[WIP] SMIRFF ForceField implementation

This begins the SMIRFF ForceField implementation.
For discussion of format, see: https://github.com/open-forcefield-group/open-forcefield-data/issues/9
Currently, only SMIRFF bond types are implemented, but the implementation for other force terms is very simple and should proceed quickly. I want to do more testing to make sure the current machinery is working for bonds, however.

Note that this implementation doesn't yet handle constraints---all bonds are added as harmonic bonds for now.
I propose we add a general constraint scheme later, perhaps with an SMIRKS-styled syntax:
<Constraints>
  <!-- bonds involving hydrogen -->
  <Constraint smirks="[#1:1]-[*:2]"/> <!-- add constraint between atoms 1 and 2 using equilibrium bond distance -->
  <!-- angles involving hydrogen -->
  <Constraint smirks="[#1:1]-[*:2]-[#1:3]"/> <!-- add constraint between atoms 1 and 3 using auto-calculated distance from equilibrium bond and angles -->
</Constraints>

I've tried to make adding a new force generator require only a minimal amount of work. For harmonic bond forces, this is:
class HarmonicBondGenerator(object):
    """A HarmonicBondGenerator constructs a HarmonicBondForce."""

    class SMARTYBondType(object):
        """A SMARTY bond type."""
        def __init__(self, node):
            self.smirks = _validateSMIRKS(node.attrib['smirks'], node=node)
            self.length = _convertParameterToNumber(node.attrib['length'])
            self.k = _convertParameterToNumber(node.attrib['k'])

    def __init__(self, forcefield):
        self.ff = forcefield
        self._bondtypes = list()

    def registerBond(self, node):
        """Register a SMARTY bondtype definition."""
        bond = HarmonicBondGenerator.SMARTYBondType(node)
        self._bondtypes.append(bond)

    @staticmethod
    def parseElement(element, ff):
        # Find existing force generator or create new one.
        existing = [f for f in ff._forces if isinstance(f, HarmonicBondGenerator)]
        if len(existing) == 0:
            generator = HarmonicBondGenerator(ff)
            ff.registerGenerator(generator)
        else:
            generator = existing[0]

        # Register all SMARTY bond definitions.
        for bond in element.findall('Bond'):
            generator.registerBond(bond)

    def createForce(self, system, topology, **kwargs):
        # Find existing force or create new one.
        existing = [system.getForce(i) for i in range(system.getNumForces())]
        existing = [f for f in existing if type(f) == openmm.HarmonicBondForce]
        if len(existing) == 0:
            force = openmm.HarmonicBondForce()
            system.addForce(force)
        else:
            force = existing[0]

        # Iterate over all defined bond types, allowing later matches to override earlier ones.
        bonds = ValenceDict()
        for bond in self._bondtypes:
            for atom_indices in topology.getSMIRKSMatches(bond.smirks):
                bonds[atom_indices] = bond

        # Add all bonds to the system.
        for (atom_indices, bond) in bonds.items():
            force.addBond(atom_indices[0], atom_indices[1], bond.length, bond.k)

parsers["HarmonicBondForce"] = HarmonicBondGenerator.parseElement

I'll next write these for HarmonicAngleForce, PeriodicTorsionForce, and NonbondedForce.

I'll also note that the current createSystem function signature is
system = forcefield.createSystem(topology, mols)

where mols is a list of openeye.oechem.OEGraphMols.
I can change this to SDF if that is preferred, but is there additional information we need in the tags that must be preserved in this case?

Matching of molecules identified in the Topology object to the molecules is currently done using networkx based on graph isomorphism, using only elements and bond connectivity. I'm not sure if this has the potential to match the molecules incorrectly, but if it does, we would have to figure out what other properties to match on.

I can finish this PR up tonight, but it would be great to get comments from @davidlmobley and @pgrinaway (who has been asking for this for some time).
The biggest issues I can see right now are:

The charges will have to be taken from the provided OEMols, which is fine for now, but will eventually have to be replaced by a charging scheme.
There is no understanding of polymeric entities. If you have a protein that consists of many amino acids, the valence and Lennard-Jones terms will be typed, but you still need to provide an OEMol for the whole protein from which the charges are taken. I'm also not sure how well the NetworkX graph isomorphism algorithm scales for very large molecules (subgraphs) like proteins.

@jchodera :

...where mols is a list of openeye.oechem.OEGraphMols that specify the unique "reference molecules" present in the system. These reference molecules will also carry the partial charges used.
I can change this to SDF if that is preferred, but is there additional information we need in the tags that must be preserved in this case?

I'm not totally sure what you're asking about tags, since if you change it to taking in SDF files, you'd be pulling in whatever tags are in the SDF files so I don't see a significant difference (in terms of the result) than what you'd get pulling in info from OEMols. But, I'm assuming you're asking what would be in the tags. It would be something like:

partial_bond_orders
partial_charges
atom_types (we probably want to track these just for, er, "historical" reasons at present, though obviously they're going to be unimportant to the force field)
However, Christopher Bayly notes that these names should be revised so they are very certain to never clash with any tags anyone else would create, to avoid unintended behaviors/clashes. He suggests adding the origin to the tags to achieve this, so maybe something more like:
OpenEyeAM1BCC_partial_charges
OpenEyeAM1_partial_bond_orders
antechamber_gaff_atom_types and possibly antechamber_sybyl_atom_types
(the last one I'm pretty ambivalent on since we don't anticipate significant functional importance to the atom types, but we may need these - especially sybyl atom types - down the road to get back into file formats which require atom types, such as .mol2)

In the interests of getting going quickly, I'm really OK with just having everything come in as OEMols for now, even though as we discussed on the phone last week there's some preference for taking SDFs.
In terms of constraints - presumably we can get by without constraints for everything in AlkEthOH for now. It does have water, but that could be treated as flexible water (which would be more in keeping with the spirit of what we're doing right now anyway).
Otherwise, I think this looks good to me (but do you want me to try and do code review?).
Thinking of testing - I was thinking a sensible test for me to run once you think you have this working would be to do energy evaluations in OpenMM for the provided AlkEthOH conformations via parameters coming in from .prmtop and .crd files versus from this implementation of SMIRFF. This should check two things at once:

Has Bayly input his SMIRFF file properly
Are the parameters parsed properly to result in the same energies

Thoughts?

Thanks! Would be great if you could also look through the code to see if it makes sense or has appropriate documentation, since blocks of it will be replicated and modified next.
Do you have any input files I could use for more thorough testing? I am only testing against single molecules in vacuum right now.

@jchodera - I'll review the code, though it might not be til late.
Input files - anything in particular you want to look at? Solvation Toolkit should be able to set up any mixture you want pretty easily via an API we discussed previously (https://github.com/mobleylab/solvationtoolkit) and I almost have it conda installable (https://github.com/omnia-md/conda-recipes/pull/540 - I just have to bypass a couple software clashes I think).
I'll generate a couple of simple mixtures of alkanes or cyclohexane or something for you and attach them momentarily.

I'll generate a couple of simple mixtures of alkanes or cyclohexane or something for you and attach them momentarily.

Great!  A small number of "things that should work" would be great.

OK, @jchodera - attached please find mixtures of (cyclohexane, ethanol) and (propane, methanol, butanol). These are (40%,60%) and (20%, 30%, 50%) respectively.
Within the data directory, you'll find subdirectories for monomers, which has the monomers in .mol2 and .sdf formats; then there is a packmol_boxes directory with PDBs of the solvated boxes. These are out of packmol, and are cubic. (Note I also have AMBER .prmtop and .crd files there if it's easier for you to load those than PDBs; those are in the amber directory).
I expect you can just load:

data/monomers/ethanol.sdf and cyclohexane.sdf and data/packmol_boxes/cyclohexane_ethanol_0.4_0.6.pdb
data/monomers/methane.sdf, propane.sdf, and butanol.sdf and data/packmol_boxes/propane_methane_butanol_0.2_0.3_0.5.pdb

As noted if it's easier for you to get a Topology from AMBER files those are there as well.
If you'd like anything else generated, I can easily do so. For example, I could blast through AlkEthOH and generate mixtures of every molecule paired with another molecule, or something along those lines. LMK.
data.tar.gz

Thanks! This is a great start. Let me make sure this works first.

@davidlmobley: I've implemented tests based on the nice dataset you provided, but this has uncovered a problem in SMIRKS typing the OH bond in ethanol.
I'm using the monomers/ethanol.mol2 file as a source for the ethanol molecule template, and while I can type C-H with [#6:1]~[#1:2] just fine, I can't match O-H with [#8:1]~[#1:2].
See the test code here, which succeeds with [#6:1]~[#1:2],
[LSKI1497:open-forcefield-group/smarty/smarty.open-forcefield-group] choderaj% python smarty/tests/test_forcefield.py
1 reference molecules loaded
('C1', 'H1')
('C1', 'H2')
('C1', 'H3')
('C2', 'H4')
('C2', 'H5')

but fails with [#8:1]~[#6:2]
[LSKI1497:open-forcefield-group/smarty/smarty.open-forcefield-group] choderaj% python smarty/tests/test_forcefield.py
1 reference molecules loaded
Traceback (most recent call last):
  File "smarty/tests/test_forcefield.py", line 96, in <module>
    test_smirks()
  File "smarty/tests/test_forcefield.py", line 92, in test_smirks
    raise Exception("Pattern '%s' did not match any molecules in set" % (smirks))
Exception: Pattern '[#8:1]~[#1:2]' did not match any molecules in set

Perhaps the SMIRKS syntax is incorrect here?

Another clue here: If I change to using the SDF files, it does seem to perceive this bond, but (of course) the atom names are empty:
[LSKI1497:open-forcefield-group/smarty/smarty.open-forcefield-group] choderaj% python smarty/tests/test_forcefield.py
1 reference molecules loaded
('', '')

@jchodera :

I'm using the monomers/ethanol.mol2 file as a source for the ethanol molecule template, and while I can type C-H with [#6:1]~[#1:2] just fine, I can't match O-H with [#8:1]~[#1:2].

I expect this is because the .mol2 files use GAFF atom types (I should have emphasized the importance of this when I was passing them on to you) so it's probably not perceiving the elements properly. You MAY be able to fix this by using the forcefield-flavor reader as we had to use the other week when working on Smarty. Alternatively, you can use antechamber to get back SYBYL types. (To test, you could write your OEMols back to .mol2 files and see how the atoms are typed. I'm guessing the oxygens might be listed as "Os" or something.)

Aha! Thanks!

I also read through the code and it generally looked good to me though there were some things which are hard to follow, not knowing the inner workings of OpenMM. BUT, I did also see a couple potential issues:

Line 96 of forcefield.py: resname = molecule.GetTitle(); is this going to be important for anything? If so we'll need to check that there is actually a title... What if it is blank? Won't line 97 fail? Or what if it is non-unique? (i.e. multiple molecules have the same residue name?) We have some code in openmoltools which ensures no mixtures are set up involving monomers which have the same residue names when using packmol as this causes failures elsewhere, but we may need something similar here. Inevitably someone is going to feed in molecules with no titles and/or molecules with non-unique residue names, I would imagine.
Aren't we calling the atom type sampler Smarty and the forcefield Smirff? So this code might need a nomenclature change: """Register a SMARTY bondtype definition."""
bond =HarmonicBondGenerator.SMARTYBondType(node)

Thanks for the comments!

generateTopologyFromOEMol() function is actually a duplicate from openmoltools, and is just a utility function. The resname isn't used anywhere, and this shouldn't fail if the molecule title is blank.
Good point about SMIRFF. I'll make that change.

OK, all tests pass locally now!
Extending the forcefield parsing to handle the rest of the forces will have to wait until tomorrow.
@pgrinaway: Would still love input/feedback if you had any!

I think this is looking really great! It will be nice to have networkX as a part of this. The one minor comment that I will say is that it's best to stick with python style (method_name not methodName). But aside from that very minor comment, I think this is great!

Thanks, @pgrinaway! Will make a note to adopt PEP8 syntax, but for now, there are advantages to keeping the same method naming scheme as the original simtk.openmm.app.ForceField and trying to make it as similar as possible.

I've added angles, torsions, and Lennard-Jones parameters. This is just missing charges, which I'll add tomorrow.
I may have some logic incorrect with torsions. Currently, all torsions are assumed to be symmetric so that matches for atom indices (i,j,k,l) and (l,k,j,i) are the same thing, which may not be true for improper torsions. Perhaps someone could comment on whether that logic?

@jchodera :

I may have some logic incorrect with torsions. Currently, all torsions are assumed to be symmetric so that matches for atom indices (i,j,k,l) and (l,k,j,i) are the same thing, which may not be true for improper torsions. Perhaps someone could comment on whether that logic?

Weren't you the one who told me that impropers aren't symmetric? I thought you said permuting the atom order can be very important?
@swails I'm sure could straighten us out... Jason, in AMBER-style force fields, are impropers (i,j,k,l) and (l,k,j,i) the same typically (symmetric) or would the order result in important differences?
Regardless, I would guess that this would not be an issue immediately as there are probably no impropers in AlkEthOH. @bannanc - maybe you can check the info you have on parm@frosst and see if you can tell anything on this?
One thing I think we'll be in a position to do, @jchodera , is to soon cross-check the energies produced by this with the direct tleap implementation of parm@frosst in the AlkEthOH set. I can probably add part of that (not the whole thing) as a test once we do so.

I tried to get caught up on the discussion happening here, but I'm afraid I have only a partial picture.
As for the impropers in Amber, there are two different "symmetries" in atom indices of note here.  The first is the one that tleap uses when assigning impropers.  The second is the transformations that result in identical energies within the prmtop.  The following is how I believe that tleap assigns impropers:

It definitely reorders all of the improper atom types (upon reading) to be in alphabetical order (by type, obviously), with wild-cards coming first (see zParmSetOrderImproperAtoms in parmSet.c).
At potential improper centers (not sure how this is defined), tleap checks various permutations of the atom types involved in the potential improper and sees if there is an exact or wild-card match in the database.  If it finds one, it puts the central atom in the 3rd position and orders the remaining 3 atoms (in positions 1, 2, and 4) according to atom type name (and, I believe, possibly residue number).  So it's possible you'd see some permutations of i, j, k, l where i, j, and l can be in any order if the atom type name and residue number are identical (indeed, I've seen prmtop files where identical residues can have different orderings since tleap does not use a stable sort for that).

Once it's in the prmtop, the energy expression is equivalent for i-j-k-l and l-k-j-i.  tleap swaps the order of improper torsions IFF the first atom in the system (which has an index of 0) is either in position k or l, since impropers assign the 3rd and 4th indices to negative numbers to indicate exclusion from the 1-4 list and that it is an improper.  Since -0 == 0, the first atom has to come in one of the first two positions.
I'm not sure if this answered your question or not... Assigning impropers is confusing for all packages :(

@swails: Thanks so much for the lucid clarification!
The code is now done, but there are two issues we should sort out with @cbayly13:
Ambiguity in impropers
There is a real issue that @swails brings up regarding the ill-determinedness of impropers.
Consider an improper that keeps the nitrogen in a peptide bond planar.  We could specify a specific enough SMIRKS string that there is no ambiguity in the improper, such as [C:1](=O)-[N:3](H:4)-[C:2], but there is also a way to specify the SMIRKS string so that the improper is ambiguous: (e.g. [C:1]-[N:3](H:4)-[C:2], where the carbons connected to the nitrogen can be matched in either way). In this case, the SMIRKS would match both ways, and we would accidentally apply the torsion twice. So I should probably add error checking to make sure the same set of atoms isn't accidentally matched twice, throwing an exception if this happens---presuming we want to avoid ambiguity in impropers.
Units for SMIRFF XML format
@cbayly13 didn't specify the units in his SMIRFF XML example, so I've had to guess these corresponded to the standard Amber choices. I'm not sure I guessed correctly---in fact, I'm pretty sure I didn't. The energies are finite, but they are weird, and you guys can help fix that with further testing.
What do you think about proposing a way to attach units to the file to have them automatically converted from whatever you like?  We could extend the XML format to include units:
<HarmonicBondForce length="angstroms" k="kilocalories_per_mole/angstroms">
   <!-- length is in angstroms; k is in kcal/mol/angstrom -->
   <Bond smirks="[#6X4:1]-[#6X4:2]" length="1.626" k="310.0"/> <!-- CT-CT from frcmod.Frosst_AlkEthOH -->
...
</HarmonicBondForce>

or we could even specify units in a per-attribute basis:
<HarmonicBondForce>
   <!-- length is in angstroms; k is in kcal/mol/angstrom -->
   <Bond smirks="[#6X4:1]-[#6X4:2]" length="1.626*angstroms" k="310.0*kilocalories_per_mole/angstroms"/> <!-- CT-CT from frcmod.Frosst_AlkEthOH -->
...
</HarmonicBondForce>

@bannanc - can you cross-check these files with the parameters in the AlkEthOH test set here https://github.com/open-forcefield-group/open-forcefield-data/tree/master/Model-Systems/AlkEthOH_distrib (and perhaps see also the AMBER input files in this PR https://github.com/open-forcefield-group/open-forcefield-data/pull/17 and let us know the whether the units are the same/different from what is in the AMBER files/frcmod files?)

@jchodera : I like this style:

I DEFINITELY think these files should have units. If we get to design our own format, it ABSOLUTELY should have units. That's one of my pet peeves about existing simulation file formats - they don't carry units so you have to go digging through the docs to even find out what units things are in, which is so annoying. Should have thought of it before...

OK, let me add the units handling before we merge this.

@jchodera and @davidlmobley
I'm comparing values in the Frosst_AlkEtOH.ffxml file with the Amber force field file for AlkEthOH set (frcmod.Frosst_AlkEtOH here)
They appear to have the same values in the majority of cases so I would conclude everything is in AMBER units.
However, for the bond length for CT-CT in the frcmod file is 1.526 and it's 1.626 in the xml file.
Also, unless I'm missing something, in the xml file there are no sigma and epsilon values for carbons or oxygens.

@bannanc - @cbayly13 hand-typed the XML file so probably he's mis-typed 1.526 as 1.626 I would imagine.
@jchodera - does the sigma and epsilon issue explain your weird energies? Do you have carbons and oxygens without sigmas and epsilons?

REGARDING MISSING SIGMAS AND EPSILONS: It looks like the .ffxml file here is only the "abbreviated" version drawn from John's example here https://github.com/open-forcefield-group/open-forcefield-data/issues/9#issue-154386766 and one of us, NOT @jchodera , should go ahead and manually convert the rest of this file https://github.com/open-forcefield-group/open-forcefield-data/blob/master/Model-Systems/SMIRFF_prototype/smarff_mockup1.Frosst_AlkEthOH into the .ffxml format. (Note that there are also missing entries for torsions, etc - basically every where he had a "..." in his example implementation there is stuff missing (torsions and nonbonded only, it looks like).)
There is no reason for @jchodera to do this conversion, though, as we can easily do that on this end.
@jchodera - does this explain your weird energies?

Thanks, everyone!
Let me just get the units thing in and we can merge this, then you can fix up the .ffxml file.

Types are now implemented.
I imagine there is still a lot we can do to provide more useful error feedback when there are typos or mistakes in the ffxml file, but we can add those after this PR is merged or as we find they are needed to help avoid common mistakes.

Types are specified using this format:
<PeriodicTorsionForce phase_unit="degrees" k_unit="kilocalories_per_mole">
...

Note that not all types have a corresponding type_unit attribute. Those are assumed to be dimensionless, so it's important to remember that if you accidentally make a typo and use, for example, phrase_unit="degrees" instead, it will assume the phase is unitless or in natural OpenMM units (radians).  So we can probably harden this further by enforcing units be specified when we expect them to be.
This should be ready to merge when all tests pass.

One other thought for the record (for me to think about later) - we need to add something which will catch cases where we just don't have parameters defined for some of the atoms, i.e. we should never be able to run a system where we just don't have LJ parameters for some of the atoms. Presumably we should add some sort of exception handling to catch this...

I can certainly add that. I just took out some code that looked for bonds
in the Topology that didn't have HarmonicBondForce terms.
We should probably have an option to do thorough checking. But we can add
in a separate PR. If you can come up with what we should check for in an
issue, I can quickly add it in a separate PR.

I'll get back to that, @jchodera . So far this looks good, so I'd suggest you merge once tests pass and we (on my end) can work on testing more extensively (and fix the issue with the incomplete ffxml file) very soon.


Actually check that __toString method exists

Check before we try to cast to string.

Fixed.

The build is failing because the line is too long. Do you mind breaking that statement into multiple lines?

I've split it into multiple lines, but do you prefer trailing conditionals or the other way round? :)

The way you've formatted it is fine.
Oops! One more error:
 84 | ERROR | [x] Expected 0 spaces after opening bracket; newline
    |       |     found
    |       |     (PSR2.ControlStructures.ControlStructureSpacing.SpacingAfterOpenBrace)

You can run composer test locally before pushing to see what all the build will complain on, if there are errors.

I think we need to update the phpcs rule. I'm following the draft PSR-12: https://github.com/php-fig/fig-standards/blob/master/proposed/extended-coding-style-guide.md#51-if-elseif-else

Expressions in parentheses MAY be split across multiple lines, where each subsequent line is indented at least once. When doing so, the first condition MUST be on the next line. The closing parenthesis and opening brace MUST be placed together on their own line with one space between them. Boolean operators between conditions MUST always be at the beginning or at the end of the line, not a mix of both.
<?php

if (
    $expr1
    && $expr2
) {
    // if body
} elseif (
    $expr3
    && $expr4
) {
    // elseif body
}

Anyway, that phpcs rule is wrong. PSR2 does not care if you add a newline. It only cares about space: https://www.php-fig.org/psr/psr-2/#5-control-structures

There MUST NOT be a space after the opening parenthesis

There MUST NOT be a space after the opening parenthesis

A newline character is technically a space character. :smile:
At any rate, I have updated the project to use PHP CodeSniffer 3.3.1 and the new PSR-12 sniffs. Unfortunately, phpcs currently has a bug with the specific rule that covers control structure spacing, so I'm ignoring that rule for now:

https://github.com/squizlabs/PHP_CodeSniffer/issues/2113
1be7a854f97f7d5828cf92a4b17d632902bb2e53

Thanks for your contribution! 🎉

Oops! Now, it should be passing on Travis CI. f139239d39dfa0ac1e147ca89a179e8bdc44bda5
:smile:

A newline character is technically a space character.

Space is space. Whitespace is whitespace. Space is whitespace yes, but whitespace is not space. 😂


What does PIXEL_MEANS do?

# Pixel mean values (BGR order) as a (1, 1, 3) array
# We use the same pixel mean for all networks even though it's not exactly what
# they were trained with
__C.PIXEL_MEANS = np.array([[[102.9801, 115.9465, 122.7717]]])

What is the purpose of pixel means?
Do I need to change it if I'm using a cusotm dataset?
If yes, then how exactly do I calculate this value?

@CodeJjang this is aimed to adapt to the pre-trained caffe models, which you typically do not need to change.

Thanks


[AutoRelease] t2-storage-2023-08-07-94171(can only be merged by SDK owner)

https://github.com/Azure/sdk-release-request/issues/4391
Recording test success
https://dev.azure.com/azure-sdk/internal/_build?definitionId=842
BuildTargetingString
azure-mgmt-storage
Skip.CreateApiReview
true

issue link:https://github.com/Azure/sdk-release-request/issues/4391


How can I get the source code of latest relase?

Hi @frawau
Thanks for your excllent work! I can easily use it to process BLE advertisement.
In this repo, I only can find the latest release is 0.2.4, but in PyPi, the latest version is 0.2.8, so could you help me to figure out which one I should use? how can I get source code of latest relase?
Thanks again!

Hi,
The sources in this github repo  are the latest ones. Look int setup.py and  aioblescan/init.py   It is 0.2.8   What make you think it is 0.2.4?

I think he refers to the "releases" on the main page on github
https://github.com/frawau/aioblescan/releases

I see. That is because I changed the way I push releases to PyPi.  I now use twine to push my releases, so I no longer need to create those "release" bundles.  @allenzt Just clone the repo and you'll get the latest version. You can also download it as a zip. @Ernst79 Thanks for the pointer.

@frawau @Ernst79 Many thanks for your help, I got it!


Always returns Authentication failed

Hi, I used the middleware for a time and it's works ok, an in a time to here always return error in the authentication when I try to insert another user. I return to the old status but don't work.
$app->add(new Tuupola\Middleware\HttpBasicAuthentication([ 		"secure" => false, 	    "users" => [ 	        "test" => "secret",                 "test-2" => "secret2" 	    ], 	    "error" => function ($response, $arguments) { 	        $data["status"] = "error"; 	        $data["message"] = $arguments["message"]; 	        return $response 	            ->withHeader("Content-Type", "application/json") 	            ->getBody()->write(json_encode($data, JSON_UNESCAPED_SLASHES | JSON_PRETTY_PRINT)); 	    } 	]));
I'm using version 3 and have php 7.1. What can do the problem?

I have the same problem, does anyone know how to solve it?

What is the returned error message?

Closing due no feedback.


Databinding issue

Describe the bug
I am filling my datagrid with an observablecollection containing objects with 3 fields, all strings
I am creating DataTemplates and setting combo boxes (from syncfusion) and the itemssource is working fine, and selected item seems to be working as well, but when I pick a different value, I can see that syncfusion detects the change, but I can not detect the databinding being updated.. so no update is propagated to the underlying property.
To Reproduce
My class:
using CommunityToolkit.Mvvm.ComponentModel;
namespace SharedModels.Models
{
public class SatelliteModeConfiguration : ObservableObject
{
private string _viewPath = String.Empty;
private string? _decorations;
private bool _isDirty;
    public SatelliteModeConfiguration() { }
    public SatelliteModeConfiguration(string mode, string viewPath, string decorations)
    {
        Mode = mode;
        _viewPath = viewPath.Trim();
        _decorations = decorations;
    }

    public string Mode { get; set; } = string.Empty;

    public string ViewPath
    {
        get => _viewPath;
        set
        {
            if (_viewPath == value)
                return;
            _viewPath = value;
            IsDirty = true;

            if (!ChangedProperties.Contains(nameof(ViewPath)))
                ChangedProperties.Add(nameof(ViewPath));
            OnPropertyChanged();
        }
    }

    public string Decorations
    {
        get => _decorations;
        set
        {
            if (_decorations == value)
                return;
            IsDirty = true;
            if (!ChangedProperties.Contains(nameof(Decorations)))
                ChangedProperties.Add(nameof(Decorations));
            _decorations = value;
            OnPropertyChanged();
        }
    }

    public bool IsDirty
    {
        get { return _isDirty; }
        set
        {
            if (_isDirty == value)
                return;
            _isDirty = value;
            OnPropertyChanged();
        }
    }

    public List<string> ChangedProperties { get; set; } = new();
}

}
SelectedSatellite.Config.Modes = public ObservableCollection Modes
My grid:
<dg:DataGrid Grid.Row="5" Grid.Column="0" Grid.ColumnSpan="2" ItemsSource="{Binding SelectedSatellite.Config.Modes}" IsEnabled="{Binding SelectedSatellite.IsConnected, Mode=OneWay}">
dg:DataGrid.Columns
<dg:DataGridColumn Title="Mode" PropertyName="Mode" />
<dg:DataGridColumn Title="View" PropertyName="ViewPath">
dg:DataGridColumn.CellTemplate

<control:SfComboBox
ItemsSource="{Binding Source={RelativeSource AncestorType={x:Type viewModels:DevicesViewModel}}, Path=SelectedSatellite.Templates, Mode=OneWay, Converter={StaticResource PrefixListItemsConverter}, ConverterParameter=Templates/}"
SelectedItem="{Binding Mode=TwoWay}"
IsEnabled="{Binding Source={RelativeSource AncestorType={x:Type viewModels:DevicesViewModel}}, Path=SelectedSatellite.IsConnected, Mode=OneWay}"/>

</dg:DataGridColumn.CellTemplate>
</dg:DataGridColumn>
<dg:DataGridColumn Title="Decorations" PropertyName="Decorations">
dg:DataGridColumn.CellTemplate

<control:SfComboBox
ItemsSource="{Binding Source={RelativeSource AncestorType={x:Type viewModels:DevicesViewModel}}, Path=SelectedSatellite.Decorations, Mode=OneWay}"
SelectedItem="{Binding Mode=TwoWay}"
IsEnabled="{Binding Source={RelativeSource AncestorType={x:Type viewModels:DevicesViewModel}}, Path=SelectedSatellite.IsConnected, Mode=OneWay}"/>

</dg:DataGridColumn.CellTemplate>
</dg:DataGridColumn>
</dg:DataGrid.Columns>
dg:DataGrid.RowsBackgroundColorPalette
dg:PaletteCollection
#F2F2F2
#FFFFFF
</dg:PaletteCollection>
</dg:DataGrid.RowsBackgroundColorPalette>
</dg:DataGrid>
Expected behavior
I would expect the underlying property to be updated according to the selection (and the combobox I use any other places in my app with no problems)
Screenshots
N/A
Desktop (please complete the following information):

OS: Windows + Android
Browser [e.g. chrome, safari]
Version [e.g. 22]

Smartphone (please complete the following information):

Device: [e.g. iPhone6]
OS: [e.g. iOS8.1]
MAUI

Additional context
Add any other context about the problem here.

I posted in another thread the following code to force updates:
Forcing the CollectionChanged event to fire is something that I have accomplished in my app by calling the following workaround method (ForceNotifyCollectionChanged) after every data change. After MAUI fixes the bug, this stupid code could be removed..
    public ObservableCollection<RecordPhoto> RecordPhotos { get; set; }

    private async Task OnDeletePhoto(RecordPhoto? photo)
    {
        this.RecordPhotos.Remove(photo);

        var removed = this.dbContext.RecordPhotos.RemoveIfExists(photo);

        if (removed)
        {
            _ = await this.dbContext.SaveChangesAsync();
        }

        this.ForceNotifyCollectionChanged();
    }

    private void ForceNotifyCollectionChanged()
    {
        // TODO: Remove this whenever MAUI updates the collection correctly. https://github.com/dotnet/maui/issues/8534
        var tempRecordPhoto = new RecordPhoto(null);
        this.RecordPhotos.Add(tempRecordPhoto);
        _ = this.RecordPhotos.Remove(tempRecordPhoto);
    }


Add REST API parameter type documentation

Add support to generate Swagger parameter type documentation and JSON
schemas, as well as support for examples. Add documentation for the
instance creation API.

lgtm

[Current coverage][cc-pull] is 43.33%

Merging [#170][cc-pull] into [master][cc-base-branch] will decrease coverage by 0.10%

@@             master       #170   diff @@
==========================================
  Files           696        696
  Lines         31843      31915    +72
  Methods           0          0
  Messages          0          0
  Branches       4754       4781    +27
==========================================
- Hits          13832      13831     -1
- Misses        16878      16951    +73
  Partials       1133       1133

Powered by Codecov. Last updated by [4898cff...32eb850][cc-compare]
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Stm32 common SPI

This adds an initial common shared SPI driver for all STM32 supported MCUs.
For now I disabled support for slave on F3/F7, which have internal FIFOs. The TX FIFO is not configurable on size always generates a TXE interrupt when it is half full, and it does not seem to have a flush operation, so when working as slave, after SS is asserted there is no way to flush whatever was already presented in the FIFO and it will be sent later after a new communication, breaking functionality of some apps like spitest. I will open an issue to look into this after all common driver framework is in place.

PS: there are some #if 0, FIXME and TODO in the code. I would prefer to leave them there if it is in one of the two driver files and hw/mcu/stm/stm32_common!

@ccollins476ad LOL, of course, it works on F1/L1/F4 as master/slave and F3/F7 as master only (for now)!


BasicVSR BD在Vid4上测试只有20dB

我用BasicVSR BD的模型在Vid4上测试只有20dB，请问是哪里出现了问题呢？更改的地方如下：

@Z-Fran
Please check this issue.

Sorry for the late reply. I have tested Vid4/BDx4 with the same config as you,  and PSNR is 27.98dB. Please check your data  or fetch latest code.


move spriter and stagger to es6

Hey @oxyflour! Thanks a lot. Looks great!
Few minor issues I should to point out:

something seems to be wrong with indentation here and there http://take.ms/4rRzy . We should have 2 spaces indentation everywhere.
all method declarations should have space after their names:

  // was
  _declareDefaults() {
  // should be
  _declareDefaults () {

This nuance makes the code a little bit more readable and also comes handy when you try to distinguish method declaration vs method call in a search. For instance if you search method and hit space - you will have method declaration, but if you search method and hit ( you will have all the method's calls.

Please don't forget to use curly braces after if and else statements even if it is followed by only one statement:

  // if number was set
  if (typeof name === 'number') { return name; }

Sorry for the inconvenience - we should make js style guides probably.
You did a great job, thanks a lot again!

@legomushroom Thank you for your detailed instructions! I should have been more careful. BTW, maybe we can add a new wiki page about code styles?

@oxyflour would be nice. could you take care of it?


Update proposal document on SPARK-18278

There's probably some details that are out of date on the document that's attached to the ticket. We should update the proposal to include the new submission architecture and the CustomResource support.

I'll do this item in the shared public doc. There's quite a bit of updating to be done.

This is done and the artifact is uploaded to the JIRA.


Add pagination bullets

How can i add the pagination bullets? currently i am only see the arrows pagination. thanks.

did u find any solution for this?


No graphs in system statistics

Graphs shown correctly when selecting framed theme but with _authentic theme, graphs window appears black.
Pls see attached screenshots.

Hi,
I think this is due to outdated Virtualmin version. Please consider upgrading.

TKS I'll have a look (if I can find how to upgrade Virtualmin Pro :) )

I'll be glad to help with the upgrade. Let me know if you have any difficulties.
In case you have valid license, there should be no problem.
Go to console and run:
yum clean all && yum update

Do you have Virtualmin there upon the packages?

TKS a lot for you rapid answer
II already tried it before but no success.
I get this:
-bash-4.1# yum clean all && yum update
Limpiando repositorios:Webmin base epel extras remi-safe rpmforge updates webtatic
…
…
…
"No se han seleccionando paquetes para ser actualizados
-bash-4.1#!
(In English: there are no selected packages to be updated.)
"Packake details “ says I have latest version (5.99) ??
Perhaps I’m not using the correct repository.
...___Albert

El 14 abr 2018, a las 12:39, Ilia Rostovtsev<EMAIL_ADDRESS>escribió:
I'll be glad to help with the upgrade. Let me know if you have any difficulties.
In case you have valid license, there should be no problem.
Go to console and run:
yum clean all && yum update
Do you have Virtualmin there upon the packages?
—
You are receiving this because you modified the open/close state.
Reply to this email directly, view it on GitHub https://github.com/qooob/authentic-theme/issues/1107#issuecomment-381320111, or mute the thread https://github.com/notifications/unsubscribe-auth/AI1GB880Ohw7P-IqDGiuPCQhAEcX9RGiks5todHNgaJpZM4TVA5i.

What is the output of:
yum repolist

-bash-4.1# yum repolist
Complementos cargados:fastestmirror
Loading mirror speeds from cached hostfile

base: mirror.uv.es
epel: mirror.uv.es
extras: mirror.uv.es
remi-safe: mirror.netweaver.uk
rpmforge: mirror.de.leaseweb.net
updates: mirror.uv.es
webtatic: uk.repo.webtatic.com
id del repositorio                                nombre del repositorio                                                                     estado
Webmin                                            Webmin Distribution Neutral                                                                   116
base                                              CentOS-6 - Base                                                                             6.706
epel                                              Extra Packages for Enterprise Linux 6 - x86_64                                             12.493
extras                                            CentOS-6 - Extras                                                                              53
remi-safe                                         Safe Remi's RPM repository for Enterprise Linux 6 - x86_64                                  2.329
rpmforge                                          RHEL 6 - RPMforge.net - dag                                                                 4.718
updates                                           CentOS-6 - Updates                                                                          1.185
webtatic                                          Webtatic Repository EL6 - x86_64                                                              243
repolist: 27.843
-bash-4.1#

El 14 abr 2018, a las 12:56, Ilia Rostovtsev<EMAIL_ADDRESS>escribió:
What is the output of:
yum repolist
—
You are receiving this because you modified the open/close state.
Reply to this email directly, view it on GitHub https://github.com/qooob/authentic-theme/issues/1107#issuecomment-381321001, or mute the thread https://github.com/notifications/unsubscribe-auth/AI1GBwBJpg_WW0iG83KNqZQJvjyvd-Qqks5todXugaJpZM4TVA5i.

I thing I found it
Need to install this repository.
http://software.virtualmin.com/gpl/centos/6/i386/virtualmin-release-latest.noarch.rpm
I’l try right now

El 14 abr 2018, a las 12:56, Ilia Rostovtsev<EMAIL_ADDRESS>escribió:
What is the output of:
yum repolist
—
You are receiving this because you modified the open/close state.
Reply to this email directly, view it on GitHub https://github.com/qooob/authentic-theme/issues/1107#issuecomment-381321001, or mute the thread https://github.com/notifications/unsubscribe-auth/AI1GBwBJpg_WW0iG83KNqZQJvjyvd-Qqks5todXugaJpZM4TVA5i.

Okay, I see now. Contact me using my website's contact form. I could help you further, if you proceed here, make sure you're not going to leak your Virtualmin Pro license id and key, that looks like
0000000:XuwXKskXl

No, not i386 in your case.

Simply create the file in your /etc/yum.repos.d.
Run nano /etc/yum.repos.d/virtualmin.repo
Add as content:
[virtualmin]
name=RHEL/CentOS $releasever - $basearch - Virtualmin
<EMAIL_ADDRESS>enabled=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-virtualmin-6
gpgcheck=1

[virtualmin-universal]
name=Virtualmin Distribution Neutral Packages
<EMAIL_ADDRESS>enabled=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-virtualmin-6
[RPM-GPG-KEY-virtualmin-6.zip](https://github.com/qooob/authentic-theme/files/1910276/RPM-GPG-KEY-virtualmin-6.zip)
gpgcheck=1

Where 0000000:XuwXKskXl your license id/key.

RPM-GPG-KEY-virtualmin-6.zip

You can get your credentials by signing to virtualmin.com website, and going to Account/Software Licenses.

Solved!
Now I have Virtualmin Pro version 6.02 and stats working like a charm.
TKS a lot for your helpful messages.


import has the wrong type, but doesn't seem to be adapter version mismatch

Similar to #7505, I'm running into a problem with a "has the wrong type" error, but unlike that previous issue, I believe I do have the correct adapter version. I'm running wasmtime 17.0.1 with the reactor adapter taken from the corresponding release.
AnyError(import<EMAIL_ADDRESS>has the wrong type

Caused by:
    0: instance export `incoming-request` has the wrong type
    1: expected resource found nothing))

$ wasm-tools component wit test_plugin.wasm
package root:component;

world root {
  import<EMAIL_ADDRESS>  import<EMAIL_ADDRESS>  import<EMAIL_ADDRESS>  import<EMAIL_ADDRESS>  import<EMAIL_ADDRESS>  import<EMAIL_ADDRESS>  import<EMAIL_ADDRESS>  import<EMAIL_ADDRESS>  import<EMAIL_ADDRESS>  import<EMAIL_ADDRESS>  import<EMAIL_ADDRESS>  import<EMAIL_ADDRESS>  import<EMAIL_ADDRESS>
  export<EMAIL_ADDRESS>}

I'm not particularly confident in the correctness of any of these, even though everything compiles OK:

the world definitions in my wit files
how things are set up w/ wasmtime's generate macros
how things are set up w/ wit-bindgen's generate macros
how I'm currently using the wasmtime runtime

However, I did have this previously working with a simpler API definition that didn't really try to do anything with WASI beyond using stdout/stderr.
Full codebase in this branch, along with wit definitions: https://github.com/bulwark-security/bulwark/tree/api-refactor
Unfortunately, I've exhausted everything I can think of to debug this. The error message just doesn't give a whole lot to go on and I'm wondering if there might be something that could be done to significantly improve that error message, because it has seemed to come up a lot.

I think you are missing an add_to_linker that provides wasi:http/types here: https://github.com/bulwark-security/bulwark/compare/main...api-refactor#diff-3f2325fd7fe144935eb0a48fb3ced5e8afd4a3cc28a6ac7d86a629db1af865ccR282
This one will provide it, if you need the outgoing-handler as well that is nearby https://docs.rs/wasmtime-wasi-http/latest/wasmtime_wasi_http/bindings/wasi/http/types/fn.add_to_linker.html

Wow, thanks, at first glance, that does indeed seem to have been the issue. I think I do need the outgoing-handler one too, but interestingly, omitting it doesn't seem to have failed anything on instantiation. Not sure I understand why the http types one would fail on instantiation but outgoing-handler wouldn't?
I'm also really interested in understanding your thought process for how you found the problem so quickly because I've been trying to figure it out for the better part of a week. 😬
Even with a likely root cause now, I think I feel like my comment on the error message still applies. This feels like a good opportunity to give implementors more useful information.

Just noticed that wasm-tools component wit test_plugin.wasm output shows import<EMAIL_ADDRESS>but not import<EMAIL_ADDRESS>so presuming that's why... but I guess I'm not sure I understand why it's missing. Shouldn't the include have pulled it in?

My thought process was: if its just HTTP that gets the complaint and not the rest of WASI, then you probably just weren't aware that our HTTP implementation lives in a separate crate. Missed add_to_linker is a sizable minority of the bug reports we get, so thats always one of the first things I rule out.
If you did an include wasi:http/proxy; that should have pulled in the outgoing-handler import, and require an incoming-handler export be present. That's what we'd expect you to use if you were trying to provide a superset of the proxy world (meaning a proxy component that doesnt know anything about bulwark would execute just like it does in plain old wasmtime serve).

This include: https://github.com/bulwark-security/bulwark/blob/api-refactor/wit/platform.wit#L4

I took a look but I'm having a hard time getting oriented to reproduce - can you describe how to build the sample guest code, and run the host code, at the current commit?

I'll note that when creating a component if an interface isn't used it'll be omitted from the final component. To that end can you confirm that dist/plugins/bulwark_blank_slate.wasm is using wasi:http/outgoing-handler? If it's not then that's expected behavior that the import doesn't show up, but if it is then something indeed odd is happening!

Sorry, looping back to this quite a bit later. Yeah, that might be it. That specific component isn't using wasi:http/outgoing-handler. I'll have to write one that does and re-check. Might be working as intended!

Confirmed, working as intended, thanks. Once I recompiled a component that used wasi:http/outgoing-handler it started to show up.

Ok sounds good, thanks for the follow-up! I think that means everything here is working as expected, so I'm going to close. (if I missed something though let me know)


Tool to ingest ZTF source features

This PR implements a tool to ingest ZTF source features produced by @mcoughlin + external features (from cross-matches) + dmdt's.

Failure on the CI is unrelated (something's up with the TNS), so should be mergeable @kmshin1397.


Richer grammars

What are you trying to do?
Being able to specify grammars is great, but it seems a bit underutilized at the moment. This is mostly a thought dump on how it could be improved from experimentation...
How should we solve this?

Using llama.cpp grammar directly would be pretty powerful and nice to have
Specifying jsonschema for json. Llama.cpp json is usually forced into a specific key order and ollama json isn't schema'd at all
Changing the format on the fly is useful, but I think it would be nice to have a way to specify a grammar in the Modelfile.

What is the impact of not solving this?
Not having either of the first two ideas is annoying, since there's no way to guarantee that a model generates a response in a format I want. The third idea allows one to make a "llm api", where a model generates a specific response every time (imagine bundling a "summary llm" that always responds with {"summary":"..."} as a Modelfile.)
Anything else?
No response

There are a few open PRs for this behaviour - the most recent one being https://github.com/ollama/ollama/pull/3618 it would be amazing to get this merged in. It's a 2 line change that exposes the llama.cpp GBNF functionality via modelfile parameters. Its not my patch but I've compiled it and used it locally and it works really well.

Specifying grammars in the Modelfile is one thing. It would be much more useful to be able to send a grammar string in the request, similar to llama.cpp server.
Is that possible with Ollama now? There's nothing about grammars in the api docs.

Is that possible with Ollama now?

No, it's not. But it's a nice proposition, I think.

Yes you can send the grammar as an option when you submit a request with this patch enabled.  It just isn't documented!
Here's an example:
POST http://localhost:11434/api/chat
{
  "model":"llama3:8b",
  "stream": false,
  "messages":[
    {"role":"user", "content": "The sky is blue, true or false?"}
  ],
  "options":{
    "grammar": "root ::= (\"true\" | \"false\")"
  }
}

Response:
{
  "model": "llama3:8b",
  "created_at": "2024-04-21T20:53:15.212659393Z",
  "message": {
    "role": "assistant",
    "content": "true"
  },
  "done": true,
  "total_duration": 545867966,
  "load_duration": 5912270,
  "prompt_eval_duration": 213384000,
  "eval_count": 2,
  "eval_duration": 202538000
}

It just isn't documented!

So, I can add docs about it in #3618.

That's really really cool. Though as far as i can see it not merged into main yet.

This would be so nice to have, one step closer to ditching my custom python bindings for llamacpp and being able to use ollama now that they also started supporting concurrent models. Sending a grammar together with the request is a great feature to support.

I added support for this and JSON schema in #5348.

Hey all, I know there's an automated ping here but just to better align everyone please check out and comment on my new call to the Ollama team for clarity here. As always please be civil and stay on topic! 😄 - https://github.com/ollama/ollama/issues/6237

Hey! Thanks for raising this! Going to close this out as we're supporting structured outputs through https://github.com/ollama/ollama/pull/7900
Left a comment with some background as well: https://github.com/ollama/ollama/issues/6237#issuecomment-2518836758


[release-v1.15] fix: add case for DNS resolve fail in TestDialUnreachable

Backport of https://github.com/knative/func/pull/2619/files

/cherry-pick release-v1.16

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/approve
/lgtm

/retest-required

/override "Red Hat Konflux / serverless-operator-135-ec / kn-plugin-func-func-util-115"

/override ci/prow/417-e2e-oncluster-test
/override ci/prow/417-images
/override ci/prow/417-unit


[Not an issue] Raspberry Pi3 B not supported.

Can anyone let me know why is it that Raspberry Pi 3 model B not supported. is there any hardware limitation?

Yes. Raspberry Pi 3 B/B+ does not support usb otg mode, which is required for this to work.
Duplicate #140, #157


Integration with django-admin-sortable2

I'm using Admin sortable 2 in admin to order models by dragging them around. Parler works well with SortableAdminMixin but it doesn't work with SortableInlineAdminMixin. So basically, if the model is both translatable and inline, the two apps are not compatible. Just wonder if there's any tip or plan on integrating Admin sortable 2's SortableInlineAdminMixin.

@georgema1982 can this issue be closed now?
Simply add SortableInlineAdminMixin to your TranslatableTabularInline and override property template. Check both base templates for conflicting issues.

Ok, please close this. But I do hope there's a recipe on how to combine the two in the django-parler's document the same as how to combine parler with mptt

Glad to know you worked it out!
I'd be happy to accept a pull request which adds such recipe to the documentation.


Flatten kafka_consumer

What does this PR do?

This PR merges kafka_consumer.py and new_kafka_consumer.py into one file to make it easier to understand the check.
Motivation

Additional Notes

Review checklist (to be filled by reviewers)

[ ] Feature or bugfix MUST have appropriate tests (unit, integration, e2e)
[ ] PR title must be written as a CHANGELOG entry (see why)
[ ] Files changes must correspond to the primary purpose of the PR as described in the title (small unrelated changes should have their own PR)
[ ] PR must have changelog/ and integration/ labels attached
[ ] If the PR doesn't need to be tested during QA, please add a qa/skip-qa label.

Closing this PR in favor of https://github.com/DataDog/integrations-core/pull/13929


fixed filenames

Description
removed the @ symbol from the filename
closes #757
Attach Screenshot

Note 2 code reviewer approval needed. Approach in twitter group & discord channel.

Good job @madhusudanbabar


Azure Files performance tier

@mlearned Could you review this pull request? Thanks!

@ktoliver, can you resolve the merge conflict? Thanks!
#sign-off

@laurenhughes: I'm sorry - only the author of this article, @mlearned, can sign off on your changes. But we do have an exception process - if you are on the Microsoft content or product team for this product area, you can ask the PR review team to review and merge it by sending mail to the techdocprs alias.


generating LLC client

API changes have been detected in azure-ai-language-questionanswering. You can review API changes here

API changes have been detected in azure-ai-language-questionanswering. You can review API changes here


fix(url): ssl secured URL is added for infotips

Note: If there are pending changes to the PR, prefix the PR title with "WIP" and add the label "DO NOT MERGE"
Mandatory

[ ] What does this PR do?

[ ] What issue/task does this PR references?

[ ] Are the tests Included?

Optional

[ ] Is the documentation Included?

[ ] Are the Release Notes included?

[ ] @mention(s) to expected reviewer(s) included

Ike Plugins (test-keeper)
Thank you @sanbornsen for this contribution!

It appears that no tests have been added or updated in this PR.
Automated tests give us confidence in shipping reliable software. Please add some as part of this change.
If you are an admin or the reviewer of this PR and you are sure that no test is needed then you can use the command /ok-without-tests as a comment to make the status green.
Your plugin configuration is stored in the file.

@sanbornsen Your image is available in the registry. Run docker pull registry.devshift.net/fabric8-ui/fabric8-planner:SNAPSHOT-PR-2612 && docker run -it -p 5000:8080 registry.devshift.net/fabric8-ui/fabric8-planner:SNAPSHOT-PR-2612 and visit http://localhost:5000 to access it.


Fix typo (CofeeScript)

Just a typo fix: CofeeScript => CoffeeScript

Thank you!

My pleasure! 👍


Is esp32-smbus thread safe?

I am using esp32-i2c-lcd1602 and esp32-mcp342x on a single i2c bus and occasionally the LCD becomes corrupt. I have one task updating the LCD, and a different task polling the MCP342x.
Is it safe to use these simultaneously, or do I need to apply my own mutex to ensure they don't occur at the same time?
This issue suggests that at least some of the underlying I2C APIs are already protected by a mutex, but it's not very clear to what extent.
Thanks!

@lukecyca esp32-smbus makes use of the ESP-IDF I2C master component, which is not thread-safe between transactions as far as I understand. You have to protect access to the bus yourself. I do this at the top level, for example: https://github.com/DavidAntliff/esp32-poolmon/blob/master/main/sensor_light.c#L104

Thanks! That is the answer I was hoping for.


rj/adc refactor

Don't reset the peripheral in the DMA1/2 StreamsTuple::new method
Initial Octo SPI support
Remove address_size from config, add write/read_extended methods
Add example for OCTOSPI
Don't need to explicitly invalidate icache, since enable_icache does it for us.
qspi read seems to be working
enable fmode in setup, only write address if needed
consolidate setup
Octospi support for RM0455 parts, mostly commented out for now
Test Octospi example on a part that has octospi
Add missing feature gates to docs, correct qspi -> quadspi in docs
v0.10.0
Fixing i2s lints
Fixing all clippy lints, elevaing warnings to errors
Adding changelog
Fixing various clippy lints
Add an example of QSPI used for flash memory
Avoid creating intermediate references to packed fields
Bump MSRV for bors also
Fixing lint
Fix inverted UART parity configuration
Adding InputPin trait implementation for Alternate Pins
Tidy peripheral_target_address macro, implement for I2C123
Simplify device signature API
Make more CRC methods const
Ethernet: Disable RA in filtering, fix MAC address setting
Clamp scldel/sdadel to 4-bit and update divider calculations
Add initial support for MDMA
[mdma] Add word endianness exchange
[mdma] Limit transfer length based on both source and destination
[mdma] Use block mode to support up lengths up to 65536
[mdma] Add configuration methods for trigger and transfer length
[mdma] Add support for hardware requests and peripheral transfers
[mdma] Rename transfer to avoid confusion and explain in docs
[mdma] Add support for packing/alignement modes
[mdma] Swap CTCI and TCI interrupts in the API
[mdma] Remove old macro parameters, not needed now
[mdma] Fix and document mdma example
[mdma] Add accessors for buffer and block transfer complete flags
[mdma] Add TargetAddress implementations for QSPI
Compatibility with constant source buffers support (#178)
[mdma] fix examples in stable rust
[mdma] Add mdma example using the qspi peripheral
[mdma] qspi only on rm0433, rm0399 parts
[mdma] replace generic config with concrete for mdma-only methods
[mdma] ITCM can be up to 256kB
[mdma] Rename buffer_bytes to transfer_length in the internal API
[mdma] Rename {buffer,block}_bytes to {buffer,block}_length
[mdma] add support for setting AXI burst length
[mdma] Delay after interrupt clear (#195) and trait update from (#226)
[mdma] Refactor transfer length so that it is set in one place only
rename example with underscore
[mdma] limit burst length to meet constraints
Improvements to DMA docs
tidy Cargo.toml diff
Add docs to qspi_mdma example
[mdma] fix set_buffer_transfer_complete_interrupt_enable method
[mdma] add packing options for trunctions, fix length calculation
[mdma] refactor source/destination address setting
Improve DMA docs
[mdma] implement next_transfer for mdma
[mdma] add MdmaTransferRequest values for rm0455 and rm0468 parts
Fix unused import
Tidy clippy notes
[mdma] implement streams 8-15
Allow parallel conversion on multiple ADCs
Mark change to I2S constructor as breaking
crc dr registers updated
replace pac variant with Option
unsafe is now unnessesary
pac updates for RM0455 parts
Use RTIC v0.5 alongside cortex-m v0.7
Pick cortex-m-rt ^v0.6.15 to prevent multiple linking of cortex-m-rt
update cfg-if and rtt-target dependencies
Upgrade stm32-rs to v0.14.0
implement IoPin
Support cortex-m-rt 0.7.0
further improve usart capabilities
Add glue to make embedded-sdmmc work nicely
Remove INSERT AFTER .bss to fix infinite loop on boot when zeroing bss. Fixes #263.
added example code
example format fix
rust is default
cross-referencing examples now
complete x-ref set
Add synchronous flag to serial_unchecked method
Set synchronous bits on USART peripheral only, for others they are reserved
Add builder methods for usart configuration fields
Add an example of more synchronous USART operation
Add feature flag for stm32h735
RCC and PWR updates for STM32H735
EXTI and GPIO updates for STM32H735
Update most of the non-optional peripherals for STM32H735
Frequency limits, voltage scaling and wait states for STM32H735
Tidy up ugly macro in ethernet and remove GPIOI pins for STM32H735
Tidy up USB support for STM32H735
Tidy up FMC for STM32H735
Add OCTOSPI rec for RM0455 devices
Tidy up DMA for STM32H735
Add STM32H735 to README
Add tested ethernet example for STM32H735
Make d3cr register macro available even without smps flag
Initial ADC support for STM32H735
spelling
Rework examples for RM0468 devices
Make ethernet::DesRing generic over the number of buffers
Avoid creating references to packed fields
Update changelog: ethernet::DesRing generic over the number of buffers
Implement Default for ethernet::DesRing
change Self::Error to Never and unwrap
Initial Octo SPI support
Remove address_size from config, add write/read_extended methods
Add example for OCTOSPI
qspi read seems to be working
enable fmode in setup, only write address if needed
consolidate setup
Octospi support for RM0455 parts
Test Octospi example on a part that has octospi
Update MDMA support for quadspi
Implement pin traits for octospi
Fix unused enum warning
Add basic docs for octospi indirect mode
Add MDMA peripheral targets for OCTOSPI
update MSRV to 1.52.0
add MSRV 1.52.0 badge
add spi extensions
update SPI trait names
README update
Edit text for:
Avoid stale dependencies in README (eg. cortex-m-rt 0.6 !)
Re-order examples readme
Make new section in examples readme a major section
set ulpi pin speed to VeryHigh
fix copy-pasta oppsie
improve spi traits
fix typo
improve USB1_ULPI::new doc comment
ethernet::new
rand_core impl & support all integers in rng
impl rand_core::CryptoRng
add error code offset & add comments about alignment
derive Default implementation for MdmaBurstSize
Tidy a 'type alias is never used' warning
octospi: allow unused imports
Example: tidy unused import
Fix the rt feature for stm32h7 0.14.0
Add "rt" to the default features
Delete qspi.rs, should have disappeared in PR #230
Move/add example links for qspi and octospi
Utilise the SPI FIFO in the Transfer and Write implementations
change enum values
fix sdcard size truncation
fix @richardeoin's comments
update smoltcp from 0.7.0 to 0.8.0
Add OCTOSPI Hyperbus support and an example for HyperRAM usage
Improve error diagnostics when kernel clocks are stopped
Allow LSI clock as source for the RNG peripheral
stringify consumer name for error message
update clock method name in octospi
Disable ethernet MAC MMC counter interrupts
serial: document parity and word length configuration
serial: remove WordLength configuration but set it automatically based on parity
Fix docs.rs quadspi feature
Add DMA to top-level docs
v0.11.0
Changelog: fix merge diff leftovers
Add backup domain voltage regulator control
Update changelog
Add optional formatting of some types with defmt
remove release mode requirement from USB examples
Migrate to Rust 2021 as part of the public testing
Increase MSRV to 1.56.1
Upgrade examples to rtic v1.0.0
Allow unsafe with log-itm feature flag for examples
Pick up a depreciation warning from cortex-m v0.7.4
Tidy nested lock calls
Document defmt feature
defmt: Use Debug2Format for ADC Resolution
DWT::cycle_count requires cortex-m 0.7.4
add more traits to spi error
fix clippy error
impl countdown
add fugit for Countdown
update msrv -> 1.57.0
Actually write both words
Always enable the embedded-hal/unproven feature
update embedded dma -> 0.2.0
Add notes about internal USB regulator to examples
Add example using RTIC
Upgrade to synopsys-usb-otg v0.3.0
add serial over usb with external phy using interrupts example
revertme: PAC doesn't use include USB interrupts for rm0468 parts
Document ULPI Transciever Delay
Add support for VOS0 on rm0468 chips
Avoid 'unused import RCC' warning for rm0468
try debug output
Wait until VOS0 is stabilized before returning from power freeze
PD12 is linked to TIM4 via AF2
Missing TIM15 pins
initial flash implementation
flash behind feature flag, only rm0433 supported
improve flash bank interface
add flash example
use little endian for writing and reading flash, enhance Bank enum impl
Read only the CNT field when reading timer CNT register
Implement tick_timer() for LPTIM'ers
Add more documentation to the tick_timer method on TimerExt
Add priv_set_tick_freq method for LP Timers
LP Timer counter method should return u16 (all LP Timers are 16-bit)
Update changelog for timers
Add example for the LPTIM2 tick_timer method
Support VOS2 and VOS3
Fix arithmetic error in spi divider calculation
Error on DuplexFailed errors rather than blocking
spi: Update changelog
Read SPI SR again to prevent false errors
fix: pull-request feedback
ensure github action only checks flash example with rm0433
serial: add reconfigure method
serial: add join method
serial: add config to swap tx/rx pins
serial: fix txrx swap
serial: remove redundant enable
serial: don't reset enabled events when reconfiguring
Use union merge in changelog
serial: remove outdated comment
Add serial changes to Changelog
serial: improve doc comments
Update examples/flash.rs
Update examples/flash.rs
Update examples/flash.rs
fix: lock flash bank and cleanup if write out-of-bounds occurs
flash module doc improvments
cleanup flash example to be more similar to other examples
main RCC registers debug prints
make logging optional
fix formatting
adjust feature flags
Fix clippy lints in flash example
Added flash to CHANGLOG
Docs and clippy lints for ethernet
add comments, better indentation, and add divider offset
typo
print raw values in hex so there is less confusion with the divider representation.
port f4 gpios
gpio reexport
changelog
add comment about dev-dependencies
Add ChannelA/B types for SAI, add DMA implementation
FDCAN support using the fdcan crate
Add can flag to CI
can: set watermark to RX_FIFO_MAX / TX_EVENT_MAX
can: Update example with new API
Use fdcan crate from crates.io
review fixes
Add inner and inner_mut functions to peripherals where it's easy to do so
Add stable check back in CI
Replace crate::Never with core::convert::Infallible
serial: add invertrx and inverttx
serial: add serial-inverted-loopback example
Support eMMC using SDMMC module
Build sdmmc example for all families
CAN GPIO
rustfmt cleanup of serial.rs
Add slope method to ADC and depreciate max_sample
Annotate methods with #[must_use]
Include REC in free method for qei
Add more documentation for REC objects and highlight where they are dropped
fugit units
MHz
fugit: Changelog
Add begin_write_extended and begin_read_extended methods
gpio rework
[add] Add Rx and Tx fifo capacity and Fifo interrupt event
Update CHANGELOG.md
format code with cargo fmt
add Rx and Tx fifo capacity - review comments
add Rx and Tx fifo capacity - formatting inside macro
v0.12.0
Add "can" feature flag to docs list
Expose PinMode as public
Use the word "sealed" in documentation of PinMode
Fix docstrings using duration types
Fix docstrings with rate type extensions
Document the RMII TXD1 pin in ethernet examples
v0.12.1
fix: flash bank impl visibility
Convert ResetMode to own witness pin and track past pin mode
sdmmc: wait for the card to return to transfer mode after each write
sdmmc: Add back-to-back writes in example
Refactor ResetMode
Add example that uses with_input method
flash: document sector_address method
v0.12.2
adc: simplify cr reads and sample time code

wrong repo


Routing using $templateUrl with content put in cache with $templateCache does not seen to work

Hello,
Thanks for your amazing lib that shifted angular dev to another level. Dealing with states inside each component would have been so painful before.
So I'm refactoring my code from using the core angular routing to the angular ui router, and I have some issues with the $templateCache.
Step 1 : I declare my html code in $templateCache

Step 2 : I check that the $template cache works with the core routing feature

Step 3 : I create a new routing file and remove the core routing file and use the same template url

Step 4 : I load the page to test, and in the console log, I see that angular is trying to load the url template without considering the cache version

I'm pretty new to angular ui router, so maybe there is some obvious reason it does not work.
In reading the api, I found $templateFactory that may help, but I didn't get how to use it while declaring the states.
If anyone can help me understand, it would be so great.
Thanks
Best regards
Bobby

@guilbep @Crotery Thanks, saved me a lot of debugging effort. :+1:

@Crotery Thanks :+1:

Someone want to add this to the FAQ?

Don't know what will be the question and the answer. The core problem is still hidden, at least for me.  We've just hardcoded absolute urls, so our production works nice. But ui-router still downloads all tpls on developer's machines, and there is no guarantee that other project will not have such issue.
What about
Q. Trying to put ui-router templates to $templateCache by hand, but ui-router still downloads them.
A. Sometimes angular adds slashes, absolute paths or even absolute urls (http://...) to $templateCache. Make sure you also put same urls to cache.
?


Indicator reacts to touch , even on outside the boundaries

When i touch outside the slider boundaries , indicator pops up and reacts to touch in it's parent
I checked the latest release but this bug doesn't solved for me yet.
Check this screenshot for more detail:

Same issue here

any solution @BehnamMabodi @AnderWeb

Same issue here

any solution @BehnamMabodi  @AnderWeb


CI: ensure broken code builds are detected early

We should create a GitHub Action that compiles all of the Go code as well as tests, so that contributors don't have to wait for CI run to find out they made a typo in test code or missed something.

IMO govet should also be part of this, at the moment it's lost somewhere in the middle of the Travis unit-tests output.

@joestringer yes, for sure! we have a PR for golangci-lint (#11528), which may include govet (something to check).

I would say that this is done by our smoke tests now, closing the issue.

@nebril I think it's still not early enough, I was implying the we should run go test -c.

I've added this as a good-first-issue to figure out how to get go test -c (test compilation) to occur early on during the github actions builds.

This is no longer an issue today, closing.


feat: Multivariate Anomaly Detection

Additions:

Beta VAE to balance the KLD and Log likelihood loss
RobustMahalanobis Distance for multivariate thresholding
Percentile based thresholding with aggregation
Allow a tag suffix in docker workflow when using the github UI
Exponential moving average in postprocess output
Introduce pytests instead of unittests for newer test cases
Improve synthetic anomaly generator module
Per feature anomaly score when using certain thresholding models
Score config for different feature and window aggreation methods

Removal:

backtesting cli tool (since this will be added in a separate backtesting tool UI)

Have you evaluated the quality difference between plain VAE v.s. conv1d VAE in anomaly detection?

Yes, conv1d has much better quantitative scores.

Also, I am not sure how do we test pytest files. can you add a step in README for it too.
Added some minor comments otherwise LGTM.

Simple make test will work, already in README.


What are the steps to start / build nunuStudio ?

Hello
I am sorry I can't figure how to launch nunuStudio with the latest source from github. Could you please detail what "npm" commands I need to type in order to either build or start nunuStudio (on linux) ?
Or even better do you plan to update the released binaries ? I haven't tried the other platforms but the one for Linux seems very outdated (2019!) . But beside being outdated it works well and it is very easy to launch. That would be great if we could have the latest build released !

Hello
To build the code you will need to run these three commands.
Some of the deps are not present in npm so i have added napa to handle these.
npm install
npm install napa
npm run build

Thanks a lot!

Sorry to bother it still doesn't work
Everything goes well until I run
npm run build
it gives me this error

node:internal/crypto/hash:67
  this[kHandle] = new _Hash(algorithm, xofLen);
                  ^

Error: error:0308010C:digital envelope routines::unsupported
    at new Hash (node:internal/crypto/hash:67:19)
    at Object.createHash (node:crypto:130:10)
    at module.exports (/home/zfx/logiciels/nunuStudio/node_modules/webpack/lib/util/createHash.js:135:53)
    at NormalModule._initBuildHash (/home/zfx/logiciels/nunuStudio/node_modules/webpack/lib/NormalModule.js:417:16)
    at handleParseError (/home/zfx/logiciels/nunuStudio/node_modules/webpack/lib/NormalModule.js:471:10)
    at /home/zfx/logiciels/nunuStudio/node_modules/webpack/lib/NormalModule.js:503:5
    at /home/zfx/logiciels/nunuStudio/node_modules/webpack/lib/NormalModule.js:358:12
    at /home/zfx/logiciels/nunuStudio/node_modules/loader-runner/lib/LoaderRunner.js:373:3
    at iterateNormalLoaders (/home/zfx/logiciels/nunuStudio/node_modules/loader-runner/lib/LoaderRunner.js:214:10)
    at Array.<anonymous> (/home/zfx/logiciels/nunuStudio/node_modules/loader-runner/lib/LoaderRunner.js:205:4)
    at Storage.finished (/home/zfx/logiciels/nunuStudio/node_modules/webpack/node_modules/enhanced-resolve/lib/CachedInputFileSystem.js:55:16)
    at /home/zfx/logiciels/nunuStudio/node_modules/webpack/node_modules/enhanced-resolve/lib/CachedInputFileSystem.js:91:9
    at /home/zfx/logiciels/nunuStudio/node_modules/graceful-fs/graceful-fs.js:123:16
    at FSReqCallback.readFileAfterClose [as oncomplete] (node:internal/fs/read_file_context:68:3) {
  opensslErrorStack: [ 'error:03000086:digital envelope routines::initialization error' ],
  library: 'digital envelope routines',
  reason: 'unsupported',
  code: 'ERR_OSSL_EVP_UNSUPPORTED'
}

Node.js v17.3.0

I suppose I will have to try on an other machine with a fresh node/npm install unless you have a solution ?
May I ask why don't you put a prebuilt version on nunuStudio website ? The builts available seem very far behind the latest branch of nunustudio.

@shantee Readme says you gotta use Node LTS which is currently version 16.15. You used v17.3.0 I assume some dependencies fail here.


Request to add new exchanges - Exbitron, Txbit, as well as an error when loading SafeTrade exchange data.

Hello, thank you so much for your hard work! This is the best cryptocurrency price tracking app!
I ask you to add exchanges: Exbitron - https://www.exbitron.com / and also Txbit - https://www.txbit.io / there are interesting coins on these exchanges that need to be tracked.
SafeTrade - when trying to load the list message: Last sync: never "Error: Authentication required (403)"
Thank you! Be healthy and happy!

Regarding SafeTrade

Please try again, maybe it is a temporary issue on the exchange side. I can't reproduce this.
If you still have this issue, try to open directly SafeTrade API url from the browser on your device: https://safe.trade/api/v2/peatio/public/markets
This may show the details of the issue (maybe network/proxy issue, maybe this exchange inaccessible from your IP region).

Exbitron, Txbit
I will analyze the API of these exchanges and then add it to the app.

Thank you for the feedback.

Exbitron and Txbit added in the app v2.64


[Request] Gephi

Package Request
Information
Name: Gephi
Description: Gephi is the leading visualization and exploration software for all kinds of graphs and networks. Gephi is open-source and free.
Homepage: https://gephi.org/
Download link(s): https://github.com/gephi/gephi
Some indication of popularity/repute: 4.6k Stars

@DOFfactory I've added it, check it out! The Scoop version doesn't include the Java runtime like the full installer so you'll need to install oraclejre8 or liberica8-jdk from the Java bucket (or an equivalent Java 8 version)

Hm, thanks for this, unfortunately I am still getting an error

I tried installing both oraclejre8 and liberica8-jdk separately. In both instances I have the JAVA_HOME environment set correctly, no idea what is the issue with Gephi here...

Thanks, it works now!


Remove version: FutureScholars.Paperlib version 1.9.1

All urls in manifest result in 404s, no longer available
Microsoft Reviewers: Open in CodeFlow

URL: https://github.com/GeoffreyChen777/paperlib/releases/download/release-electron-1.9.1/Paperlib_1.9.1.exe
Response status code does not indicate success: 404 (Not Found).
(Automated message - build 727)


runtime: TestGdb{AutotmpTypes,Const} failing as of CL 171823

I don't know whether CL 171823 was the cause, or if there was some incidental change to the builder, but the solaris-amd64-oraclerel builder is now consistently failing (https://build.golang.org/log/92fe055b8bae545fdae60bdda9575ca85bff728e) in the runtime test:
--- FAIL: TestGdbAutotmpTypes (11.23s)
    runtime-gdb_test.go:65: gdb version 8.0
    runtime-gdb_test.go:446: building source exit status 2
        # command-line-arguments
        runtime.morestack: nosplit stack overflow
        	744	assumed on entry to runtime.sigtramp (nosplit)
        	736	on entry to runtime.sigtrampgo (nosplit)
        	568	after runtime.sigtrampgo (nosplit) uses 168
        	560	on entry to runtime.sigfwdgo (nosplit)
        	488	after runtime.sigfwdgo (nosplit) uses 72
        	480	on entry to runtime.dieFromSignal (nosplit)
        	456	after runtime.dieFromSignal (nosplit) uses 24
        	448	on entry to runtime.setsig (nosplit)
        	384	after runtime.setsig (nosplit) uses 64
        	376	on entry to runtime.sigaction (nosplit)
        	328	after runtime.sigaction (nosplit) uses 48
        	320	on entry to runtime.sysvicall3 (nosplit)
        	264	after runtime.sysvicall3 (nosplit) uses 56
        	256	on entry to runtime.sysvicall3Err (nosplit)
        	168	after runtime.sysvicall3Err (nosplit) uses 88
        	160	on entry to runtime.asmcgocall (nosplit)
        	152	on entry to gosave (nosplit)
        	144	on entry to runtime.badctxt (nosplit)
        	120	after runtime.badctxt (nosplit) uses 24
        	112	on entry to runtime.throw (nosplit)
        	72	after runtime.throw (nosplit) uses 40
        	64	on entry to runtime.fatalthrow (nosplit)
        	16	after runtime.fatalthrow (nosplit) uses 48
        	8	on entry to runtime.systemstack (nosplit)
        	0	on entry to function pointer
        	-8	on entry to runtime.morestack (nosplit)
--- FAIL: TestGdbConst (11.71s)
    runtime-gdb_test.go:65: gdb version 8.0
    runtime-gdb_test.go:512: building source exit status 2
        # command-line-arguments
        runtime.morestack: nosplit stack overflow
        	744	assumed on entry to runtime.sigtramp (nosplit)
        	736	on entry to runtime.sigtrampgo (nosplit)
        	568	after runtime.sigtrampgo (nosplit) uses 168
        	560	on entry to runtime.sigfwdgo (nosplit)
        	488	after runtime.sigfwdgo (nosplit) uses 72
        	480	on entry to runtime.dieFromSignal (nosplit)
        	456	after runtime.dieFromSignal (nosplit) uses 24
        	448	on entry to runtime.setsig (nosplit)
        	384	after runtime.setsig (nosplit) uses 64
        	376	on entry to runtime.sigaction (nosplit)
        	328	after runtime.sigaction (nosplit) uses 48
        	320	on entry to runtime.sysvicall3 (nosplit)
        	264	after runtime.sysvicall3 (nosplit) uses 56
        	256	on entry to runtime.sysvicall3Err (nosplit)
        	168	after runtime.sysvicall3Err (nosplit) uses 88
        	160	on entry to runtime.asmcgocall (nosplit)
        	152	on entry to gosave (nosplit)
        	144	on entry to runtime.badctxt (nosplit)
        	120	after runtime.badctxt (nosplit) uses 24
        	112	on entry to runtime.throw (nosplit)
        	72	after runtime.throw (nosplit) uses 40
        	64	on entry to runtime.fatalthrow (nosplit)
        	16	after runtime.fatalthrow (nosplit) uses 48
        	8	on entry to runtime.systemstack (nosplit)
        	0	on entry to function pointer
        	-8	on entry to runtime.morestack (nosplit)
FAIL
FAIL	runtime	60.061s

CC @ianlancetaylor @mknyszek

I maintain the host running that builder and neither has changed in a week.  So it's pretty certain
that Ian's patch is the culprit.

Yes.  The test builds a program with -gcflags=all=-N -l, which disables optimizations.  My CL introduced another function call, and that seems to been enough to cause an overflow in the linker's nosplit stack check when not optimizing.


Working with data in ts format

Hi, I saw in one of the documents presented at Juliacon you have run experiments on datasets from http://www.timeseriesclassification.com/.  I have two queries to it.

Can you point me towards the script used?
I'm particularly interested in working with Multivariate data? Is there support available?

Thanks
Bhaskar

Hi,
Thanks for taking interests on TSML. I suggest you read the docs and get back here for any questions. TSML is used to transfom data consisting of Date, Value columns into matrix features using sliding windows. You can also add other variables and concatenate the matrices. I have examples how to do this in the documentation. Please follow the examples from here: https://ibm.github.io/TSML.jl/stable/man/valueproc/

Once you transform the data into matrix form, TSML pipeline is compatible with AutoMLPipeline syntax so you can do machine learning prediction and regression using a more richer set of operators using AutoMLPipeline: https://github.com/IBM/AutoMLPipeline.jl
If you want to add your own operators to be part of the pipeline, you can using the AMLPipelineBase: https://github.com/IBM/AMLPipelineBase.jl for the type abstract hierarchy and add your operations as described in how to extend it which is described in its README.

Sure. Thank you! I will read the doc and come back here :)
On Tue, 10 Aug 2021 at 15:52, Paulito Palmes, PhD @.***>
wrote:

Once you transform the data into matrix form, TSML pipeline is compatible
with AutoMLPipeline syntax so you can do machine learning prediction and
regression using a more richer set of operators using AutoMLPipeline:
https://github.com/IBM/AutoMLPipeline.jl
If you want to add your own operators to be part of the pipeline, you can
using the AMLPipelineBase: https://github.com/IBM/AMLPipelineBase.jl for
the type abstract hierarchy and add your operations as described in how to
extend it which is described in its README.
—
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Logger filepath fix

Makes logging more robust: Windows paths do not use forward slashes.

WINDOWS IS TRASH
(i'll fix this later)

Will add automated testing for execution to pipeline for the future, see #16


fixed editable true functionality

This simple change will make "editable: true" work properly.

Hi @PiotrObrebski,
Unfortunately this breaks many things. Please see the failing CI build.

Which issue does this resolve?
Also please provide a codepen to demonstrate the failing and the fixed case.
https://github.com/amsul/pickadate.js/search?q=editable&type=Issues

Hi @DanielRuf,
in my project, someone made a mistake initializing your picker.js. Sorry for taking your time. This commit solves only my case.

Hi @DanielRuf,
In my project, someone made a mistake initializing your picker.js. Sorry for taking your time. This commit solves only my case.

No problem. I'm glad that you could resolve it.


containerd ulimit parameters are not set in containers after changing in containerd.service file

Description
we have installed the containerd in ubuntu , so we try to change the ulimit of the containers created but after changing the LimitNOFILE=1048576 containers ulimit values are not change please help on this
Steps to reproduce the issue

create a ubuntu container using nerdctl
change the conatinerd.servive file with LimitNOFILE=1048576
and check the ulimit value inside the conatiners

Describe the results you received and expected
still ulimit value is 1024
What version of containerd are you using?
v1.6.19
Any other relevant information
using nerdctl
Show configuration if it is related to CRI plugin.
no

Whether using ctr or nerdctl, RLIMIT_NOFILE will be set to 1024 by default.
https://github.com/containerd/containerd/blob/584d13d5cb350b48e64eb7c7b0e3e935b941e0d1/oci/spec.go#L159-L164
nerdctl can set RLIMIT_NOFILE with --ulimit=nofile=10000

thanks a lot @Iceber  for your comment but not error  has changed to FATA[0000] failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: error during container init: error setting rlimits for ready process: error setting rlimit type 7: operation not permitted: unknown
can you please suggest

There are no errors in my environment. Are you using rootless containerd?

yes

i have configured the LimitNOFILE=1048576 in /etc/systemd/system/containerd.service but conatiners ulimit is still 1024

check your nerdctl version, nerdctl seems to have fixed this issue https://github.com/containerd/nerdctl/pull/588

@Iceber  i m using the nerdctl version 1.2.1 is there any issue with that , which version of nerdctl issue is fixed?


A question about VCF format conversion

I am a master's student studying plants and VCF format is a commonly used SNP format for me. I use this command to processing my data ：

After the phenotype is added, an additional file of the phenotype is output. The output phenotype file is not in the same order as my original phenotype file. After I checked it, it seemed that in subsequent GWAS analyses, it seemed that the output phenotype file had to be used instead of my original phenotype file. But this is not emphasized in your ReadMe. I would like to ask what is the reason for this?
And by the way, in the given command, the row that adds the phenotype is commented out, but shouldn't the line that adds the phenotype be important?
Thank you very much for answering my questions!!！

Thank you for the question.
Yes, if the phenotype file is provided, rMVP will automatically re-order the individuals in phenotype file to be consistent with that in genotype file, we recommend providing phenotype file since it can help users avoid some potential problems. However, it's not mandatory, because some users are only interested in parts of functions in rMVP, e.g., genotype numeric coding, PCA and Kinship calculation, in which the phenotype file is not involved. Therefore we command out this line in the tutorial script to tell the users that the phenotype file is optional, it does not represent unimportance.

Thank you for your answer
The reason I asked this question was because in the subsequent GWAS analysis, the phenotype file I provided is the original one, not a reorganized version, leading to consistent issues with the results. I think you can mention this in the README of GWAS analysis, maybe it will be more comprehensive!


Add exponential backoff for deletion failures.

Fixes: #1657.
Note for potential broader use toward #1619.

LGTM


[Task]: Create a scheduled task trigger (cronjob) in CS to fetch and store the ACTIONS API response for all the integrations one by one (or all at once)

SubTasks
Create a scheduled task trigger (cronjob) to fetch the ACTIONS API response for all the integrations one by one (or all at once depending on the paragon actions api) and store the response in the Cloud Service database.

Hey team! Please add your planning poker estimate with Zenhub @AmanAgarwal041 @sneha122

There are some unknowns in this task depending on the actions Api, hence giving a higher story point

Setting the final estimate to 2 as per planning poker estimate.


Update non-monotonic timers to be monotonic.

Currently, Luau has left severe adverse effects associated with its current non-monotonic timer, tick().
Some of these adverse effects end-up being game-breaking on specific platforms or in specific conditions. For instance, on some non-Windows machines, tick() counts backwards instead of forwards. This is suboptimal and has unintended consequences in Adonis.
A Roblox engineer has also stated on considering deprecating tick() because of these arbitrary adverse effects and misleading principles (though that'd be a tough call, considering how many experiences rely on tick()): https://devforum.roblox.com/t/luau-recap-june-2020/632346 (under os. enhancements)
time() is optimal as a monotonic timer and avoids common pitfalls and adverse effects that tick() consists. Unlike tick(), it runs the total experience simulation time (meaning this will likely always return studio if no simulation is ran, impacting plugins).
Cheers!

Stfu, give feedback, not #DoNotMerge

Nope, this commit is completely busted.
This page is completely incorrect, time() is NOT a global. os.time() is the only way to access it.
Adonis crashes immediately.

None of the changes that I've made (even if time() were not to exist should not impact crashing). The most that should occur should just be several errors to output.
If you can send me a place file if it is reproducable, that'd be great and i'll definitely make changes to it. At the moment, I can not reproduce crashes.
If you're running your tests outside of the Luau environment (such as a CLI), it is possible that time() does not exist as a global. However, in Luau, this is supported. time() is restricted to the elapsed time of simulation within Roblox. If no simulation is running, time() will always return 0.
os.time() and time() are completely different. While both are monotonic timers, os.time() is great if you want a UNIX timestamp, but the resolution is excessive for these changes.
Generally speaking for all of Roblox's monotonic timers:
Any UNIX timestamp needed should always use os.time(), formatted time should use DateTime, performance comparisons should use os.clock(), and everything else should use time().

Stfu, give feedback, not #DoNotMerge

cool mans cant read up lmao

Nope, this commit is completely busted.
This page is completely incorrect, time() is NOT a global. os.time() is the only way to access it.
Adonis crashes immediately.

None of the changes that I've made (even if time() were not to exist should not impact crashing). The most that should occur should just be several errors to output.
If you can send me a place file if it is reproducable, that'd be great and i'll definitely make changes to it. At the moment, I can not reproduce crashes.
If you're running your tests outside of the Luau environment (such as a CLI), it is possible that time() does not exist as a global. However, in Luau, this is supported. time() is restricted to the elapsed time of simulation within Roblox. If no simulation is running, time() will always return 0.
os.time() and time() are completely different. While both are monotonic timers, os.time() is great if you want a UNIX timestamp, but the resolution is excessive for these changes.
Generally speaking for all of Roblox's monotonic timers:
Any UNIX timestamp needed should always use os.time(), formatted time should use DateTime, performance comparisons should use os.clock(), and everything else should use time().

Turn out I was wrong about time() not being a global constant, roblox wiki, believe it or not, it correct.
I was getting a nil constant error from using it.
If @Sceleratis could approve the workflow that'd be nice. Testing it after that would be trivial.

If @Sceleratis could approve the workflow that'd be nice. Testing it after that would be trivial.

👍

@Sceleratis It failed to post in the nightly channel.

os.clock() is better

os.clock() is better
if you can use os.clock() in a schenario where you can use time() then use os.clock()

This is correct, but wouldn't os.clock be slower? If it's a few milliseconds even then I'd recommend it over time()

@Sceleratis It failed to post in the nightly channel.

I manually posted it in #development

os.clock() is better
if you can use os.clock() in a schenario where you can use time() then use os.clock()

This is correct, but wouldn't os.clock be slower? If it's a few milliseconds even then I'd recommend it over time()

The performance difference between os.time() and time() are negligible (at least should be negligible). The only timer provided by Roblox that genuinely has some questionable performance is workspace.DistributedGameTime, but if you're using that in 2021 for production-value work, you've got more issues to worry about 😬.
The biggest difference is that time() considers the simulation environment, whereas os.time() only cares about a UNIX timestamp. This is a pretty big difference when considering clients with high network latency (one instance that would cause unexpected interruptions, there are a plethora of cases where a client may need simulation to be paused) -- time() will intentionally lag behind to avoid the simulation timer skipping a tick, whereas os.time() will continue ticking.

Did some testing with this branch to make sure it works and as far as I can tell this seems to be an acceptable drop-in replacement for any usage of tick() in Adonis so I'm gonna go ahead and merge it now.


Get value tests

Signed-off-by: Maciej Byczko<EMAIL_ADDRESS>

Will have to be made from scratch, too many changes on main branch


Feature request: "Cycle" task

Feature Request
Feature Information:

What should it do?
a task "cycle", which can have additional tasks added inside of it, and each time that parent task is run, it executes the next task in it's list

For example:
 Trigger: Simple Time Interval 10 minutes
    Task: Cycle
        Task: Send message to everyone on the server
            MessageOne
         Task: Send message to everyone on the server
             MessageTwo
         Task: Send message to everyone on the server
             MessageThree

would send "MessageOne", then "MessageTwo", then "MessageThree", one after the other, with one message every 10 minutes, repeating after "MessageThree"

Is it specific to a given application module?
No

I confirm:

[x] that I have searched for an existing feature request matching the description.

This can already be done with one trigger and three tasks. Unless I'm misunderstanding.

Ohh I see what you're saying. Instead, you'd just do three triggers of every X minutes. Each with one of the messages. I think that's what you're wanting.

let me add some "pseudocode" (python xD)
import time

i = 0
taskList = [
    lambda: print("MessageOne"),
    lambda: print("MessageTwo"),
    lambda: print("MessageThree")
    # you have the ability to easily add as many of these as you like
]
while True:
    taskList[i]()
    i += 1
    i %= len(taskList)
    time.sleep(10*60) # 10 minute sleep

the current way, as far as i can see, say you want this to trigger at 5pm every day, you'd have to manually work out the timings, so that it plays the next message at the correct time, and then cycles back

i suppose, rather than that while loop if you put the taskList[i](), and the i+=1 and i%=len(taskList) parts in a def trigger():, that's more like what would happen in AMP, like, whatever you set the trigger to, those three lines get called every single time it triggers

Perhaps the Wait Task would be what you want then?

https://paste.gg/p/TheStraying11/83783d3e762844e1bb9d051d9af219bf
here is a more robust example that shows its usefulness over the "Wait" task, while the first two are just harder to do with just "Wait", specifically the last trigger I define, cannot be done with a wait

you could have for example, a trigger where, if a player performs a certain action, a certain number of times, they get banned, but before that they are given warnings


can not import cpp files?

Hi, it is wrong when i train the command:
python3 train.py config/shapenet/pvcnn/c1.py
details coud be senn as below:

This is probably due to the CUDA environment configuration. You could add these lines into your .bashrc:
export CUDA_PATH=/usr/local/cuda
export PATH=$CUDA_PATH/bin:$PATH
export LD_LIBRARY_PATH=$CUDA_PATH/lib64:$LD_LIBRARY_PATH

Remember to restart the terminal after this.