Add example host-guest complex setup and simulation using SMIRNOFF

This adds an example which sets up:

generation of guest from SMILES
2D structure depiction of the guest
3D conformer generation/charging of guest
Docking into the host
3D structure depiction of the complex
solvation of the complex
parameterization w/ SMIRNOFF99Frosst
minimization and super short MD with OpenMM
visualization of simulation

This could be extended in the future to also generate Yank inputs for binding free energy calculation, for example.
As written this is fairly concise, but I think it's kind of cool and could enable research projects fairly easily I think.
@nhenriksen or @slochower , interested in reviewing for me?

Yes, sounds great. I can review tomorrow afternoon or Friday morning.
Sent from my iPhone

On Aug 30, 2017, at 17:37, David L. Mobley<EMAIL_ADDRESS>wrote:
This adds an example which sets up:
generation of guest from SMILES
2D structure depiction of the guest
3D conformer generation/charging of guest
Docking into the host
3D structure depiction of the complex
solvation of the complex
parameterization w/ SMIRNOFF99Frosst
minimization and super short MD with OpenMM
visualization of simulation
This could be extended in the future to also generate Yank inputs for binding free energy calculation, for example.
As written this is fairly concise, but I think it's kind of cool and could enable research projects fairly easily I think.
@nhenriksen or @slochower , interested in reviewing for me?
You can view, comment on, or merge this pull request online at:
https://github.com/open-forcefield-group/openforcefield/pull/56
Commit Summary
Add skeletons of setup notebook I'm working on
Add demo of docking, setup, MD simulation of SMIRNOFF host-guest system
Update main README.md to point to new example
File Changes
M README.md (3)
M examples/README.md (1)
A examples/host_guest_simulation/OA.mol2 (399)
A examples/host_guest_simulation/README.md (17)
A examples/host_guest_simulation/hbonds.ffxml (11)
A examples/host_guest_simulation/smirnoff_host_guest.ipynb (634)
Patch Links:
https://github.com/open-forcefield-group/openforcefield/pull/56.patch
https://github.com/open-forcefield-group/openforcefield/pull/56.diff
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@jchodera - builds are failing because your encrypted OE license on here is expired. Do you want to fix, or should I do it with mine?

I'll do that right now!

See #57.

We don't have a way of automatically testing these Jupyter notebooks to make sure they run, do we?
If not, there is a plugin for py.test that we can use.
Once we start adding documentation too (which we should probably do soon!) we can use nbsphinx to render the these notebooks as sphinx help.

Currently no testing for jupyter notebooks here, @jchodera . That's on the list of things to do, but finishing the paper is a priority first.

@davidlmobley Just getting to this today... I really appreciate the detailed instructions you put at the top of the jupyter notebook for the requirements. Incidentally, for unrelated reasons, I had to reset some of my conda environments I was glad to see your notes about installing the dependencies.
While trying to install oeommtools, I ran into the following error:
$ conda install -c nividic -c omnia oeommtools
Fetching package metadata ...............
Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in conflict:
  - oeommtools -> python >=3.5,<3.6.0a0 -> openssl 1.0.1*
  - oeommtools -> python >=3.5,<3.6.0a0 -> xz 5.0.5
  - python 3.6*
Use "conda info <package>" to see the dependencies for each package.

...and I'm curious if you've come across before.

To be clear, I didn't follow your instructions exactly. Because of how I had things setup on my machine previously, I used a hybrid approach that possibly messed things up. I created environment.yaml with:
name: openforcefield
channels:
  - anaconda
  - conda-forge
dependencies:
  - anaconda::numpy
  - anaconda::networkx
  - anaconda::lxml
  - anaconda::openmoltools
  - anaconda::parmed
  - anaconda::matplotlib
  - anaconda::pandas
  - anaconda::ipykernel
  - pip:
    - git+https://github.com/open-forcefield-group/openforcefield@548f04d005a51c03b40f1b4fa0ec32b80ae10775
    - https://pypi.anaconda.org/openeye/label/beta/simple/openeye-oenotebook/0.8.1/OpenEye-oenotebook-0.8.1.tar.gz

I installed that into a new conda environment, which requires adding
[global]
extra-index-url = https://pypi.anaconda.org/OpenEye/simple

to pip.conf. Then I got the above error after trying conda install -c nividic -c omnia oeommtools.

It would be really great to get oemmtools onto conda-forge to simplify this whole process. We can just make it a dependency of openforcefield at that point.

I've not run across that before, @slochower . @nividic , can you take a look at this? It's the oeommtools dependency causing problems here.
@slochower - might be useful to have the final contents of your environment for troubleshooting purposes.

Here are the packages in my openforcefield environment:
$ conda list
# packages in environment at /home/dslochower/data/applications/anaconda3/envs/openforcefield:
#
alabaster                 0.7.10                   py36_0    anaconda
ambermini                 16.16.0                       7    http://conda.binstar.org/omnia
babel                     2.5.0                    py36_0    anaconda
bleach                    2.0.0                     <pip>
cycler                    0.10.0                   py36_0    anaconda
dbus                      1.10.20                       0    anaconda
decorator                 4.1.2                    py36_0    anaconda
docutils                  0.14                     py36_0    anaconda
entrypoints               0.2.3                     <pip>
expat                     2.1.0                         0    anaconda
fftw3f                    3.3.4                         2    http://conda.binstar.org/omnia
fontconfig                2.12.1                        3    anaconda
freetype                  2.5.5                         2    anaconda
glib                      2.50.2                        1    anaconda
gst-plugins-base          1.8.0                         0    anaconda
gstreamer                 1.8.0                         0    anaconda
hdf5                      1.8.17                        2    anaconda
html5lib                  0.999999999               <pip>
icu                       54.1                          0    anaconda
imagesize                 0.7.1                    py36_0    anaconda
ipykernel                 4.6.1                    py36_0
ipykernel                 4.6.1                     <pip>
ipython                   6.1.0                     <pip>
ipython                   6.1.0                    py36_0
ipython-genutils          0.2.0                     <pip>
ipython_genutils          0.2.0                    py36_0
ipywidgets                7.0.0                     <pip>
jedi                      0.10.2                    <pip>
jedi                      0.10.2                   py36_2
jinja2                    2.9.6                    py36_0    anaconda
jpeg                      9b                            0    anaconda
jsonschema                2.6.0                     <pip>
jupyter                   1.0.0                     <pip>
jupyter-client            5.1.0                     <pip>
jupyter-console           5.2.0                     <pip>
jupyter-core              4.3.0                     <pip>
jupyter_client            5.1.0                    py36_0
jupyter_core              4.3.0                    py36_0
libffi                    3.2.1                         1    anaconda
libgcc                    5.2.0                         0    anaconda
libgfortran               3.0.0                         1    anaconda
libiconv                  1.14                          0    anaconda
libpng                    1.6.30                        1    anaconda
libsodium                 1.0.10                        0
libxcb                    1.12                          1    anaconda
libxml2                   2.9.4                         0    anaconda
libxslt                   1.1.29                        0    anaconda
lxml                      3.8.0                    py36_0    anaconda
markupsafe                1.0                      py36_0    anaconda
matplotlib                2.0.2               np113py36_0    anaconda
mdtraj                    1.8.0                    py36_2    conda-forge
mistune                   0.7.4                     <pip>
mkl                       2017.0.3                      0    anaconda
nbconvert                 5.3.0                     <pip>
nbformat                  4.4.0                     <pip>
networkx                  1.11                     py36_0    anaconda
nose                      1.3.7                     <pip>
notebook                  5.0.0                     <pip>
numexpr                   2.6.2               np113py36_0    anaconda
numpy                     1.13.1                   py36_0    anaconda
numpydoc                  0.7.0                    py36_0    anaconda
OpenEye-oenotebook        0.8.1                     <pip>
OpenEye-toolkits          2017.6.1                  <pip>
OpenEye-toolkits-python3-linux-x64 2017.6.1                  <pip>
openforcefield            0.0.3                     <pip>
openmm                    7.1.1                    py36_0    http://conda.binstar.org/omnia
openmoltools              0.8.1                    py36_0    http://conda.binstar.org/omnia
openssl                   1.0.2l                        0    anaconda
pandas                    0.20.3                   py36_0    anaconda
pandocfilters             1.4.2                     <pip>
parmed                    2.7.3                    py36_1    http://conda.binstar.org/omnia
path.py                   10.3.1                   py36_0
pcre                      8.39                          1    anaconda
pexpect                   4.2.1                    py36_0
pexpect                   4.2.1                     <pip>
pickleshare               0.7.4                     <pip>
pickleshare               0.7.4                    py36_0
pip                       9.0.1                    py36_1    anaconda
prompt-toolkit            1.0.15                    <pip>
prompt_toolkit            1.0.15                   py36_0
ptyprocess                0.5.2                     <pip>
ptyprocess                0.5.2                    py36_0
pygments                  2.2.0                    py36_0    anaconda
pyparsing                 2.2.0                    py36_0    anaconda
pyqt                      5.6.0                    py36_2    anaconda
pytables                  3.4.2               np113py36_0    anaconda
python                    3.6.2                         0    anaconda
python-dateutil           2.6.1                    py36_0    anaconda
pytz                      2017.2                   py36_0    anaconda
pyzmq                     16.0.2                    <pip>
pyzmq                     16.0.2                   py36_0
qt                        5.6.2                         5    anaconda
qtconsole                 4.3.1                     <pip>
readline                  6.2                           2    anaconda
requests                  2.14.2                   py36_0    anaconda
scipy                     0.19.1              np113py36_0    anaconda
scripttest                1.3                       <pip>
setuptools                27.2.0                   py36_0    anaconda
simplegeneric             0.8.1                    py36_1
simplegeneric             0.8.1                     <pip>
sip                       4.18                     py36_0    anaconda
six                       1.10.0                   py36_0    anaconda
snowballstemmer           1.2.1                    py36_0    anaconda
sphinx                    1.6.3                    py36_0    anaconda
sphinxcontrib             1.0                      py36_0    anaconda
sphinxcontrib-websupport  1.0.1                    py36_0    anaconda
sqlite                    3.13.0                        0    anaconda
terminado                 0.6                       <pip>
testpath                  0.3.1                     <pip>
tk                        8.5.18                        0    anaconda
tornado                   4.5.2                    py36_0
tornado                   4.5.2                     <pip>
traitlets                 4.3.2                    py36_0
traitlets                 4.3.2                     <pip>
wcwidth                   0.1.7                    py36_0
wcwidth                   0.1.7                     <pip>
webencodings              0.5.1                     <pip>
wheel                     0.29.0                   py36_0    anaconda
widgetsnbextension        3.0.2                     <pip>
xz                        5.2.3                         0    anaconda
zeromq                    4.1.5                         0
zlib                      1.2.11                        0    anaconda

@slochower - do you want to try again in a clean conda env? Gaetano ( @nividic ) and I do not have these issues with oeommtools, and it also passes Travis tests (and the https://github.com/oess/openmm_orion repo, which depends on it, also passes tests). So we suspect the problem is on your end but neither of us has had a chance to dig into your details.

@davidlmobley Sure -- I'll try to start from a new environment this afternoon and get back to you.

fwiw, I tried with a fresh conda environment on friday and got the same problem.

Well, that's very odd. I don't get how it could be passing on Travis on https://github.com/oess/openmm_orion then. ( @nividic ? )
I'll have to look into this but it may take me a while to get to it.

@davidlmobley  and @slochower. I've just finished to test the oeommtools installation on Linux 14.04 in a virtual machine. I started from scratch installing conda and then I installed the oeommtools package as specified on the git hub repo. I was not able to reproduce the problem in any way. Currently, I'm using the package also on OS X and Linux 16. @slochower please if you have time, can you try to install the package as I did in a virtual machine or in a different computer? If this is taking to much time try to remove completely conda and reinstall it from scratch, then try to install just the oeommtools package.

@nividic thanks. I'm trying with Ubuntu 16.04.3 LTS. I'm going to give installation another shot this afternoon. One thought -- perhaps we need to install a oemmtools before the other dependencies?

Is this a python 3.6 specific issue? The oess/oemmtools travis only tests python 3.5, but @slochower's issue is a 3.6 issue:
$ conda install -c nividic -c omnia oeommtools
Fetching package metadata ...............
Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in conflict:
  - oeommtools -> python >=3.5,<3.6.0a0 -> openssl 1.0.1*
  - oeommtools -> python >=3.5,<3.6.0a0 -> xz 5.0.5
  - python 3.6*
Use "conda info <package>" to see the dependencies for each package.

I think that either means (1) there is something non-3.6-compliant, or, more likely, (2) a different version of a dependency is being picked up when 3.6 is used than when 3.5 is used on travis.

I retested the openforcefield installation with oeommtools in a python 3.5 environment and I do not have any problems. @jchodera I'm going to test python 3.6

The problem is python 3.6...I'm working on it

@davidlmobley @slochower @nhenriksen The problem with python 3.6 should have been fix now

Should I still use the same command ($ conda install -c nividic -c omnia oeommtools) to install? Or do I need to grab directly from your Github? I tried a second ago and it failed in a new test environment.
$ conda list
# packages in environment at /home/dslochower/data/applications/anaconda3/envs/testenvironment:
#
openssl                   1.0.2l                        0
pip                       9.0.1                    py36_1
python                    3.6.2                         0
readline                  6.2                           2
setuptools                27.2.0                   py36_0
sqlite                    3.13.0                        0
tk                        8.5.18                        0
wheel                     0.29.0                   py36_0
xz                        5.2.3                         0
zlib                      1.2.11                        0
(testenvironment) Tue Sep 05 08:27:48 warthog:~/data/projects/openforcefield/openforcefield-binding/build
$ conda install -c nividic -c omnia oeommtools
Fetching package metadata ...............
Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in conflict:
  - oeommtools -> python >=3.5,<3.6.0a0 -> openssl 1.0.1*
  - oeommtools -> python >=3.5,<3.6.0a0 -> xz 5.0.5
  - python 3.6*
Use "conda info <package>" to see the dependencies for each package.

@slochower - I think they've migrated to this one: conda install -c OpenEye/label/Orion -c omnia oeommtools
(I need to update my PR to reflect this.)

@davidlmobley @nividic Great! That worked.

Yay! And you guys are up and running with the OpenEye tools again?

@nividic : It would be great if you could cut separate releases (even just minor x.y.z updates of the z) and match the version numbers for each conda package you upload. It gets to be pretty hard to update the packages when bugfixes are released otherwise.
https://anaconda.org/OpenEye/oeommtools/files

Yup, should be. This'll be first test.

(LMK if you have issues when testing it out.)

@davidlmobley  This may be a separate issue, but...
I created a brand new environment, installed oemmtools as above (conda install -c OpenEye/label/Orion -c omnia oeommtools). Then installed openforcefield using the suggested command (conda install -c omnia openforcefield) and finally tried to grab openeye-oenotebook using pip install -i https://pypi.anaconda.org/openeye/simple openeye-oenotebook. I got:
$ pip install -i https://pypi.anaconda.org/openeye/simple openeye-oenotebook
Collecting openeye-oenotebook
  Could not find a version that satisfies the requirement openeye-oenotebook (from versions: )
No matching distribution found for openeye-oenotebook

Is this another python 3.5 vs. 3.6 issue?

can confirm.
Also related to the instructions in the PR @davidlmobley, I had trouble with pip install -i https://pypi.anaconda.org/openeye/simple openeye-oenotebook ("Could not find a version that satisfies ...").  I solved this by finding a .whl file and downloading and installing that:  pip -v install OpenEye_oenotebook-0.8.1-py2.py3-none-any.whl

@jchodera I'm going to set the oeommtools git hub tag as the conda repo version and I'll keep them in synchro.

@mattgeballe - some issues with oenotebook noted here: https://github.com/open-forcefield-group/openforcefield/pull/56#issuecomment-327309920 -- maybe there is no Python 3.6 version yet? Can you comment?

In order to install the latest packmol release, I have temporary added my conda channel to the installation string:
conda install -c openeye/label/Orion oeommtools -c nividic -c omnia

When packmol will be available on the omnia channel  I'll remove my repo...I'm sorry about that

@nhenriksen @slochower - so this is mostly working for you, except that I need to add (what info exactly?) to the Jupyter notebook? I'm not familiar with whl files so maybe you can tell me what I need to tell people...?

When packmol will be available on the omnia channel I'll remove my repo...I'm sorry about that

Sorry for the delay---looks like @andrrizzi and @lnaden were tied up. I can do this now.
Do you want 17.221 from https://github.com/mcubeg/packmol/releases?

Working on getting the new packmol built here.

@davidlmobley I think the problem stems from the fact that the openeye-oenotebook package is not listed on https://pypi.anaconda.org/openeye/simple/ .  So it can't be found by running pip install -i https://pypi.anaconda.org/openeye/simple openeye-oenotebook.
The approach I used is fixed to a specific release version that I found on here: https://anaconda.org/OpenEye/OpenEye-oenotebook/files
To install, run:
pip install https://anaconda.org/OpenEye/OpenEye-oenotebook/0.8.1/download/OpenEye_oenotebook-0.8.1-py2.py3-none-any.whl

@jchodera YES please the 17.221 would be ok

@nhenriksen -

@davidlmobley I think the problem stems from the fact that the openeye-oenotebook package is not listed on https://pypi.anaconda.org/openeye/simple/ . So it can't be found by running pip install -i https://pypi.anaconda.org/openeye/simple openeye-oenotebook.

Now that you mention it, I remember noticing the same thing. I think I installed via a download link from the website, which was a bit annoying; I never figured out how to do it via pip. @mattgeballe -- any prospects of making the "obvious" pip method for installing (pip install -i https://pypi.anaconda.org/openeye/simple openeye-oenotebook) work properly?

I haven't tested it yet, but I wonder if linking to https://pypi.anaconda.org/openeye/label/beta/simple/openeye-oenotebook instead of https://pypi.anaconda.org/openeye/simple will get the job done because I do see relevant-looking packages at the former URL.

@jchodera Thanks for packmol. I have noted that the packmol version that you selected is "1!17.221". Is it what you wanted or the "!" is a typo?

@nividic thats actually for setting the Version Epoch

This should ensure that this version is grabbed by default instead of the older date-based version. Let me know if that doesn't work.

@davidlmobley Thanks for working on this! I forgot to pick things up while waiting on install instructions for openeye-oenotebook, but I can do the manual install -- https://github.com/open-forcefield-group/openforcefield/pull/56#issuecomment-327574956 -- and test the notebook, if you think it'd still be useful.

@slochower - I think it's working now, or at least, it sounded like it was for @nhenriksen . Maybe you can just doublecheck with him? If not it would be good to have one of you confirm, but if he's already checked I see no reason for you to doublecheck.
Though, you may also want to try this out since this should give you an easy way to do on-the-fly modification of force field parameters for your host guest systems, which sounds like it would help you. (My recollection is it's as simple as something like ff.changeParameter(...) or similar).
The better long-term solution, of course, is for me to implement automated testing of the provided Jupyter notebooks under multiple Python versions, but it'll take a while to get to that.

@davidlmobley just to clarify, I did get openeye-oenotebook installed correctly, but I wasn't able finish testing the whole notebook yet.

OK, thanks. So @nhenriksen or @slochower - it would be great if one of you could test. It'd be good to make sure I didn't forget any prereqs or something. :)

@davidlmobley I finally got around to giving this a go with CB7 as the host and heptane as a guest, and I have a few comments.
First, regarding prereqs. I still had some problem initially, but here is the final set of steps that got it working:

Install Anaconda3
./Anaconda3-4.4.0-Linux-x86_64.sh
conda update --all
Install OpenMM
Install Prereqs
conda install -c omnia openforcefield
conda install -c OpenEye/label/Orion -c omnia oeommtools
pip install -i https://pypi.anaconda.org/openeye/simple openeye-toolkits
pip install https://pypi.anaconda.org/openeye/label/beta/simple/openeye-oenotebook/0.8.1/OpenEye_oenotebook-0.8.1-py2.py3-none-any.whl
conda install -c OpenEye/label/Orion -c omnia pdbfixer

Note that the openeye-toolkits step is not in your instructions and your wording for the oeommtools installation requires the user to add the package name to the end of command you give, which could be made simpler by just making the command complete.  Also, I used conda to install pdbfixer.
The rest of the notebook went fine, except that there seemed to be some problems with the CB7 topology.  Docking went fine, and the complex.pdb looks totally correct:

But the solvation step introduced some problems.  Somehow the coordinates of CB7 in complex_solvated.pdb got messed up, bizarrely starting in the middle of the molecule (i.e., about half the coordinates directly match complex.pdb, but then the rest appear to be shifted nonsensically).  The result is spaghetti CB7. I did check the CONECT lines and they appear to be correct.  Just the coordinates of some CB7 atoms have changed:

Despite the spaghetti, the minimization and MD completed, although it resulted in CB7 being twisted inside-out.  I was hoping it would be a mobius strip, but alas, it looks like just a regular twist:

So it looks like the CB7 topology got scrambled somehow, but other than that, things worked pretty well.  I've attached the CB7 mol2 for debugging.
cb7.tar.gz

Thanks for testing, @nhenriksen . I've noted this and will revisit. Somewhat weird you had these problems and I didn't; presumably a version of something has changed/is different.

@nhenriksen - I'm trying to look into the issue you raised here, but I can't extract the cb7 file you used. Can you re-attach if you still have it, or say where you got it from?

@davidlmobley oops, I have no idea what I did to that file .... possibly tar'ed something twice.  See if this works.
cb7.tar.gz

Thanks. In the meantime I was able to reproduce the issue (while offline) using files from benchmarksets. Working on sorting it out.

@nhenriksen I believe I have fixed your issue; see #66 . Basically it's just that the solvation tools are sort of finicky and I'd botched something.


finalize: pass the last emitted value to the callback

Feature Request
Is your feature request related to a problem? Please describe.
When my observable completes, errors, or gets unsubscribed, I need to do a cleanup using the last emitted value.
Describe the solution you'd like
I'd like to get the last emitted value as an argument to finally's callback
Describe alternatives you've considered
All the alternatives look too clumsy.
Additional context
Another issue about adding a callback argument to finalize: #2823

IMO, this is something that should be handled in a user-land operator or observable. I don't think it's something that should be added to finalize.

You can compose this pretty easily with existing operators:
https://stackblitz.com/edit/rxjs-fkavym

function finalizeWithValue<T>(callback: (value: T) => void) {
  return (source: Observable<T>) => defer(() => {
    let lastValue: T;
    return source.pipe(
      tap(value => lastValue = value),
      finalize(() => callback(lastValue)),
    )
  })
}

I agree with @cartant that this should probably be a user land thing.


Add Pagefelt

added pagefelt application
By submitting this pull request, I promise I have read the contribution guidelines twice and made sure my submission follows it.
⬆⬆⬆⬆⬆⬆⬆⬆⬆⬆

Please follow the contributing guidelines and the existing formatting.


Window not being destroyed

It seems that this causes abandoned memory.
For some reason, when using .register(), closing the window would not destroy it.
https://github.com/Wouter01/SwiftUI-WindowManagement/blob/adbebf5d7df325f3d7bf07dc832e5e162a9003f5/Example/WindowManagementProject/WindowManagementProjectApp.swift#L32

Sorry for the late reply. You're right that this is causing memory issues. However, I'm personally not using the library anymore, and I don't think it's safe enough for production apps. I will archive this repo


Support lerna repositories

I'd like to use greenkeeper for our monorepo for React Server, but it only updates the top-level package.json, and not the individual package's dependencies.  In this pull request, greenkeeper updates the root package.json, but none of the ones in packages (for instance React Server proper or our cli.  We use a tool called lerna to manage our monorepo; updating the dependencies with david would be accomplished as follows: lerna exec -- david u

Heya, this is a good feature request. I’m closing this as a duplicate of https://github.com/greenkeeperio/greenkeeper/issues/139


Proposal: Stream compatible RegExp implementation

I think it would be cool to take the parser and AST you have created, and generate a Node.js Stream compatible version.
API would go something like this:
var input = createInputStream('hello how are you');
var streamRegex = new StreamRegex('\\w+');
var arr = [];
input.pipe(streamRegex.match())
 .on('data', function(chunk) {
   arr.push(chunk.toString('utf8'));
 });

console.log(arr);
// ['hello', 'how', 'are', 'you']

Goals / Ideas:

Equivalents for match, test, split, and replace
Work with very large inputs (i.e. larger than available memory). This would be the key advantage of using a Stream based version over the default.
no copying of buffer data, use Buffer.concat() and buf.slice()
work with multiple encodings
be fast

I've searched, but have not found anything that operates this way. I did find this, but it converts the buffers to strings, and concats them (violating 2, and 3 above).
Obviously this would be a separate project from this one, but it could certainly share the parser and AST at a minimum (and likely more). I may try implementing myself, but it would be nice to have buy in / input from the contributors here, especially if I end up wanting to refactor some of the code here to facilitate reuse in my project (and help from experts on the problem domain would certainly be welcome).
I think it could be pretty powerful. Thoughts?

Obviously this would be a separate project from this one,

I agree - creating a stream based RegExp engine is out of the scope of this project. Therefore, I am going to close this issue.

Work with very large inputs (i.e. larger than available memory)

This sounds like a good idea at first, but note, that it is trivial to write a RegExp that might match the entire stream input like /.+TheEnd$/. Therefore, designing a streaming based RegExp might require restricting the expressiveness of the RegExp language.


Configure context to prevent a hanging call

When using interfaces with MTU=9000, we sometimes see how cilium-agent
gets stuck when doing this Rest call. Eventually it gets killed by
Kubernetes because it exceeds the liveness probe and as a result there
are no useful logs.
This patch uses contexts to provide a timeout to the call. The 120s are
used since this number is defined in one of the examples for the
livenessProbe.initialDelaySeconds
https://github.com/cilium/cilium/blob/master/install/kubernetes/quick-install.yaml#L364
We can discuss if perhaps makes sense to generalize all calls to include
such a timeout with a globally defined timeout variable
Fixes: #10506
Signed-off-by: Manuel Buil<EMAIL_ADDRESS>Please ensure your pull request adheres to the following guidelines:

[X] For first time contributors, read Submitting a pull request
[X] All code is covered by unit and/or runtime tests where feasible.
[X] All commits contain a well written commit description including a title,
description and a Fixes: #XXX line if the commit addresses a particular
GitHub issue.
[X] All commits are signed off. See the section Developer’s Certificate of Origin
[X] Provide a title or release-note blurb suitable for the release notes.
[X] Thanks for contributing!

Fixes: #10506
<!-- Enter the release note text here if needed or remove this section! -->

I can't reproduce the issue anymore. I suspect it got fixed with the client-go update. Therefore, I close this


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doc(data/list/basic): improve docstrings [ci-skip]

Fixed a few wrong docstrings (split_at, sigma, pw_filter, and erase_dup) and made spacing around examples consistent throughout. link to relevant zulip thread.
TO CONTRIBUTORS:
Make sure you have:

[x] reviewed and applied the coding style: coding, naming

For reviewers: code review check list

@johoelzl @digama0 This PR looks good to me.

@bryangingechen Could you resolve the conflicts in this file?

This should be OK now. @digama0


[Bug]: adminjs/logger not working

Contact Details
Slack
What happened?
Trying to get adminjs/logger setup and can't seem to get it to work. I have gotten to a point where I think I am close but still no luck. Here is my setup:
Model
@Entity({ name: "logs" })
export class Log extends BaseEntity implements ILog {
    @PrimaryGeneratedColumn()
    public id: number;

    @CreateDateColumn({ name: "created_at" })
    public createdAt: Date;

    @UpdateDateColumn({ name: "updated_at" })
    public updatedAt?: Date;

    @Column({ name: "record_id", type: "integer", nullable: false })
    public recordId: number;

    @Column({ name: "record_title", type: "text", nullable: true, default: "" })
    public recordTitle: string | null;

    @Column({ name: "difference", type: "jsonb", nullable: true, default: {} })
    public difference: Record<string, unknown> | null;

    @Column({ name: "action", type: "varchar", length: 128, nullable: false })
    public action: string;

    @Column({ name: "resource", type: "varchar", length: 128, nullable: false })
    public resource: string;

    @Column({ name: "user_id", type: "varchar", nullable: false })
    public userId: string;

    @ManyToOne(() => User)
    @JoinColumn()
    user: User;
}

AdminJS
        // Setting up the adminJs app
        const admin = new AdminJS({
            // databases: [AppDataSource],
            rootPath: "/admin",
            resources: [
                User,
                JobTitle,
                Department,
                UserHistory,
                UserHierarchy,
                ProxyPermission,
                Permission,
                AccessToken,
                createLoggerResource({
                    resource: Log,
                    featureOptions: {
                        propertiesMapping: {
                            recordTitle: "recordTitle", //field to store logged record's title
                        },
                        userIdAttribute: "userId",
                    },
                }),
            ],
        });

The error that I am getting is really not an error but its output in the console:
[AdminJS]: There is no property of the name: "user". Check out the "listProperties" in the resource: "Log"
I've tried both methods mentioned in the docs and neither is getting it to work. I'm not sure if I am missing something and that is causing it not to work. Please provide some guidance. Thank you for your help
Bug prevalence
When visiting the admin panel and deleting, adding, editing any entry in any table
AdminJS dependencies version
"@adminjs/express": "^5.1.0",
"@adminjs/logger": "^4.0.1",
"@adminjs/typeorm": "^4.0.0",
"adminjs": "^6.8.7",

What browsers do you see the problem on?
Chrome
Relevant log output
No response
Relevant code that's giving you issues
No response

You're missing user mapping in propertiesMapping
Here's an example of featureOptions that we used in one of our projects.
{
  propertiesMapping: {
    user: 'userId',
    action: 'actionName',
    resource: 'resourceId',
  },
  resourceOptions: {
    resourceId: 'Log',
    navigation: logsNavigation,
    actions: {
      list: {
        isAccessible: or(forAdmins, forSuperAdmins),
      },
      show: {
        isAccessible: or(forAdmins, forSuperAdmins),
      },
    },
  },
  userIdAttribute: 'id',
}

@dziraf, great that resolved the output that I was getting but it still isn't logging anything. Is there something else that I am missing that needs to be added? Here is my adminJs config:
        const adminJs = new AdminJS({
            databases: [AppDataSource],
            rootPath: "/admin",
            resources: [
                createLoggerResource({
                    resource: Log,
                    featureOptions: {
                        userIdAttribute: "id",
                        propertiesMapping: {
                            user: "userId",
                            resource: "resource",
                            action: "action",
                        },
                        resourceOptions: {
                            navigation: {
                                name: "SectionName",
                                icon: "iconName",
                            },
                        },
                    },
                }),
            ],
        });

Also, does this log anytime a save/delete/edit happens on every entity or does it only log what is done through the adminJS portal?


REVIEW SOON BUT DO NOT COMMIT UNTIL 1.1.0 is ready - Updated Installation Steps

Updated compiling-babelfish-from-source.md with installation steps from Emanuel (based on jdbc_unit_tests.yml).  Contains multiple FIXMEs - DO NOT COMMIT until FIXMEs are resolved and the steps are tested.
Signed-off-by: susanmdouglas<EMAIL_ADDRESS>Description
Updated compiling-babelfish-from-source.md with installation steps from Emanuel (based on jdbc_unit_tests.yml).  Contains multiple FIXMEs - DO NOT COMMIT until FIXMEs are resolved
Issues Resolved
This commit updates the installation, but contains a number of FIXMEs and needs to be tested before committing.
Check List

[x ] Commits are signed per the DCO using --signoff

By submitting this pull request, I confirm that my contribution is made under the terms of the BSD-3-Clause License.

@susanmdouglas-aws I've made my review and done the modifications, could you please review back?


Add option to dump stack trace (especially handy for Plugin developers)

What's the best (industry standard?) way of doing this? --stack? --verbose/-v<Level>?

@duaraghav8 --verbose/-v seems like a more flexible option.

@mushketyk Yes. But I'm not very keen on also adding -v (because the uppercase -V is short for --version). It causes confusion.
Also, since this verbose info is aimed at developers (and not users), I also thought that --dev could be a suitable flag name. Because right now, its just stack traces. Eventually, verbose info will include all content being printed on screen that may be useful to anyone developing solium or something on top of it.
So with that in mind^, would you side toward --dev or --verbose?

Great @mushketyk! Please go ahead and implement --debug, #186 is going to take some time before merging so I'll take care of conflicts.
It'll take time primarily because so far, everything in solium was being done synchronously and I'm planning to parallelise your version check code so it doesn't block the linting. I'll handle this so you need not worry about any conflicts.

--debug option is already live by now, forgot to close this issue earlier.
Thanks for contributing!


Fixed output file bugs in classic mode.

When no OUTFILE specified in global file, output default files;
When OUTFILE is specified but no corresponding OUTVAR specified, raise
an error.

Thanks, this looks great.

@jhamman Updated PR as suggested.

@jhamman : Ran uncrustify on the changed two files. (it seems that several other files are not under the desired format if I understood it correctly, but I didn't change them)

Thanks @yixinmao - this is great!


Fix failing legacy tests

What
Addresses error seen in old ruby versions since #151 :
[!] There was an error parsing `Gemfile.legacy`:
[!] There was an error while loading `postmark.gemspec`: undefined method `metadata' for #<Gem::Specification:0x2e5d6c8>. Bundler cannot continue.

@ibalosh do you have an idea as to what might be up with the integration tests here...? 🤔 :

yo @balvig
checked it out, and seems to be passing now. The account which integration tests use got suspended :D
Account is named Postmark Ruby Library in Tele...
Seems some old wildbit.com address got it suspended (maybe you have a .env file in postmark-gem folder with some old addresses,  I know.. this is clunky..

Thanks a lot @ibalosh!
Should've thought to check out the account. Super helpful! 🙏


Documentation updates

The text "Replace both occurrences" needs to be reworded as the two changes are independently identified.
The text "Uri redirectUri = new Uri(Request.Url.GetLeftPart(UriPartial.Authority.ToString());" should instead be "Uri redirectUri = new Uri(Request.Url.GetLeftPart(UriPartial.Authority).ToString());"

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


Post.Service

Minispace.Services.Post
Core
Core repository will contain the objects and dtos for the 'Students'  and the 'Post' databases of cluster.
Post:
Post object:

postId: guid

eventId: guid

author:

textContent: string

image/video?: string(binary)

method(): Type

Studnet

guid SudetntId
string StudentFullName

Endpoints:
Endpoints for the evetns:

POST: /post
PUT: /post/{post_id}
GET: /post/get
DELETE: /post/{post_id}

Content length
Maximum signs 5000
Diagram: https://app.diagrams.net/#G1BsP1sv_9fAmCtE4uVDHizcFcp7TqqvXc#{"pageId"%3A"9VrkRtQQe1OaMDu59Q1v"}

Due to the fact that we would like to have Posts Service working for frontend development in a relatively short time, I decided to take care of preparing it. @olegkiprik, in that situation you will be assigned to some other service. I think Reactions Service can be a great option for you to begin in a quite smooth way. What do you think?

I'm sorry about my slow responsiveness. I agree with your suggestion.

Is this service working/finished? If so we should merge it with dev

[ ] background worker for posts publish date

I provided necessary changes, but I think that now GetPosts request returns all posts regardless of their state. It shouldn't probably work like that, so what endpoints do we need for getting posts?

So far i added an endpoint for getting all posts for organizer. Do we want something more @an2508374 ?

Also right now state reported doesn't have any functionality and aren't in draft and hidden functionally the same state?

So far i added an endpoint for getting all posts for organizer. Do we want something more @an2508374 ?

Thank you @eggwhat, I think endpoints which we have now will be sufficient.

Also right now state reported doesn't have any functionality and aren't in draft and hidden functionally the same state?

State reported will be used if user reports a post and then only admin can republish or delete that post. And I agree that in draft and hidden are functionally the same state - in both a post is not visible for public and its content can be edited.

[ ] endpoint for getting user posts for events that user signed up to


What's NbBitcoin useful? How?

Read https://programmingblockchain.gitbooks.io/programmingblockchain/content/


remove redundant notebook

closes #656
We are retaining notebooks/Using_Cache.ipynb which covers use of the image cache. This top-level notebook is not needed.

/merge


Why not implement java-sdk-springboot as a spring boot starter?

Describe the proposal
Hi, I'm a java learner of dapr, i wonder why not implement  dapr-sdk-springboot according to spring boot common starter rules, that would be nicer for spring boot users.

@darren-wang Can you provide an example of how it would work for the end user? I am not a spring boot expert, so I am eager to learn how we can better integrate with it.

@darren-wang Can you provide an example of how it would work for the end user? I am not a spring boot expert, so I am eager to learn how we can better integrate with it.

@darren-wang Can you provide an example of how it would work for the end user? I am not a spring boot expert, so I am eager to learn how we can better integrate with it.

HI, please check PR:
https://cla.opensource.microsoft.com/dapr/java-sdk?pullRequest=457

@darren-wang Can you provide an example of how it would work for the end user? I am not a spring boot expert, so I am eager to learn how we can better integrate with it.

HI, please check PR:
https://cla.opensource.microsoft.com/dapr/java-sdk?pullRequest=457

@darren-wang We are closing on the release, so I took the liberty to have a PR where we incorporate your solution into  the sdk-springboot package directly. It is OK for that package to be springboot specific - that is the intent. We might refactor spring only stuff out of it later. The priority now is on springboot apps. Please, take a look a the PR.

@darren-wang We are closing on the release, so I took the liberty to have a PR where we incorporate your solution into  the sdk-springboot package directly. It is OK for that package to be springboot specific - that is the intent. We might refactor spring only stuff out of it later. The priority now is on springboot apps. Please, take a look a the PR.

Closed by https://github.com/dapr/java-sdk/pull/457 and https://github.com/dapr/java-sdk/pull/459

Closed by https://github.com/dapr/java-sdk/pull/457 and https://github.com/dapr/java-sdk/pull/459

Reopening since PR is not merged yet.

Reopening since PR is not merged yet.


Add uninstall methodology

We should have a way to uninstall the various services. This can be useful for POC or dev environments that are short lived that need to be upgraded without regard for existing data.

Great idea! We have added this to our backlog. We won't get to it near term.

I could really use this right about now. Trying to get my env just right and it would be nice to have a clean slate each time. Normally i would dockerize but we have contraints.

I also have high need for this! Please implement!

Hi,
This PR by @anuj-apdev - https://github.com/confluentinc/cp-ansible/pull/1302 takes care of the ask.
This'll clear off anything that got installed by CP-Ansible. We'll continue to take feedback and improve the playbook.

Closing this as per @utkarsh5474 comment, closing this one.


Docs improved: more details about caching and memory for segments on historicals

More info about Local cache for caching docs page + clarification what total_memory is in Performace FAQ page. Info taken from this Druid User group post.

Thanks for the contrib! Do you mind signing http://druid.io/community/cla.html?
WIll merge after that

Signed. Thanks for your help too!

thanks @itsmee!


refactor: iteration on generating CSV

addressing https://github.com/GaloyMoney/galoy/issues/4094

please run codegen too
buck2 clean #required to avoid cache issues in update schemas
buck2 run //dev:update-schemas
./dev/bin/codegen.sh

We have buck2 run //dev:codegen as well that does the same as ./dev/bin/codegen.sh


openmpt123: 0.5.9 -> 0.5.10

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/openmpt123/versions.
meta.description for openmpt123 is: "A cross-platform command-line based module file player"
meta.homepage for openmpt123 is: "https://lib.openmpt.org/libopenmpt/"
meta.changelog for openmpt123 is: ""
Updates performed

Version update

To inspect upstream changes
Impact

Checks done (click to expand)

built on NixOS

The tests defined in passthru.tests, if any, passed

/nix/store/kizl7frzfn60b0vibq8a65acwrzhn0qa-openmpt123-0.5.10/bin/openmpt123 passed the binary check.

1 of 1 passed binary check by having a zero exit code.

1 of 1 passed binary check by having the new version present in output.

found 0.5.10 with grep in /nix/store/kizl7frzfn60b0vibq8a65acwrzhn0qa-openmpt123-0.5.10

found 0.5.10 in filename of file in /nix/store/kizl7frzfn60b0vibq8a65acwrzhn0qa-openmpt123-0.5.10

directory tree listing: https://gist.github.com/1a54fe36b12885adbb9cb28e86a62eb2

du listing: https://gist.github.com/d320c50a2aceeb4f20ee966cbcf83d90

Rebuild report (if merged into master) (click to expand)

13 total rebuild path(s)

4 package rebuild(s)

4 x86_64-linux rebuild(s)
4 i686-linux rebuild(s)
1 x86_64-darwin rebuild(s)
4 aarch64-linux rebuild(s)

First fifty rebuilds by attrpath
audacious
audaciousQt5
gjay
openmpt123

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/kizl7frzfn60b0vibq8a65acwrzhn0qa-openmpt123-0.5.10 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A openmpt123 https://github.com/r-ryantm/nixpkgs/archive/4cb042ecb50b5bf8af767bf910f0adfaa541e546.tar.gz

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/kizl7frzfn60b0vibq8a65acwrzhn0qa-openmpt123-0.5.10
ls -la /nix/store/kizl7frzfn60b0vibq8a65acwrzhn0qa-openmpt123-0.5.10/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review run on x86_64-linux 1

3 packages built:

audacious
gjay
openmpt123

Maintainer pings
cc @OPNA2608 for testing.

Result of nixpkgs-review pr 129414 at 4cb042ec run on aarch64-linux 1

3 packages built successfully:

audacious (audaciousQt5)
gjay
openmpt123


When input is required the _validateCount increases while the validate function is not being called

Have regular input with native required prop. When this input is empty, browser traps the submit event and displays the native popup window requiring user to fill this input.
Currently the _validateCount increases with every submit while the validate function is not being called.
Here is codesandbox demo with two inputs.
Steps:

open console
submit the form
observe that nothing is logged, the input has popup "please fill out this form"
submit the form again
in console it logs {name: "first", validateStatus: "valid", _validateCount: 1}

For me the increasing _validateCount is a problem, as I use it in conjunction with the aria-invalid prop.
When a field is required, I set the aria-invalid to _validateCount > 0 && validateStatus === "invalid"
Since the "valid" is initial value of the _validateStatus atom, my inputs get the aria-invalid="false" prop which colors inputs in green when you submit twice
I understand that the atoms prefixed with _ are internals, and likely should not be used for this aria-invalid behavior.
I think the solution here is not to stop the validateCount from increasing, but instead have a new validatedCount atom which will indicate that the field did validate in the past. Since the validate function did not run, it will stay 0, so I won't see the false-positive value of aria-invalid=false.
Also this would solve one other issue for me - the _validateCount is not being reset when the form state is reset (which is ok, since it's internal thing) so having the validatedCount would be a public API.
This started like a bug initially, but since I don't have other solution in mind consider this a feature request.

For more background, here is the aria-invalid behavior
https://github.com/MiroslavPetrik/form-atoms-field/commit/334d276bf08b36e6a012caa60164cff68b161712

Is there a reason checking for an error count doesn't suffice for the aria-invalid case?

Validate count is an internal that's used as an ID to prevent race conditions. It doesn't really need to be so accurate as designed.

Is there a reason checking for an error count doesn't suffice for the aria-invalid case?

By definition the validateStatus already indicates the error count:

when 0 errors then "valid"
when > 0 errors then "invalid"

So practically I'm already using the error count.
The validateStatus is part of the problem, because it has initial value of "valid" which causes my inputs to be highlighted green when the validateCount increments.
In reality, since the validation did not run, the validateStatus could be undefined since we don't know the real field validation status...
What do you think about that?

As another approach, I've used the submitCount from the formAtom.
It requires a context to provide the formAtom (since the field atoms do not have the 'submitCount'), so all the field components can access the form state.
It fixes the 'false positive' case when the validateStatus is initially "valid" but the validation did not run.
With this change, the inputs are colored green only when they are properly filled & form is submitted.
But it has another drawback, that we don't have the field set to aria-invalid="false" right away when it's filled properly - e.g. when required checkbox is checked.
The submitCount > 0 helps to distinguish the "initially pseudo-valid" from "valid after real user change" scenarios.
But it's too strict since we could color the input green as soon as the user checks the input, but that requires some other state to rely on:

start validateStatus as undefined so it becomes valid after validation when user did real change
count validateDCount for each field properly from 0, also respecting the reset action
add changed atom indicating whether user acted with change event on the field (notice that dirty atom cannot be used)

Couldn't you just choose to validate on mount and then check dirty and touched in your validator?

The root issue is that the initial validation status ("valid") without user changing the input is indistinguishable from "valid" state after user caused some validation event.
Validate on mount - how would you do that? I've already tried to call validate function in an effect hook. IMHO this is bad practice as it points out either that the initial value for the validateStatus is poorly chosen or simply it is missing initializer.
I have animated styles on my inputs, so the quick change from "valid" to "invalid" animates the form when rendered which is bad.

I would argue any initially invalid state is bad UX? Like "why are you yelling at me? I didn't even do anything yet"
Do other form libraries validate right away?

Works as designed


Add option to enable gen128Bit for tracer

Signed-off-by: Jingwen Peng<EMAIL_ADDRESS>

 Thank you for your submission, we really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.

Coverage decreased (-0.2%) to 85.413% when pulling 1fd68baf9b151f03abd05df79495e96175e16342 on pengsrc:master into 1f15fec2472dd7d062508f9c13083a1f0a91ed0f on uber:master.

thanks for this, do you mind adding a small test to cover the new option?

No problem, I'll add it.

Coverage decreased (-0.08%) to 85.532% when pulling 3ccac6f59cc8c3fff7cdab297f9d251c42b4cacf on pengsrc:master into 1f15fec2472dd7d062508f9c13083a1f0a91ed0f on uber:master.

Coverage increased (+0.1%) to 85.71% when pulling 63ce24db7389562c4985f2b43bcd496811ebfaab on pengsrc:master into 1f15fec2472dd7d062508f9c13083a1f0a91ed0f on uber:master.

@black-adder Hi, the related tests have been added, please check that.

Thanks for this nice advice!


Progress bar when run npm run build

This is the new thread for #935. Four years after there's still no progress.

When running npm run build, it takes a long time to build.
How to implement a progress bar when building?

I support this issue :+1:

Hi @Menci, is this issue still open ?


🚀 Feature: Authelia and other SSO management

🔖 Feature description
I am using the SSO Authelia and it will be amazing to rely on it to identify my users. I guess it will also work for other SSO applications.
🎤 Pitch
It will simplify the user management for my users.
Below, headers that can be retrieved to identify a user:
HTTP_REMOTE_USER (login)
HTTP_REMOTE_NAME (fullname)
HTTP_REMOTE_EMAIL
It will be nice to a place where to setup these so Pingvin Share can use it.
Thanks in advance for your consideration

There is already an issue #109 for this request, Unfortunately I have no experience with implementing OAuth2 so we have to wait for someone that wants to work on this feature.


Closes vulnerabnility in tunnel-agent

vulnerability details:
https://snyk.io/vuln/npm:tunnel-agent:20170305
Closed by upgrading to latest version of tunnel-agent

The caret should do the work, shouldn't it? But I don't mind to explicitly set that version. Other thoughts?

in this case no @mathiask88
The carat will only match patch level because of the trailing 0. Carat is one of the more confusing parts of semver. Plus you want to exclude vulnerable versions (anything below 0.6.0).

@designfrontier Oh yes, your right. Then I am +1 for this. I checked the other ^0.x.x dependencies and they are all fine.
/cc @ralphtheninja @juliangruber

@designfrontier Thanks!

The history looks a bit odd because last time I published 2.1.2 I forgot to update upstream master branch. Sorry about this. Anyway, released this as a new minor because of bf033af

Thanks y'all!


Allow process comparisons

As seen in the procfile buildpack work. I want to be able to compare equality of Process variables.

Should we add Eq / PartialEq to more of the structs in libcnb-data?

@edmorley

Should we add Eq / PartialEq to more of the structs in libcnb-data?

Probably, yeah. It's a little bit more complicated with structs that take generic metadata since we cannot derive due to the fact that the generic type might implement PartialEq itself. We would need smth. like this:
impl<T: PartialEq> PartialEq for SomeType<T> {
    // Implement me!
}


Remove deprecated API endpoints by April 1, 2019

GitHub Developer API announcement:
https://developer.github.com/changes/2019-01-29-life-after-github-services/
These deprecated API endpoints need to be removed, preferably by April 1, 2019.
This would be a great PR for any new contributor to this repo or a new Go developer.
All contributions are greatly appreciated!
Feel free to volunteer for any issue and the issue can be assigned to you so that others don't attempt to duplicate the work.
Please check out our CONTRIBUTING.md guide to get started.
Thank you!

Hi @gmlewis , if it is okay with you I would like to ask some questions.
Since the announcement told us that there will be 3 endpoints affected which I found here, does this mean that we are going to replace it by using GitHub Apps?

Yes, that is my understanding from the announcement. Others may have more insights.

For this specific issue, do we need to only remove the codes that use the 3 service hooks endpoints, or including making the GitHub Apps for the hooks?

For this specific issue, only the deprecated endpoints need to be removed.
We have a number of other open (and closed) issues for GitHub Apps webhooks:
https://github.com/google/go-github/issues?utf8=✓&q=is%3Aissue+"GitHub+Apps"


Document review process

There are 3 different docs across which brings misunderstanding. We should merge them into one.
v0.5 Submission rules
v0.6 Submission rules changes
Submission categories

Merged.


Exception-free support?

Can this wrapper be used with fno-exceptions or in environments with exceptions completely disabled? As far as I see, I found only info about exception handling with try-catch, so I would be glad to receive any info about this question

Hello,
sorry but this project has been built with exceptions in mind, around the concept of RAII
Sébastien


testing: first pass at related code api

This adds relatedCode?: readonly Location[]; on the TestItem as discussed in https://github.com/microsoft/vscode/issues/126932, and wires up test decorations to that.

I'm going to rework this


ARROW-11490: [C++] BM_ArrowBinaryDict/EncodeLowLevel is not deterministic

Clearing out previous values before generating new data.  This will allow the benchmark to be more consistent when run with benchmark_repetitions

Thanks for the PR @westonpace, thanks for the review @cyb70289 !


Parsing gives incorrect data instead of failing for unknown format

Parsing '2001W05' (ISO8601 for the fifth week of 2001) with arrow gives you back 2001-05-01 which is totally wrong. Expected behavior is to either parse it correctly or throw an error when it find an unsupported format.
(Followup to #291)

I want to add a couple of examples. They're not ISO8601 related, but perfectly match the issue title.
>>> arrow.get('31.12.2017')
<Arrow [2017-01-01T00:00:00+00:00]>

>>> arrow.get('12/31/2017')
<Arrow [2017-01-01T00:00:00+00:00]>

I would prefer an error in such cases, like in the following case:
>>> arrow.get('31 Dec 2017')
...
arrow.parser.ParserError: Could not match input to any of [u'YYYY-MM-DD HH:mm'] on '31 Dec 2017'

Hi, I'm interested in taking a crack at this issue. Has it been addressed yet?


feat(conceal): conceal \set{} command

conceals usage of the \set{} command, replacing it with curly braces.
sample input:
$$
x \in \set{ 0, 1 }^{*}
$$

unconcealed:

concealed:

i've mostly followed the coding style of the surrounding code, with a few deviations:

use of a regex literal in favor of constructing regex from a string
naming the regex literal setRegex as opposed to the generic symbolRegex used elsewhere
space between : and Concealment[] in the two places where it's used. no space is how it's written from concealFraction, which i based this code off of, but there is a space otherwise for parameter types
single-line if statements are wrapped in braces regardless to make control flow more explicit

Looks good to me, thanks!


Documentation: command-line options

Currently we can only know command-line options by the command line --help option.
Issues #79 and #85 are examples that could have been solved with documentation.

merged #93 and published.

build process: https://readthedocs.org/projects/sphinx-intl/builds/21950993/
build result: https://sphinx-intl.readthedocs.io/en/master/refs.html#sphinx-intl


fix: Correct typo credentials_arn -> credential_arn

Description

Correct typo credentials_arn -> credential_arn

Motivation and Context

Resolves #35

Breaking Changes

No, it wasn't correct to begin with

How Has This Been Tested?

[ ] I have updated at least one of the examples/* to demonstrate and validate my change(s)
[ ] I have tested and validated these changes using one or more of the provided examples/* projects
[x] I have executed pre-commit run -a on my pull request

This PR is included in version 2.1.1 :tada:


x509: certificate is not valid for any names

This is most likely a PEBKAC since I am probably not understanding the instructions correctly, so here's my issue.
I've gotten the CID, GID and bot token and I can start the bridge fine with mumble-insecure set to true. But when I run it with it set to false, it won't connect;
2021/11/24 21:30:59 To Discord Jitter Buffer:  50  ms
2021/11/24 21:30:59 To Mumble Jitter Buffer:  50  ms
2021/11/24 21:30:59 Discord Bot Connected
2021/11/24 21:30:59 Discord bot looking for command !mumble-discord
2021/11/24 21:30:59 CREATE event registered
2021/11/24 21:30:59 bridge starting in constant mode
2021/11/24 21:30:59 Attempting to join Discord voice channel
2021/11/24 21:31:00 Discord Voice Connected
2021/11/24 21:31:00 Attempting to join Mumble
2021/11/24 21:31:00 x509: certificate is not valid for any names, but wanted to match ???
2021/11/24 21:31:01 Bridge died

I did try generate a certificate (which is optional it says) but it doesn't work still. I replaced the mumble address with question marks.

That sounds like an issue with your Mumble host certificate; can you verify that the certificate on your mumble host has the host as its CommonName or SAN? I.e. if the ??? was "mumble.example.com" then the certificate would have "mumble.example.com" as either the CommonName or a SubjectAlternativeName.

@stryan I am not really sure what CommonName or SAN is, but when I view the info of the server and the "Certificate Chain Details", it does say
Issued by:
Common Name: Murmur Autogenerated Certificate v2

You are correct that the address is mumble.example.com.

Ah, you're using the Mumble generated certificate. The auto-generated certificate doesn't actually know what you're calling your server so it doesn't have the right names on it.
I don't think Murmur has a way of automatically generating an actual trusted certificate for your server, though I'm not at home to verify this. So if you're not providing one manually through the
sslCert=cert.pem
sslKey=key.pem

options in Murmur.ini, you'll probably need to use the -mumble-insecure option to connect.
If you want to use the server outside of small-scale or testing purposes, you can grab a free certificate from Let's Encrypt. That will work without the -mumble-insecure option
as a side-note; I do suspect this problem will keep coming up for others. I might take a look at adding some kind of TOFU-style system to the bridge for auto-generated and self-signed certificates. I know Gumble uses something similar for self-signed certs.

I am using this on a very small scale basis (or testing) so that's not a problem really. Thanks for your support, and yeah I think this issue might come up to more people.


Package Structure

Awesome idea and really useful for classes that I teach.
I thought a package structure might be helpful, so I implemented one.
Although spread/gather is not yet implemented, this branch has a slightly different, yet powerful api as it allows the user to specify different datasets as well as the by-argument for joins.
One downside though is that the extra-joins (where multiple observations of y are added) are not yet correctly implemented.
Do you think this will be helpful?
To give you a brief overview:
library(tidyAnimatedVerbs)
#> Loading required package: tidyverse
#> Loading required package: gganimate
#>
#> Attaching package: 'tidyAnimatedVerbs'
#> The following object is masked from 'package:dplyr':
#>
#>     combine

singer <- data_frame(name = c("Mick", "John", "Paul", "Matthew", "Mick"),
                     band = c("Stones", "Beatles", "Beatles", "Muse", "Foreigner"),
                     age  = c(75, 40, 76, 40, 73))

instr <- data_frame(name = c("Mick", "John", "Mick", "Keith"),
                    band = c("Stones", "Beatles", "Foreigner", "Stones"),
                    plays = c("guitar", "bass", "guitar", "guitar"))

singer
#> # A tibble: 5 x 3
#>   name    band        age
#>   <chr>   <chr>     <dbl>
#> 1 Mick    Stones       75
#> 2 John    Beatles      40
#> 3 Paul    Beatles      76
#> 4 Matthew Muse         40
#> 5 Mick    Foreigner    73

instr
#> # A tibble: 4 x 3
#>   name  band      plays
#>   <chr> <chr>     <chr>
#> 1 Mick  Stones    guitar
#> 2 John  Beatles   bass
#> 3 Mick  Foreigner guitar
#> 4 Keith Stones    guitar

animate_left_join(singer, instr, by = c("name", "band"), text_size = 5)

Created on 2018-08-22 by the reprex package (v0.2.0).

One small update: joins with extra rows are now fully supported.
Also the user can tweak the plots easier:
library(tidyAnimatedVerbs)
#> Loading required package: tidyverse
#> Loading required package: gganimate

singer <- data_frame(name = c("Mick", "John", "Paul", "Matthew", "Mick"),
                     band = c("Stones", "Beatles", "Beatles", "Muse", "Foreigner"),
                     age  = c(75, 40, 76, 40, 73))

instr <- data_frame(name = c("Mick", "John", "Mick", "Keith"),
                    band = c("Stones", "Beatles", "Foreigner", "Stones"),
                    plays = c("guitar", "bass", "guitar", "guitar"))

singer <- singer %>% slice(c(1:3, 1, 5))
instr <- instr %>% slice(c(1, 1:3))

singer
#> # A tibble: 5 x 3
#>   name  band        age
#>   <chr> <chr>     <dbl>
#> 1 Mick  Stones       75
#> 2 John  Beatles      40
#> 3 Paul  Beatles      76
#> 4 Mick  Stones       75
#> 5 Mick  Foreigner    73
instr
#> # A tibble: 4 x 3
#>   name  band      plays
#>   <chr> <chr>     <chr>
#> 1 Mick  Stones    guitar
#> 2 Mick  Stones    guitar
#> 3 John  Beatles   bass
#> 4 Mick  Foreigner guitar

animate_left_join(
  singer, instr, by = c("name", "band"),
  text_size = 5,
  text_family = "LM Roman 10",
  title_size = 15,
  title_family = "LM Roman 10",
  color_fun = viridis::magma,
  color_other = "#decbe4",
  color_header = "#525252"
)

Created on 2018-08-22 by the reprex package (v0.2.0).

Wow, @DavZim! I'm really impressed by the amount of work you put into this! I normally do my work inside a package structure, but I didn't think there would be a need this time. Thank you for proving me wrong! :smile:
I really like that the user can now specify arbitrary data frames to animate and the number of parameters that can be tweaked in the plot output. There are a few places where I animated the operations using three key frames that I like a little more, but I think it's a reasonable trade-off for the ability to easily change the input data.
How would you like to work together? I like the direction and think a package structure is a good idea, so we definitely agree there. I'm happy to dig into the code whenever you're ready, but I don't want to get in your way if you're actively working on it still. As far as working together, I'm happy with anything from taking over completely when you're done (or tired of working on this) through letting you take the lead and providing input via code review. Just let me know what you'd like.
As some quick thoughts overall:

Would it be possible to parameterize the inclusion of the column headers? I think in certain cases it looks better without them.

There's some cleaning up to do around the use of ... to make sure that they are used or that the additional arguments are passed to the right functions. It seems like animate_join() passes ... to multiple functions and we might need to make sure the extra arguments end up in the right place.
You can also use #' @inheritDotParams <function name> to automatically generate documentation for those parameters (in place of #' @param ... passed to <function>).

There are a few references to base_plot() in the documentation that I think should be static_plot().

Oh and definitely at a minimum can you update the DESCRIPTION to include your information?

Glad that you like it :)
True, the three-piece movement makes understanding the operation easier. I think that could be implemented at one point.
For now, I would try to finish the gather/spread functionality, then I think we can try to merge the branches or at least go into more detail with code review etc.
Given that its night over here (Europe), I think I will try to finish that tomorrow.
My goal is to also supply basic information for something like filter, mutate, summarise, group-by mutate & summarise, and maybe separate and unite. And maybe in the longer run a small shiny app that the user can see the functionality with different datasets for different cases (i.e., the extra matches in joins).
That would make it a lot easier for me to teach dplyr/tidyverse-functionality.
Regarding your points: the ellipsis was more of a brute force approach than precision, so we should try to clean that for sure :D
I haven't used ellipsis too much, therefore I am unsure what exactly to do. Once this branch is up to date we can go into this.
Overall, I am definitely happy to work together. Again, right now I would like to finish the background for the gather/spread functionality, then we can move forward together.
Looking forward to it!
Best,
David

I've added the animate_gather and animate_spread functions.
I think we can try to move it forward by merging the branches. Also, if you find some time you can change/update the code.
One of the biggest issues right now is that the new animate tidy functions do not pass the ellipsis through.

library(tidyAnimatedVerbs)
#> Loading required package: tidyverse
#> Loading required package: gganimate
long <- data_frame(
  year = c(2010, 2011, 2010, 2011, 2010, 2011),
  person = c("Alice", "Alice", "Bob", "Bob", "Charlie", "Charlie"),
  sales = c(105, 110, 100, 97, 90, 95)
)
wide <- data_frame(
  year = 2010:2011,
  Alice = c(105, 110),
  Bob = c(100, 97),
  Charlie = c(90, 95)
)

animate_spread(long, key = "person", value = "sales")

Created on 2018-08-23 by the reprex package (v0.2.0).

Very cool! I love how slightly different approaches to laying out the animation and movement lead to complimentary visualizations of the process. Like how we ended up with two similar animations for spread/gather but that are also different in a way that highlights different parts of the action.
I think it would be good to take a small step back and look at the overall structure. I'm interested to see what you think, but for me the three key steps to solve for these types of animations is

The layout of the data at each key frame

In part this is specific to the animated function (i.e. left_join() vs right_join()
On the other hand, the process of laying out a data frame for ggplot is the same except for translations in the x or y dimensions

Adding extra elements to key frames so that all objects are tracked throughout the animation (e.g. move to the right place)
Tweaking the plot or animation output (e.g. tweaking enter/exit behavior, ease_aes() or plot labels)

From a quick look through the code it seems like we're headed in this direction although maybe not completely there. I think that one of the benefits of making this a package rather than a collection of "hand-crafted" scripts is that we can add an additional layer of abstraction that will make it easier to build out more animations (for things like filter, mutate, etc.).
It's hard to tell from looking at the GitHub diffs (hoping to pull the code and dig in soon), but how much overlap is there between underlying functions among the "joins", "sets" and "gather/spread" animations? To be more concrete, which functions would you use to build a new animation in a different class (say filtering)? Is there a function that handles the core of step 2, or is this logic different for each animation group?
As a final question, if you could quickly describe the function layout as it is now, that would be very helpful to orient me as I dive in.
Thanks again!

The underlying structure is definitely something that we need to think about.
My general goal was to first process the data using processing_long or processing_wide, or the process_join function for sets/joins.
 That is the .x, .y values for plotting, colors, ids, etc. (a nice gimmick is that the processed data can be immediately plotted using static_plot).
I would love to cut the number of preprocessors but didn't find a solution yet.
The major issue is here that we need to be able to id each element of a plot (best in a standardised way). I tried this using the variables .id_map (linking in a spread/gather function to the id, i.e., year in the example) and .key_map (linking to the respective key), as well as the element type in .type. But I feel this is hard to generalize for different data structures.
The outputs are then used in the higher functions animate_join/animate_set or gather_spread, where the movement is coordinated.
A basic Minimum Working Example is provided here: https://gist.github.com/DavZim/2e829ae24b2e272c409899e01d420479
All joins/sets are done in a single movement, whereas the gather/spread functions take multiple steps (for each key-value one to be precise, plus initial and final states) if detailed = TRUE in animate_gather/spread. This handling is done in the gather_spread helper function.
To summarise:
The user can call animate_* functions that all take more or less the same inputs (depending on the function it may take a by argument or keys/values).
The idea is to have data-processors (specific to the different type of function, joins+sets, long, and wide format) that transform the data into a standard format. Then we have a move_together function for the joins or use the gather_spread function for gather/spread that handle the movement of the tiles.
Colorings are done in add_color_join/tidyr.
To answer your question, all functions have a similar structure, but are not (yet?) interchangeable. For a new function (say group_by + summarise), one would need to specify a process-function that converts the input data into the processed form (with plotting information and all), and a second function that then specifies how the different steps (from input (or lhs) to output (rhs)) are displayed. If we find a unifying approach, that would be awesome.
Drawbacks/stuff to improve.
I think I was a bit sloppy at designing the structure of the processed data, i.e., the data from joins/tidyr looks quite different to me now, and sometimes it needs to have multiple entries so that entries do not disappear, this is something that we could improve using nested data-frames, where we save the idea.
Ellipsis ... are not carefully done as you mentioned earlier. Currently the tidyr-functions do not pass them on at all...
closely related: the ... arguments in animate_gather are not fully working (working for one case at least). In the future this should work as well animate_gather(wide2, key = "person", value = "sales", -year, -region) or animate_gather(wide2, key = "person", value = "sales", -year:region)

Also a minor thing: I didnt figure out how to make the output for the tidyr-functions as pretty as yours/as the joins...

@DavZim Holding off on merging for now in case you have few more updates to push. Let me know when this is ready to merge into a pkg branch (see #12)

I think you can merge as I don't have any updates currently. bind_cols and bind_rows prove to be a bit more complicated to integrate them into the join-family. It might be easier to write new functions.

@DavZim Okay, I merged this pretty much as-is into the pkg branch.
The biggest thing I changed was not depending on the tidyverse and starting to think about global imports.
This probably broke the package, but mostly because we need to add the package name qualifiers to non-imported packages. Anywhere that the code breaks for this reason should require a qualifier. E.g. gather(df, key, val) will need tidyr:: added.
Also I didn't add stringr to Imports so that we can remember to replace those functions with base R, until that's fixed we can just library(stringr) around it.


Add info about Kafka partitions to Kafka Source for tracing purposes

Problem
A short explanation of the problem, including relevant restrictions.
For users of Kafka eventing source who want to understand the performance of their system running eventing with Apache Kafka in various cluster setups like single/multi tenant, single/multi regions etc or for troubleshooting reasons, it will be helpful to provide some partition information (below) to kafka source since only kafka consumer knows form which partition it is reading from. Will be useful to also understand the impact of broker rebalancing from Kafka on eventing. Some useful info are:

How the x events being consumed by a Kafka source/consumers were spread across the y partitions in that topic?
Partition number that an event was consumed from by a consumer (vreplica) and any other metadata could be added?
Other Kafka broker details?

This can be optional information added (users can turn on/off this detail)
Persona:
Which persona is this feature for?
Exit Criteria
A measurable (binary) test that would indicate that the problem has been resolved.
Partition info for each event or group of events is visible in the source, and can be consumed by tools like KPerf to measure performance.
Time Estimate (optional):
How many developer-days do you think this may take to resolve? Unknown
Additional context (optional)
Add any other context about the feature request here.
Partition-id could be added as key-value pair to tracestate in https://github.com/cloudevents/spec/blob/v1.0.1/extensions/distributed-tracing.md#tracestate (info from @aslom )

Setup tracing config with zipkin backend for Kafka source and this is all the info (key/value pairs) being forwarded under Tags.

There is no info about the Kafka producer + partitions...

this is relevant: https://github.com/open-telemetry/opentelemetry-specification/blob/main/specification/trace/semantic_conventions/messaging.md#apache-kafka
In particular messaging.kafka.partition

/remove-lifecycle stale

/remove-lifecycle stale

/reopen


discovery(engine): refactor agent to use list api

What problem does this PR solve?

Issue Number: ref https://github.com/pingcap/tiflow/issues/6867
What is changed and how it works?
Refactor discovery.Agent to use ListMasters and ListExecutors API.
Check List
Tests

Unit test
Integration test
Manual test (add detailed scripts or steps below)
No code

Questions
Will it cause performance regression or break compatibility?
Do you need to update user documentation, design documentation or monitoring documentation?
Release note
None

Codecov Report

Merging #6891 (24c6253) into master (7c5032c) will decrease coverage by 5.4571%.
The diff coverage is 50.6686%.

Flag
Coverage Δ

cdc
?

dm
52.0523% <52.6690%> (+0.0537%)
:arrow_up:

engine
62.5105% <49.2346%> (-0.1249%)
:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.
@@               Coverage Diff                @@
##             master      #6891        +/-   ##
================================================
- Coverage   59.9224%   54.4653%   -5.4572%
================================================
  Files           783        417       -366
  Lines         89519      51620     -37899
================================================
- Hits          53642      28115     -25527
+ Misses        31168      20818     -10350
+ Partials       4709       2687      -2022

/merge

/run-leak-test


About SPECIFIERS in Custom log

Hi
I have 2 questions about that https://goaccess.io/man#custom-log

Should all the following 3 fields be used in one command?

GoAccess requires the following fields:
a valid IPv4/6 %h
a valid date %d
the request %r
I saw in some links that all 3 did not come in one order, But it is required in the document.

Is there any use of duplicate SPECIFIERS in the command?
When we have two parameters with a byte value, Or we have 3 different durations

we can use commands like this?
goaccess access.log --log-format='{ "time": "%dT%t+%^",  "byte_out": "%b",  "byte_in": "%b", "delivery_duration": "%L", "connection_duration": "%L", "total_duration": "%L"  }' --date-format='%Y-%m-%d' --time-format=%T
thanks

Hi, regarding your questions.

Yes, those fields are required.
You can use a specifier multiple times, however, only the last one will prevail.

about question two:
it's that mean only the last one will be analyzed and shown on the output?
and others have no effect on output?
if send or show one example will be great.

That's correct. I'd not use the same specifier multiple times, thus I don't have an example to show. Please pair a field with only one specifier.


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Feature/lit 2494 js sdk get rid of lit third party libs

Description
This PR removes the lit-third-party-libs completely and uses Lit Action to hash data to ipfs cid instead. This is the repo that bundles the package.
Type of change

[x] Reduce bundle size & redundancy

How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

[x] e2e

yarn test:e2e:nodejs --filter=test-lit-action-get-ipfsid.mjs

yarn test:e2e:nodejs --filter=test-lit-action-run-target-node.mjs

Checklist:

[] My code follows the style guidelines of this project
[] I have performed a self-review of my code
[ ] I have commented my code, particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation
[ ] My changes generate no new warnings
[ ] I have added tests that prove my fix is effective or that my feature works
[ ] New and existing unit tests pass locally with my changes
[ ] Any dependent changes have been merged and published in downstream modules

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you all sign our Contributor License Agreement before we can accept your contribution.1 out of 2 committers have signed the CLA.:white_check_mark: Ansonhkg:x: cairomassimoYou have signed the CLA already but the status is still pending? Let us recheck it.


Run tortoise 30 seconds into the layer

Today the tortoise is being fed on a layer's tick with blocks from the previous layer. In addition, late blocks are considered "late" (not for hare) only if they are published not within their layer timeframe.
Since all honest blocks should arrive within delta time (propagation limit = 30 seconds) from the layer's tick, we can let the tortoise eat blocks after delta time. All other blocks should be considered late.
The benefit is that we get confirmation 4:30 minutes earlier compared to today, and also classify late blocks correctly.
Note that Hare CPs start exactly after 30 seconds, so we should consider this before implementing.

#1860

lets wait with the whole hare cp thing till we have proof its a problem

Done https://github.com/spacemeshos/go-spacemesh/pull/1860


The number of matched key points is not stable

AKAZE2 sporadically loses some descriptor matches.
$ ./akaze_match.exe img1.ppm img4.ppm H1to4p --descriptor 5
AKAZE_Impl2 constructor called
AKAZE_Impl2 constructor called
AKAZEFeaturesV2 constructor called
hardware_concurrency: 8
AKAZEFeaturesV2 constructor called
hardware_concurrency: 8
Number of Keypoints Image 1: 1822
Number of Keypoints Image 2: 1091
A-KAZE Features Extraction Time (ms): 120.327
Matching Descriptors Time (ms): 16.2663
Number of Matches: 959
Number of Inliers: 889
Number of Outliers: 70
Inliers Ratio: 92.7007

$ ./akaze_match.exe img1.ppm img4.ppm H1to4p --descriptor 5
AKAZE_Impl2 constructor called
AKAZE_Impl2 constructor called
AKAZEFeaturesV2 constructor called
hardware_concurrency: 8
AKAZEFeaturesV2 constructor called
hardware_concurrency: 8
Number of Keypoints Image 1: 1822
Number of Keypoints Image 2: 1091
A-KAZE Features Extraction Time (ms): 122.356
Matching Descriptors Time (ms): 16.2488
Number of Matches: 957  <--- OOPS TWO LESS!!
Number of Inliers: 889
Number of Outliers: 68  <--- OOPS TWO LESS!!
Inliers Ratio: 92.8945

The following commit is to fix this issue.

59a800f Fix the bug that the last byte of desc[] is partially not initialized

The fix has been verified by the reporter, so I'm closing the issue.


CUDA out of Memory

System Specs: Ryzen 9 5900HX, NVidia 3070 Mobile, Arch Linux (EndeavorOS) on Kernel 5.17.2
Whenever I try to run a model that is relying on CUDA, for example cugan, the program exits with

Error: Failed to retrieve frame 0 with error: CUDA out of memory. Tried to allocate 148.00 MiB (GPU 0; 7.80 GiB total capacity; 5.53 GiB already allocated; 68.56 MiB free; 5.69 GiB reserved in total by PyTorch)

and stops after having output 4 frames.
However, TensorRT works fine for models that support it (like RealESRGAN for example).
Edit: Running nvidia-smi while the command is executed reveals that vspipe is allocating GPU Memory, but <2 GiB of VRAM, far from the 8GiB my model has.

Different models and implementations have different requirements. In it's current state, cugan does have tiling added, so you can just adjust the tiling size. I did hear that 8gb vram was not enough for higher resolutions for ond person though, so your gpu might not even be sufficient and you would need to accept it. I was mainly testing with 16gb vram.

Thank you for the explanation. I will try adjusting the tiling size and report back on my findings.
If I may ask; if the amount of VRAM my GPU has is the problem on CUDA Models, why does TensorRT work?

The architectures cugan and esrgan are fundamentally different. Not only the backend plays a role in vram usage.

I guess I can close this issue, since this is just a hardware limitation.


Document differences between file-based Cordova app vs HTTP(S) web app

While most apps would be based on a http: or https: origin domain, a Cordova app would be based on some kind of a file:// index URI path. I think both this difference and the potential consequences are not clear at all in the Cordova documentation. Examples of potential consequences include:

Problems with postMessage call such as https://github.com/apache/cordova/issues/177
CORS (??? ???)

It seems to be not 100% clear that a script tag to include cordova.js is needed when embedding an existing SPA web app in Cordova (see issue #852)
etc. etc.

Also related: #943 - improve WebView documentation


Reintroduce a LOOSE SemverType again

In contrast to @vdurmont's original, this library has only SemverType.STRICT. Which means there is no elegant way to make
RangesListFactory.create("[1.0.0,2.0.0]").isSatisfiedBy(Semver("1.23")) == true

if the version string "1.23" is user-provided. However, "1.23" could be trivially fixed to be a Semver by appending ".0" so it reads "1.23.0", and it would be nice if this library could do this internally in a LOOSE mode.

Maybe it's a time for this removal and should be done to reduce misunderstandings 🤔

I agree. Anyway, let me close this issue, as it's resolved.


Feature: Implement Default Parameters Requirements

Problem
Currently the only "requirements" of the the BaseLayerParams.default_parameters property is that it is of type DefaultParams: https://github.com/DiogenesAnalytics/autoencoder/blob/ca2c35b185c0c106b282d6bea6077aa7ba04c3cf/src/autoencoder/model/base.py#L16-L62
But there will likely be a need for even more intense requirements of this data structure (i.e. in order to determine which layers are input, encoding, decoding ...).

Solution
This can be resolved by simply flipping the instance dict with the default parameters dict:
# loop over layer_name/params in defaults
for layer_id, params in self.default_parameters.items():
    # now find corresponding layer_id in constructor args
    try:
        yield layer_id, self.__dict__[layer_id]
    except KeyError as error:
        raise KeyError(
            "Constructor arguments must match "
            "the keys of the default_parameters dictionary."
        ) from error

Implemented with:<PHONE_NUMBER>d414459a9762f879e744d29521a82c


unknown option protein

Hi,
The following (attachment error is obtained when I attempt to dock:

I am a novice. Kindly help resolve the error. Thank you.

Hi, that unknown option in the config.txt file

@diogomart thanks for the reply. So this is how my config file looks like:

is there something that I am missing here which requires rectification?

Hi @dnapolren
The words you use in config file need to match exactly with the given names in the help message (protein -> receptor, centre -> center)

@rwxayheee thank you so much. will work on it.

Thank you all. The suggestions worked. :)


Does not work in Version 4.0.2

Python: Traceback (most recent call last):
File "C:\Users\myw\AppData\Roaming\Blender Foundation\Blender\4.0\scripts\addons\Rhino-to-blender-main_init_.py", line 339, in execute
bpy.ops.export_scene.obj(filepath=os.path.join(os.path.dirname(file), 'assets', 'Blender to Rhino-mesh.obj'), use_selection=True,axis_forward='Y',axis_up='Z')
File "D:\blender-4.0.1-windows-x64\blender-4.0.1-windows-x64\4.0\scripts\modules\bpy\ops.py", line 109, in call
ret = _op_call(self.idname_py(), kw)
AttributeError: Calling operator "bpy.ops.export_scene.obj" error, could not be found

Same problem, but I have "line 64" instead of line "339"

Fixed!! https://github.com/chenpaner/Rhino-to-blender/releases/tag/1.1.1


input width in designer

noticed that the width of a new property i am working on is not set to 100%.

turns out I am passing in the wrong setWidth flag for controls in TabsView, so I did a refactoring and removed the unnecessary flag and use the view parameter instead.

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 41.61%

Totals

Change from base Build<PHONE_NUMBER>:
0.0%

Covered Lines:
27086

Relevant Lines:
59040

💛  - Coveralls


Using useCookie in server plugin results in unhandledRejection on 404 pages

Environment
Node 18.15.0
Nuxt 3.4.3
Reproduction
Create a page and use  in app.vue
Create server plugin that uses useCookie
Go to an unknown page
GOOD
Nuxt 3.4.3 without using useCookie shows 404 fine
source: https://github.com/hecktarzuli/nuxt-bugs
url: https://nuxt-bugs.vercel.app/foo
BAD
Nuxt 3.4.3 using server plugin with useCookie shows 500 in vercel (crash) / 200 in dev for pages that should be 404.
source: https://github.com/hecktarzuli/nuxt-bugs/tree/usecookie-server-plugin-no-404
url: https://nuxt-bugs-ldou8053t-hecktarzuli.vercel.app/foo

Vercel Crashes

Dev Exception

Describe the bug
When reading a cookie via useCookie in server plugin, if you hit a 404 page it throws an unhandled exception.  Plugins should be able to read and set cookies on 404 responses.
Additional context
This seems to work fine in 3.4.2
Logs

In fact, your problem is essentially the same as the one I encountered (https://github.com/nuxt/nuxt/issues/20578)
Because useCookie is also add app:error hook.
https://github.com/nuxt/nuxt/blob/1464294d6abe13b54fdb8d204732345551c8e647/packages/nuxt/src/app/composables/cookie.ts#L55

Let's track it there.

same problem.
------------------------------
- Operating System: Darwin
- Node Version:     v20.13.1
- Nuxt Version:     3.11.2
- CLI Version:      3.12.0
- Nitro Version:    2.9.7
- Package Manager<EMAIL_ADDRESS>- Builder:          -
- User Config:      devtools, modules, plugins, nitro, image, colorMode, tailwindcss, eslint, ui, typescript, supabase, runtimeConfig, routeRules, vite, security
- Runtime Modules<EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS>- Build Modules:    -
------------------------------


Include Fonts in Examples

This PR include the examples' fonts in the function itself to ensure they are embedded on export

When exporting the business card type is exported and seen correctly, but for the IG posts:
https://user-images.githubusercontent.com/13511560/141500639-4412615b-5b47-4d91-b31c-818e9bc38d2b.mov

that is odd because the code is exactly the same in both.

I haven't changed a thing, tested and it works as expected.
Can you give it another try? The right version should have a folder /assets/ with the fonts inside, and a styles.css file with the font-face references.

Hey! I just did and yeah, it's that set up and I also checked that I yalc-ked correctly. I just did again twice and same thing. Just to clarify, the preview in the tool it self shows the font correctly, it's just the video export the one that isn't showing the typeface.

@fdoflorenzano try again.