenomic/lib/redux/createStore'
import * as phenomicReducers from 'phenomic/lib/redux/modules'

const additionalState = {test: 'hi'}
const combinedInitialStateObject = { ...(typeof window !== 'undefined') && window.__INITIAL_STATE__, ...additionalState }
const store = createStore(
  combineReducers(phenomicReducers),
  combinedInitialStateObject
)
console.log('combinedStateObject', combinedInitialStateObject)
export default store

The store when it gets combined with the pages key drops my custom test key

This is how redux work. You're adding a state tree that no reducer can handle, so it throws error.
I don't have any live example for you but this is mostly redux stuff. What are you trying to achieve here ?

It's possible (or it was) to set whatever initial state you wanted in createStore
Does redux strip it out now if there is no reducer to act on that key?
I will setup a new reducer and test this out. I still need to set the intial state somewhere and I don't see where you would do this other than createStore here. Going to follow the ducks pattern https://github.com/erikras/ducks-modular-redux#example

Like it has been explained, you probably just miss a reducer, that's how redux works.
Anyway, do not count too much on Phenomic store as it is going to be removed (you will have to handle it yourself). Please track #40.
I will try to provide instructions when it will be remove so people can keep their custom reducers using a custom store.

@moox @thangngoc89 yep this was my fault. Importing stuff all wrong =/
Fixed it though and now have userAuth setup in redux! =)

For anyone else interested. Redux will throw errors if you don't setup the corresponding reducer to handle the state key passed in.
I hadn't seen this before


Dictionary Website

Description
This is a Dictionary website which can be used to know meanings , pronunciation of words
Stack:

[x] Html
[x] CSS
[x] JavaScript

Hi @Ayush7614 This issue was open since a long time. Would love to volunteer to solve it if it is available for grab.


test ngclient with simulated repo

I'm not sure if this is quite ready but I do think I need other people to comment on this.

Add a RepositorySimulator as a test utility
Add some tests that demonstrate how to use RepositorySimulator
Add "--dump" option to the tests to show how to debug (or just how to create repository test data if that's needed)
Include the fix from #1565: let's review that one there even if we merge all together

So I've not tried to implement any real test coverage yet: I'm making a PR now since there's a lot of activity around client tests and maybe this will help others if it turns out reasonable. At the very least the folks creating tests should have opinions :) I do think that if this looks like a good solution we should move most updater tests to this testing style and have extensive coverage here -- and only leave existing tests as smoke test for the whole stack with a network connection etc.
The note worthy aspects of this are

test_updater_with_simulator.py  is tiny for what it does: 125 lines includes one test with 5 different repository versions and another with 4 different repository versions. I think our current tests never have that many versions anywhere
it should also be quite fast (although I've not benchmarked this) as network connections are not created and the only file access is by ngclient itself
python3 test_updater_with_simulator.py -vvv will be fairly informative: you can see all the metadata versions that get loaded
python3 test_updater_with_simulator.py --dump is quite good for debugging: it stores a repository version every time the client refreshes. These versions can be easily diffed: diff /tmp/tmp614pepb4/test_keys_and_signatures/2 /tmp/tmp614pepb4/test_keys_and_signatures/3
Writing the tests is not as simple as I'd hope (with e.g. publish_root() complication) but maybe still understandable
I'm still not quite sure what exactly we should check when a refresh succeeds... but this is not unique to my approach here

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

16 of 16 (100.0%)  changed or added relevant lines in 2 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage increased (+0.1%) to 96.84%

Totals

Change from base Build<PHONE_NUMBER>:
0.1%

Covered Lines:
3889

Relevant Lines:
3989

💛  - Coveralls

One side question, any ideas how this "client-testing" repository simulator can evolve into repository code and/or a repository testing suit?

Since we have already publish_root(), I think an explicit invocation of a public signing method of the simulator would be better than signing on fetch. This gives you the flexibility to choose creating valid and correctly signed metadata or invalid one, depending on the needs of the test case.

You do have a point... I've tried it but finally ended with the implicit sign because:

incorrect signatures are likely a small minority of tests
large majority of tests would have to add many  sign() calls if signing is explicit -- and I really like the fact that many repo changes now are literally one or two line lines
incorrect signatures can still be done: I included test_keys_and_signatures() to show that -- it's a bit complex because you have to make a mental connection between the signers and the implicit signing, but it is flexible: I think you can do whatever test you need with it

All that said, I'm not married to implicit signing:  if you think the explicit version is definitely clearer, I can change it

any ideas how this "client-testing" repository simulator can evolve into repository code and/or a repository testing suit?

No clear ones, but I figure between this work, repository-editor-for-tuf and Warehouse usage we would have examples where we can start looking at patterns and see what could be in a Metadata API or separate library.
repository testing is tricky... as a first step it would be nice to have a "repository workflow" in the spec that defines in detail how some common thing should be done (new timestamp, new snapshot, common key rotations, adding new targets, adding new delegation, key rotation with ffwd attack recovery, etc).

@sechkova approved with some valid comments... I think I'm going to make an executive decision and merge it with this approval: this is a testing utility and it's not supposed to be a complete design or "final api" in any way, so let's get other people to try this out, modify/improve it -- we can even remove it without big issues it if it turns out to not work in reality.
The one change I'll do before merge is rebase on #1565 to get the docstring fixes for it.


Adding replay controls for directory and no replay

Getting this error
core/Halite.cpp: In member function ‘GameStatistics Halite::runGame(std::vector<std::basic_string<char> >*, unsigned int, unsigned int, bool, std::string)’:
core/Halite.cpp:388:9: error: ‘enabledReplay’ was not declared in this scope
     if (enabledReplay) {

that last commit should have been a fix for that

when I undid the spacing, I reverted that change and forgot to add it back in.

this doesn't redirect the error reports, I don't know if that is desired as well.


Relicense under MIT

This PR makes the license of the code clear and updates the licence to MIT.

Bump. This should be easy to review/merge.


Naming web worker chunks

Forgive me if this issue should be in the worker-loader repository.  Poking through the code, I saw webpack/lib/webworker so I wasn't sure.
Is it possible to name web worker chunks like you can name chunks using a third parameter in require.ensure()?
I have two web workers to load and when I don't include [hash] in the output filename, only one gets created, or more accurately, they both get created with the same name, so only one exists at the end of compilation.  Even including [id], doesn't work--they both, apparently, have an id of 0.
However, when I do include [hash], every time I make a change to the code a new file is created, leaving my output folder full of old versions of the worker file.  Periodically deleting all the output is quite annoying.
Thanks!

It doesn't appear to be documented at code splitting, but I've been doing this for a while. Just pass a string as the third parameter to require.ensure like so:
require.ensure([], function() { var tmp = require("some-module"); }, "page/some-module");

You can put slashes in the string and it will create subfolders. You have to make sure that your output.chunkFilename contains "[name]" somewhere in it and that will get replaced with the name that you pass in.

I think I mispoke.  For loading workers, I'm not using require.ensure().  I don't want to get into an async mess, so I'm doing a simple
import myWorker from 'worker!./myWorker.js';

+1

@dfoverdx Safe to close?

https://github.com/webpack/worker-loader/issues/5

[…] It is now possible to specify the name in the loader query.


cmd/go: go mod download doesn't do anything if you give it a module without a version

So, I didn't realize that go mod download required an @version at the end... I presumed it would default to @latest just like it would if you import a library without specifying a version in your go.mod.  However, instead, go mod download just silently fails.
What did you do?
(in a directory outside GOPATH with a go.mod that did not include github.com/lib/pq)
go mod download github.com/lib/pq
What did you expect to see?
some version of lib/pq downloaded, or an error
What did you see instead?
nothing happened and no error
System details
go version go1.11 darwin/amd64
GOARCH="amd64"
GOBIN=""
GOCACHE="/Users/finchnat/Library/Caches/go-build"
GOEXE=""
GOFLAGS=""
GOHOSTARCH="amd64"
GOHOSTOS="darwin"
GOOS="darwin"
GOPATH="/Users/finchnat"
GOPROXY=""
GORACE=""
GOROOT="/Users/finchnat/sdk/go1.11"
GOTMPDIR=""
GOTOOLDIR="/Users/finchnat/sdk/go1.11/pkg/tool/darwin_amd64"
GCCGO="gccgo"
CC="clang"
CXX="clang++"
CGO_ENABLED="1"
GOMOD="/Users/finchnat/dev/test/go.mod"
GOROOT/bin/go version: go version go1.11 darwin/amd64
GOROOT/bin/go tool compile -V: compile version go1.11
uname -v: Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64
ProductName:	Mac OS X
ProductVersion:	10.13.6
BuildVersion:	17G65
lldb --version: lldb-9<IP_ADDRESS>
  Swift-4.1

Notably, I'd prefer "no version" to default to @latest ... but it at the very least should tell me I gave it something invalid.

'go mod download' should report errors and failure if any.

$ go mod download somethingveryfake.com/fake
$

Issue is related to #31237, an error message displays with the submitted fix which seems to solve the issue:
$GOPATH\src\mymod>set GO111MODULE=on

$GOPATH\src\mymod>goissue mod download rsc.io/doesnotexist
go: cannot find main module; see 'go help modules'


Add installation instructions for fANOVA to README.md

The README doesn't mention that it's necessary to install fANOVA

Thanks for pointing this out, I fixed that and added instructions for the fANOVA installation


Extend Github Public Samples Build Timeout to 90 minutes

This change extends the GitHub Public Samples Build Timeout to 90 minutes to counteract the increased execution time due to the OpenCV Build Task

All the tasks were placed underneath a job so that the timeoutInMinutes flag could be added globally

why does it look like the whole file changed? is there a whitespace or line-ending change?

why does it look like the whole file changed? is there a whitespace or line-ending change?

All the tasks were placed underneath a job so that the timeoutInMinutes flag could be added globally


feat(cli): --inspect-brk support

[x] I have read the contribution documentation for this project.
[x] I agree to follow the code of conduct that this project follows, as appropriate.
[x] The changes are appropriately documented (if applicable).
[x] The changes have sufficient test coverage (if applicable).
[x] The testsuite passes successfully on my local machine (if applicable).

Summarize your changes:
A simple change to support passing --inspect-brk option to electron.

@malept, could you take a look at this issue and provide your feedback please?

Any progress on this?


Plaintext Output

We're including your project in our GitLab CI pipelines, but it seems that the coloring codes aren't represented the same as they would be in GitHub?

Is there an option for plaintext output? Or better, a way to get these color codes to show up properly in GitLab MRs?

I'm not sure if this is helpful, but linking just in case: https://gitlab.com/gitlab-org/gitlab-foss/-/issues/24167


Python Extension

VSCode Version: 1.46
OS Version: Windows 10

Steps to Reproduce:

I am using Django and when I create a model and then I use it in my views to extract information from the database. The extension shows that this model has no objects member but my code works fine.
I just want you to handle this error. I can even share screenshots of the error if you want.

Does this issue occur when all extensions are disabled?: Yes/No
Yes

Please file issue against the extension.

okay thanks...


dfm add ~/.emacs.d does not add to tracked files.

Traceback (most recent call last):
File "/usr/local/bin/dfm", line 11, in
sys.exit(dfm())
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/usr/local/lib/python3.6/site-packages/dfm/cli.py", line 182, in add
add_file(f, profile)
File "/usr/local/lib/python3.6/site-packages/dfm/lib/init.py", line 147, in add_file
link_file(new_path, bytes(old_file), force=True)
File "/usr/local/lib/python3.6/site-packages/dfm/lib/init.py", line 96, in link_file
if CONFIG['verbose']:
KeyError: 'verbose'
It does end up linking the file, but it doesn't look like it adds it to git tracking. I tried to commit afterwards, and my .emacs.d was untracked.

The stack trace was caused by a completely unrelated error which caused the program to crash before it got to adding the file in git, I've fixed this bug and tested dfm add on my local box and it's working, pushing a fix soon


Merge without target-item

Hi,
first of all, thank you for your library. It makes my life much easier. :+1:
I was expecting that if I set "newTranslationTargetsBlank": true, there would be no translation and when building the app the original language would be used. So, it would be clear to any user that there is still a translation missing here.
Unfortunately, however, a <target/> is inserted into the xlf file, which ensures that the string is no longer displayed at all and content is suddenly missing from the app.
Is it possible to do the merge in a way that the new strings are taken over and no <target/> is inserted?
Example:
Instead of this
...
    <unit id="1234565678984936453432">
      <segment state="initial">
        <source>Original</source>
        <target/>
      </segment>
    </unit>
...

I would find this better
...
    <unit id="1234565678984936453432">
      <segment state="initial">
        <source>Original</source>
      </segment>
    </unit>
...

Hi @Vorlif
not sure if I get your intend here. To leave texts in the original/source language until they are translated, I'd be recommended to set newTranslationTargetsBlank: false - that way the target is populated with the source:
...
    <unit id="1234565678984936453432">
      <segment state="initial">
        <source>Original</source>
        <target>Original</target>
      </segment>
    </unit>
...

Would this solve your problem?

Hi @daniel-sc
Thanks for your quick reply. newTranslationTargetsBlank: false would be a workaround for me, but not a nice solution. I would like to leave the missing translations blank and display the original text as a fallback.
Through <target/>, it is assumed that the translation is an empty string and this empty string is also displayed in the frontend. So nothing is displayed. But without <target/> it is assumed that no translation is available and the original language (which should be translated) is displayed as fallback. This would also be more in line with the real intention.
I know that newTranslationTargetsBlank: false has the same effect in the frontend. But it also puts the original language as translation everywhere and I would like to avoid that.
But I can understand if you say that's not your library's job. I just thought I would propose it once.

I understand - maybe it makes sense to add a third option (besides true/false) such as "noTargetElement".
Not sure when I find time for this, but I'll definitely give it a try - but if you'd like to create a PR I'd be happy to help!


Update processFileContent to support DevSecOps token format

I noticed that even though the extension had been updated to support the DevSecOps setup, it didn't appear to be supporting tokens during file import. This is my attempt at implementing this, currently untested though.

This is my attempt at implementing this, currently untested though.
Thanks for the update! Does the change fixes the issue on your side, so you
tested it on a limited set of files?

On Wed, Jan 11, 2023 at 10:14 PM matt0x5B @.***> wrote:

I noticed that even though the extension had been updated to support the
DevSecOps setup, it didn't appear to be supporting tokens during file
import. This is my attempt at implementing this, currently untested though.
You can view, comment on, or merge this pull request online at:
https://github.com/lispercat/sailpoint-iiq-dev-accelerator/pull/39
Commit Summary

c6eadd7
https://github.com/lispercat/sailpoint-iiq-dev-accelerator/pull/39/commits/c6eadd7f2914bf7738cdf1711ba63c273f952275
Update processFileContent to support DevSecOps token format

File Changes
(1 file
https://github.com/lispercat/sailpoint-iiq-dev-accelerator/pull/39/files
)

M client/src/iiq-commands.ts
https://github.com/lispercat/sailpoint-iiq-dev-accelerator/pull/39/files#diff-fefd9afedc7abb17b1a8574db92509e31b3bc616502854558711081d887f9895
(19)

Patch Links:

https://github.com/lispercat/sailpoint-iiq-dev-accelerator/pull/39.patch
https://github.com/lispercat/sailpoint-iiq-dev-accelerator/pull/39.diff
—
Reply to this email directly, view it on GitHub
https://github.com/lispercat/sailpoint-iiq-dev-accelerator/pull/39, or
unsubscribe
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You are receiving this because you are subscribed to this thread.Message
ID: @.***>

@matt0x5B could you please answer the question? I don't use the feature so it needs to be tested somehow to get merged.

Closing for inactivity


Attachments_First() from codeunit 8904 "Email Message" is not working as expected

BC 21.5 US Saas.
I was trying to download the attachments from sent email Sample code is attached and
codeunit 8904 "Email Message" called below procedure is not working as expected.
/// <summary>
/// Finds the first attachment of the email message.
/// </summary>
/// <returns>True if there is any attachment; otherwise - false.</returns>
procedure Attachments_First(): Boolean
begin
    exit(EmailMessageImpl.Attachments_First());
end;

Download Email Attachments.txt

This issue should be moved to the https://github.com/microsoft/ALAppExtensions repository since it's related to the System Application.
@bineshsingh you simple embed your example code inline. Then it's easier to check.
Could you please elaborate what isn't working as expected?
This would make it easier to improve the System Application Code.


Suggestion: Scroll history of current chat via keyboard

This is a great UI, it's almost 100% what I want!
It's perfect for my requirements, but for one thing. It seems to be necessary to use the mouse to scroll up and down through a chat.
I'd like to be able to use this program through the full-screen TTY Linux session (via Ctrl+Alt+F5) where using the mouse isn't an option.
Would it be possible to make this 100% keyboard-only compatible, by perhaps allowing the use of the PageUp and PageDown keys to scroll through the chat history?
Thanks, and I hope you give this feature a thought!

Hey thank you so much for the kind words :)
This has popped up before, it's something that I also miss.
The difficulty is that the underlying markdown widget does not get focus (it's only a view) and does not support afaik keyboard scrolling.  It is hard to capture keyboard events without messing with the terminal's own events.
Let me think a bit about it, perhaps I can can figure out something by binding to the inputs.

As a workaround, it is possible to use an app call homerow allows for keyboard only scrolling of the chat history via a keyboard shortcut.


Stopped working: Remember client position

Please check if your issue is not a duplicate by searching existing issues
Describe the bug
Until 1.6.23, my windowed client was opening fine on Monitor 1. After latest update, it now loads at same position but on Monitor 2 (main display). I recall having this in the past but it seems it was fixed on 1.6.22.
Unchecking  "Remember client position", reloading client and checking again does nothing.
Nothing else has changed on my PC setup (i.e. no Windows updates, no hardware changes).

The behavior was changed to reset the client position if it is partially off screen instead of completely off screen, due to users getting the client stuck in ways which they were unable to move or fix the size of it. Is your normal client position partially off screen?

Hi Adam, thanks for your reply.
That makes sense! I had originally the client windowed and resized to the whole screen. It was probably a couple pixels over boundaries. After the update It was keeping the same size but loading on my second monitor (which is smaller resolution), hence i thought the issue had came back.
I just resized the client to one pixel smaller than the screen res and it worked!
Thanks for the info! 👍 This can be closed.


Project Setup Guidelines have wrong run command in README.md

In README.md the section Project Setup Guidelines specify to execute: Run main.go.
This is not a valid command and should be go run main.go.
Edit: I'll fork and create a branch to update this and submit a PR shortly.

Just merged ! Thanks @benjmarshall !


Can't save configuration

Every time I press "save" Discord Webhook Url and Server Url fields are wiped out and the page reloads without saving anything.
Also when pressing " Send test notification" this error occurs "Uncaught (in promise) TypeError: Cannot read property 'UserId' of undefined at configurationpage?name=DiscordJS&v=10:1502"

There's a bug with jellyfin-web where clicking save the first time refreshes the page. Just reenter the details and hit save; then you should be able to test

I've done it 3 times but it's still reloading

I just tested with my instance and was able to save successfully
Steps I took to save:

Load plugin config
Save
Let page automatically reload
Save again without refreshing

As shown here, it's not working for me. I also tried another browser without any luck

Close it by accident sorry

Just built 1.2020.910.255. Can you update the plugin and try now?

It worked! Thank you so much

perfect!
For future reference -> e.preventDefault; -> e.preventDefault();


Futures are not Send

This is a real problem when trying to do something with the API of this crate.
Can we work towards a Send interface? What needs to be done?

I think this is due to a limitation with Actix. Not sure how to resolve it and make it so there's still a shared interface

Would be really nice if this could be fixed, because it makes implementing something useful with this library absolutely impossible!

You're welcome to put a PR for it. I am not getting paid to maintain or develop this library and do it in my freetime


Exception handling tries to use function.name

While testing AirLift code, I must have triggered the RuntimeError in WSGIApp.__call__. Which lead to this error:
Traceback (most recent call last):
  File "code.py", line 1, in <module>
  File "counting.py", line 23, in <module>
  File "robot_wifi.py", line 52, in start_wifi_server
  File "adafruit_esp32spi/adafruit_esp32spi_wsgiserver.py", line 105, in update_poll
  File "adafruit_wsgi/wsgi_app.py", line 74, in __call__
AttributeError: 'function' object has no attribute '__name__'

CircuitPython does not implement the function.__name__ magic. The following demonstrates this:
Adafruit CircuitPython 7.3.0-beta.2 on 2022-04-27; Raspberry Pi Pico with rp2040
>>> def a():
...     return 1
...
...
>>> a.__name__
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'function' object has no attribute '__name__'

This is different from CPython:
Python 3.7.4 (v3.7.4:e09359112e, Jul  8 2019, 14:54:52)
[Clang 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> def a():
...   return 1
...
>>> a.__name__
'a'

The current exception handler looks like:
                raise RuntimeError(
                    "Proper HTTP response return not given for request handler '{}'".format(
                        route["func"].__name__
                    )
                ) from err

I recommend maybe a getattr with a default?
>>> getattr('a', '__name__', '')
''

Which means where it is available it will format in the name, otherwise it's empty.

Or perhaps use the route name...


Enable tracing of prometheus scrape requests to be disabled

When the helm chart is installed with both zipkin and prometheus enabled, and a service is deployed with annotation prometheus.io/scrape: "true", it results in the prometheus scrape requests being traced by the service's inbound proxy.
For example, the following shows multiple trace instances for a service, without any "business request" actually being sent to the service:

The details for one of the trace instances shows that it is a request to the exposed /metrics endpoint from prometheus, that is creating the trace instance.

This PR introduces a new value on the prometheus chart prometheus.tracing.sampled (default to true to maintain current behaviour and not install nginx), that can be used to install a nginx proxy that will add the X-B3-Sampled: 0 header to the scrape request.

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Hi @objectiser. Thanks for your PR.
I'm waiting for a istio member to verify that this patch is reasonable to test. If it is, they should reply with /ok-to-test on its own line. Until that is done, I will not automatically test new commits in this PR, but the usual testing commands by org members will still work. Regular contributors should join the org to skip this step.
I understand the commands that are listed here.

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository.

cc: @jeffmendoza
Any particular reason to use an nginx proxy here?  Can this wait until Tracing configuration is supported in a more first-class way within Istio (allowing path exclusion, etc.)?

I guess it depends how long until such a mechanism is implemented, as currently it can lead to a lot of unnecessary trace instances. But no problem if you want to close.

I can try to convert nginx config to envoy config as a follow-up. That should be trivial.
What is interesting, is whether we should be tracing at all for in-mesh requests, and how to make it easier to turn off tracing selectively for istio-internal services.

Based on comments, will close this issue.
I have created a blog post in case any users require a solution in the short term.


Fixes #2854 and #2856

Fix #2854: issue with unit selector
Fix #2856: scanner should be restarted only if the bottom view is col…

Looks good to me. Thanks @deniger


Create a consistent layout for content pages

We need to create a consistent layout for content pages to follow.

Layout is made in df4e9908c1c3d98d87ccd32192e5d05550f606d8


WIP Inline File Renaming #150

Closes #150
Todo: Fix issue where clicking rename directory button while that directory is not currently being renamed toggles the directory open/close.

This may be of interest as a reference https://github.com/vizhub-core/vizhub/blob/01cadfb78a2611df32f981b1fd8136b70447de9e/vizhub-v2/packages/neoFrontend/src/pages/VizPage/Body/Editor/FilesSection/index.js#L14

This change may help here https://github.com/vizhub-core/vzcode/pull/182/files#diff-017595a8c9d711c40f5137aa936038881760cacffebe8c98ded565b9302dee99R34 - there's a possibility that the rename function was not working properly before because of this missing dependency. Maybe pull this change into this branch once it lands, hopefully that will help get this inline file renaming feature working properly.

Let me know if you want to tap out @michaelkrar , I can potentially take over this PR to land it if you're out of energy for it (I know what that's like - sometimes it's tough to get it over the finish line). The bulk of the feature is done and you've done amazing work here. Thanks!

This PR is getting stale, some merge conflicts are arising.
Also I was thinking, how can we get this merged? We need to maintain working order. One idea: disable the rename UI entirely for directories, then re-enable it at a future time to close #103 .

Hi sorry for the delay I have not been checking my email for github notifications. Going on I will make sure to respond faster. I temporarily undid the default file name feature and cleaned up the changes. I also changed the two lambda functions I wrote in Item.jsx to be useCallback. Let me know if anything else needs to be changed before merge.

Amazing! Thank you so much for your work on this. I'll take it from here re: final cleanup and merge.

Notes on local testing:

There's a strange behavior of when you are typing something, then if you move the mouse outside the text area, it switches back to a regular file listing

Hooray! Inline File Renaming landed! Thank you  @michaelkrar  for the excellent work.
I've identified a few minor improvements that can be made and split them out into new issues. See https://github.com/orgs/vizhub-core/projects/2/views/1?filterQuery=assignee%3Amichaelkrar


Polar_Cartesian_Conversion

Submission Title
Polar_Cartesian_Conversion
Submission Type
Maths_And_Stats
Submission Description
Converting Polar Coordinates to Cartesian
Folder Related To
Maths_And_Stats => Geometry => Polar_Cartesian_Conversion => Polar_Cartesian_Conversion.extension
Contributors

[ ]  C++ -
[ ]  C -
[ ]  Python -
[ ] Java -
[ ] JavaScript -
[ ] TypeScript -
[ ] Golang -
[ ] Ruby -
[ ] php -
[ ] Swift -
[ ] C# -

I will do it in python

Please assign me for Golang.

Please check my PR, thanks

Hello, I would like to add the code for this problem in CPP.

thanks everyone :v:


is it giving insta ban or something like this?

Cause smef said that indigo is dead now and i have a fix of it, will i be banned if i use it becaute of VMT?

i can test it for u


[media-common] Image values separate organisation

In the media-common chart the image definitions are as follows:
image:
  organization: ""
  repository: ""
  pullPolicy: IfNotPresent
  tag: ""

Which separates the organisation part from the image name part. For update automation flux requires the repository value to be in the owner/image-name format. I think it would be possible to workaround that, by creating a dummy value for the repository and point flux to use that, but this makes it very hacky and one would need to maintain three repetitive fields for custom images and additional annotations for flux. Were there any specific design decisions to separate them?

Actually the proposed workaround does not seem to work with Flux. I tried for example for radarr:
...
metadata:
  name: radarr
  namespace: media
  annotations:
    fluxcd.io/automated: "true"
    repository.fluxcd.io/app: image.repo
    tag.fluxcd.io/app: image.tag
    filter.fluxcd.io/app: regexp:^3\.\d+\.\d+\.\d+-ls.*
spec:
  values:
    radarr:
      image:
        # those are chart values concatenated in the pod definition as organization/repository
        organization: linuxserver
        repository: radarr
        # repo is a dummy value(not used by the chart) using the correct notation for a repository
        repo: linuxserver/radarr
        tag: <IP_ADDRESS>24-ls21
...

Flux just ignores this and tries to query dockerhub for index.docker.io/library/radarr looks like because values.repository is already set and a default path to look for in Flux.
caller=images.go:159 component=sync-loop err="fetching image metadata for index.docker.io/library/radarr: item not in cache, last error: errors:\ndenied: requested access to the resource is denied\nunauthorized: authentication required\n"

I can't actually workaround that without changing the chart itself.
BTW: Non dockerhub registries can and do contain a longer paths not only consisting of a organisation and a image name, like cloud/media/custom/radarr which does not really fit in the organization option.

We just added the k8s@home common library chart. I will be creating a PR to update sonarr/radarr/etc to use it, similar to Jackett (https://github.com/k8s-at-home/charts/pull/113). That should resolve this issue I think.

Not a big fan of the dependency umbrella (makes hard to track changes affecting a chart) but yeah it's merged together again and should be fixed after merge.


Improve Get-PnPPlannerPlan error message

Type

[x] Bug Fix
[ ] New Feature
[ ] Sample

Related Issues?
Improves #4494
What is in this Pull Request ?
Improve Get-PnPPlannerPlan error message when no plan with the specified name is found.
Before the same error was shown when 0 plans were found and when 2+ were found:

Now a different error is shown when 0 plans are found, making it more clear that no plan was found at all. When multiple plans are found, the count is displayed too. The title of the plan passed as parameter is also included in the error message:

The plan is returned as usual when it's found and it's unique.

Thanks @jackpoz , much appreciated !


Allow building presentation with multiple VCs

The document.createPresentation() takes the fields as string array, instead it should take it as object and option to tell which VC it wants the fields from.
Sample
{
  “fields”: [
      { “k”: “email”, “v”: [ “did1”, “did2” ] },
      { “k”: “name”, “v”: [ “did1”, “did2”, “aadhaarDid”, “panDid” ] },
      { “k”: “company”, “v”: [ “self” ] },
      { “k”: “event”, “v”: [] }
]
}

Hello @Prashant-Mutnale , Could you please elaborate on this issue a bit? Need some more clarity on this issue.

The VC export is been take out now.
Thanks @Ris-code


Additional files

I use wordpos in an action. It's currently inpossible to publish that package because it has additional files in dist:

And only dist/index.js is added to the Automatic compilation commit. After looking into the code I think it's not possible to add the whole dist folder with your package. But correct me if I'm working.

https://github.com/JasonEtco/build-and-tag-action/pull/24 added this pull request because I stumbble with that requirement as well

Hi @JasonEtco, would it be possible to incorporate this feature? (There are already open PRs #18 and #24 which have possible implementations of this.)
In addition to not supporting actions that need additional files, this also doesn't allow including licenses, which seems like bad OSS etiquette at a minimum and violating license agreements with a stricter stance. This comment also points out that the marketplace page for older versions end up with blank descriptions because there is no README.
I also like this comment's suggestion of using the files keyword on the package.json spec which is intended to allow for specifying exactly this kind of thing.

yes, please !!

You can try this action: https://github.com/marketplace/actions/github-versioned-release


elevation and snow persistence

make elevation/snow persistence section with:

[ ] make a mountain graphic - either diagram, 3d map, or annotated image - that captures the elevation range of interest of upper colorado monitoring and modeling efforts
[x] meet with graham sexton about what work is being done with elevation
[ ] determine focal elevational range, gages of interest, and general patterns to communicate

Likely next steps pending steps above:

[ ] show gage locations on the mountain
[x] pair with animated hydrographs showing water year progression in snow and discharge
[x] order gage hydrographs by snow persistence (https://www.sciencebase.gov/catalog/item/5f63790982ce38aaa23a3930) or elevation
[ ] add snow animation  to play simultaneously over mountain. may be more effective to use simple css effect with a drawn diagram rather than overlaying snow rasters on top

This resulted  in the ridgeline interactive chart. This idea is solid though and should be executed once obstacles to rendering a rayshader animation are sorted out.


an error found in the Transitioner example

Current Behavior

this is my setting
<Transitioner
   configureTransition={this._configureTransition}
   navigation={this.props.navigation}
   render={this._render}
   onTransitionStart={this.onTransitionStart}
   onTransitionEnd={this.onTransitionEnd}
/>

the same as Transitioner doc
then there is a prompt that " cannot read property 'forEach' of undefined "
in ScenesReducer.js 99:19
nextState.routes.forEach

I log the "nextState" is
{
  key: "id-1501060202060-2",
  params: undefined,
  routeName: "Index"
}

so that i found the props 'navigation' of Transitioner need the property 'index' and 'routes'
navigation prop
Is the example Transitioner doc  wrong?
Expected Behavior

Environment

software
version

react-navigation
1.0.0-beta.11

react-native
0.44.3

node
7.10.0

npm
4.2.0

Ah, I just ran into this too. Is there an example of how to set up Transitioner that you've found that works?

I'm seeing this error outside the context of a transitioner.

Pinging OP @linjiajian999  since this issue has not been active for a while, and it's related to an old version of the lib.
Please let me know if you want this to remain open; if I get no answer in the next 7 days I will close it.

Hi there @linjiajian999 ,
In an effort to cleanup this project and prioritize a bit, since this issue had no follow up since my last comment I'm going to close it.
If you are still having the issue with the latest version (especially if it's a bug report) please check the current open issues, and if you can't find a duplicate, open a new one that uses the new Issue Template to provide some more details to help us solve it.

@kelset okay. I will test it again in the new version and give the relevant report later.

Has anyone else fixed this nextstate.routes.foreach issue? I opened up a stackoverflow post just now for what I believe is the same problem as everyone here: https://stackoverflow.com/questions/47848999/redux-with-react-navigation-nested-navigators-typeerror-undefined-is-not-an-ob
I think it is definitely because of the nested navigators but I am unsure how to resolve the issue.
Any luck finding anything?


Fix for time validation

:tada: This PR is included in version 1.13.1 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


Service exited due to Trace/BPT trap: 5

Hi there, I’m trying to run the Groceries app for the first time, and it seems to be exiting with the system.log message below. Can anyone help?
I've tried both the angular-start and master branch. Same error.
tns 2.2.1
Simulator Version 10.0 (SimulatorApp-700.5.3
Xcode Version 8.0 (8A218a)
Sep 13 19:05:44 CHRISTOPHERs-MacBook-Pro com.apple.CoreSimulator.SimDevice.499CBAD2-C487-495B-A343-DFB9A16D127D.launchd_sim[25503] (UIKitApplication:org.nativescript.groceries[0x5f5][25953]): Service exited due to Trace/BPT trap: 5

I apologise, this is probably a Stack Overflow question.

Same here. I think we should reopen this issue.

Same since updating to xcode 8 one of my apps is giving me this and I can't figure it out.

Hey @ChrisFlannagan , @loicjaures , @cck197
Possible reason for your trap 5 error is because you have not provbide TeamID for your project.
Sinci XCode 8 and iOS 10 , Apple had made some changes and now deploying on real device with Xcode8 and iOS10 is allowed only after provided team id.
To provide your team id in the project you are trying to build do the following:
Open app/App_Resources/iOS/buld.xcconfig and unccoment DEVELOPMENT_TEAM
DEVELOPMENT_TEAM = <YOUT_TEAM_ID_HERE>;

If you have set team id it can be seen in Keychain Access app in your Mac OS.
If you need more information about the new developer tools and requirments you can follow this link

I'm still getting this error, has anyone been able to solve it? It pretty much makes development impossible.


How to handle composite ids?

I'm working with a table that doesn't have its own id, it just has two foreign keys and a few properties.
Are there any gotchas that I might run into with this table?

This is being tracked in #93. Closing this issue due to lack of activity.

@tgriesser I'm not sure how you handle composite keys here... withPivot will allow you to pull more columns out from your associative table but it is not generating multiple on's in my join.


Update Cargo.lock

Description
This PR fixes a small glitch in the latest release: Cargo.lock is not up-to-date (It still references 0.2.6). This affects the source archives of the github release only. It does NOT affect the release on crates.io.
Type of change
Please delete options that are not relevant.

[x] Updates Cargo.lock

@skraus-dev Here is a pre-push hook script, that checks Cargo.lock whenever a tag is pushed and prevents the push if Cargo.lock is not up-to-date:
#!/bin/bash
## hook to check if Cargo.lock is up to date when pushing a tag

tagref=$(grep -Po 'refs/tags/([^ ]*) ' </dev/stdin | head -n1 | cut -c11- | tr -d '[:space:]')

if [[ "$tagref" == ""  ]]; then
    ## pushing without --tags , exit normally
    exit 0
fi

echo "Checking Cargo.lock state ..."
if cargo fetch --locked >/dev/null 2>&1 ; then
    # Cargo.lock is up-to-date
    exit 0
fi

echo "Pushing a tag, but Cargo.lock is out of date" >&2
exit 1

In order to use this, save this as .git/hooks/pre-push in your local working copy and make it executable.

Why I stumbled over this:
In my rpm packaging, during setu and build phase, the following commands are run:
cargo fetch --locked

cargo build --frozen --all-features --all

This is done in order to make shure, that exactly the same dependencies like in the upstream the release are used.
I believe, the same applies to the AUR package by @mpldr
For my rpm package, I simply removed the --locked temporarily for the 0.2.7 packaging.


Reduce log chatter.

Make it easier to see what tests are running and help concentrate on important messages.
bazel test --test_output=streamed  //verilog/tools/ls/...

CC: @glatosinski - FYI, might be needed to git rebase to patch these changes into your copy.

Codecov Report
Base: 92.97% // Head: 93.00% // Increases project coverage by +0.02% :tada:

Coverage data is based on head (e5eb5ee) compared to base (4779bd9).
Patch coverage: 95.46% of modified lines in pull request are covered.

: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
Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1712      +/-   ##
==========================================
+ Coverage   92.97%   93.00%   +0.02%
==========================================
  Files         352      352
  Lines       25238    25477     +239
==========================================
+ Hits        23465    23694     +229
- Misses       1773     1783      +10

Impacted Files
Coverage Δ

verilog/tools/ls/symbol-table-handler.cc
86.59% <64.28%> (-2.09%)
:arrow_down:

verilog/tools/ls/autoexpand.cc
96.86% <97.80%> (+0.01%)
:arrow_up:

verilog/tools/ls/lsp-parse-buffer.cc
95.45% <100.00%> (ø)

verilog/tools/ls/verilog-language-server.cc
94.59% <100.00%> (ø)

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

:umbrella: View full report at Codecov.
:loudspeaker: Do you have feedback about the report comment? Let us know in this issue.


[Upstream] 3D pooling

This upstreams #774, #854 and #997.

Can one of the admins verify this patch?


fix: avoid race condition when building chain processors

Background
I'm surprised this hasn't flared up before. Pigeons will usually "build processors" before every operation, meaning they will ask Paloma for the latest chain configuration and compare their local setup. In case there's a difference, they will rebuild their local setup to match what's asked for by Paloma.
The code for this was not written with concurrency in mind, but is part of most of our background tasks which all run concurrently. Therefore, updating the internal state would interfere with each other, leading to contradicting results, a ton of update calls, invalid and incomplete data in the valsets and more.
This change adds a read/write mutual exclusion lock around the code in question, ensuring that reads stay performant, but don't interfere with updating the internal state any longer.
Testing completed

[x] test coverage exists or has been added/updated
[x] tested in a private testnet

Breaking changes

[x] I have checked my code for breaking changes

To reflect: we now have a new set of mutex locks to prevent race conditions on getting chain infos. Yes, surprised this was not an issue before. Any tests needed here?

@taariq There's tests in place that verify the func works as expected.


[#139196683] Monitor BBS health

What
This is set of PRs to deploy BBS monitoring solution. It adds new cf.bbs.Healthy and cf.bbs.ResponseTime metrics.
It consists of:

https://github.com/alphagov/paas-bootstrap/pull/55 - WHICH MUST BE DEPLOYED FIRST
https://github.com/alphagov/paas-datadog-bbs-integration/pull/1 - Provides BBS check and tests.
https://github.com/alphagov/paas-datadog-for-cloudfoundry-boshrelease/pull/13 - Integrates BBS check into BOSH release and provides default config
https://github.com/alphagov/paas-datadog-for-cloudfoundry-boshrelease/pull/13 - Implements new mechanism to copy custom checks into datadog agent directory
This PR

How to review

deploy from this branch and check if cf.bbs.Healthy and cf.bbs.ResponseTime are available in DD for your env. Check if monitor works
Review and merge https://github.com/alphagov/paas-datadog-bbs-integration/pull/1
update git submodule in  https://github.com/alphagov/paas-datadog-for-cloudfoundry-boshrelease/pull/13 to point to master branch of alphagov/paas-datadog-bbs-integration
Merge https://github.com/alphagov/paas-datadog-for-cloudfoundry-boshrelease/pull/13 - this will trigger final build for paas-datadog-for-cloudfoundry-boshrelease
Once https://github.com/alphagov/paas-datadog-for-cloudfoundry-boshrelease/pull/13 is merged, replace TMP commit with final build of the release.

Who can review
not @mtekel or @combor

Merging, but won't take effect until I deploy alphagov/paas-bootstrap#55 in all environments.