[Fix] mlflow attr

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Motivation
This PR is written to update the attributes used in the mlflow callback class due to the update of the Ray framework to a new version.
Modification

Updated the self.client and self.experiment_id attributes.
Changed self.save_artifact to self.should_save_artifact.

Checklist

Pre-commit or other linting tools are used to fix the potential lint issues.
The modification is covered by complete unit tests. If not, please add more unit test to ensure the correctness.
If the modification has potential influence on downstream projects, this PR should be tested with downstream projects, like MMDet or MMCls.

The documentation has been modified accordingly, like docstring or example tutorials.

Codecov Report

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Patch has no changes to coverable lines.

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #135   +/-   ##
=======================================
  Coverage        ?   61.65%
=======================================
  Files           ?       63
  Lines           ?     1961
  Branches        ?      312
=======================================
  Hits            ?     1209
  Misses          ?      648
  Partials        ?      104

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UI elements won't update asynchronically

I'm a bit lost. In order to update the UI after an asynchronous task finished, the following event handlers return False (no page update) and call update() after modifying the UI elements. But somehow the UI does not refresh.
import asyncio
import justpy as jp

def create_page():
    wp = jp.WebPage()
    container = jp.Div(a=wp)

    def change(self, msg):
        async def change_async():
            change_div.text += '!'
            await container.update()
        asyncio.get_event_loop().create_task(change_async())
        return False

    def insert(self, msg):
        async def insert_async():
            jp.Div(text='a new div', a=container)
            await container.update()
        asyncio.get_event_loop().create_task(insert_async())
        return False

    change_div = jp.Div(text='Change this div!', a=container, on_click=change)
    insert_div = jp.Div(text='Insert new div!', a=container, on_click=insert)

    return wp

jp.justpy(create_page)

When removing return False, the elements get updated, but show an outdated state from before the tasks finished.
What am I doing wrong?

Since you are updating a Div and not a WebPage, you need to add temp=False when creating container so that justpy will assign an id to it and you need to tell container which pages it is on:
container = jp.Div(a=wp, temp=False)
container.add_page(wp)

This is discussed here: https://justpy.io/tutorial/pushing_data/#simple-message-board

Oh, I see. Thanks for your help!
I read about temp=False some time ago, but wasn't aware that it is crucial in this case.
And I thought a=wp is equivalent to add_page(wp) - like a=container and container.add(...) seem to be.

It is very difficult to determine automatically which page a component is on. The component can be added to another component that then is added to another component and so on until a component is added to a page. a=wp is just shorthand for add. This adds a component to another component or page as a direct child. add_page is something different. It is a mechanism for the programmer to tell the framework on which pages it will find the component if it wants to just update the component.


Feature/python cicd

Description
This pull request adds a github action that would automatically build and upload OpenCC python packages to PyPI.
The goal is to make the process of deployment smoother and much less of a hassle than it is right now.
Currently, the action is setup to be triggered manually (though it can be modified to be executed on new releases etc.).
Just 1 additional thing would need to be done. @BYVoid @sgalal would have to help configure the package secret PYPI_TOKEN.
This was a long-overdue feature that I've only just had time to work on.
It was briefly mentioned on https://github.com/BYVoid/OpenCC/issues/477.
Changes

Added new github action Build and upload python package to PyPI
Added new shell scripts to facilitate the building and uploading of python packages

release-pypi-linux.sh
release-pypi-macos.sh
release-pypi-windows.sh

Removed previous helper scripts used for python packaging.

bdist_array.sh
bdist_array.cmd
BUILD.md
python/Dockerfile.posix

Looks good! Since I do not have access to PyPI I cannot get the token. Need help from @BYVoid

Thank you very much. @mingruimingrui, since you have the PyPI admin access, can you suggest how to set up the PYPI_TOKEN?

@BYVoid Thanks, however, I can't add the secret to this repository.
I'll add some instructions to help you out.

Create a new token at OpenCC PyPI repository settings.
https://pypi.org/manage/project/opencc/settings/

Navigate to OpenCC GitHub repository settings and find the secrets in the sidebar.
https://github.com/BYVoid/OpenCC/settings/secrets
There should be some New Secret button. Use it to add the PYPI_TOKEN secret.
Make sure the name is PYPI_TOKEN and the value is the token generated from PyPI.

Thanks. Done.


Ansible 101 Live Stream Episode 7 Agenda - May 6

Previous episode agenda: #244
Video link: https://www.youtube.com/watch?v=FaXVZ60o8L8

[x] Thank you SO MUCH to GitHub Sponsors and Patreon Patrons:

GitHub: @mglaman, @daverunscouk, @matthewcosgrove
Patreon: @mgrennan, Deanna P

[x]  Questions and notes from last week's episode:

Baptiste M-M: "Any hints when a team work on a same playbook, is there any way to avoid password sharing ?"

See Vault docs — including --vault-id which can allow multiple passwords for a vault (e.g. dev vault or prod vault) (thanks to Yann L for pointing that out!)

Rolling Pictures: "dumb question: do we need any config mgmt tool like Ansible if we are working in Docker?"
Patrick Köll: "should i structure the playbooks as roles or would you recommend using collections?"
StormWolf01: "To anyone who doesn't have access to an EC2 instance, just just launch a VM with vagrant, as shown in the previous tutorial, and have the ansible playbook executed on that VM. This seems pretty obvious, but it took me 10 minutes to realize." (link)
Aaron Kulbe: "How long are you going to continue the live streaming past Device42 sponsorship?" (🤷♂)

[x] Ansible Galaxy (chapter 6)

[x] See my AnsibleFest presentation: There's a Role for That!

[x] Testing Ansible Playbooks with yamllint, ansible-lint, and Molecule (chapter 11, sorta; see #101)

Next agenda: #261 — great video today, woohoo!


python310Packages.universal-pathlib: 0.0.24 -> 0.1.0

Changelog: https://github.com/fsspec/universal_pathlib/releases/tag/v0.1.0
Description of changes

Things done

Built on platform(s)

[x] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[x] Tested basic functionality of all binary files (usually in ./result/bin/)
23.11 Release Notes (or backporting 23.05 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

Result of nixpkgs-review pr 246971 run on x86_64-linux 1

10 packages built:

browsr
browsr.dist
python310Packages.textual-universal-directorytree
python310Packages.textual-universal-directorytree.dist
python310Packages.universal-pathlib
python310Packages.universal-pathlib.dist
python311Packages.textual-universal-directorytree
python311Packages.textual-universal-directorytree.dist
python311Packages.universal-pathlib
python311Packages.universal-pathlib.dist


devede broken on 19.03

Issue description
The devede package is broken in 19.03.
Steps to reproduce
~> nix-shell -p devede --run devede_ng.py
Traceback (most recent call last):
File "/nix/store/545kqgnp1qaz9fx5lh1vjq2341h26mps-devede-4.8.8/bin/..devede_ng.py-wrapped-wrapped", line 22, in
gi.require_version('Gtk', '3.0')
File "/nix/store/9jyqlkf8q1disirs79pqh5pwcdxhmd9f-python3.7-pygobject-3.30.4/lib/python3.7/site-packages/gi/init.py", line 129, in require_version
raise ValueError('Namespace %s not available' % namespace)
ValueError: Namespace Gtk not available
Technical details
Please run nix-shell -p nix-info --run "nix-info -m" and paste the
results.

system: "x86_64-linux"
host os: Linux 4.19.36, NixOS, 19.03.172347.7936400662b (Koi)
multi-user?: yes
sandbox: yes
version: nix-env (Nix) 2.2.2
channels(root): "nixos-19.03.172347.7936400662b"
channels(aaron): ""
nixpkgs: /nix/var/nix/profiles/per-user/root/channels/nixos

@aanderse See https://github.com/NixOS/nixpkgs/issues/56943.
You need to disable strictDeps like the commits that reference the issue until we can fix it.

Yeah I have seen one of these already and didn't have time to test/fix this tonight so just wanted to get it logged. I'll self assign and circle back to this hopefully in the next few days.

@worldofpeace in this case adding strictDeps = false; did not fix the issue, but adding gobject-introspection to buildInputs did.


Pretty-print json body

Detailed Description
This is separate/additional to the log format. 'http' format works for me for showing headers, but when a body comprised of json is logged it's all in one line with no line breaks or indentation.
This would apply to the 'json' log format too, I'm not sure if in this case the entire output should be pretty-printed or just the body.
Context
I work with a Spring Boot webservice which returns large bodies of deeply nested json, currently it is output as one long line so to make sense of it I need to copy/paste it into some editor and use its formatting tool.

Thanks.
I prefer the http output rather than json. It would be quite easy to add formatting to application/json bodies using Jackson at the point you linked to in DefaultHttpLogFormatter but I'm not sure that all users would want that.
I could subclass it for my own personal use - if you'd consider making the class non-final and some of the methods non-private - but that's not a contributable solution.
How about adding pluggable body formatters? A new interface BodyFormatter, property Map<mime type, BodyFormatter> and accompanying method addBodyFormatter() might be enough.
At a later date, if it's used enough, add a config property to provide the Map.

if you'd consider making the class non-final and some of the methods non-private

I'm not a big fan of implementation inheritance. For now the pattern for extending formatters is to compose them and use the prepare methods directly (which are exposed). In order to allow a custom body formatting, we would need to expose some more of those internals.

Actually this was relatively easy to do by adding a BodyFilter. I'm using Spring Boot so I override the default BodyFilter bean with one that merges with it.
https://gist.github.com/molexx/0ef227a7f7299a6aacb04f9d44559af8
Feedback welcome :-)

That's a pretty good use of a BodyFilter. @nsmolenskii actually contributed a body filter that implements compacting, see #357. Might be even worth adding your pretty-print filter as a built-in filter, but that requires that we fully extract the compacting from the formatter, see https://github.com/zalando/logbook/pull/357#issuecomment-427754680.

See also #361.

Are you intending on making the compacting body filter part of the default?

Yes.

If so then I should probably not merge with the default otherwise the body will be compacted and then pretty-printed which is inefficient.

Yes, that's true.

but I would want the max length filter which is currently set in LogbookAutoConfiguration.java.

I'd go with a pure programmatic configuration in that case:
merge(prettyPrintJson(), truncate(80));

Maybe an array of BodyFilters could be added to the config yaml?

I'd limit the configuration to a really small use case and let users go crazy with a programmatic configuration.

@molexx Would you care contributing your pretty print filter to the 2.x release?

Sure, but I'll be a few days. Feel free to copy/paste from my gist in the meantime.

No pressure, take your time.


global do_exec to help linters and humans understand the code

Declaring global do_exec will help both linters and humans understand that do_exec() is defined in the exec() call.  Discovered via #104.

Aha, now it makes sense!


enh: new tmq get raw response

Codecov Report
Attention: Patch coverage is 85.08772% with 17 lines in your changes missing coverage. Please review.

Project coverage is 68.80%. Comparing base (fbc4aa0) to head (0f51c18).

Files
Patch %
Lines

controller/ws/tmq/tmq.go
85.08%
11 Missing and 6 partials :warning:

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #318      +/-   ##
==========================================
- Coverage   68.85%   68.80%   -0.06%
==========================================
  Files          85       85
  Lines        9730     9805      +75
==========================================
+ Hits         6700     6746      +46
- Misses       2352     2377      +25
- Partials      678      682       +4

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


Update equations in ./notes/SD3_zh-CN.md

Some eqations could be interpreted by the Github, please check the reason and update it

I think I might be able to fix these issues.


refactor: Query classes and related code

In this PR:

Query class has been renamed DeepRankQuery and converted into a dataclass and all common arguments are defined in the parent class instead of the children.
ProteinProteinInterfaceResidueQuery and ProteinProteinInterfaceAtomicQuery were merged into a single child dataclass of DeepRankQuery, as were SingleResidueVariantResidueQuery and SingleResidueVariantAtomicQuery

resolution is now given as a keyword instead of being a separate class

Moved as much as possible into parent class

unbound functions were unified and made internal methods of parent.
unused/obsolete functions removed

code related to adding hydrogens
_get_atom_node_key function
potentially more

build function is largely defined in parent class, with specifics defined in child class as internal _build_helper methods.

it feels like build function could be further unified, but my tests doing this kept failing.

Reorganized module

QueryCollection at the bottom now

Update external modules

tests
docs
notebooks
etc

Not yet done:

Unify build_atomic_graph and build_residue_graph from buildgraph.py (#506)
Separate radius from distance_cutoff for PPI Queries (#504)

fixes: #480 and #490
Final TO DO list:

[x] Move parameters to parent class
[x] Switch to dataclasses
[x] Unify atomic and residue version of each query into one

[x] fix all tests, linting, READMEs, notebooks until here

[x] Move as much as possible into parent class

[x] Make main build function in parent, have specific helper functions in child classes.
[x] Remove unbound functions or make them methods or parent if still useful.
[x] Unify build methods for PPI and SVR (if possible)

[x] Make sure all tests and external modules work with new classes
[x] Update docstrings

[x] Check how this should work with inheritance, what is listed in which docstring, etc
[ ] Check if it's possible to inherit docstrings.

Haven't found a nice way of doing this.

[x] Check for all methods as well (not all necessarily require one).

[x] Remove code related to inlcuding hydrogens

[x] check that this is indeed OK

[ ] Clarify distance_cutoff vs radius across different Query classes (see here)

Moved to PR #504 instead

[x] Resolve conflicts with #497

[x] Potentially others

[x] Check all #TODOs throughout script
[ ] Refactor duplicate code from buildgraph module

Will be a new PR for issue #506

reopened as #486

How do you feel about current class names? They are a bit long.
Other options are

ProteinProteinInterfaceQuery and SingleResidueVariantQuery (current)
PPIQuery and SRVQuery (starting capitals are a bit odd maybe)
PpiQuery and SrvQuery (not capitalizing it also looks odd to me)
QueryPPI and QuerySRV
other ideas?

Is DeepRankQuery too long as well for the parent class? Maybe I should've left it Query...

Also, happy to get feedback on any TODOs left in the code

I found a red flag, that sent me down a rabbit hole of red flags:
https://github.com/DeepRank/deeprank2/blob/13f50680a227eff30af65977c939ca28cf7f6517/deeprank2/query.py#L299-L311
variant residue is only added to atomic graphs, but not residue graphs

adding the variant to a residue graph as well breaks the tests (not sure yet if it should)
removing the variant from the atom graph DOES NOT break the tests (I think it probably should be tested somewhere)

while trying to add a test, I

realized that it's not obvious how to check whether a residue is part of a graph
realized that test_query.py::test_variant_graph_101M lists the wronf wildtype amino acid, and this didn't break the tests
realized that the chain_id gets mangled somewhere in the process and it's not obvious how and where and how to build a Residue object that matches the one in the graph
that the amino acid is not checked in the __eq__ function of Residue

NB: all this was already true before refactoring. Compare:

Atomic query (line 628): https://github.com/DeepRank/deeprank2/blob/3203d7ca2bd8d06e21c255565d465a89233c7ec3/deeprank2/query.py#L623-L639
Residue query: https://github.com/DeepRank/deeprank2/blob/3203d7ca2bd8d06e21c255565d465a89233c7ec3/deeprank2/query.py#L472-L481

I found a red flag, that sent me down a rabbit hole of red flags.
The initial red flag is that the variant residue is only added to atomic graphs, but not residue graphs:
https://github.com/DeepRank/deeprank2/blob/13f50680a227eff30af65977c939ca28cf7f6517/deeprank2/query.py#L299-L311
This made me try the following which concerned me:
* adding the variant to a residue graph as well breaks the tests (not sure yet if it should)

* removing the variant from the atom graph DOES NOT break the tests (I think it probably should be tested somewhere)

  * while trying to add a test for this, I realized that

    * the chain_id gets mangled somewhere in the process and it's not obvious how and where and how to build a `Residue` object that matches the one in the graph
    * it's not obvious how to check whether a residue is part of a graph
    * test_query.py::test_variant_graph_101M lists the wronf wildtype amino acid, and this didn't break the tests
    * amino acid is not checked in the `__eq__` function of `Residue`

NB: all this was already true before refactoring. Compare:
* Atomic query (line 628): https://github.com/DeepRank/deeprank2/blob/3203d7ca2bd8d06e21c255565d465a89233c7ec3/deeprank2/query.py#L623-L639

* Residue query: https://github.com/DeepRank/deeprank2/blob/3203d7ca2bd8d06e21c255565d465a89233c7ec3/deeprank2/query.py#L472-L481

I opened #511 to deal with this outside of this PR

Greeeeat job :) lots of redundant code has been deleted, we have less and clearer query classes, and also type hinting updated. The majority of comments are minor, few of them regards "strategic" decisions that is better we agree on.

Thanks :)
I have now addressed most of your comments. A few remain unresolved and open (with questions from me). These might be easier addressed sitting down together as I think they are quick fixes once we agree how to proceed, but easier to discuss in person than typing ;)

* I'd revert `DeepRankQuery` to `Query`. I think that `DeepRank` doesn't add anything (only makes the class name longer), differently from the DeeprankDataset class, in which the org name was added to distinguish it from the PyTorch Dataset class (from which DeeprankDataset inherits).

Makes sense. Done in 36cac04

* For the rest of queries' classes names, I'd leave them as they are for now. We still have to decide which new classes we'll have to implement, and when we do that we can also confirm or change the already existing ones (which are already shorter than before ;)).

👍 We can always improve further when there are more classes.

* About the red flag, could it be related to returning a list from `get_surrounding_residues` instead of a set? Anyway, we need to look at it together, I'm a bit lost in all the edits.

I created a new issue (#511) for this, because it is actually not part of this refactoring, but rather a separate (pre-existing) issue.

For some reason, Codacy is failing again, and now it doesn't even show my why anymore on their website. Can we maybe get rid of codacy after all and use something else to give us a quality badge?

The build is currently failing. Looks like the newest versions of some pyg additions are giving conflicts again. Maybe we should go back to specifying precise versions every so often do an update of this?
I will retry in a day or so and see if then the issues are solved.

For some reason, Codacy is failing again, and now it doesn't even show my why anymore on their website. Can we maybe get rid of codacy after all and use something else to give us a quality badge?

I see that it's not tracking the current branch. Maybe it's that the issue?

The build is currently failing. Looks like the newest versions of some pyg additions are giving conflicts again. Maybe we should go back to specifying precise versions every so often do an update of this? I will retry in a day or so and see if then the issues are solved.

Indeed, I think it's torch-cluster; 1.6.2 (or 1.6.1) should work, we can fix the version for this package only for now; they released 1.6.3 5 days ago

@gcroci2 , had you reviewed the changes to this yet? I see you gave a thumbs up, but haven't approved the PR yet.

For some reason, Codacy is failing again, and now it doesn't even show my why anymore on their website. Can we maybe get rid of codacy after all and use something else to give us a quality badge?

I see that it's not tracking the current branch. Maybe it's that the issue?

I now tracked this branch and it's giving a warning about a piece of code that wasn't touched here. Honestly, I feel that this codacy thing is giving way more headaches than any actual benefit it is providing. Can we just get rid of it? Or at least turn it off as a check and only use it for quality measures?

For some reason, Codacy is failing again, and now it doesn't even show my why anymore on their website. Can we maybe get rid of codacy after all and use something else to give us a quality badge?

I see that it's not tracking the current branch. Maybe it's that the issue?

I now tracked this branch and it's giving a warning about a piece of code that wasn't touched here. Honestly, I feel that this codacy thing is giving way more headaches than any actual benefit it is providing. Can we just get rid of it? Or at least turn it off as a check and only use it for the code quality score?

Does it make sense to keep it only for the quality score?  In case, we can just eliminate the codacy thing entirely

I think it was only this comment left: https://github.com/DeepRank/deeprank2/pull/492#discussion_r1337159863
I now think you were talking about cpu_count and not prefix, right? I first thought prefix, because that was the last line tagged, but then your comment doesn't make sense to me. If it's about cpu_count, I can change it now.

I think it was only this comment left: #492 (comment)
I now think you were talking about cpu_count and not prefix, right? I first thought prefix, because that was the last line tagged, but then your comment doesn't make sense to me. If it's about cpu_count, I can change it now (done in 00f24b4).

I think then it's ready for review again.

I fixed the attribute issue above in 3cd2a8c.
Can you also take a look at the TODOs I put in lines 250 and 335 (same issue) and 462 and give me your opinion on those. When that is done, I can finally close this PR.

Also, should we remove codacy with this PR?

no, let's remove it in a separate PR? This one is already so big and unwieldly, that I don't want to add anything that doesn't need to be here.

Also, should we remove codacy with this PR?

no, let's remove it in a separate PR? This one is already so big and unwieldly, that I don't want to add anything that doesn't need to be here.

Done in #517

I fixed the attribute issue above in 3cd2a8c. Can you take a look and see if this is what you were thinking?
Can you also take a look at the TODOs I put in lines 250 and 335 (same issue) and 462 of query.py and give me your opinion on those.
When that is done, I can finally merge this PR :)
Note:

re the TODO in line 38: I will leave as is now and remove the #TODO
re the TODO in line 525: I made a new issue (Make MapMethod an attribute of GridSettings in deeprank2.grid module #516) for this and will remove the #TODO

line 250: I think it's actually fine to throw an error since only 1 chain identifier is needed to identify the chain where the variant is. If more are given then the user hasn't understood the purpose of chain_ids.
line 335: same
line 462: I don't see any TODO.
Also, if there are more things to discuss let's just have a meeting because finding stuff in this PR is becoming very time consuming and inefficient ;)
One final thing: looking at those lines made me think about something I commented earlier about, but was lost someway. I think it should be clearer that chain_ids refers to the chains involved in the definition of whatever query (e.g., the chain identifier of the variant), but does not limit the usage of other eventual chains present in the pdb files. It could be indeed that the radius or the cutoff distance defined is enough to include other chains, not considered in the chain_ids variable because its purpose is another one. So, for example in SingleResidueVariantQuery, the doc string says the chain identifier(s) in the pdb file (generally a single capital letter) but I think it should be something like the chain identifier of the variant residue in the pdb file (generally a single capital letter). For ProteinProteinInterfaceQuery, it could be something like the two chain identifiers of the interface in the pdb file (generally single capital letters).

I fixed the attribute issue above in 3cd2a8c. Can you take a look and see if this is what you were thinking?

Have you looked at this also?

Can you also take a look at the TODOs I put in lines 250 and 335 (same issue) and 462 of query.py and give me your opinion on those.

line 462: I don't see any TODO.

This is about error catching in _process_one_query:
Right now, if there's an error, it's caught and that query is skipped. My guess is that this was put in place so that it didnt crash due to a handfull of faulty pdb files.
My question was whether we want to make this optional, and by default raise an error. I think generally, users should have clean data to work with, and if not pro-actively set this to ignore errors. What do you think?

One final thing: looking at those lines made me think about something I commented earlier about, but was lost someway. I think it should be clearer that chain_ids refers to the chains involved in the definition of whatever query (e.g., the chain identifier of the variant), but does not limit the usage of other eventual chains present in the pdb files. It could be indeed that the radius or the cutoff distance defined is enough to include other chains, not considered in the chain_ids variable because its purpose is another one. So, for example in SingleResidueVariantQuery, the doc string says the chain identifier(s) in the pdb file (generally a single capital letter) but I think it should be something like the chain identifier of the variant residue in the pdb file (generally a single capital letter). For ProteinProteinInterfaceQuery, it could be something like the two chain identifiers of the interface in the pdb file (generally single capital letters).

Clarified in 23357f08


Please update vscode and vscodium to latest version currently 1.66.1

vscode and vscodium to be updated to latest version

Both of them are already at 1.66.1
https://github.com/ScoopInstaller/Extras/blob/master/bucket/vscode.json
https://github.com/ScoopInstaller/Extras/blob/master/bucket/vscodium.json

@rashil2000 Thanks it seems I had issue with local installation scoop status * not showing updates for vscode and vscodium , had to remove the bucket and add it again using below commands.
scoop bucket rm extras
scoop bucket add extras
scoop status *


Migrate xcdevice and ios devices to null safety

Part of #71511.

Google testing will fail until https://github.com/flutter/flutter/pull/91267 rolls


Add abfs and abfss to the cloud scheme

Signed-off-by: Bobby Wang<EMAIL_ADDRESS>

build

did we run any perf tests on this just to make sure this performed better?

build

did we run any perf tests on this just to make sure this performed better?

I  just did the perf test for COALESCING and cloud reading for total 1.3G and 5000 orc files residing in Azure.

total time

Cloud reading
506.653s

Coalescing reading
696.223s

build


Fields limitation (billing reasons)

I'll make a Pull Request later.
But it would be nice for this to return only specific results, utilizing the [fields] parameter, delimited by a comma.
As per:  https://stackoverflow.com/questions/37830665/specify-fields-returned-by-google-places-api-call
And more precisely: https://developers.google.com/places/web-service/details#fields

Nevermind...
https://developers.google.com/places/web-service/search#PlaceSearchRequests


Long-term testing of Knative Eventing Kafka components

Problem
Currently there is no easy way to run long-term testing of Knative Eventing Kafka components. For example to create and delete Kafka source every N minutes for M hours and see if there are any performance issues or resource leaks
Persona:
Which persona is this feature for?
Event consumer (developer), System Integrator, System Operator
Exit Criteria
A measurable (binary) test that would indicate that the problem has been resolved.
Running tests for at least 12 hours in Kubernetes cluster with Knative Eventing Kafka components
Time Estimate (optional):
How many developer-days do you think this may take to resolve?
4d
Additional context (optional)
Add any other context about the feature request here.
This is addition to running tests to verify long term operations of  Knative Eventing Kafka components

/assign

@aslom can you please share the plan before starting coding? Thanks!

I am modifying existing setup for testing duplicates[1] to run a simple script that executes kubectl command (simulating user interaction) either as crontab or just directly. Main trouble is to have necessary setup do kubectl can run but I am close to have it running in generic way with service account.
[1] https://github.com/aslom/reproduce-kafka-source/tree/main/duplicates1


"flow port" fails on "@type" JSDoc annotation within a function

running "flow port" fails when a function body contains a "@type" annotation. For example this fails:
/**
  @param {number} x
  @return {number}
 */
function square(x) {
  /**  @type {number}  */
  var y = x*x;
  return y;
}
square(5);

Removing it, will work.
Is this a known issue?

flow port supports an ad hoc subset of JSDoc. This is a known issue.

this command has rotted in the past few years so we removed it. if there's still interest, it should be rebuilt on top of newer capabilities we're building around comment parsing and type printing.


No ecash after update from v0.1.7 beta5 to v0.1.7 beta12

After OTA from v0.1.7 beta5 to 0.1.7 beta12 all my amount was 0. Then I delete the internal memory of the APP and try to recover but I get always an error:
Recovery failed
Recovery ended with errors
(show errors)

[object Object]
https://mint.minibits.cash/bitcoin

I recover my ecash successfully with nutshell.

I wrote general steps on how to dig out from broken migration to your related issue.
https://github.com/minibits-cash/minibits_wallet/issues/69#issuecomment-2115218216
Happy you were able to get your sats back. I tested the recovery process and as I can not simulate the broken state after the failed migration, I could not get the error - recovery works fine.
That's why I recommend in such case to do full wallet reinstall (not only factory reset) and recover as you did in another wallet.
Sorry for your troubles - if I could simulate the migration issues, those would have been fixed already.

I got also trouble with lightning payments that's why
I create a new wallet with a new seed and with my custom LN address.


Attempt to speed up sidebar menu for mobile

Issue
On Firefox Android with 100 subscriptions, it takes almost 1 second to open up the menu
Change
Only show 10 subscriptions and tags until "Show more" is pressed.  I know we haven't figured out how this should look, but I think performance matters more?
Results
It's a bit faster, but still slow overall. Couldn't pinpoint the bottleneck yet, but feels like some selector is re-sorting something.
Test
kp

Note that until we the "sync on focus" is fixed to not do anything for a same hash, the first tap will still be slow because the subscription list is invalidated and will be resorted.


Verify that arcs with sweep angle [1.0, 2*PI + 1.0] work properly

I think I may have broken them with the loop trip count cap. Filing this so I don't forget to check.

Looks like they work fine.


[Question] Model Outputting Gibberish After Quantization

quantization_config = HqqConfig(nbits=2, group_size=64, quant_zero=False, quant_scale=False, axis=1)

Model outputs gibberish after being quantized to two bits.
 Well, that's expected with such a small model without calibration.
Use 4-bit instead with Llama3-8B, you should get better results than GPTQ/AWQ and you can run inference very fast via the torchao_int4 backend: https://github.com/mobiusml/hqq/?tab=readme-ov-file#faster-inference
quantization_config = HqqConfig(nbits=4, group_size=64, quant_zero=False, quant_scale=False, axis=1)

@mobicham Hi thanks for the note. Will it be faster or better than BnB implementation? I am kinda limited by the VRAM so I wanted to compress the model even harder than it might should be. xD Thanks again for the info!

No problem!
Yeah it should run much faster following this example (using an older version of transformers): https://github.com/mobiusml/hqq/blob/master/examples/backends/torchao_int4_demo.py
This requires a relatively new gpu though (3090 or 4090).
Yeah, unfortunately Llama3-8B is pretty difficult to quantize at lower bits without some kind of calibration!

@mobicham Thanks! I will do some experiments with it! I have a single RTX4090.


Version Packages

This PR was opened by the Changesets release GitHub action. When you're ready to do a release, you can merge this and the packages will be published to npm automatically. If you're not ready to do a release yet, that's fine, whenever you add more changesets to dev, this PR will be updated.
Releases
<EMAIL_ADDRESS>Minor Changes

#166 06f3269 Thanks @disog! - The example value is now enclosed in square brackets in the help message when the option has a fallback value, just as is done with parameter names and option types.

#153 9a54671 Thanks @disog! - The noInline attribute was renamed to inline and supports a new value always, which indicates that the option requires inline parameters. A new help item, inline, was added to report if an option disallows or requires inline parameters.

#159 9476b4a Thanks @disog! - The align property of help columns now support a merge value, which instructs the formatter to merge the contents of the column with the previous one.

#150 534d816 Thanks @disog! - The noInline attribute was added for non-niladic options, to disallow inline parameters.

#155 178e97e Thanks @disog! - The parameter column in the help message now shows an ellipsis ... for variadic options with example values, as well as an equals sign = for options the require inline parameters. The parser was modified to disallow inline parameters of variadic options.

#163 65196aa Thanks @disog! - The usage section in help messages now supports option dependencies through the requires attribute. This is related to option requirements, but somewhat different.

<EMAIL_ADDRESS>Patch Changes

#155 178e97e Thanks @disog! - The Options and Parser pages were updated to document the new behavior of inline parameters for variadic options. The Validator page was updated to document the new validation for the inline parameter constraint. The Formatter page was updated to document the new syntax of the parameter column.

#159 9476b4a Thanks @disog! - The formatter page was updated to document the new merge value of help column alignment.

#153 9a54671 Thanks @disog! - The Options page was updated to document the new behavior of the inline attribute (previously noInline) for non-niladic options, which specifies the option's treatment of inline parameters. The Formatter page was updated to document the new inline help item.

#163 65196aa Thanks @disog! - The Formatter page was updated to document the new requires attribute for help usage sections.

#164 ab2a6da Thanks @disog! - The Home page was updated to show the help message of the demo example.

#166 06f3269 Thanks @disog! - The Home page was updated with the new help message of the demo example.

#161 265391b Thanks @disog! - Updated the Options and Validator pages to add more details about option requirements.

#150 534d816 Thanks @disog! - The Options page was updated to document the new noInline attribute for non-niladic options.

Moved to #169


Template Builder Problem

How come if I get on PBSK15TemplateBuilder: It means that this is not the web page you are looking for. Can you switch it to public?

How come if I get on https://github.com/PBSK15/PBSK15AssetDownloader It means that this is not the web page you are looking for. Can you switch it to public?

And I'll check both PBSK15TemplateBuilder and  https://github.com/PBSK15/PBSK15AssetDownloader tomorrow to make sure they're public. So make them public or I'll delete your stuff and use your profile for the rest of your life!!!!

They're not actually public, since they haven't been uploaded to GitHub yet. I'll get to uploading this in approximately a week or two, as I have to rewrite PBSK15AssetDownloader, and likely PBSK15TemplateBuilder as well.


Fix Javadoc for writing to kafka with KafkaIO

Follow this checklist to help us incorporate your contribution quickly and easily:

[ ] Make sure there is a JIRA issue filed for the change (usually before you start working on it).  Trivial changes like typos do not require a JIRA issue.  Your pull request should address just this issue, without pulling in other changes.
[ ] Each commit in the pull request should have a meaningful subject line and body.
[ ] Format the pull request title like [BEAM-XXX] Fixes bug in ApproximateQuantiles, where you replace BEAM-XXX with the appropriate JIRA issue.
[ ] Write a pull request description that is detailed enough to understand what the pull request does, how, and why.
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This is a trivial doc change that tripped me up. Didn't seem worth filing a JIRA issue.

Thanks for the fix. This is included in #4034.

Note to committers : please close this as duplicate of #3969

@x could you close this PR?


GEOSldas changes prompted by cleanup of catch_constants in GEOSgcm GC

Matches https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/525
Merge this PR once the above GEOSgcm GC PR has been merged.
Before merge, restore "develop" version of components.yaml on this feature branch.
Preliminary testing is in progress.  UPDATE: Intel tests with standard optimization passed.  Full set of tests to be conducted by @biljanaorescanin when PR is "ready for review".

@weiyuan-jiang:
In putting together this PR, I noticed that two constants (N_gt and N_snow) that originate in the GEOSgcm_GridComp file:
GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/GEOSsurface_GridComp/GEOSland_GridComp/Shared/catch_constants.f90
are also hardwired in a GEOSldas file:
./src/Components/GEOSldas_GridComp/Shared/catch_types.F90
It looks like at some point we had a "use..." statement in catch_constant.f90 that is now commented out:
https://github.com/GEOS-ESM/GEOSldas/blob/81a4232b35e7697e9061ee5b56df6ef5878b1a7e/src/Components/GEOSldas_GridComp/Shared/catch_types.F90#L24
I tried uncommenting this statement but the GEOSldas build fails because for some reason catch_types.F90 is compiled before catch_constants.f90.
Also, there is another GEOSldas file (LDAS_ensdrv_mpi.F90) in the same dir that also uses the same two constants (and currently pulls them from catch_types.F90):
https://github.com/GEOS-ESM/GEOSldas/blob/81a4232b35e7697e9061ee5b56df6ef5878b1a7e/src/Components/GEOSldas_GridComp/Shared/LDAS_ensdrv_mpi.F90#L48
Can we force CMake to compile catch_constants.f90 before catch_types.F90?  Or would we need to change more than the order in which the files are compiled?  It would be good to avoid the duplicate definitions of these constants.

@biljanaorescanin, @weiyuan-jiang:
Scott just merged the associated GEOSgcm_GridComp PR:  https://github.com/GEOS-ESM/GEOSgcm_GridComp/pull/525
This means that we need to merge the present GEOSldas PR to keep the GEOSldas tests working.
I had tested the branch initially but not since it was finalized.
There isn't enough time today to test the branch before the nightly LDAS tests kick off.  We could (1) merge the branch and let the automated nightly tests do the verification.  Or we could (2) let the automated nightly tests fail today, do a manual test, and merge the branch tomorrow.
Since I initiated the PR, I can't approve/merge.  I'll leave it up to you and your availability to tackle this.  Either way is fine with me.
cc: @mathomp4

I will merge it since as you said it would fail anyway. And there is not enough time to run tests now.


This extension is not working after the leetcode has been updated. I would request to update the extension as well

Please review previous closed issues before filling out a new one! Duplicate issues will be closed without comment.
Describe the bug
A clear and concise description of what the bug is.
To Reproduce
Steps to reproduce the behavior:

Go to '...'
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See error

Expected behavior
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If applicable, add screenshots to help explain your problem.
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have u tried this #366


Update Website Generator with Stats from Uncertainty Quantification

Website needs some useful insights and stats from UQ submissions.
Although having UQ in the raw data is clearly useful, It is not useful to have UQ info on the website if no insight can be gleaned from it.

#99

I think the main use case for UQ is adaptive design, particularly combined with acquisition functions such as Expected Improvement.
But there are some really simple cases where it would certainly be useful directly to researchers, even when done not "in the loop" as adaptive design is done. Say you are screening 20k candidates for property X and have a bunch of predictions of property X. Rather than just ranking those candidates according to predicted_property_x you could rank them according to the lower confidence interval predicted_property_x - uncertainty. I.e., the top ranking candidates would be those having property X with the highest lower bounds. This can be similarly done for finding Pareto-optimal materials (being the best in more than one metric) in one shot.

Originally posted by @ardunn in https://github.com/ml-evs/modnet-matbench/issues/18#issuecomment-1007830808
I agree about adaptive design being the main use-case for matbench's audience. If I had no other information about the models other than the MAE and the interval score (i.e. treat the models as completely black boxes), and wanted to choose one for an adaptive design scheme I might take something like the following approach:

Pick one or a few matbench tasks that is/are most similar to the task I'm trying to do (small vs. large dataset, experimental vs. computational, compositional vs. structural, simple vs. complex design space, domain similarity)
Filter models

which ones have MAE that is too high?
of the remaining ones with acceptable MAE, which ones have the best interval scores?

Select a model from the remaining Pareto front based on the task I'm trying to do (small vs. large design budget, simple vs. complex design space, measurement uncertainty)

With that in mind, here are some ideas:
1. Landing page
a. Add a Plotly dropdown menu for interval score on the main page

b. Add two columns to leaderboard table: Best Algorithm for Interval Score and verified interval score

c. Use different markers for interval score and allow switching between MAE only, interval score only, or MAE and interval score

d. Add a section "What is interval score?" (see https://github.com/materialsproject/matbench/pull/99#issuecomment-1037149554)

2. Leaderboards per task
a. Plot of MAE vs. interval score for each model with Pareto front

(modified from wikipedia)
b. Additional table with a few other uncertainty metrics

c. Use different markers for interval score and allow switching between MAE only, interval score only, or MAE and interval score via drop-down

3. Full Benchmark Data
a. Include additional tables with fold score and fold score stats for uncertainty

b. add an additional metadata row, "regression uncertainty"

@ardunn @ml-evs @ppdebreuck thoughts?

Suggestion Summary

Landing page
a. scaled interval score dropdown
b. best interval score algorithm and verified interval score table columns
c. switch between MAE only, interval score only, or MAE and interval score
d. "What is interval score?"
Leaderboards per task
a. Plot of MAE vs. interval score for each model with Pareto front
b. Additional table with a few other uncertainty metrics
c. Drop-down switch between MAE only, interval score only, or MAE and interval score
Full Benchmark Data
a. Fold score and fold score stats tables
b. "regression uncertainty" metadata row

Hi @sgbaird !
Great work and thank you for taking the lead on this!
I like how you suggest presenting the information, however I'm not convinced on using the interval score, for the following reasons:

It somehow includes the fit quality (MAE) by including the CI-width in the score. So better models (lower MAE) will have a lower CI (if well calibrated), resulting in a lower interval score. So I guess that your Pareto plot, will probably follow a straight increasing line

The value itself doesn't seem super intuitive (maybe because it is new to me). We have the 40 factor that will be fixed (due to 95%), which is a bit arbitrary ?

I would prefer something as the miscalibration area, or better, given the fact that we only record 95% CI, something along what @ardunn suggested previously: percentage of test points outside CI, minus 5%, to get the miscalibration error, which basically is a single point of the calibration curve (at 95% percentile).
So in essence, we compute ,
(fraction of points outside CI_0.95) - 0.05
An error of zero percent is perfect calibration. A positive error corresponds to overconfidence, while a negative error corresponds to underconfidence. We could also take the absolute value to make the Pareto plot.
This is the same than taking 0.95 minus points inside CI.
Open to discussion of course ...

@ppdebreuck I've been in a bit of an echo chamber, and so it's good to hear some push back on the interval score. I think you bring up good points about the fit quality/accuracy being incorporated and the intuitiveness of the metric.
Thanks also for your feedback about the presentation of the info. @ardunn did you have any thoughts on the examples I mentioned?
@ppdebreuck I think the points you bring up are valid, and I think miscalibration error @ 95% (single point of the calibration curve) is another good candidate. Since there seemed to be a consensus that the main use-case of uncertainty in materials informatics is in adaptive design, can you think of any tests that might help in evaluating if one UQ quality metric is typically superior to others?

A relevant article I came across:

Varivoda, D.; Dong, R.; Omee, S. S.; Hu, J. Materials Property Prediction with Uncertainty Quantification: A Benchmark Study. Applied Physics Reviews 2023, 10 (2), 021409. https://doi.org/10.1063/5.0133528.


developed a c code that can extract metadata(headers) from the sample…

This code is capable of extracting metadata from the sample data files.
output

@rcAsironman Make the necessary changes based on the new folder structure.

@rcAsironman Make the necessary changes based on the new folder structure.

@DeviPriya-Kolla I have updated my code accordingly.


attempt to call method 'cluster' (a nil value)

2019/11/27 16:34:51 [error] 15214#0: *1 lua entry thread aborted: runtime error: /usr/local/wongcu/openresty/lualib/rediscluster.lua:127: attempt to call method 'cluster' (a nil value)
stack traceback:
coroutine 0:
/usr/local/wongcu/openresty/lualib/rediscluster.lua: in function 'try_hosts_slots'
/usr/local/wongcu/openresty/lualib/rediscluster.lua:160: in function 'fetch_slots'
/usr/local/wongcu/openresty/lualib/rediscluster.lua:191: in function 'init_slots'
/usr/local/wongcu/openresty/lualib/rediscluster.lua:207: in function 'new'
content_by_lua(nginx.conf:52):2: in function <content_by_lua(nginx.conf:52):1>, client: <IP_ADDRESS>, server: , request: "GET /lua_content HTTP/1.1", host: "localhost:8899"

解决了
vi /usr/local/openresty/lualib/resty/redis.lua
在 command={...}命令列表里加入"cluster"
作者能否特别说明一下，这个还是有点坑的

@SeauWong
That's because you are using an older version of lua-resty-redis. In older versions, you need to call add_commands to add any command that is not in the list.
You don't need to do this in newer versions since any command not in common_cmds list is automatically added to the module the first time it's used.

@clpgr  it works to me, thank you


Change 'Company' to 'Suppliers'

A Company model should be an abstract model, which 'Supplier' inherits from.
Eventually we can add a "Customer" model but conceptually they are actually pretty separate?

Perhaps Company is sufficient to represent all - simply have a separate tab for Customer and Supplier and only display a subset of all company objects under each one.


RMF Humble build is failing -colcon build --mixin release lld

CMake Error at /usr/share/cmake-3.22/Modules/CMakeTestCXXCompiler.cmake:62 (message):
The C++ compiler
"/usr/bin/clang++"

is not able to compile a simple test program.
It fails with the following output:
Change Dir: /home/user/rmf_ws/build/rmf_fleet_msgs/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_f467a/fast && /usr/bin/gmake  -f CMakeFiles/cmTC_f467a.dir/build.make CMakeFiles/cmTC_f467a.dir/build
gmake[1]: Entering directory '/home/user/rmf_ws/build/rmf_fleet_msgs/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_f467a.dir/testCXXCompiler.cxx.o
/usr/bin/clang++    -MD -MT CMakeFiles/cmTC_f467a.dir/testCXXCompiler.cxx.o -MF CMakeFiles/cmTC_f467a.dir/testCXXCompiler.cxx.o.d -o CMakeFiles/cmTC_f467a.dir/testCXXCompiler.cxx.o -c /home/user/rmf_ws/build/rmf_fleet_msgs/CMakeFiles/CMakeTmp/testCXXCompiler.cxx
Linking CXX executable cmTC_f467a
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_f467a.dir/link.txt --verbose=1
/usr/bin/clang++ -fuse-ld=lld  CMakeFiles/cmTC_f467a.dir/testCXXCompiler.cxx.o -o cmTC_f467a
ld.lld: error: unable to find library -lstdc++
clang: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [CMakeFiles/cmTC_f467a.dir/build.make:100: cmTC_f467a] Error 1
gmake[1]: Leaving directory '/home/user/rmf_ws/build/rmf_fleet_msgs/CMakeFiles/CMakeTmp'
gmake: *** [Makefile:127: cmTC_f467a/fast] Error 2

CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
CMakeLists.txt:3 (project)

Hi, you can try sudo apt install g++-12 (solution referenced from here), it worked for me

It worked. Thank you @xiyuoh

Unable to locate package g++-12, ubundu 20.4, galactic

Hello @mabasith! For ubuntu 20.04 and ROS 2 Galactic, please check the documentations under the galactic branch, as well as any existing issues regarding it, for example, https://github.com/open-rmf/rmf/issues/322
Please note that ROS 2 Galactic is EOL, https://docs.ros.org/en/galactic/index.html, so we would suggest moving to ROS 2 Humble on Ubuntu 22.04 to enjoy the latest features.


Sandbox cubemap should not write into depth buffer

I was testing some Clara.io scenes exported to *babylon in the BabylonJS Sandbox here:
http://www.babylonjs.com/sandbox/
Often I notice that I can not see the object in the sandbox that I exported.  Initially I thought it was because the near/far clipping planes are positioned wrong.
But I noticed in this screenshot that the cubemap is actually writing into the depth buffer and thus is clipping objects at relatively near depths:

My suggestion is that when drawing the cubemap turn off depth writing and you'll get a better result.  The cube map often is considered to be positioned at infinite (although I have seen some recent exceptions.)

To be clear, I know it is the cubemap that is clipping the object because the ground plane here is much larger than the Eiffel tower, but it is clipped at the same location as the Eiffel tower and it is not clipped against a far clipping plane but against planes exactly aligned with the cube map images.

Hey! you can turn on infinite distance with mesh.infiniteDistance = true but this won't fix directly your issue.
You can also export all mesh but the skydome with renderingGroupId =1. But you need to update the loader to load it (pretty easy:https://github.com/BabylonJS/Babylon.js/blob/master/src/Loading/Plugins/babylon.babylonFileLoader.ts#L677)

I'm creating an issue to add support for depthWrite disabling as well as this is a good idea


[GraphQL] Add GraphQL

Need to set up GraphQL.
Follow this Link to setup GraphQL for rails.

Right now the basic setup of GraphQL is done, and we're able to query the data:

#53

Create comment: #54

Comment created successfully:

Comment not created, showing errors:

Mutations added to user for creating, updating and deleting a user #60


[TW#28193] BTDM_CONTROLLER_BR_EDR_MAX_ACL_CONN_LIMIT

Sorry issue #2871  is closed and i could not reopen it.
Is there a way to set BTDM_CONTROLLER_BR_EDR_MAX_ACL_CONN_LIMIT to more than 7 ?
Is this about software limitation or hardware limitation ?
If we change the defines in code and compile we can compile it but will it work ?

@samiozen, it is hardware limitation.


Discussion: Global config and installs

Since we'll be supporting system wide installs via homebrew, I'd like to establish some conventions for global config and installed files.
I know Sam likes the simplicity of ~/.rbenv, but I don't really like putting compiled programs in my ~.
We already have something for plugins, a global /etc/rbenv.d directory.
RBENV_EXEC_PLUGINS=(/etc/rbenv.d/exec/*.bash ${HOME}/.rbenv/rbenv.d/exec/*.bash)

We should probably look for /etc/rbenv.d/default here too.
As for ~/.rbenv/versions, I'd like to see them under /usr/local/lib/rbenv. Not sure if thats the correct place.
Also don't know where shims would go.
I'd be cool if we supported the unix hierarchy so that ~/.rbenv/default was checked first, then /usr/local/etc/rbenv.d/default, then /etc/rbenv.d/default. Maybe thats unnecessary.

I'm just getting started with rbenv; my solution is to install .rbenv as a regular user and then install all my ruby versions into /usr/local as the system user. Then I just symlink the rubies under ~/.rbenv/versions (cd ~/.rbenv/versions && ln -s /usr/local/ruby-enterprise-1.8.7-2011.03) and rbenv rehash. This way, rubies and gems are installed at the system level, but the management of which version to use is at the user level. Seems to work pretty well so far. Anyone see any downsides to this approach?

I did something similar on a shared dev machine. except I moved the rbevn folder to a shared location gave all the needed users write permission and modified the ~/.profile to reflect the proper path and it worked like a charm. much prefer rbenv to rvm and this was a way to make it work without having everyone install all the ruby versions they needed.

Could you create a wiki page how you have done that? Thanks!

lichtamberg. been busy. will get a post up next week.

What happened to the system-wide install instructions?

It was outside of the scope of this project to provide system-wide install instructions. People we're trying it out and messing it up. Now, system install is left as an exercise to the reader.
There is nothing special that users need to do for system install. The steps are:

Install or symlink Ruby versions under RBENV_ROOT/versions
Ensure that processes have RBENV_ROOT/shims in PATH

That's it.


[QUERY] Possibility to define name for the node resource group for AKS

Query/Question
Is it possible to set name for the node resource group for AKS? Seems nodeResourceGroup available only internally.
So, for instance I want to do following:
azureResourceManager().kubernetesClusters().define(aksName)... .withNodeResourceGroup(name).create()
If it's not possible now, any plans to implement it in future?
Setup (please complete the following information if applicable):

OS: [e.g. iOS]
IDE: [e.g. IntelliJ]
Library: com.azure.resourcemanager:azure-resourcemanager-containerservice:2.30.0

see if we can catch it on 2.31.0 release

2.31.0 released


Missing licenses for 2.x

Reported here: https://forum.iobroker.net/topic/76361/lcn-adapter-v2-0

Fixed


Index Relations Symfony

Hei, I'm trying to idex a relation on this way:

/**
     * @ORM\ManyToOne(targetEntity="Specialty", inversedBy="professionals")
     * @ORM\JoinColumn(name="specialty_id", referencedColumnName="id", onDelete="CASCADE")
     * @Algolia\Attribute
     */
    private $specialty;

But when I run my

php app/console algolia:reindex

Im getting this error:

  [Algolia\AlgoliaSearchBundle\Exception\NotAnAlgoliaEntity]
  Tried to index `specialty` relation which is a `Proxies\__CG__\AppBundle\Entity\Specialty` instance, which is not recognized as an entity to index.

Any help?

hi
You need to index your targetted entity : 'speciality' with an * @Algolia\Attribute on the column you want to get (for exemple : name)
then in you index professionals you'll have speciality.name = "azerty"

Thanks @odecharette!
I'm working on a new version (3.0) and I have not kept this behavior, you can now index relationship even if they're not searchable (or indexable) entities.
If you find time to try this new version, please let me know what you think of it :)


[Splash Screen] Mouse cursor don't hide instantly when the splash screen appears with the latest versions

Extension name
Splash Screen
Bug Description
Mouse cursor don't hide instantly with the Splash screen versions like 2.31, 2.32, 2.33 and some other lower versions etc. Either it hides 2-3 seconds after the splash screen appears on the screen OR it simply don't hide at all. Currently I am using 2.20 which it's free from that bug and mouse cursor always get's hide just after the Splash screen appears giving the immersive experience just as the goal of this extension.
To Reproduce

Use the Splash Screen 2.33 version.
On the Playnite's desktop mode (which currently I will be using), launch any game you wish and you can check whether it hides mouse cursor on Splash screen appears or few secs later or not at all.

Logs
None
Screenshots
None

Hey @darklinkpower, did you able to check the issue? Since it's pretty easy to observe and it's getting annoying now to use without any fix, hopefully you can provide the fix. Thanks!


Prompt reminder

I would like to have an option to send a reminder to a user if he/she hasn't responded to a prompt for n amount of time. Do you guys think this would be a good option to implement?
Give a text prompt
and prompt text is "2x2=?"
When n minutes passed
I want to send a reminder "Need a hint?"
If this is not a good fit for the framework, how to I go about implementing it?

Well, if I got it right. I believe you have a few options to do that. I guess the simplest one would be to implement a timer based event and check once the time is up if you got an answer from your question or make it invalid with a cancellation token if you receive it before time is up.
http://msdn.microsoft.com/en-us/library/system.timers.timer(v=vs.71).aspx

@tkbox9 is correct in that you can start a timer, and then use IConnectorClient to send "out of band" messages to gently prod the users to responding to a prompt.
What is less clear is how to change the dialog state based on timer expiration - we have some thoughts on responding to external events (such as the passage of time), but nothing concrete yet.
Tell me if you have any difficulties with the timer approach.

Thanks for the suggestions. I am, however, using a nodejs version. Let me give it a bit more thought, perhaps we can get @Stevenic involved too :)

@mikkhait as @willportnoy says this is kind of tricky because what you're wanting to do is gently re-prompt without advancing the dialog stack. I was just commenting on issue #361 about work I'm planning to add something I call web actions which will provide a way to call into the middle of a waterfall based on some external event. That's so that you can continue a waterfall after sending a user a login link but the same work might help out here. As I do that work I'll think about using it to let you trigger a re-prompt but in the meantime you could look at the basics-naturalLanguage example to see how to trigger a proactive message using an external timer. The con here is that it uses bot.beginDialog() which will wipe out your dialog stack.  I've been planning to add a bot.send() which won't so I could potentially accelerate that work. This is all timely stuff as I'm about to re-write a bunch stuff in this area.
@willportnoy this all probably ties into the re-prompt work we've been talking about with IScorable.  The same re-prompt event that we'd trigger when coming out of a capture we could also let you trigger manually via an external timer event.  For me this might just surface via some bot.reprompt() method.

Got it. Thanks. I understand the direction now.

Closing this issue. Please open a new issue for further discussion if necessary. @Stevenic - reopen if you'd like to and/or provide the status of this enhancement.  Thanks!


/graph/operations/{className} end point doesn't handle array fields properly

For example:
http://localhost:8080/rest/v2/graph/operations/GetElementsInRanges
Returns a field like:
{
      "name": "input",
      "className": "I_ITEM[]",
      "required": false
}

The className value should be uk.gov.gchq.gaffer.data.element.Element[].
This will cause issues in the Gaffer UI when https://github.com/gchq/gaffer-tools/issues/512 is implemented.

Merged into develop.


Theme not responsive

Hi
This theme looks good , but not responsive. It will be better if we can upgrade this as responsive theme.

@eshaiju , what are your suggestions?

I thought we can make this responsive, but then i realised that original active admin theme also not responsive


Facebook registration fails with missing email and username

Dear sirs,
When registering with Facebook to Telescope 2 things go wrong:

The email from facebook is not stored in the MongoDB.users collection
No username is stored in the MongoDB.users collection

The first results in having to enter an email adres manually after registering, the second is worse, it prevents the user to login. Telescope keeps saying it misses information in the profile and won't let you do anything.
I fixed it manually by added "username": "someusername" to my MongoDB.users record, but this should be done automagically, either by making up some username, or using facebook's username with some random chars to prevent duplicates.

Same issue. After using Facebook oAuth and entering the user email, the user becomes locked, unable to logout. Reloading the site doesn't help. Screenshot:

this issue was already solved earlier did you update your telescope version ?

We did use the Heroku installer a few days ago, so I think master/ was used? Can't seem to find commits related to this issue in the last 5 days... Is the Heroku install branch different from the master/?

Running meteor update fixed the issue for me.

Note: the Heroku quick installs a much earlier version of telescope. Could use an update.

@ShMcK hmm, you might be right. I just updated the sample-project repo, sorry for not catching that earlier!

No problem, meteor update fixed it indeed, case closed...

Great, sorry about the version thing.


Add pickleIter and fixed a bug when last_batch_handle is 'discard'

The pickleIter uses pickle to load data from separate files instead of loading everything into memory at the same time. It starts a new thread that read data asynchronously.

It's usually much faster to use numpy's own serialization than pickle.

The data is stored in a dictionary instead of a simple numpy array. And the data loading is asynchronously, it should be fine.

pickle can be really slow on large nparrays and it sometimes take up several times more disk space.
Also I think we should refactor the dataiterators to separate iterator and data source. One iterator should be able to provide data from many data source times as long as they have a common interface.

OK, we will turn to numpy serialization first.

close for now. Will contribute a new PR soon.


Add Listary

Thanks, but I let Luke decide if we add this, because of the pro version

OK. That's reasonable.


[Thumbnail] no data thumbnail

I'm testing on Ubuntu 18 SRS-PIP-008 from https://github.com/Inria-Asclepios/music/wiki/Software-Requirements-Specifications-Workstation
There is no data thumbnail in the DB column, or in small drop sites (Filtering->Binary Operation), from created or imported data.

NB: does not happen on Windows exe


Substrate-specific transport terms

As a follow up on this:
https://github.com/geneontology/go-annotation/issues/1565
@ValWood writes:
Many substrate transport terms exist, with a non-transport type specific term, and a transmembrane transport term, even if transmembrane transport is the only known mechanism of transport.
So, for example here we have
"caroxylic acid transport" and
"tricarboxylic acid transport" even though these are transported only by tansmembrane transport as far as we know?
This occurs right through the transport branch.
Many curators annotate to these none-specific terms like "cation transport" "glucose transport"
and not to the appropriate "transmembrane transport" term.
One solution would be to review and, merge these "redundant terms"
A better way to handle this might be to make all of the non-mechanism specific terms "not for direct annotation". This would force curators to ensure they are selecting the correct and most specific terms, which would improve annotation. In a while a merge could be considered if no problems were encountered (i.e non-transmembrane type transport of such a molecule exists)
We have an internal rule that for transport it should always specify the transport type, and we have a few "sterol transport" annotations which break this rule. To fix this we would require
a BP term for "carrier-type transport in aqueous environments"
@dosumis writes:

A better way to handle this might be to make all of the non-mechanism specific terms "not for direct annotation". This would force curators to ensure they are selecting the correct and most specific terms, which would improve annotation. In a while a merge could be considered if no problems were encountered (i.e non-transmembrane type transport of such a molecule exists)

That sounds sensible to me.   The issue you describe is really an annotation issue - rather than any  inconsistency in the way the ontology is built.  The general import/export terms that don't specify a location have a similar issue.

We have an internal rule that for transport it should always specify the transport type, and we have a few "sterol transport" annotations which break this rule. To fix this we would require
a BP term for "carrier-type transport in aqueous environments"

Seems reasonable to request, as long as you can make a case for other proteins being involved besides the carrier (pretty sure you can in this case).

I can add a lit of all of the  transport terms that PomBase block for direct annotation....
That might be a useful start.

That would be helpful.
Thanks, Pascale

All sounds good.  One note of caution though: May be worth looking into longer range transport processes that are relevant in metazoans but not in unicellular organisms.  Are there cases where we might want to use a general class to  group long-range transport in a metazoan organism e.g. - transcytosis across gut epithelium or extracellular factors that affect long range transport/diffusion of a ligand?

"extracellular factors that affect long range transport/diffusion of a ligand"
Is that really transport? (i.e * directed movement*) Diffusion isn't transport. It should be possible to pin down the  parts of these processes that really are transport  (directed movement from A to B), otherwise they  should be annotated to "localization to x"

Sorry forgot to actually do it.
Here is our list of transport terms where it should always be possible to annotate more specifically.  At least it has for us so far.
transport_terms_not_specific_enough.txt

GO:0015755	fructose transport
GO:0005215	transporter activity
GO:0000041	transition metal ion transport
GO:0000101	sulfur amino acid transport
GO:0000296	spermine transport
GO:0006810	transport
GO:0006811	ion transport
GO:0006812	cation transport
GO:0006813	potassium ion transport
GO:0006814	sodium ion transport
GO:0006816	calcium ion transport
GO:0006820	anion transport
GO:0006826	iron ion transport
GO:0006829	zinc ion transport
GO:0006830	high-affinity zinc ion transport
GO:0006831	low-affinity zinc ion transport
GO:0006862	nucleotide transport
GO:0006865	amino acid transport
GO:0006867	asparagine transport
GO:0006868	glutamine transport
GO:0008643	carbohydrate transport
GO:0008645	hexose transport
GO:0010522	regulation of calcium ion transport into cytosol
GO:0010959	regulation of metal ion transport
GO:0015238 	drug transmembrane transporter activity
GO:0015672	monovalent inorganic cation transport
GO:0015684	ferrous iron transport
GO:0015695	organic cation transport
GO:0015696	ammonium transport
GO:0015697	quaternary ammonium group transport
GO:0015698	inorganic anion transport
GO:0015711	organic anion transport (transmembrane?)
GO:0015718	monocarboxylic acid transport
GO:0015748	organophosphate ester transport
GO:0015749	monosaccharide transport
GO:0015755	fructose transport
GO:0015758	glucose transport
GO:0015780	nucleotide-sugar transport (transmembrane?)
GO:0015781	pyrimidine nucleotide-sugar transport
GO:0015788	UDP-N-acetylglucosamine transport
GO:0015801	aromatic amino acid transport
GO:0015802	basic amino acid transport
GO:0015803	branched-chain amino acid transport
GO:0015804	neutral amino acid transport
GO:0015807	L-amino acid transport
GO:0015809	arginine transport
GO:0015816	glycine transport
GO:0015817	histidine transport
GO:0015818	isoleucine transport
GO:0015819	lysine transport
GO:0015820	leucine transport
GO:0015821	methionine transport
GO:0015822	ornithine transport
GO:0015823	phenylalanine transport
GO:0015824	proline transport
GO:0015826	threonine transport
GO:0015827	tryptophan transport
GO:0015828	tyrosine transport
GO:0015829	valine transport
GO:0015838	amino-acid betaine transport
GO:0015844	monoamine transport
GO:0015846	polyamine transport
GO:0015848	spermidine transport
GO:0015849	organic acid transport
GO:0015850	organic hydroxy compound transport
GO:0015857	uracil transport
GO:0015870	acetylcholine transport
GO:0015871	choline transport
GO:0015872	dopamine transport
GO:0015879	carnitine transport
GO:0015904 	tetracycline transport
GO:0015931	nucleobase-containing compound transport
GO:0015986	ATP synthesis coupled proton transport
GO:0016482	cytoplasmic transport
GO:0022804	active transmembrane transporter activity
GO:0022884	macromolecule transmembrane transporter activity
GO:0030001	metal ion transport
GO:0031460	glycine betaine transport
GO:0031919	vitamin B6 transport
GO:0031920	pyridoxal transport
GO:0031922	pyridoxamine transport
GO:0031923	pyridoxine transport
GO:0032328	alanine transport
GO:0032329	serine transport
GO:0032386	regulation of intracellular transport
GO:0032388	positive regulation of intracellular transport
GO:0034762	regulation of transmembrane transport
GO:0042883	cysteine transport
GO:0042886	amide transport
GO:0043269	regulation of ion transport
GO:0043270	positive regulation of ion transport
GO:0044765	single-organism transport
GO:0045117	azole transport
GO:0046907	intracellular transport
GO:0046942	carboxylic acid transport
GO:0051028	mRNA transport
GO:0051049	regulation of transport
GO:0051050	positive regulation of transport
GO:0051051	negative regulation of transport
GO:0051180	vitamin transport
GO:0051608	histamine transport
GO:0051924	regulation of calcium ion transport
GO:0051928	positive regulation of calcium ion transport
GO:0051937	catecholamine transport
GO:0060401	cytosolic calcium ion transport
GO:0060402	calcium ion transport into cytosol
GO:0070838	divalent metal ion transport
GO:0071579	regulation of zinc ion transport
GO:0071582	negative regulation of zinc ion transport
GO:0071702	organic substance transport
GO:0071705	nitrogen compound transport
GO:0071804	cellular potassium ion transport
GO:0072337	modified amino acid transport
GO:0072348	sulfur compound transport
GO:0072511	divalent inorganic cation transport
GO:0072512	trivalent inorganic cation transport
GO:0072531	pyrimidine-containing compound transmembrane transport
GO:0090481	pyrimidine nucleotide-sugar transmembrane transport
GO:1900751	4-(trimethylammonio)butanoate transport
GO:1901264	carbohydrate derivative transport
GO:1901374	acetate ester transport
GO:1901679	nucleotide transmembrane transport
GO:1902023	L-arginine transport
GO:1902024	L-histidine transport
GO:1902495	transmembrane transporter complex
GO:1902582	single-organism intracellular transport
GO:1903649	regulation of cytoplasmic transport
GO:1903651	positive regulation of cytoplasmic transport
GO:1903789	regulation of amino acid transmembrane transport

Hi
sorry what is the plan here?

Are you suggesting that these terms are deleted or marked as do not annotate?
When you say we should be able to annotate to a more specific term, these terms are very different, what are the child terms options? Please can you provide the terms you think people can  use instead. Obviously this is difficult for the very general terms such as ion transport, but an example of one option, or to use AE or Noctua to specify

Using QuickGO I have identified that there are 2000 manual expt annotations to these terms
UniProt | 17.79 | 396
MGI | 17.21 | 383
RGD | 11.77 | 262
ZFIN | 10.20 | 227
SGD | 10.02 | 223
FlyBase | 8.67 | 193
TAIR | 3.82 | 85
EcoCyc | 3.46 | 77
WormBase | 3.41 | 76
PseudoCAP | 2.88 | 64
I think you need to let all these groups know what you are proposing.
Also I think these general terms might be useful when used by InterPro etc, because there may not be a specific substrate for all members of a protein family might not be. note there are 4 million annotations directly using these terms. This is confirmed by the statistics for these terms which confirms 61% of annotations using these exact terms are provided by Interpro:
InterPro | 61.54 | 2,465,983
UniProt | 35.17 | 1,409,305
GOC | 2.52 | 100,833
Ensembl | 0.26 | 10,398
EnsemblFungi | 0.18 | 7,346
GO_Central | 0.18 | 7,315
EnsemblMetazoa | 0.03 | 1,115
RGD | 0.02 | 990
EnsemblPlants | 0.02 | 846
MGI | 0.02 | 661
Thanks
Ruth

Hi Ruth,
We are saying that most of these should really be transmembrane transport (for example glucose). They will not get a 'do not annotate' tag (at least that's not the plan at this point).
OK ?

Are there no cases where these things are transported across tissues or around organisms? These merges seem a bit dangerous.

Across organisms I haven't seen.
I have come across intestinal absorption and transepithelial transport, these have not been put under transmembrane. OK ?
I'll post a comment if I find anything that looks different - so far all transport I looked at was mediated by normal TM transporters.
Thanks, Pascale

I also think that for each one you need to be sure that there is no case where there is endocytosis so that the transport is not across the membrane. As mentioned before iron transport is not always (ever?) transmembrane therefore
GO:0072511	divalent inorganic cation transport
GO:0072512	trivalent inorganic cation transport
for example should not be merged with transmembrane transport
In future please make sure someone from each group contributing annotations that will be affected is included on the ticket. In this case UCL has no direct annotations to the terms listed, however we do have annotations to the child terms.
There is such a long list of terms above, who is going to be responsible for checking that for each term there is not an endocytosis mechanism?
Ruth

Hi @RLovering
Thanks for the feedback. Here's what I do: For each term:

check EXP annotations; if all annotated proteins are TM transporters (or if there are no annotations), then change term label (or merge with TM transporter if it exists)
otherwise postpone. So far all terms were in that category.

As mentioned in the previous ticket, I am not touching iron and lipids for now.
Thanks, Pascale

Look closely at the kidney and maybe transport into and out of the nervous system.

Thanks Pascale
but how are we to know which ones you are doing? the terms I have listed above are in your full list. but according to you they were in the category for merging.
so why are they in the list?
Ruth

Hi @RLovering
You're right, I don't know a priori which terms are excluded. I've been adding them at the bottom of the list (the part that starts with ??). I'm doing the straight forward ones first.

@pgaudet  this might be done. Maybe you can close and just request  any more as we see them (which is what I have been doing)

I agree more works need to be done but this ticket is not really useful to describe it.


helm: fix poststart-eni.bash execution in agent DS

This change fixes malformed bash -c call in postStart agent hook, which caused the script to not be executed.
This fixes a bug introduced in https://github.com/cilium/cilium/pull/24134

/test

/test-runtime

This PR has been superseeded by https://github.com/cilium/cilium/pull/24389 , but I think we need to backport only change from this PR into 1.13

Since the PR was superseded, but https://github.com/cilium/cilium/pull/24389 is not marked for backporting , I only changed indentation in this PR. This will allow us to backport the change to 1.13 with a small conflict.

After consideration, I will make a separate 1.13 PR. Closing this one.


Initial pull request

Have you consider to use rubocop together with overcommit here? If yes, rubocop and overcommit config files are needed.


⚠ Turnos 24x7 has degraded performance

In 21810e3, Turnos 24x7 (https://reservas-dev.alternativasinteligentes.com/) experienced degraded performance:

HTTP code: 200
Response time: 888 ms

Resolved: Turnos 24x7 performance has improved in 6dbfd5d.


install v1.16.0 fails: "can't open config file: /usr/lib/ssl/openssl.cnf"

Neither microk8s v1.16.0 (920) nor edge (922) installs on my Centos 7.6 1810 VM. v1.15.3 installs without error.
sudo yum install epel-release
sudo yum install snapd
sudo systemctl enable --now snapd.socket
sudo ln -s /var/lib/snapd/snap /snap  # enable classic snap support

At this point, here is how things look wrt openssl.cnf
ll /etc/ssl/  # output:
total 0
lrwxrwxrwx. 1 root root 16 Sep 27 12:20 certs -> ../pki/tls/certs

ls -la `sudo find /|grep openssl.cnf` # output

-rw-r--r--. 1 root root 10923 Oct 30  2018 /etc/pki/tls/openssl.cnf
lrwxrwxrwx. 1 root root    14 Sep 27 12:20 /usr/share/man/man5/openssl.cnf.5ssl.gz -> config.5ssl.gz

Nothing looks wrong. Following the instructions at https://snapcraft.io/docs/installing-snap-on-centos, I reboot.
Note that I've done nothing else significant up to now, I did the above steps on a new VM.
Then
sudo snap install microk8s --channel=1.16/stable --classic  # output:

error: cannot perform the following tasks:
- Run install hook of "microk8s" snap if present (run hook "install":
-----
+ export LD_LIBRARY_PATH=/snap/microk8s/920/lib:/snap/microk8s/920/usr/lib:/snap/microk8s/920/lib/x86_64-linux-gnu:/snap/microk8s/920/usr/lib/x86_64-linux-gnu
+ LD_LIBRARY_PATH=/snap/microk8s/920/lib:/snap/microk8s/920/usr/lib:/snap/microk8s/920/lib/x86_64-linux-gnu:/snap/microk8s/920/usr/lib/x86_64-linux-gnu
+ export PATH=/snap/microk8s/920/usr/sbin:/snap/microk8s/920/usr/bin:/snap/microk8s/920/sbin:/snap/microk8s/920/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/bin:/usr/local/bin
+ PATH=/snap/microk8s/920/usr/sbin:/snap/microk8s/920/usr/bin:/snap/microk8s/920/sbin:/snap/microk8s/920/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/bin:/usr/local/bin
+ source /snap/microk8s/920/actions/common/utils.sh
+ cp -r /snap/microk8s/920/default-args /var/snap/microk8s/920/args
+ mkdir /var/snap/microk8s/920/certs
+ cp /snap/microk8s/920/certs/csr.conf.template /var/snap/microk8s/920/certs/csr.conf.template
+ produce_certs
+ for key in serviceaccount.key ca.key server.key front-proxy-client.key
+ '[' -f /var/snap/microk8s/920/certs/serviceaccount.key ']'
+ openssl genrsa -out /var/snap/microk8s/920/certs/serviceaccount.key 2048
WARNING: can't open config file: /usr/lib/ssl/openssl.cnf
Generating RSA private key, 2048 bit long modulus
..................................................................................+++
.................................................................+++
unable to write 'random state'
e is 65537 (0x10001)
+ for key in serviceaccount.key ca.key server.key front-proxy-client.key
+ '[' -f /var/snap/microk8s/920/certs/ca.key ']'
+ openssl genrsa -out /var/snap/microk8s/920/certs/ca.key 2048
WARNING: can't open config file: /usr/lib/ssl/openssl.cnf
Generating RSA private key, 2048 bit long modulus
...................................+++
...............................................................................................................+++
unable to write 'random state'
e is 65537 (0x10001)
+ for key in serviceaccount.key ca.key server.key front-proxy-client.key
+ '[' -f /var/snap/microk8s/920/certs/server.key ']'
+ openssl genrsa -out /var/snap/microk8s/920/certs/server.key 2048
WARNING: can't open config file: /usr/lib/ssl/openssl.cnf
Generating RSA private key, 2048 bit long modulus
.+++
............................................+++
unable to write 'random state'
e is 65537 (0x10001)
+ for key in serviceaccount.key ca.key server.key front-proxy-client.key
+ '[' -f /var/snap/microk8s/920/certs/front-proxy-client.key ']'
+ openssl genrsa -out /var/snap/microk8s/920/certs/front-proxy-client.key 2048
WARNING: can't open config file: /usr/lib/ssl/openssl.cnf
Generating RSA private key, 2048 bit long modulus
...............................+++
....+++
unable to write 'random state'
e is 65537 (0x10001)
+ '[' -f /var/snap/microk8s/920/certs/ca.crt ']'
+ openssl req -x509 -new -nodes -key /var/snap/microk8s/920/certs/ca.key -subj /CN=<IP_ADDRESS> -days 10000 -out /var/snap/microk8s/920/certs/ca.crt
WARNING: can't open config file: /usr/lib/ssl/openssl.cnf
Unable to load config info from /usr/lib/ssl/openssl.cnf
-----)

Now, here is how things stand with regard to openssl.cnf:
ls -la `sudo find /|grep openssl.cnf`   # output:
-rw-r--r--. 1 root root 10923 Oct 30  2018 /etc/pki/tls/openssl.cnf
lrwxrwxrwx. 1 root root    14 Sep 27 12:20 /usr/share/man/man5/openssl.cnf.5ssl.gz -> config.5ssl.gz
-rw-r--r--. 1 root root 10835 Feb 27  2019 /var/lib/snapd/snap/core/7713/etc/ssl/openssl.cnf
lrwxrwxrwx. 1 root root    20 Feb 27  2019 /var/lib/snapd/snap/core/7713/usr/lib/ssl/openssl.cnf -> /etc/ssl/openssl.cnf       ##### this is a broken symlink

Disabling selinux made no difference.
If I install v1.15.3, it's still a broken link, and installation works.
[mb@mb-centos7-1810-c ~]$ snap list
Name      Version  Rev   Tracking  Publisher   Notes
core      16-2.41  7713  stable    canonical✓  core
microk8s  v1.15.3  825   1.15      canonical✓  classic

(At the moment Centos 7.6 1908 is the latest; I am tied to 1810 for an unrelated compatibility reasons.)

I'm having the same issue. I see the following results for the config file:
sudo find / -name *openssl.cnf /etc/ssl/openssl.cnf find: File system loop detected; ‘/.snapshots/1/snapshot’ is part of the same file system loop as ‘/’. /.snapshots/2/snapshot/etc/ssl/openssl.cnf -snipped- /.snapshots/14/snapshot/etc/ssl/openssl.cnf /snap/core/7713/etc/ssl/openssl.cnf /snap/core/7713/usr/lib/ssl/openssl.cnf
So it looks to me like it's trying to use the packaged config file but for some reason resolving the host's filesystem instead of the mounted one.

There should be a fix on edge by tomorrow (sudo snap install microk8s --classic --edge). Please let me know if it worked for you too.
Thank you @DomFleischmann for your work.

# snap info microk8s
 ...
installed:        v1.16.0             (927) 187MB classic

Thank you for the quick response.


TypeError: Cannot read property '$$phase' of null

This error is called on this line:
          $element
            .on('dp.change', function (e) {
              if (ngModelCtrl) {
                $timeout(function () {
                  ngModelCtrl.$setViewValue(e.target.value); // TypeError: Cannot read property '$$phase' of null
                });
              }
            })
            .datetimepicker(options);

I think $setViewValue should be wrapped in something like this:
  $scope.$applyAsync(function() {
    ngModelCtrl.$setViewValue(e.target.value);
  });

and if should remove listeners by $element.off with the event handler on $scope.$on('$destroy', ...)

The problem is that $timeout puts a promise in $digest cycle. But when the scope which holds datetimepicker is destroyed, also does the model. So, in the end (after local scope is destroyed), $digest finds a promise and executes it. This promise calls $setViewValue on a model that dont exist anymore (its scope is destroyed).
So, to solve this you should do something like this:
var promise = $timeout(...);
scope.$on('$destroy', function() {
  $timeout.cancel(promise);
  $element.off();
});

Worked for me.


Fix CompactionIT after changes in #4127

This increases the value of table.file.max.prop to 1001, which is the value already used by testErrorDuringUserCompaction, so that the tests get the expected values

It looks like there are 3 failing tests. Can this same fix be used for all of them? See #4135


Changing invalid request state detection logic in NettyMessageProcessor.

Previously NettyMessageProcessor used to be ready for subsequent requests on the same channel only after NettyResponseChannel reported that responses had been fully sent out (including sending of LastHttpContent  which is an artifact of Netty and has no meaning in responses with Content-Length set). This created a race condition between the server and client in the scenario where clients detect that they have fully received a response and send another request while the server still hadn't realized that the response has been fully sent out. This race condition became more pronounced and started inducing errors when the NonBlockingRouter was used.
This commit fixes this problem by declaring the NettyMessageProcessor ready for subsequent requests
as soon as the current request is fully received from the client. This way, there are no race conditions
because NettyMessageProcessor is ready even before the response sending has started. The only way this can cause an error is if the client sends a request without waiting for the previous response in which
case that would be a bug with the client and not the server.
Primary Reviewers: @pnarayanan
Expected time to review : 15 mins
@pnarayanan debugged the issue with me and has tested the fix so he has the most context to review.
Built (./gradlew build and ./gradlew test) and formatted.

@pnarayanan : @dniq merged it by mistake ! Please take a look - will make changes suggested. The PR doesn't break the build so I'm not going to revert it (it creates another commit)

LGTM.


MeshLine.load submeshes & boundaries

MeshLine.load warns

UserWarning: Unable to load submeshes

for any input, and fails to read any subdomains and boundaries present.
The immediate cause is that 'line' is absent from the keys in
https://github.com/kinnala/scikit-fem/blob/dadd4bac13ca66786c6a545fbb3f139c8b34836a/skfem/mesh/mesh.py#L286-L291
While the one-dimensional examples to date just use MeshLine.__init__, and this suffices for most purposes, it is occasionally useful to generate even one-dimensional meshes externally in Gmsh; e.g. for problems like the ‘composite wall composed of n slabs of thicknesses l1, …, ln and conductivities K1, …, Kn’ of Carslaw & Jaeger (1959, Conduction of Heat in Solids, §3.2 ‘Steady temperature’, Oxford University Press).
Minimal example: line.geo.gz.
Point(1) = {0, 0, 0};
Point(2) = {1, 0, 0};
Line(1) = {1, 2};

Generate mesh with
gmsh -1 line.geo

and attempt to load with
MeshLine.load('line.msh')

Just adding 'line': 'vertex' seems to be enough to get MeshLine.load to not warn and to successfully read the subdomain defined by the addition line in line.geo
Physical Curve("domain") = {1};

MeshLine.load is not loading the boundaries correctly; e.g. for
Point(1) = {0, 0, 0};
Point(2) = {1, 0, 0};
Line(1) = {1, 2};
Physical Point("left") = {1};
Physical Point("right") = {2};
Physical Curve("domain") = {1};

which produces line.msh.gz, containing
$PhysicalNames
3
0 1 "left"
0 2 "right"
1 3 "domain"
$EndPhysicalNames

I'm wondering whether the problem follows from MeshLine._build_mappings sorting .p whereas that method of other descendents, e.g. MeshTri, MeshTet, doesn't.

Yes, this is the problem.  In the above example, at
https://github.com/kinnala/scikit-fem/blob/9ff1fd5c76a5b3044df563721c0c80fe6069e651/skfem/mesh/mesh.py#L314-L316
we have facets == array([[0], [1]]), but bndfacets == array([0, 5]), i.e. facets is numbered as in line.msh but bndfacets uses the reordered nodal indices.
Then dic == {{(0,): 1, (1,): 2} (input order) so in
https://github.com/kinnala/scikit-fem/blob/9ff1fd5c76a5b3044df563721c0c80fe6069e651/skfem/mesh/mesh.py#L324-L326
the if-clause does get 'left' but only by luck since node 0 survived the permutation but misses 'right' since self.external.points[1] at x = 1.0 has been renumbered as self.p[:, 5]; i.e. index only contains one entry
array([[1, 0]])

I don't know how to fix this.  I don't think it can be done at this point of _parse_submeshes since the permutation of the points is not remembered.

I can't recall now the exact reason for doing the sort in _build_mappings. There could have been some technical problem but maybe its only because mesh.p was easier to interpret this way.

I think you could as a workaround (for 1D meshes) re-sort self.external.points in _parse_submeshes and by that way obtain the correspondence 0<->0, 1<->5 by setting the kwarg return_index or return_inverse to True in np.sort.

I can't recall now the exact reason for doing the sort in _build_mappings. There could have been some technical problem but maybe its only because mesh.p was easier to interpret this way.

That sorting is relied upon in a couple of places:

the argument t that is passed to MeshLine.__init__ is always silently ignored and
MeshLine.t and MeshLine.facets are defined in terms of the sorted MeshLine.p.

https://github.com/kinnala/scikit-fem/blob/625ac42ed2185982752c49def5259c6f4e6fa4a2/skfem/mesh/mesh_line.py#L44-L47

So if it's O. K. to drop the sorting of the p, there's a fix in #176.

Nothing left here I presume.


fix(SESI-261): clamp max width column to 75% of visualization width

:tada: This PR is included in version 1.2.3 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


Update Co-Chair Statuses

Removes Community Committee Co-Chair label on @racehlnicole's line and removes Co- from @bnb's line.
This should be able to be merged if @rachelnicole has no objections.
Ref: https://github.com/nodejs/community-committee/issues/251

LGTM <3


Error: Unable to load valid module manifest data

Error: Unable to load valid module manifest data from "https://github.com/jessev14/pf2e-staves/releases/download/1.2.5/module.json"
The requested manifest at "https://github.com/jessev14/pf2e-staves/releases/download/1.2.5/module.json" did not provide module manifest data.
at Module.installPackage (file:///home/ubuntu/foundry/resources/app/dist/packages/views.mjs:1:1634)
at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
at async SetupView.handlePost (file:///home/ubuntu/foundry/resources/app/dist/server/views/setup.mjs:1:1980)
error @ setup.js:292

a refresh fixed it. weird closing.


Discussions from AGAGE69

The following is a summary of the outstanding discussion and outcomes from AGAGE69. Some of these points may be better split into individual issues.

[ ] Should the folder named ‘event’ be changed to something more descriptive?

[ ] - Update/check data policy as it was likely taken from an out-of-date version on the AGAGE website

[ ] - Debate over whether to keep all gases as lowercase. Seemed the opinion was that it should stay that way.

[ ] - The instruments for CMN are currently separated and need to be combined into a single record

[x] - There may be some problems with “non-AGAGE” measurements at an AGAGE site (e.g., measurements may be made as part of a previous network that is not ALE/GAGE/AGAGE but would like to be considered as AGAGE).

[ ] - Whether to include the instrument in the filename [vote was to remove instrument]

[ ] - The time in the netcdf files does not currently state that the time is UTC

[ ] - CHECK: CGO CH3CCl3 CGAA data may have had pollution events removed in the record. Need to add to the README that this has been done. Need to double check whether that has been done to other compounds as well. Paul F. suggests to look at all compounds. It should be obvious by eye if there is a difference between CGAA and ALE.

[ ] - Overlap of instruments: should instruments switch cleanly at one time, or be able to temporarily switch back and forth.

[ ] - Decision was for this to be a decision from data managers.

[ ] - May be some issues when changing between two of the same instrument (e.g,, 2 picarros). This is already noted in issue #44.

[ ] - Known outstanding issues:

[ ]  _pdd naming of H2 data files

[ ]   - Unable to output Met Office baselines flags

[ ]   - Actions: Station PIs to report whether to use CFC-11 ALE/GAGE “S” or “P”

[ ]     - Who will be responsible for maintaining this going forward? Ray Wang volunteered that he may be most appropriate

Question around outputting in other file formats:

A human readable file format would be useful
Perhaps give the user the ability to output in multiple formats
A web tool may be best to output in a couple of desired formats

From Ray Wang's talk:

Add "event" to filename...
... but what about hourly Picarro data?
Change mf_N to mf_count?
Underscores in filename: AGAGE_ALE-GCMD_CGO_cfc-11_event_version.nc
Make filename all lower case?
Include Picarro model number in filename? Probably not for now?
Remove "v1" for version string

Proposed alternate naming: {network}{-instrument, optional}{site}{species}_{extra, optional-}{version}.nc
I.e., keep hyphens for the optional extra bits: instrument and "extra" string (e.g., "baseline-flag", "monthly-baseline"). This way, we always have three underscores, and the user always knows that site will be after the first underscore and species after the second.

Couldn't decide on a better term than "event", so current idea is just to ignore it. Hard to get something that describes the high-frequency in-situ data combined with the hourly Picarro data. High-frequency files will just be directly in the species folder, and then individual instruments and monthly means will be in sub-folders