What caused the different results?

Dear Dr.@MichaelHiller,
Thank you!
I have modified these scripts and ran successfully. To ensure that I properly ran these scripts, I tried to replicate the results of the Loss of Vitamin C Synthesis dataset which you provided in the latest Forward genomics paper(just for a quick test, I picked up CDS053214 element ).  However, I got a series of different global %id values.
The global percentID your provied:
species ailMel1 bosTau7 calJac3 canFam3 cavPor3 choHof1 chrPic1 dasNov3 dipOrd1 echTel1 equCab2 eriEur1 felCat5 galGal4 gorGor3 hetGla2 hg19 loxAfr3 macEug2 melGal1 melUnd1 micMur1 mm10 monDom5 myoLuc2 nomLeu2 ochPri2 ornAna1 oryCun2 otoGar3 oviAri1 panTro4 papHam1 ponAbe2 proCap1 pteVam1 rheMac3 rn5 saiBol1 sarHar1 sorAra1 speTri2 susScr3 taeGut1 tarSyr1 triMan1 tupBel1 turTru2 vicPac1
CDS053214 0.92156862745098 0.92156862745098 0 0.901960784313726 0.794117647058823 NA NA 0.92156862745098 0.882352941176471 0.911764705882353 0.950980392156863 0.929292929292929 0.941176470588235 NA 0 0.852941176470588 0 0.950980392156863 NA NA NA 0.911764705882353 0.911764705882353 NA 0.225490196078431 NA 0.92156862745098 NA 0.901960784313726 0.950980392156863 NA 0 0 0 0.892156862745098 NA 0 0.872549019607843 0 NA NA 0.892156862745098 0.931372549019608 NA NA 0.950980392156863 0.970588235294118 0.941176470588235 0.950980392156863

My result:
species ailMel1 anoCar2 bosTau7 calJac3 canFam3 cavPor3 choHof1 chrPic1 danRer7 dasNov3 dipOrd1 echTel1 equCab2 eriEur1 felCat5 fr3 gadMor1 galGal4 gasAcu1 gorGor3 hetGla2 hg19 latCha1 loxAfr3 macEug2 melGal1 melUnd1 micMur1 mm10 monDom5 myoLuc2 nomLeu2 ochPri2 oreNil2 ornAna1 oryCun2 oryLat2 otoGar3 oviAri1 panTro4 papHam1 petMar1 ponAbe2 proCap1 pteVam1 rheMac3 rn5 saiBol1 sarHar1 sorAra1 speTri2 susScr3 taeGut1 tarSyr1 tetNig2 triMan1 tupBel1 turTru2 vicPac1 xenTro3
CDS053214 0.882352941176471 NA 0.911764705882353 0 0.862745098039216 0.794117647058823 NA NA NA 0.911764705882353 0.843137254901961 0.92156862745098 0.92156862745098 0.901960784313726 0.892156862745098 NA NA NA NA 0 0.852941176470588 0 NA 1 NA NA NA 0.882352941176471 0.872549019607843 NA 0.215686274509804 0 0.872549019607843 NA NA 0.862745098039216 NA 0.901960784313726 0 0 0 NA 0 0.911764705882353 NA 0 0.852941176470588 0 NA NA 0.872549019607843 0.92156862745098 NA NA NA 0.950980392156863 0.92156862745098 0.911764705882353 0.92156862745098 NA

There are two main differences: 1.the results from yours include id% of 50 species and mine include 60 species. 2. The id% value are different.
I'm wondering whether this is caused by my faults or by different input data or parameters.
Here are my commands:

extract maf (download from UCSC)

/xieduo/software/ForwardGenomics_20200324/bin/mafIndex chr14.maf chr14.maf.bb -chromSizes=mm10.chrom.sizes
/xieduo/software/ForwardGenomics_20200324/bin/mafExtract chr14.maf.bb out.maf -regionList=CDS053214.bed -leaveEdgeMeta

reconstruct ancestral sequences

perl /xieduo/software/ForwardGenomics_20200324/scripts/Maf2SpanningSeq_PRANK.perl out.maf CDS053214  -runPrank -treeFile /xieduo/01.B10K/07.Forward_genomics/test/identity/tree.nh -keepTemporaryFiles -genomePath genomes -BDBFile testBDB

and here is the tree I used from UCSC mod file(ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/phastCons60way/mm10.60way.phastCons.mod).  This tree consist of 60 species and I noticed that the tree you provided consist of 50 speices(https://bds.mpi-cbg.de/hillerlab/ForwardGenomics/loss_of_vitaminCsynthesis/tree.nh). Did you used 50 species tree to run this script?

compute global id%

perl /xieduo/software/ForwardGenomics_20200324/scripts/GetGlobalAndLocalPercentID.perl testBDB CDS053214 -treeFile /xieduo/01.B10K/07.Forward_genomics/test/identity/tree.ancestor.nh -allowedAncestralNodes mm10-loxAfr3,mm10-susScr3,mm10-hg19  -global

The tree.ancestor.nh was derived from tree.nh by running tree_doctor -a tree.nh.

I'm questioning this difference may be caused by 3rd step in which I used a differentallowedAncestralNodes or species treee from yours. What do you think?
Thank you!
 In fact, your values are slightly lower, which is exactly what you expect if you take a more distant ancestor.
We have fewer species, because we reconstructed a mammal ancestor and by definition no non-mammal species can then get a %id value (e.g. you have anoCar2 = lizard).
Please reproduce it with the exact same tree, alignment, ancestor etc. If there are still differences, I can have a look.
Best
Michael

Dear Dr.@MichaelHiller ,
Thank you for your reply!
I have two quick questions.
First, which species tree you used to reconstructed the ancestral sequence and compute %id value respectively? Were they same? Was this species tree?
Second, how did you set the -allowedAncestralNodes option when you ran the GetGlobalAndLocalPercentID.perl script? I'm wondering this because of some elements the most recent common ancestor may be absent.
Best,
Duo

Hi Duo,

Yes, we used the tree that we deposited in the loss_of_vitaminCsynthesis/ directory.
The boreoeutherian mammal ancestor. This will be mouse-{any species such that mouse-species has the boreoeutherian ancestor is the MRCA}.
I think this should work
-allowedAncestralNodes mm10-ailMel1,mm10-bosTau7,mm10-canFam3,mm10-equCab2,mm10-eriEur1,mm10-felCat5,mm10-myoLuc2,mm10-oviAri1,mm10-pteVam1,mm10-sorAra1,mm10-susScr3,mm10-turTru2,mm10-vicPac1

The reason for specifying them all is that

pig is listed first in the tree.nh --> if pig has aligning seq, then mm10-susScr3 will be the ancestor name
if pig is missing (assembly gap, other reason) but alpaca (vicPac1, which is second in the tree) is present, then this ancestor will be called mm10-vicPac1.

Pls give it a try

Dear Dr. @MichaelHiller ,
Thank you for your quick reply!
This species tree contains 50 species but the MAF file contains 60 species, they are inconsistent. This inconsistency caused error in the reconstruction of ancestral sequence (see below). How can I avoid this problem?:
I used this species tree to run the Maf2SpanningSeq_PRANK.perl script but it failed:
perl /xieduo/software/ForwardGenomics_20200324/scripts/Maf2SpanningSeq_PRANK.perl out.maf CDS053214  -runPrank -treeFile /bds.mpi-cbg.de/hillerlab/ForwardGenomics/loss_of_vitaminCsynthesis/tree.nh -keepTemporaryFiles -genomePath genomes -BDBFile testBDB1
retrieve 99 bp sequence for xenTro3 GL173375:430100-430199 from 2bit file: genomes/xenTro3.2bit
retrieve 102 bp sequence for macEug2 GL139024:11872-11974 from 2bit file: genomes/macEug2.2bit
retrieve 102 bp sequence for sarHar1 chr1_GL834967_random:216766-216868 from 2bit file: genomes/sarHar1.2bit
retrieve 102 bp sequence for loxAfr3 scaffold_22:7524042-7524144 from 2bit file: genomes/loxAfr3.2bit
retrieve 102 bp sequence for anoCar2 chrUn_GL344527:26117-26219 from 2bit file: genomes/anoCar2.2bit
retrieve 102 bp sequence for ochPri2 scaffold_80:294298-294400 from 2bit file: genomes/ochPri2.2bit
retrieve 102 bp sequence for ornAna1 Contig7426:18795-18897 from 2bit file: genomes/ornAna1.2bit
retrieve 102 bp sequence for speTri2 JH393485:472152-472254 from 2bit file: genomes/speTri2.2bit
retrieve 102 bp sequence for micMur1 scaffold_86763:4487-4589 from 2bit file: genomes/micMur1.2bit
retrieve 102 bp sequence for hetGla2 JH602071:22403740-22403842 from 2bit file: genomes/hetGla2.2bit
retrieve 102 bp sequence for rn5 chr15:48899714-48899816 from 2bit file: genomes/rn5.2bit
retrieve 102 bp sequence for susScr3 chr14:12481256-12481358 from 2bit file: genomes/susScr3.2bit
retrieve 102 bp sequence for melUnd1 JH556573:907725-907827 from 2bit file: genomes/melUnd1.2bit
retrieve 102 bp sequence for eriEur1 scaffold_375434:5585-5687 from 2bit file: genomes/eriEur1.2bit
retrieve 102 bp sequence for galGal4 chr3:104725221-104725323 from 2bit file: genomes/galGal4.2bit
retrieve 102 bp sequence for dipOrd1 scaffold_16090:8223-8325 from 2bit file: genomes/dipOrd1.2bit
retrieve 102 bp sequence for turTru2 JH477170:152063-152165 from 2bit file: genomes/turTru2.2bit
retrieve 28 bp sequence for myoLuc2 GL429768:39134474-39134502 from 2bit file: genomes/myoLuc2.2bit
retrieve 102 bp sequence for otoGar3 GL873593:3080745-3080847 from 2bit file: genomes/otoGar3.2bit
retrieve 102 bp sequence for canFam3 chr25:30038778-30038880 from 2bit file: genomes/canFam3.2bit
retrieve 102 bp sequence for felCat5 chrB1:49993618-49993720 from 2bit file: genomes/felCat5.2bit
retrieve 102 bp sequence for mm10 chr14:66008038-66008140 from 2bit file: genomes/mm10.2bit
retrieve 102 bp sequence for dasNov3 JH565766:103638-103740 from 2bit file: genomes/dasNov3.2bit
retrieve 102 bp sequence for monDom5 chr1:504228908-504229010 from 2bit file: genomes/monDom5.2bit
retrieve 102 bp sequence for echTel1 scaffold_321843:32718-32820 from 2bit file: genomes/echTel1.2bit
retrieve 102 bp sequence for tupBel1 scaffold_150490.1-215242:85968-86070 from 2bit file: genomes/tupBel1.2bit
retrieve 102 bp sequence for equCab2 chr2:56161551-56161653 from 2bit file: genomes/equCab2.2bit
retrieve 102 bp sequence for bosTau7 chr8:78860500-78860602 from 2bit file: genomes/bosTau7.2bit
retrieve 102 bp sequence for proCap1 scaffold_16290:7312-7414 from 2bit file: genomes/proCap1.2bit
retrieve 102 bp sequence for triMan1 JH594697:4001713-4001815 from 2bit file: genomes/triMan1.2bit
retrieve 102 bp sequence for vicPac1 scaffold_24478:41949-42051 from 2bit file: genomes/vicPac1.2bit
retrieve 102 bp sequence for melGal1 chr2:110544788-110544890 from 2bit file: genomes/melGal1.2bit
retrieve 102 bp sequence for cavPor3 scaffold_1:63491694-63491796 from 2bit file: genomes/cavPor3.2bit
retrieve 102 bp sequence for chrPic1 JH584860:2174318-2174420 from 2bit file: genomes/chrPic1.2bit
retrieve 102 bp sequence for oryCun2 chr2:42109078-42109180 from 2bit file: genomes/oryCun2.2bit
retrieve 102 bp sequence for ailMel1 GL192389.1:705067-705169 from 2bit file: genomes/ailMel1.2bit
total number of bases to be aligned for CDS053214: 3595
Running prank: set -o pipefail; prank -d=/dev/shm/prank.in.QRFkuj2HK.fa -t=/dev/shm/prank.in.QRFkuj2HK.fa.tree.nh -o=/dev/shm/prank.in.QRFkuj2HK.fa -showtree -showanc -prunetree -once -seed=10 > /dev/shm/prank.in.QRFkuj2HK.fa.prankout   ...
ERROR: grep "Reading the alignment file failed. Exiting" /dev/shm/prank.in.QRFkuj2HK.fa.prankout -c failed

Then I looked into the /dev/shm/prank.in.QRFkuj2HK.fa.prankout file:
-----------------
 PRANK v.170427:
-----------------

Input for the analysis
 - aligning sequences in '/dev/shm/prank.in.QRFkuj2HK.fa'
 - using alignment guide tree '/dev/shm/prank.in.QRFkuj2HK.fa.tree.nh'
 - option '+F' is not used; it can be enabled with '+F'
 - external tools available:
    MAFFT for initial alignment

Of the 36 sequences, only 26 match the tree leaves.
The data can be pruned to match the tree using the flag '-prunedata'. Now exiting.

The unmatched sequences are:
  xenTro3
  macEug2
  sarHar1
  anoCar2
  ornAna1
  melUnd1
  galGal4
  monDom5
  melGal1
  chrPic1

I think this was caused by the discordance between the tree(50 species) and the MAF file(60 species). How did you avoid this problem?
Thank you!
Best,
Duo

Dear Duo,
our 50-species tree excludes the non-mammalian species, such as xenTro3, galGal4, etc. We don't need them if we reconstruct the boreoeutherian ancestor.
Two ways to hopefully fix the prank crashes.

Pls use -prunedata as an additional flag when running prank.
Can you try to use mafSpeciesSubset (kent src code) to only keep the species listed in the tree.nh file? Then run the script as is.

Let me know if that works (or not).

Michael

Duo,
why don't you try to recapitulate the vision loss scenario https://bds.mpi-cbg.de/hillerlab/ForwardGenomics/loss_of_vision/
There you will get the tree, the CDS, and the multiple alignment. All should match.

Dear Dr. @MichaelHiller ,
Thank you!
I' ll give it a try give you feedback later!
Best,
Duo

Dear Dr. @MichaelHiller ,
I tried to recapitulate the the vision loss scenario, but the result also confused me (for convience, I random picked one element(CDS147317) to replicate your analysis).
There are two major differences:
First, the global IDs you computed, in general, are higher than mine. For example, the global IDs of canFam3 of yours and mine are 0.946902655 and 0.920353982 respectively. I question whether this difference caused by the different version of prank. I used prank-msa-170427. And how about you?
species	hiller	duo
anoCar2	NA	NA
bosTau7	NA	NA
canFam3	0.946902655	0.920353982
cavPor3	0.946902655	0.920353982
chrAsi1	0.92920354	0.938053097
equCab2	0.955752212	0.920353982
felCat5	0.96460177	0.920353982
galGal4	NA	NA
hg19	0.973451327	0.946902655
loxAfr3	0.96460177	0.973451327
macFas5	0.973451327	0.92920354
micOch1	0.884955752	0.85840708
mm10	0.89380531	0.876106195
monDom5	NA	NA
nanGal1	0.92920354	0.884955752
ochPri3	0.92920354	0.902654867
oryCun2	NA	0.690265487
otoGar3	0.92920354	0.902654867
rn5	0.902654867	0.867256637
speTri2	0.92920354	0.92920354
triMan1	0.955752212	0.982300885
xenTro7	NA	NA

Second,  the global ID of oryCun2 is absent in your result but not in mine. I examined the alignment(MAF) and found there are some gap in the sequence of oryCun2. So did you filter the sequences such as that by additional step(s)?
s oryCun2.chrUn0214         244005 83 +    422373 NNANGGGTNNGTGTTTGGGGGNNTTGNNNNGGTTGGGGNCNCTTGANGACCACTGCTTGNTGCCTTCCCCCAGGNCCTTCAGC

Here are the commads I used:
zcat conservedCDS.bed.gz|randomLines stdin 1 stdout >data.test

mafIndex out.maf out.maf.bb -chromSizes=/pub/database/hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/mm10.chrom.sizes
mafExtract out.maf.bb CDS147317.maf -regionList=data.test -leaveEdgeMeta
perl /PUB/USER/xieduo/software/ForwardGenomics_20200324/scripts/Maf2SpanningSeq_PRANK.perl CDS147317.maf CDS147317  -runPrank -treeFile /pub/database/bds.mpi-cbg.de/hillerlab/ForwardGenomics/loss_of_vision/tree.nh -keepTemporaryFiles -genomePath /USER/xieduo/01.B10K/07.Forward_genomics/test/loss_of_vision_test/genomes -BDBFile testBDB
perl /PUB/USER/xieduo/software/ForwardGenomics_20200324/scripts/GetGlobalAndLocalPercentID.perl testBDB CDS147317 -treeFile /pub/database/bds.mpi-cbg.de/hillerlab/ForwardGenomics/loss_of_vision/tree.nh  -allowedAncestralNodes mm10-loxAfr3,mm10-bosTau7,mm10-hg19,mm10-oryCun2,mm10-cavPor3  -global >identity

Do you have any idea? Did I leave out some important options when ran your scripts?
Thank you!
Best,
Duo

Dear Duo,
we have NA for rabbit, as the first maf block in this coding exon is missing in the maf (likely because the rabbit assembly is incomplete here). The reason for doing this is that if only a partial exon or CNE seq is given, this may lead to severe alignment errors.
Pls set -noMissingSeq for Maf2SpanningSeq_PRANK.perl to enable this (without this parameter, rabbit would not be excluded).
We have exactly the same prank version, so this does not explain the differences.
 Not sure where the difference are.
I have uploaded a script to read out the bdb file with the ancestral seqs.
Pls run
ReadBDB.perl testBDB
and compare if you get these exact same results:
value for CDS147317:
>mm10
CCATCTCGTTGAGGCTGGCGAAGCCTGGGGCCATGGGGGTGTGCTTAGGGGATTTGCCCAGGTTGGGGGCGCTCGAGGACCACTGCTTGCTTCCTTCCCCCAGGGCCTTGAGC
>mm10-rn5
CCATCTCATTGAGGCTGGCGAAGCCTGGGGCCATGGGGGTGTGCTTAGGGGATTTGCCCAGGTTGGGGGCGCTCGAGGACCACTGCTTGCTTCCTTCCCCCAGGGCCTTGAGC
>rn5
CCATCTCATTGAGGCTGGCGAAGCCTGGGGCCATGGGGGTGTGCTTAGGGGATTTGCCCAGGTTGGGGGCGCTCGAGGACCACTGCTTGCTTCCTTCCCCCAGGGCCTTGAGC
>mm10-micOch1
CCATCTCATTGAGGCTGGCGAAGCCTGGGGCCATGGGGGTGTGCTTGGGGGATTTGCCCAGGTTGGGGGCGCTTGAGGACCACTGCTTGCTTCCTTCCCCCAGGGCCTTGAGC
>micOch1
CCATCTCATTGAGGCTCGCAAAGCCTGGGGCCATGGGGGTGTGCTTGGGGGATTTGCCCAAGTTTGGGGCGCTTGAGGACCACTGCTTGCTTCCTTCCCCCAGGGCCTTGAGC
>mm10-nanGal1
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGGGTGTGCTTGGGGGATTTGCCCAGGTTGGGGGCGCTTGAGGACCACTGCTTGCTTCCTTCCCCCAGGGCCTTGAGC
>nanGal1
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGGGTGTGCTTGGGGGATTTGCCAAGGTTGGGGGCGCTTGAGGACCACTGCTTGCTTCCTTCCCCCAGGGCCTTGAGC
>mm10-speTri2
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGATTTGCCCAGGTTGGGGGCACTTGATGACCACTGTTTGCTTCCTTCCCCCAGGGCCTTCAGC
>speTri2
CCATCTCGTTGAGGCTGGCAAAACCAGGGGCGATGGGTGTGTGTTTGGGGGATTTTCCCAGGTTGGGGGCACTTGATGACCACTGTTTGCTCCCTTCCCCCAGAGTCTTCAGC
>mm10-cavPor3
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGATTTGCCCAGGTTGGGGGCACTTGATGACCACTGTTTGCTTCCTTCCCCCAGGGCCTTCAGC
>cavPor3
CCATCTCATTGAGGCTGGCAAAGCCGGGGGCGATGGGGGTGTGTTTGGGGGATTTGCCTAGGTTGGGGGCACTTGATGACCACTGTTTGCTTCCTTCCCCCAGGGCCTTGAGC
>mm10-oryCun2
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGATTTGCCCAGGTTGGGGGCACTTGATGACCACTGTTTGCTTCCTTCCCCCAGGGCCTTCAGC
>oryCun2
------------------------------CGATGGGTGTGTGTTTGGGGGACTTGCCCAGGTTGGGGGCGCTTGACGACCACTGCTTGCTGCCTTCCCCCAGGGCCTTCAGC
>oryCun2-ochPri3
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGACTTGCCCAGGTTGGGGGCGCTTGATGACCACTGCTTGCTTCCTTCCCCCAGGGCCTTCAGC
>ochPri3
CCATTTCGTTGAGGCTGGCGAAGGCAGGGGCGATGGGTGTATGTCTGGGGGACTTGCCCAGGTTGGGGGCGCTGGATGACCACTGCTTGCTTCCTTCCCCCAGGGCCTTCAGC
>mm10-hg19
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGATTTGCCCAGGTTGGGGGCACTTGATGACCACTGTTTGCTTCCTTCCCCCAGGGCCTTCAGC
>hg19
CCATCTCATTGAGGCTGGCAAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGACTTGCCCAGGTTGGGGGCACTTGATGACCACTGTTTGCTTCCTTCCCCCAGCCCCTTCAGC
>hg19-macFas5
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGACTTGCCCAGGTTGGGGGCACTTGATGACCACTGTTTGCTTCCTTCCCCCAGCCCCTTCAGC
>macFas5
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGACTTGCCCAGGTTGGGGGCACTCGATGACCACTGTTTGCTTCCTTCCCCCAGCCCCTTCAGC
>hg19-otoGar3
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGATTTGCCCAGGTTGGGGGCACTTGATGACCACTGTTTGCTTCCTTCCCCCAGGGCCTTCAGC
>otoGar3
CCATCTCATTGAGGCTGGCAAAGCCCGGGGCCATGGGTGTGTGTTTGGGGGATTTGCCCAGATTGGGGGCACTTGATGACCATTGTTTGCTTCCTTCCCCGAGGGTCTTCAGC
>mm10-equCab2
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGATTTGCCCAGGTTGGGGGCACTTGATGACCACTGTTTGCTTCCTTCCCCCAGGGCCTTCAGC
>equCab2
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGGGTGTGTTTGGGGGATTTGCCCAGGTTGGGGGCGCTCGATGACCACTGTTTGCTCCCTTCCCCCAGGGCCTTCAGC
>equCab2-felCat5
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGATTTGCCCAGGTTGGGGGCGCTTGATGACCACTGTTTGCTTCCTTCCCCCAGGGCCTTCAGC
>felCat5
CCATCTCATTGAGGCTGGCGAAGCCTGGGGCGATCGGTGTGTGTTTGGGGGATTTGCCCAGGTTGGGGGCACTGGATGACCACTGTTTGCTTCCTTCCCCCAGGGCCTTCAGC
>felCat5-canFam3
CCATCTCATTGAGGCTGGCGAAGCCTGGGGCGATCGGTGTGTGTTTGGGGGATTTGCCCAGGTTGGGGGCGCTTGATGACCACTGTTTGCTTCCTTCCCCCAGGGCCTTCAGC
>canFam3
CCATCTCGTTGAGGCTGGCGAAGCCTGGGGCTATCGGTGTGTGTTTGGGGGATTTGCCCAGGTTGGGGGCGCTTGATGACCACTGTTTGCTTCCTTCCCCCAGGGCCTTCAGC
>mm10-loxAfr3
CCATCTCATTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGACTTGCCCAGGTTGGGGGCACTTGATGACCACTGTTTGCTTCCTTCCCCCAGGGCCTTCAGC
>loxAfr3
CCATCTCGTTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGACTTGCCCAGGTTGGGGGCACTTGATGACCACTGTTTGCAGCCCTCCCCCAGGGCCTTCAGC
>loxAfr3-triMan1
CCATCTCGTTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGACTTGCCCAGGTTGGGGGCGCTTGATGACCACTGTTTGCTGCCTTCCCCCAGGGCCTTCAGC
>triMan1
CCATCTCGTTGAGGCTGGCAAAGCCAGGGGCGATGGGTGTGTGTTTCGGGGACTTGCCCAGGTTGGGGGCGCTTGATGACCACTGTTTGCTGCCTTCCCCCAGGGCCTTCAGC
>loxAfr3-chrAsi1
CCATCTCGTTGAGGCTGGCGAAGCCAGGGGCGATGGGTGTGTGTTTGGGGGACTTGCCCAGGTTGGGGGCGCTTGATGACCACTGTTTGCTGCCTTCCCCCAGGGCCTTCAGC
>chrAsi1
CCATCTCGTTGAGGCTGGCGAAGCCAGGGGCAATGGGTGTGTGTTTGGGGGACTTGCCCAGGTTGGGGGCGCTCGATGACCACTGTTTGCAGCCTTCCCCCAGCGTCTTCAGC
>mm10-monDom5
CCATCTCTGTGAGGCTGGCGAAGCCAGGGGCCATGGGCGTGTGCTTGGGAGACTTGCCCAGGTTGGGGGCACTGGATGACCACTGTTTGCATCCTTCTCCCAGGGCCTTCAGC
>monDom5
CCATCTCTGTGAGGCTGGAGAAGCCAGGGGCCATGGGCATGTGCTTGGGAGACTTGCCCAGGTTAGGGGCACTGGACGACCACTGCTTGCACCCCTCTCCCAGGGCCTTCAGC
>mm10-galGal4
CCATCTCTGTGAGGCTGGCGAAGCCAGGAGCCATGGGCGTGTGCTTCGGAGACTTGCCCAGGTTGGGGGCACTGGATGACCACTGTTTGCTGCCTTCTCCCAGAGCCTTCAGC
>galGal4
CCATCTCTGCTAAGCTGGTGAATCCTGGAAAAGCAGGCGCAGTTCTCTGGATCTTCCCTAGGTTTGGTGCACTGGATGACCACTGTTTGTATCCTTCTACCAAAGCTTTCAGA
>galGal4-anoCar2
CCATCTCTGTGAGGCTGGCGAAGCCCGGAGCCATGGGCGTGTGCTTCGGAGACTTGCCCAGGTTGGGAGCACTGGATGACCACTGTTTGCTGCCTTCTCCCAGAGCCTTCAGC
>anoCar2
CCATCTCGTTGAGGCTAGCAAAGCCCCCAGCCAACGGCATGTGCTTCGGAGACTTGCCCAGGTTGGGAGCACTGGAGGACCACTGCTTGCTGCCTTCAGCCAGAGACTTCAAC
>mm10-xenTro7
CCATTTCAGTGAGGCTGGCAAACCCAACACTTATGGGAGTGTGCTTAGGAGATTTGCCCAGGTTGGGAGCACTGCATGACCACTGTTTGCTGCCTTCTCCAAGAGTCTTCAGC
>xenTro7
CCATTTCAGTGAGGCTGGCAAACCCCACACTTATGGGAGTGTGCTTAGGAGATTTGCCCAGGTTGGGAGCACTGCTTGACCACTGTTTGCTGCCTTCTCCAAGAGTCTTCAGC

Dear Dr. @MichaelHiller ,
Thank you for your information!
I found my ancestor sequences are different from yours(see below). That is, we used the same inputs(the sequences of extant species) and the same version of prank, but produced different ancestral sequences. It confused my again.
faCmp -sortName my.fa hiller.fa
sorting my.fa
sorting hiller.fa
equCab2-felCat5 in my.fa differs from equCab2-felCat5 at hiller.fa at base 25 (t != a)
felCat5-canFam3 in my.fa differs from felCat5-canFam3 at hiller.fa at base 19 (a != g)
galGal4-anoCar2 in my.fa differs from galGal4-anoCar2 at hiller.fa at base 8 (t != g)
hg19-macFas5 in my.fa differs from hg19-macFas5 at hiller.fa at base 19 (a != g)
hg19-otoGar3 in my.fa differs from hg19-otoGar3 at hiller.fa at base 19 (a != g)
loxAfr3-chrAsi1 in my.fa differs from loxAfr3-chrAsi1 at hiller.fa at base 7 (a != g)
loxAfr3-triMan1 in my.fa differs from loxAfr3-triMan1 at hiller.fa at base 90 (a != t)
mm10-cavPor3 in my.fa differs from mm10-cavPor3 at hiller.fa at base 19 (a != g)
mm10-equCab2 in my.fa differs from mm10-equCab2 at hiller.fa at base 25 (t != a)
mm10-galGal4 in my.fa differs from mm10-galGal4 at hiller.fa at base 9 (c != t)
mm10-hg19 in my.fa differs from mm10-hg19 at hiller.fa at base 19 (a != g)
mm10-loxAfr3 in my.fa differs from mm10-loxAfr3 at hiller.fa at base 7 (g != a)
mm10-micOch1 in my.fa differs from mm10-micOch1 at hiller.fa at base 19 (a != g)
mm10-monDom5 in my.fa differs from mm10-monDom5 at hiller.fa at base 7 (a != t)
mm10-nanGal1 in my.fa differs from mm10-nanGal1 at hiller.fa at base 31 (c != g)
mm10-oryCun2 in my.fa differs from mm10-oryCun2 at hiller.fa at base 4 (t != c)
mm10-speTri2 in my.fa differs from mm10-speTri2 at hiller.fa at base 19 (a != g)
mm10-xenTro7 in my.fa differs from mm10-xenTro7 at hiller.fa at base 25 (c != a)
oryCun2-ochPri3 in my.fa differs from oryCun2-ochPri3 at hiller.fa at base 19 (a != g)
my.fa and hiller.fa have 19 sequences that differ

Then I investigated where our ancestral sequences are different. I found there may be some differences in the inference of ancestral sequence. For example,  in mm10-micOch1, we can see

At first differential site, your ancestral base is same as the ingroup base and mine is same as outgroup base: the ingroup(mm10 and rn5) and outgroup(micOch1) is G and  A respectively, but your infered ancestral base is G and mine is A. However, the second differential site showed a different pattern: the ingroup(mm10 and rn5) is A and outgroup(micOch1) is G, then your infered ancestral base is G and mine is A.
Here is my prank command reported by Maf2SpanningSeq_PRANK.perl
Running prank: set -o pipefail; prank -d=/dev/shm/prank.in.1KghANguP.fa -t=/dev/shm/prank.in.1KghANguP.fa.tree.nh -o=/dev/shm/prank.in.1KghANguP.fa -showtree -showanc -prunetree -once -seed=10 > /dev/shm/prank.in.1KghANguP.fa.prankout

I have uploaded my inputs and outputs of prank files here.
Would you please compare where my results are different yours?
Best,
Duo

I guess here is the key difference. Input.fa (except the sort order of the species) and tree is the same.
But prankout differs:
my output
-----------------
 PRANK v.170427:
-----------------

Input for the analysis
 - aligning sequences in '/tmp//prank.in.bkL1eVBfm.fa'
 - using alignment guide tree '/tmp//prank.in.bkL1eVBfm.fa.tree.nh'
 - option '+F' is not used; it can be enabled with '+F'
 - external tools available:
    MAFFT for initial alignment
    Exonerate for alignment anchoring
    BppAncestor for ancestral state reconstruction

Generating multiple alignment: iteration 1.

Alignment score: 170

Writing
 - alignment guide tree to '/tmp//prank.in.bkL1eVBfm.fa.best.dnd'
 - alignment to '/tmp//prank.in.bkL1eVBfm.fa.best.fas'
 - ancestors to '/tmp//prank.in.bkL1eVBfm.fa.best.anc.fas' and '/tmp//prank.in.bkL1eVBfm.fa.best.anc.dnd'

Analysis done. Total time 1s

Your output

-----------------
 PRANK v.170427:
-----------------

Input for the analysis
 - aligning sequences in '/dev/shm/prank.in.1KghANguP.fa'
 - using alignment guide tree '/dev/shm/prank.in.1KghANguP.fa.tree.nh'
 - option '+F' is not used; it can be enabled with '+F'
 - external tools available:
    MAFFT for initial alignment

Generating multiple alignment: iteration 1.

Alignment score: 347

Writing
 - alignment guide tree to '/dev/shm/prank.in.1KghANguP.fa.best.dnd'
 - alignment to '/dev/shm/prank.in.1KghANguP.fa.best.fas'
 - ancestors to '/dev/shm/prank.in.1KghANguP.fa.best.anc.fas' and '/dev/shm/prank.in.1KghANguP.fa.best.anc.dnd'

Analysis done. Total time 8s

Looks like you are somehow missing
Exonerate for alignment anchoring
BppAncestor for ancestral state reconstruction
BppAncestor is key for ML-based reconstruction (my understanding).
Pls install that and check if this explains the difference.
Michael

Dear Dr. @MichaelHiller,
Thank you information and patience again!
I have replicated your results now, after I downloading the Pre-compiled executables for Linux version of prank. Do you used this version instead of compling prank from source code? This is the key difference. I installed prank from source code, and installed exonerate and bpp before. But I got the same results as previous when I just add these software into path. However, I obtained the same results as yours(please pay attention to the Alignment score) when I used the Pre-compiled executables version of prank.
I think this is caused by the different versions of bppancestor. My bppancestor is version 2.4.0 but the Pre-compiled version bppancestor  is version 0.5.0 (see below).
When I ran the prank installed from source:
The verisons of exonerate and bppancestor
exonerate from exonerate version 2.2.0
Using glib version 2.4.7
Built on Oct 17 2008
***
******************************************************************
*     Bio++ Ancestral Sequence Reconstruction, version 2.4.0     *
* Authors: J. Dutheil                       Created on: 10/09/08 *
*          B. Boussau                       Last Modif: 19/02/18 *
******************************************************************

The output of prank:
-----------------
 PRANK v.170427:
-----------------

Input for the analysis
 - aligning sequences in '/dev/shm/prank.in.BxDS0UApP.fa'
 - using alignment guide tree '/dev/shm/prank.in.BxDS0UApP.fa.tree.nh'
 - option '+F' is not used; it can be enabled with '+F'
 - external tools available:
    MAFFT for initial alignment
    Exonerate for alignment anchoring
    BppAncestor for ancestral state reconstruction

Generating multiple alignment: iteration 1.

Alignment score: 347

Writing
 - alignment guide tree to '/dev/shm/prank.in.BxDS0UApP.fa.best.dnd'
 - alignment to '/dev/shm/prank.in.BxDS0UApP.fa.best.fas'
 - ancestors to '/dev/shm/prank.in.BxDS0UApP.fa.best.anc.fas' and '/dev/shm/prank.in.BxDS0UApP.fa.best.anc.dnd'

Analysis done. Total time 5s

However, when I used the Pre-compiled executables for Linux version, I got the same results with yours:
The version of exonerate and bppancestor
exonerate from exonerate version 2.2.0
Using glib version 2.4.7
Built on Oct 17 2008
Branch: unnamed branch
***
******************************************************************
*     Bio++ Ancestral Sequence Reconstruction, version 0.5.0     *
* Authors: J. Dutheil                       Created on: 10/09/08 *
*          B. Boussau                       Last Modif: 17/06/11 *
******************************************************************

The output of prank:
-----------------
 PRANK v.170427:
-----------------

Input for the analysis
 - aligning sequences in '/dev/shm/prank.in.4RpdYKxha.fa'
 - using alignment guide tree '/dev/shm/prank.in.4RpdYKxha.fa.tree.nh'
 - option '+F' is not used; it can be enabled with '+F'
 - external tools available:
    MAFFT for initial alignment
    Exonerate for alignment anchoring
    BppAncestor for ancestral state reconstruction

Generating multiple alignment: iteration 1.

Alignment score: 170

Writing
 - alignment guide tree to '/dev/shm/prank.in.4RpdYKxha.fa.best.dnd'
 - alignment to '/dev/shm/prank.in.4RpdYKxha.fa.best.fas'
 - ancestors to '/dev/shm/prank.in.4RpdYKxha.fa.best.anc.fas' and '/dev/shm/prank.in.4RpdYKxha.fa.best.anc.dnd'

Analysis done. Total time 9s

Anyway, we finally fixed this problem. Thank you for your patience! I think you can add some lines to a readme of your script directory, and I would like to reorganize this issue and my commands to a readme if you need! I think it is necessary, because there are some tricks when running these script.
Thank you!
Best,
Duo

Hi Dou,
good catch, we are indeed running bppancestor

Bio++ Ancestral Sequence Reconstruction, version 0.5.0     *

Authors: J. Dutheil                       Created on: 10/09/08 *

     B. Boussau                       Last Modif: 17/06/11 *

I guess we have to update prank and likely give it a fresh installation to get the lastest bppancestor version.
Glad that the differences are resolved.
Thanks
Michael


Custom headers in package requests

The issue I face is the following. We have some mfe applications stored in an s3 bucket. We want to protect the code stored in the s3 bucket with an authorizer that will check if an authorization token exists in the request. Is there some way to include a custom header containing this auth token in every request of the mfe packages? I have managed to include the auth token for the remoteEntry.js request using a Promise Based Dynamic Remotes approach combined with XHR requests, but this solution can't work because we need the auth token for every request of every file stored in the s3 bucket, not just the remoteEntry.js files.
Another thought would be to include the token as a url param, but I end up, that there is the same issue as before. I can't think of a way that the url param will be included in all package requests and not only in the remoteEntry.js one.
Is there a solution for this? If not, is it planned to support such functionality in the future?

You can override the chunk loading global on node.js side so all imports use your fetch client over mine.
globalThis.webpackChunkLoad
***/ 				      const vm = require('vm');
/******/ 				      (globalThis.webpackChunkLoad || globalThis.fetch || require("node-fetch"))(url).then(function (res) {
/******/ 				        return res.text();
/******/ 				      }).then(function (scriptContent) {
/******/ 				        try {
/******/ 				         const m = require('module');
/******/
/******/ 				         const remoteCapsule = vm.runInThisContext(m.wrap(scriptContent), 'node-federation-loader-' + name + '.vm')
/******/ 				         const exp = {};
/******/ 				         let remote = {exports:{}};
/******/ 				         remoteCapsule(exp,require,remote,'node-federation-loader-' + name + '.vm',__dirname);
/******/ 				         remote = remote.exports || remote;
/******/ 				          globalThis.__remote_scope__[name] = remote[name] || remote;
/******/ 				          globalThis.__remote_scope__._config[name] = url;
/******/ 				          callback(globalThis.__remote_scope__[name])
/******/ 				        } catch (e) {
/******/ 				          console.error('executeLoad hit catch block', e);
/******/ 				          e.target = {src: url};
/******/ 				          callback(e);
/******/ 				        }
/******/ 				      }).catch((e) => {
/******/ 				        e.target = {src: url};
/******/ 				        callback(e);
/******/ 				      });

So I just need to declare a function globalThis.webpackChunkLoad? Where can i find your implementation of fetch so I can use it as a guideline? And also at which location of my code should I place this function?

my implementation is globalThis.webpackChunkLoad = require('node-fetch')
its vanillia, what it expects is fetch to return a response, then i call res.text() and return that.
globalThis.webpackChunkLoad = (url)=> myCustomFetch({url,whatever})

then webpack will do this with it. globalThis.webpackChunkLoad(url).then(res=>res.text()).then(wrapModuleForVM).then(execteWrappedModuleInVM)


Set up CI with Azure Pipelines

OPS Build status updates of commit 26227ac:
:clock10: Preparing: average preparing time is 1 min(s) 59 sec(s)

OPS Build status updates of commit 26227ac:
:clock10: Incremental building: average incremental building time is 19 sec(s)

OPS Build status updates of commit 26227ac:
:white_check_mark: Validation status: passed

File
Status
Preview URL
Details

azure-pipelines.yml
:white_check_mark:Succeeded

For more details, please refer to the build report.
Note: If you changed an existing file name or deleted a file, broken links in other files to the deleted or renamed file are listed only in the full build report.


Request for support for loock.lock.t1pro XMZNMSTO3YD

I use the loock.lock.t1pro XMZNMSTO3YD，and I try to make it work by myself.
I find the this(https://github.com/AlexxIT/XiaomiGateway3/issues/973#issue-1574378322)， but the problem still hasn't been resolved。
And then i find this snippet in device https://github.com/AlexxIT/XiaomiGateway3/blob/72e26fcc03741d624241e281eeefb8d51ca46fd8/custom_components/xiaomi_gateway3/core/converters/devices.py#L1493
so， i just fix the num 2444 to 3899， and change the model name。
unfortunately ，it doesn‘t work。

How can i fix it？

 I can see that lock works without any problems with default converters.

@Blear thanks! I can see that lock works without any problems with default converters.

yes,that's good ,I tested the automation of the door lock and it runs very well .
I think this issue can be closed now..

 But the result will still be the same

Thanks to you, I will write a more accurate converter for this model. But the result will still be the same

The sensor Contact doesn't seem to work, the status is always closed when the door is open

Can't do anything with it. Lock sends this messages

Can't do anything with it. Lock sends this messages

oh, that's okay .the automated scenarios are enough for me to use

https://github.com/AlexxIT/XiaomiGateway3/releases/tag/v4.0.0


Better defaults and user modification of defaults through CR

For issue #37
Adding couchbase deployment
make operator and pod versions and urls variables changeable by CR
move default vars to defaults dir
making operator and pod versions and URLs user-configurable

rerun smoke

/rerun

/rerun all

/rerun all

/rerun all

/rerun minishift

/rerun all

/rerun all

Seems to be failing on my 3.11 minishift environment at creating clusterrolebinding for the cb-operator :/ despite the other clusterrole, clusterrolebinding being applied successfully.

Please apply rebase and also update the docs reflecting the new changes.

Updates done, and tests passed locally on minishift.

Looks good for most part, we just need to edit the templates to make use of benchmark namespace instead of defaulting to current namespace. Another way we can do this, for now we can merge this if I'm able to get it to work locally and then make changes in #50

We currently use meta.namespace across other workloads, and the existing CI system (minishift, at least) would run tests within the benchmark namespace context already. I don't like the idea of hard-coding the benchmark namespace all over the place; I already don't like how much of this is in the deploy/ directory files.

Test passed for me on local minikube (after dealing with lab-related network annoyances)

Test passed on minishift if all other images were cleared from cache and rerun thrice. Will merge this as discussion related to namespace can take place at #54 .


[google_sign_in] PlatformException(sign_in_failed, com.google.android.gms.common.api.ApiException: 10: , null, null)

After run await GoogleSignIn().signIn();
get in Console (Nexus 5X_API 32:5554)
PlatformException(sign_in_failed, com.google.android.gms.common.api.ApiException: 10: , null, null)
D/TransportRuntime.SQLiteEventStore( 6791): Storing event with priority=DEFAULT, name=FIREPERF for destination cct
D/TransportRuntime.JobInfoScheduler( 6791): Upload for context TransportContext(cct, DEFAULT, MSRodHRwczovL2ZpcmViYXNlbG9nZ2luZy1wYS5nb29nbGVhcGlzLmNvbS92MS9maXJlbG9nL2xlZ2FjeS9iYXRjaGxvZ1xBSXphU3lDY2traUg4aTJaQVJ3T3MxTEV6RktsZDE1YU9HOG96S28=) is already scheduled. Returning...

Hi @Joldersman, Thanks for filing the issue. Please ensure that you have added the sha1 fingerprint in the firebase console. if the issue persists please share the output of flutter doctor -v the version of the google_sign_in plugin along with the steps to reproduce the issue.
duplicate of https://github.com/flutter/flutter/issues/56235 (closed)


Update Kontrol documentation

We should bring our documentation (https://docs.runtimeverification.com/kontrol) up to date.
There're features that are not yet covered there, including external computation, CSE, new flags such as kontrol build --no-minimize, and many others.

I think we should plan a structure in a branch, holding everything we'd like to express. Then, it will be easier to complete our doc step by step by checkouting this branch.
What do you think?


JOSS Review Comments

Hello, and congrats on your JOSS submission! Overall, the package is in a very good state, the paper is well written, and I've ticked most of the items on my reviewer checklist already.
I have a few minor comments that shouldn't take too long to address. Please let me know if these make sense, I'm happy to discuss them further if needed:
The Paper

[x] 1. Generally, it is advisable to include code examples in the README.md and the documentation, but not in the JOSS paper, as the interface might change and the examples might become outdated. However, this seems unlikely in your case; I encourage you to consider the point, but I won't insist on it.
[x] 2. There is, however, a small issue with the code examples; see my comments in the "Repository" section.

The Repository

[x] 1. Please add a link to the documentation in the repository's About section; here is a guide on how to do so.
[x] 2. I tried following the code examples given in README.md (as well as in the paper and the documentation). Seems that the use of I as a shorthand for the identity matrix requires me to import LinearAlgebra.jl. You do mention later on that LinearAlgebra is a dependency of the package, but the code examples should work as standalone pieces of code. Please add using LinearAlgebra to the examples.
[x] 3. The text in the Dependencies section of README.md is confusing; you don't "need to install" anything, as the Julia package manager install dependencies for you when you install the package via ]add MultiPrecisionArrays. Please clarify this.
[x] 4. The community guidelines need to be improved. You can add issue templates (such as these, which were created automatically following this tutorial so that bug reports and other issues are more concise and targeted.
[x] 5. Related also to the community guidelines, I was surprised to see that you specifically ask potential contributors not to make pull requests in README.md! What is the reason for this?

The Code

[x] 1. An alternative solution to the missing using LinearAlgebra on the examples would be to re-export some of the functionality of LinearAlgebra for the user's convenience. You can use the Reexport.jl package for this. If you just want to re-export the identity, you can add using Reexport; @reexport import LinearAlgebra.I to the Examples module. If you think that the users of your package are likely to need the full functionality of LinearAlgebra, you could instead add using Reexport; @reexport using LinearAlgebra to your main module, but this might be overkill.
[x] 2. I noticed there's exactly one line missing test coverage, and it's an end statement. I have no idea why it's not covered, when the loop code has been executed, so I suspect a bug in the coverage code. Out of curiosity, I have asked about this on the Julia discourse.
[x] 3. There are many commented lines in the code. Some of these are explanatory (e.g. "# Scale first column" in src/Factorizations/hlu!.jl), but some are just old commented code (e.g. "#    residterm ? tf=1.0 : tf=.9" in src/Solvers/mpkrir.jl). The latter are not acceptable, as they only clutter the code and confuse the user, and are unnecessary, as old code can always be recovered thanks to version control. If you find the commented old code helpful for development, I invite you to create a separate development branch where the code can be "messy", but contributions to the main branch should always be "tidy" for the sake of code readability.
[x] 4. There is no consisting code formatting across the repository. You should be using JuliaFormatter, or an equivalent tool, to enforce consistent formatting on your main branch. One easy way to do so (not necessarily the optimal way) is to add a format command to your unit tests, such as this one, which enforces a given configuration across the entire codebase; I find this approach helpful as I always manually run my unit tests before committing changes to a branch.

The Documentation

[x] 1. There is, again, a small issue with the code examples; see my comments in the "Repository" section.

Hi @rafaelbailo . Thanks again for the thoughtful review. Here is a point-by-point reply to your report. I have mostly followed your suggestions. The exception is the "no PR please" statement in the readme. I have explained that in my response
-- Tim
The Paper

Code examples in JOSS papers: I eliminated that section as you suggested.

The Repository

link to documentation in About section: Done

LinearAlgebra.jl: I used your idea about Reexport.jl

Dependencies section: I reworded the part about "install"

Community guidelines:
A) Issue templates: Done
B) I would like to avoid PRs until I get QR and
nonlinear solvers finished sometime in the next 6-12 months. These
two things are tricky and I do not want to have to deal with PRs at
the same time. After that's done, PRs will be welcome.

The Code:

LinearAlgebra.jl alternative: Done

CodeCov has done that to me before. I think it's harmless.

Stray comments: Cleaned up

Formatting: Done

Docs: fixed in item 1 of Repository

Hi @ctkelley, thank you for the prompt response and all the work! Fair enough about the PRs, I completely understand that you don't want to juggle PRs while working on core components of the package. I'm closing this as completed and recommending acceptance on the review issue. 👍🏻

Thanks again.
— Tim
On Wed, Sep 25, 2024 at 3:27 AM Rafael Bailo @.***>
wrote:

Hi @ctkelley https://github.com/ctkelley, thank you for the prompt
response and all the work! Fair enough about the PRs, I completely
understand that you don't want to juggle PRs while working on core
components of the package. I'm closing this as completed and recommending
acceptance on the review issue. 👍🏻
—
Reply to this email directly, view it on GitHub
https://github.com/ctkelley/MultiPrecisionArrays.jl/issues/51#issuecomment-2373273980,
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You are receiving this because you were mentioned.Message ID:
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preventChanges - add an option

preventChanges presently throws is a patch is mutating given fields. An option to just remove those fields from context.data and continue with the patch may be useful.

The cleanest implemention may be a discardChanges hook. That would be yet another tiny hook. Any better suggestions?

Changed signature in Buzzard version: https://feathers-plus.github.io/v1/feathers-hooks-common/index.html#preventchanges . Deprecated old signature.


fix(suspense): don't run post flush callbacks in suspended component (fix #6811)

As described in #6811 post flush watchers are executed in suspended components that are currently being switched out. This has huge implications for example in routing, where switching pages executes both post flush watchers both on the new page and also on the old page. This PR fixes this issue and causes post flush watchers to be executed ONLY on the new component.
Closes #6811

Fixes #6811

So apparently this completely breaks post-flsuh watchers in Suspense. I'll add more tests and try to do a proper fix.

@adamjedlicka Is it still your intention to continue working on this PR? If I've understood your previous comment, it sounds like this isn't currently a valid fix. If you don't have time to work on it then should it maybe be closed?


Firebase auth error -23, "limits exceeded" on staging server

I can authenticate the user on iOS without any issues, so Firebase is accepting auth requests for this user. It is working for iOS auth on both our staging AND production Firebase URLs.
However, on Android simulator/device I cannot login with same user on the staging Firebase.
I have tried using older login example with 'com.firebase:firebase-client-android:2.0.3+'  as we well as newer example using Google GSM and com.google.firebase:firebase-auth:9.0.2. Both return auth error -23 with message "limits exceeded".
Does this require some additional settings or config in the Firebase dashboard?
Thanks,
Anthony

Update - we enabled Google auth as well as email/pwd in our Firebase dashboard under Authorization -> Sign In Method. Also added SHA1 from ~/.android/debug.keystore. Here is the latest stack trace:
06-13 16:23:59.599 10460-10460/com.helium.mobile.android.pulse D/com.helium.mobile.android.pulse.util.Preferences: signInWithEmail:onComplete:false 06-13 16:24:02.373 10460-10530/com.helium.mobile.android.pulse E/DynamiteModule: Failed to load module descriptor class: Didn't find class "com.google.android.gms.dynamite.descriptors.com.google.firebase.auth.ModuleDescriptor" on path: DexPathList[[zip file "/data/app/com.helium.mobile.android.pulse-1/base.apk"],nativeLibraryDirectories=[/data/app/com.helium.mobile.android.pulse-1/lib/x86, /vendor/lib, /system/lib]] 06-13 16:24:06.523 10460-10460/com.helium.mobile.android.pulse W/com.helium.mobile.android.pulse.util.Preferences: signInWithEmail                                                                                com.google.firebase.FirebaseTooManyRequestsException: We have blocked all requests from this device due to unusual activity. Try again later.                                                                                at com.google.android.gms.internal.zzacq.zzbN(Unknown Source)                                                                                at com.google.android.gms.internal.zzacn$zzg.zza(Unknown Source)                                                                                at com.google.android.gms.internal.zzacy.zzbO(Unknown Source)                                                                                at com.google.android.gms.internal.zzacy$zza.onFailure(Unknown Source)                                                                                at com.google.android.gms.internal.zzact$zza.onTransact(Unknown Source)                                                                                at android.os.Binder.execTransact(Binder.java:453)

Here is more info on how I'm calling the Firebase auth:
Init mAuth per google Firebase example:
mAuth = FirebaseAuth.getInstance();
mAuthListener = new FirebaseAuth.AuthStateListener() {             @Override             public void onAuthStateChanged(@NonNull FirebaseAuth firebaseAuth) {                 FirebaseUser user = firebaseAuth.getCurrentUser();                 if (user != null) {                     // User is signed in                     Log.d(TAG, "onAuthStateChanged:signed_in:" + user.getUid());                 } else {                     // User is signed out                     Log.d(TAG, "onAuthStateChanged:signed_out");                 }                 //updateUI(user);             }         };
Initially user is NULL so onAuthStateChanged:signed_out gets logged. Next, after signing in with email and pwd (same user credentials are working with iOS Firebase SDK) the onCompleteListener is called and the Exception is produced (shown in last comment) in the if (!task.isSuccessful()) block:
mAuth.signInWithEmailAndPassword(email, pwd)                 .addOnCompleteListener(this, new OnCompleteListener<AuthResult>() {                     @Override                     public void onComplete(@NonNull Task<AuthResult> task) {                         Log.d(TAG, "signInWithEmail:onComplete:" + task.isSuccessful());                         if (!task.isSuccessful()) {                             Log.w(TAG, "signInWithEmail", task.getException());                             Toast.makeText(SignInActivity.this, "Authentication failed.",  Toast.LENGTH_LONG).show();                         }                     }                 });

@mutablestudio is it possible you have an infinite loop in your application somewhere?  In your logs the Firebase server is saying it's getting too many requests from your client.

@mutablestudio it's been a few weeks since the last reply on this thread and I have heard no additional reports of this issue.  I am going to mark this as closed, please re-open this issue if you are still stuck.


fix: condition to not create sm credentials

Description
https://github.com/terraform-ibm-modules/terraform-ibm-cos/issues/695
Release required?

[x] No release
[ ] Patch release (x.x.X)
[ ] Minor release (x.X.x)
[ ] Major release (X.x.x)

Release notes content

Run the pipeline
If the CI pipeline doesn't run when you create the PR, the PR requires a user with GitHub collaborators access to run the pipeline.
Run the CI pipeline when the PR is ready for review and you expect tests to pass. Add a comment to the PR with the following text:
/run pipeline

Checklist for reviewers

[ ] If relevant, a test for the change is included or updated with this PR.
[ ] If relevant, documentation for the change is included or updated with this PR.

For mergers

Use a conventional commit message to set the release level. Follow the guidelines.
Include information that users need to know about the PR in the commit message. The commit message becomes part of the GitHub release notes.
Use the Squash and merge option.

/run pipeline

/run pipeline

/run pipeline

/run pipeline

:tada: This issue has been resolved in version 8.10.2 :tada:
The release is available on:

GitHub release
v8.10.2

Your semantic-release bot :package::rocket:


NEW: Clarifying prerequisites

Current coverage is 51.37% (diff: 100%)

Merging #66 into master will not change coverage

@@             master        #66   diff @@
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  Files            19         19
  Lines          1851       1851
  Methods           0          0
  Messages          0          0
  Branches          0          0
==========================================
  Hits            951        951
  Misses          779        779
  Partials        121        121

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Remove Nth Node From End of List

Great work @ak84349 please give this repo a star if it really helped you to complete your PR.
Also follow me for follow back if you want to get connected with me for any such open source contribution program. Thank you 😊


Add protractor support

The seed project should integrate protractor and a couple of example e2e tests using it.

Fixed


Articles on dart-lang.org have scary "obsolete" message

For example https://www.dartlang.org/articles/libraries/zones. This is the top Google result for "dart zones", but it has a big red error message on the top saying "Content of this page might be obsolete."
I fear this will turn away users if we don't have an appropriate substitute.

@kwalrath

I'm not sure what to do about the articles. The banners are there because most of the articles do have some obsolete content. In fact, most of the articles would have been published on Medium, rather than dartlang.org, if that had been an option at the time. Many of the writers are not inclined to update their articles and/or are no longer with Google.
How about I get each article reviewed by the most knowledgable people I can find on the subject, and then add a note at the top of each article that addresses the following points:

Who should read (or not read) the article, and why (or why not).
What's changed since the article was written.
What's still true.
What's important.
Where else they can find information on this topic.

For articles that have important content, we should consider either updating the article or writing more maintainable documentation somewhere — perhaps in the dart-lang/sdk repo, where engineers working on the source code are more likely to encounter and update it.
What do you think?

That sounds good to me.  For Zones (@lrhn), I don't think we actually changed much at all for Dart 2.

I think that's a solid solution. It will take time however, is there something we can do avoid scaring users in the meantime though? Perhaps changing the message to something like "This is a community-contributed article and may be out of date," and using a yellow banner instead of red.

Sure, we can change the banner easily. I'll do that today.

https://github.com/dart-lang/site-www/issues/663 is the tracking bug for reviews.

The less scary warnings are up, e.g. https://www.dartlang.org/articles/libraries/zones:

(although that screenshot makes me realize that I need to change the sides of the page from red to yellow)

Thanks! I think that's much less likely to scare away a potential user who is just Googling for documentation.

I think this can be closed now?

Yes, we can close it since dart-lang/site-www#663 is tracking this.


cmd/compile: spurious error for goto jumping over non-var declarations

The compiler issues an error message for a goto jumping over type or const declaration, like
package main

func main() {
    goto L1
    type A int
L1:
}

The specification forbids only jumping over variable declarations.

/cc @griesemer @alandonovan @ianlancetaylor

Fails on gccgo as well:
/home/iant/foo.go:4:5: error: goto jumps over declaration of ‘A’
goto L1
^
/home/iant/foo.go:5:10: note: ‘A’ defined here
type A int
^

Passes with gotypes.

Exact dup of #8042.
Also see the old thread for a tentative fix (it was reverted but maybe it's salvageable).

Closing as duplicate of #8042.


Add simple arm example

Extended the spawn scripts to support loading custom models in the mbzirc_custom directory (similar to the way we added support for loading custom sensors in https://github.com/osrf/mbzirc/pull/105)
Added a new mbzirc_simple_arm example model that can be attached to the USV. The install cmds in the CMakelists.txt is commented out on purpose as this is supported to be an example only.
Other changes: updated naming style of a few functions to be snake_case to be consistent with other functions
Here is the accompanying documentation page on the wiki with instructions on testing the simple arm model at the end of the page:
https://github.com/osrf/mbzirc/wiki/Custom-Arm

Did you forget to push the mbzirc_simple_arm/launch/ directory?

oops, just added the bridge launch file. 8246a22

Did you forget to push the mbzirc_simple_arm/launch/ directory?

oops, just added the bridge launch file. 8246a22

Apparently there are some conflicts.


Add configurable options to RES Tool

Suggested already on initial release
https://www.reddit.com/r/Enhancement/comments/2kly10/i_made_a_cross_platform_application_for_backing/cmir4k1

Done in https://github.com/Nikola-K/RESTool/commit/bb011094f7b2e4f7d16b19da13b23616bf38e935


WIP: Call create api plugin in sdk command

Description
Call the plugin to execute the sdk command.
Steps to check it locally

Run operator-sdk add api --api-version=cache.example.com/v1alpha1 --kind=Memcached in a Helm project. It should create the API.

/hold
Blocked by: https://github.com/operator-framework/operator-sdk/pull/3229

It will change. Closing for now but I might will re-open this one.


fix: use the right stage name in the logs

when retrieving the running build logs, the stage name used to be hardcoded to "pipeline".
this change set the stage name to its real value.
this is needed by https://github.com/jenkins-x/jx-pipelines-visualizer/pull/72 to map the logs by stages/steps in the UI

Hi @vbehar. Thanks for your PR.
I'm waiting for a jenkins-x or todo 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.
Once the patch is verified, the new status will be reflected by the ok-to-test label.
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 jenkins-x/lighthouse repository.

Hi @vbehar. Thanks for your PR.
I'm waiting for a jenkins-x or todo 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.
Once the patch is verified, the new status will be reflected by the ok-to-test label.
I understand the commands that are listed here.

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feat: added toast for run succesfull query

Description

Added toast to show query successful run after loading

Related issue(s)
 feat #37

@prash240303 kindly rebase and resolve the conflicts.
The toast also occurs when loading the site for the first time. It should occur only when query is being run.

fixed it


Uncaught SyntaxError: Unexpected token < in JSON at position 0

I followed the steps in the readme file and got this error whenever I run the application.
Uncaught SyntaxError: Unexpected token < in JSON at position 0
at JSON.parse ()
at HTMLIFrameElement. (index.js:212)
Any advice? Thank you in advance!

@markstur take a look at this when you're back

Closing as cannot reproduce.  Wonder if this was a temporary error w/ a not-ready state that is fixed on retry.  Could use more info.


Add robots.txt & sitemap.xml

I have added a basic robots.txt.
Adding robots.txt requires the project to have a sitemap.xml file for SEO purposes, so I have added a sitemap.xml file as well.
This PR resolves #51 & #50

Hi @mindninjaX , thanks for your work, but I won't merge this PR. We are looking for something that will be generated on build to populate files with all the website routes, using Gatsby plugins such as gatsby-plugin-robots-txt and gatsby-plugin-sitemap

Oh in that case I can try making use of plugins and send a new PR?

A PR is currently in the work for the sitemap part, you still can do the PR for the robots.txt if you still want to. A simple robots.txt generation without any policy at the moment would be great. Someone from the @CodeursEnSeine/codeursenseinewebsite team will add policies later in an other PR.


Fix: User not scrolled to top of chats list when scrolling down and deleting search

Explanation of Change

This fix will resolve scroll issue when removing search input value to empty in BaseSelectionList and the SearchRouter
Fixed Issues

$ https://github.com/Expensify/App/issues/50562
PROPOSAL: https://github.com/Expensify/App/issues/50562#issuecomment-2454175067
Tests

Open app
Log in to an account with a large list of chats
Tap on the search icon on the top right corner
Write a few letters to trigger some results
Scroll down to the middle of the results
Select all the content in the search input and delete it
Verify the chats list is updated and the user is navigated to the top of it

[X] Verify that no errors appear in the JS console

Offline tests

Same as test
QA Steps

Same as test

[X] Verify that no errors appear in the JS console

PR Author Checklist

[X] I linked the correct issue in the ### Fixed Issues section above
[X] I wrote clear testing steps that cover the changes made in this PR

[X] I added steps for local testing in the Tests section
[X] I added steps for the expected offline behavior in the Offline steps section
[X] I added steps for Staging and/or Production testing in the QA steps section
[X] I added steps to cover failure scenarios (i.e. verify an input displays the correct error message if the entered data is not correct)
[X] I turned off my network connection and tested it while offline to ensure it matches the expected behavior (i.e. verify the default avatar icon is displayed if app is offline)
[X] I tested this PR with a High Traffic account against the staging or production API to ensure there are no regressions (e.g. long loading states that impact usability).

[X] I included screenshots or videos for tests on all platforms
[X] I ran the tests on all platforms & verified they passed on:

[X] Android: Native
[X] Android: mWeb Chrome
[X] iOS: Native
[X] iOS: mWeb Safari
[X] MacOS: Chrome / Safari
[X] MacOS: Desktop

[X] I verified there are no console errors (if there's a console error not related to the PR, report it or open an issue for it to be fixed)
[X] I followed proper code patterns (see Reviewing the code)

[X] I verified that any callback methods that were added or modified are named for what the method does and never what callback they handle (i.e. toggleReport and not onIconClick)
[X] I verified that comments were added to code that is not self explanatory
[X] I verified that any new or modified comments were clear, correct English, and explained "why" the code was doing something instead of only explaining "what" the code was doing.
[X] I verified any copy / text shown in the product is localized by adding it to src/languages/* files and using the translation method

[X] If any non-english text was added/modified, I verified the translation was requested/reviewed in #expensify-open-source and it was approved by an internal Expensify engineer. Link to Slack message:

[X] I verified all numbers, amounts, dates and phone numbers shown in the product are using the localization methods
[X] I verified any copy / text that was added to the app is grammatically correct in English. It adheres to proper capitalization guidelines (note: only the first word of header/labels should be capitalized), and is either coming verbatim from figma or has been approved by marketing (in order to get marketing approval, ask the Bug Zero team member to add the Waiting for copy label to the issue)
[X] I verified proper file naming conventions were followed for any new files or renamed files. All non-platform specific files are named after what they export and are not named "index.js". All platform-specific files are named for the platform the code supports as outlined in the README.
[X] I verified the JSDocs style guidelines (in STYLE.md) were followed

[X] If a new code pattern is added I verified it was agreed to be used by multiple Expensify engineers
[X] I followed the guidelines as stated in the Review Guidelines
[X] I tested other components that can be impacted by my changes (i.e. if the PR modifies a shared library or component like Avatar, I verified the components using Avatar are working as expected)
[X] I verified all code is DRY (the PR doesn't include any logic written more than once, with the exception of tests)
[X] I verified any variables that can be defined as constants (ie. in CONST.js or at the top of the file that uses the constant) are defined as such
[X] I verified that if a function's arguments changed that all usages have also been updated correctly
[X] If any new file was added I verified that:

[X] The file has a description of what it does and/or why is needed at the top of the file if the code is not self explanatory

[X] If a new CSS style is added I verified that:

[X] A similar style doesn't already exist
[X] The style can't be created with an existing StyleUtils function (i.e. StyleUtils.getBackgroundAndBorderStyle(theme.componentBG))

[X] If the PR modifies code that runs when editing or sending messages, I tested and verified there is no unexpected behavior for all supported markdown - URLs, single line code, code blocks, quotes, headings, bold, strikethrough, and italic.
[X] If the PR modifies a generic component, I tested and verified that those changes do not break usages of that component in the rest of the App (i.e. if a shared library or component like Avatar is modified, I verified that Avatar is working as expected in all cases)
[X] If the PR modifies a component related to any of the existing Storybook stories, I tested and verified all stories for that component are still working as expected.
[X] If the PR modifies a component or page that can be accessed by a direct deeplink, I verified that the code functions as expected when the deeplink is used - from a logged in and logged out account.
[X] If the PR modifies the UI (e.g. new buttons, new UI components, changing the padding/spacing/sizing, moving components, etc) or modifies the form input styles:

[X] I verified that all the inputs inside a form are aligned with each other.
[X] I added Design label and/or tagged @Expensify/design so the design team can review the changes.

[X] If a new page is added, I verified it's using the ScrollView component to make it scrollable when more elements are added to the page.
[X] If the main branch was merged into this PR after a review, I tested again and verified the outcome was still expected according to the Test steps.

Screenshots/Videos

Android: Native
https://github.com/user-attachments/assets/a5edd6b2-5741-4d14-855d-54b8017bd05c

Android: mWeb Chrome
https://github.com/user-attachments/assets/8f66dd8e-0c3c-41c3-a0a5-d4d751a5752e

iOS: Native
https://github.com/user-attachments/assets/7442e2ba-1830-4163-9d52-6278cb35abed

iOS: mWeb Safari
https://github.com/user-attachments/assets/110269ce-9d29-4ab5-9ba1-3b0c55b042c1

MacOS: Chrome / Safari
https://github.com/user-attachments/assets/f93d9fb0-3d2c-46ee-8f5b-74493c1446a3

MacOS: Desktop
https://github.com/user-attachments/assets/0b22f56c-67f9-4d97-bdf0-91aebdb48aca

When going from empty to some query we are not scrolling back up and I think we should?
https://github.com/user-attachments/assets/7722d8d4-42ab-4441-85b5-d138d954a4a7

Yeah, I think we should because that is what we do when it is not empty and we type something else...but we can ask the @Expensify/design team for help here 😄
https://github.com/Expensify/App/pull/52606#issuecomment-2485955506

Yeah I agree with scrolling back to the top once someone starts inputting a query.

@rlinoz not sure why you experience this. My code changes doesn't change that behavior
Uploading Kapture 2024-11-20 at 08.32.00.mp4…

:hand: This PR was not deployed to staging yet because QA is ongoing. It will be automatically deployed to staging after the next production release.


🚀[Feature]: Add functionality to autorefresh managed IATs when expired

Description
When running the GitHub module as a GitHub App via automation:
In function app for automation, we want to be able to have context retained and ready when a function is called towards a target.
When the IAT is detected and we have the context for the app, refresh the IAT.
Scenario:

Automation is running in the context of a GitHub App (no IATs currently defined).
Automation needs to run Delete-GitHubTeam -Name 'someTeam' -Organization 'someOrg'.

Delete-GitHubTeam requires, IAT, UAT or PAT, Team permission

Module gets the context matching the request:

Type = IAT
Permissions contains 'Teams'
TargetType = 'organization'
Target = 'someOrg'

If the IAT is found:

Module checks that the time now is greater than my TokenExpirationDate (subtract a var offset that can be stored in config)
Check if parent is available:

Type = 'App'
ClientID = $me.ClientID

Recreate context for the IAT (or just refresh the token)

Should the 'parent' be stored in the context of the managed IAT, or should the function assume a naming convention?


Sort File Names When Updating File List

This PR sorts the acquired sources and headers list before writing it to the project file.
This should prevent unwanted diffs and guarantee consistent output.
To test, checkout this branch and run python3 update_filelist.py. If everything works correctly, no diffs should be produced in the chatterino.pro file.

@Mm2PL reported that his file list gets sorted differently. He is on an older sort version though. Additional testing much appreciated.

Now uses built-in Python sorting instead of relying on the sort command.


document.body.toggleClass is not a function

In a form like this https://webslides.tv/demos/components#slide=92
when you press enter to submit the form, Chrome 56 throws an exception:
Uncaught TypeError: document.body.toggleClass is not a function
    at Grid.onKeyPress_ (webslides.js:984)
onKeyPress_ @ webslides.js:984

in this line you try to toggle body class with:
document.body.toggleClass('baseline');

but the function is not defined...
I think that the correct function is classList.toggle("..")
Also when you add the class to the body, the associated style try to load an image which doesn't exists:
body.baseline {
  background: url(../images/baseline.png) left top .8rem/.8rem;
}

throws this error:
GET https://webslides.tv/images/baseline.png 404 (Not Found)

Thanks @jerolba I already noticed this and it's fixed on our dev branch but will merge this!


Amazon SES?

Never really played with Django, so something new for me to learn.
How would I get Amazon SES to work with this and not MAILGUN (overpriced imo)
Thanks!
https://anymail.dev/en/stable/esps/amazon_ses/

You should be able to use anymail as you indicated. You should be able to modify it in settings and follow the general instructions in the link you sent. I was going to use send grid and decided against it in the end.

You should be able to use anymail as you indicated. You should be able to modify it in settings and follow the general instructions in the link you sent. I was going to use send grid and decided against it in the end.

Alright, thanks! I haven't gotten into this at all but it seems like a small project.

@CodeMeZone it is possible, but requires installing additional library. It would probably involve changing settings.py, unfortunately I think it is quite hard to support all this options through .env
But thanks for looking into the project! I'm working on docker version - takes time because I am not a big expert with it

@garrrikkotua I guess we're both trying something new lol!
Hmm.. I guess it's something that I'll try my best at.


Small typo

Probably better to use "as" rather than "and."

Sorry for my english :laughing:

I think this should be able to be merged now!
Please review.

Couldn't merge this because you didn't edit the jade file, but I made this change in 326b8736fa35edcca68e13196943a3d956d30bdd


Reconcile PyTorch pass pipelines with those upstream in torch-mlir (if needed)

We have some people running "e2e" test workflows in torch-mlir that end up differing when running through IREE. I suspect the pipelines may have drifted a bit.
linalg:

IREE: https://github.com/openxla/iree/blob/main/compiler/plugins/input/Torch/InputConversion/Passes.cpp
torch-mlir: https://github.com/llvm/torch-mlir/blob/main/lib/Dialect/Torch/Transforms/Passes.cpp (maybe other files too?)

onnx:

IREE: https://github.com/openxla/iree/blob/main/compiler/plugins/input/Torch/PluginRegistration.cpp

Related: https://github.com/nod-ai/SHARK-TestSuite/issues/47

Related https://github.com/nod-ai/SHARK-TestSuite/issues/225


Approaching version 1

This pull request will close a number of issues to progress towards an initial release.
Core Changes

A condition builder / factory has been added to make creating and modifying conditions easier in the future

site admin (closes #6) and repo owner (closes #7) were added based on known context and basic request to graphql endpoint.

Action will now opt to taking a workflow token argument, defaulting to github.token
Action will not take an endpoint argument, closed in #21 with github.apiUrl or github.graphqlUrl (whichever is used).
At present, only one request is made to the graphql endpoint (closes #10).

Backend changes

Jest has been removed in favour of Ava
NPM has been exchanged in favour of Yarn
Ava will attempt to mock the context by providing injecting a false environment for @action/github to use.
Test action matrix has been prepared for future implantations (closes #24).
allcontributors has been added with @dependabot being the first to populate the list :tada:

Concerns

The Graphql Explorer did not respond well to the query written when asking for variables (even when provided). The data explorer also reset the variables context whenever the query was modified (likely due to lack of state continuity upon refreshing or reloading components).

Query failed due to my concerns with GraphQL variables, which I may not be providing correctly...

Reason to query failing is how the request has been formed at bf5004d

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 3173b40..f8d4a22 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -40,7 +40,12 @@ jobs:
       - uses: actions/checkout@v2
       - name: Debug Context
         run: |
-          echo "${{ toJSON(github) }}"
+          echo Actor: ${{ github.actor }}
+          echo Owner/Repo: ${{ github.repository }}
+          echo Event: ${{ github.event_name }}
+          echo Event Action: ${{ github.event.action }}
+          echo Run No.: ${{ github.run_number }}
+          echo Run ID: ${{ github.run_id }}
       - uses: ./
         env:
           ACTIONS_STEP_DEBUG: true
diff --git a/src/condition.ts b/src/condition.ts
index 93e8d1e..950eb6c 100644
--- a/src/condition.ts
+++ b/src/condition.ts
@@ -12,7 +12,7 @@ export default class ConditionBuilder {
 	constructor(private readonly key: string) {}

 	useCheck(predicate: ConditionPredicate): ConditionBuilder {
-		this.check = (data, context) => predicate(data, context);
+		this.check = predicate;
 		return this;
 	}

diff --git a/src/main.ts b/src/main.ts
index 4185cd4..5199c83 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -1,24 +1,24 @@
 import * as core from '@actions/core';
-import { context, getOctokit } from '@actions/github';
-import { OctokitResponse } from '@octokit/types';
+import {context, getOctokit} from '@actions/github';
+import {OctokitResponse} from '@octokit/types';

-import { accessGroups } from './access';
-import { DataQuery, logAndExport } from './util';
+import {accessGroups} from './access';
+import {DataQuery, logAndExport} from './util';

 async function run(): Promise<void> {
 	try {
-		const { actor } = context; // core.getInput('user') - future
-		const { owner, repo } = context.repo;
+		const {actor} = context; // Core.getInput('user') - future
+		const {owner, repo} = context.repo;

-		const token: string = core.getInput('github-token', { required: false });
+		const token: string = core.getInput('github-token', {required: false});

 		const octokit = getOctokit(token, {
 			baseUrl: context.apiUrl,
 		});

-		const { data }: OctokitResponse<DataQuery> = await octokit.graphql(
+		const {data}: OctokitResponse<DataQuery> = await octokit.graphql(
 			`
-      query accessData($owner: String!, $actor: String!, $repo: String!) {
+      query accessData($owner: String!, $repo: String!, $actor: String!) {
 				user(login: $actor) {
 					...Access
 				}
@@ -27,9 +27,11 @@ async function run(): Promise<void> {
 						...Access
 					}
 					collaborators(query: $actor) {
-						nodes {
-							...Access
-
+						edges {
+							node {
+								...Access
+							}
+							permission
 						}
 					}
 				}
@@ -39,7 +41,8 @@ async function run(): Promise<void> {
 				login
 				isViewer
 				isSiteAdmin
-			}
+				__typename
+			}
       `,
 			{
 				owner,
@@ -50,10 +53,10 @@ async function run(): Promise<void> {

 		core.debug(`Access Data: ${JSON.stringify(data)}`);

-		const { groups, highestGroup } = accessGroups(context, data);
+		const {groups, highestGroup} = accessGroups(context, data);

-		logAndExport('groups', groups, `${context.actor} has access to %s`);
-		logAndExport('highest-group', highestGroup, `${context.actor} groups.first -> %s`);
+		logAndExport('groups', groups, `${actor} has access to %s`);
+		logAndExport('highest-group', highestGroup, `${actor} groups.first -> %s`);
 	} catch (error: unknown) {
 		core.setFailed((error as Error).message);
 	}
diff --git a/tsconfig.json b/tsconfig.json
index e6cc392..91e3dba 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -6,10 +6,7 @@
     "rootDir": "./src",
     "strict": true,
     "noImplicitAny": true,
-    "esModuleInterop": true,
-    "typeRoots": [
-      "node_modules/@types"
-    ]
+    "esModuleInterop": true
   },
   "include": [
     "./src/**/*.ts",


Uncaught TypeError: Cannot read property 'body' of undefined

opening a new file using atom ~/.newfile, resulted in the following error:
Atom Version: 1.0.0
System: Mac OS X 10.10.3
Thrown From: slack-chat package, v3.2.8
Stack Trace
Uncaught TypeError: Cannot read property 'body' of undefined
At /Users/Jean/.atom/packages/slack-chat/node_modules/sc-client/lib/app.js:112

TypeError: Cannot read property 'body' of undefined
  at /Users/Jean/.atom/packages/slack-chat/node_modules/sc-client/lib/app.js:112:28
  at done (/Users/Jean/.atom/packages/slack-chat/node_modules/sc-client/node_modules/needle/lib/needle.js:355:7)
  at ClientRequest.had_error (/Users/Jean/.atom/packages/slack-chat/node_modules/sc-client/node_modules/needle/lib/needle.js:362:5)
  at emitOne (events.js:77:13)
  at ClientRequest.emit (events.js:166:7)
  at TLSSocket.socketCloseListener (_http_client.js:230:9)
  at emitOne (events.js:82:20)
  at TLSSocket.emit (events.js:166:7)
  at TCP.close (net.js:464:12)

Commands
     -0:08.9.0 tree-view:reveal-active-file (atom-workspace.workspace.scrollbars-visible-when-scrolling.theme-one-dark-syntax.theme-one-dark-ui)
     -0:03.8.0 core:close (atom-text-editor.editor.is-focused)
     -0:03.8.0 tree-view:reveal-active-file (atom-workspace.workspace.scrollbars-visible-when-scrolling.theme-one-dark-syntax.theme-one-dark-ui)

Config
{
  "core": {
    "disabledPackages": [
      "atom-ctags",
      "goto",
      "ask-stack",
      "wrap-guide"
    ],
    "audioBeep": false,
    "projectHome": "/Users/Jean/code"
  },
  "slack-chat": {
    "api_key": "xxx",
    "api_secret": "yyy",
    "notifications": false,
    "api_token": "zzz"
  }
}

Installed Packages
# User
autocomplete-ctags, v0.2.0
autocomplete-paths, v1.0.2
docblockr, v0.7.2
file-icons, v1.5.8
git-projects, v1.14.1
highlight-selected, v0.10.1
language-docker, v1.1.3
language-gherkin, v1.0.2
linter, v1.1.0
linter-rubocop, v0.2.7
minimap, v4.10.0
minimap-highlight-selected, v4.3.0
multi-wrap-guide, v0.20.0
slack-chat, v3.2.8
synced-sidebar, v0.4.0

# Dev
No dev packages

Its still occurring any solution?

Toggling "Load conversations on startup" in Slack Chat settings and restarting atom helps me to avoid this error.


YARP Sidecar

Create a development only sidecar for use in simplifying the developer experience. YARP is service discovery aware and thus can be used to send traffic from the gateway to multiple replicas.
Discussion here:
https://github.com/NapalmCodes/Aspire.Hosting.Krakend/issues/25

Work in progress: https://github.com/NapalmCodes/Aspire.Hosting.Krakend/tree/sidecar

Implemented


Create a coc.nvim extension

Problem

The vscode extension looks great, I'd love to see it as a coc.nvim extension.
Proposed solution
Convert the vscode extension to a coc extension, https://github.com/neoclide/coc.nvim/wiki/Using-coc-extensions

Hey! It looks like coc.nvim already supports Sorbet
https://github.com/neoclide/coc.nvim/wiki/Language-servers#using-sorbet

Hey! It looks like coc.nvim already supports Sorbet
https://github.com/neoclide/coc.nvim/wiki/Language-servers#using-sorbet

Yeah but that's not really the same as the extension, it has a subset of the features only...


Re-enable pusher-http-haskell

It is now GHC 8 compatible.

There are still some upper bounds:
QuickCheck-2.9.1 (Stackage upper bounds) is out of bounds for:

[ ] pusher-http-haskell-<IP_ADDRESS> (>=2.7 && < 2.9). Will Sewell<EMAIL_ADDRESS>@willsewell. @pusher-community

aeson-<IP_ADDRESS> (Adam Bergmark<EMAIL_ADDRESS>@bergmark) is out of bounds for:

[ ] pusher-http-haskell-<IP_ADDRESS> (>=0.8 && < 0.12). Will Sewell<EMAIL_ADDRESS>@willsewell. @pusher-community

http-client-<IP_ADDRESS> is out of bounds for:

[ ] pusher-http-haskell-<IP_ADDRESS> (==0.4.*). Will Sewell<EMAIL_ADDRESS>@willsewell. @pusher-community

This should now be ok with pusher-http-haskell-<IP_ADDRESS>.


Projects

Updated projects (everything works locally and on Colab // Kaggle).
Only 2 things are required:

to change tonic repo origin in Macrocircuits project when it is going to be forked to Neuromatch organization;
agree on final versions of project guidance.

The changes are implemented.


VS code: Taking longer time than expected to deploy workflow from VS code to logic app only in NuGet Artifact.

Describe the Bug with repro steps
1.Create a new workflow app using VS Code.
2.Create a stateful/stateless workflow
3.Open the workflow.json file in designer and author a new workflow.
4.Add http request trigger.
5.Add Inline javascript action and add a Response action, where the body is the output from the Run in-line JavaScript action (Inline javascript test case)or else add some parameters with request and any action like response or compose(workflow parameters test case).
6..Save, debug and run it.
7..Create a logic app from logic apps tree in resources blade.
8.Deploy the workflow from VS code to logic app in NuGet Artifact.
9..Expected: Should able to deploy the workflow from VS code to logic app in NuGet Artifact within less than 10min.
Actual: It is taking more than 45-50 minutes to create a zip package and deploy the workflow from VS code to logic app only in NuGet Artifact.
Note: Issue repro only in nuget artifact, to create a zip package and deploy the workflow, but the deployment is getting success enough though it is taking longer time by getting the error as shown below.
What type of Logic App Is this happening in?
Standard (VSCode)
Are you using Preview Designer or GA Designer
Preview
Workflow JSON
No response
Screenshots or Videos

Browser
VS Code
Additional context
Artifacts details:
1.VS Code extension: vscode-azurelogicapps-2.18.0.vsix
2.NuGet package: https://artprodeussu2.artifacts.visualstudio.com/A41bf5486-7392-4b7a-a7e3-a735c767e3b3/b32aa71e-8ed2-41b2-9d77-5bc261222004/_apis/artifact/cGlwZWxpbmVhcnRpZmFjdDovL21zYXp1cmUvcHJvamVjdElkL2IzMmFhNzFlLThlZDItNDFiMi05ZDc3LTViYzI2MTIyMjAwNC9idWlsZElkLzczNTE1ODYzL2FydGlmYWN0TmFtZS9kcm9wX2J1aWxkX0J1aWxkQXJ0aWZhY3RzX1dpbmRvd3M1/content?format=file&subPath=%2FMicrosoft.Azure.Workflows.WebJobs.Extension.1.23.1.nupkg
3.Extension Bundle (CDN URL): https://cdnforlogicappsv2.blob.core.windows.net/logicapps-vendortesting
4.Extension Bundle (Direct Download): https://cdnforlogicappsv2.blob.core.windows.net/logicapps-vendortesting/ExtensionBundles/Microsoft.Azure.Functions.ExtensionBundle.Workflows/1.23.1/Microsoft.Azure.Functions.ExtensionBundle.Workflows.1.23.1_any-any.zip

That specific process of creating the zip package and uploading is done via the VSCode Azure SDK for Node.js package. After analyzing it, it might be taking so much time due to the internet upload speed.  I put a known issue label on this in the meantime we discuss on this with the team,

Internet upload and download speed is 20MBPS.

I had a talk with one of the team members of App Service Tools. The amount of time will totally depend on the project size and the internet speed. As for now, they aren't sure how they can improve the performance of it. But I will keep this open as a known issue.


test: 7.2.0 Analysis Snapshot Protocols

Overview
Add protocols pulled from v7.2.0 pull requests for Analysis Snapshot testing. All work filed under RQA-2434
Test Plan

Run new protocols locally and verify results
Run in workflow dispatch action and verify success

Changelog
Here are the protocols added and where I found them:

RQA-2098

Flex_P1000_96_Gripper_TC_TM_HS_AnalysisError_GripperCollisionWithTips.json

https://github.com/Opentrons/opentrons/pull/14491

Flex_None_None_TC_2_14_verifyThermocyclerLoadedSlots.py
Flex_None_None_TC_2_15_verifyThermocyclerLoadedSlots.py
Flex_None_None_TC_2_16_verifyThermocyclerLoadedSlots.py
Flex_None_None_TC_2_17_verifyThermocyclerLoadedSlots.py
OT2_None_None_TC_2_14_VerifyThermocyclerLoadedSlots.py
OT2_None_None_TC_2_15_VerifyThermocyclerLoadedSlots.py
OT2_None_None_TC_2_16_VerifyThermocyclerLoadedSlots.py
OT2_None_None_TC_2_17_VerifyThermocyclerLoadedSlots.py

https://github.com/Opentrons/opentrons/pull/14475

Flex_None_None_TC_2_16_AnalysisError_TrashBinAndThermocyclerConflict.py
OT2_None_None_2_16_verifyDoesNotDeadlock.py
OT2_None_None_HS_2_16_AnalysisError_HeaterShakerConflictWithTrashBin1.py
OT2_None_None_HS_2_16_AnalysisError_HeaterShakerConflictWithTrashBin2.py

https://github.com/Opentrons/opentrons/pull/14547

Flex_P1000_96_None_TC_2_16_AnalysisError_pipetteCollisionWithThermocyclerLid.py

https://github.com/Opentrons/opentrons/pull/14522

Flex_P1000_96_None_TC_2_16_AnalysisError_pipetteCollisionWithThermocyclerLidClips.py

Dispense functionality validation

OT2_P300M_P20S_TC_HS_TM_2_15_dispense_changes.py
OT2_P300M_P20S_TC_HS_TM_2_16_dispense_changes.py
OT2_P300M_P20S_TC_HS_TM_2_17_dispense_changes.py

https://github.com/Opentrons/opentrons/pull/14253

OT2_P300S_None_2_16_verifyNoFloatingPointErrorInPipetting.py

Review requests
There are a few pull requests that I had questions about. I will @ the people that worked on them to answer the questions

https://github.com/Opentrons/opentrons/pull/14437

@sfoster1, Can I use the protocol found in RABR-23 to get this to happen? Is there another way?

https://github.com/Opentrons/opentrons/pull/14509

@SyntaxColoring, can analysis capture this change or is this only relavant during actual protocol runtime?

https://github.com/Opentrons/opentrons/pull/14510

@TamarZanzouri or @SyntaxColoring, can I raise a generic python exception inside the protocol to trigger this functionality?

https://github.com/Opentrons/opentrons/pull/14512

@Laura-Danielle or @SyntaxColoring, Iant to validate my logic. This not a good canidate for snapshot testing because you have to run LPC and Calibration which is not taken into account during analysis. Can you confirm?

Risk assessment
None

I'd expect you can use RABR-23 to test #14437 yeah

fix(robot-server): Fix error parsing persisted loadModule commands #14509

@SyntaxColoring, can analysis capture this change or is this only relavant during actual protocol runtime?

Analysis can't capture it. It's only relevant when robot-server retrieves details about runs and analyses stored from prior boots.

fix(robot-server): append error to analysis error list in case an internal error occurred #14510

@TamarZanzouri or @SyntaxColoring, can I raise a generic python exception inside the protocol to trigger this functionality?

Unfortunately no. The hole that that PR plugged is only for exceptions raised by certain Opentrons internal code.

refactor(api): Save and load tip length calibrations from tiprack uri #14512

@Laura-Danielle or @SyntaxColoring, Iant to validate my logic. This not a good canidate for snapshot testing because you have to run LPC and Calibration which is not taken into account during analysis. Can you confirm?

Yep, I agree. That fix is for robot runtime behavior, which we can't cover with these analysis tests. Theoretically, we could do a similar snapshot thing for robot runtime behavior. I guess that would be g-code-testing.


Create Database Artifacts Using Core Data Services (CDS) for SAP HANA Cloud

Tutorials: https://developers.sap.com/tutorials/hana-cloud-cap-create-database-cds.html
Write here how you think we can improve the tutorial ...
Step 3 Deploy Objects into the Databaee -  Use the  SAP HANA Projects view ??
I would if it existed but it does not appear on the left side options
I have

MyHANNAAPP
NPM SCRIPTS
CAP DATA MODELS AND SERVICES
TIMELINE

How can i active this view

Go back to the previous tutorial when you created your Dev Space: https://developers.sap.com/tutorials/hana-cloud-cap-create-project.html
In the first step when creating the space you need to select the additional SAP HANA Tools and Calculation View editor.

If you are missing the SAP HANA Projects view, then you didn't select the SAP HANA Tools at this step. If you stop your dev space and then press the Edit Icon, it will return you to this same screen as when you were creating your Dev Space.  Add the two tools as specified in the tutorial, save and restart the Dev Space.  When you reload the Business Application Studio you should then have the SAP HANA Projects View.


nixos/dendrite: remove

Motivation for this change
This module is still in flux and should not be included in the 21.05 release until we stabilize the situation regarding dynamic user and accessing user-owned tls certs/keys.
cc @dotlambda
Things done

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

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

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

Result of nixpkgs-review pr 124524 at 3c9702f3 run on aarch64-linux 1

1 package failed to build:

nixos-install-tools

Note that build failures may predate this PR, and could be nondeterministic or hardware dependent.
Please exercise your independent judgement. Does something look off? Please file an issue or reach out on IRC.

Done.


feature: support LDAP auth plugin

@moonming  is there a base package to perform or have to write from scratch ?

maybe it‘s useful for the  feature，  https://github.com/lualdap/lualdap

@soulsoul hm what I dont get is this is also a client not an sdk which provides an interface.I actually had a look on this
Cc @moonming @membphis


add CEXL docs

Add md documentation for cexl.

This change is

Codecov Report

Merging #264 into master will increase coverage by 0.07%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #264      +/-   ##
==========================================
+ Coverage   83.67%   83.75%   +0.07%
==========================================
  Files          49       49
  Lines        2745     2745
==========================================
+ Hits         2297     2299       +2
+ Misses        424      423       -1
+ Partials       24       23       -1

Impacted Files
Coverage Δ

pkg/expr/func.go
100% <ø> (ø)
:white_check_mark:

pkg/adapterManager/parallelManager.go
95.23% <ø> (ø)
:white_check_mark:

adapter/prometheus/server.go
89.47% <ø> (+10.52%)
:white_check_mark:

Continue to review full report at Codecov.

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Can this doc be either moved to istio/istio repo or atleast can we link from istio/istio to this doc?
We are trying to collate all docs there.

Can we close this PR?


EDU-290 Create plugin selector dialog

Closes https://educandu.atlassian.net/browse/EDU-290

Looks really really nice, this plugin selection modal! 🥳

Looks really really nice, this plugin selection modal! partying_face

Thankya :relaxed:


read and render results document

when wanting to display different output modes, e.g. plain or verbose, the whole program needs to run again
with the results document saved by the user, we could also take that as an input and render per the specified arguments
alternatively/additionally, we could think about a "workspace option" combining the results and/or freeze output (underused, currently I think) to speed up subsequent runs
uses cases for this would be:

rule dev
results exploration

this will require a bit of refactoring so let's agree if this is worth it and how to do it, first

rendering an existing results document is a great idea!

Could you please explain it a bit more and guide me how to do it ?

For the rendering of an existing result document (JSON), we'll have to:

find a good way to provide the result file to capa
render the loaded results per the arguments

@williballenthin is adding a new format FORMAT_RESULT a correct approach as by this we can reuse args.sample to accept json file as cited by @mr-tz ,and rather than flag we can just compare the buf.read of the file to be {"meta": to ensure its a results.json file

Yes, an explicit new FORMAT and auto-detection via the first few bytes (and subquential successful loading) sound great.


Account linking in Myaccount doesn't work for suborg users

Describe the issue:

Create a sub org
Switch to it and create two users
Go to Applications section and copy the myaccount URL (org qualified URL)
Login by one suborg user
Go to Personal Info section and try to link other user account
Request fails with following error

{
    "code": "UAA-8540",
    "message": "Error while adding associations of user: bob",
    "description": "Cross tenant association is not allowed",
    "traceId": "b1296d56-4ed9-41fc-b81b-d816ae8a1b95"
}

Reason:

The shown tenant domain is incorrect. The suborg's tenant domain needs to be appended to the username in order to work the flow

Working when suborg's tenant domain is appended.

need to analyze the logic here: https://github.com/wso2/identity-apps/blob/b5e1770bc2c6d2e813ade315323f113b0f1ae562/apps/myaccount/src/components/linked-accounts/linked-accounts.tsx#L95


Min/Max values for ranges

Is there a way to specify a minimum and maximum value for the lower and upper values.
For example:
A slider with an overall range of 1-100.
Minimum value has a range of 1-30
Maximum value has a range of 60-100
Is this possible?

No this is not possible. I think you should use two separate sliders for this use case.