analysis TI with alchemical_analysis.py errors

Dear Prof. Mobley,
I run a TI analysis with AMBER and I installed and I am trying to use your alchemical_analysis.py script for the example that comes with the with it, from the sampes/amber directory as it is. The scripts runs, but I get an error I don’t understand, probably my python ignorance, here it is the ouptut, it seems it starts to run, but it gives a mbar_lambdas error.
/Users/admin/Data/TOOLS/alchemical-analysis-master/samples/amber
03:24 PM Sun Dec 13$  ../../alchemical_analysis/alchemical_analysis.py -a AMBER -d data/* -m TI -p ti00* -q out
Started on Sun Dec 13 15:25:08 2015
Command line was: ../../alchemical_analysis/alchemical_analysis.py -a AMBER -d data/0.0 data/0.1 data/0.2 data/0.3 data/0.4 data/0.5 data/0.6 data/0.7 data/0.8 data/0.9 data/1.0 -m TI -p ti00* -q out
Loading in data from data/0.0/ti002.out...  50 data points, 10 DV/DL averages
Loading in data from data/0.0/ti003.out...  50 data points, 10 DV/DL averages
Sorting input data by starting time and lambda
Traceback (most recent call last):
File "../../alchemical_analysis/alchemical_analysis.py", line 1224, in
main()
File "../../alchemical_analysis/alchemical_analysis.py", line 1172, in main
nsnapshots, lv, dhdlt, u_klt = parser_amber.readDataAmber(P)
File "/Users/admin/Data/TOOLS/alchemical-analysis-master/alchemical_analysis/parser_amber.py", line 582, in readDataAmber
if len(dvdl_all) != len(mbar_lambdas):
UnboundLocalError: local variable 'mbar_lambdas' referenced before assignment
If I use your script run.sh I get a different error:
./run.sh
Traceback (most recent call last):
File "../../alchemical_analysis//alchemical_analysis.py", line 1224, in
main()
File "../../alchemical_analysis//alchemical_analysis.py", line 1200, in main
Deltaf_ij, dDeltaf_ij = estimatewithMBAR(u_kln, N_k, P.relative_tolerance, regular_estimate=True)
File "../../alchemical_analysis//alchemical_analysis.py", line 290, in estimatewithMBAR
O = MBAR.computeOverlap()[2]
IndexError: invalid index to scalar variable.
/Users/admin/Data/TOOLS/alchemical-analysis-master/samples/amber
03:41 PM Sun Dec 13$ more run.sh
../../alchemical_analysis//alchemical_analysis.py
-a AMBER
-d data
-p '[01].*/ti00[2-9]'
-q out
-o .
-r 5
-u kcal
-s 0
-g
-w \

run.log
/Users/admin/Data/TOOLS/alchemical-analysis-master/samples/amber

Could you please help me understand what I am doing wrong?
Thanks a lot in advance,
Fabian
Dr. Fabian Glaser
Head of the Structural  Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel:    +972 4 8293701
http://bku.technion.ac.il

I forgot to mention that I am running this on my Mac El capitan with python 2.7.10
Thanks,
Fabian

Have you run pmemd with ifmbar=0 (or not set this at all so it defaults to 0)?  This is a bug in the AMBER parser.  Please checkout the version from my branch: https://github.com/halx/alchemical-analysis.

I didn't use ifmbar... should I run production again?
Or use the version you suggest?
Thanks!!
Fabian
Technion, Israel

Use my branch.
You may want to use ifmbar>0 as the computational cost is rather smalle.  But this is only useful with equally spaced lambdas because AMBER currently does not allow you to use arbitrary lambdas.

Thanks a lot for your kind help,
I did succeed with your branch, and it worked only for TI, now I don’t understand why the results are so different from the Kaus paper…. the output is below. And several questions…. sorry for so many….
First, only TI calculation worked, why?
Second there are two values of TI, -19.525 and -82.289 what is their difference?
Third, in any case those values are far far away from the published in the paper, with a similar procedure (although they did 5 ns and I did 3 ns production, and they did NVT production and I did NPT as you suggested).
They published
Model System 		Method 	DF0:0􀀀>1:0  	DF0:1􀀀>0:9 	DDFend
Solvation Free Energy 	TI 		-66.74  		-49.33    		-19.29
MBAR 	-65.62		-47.15		 -18.47
And as you can see below my calculation yielded -82 …… The preparation of the system is identical I followed their procedure… so I really don’t know where the culprit is.  I used the amber AM1-BCC method for charges and they used RESP, since I don’t have Gaussian, can this be the source of such a difference in TI?
Any help will be most welcomed.
Here is my output:
$ alchemical_analysis.py -a AMBER -d data/* -m all -p prod* -q out
Started on Mon Dec 14 12:01:15 2015
Command line was: /Users/admin/Data/TOOLS/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py -a AMBER -d data/0 data/0.1 data/0.2 data/0.3 data/0.4 data/0.5 data/0.6 data/0.7 data/0.8 data/0.9 data/1 -m all -p prod* -q out
Loading in data from data/0/prod0.out...  100 data points, 1 DV/DL averages
Sorting input data by starting time and lambda
Note: BAR/MBAR results are not computed.
Skipping first 0 steps (= 0.000000 ps)
Note: extrapolating missing gradient for lambda = 1.0: -19.524776
The gradients from the correlated samples (kcal/mol):
0.00000   -19.525
1.00000   -19.525
TI =   -19.525
The correlated DV/DL components from every_single step (kcal/mol):
Lambda       BOND     ANGLE     DIHED    1-4 NB   1-4 EEL   VDWAALS     EELEC RESTRAINT
0.00000     0.000     0.000     0.000     0.000     0.000    -0.245   -19.279     0.000
TI =     0.000     0.000     0.000     0.000     0.000    -0.245   -19.279     0.000
Number of correlated and uncorrelated samples:
State            N          N_k        N/N_k
 0          100           62         1.61
 1          100          100         1.00

Estimating the free energy change with TI, TI-CUBIC, DEXP, IEXP, GINS, GDEL, UBAR, RBAR...

States           TI (kJ/mol)     TI-CUBIC (kJ/mol)         DEXP (kJ/mol)         IEXP (kJ/mol)         GINS (kJ/mol)         GDEL (kJ/mol)         UBAR (kJ/mol)         RBAR (kJ/mol)

0 -- 1       -82.289  +-  3.867    -82.289  +-  3.867     -0.000  +-  0.000      0.000  +-  0.000     -0.000  +-  0.000      0.000  +-  0.000      0.000  +-  0.000      0.000  +-  0.000

TOTAL:      -82.289  +-  3.867    -82.289  +-  3.867      0.000  +-  0.000      0.000  +-  0.000      0.000  +-  0.000      0.000  +-  0.000      0.000  +-  0.000      0.000  +-  0.000

IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII   The above table has been stored in   IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII           data/0/results.txt           IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII     while the full-precision data      IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII (along with the simulation profile) in IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII         data/0/results.pickle          IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

Time spent: 0 hours, 0 minutes, and 0.25 seconds.
Finished on Mon Dec 14 12:01:16 2015
/Users/admin/Data/TUTORIALS/AMBER/A9/1HNN
12:01 PM Mon Dec 14$
THANKSS!!
Dr. Fabian Glaser
Head of the Structural  Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel:    +972 4 8293701
http://bku.technion.ac.il

All the results and input files and everything is here
https://www.dropbox.com/sh/nzs2t2zs1nh6mq1/AADK1vyHEVG3ECuAOoQFjFO3a?dl=0
If you want to take a look....
Thansk!!!
Fabian

You will not get any results for the FEP family of analyses unless you run
your simulations with ifmbar > 1 (and ensure that the lambdas generated
with bar_l_min, bar_l_max and bar_l_incr match all your chosen clambdaS)
The first TI result is based on the correlated data set.  The last one from
the uncorrelated one and thus is the relevant one.  In practice thought
both should be fairly close to each other.
The analysis tool is a bit odd in how you specifiy how it should find the
input files.  I do not know what the directory layout of your files are (I
suspect it is the same as in tool's sample directory) but what you probably
want is something like -d data -p '[01]./prod' -q out (other variants are
possible too).  None of these command-line options takes more than one
argument.  If you want to read in more than one files then you will need to
familiaries yourself with glob patterns.  This is done as
glob(datafile_directory/prefix*suffix) where datafile_directory is -d,
prefix is -p and suffix is -q.
You have effectively only read in one single file.   "Loading in data"
tells you what file the parser is reading.
On 14 December 2015 at 10:21, fglaser<EMAIL_ADDRESS>wrote:

Thanks a lot for your kind help,
I did succeed with your branch, and it worked only for TI, now I don’t
understand why the results are so different from the Kaus paper…. the
output is below. And several questions…. sorry for so many….
First, only TI calculation worked, why?
Second there are two values of TI, -19.525 and -82.289 what is their
difference?
Third, in any case those values are far far away from the published in the
paper, with a similar procedure (although they did 5 ns and I did 3 ns
production, and they did NVT production and I did NPT as you suggested).
They published
Model System Method DF0:0􀀀>1:0 DF0:1􀀀>0:9 DDFend
Solvation Free Energy TI -66.74 -49.33 -19.29
MBAR -65.62 -47.15 -18.47
And as you can see below my calculation yielded -82 …… The preparation of
the system is identical I followed their procedure… so I really don’t know
where the culprit is. I used the amber AM1-BCC method for charges and they
used RESP, since I don’t have Gaussian, can this be the source of such a
difference in TI?
Any help will be most welcomed.
Here is my output:
$ alchemical_analysis.py -a AMBER -d data/* -m all -p prod* -q out
Started on Mon Dec 14 12:01:15 2015
Command line was:
/Users/admin/Data/TOOLS/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py
-a AMBER -d data/0 data/0.1 data/0.2 data/0.3 data/0.4 data/0.5 data/0.6
data/0.7 data/0.8 data/0.9 data/1 -m all -p prod* -q out
Loading in data from data/0/prod0.out... 100 data points, 1 DV/DL averages
Sorting input data by starting time and lambda
Note: BAR/MBAR results are not computed.
Skipping first 0 steps (= 0.000000 ps)
Note: extrapolating missing gradient for lambda = 1.0: -19.524776
The gradients from the correlated samples (kcal/mol):
0.00000 -19.525
1.00000 -19.525
TI = -19.525
The correlated DV/DL components from every_single step (kcal/mol):
Lambda BOND ANGLE DIHED 1-4 NB 1-4 EEL VDWAALS EELEC RESTRAINT
0.00000 0.000 0.000 0.000 0.000 0.000 -0.245 -19.279 0.000
TI = 0.000 0.000 0.000 0.000 0.000 -0.245 -19.279 0.000
Number of correlated and uncorrelated samples:
State N N_k N/N_k
0          100           62         1.61
1          100          100         1.00
Estimating the free energy change with TI, TI-CUBIC, DEXP, IEXP, GINS,
GDEL, UBAR, RBAR...
States TI (kJ/mol) TI-CUBIC (kJ/mol) DEXP (kJ/mol) IEXP (kJ/mol) GINS
(kJ/mol) GDEL (kJ/mol) UBAR (kJ/mol) RBAR (kJ/mol)
0 -- 1 -82.289 +- 3.867 -82.289 +- 3.867 -0.000 +- 0.000 0.000 +- 0.000
-0.000 +- 0.000 0.000 +- 0.000 0.000 +- 0.000 0.000 +- 0.000
TOTAL:      -82.289  +-  3.867    -82.289  +-  3.867      0.000  +-  0.000      0.000  +-  0.000      0.000  +-  0.000      0.000  +-  0.000      0.000  +-  0.000      0.000  +-  0.000

IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
The above table has been stored in
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
data/0/results.txt
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
while the full-precision data
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
(along with the simulation profile) in
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
data/0/results.pickle
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
Time spent: 0 hours, 0 minutes, and 0.25 seconds.
Finished on Mon Dec 14 12:01:16 2015
/Users/admin/Data/TUTORIALS/AMBER/A9/1HNN
12:01 PM Mon Dec 14$
THANKSS!!
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
—
Reply to this email directly or view it on GitHub
https://github.com/MobleyLab/alchemical-analysis/issues/45#issuecomment-164401082
.

Hi,
Oh I see, this is much better now, thanks! Yes the structure of the dirs are as in the tutorial. Now the correlated IT value is almost perfect -67.201 vs -66.74 as in the paper, but the uncorrelated one (is this the second value ? TOTAL:     -281.312  +-  2.176 ???) is completely different....
Any idea why they are so different?? And how can I correct my mistake?
This is only a control run for me, once I get the right uncorrelated values I will work on my molecule.
Here is the full output,
THanks!!
$$alchemical_analysis.py -a AMBER -d data -m TI -p '[01]./prod' -q out
Started on Mon Dec 14 14:59:38 2015
Command line was: /Users/admin/Data/TOOLS/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py -a AMBER -d data -m TI -p [01]./prod -q out
Loading in data from data/0.1/prod0.1.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.2/prod0.2.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.3/prod0.3.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.4/prod0.4.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.5/prod0.5.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.6/prod0.6.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.7/prod0.7.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.8/prod0.8.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.9/prod0.9.out...  100 data points, 1 DV/DL averages
Sorting input data by starting time and lambda
Note: BAR/MBAR results are not computed.
Skipping first 0 steps (= 0.000000 ps)
Note: extrapolating missing gradient for lambda = 0.0: -15.816537
Note: extrapolating missing gradient for lambda = 1.0: -125.537551
The gradients from the correlated samples (kcal/mol):
0.00000   -15.817
0.10000   -24.593
0.20000   -32.826
0.30000   -44.704
0.40000   -56.149
0.50000   -61.926
0.60000   -65.991
0.70000   -77.821
0.80000  -103.103
0.90000  -134.217
1.00000  -125.538
TI =   -67.201
The correlated DV/DL components from every_single step (kcal/mol):
Lambda       BOND     ANGLE     DIHED    1-4 NB   1-4 EEL   VDWAALS     EELEC RESTRAINT
0.10000     0.000     0.000     0.000     0.000     0.000    21.143   -45.736     0.000
0.20000     0.000     0.000     0.000     0.000     0.000    43.638   -76.464     0.000
0.30000     0.000     0.000     0.000     0.000     0.000    61.012  -105.717     0.000
0.40000     0.000     0.000     0.000     0.000     0.000    82.468  -138.618     0.000
0.50000     0.000     0.000     0.000     0.000     0.000    16.425   -78.352     0.000
0.60000     0.000     0.000     0.000     0.000     0.000    22.832   -88.823     0.000
0.70000     0.000     0.000     0.000     0.000     0.000    14.154   -91.975     0.000
0.80000     0.000     0.000     0.000     0.000     0.000    -1.906  -101.198     0.000
0.90000     0.000     0.000     0.000     0.000     0.000     2.224  -136.441     0.000
TI =     0.000     0.000     0.000     0.000     0.000    54.055  -121.256     0.000
Number of correlated and uncorrelated samples:
State            N          N_k        N/N_k
 0          100          100         1.00
 1          100          100         1.00
 2          100           85         1.18
 3          100           57         1.76
 4          100          100         1.00
 5          100          100         1.00
 6          100           97         1.03
 7          100           66         1.52
 8          100          100         1.00
 9          100          100         1.00
10          100          100         1.00

Estimating the free energy change with TI...

States           TI (kJ/mol)

0 -- 1        -8.454  +-  0.333
1 -- 2       -12.068  +-  0.506
2 -- 3       -16.160  +-  0.597
3 -- 4       -20.983  +-  0.569
4 -- 5       -24.701  +-  0.445
5 -- 6       -26.775  +-  0.432
6 -- 7       -30.216  +-  0.564
7 -- 8       -37.965  +-  0.551
8 -- 9       -49.648  +-  0.448
9 -- 10      -54.341  +-  0.337

TOTAL:     -281.312  +-  2.176

The above table has been stored in
data/results.txt
while the full-precision data
(along with the simulation profile) in
data/results.pickle

Time spent: 0 hours, 0 minutes, and 1.02 seconds.
Finished on Mon Dec 14 14:59:39 2015

By the way I don't find any indication as if the value they published in their paper is correlated or uncorrelated data.....
Will this procedure work also for a larger molecule much more flexible like darunavir reasonably well?
Improving the Efficiency of Free Energy Calculations in the Amber
Molecular Dynamics Package
Joseph W. Kaus,*,† Levi T. Pierce,†,‡ Ross C. Walker,†,‡ and J. Andrew McCammon†,§,∥,⊥
†Department

Oh, I saw the uncorrelated flag  -n UNCORR, but using it does not produce any new output.... only the correlated lambda value....
Here it is
alchemical_analysis.py --uncorr=UNCORR  -a AMBER  -d data -m TI  -p '[01]./prod' -q out
Started on Mon Dec 14 15:45:44 2015
Command line was: /Users/admin/Data/TOOLS/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py --uncorr=UNCORR -a AMBER -d data -m TI -p [01]./prod -q out
Loading in data from data/0.1/prod0.1.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.2/prod0.2.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.3/prod0.3.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.4/prod0.4.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.5/prod0.5.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.6/prod0.6.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.7/prod0.7.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.8/prod0.8.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.9/prod0.9.out...  100 data points, 1 DV/DL averages
Sorting input data by starting time and lambda
Note: BAR/MBAR results are not computed.
Skipping first 0 steps (= 0.000000 ps)
Note: extrapolating missing gradient for lambda = 0.0: -15.816537
Note: extrapolating missing gradient for lambda = 1.0: -125.537551
The gradients from the correlated samples (kcal/mol):
0.00000   -15.817
0.10000   -24.593
0.20000   -32.826
0.30000   -44.704
0.40000   -56.149
0.50000   -61.926
0.60000   -65.991
0.70000   -77.821
0.80000  -103.103
0.90000  -134.217
1.00000  -125.538
TI =   -67.201
The correlated DV/DL components from every_single step (kcal/mol):
Lambda       BOND     ANGLE     DIHED    1-4 NB   1-4 EEL   VDWAALS     EELEC RESTRAINT
0.10000     0.000     0.000     0.000     0.000     0.000    21.143   -45.736     0.000
0.20000     0.000     0.000     0.000     0.000     0.000    43.638   -76.464     0.000
0.30000     0.000     0.000     0.000     0.000     0.000    61.012  -105.717     0.000
0.40000     0.000     0.000     0.000     0.000     0.000    82.468  -138.618     0.000
0.50000     0.000     0.000     0.000     0.000     0.000    16.425   -78.352     0.000
0.60000     0.000     0.000     0.000     0.000     0.000    22.832   -88.823     0.000
0.70000     0.000     0.000     0.000     0.000     0.000    14.154   -91.975     0.000
0.80000     0.000     0.000     0.000     0.000     0.000    -1.906  -101.198     0.000
0.90000     0.000     0.000     0.000     0.000     0.000     2.224  -136.441     0.000
TI =     0.000     0.000     0.000     0.000     0.000    54.055  -121.256     0.000
Number of correlated and uncorrelated samples:
State            N          N_k        N/N_k
 0          100          100         1.00
 1          100          100         1.00
 2          100           85         1.18
 3          100           57         1.76
 4          100          100         1.00
 5          100          100         1.00
 6          100           97         1.03
 7          100           66         1.52
 8          100          100         1.00
 9          100          100         1.00
10          100           99         1.01

Estimating the free energy change with TI...

States           TI (kJ/mol)

0 -- 1        -8.454  +-  0.333
1 -- 2       -12.068  +-  0.506
2 -- 3       -16.160  +-  0.597
3 -- 4       -20.983  +-  0.569
4 -- 5       -24.701  +-  0.445
5 -- 6       -26.775  +-  0.432
6 -- 7       -30.216  +-  0.564
7 -- 8       -37.965  +-  0.551
8 -- 9       -49.648  +-  0.448
9 -- 10      -54.341  +-  0.337

TOTAL:     -281.312  +-  2.176

The above table has been stored in
data/results.txt
while the full-precision data
(along with the simulation profile) in
data/results.pickle

Time spent: 0 hours, 0 minutes, and 0.43 seconds.
Finished on Mon Dec 14 15:45:44 2015
/Users/admin/Data/TUTORIALS/AMBER/A9/1HNN

Lastly, a few theoretical questions for my real example:
For a molecule like this one https://en.wikipedia.org/wiki/Ritonavir much larger and flexible that the one of the example I am using now, will this method provide a relatively accurate result?
How many lambda jumps should I use 10, 20? How many ns of production? I used 3 ns per lambda in this example.
Will 5 or 10 be enough for such a large molecule?
Will this method work for a mixture of acetone and water?
Thanks a lot in advance,
Fabian

Why don't you sample the end-points at lambda=0 and 1?  Also, include
TI-cubic in the analysis and look at the gradient plots (-g flag).  Your
data does not seem to very correlated so you can reduce ntpr.  100 data
points only doesn't look like very much.  Maybe you continue your
simulation with this in mind and also compute the MBAR energies?
As for the molecules you are actually interested in,  I guess this will be
very challenging.  Simulation time will depend on convergence and
correlation.  Lambda spacing depends on the steepness of the gradient (TI)
or energy overlap (FEP).  What are you after: relative or absolute free
energies?
I think the -n flag does not apply to TI and you can safely ignore it.
On 14 December 2015 at 13:17, fglaser<EMAIL_ADDRESS>wrote:

Hi,
Oh I see, this is much better now, thanks! Yes the structure of the dirs
are as in the tutorial. Now the correlated IT value is almost perfect
-67.201 vs -66.74 as in the paper, but the uncorrelated one (is this the
second value ? TOTAL: -281.312 +- 2.176 ???) is completely different....
Any idea why they are so different?? And how can I correct my mistake?
This is only a control run for me, once I get the right uncorrelated
values I will work on my molecule.
Here is the full output,
THanks!!
$$alchemical_analysis.py -a AMBER -d data -m TI -p '[01]./prod' -q out
Started on Mon Dec 14 14:59:38 2015
Command line was:
/Users/admin/Data/TOOLS/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py
-a AMBER -d data -m TI -p [01]./prod -q out
Loading in data from data/0.1/prod0.1.out... 100 data points, 1 DV/DL
averages
Loading in data from data/0.2/prod0.2.out... 100 data points, 1 DV/DL
averages
Loading in data from data/0.3/prod0.3.out... 100 data points, 1 DV/DL
averages
Loading in data from data/0.4/prod0.4.out... 100 data points, 1 DV/DL
averages
Loading in data from data/0.5/prod0.5.out... 100 data points, 1 DV/DL
averages
Loading in data from data/0.6/prod0.6.out... 100 data points, 1 DV/DL
averages
Loading in data from data/0.7/prod0.7.out... 100 data points, 1 DV/DL
averages
Loading in data from data/0.8/prod0.8.out... 100 data points, 1 DV/DL
averages
Loading in data from data/0.9/prod0.9.out... 100 data points, 1 DV/DL
averages
Sorting input data by starting time and lambda
Note: BAR/MBAR results are not computed.
Skipping first 0 steps (= 0.000000 ps)
Note: extrapolating missing gradient for lambda = 0.0: -15.816537
Note: extrapolating missing gradient for lambda = 1.0: -125.537551
The gradients from the correlated samples (kcal/mol):
0.00000 -15.817
0.10000 -24.593
0.20000 -32.826
0.30000 -44.704
0.40000 -56.149
0.50000 -61.926
0.60000 -65.991
0.70000 -77.821
0.80000 -103.103
0.90000 -134.217
1.00000 -125.538
TI = -67.201
The correlated DV/DL components from every_single step (kcal/mol):
Lambda BOND ANGLE DIHED 1-4 NB 1-4 EEL VDWAALS EELEC RESTRAINT
0.10000 0.000 0.000 0.000 0.000 0.000 21.143 -45.736 0.000
0.20000 0.000 0.000 0.000 0.000 0.000 43.638 -76.464 0.000
0.30000 0.000 0.000 0.000 0.000 0.000 61.012 -105.717 0.000
0.40000 0.000 0.000 0.000 0.000 0.000 82.468 -138.618 0.000
0.50000 0.000 0.000 0.000 0.000 0.000 16.425 -78.352 0.000
0.60000 0.000 0.000 0.000 0.000 0.000 22.832 -88.823 0.000
0.70000 0.000 0.000 0.000 0.000 0.000 14.154 -91.975 0.000
0.80000 0.000 0.000 0.000 0.000 0.000 -1.906 -101.198 0.000
0.90000 0.000 0.000 0.000 0.000 0.000 2.224 -136.441 0.000
TI = 0.000 0.000 0.000 0.000 0.000 54.055 -121.256 0.000
Number of correlated and uncorrelated samples:
State N N_k N/N_k
0          100          100         1.00
1          100          100         1.00
2          100           85         1.18
3          100           57         1.76
4          100          100         1.00
5          100          100         1.00
6          100           97         1.03
7          100           66         1.52
8          100          100         1.00
9          100          100         1.00
10          100          100         1.00
Estimating the free energy change with TI...
States TI (kJ/mol)
0 -- 1 -8.454 +- 0.333
1 -- 2 -12.068 +- 0.506
2 -- 3 -16.160 +- 0.597
3 -- 4 -20.983 +- 0.569
4 -- 5 -24.701 +- 0.445
5 -- 6 -26.775 +- 0.432
6 -- 7 -30.216 +- 0.564
7 -- 8 -37.965 +- 0.551
8 -- 9 -49.648 +- 0.448
9 -- 10 -54.341 +- 0.337
TOTAL:     -281.312  +-  2.176

The above table has been stored in
data/results.txt
while the full-precision data
(along with the simulation profile) in
data/results.pickle
Time spent: 0 hours, 0 minutes, and 1.02 seconds.
Finished on Mon Dec 14 14:59:39 2015
—
Reply to this email directly or view it on GitHub
https://github.com/MobleyLab/alchemical-analysis/issues/45#issuecomment-164433562
.

I tried, the TI is less similar to the paper with 0 and 1.... TI =   -72.664 why is that? :-( and I get a new error, the figures are great tahnsk!!
The objective is to learn about the differences of solubility, any measure that will teach me what is more soluble and maybe a hint about  why will be great about this two guys which are given together for HIV:
https://en.wikipedia.org/wiki/Ritonavir
https://en.wikipedia.org/wiki/Darunavir
So I thought to calculate TI of hydration of each one and compare them,  I have an idea of what should be the result.
Here is the result with 0 and 1:
alchemical_analysis.py  -a AMBER  -d data -m TI-cubic  -p '/prod' -q out -g
Started on Mon Dec 14 16:42:31 2015
Command line was: /Users/admin/Data/TOOLS/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py -a AMBER -d data -m TI-cubic -p /prod -q out -g
Loading in data from data/0/prod0.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.1/prod0.1.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.2/prod0.2.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.3/prod0.3.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.4/prod0.4.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.5/prod0.5.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.6/prod0.6.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.7/prod0.7.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.8/prod0.8.out...  100 data points, 1 DV/DL averages
Loading in data from data/0.9/prod0.9.out...  100 data points, 1 DV/DL averages
Loading in data from data/1/prod1.0.out...  100 data points, 1 DV/DL averages
Sorting input data by starting time and lambda
Note: BAR/MBAR results are not computed.
Skipping first 0 steps (= 0.000000 ps)
The gradients from the correlated samples (kcal/mol):
0.00000   -19.525
0.10000   -24.593
0.20000   -32.826
0.30000   -44.704
0.40000   -56.149
0.50000   -61.926
0.60000   -65.991
0.70000   -77.821
0.80000  -103.103
0.90000  -134.217
1.00000  -231.084
TI =   -72.664
The correlated DV/DL components from every_single step (kcal/mol):
Lambda       BOND     ANGLE     DIHED    1-4 NB   1-4 EEL   VDWAALS     EELEC RESTRAINT
0.00000     0.000     0.000     0.000     0.000     0.000    -0.245   -19.279     0.000
0.10000     0.000     0.000     0.000     0.000     0.000    21.143   -45.736     0.000
0.20000     0.000     0.000     0.000     0.000     0.000    43.638   -76.464     0.000
0.30000     0.000     0.000     0.000     0.000     0.000    61.012  -105.717     0.000
0.40000     0.000     0.000     0.000     0.000     0.000    82.468  -138.618     0.000
0.50000     0.000     0.000     0.000     0.000     0.000    16.425   -78.352     0.000
0.60000     0.000     0.000     0.000     0.000     0.000    22.832   -88.823     0.000
0.70000     0.000     0.000     0.000     0.000     0.000    14.154   -91.975     0.000
0.80000     0.000     0.000     0.000     0.000     0.000    -1.906  -101.198     0.000
0.90000     0.000     0.000     0.000     0.000     0.000     2.224  -136.441     0.000
1.00000     0.000     0.000     0.000     0.000     0.000    24.306  -255.390     0.000
TI =     0.000     0.000     0.000     0.000     0.000    27.402  -100.066     0.000
Number of correlated and uncorrelated samples:
State            N          N_k        N/N_k
 0          100           62         1.61
 1          100          100         1.00
 2          100           85         1.18
 3          100           57         1.76
 4          100          100         1.00
 5          100          100         1.00
 6          100           97         1.03
 7          100           66         1.52
 8          100          100         1.00
 9          100          100         1.00
10          100           90         1.11

Estimating the free energy change with TI-CUBIC...

States     TI-CUBIC (kJ/mol)

0 -- 1        -9.199  +-  0.555
1 -- 2       -11.949  +-  0.575
2 -- 3       -16.071  +-  0.681
3 -- 4       -21.094  +-  0.651
4 -- 5       -24.903  +-  0.514
5 -- 6       -26.683  +-  0.500
6 -- 7       -29.701  +-  0.644
7 -- 8       -37.963  +-  0.630
8 -- 9       -48.203  +-  0.510
9 -- 10      -74.725  +-  0.720

TOTAL:     -300.490  +-  2.306

The above table has been stored in
data/results.txt
while the full-precision data
(along with the simulation profile) in
data/results.pickle

Plotting the free energy breakdown figure...
Plotting the TI figure...
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/axes.py:4747: UserWarning: No labeled objects found. Use label='...' kwarg on individual plots.
warnings.warn("No labeled objects found. "
Traceback (most recent call last):
File "/Users/admin/Data/TOOLS/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py", line 1224, in
main()
File "/Users/admin/Data/TOOLS/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py", line 1216, in main
plotdFvsLambda()
File "/Users/admin/Data/TOOLS/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py", line 1010, in plotdFvsLambda
plotTI()
File "/Users/admin/Data/TOOLS/alchemical-analysis-master/alchemical_analysis/alchemical_analysis.py", line 999, in plotTI
for l in lege.legendHandles:
AttributeError: 'NoneType' object has no attribute 'legendHandles'
/Users/admin/Data/TUTORIALS/AMBER/A9/1HNN

As far as I can tell from the paper they have found a solvation free energy around -66 kcal/mol so you do not seem to be far off.   What I find more worrisome is that the correlated and uncorrelated result is so different.  Have you plotted your results and compared this with the output plots from the tool?
The error message may be some bug in the main code but it looks like it is only one of the plotting routines.

Sorry for the delay getting involved in this. I'm tied up here grading
finals but can start dealing with issues on this code in a day or two.
On Tue, Dec 15, 2015 at 7:37 AM, Hannes Loeffler<EMAIL_ADDRESS>wrote:

As far as I can tell from the paper they have found a solvation free
energy around -66 kcal/mol so you do not seem to be far off. What I find
more worrisome is that the correlated and uncorrelated result is so
different. Have you plotted your results and compared this with the output
plots from the tool?
The error message may be some bug in the main code but it looks like it is
only one of the plotting routines.
—
Reply to this email directly or view it on GitHub
https://github.com/MobleyLab/alchemical-analysis/issues/45#issuecomment-164800996
.

--
David Mobley
Associate Professor
Department of Pharmaceutical Sciences
Department of Chemistry
3134B Natural Sciences I
University of California, Irvine
Irvine, CA 92697
<EMAIL_ADDRESS>work<PHONE_NUMBER>
cell<PHONE_NUMBER>

OK, @fglaser , to respond to some of this which still seems to be unresolved:

Now the correlated IT value is almost perfect -67.201 vs -66.74 as in the paper, but the uncorrelated one (is this the second value ? TOTAL: -281.312 +- 2.176 ???) is completely different....

I think the major issue you're noticing here is a units one. Specifically, it appears @halx 's AMBER parser is printing out "correlated" values using kcal/mol but the total is in kJ/mol. I've created an issue to fix this so these are consistent. But you'll notice that 67.201*4.184 = 281.17, so you're in rather good shape here.

By the way I don't find any indication as if the value they published in their paper is correlated or uncorrelated data.....

Often people do NOT subsample at intervals of the autocorrelation time, which means they're using correlated data. This doesn't mean that it's correct to do so.

Will this procedure work also for a larger molecule much more flexible like darunavir reasonably well?

The key questions here are:
a) What are the relevant timescales in your system, and
b) How important are they for the property you are computing
i.e. if there are flexible rotatable bonds that impact the conformation which is important for the solvation free energy and are only adequately sampled on timescales of hundreds of nanoseconds, then you will either need to run simulations which are hundreds of nanonseconds long, or be tricky somehow. So whether it will work on darunavir in particular is something I can't really answer without knowing more about the molecule (i.e. knowing timescale for bond rotation, etc.).

For a molecule like this one https://en.wikipedia.org/wiki/Ritonavir much larger and flexible that the one of the example I am using now, will this method provide a relatively accurate result?

See above - depends on timescales. TI gives correct results in the limit of infinite sampling; the key question for any system is how fast you approach that limit. The more flexibility/the slower the timescales, the slower you approach that limit. Again I can't tell you anything in specific without knowing details of the timescales of your system. You might want to look at bond rotation timescales in your simulations for example, to get an idea of that.

How many lambda jumps should I use 10, 20? How many ns of production? I used 3 ns per lambda in this example.

Lambda spacing is not going to be as sensitive to the molecule, other than that for relatively nonpolar molecules or very small molecules one could get by with fewer lambda values. But in general if you have a lambda schedule which works for a reasonably-sized polar molecule it ought to work fairly well for most other cases you would want to look at, provided you sample enough.

Will 5 or 10 be enough for such a large molecule?
I expect not.

Will this method work for a mixture of acetone and water?
We've done some work recently treating solvents other than pure water, and yes, there's no methodological reason that won't work (it's worked well for us). You might want to see github.com/mobleylab/solvationtoolkit.

The objective is to learn about the differences of solubility, any measure that will teach me what is more >soluble and maybe a hint about why will be great about this two guys which are given together for HIV:

https://en.wikipedia.org/wiki/Ritonavir
https://en.wikipedia.org/wiki/Darunavir

So I thought to calculate TI of hydration of each one and compare them, I have an idea of what should >be the result.

Do keep in mind that solubility is determined by other factors aside from the solvation free energy. In fact, ritonavir is famous for solubility problems that originated specifically from issues OTHER than the solvation free energy (several different crystal polymorphs of ritonavir are possible and these have dramatically different solubilities and dramatic effects on oral bioavailability; this actually resulted in ritonavir being withdrawn from the market at one point, i.e. see http://www.nature.com/nrd/journal/v3/n1/box/nrd1280_BX2.html).
I'm marking this issue as closed for now, as I don't see any actual problems with the tool that aren't already solved. But please re-open if you have further issues.

Dear Prof. Mobley,
Thanks a lot for your informative answer, trully I don't have the details of rotation time scale of my system, but I think I'll give it a go. I know bioavailability is a complicated issue. I just want to learn about the process of the precipitation or desolvation or both, and since not much is known for this two guys and specially their combination, I think I maybe able to help my colleague. In any case I'll bug you from time to time with some questions. The main problem as I understand with those molecules is running time.
Now if I need to run 500 ns to get some approximate value is a problem, I guess I can try to use accelerated MD, which I never used... if you happen to know some additional bibliography yours or other's on this issue of studying the precipitation / desolvation of drugs into water or water / acetone mixtures, I'll be more than thankfully to get links.
Or any other suggestion that can help to understand the complicated process of nano precipitation of drugs in general with simulation.
At least  I know know with yours and Hannes great help to run IT... It's a beginning.
Best wishes and happy new year,
Fabian Glaser PhD,
Technion Israel

In terms of references on solubility - you'll want to look at Mike
Schnieders' (Iowa) work on this with the AMOEBA force field, and probably
the work of Sanz and Vega. We're working on some actual solubility
calculations ourselves but the work is not complete yet. We're also doing a
lot on relative solubility and solvation in mixtures, though not in
water/acetone at present.
On Mon, Dec 21, 2015 at 5:57 AM, fglaser<EMAIL_ADDRESS>wrote:

Dear Prof. Mobley,
Thanks a lot for your informative answer, trully I don't have the details
of rotation time scale of my system, but I think I'll give it a go. I know
bioavailability is a complicated issue. I just want to learn about the
process of the precipitation or desolvation or both, and since not much is
known for this two guys and specially their combination, I think I maybe
able to help my colleague. In any case I'll bug you from time to time with
some questions. The main problem as I understand with those molecules is
running time.
Now if I need to run 500 ns to get some approximate value is a problem, I
guess I can try to use accelerated MD, which I never used... if you happen
to know some additional bibliography yours or other's on this issue of
studying the precipitation / desolvation of drugs into water or water /
acetone mixtures, I'll be more than thankfully to get links.
Or any other suggestion that can help to understand the complicated
process of nano precipitation of drugs in general with simulation.
At least I know know with yours and Hannes great help to run IT... It's a
beginning.
Best wishes and happy new year,
Fabian Glaser PhD,
Technion Israel
—
Reply to this email directly or view it on GitHub
https://github.com/MobleyLab/alchemical-analysis/issues/45#issuecomment-166310783
.

--
David Mobley
<EMAIL_ADDRESS>949-385-2436


Error when calling zwlr_layer_surface_v1::get_popup

Hyprland Version
Hyprland, built from branch main at commit ecf98069f655a4e54943ec70d638ddcf429211d1
Bug or Regression?
Bug
Description
Calling zwlr_layer_surface_v1::get_popup with an xdg popup object that was created by calling xdg_surface::get_popup with the "parent" argument set as NULL yields the following error message: Request<EMAIL_ADDRESS>expects an argument of interface xdg_popup but zxdg_output_manager_v1 was provided instead. Or at least Smithay (the library I'm using) says so. As far as I can see WAYLAND_DEBUG=1 log (attached here) doesn't show anything suspicious and neither does the Hyprland log. Is it possible that Hyprland creates/assigns the wrong object somehow? Otherwise, it may be a library issue...
How to reproduce
Smithay provides an abstraction for creating popups: https://github.com/Smithay/client-toolkit/blob/master/src/shell/xdg/popup.rs#L76 which is what I'm using in my code.
Crash reports, logs, images, videos
wayland_debug.log

Can you test sway-git? I don't think it's me handling this.

True, also happens on sway-git. So this is handled in wlroots then?

yeh

The bug was in my own code... was mixing Wayland objects created by different connections which apparently isn't how this works.


How to get started with Facets for a simple one-page website?

Hello,
I've just discovered Facets and SandDance (by Microsoft); both seem to be amazing tool to visualize data.
However, it's not easy to get started with Facets (Bazel & Cie).
Is there a simple way to build a simple one-page website displaying a Facet Dive (no Jupyter, no build, etc.) ?
I didn't succeed in doing so even if I tried to get started copying https://pair-code.github.io/facets/quickdraw.html ...
Thanks a lot.

The best way will be to follow how quickdraw.html was made. See the source here: https://github.com/PAIR-code/facets/tree/gh-pages
basically this approach required 3 files:
facets.html which is the compiled facets code for the visualizations. You should be able to use the provided https://github.com/PAIR-code/facets/blob/master/facets-dist/facets-jupyter.html file from the repo.
quickdraw.html which loads all necessary code (the webcomponents-lite js file) and when web components are ready, it loads the facets html file and when that is loaded it creates the facets-dive element.
quickdraw.js which sets the data and options on the facets-dive object to get it to display the dataset.

First, thanks for your message.
I've cloned gh-page as you suggest, run it into VSCode with Live-server to avoid CORS issues and used facets-jupyter.html (renamed facets.html).
However, quickdraw.html is empty (without any console errors).
Not so easy to get started for a simple dataviz :)

definitely true that facets is not simple at all to embed into a website. it was built to be easily usable in notebooks such as colab, and to be used in other webapps with complex build environments such as the what-if tool.

I tried another method with the Jupyter notebook suggested on README (Facets Dive and Overview Colab Example).
Is it possible to export the embedded Facets Dive into a webpage (the notebook displaying html)?
If yes, do you know how to?
Thanks again.

I haven't tried exporting the html from a notebook to use on a webpage, so unfortunately can't help with that flow

Solved.
from google.colab import files
with open('facets.html', 'w') as f:
  f.write(html)
files.download('facets.html')

The webpage is super heavy (12 mo including data), but It works.


Removed vulnerable package - DotNetZip and installed and set up Systm.IO.Compression

Removed vulnerable package - DotNetZip and installed and set up Systm.IO.Compression

Thanks for your pull request, @VasilenaDaskalska!
Could you tell us why you close it?


Adding table_prefix to ScyllaDBStore.

Closes #50
Proposed Changes

Adding a table_prefix setting for ScyllaDBStore

Codecov Report

Merging #57 (5c942ee) into main (6ea532d) will decrease coverage by 0.35%.
The diff coverage is 60.00%.

Impacted Files
Coverage Δ

narrow_down/scylladb.py
96.07% <33.33%> (-1.91%)
:arrow_down:

narrow_down/_minhash.py
100.00% <100.00%> (ø)


Line wrapping JTextField built from onActivate while in a MultiplexingPluginPanel causes client resize

Type
Incorrect behavior
Operating System
Windows
OS Version
Windows 11
Bug description
I was getting this client resize issue in various ways and have mostly found workarounds, most of them were with calling revalidate on a PluginPanel. But I have recently found a case when building the panel inside of a MultiplexingPluginPanel and using the onActivate function. Here is an example plugin stripped down to show the issue. https://github.com/adamk33n3r/client-resize-issue
Screenshots or videos
If onActivate calls it like SwingUtilities.invokeLater(() -> this.build(), then the
resize issue happens immediately when the panel is pushed on.

If onActivate calls it like this.build(), then the resize issue happens when restoring the
panel from collapse and when switching panel tabs (like to settings and back).

RuneLite version
RL: <IP_ADDRESS>
Launcher: 2.7.1
Logs
No response

FYI, I'm using the onActivate function to rebuild panels as I step up the chain because in Watchdog if I edit the name of an alert in an alert group, step up to the alert group, I need to rebuild the panel to show the new name. I tried thinking of other ways of handling this, but onActivate is really what I need, and it's sad that when I tried to delay it with invokeLater it made it even worse somehow lol.
I know previously, calling reavalidate() when there was a multiline text area would cause this issue to happen, so that may be related to this.


Fix: Make separate Favicons for light and dark theme

Description
Make separate Favicons for light and dark theme
we have one right here /public/favicon-dark.svg
Screenshots
No response
Additional Information
No response

Can I work on this issue?

Can I work on this issue?

sure @Shivam-Amin go ahead

I think this issue is already fixed, isn't it?


Papertrader not working anymore in develop branch

Note: this is the technical bug tracker, please use other platforms for getting support and starting a (non technical) discussion. See the getting help page for details.
I'm submitting a ...
[*] bug report
[ ] question about the decisions made in the repository
Action taken (what you did)
The whole last week I tried to run the latest code of the develop branch, but the papertrader seems not to be working anymore.

Exchange: kraken
Currency: EUR
Asset: XRP
Type: papertrader
Strategy
Name
RSI_Bull_Bear_Adx_Stop
Parameters
{
"SMA_long": 1000,
"SMA_short": 50,
"BULL_RSI": 10,
"BULL_RSI_high": 80,
"BULL_RSI_low": 60,
"BEAR_RSI": 15,
"BEAR_RSI_high": 50,
"BEAR_RSI_low": 20,
"BULL_MOD_high": 5,
"BULL_MOD_low": -5,
"BEAR_MOD_high": 15,
"BEAR_MOD_low": -5,
"ADX": 3,
"ADX_high": 70,
"ADX_low": 50,
"Stop_Loss_Percent": 50
}

The result is error messages and a non-running Gekko, immediately after start:

This is an archived Gekko, it is currently not running anymore.
This is Gekko crashed with the following error: This Gekko instance encountered an error and can't continue

No error messages in the log files in the /logs directory. I tried it with other exchanges as well.
Expected result (what you hoped would happen)
A running papertrader.
Actual result (unexpected outcome)
Papertrader crashes immediately, no errors to be found in the logs.
Other information (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, eg. stackoverflow, etc)

Works great for me:

Can you try with a default strategy that comes with Gekko?

Mike, I can't reproduce it anymore as well, I created a new built and tried several strategies and exchanges now with the papertrader. I think that I made a mistake somewhere, I won't be able to discover where it went wrong though, my apologies for that.
Now that I managed to get it working I'll start running a new test instance for the coming days with the latest develop code. Again, my apologies.

And I did reproduce it, but not with the standard strategies. But with a lot of strategies I successfully used before, I encounter this error.

It turns out that when the following line is in the strategy file, it crashes:
this.addTulipIndicator(...)

I'm not sure if you are using the UI or the CLI to start, but I just some default configs for the two tulip methods: tulip-macd and tulip-adx, for some reason they were not included in the default config.
For me Gekko works fine using the sample config (that passes the correct config). Can you check if that also works for you?

Will check it asap and let you know! Im using the UI. What I did this morning was completely strip the strategy and adding line for line to see where it went wrong (could not find useful logs related to this issue). And it crashed on the addTulipIndicator... very strange.

I found the issue. In my deployment scripts, I injected the following line in Dockerfile:
RUN npm install mathjs convnetjs
This is necessary for some (external) indicators. It turns out that not injecting this line solved the problem. I don't know anymore which indicators required these libraries, and I don't know if this is going to be another issue for me, but that's not related to Gekko then. I can't judge if this is a problem that should be solved.
With this issue, I noticed that when a strategy crashes in the init method, no errors are found in the log files (don't know if this is by design or not).

Great that you figured it out! in my experience docker is great for
automating builds that work, but when experimenting/debugging that
container layer only gets in the way.
On Sun, 22 Jul 2018, 16:37 bald123<EMAIL_ADDRESS>wrote:

I found the issue. In my deployment scripts, I injected the following line
in Dockerfile:
RUN npm install mathjs convnetjs
This is necessary for some (external) indicators. It turns out that not
injecting this line solved the problem. I don't know anymore which
indicators required these libraries, and I don't know if this is going to
be another issue for me, but that's not related to Gekko then. I can't
judge if this is a problem that should be solved.
With this issue, I noticed that when a strategy crashes in the init
method, no errors are found in the log files (don't know if this is by
design or not).
—
You are receiving this because you commented.
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Non-Node.js env

Our use case doesn't depend on Node.js.
https://github.com/devongovett/rsc-html-stream/blob/1ff7350f280243ee23f7133c26892f9b9065a663/server.js#L15
Can you use setTimeout instead?
I'm not sure if we need to wait for a tick, though.

I think it should work. Will have to check what next.js uses again. The delay is necessary to ensure the app shell is flushed before the script tags are added to the stream. That might be the whole page, or maybe not in the case of suspense, but it should always be a valid spot to insert the scripts.

Yeah looks like they use setTimeout when setImmediate isn't available. But I think setTimeout is probably fine in all cases. https://github.com/vercel/next.js/blob/canary/packages/next/src/lib/scheduler.ts#L28

published in 0.0.3


Possibility for tslint inside mdx files?

Hello! First I would like to thank you for this amazing project! I am loving it!
My question is for Docz configured to use Typescript:
I was wondering if there is a way to have type checking, or tslint active inside the mdx files for the parts that use ts components?
As it is right now, if I misstype a component prop, my editor doesn't highlight it as an error.
Thank you for taking the time to read this!

You can simply using modifyBundlerConfig to add your tslint or eslint loader ✌

@pedronauck could you add an example of how to do this?


Add MIT license and GitHub info to Components page

What we've changed
Fixes #1810.
This PR adds info to the Components page on the main Design System site.
It tells users:

that our code is public and available under an MIT license
where they can find our repos

I also replaced some instances of the passive voice, to make the text more direct.
Why we've changed it
We're adding this info because a user reported they'd had to dig around before they found out we use MIT. See #1810 for full details.
Other gov teams have previously added similar info to their sites. For example, data.gov.uk and Verify.

@vanitabarrett Thanks for reviewing! I'll send this PR for 2i now.

Content has passed pre-i. I'll send it for 2i now.


Windows support for control_robot.py as well as support for recording a policy without a leader arm.

What this does
rewrites mac specific code to be multiplatform.
adds ability to use koch arm as both leader arm and follower arm.
How it was tested
Manual testing with a physical arm.
note: not tested on linux or mac...
How to checkout & try? (for the reviewer)

configure factory.py with your follower arm. Remove a reference to a leader arm in the configuration.
python -m control_robot record_dataset --fps 30 --root tmp/data --repo-id example/koch_test --num-episodes 1 --run-compute-stats 1 --push-to-hub 0
move the follower around to record some movement for 10 seconds.
python -m control_robot record_dataset --fps 30 --root tmp/data --repo-id travis/koch_test --num-episodes 1 --run-compute-stats 1 --push-to-hub 0
You should see your motions replay on the follower arm.

Should be working on windows.

By any chance, could we split this PR in two?

Add windows support for control_robot.py
Add support for data recording without leader arm

We can merge the first PR as soon as possible. By the way, did you have any issue with OpenCVCamera on Windows?
For the second PR, could we add a test called test_robot_without_leader_arm? It would be similar to this one, but lighter: https://github.com/huggingface/lerobot/blob/main/tests/test_robots.py#L12-L128 We should add it on the same test_robots.py file. Let me know if you are not inspired and I will do it.
Thanks for your contributions ;)

I hadn't used the camera feature yet. So I can't really comment on it. It could be the case that it still doesn't work. I'll do what's asked here after lunch.

I splited the PR in two by isolating your contribution with the say function in this PR: https://github.com/huggingface/lerobot/pull/355


[BUG]Syntax error in ppl commands redirecting to blank page

What is the bug?
New ppl commands have been introduced by ml-commons plugin to allow users to process the queried data from index before performing ML and AD operations.
We recently found out a bug when sending such ppl requests on OS dashboards. Whenever there is a syntax error in the ppl request, instead of throwing error to the user, the page just goes blank(refer to the screenshots attached) which is not desirable. When sending the same requests on other platforms like postman, everything works fine and error message is thrown to the user.
How can one reproduce the bug?
Steps to reproduce the behavior:

Go to OpenSearch Dashboards
Go to Dev Tools
Send a PPL API request with a syntax error as shown below (the correct parameter to be used is "centroids" and not "centroid").
e.g:

POST _plugins/_ppl
{
  "query": "source=iris_data | fields petal_length_in_cm,petal_width_in_cm | kmeans centroid=3"
}

The page goes blank as shown in the attachment

What is the expected behavior?
Ideally, it should have thrown a syntax error as shown below:
{
  "error": {
    "reason": "Invalid Query",
    "details": "Failed to parse query due to offending symbol [centroid] at: 'source=iris_data | fields petal_length_in_cm,petal_width_in_cm | kmeans centroid' <--- HERE... More details: Expecting tokens in {<EOF>, 'CENTROIDS', 'ITERATIONS', 'DISTANCE_TYPE', '|'}",
    "type": "SyntaxCheckException"
  },
  "status": 400
}

This is happening for any PPL request that has some syntax error in its body. We have been seeing this behavior only with PPL commands and not with any other ML or AD APIs.
Do you have any screenshots?

@rbhavna, thank you for posting the bug!
Could you please, rename it to be a bit more verbose?

@jngz-es may have some context?

Closing as stale / the query UI has changed a bit since this issue was opened so the bug is probably not relevant anymore


Error - UNIQUE constraint failed.

This error occurs when:

install app
create one or more todo tasks
close and reopen the app
Create a new todo task and press save

App crashes.
This is due to task Id restarts from 1 after reopening. And the ID is marked as "PrimaryKey" so it should be unique. But the new task about to create after reopening the app is trying to assume ID 1 which is already taken.

Instead of keeping the LiveData observe in a separate function, moved it to oncreate method


feat(p-select-dropdown): add lg size

To Reviewers

[ ] Skipping review is not a problem (style, chore ONLY)
[X] Not that difficult

Type of Change

[ ] New feature
[ ] Bug fixes
[X] Feature improvement

[ ] These changes require a usage change

[ ] Others (performance improvement, refactoring, CI/CD, etc.)

Checklist

[X] Updated Storybook documents
[ ] Tested with console(if usages are changed)

Description

add large size props

Things to Talk About

:tada: This PR is included in version 1.1.0-beta.468 :tada:
The release is available on:

npm package (@beta dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


Errors when run the Remove Anything Video

hi， when I run the remove_anything_video.py, comes the errors as following:
(Inpaint_Anything) E:\Sydney University\CVProject\Project\Inpaint_Anything\Inpaint-Anything-main>python remove_anything_video.py --input_video ./example/video/paragliding/original_video.mp4 --coords_type key_in --point_coords 652 162 --point_labels 1 --dilate_kernel_size 15 --output_dir ./results --sam_model_type "vit_h" --sam_ckpt ./pretrained_models/sam_vit_h_4b8939.pth --lama_config lama/configs/prediction/default.yaml --lama_ckpt ./pretrained_models/big-lama --tracker_ckpt vitb_384_mae_ce_32x4_ep300 --vi_ckpt ./pretrained_models/sttn.pth --mask_idx 2 --fps 25
Detectron v2 is not installed
Traceback (most recent call last):
File "E:\Sydney University\CVProject\Project\Inpaint_Anything\Inpaint-Anything-main\remove_anything_video.py", line 384, in
model = RemoveAnythingVideo(args)
File "E:\Sydney University\CVProject\Project\Inpaint_Anything\Inpaint-Anything-main\remove_anything_video.py", line 117, in init
self.segmentor = self.build_segmentor(
File "E:\Sydney University\CVProject\Project\Inpaint_Anything\Inpaint-Anything-main\remove_anything_video.py", line 131, in build_segmentor
return build_sam_model(**kwargs)
File "E:\Sydney University\CVProject\Project\Inpaint_Anything\Inpaint-Anything-main\sam_segment.py", line 39, in build_sam_model
sam.to(device=device)
File "D:\Anaconda\envs\Inpaint_Anything\lib\site-packages\torch\nn\modules\module.py", line 1145, in to
return self._apply(convert)
File "D:\Anaconda\envs\Inpaint_Anything\lib\site-packages\torch\nn\modules\module.py", line 797, in _apply
module._apply(fn)
File "D:\Anaconda\envs\Inpaint_Anything\lib\site-packages\torch\nn\modules\module.py", line 797, in _apply
module._apply(fn)
File "D:\Anaconda\envs\Inpaint_Anything\lib\site-packages\torch\nn\modules\module.py", line 797, in _apply
module._apply(fn)
File "D:\Anaconda\envs\Inpaint_Anything\lib\site-packages\torch\nn\modules\module.py", line 820, in apply
param_applied = fn(param)
File "D:\Anaconda\envs\Inpaint_Anything\lib\site-packages\torch\nn\modules\module.py", line 1143, in convert
return t.to(device, dtype if t.is_floating_point() or t.is_complex() else None, non_blocking)
File "D:\Anaconda\envs\Inpaint_Anything\lib\site-packages\torch\cuda_init.py", line 239, in _lazy_init
raise AssertionError("Torch not compiled with CUDA enabled")
AssertionError: Torch not compiled with CUDA enabled
I think the problem is the Cuda version is not compatible with Torch version, but when I download the new version of Torch, comes a lot of other problems, even the other function remove,fill, and replace can not be used(it can be run correctly before), so do you know how to solve this problem?and do you have any recommend suitable cuda version?

The installation requires commond is :python -m pip install torch torchvision torchaudio， this code install the pytorch without the cuda, but somewhere in the remove_anything_video.py it seems using the cuda, so here comes the problem I guss, so maybe should update the requires or delete the cuda parts.

另一个问题是remove anything video提供的checkpoints文件格式似乎不对，我通过您在Usage上的链接下载并且解压后，尽管他的名称是OSTrack_ep0300.pth，但是实际的格式仍然是文件夹格式而不是.pth格式，所以导致没法调用，希望您能解答我的问题

另一个问题是remove anything video提供的checkpoints文件格式似乎不对，我通过您在Usage上的链接下载并且解压后，尽管他的名称是OSTrack_ep0300.pth，但是实际的格式仍然是文件夹格式而不是.pth格式，所以导致没法调用，希望您能解答我的问题

You can rename it or re-download from here.

Have you tried using conda instead? I find that installation has lesser issues when using conda.
Here is the command, you will need to create an env first however.
conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia

@Zixuan-Xu-GodVision Have you tried using conda instead? I find that installation has lesser issues when using conda. Here is the command, you will need to create an env first however.
conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia
# other commands
# pip install ...

Yeah, I tried, but after using conda to install, something else still wrong, so I think simply way to run it directly change the cuda to cpu

The installation requires commond is :python -m pip install torch torchvision torchaudio， this code install the pytorch without the cuda, but somewhere in the remove_anything_video.py it seems using the cuda, so here comes the problem I guss, so maybe should update the requires or delete the cuda parts.

Firstly, change the device to "cpu" and check out if it runs normally.
https://github.com/geekyutao/Inpaint-Anything/blob/a68eff249a07ea081e584ad262cbfbba8dc2a196/remove_anything_video.py#L334
You then need configure torch and cuda according to your device (e.g., GPU type). I'm afraid I can't help you without enough context.

Thanks for replying, after chnage to "cpu", it can not run normally,
but I figure it out , using conda to install the pytorch again.

I was having this problem too while trying to run with CPU only. The problem is that remove_anything_video.py calls functions like build_sam_model in sam_segment.py (and also in sttn_video_inpaint.py) without specifying the device. It's usually an optional parameter that defaults to "cuda". I tried fixing that, but also it seems like pytracking/lib/test/tracker/ostrack.py also assumes you have cuda instead of cpu and I couldn't figure out quickly how to switch it


Find better calendar

Current calendar plugin uses jQuery, I would like to get rid of jQuery dependency and go vanilla.

Many design components still use jquery - lets skip this for now.


Security

I don't know if it is just hackers in runescape or this plugin but i have installed and uninstalled it twice now and both times i've logged out, checked my email and have received emails for a single use code both times meaning someone has been trying to get access through forgot password. i have since uninstalled the plugin and i probably will not be reinstalling it.
Edit: i forgot to mention i have been playing runescape for about a week and a half now, and i haven't had this problem until i installed this plugin.

Update: After uninstalling the Plugin, running a Windows Defender scan AND activating 2 factor authentication i have since stopped receiving the emails. I'll install it one last time and if i start receiving them again someone is doing some shady things with this plugin.

Update: I've stopped receiving the emails but that doesn't really mean anything. All that tells me is whoever is doing the shady stuff got spooked and stopped. I'll be leaving this plugin uninstalled until access to the 3rd party website my IP is being broadcast to is released.

Update: I don't think it's this plugin but i don't know anything about programming or anything so i don't actually know. i have activated 2 factor authentication on my email account, and phone verification so i was told i could safely ignore the emails. but i would seriously like an answer to this.
I'm sure you would like to know if your own plugin is compromised since it doesn't seem like you're around on github a lot.

This plugin is incapable of leaking your email; it only contacts ttsplugin.com and readaloud.app with the text to be converted into audio

All pluginhub plugins are verified to not contain malware like that, and since their open source, you can always re-check yourself.


Crashes on specific mod

Describe your bug here.
I downloaded a modpack from the discord but some mods would crash and give me this error:Paths.hx (line 443)
Character.hx (line 226)
Boyfriend.hx (line 16)
PlayState.hx (line 1212)
flixel/FlxGame.hx (line 642)
flixel/FlxGame.hx (line 729)
flixel/FlxGame.hx (line 682)
flixel/FlxGame.hx (line 556)
openfl/events/EventDispatcher.hx (line 402)
openfl/display/DisplayObject.hx (line 1399)
Uncaught Error: Null Object Reference

Crash Handler written by: sqirra-rng
here's the mod link if u wna check it out https://www.mediafire.com/file/csf1sacx5m2jugz/OG_Modpack_V3.zip/file

Command Prompt/Terminal logs (if existing)
No response
Are you modding a build from source or with Lua?
Lua
What is your build target?
Windows
Did you edit anything in this build? If so, mention or summarize your changes.
no

This bug usually happens, and really no one knows why. My guess there was something that was used but it had no value or was nil or null
 d


Added/removed accessConfigs after inital instance creation do not get recognized

What happened?
Deploying an instance with a public IP initially and removing it afterwards does not get recognized by pulumi.
Example
Deploying an instance with a public IP like this:
new gcp.compute.Instance('my-instance-name', {
    name: 'my-instance-name',
    zone: 'europe-west4-a',
    machineType: 'f1-micro',
    networkInterfaces: [
      {
        subnetwork: args.subnetworkId,
        accessConfigs: [
          {
            networkTier: 'PREMIUM',
          },
        ],
      },
    ],
    bootDisk: {
      initializeParams: {
        image: 'ubuntu-2204-jammy-v20230727',
      },
    },
  });

And then removing the accessConfigs block like this:
new gcp.compute.Instance('my-instance-name', {
    name: 'my-instance-name',
    zone: 'europe-west4-a',
    machineType: 'f1-micro',
    networkInterfaces: [
      {
        subnetwork: args.subnetworkId,
        // accessConfigs: [
        //   {
        //     networkTier: 'PREMIUM',
        //   },
        // ],
      },
    ],
    bootDisk: {
      initializeParams: {
        image: 'ubuntu-2204-jammy-v20230727',
      },
    },
  });

And doing pulumi up again, results in no update/change of the instance.
Output of pulumi about
CLI
Version      3.88.0
Go Version   go1.21.2
Go Compiler  gc

Plugins
NAME    VERSION
nodejs  unknown

Host
OS       darwin
Version  13.6
Arch     arm64

Additional context
This also does not work the other way round:

Instance without public IP address
Add accessConfigs block to networkInterfaces
pulumi up -> results in no changes

Contributing
Vote on this issue by adding a 👍 reaction.
To contribute a fix for this issue, leave a comment (and link to your pull request, if you've opened one already).

Unfortunately, it looks like this issue hasn't seen any updates in a while. If you're still encountering this problem, could you leave a quick comment to let us know so we can prioritize it?

Hi, just tested this again: Removing the accessConfigs block now results in a diff/replace. So everything working as expected. Thank you for following up on this.
Tested with
> pulumi about

CLI
Version      3.134.0
Go Version   go1.23.1
Go Compiler  gc

Plugins
KIND      NAME    VERSION
resource  gcp     7.38.0
language  nodejs  3.134.0-dev.0

Host
OS       darwin
Version  14.7
Arch     arm64


Hello. Status?

Hello.
I'm interested in writing some automated Betfair trading in Swift. I started a similar project and stumbled on this repo.
I just wanted to say hello and ask where you got to with this project, and what made you stop?
I started writing code for the authentication part and hit the immediate stumbling block of their tricky certificate based auth. I noticed in the master branch you used Kitura, and dropped it in the development branch?
Thanks!
Adam

Sorry for the delay on the reply. I gave up as I moved onto some other unrelated side projects. I did have some success with this placing orders and seeing some good returns on it. I’d still give the usual warning of make sure you test anything using this library extensively before placing live orders though.
In the development branch my plan was to move over to NIO libraries instead of Kitura. I can’t 100% remember where I got up to but I’ll try and answer any questions you’ve got.

Sorry for the delay on the reply. I gave up as I moved onto some other unrelated side projects. I did have some success with this placing orders and seeing some good returns on it. I’d still give the usual warning of make sure you test anything using this library extensively before placing live orders though.
In the development branch my plan was to move over to NIO libraries instead of Kitura. I can’t 100% remember where I got up to but I’ll try and answer any questions you’ve got.

All good thanks mate. I found a pretty mature Python lib in the end and went with that.

All good thanks mate. I found a pretty mature Python lib in the end and went with that.


Add support for readonly-tags

Hi,
As suggested I created draft for read-only tags.
Issues that I believer deserve mentioning:
If You try to remove readonly tag by backspace, nothing will happen, even if You have tags earlier, that could be removed.
If next tag for removal by backspace is "readonly" tag, then the feature is disabled. Tags before "readonly" one, can still be removed by taping on the "x" button.
I merged my repo with newest master, to add support for disabled tags as well. I noticed it too late.

@Istalacar could you review what's currently on master? i've given it some thoughts and I'd rather use the officially supported "disabled" attribute. Could you give it a try and see how that fits with your proposal ?

@Istalacar ok i see, but then maybe we can just use disabled, and not using readonly? what is the use case for this ?


add support for nuki-extended adapter devices

Hi,
probably it's possible to add nuki-extended adapter. There are different things that can be connected to the nuki bridge and I have two of them.
One of the devices has just the batteryCritical State and one has batter berrtyChargeState with the percentage.

Can you give me the whole path of batteryChargeState, please? Then I will look if I get it implemented.

The Lock:
nuki-extended.0.smartlocks.schloss.state.batteryChargeState

The Opener:
nuki-extended.0.openers.opener.state.batteryCritical

But the 'opener' and 'schloss' in the object path is the name of my device so this will change for different persons and locks.

Yes okay thanks. I will look the next days. The opener doesn't have the state batteryChargeState?

Okay I added Nuki Extended. But we have to test if it works. I have to lookout for the datapoint batteryCritical. Otherwise it will not work. I hope the timestamp of this datapoint is refreshing sometimes so it will not shown as an offline device. Maybe you can try it and tell me


Import Task is just cancelld without any reason

The import Sol. Task everey day stops after different time periods without any reason.

whereas the import in the solution history is correct and has no issues at all.
Its not a timeout, as its always a different timeframe.

I guess it was a general Pipelinie Timeout. Ill try again.


Fix re_dirs check in RegExpWatcher

Thanks. Do you want me to do a release now or in a few days incase you find any other problems?

ok, I'll release in a few days. If I forget please remind me.


Enabling generateAsInternal in combination with nonempty sealedClassesForEnumsMatching generates invalid classes definitions

Version
4.0.1
Summary
I have my apollo service defined in build.gradle.kts as follows:
apollo {
    service("myService") {
        packageName.set("...")
        schemaFile.set(file("..."))

        introspection {
            ...
        }
        generateAsInternal = true
        sealedClassesForEnumsMatching.set(setOf(".*"))
    }
}

I enabled sealedClassesForEnumsMatching just recently, because I wanted to access the raw value of the UNKNOWN__ constant. However, the generated classes for UNKNOWN__ constant looks like this:

private internal class UNKNOWN__MyModelClass(
  override val rawValue: String,
) : MyModelClass.UNKNOWN__ {
  override fun equals(other: Any?): Boolean {
    if (other !is UNKNOWN__MyModelClass) return false
    return this.rawValue == other.rawValue
  }

  override fun hashCode(): Int = this.rawValue.hashCode()

  override fun toString(): String = "UNKNOWN__($rawValue)"
}

If i disable generateAsInternal = true the problem doesn't occur, only private modifier remains on the generated class' definition.
The build then fails on invalid syntax.
I believe this is a bug.
Steps to reproduce the behavior
No response
Logs
No response

Thanks for reporting! This was indeed a bug in the codegen - a fix is in #6213.

The fix will be in the next release. In the meantime you can test it with the snapshots.

The fix is now available in 4.1.0


Match data from previous transcation

Just a heads up on what I'm working on adding now.
When we get a new transaction I now look for a previous transaction for this payee, and get the category set, and the payee actually used (some people tidy up the names of the payees).
Are you happy for me to sneak this in before 1.0?

Yeah, that is a good idea. Auto filling the category based on the previous transaction will work really nicely.

resolved with check in 484f4e81f11afc518f7ad46139c7f026b9cdbea2

@rossdargan with big changes like that, we should really still use branches and PR them in so that we can test.

Fair point - to be honest it's more my lack of familiarity with git that's caused it.

No worries. Just for future note :) not all changes need a new branch, just bigger ones like this.


Show additional information for unexpected error if available

We have the info present within the content record, so we just have to recognize that additional info is there and display it correctly.
I believe this will be related to our continued narrowing of AgentError.

The screenshot on this issue description is outdated, from an older publisher version. PR #2430 introduced some changes to use a better message.
Recent screenshot showing current behavior

I believe this will be related to our continued narrowing of AgentError.

Yes, we still have to keep an eye open for this kind of "unexpected error..." messages, we could (should) do a search for bare errors in our API handlers and list those that have a raw message instead of an Agent|OperationError


Add username and ssh to image validation

Add validation to make sure username and ssh-key are presented in the request when creating a new image.
Small updates to the testing -> moving to test table form.

Let me know when I can merge this so we don't break the currently working UI.

Thanks @biancarosa !


feat: handle delete for CRP controller

Description of your changes
delete all the policy snapshots & resource snapshots when CRP is in the deleting state
Fixes #
I have:

[X] Run make reviewable to ensure this PR is ready for review.

How has this code been tested
added UT
Special notes for your reviewer

This PR is supposed to be sent after the prev. one is merged? If so, I will wait until it happens to review it.


Move some types back to aw project #5306

Closes #5306

If so, better to mention the "why" in the commit message and PR title

This is necessary because they belong to the app, but not the AlphaWallet logic?

yes, there some types, those actually related to the app, and not its functionality that was moved to the pod


Make thumb in slider component more customizable.

Should be able to customize thumb in slider component.
Expected Behavior
Customizing thumb should be flexible and have a separate prop for customizing thumb with images or icons.
Current Behavior
currently there is no option to customize the thumb with images. By default is is of type button and styles are applied on that but there is option to change the type of thumb.
Examples

Context
currently I'm trying to add a mdi-react LabelIcon as a thumb to the slider but it is not allowing me to do that. Because it is a button and there is option to override that I'm blocked.

Please come up with a solution as early as possible.

https://github.com/mui-org/material-ui/pull/12485

Thank you.

https://github.com/mui-org/material-ui/pull/12600

This was shipped with<EMAIL_ADDRESS>in #12600. Is this sufficient for your use case @ksairamya?

yes this is sufficient @eps1lon .  Thank you for working on it.


Instagram: Unable to extract data

DO NOT REMOVE OR SKIP THE ISSUE TEMPLATE

[X] I understand that I will be blocked if I intentionally remove or skip any mandatory* field

Checklist

[X] I'm reporting that yt-dlp is broken on a supported site
[X] I've verified that I'm running yt-dlp version 2023.07.06 (update instructions) or later (specify commit)
[X] I've checked that all provided URLs are playable in a browser with the same IP and same login details
[X] I've checked that all URLs and arguments with special characters are properly quoted or escaped
[X] I've searched known issues and the bugtracker for similar issues including closed ones. DO NOT post duplicates
[X] I've read the guidelines for opening an issue
[ ] I've read about sharing account credentials and I'm willing to share it if required

Region
Turkey
Provide a description that is worded well enough to be understood
Unable to parse the profile page to get the image and video content for downloading
Provide verbose output that clearly demonstrates the problem

[X] Run your yt-dlp command with -vU flag added (yt-dlp -vU <your command line>)
[ ] If using API, add 'verbose': True to YoutubeDL params instead
[X] Copy the WHOLE output (starting with [debug] Command-line config) and insert it below

Complete Verbose Output
C:\Users\X\Downloads>yt-dlp.exe https://instagram.com/barbara_cicero_ -vU
[debug] Command-line config: ['https://instagram.com/barbara_cicero_', '-vU']
[debug] Encodings: locale cp1254, fs utf-8, pref cp1254, out utf-8, error utf-8, screen utf-8
[debug] yt-dlp version<EMAIL_ADDRESS>[f780bb52b] (win_exe)
[debug] Python 3.8.10 (CPython AMD64 64bit) - Windows-10-10.0.19045-SP0 (OpenSSL 1.1.1k  25 Mar 2021)
[debug] exe versions: ffmpeg 4.2.2, ffprobe 4.2.2
[debug] Optional libraries: Cryptodome-3.18.0, brotli-1.0.9, certifi-2023.07.22, mutagen-1.46.0, sqlite3-2.6.0, websockets-11.0.3
[debug] Proxy map: {}
[debug] Loaded 1857 extractors
[debug] Fetching release info: https://api.github.com/repos/yt-dlp/yt-dlp/releases/latest
Available version<EMAIL_ADDRESS>Current version<EMAIL_ADDRESS>Current Build Hash: 9cb23e2fd45fc307c6ebe0d477539fdd760e06fe1703d2289acab103106ef2a7
yt-dlp is up to date<EMAIL_ADDRESS>[instagram:user] Extracting URL: https://instagram.com/barbara_cicero_
[instagram:user] barbara_cicero_: Downloading webpage
ERROR: [instagram:user] barbara_cicero_: Unable to extract data; please report this issue on  https://github.com/yt-dlp/yt-dlp/issues?q= , filling out the appropriate issue template. Confirm you are on the latest version using  yt-dlp -U
  File "yt_dlp\extractor\common.py", line 715, in extract
  File "yt_dlp\extractor\instagram.py", line 610, in _real_extract
  File "yt_dlp\extractor\instagram.py", line 543, in _parse_graphql
  File "yt_dlp\extractor\common.py", line 1263, in _search_regex

C:\Users\X\Downloads>

Duplicate of #4394


SCM decorations are single pixel wide and sometimes not visible at all

Not sure if this was intentional but it's very small now:

They are invisible when zooming out once:

Version: 1.71.0-insider (user setup)
Commit: 8e42bda5487a953d59fab7792eedd4ca209cabba
Date: 2022-08-16T05:18:32.502Z
Electron: 19.0.12
Chromium: 102.0.5005.167
Node.js: 16.14.2
V8: <IP_ADDRESS>-electron.0
OS: Windows_NT x64 10.0.22000
Sandboxed: Yes

I preferred the old style:

Version: 1.69.2 (user setup)
Commit: 3b889b090b5ad5793f524b5d1d39fda662b96a2a
Date: 2022-07-18T16:12:52.460Z
Electron: 18.3.5
Chromium: 100.0.4896.160
Node.js: 16.13.2
V8: <IP_ADDRESS>-electron.0
OS: Windows_NT x64 10.0.22000

The mouse target is also 1 pixel wide now

Deleted lines are much harder to see and use now

do you have any repro steps? I can't seem to see that, assume it was unintentional:

This is in a PR so likely related to the comments changes

Still an issue after https://github.com/microsoft/vscode/issues/158299 and https://github.com/microsoft/vscode/issues/158521 fixes:

This does seem likely to be related to the comments changes. I'm looking into it.

I have "editor.folding": false set, it works fine when I enable folding again


adding assignmentExpression entity, assigning init of loopControl to it

Created an entity FastFortranAssignmentExpression that has leftPart and rightPart of FastFortranVariable.
Change type of init in loopControlExpression to FastFortranAssignmentExpression

Didn't we have a TFASTAssignementExpression ?
I assume we should. And FastFortranAssignmentExpression would use it


(YNAB::ApiError)

Have spun this up and I'm having a little issue. It's running on a docker instance.
The webhook has been registered and succesfully received as per this line:
I, [2023-12-30T18:38:42.773650 #7]  INFO -- : Completed 200 OK in 1ms (Views: 0.1ms)
The issue I'm having is the 400 bad request to the YNAB api endpoint.
I, [2023-12-30T18:38:42.773650 #7]  INFO -- : Completed 200 OK in 1ms (Views: 0.1ms)
D, [2023-12-30T18:38:42.877115 #7] DEBUG -- : ETHON: performed EASY effective_url=https://api.youneedabudget.com/v1/budgets/{YNAB_BUDGET_ID}/transactions response_code=0 return_code=ssl_cacert total_time=0.21707299999999996
E, [2023-12-30T18:38:42.877596 #7] ERROR -- : YNAB::Client.create_transaction failure
E, [2023-12-30T18:38:42.877625 #7] ERROR -- : YNAB::Client.create_transaction Response:
E, [2023-12-30T18:38:42.877639 #7] ERROR -- : Peer certificate cannot be authenticated with given CA certificates (YNAB::ApiError)
/usr/local/bundle/gems/ynab-1.5.0/lib/ynab/api_client.rb:65:in `call_api'
/usr/local/bundle/gems/ynab-1.5.0/lib/ynab/api/transactions_api.rb:126:in `create_transaction_with_http_info'
/usr/local/bundle/gems/ynab-1.5.0/lib/ynab/api/transactions_api.rb:87:in `create_transaction'
/usr/local/bundle/bundler/gems/f2ynab-3ee8170dd7ec/lib/f2ynab/ynab/client.rb:52:in `create_transaction'
/usr/local/bundle/bundler/gems/f2ynab-3ee8170dd7ec/lib/f2ynab/ynab/transaction_creator.rb:16:in `create'
/usr/local/bundle/bundler/gems/f2ynab-3ee8170dd7ec/lib/f2ynab/webhooks/monzo.rb:53:in `import'
/app/app/controllers/monzo_controller.rb:12:in `receive'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_controller/metal/basic_implicit_render.rb:6:in `send_action'
/usr/local/bundle/gems/actionpack-5.2.1/lib/abstract_controller/base.rb:194:in `process_action'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_controller/metal/rendering.rb:30:in `process_action'
/usr/local/bundle/gems/actionpack-5.2.1/lib/abstract_controller/callbacks.rb:42:in `block in process_action'
/usr/local/bundle/gems/activesupport-5.2.1/lib/active_support/callbacks.rb:132:in `run_callbacks'
/usr/local/bundle/gems/actionpack-5.2.1/lib/abstract_controller/callbacks.rb:41:in `process_action'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_controller/metal/rescue.rb:22:in `process_action'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_controller/metal/instrumentation.rb:34:in `block in process_action'
/usr/local/bundle/gems/activesupport-5.2.1/lib/active_support/notifications.rb:168:in `block in instrument'
/usr/local/bundle/gems/activesupport-5.2.1/lib/active_support/notifications/instrumenter.rb:23:in `instrument'
/usr/local/bundle/gems/activesupport-5.2.1/lib/active_support/notifications.rb:168:in `instrument'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_controller/metal/instrumentation.rb:32:in `process_action'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_controller/metal/params_wrapper.rb:256:in `process_action'
/usr/local/bundle/gems/actionpack-5.2.1/lib/abstract_controller/base.rb:134:in `process'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_controller/metal.rb:191:in `dispatch'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_controller/metal.rb:252:in `dispatch'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/routing/route_set.rb:52:in `dispatch'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/routing/route_set.rb:34:in `serve'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/journey/router.rb:52:in `block in serve'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/journey/router.rb:35:in `each'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/journey/router.rb:35:in `serve'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/routing/route_set.rb:840:in `call'
/usr/local/bundle/gems/rack-2.0.6/lib/rack/etag.rb:25:in `call'
/usr/local/bundle/gems/rack-2.0.6/lib/rack/conditional_get.rb:38:in `call'
/usr/local/bundle/gems/rack-2.0.6/lib/rack/head.rb:12:in `call'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/middleware/callbacks.rb:28:in `block in call'
/usr/local/bundle/gems/activesupport-5.2.1/lib/active_support/callbacks.rb:98:in `run_callbacks'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/middleware/callbacks.rb:26:in `call'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/middleware/executor.rb:14:in `call'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/middleware/debug_exceptions.rb:61:in `call'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/middleware/show_exceptions.rb:33:in `call'
/usr/local/bundle/gems/railties-5.2.1/lib/rails/rack/logger.rb:38:in `call_app'
/usr/local/bundle/gems/railties-5.2.1/lib/rails/rack/logger.rb:28:in `call'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/middleware/remote_ip.rb:81:in `call'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/middleware/request_id.rb:27:in `call'
/usr/local/bundle/gems/rack-2.0.6/lib/rack/runtime.rb:22:in `call'
/usr/local/bundle/gems/activesupport-5.2.1/lib/active_support/cache/strategy/local_cache_middleware.rb:29:in `call'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/middleware/executor.rb:14:in `call'
/usr/local/bundle/gems/actionpack-5.2.1/lib/action_dispatch/middleware/static.rb:127:in `call'
/usr/local/bundle/gems/rack-2.0.6/lib/rack/sendfile.rb:111:in `call'
/usr/local/bundle/gems/railties-5.2.1/lib/rails/engine.rb:524:in `call'
/usr/local/bundle/gems/puma-3.12.0/lib/puma/configuration.rb:225:in `call'
/usr/local/bundle/gems/puma-3.12.0/lib/puma/server.rb:658:in `handle_request'
/usr/local/bundle/gems/puma-3.12.0/lib/puma/server.rb:472:in `process_client'
/usr/local/bundle/gems/puma-3.12.0/lib/puma/server.rb:332:in `block in run'
/usr/local/bundle/gems/puma-3.12.0/lib/puma/thread_pool.rb:133:in `block in spawn_thread'
I, [2023-12-30T18:38:42.877950 #7]  INFO -- : Completed 400 Bad Request in 221ms (Views: 0.2ms)

I wonder if the following (from above) is a problem but my research is struggling - any ideas?
E, [2023-12-30T18:38:42.877596 #7] ERROR -- : YNAB::Client.create_transaction failure
E, [2023-12-30T18:38:42.877625 #7] ERROR -- : YNAB::Client.create_transaction Response:
E, [2023-12-30T18:38:42.877639 #7] ERROR -- : Peer certificate cannot be authenticated with given CA certificates (YNAB::ApiError)

Thanks in advance!

I wonder if it the fact I'm running this with Cloudflare as MITM may be impacting my results - the DNS was setup < 60 minutes ago so perhaps the SSL cert is not created...

Some gems/libraries will likely need to be updated. I unfortunately don't have the time to do this right now though.

Thanks - will use baked in YNAB updates for now.

Did not resolve issue myself. Closing.


Remove references to debug_guilds

As discord fixed the 1 hour delay in global command registration, it is no longer necessary to register guild commands instead of global commands when testing. Because of this, the guide has no reason to reference debug_guilds as it's an unnecessary detail that will just confuse the user. Removing all references should provide the guide with more clarity.

#232


Added cognitive services accounts

Change
Added cognitive services accounts
Type of Change
Please delete options that are not relevant.

[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update (Wiki)

Checklist

[x] I'm sure there are no other open Pull Requests for the same update/change
[x] My corresponding pipelines / checks run clean and green without any errors or warnings
[x] My code follows the style guidelines of this project
[x] I have commented my code, particularly in hard-to-understand areas
[x] I have made corresponding changes to the documentation (readme)
[x] I did format my code

@MrMCake I checked to include the privateDnsZoneGroups as part of the privateEndpoints resource, but seems like its a different resource that needs to be declared separately 😊


More Converting operations

When working with specific local settings, we still can get data in international format. And it should be parsed rather than rejected. Here we have fallback on parsing doubles with POSIX number format. (This was made for convertTo function but also works on primary parsing. For example, readCsvWithFloats test now passes on my computer without switching to empty locale manually.) May be, we should have similar logic in date, time and some other parsers.
Also some new converters (to Boolean and LocalTime) have been added.

Hi! Thank you for the PR. Parsing numbers is quite an old problem here :) https://github.com/Kotlin/dataframe/issues/9

Review current version, please.
Also do you think we should make rendering test locale-independent as was suggested here?

Review current version, please.
Also do you think we should make rendering test locale-independent as was suggested here?

Sure. I guess right now it's impossible to run all tests on a PC with locale that uses comma? Would be nice to fix it

Sure. I guess right now it's impossible to run all tests on a PC with locale that uses comma?

Until now I used export LANG=C.UTF-8 command in bash session to avoid problems.

Would be nice to fix it

Done. Double printing is unified by DecimalFormatSymbols.getInstance().decimalSeparator and LocalDate parsing is forced by using en_US explicitly.


Attack an ensemble of models

Hi Muzammal,
Have you test your approach when white-box models are an ensemble of Inc-v3, Inc-v4, IncRes-v2 and Res-152? The reported results in Tab.6 is really impressive! And I want to know if you attack an ensemble of models, How much can your experimental results improve?
Thanks~

Hi,
We haven't experimented with ensemble. All of the generators are trained against single model at a time. The pretrained generators are available. You are welcome to attack ensemble of models.
Best Regards,


Support converting Vega specs to Vega-editor compatible URLs

Inspired by @NickCrews's idea in https://github.com/altair-viz/altair/issues/3188, vl-convert could potentially support converting Vega/Vega-Lite specifications to share URLs that are compatible with the Vega editor.
I haven't looked into the details, but @NickCrews mentioned that the editor is using the lz-string JavaScript library for URL-compatible compression. There is a Rust port of this library at https://docs.rs/lz-str/latest/lz_str/. If this library is compatible with the what the Vega editor needs, this might be a pretty easy and useful addition to vl-convert.

I don't really understand how all the vega parts fit together, if this is added here, would it be accessible from altair?
Specifically, vega editor uses the LZstring.decompressFromEncodedURIComponent method. The python port I mentioned in the above issue did not have this flavor. But the rust port you linked does! So it might just work out of the box! I would just try passing some json to the rust lib and see if it works as a 10 minute prototype

This turned out to be pretty straightforward, so I opened a PR at https://github.com/vega/vl-convert/pull/104. Regardless of what else happens with the Vega editor, this is a nice feature to have in VlConvert.

I don't really understand how all the vega parts fit together, if this is added here, would it be accessible from altair?

vl-convert-python is an optional dependency of Altair that we already use for PNG and SVG image export. We would probably want to have Altair provide a convenience chart.to_url() method, but it will be usable with vl-convert directly like this:
import vl_convert as vlc
vlc.vegalite_to_url(chart.to_json())


How about replacement jq with jaq?

At the time of v0.1.0, the author deemed it most appropriate to use the original jq.
However, managing C-related stuff during build time had to be undertaken, and this was underestimated at the release of v0.1.0. After actually releasing and taking a look the installation error issues that were raised, it became apparent that continuing to use jq might not be the best decision.
Then, there is a project in Rust called jaq, which is a jq-clone. I hope to discuss whether or not to replace jq with jaq, and whether it is feasible to do so.
Here's a rough outline of the pros and cons:
jq (j9)

pros

As an original implementation, all filters defined here are, of course, available for use

cons

Requires management of C dependencies, which might pose issues during build phase

https://github.com/ynqa/jnv/issues/6
https://github.com/ynqa/jnv/issues/13
https://github.com/ynqa/jnv/issues/1

jaq

pros

pure Rust, there is no need to manage C dependencies

cons

jq-clone, not all filters may be supported

e.g. https://github.com/01mf02/jaq/issues/112
My concern is with this point. Ideally, it would be better if all features were available for use (Or maybe it's sufficient if only the basic filters are available...?)

I say it’s okay to have jaq’s reduced set of available filters, if more people can build and use jnv. 😊

I agree with @dwvisser and would personally prefer an easy-to-build pure rust tool over packaging C deps. ripgrep took a similar approach where the rust regex crate they use lacks some features (eg look-ahead/behind is not supported) but in return doesn't depend on C.

I would like to start using this tool if it was pure Rust. Even if there weren't a complete match of filters.
jq was unmaintained entirely for a number of years. At least if you only have Rust dependencies it will be easier to manage if such a situation happens again.

Can you maybe try out how it works with jaq, allowing choice of jaq and jaq, then deprecate jq if jaq is good enough.

I'm also having some issues compiling j9-sys
https://github.com/conda-forge/staged-recipes/pull/25806#issuecomment-2041434460
checking host system type...
  --- stderr
  configure.ac:11: installing 'config/ar-lib'
  configure.ac:8: installing 'config/compile'
  configure.ac:19: installing 'config/config.guess'
  configure.ac:19: installing 'config/config.sub'
  configure.ac:9: installing 'config/install-sh'
  configure.ac:9: installing 'config/missing'
  Makefile.am: installing 'config/depcomp'
  configure.ac: installing 'config/ylwrap'
  parallel-tests: installing 'config/test-driver'
  Invalid configuration `/home/conda/staged-recipes/build_artifacts/jnv_1712488275842/_build_env/bin/x86_64-conda-linux-gnu': more than four components
  configure: error: /bin/sh /home/conda/staged-recipes/build_artifacts/jnv_1712488275842/work/target/x86_64-unknown-linux-gnu/release/build/j9-sys-b50a7ed31c9b8fd9/out/jq_build/config/config.sub /home/conda/staged-recipes/build_artifacts/jnv_1712488275842/_build_env/bin/x86_64-conda-linux-gnu failed
  thread 'main' panicked at /home/conda/staged-recipes/build_artifacts/jnv_1712488275842/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/autotools-0.2.6/src/lib.rs:781:5:

Switching to jaq would fix this 😅