KeyError: ('C', 1, 'm')

hello，
I got an error when I used mathphaser：
/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/meth_phaser_parallel:235: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass (name,) instead of name to silence this warning.
phased_df_chr.get_group(chromosome).iterrows()
/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import require
Traceback (most recent call last):
File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 1471, in
main(sys.argv[1:])
File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 1437, in main
) = get_assignment_max(
File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 898, in get_assignment_max
base_modification_list = get_base_modification_dictionary(  # build the dictionary with snp phased reads
File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 243, in get_base_modification_dictionary
for i in mm[methylation_identifier]:  # Remora only output one type of score: c 1 m/c 0 m, but this part can be improved for other methlyation callers
KeyError: ('C', 1, 'm')
My run command is：meth_phaser_parallel -b sample.whatshap.haplotagged.bam -r ref.fa -g sample.phased.gtf -vc sample.haplotype.phased.VCF -o path/to/output
why this happened？
Any help to overcome this is appreciated!
Best

Could you please attach one read from your bam file? I am suspecting there are some bugs with the methylation signal reading. Thanks!
Get Outlook for iOShttps://aka.ms/o0ukef

From: Wshengquan @.>
Sent: Monday, July 15, 2024 8:44:03 AM
To: treangenlab/methphaser @.>
Cc: Subscribed @.***>
Subject: [treangenlab/methphaser] KeyError: ('C', 1, 'm') (Issue #22)
hello，
I got an error when I used mathphaser：
/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/meth_phaser_parallel:235: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass (name,) instead of name to silence this warning.
phased_df_chr.get_group(chromosome).iterrows()
/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import require
Traceback (most recent call last):
File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 1471, in
main(sys.argv[1:])
File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 1437, in main
) = get_assignment_max(
File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 898, in get_assignment_max
base_modification_list = get_base_modification_dictionary( # build the dictionary with snp phased reads
File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 243, in get_base_modification_dictionary
for i in mm[methylation_identifier]: # Remora only output one type of score: c 1 m/c 0 m, but this part can be improved for other methlyation callers
KeyError: ('C', 1, 'm')
My run command is：meth_phaser_parallel -b sample.whatshap.haplotagged.bam -r ref.fa -g sample.phased.gtf -vc sample.haplotype.phased.VCF -o path/to/output
why this happened？
Any help to overcome this is appreciated!
Best
—
Reply to this email directly, view it on GitHubhttps://github.com/treangenlab/methphaser/issues/22, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADDV4HSJUIW34QP42SJNL7DZMPG2HAVCNFSM6AAAAABK4SWL4WVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQYDQNZYGU2TQOA.
You are receiving this because you are subscribed to this thread.Message ID: @.***>

Thanks for your reply. Here's one of my reads:
8e9d05a0-9447-4b61-9600-1d9e92384702    0       1       1       60      1513S328M2I1M1I255M2D501M4D2M1I41M1I232M2D841M3S        *       0       0       GGGAACTCCTCCTTTTTTTTTCCTAAGAAATTATCTAAATAATAAATTTTGTTGAAGTGTTTGTC
TAGGATTTCAAGGTAACGGCCTAGAAGTCACCATCTAACCACTGTGGCAAATCCGTATGAGTGACATTAGAAGAAGTAATCTTTTGTCTATCATTTTTAATTTTATTAAGTTGAATACATAATTTTACAATTTTATAGTCGCTAATGACTAATTGGTTAATTATCCAGCCAATGAAACTAGTAGAGGGAGTTTAGGAAATGCAGAATAATTAGGCATTTCCTAGGACTTGTGTAAATTAGAATATGACGGTAGCATTTTTATGGTTGTAAAATCAGAGGGAAGGCATATATATAGCTGTTGTAGTTTTTGTTTTTGTTTTTGTTTTTTTTTTAATGGCTACACCCACGGCATGTGGAAGTGTCCCTGGTTCCTGGTTTCTGGGCCAGGGATTGAATCCAAGCCACAGCTGCAGCAATACCAGATCCTTTAACCCACCGCACTGGGCTGGTGATTGAACCCTGACCTACACAGCAACCCAAGCTGCTGCAGTTGAAGTCTTAATCCGCTGTGTCGCAGCAGGAATTCCCATATAGCAGTTTTTAAAACAGTTAAAACTATCTATTTTGTCAAACAGTCATTTTGATGAGACATATTTTATGAATTTTTTCGTATGTAACTAAATATCTGATATTAATACTTTAGAGTTGTTTGAAAGTAATTTTTTGCTTTATATCATGTAACCTAGTAACTGAAGCCATTGCATATATATAAATGGCAGTACATTAATATTGTTTCTGAGAGCCCATTGGAAACAGGAGGTCACTTCACTATCTGTTGGTATGCTTGTAATCTGATTTATTAATTCCTTCTGGAGGTTGAAAAGGGTTATCAGTTGATTTGCCTAAAAAAATCATTAATAAAATTTACAGTTAAAGAAAATTTTTGTAACTTCTGTCTTCACTTGTTGGAATGTGTGTGAAAGAACACACAGATCTTGGTCCAGCTGCCCTAGTAGCCACAGTTTACTTGTCGGCTCCCTGTCCAAGAGTACACATGCCACATGGCCATGGAAGGGAATCCTGTATAGAAACAATGACAGGTATCTGGGTGGCTGTCATTGTCTAATTCTCCTGACAGAATCAGCAGTCTGAGTGACTCATTAACCGTTGTCTCTGACTGTTTCAGCGATTTGCTGCTGTAATCATGAGAATAAGAGAAACCCGCAGACACCGCACTAAATATCAGCTCTGGGAAAATGGTGTGCACGGGAGCCAAGAGGTGGGTCTAAAAGGGTTCATTGTCCTAGTCTGTGCGTTAGGAAAGAAAAGGCTGTATGTCGTGGTTTCTAGGTATTAGGTTACTACTGTGATACATTGTCATTGTTGCTTTCTGTTAAGGTGGTTGATTTTCATCACTGCAGACAGCAGTAACTTCATTTTCTTAAAATCAGGCATGAGTAAGGATGTGTGTTATCATCTGATTTCCATATAGTTGAGCGTGATTATGTGCTTAATTTTTGTCATTTCTCACCCCTGCTCTTGAGAGCTTTTGTTGATAATGTTGTTATTGCTTTCATTCTGCTTTTATTTTGTAAGCCCTGCACTCATTCATCGCTGTACCCGAATATGAGGTAAGGAGTGGTAAAGAAAGACTGGACATAAAAGAGGAATTAGCATTTGCACTCTTCAGATATAAATGCCATCAGTATTTTCCTATTAAAATGAAGCTTGTTTTCATCTCAGTGGAAATCTGTGGCTAAAGTACAACAATAGTAATGATAATGGTGAGGCTGTTGTACTTCACATCTATAAAATCTTGCATCAATAATTTGATTAACCAGATTCCTTTGGGTAGGCCTACGTTTTCTGTCAGAGACACAGGAATACTTTATAAATAAAATTGTTAATGTCTGTTGATCTTTTTTCATTGGAAGAGGGTGACCAGTTTACCTTTTGAAAAAAAACTTTCCTAATTTGGGCTTTTTTTTTTTTCTCCTTTTTAGGGCTGTACCCATGGCATATGAAAGTTCCTGTGCTAAGGGTTGATCAGAGCTGCAGCTGCCAGGTTACGCTACAGCAACACCAGATCAGGTTGTCTGTGGCCTTTGCCATAGCTTGGGGCAGCACCGGATCCTTAACCCACTGAGTGAGGCCAGGGATTGAACCTGCATCCTCCTGGATACTAGTTGGGTTCTTAACCTGCTGAGCCACAATGGGAACTCCTGGGCTTTTTATAAGTTATACGTTAAATAATTATTTTAGCTGTCTTTGAGTATGAATATCTCACTTTTTCTTTCCTTAGTGAAGAACAGTCCAGACTAGCAGCAAGAAAATATGCCAGAGTTGTACAGAAGTTGGGTTTTCCAGCTAAATTCTTGGACTTCAAGATTCAGAACATGGTGGGGAGCTGTGATGTGAAGTTCCCTATAAGGTTAGAAGGCCTTGTGCTTACCCACCAACAGTTCAGTAGGTAAGTCTGAAATGGATTGTGATTGCTTTTGGCAACAATTAATTTATAACCTATTTAAACACTGTTCATGATTTTTAAAAAACATGCAAAGTAATTGGTATATGAAATCAAATTATTTTGGTTTTTTCATCTTCAGGACCATAGCAGTGGCATATGGAAGTTTCCGGGCCAGGGGTCAAATCAGAGCTGCAACTGCCAACCTCCACCACGGCCACAGCAGTGCCAGGTCCCAGCTATGTCTGTGATTTACATCGCAGCTCAGGGCGAAACCAGATCCTTAACCCACTGAGCAGGGCCAGGGATCGAACCTGAATCCTCACTGATACAGTTTTGTTACCACTGAGCCACCATAGGAGCTCCCAAATGATTCACATATAGATGTTTTACTATTGAAATTTCTCCCATTCCTACCATTCTCACTGGTCTTCTACTTCTTAATGATACCCCAGACTCCCCTTTACTAGGATGAAATTGGTTCCCCTTCTGTATGTTTCATCGTTTCATTGCTCAATGAATACATTTCAAATGCATGAATTAGAAGTTCCTGTTATGGTGGATATGACATTTCTTTCTCTTTGTTTTCCCTGCTGCTCTCCTGGTGAAGACTTTAAAGGCAGGCTTGCCCATCTCTGCAGACCCTGCTTGCAGCATGCGCCTGGCGTGCTGTGCCCTTAATTGCACCAGGGCCTTTGCACATCCCGCTTTTATGCCTGGTGCTCTTGTTTCACTCTTCACCTAGGAAACTCCCACCGGCATTTCATGTATCCATCCAGGCATCTTTTCTTCAGAGAAGCCTGTCTTGAATTTTTCACTGGGCTAAACACACACACACCTAACTATTTTCAGTCTCTCTAACTAACAAAATGAGATGACTAGGATTAGAAAAAAACATACCAGTAGTGCATTTGGTCTGACAACACAGCGAAAGGTTCATTGTCTAACCAGTATCTTTTCTATCACTTTTGGTTAAGTCGCCTGACCTAGGTTAACACTTTGAGGATATTTCAGTTTAAGGAGATGAGATGTGAATGATTAGAAGGTAAACTGTGTGACTGTCATATCTTAGACATAAGTAATTCATTAGGCTCTTGTAAATCAGTGTACTTCACTTGTCCAGAGTGAAACTTGATGAGGGGCAGAGACTACAGAACATATTTATAAAGCTCTTGTTCTCATGTCTGGAAATTCAGATTCATTAGAAGTAAGAGTTCGTTGGCCTTCAGGTGCCAATTACAAGTCAGCTTGAG      ISQKMJSFEB===:;AABFJECHEFHMHJNGQSQMJMMSHISJKMSCKSSSS9557JFJJEJFSFJLLGSSIHLIJHJSKIMSSSLKKSJPIILOSKLKIHNIHIKSQJSHSNOLIGNSLLJSKPJIIIO>LHA@BDNJLKIJKSMJSLLSSMMISMGJIILSOOKHSSLSRNSJHINMSSJSMIPLJSSJJSGJSKSIPIMSISISMKKIPOHKKHSIPJOHNNKKHKIMJLHMOJPJSKMIKQLHIHHSQIJHSNLKKHJNOSJJSMJSSJKKSLEOJIJHISSHPIJLMLSIIMSPQSJSIJSLIJSHJRKKJLIGE@88=;0///GNISJKSLFGISSISJJSNSKKHJKOJIF::9989ABCEKHEISLPSSSIHGKFJRGI@>;AEISSSSHGEESSSKOKIMSISKHJHHSSSKPSLGLISSJEHSQPLGLNKOSJIGECED@A;;:99:44459CEDBFJJHKJSGHFSLSJHSSSOSMJSMHSQSLGGMJJISNIIGLKPJSSSILKICEKIHJJSJHSKNSKKII<=<;8((((((///0@IFICB>;788956,&&&&&+,//3333336JSJKNKGGSDDDSINSMKHSKSSSLKJSJQKHG?<<=J;;/////;>.BHEHJLQJJNLGSMNIGKNSSJSISJSSISSQISHPMPSSINJSLSRSLJHISHSSISSKNSSISOSIHSISSISSQGJSSPRSHHNLJKKKSKPSSSIKCSFDEJGHOJIFMSJLJHSLISKSJSSISJSHKILHOLSPKHFFSLHSNSMKSKJJOSLSPS(((((GKKJOSLQHSSHJSISKSOMOKEH;;::;FSINPMLILSMOSSKRJRMSSMKIPSSLSISSSSGHGKJHMOJIMSHNHIHSONSSSMSSOKHSJFLNLSSOMSKHKKSSEEJKSSSSSSSSGJSKJSOSSMKSJMIFHSGSKSLSJNSKJSSHHMLIHRMMHSKHRGIJHSLLSSQHSLIISJB99:?GLEJESIPSMSSH>:;:;JRFOSLIOKFSKKKSSHOSJSIJS>==<:<9;;ACGMF@AEPKFHSKNSNERSSOJGKKSMSJHRKLHHNOHKKSSSPSJKKMIRJHKMLHSNSSSSSISSQS===>===MSQMNJNSPNSHGSGHGLLFGMLSFIILJNKSNRHMKKKKIIKKJKKJSLSJIIGLLIHD410,++)'&&'''%%%&&&&(((&&'(&'($$$%'(()3457@>.,,,,1&&&((-+++@BIRKSISIPSSMKHJISSJLE?@BBAGSKSJSPSKIPHSKSSSSNSSHHMSJGDCCJMSSSLNSSMLHKL
SMSJJMKSSKOMNSSHSSMMLSMJKSSISGSJOJOFIN>>==>SJSKSSKISSISSKNISSLHFSSSSRHGISIIGHGN@@CCBGOKGFHIKHKJISHRHJSSKSHSSKISIHRHKSKSGEJNMSJHSJNNSJNSGJHSJJSSHHSMOSSSHSSJSJHSPSLSGSKSNKNNGGHLGHSNPSJNPKJOSSGJNSSSKKHSLSSSLJSSILKSIGNSSSLISKSRHSILKDHIIPSSHSOSRSSMLMMOKLIHGNKQMJSOFEFLBFEPOFIKHLSHSKNGSSSECLHJJHLSSMSIKSSSSSSSSHHINMSJGEKIKSIJB><<<==:4433/00HSIIGEJHKJGSSSSJSSSISGLJSGIRLNILSMHHJGSLHIJSNINGSSMJJHHHJDDFHLNQIKLSKSMKKSSMOKMLJIMJIJSSHSMSOLSKSNSKSSSGOHIPSSHGISLSJKJSOLOJOGKNSMPKSSFSEQKJKISPJLOSSMHLJJSGIJC>@,,--.HGEGHGB80--,++(&'()((()BFADGR<<;;;<CECDMMSIJSSKSSKKSSHILSSQLSNA@AA@HHSNPIKLJSSSSHSKSLSFNKEGFMF:<20GJSFEHGKSKGNLSLSSLSLIJHQSISHMB76S:9989JSSSKFIJESKMSLHISHKSGS8GEIGSFSSGIEAA55=?@BJIKSQLRLGOHKHJIIHONHSSSNSLLJGSLKLGSSGME<;>100004100000EIELIJGCNIHMMHHMSSJHI?:98,,)((%%%$$%''&),-2367622658EIFCABB?8889ESNSKSLGFIJFDJFEGGJSLSSIQSHSFGHSIQSSJFDDCCESPSKMPSJILJKHLNSHJHMHKJIFHJ
FCDCDOPSIHOJJSMLJSSHKIIKIPGMIKSSM?>>?H;;<<<EFFGSQBCLIKFHLGSISISPJSRLSKSSQIHSSNJDMNLKSGHKFGISKSPSKILSKNSHSDHHSHA@@JSISSSGJOJRSQJHHKHSSISGLSHKSGISSJMSJGKNOSIISSNKSJSLKLIH@NRIENINESIJLJKHSNISSHSISEBFEFNSHMHSLOKHLJSOSIIIS
JSPIJIMSLSKKSILSPSQHKMSHMSKGKLKLIKKSSHHHIKGILIEQMLOSHSNGHFFHHPSDRKEMHLKSSSSSHMRSJGSSSJHQMSSMMSSJJHOKSLKJPSIQKFIJMJLSMKNSLLSIOSKSJSSSJJCF>;;@AASSMPSSJSSNNNSSSKHSHKSJSJRHPHLSKKHKHFCODJHHEGECB)&&&&*((112GOKIKHFGSSLHHKSSNISLI@MJSSFHFLSSLNLMJJSSJNS??>??SSKSQHIKLPSIGJSJBA642222>??AFKFHSIILGQSHILSMLIJKJILJJOSHSSKIHHRGJSPSSFSGIJSL;:981023356AADCCCEHSHHOSJHQISLPKMFHH:4554448=@GNSNJMILHSKJKKMSMSNKIJISKJSKS<<1111364311BEEESNSSJSMLLSNHILSLJSJNJKJMJJHKOSLHIIFFEHEFLLSNG;40()*3767@ADCSSHSGSSPSHMSQJOIAFC?>>>>A33333;@>2?:9:69<?<GH56DBBDEGSLGPJSMSFSHRSJGSIGMSPSSIOJIIGSKSNKSKSHPSKLSSSSJSHIJSS?D-----SSNKLHMSFSILSHOSLSKIIJIIKSSSJISIHKLLSJISKPQISKKSLGAISKGFEB7D@?
??KIGHFAAJLSJJGSMFSPFMISKSJSMLIJKFKJSSSILMMHIGGSPSKKHSSRSJSLNKPOSLNSJONQIISRLISKNJHQIJGQSLIISNSHPSHSMSJKSGSOMRSOISSJSLSJGLKHSLSHIKSMSJSLSGKHJRKKGJKFKHIILJIB@90/42//1932222344444:;<CJFKSILLMFJSHIEE==CCSSJLHSGHIJSJLSJSSISSSSNJNGSKGIFSJSSIKPLKJSSPSJSHRSJISSJSSJSHSKIHMSSSQJHJSSGGSSHSKSRIIJKSJKME))*477>BBCJGSSPHKLSLKJPIKSSSSOHMSHKSGSISOSSSSPSGILFHIGEJ=<;;;KSPHSGNLSKGFGFIHSSJJSJMHRSSLMPKKKOSJHNHOMLSQNLLGKQSSSJFSHSISFNSQSIHJHSSQILNSSIHJISSIHFJHSISGNFGSLGKNOIKHQJSHSQSHRIISJNSGHSIGNJSSKLSSOJGSSLJOSLSISPHJHHJMIIKJHSMSLLNSJKSPHJSSSRISLKJSSHLMSJKSJILHJKSIJSFGDDCDBBCSIKSFFGDACHSSMJSSSKLSRKFKIJHGFDPQESSJHISSSLKJJIPKJJGSSJSGKHGF>=DJISSSSIJSKSKJQISMSH=;:98888
755.)&%      qs:i:21 du:f:9.5696     ns:i:47848      ts:i:592        mx:i:3  ch:i:843        st:Z:2024-04-08T11:56:24.693+00:00      rn:i:5741       fn:Z:PAW37422_pass_b74e10a2_68ebe454_253.pod5   sm:f:100.808    sd:f
:28.356     sv:Z:quantile   dx:i:0<EMAIL_ADDRESS>      MN:i:3722            MM:Z:A+a.,0,17,2,6,3,0,0,3,12,0,12,2,13,1,9,5,0,3,12,8,0,0,0,0,0,0,0,0,2,7,0,0,0,2,0,0,3,0,0,0,2,9,63,0,0,0,3,0,0,47,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,13,0,0,0,1,0,0,6,2,0,0,0,0,0,0,0,0,0,0,0,0,0,8,0,0,4,0,3,1,1,0,17,0,0,0,50,0,1,23,39,0,0,43,1,3,0,0,0,0,4,0,0,0,0,0,0,0,0,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,1,12,1,14,0,0,0,3,4,0,0,0,0,0,0,0,3,2,0,3,6,0,39,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,2,1,0,0,1,0,0,2,2,8,0,17,4,0,0,0,12,14,0,1,0,0,0,4,0,0,0,1,0,0,0,1,2,5,0,0,1,33,12,0,0,12,0,1,41,1,0,6,1,1,4,8,0,0,0,0,0,0,0,0,0,0,0;C+h.,9,0,2,3,0,2,0,6,3,2,2,0,1,1,7,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,5,3,1,0,0,0,0,0,3,0,0,0,0,0,1,1,0,0,1,11,14,0,0,1,0,0,0,13,0,0,0,0,0,0,0,0,0,1,0,0,2,0,0,0,2,0,0,0,0,0,0,0,0,4,0,0,0,0,1,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,2,3,0,0,0,0,0,0,0,0,1,0,2,2,0,0,0,5,6,4,0,0,0,0,0,0,8,1,0,1,0,0,16,4,6,0,1,0,1,0,0,1,2,0,0,0,9,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,8,0,0,5,2,3,0,0,4,1,0,0,0,0,0,1,12,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,0,0,22,0,8,3,0,0,3,1,0,4,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,1,0,1,0,0,0,0,0,0,5,1,0,0,1,2,2,8,16,0,0,0,0,0,0,7,1,1,4,9,2,0,0,0,8,1,0,0,0,0,0;C+m.,9,0,2,3,0,2,0,6,3,2,2,0,1,1,7,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,5,3,1,0,0,0,0,0,3,0,0,0,0,0,1,1,0,0,1,11,14,0,0,1,0,0,0,13,0,0,0,0,0,0,0,0,0,1,0,0,2,0,0,0,2,0,0,0,0,0,0,0,0,4,0,0,0,0,1,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,2,3,0,0,0,0,0,0,0,0,1,0,2,2,0,0,0,5,6,4,0,0,0,0,0,0,8,1,0,1,0,0,16,4,6,0,1,0,1,0,0,1,2,0,0,0,9,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,8,0,0,5,2,3,0,0,4,1,0,0,0,0,0,1,12,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,0,0,22,0,8,3,0,0,3,1,0,4,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,1,0,1,0,0,0,0,0,0,5,1,0,0,1,2,2,8,16,0,0,0,0,0,0,7,1,1,4,9,2,0,0,0,8,1,0,0,0,0,0;
ML:B:C,14,13,53,12,35,21,16,14,112,191,38,66,13,12,12,39,111,24,13,22,80,72,66,148,40,35,28,14,28,35,40,29,16,13,26,251,29,241,106,70,12,171,107,16,21,12,12,16,18,12,12,17,15,12,17,22,13,14,22,25,46,18,71,17,24,17,23,17,48,20,25,15,20,15,78,20,139,100,80,74,146,146,112,125,167,117,108,87,25,51,12,38,46,12,15,13,12,111,18,21,20,19,14,12,31,26,30,41,59,39,17,12,13,56,77,45,31,14,53,29,222,132,113,74,21,97,14,14,18,17,22,25,34,16,68,14,210,38,14,25,16,159,12,13,102,13,15,17,18,34,126,38,22,33,25,19,39,93,47,76,15,21,15,39,14,15,14,32,21,35,43,62,49,51,64,36,36,15,21,62,45,255,255,29,42,38,40,17,227,32,37,29,15,226,91,21,156,42,85,112,128,14,132,14,88,206,12,14,13,16,15,15,40,38,53,51,53,63,30,26,87,12,159,14,14,13,90,21,12,14,24,63,22,13,14,12,20,112,133,55,43,108,31,138,13,16,17,59,29,182,18,15,8,0,3,8,3,1,1,3,4,2,5,5,16,8,2,9,28,40,33,25,33,18,30,125,7,51,6,2,2,2,2,1,4,5,4,4,3,2,4,8,15,100,9,8,12,12,147,19,13,30,6,7,5,2,9,16,15,12,9,6,5,4,2,3,3,11,5,6,6,3,14,255,30,10,7,22,5,8,11,6,6,4,6,8,10,6,7,6,5,5,5,3,4,0,0,7,11,9,7,0,5,2,29,27,71,47,3,7,2,2,1,37,78,28,7,8,17,18,1,11,9,4,11,7,9,5,2,1,2,3,3,2,2,2,6,3,44,9,23,39,1,3,9,7,18,6,7,8,7,4,21,8,13,7,6,6,4,47,6,7,5,9,15,19,34,22,11,11,0,5,4,6,13,130,57,230,22,11,11,21,9,12,21,27,86,5,5,7,8,10,10,14,16,5,7,5,4,7,7,9,7,8,3,3,4,11,5,7,1,24,5,4,8,7,7,9,49,7,6,6,4,3,4,2,8,2,5,5,8,11,12,3,10,6,17,11,2,12,3,2,2,5,5,2,6,4,20,24,9,16,13,10,11,13,12,14,4,12,4,2,2,25,28,3,4,6,3,4,2,6,11,10,13,11,10,10,3,3,7,7,3,4,2,0,1,3,12,1,3,2,15,6,4,10,13,8,14,11,9,4,4,9,15,14,8,10,7,3,4,4,5,20,15,16,4,18,1,8,8,11,12,5,4,6,3,3,20,8,7,8,13,4,3,11,7,3,5,13,66,13,2,3,3,7,7,9,12,4,3,1,3,2,106,92,5,5,17,10,2,39,21,8,10,9,5,63,7,16,255,13,24,12,37,254,252,22,12,13,13,240,13,254,16,36,40,40,39,52,50,24,24,20,79,19,13,14,12,12,254,16,12,13,14,15,13,14,22,9,7,18,17,14,240,36,235,17,225,12,16,18,12,22,38,16,22,17,13,16,16,13,17,16,22,22,18,28,12,14,0,6,12,23,46,18,22,20,18,19,12,21,16,18,15,20,31,13,18,15,13,18,13,255,16,17,18,200,255,19,18,43,65,137,90,25,37,253,12,254,55,38,37,18,12,15,26,254,244,12,12,21,17,20,14,42,254,12,14,14,14,12,12,14,12,27,246,13,11,254,12,15,19,100,18,16,247,22,13,26,12,13,14,13,12,13,14,16,17,13,14,27,36,42,44,29,33,255,14,25,232,85,94,110,8,70,26,29,59,31,4,234,51,44,18,18,21,28,27,28,26,27,17,20,15,14,17,19,17,14,20,13,15,15,24,14,16,254,12,15,12,16,18,16,19,50,13,22,21,15,13,14,12,12,45,18,16,20,27,13,252,20,19,41,29,14,12,14,13,16,21,21,12,24,19,224,55,35,26,30,34,26,31,24,28,13,212,251,22,31,229,76,246,28,23,19,20,12,24,36,23,23,244,23,25,17,17,21,20,18,16,13,17,14,16,47,254,14,16,11,12,12,21,24,16,24,26,23,16,15,58,26,23,20,28,26,16,14,13,17,31,29,29,251,79,254,21,16,20,28,20,19,22,23,28,11,12,248,15,25,12,12,12,21,14,20,14,189,10,14,13,24,28,14,16,21,15,13,254,22,253,15,2,13,16,30,19,12,29,234,16,24,29,22,22,30 NM:i:25 ms:i:4282       AS:i:4276       nn:i:0  de:f:0.00860507 tp:A:P  cm:i:350        s1:i:1968       s2:i:0  MD:Z:169G154G1G154T72C23C0A4^TA501^TTGG3T77A55A38A98^TG119T721  rl:i:400        SA:Z:1,5438,-,2207S1514M1I,60,15;
Is there an error because the label of methylation recorded in my bam file is MM instead of mm

I see. The read you are showing here only has 6mA calls, but MethPhaser can only phase with 5mC calls.

MM:Z:A+a? is for 6mA calls. C+m? is for 5mC.

MM:Z:A+a.,0,17,2,6,3,0,0,3,12,0,12,2,13,1,9,5,0,3,12,8,0,0,0,0,0,0,0,0,2,7,0,0,0,2,0,0,3,0,0,0,2,9,63,0,0,0,3,0,0,47,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,13,0,0,0,1,0,0,6,2,0,0,0,0,0,0,0,0,0,0,0,0,0,8,0,0,4,0,3,1,1,0,17,0,0,0,50,0,1,23,39,0,0,43,1,3,0,0,0,0,4,0,0,0,0,0,0,0,0,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,1,12,1,14,0,0,0,3,4,0,0,0,0,0,0,0,3,2,0,3,6,0,39,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,2,1,0,0,1,0,0,2,2,8,0,17,4,0,0,0,12,14,0,1,0,0,0,4,0,0,0,1,0,0,0,1,2,5,0,0,1,33,12,0,0,12,0,1,41,1,0,6,1,1,4,8,0,0,0,0,0,0,0,0,0,0,0;C+h.,9,0,2,3,0,2,0,6,3,2,2,0,1,1,7,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,5,3,1,0,0,0,0,0,3,0,0,0,0,0,1,1,0,0,1,11,14,0,0,1,0,0,0,13,0,0,0,0,0,0,0,0,0,1,0,0,2,0,0,0,2,0,0,0,0,0,0,0,0,4,0,0,0,0,1,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,2,3,0,0,0,0,0,0,0,0,1,0,2,2,0,0,0,5,6,4,0,0,0,0,0,0,8,1,0,1,0,0,16,4,6,0,1,0,1,0,0,1,2,0,0,0,9,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,8,0,0,5,2,3,0,0,4,1,0,0,0,0,0,1,12,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,0,0,22,0,8,3,0,0,3,1,0,4,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,1,0,1,0,0,0,0,0,0,5,1,0,0,1,2,2,8,16,0,0,0,0,0,0,7,1,1,4,9,2,0,0,0,8,1,0,0,0,0,0;C+m.,9,0,2,3,0,2,0,6,3,2,2,0,1,1,7,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,5,3,1,0,0,0,0,0,3,0,0,0,0,0,1,1,0,0,1,11,14,0,0,1,0,0,0,13,0,0,0,0,0,0,0,0,0,1,0,0,2,0,0,0,2,0,0,0,0,0,0,0,0,4,0,0,0,0,1,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,2,3,0,0,0,0,0,0,0,0,1,0,2,2,0,0,0,5,6,4,0,0,0,0,0,0,8,1,0,1,0,0,16,4,6,0,1,0,1,0,0,1,2,0,0,0,9,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,8,0,0,5,2,3,0,0,4,1,0,0,0,0,0,1,12,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,0,0,22,0,8,3,0,0,3,1,0,4,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,1,0,1,0,0,0,0,0,0,5,1,0,0,1,2,2,8,16,0,0,0,0,0,0,7,1,1,4,9,2,0,0,0,8,1,0,0,0,0,0;
MM has not only A+a but also C+m

I see, yes indeed this is a bug of MethPhaser. I would suspect that there is some reads that only have 6mA call but do not have 5mC calls. I will try to apply a filter to skip those reads.

I've made the changes, could you please check the MethPhaser version of https://github.com/treangenlab/methphaser/tree/Fu-Yilei-patch-1? Or if you could provide an example BAM file I can do the test.

subset.zip
This is a subset of my data.
Do I need to reinstall mathphaser

yeah you need to clone the version in the branch I provided

Thank you very much for your help, waiting for your test success using the subset file

I used the new version you changed yesterday, but the error is still reported, but it seems to be different：
/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/meth_phaser_parallel:235: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas
phased_df_chr.get_group(chromosome).iterrows()
/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import require
Traceback (most recent call last):
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 1477, in
main(sys.argv[1:])
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 1443, in main
) = get_assignment_max(
^^^^^^^^^^^^^^^^^^^
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 910, in get_assignment_max
assignment_df = get_base_modification_list_snp_block(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 605, in get_base_modification_list_snp_block
for i in mm[methylation_identifier]:
~~^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: ('C', 1, 'm')

sorry forgot to change one spot in the code, now should be fine :)

I tried again, but I got a mistake：
/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/meth_phaser_parallel:235: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass (name,) instead of name to silence this warning.
phased_df_chr.get_group(chromosome).iterrows()
/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import require
Traceback (most recent call last):
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 1471, in
main(sys.argv[1:])
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 1437, in main
) = get_assignment_max(
^^^^^^^^^^^^^^^^^^^
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 898, in get_assignment_max
base_modification_list = get_base_modification_dictionary(  # build the dictionary with snp phased reads
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 243, in get_base_modification_dictionary
for i in mm[methylation_identifier]:  # Remora only output one type of score: c 1 m/c 0 m, but this part can be improved for other methlyation callers
~~^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: ('C', 1, 'm')

Sorry about the back and forth. Was this the program from this patch? https://github.com/treangenlab/methphaser/tree/Fu-Yilei-patch-1

I did reinstall it from here : https://github.com/treangenlab/methphaser/tree/Fu-Yilei-patch-1
My input file takes up too much memory and cannot be uploaded to you via github, even after compression. How should I give you my input file

you could limit your vcf, gtf and bam to the first 3 phaseblock on chr1. I think those could be sufficient. Thanks.

“you could limit your vcf, gtf and bam to the first 3 phaseblock on chr1. I think those could be sufficient.”
I'm sorry, how do I do this? This is my first contact with haplotype related knowledge, I really do not know how to do

Hey no worries!
For gtf file, keep only first 3 lines.
For bam file, use samtools with samtools view function with specifying region chr1:0-x (x = the phaseblock end of the 3rd phaseblock)
for vcf file, use vcftools view chr1:0-x too.
I have put the samtools and vcftools repo here: https://samtools.github.io/bcftools/bcftools.html#view https://www.htslib.org/doc/samtools-view.html

Thank you very much for your help
train.gz
I made specific operations in the files according to the suggestions you gave me but I kept the first chromosome in the gtf file.
The reference genome I used was this version of the pig genome downloaded from ensemble：

Hey sorry for the delay, but I still need a week or so to actually look into this issue. I would suspect that there are some reads only have 6ma or 5hmc but does not have 5mc on it so the bug exists. I don't have a huge amount of time to debug this right now but will look into it next week. Thanks!

Question in this vane...can Methphaser process C+h tag info, or would this also cause a hang-up or poor phasing?

MethPhaser ignores C+h because it is not very accurate in some basecaller versions. As long as you have C+m MethPhaser can do phasing.

Hi,
As long as I have your attention, I've noticed that Methphaser works better
and worse depending on some use cases. I'm assuminng this most likely has
to do with the underlying heterozygosity in methylation between the
alleles. Do you have any information on which regions here work better or
worse?
Best regards,
Dvid
On Mon, 5 Aug 2024 at 18:04, Yilei Fu @.***> wrote:

MethPhaser ignores C+h because it is not very accurate in some basecaller
versions. As long as you have C+m MethPhaser can do phasing.
—
Reply to this email directly, view it on GitHub
https://github.com/treangenlab/methphaser/issues/22#issuecomment-2269419159,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/A7KF4B3LDRMDNUN62O7V333ZP6PCPAVCNFSM6AAAAABK4SWL4WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRZGQYTSMJVHE
.
You are receiving this because you commented.Message ID:
@.***>

Sorry this depends. First the landscape of human genome methylation is still not fully revealed. This would require a large population scale analysis to discover so I cannot tell you which region usually has more heterozygosity and which region does not. On the other hand, the input sample type also affects a lot. For example we included a blood sample which has shitty ONT reads in our paper, and it shows that the improvement is not huge because the SNP phasing is already shitty. Happy to chat more if you like.
I think you can understand this as: when you have a reasonable SNP phased genome and the gap is not too large, MethPhaser can come in and help

Hi,
Sure I have a bunch of questions, would love to learn more about the program and maybe some more insights you have.

Long time no see. I have been testing other processes recently, so I am very sorry for not communicating with you in time.May I ask whether this process has been successfully run out with the data I gave


SAA-1965: Add scheduled instance start and end time to each attendance result

Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 84.32%. Comparing base (0847286) to head (0b5d0d4).

Additional details and impacted files
@@            Coverage Diff            @@
##               main    #1040   +/-   ##
=========================================
  Coverage     84.32%   84.32%
- Complexity     3677     3679    +2
=========================================
  Files           381      381
  Lines         12387    12393    +6
  Branches       1062     1062
=========================================
+ Hits          10445    10451    +6
  Misses         1459     1459
  Partials        483      483

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.


with path

@rultor release, tag is 0.0.4

@rultor release, tag is 0.0.4

@yegor256 OK, I will release it now. Please check the progress here


Add public API analysers

We should add the Microsoft.CodeAnalysis.PublicApiAnalyzers analyser to avoid making unintentional binary-breaking changes.
Examples:

https://github.com/domaindrivendev/Swashbuckle.AspNetCore/pull/2418#pullrequestreview-2000191284.
https://github.com/domaindrivendev/Swashbuckle.AspNetCore/pull/2610#discussion_r1565295657
https://github.com/domaindrivendev/Swashbuckle.AspNetCore/pull/2677#discussion_r1565538897
https://github.com/domaindrivendev/Swashbuckle.AspNetCore/pull/2718#discussion_r1566883950
https://github.com/domaindrivendev/Swashbuckle.AspNetCore/pull/2803#discussion_r1566871645

Will do a PR for this once 6.7.0 ships.


no such file or directory: dcosqb.c

Trying to install scipy via pip or homebrew (both give me the same error) crashes with the above clang error. I'm on Yosemite, trying to install scipy into a virtualenv; I was able to do so before upgrading to Yosemite. Googling led to me uninstalling and reinstalling gcc and libmpc, with no success. Any suggestions?

I've not seen this one before. Can you please put your complete build log in a gist and link to it?

Also, tell us how you installed Python itself, your Fortran compiler, and the output of
$ gcc --version
$ gfortran --version

Here's the gist: https://gist.github.com/sirpercival/f1e6e56939a79ad5a540
I'm using the version of python included with Kivy. Thanks!

Here's the error:
f77.sh:f77: scipy/fftpack/src/dfftpack/dcosqb.f
/usr/stsci/iraf/iraf/unix/hlib//f77.sh: line 183: /usr/stsci/iraf/iraf/unix/bin.macosx//f2c.e: No such file or directory
clang: error: no such file or directory: 'dcosqb.c'
clang: error: no input files

You do have gfortran installed but also this weird f77.sh compiler, I've never seen that on OS X:
Fortran f77 compiler: /usr/stsci/iraf/iraf/unix/hlib//f77.sh -Wall -g -ffixed-form -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops

Fortran f90 compiler: /usr/local/bin/gfortran -Wall -g -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops

Fortran fix compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops

You need to remove that compiler from your path, so the build starts using gfortran for Fortran 77 files.


Document what goes into github.properties

What are, and how do we define:
github_oauth
github_oauth_scheme
github_secret
github_client
Is it ok that they are just left to DEFAULT?

When they are DEFAULT it won't login.
I will change the install guide later today, forgot it when creating the PR

Until I fix it here's the steps.

You need to create a github application (https://github.com/settings/applications/new)
Create a github.properties in the root folder of the repo
Add these three value too the github.properties

GITHUB_CLIENT=your_application_client_id
GITHUB_SECRET=your_application_client_secret
GITHUB_CALLBACK=your_callback_url

(The callback url need to be in the format "your_schema://whatever_you_want")

Hey
If you are using GithubAndroidSdk from @alorma,
I changed how properties can be loaded.
Now, it supports manifest and buildconfig, or you can use a file, etc.
I will upload a new release to bintray today afternoon.

I added a gitter chat for discuss Android SDK
https://gitter.im/gitskarios/GithubAndroidSdk

It's added to the README so I'll close this now


Vagrant to use group_vars/all.yml

Addresses #929

Vagrant is looking for group_vars in the inventory directory, added a sym link to group_vars

Confirmed on Virtualbox + CoreOS & VirtualBox + CentOS

Removes the Virtualbox 1.8 dependency

Removes variables in inventory file

1:1 match to the BM deployment in using group_vars as it should.

CC @adamschaub @rutsky @danehans

@stephenrlouie currently Vagrant controls not only some variables in inventory file, but also whole inventory generation: list of nodes with their addresses (which in some cases only Vagrant can know), number of nodes, master/etcd/node separation.
I don't think it's feasible to leave all this items configuration on user, when Vagrant can do this job automatically.
Yes, there is a problem that group_vars are not applied in Vagrant+Ansible run. Some of these variables are explicitly set by Vagrant, but in general I would expect to have ansible-related solution: somehow add group_vars from parent directory to search path of Ansible in vagrant directory.

@rutsky sorry for the very late response, had to prioritize other work, then I was traveling.
Contrib would still use vagrant to generate the inventory, this addition is putting group_vars in the search path of ansible, as far as I know there is no other way to do this. You can specify role paths, but cannot specify group_var paths to search on.
Copied from [ansible's site] (http://docs.ansible.com/ansible/intro_inventory.html)

Tip: In Ansible 1.2 or later the group_vars/ and host_vars/ directories can exist in the playbook directory OR the inventory directory. If both paths exist, variables in the playbook directory will override variables set in the inventory directory

Goal:

remove the 1.8 dependency and the python_interpreter lines from the vagrantfile
let us support a playbooks directory to store top level playbooks as in #967

I understand the addition of a script to generate the link isn't ideal, but from what I know ansible does not provide any way to set the group_var path.

Let's rebase and merge after #967 is merged

@ingvagabund seems like ansible upstream doesn't want to make it configurable. https://github.com/ansible/ansible/issues/13051

I'm hesitant to merge this PR, it is very sloppy and we need a better way to do this.

@ingvagabund seems like ansible upstream doesn't want to make it configurable. ansible/ansible#13051

Sorry, I meant make it configurable for the setup.sh file. Something like:
$GROUP_VARS_DIR=${1:-../../../../../group_vars/}

ln -fs ${GROUP_VARS_DIR} .vagrant/provisioners/ansible/inventory

@ingvagabund I get an invalid path doing $GROUP_VARS_DIR=${1:-../../../../../group_vars/}
It works if it was just in the ln -fs line though.

@ingvagabund should be good for configuration now

This is much more better. User can carry his own steps to set the group_vars or call the setup.sh.

@jasonbrooks, @stephenrlouie what about to put a code into Vagrantfile:207 (cluster_ansible_provision function) to check if ../inventory/ group_vars directory exists and if so copy the directory under .vagrant/provisioners/ansible/inventory? No need for the setup.sh function then. Each time group_vars/main.yml gets changed, changes get reflected to vagrant as well.

The ansible playbook is already hardcoded in Vangrantfile (../playbooks/deploy-cluster.yml) anyway.

Updating the Vagrantfile here https://github.com/kubernetes/contrib/pull/1606.

Resolved via #1606.


problem in checkpoint

I used tf 0.9.
When I restore the checkpoint i get the error:
Traceback (most recent call last):
File "", line 1, in
runfile('/media/m/E/Deep/proj/1/t.py', wdir='/media/m/E/Deep/proj/1')
File "/home/m/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 714, in runfile
execfile(filename, namespace)
File "/home/m/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 89, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File "/media/m/E/Deep/proj/1/t.py", line 70, in
saver.restore(sess, ckpt.model_checkpoint_path) # restore all variables
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/training/saver.py", line 1105, in restore
{self.saver_def.filename_tensor_name: save_path})
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 333, in run
The optional options argument expects a [RunOptions] proto. The options
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 573, in _run
elif isinstance(fetches, dict):
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 648, in _do_run
for fetch, result in zip(unique_fetches, results):
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/client/session.py", line 668, in _do_call
"""Runs a step based on the given fetches and feeds.
NotFoundError: Tensor name "global_step_7" not found in checkpoint files ./ckpt_dir/model.ckpt-0
[[Node: save_18/restore_slice_438 = RestoreSlice[dt=DT_INT32, preferred_shard=-1, _device="/job:localhost/replica:0/task:0/cpu:0"](_recv_save_18/Const_0, save_18/restore_slice_438/tensor_name, save_18/restore_slice_438/shape_and_slice)]]
Caused by op 'save_18/restore_slice_438', defined at:
File "/home/m/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/start_ipython_kernel.py", line 205, in
ipythonkernel.start()
File "/home/m/anaconda3/lib/python3.5/site-packages/ipykernel/kernelapp.py", line 442, in start
ioloop.IOLoop.instance().start()
File "/home/m/anaconda3/lib/python3.5/site-packages/zmq/eventloop/ioloop.py", line 162, in start
super(ZMQIOLoop, self).start()
File "/home/m/anaconda3/lib/python3.5/site-packages/tornado/ioloop.py", line 883, in start
handler_func(fd_obj, events)
File "/home/m/anaconda3/lib/python3.5/site-packages/tornado/stack_context.py", line 275, in null_wrapper
return fn(*args, **kwargs)
File "/home/m/anaconda3/lib/python3.5/site-packages/zmq/eventloop/zmqstream.py", line 440, in _handle_events
self._handle_recv()
File "/home/m/anaconda3/lib/python3.5/site-packages/zmq/eventloop/zmqstream.py", line 472, in _handle_recv
self._run_callback(callback, msg)
File "/home/m/anaconda3/lib/python3.5/site-packages/zmq/eventloop/zmqstream.py", line 414, in _run_callback
callback(*args, **kwargs)
File "/home/m/anaconda3/lib/python3.5/site-packages/tornado/stack_context.py", line 275, in null_wrapper
return fn(*args, **kwargs)
File "/home/m/anaconda3/lib/python3.5/site-packages/ipykernel/kernelbase.py", line 276, in dispatcher
return self.dispatch_shell(stream, msg)
File "/home/m/anaconda3/lib/python3.5/site-packages/ipykernel/kernelbase.py", line 228, in dispatch_shell
handler(stream, idents, msg)
File "/home/m/anaconda3/lib/python3.5/site-packages/ipykernel/kernelbase.py", line 391, in execute_request
user_expressions, allow_stdin)
File "/home/m/anaconda3/lib/python3.5/site-packages/ipykernel/ipkernel.py", line 199, in do_execute
shell.run_cell(code, store_history=store_history, silent=silent)
File "/home/m/anaconda3/lib/python3.5/site-packages/IPython/core/interactiveshell.py", line 2723, in run_cell
interactivity=interactivity, compiler=compiler, result=result)
File "/home/m/anaconda3/lib/python3.5/site-packages/IPython/core/interactiveshell.py", line 2831, in run_ast_nodes
if self.run_code(code, result):
File "/home/m/anaconda3/lib/python3.5/site-packages/IPython/core/interactiveshell.py", line 2885, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 1, in
runfile('/media/m/E/Deep/proj/1/t.py', wdir='/media/m/E/Deep/proj/1')
File "/home/m/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 714, in runfile
execfile(filename, namespace)
File "/home/m/anaconda3/lib/python3.5/site-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 89, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File "/media/m/E/Deep/proj/1/t.py", line 57, in
saver = tf.train.Saver()
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/training/saver.py", line 845, in init
restore_sequentially=restore_sequentially)
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/training/saver.py", line 515, in build
filename_tensor, vars_to_save, restore_sequentially, reshape)
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/training/saver.py", line 271, in _AddRestoreOps
values = self.restore_op(filename_tensor, vs, preferred_shard)
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/training/saver.py", line 186, in restore_op
preferred_shard=preferred_shard)
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/ops/io_ops.py", line 201, in _restore_slice
file_pattern, tensor_name, shape_and_slice, base_type,
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/ops/gen_io_ops.py", line 325, in _restore_slice
def _restore_slice(file_pattern, tensor_name, shape_and_slice, dt,
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/ops/op_def_library.py", line 704, in apply_op
op_def=op_def)
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/framework/ops.py", line 2249, in create_op
# specified for this op_type.
File "/home/m/anaconda3/lib/python3.5/site-packages/tensorflow/python/framework/ops.py", line 1224, in init
raise TypeError("Control input must be an Operation, "
how can i solve this problem?

Are you sure that the ckpt_dir/model.ckpt-0 file exists in your checkpoint directory?  Normally a later step would be loaded, after some training had been done. But basically tf.restore is trying to restor me a specific file. Make sure the file you specify is there.

Yes , this file exists.
This is my code:
`import tensorflow as tf
import input_data
import os
checkpoint_dir='./ckpt_dir/'
mnist = input_data.read_data_sets("MNIST_data", one_hot = True)
x = tf.placeholder(tf.float32, shape = [None , 784])
y_ = tf.placeholder(tf.float32, [None, 10])
sess = tf.InteractiveSession()
def load_model(sess, saver, checkpoint_dir ):
ckpt = tf.train.get_checkpoint_state(checkpoint_dir)
if ckpt and ckpt.model_checkpoint_path:
print(ckpt.model_checkpoint_path)
saver.restore(sess, ckpt.model_checkpoint_path)
else:
if not os.path.exists(checkpoint_dir):
os.makedirs(checkpoint_dir)
sess.run(init)
return
def weight_variable(shape):
initial = tf.truncated_normal(shape, stddev = 0.1)
return tf.Variable(initial)
def bias_variable(shape):
initial = tf.constant(0.1, shape= shape)
return tf.Variable(initial)
def conv2d(x, W):
return tf.nn.conv2d(x, W, strides = [1, 1, 1, 1], padding = "SAME")
def max_pool_2x2(x):
return tf.nn.max_pool(x, ksize = [1, 2, 2, 1], strides = [1, 2, 2, 1],
padding = "SAME")
W_conv1 = weight_variable([5, 5, 1, 32])
b_conv1 = bias_variable([32])
x_image = tf.reshape(x, [-1, 28, 28, 1])

h_conv1 = tf.nn.relu(conv2d(x_image, W_conv1))
h_pool1 = max_pool_2x2(h_conv1)

W_conv2 = weight_variable([5, 5, 32, 64])
b_conv2 = bias_variable([64])
h_conv2 = tf.nn.relu(conv2d(h_pool1, W_conv2))
h_pool2 = max_pool_2x2(h_conv2)
W_fc1 = weight_variable([7764, 1024])
b_fc1 = bias_variable([1024])
h_pool2_flat = tf.reshape(h_pool2, [-1, 7764])
h_fc1 = tf.nn.relu(tf.matmul(h_pool2_flat, W_fc1) + b_fc1)

keep_prob = tf.placeholder(tf.float32)
h_fc1_drop = tf.nn.dropout(h_fc1, keep_prob)

W_fc2 = weight_variable([1024, 10])
b_fc2 = bias_variable([10])
y_conv = tf.nn.softmax(tf.matmul(h_fc1_drop,W_fc2) +b_fc2)

cross_entropy = tf.reduce_mean(-tf.reduce_sum(y_ * tf.log(y_conv), reduction_indices = [1]))
train_step = tf.train.AdamOptimizer(1e-4).minimize(cross_entropy)
correct_prediction = tf.equal(tf.argmax(y_conv, 1), tf.argmax(y_, 1))
accuracy = tf.reduce_mean(tf.cast(correct_prediction, tf.float32))
init = tf.initialize_all_variables()
saver = tf.train.Saver()
load_model(sess, saver, checkpoint_dir)
for i in range(1):
batch = mnist.train.next_batch(50)
if i%10 == 0:
train_accuracy = accuracy.eval(feed_dict = {x : batch[0] , y_ : batch[1], keep_prob : 1.0})
print("step %d, training accuracy %g"%(i, train_accuracy))
train_step.run(feed_dict = {x : batch[0], y_ : batch[1], keep_prob : 0.5})

print("test accuracy %g"%accuracy.eval(feed_dict={
x: mnist.test.images, y_: mnist.test.labels, keep_prob: 1.0}))
tf.scalar_summary("accuracy", accuracy)
saver.save(sess,checkpoint_dir+'model.ckpt')`

You are repeatedly creating the Saver, that's why you have 8 global_steps. You can fix it by either explicitly creating a new graph tf.Graph(), or reset the default graph by calling tf.reset_default_graph().

If you print out your graph now by calling tf.train.write_graph, you will see that you have 8 copies of what you are building.

The saver should only be called once after you have created the graph, and must be called before init = tf.initializes_all_variable() because without arguments the Saver adds operations to the graph.

tf.initialize_all_variables() just creates an op. It doesn't initialize anything. You need to explicitly run it by calling

sess.run(init)
or
init.run()
Hope that helps.
Sherry

Please reopen if this doesn't fix the problem.

@sherrym
i cant solve this problem. if you can do this with my code can you past it here?


Endpoints /.well-known/* are not included

Describe the bug
We are hosting some endpoints under the /.well-known/ path prefix, this prefix is quite standard and enforced by Android et iOS domain checks.
During the "adapt" phase, endpoint files are not copied by the builder writeServer() funnction. Paths starting with a dot are explicitly filtered out.
Reproduction
I created a reproduction app there https://github.com/trecloux/svelte-kit-dot-path-filtered-out
Logs
No response
System Info
System:
    OS: Linux 5.16 Arch Linux
    CPU: (8) x64 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
    Memory: 373.44 MB / 31.20 GB
    Container: Yes
    Shell: 5.8 - /bin/zsh
  Binaries:
    Node: 17.2.0 - ~/.nvm/versions/node/v17.2.0/bin/node
    Yarn: 1.22.17 - ~/.nvm/versions/node/v17.2.0/bin/yarn
    npm: 8.1.4 - ~/.nvm/versions/node/v17.2.0/bin/npm
  Browsers:
    Chromium: 97.0.4692.71
    Firefox: 96.0
  npmPackages:
    @sveltejs/adapter-node: next => 1.0.0-next.61
    @sveltejs/kit: next => 1.0.0-next.229
    svelte: ^3.44.0 => 3.46.1

Severity
blocking an upgrade
Additional Information
No response

dot prefixed files are often hidden files in a lot of filesystems, and I think hidden files shouldn't be used by Svelte at all. You typically have other dot prefixed files in project You would never want to include, and because it's complicated to decide which dot files should or shouldn't be included, I think better solution than including every dot file should be having config in svelte.config.js where we would be able to tell, which files to include, that are prefixed with dot.

Serve .well-know/file from static folder. I am using the same in production in a project

Serve .well-known/file from static folder. I am using the same in production in a project

Unfortunately, I'm using dynamic content there

I'm automatically rotating keys in a JWKS served from .well-known/jwks.json, and so dynamically generating the content. I could change this to serve the key set from static, but would need to re-build/re-deploy each time I rotated the keys. Being able to 'map' the path in svelte.config.js would be useful if the use of dot prefixed files should be avoided.

https://www.rfc-editor.org/rfc/rfc8615 defines the use of well-known URIs. I wonder if adding  __well-known as a root route could be a place-holder for the .well-known path, be mapped automatically by SvelteKit?

Figured out a workaround. Rename .well-known directory to well-known and rewrite request via hooks. Tested with adapter-node.
I had some problems with content-encoding though, so I manually cleared some headers.
// src/hooks.js
export const handle = ({ event, resolve }) => {
  if (event.url.pathname.startsWith('/.well-known')) {
    const url = new URL(event.url);
    url.pathname = url.pathname.replace('/.well-known', '/well-known');
    const res = await fetch(url.href, {
      method: event.request.method,
      headers: event.request.headers,
    });
    // Some content-encoding related headers cause invalid response. So, we pick
    // the desired ones. There might be a better way to do this.
    const headers = new Headers();
    headers.set('content-type', res.headers.get('content-type'));
    headers.set('cache-control', res.headers.get('cache-control'));
    return new Response(res.body, { headers });
  }

  return resolve(event);
};

I think adapters should respect config.kit.routes and/or include .well-known as an exception.

I think adapters should respect config.kit.routes and/or include .well-known as an exception.

I agree. I think the blanket filter is a bug, but besides @sidvishnoi 's workaround you can work around it this way as well:
Rename .well-known to [...wellKnown=wellKnown]
src/routes/.well-known => src/routes/[...wellKnown=wellKnown]/

and then: src/params/wellKnown.ts is
import type { ParamMatcher } from '@sveltejs/kit';

export const match: ParamMatcher = (param) => {
  const isWellKnownPath = /^\.well-known$/i.test(param);
  return isWellKnownPath;
};

That way the file doesn't start with a . and isn't filtered by the adapter.


Bug: Segmentation violation when running on Ubuntu 22.04

Describe the bug
I've tried using the pre-built release and building from source, but I receive the following error when running:
❯ ./gollama
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x50 pc=0x545177]

goroutine 1 [running]:
net/url.(*URL).EscapedPath(0x0)
	/usr/local/go/src/net/url/url.go:705 +0x17
net/url.(*URL).JoinPath(0x0, {0xc00020dd58, 0x1, 0x8?})
	/usr/local/go/src/net/url/url.go:1201 +0x2f
github.com/ollama/ollama/api.(*Client).do(0xc00011c480, {0x8a3d68, 0xb7dc40}, {0x79cb06, 0x3}, {0x79ee2a?, 0x410305?}, {0x0?, 0x0?}, {0x721fa0, ...})
	/home/joelt/go/pkg/mod/github.com/ollama/ollama@v0.1.44/api/client.go:104 +0xe5
github.com/ollama/ollama/api.(*Client).List(0xc00011c480, {0x8a3d68, 0xb7dc40})
	/home/joelt/go/pkg/mod/github.com/ollama/ollama@v0.1.44/api/client.go:300 +0x85
main.main()
	/home/joelt/tools/gollama/main.go:112 +0x554

To Reproduce
Steps to reproduce the behaviour:

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

Expected behaviour
A clear and concise description of what you expected to happen.
Screenshots

If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):

OS: Ubuntu 22.04
Gollama 1.11.1

Thanks for the bug report, I'll look into this!
@jralmaraz I wonder if it's related to recent logging/config changes, perhaps trying to access a log or config file that doesn't exist?

@joelclimbsthings could you please try updating gollama (e.g. go install github.com/sammcj/gollama@HEAD) and let me know if the problem is resolved?

@sammcj That worked! That's for the quick fix 🙇🏻
I did get a small error regarding parsing the Ollama URL from the config, but fixed it be replacing <IP_ADDRESS>:11434 with http://<IP_ADDRESS>:11434. And the linking worked, thanks!

Ah great thanks for letting me know. I'll update the default config handler to make that a bit more reliable.


Training on a larger dataset

Hi,
Co-author of 1911.11071 here. Nice work! Glad to see that you are building an openly available API for machine learning prediction of QAOA parameters.
I would suggest incorporating the large-scale datasets in available QAOAKit (https://github.com/QAOAKit/QAOAKit) into the training set for MaxCut. It can potentially significantly improve the performance. Happy to help with any issues you might have using QAOAKit.

Hi @rsln-s,
Thank you for pointing me to this resource. It was not on my radar!
It looks like the data is focused on the MaxCut problem. Are there plans to extend it to other popular graph problems?
In my approach, I more or less followed the methodology from the paper, but I also generated data for Vertex Cover, Graph Partition and Stable Set. More problems are planned, not necessarily based on graphs. I am currently evaluating the prediction quality of Kernel Density Estimation for different values of a bandwidth parameter.

The data is indeed focused on MaxCut for now. Note that the dataset is quite large!
We are indeed very interested in adding new datasets for other problems (including beyond graphs) and welcome contributions.


Fix KML descriptions that link to relative paths

If a KML description included a relative path, the browser request would end up using whatever server the application was hosted on as the base path, this is because the KML HTML would be injected into the InfoBox as-is. The end result is that relative images and links inside of KML files would not load properly.
To fix this, we now expand all relative paths into absolute paths that use the KML's source Uri as the bas.
I added a test that fails in master and passes in this branch; but if you want to test this manually, you can unzip gdpPerCapita2008.kmz into it's own subdirectory and load the KML.  Click on any item and it will be missing images in master, but they properly show up in this branch (the KMZ itself always worked because it goes through a different code path).

:+1: thanks @mramato!


File overwrite error

CKAN tried to overwrite a file from Interstellar Fuel Switch CKAN version while installing Interstellar Fuel Switch Core.
I think the error is likely on my end, and I wouldn't file the report, except the log told me to. The log also suggests updating CKAN, which I've done (version 1.6.22). The log follows:
"About to remove:
Done!
About to install...

InterstellarFuelSwitch-Core 1.11 (cached)

Oh no! We tried to overwrite a file owned by another mod!
Please try a ckan update and try again.
If this problem re-occurs, then it maybe a packaging bug.
Please report it at:
https://github.com/KSP-CKAN/CKAN-meta/issues/new
Please including the following information in your report:
File           : GameData/InterstellarFuelSwitch/Plugins/InterstellarFuelSwitch.dll
Installing Mod : InterstellarFuelSwitch-Core 1.11
Owning Mod     : InterstellarFuelSwitch
CKAN Version   : v1.6.22-0-g007717d (beta)
Your GameData has been returned to its original state.
Error!"

did you by any chance install interstellarfuelswitch back when there was only 1 mod and not a core package?

Yes, I believe I did. I unchecked it, went to changes, tried to install the new core version, and I got an unhandled exception regarding GameData/CommunityResourcePack/ResourceConfigs/CarbonDioxide.cfg.
I'm going to try deleting my insterstellar fuel switch folder and trying again.

Has this issue been resolved?

Closing this issue as there's no activity. If there's more to add or new developments, I'm happy to reopen this.


Each node different styles (width,height,styles) - Enhancement Feature

@bkrem same goes for the text attribute each node text/attributes can be positioned individually.
I hope you get my idea its pretty clear in the demo picture below :) waiting for you reply and what are you thoughts about this features :)

Hey @iqbalhussain931, this is great, thanks for taking the time to make a sketch! 👏
Will try to get this implemented after work at some point this week, might take longer though if breaking changes can’t be avoided, i.e. it needs to be published as v2. Should be possible as a minor release though hopefully.
Also hey if you feel like it feel free to work on it and shoot me a PR! :)

I understand sure that your time @bkrem and though i am at a beginners level on react but would loved to be a part of this but surely will need your help too :)

Hey @bkrem
how are you? :)
just wanted to take a follow up on the feature as discussed with you.

Hey, haven’t had time during the week to work on the library but I’ll start on this tomorrow!
Until I get paid for open source I unfortunately have to prioritise my job 😛

Resolved in #82, closing.


Message.content as template

Introduce Message.content_as_template flag which is True by default
Introduce Message.generate_content() ? Or turn Message.content into a dynamic property ? It should use other fields of the message as variables to fill in the Message.content template (if content_as_template is True)
Make sure openai_chat_completion (and render_conversation in ForumVersusGaia - move it to AgentForum actually) use the new method / dynamic property that fills in the content template

Setting "Complexity" to "Large" because it needs to be thought through, how to reconcile this generate_content() method with plain content property (which may be an unfilled template) in terms of outside code.


Consider removing Temu and Shein

About this discussion
Temu is a (suspected) spyware application currently under investigation from the US government, and their sister app has been banned off of Google Play and the Apple App Store for containing malicious code. Shein is based on the same base as Temu and their businesses have ties. Lawnicons should not be supporting such apps or businesses.

It's just a set of icons.
If you evaluate each app to see if it complies with the laws of one country or another, there will be plenty of apps that don't comply with US laws (for example), but do comply with the laws of other countries. Revanced, Sberbank, Tinkoff, etc.
Apps that are harmful suck. People are capable of deciding for themselves what to install on their phone. In my opinion, the most important thing is that the user feels comfortable using a set of icons. Lawnicons are used all over the world. If you make a set of icons that will be cleared of apps that are suspicious in any way or violate any law of any country, then such a set will not be comfortable for anyone.
If there is a virus embedded in the app and there is proof, only then in my opinion you should consider deleting it. However, your options are quietly available on Google Play right now.

Temu has spyware.
https://www.thecorporatelawjournal.com/technology/chinese-marketplace-temu-faces-class-action-lawsuit-for-spyware-and-malicious-business-practices
https://www.classaction.org/news/data-breach-class-action-claims-temus-in-app-web-browser-secretly-tracks-users
https://www.usatoday.com/story/tech/columnist/komando/2023/04/20/delete-temu-app-cybersecurity-expert-advice/11667796002/https://www.fashiondive.com/news/temu-class-action-lawsuit-data-collection/699328/

The fact that it's even owned by a company that has put out virus and spyware ridden apps should be a huge immediate red flag.

Also, "it's just a set of icons" isn't a great argument. By putting an app in an icon pack, it holds some meaning like "oh, people use this app since this big project has an icon for it. I should be fine using it too"

Temu has spyware.

It's a reason to evaluate your trust in an app. If you don't trust the app, you don't install it.

Also, "it's just a set of icons" isn't a great argument. By putting an app in an icon pack, it holds some meaning like "oh, people use this app since this big project has an icon for it. I should be fine using it too"

The presence of an icon in any set has no bearing on the decision to install an app. The reason is that a person makes a decision to install the app based on its usefulness, rather than going to check whether there is an icon in the set before installing the app. Also, the presence of an icon doesn't affect whether a person uninstalls the app or not. People who like the app without an icon will either install some suitable icon on it or request an icon for that app.
There are also plenty of people who don't care what data is collected about them. They will make good use of any app. If you want dry stats, making a Temu icon was asked 2 times, as was Shein. At the moment, it's 4 vs 1.
I've said enough. I wouldn't remove any icon if at least a meaningful number of people are using the app, as it has no effect on installing or uninstalling apps. Especially when it comes to apps that are available on Google Play. It's not just up to me, though.
If someone wants to join the discussion, they will do so. Thank you for being concerned about it.

Arguably if it was removed it would just lead to requests, issues, and PRs


Error upon clicking "Create Army"

This error occurred shortly after clicking Create Army. After doing so, the button is now greyed out. There were 2 unselected buttons, since they were extras created by the Battlescribe formatting for the Talos Pain Engine.

Does this happen consistently, and if so can you upload the roster file that's having the issue?

I've updated with better logging for these cases, and some code that should always unlock the button so you can try again. If you're still able to reproduce the error with the new version let me know, and please send me the roster file and roster code that's giving you the error.

I get this same error (though it now just says "got error") with the following roster.
2k - Medium Nids.zip

It looks like in your case the Acid Maw genestealers are tripping it up. I will see if I can get this fixed.

Ok these issues should be fixed now. Let me know if you see problems like this again.


Fix cluster event queue processing

Fix eventually broken cluster event queue processing

👍

Coverage decreased (-0.01%) to 9.268% when pulling a7f79a33f3f6fa71528c754be88f968c0c3cff6d on fix/clusterevent-queue into 2fe22ff61451f592471de465593cb057faa74c7e on master.

👍


updated info about NDES server name

https://github.com/MicrosoftDocs/windows-itpro-docs/issues/2450

@nenonix @JohanFreelancer9 Copy editing is needed for this PR. Thanks.

@mapalko Would you be able to review and merge this PR for a document that you have authored? The PR is based on issue #2450.
Thanks.

I reviewed it and the change looks good.. I don't have merge rights. @DaniHalfin can you help merge this

@DaniHalfin Can you merge this PR that has passed review via mapalko ?
Thanks.


Add support for BigInt and BigDecimal

Cross source code seems a bit like an overkill but it clearly shows what to do when we drop Scala 2.10 support.

Bug bankruptcy


MM-13494 Remove fixed class from body when announcement bar is unmounted

Summary
Remove fixed class from body when announcement bar is unmounted.
Ticket Link
https://mattermost.atlassian.net/browse/MM-13494

cherry picked be5af8fb3816500d4c50ea04c3ac19350a668426 into release branch 5.6


Enable filtering on populate parameter in em.find()

Is your feature request related to a problem? Please describe.
We have Fee and Discount entities with a nullable (and inversed) 1:many relation of fee.discounts. Each of these also has a nullable many:1 relation with Organisation. I need to select only fees and associated discounts that (among other things) match a particular organisation or none at all, i.e. excluding all other organisations.
As it stands I can construct a "match or null" where clause on em.getRespository(Fee).find() to retrieve the fee entities, but I can only populate all discounts for a fee or none at all.
Describe the solution you'd like
I'd like to be able to filter the relation populated like I can filter the primary entity.
Describe alternatives you've considered
We've encountered this requirement numerous times while using mikro-orm. As a workaround we currently either:

populate all entities in the relation and filter in the application code, or
execute multiple queries, or
use QueryBuilder to select multiple rows per primary entity (each with the relation matching a where on the join) and map result columns to entities manually

1 & 2 are suboptimal performance-wise. 3 is better for the db but feels unwieldy and unnecessary - constructing a (psuedo-)sql query and deserialising results is... why we have an ORM :)
Additional context
LLBL achieves this via the PrefetchPath to which you can attach a predicate, sort etc.
Sequelize enables the same via an include statement during eager loading. IMHO, a similar syntax wouldn't look out of place here.
Looks like work is well underway on LoadStrategy at #556. Could this be achieved via the subquery option suggested in #440?

I'd like to be able to filter the relation populated like I can filter the primary entity.

As discussed on slack, this is already possible, the partial condition that apply to child/populated entity will be propagated to the query that loads it.
const res = await orm.em.find(Author2, { books: { title: { $in: ['b1', 'b2'] } } }, ['books']);
// [query] select "e0".* from "author2" as "e0" left join "book2" as "e1" on "e0"."id" = "e1"."author_id" where "e1"."title" in ($1, $2) [took 6 ms]
// [query] select "e0".*, "e0".price * 1.19 as "price_taxed" from "book2" as "e0" where "e0"."author_id" in ($1) and "e0"."title" in ($2, $3) order by "e0"."title" asc [took 5 ms]

1 & 2 are suboptimal performance-wise. 3 is better for the db but feels unwieldy and unnecessary - constructing a (psuedo-)sql query and deserialising results is... why we have an ORM :)

First of all, the approach with multiple queries can be actually faster when the DB is really large. Having too complex queries can result in real slowness, I've been there. I don't know why everybody thinks that more simple queries are always slower, that is simply not true, and its not true especially for large databases (and we are talking about those anyway, right?).
Why do you think we need subqueries? How is that different from joined query? (from my experience, subqueries are usually slower)

Sequelize enables the same via an include statement during eager loading. IMHO, a similar syntax wouldn't look out of place here.

I said it somewhere already, I can't understand why we should have so complex api, why not use a query builder for that? QB does work with entities, and support mapping results to entities. Also supports auto-joining, so the API is really similar to the one from EM. And with #556 it will also support mapping of multiple (nested) entities from single (joined) query.

this is already possible the partial condition that apply to child/populated entity will be propagated to the query that loads it

That's great news! Alas, I'm struggling to get this working - I've created a test case to demonstrate. Be great if you could set me straight on what we're doing wrong :)

I don't know why everybody thinks that more simple queries are always slower, that is simply not true

You're right of course - I meant to say "1 and 2 are potentially suboptimal". OTOH, complex single queries can be faster the multiples if they're correctly designed, planned and optimised. If em.find() supports both then we have the option to choose.

Why do you think we need subqueries?

I don't. You're right: joins can be, although are not always are, better optimised. I was just asking if that's how we'd achieve populate filtering using the forthcoming changes on #556, given that's what Will had mentioned originally at #440.

why not use a query builder... it will also support mapping of multiple (nested) entities from single (joined) query

Because it doesn't support nested mapping yet :) Once it does, we can certainly use QB to achieve this. However, being able to specify a different filter on populate is so useful it deserves to be an option on higher-level find APIs (hence this issue!). QB logic sql re-written in a mikro DSL. Powerful (and great to have at hand) but verbose and somewhat cumbersome for a task we've required multiple times already on our current project.

Your problem with first query is the { foos: null } in the query condition, this is not yet supported (not even sure if we will support it like this, I was thinking about adding new operators for this use case, $empty and $size). Here is an issue about it #548.
You can do this:
const result1 = await orm.em.find(Bar, { $or: [{ foos: { prop: 'a' } }, { foos: { id: null } }] }, ['foos']);

which does produce this query:
select "e0".* from "bar" as "e0" left join "foo" as "e1" on "e0"."id" = "e1"."bar_id" where ("e1"."prop" = 'a' or "e1"."id" is null)

Still not what you want, as it will return only one entity. In fact there are relations set in both your entities.
So the question is more like - what SQL are you expecting to solve this?
In the comment you have:

Goal: find all bars but only populate the foo relation if foo.prop is 'a', i.e.

Well but this is not what you are doing in the query above. You are requesting bars that either have a relation with foo.prop = a, or there is no relation at all. The condition is first applied to the root entity, so you can't get all bars this way.
If you want to have all bars but populate only something, correct solution (and I am pretty sure that also the fastest when it comes to big data) is to do one query to load the roots and another to populate:
const result1 = await orm.em.find(Bar, {});
await orm.em.populate(result1, ['foos'], { foos: { prop: 'a' } } as any); // there are some issues in v4 typings of the populate method, so had to cast as any otherwise the type of result1 was not used as T
expect(result1).toHaveLength(2);
expect(flatMap(result1, b => b.foos.getItems())).toHaveLength(1);

Doing it otherwise just seems overcomplicated. Also your links to other solutions are about something different I think, I don't think they can do this in single query (and let me say it one more time, the solution in typeorm looks terrible, I would never let this pass my code review :trollface:, if we want to optimise for performance, its much easier to use raw sql instead).
Let's put it this way - if you want to do it in single query, how do you think the query should look like?
If you are fine with multiple queries, then my approach with em.populate() feels much more readable.

Btw I don't understand what are you expecting from having 1:m nullable. Its an inverse side, collection, it can't be nullable, there is nothing to be nulled (you can have it there, but its a no-op, nullable have a meaning only on owning sides).

Closing due to inactivity. As said above, this is already possible, conditions are propagated to the populate queries, and in v4 it is possible to use the joined strategy too. I don't see a value in having another strategy, introducing the joined one ended up being the second most complex thing in the whole ORM development (right after composite keys).


Add shields to README

Add shields from shields.io to show current NPM package and other information.

Already done with release 1.0.0, so closing this issue.


totally cosmetic :-)

The picture in the Readme.md is not displayed on my screen.

After the short investigation we realised that there was no issue :)


UriNotifier#addUrisToNotify sample code in JS Docs

I was looking on how to force my cursor to update when I add new entry (modify data) and found something called UriNotifier#addUrisToNotify (btw. such things could be added to WIKI:) ) but the sample code in JS Doc has a missing bracket here
      if (Student.TABLE.equals(table) {

and it should be
      if (Student.TABLE.equals(table)) {

on the side note, the example contained
uris.add(Student.CONTENT_URI);
Is the CONTENT_URI automatically generated? If so what my Table spec needs to have as my generated class doesnt have it.

No, the content uri is not automatically generated. If you declare any public static final fields in your spec files though, they will be copied to the generated model class.
Thanks for the note about the javadocs, we'll fix it. And yes, the UriNotifier is a relatively new feature so we haven't written a wiki page for it yet. We'll get to it :) Thanks!

:) thanks for your help:)

Had a little extra time this afternoon so I added a wiki page for the UriNotifiers. Thanks again for the feedback, feel free to keep it coming!

Thanks for the WIKI page:)


Refactor of SetSubnodeOwner including rebase of PR #159

This refactoring was done to limit the gas used and make the code more readable. Some of the methods used include:

Removing duplicate calls to getData()
Adding comments to all parts of the code
Reducing the number of calls to external functions

The overall gas used by setSubnodeOwner was reduced by:
Min - Max - Average
60391  ·     131996  ·      123610
55282  ·     124713  ·      116696
(-5,109)      (-7,283)       (-6,914)

NameWrapper has been deployed to mainnet, so closing this PR


What is the correct parameter combination for using dynamic RoPE scaling ?

Hi Team, First of all thanks for the awesome piece of software !!
I want to use upstage/Llama-2-70b-instruct-v2 model with --max-input-length=8192 --max-total-tokens=10240 which originally supports max_position_embeddings=4096.
I tried running the following command :
docker run -it --rm --gpus all --shm-size 80g --name llama2_70b_instruct_v2 -p 8560:80 -v ~/tgi_data:/data \
  ghcr.io/huggingface/text-generation-inference:sha-f91e9d2  --num-shard=8 \
  --model-id upstage/Llama-2-70b-instruct-v2 --revision 5f9c77b2c0397cf83d2f97740483f107c7109e8c \
  --dtype=float16 \
  --max-input-length=8192 --max-total-tokens=10240 --rope-scaling=dynamic --rope-factor=2.5 \
  --max-batch-prefill-tokens=40100 \

Does it look correct ?

Though this ended up with:
Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/site-packages/text_generation_server/models/flash_causal_lm.py", line 727, in warmup
    _, batch = self.generate_token(batch)
  File "/opt/conda/lib/python3.9/contextlib.py", line 79, in inner
    return func(*args, **kwds)
  File "/opt/conda/lib/python3.9/site-packages/text_generation_server/models/flash_causal_lm.py", line 825, in generate_token
    raise e
  File "/opt/conda/lib/python3.9/site-packages/text_generation_server/models/flash_causal_lm.py", line 813, in generate_token
    out = self.forward(
  File "/opt/conda/lib/python3.9/site-packages/text_generation_server/models/flash_causal_lm.py", line 789, in forward
    return self.model.forward(
  File "/opt/conda/lib/python3.9/site-packages/text_generation_server/models/custom_modeling/flash_llama_modeling.py", line 475, in forward
    hidden_states = self.model(
  File "/opt/conda/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1501, in _call_impl
    return forward_call(*args, **kwargs)
  File "/opt/conda/lib/python3.9/site-packages/text_generation_server/models/custom_modeling/flash_llama_modeling.py", line 428, in forward
    cos, sin = self.layers[0].self_attn.rotary_emb.get_cos_sin(
  File "/opt/conda/lib/python3.9/site-packages/text_generation_server/utils/layers.py", line 470, in get_cos_sin
    self._update_cos_sin_cache(dtype, position_ids.device, max_s)
  File "/opt/conda/lib/python3.9/site-packages/text_generation_server/utils/layers.py", line 501, in _update_cos_sin_cache
    newbase = self.base * ((self.scaling_factor * seq_len / self.max_position_embeddings) - (self.scaling_factor - 1)) ** (self.dim / (self.dim - 2))
NameError: name 'seq_len' is not defined

Looks like typo in the code, should it have been seqlen  instead of seq_len ?

When I am using the above model without RoPE scaling on 8xA100-40GB GPUs, it can churn out 1534 tokens per sec,  with an prompt heavy set up of ~883 input tokens, ~76 output tokens(best_of=1, so no hidden output tokens) per request.
Is this expected performance or can I do better on the above set up?
FYI: tried fp16 on vllm, gptq(4bit), bitsandbytes(8bit) models all ended up with similar TPS (tokens per second).

I think you don't need factor for dynamic most of the time (the factor will be applied, never tried myself, but my understanding is that it's not required).
Indeed https://github.com/huggingface/text-generation-inference/pull/783

Is this expected performance or can I do better on the above set up?

I cannot tell you I haven't tried that particular setup. Performance measurements is always tricky and for actual loads I usually prefer live metrics from live systems rather than one off benchmarks. (Although those are super helpful understanding how your system behaves, I don't necessarily use them as a source of truth).
TPS is throughput and is really not what you want to be measuring imho. The critical measurement you want to be measuring is latency (that we usually refer to as ms/token and text-generation-benchmark will do just that.
Ideally you find the breaking point for memory-bound/compute-bound, and stop answering requests whenever you start becoming compute-bound (usually it's a number of stacked requests/tokens)
Throughput is important, but you generally don't want to have a running system close to throughput capacity, it will start to fall down rapidly whenever you get more load than throughput, so safety margins are important.


Adaptive scaling to display

experimental scaling of all widgets as function of display width and height

With recent PR #79,we switched to system resizing on rendered qt objects and this PR became irrelevant.


[Analyse] CSS Framework for Indigo Layout

– for decreasing of dev. time and getting the powerfull documentation about the HTML, CSS we have decided use CSS framework.
The main goal is to check several modern frameworks, create the test page and provide to the team some of the summary information with examples.
Possible frameworks:

Tailwind CSS - https://tailwindcss.com/
Bulma - https://bulma.io/
Codyhouse - https://codyhouse.co/

Should be checked:

Build one example HTML and CSS for https://www.karriere.de/ - the first screen will be enough
Take the principle: one HTML, one CSS for each project (karriere.de, wiwo.de, handelsblatt.com) - the difference in configuration (color, padding, margin, fonts, icons, customization).
Mobile/Responsive version
AMP version
Dark/Light theme (not necessary for the projects, but …)
What of the size of final minified CSS
Check complexity and learning speed.
CSS Modules ? https://vue-loader.vuejs.org/guide/css-modules.html#usage

Interesting links:

https://2019.stateofcss.com/technologies/css-frameworks/

➤ Ilya Kitayev commented:
https://git.awescode.com/awes-io/framework-comparasion ( https://git.awescode.com/awes-io/framework-comparasion )


[SILGen] Fix the type of closure thunks that are passed const reference structs

The thunk's parameter needs the @in_guaranteed convention if it's a const reference parameter. However, that convention wasn't being used because clang importer was removing the const reference from the type and SILGen was computing the type of the parameter based on the type without const reference.
This commit fixes the bug by passing the clang function type to SILDeclRef so that it can be used to compute the correct thunk type.
This fixes a crash when a closure is passed to a C function taking a pointer to a function that has a const reference struct parameter.
rdar://131321096

@swift-ci please test

@swift-ci please test

@swift-ci please smoke test

@swift-ci please test

@swift-ci Please Build Toolchain macOS Platform


demo issue

when I run the demo, I got a error,please help me,thank you.
the error information as following:
y = net(xx)
File "/home/bupt-sse3/anaconda3/lib/python3.5/site-packages/torch/nn/modules/module.py", line 489, in call
result = self.forward(*input, **kwargs)
File "/home/bupt-sse3/repulsion_loss_ssd-master/ssd.py", line 103, in forward
self.priors.type(type(x.data))                  # default boxes
File "/home/bupt-sse3/repulsion_loss_ssd-master/layers/functions/detection.py", line 54, in forward
ids, count = nms(boxes, scores, self.nms_thresh, self.top_k)
ValueError: not enough values to unpack (expected 2, got 0)

Same issue, did u solve it?

i got the same result.

I changed the code as follows and worked for me.
In detection.py of line 49
from
if scores.dim() == 0:
continue
to
if scores.size(0) == 0:
continue


Russian and Ukrainian translation

Add the Russian and Ukrainian translate files, I'd be glad to translate the mod!

Hi DenTheUA, I added them.
Can you manage to do this until tomorrow?
I plan to release the new version then and it would be cool to have your translation in there, too :)

Btw.: They are here: https://github.com/TheOnlySilverClaw/Reforged/tree/master/resources/assets/reforged/lang
(the ru_RU.lang and uk_UA.lang)

Wow, thanks for translating both now :)
The Ukrainian translation will be in the update 0.7-pre4 then.
Thanks 1000 times ^^

If you need me,then you know where to f-i-i-i-i-i-i-i-i-i-i-ind me^_^


Added optional auto-run argument.

Aside from the version conflict this is fine, although I wonder if it might be better to have a "headless" mode - where no interface is necessarily shown, but you can still have things like qt message dialogs or even progress dialogs.


Adding Default Message to README.md

Added information about defaultMessage prop to README file.

@awran5 added the new prop information to README as discussed.


Bot token expired

I don't have eyes

I don't have eyes

what was wrong i have the same issue and when i try doing it in Config.json it gives me the error :/


Community Bridge demo

Present to the board.

Demo 1 of 2 provided to @danlopez00 as there are multiple sub-products with varying degree of GTM readiness. EasyCLA, Security, and Dev Analytics were demoed. Getting the next set of demos from the product team is scheduled for next week. A summary demo will be compiled and shared with the CDF

Update: CB is slated for a release in the next couple of weeks.  However, CDF now has 2 main URLs:
https://people.communitybridge.org/project/515e26a1-9e56-49e6-bb87-ce5544e8ee10
https://funding.communitybridge.org/projects/continuous-delivery-foundation
These are only preliminarily setup and will take some time to refine and get the pages setup appropriately

Closing. Will open a new ticket when product teams are ready with updates


Fix max width and margin of comment box on conversation page

Fix regression from #23937
The changes should only be limited to .conversation-holder .comment-code-cloud, otherwise it will affect the .comment-code-cloud in conversation tab
Before:

After:

It's still limited in the "Files" tab, right?

It's still limited in the "Files" tab, right?

yep


[SPARK-30954][ML][R]Make  file name the same as class name

This pr solved the same issue as pr27919, but this one changes the file names based on comment from previous pr.
What changes were proposed in this pull request?

Make some of  file names the same as class name in R package.
Why are the changes needed?

Make the file consistence
Does this PR introduce any user-facing change?

No
How was this patch tested?

run ./R/run-tests.sh

Can one of the admins verify this patch?

Can one of the admins verify this patch?

ok to test

cc @zhengruifeng and @srowen

Test build #119945 has started for PR 27940 at commit 575d4d4.

Merged build finished. Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder-K8s/24668/
Test PASSed.

Yep seems OK. CC @felixcheung just FHI

Test build #119945 has finished for PR 27940 at commit 575d4d4.

This patch fails PySpark unit tests.
This patch merges cleanly.
This patch adds no public classes.

Merged build finished. Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/119945/
Test FAILed.

retest this please

Merged build finished. Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder-K8s/24673/
Test PASSed.

Test build #119951 has started for PR 27940 at commit 575d4d4.

Merged build finished. Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder-K8s/24675/
Test PASSed.

Test build #119951 has finished for PR 27940 at commit 575d4d4.

This patch passes all tests.
This patch merges cleanly.
This patch adds no public classes.

Merged build finished. Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/SparkPullRequestBuilder/119951/
Test PASSed.

Ok

Thank you, @felixcheung !


bboxHexEstimate: Calculated area is way too big

I noticed that maxPolygonToCellsSize is giving me numbers way too big for my input geometries. I could track it down to bboxHexEstimate. There the calculated area is way to big.
Here is an example geometry:
Polygon ((7.54402069689999966 47.13895667900000319, 7.54419258430000017 47.13895667900000319, 7.54419258430000017 47.15093149700000197, 7.54402069689999966 47.15093149700000197, 7.54402069689999966 47.13895667900000319))

It is a street. So it is quite long but narrow.
bboxHexEstimate calculates a distance (bbox diagonal) of 1.33km. This sounds about right. But the calculated area then is 103.87km2 which is way too big. We call polygonToCells with an index resolution of 15 and this causes memory problems in our application.
I do not understand your formula to calculate the bbox area:
double a = d * d / fmin(3.0, fabs((p1.lng - p2.lng) / (p1.lat - p2.lat)));
But it seems to work really bad for bboxes where one side is much much longer than the other.
Do you have any idea how to fix this?

As it happens, I was also looking at this function recently ^^
From my understanding there are two issues here:

the quotient of the bbox sides is wrong
the capping to 3 seems to be hurting (at least in this case).

The ratio is always computed as lng diff/lat diff, which gives value < 1 for vertical narrow shapes like yours (and since we divide the squarred diagonal by this ratio, the result is a larger number).
With the current formula we get:

estimated area: ~123km²
351,145,612 cells

Which is way too big, indeed...
If we fix the formula by making sure we always compute ratio as length/width:
double d1 = fabs(p1.lng - p2.lng);
double d2 = fabs(p1.lat - p2.lat);
double length = fmax(d1, d2);
double width = fmin(d1, d2);
double ratio = length/width;
// Derived constant based on: https://math.stackexchange.com/a/1921940
// Clamped to 3 as higher values tend to rapidly drag the estimate to zero.
double a = (d * d) / fmin(3, ratio);

We get better result:

estimated area: ~0.6km²
1,680,136 cells

But we can get an even better estimation, by removing the capping to 3:
double d1 = fabs(p1.lng - p2.lng);
double d2 = fabs(p1.lat - p2.lat);
double length = fmax(d1, d2);
double width = fmin(d1, d2);
double ratio = length/width;
// Derived constant based on: https://math.stackexchange.com/a/1921940
double a = (d * d) / ratio;

Now we get

estimated area: ~0.025km²
72,362 cells

Given that the polyfill of your shape actually returns ~20k cells at res 15, we only over-estimate by a factor 3.5 (instead of ~x17,000)
Now those are just my 2 cents, I'm not an expert on H3 internals though ^^
(like maybe removing the capping to 3 have adverse effects in other cases).

Thanks for your detailed analysis @grim7reaper.
I would be more than happy even with your first example where capping to 3 is still present.
Shall I create a pull request containing these changes?

At first I didn't understand how the formula from the linked Stackexchange issue was reduced from $d^2 \over \sqrt{2 + r^2 + {1 \over r^2}}$ to $d^2 \over r$. But I think that's just a (rough) approximation, right?

Yes, I think you can make a PR (not sure if it breaks any existing tests though).
You can probably also add your shape as a unit test to avoid future regression.

But I think that's just a (rough) approximation, right?

Yup, that's my guess too, probably considered that $2+\frac{1}{r^2}$ were negligible in this case
To be confirmed by the authors.


Anyway I can change the note offset itself?

Describe your problem here.
for clarification, the note trail moves with the note when using setPropertyFromGroup('unspawnNotes', i, 'offsetX', value); or setPropertyFromGroup('unspawnNotes', i, 'offsetY', value); and I clearly don't want that

Are you modding a build from source or with Lua?
Lua
What is your build target?
Windows x64
Did you edit anything in this build? If so, mention or summarize your changes.
No response

`    for i=0,getProperty('unspawnNotes.length')-1 do
if not getPropertyFromGroup('unspawnNotes',i,'isSustainNote') then
setPropertyFromGroup('unspawnNotes',i,'offsetX',value)
setPropertyFromGroup('unspawnNotes',i,'offsetY',value)
end
end`

`    for i=0,getProperty('unspawnNotes.length')-1 do
if not getPropertyFromGroup('unspawnNotes',i,'isSustainNote') then
setPropertyFromGroup('unspawnNotes',i,'offsetX',value)
setPropertyFromGroup('unspawnNotes',i,'offsetY',value)
end
end`

I should have known that, thanks.


TypeScript examples based on NodeJS examples

Mostly boilerplate for setting up tsconfig and package.json / esm for those who don't live in a Deno-tastic world.

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.Justin Pettit seems not to be a GitHub user. You need a GitHub account to be able to sign the CLA. If you have already a GitHub account, please add the email address used for this commit to your account.You have signed the CLA already but the status is still pending? Let us recheck it.


TFLite: Missing activation in built-in Mul operation

ReLU activation went missing despite appearing in the graph as an activation function in the Mul operation.
Hope this fixes a TODO marked by @ekaterinaignasheva

@guydavid Can you please resolve conflicts? Thanks!

Seems auto-merge is not happening but the changes are now committed so we can close this. Thank you for the PR.
@chanshah thank you for importing this PR internally.


Remove Standard Assets

These don't appear to be used.

This repository is move to read-only and will be unmaintained going forward. Marking all issues as Closed.


update storage connections using oVirt java sdk

Force updating a storage server connection has been added in oVirt 3.6.10 (https://gerrit.ovirt.org/#/c/64531/). Hence, updating connections and IQNs through the API,
instead of directly manipulating engine's DB.

@mureinik

@xandradx

Thanks !
I will update configuration section on README.


Make ActivityUpdate subclasses public

Is there a reason for all entities that extend from ActivityUpdate to not be public?
From my understanding, if we had access to _ActiveActivityUpdate, instead of doing
_liveActivities.activityUpdateStream.listen((update) async {
      final updatedToken = await _liveActivities.getPushToken(activityId: update.activityId);
      ...
    });

We could do just
_liveActivities.activityUpdateStream.listen((update) async {
      final updatedToken = update is _ActiveActivityUpdate ? update.activityToken : null;
     ...
    });

It's now published on pub.dev 👍
Thanks to @arnar-steinthors :)


Typo issue on the TrustedMailOutboundEnabled

Minor correction expected to the description section since it show TrustedMailInboundEnabled instead of TrustedMailOutboundEnabled

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: a59cfe39-9c00-1a50-be14-0d8e58754529
Version Independent ID: c8c00bed-da63-654e-d44f-6c83d967821e
Content: Set-RemoteDomain (exchange)
Content Source: exchange/exchange-ps/exchange/mail-flow/Set-RemoteDomain.md
Service: exchange-powershell
GitHub Login: @chrisda
Microsoft Alias: chrisda

@nramouche, OK. Fixed.


can no longer build at all

Running cargo r I get this issue:
thread 'main' panicked at 'called `Option::unwrap()` on a `None` value', /home/raj/.cargo/registry/src/index.crates.io-6f17d22bba15001f/blue_engine-0.4.28/src/render.rs:59:14
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

I see, please write your OS and environment, I do not know how to reproduce it yet

I use same os as you man lol
Sent from Proton Mail mobile
-------- Original Message --------
On 4 Jan. 2024, 3:50 pm, Elham Aryanpur wrote:

I see, please write your OS and environment, I do not know how to reproduce it yet
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you authored the thread.Message ID: @.***>

Moved to 0.5, no longer having issues, closing ticket.

I am on 0.5 and still issue persists.

thread 'main' panicked at 'called `Option::unwrap()` on a `None` value', /home/raj/.cargo/registry/src/index.crates.io-6f17d22bba15001f/blue_engine-0.5.0/src/render.rs:59:14
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

This happened because wgpu can't find your GPU, so the engine stops

@Gipson62 I don't know why doing a ful system update messes chnages my drivers, thanks for letting me know.

Know that when you get this type of error (in render.rs line 59) it's a GPU error from wgpu. And yeah, sometimes drivers are messed up on some Linux distro because of system updates.

Yeah gipson is right, that error is from engine not being able to get access for rendering, which means driver not working correctly

Yep now working thanks


App will not connect

So when I click on the link to start it, it shows up the window with "getting your service id" "Figuring POI" and spinning circle and than throws this error
Unhandled Promise Rejection
NonError: 'Could not get POI list'
    at module.exports.input (/Applications/aussiebb_aunt.app/Contents/Resources/app.asar/node_modules/ensure-error/index.js:14:10)
    at handleError (/Applications/aussiebb_aunt.app/Contents/Resources/app.asar/node_modules/electron-unhandled/index.js:21:10)
    at process.on.error (/Applications/aussiebb_aunt.app/Contents/Resources/app.asar/node_modules/electron-unhandled/index.js:100:4)

I can log in just fine with AussieBB app on my ipad and via web page
This is on my Mac running mojave

This is in relation to the DDoS issue the main webserver / api is having. It should pass as the heat / webservers come back up.

Closing this as it seems to be working fine on my end now the DDoS issues have passed.


MZMINE CANNOT PERFORM MASS DETECTION

Hello all;
I am experiencing an issue in data upload step.
When I try to upload my data it cannot perform the mass detection. See the error message below

Data is acquired in 6546 Q-TOF Agilent and data seems to be fine when I open it up in MH 11

The parameter settings for MSConvert are as seen in the screeshot below:

The project contains 30+ files but I am adding one example datafile in zipfile below and but the issue shows up in every data file.
https://drive.google.com/file/d/1BPKlQy3B6o6AirO0BLIO7gaEoE0ooErF/view?usp=sharing
It is likely a file conversion issue but I just couldn`t figure out how to solve the issue.

I have also tried 64 bit with zlib conversion and and 32 bit w/wo zlib.
I have no clue on what I am doing wrong as I do almost the same thing I always do.

Thanks for reaching out this is not an issues just a warning.
Some scans in your file are empty which is the case for some instruments but also sometimes die to heavy preprocessing.
You should be able to just do regular processing and if you get results than you don't have to worry at all.


Text overlap issue

Currently the text that has to be written is overlapping with the "Type here:" text.

Please assign me this issue under hacktoberfest.

done