Propose unit cell concept

So I'd note that this definition will be easier to write if we have agreed on the concept of a crystal structure model which we have a draft of here. Can we agree on that first, and then the unit cell concept should fall out of it?
I note that the present draft for unit cell includes ideas of disorder, whereas the simple crystal structure model described above doesn't explicitly allow for that. We could either adjust the crystal structure model description to allow for the unit cell to have "disordered" contents while having fixed dimensions, or we could have the basic unit cell with well-defined contents and then a separate concept that allows for various forms of disorder.

I have summarized thoughts on the "unit cell" (and, incidentally, of the "crystal") definitions from today's discussions:
crystal-unit-cell-concept.txt

After reviewing the EMMO ontologies for data and semiosis, and bearing in mind last weeks' discussion, I think perhaps it makes more sense to pursue "unit cell" as the key concept instead of "crystal structure model" (see #12 and a discussion topic #17). How I think this might work:

The unit cell parameters listed in databases and derived from experiments are "secondary data", that is, data derived from primary data. We can use the data ontology to describe these values.
Separately, we use the "reductionistic" perspective to describe crystalline materials as being composed of many non-overlapping unit cells.
We then use semiosis to state that the unit cell parameters found in CIF files are interpreted by the publisher of the CIF data to be parameters of the unit cell we have described in the reductionistic perspective.
The same process can be used to capture the other information that arises from a crystallographic experiment.

I had initially understood that we should not think about working with the reductionistic perspective because we weren't 100% sure that a material really was a crystal, so could not properly assign any individual to the entity "crystalline material". However, if we are simply interpreting a piece of data as a unit cell parameter, then we are not committing the ontology to assert that any given material is crystalline / aperiodic / periodic. A search for a crystalline material could be expressed as "find a material to which at least one publisher has assigned unit cell parameters".
My question to @emanueleghedini, @jesper-friis and @francescalb as EMMO experts is, does that sound like a reasonable way to proceed?

I'm a bit worried that this is taking us in a direction of an ontology that will be difficult for our use cases of materials/crystallography databases that are primarily built on theory and computation, and thus work entirely with models (in the arguably most common use of that word in science).
Nevertheless, with a completely reductionist perspective, isn't "unit cell" also a model abstraction? Don't we need to get to the cell parameters bottom-up through something like this?:

An experimental x-ray diffraction pattern is-a semiotic sign; which has been created via an x-ray experiment performed on a sample.
An essentially sharp diffraction pattern is-a experimental x-ray diffraction pattern; where most of the intensity of the diffraction is concentrated in relatively sharp Bragg peaks.
A diffraction 2*theta peak value is a semiotic sign; which is interpreted from an essentially sharp diffraction pattern.
A lattice constant or angle is-a semiotic sign; which is the result of a mathematical equation on a set of diffraction 2*theta peak values.

But this would leave us completely without the abstract concepts of "unit cells" and "periodic crystals". So, can we get there via "semiotic representations", or, is that just another word for models? E.g.,

A crystalline solid represents a sample with an essentially sharp diffraction pattern.
A unit cell is-a constituent part of a crystalline solid.

I don't think "unit cell" has to be seen as a model abstraction. If the EMMO physicalistic perspective is able to posit things like "gluons", "gravitons", and "fields" and so on, then I think we can happily introduce a "crystalline solid" composed of many non-overlapping "unit cells".
I believe that all of the examples above ("diffraction pattern" through to "lattice constant") are simply types of data in EMMO. These numbers then have to be interpreted by somebody in order to see them as relating to the lattice parameters of a unit cell in a material, at least, that is how I think EMMO wants to describe the process.
I agree that it seems strange that we are sidelining models, when essentially all the experimental results come from applying a model, but on the other hand that means we don't actually have to reproduce the models in all their detail and variation. Instead we only need to introduce those aspects that the "interpreter" cares about (e.g. the choice of extinction model can be ignored). And the fact that models posit an infinite crystal is irrelevant, as the people interpreting the results of the model are happy to see the resulting lattice parameters as facts about an actual space-limited object.
Another "win" as I see it is that the whole aperiodic/periodic thing goes away. We construct in the physicalistic (reductionistic?) perspective distinct aperiodic and periodic crystals, and whether or not a particular material is seen as one or the other just depends on the model from which the parameters in the data base are derived.
At least that's how I see it but I would dearly love the ontologists to (a) confirm that this is viable (b) provide a pointer to how other domains have implemented models, where a "model" is a mathematical equation that has free parameters whose values can be chosen so that the result of calculations using the equation best match observed values.


[bp/1.28] tracing: dd-trace-cpp v0.1.12 (#31526)

We use Istio and see issues with the datadog tracer in Envoy 1.27/1.28. We're opening this backport as we believe that the later version of the tracer library should resolve some (hopefully all) the issues we see.
As with the last backports I opened, I ran the unit tests locally (using libc++).
Commit Message: [bp/1.28] Datadog: tracing: dd-trace-cpp v0.1.12
Additional Description:
This is the backport of #31526
Risk Level: low
Testing: local unit tests
Docs Changes: n/a
Release Notes: n/a
Platform Specific Features: n/a
Fixes: #30957, #29354, and #31360.

None of the issues in the Envoy Datadog extension that I've addressed since v1.27 involved changes to the dd-trace-cpp library. Instead, the bugs were introduced in changes that I made to Envoy.
I doubt that backporting a more recent dd-trace-cpp onto Envoy's release branches will fix any bugs, and so I think that it's inappropriate to do so.
@Smeb has described the tracing issues that he's encountered since upgrading to an Istio version that uses Envoy versions that contain Datadog tracing bugs. Let's address those issues individually. They likely will not involve changes to dd-trace-cpp, nor backporting dd-trace-cpp releases onto Envoy releases.

Closed based on the above comment.


Pausing tree disables white-listed Area2D's signals

Godot version
3.5 RC4
System information
Windows 10
Issue description
When pausing the scene tree, and an Area2D is white-listed to process while paused, the body_entered signals are not fired.
https://user-images.githubusercontent.com/21325943/174443994-07604fb1-872c-4970-9832-774e41b76f69.mp4
Steps to reproduce

Create a scene with a white-listed branch.
Have the branch contain a moveable body and Area2D
Set Area2D's body_entered signal to notify when body has entered.
pause tree and move body over Area2D

Minimal reproduction project
CollisionBug.zip

I believe this has already been reported.

I looked through https://github.com/godotengine/godot/issues/45334 but I couldn't find it.

https://github.com/godotengine/godot/issues/61420 I think is what I remember. Not all issues are listed on the tracker

Ah! That one is specific to 4.0, and has a different result with the new pause system, causing the signal to be removed entirely or throw errors.

Workaround: call Physics2DServer.set_active(true) after pausing the tree.
A side effect of get_tree().paused = true is to disable the physics engine. It is documented, just not very clearly:
https://docs.godotengine.org/en/stable/classes/class_scenetree.html#class-scenetree-property-paused

Hm. This does resume the physics server, but still seems like an unintentional side-effect. It's a far-reaching workaround, because with the pause system currently, it means either:

White-listed nodes don't behave as white-listed (physics disabled for all).
Paused nodes don't behave as paused (physics enabled for all).

I don't think this can be resolved unless something like https://github.com/godotengine/godot/pull/46191 is backported in a backwards-compatible manner, which sounds too difficult to do.

@Calinou The mentioned rewrite introduces it's own set of (worse?) Area2D bugs (mentioned a few comments above), but you're absolutely right. It's probably not worth spending the effort to backport the fix to 3.x in the long-run and just focus on 4.0. It seems like, for now, the best solution is either a custom pause system in 3.x or wait for Area2D to be fixed in 4.0.
As reference for anyone else who needs to be able to pause in 3.x without this bug, nodes have the following methods you can use to emulate a custom system, by iterating through a branch:
set_physics_process()
set_physics_process_internal()
set_process()
set_process_internal()
set_process_input()
Keep in mind it can be brittle so node reparenting should be kept to a minimum.

Closing since it can't be fixed in 3.x


Bottom Modal rebuild multiple times when I focus textfield

I have a textfield in a modal bottom sheet. And when I focus the textfield, the bottom modal is rebuild 20-30 times.
Only test on iOS emulator.
Here is a minimum reproducible code :
https://gist.github.com/camilledelouis/41c7fc17d4c2878bb2739e0d43d4873b

@camilledelouis
What Flutter version are you seeing this behavior on ?
There was a recent fix made related to similar scenario that you can take a look https://github.com/flutter/flutter/issues/126833
Also, see below related open issues for your reference:
https://github.com/flutter/flutter/issues/113192
https://github.com/flutter/flutter/issues/105184


ftp list function only returning a String

This one is only for ease of use:
It would be great if the list function return a Struct containing all of the information in the String.
I will do yet another pull request adding the code that I made for this, but I would like the openssl issue #69 to be resolved first because the list function doesn't work without this update.

This is ready on my fork (because I needed it), but I won't create a PR until #69 isn't merged because it is based on that.

@Luxed Can you please create a PR ? This feature interest me also 😃

@benjaminbours Well... This is 2 years old now.
I looked at my branch and I'm not that happy about what I did. I don't like the fact that everything is based on the given string, so if the returned string doesn't have a fixed format, this entire module would break.
If are willing to make the PR yourself, the changes are on my branch, feel free to fork/merge that into your branch, fix everything up and test to see if this still works.

It's ok forget it 😄By the time, I checked specification about FTP and it seems there is no official specification about the response format of the LIST command.
Here are some useful ressources I found about it during my search => https://files.stairways.com/other/ftp-list-specs-info.txt
http://cr.yp.to/ftpparse.html => This one could be a Rust crate by itself, it seems to cover most of the case and I think FileZilla for exemple.

I have created a crate that can parse FTP-server's answer  (LIST command): ftp-cmd-list-parse

I have created a crate that can parse FTP-server's answer  (LIST command): ftp-cmd-list-parse


Anchor integration test doesn't exit when program panics

When running anchor test, if the program panics, the process hangs and does not exit.
It can be replicated by a simple program that say has a lot of un-boxed accounts so the access violation is thrown. Please see below an example of the log output.
The program just hangs after these logs forever. I waited up to 10 minutes before killing the process (successful test finishes in 9 seconds).
Found a 'test' script in the Anchor.toml. Running it as a test suite!

Running test suite: "/home/sohrab/workspaces/hello_anchor/Anchor.toml"

yarn run v1.22.18
$ /home/sohrab/workspaces/hello_anchor/node_modules/.bin/ts-mocha -p ./tsconfig.json -t 1000000 tests/**/*.ts

  hello
Transaction simulation failed: Error processing Instruction 0: Program failed to complete
    Program Fg6PaFpoGXkYsidMpWTK6W2BeZ7FEfcYkg476zPFsLnS invoke [1]
    Program Fg6PaFpoGXkYsidMpWTK6W2BeZ7FEfcYkg476zPFsLnS consumed 3688 of 1400000 compute units
    Program failed to complete: Access violation in stack frame 3 at address 0x200003e38 of size 8 by instruction #4580
    Program Fg6PaFpoGXkYsidMpWTK6W2BeZ7FEfcYkg476zPFsLnS failed: Program failed to complete
    1) panics!

  0 passing (33ms)
  1 failing

  1) hello
       panics!:
     Error: failed to send transaction: Transaction simulation failed: Error processing Instruction 0: Program failed to complete
      at Connection.sendEncodedTransaction (/home/sohrab/workspaces/common/temp/node_modules/.pnpm/@solana+web3.js@1.36.0/node_modules/@solana/web3.js/src/connection.ts:3964:13)
      at processTicksAndRejections (node:internal/process/task_queues:96:5)
      at async Connection.sendRawTransaction (/home/sohrab/workspaces/common/temp/node_modules/.pnpm/@solana+web3.js@1.36.0/node_modules/@solana/web3.js/src/connection.ts:3921:20)
      at async sendAndConfirmRawTransaction (/home/sohrab/workspaces/common/temp/node_modules/.pnpm/@project-serum+anchor@0.24.2/node_modules/@project-serum/anchor/src/provider.ts:284:21)
      at async AnchorProvider.sendAndConfirm (/home/sohrab/workspaces/common/temp/node_modules/.pnpm/@project-serum+anchor@0.24.2/node_modules/@project-serum/anchor/src/provider.ts:144:14)
      at async MethodsBuilder.rpc [as _rpcFn] (/home/sohrab/workspaces/common/temp/node_modules/.pnpm/@project-serum+anchor@0.24.2/node_modules/@project-serum/anchor/src/program/namespace/rpc.ts:29:16)
      at async Context.<anonymous> (file:///home/sohrab/workspaces/hello_anchor/tests/hello.ts:84:5)

Can you attach your test code and anchor program? Repo / branch with simple way to reproduce is preferred.

I set up a couple of different projects but can't seem to replicate it consistently. Def modifying the tutorial-3 code to panic, it did not hang as I described above. But it is still happening in some of the other projects. 🤷
For the sake hygiene, I'll close this for now till I can reliably reproduce it.


Network selector redesign

I think a leaner design will be beneficial for the overall composition of the dashboard, and also to the behavior of the component when resizing.
Please let me know what you think.
@tetogomez @xavier506
https://zpl.io/VDNxePq

You can find logos here: https://zpl.io/29mRr0W
And the component guide here: https://zpl.io/bzdB4P8


Compatibility with PF2e Spell Summary

It would be nice if this had some compatibility with PF2e Spell Summary (https://github.com/reonZ/pf2e-spells-summary) As it helps cut down on the space the spell lists take up. Currently the spells will not cast while they are in the collapsed version of the Spell List.

This should be doable, but this module was funded by a commission. I unfortunately don't have the means to implement and maintain compatibility with other modules in my free time.
I'm happy to accept a pull request if you'd like to implement it yourself. Or you can reach out to me on Discord to discuss funding the development enso#0361.


Enhance Readme

We need to remove clutter from our Readme.md file.
Requirements

Need to remove the Roadmap section
Fix grammatical mistakes, if any

In the future, we will migrate the Roadmap to a better place where managing will be much easier

Hey @chilarai, i would like to work on this issue

@hemantwasthere sure.

Thanks @chilarai for assigning the issue

Hey @chilarai, I have opened a PR please check it out

Closed with PR #110


WIP: Don't add additional scope when profile is not enabled

The additional scope break some clippy lint detection (like missing_errors_doc)
This Fix #75
WIP: the change affect only when no profiling instrumentation is enabled.
But if the puffin (by example) instrumentation is enabled, the problem is here again.
And when I have tried remove the additional brace too in impl_block of profile-with-puffin, the macro failed with :
error: custom attribute panicked
 --> profiling/examples/simple.rs:8:1
  |
8 | #[profiling::all_functions]
  | ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  |
  = help: message: expected curly braces

The correct fix would be to find a way to pass doc comments through, and I think this is actually happening.


Monad transformers should implement the interfaces of the nested types being manipulated.

This would allow, for example, values to be added to every List nested inside a Stream via a ListT
     Stream<List<Integer>> nested = Stream.of(list1,list2,list3);
     Stream<List<Integer>> tenAdded = nested.map(list->list.add(10));

With a List Transformer this would look like
     ListT<Integer> tenAdded = ListT.fromStream(Stream.of(list1,list2,list3))
                                                        .add(10);
           //underlying structure is still Stream<List<Integer>>

ListT should extend ListX
SetT should extend SetX
StreamT should extend ReactiveSeq
StreamableT should extend Streamable
ReaderT should extend Reader
TryT should extend Try
MaybeT should extend Maybe
EvalT should extend Eval
XorT should extend Xor
FutureWT should extend FutureW

Complex to implement, benefit probably not worth the effort at this stage.


fix(tsconfig): enforce verbatimModuleSyntax and fix files

Description:
By enabling verbatimModuleSyntax we will be forced to specify when we're importing a type.
Using the verbatimModuleSyntax flag on a clean install triggered an error upon pnpm wagmi-generate script call.
So to keep the usefulness of the tsc checks I moved away the check from the pre-commit husky hook and moved it to a pre-push git hook.
This means, that whoever wants to use it, needs to set it up locally by running the following command:
$ pnpm git:config:hooks

[!WARNING]
This will define the githooks/ directory as the source of hooks for the repo's git config.
If you have your configs, please be sure to add what's inside githooks/pre-push file into your setup, so you too run the tsc command before pushing.

Steps:
tsc should pass without errors (that is, the build pass)
Type of change:

[x] New feature
[ ] Bug fix
[x] Breaking change
[x] Enhancement
[x] Refactoring
[x] Chore

How Has This Been Tested?

[x] Manual testing
[ ] Automated tests
[ ] Other (explain)

Remember to check that:

Your code follows the style guidelines of this project
You have performed a self-review of your code
You have commented your code in hard-to-understand areas
You have made corresponding changes to the documentation
Your changes generate no new warnings

Screenshots
(Add screenshots or videos to help test this pull request)

@nicosampler please re-check this, as it's completely different from what you approved


Validate ClientHello session_id field length and send alert on failure (1.0.1)

RT#4080

+1, subject to the same nit as in #545 being fixed.

Nit fixed just now.

+1

+1 same temrs

Patch applied. Thanks.


Keras Unable to clone_model a load_model result saved in TF format

Please make sure that this is a bug. As per our
GitHub Policy,
we only address code/doc bugs, performance issues, feature requests and
build/installation issues on GitHub. tag:bug_template
System information

Have I written custom code (as opposed to using a stock
example script provided in TensorFlow): Yes, see attached example
OS Platform and Distribution (e.g.,
Linux Ubuntu 16.04): CentOS 7
Mobile device (e.g. iPhone 8, Pixel 2, Samsung Galaxy) if
the issue happens on mobile device: N/A
TensorFlow installed from (source or
binary): Binary
TensorFlow version (use command below): 2.0.1
Python version: 3.6.8
Bazel
version (if compiling from source): N/A
GCC/Compiler version (if compiling from
source): N/A
CUDA/cuDNN version: N/A
GPU model and memory: N/A

You can collect some of this information using our environment capture
script
You can also obtain the TensorFlow version with: 1. TF 1.0: python -c "import tensorflow as tf; print(tf.GIT_VERSION, tf.VERSION)" 2. TF 2.0: python -c "import tensorflow as tf; print(tf.version.GIT_VERSION, tf.version.VERSION)"
Describe the current behavior
Attempting to clone a loaded model that had been saved in TF format (i.e. a directory rather than .h5) creates an error.  This appears to be because the loaded model is of a slightly malformed type.
Describe the expected behavior
clone_model should be able to clone derived types.  load_model should return a true model instance even when loading a TF format model.
Standalone code to reproduce the issue
Provide a reproducible test case that is the bare minimum necessary to generate
the problem. If possible, please share a link to Colab/Jupyter/any notebook.
import tensorflow as tf

# make dummy functional model
x = tf.keras.layers.Input(10)
y = tf.keras.layers.Dense(10)(x)

a = tf.keras.models.Model(x,[y])

# save model with tf format
a.save('foo_model')

print('Type of a is {0}'.format(type(a)))
print('a._is_graph_network = {0}'.format(a._is_graph_network))

# read in the model
b = tf.keras.models.load_model('foo_model')

print('Type of b is {0}'.format(type(b)))
print('b._is_graph_network = {0}'.format(b._is_graph_network))

# Try to clone b, errors because b is not of correct type.
c = tf.keras.models.clone_model(b)

Other info / logs Include any logs or source code that would be helpful to
diagnose the problem. If including tracebacks, please include the full
traceback. Large logs and files should be attached.
Output
Type of a is <class 'tensorflow.python.keras.engine.training.Model'>
a._is_graph_network = True
Type of b is <class 'tensorflow.python.keras.saving.saved_model.load.Model'>
b._is_graph_network = False
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~/proj/keras_load_clone.py in <module>()
     21
     22 # Try to clone b, errors because b is not of correct type.
---> 23 c = tf.keras.models.clone_model(b)

~/.local/lib/python3.6/site-packages/tensorflow_core/python/keras/models.py in clone_model(model, input_tensors, clone_function)
    420   else:
    421     return _clone_functional_model(
--> 422         model, input_tensors=input_tensors, layer_fn=clone_function)
    423
    424

~/.local/lib/python3.6/site-packages/tensorflow_core/python/keras/models.py in _clone_functional_model(model, input_tensors, layer_fn)
    163                      'got a `Sequential` instance instead:', model)
    164   if not model._is_graph_network:
--> 165     raise ValueError('Expected `model` argument '
    166                      'to be a functional `Model` instance, '
    167                      'but got a subclass model instead.')

ValueError: Expected `model` argument to be a functional `Model` instance, but got a subclass model instead.

I've tried overwriting the _is_graph_network attribute, but that just pushes off the problem to another line.
The reason I have to load and then clone is so I can recreate old models with specific datatypes (because TF 2.0.1 can't save mixed_float16 models, I had to save as float32 and fix after loading).  Normally, one would just rebuild the model from the actual commands, but I've made backward-compatibility breaking changes since then.  I'd like to still be able to use my old models.  I'm looking at just updating to TF2.2, but I don't control my environment so that may not be an option.

@dvbuntu,
I was able to reproduce the issue with TF v2.0.1 and TF v2.1.0. However, I was able to run the code without any issues with TF-nightly. Please find the attached gist. Thanks!

Good to hear it's fixed in the 2.2.  I'll just this example to push for the upgrade.

@dvbuntu,
Please feel free to close the issue if resolved. Thanks!


Support circular vite configs

I ran into problems trying to use Svelte since it has a circular config.

Released in: https://github.com/aklinker1/vite-plugin-web-extension/releases/tag/v1.4.3


Can not import connections from a csv file into Dbeaver

Hi,
Even after formatting the columns as mentioned in the documentation, I am still not able to import connections from a csv file into DBeaver.

Shirish

@shirishkale could you provide steps to reproduce an issue? is there something in the logs?

The database connections are never imported from the xml / csv files.
Please find attached csv, xml as well as process screenshot
conn_import_test.csv
s
dbeaver import screenshots.docx
.

@shirishkale
i was able to import connections from your example. But i was need to change column header to lowercase and switch file encoding to UTF-8 from UTF-8-BOM. Could you check if it works for you?
new2.csv

Yes it works
Thanks


Unlisted dependency: irods-dev

irods-dev provides rodsClient.h, which is required to build kanki

Hi,
Sorry I forgot to comment on this earlier. Will start again working on a release, and will fix all these that have been hanging. Thanks for the report!

it's happening... :)


No links to app on blog post

I was checking out the blog post for Carbon, and it seems that there are no links to carbon.now.sh.
It'd be cool to have that link as well as a link to this repo in there 😃

Updated https://dawnlabs.io/blog/carbon/ 😄


Refactor check union, intersection and difference to use a common function

Most of the logic in these functions are shared with exception of the early termination, so we should see if we can combine them into a single function.
Reference: https://github.com/authzed/spicedb/blob/main/internal/graph/check.go#L323

They all make use of dispatchAllAsync now


chore: Update using directives to a version that doesn't support mult…

…iline

Can you also remove invalid example from documentation?

I realized we have some more invalid syntax, so trying to update it altogether. Not sure which tests will fail, so will need to check on CI :sweat_smile:


Legacy cdn of pdfjs-dist fails

Attach (recommended) or Link to PDF file here:
Configuration:

Web browser and its version:
Operating system and its version:
PDF.js version:
Is a browser extension:

Steps to reproduce the problem:

npm i ng2-pdf-viewer
npm i pdfjs-dist
console log with

<EMAIL_ADDRESS>404
<EMAIL_ADDRESS>404
What is the expected behavior? (add screenshot)

cnd of legacy build exists

What went wrong? (add screenshot)

Link to a viewer (if hosted on a site other than mozilla.github.io/pdf.js or as Firefox/Chrome extension):
https://www.npmjs.com/package/ng2-pdf-viewer

Thanks for your help will check cdn legacy availability for my IP.


add support for attaching to pids by-number

Can you move the isInteger function out side of the else block?


Making perturbation alpha into list input and bugfixes

See issues #35 #36

Allowing for alphas to be a list input to perturbation/atcf.py so that each ensemble member has a different perturbation of the error
In the best track perturbation test making a separate call to perturb the radius_of_maximum_winds since that has a different alpha range
Trying to fix bug for negative along_track perturbation due to variable index range, still having issues need figure out
Noting problem with radius_maximum_winds perturbation always ending up as 200 nm, need to fix

This requires more fixes to come for the AlongTrack and RadiusOfMaxmimumWinds perturbations.

Cross-track example perturbed tracks with test from this PR (make sense?):

Here are the reference figures for the test we want to do (alpha = [-1,1] for track and Vmax; and [0.25,0.75] for Rmax) using the original make_storm_ensemble.py script from the Storm-Surge-Mesh-Subetting repository:

Cross-track example perturbed tracks with test from this PR, quite different from the original one.. :

@zacharyburnettNOAA could there be some issue with the units or something like that?

The wind speed one looks fine for the current PR:

New result for Rmax after correction looks good:

Found mistake in the cross_track and along_track errors, I never entered them in correctly, and instead just copied them from the intensity (Vmax) errors. Here are new plots for cross-track and along-track perturbations using the Storm-Surge-Mesh-Subsetting repository:

@WPringle sorry I did not see this on Friday. It looks like I accidentally assigned .us_statute_mile instead of .nautical_mile in the errors; which unit are the values in?

@WPringle sorry I did not see this on Friday. It looks like I accidentally assigned .us_statute_mile instead of .nautical_mile in the historical_forecast_errors; which unit are the values in?
https://github.com/noaa-ocs-modeling/EnsemblePerturbation/blob/d99a723f4a9dabb3ba3e5f63cf5c99b899657839/ensembleperturbation/perturbation/atcf.py#L410-L414

No, this is fine actually thanks! The values in the array are statute miles here but we want them to be converted to nautical miles for use in the vortex file. (we could just manually compute these values in nautical miles to avoid confusion).
The problem was the dataframe was just populating nans due to the format of how the values were entered.

tests look okay and the tracks are now being correctly perturbed as shown in your diagrams; I will merge this

Can please wait, I need to go through the tracks perturbation. The plots above were not for this script (for the old one). I'm happy with the Vmax and Rmax for this script but I think there is still an issue with the cross-track/along-track. Will try to get it sorted this afternoon.

I am having some difficulty understanding the along track perturbation methodology; would it be okay if we had a google meet or something to talk about it?

Ok now the cross-track is behaving as expected; the order of longitude and latitude was switched. Last thing is to figure out the along-track

So the new code for along_track interpolation seems to work ok now, but the extrapolation at the beginning is strange. It should look like the black line but its being extrapolated as the red-line (from where the black line starts).

@zacharyburnettNOAA So the new code for along_track interpolation seems to work ok now, but the extrapolation at the beginning is strange. It should look like the black line but its being extrapolated as the red-line (from where the black line starts). I don't quite get the extrapolation as you did it but should be easy fix for the sign.

looks like this was because the numpy.flip function was flipping both axes (because I forgot to specify axis=0), fixed in 455d43f

@WPringle from what I can see, this seems pretty good. Let me know if there are any more outstanding issues aside from the 4 you specified at the beginning


Note UFUNCTION(meta=(BlueprintAutocast)) Requirements

BlueprintAutocast requires the function to be static, public, BlueprintPure, have at least 1 input, and have a return output.
Only the first input will be considered for auto conversion, but you can have multiple.
These requirements are checked in EdGraphSchema_K2.cpp
https://github.com/EpicGames/UnrealEngine/blob/072300df18a94f18077ca20a14224b5d99fee872/Engine/Source/Editor/BlueprintGraph/Private/EdGraphSchema_K2.cpp#L2440

@uextm Thank you for this


Rename to Moonslide

Rename Repository
Fix Links in README.md
Replace global object RevealEditor with Moonslide.
replace all reveal-editor like strings in project with moon-slide like strings

Done with #110


desktopBackgroundImage render issue in electron two package structure

Hi, Myxvisual:
Problem description
I use the two package.json structure suggested of electron(https://www.electron.build/tutorials/two-package-structure
), i found the desktopBackgroundImage couldn't be rendered out.
Link to minimal working code that reproduces the issue
I use the default example:
export default class AppUWP extends React.Component {
  render() {
    return (
      <UWPThemeProvider
        theme={getTheme({
          themeName: "dark", // set custom theme
          accent: "#0078D7", // set accent color
          useFluentDesign: true, // sure you want use new fluent design.
          desktopBackgroundImage: require("./components/images/blurBackground/jennifer-bailey-10753.jpg") // set global desktop background image
        })}
      >
        <MyComponent />
      </UWPThemeProvider>
    )
  }
}

And get the result in html:
For two package structure:

There is not background, but when i manually enter the address(http://localhost:3000/63dd844671a9043144eea6a44690a067.jpg) in explorer, there will the picture shown out.
For one package structure:

the background work normal.
Versions

React-UWP: 1.2.31
React: 16.1.1
Browser:

two package structure:
https://github.com/mjangir/reactron
one package structure:
https://github.com/csepulv/electron-with-create-react-app
I trace the code to react-uwp/theme/index.js
at Theme.prototype.render function , there createElement("theme-root") element and set "desktopBackground"  to backgroundStyle.background, i want to understand how how the framework render the background  that i could do further debug?
thanks

Get the answer,
This issue is not directly caused by UWP but referred to UWP structure. In UWP the desktopBackgroundImage coded as the a tag  with CSS, this tag is sibling node of the app root node, not the child of the app root node. So we could see:

...

the background div is controlled by CSS syntax z-index, there set to -1, that means put to bottom:
.fluent-background-1745310480 {
  position: fixed;
  z-index: -1;
  top: 0px;
  left: 0px;
  width: 100%;
  height: 100%;
  background: url(http://localhost:3000/63dd844671a9043144eea6a44690a067.jpg) no-repeat fixed top left / cover;
  pointer-events: none;
}

But there may some global CSS attribute for root app, like here in my used boilerplate:
  #app {
    background-color: #fafafa;
    min-height: 100%;
    min-width: 100%;
  }

You could see it's not used the z-index to control. And unfortunately, there the default z-index value will be defined to auto, that means start from last number(That's ZERO). So the z-index number in app root is ZERO and z-index in background is -1. That cause  app root color cover the whole background image. We could see the background insight.


Output files for detections

If no detection is found for a given sound file, then don't output an empty corresponding detection file for e.g. Raven, Kaleidoscope...

For consistency we will always output a file.


Using old code getting error in my application

Hi,
I am using old transactions create and transactions execute while trying to execute I am getting the below error
{:success=>false, :err=>{:code=>"400", :msg=>"Non 200 HTTP Status", :display_text=>"", :display_heading=>"", :error_data=>{}}, :data=>{}}
But, Same codebase working in other application. Could you please let me know old api's will work or not
@credentials = OSTSdk::Util::APICredentials.new(api_key, api_secret)
@transaction_object = OSTSdk::Saas::TransactionKind.new(environment, credentials)
Above one, I am using it
Regards

Please check below code for full details which is getting above errors.
require('ost-sdk-ruby')
class OstService
attr_accessor :credentials, :environment, :company_uuid
def initialize
@environment = ENV["OST_ENV"]  # possible values sandbox / main
@company_uuid = ENV["COMPANY_UUID"]
puts ENV.inspect
api_key = ENV["OST_API_KEY"] # replace with the API Key you obtained earlier
api_secret = ENV["OST_API_SECRET"] # replace with the API Secret you obtained earlier
@credentials = OSTSdk::Util::APICredentials.new(api_key, api_secret)
end
def send_coins_to_vessel_owner(vessel_id, coins=0)
return {success: false, err: {msg: "Invalid Params"}} if vessel_id.blank?
vessel = User.find_by(id: vessel_id)
name = "incentivevessel " + SecureRandom.hex(1).to_s
send_coins(company_uuid, vessel.uuid, coins, name, "company_to_user")
end
def send_coins(from, to, coins, trns_name, trns_kind)
return {success: false, err: {msg: "Invalid details"}} if from.blank? && to.blank?
result_ins = transaction_object.create(name: trns_name, kind: trns_kind, currency_type: 'bt', currency_value: coins, commission_percent: '0').to_json
Rails.logger.error("Response for transaction create vtt ontime incentive: #{result_ins}")
if result_ins[:success]
result = transaction_object.execute(from_uuid: from,
to_uuid: to, transaction_kind: trns_name).to_json
return result
Rails.logger.error("Response for transaction execute vtt ontime incentive: #{result}")
else
return result_ins
end
end
private
def transaction_object
@transaction_object = OSTSdk::Saas::TransactionKind.new(environment, credentials)
end
end

Hi,
I have removed the commission_percent. But, still, I am facing the same issue.
Regards.

Hi, I am facing the same problem. We are still using the older version (0.9) and locally everything works, but in our staging environment I'm getting the Non 200 HTTP Status error.

Just found out the problem. The name of the user had more than 20 chars (it seems to be the maximum), but this error message isn't that helpful:
{:success=>false, :err=>{:code=>"400", :msg=>"Non 200 HTTP Status", :display_text=>"", :display_heading=>"", :error_data=>{}}, :data=>{}}


Pb/filters

This PR adds:

filters
rewritten README and swagger documentation

This is extensive, but should be backwards compat. Happy to walk people through it and discuss front-end integration.

Looks good from first glance. From the doc and the image below: should "series" and "call number" be removed from the search box filter search?

I'm going to try it locally, but if it's backwards compatible, there shouldn't be an issue merging.

When I try these filters

http://local.nypl.org:3003/api/v0.1/discovery/resources?filters[dateCreated]=1999
http://local.nypl.org:3003/api/v0.1/discovery/resources?filters[language]=lang:eng

I get the following error:

error: "[query_parsing_exception] query_string must be provided with a [query], with { index=resources-2017-05-08 line=1 col=212 }"

This one returns results http://local.nypl.org:3003/api/v0.1/discovery/resources?q=hamilton&filters[dateCreated]=1999&per_page=4 but it doesn't seem like dateCreated of 1999 was picked up.

Please pull latest. Documentation was about the createdYear filter and I neglected to make the q param optional per docs.

Looks good from first glance. From the doc and the image below: should "series" and "call number" be removed from the search box filter search?

My understanding is the search box drop-down controls a special search_scope param, which governs what properties the q param matches against. It's different from this new filters param, which can be used in tandem to search_scope & q pairs. The filters param should typically be used solely in conjunction with aggregations ("facets") to match specific property values (i.e. no partial/ fuzzy matching when using filters, so it really shouldn't be entered by a user).

That makes sense. Thanks, all the examples work now.
I need to better understand making ES queries but that shouldn't block this PR.

I trust you both.


Create the components/actions for the filtered product, purchasing history, use order mgmt pgs

see comment on issue #73


training problem

Dear author, I encountered a problem while training the model. No matter how I modified my configuration parameters, I was unable to obtain data through the dataloader when using GCC12m for training, and the algorithm got stuck endlessly at this stage. If you could give me some guidance on this issue, I would greatly appreciate it.

Thank you for your interest in our research. We recommend checking your library versions and environments first.

Thank you for your suggestion, but it doesn't seem to be an environmental issue because my code can successfully train on the cc3m dataset, but switching to cc12m won't work.

If so, it might be worth checking if there's an issue with the cc12m dataset.


The client-side rendered virtual DOM tree is not matching server-rendered content

Hi there,
I can't use CodeSandbox to reproduce the error because when I try to add the vue-server-renderer to the dependencies it gives me an Internal Server Error :man_shrugging:
So here's the minimal configuration I got in place that is giving me troubles.
main.server.js
import Vue from 'vue';
import router from './modules/router';
import App from './App.vue';

// Receives the context of the render call, returning a Promise resolution to the root Vue instance.
export default () => Promise.resolve(
    new Vue({
        router,
        render: h => h(App)
    })
);

App.vue
<template>

        <router-view></router-view>

</template>

router.js
import Vue from 'vue';
import Router from 'vue-router';

Vue.use(Router);

const Layout = {template: '
ciao
'};

export default new Router({
    routes: [
        {
            path: '/',
            name: 'Layout',
            component: Layout
        }
    ]
});

$ npm list | grep vue
306:├─┬<EMAIL_ADDRESS>752:├─┬<EMAIL_ADDRESS>901:├──<EMAIL_ADDRESS>902:├─┬<EMAIL_ADDRESS>946:│ ├──<EMAIL_ADDRESS>947:│ ├─┬<EMAIL_ADDRESS>950:│ └──<EMAIL_ADDRESS>npm951:├──<EMAIL_ADDRESS>952:├──<EMAIL_ADDRESS>953:├─┬<EMAIL_ADDRESS> 971:├─┬<EMAIL_ADDRESS>974:├─┬<EMAIL_ADDRESS>977:├──<EMAIL_ADDRESS>978:├──<EMAIL_ADDRESS>ERR! peer dep missing<EMAIL_ADDRESS>required by<EMAIL_ADDRESS>npm ERR! peer dep missing<EMAIL_ADDRESS>required by<EMAIL_ADDRESS>
webpack.server.config.js
const path = require('path');
const webpack = require('webpack');
const VueSSRPlugin = require('vue-ssr-webpack-plugin');

module.exports = {
    // The target should be set to "node" to avoid packaging built-ins.
    target: 'node',
    // The entry should be our server entry file, not the default one.
    entry: './src/main.server.js',
    output: {
        path: path.resolve(__dirname, './dist'),
        publicPath: '/dist/',
        filename: 'build.js',
        // Outputs node-compatible modules instead of browser-compatible.
        libraryTarget: 'commonjs2'
    },
    module: {
        rules: [
            {
                test: /\.vue$/,
                loader: 'vue-loader',
                options: {
                    loaders: {}
                    // other vue-loader options go here
                }
            },
            {
                test: /\.js$/,
                loader: 'babel-loader',
                options: {
                    presets: [
                        'env',
                        'es2015'
                    ]
                },
                exclude: /node_modules/
            },
            {
                test: /\.css/,
                loader: 'style-loader!css-loader'
            },
            {
                test: /\.(png|jpg|gif|svg)$/,
                loader: 'file-loader',
                options: {
                    name: '[name].[ext]?[hash]'
                }
            }
        ]
    },
    resolve: {
        alias: {
            'vue$': 'vue/dist/vue.esm.js'
        }
    },
    // We can remove the devServer block.
    performance: {
        hints: false
    },
    // Avoids bundling external dependencies, so node can load them directly from node_modules/
    externals: Object.keys(require('./package.json').dependencies),
    devtool: '#source-map',
    // No need to put these behind a production env variable.
    plugins: [
        // Add the SSR plugin here.
        new VueSSRPlugin(),
        new webpack.DefinePlugin({
            'process.env': {
                NODE_ENV: '"prod"'
            }
        }),
        new webpack.optimize.UglifyJsPlugin({
            sourceMap: true,
            compress: {
                warnings: false
            }
        }),
        new webpack.LoaderOptionsPlugin({
            minimize: true
        })
    ]
};

I get that only when using the router, it renders fine otherwise. Maybe I got the deps wrong?
Along with that error I also get:
Uncaught TypeError: Cannot read property 'toLowerCase' of undefined

Does anybody know what's going on? Thanks!

I can't use CodeSandbox to reproduce the error because when I try to add the vue-server-renderer to the dependencies it gives me an Internal Server Error. Can anybody take a look at this anyway please?

You could provide a repository on github that we can run. It's extremely difficult to debug printed code.

@LinusBorg just created one here for you.
I'm using docker and a Makefile to run everything. Just do make dbuild install to make the container image and run npm install then do make wbuild ssr and it should be testable on http://localhost:8080.
If you want the client version just do make wbuild run and there you got the webpack dev server again on http://localhost:8080.

@LinusBorg just did it properly here https://github.com/vuejs/vue/issues/6830


Open email app in compose view with content

Building on the work started by @azorychta. All of the launch schemes were taken from their PR.
Built in collaboration with @krispypen.
Supported on android and iOS for the to, cc, bcc, subject and body fields.
Should close https://github.com/HomeXLabs/open-mail-app-flutter/issues/6

Wow! Thank you. We will take a look very soon.

@diskwriter thanks again for the PR! Let us know if you are happy to work on the feedback or if you would prefer we do it.

@dw2kim @MisterJimson
Thanks a lot for the review! Happy to work on the feedback; I'll pick it up somewhere tomorrow.

@dw2kim Resolved your comments! Could you take another look? Thanks!
cc/ @MisterJimson


Fix Pandora logo color

fixed in https://github.com/inttter/md-badges/commit/d46735e2c1a136b9f97e97d52704b423750bc9b0


feature/wa-55: improved questionnarie component accesibility

Could we validate the UX?. When you move with the left and right keys, I could observe that the question selected also move in direction to key

this will be solved in a bug ticket in the future


BREAKING CHANGE: update to eye v9.0.1

BREAKING CHANGE: update to eye v9.0.1

:tada: This PR is included in version 10.7.5 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release
v10.7.5

Your semantic-release bot :package::rocket:


shimv2: Add a "--version" cli option

All components should support a --version option to allow clear identification of the version of the component being used.
Note that the build changes are required to allow the shim binary to access the golang code generated by the build (such as the version variable).
This is a backport of https://github.com/kata-containers/kata-containers/pull/308.
Fixes: #2886.
Signed-off-by: James O. D. Hunt<EMAIL_ADDRESS>

/test-ubuntu


return single instance of linked results from ocr searches

closes isanteplus/openmrs-module-registrationapp#36

closes isanteplus/openmrs-module-registrationapp#36


Support for multiple Database configurations

Is there any way to achieve the following?
Use akka-persistence-sql-async for two kinds of persistent actor
One type is in mysql database A and the other is in mysql database B
They require different configuration details.

@justinhj You mean that you want to select the database for a particular PersistentActor, right?
That needs a logic to select a connection at run-time and I have no good idea.

Ok thanks, just checking I wasn't missing some obvious way of doing it.


Storing a BootEntry's ID inside it?

I'm currently writing a boot menu-type program, where I choose one of the boot entries, then set BootNext to it. So far, I've managed to find the boot entry I need using the VarManager::get_boot_entries method, however I don't know the BootEntry's ID in order to write it into the BootNext variable. That value isn't stored in a Boot#### variable, but is instead the name of that variable, so it doesn't get parsed from the variable's content.
For now, I have workarounds available, including performing parallel iteration over the get_boot_entries() and get_boot_order(), or getting the boot order list manually from the BootOrder variable. However, I think it would be easier if the ID were part of a BootEntry.

Hey !
I presume you were using v1.4.0. Since then, I fixed the issue in main by making get_boot_entries() return a tuple of (BootEntry, Variable) (See https://github.com/iTrooz/efiboot-rs/blob/d81047c2bfe507102966dc5d5619036e6a4f29f8/efiboot/src/cli/boot/get_entries.rs for usage)
Please note that the current API on the main branch is heavily in beta. I reserve myself the right to do breaking changes at any moment, until I make a 2.0 release, at which point the API will be stable. Until then, there should be no new release.
Its ok if you want to use it, but be ready to modify your code a bit when updating

Thanks for your reply. I think I'll stick to the released version for now, because I don't know when I'll be coming back to this project, and I am able to work around the issue. I might reconsider if I encounter something that can't be worked around that I need.
Though I did notice one such thing, and it is that some of the user-visible types, like the BootEntry, or FilePathList, don't have Debug implementations, which you might want if you're using this as a library like I am. You probably also fixed that already as well, though.
Though, if you're going to be changing APIs for 2.0, then you may still consider embedding the boot ID into the record. One thing I was confused about is how in v1.4 you were parsing the u16 boot IDs only to then put them into a string instead of exposing the sequence of u16s like you do now  -- doing that didn't make a sense to me, because by embedding the numbers into the string you now have to parse them back out of the string, adding a place for errors where there shouldn't be.
But then, in your linked sample, you end up needing to parse the number back out of the string, because it's being thrown away at some point before. That except will never trigger, but its presence is making it seem like it could, which is the downside of passing strings everywhere.
So, my recommendation for v2.0 (or maybe v3.0 as it's a fairly involved thing) is to put all the (important) EFI-standard variable names into their own structs. Then, you would be able to return a BootNumberVariable { boot_id: u16 } from that iterator, instead of a generic Variable with opaque string names.

Though, if you're going to be changing APIs for 2.0, then you may still consider embedding the boot ID into the record.

I don't think I'll do this, because I want to have one type dedicated to the variable content, with no relation to where it comes from. That said, I could imagine a type which combines the variable's identifier, and its content. I don't see the need for it, rather than a tuple like I'm doing now, though.

But then, in your linked sample, you end up needing to parse the number back out of the string, because it's being thrown away at some point before. That except will never trigger, but its presence is making it seem like it could, which is the downside of passing strings everywhere.

Indeed, this is one of the things which may change before 2.0

So, my recommendation for v2.0 (or maybe v3.0 as it's a fairly involved thing) is to put all the (important) EFI-standard variable names into their own structs. Then, you would be able to return a BootNumberVariable { boot_id: u16 } from that iterator, instead of a generic Variable with opaque string names.

I think this is a good idea ! Specifically, I could make a BootVariable type, which would be a "specialisation" of the Variable type, and which implements .into::<Variable>()
In general, I don't have a lot of experience building APIs, so your feedback is really interesting ! Thank you !

I want to have one type dedicated to the variable content, with no relation to where it comes from

How about an enum?
/// Different categories of variables to choose from
#[derive(derive_more::From, Debug, Clone)]
pub enum VariableName {
  Efi(EfiStandardVariableName),
  Vendored(VendoredVariableName),
}

/// Vendor-specific variables are opaque
#[derive(Debug, Clone)]
pub struct VendoredVariableName {
  pub uuid: ...,
  pub name: ...String...,
}

/// EFI Standard variables are either the ones we care about explicitly,
/// or just the ones that have that vendor UUID
#[derive(derive_more::From, Debug, Clone)]
pub enum EfiStandardVariableName {
  Specific(SpecificEfiVariableName),
  Generic(...String...),
}

/// This is where we list all the variable names that are semantically meaningful to our app
#[derive(derive_more::From, Debug, Clone, Copy)]
#[non_exhaustive]
pub enum SpecificEfiVariableName {
  BootOrder,
  BootEntry(BootEntryVariableName),
  // ...
}

/// After cascading through a few of the enums, we finally get to this struct,
/// which is unambiguous in its meaning.
/// It can even be made Copy at this point, because it's just a number
#[derive(PartialEq, Debug, Clone, Copy)]
pub struct BootEntryVariableName {
  pub boot_id: u16,
}

Once you have this, you can add a cascade of parse implementations, and the presence of the generic options ensures that whatever string you put in, you will get an instance of VariableName.
impl VariableName {
  pub fn new(uuid: ..., name: ...String...) -> Self {
    if uuid == MAGIC_EFI_VENDOR_UUID {
      EfiStandardVariableName::parse(name).into()
    } else {
      VendoredVariableName { uuid, name }.into()
    }
  }
}

impl EfiStandardVariableName {
  pub fn new(name: ...String...) -> Self {
    match SpecificEfiVariableName::try_from_name(name) {
      Some(specific) => specific.into(),
      None => Self::Generic(name),
    }
  }
}

impl SpecificEfiVariableName {
  pub fn try_from_name(name: ...String...) -> Option<Self> {
    if name == "BootOrder" {Some(Self::BootOrder)}
    else if let Some(boot_id) = parse_boot_entry_id_from_bootXXXX(name) {Some(BootEntryVariableName {boot_id}.into())}
     else {None}
   }
}

This all looks scarily verbose, but it's the kind of code you write once and then never touch it again. Also, you can reduce the amount of code being written with clever use of macros: for example, derive_more, which I've mentioned here, will generate the From implementations for your enums automagically.

Hey ! Sorry about the long delay
For now I'm not in the mood to think about/discuss Rust architecture stuff (I'm currently handling another project), but I'll check this out in detail when I come back to this project
Thanks !

Hey ! Finally got time to properly review your suggestion
So, for now I don't think if is useful to add this whole enum system, because the useful case I see for it is a boot entry having access to its boot id. So for now, I added a BootVariable type which is composed of the Boot Entry (purely the parsed content of the variable), and a boot id.
If I see the need for more "special" variable types like this in the future, I'll add the enum you suggested to help
I'm closing this issue since the initial problem is solved

By the way, is this project open source ?

I'm currently writing a boot menu-type program, where I choose one of the boot entries, then set BootNext to it

I'd love to take a look at it, and potentially contribute :)


Generalize number of nodes (i.e., don't restrict to multiples of 12)

I am working on this but don't current have write privileges.


[QUESTION] site problem

Hi, have i to download bitcoin core to use this script?

You need bitcoind to use this script.
https://github.com/bitcoin/bitcoin/

Thanks. After that i had installet it. Have i to do other things?

And can i use electrum instead of bitcoind?

Done bitcoind now have i to import my wallet in bitcoin core?


Issue with Sorting input data by starting time (parser_amber.py)

Hello there,
I am getting this error when I try to use alchemical_analysis.py which is coming from amber MDOUT file  parsing. I had it write out the offending variables ( found, uniq in parser_amber.py)
Command line was: ./alchemical-analysis/alchemical_analysis/alchemical_analysis.py -a AMBER -d data -p [01].*/ti00[2-9] -q out -o . -r 5 -u kcal -s 0 -g -w
Loading in data from data/0.4/ti003.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.4/ti002.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.7/ti003.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.7/ti002.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.6/ti003.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.6/ti002.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.0/ti003.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.0/ti002.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.9/ti003.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.9/ti002.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.2/ti003.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.2/ti002.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.1/ti003.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.1/ti002.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.5/ti003.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.5/ti002.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.3/ti003.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.3/ti002.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.8/ti003.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/0.8/ti002.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/1.0/ti003.out...  6000 data points, 6000 DV/DL averages
Loading in data from data/1.0/ti002.out...  6000 data points, 6000 DV/DL averages
Sorting input data by starting time
found:  [200.0, 200.0] 2 uniq:  set([200.0]) 1
ERROR: Same starting time occurs multiple times.
The header for parser_amber.py says
"Relevant namelist variables in MDIN: ntpr, ntave, ifmbar and bar*,
do NOT set t as the code depends on a correctly set begin time"
and it appears the issue stems from the begin time mentioned here. I am not exactly sure what this time it mentions here is.
Any thoughts appreciated.
Thanks!
Emmanuel

Hi Emmanuel,
the begin time is stored in the restart file and reported also in the MDOUT
file.  The parser uses this to unambiguously reassemble the data for each
lambda. Sander/pmemd allow the user to set this time to any value through
the namelist variable 't'.  Don't do this!  Check your output files (MDOUT)
for each clambda and look for the string "begin time read from input coords
=".  They should never be the same for a given clambda.
Cheers,
Hannes.
On 3 April 2016 at 19:07, baribefe<EMAIL_ADDRESS>wrote:

Hello there,
I am getting this error when I try to use alchemical_analysis.py which is
coming from amber MDOUT file parsing. I had it write out the offending
variables ( found, uniq in parser_amber.py)
Command line was:
./alchemical-analysis/alchemical_analysis/alchemical_analysis.py -a AMBER
-d data -p [01].*/ti00[2-9] -q out -o . -r 5 -u kcal -s 0 -g -w
Loading in data from data/0.4/ti003.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.4/ti002.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.7/ti003.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.7/ti002.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.6/ti003.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.6/ti002.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.0/ti003.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.0/ti002.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.9/ti003.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.9/ti002.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.2/ti003.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.2/ti002.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.1/ti003.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.1/ti002.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.5/ti003.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.5/ti002.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.3/ti003.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.3/ti002.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.8/ti003.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/0.8/ti002.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/1.0/ti003.out... 6000 data points, 6000 DV/DL
averages
Loading in data from data/1.0/ti002.out... 6000 data points, 6000 DV/DL
averages
Sorting input data by starting time
found: [200.0, 200.0] 2 uniq: set([200.0]) 1
ERROR: Same starting time occurs multiple times.
The header for parser_amber.py says
"Relevant namelist variables in MDIN: ntpr, ntave, ifmbar and bar*,
do NOT set t as the code depends on a correctly set begin time"
and it appears the issue stems from the begin time mentioned here. I am
not exactly sure what this time it mentions here is.
Any thoughts appreciated.
Thanks!
Emmanuel
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Thanks for the quick reply Hannes!
So just going into each MDOUT file (for each lambda) and chaning this to a different number should fix the problem?
Thanks again.
Emmanuel

Yes.  The code currently only requires to find a unique set of begin times.
On 3 April 2016 at 20:52, baribefe<EMAIL_ADDRESS>wrote:

Thanks for the quick reply Hannes!
So just going into each MDOUT file (for each lambda) and chaning this to a
different number should fix the problem?
Thanks again.
Emmanuel
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Just to clarify, this is resolved?
Thanks, Hannes, for the help. I never would have guessed this was the
problem.
On Sun, Apr 3, 2016 at 11:11 PM, Hannes Loeffler<EMAIL_ADDRESS>wrote:

Yes. The code currently only requires to find a unique set of begin times.
On 3 April 2016 at 20:52, baribefe<EMAIL_ADDRESS>wrote:

Thanks for the quick reply Hannes!
So just going into each MDOUT file (for each lambda) and chaning this to
a
different number should fix the problem?
Thanks again.
Emmanuel
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Department of Chemistry
3134B Natural Sciences I
University of California, Irvine
Irvine, CA 92697
<EMAIL_ADDRESS>work<PHONE_NUMBER>
cell<PHONE_NUMBER>

Yes, it is! I just made the changes and ran it again this morning.
Thanks again for your help!
Cheers,
Emmanuel

I have just realized that pmemd16 reads the initial begin time from the restart file but then resets its own counter.  If for instance I have 500.0 ps MD runs and the initial time was, say 1000.0 ps the begin times of consecutive runs would be: 1000.0, 500.0, 1000.0, 1500.0, etc.
I think that's a silly bug (older versions got this right) and I will see what the AMBER mailing list will respond.

Ok.  This is only an issue if the first MD run starts with irest=0 i.e. if it is not a restart run.  In a typical setup protocol where one does first do some sort of "equilibration" that is prior MD runs this is not an issue.

Thanks a lot for letting me know.
Cheers,
Emmanuel
On Fri, Aug 26, 2016 at 10:36 AM, Hannes Loeffler<EMAIL_ADDRESS>wrote:

Ok. This is only an issue if the first MD run starts with irest=0 i.e. if
it is not a restart run. In a typical setup protocol where one does first
do some sort of "equilibration" that is prior MD runs this is not an issue.
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Change public references to Firefox Accounts to just account.

Fixes #248
Screenshots
Inaccessible login page
As far as I can tell this page is not used, however there are so many references to login I'm slightly afraid it might break something. So I kept it, and removed all the fluff. It's super bare (and ugly), but it also shouldn't be used anyways.
Before

After

User Profile Edit
I'm tempted to just remove the help text for the email box, since it's a little awkward with the link right below it.
"Manage other account details..." takes you to the Firefox/Mozilla accounts page like it did before. Somehow naming it "Manage account..." didn't seem like a good idea.
Before

After
(Ignore the Firefox logo at the top, this is just the site running in docker.)

There's also internal references to Firefox Accounts like in the documentation. Should those remain, be changed to Mozilla Accounts (as it is a technical reference) or just be renamed to accounts?
I could not find any other public facing reference to Firefox Accounts, or a privacy policy link. So that's nice. The localized text will be broken and display english, but considering how much we wanted to remove the Firefox Accounts branding, I think that's fine until we do the re-write.

Oh yeah, the l10n strings are also going to need a search and replace. That can be a separate PR.


Minor bootstrap improvement, py36

Codecov Report

Merging #127 into master will increase coverage by 0.03%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #127      +/-   ##
==========================================
+ Coverage   87.18%   87.21%   +0.03%
==========================================
  Files          13       13
  Lines        1912     1909       -3
  Branches      359      358       -1
==========================================
- Hits         1667     1665       -2
- Misses        125      126       +1
+ Partials      120      118       -2

Impacted Files
Coverage Δ

wqio/bootstrap.py
78.37% <100%> (+3.37%)
:white_check_mark:

wqio/hydro.py
86.52% <100%> (ø)
:white_check_mark:

wqio/features.py
81.45% <ø> (-0.2%)
:x:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 5e80b8b...375279e. Read the comment docs.


Move .alfredworkflow to it's own repo?

I have made a bunch of improvements to my local copy of the workflow, including rewriting it from PHP into very simple javascript that runs natively through osascript… I would like to open some PRs, but that wouldn't be very useful as the workflow currently exists as basically just a binary blob as far as Git/Hub are concerned…
This way you could also utilise GitHub releases with it. @nikolaeu What do you think?

This is the Script Filter code for example:
#! /usr/bin/osascript -l JavaScript
const os = Application.currentApplication()
os.includeStandardAdditions = true
const se = Application('System Events')

const alfred = Application('Alfred 3')
const numi = Application('Numi')
const port = 15055

run = input => {
  const query = encodeURIComponent(input)
  let result
  try {
    result = os.doShellScript(`curl http://localhost:${port}/?q=${query}`)
  }
  catch (error) {
    numi.activate()
    delay(.25)
    se.processes.byName('Numi').visible = false

    alfred.runTrigger('numi', {
      inWorkflow: 'com.dmitrynikolaev.numi',
      withArgument: input
    })
  }
  const workings = `${input} = ${result}`
  items = [{
    title: result,
    arg: result,
    text: { copy: workings, largetype: workings },
    mods: {
      cmd: { subtitle: workings, arg: workings },
      alt: { arg: decodeURIComponent(input) }
    }
  }]
  return JSON.stringify({items})
}

p.s @nikolaeu Also, I have already added this workflow to homebrew-alfred… but using releases would enable better, versioned downloads…

Great work @danielbayley, and good idea on releases! Can you please create PR with plugin sources and attach binary for the workflow ?

@nikolaeu Do you mean a PR here or a seperate repo?

PR here. Actually workflow's binary already in the repo, would be great to have sources instead, and binary with release.

@nikolaeu Check out #79…
Exported binary is here: numi.alfredworkflow.zip, but the .zip extenstion needs to be removed (GitHub wouldn't let me upload otherwise…)

Amazing work @danielbayley, thank you!


surbhiahuja

Related issue

What changes does this PR do?
Screenshots (If any)
Questions

Name add in Readme file


New package: UniversityOfAmsterdam.praat version 6.4.1

Description

Resolve https://github.com/microsoft/winget-pkgs/issues/113183
Related https://github.com/microsoft/winget-pkgs/pull/113235

A previous pull request failed to pass the Azure Pipelines and closed because of stale. This is NOT a duplicate one!
Checks

[x] Have you signed the Contributor License Agreement?
[x] Have you checked that there aren't other open pull requests for the same manifest update/change?
[x] This PR only modifies one (1) manifest
[x] Have you validated your manifest locally with winget validate --manifest <path>?

[x] Does your manifest conform to the 1.5 schema?

Note: <path> is the name of the directory containing the manifest you're submitting.

Microsoft Reviewers: Open in CodeFlow

Manual validated all URLs in the manifest, and all of them are valid.
$ curl -I --socks5 localhost:57890 --compressed "https://www.fon.hum.uva.nl/praat/praat6401_win64.zip"
HTTP/1.1 200 OK
Date: Sun, 03 Dec 2023 09:36:47 GMT
Server: Apache/2.4.41 (Ubuntu)
Last-Modified: Fri, 01 Dec 2023 11:27:27 GMT
ETag: "129b0c3-60b710d8fc5c0"
Accept-Ranges: bytes
Content-Length: 19509443
Content-Type: application/zip

$ curl -I --socks5 localhost:57890 --compressed "https://www.fon.hum.uva.nl/praat/praat6401_win32.zip"
HTTP/1.1 200 OK
Date: Sun, 03 Dec 2023 09:36:56 GMT
Server: Apache/2.4.41 (Ubuntu)
Last-Modified: Fri, 01 Dec 2023 11:27:29 GMT
ETag: "126d947-60b710dae4a40"
Accept-Ranges: bytes
Content-Length: 19323207
Content-Type: application/zip

$ curl -I --socks5 localhost:57890 --compressed "https://www.fon.hum.uva.nl/"
HTTP/1.1 200 OK
Date: Sun, 03 Dec 2023 09:37:11 GMT
Server: Apache/2.4.41 (Ubuntu)
Last-Modified: Sat, 29 Oct 2022 07:48:16 GMT
ETag: "ae8-5ec2798dc3000-gzip"
Accept-Ranges: bytes
Vary: Accept-Encoding
Content-Encoding: gzip
Content-Length: 1115
Content-Type: text/html

$ curl -I --socks5 localhost:57890 --compressed "https://www.fon.hum.uva.nl/praat/"
HTTP/1.1 200 OK
Date: Sun, 03 Dec 2023 09:37:21 GMT
Server: Apache/2.4.41 (Ubuntu)
Last-Modified: Thu, 30 Nov 2023 22:14:14 GMT
ETag: "1f1d-60b65f8cc3980-gzip"
Accept-Ranges: bytes
Vary: Accept-Encoding
Content-Encoding: gzip
Content-Length: 2656
Content-Type: text/html

$ curl -I --socks5 localhost:57890 --compressed "https://www.fon.hum.uva.nl/praat/manual/General_Public_License__version_3.html"
HTTP/1.1 200 OK
Date: Sun, 03 Dec 2023 09:37:38 GMT
Server: Apache/2.4.41 (Ubuntu)
Last-Modified: Sun, 10 Sep 2023 17:09:17 GMT
ETag: "f86b-605044510c940-gzip"
Accept-Ranges: bytes
Vary: Accept-Encoding
Content-Encoding: gzip
Content-Length: 13743
Content-Type: text/html

$ curl -I --socks5 localhost:57890 --compressed "https://www.fon.hum.uva.nl/praat/manual/License.html"
HTTP/1.1 200 OK
Date: Sun, 03 Dec 2023 09:37:53 GMT
Server: Apache/2.4.41 (Ubuntu)
Last-Modified: Mon, 28 Aug 2023 15:13:06 GMT
ETag: "305-603fd219fe480-gzip"
Accept-Ranges: bytes
Vary: Accept-Encoding
Content-Encoding: gzip
Content-Length: 465
Content-Type: text/html

Reason: The pipelines warning is www.fon.hum.uva.nl.

@wingetbot waivers Add Validation-Domain


Getting 200 OK HTTP status for CORS Untrusted ORIGIN

Description
Hi Team,
This is regarding the CORS preflight request. APIM sending a 200 OK status code when the CORS is failing due to an untrusted origin. Instead, it should be sending a 4xx status code. When checking the code [1], we found that the status code is set as HttpStatus.SC_OK for both failed and successful calls. Is it possible to send the 403 status code for failed calls?
[1] https://github.com/wso2-support/carbon-apimgt/blob/f9de8855164f075aec5b0d358ca29b5c7dfbafac/components/apimgt/org.wso2.carbon.apimgt.gateway/src/main/java/org/wso2/carbon/apimgt/gateway/handlers/security/CORSRequestHandler.java#L240
Thanks,
Vikum
Steps to Reproduce
invoke the API with untrusted origin, then you will get the response with 200 status code
Affected Component
APIM
Version
3.2.0

Fixed via https://github.com/wso2/carbon-apimgt/pull/11926


Question regarding getView() and reference the View in the presenter.

This is simply a question, please label it as such.
I understand getView() is deprecated. The docs comments on the method mention the following:
/**
 * Please, use restartableXX and deliverXX methods for pushing data from RxPresenter into View.
 */

What if an Android Context is needed, in cases like parsing a local .json file from assets?
For example:
InputStream is = getView().getAssets().open("data.json");

What is the best practice for this particular case?

If you need "a" Context, I think it's best to dependency inject the application context into your presenter or abstract that dependency away so you'll get a stream from "somewhere".

We're explicitly avoiding dependency injection for this project. I was considering reading the file into a String in the Activity and then just passing the presenter the JSON String, but wanted to determine any alternatives.

App.getInstance() ?

This is quite strange, and hopefully related. I had been using .getView() as mentioned, and it worked just fine, and this question was posted as a matter of determining best practices.
However, last Friday a colleague discovered an issue with the application when running in API 25. I found it strange that I had not seen the issue, but after creating a new emulator and installing API 25, I was able to recreate it. I then switched back to the emulator I had been using for development (running API 23), and reinstalled the application. Suddenly, the above described issue appeared. After debugging the issue last Friday and today, it appeared to be a conflict between Firebase and a support library. I found it strange that the issue had suddenly appeared, and that I had not seen it before. Even old revisions that had been working, suddenly were having the same issue.
Fast forward a bit, and I seemed to have resolved the issue described above. However, for some reason, the presenter described in this original issue is no longer functioning as it was. Two issues appear to be present. getView() occasionally returns null, and the restartableLatestCache does not seem to be getting a response in some cases. Below is most of the code for the presenter:
/**
 * Presenter for the SplashActivity.
 * This presenter will parse local data files and signal it's view when completed.
 */
public class SplashActivityPresenter extends RxPresenter<SplashActivity> {

    private static final String TAG = "SplashActivityPresenter";

    /**
     * Request identifier used when parsing the local .json files is needed.
     */
    public static final int REQUEST = 1;

    /**
     * Request identifier used when the local .json files have already been parsed
     * and the Realm DB has been populated.
     */
    public static final int REQUEST_ALREADY_LOADED = 2;

    private Context mContext;

    @Override
    protected void onCreate(Bundle savedState) {
        super.onCreate(savedState);
        restartableLatestCache(REQUEST,
                () -> getData().subscribeOn(Schedulers.io()).observeOn(AndroidSchedulers.mainThread()),
                (view, response) -> {
                    Log.d(TAG, "onResponse: request");
                    view.onData();
                },
                (view, err) -> {
                    Log.d(TAG, "onError: " + err.getMessage());
                    view.onError();
                });

        restartableLatestCache(REQUEST_ALREADY_LOADED,
                () -> Observable.just(0).subscribeOn(AndroidSchedulers.mainThread()).observeOn(AndroidSchedulers.mainThread()),
                (view3, response) -> {
                    Log.d(TAG, "onResponse: request already loaded");
                    view3.onData();
                },
                (view, err) -> {
                    Log.d(TAG, "onError: " + err.getMessage());
                    view.onError();
                });
    }

    /**
     * Begin a request.
     */
    public void request(Context context) {
        mContext = context;
        Realm.getDefaultInstance().executeTransaction(realm -> {
            Bundle bundle = realm.where(Bundle.class).findFirst();
            if (bundle != null) {
                start(REQUEST_ALREADY_LOADED);
            } else {
                start(REQUEST);
            }
        });
    }

    /**
     * Creates an observable to parse the local .json files.
     * @return An Observable which will call it's subscriber's onComplete()
     * once parsing has been completed.
     */
    private Observable getData() {
        return Observable.create(subscriber -> {
            parseBundles();
            parsePhrases();
            Log.d(TAG, "getData: onComplete is about to be called.");
            subscriber.onComplete();
            Log.d(TAG, "getData: onComplete has been called");
        });
    }

    /**
     * Parses file and saves the data to Realm.
     */
    private void parsePhrases() {

        String msg = getView() == null ? "The view is null" : "The view isn't null";
        Log.d(TAG, "parsePhrases(): " + msg);
        String json = null;
        try {
            InputStream is = mContext.getAssets().open("someData.json");
            int size = is.available();
            byte[] buffer = new byte[size];
            is.read(buffer);
            is.close();
            json = new String(buffer, "UTF-8");
        } catch (IOException ex) {
            ex.printStackTrace();
            return;
        }
        JSONArray array = null;
        try {
            array = new JSONArray(json);
        } catch (JSONException e) {
            e.printStackTrace();
        }

        if (array != null) {
            for (int i = 0; i < array.length(); i++) {
                Phrase phrase = new Phrase();

                try {
                    phrase.setVideoPopupInfo(obj.getString("videoPopupInfo"));
                } catch (JSONException e) {
                    Log.e(TAG, "parsePhrases: " +  e.getMessage() );
                }

                //..A note, the above code will often throw and catch the JSONException, but this is ignored as certain JSON objects in the file don't have this property.

                Realm realm = Realm.getDefaultInstance();
                realm.beginTransaction();
                realm.copyToRealm(phrase);
                realm.commitTransaction();
            }
        }
    }

    /**
     * Parses the file and saves the data to Realm.
     */
    private void parseBundles() {
        String msg = getView() == null ? "The view is null" : "The view isn't null";
        Log.d(TAG, "parseBundles(): " + msg);
        String json = null;
        try {
            InputStream is = mContext.getAssets().open("someDataTwo.json");
            int size = is.available();
            byte[] buffer = new byte[size];
            is.read(buffer);
            is.close();
            json = new String(buffer, "UTF-8");
        } catch (IOException ex) {
            ex.printStackTrace();
        }

        JSONArray array = null;
        try {
            array = new JSONArray(json);
        } catch (JSONException e) {
            e.printStackTrace();
        }

        if (array != null) {

            for (int i = 0; i < array.length(); i++) {

                Bundle bundle = new Bundle();
                JSONObject obj = null;

                try {
                    obj = array.getJSONObject(i);
                } catch (JSONException e) {
                    e.printStackTrace();
                }

                //..Parse a number of JSON properties and save to bundle object.

                Realm realm = Realm.getDefaultInstance();
                realm.beginTransaction();
                realm.copyToRealm(bundle);
                realm.commitTransaction();
            }
        }
    }
}

getPresenter().request() is being called in the Activity's onCreate(). Moving the call to onResume() does seem to alleviate the issue of the view being null, however as most example's show this type of call being made in onCreate(), i'm curious as to what the best option is for this particular case.
Regardless, the issue of the response not being delivered occurs in all cases. As you can see, getData() creates and returns an observable. It calls the two parsing methods, and then calls subscriber.onComplete(). I can confirm this due to the two log statements placed before it. However, the restartableLatestCache for the REQUEST ID never gets the response. The call to view.onData() does not occur.
What is the issue here, and how can it be resolved? If this question is better posted as a separate issue, please let me know.

Can it be because of RxJava version update? Or support library? Support library sometimes break lifecycles.

@konmik I have all dependencies declared with explicit versions.
RxJava is compile 'io.reactivex.rxjava2:rxandroid:2.0.1', support libraries are all 25.3.1. I have not changed any of these recently.
Something interesting I've noticed: the restartableLatestCache for the REQUEST_ALREADY_LOADED seems to work as expected. If the Realm database is populated, start(REQUEST_ALREADY_LOADED) is called, and the call to view.onData() there goes through just fine.

I expanded a few of the lambdas into anonymous inner classes:
restartableFirst(REQUEST,
                new Factory<Observable<Object>>() {
                    @Override
                    public Observable<Object> create() {
                        return SplashActivityPresenter.this.getData().subscribeOn(Schedulers.io()).observeOn(AndroidSchedulers.mainThread());
                    }
                },
                new BiConsumer<SplashActivity, Object>() {
                    @Override
                    public void accept(SplashActivity view, Object response) throws Exception {
                        Log.d(TAG, "onResponse: request");
                        //view.onData();
                    }
                },
                new BiConsumer<SplashActivity, Throwable>() {
                    @Override
                    public void accept(SplashActivity view, Throwable err) throws Exception {
                        Log.d(TAG, "onError: " + err.getMessage());
                        view.onError();
                    }
                });

The following line is highlighted with a warning:
return SplashActivityPresenter.this.getData().subscribeOn(Schedulers.io()).observeOn(AndroidSchedulers.mainThread());

Unchecked assignment: 'io.reactivex.Observable' to 'io.reactivex.Observable<java.lang.Object>'. Reason: 'SplashActivityPresenter.this.getData().subscribeOn(Schedulers.io())' has raw type, so result of observeOn is erased

I suppose that may be the issue? Currently, getData() returns a plain Observable. Do I need to make it return some type, eg. Observable<T>?

I made the following changes:
I modified the below method:
private Observable<Object> getData() {
        return Observable.create(subscriber -> {
            parseBundles();
            parsePhrases();
            Log.d(TAG, "getData: " + "onComplete about to be called.");
            subscriber.onComplete();
            Log.d(TAG, "getData: onComplete has been called");
        });
}

to:
 private Observable<Object> getData() {
        return Observable.fromCallable(new Callable<Object>() {
            @Override
            public Object call() throws Exception {
                parseBundles();
                parsePhrases();
                return 0;
            }
        });
}

This appears to work. Why might the implementation using Observable.create() not work as expected?

@Orbyt https://artemzin.com/blog/rxjava-defer-execution-of-function-via-fromcallable/ ?

@TWiStErRob I have previously come across that page when looking at alternatives to .create(). Though, I'm still curious as to why .fromCallable() works in this case.
The reason for returning a 0 was simply return something, the value is not used.

I need more data on the issue, preferable a minimal repo with reproduced error. Is looks like yet another support library bug for me (I remember they broke view lifecycle inside fragment one day, so this also can be the reason).


consider removing set.seed() inside the functions

When I run BiocCheck::BiocCheck(), it was suggested to remove set.seed inside the functions, subsampleCounts.R has 1 line that set seed inside the functions (line 133)

PR welcome.

Based on the suggestions here: https://support.bioconductor.org/p/110439/, I removed the set.seed() inside the function and specify that user can define seeds before applying subsampleCounts().


D455 returns Bayer-like infrared images with Y16 format

Required Info

Camera Model
D455

Firmware Version
<IP_ADDRESS>

Operating System & Version
Debian 10

Kernel Version (Linux Only)
4.19.0-16

Platform
PC

SDK Version
2.45.0

Language
Rust/C

Segment
Robot

Issue Description
When infrared images are captured with Y16 pixel format from a D455 sensor on maximum resolution (1280x800), I get images like this:

By zooming-in we can easily see a Bayer-like pattern. Strangely enough when the images get captured with Y8 format and the same resolution. The same result can also be seen in realsense-viewer.
is this behavior intentional? if yes, can it be turned off?

@MartyG-RealSense
Please, read the issue text more carefully. My question is not about rectification, but about the Bayer-like pattern, i.e. about greatly varying measured intensity of neighboring pixels. Such effect was not present on D435 sensors.
Is this effect caused by applying a Bayer-like pattern of filters on the IR matrix level or can it be disabled somehow?

It is important in my opinion to make clear the distinction between Y8 (rectified) and Y16 (unrectified) when considering the difference between these two formats.
I will refer your question above to @agrunnet

Yes the unrectified rgb has a Bayer pattern. This is the 1280x800 resolution. The D455 has a color Bayer pattern filter. The d435 does not.
You cannot turn it off.
The other resolutions are rectified and have been de-Bayered so you won’t see the effect you mention on them.

Thanks so much for the information @agrunnet

@agrunnet
Can you please provide more details about filters used in the Bayer pattern for IR matrices? Do they simply dampen incoming light to extend dynamic range or do they filter out certain spectral ranges? Is it correct to assume that the same Bayer pattern is also used in the D450 modules?

The RGB Bayer pattern is a spectral filter red, green, green, blue. So it attenuates colors differently like a normal Bayer pattern would. It is the same in the D450 module.

Let me clarify: are you telling me that infrared cameras in D455 have different spectral sensitivity for different pixels?? It's very surprising, to say the least. Can you please point me to any official documentation which would support this statement?

That is correct. They are color cameras on the D455. The term “infrared” is more related to fact that we don’t block the inferred. Plus it is a legacy term when cameras used to be ONLY infrared.
Our stereo algo uses all colors to help determine depth. The same is true for the D415 camera.

Thank you! I guess we can close this issue then.

@newpavlov  I will see if we can do a better job in pointing this out in the documentation. We certainly don’t intend any confusion. Thanks for pointing it out.


colorscheme isn't loading

I first tried to install it manually, and created a colors folder in my .vim folder, and the entire display in vim is white (including lightline), but when I remove the colorscheme snazzy from my vimrc the lightline theme works. I tried installing it with pathogen and vim-plug, but same issue. (transparency works, so I know its reading the file). Below is my vimrc.
  1 execute pathogen#infect()
  2
  3 let g:lightline = {
  4     \ 'colorscheme': 'snazzy',
  5     \}
  6 set laststatus=2
  7 set noshowmode
  8
  9 let g:SnazzyTramsparent = 1
 10
 11 let g:SuperTabCompletionContexts = ['s:ContextText', 's:ContextDiscover']
 12 let g:SuperTabContextTextOmniPrecedence = ['&omnifunc', '&completefunc']
 13 let g:SuperTabContextDiscoverDiscovery =
 14     \ ["&completefunc:<c-x><c-u>", "&omnifunc:<c-x><c-o>"]
 15
 16 nnoremap <C-t> : hi Normal guibg=NONE ctermbg=NONE<CR>
 17
 18 set tabstop=4
 19
 20 set number

it's not letting me commit an edit to fix the formatting, sorry

Looks like you have a typo on line 9
let g:SnazzyTramsparent = 1 should be let g:SnazzyTransparent = 1


[Feature] Add Gitea Emoji

https://github.com/go-gitea/gitea/issues/8949#issuecomment-553270282

[x] upsate emojify.js to 1.1.0
[x] add gitea emoji

Is there another way to do this without modifying the vendor lib? We will eventually move to npm-sourced libs where changes like this will not be possibly any more.
If this is the only way, I suggest moving it to public/js/emojify.custom.min.js to indicate it's a customized version.

@silverwind the sad thing about this lib: it no active developement anymore ...
gitea use version v1.0.5 and the newest is v1.1.0 at https://github.com/joypixels/emojify.js
should i update to 1.1.0 and move to emojify.custom.min.js ?
since there will be no developement in the near future?

Yeah, that sounds like a good idea.

Codecov Report

Merging #8950 into master will increase coverage by <.01%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #8950      +/-   ##
==========================================
+ Coverage   41.26%   41.26%   +<.01%
==========================================
  Files         546      546
  Lines       71005    71005
==========================================
+ Hits        29300    29302       +2
+ Misses      37985    37984       -1
+ Partials     3720     3719       -1

Impacted Files
Coverage Δ

models/unit.go
62.16% <0%> (-5.41%)
:arrow_down:

models/repo_list.go
74.07% <0%> (+0.92%)
:arrow_up:

modules/log/event.go
65.64% <0%> (+1.02%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 722a7c9...8e91f9d. Read the comment docs.

Codecov Report

Merging #8950 into master will increase coverage by <.01%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #8950      +/-   ##
==========================================
+ Coverage   41.26%   41.26%   +<.01%
==========================================
  Files         546      546
  Lines       71005    71005
==========================================
+ Hits        29300    29302       +2
+ Misses      37985    37984       -1
+ Partials     3720     3719       -1

Impacted Files
Coverage Δ

models/unit.go
62.16% <0%> (-5.41%)
:arrow_down:

models/repo_list.go
74.07% <0%> (+0.92%)
:arrow_up:

modules/log/event.go
65.64% <0%> (+1.02%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 722a7c9...8e91f9d. Read the comment docs.

@silverwind done

@silverwind can you review if you have time ;)

Will put my stamp after I've tested it.

I feel like it would be cleaner to fork emojify and create a release with gitea emoji and minified version.

@sapk @zeripath to:

https://gitea.com/gitea/emoji.js ?
or https://github.com/go-gitea/emoji.js ?
or should i fork it to my account ?

My vote is https://gitea.com/gitea/emojify.js if that is the route we go.

Is there not another library that is more maintained? Aside from the realities of actually maintain and updating something like this ourselves, there are issues like this:
https://github.com/joypixels/emojify.js/issues/177
Which I guess becomes our bug now if nobody else is expected to fix it. Obviously this is already an issue and not new, but if putting in the effort to move things around anyway perhaps there is something more up to date that doesn't have these problems and even fixes this bug by allowing you to add your own?

@mrsdizzie -> https://github.com/hackmdio/emojify.js ?

I thought unicode emoji skin tone was simply a post code modifier - if there's no modifier it's supposed to be neutral.
So if emojify is simply using unicode we just delete the skin tone modifier and it should go neutral.

@sapk how to minify https://github.com/hackmdio/emojify.js?

I thought unicode emoji skin tone was simply a post code modifier - if there's no modifier it's supposed to be neutral.
So if emojify is simply using unicode we just delete the skin tone modifier and it should go neutral.

Unfortunately these aren't real emoji at all its a hack that turns something like :ok_woman: into this:
<img align="absmiddle" alt=":ok_woman:" class="emoji" src="/vendor/plugins/emojify/images/ok_woman.png" title=":ok_woman:">

Which is just: https://github.com/joypixels/emojify.js/blob/master/src/images/emoji/ok_woman.png
So its just a picture of an emoji :(

@zeripath @mrsdizzie suggestion:
we move to v1.1.0 + custom [this PR current state] ... and if https://github.com/hackmdio/emojify.js/issues/20 is resolved ... we move forward to the up-to-date fork ?

How did you go about choosing that specific fork?

@jolheiser https://www.npmjs.com/search?q=keywords:emojify

@jolheiser https://www.npmjs.com/search?q=keywords:emojify
-> most reasend updated + most activity

https://github.com/go-gitea/gitea/pull/8950#issuecomment-553476910 ?!?

@6543 I have no comment or opinion other than the one above. I think the general design of emojify is dated and limited vs what others like Github offer (using real emoji with image fall backs) but understand that is what we are already using anyway so it isn't any type of regression or current design decision. I do think the https://github.com/hackmdio/emojify.js seems a bit better as it maintains more up to date images and can maybe be a drop in replacement but personally wouldn't ever use the feature as it doesn't insert actual emojis.
Just figured if you were going to put in the effort to fork it perhaps there was a better replacement that would be a similar amount of work but end up with a better system but not meant to hold this up in any way.

Any reason why you moved the customized version back to vendor instead of public/js?

@silverwind a created a issue https://github.com/hackmdio/emojify.js/issues/21 so we will see - avter this PR is merged - I'll open a issue to track issues upcoming in this PR ...

Any reason why you moved the customized version back to vendor instead of public/js?

i don't moved ... I left it at the original place .. since this is no refactor/replacement of the emoji lib

@techknowlogick I'm ready if you are ...


Cannot upload input stream directly to Azure Storage without loading stream in memory

Cannot upload input stream directly to Azure Storage without loading stream in memory
Issue Type : Bug
Actual
The Stream instance provided in ITusStore.AppendDataAsync cannot be uploaded directly to Azure Storage. The Azure Storage SDK provides a few APIs that allow to pass an input Stream, but a NotSupportedException is thrown when supplying the input Stream directly, specifically when the SDK calls Stream.Length property.
Expected
The provided Stream should be permissive enough so that it can be redirected to another service without having to manipulate, chunk, or buffer it.
Workaround
On the client app, we can limit the chunkSize to 50 or 100MB.
When we receive the chunk, we can copy it to a MemoryStream, and use that new Stream in the Azure Storage SDK.

Hi,
The stream passed to AppendDataAsync is the HttpRequestStream provided by ASP.NET Core wrapped with support for max size and client disconnect detection. The wrapping streams just forward the Length call to the HttpRequestStream. HttpRequestStream does not support reading the length as there is no way to determine the length of a remote stream without consuming it, i.e buffering.

The provided Stream should be permissive enough so that it can be redirected to another service without having to manipulate, chunk, or buffer it.

No this is the responsibility of the store. There is no way for tusdotnet to determine the optimal buffer size for all storage solutions used by stores. There's a huge difference in the buffering needed for e.g. writing to disk or writing to a remote backend.

On the client app, we can limit the chunkSize to 50 or 100MB.
When we receive the chunk, we can copy it to a MemoryStream, and use that new Stream in the Azure Storage SDK.

This is the right idea but I wouldn't recommend using the chunkSize on the client to determine your buffer size as you would open yourself up to a denial of service attack and possible memory issues. Looking at e.g. Xtensible.TusDotNet.Azure you can see that it uses the append blob block size as the buffer.

Closing due to inactivity


refactor(bufferWhen-spec): update bufferWhen operator tests to use pipeable operators

update bufferWhen spec to use updated import sites and pipeable operators

Coverage increased (+0.2%) to 96.729% when pulling 964f9cf9789420cdb38252edb51194966764ee88 on natmegs:bufferwhen-spec-pipeable into 7e4cef4087f1f75dc5476199d80accc335bb48a0 on ReactiveX:master.


Add testing foundation (e2e, unit)

We need testing. Create a testing foundation.
I'm planning to use BrowserStack for automated browser testing.
The Ava test runner looks nice.

I'm planning to use BrowserStack for automated browser testing.

I've migrated infamous to using my builder-js-package which includes build/publish/test configs and scripts that I can share across projects. It is enables Karma + Chrome Headless for testing.
Test stubs ending with .test.js have been added. Mixin is fully tested.