CN-312 change from 'do you work in a school?' to 'what setting do you work in?'

Context
Follows on from #464
CN-312
Changes proposed in this pull request
The spec in the JIRA expects:

Rather than having a yes/no question, to avoid confusion, we’ve translated the H1 into radios.

If a user clicks on a school, a academy trust, a 16-19 organisation they will:

be shown the screen where it’s assumed they’ll have a TRN
go down the GIAS route

If a user clicks on early years they will:

shown the screen where it’s assumed they don’t have a TRN
will go down the Ofsted route

If a user clicks on other they will:

shown the screen where it’s assumed they don’t have a TRN
will go down the ‘Non-school user route’. (Tweaks to the other route will be another card)
once they have chosen their NPQ, they will see the “Tell us about where you work” and “How are you paying page” - These will eventually be removed as part of updates to the ‘Non-school user route’.

In addition to the requirements I renamed the page from work-in-school to work-setting, to keep the filenames and contents aligned and easy to follow.
The 'do you work in early years or childcare' screen has also been dropped as it's covered by the 'work setting' question.
The change was a bit more involved than expected because a more fundamental question is asked early on and had several repercussions through the rest of the journey. This is the reason this change was held off until #464 was ready.
Guidance for reviewing
I'd recommend going through the commits one by one. Most of the changes are updating other feature specs so they're aware of the page rename and early years question removal.

One other thing, should we follow this PR up with pushing the new work_setting data through to the CPD database?


Make the dashboard sections names clickable

Problem
Not a problem, just an enhancement
Solution
Make the dashboard section names

Crypto Transfers
Smart Contract Calls
HCS Messages

clickable so that it open the transaction page with the selected transaction type you clicked on.
For example when im on the dashboard and click on crypto transfers it should redirect me to this page
https://hashscan.io/mainnet/transactions?type=cryptotransfer
Alternatives
No response

any update here?


package upgrade

Hello,
I update the package and the code to integrate the last version of react-md-editor.

Hi @toxicity1985, thanks for your contribution. It is merged and released in v4.3.0!


Handle errors reading from socket during boot gracefully

Currently when Zeus receives any error reading from the command socket while waiting for a process to boot, it logs the error and then tries to parse the message anyway. Since the message shouldn't be valid when there's an error, we should instead enter an SCrashed state immediately. We could be throwing away useful debugging information bufferred from an earlier read but I don't think that'll actually happen in the existing Zeus code.

r? @nuance-stripe


Update config and fix config naming.

Support:
electric config update [--app APP] [--env ENV] [--migrations-dir PATH]

Fix naming to use app and env everywhere, including the electric.json. And update the README to match latest usage.

Messed up the last commit: the "bump the version" commit actually also makes a breaking change to the bundle format to get rid of the named data import, so rather than:
import { data as bundle } from '../migrations/dist'

We just have:
import bundle from '../migrations/dist'

Please add Closes VAX-### into the PR body

Closes VAX-###

Relates to VAX-518 but doesn't close it without other PRs across repos.


access month string from budgetHeaderValues.monthlyBudget.month momen…

GitHub Issue (if applicable): #2960
Explanation of Bugfix/Feature/Modification:
According to the debugger, monthString doesn't exist on the budget service. A little hunting around led me to budgetHeaderValues.monthlyBudget.month moment object which seems to provide the necessary value for these methods to work as intended.
Not sure if I have enough context to say this is the most logical place to access the month, but its resolved the issue on my end.

Also fixes #2962, #2957.


Add Null handling for different frames

As @ueshin pointed out in https://github.com/databricks/koalas/pull/1029#discussion_r350422624, the fix #1029 didn't cover the case below. This PR fixes it.
>>> ks.options.compute.ops_on_diff_frames = True
>>> s1 = pd.Series([True, False, True], index=list("ABC"), name="x")
>>> s2 = pd.Series([True, True, False], index=list("ABD"), name="x")
>>> s1
A     True
B    False
C     True
Name: x, dtype: bool
>>> s2
A     True
B     True
D    False
Name: x, dtype: bool
>>> s1 | s2
A     True
B     True
C     True
D    False
Name: x, dtype: bool
>>> (ks.from_pandas(s1) | ks.from_pandas(s2)).sort_index()
A    True
B    True
C    True
D    None
Name: x, dtype: object

Codecov Report

Merging #1083 into master will decrease coverage by 2.65%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #1083      +/-   ##
==========================================
- Coverage    95.2%   92.55%   -2.66%
==========================================
  Files          34       34
  Lines        6883     6886       +3
==========================================
- Hits         6553     6373     -180
- Misses        330      513     +183

Impacted Files
Coverage Δ

databricks/koalas/base.py
95.4% <100%> (+0.08%)
:arrow_up:

databricks/koalas/usage_logging/__init__.py
24.54% <0%> (-72.73%)
:arrow_down:

databricks/koalas/usage_logging/usage_logger.py
50% <0%> (-50%)
:arrow_down:

databricks/koalas/__init__.py
78.72% <0%> (-8.52%)
:arrow_down:

databricks/conftest.py
92% <0%> (-6%)
:arrow_down:

databricks/koalas/frame.py
93.43% <0%> (-3.31%)
:arrow_down:

databricks/koalas/utils.py
95.12% <0%> (-3.05%)
:arrow_down:

databricks/koalas/groupby.py
89.34% <0%> (-2.05%)
:arrow_down:

databricks/koalas/namespace.py
85.8% <0%> (-1.55%)
:arrow_down:

databricks/koalas/plot.py
93.33% <0%> (-0.96%)
:arrow_down:

... and 2 more

Continue to review full report at Codecov.

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can it be compatible with hx712 too?

Hi mate, this is not a bug, sorry to create one for this request.
My friend asked me to repair his scale, all is working except processor! It's amazing.. what a chance ))
Since I'm in love with your library I would use this too.. but the board has a hx712, can it be compatible?
Thank you

Hi!
I'm not sure. The HX712 has a slightly different serial protocol, but using the HX711 library with gain 128 (default setting) it seems like it might work. The MCU will then clock out 25 CLK pulses coresponding to a gain of 128 and rate of 10SPS on the HX712. Give it a try!

Thank you friend, I'll try then as soon I can and report here.
So if I got it right, I have just to leave the defualt settings and teorically it will work

Yes, default library settings. The assumption that it might work is just based what I learned from a quick look at the HX712 data sheet and it would be interesting to know the result if you test it, so your feedback is appreciated :)

I’m closing this issue because it has been inactive for some time.
Please reopen if you still encounter this issue with the latest version.
Thank you!

Dear friend, yes sure. I haven't have time yer to test, when I'll I'll report here ) Thanks


Update post fw v1.1.0

Description
Updates to documentation
Fixes

#36
#42
#40
#38
#35

Review 01

[x] I think the bullet indentation is off for Windows instructions
[x] Can we easily make Mac/Windows a drop-down? If not, perhaps putting windows first would be clearer since it's a shorter section
[x] I think we should remove the Oscilloscope data storage or move it out of the Data Recording section and make it VERY clear that this is for debugging purposes ONLY

Added issue #47

[x] What was updated in #35 ?

compare the new Table of Contents with the old one


Config override key flag does not work for extend option

Example command:
ruff format --check --diff --config "extend='ruff_defaults.toml'" .

This is an interesting usage of the new override system and should be supported. However, It may not have the desired result depending on your use case:
pyproject.toml

tests\
	tests.config.toml // extends pyproject.toml

Overriding the extend would override the extend value for all configurations, meaning that tests.config.toml would suddenly no longer extend the pyproject.toml. Now, that might be exactly what you want but may be unintentional if the intention was to make all configurations inherit from a base configuration.

Ah I see -- so this doesn't work because we currently apply the configuration overrides given in the --config flag after any configuration options found in any pyproject.toml/ruff.toml files have been parsed and validated. But this particular override affects which config files ruff should be looking at in the first place, so we'd need to look for it at an earlier stage in the process (I think).
I'm unlikely to have time to look at this in any more depth this week, unfortunately, but I'll work on this as soon as I'm able!

I'm okay with a fix or literally any other way to define an extend via command line! If it means a separate flag then that's cool.

Yeah, I'll have a think... if we decide that this kind of thing should be done via a separate flag, then we should probably explicitly reject trying to override extend via --config, on the grounds that it's probably not going to do what you expect, as @MichaReiser mentioned above. So whether we go with "fix behaviour of --config w.r.t. extend" or "introduce another flag", it's likely the behaviour of --config should be changed in some way here :)

+1 on this feature
This would be helpful to extend a base configuration with more specific overrides, when the path to the base config is not static and thus cannot be hard-coded into the more-specific configuration.
If that is any indication, when searching the doc I was also expecting a dedicated --extend flag, and tried out the --config override after failing to find one.
Given that --config "KEY = VALUE" has highest priority and thus needs to be applied last, it makes sense to me that --config cannot support --extend behavior as is currently the case.
I suppose a tricky part could be extend chains: with extend in the files, you can only have a linear chain of files extending one another, so the behavior is well-defined. No diamond inheritance.
With both the file passed to --config, and --extend, possibly extending another file, there can be multiple inheritance. This could reasonably result in an error unless a use-case pops up, though?

Just for some more context, can someone explain to me how --config <path> --config <some-other-override> differs from --config extend=<path> --config <some-other-override>?

Are you implying that specifying multiple configuration files is implicitly an extend operation? If so, then I suppose there is no feature request here but rather a documentation update.

I'm not sure! The configuration hierarchy is confusing and inheritance via extend is even more complicated. I'm asking for someone to try it, I guess, so we can understand what we're missing.

Oh okay, I think we can support multiple configuration files on the command line. I originally intended for it to be that way, but I think it might have been cut from scope on the initial implementation. I'd be curious to hear if it would address your use-case to support merging multiple --config file options. Also @AlexWaygood if you have any more context on why we dropped that from scope that'd be helpful, I can't remember if there were reasons it was infeasible.

If you can have more than one config file, what happens when the extend-chain is no longer linear?
ruff --config config1.toml --config config2.toml

# config1.toml
extend = "config1_base.toml"

# config2.toml
extend = "config2_base.toml"

I guess this needs to be properly documented.

Also, as a workaround for my own use-case, I template the ruff config and dynamically write a temporary file where I replace a placehold with the actual filepath to extend-from, since the CLI itself can't handle it. It's a bit ugly but it works.


Fix CI welcome message

Objective
Fixes #7424
Solution
https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#pull_request_target

By default, a workflow only runs when a pull_request_target event's activity type is opened, synchronize, or reopened.

Specify opened so that this only runs when a PR is opened
While I was in there, I fixed a couple other issues:

extra indentation that was causing the welcome message to be put in a code block.
broken relative link in message (was resolving to https://github.com/bevyengine/bevy/pull/CONTRIBUTING.md)
fixed a few other minor typos in the message

cc @mockersf

bors r+


Include a layer type property in API response

Currently, in order to distinguish between raster and vector layers one must look at the storeType property of the resource:

storeType: "coverageStore" for raster layers
storeType: "dataStore" for vector layers

While this works, the terminology seems too GeoServer oriented. It would be cleaner for a client of the API to get something like layer_type: "raster|vector" instead

Or maybe just use the spatial_representation_type property instead of a new layer_type one? It is already there in the response, but seems to always be empty

I agree @ricardogsilva this is something that I've always missed in GeoNode, a simple way to distinguish the layers.
If @afabiani agrees I would add a new attribute to the Layer model and adopt two simple constanst: RASTER, VECTOR.
I would like to also have the feature type for vector layers, but for the moment it's less relevant.

I'm pushing this forwars, but rather then chaning the field name (storeType) for the moment we will limit to change its values.
Now that the resource manager refactoring is in place we can map the values back to Geoserver storage types inside the backend implementation.
Layer.storeType values will be changed to:

dataStore -> vector
coverageStore -> raster
remoteStore -> remote

The legacy API also had a special vector_time filter, but it's useluss to me since a vector time series is already denoted by the Layer.has_time attribute.
@mattiagiupponi you know aht we need to do:

change the values everywhere they're used inside the GeoNode codebase. We must also check if they're used inside Javascript code
map the values inside the Uploader (which is GeoServer specific but pluggable
map the values inside GeoServer tasks updating the layer info
create a migration to update the values for already existing data


Help with marker_prediction_plot

Hello Yuzhou and esteemed members of the Trigos Team,
I want to begin by congratulating you on the remarkable SPIAT package. As a master's student with limited bioinformatics experience, I apologize in advance if the issues I raise may seem straightforward to resolve or are not clearly presented.
Currently, I am engaged in a project that involves comparing the results obtained from our pathologic anatomy department. I have a series of 100 TIFFs from lung tumors, which were captured using multiplex imaging and analyzed with QuPath. However, I am encountering difficulties in quality control.
Here are the specific challenges I am facing:

When using the predict_phenotypes function, I am wondering if there is a way to exclude the tumor marker (CK) from the predicted phenotypes, similar to how the nuclear marker is excluded by default. I have already utilized tumor_marker to define CK, and it has been excluded from baseline_markers. However, attempting to exclude it from markers_to_phenotype results in CK being excluded from other downstream analyses, such as marker_prediction_plot.

While using the marker_prediction_plot to assess the quality of predicted phenotypes, I encounter the following error, which seems to be dependent on the number of cells being processed (currently 8304, which I believe is not too large):

marker_prediction_plot(predicted_image, marker = "PD1")

Error in .Primitive("[")(c(2.341, 0.822, 0.048, 0.5286, 0.0752, 0.1887, :
(subscript) logical subscript too long
I sincerely appreciate any insights and assistance you can provide in resolving these issues. Thank you for your time and support.

Hi @CPUriarte ,
Thank you for your interest in using the tool.
For the first question, what is the reason for excluding the tumour marker from markers_to_phenotype argument? If the tumour marker is not predicted, it will not be included in the marker_prediction_plot as there is no prediction value for the tumour markers.
For the second question, I wonder if the issue occurred because the original phenotypes were not present in the image object. Could you post the code that includes the phenotype prediction and the data generated from that (the column names should be sufficient)?

When excluding the tumor marker from the analysis, it is automatically omitted from predictions in downstream analyses, such as the marker_prediction_plot. However, if the tumor marker is included, a misclassification occurs for TILs present in the tissue, erroneously identifying them as "Immune_1, Immune_2, Tumour_marker," even though the latter does not exist. As the current package only allows for individual cell removal, this process results in a loss of valuable information regarding those TILs.
Regarding the second issue, you were correct; my initial phenotype was not present in the image object. I have since attempted using a phenotype that is indeed present, but unfortunately, I encountered the same error.
# SELECT IMAGE SUBSET
selected_image <- "TMA1_1A_3901.tif"
selected_data <- subset(raw_measurements, Image %in% selected_image)
selected_data <- selected_data %>%
    select(-1)

# FORMATTING
x_coord <- as.numeric(t(selected_data)[1, ]) # Get X coordinates
y_coord <- as.numeric(t(selected_data)[2, ]) # Get Y coordinates

filt_measurements <- t(selected_data[, -c(1:2)]) # Delete X/Y coordinates from intensity matrix
filt_measurements <- as.data.frame(filt_measurements)
filt_measurements <- sapply(filt_measurements, as.numeric)

colnames(filt_measurements) <- str_c("CELL", as.character(1:ncol(filt_measurements)), sep = "_")
rownames(filt_measurements) <- c("DAPI", "PD1", "CD8", "CD3", "TIM3", "LAG3", "CK")
phenotype <- rep("", ncol(filt_measurements))

# CREATE SPATIAL EXPERIMENT
general_format_image <- format_image_to_spe(format = "general",
   phenotypes = phenotype,
   intensity_matrix = filt_measurements,
   coord_x = x_coord,
   coord_y = y_coord)

predicted_image <- predict_phenotypes(spe_object = general_format_image,
   thresholds = NULL,
   tumour_marker = "CK",
   nuclear_marker = "DAPI",
   baseline_markers = c("PD1", "CD8", "CD3", "TIM3", "LAG3"),
   reference_phenotypes = FALSE)

colnames(predicted_image)[1:10]
## [1] "CELL_1"  "CELL_2"  "CELL_3"  "CELL_4"  "CELL_5"  "CELL_6"  "CELL_7"  "CELL_8"  "CELL_9"
## [10] "CELL_10"

predicted_image$Phenotype[1:10]
## [1] "CK"             "PD1,CD8,CD3,CK" "CK"             "CK"             "CK"
## [6] "CK"             "CK"             "CK"             "CK"             "CK"

Sincerely thankful for your guidance,
Cyril.

Hi @CPUriarte , apologise for the late reply.
For the first issue, there shouldn't be a misclassification even if the tumour marker is excluded. I think for both issues if you could provide the data, the code and the error messages it would be easier for me to identify the problems. If you can not share the data, I suggest you send me the code and error messages along with the column names of your data. This is my email<EMAIL_ADDRESS>

I have sent you all required information, thanks for your help!

I will close the issue with a note - the function predict_phenotypes() assumes "tumour_marker" is the majority phenotype in the image. If this is not the case for a specific dataset, any marker that appears on most of the cells can be considered as "tumour_marker". This information will be updated in the documentation.


Add auto geolocation to tour page with fallback ZIP code form

http://brandnewcongress.org/tour
Assuming the intent for this page is to have me take action and RSVP to a local event, the page should make it as easy as possible to find my city. To that end, the page should allow me to auto-detect my location or enter my ZIP code, then surface my closest event at the top of the page.

Good idea.  As the tour is actually coming to a close fairly soon, I'm going to merge this into #98, which is going to be the longer term map we use.  Thanks!


[language] use short_str_lossless in ModuleId printing

This makes printing anything with a ModuleId much prettier, but without losing information.

Do you have a before/after example?

Do you have a before/after example?

This was inspired by looking at the expected value tests in https://github.com/diem/diem/pull/7234. For example, something like
Publishing a new module<PHONE_NUMBER>0000000000000000000042::M
Publishing a new module<PHONE_NUMBER>0000000000000000000043::N
Command `view storage/0x00000000000000000000000000000042/modules/M.mv`:

from there will become
Publishing a new module 0x42::M
Publishing a new module 0x43::N
Command `view storage/0x42/modules/M.mv`:

I expect there will be lots of other expected value tests I'll have to fix before landing this...

This was inspired by looking at the expected value tests in https://github.com/diem/diem/pull/7234. For example, something like
Publishing a new module<PHONE_NUMBER>0000000000000000000042::M
Publishing a new module<PHONE_NUMBER>0000000000000000000043::N
Command `view storage/0x00000000000000000000000000000042/modules/M.mv`:

from there will become
Publishing a new module 0x42::M
Publishing a new module 0x43::N
Command `view storage/0x42/modules/M.mv`:

I expect there will be lots of other expected value tests I'll have to fix before landing this...

I remember that stuff broke when we changed to print uppercase hex (#6296). Any similar risk here?

I remember that stuff broke when we changed to print uppercase hex (#6296). Any similar risk here?

Good question! That PR changed printing of AccountAddress, which is very broadly used. This one is changing the printing of ModuleId, which is only used in language tooling and VM error messages (which get threaded through json-rpc). I am fairly confident about the former, but I asked @xli about the latter.

Good question! That PR changed printing of AccountAddress, which is very broadly used. This one is changing the printing of ModuleId, which is only used in language tooling and VM error messages (which get threaded through json-rpc). I am fairly confident about the former, but I asked @xli about the latter.

Old PR, feel free to re-open.

It's not clear why this was dropped. I hadn't realized that it never landed. @sblackshear Do you still think we should do this? I really like the more readable output, as long as it isn't disruptive to switch.

I would still like to see this go in; IIRC it was breaking some tests in ways that I didn't understand.

Ah, OK. Feel free to close it for now if you don't have time. Or we could add it to our list of starter tasks?

Good idea, I'll close/create a task.


Clarification

Hey there, I am a contributor to sccache and initiator of cachepot and just stumbled upon this project.
Could you clarify how exactly the speedup gains are achieved? The README.md doesn't explain that and I see that under the hood it builds upon the sccache binary artifact.
CC @Xanewok

Sure - here's a rough breakdown of how we optimize performance:
Across All OS's:
Ramdisk (if the user is using a hard disk) OR always if the user is using WSL (3x speed improvement from our benchmarks)
Sccache (cache pre-compiled crates, especially effective with speeding up incremental builds at multi-crate cargo workspaces)
Share-generics (might be made optional soon, as our issues indicate we're trying to move to stable): -Zshare-generics=y
Increasing codegen-units, turning opt-level to 0 for debug builds.
Linux:
LLD (We're looking to change this to mold soon) Linker
Clang
Windows:
rust-lld.exe
MacOS:
ZLD Linker
-Csplit-debuginfo=unpacked

On a different note, cachepot looks super cool 😄


VSCode suggestions are not helpful after update

Hello! After upgrading to the latest version(1.54 I believe), the suggestions/auto-completes in VSCode are not working as they did before.

In the given screenshot, it should show a list of widgets, I believe. But even after I type the whole "Container", what I want doesn't show. How can I resolve this?

I restarted the IDE, it's working as expected now. I don't know why that happened.

I was about to post the following before I found this message. The vscode restart fixed it. Is this a vscode bug or a flutter extension bug?
This might be related to the last vscode update and suggestions now also coming from other modules, but now suggestions almost never suggest Widgets.
For example if I type "Containe" the suggestion list will still not suggest "Container()"

Here is MaterialApp()

Row

but the same problem happens with all widgets I've tried.


docs(readme): improve "How to commit" section

Improve How to commit section in README.md

@oliv37 thanks for helping make our docs better for new contributors 🎉🥇


Deployment Target: iOS 16

I updated the deployment target to iOS 16 and removed all deprecated code associated with iOS 15. Most of the changes involved migrating from NavigationView to NavigationStack or NavigationSplitView, with plenty of navigationDestination sprinkled in.
And since we're keeping the version of Package.resolved to 3, I configured Fastlane to use Xcode 15.3 using xcodes and updated the docs accordingly.

It seems like the the roles have reversed. Android tests are now quick and consistent and iOS tests are slow and flaky! Let's see if yeetd will improve the performance, based on https://github.com/actions/runner-images/discussions/8651#discussioncomment-7393444. I won't include this in the Mermaid diagram since I'm hoping this is a temporary workaround.

[04:16:24]: ▸ ::error file=/Users/runner/work/ez-recipes-ios/ez-recipes-ios/EZ Recipes/EZ RecipesTests/HomeViewModelTests.swift,line=67::    testGetRandomRecipeFail, Asynchronous wait failed: Exceeded timeout of 1 seconds, with unfulfilled expectations: "Fetch a random recipe".
[04:16:26]: ▸ ::error file=/Users/runner/work/ez-recipes-ios/ez-recipes-ios/EZ Recipes/EZ RecipesTests/HomeViewModelTests.swift,line=47::    testGetRandomRecipeSuccess, Asynchronous wait failed: Exceeded timeout of 1 seconds, with unfulfilled expectations: "Fetch a random recipe".
yeetd didn't help. Unit tests shouldn't exceed 1s. The longest they usually take is 0.05s to probably warm up. But I did notice a legitimate issue on iPads when using MultiPicker to search for recipes, so I'll need to fix that.


Training log

Dear authors,
Thanks a lot for sharing the code, which is quite clean and easy to read !!
I plan to train the model from scratch.
As the training takes ~10 days (c.f. issue 11), I am wondering whether it is possible to share your training log corresponding to the experiments of Lsun churches (VQGAN and Absorbing Diffusion sampler).
Finally, in the paper Sec.4.4, you mentioned that leveraging Diff Aug + $\lambda_{max} = 1$ leads to better performance. However, in the provided config, if I understand correctly, the diff aug is set to False.

Dear, authors,
I have another question about the FID evaluation.
If I understand correctly, the FID provided in the code is computed on the training set? (i.e. real and reconstructed images are both for the training set)
The details can be found in the following scripts:

calc_VQGAN_FID line 18
vqgan_utils line 78
vqgan_utils line 93-111
data_utils line 152-193

If this is true, does it make sense to report FID on the training set?
Thanks for your time !!
Best,

Hi, thanks for your interest in our paper and code! I shall answer your questions in order:

I am wondering whether it is possible to share your training log corresponding to the experiments of Lsun churches

Unfortunately we can't share training logs currently as the contain references to sensitive university info that would need to be cleaned out first. If this would be of significant use to all users though we may be able to facilitate this in the future.

However, in the provided config, if I understand correctly, the diff aug is set to False.

Good spot! That should not be set to False by default, please change it if you're trying to repeat experiments :)

If this is true, does it make sense to report FID on the training set?

This is an interesting point. I think it does make sense, as we in some ways don't want the VQGAN to generalise. We want the VQGAN to learn a latent space and a codebook that stores as much information as possible using the available data. As such reporting FID on the test/validation sets isn't really of any relevance, as the diffusion-sampler won't be affect by that data, it only cares about the latent space of the training data that the VQGAN actually used!
We would be keen to hear your thoughts on this though :)

Thanks for your reply !!!
It really helps me a lot~~
I close the issue.


Seems that bid/ask prices are swapped in wex exchange

It seems that bid and ask prices are swapped in wex->fetch_ticker() response. For example:
$wex = new \ccxt\wex();
$wex->load_markets();
print_r($wex->fetch_ticker("ETH/EUR"));

Returns a bid price (272.384) higher than the ask price (270.70566).
Array
(
    [symbol] => ETH/EUR
    [timestamp] =><PHONE_NUMBER>000
    [datetime] => 2017-10-24T14:49:40.000+00:00
    [high] => 278.387
    [low] => 246.90808
    [bid] => 272.384
    [ask] => 270.70566
    [vwap] =>
    [open] =>
    [close] =>
    [first] =>
    [last] => 271.08476
    [change] =>
    [percentage] =>
    [average] => 262.64754
    [baseVolume] => 1707.00159
    [quoteVolume] =><PHONE_NUMBER>5
    [info] => Array
        (
            [high] => 278.387
            [low] => 246.90808
            [avg] => 262.64754
            [vol] =><PHONE_NUMBER>5
            [vol_cur] => 1707.00159
            [last] => 271.08476
            [buy] => 272.384
            [sell] => 270.70566
            [updated] =><PHONE_NUMBER>
        )

)

Hi! Good catch! Thx for your report! Will fix shortly and get back to you!
On Tue, 24 Oct 2017 at 18:01, rubobaquero<EMAIL_ADDRESS>wrote:

It seems that bid and ask prices are swapped in wex->fetch_ticker()
response. For example:
$wex = new \ccxt\wex();
$wex->load_markets();
print_r($wex->fetch_ticker("ETH/EUR"));
Returns a bid price (272.384) higher than the ask price (270.70566).
Array
(
[symbol] => ETH/EUR
[timestamp] =><PHONE_NUMBER>000
[datetime] => 2017-10-24T14:49:40.000+00:00
[high] => 278.387
[low] => 246.90808
[bid] => 272.384
[ask] => 270.70566
[vwap] =>
[open] =>
[close] =>
[first] =>
[last] => 271.08476
[change] =>
[percentage] =>
[average] => 262.64754
[baseVolume] => 1707.00159
[quoteVolume] =><PHONE_NUMBER>5
[info] => Array
(
[high] => 278.387
[low] => 246.90808
[avg] => 262.64754
[vol] =><PHONE_NUMBER>5
[vol_cur] => 1707.00159
[last] => 271.08476
[buy] => 272.384
[sell] => 270.70566
[updated] =><PHONE_NUMBER>
)
)
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This issue is fixed as of 1.9.243+. WEX bid/asks are now set properly. Thx again! Let us know if you have any other questions or difficulties. Cheers!


noImplicitAny in jsconfig.json doesn't change ts behaviour

TS Template added by @mjbvz
TypeScript Version: 3.7.5

VSCode Version: 1.41.1
OS Version: Darwin x64 19.2.0

Steps to Reproduce:

Create a monorepo using lerna with yarn workspaces enabled
Create two packages
Set jsconfig.json to use "noImplicitAny": false
Import something from another package using namespace
Get an error Could not find a declaration file for module '@ns/ui/src/icons'. '**/packages/ui/src/icons/index.js' implicitly has an 'any' type.ts(7016)

I setup "noImplicitAny" and expect it work fine, but instead I see an error implicitly has an 'any' type.ts(7016)

jsconfig.json
{
  "compilerOptions": {
    "baseUrl": ".",
    "jsx": "react",
    "lib": ["dom"],
    "module": "esnext",
    "moduleResolution": "node",
    "noImplicitAny": false,
    "paths": {
      "@ms/*": ["./packages/*"]
    },
    "target": "esnext"
  },
  "exclude": ["node_modules", "**/node_modules/*", "dist"],
  "typeAcquisition": {
    "enable": true,
    "include": ["webpack-env", "jss"]
  }
}

How I import using namespace
...
import { Text } from '@ms/ui/src/text'
...

import Text from './Text'

export {
  Text,
}

My project tree looks kinda like this:
packages/
| dashboard/
|  |  src/
|  |  |  fileWhereIImport.js
|  |  package.json
|  ui
|  |  src/
|  |  |  text/
|  |  |  |  index.js
|  |  |  |  Text.js
|  |  package.json
package.json

Screenshot of an error

Does this issue occur when all extensions are disabled?: Yes

noImplicitAny doesn't control this behavior; the error message simply means "I couldn't find this module (and have thus assumed any)"


[hotfix][docs]The default value of sink.partition-commit.success-file.name shoule be _SUCCESS.

What is the purpose of the change
The default value of sink.partition-commit.success-file.name shoule be _SUCCESS.
Brief change log
(for example:)

The default value of sink.partition-commit.success-file.name shoule be _SUCCESS.

Verifying this change
This change is a trivial rework / code cleanup without any test coverage.
Does this pull request potentially affect one of the following parts:

Dependencies (does it add or upgrade a dependency): (yes / no)no
The public API, i.e., is any changed class annotated with @Public(Evolving): (yes / no)no
The serializers: (yes / no / don't know)no
The runtime per-record code paths (performance sensitive): (yes / no / don't know)no
Anything that affects deployment or recovery: JobManager (and its components), Checkpointing, Kubernetes/Yarn/Mesos, ZooKeeper: (yes / no / don't know)no
The S3 file system connector: (yes / no / don't know)no

Documentation

Does this pull request introduce a new feature? (yes / no)no
If yes, how is the feature documented? (not applicable / docs / JavaDocs / not documented)no

merged into release-1.11 by 95f0261ec2c420bc6021692d1ae9621b8f33a4b2


ci(post-release): replace set-env with set-output

:tada: This PR is included in version 1.4.4 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


Gosund WB3 OTA flash problem

Hello there,
currently having trouble with a Gosund WB3 LED Bulb https://templates.blakadder.com/gosund_WB3.html
I bought 2 (both in one pack) of them a while ago, flashed 1 already successful. Yesterday i tried to flash the second one and something went wrong. For now the LED wont turn on anymore. No AP opened.
The LED came out of the box, was installed into the socket and started it's fast pairing mode blinking.

The programs included with the Debian GNU/Linux system are free software;
the exact distribution terms for each program are described in the
individual files in /usr/share/doc/*/copyright.

Debian GNU/Linux comes with ABSOLUTELY NO WARRANTY, to the extent
permitted by applicable law.
Last login: Fri Apr 10 22:45:10 2020 from <IP_ADDRESS>
pi@raspberrypi:~ $ cd tuya-convert
pi@raspberrypi:~/tuya-convert $ dir
backups     docker      files              LICENSE    scripts
config.txt  Dockerfile  install_prereq.sh  README.md  start_flash.sh
pi@raspberrypi:~/tuya-convert $ ./start_flash.sh
tuya-convert v2.4.3
Checking for network interface wlan0... Found.
Checking UDP port 53... Occupied by dnsmasq with PID 552.
Port 53 is needed to resolve DNS queries
Do you wish to terminate dnsmasq? [y/N] y
Attempting to stop dnsmasq.service
Checking UDP port 67... Available.
Checking TCP port 80... Available.
Checking TCP port 443... Available.
Checking UDP port 6666... Available.
Checking UDP port 6667... Available.
Checking TCP port 1883... Occupied by mosquitto with PID 538.
Port 1883 is needed to run MQTT
Do you wish to terminate mosquitto? [y/N] y
Attempting to stop mosquitto.service
Checking TCP port 8886... Available.
sudo: ufw: command not found
======================================================
  Starting AP in a screen.
  Starting web server in a screen
  Starting Mosquitto in a screen
  Starting PSK frontend in a screen
  Starting Tuya Discovery in a screen

======================================================

IMPORTANT
1. Connect any other device (a smartphone or something) to the WIFI vtrust-flash
   This step is IMPORTANT otherwise the smartconfig may not work!
2. Put your IoT device in autoconfig/smartconfig/pairing mode (LED will blink fast). This is usually done by pressing and holding the primary button of the device
   Make sure nothing else is plugged into your IoT device while attempting to flash.
3. Press ENTER to continue

======================================================
Starting smart config pairing procedure
Waiting for the device to install the intermediate firmware
Put device in EZ config mode (blinking fast)
Sending SSID                  vtrust-flash
Sending wifiPassword
Sending token                 00000000
Sending secret                0101
................
SmartConfig complete.
Resending SmartConfig Packets
.....................................
IoT-device is online with ip <IP_ADDRESS>
Fetching firmware backup
mkdir: cannot create directory ‘../backups/20200410_225516’: Permission denied
./start_flash.sh: line 96: pushd: ../backups/20200410_225516: No such file or directory
======================================================
Cleaning up...
Closing AP
Exiting...

Currently i have no clue how to fix it, cause there is no sign of life.
I am far away beeing an expert on Linux, but looks like the flash didnt even start.
It failed to create the backup files already?
Could it be a misstake made by me? A Device failure?
I would be thankful for any kind of help.
Thx

Could you post the rest of your logs please?

Thx. I am sry, thought it would be enough to attach the error msg in the terminal.
smarthack-mqtt.log.txt
smarthack-psk.log.txt
smarthack-udp.log.txt
smarthack-web.log.txt
smarthack-wifi.log.txt

It failed to create the backup due to a permissions error. Looks like your device is still running the intermediate firmware.
You can chown the directory or just run as sudo. You do not need to connect a phone or put the device into pairing mode, since it already running the intermediate firmware. Just run start_flash, press enter, and plug the device back in.

Sry for the delay.
I ran it as sudo, but it fails to connect:
tuya-convert v2.4.3
Checking for network interface wlan0... Found.
Checking UDP port 53... Occupied by dnsmasq with PID 547.
Port 53 is needed to resolve DNS queries
Do you wish to terminate dnsmasq? [y/N] y
Attempting to stop dnsmasq.service
Checking UDP port 67... Available.
Checking TCP port 80... Available.
Checking TCP port 443... Available.
Checking UDP port 6666... Available.
Checking UDP port 6667... Available.
Checking TCP port 1883... Occupied by mosquitto with PID 534.
Port 1883 is needed to run MQTT
Do you wish to terminate mosquitto? [y/N] y
Attempting to stop mosquitto.service
Checking TCP port 8886... Available.
sudo: ufw: command not found
======================================================
  Starting AP in a screen.
  Starting web server in a screen
  Starting Mosquitto in a screen
  Starting PSK frontend in a screen
  Starting Tuya Discovery in a screen

======================================================

IMPORTANT
1. Connect any other device (a smartphone or something) to the WIFI vtrust-flash
   This step is IMPORTANT otherwise the smartconfig may not work!
2. Put your IoT device in autoconfig/smartconfig/pairing mode (LED will blink fast). This is usually done by pressing and holding the primary button of the device
   Make sure nothing else is plugged into your IoT device while attempting to flash.
3. Press ENTER to continue

======================================================
Starting smart config pairing procedure
Waiting for the device to install the intermediate firmware

IoT-device is online with ip <IP_ADDRESS>
Stopping smart config
Fetching firmware backup
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:--  0:00:31 --:--:--     0curl: (7) Failed to connect to <IP_ADDRESS> port 80: Connection timed out
Could not fetch a complete backup
Do you want to continue anyway? [y/N] N
======================================================
Cleaning up...
Closing AP
Exiting...

Seems the wifi.log updated:
smarthack-wifi.log-2.txt
So it was my fault, that i didnt run the command using sudo or run as root?
From my limited understanding, the backup is created before anything is uploaded?
ty


How to define the name of a schema?

Hi Jonathan,
on the documentation page, in "Tabular format for datasets" I find
"schema: Use this key to annotate the name of the schema of the table. If this key is set, ObjTables will check that its value matches the name of the schema used to interpret the table."
It's not clear to me how the name of the schema is defined in the schema file itself. Is there a metadata item "name='..'"? Could you maybe clarify this in the documentation?
Thank you!
Best,
Wolf

Yes, the name of the schema can be defined two ways

Tabular-formatted schemas: the name can be define in the metadata for the schema!!ObjTables ... name='...' ...

Python schemas: the name is the name of the Python module (equivalent to the filename)

I'll clarify this in the documentation

I added documentation


Test for action description of code actions, and simplify description for extracting method to file

Fixes #17998

FYI @RyanCavanaugh


Hot module tumblr

Fixes #4741
Tumblr made an update to it's share tool that requires a new parameter canonicalUrl which :bomb: 'ed tumblr shares . So this PR updates the dosomething_helpers_get_tumblr_intent to take in the absolute path of the page being shared, and sets the required parameter for all links.
@angaither

Looks :+1:
@sbsmith86 does this also change things for permalink shares?

@angaither yep yep

bueno!


Release of the Python binding version 0.5.8

Description

Bump version of maturin to 0.12.19
Update the rust dependencies
Prepare the release of the new version of the Python binding 0.5.8

@fvaleye - i am working on a fix for #600 that should be ready very soon.
@wjones127 also mentioned hoping to get #625 in before a release.
Could we hold off releasing until those are done?

Sure @roeap 👍
When it's done, I will merge your branches into this one!

Also note #651.

@fvaleye I believe all blocking PRs have been merged. Thanks for waiting!


Loop getting optimized out in mesh shader

When declaring a simple loop to output data from a mesh shader, the loop completely disappears when outputting glsl code (probably also for other targets, but I can't read spriv-asm and nothing is shown on screen).
Example modified from the test cases:
const static float2 positions[3] = {
  float2(0.0, -0.5),
  float2(0.5, 0.5),
  float2(-0.5, 0.5)
};

const static float3 colors[3] = {
  float3(1.0, 1.0, 0.0),
  float3(0.0, 1.0, 1.0),
  float3(1.0, 0.0, 1.0)
};
struct Vertex
{
  float4 pos : SV_Position;
  float3 color : Color;
  int index : Index;
};

const static uint MAX_VERTS = 12;
const static uint MAX_PRIMS = 4;

[outputtopology("triangle")]
[shader("mesh")]
[numthreads(3, 1, 1)]
void meshMain(
    in uint tig : SV_GroupIndex,
    out Vertices<Vertex, MAX_VERTS> verts,
    out Indices<uint3, MAX_PRIMS> triangles)
{
    const uint numVertices = 12;
    const uint numPrimitives = 4;
    SetMeshOutputCounts(numVertices, numPrimitives);

    for(uint i = tig; i < numVertices; ++i)
    {
        const int tri = i / 3;
        verts[i] = {float4(positions[i % 3], 0, 1), colors[i % 3], tri};
    }

    for(uint i = tig; i < numPrimitives; ++i)
    {
        triangles[i] = i * 3 + uint3(0,1,2);
    }
}

To test, i compiled this on the commandline with: slangc.exe test.slang -profile sm_6_6 -target glsl -entry meshMain -capability spirv_1_5 -o test.glsl
#version 450
#extension GL_EXT_mesh_shader : require
layout(row_major) uniform;
layout(row_major) buffer;

#line 27 0
layout(local_size_x = 3, local_size_y = 1, local_size_z = 1) in;
layout(max_vertices = 12) out;
layout(max_primitives = 4) out;
layout(triangles) out;
void main()
{

    SetMeshOutputsEXT(12U, 4U);

#line 46
    return;
}

@expipiplus1 This should be fixed in tandem with #2804.
The Vertices type should not be semantically an out parameter, and its subscript operator should map to a dedicated instruction that will be treated by the compiler as an external memory object and therefore DCE shouldn't apply to any read/writes on that location.

@csyonghe looks like #2804 is put for Q3 , should we move 2804 into Q1, too?

Moved #2804 to Q1.


tests: Add tests for several different ways to extract the title

Summary
Added the tests for three cases of title extraction:

<title> tag
og metatag
<title> tag in a malformed html

Related issues #493
Changes these areas

[X] Bugfixes
[ ] Feature behavior
[ ] Command line interface
[ ] Configuration options
[ ] Internal architecture
[ ] Snapshot data layout on disk

@pirate added a couple tests. Also, the parser was not raising an exception. Forcefully raise it now to try to use the HTML regex method in any case if the strict parser fails.


Built-In Rendering Library (perfomance)

Core I5, GTX 1060, can barely run the Rendering Library at 10 frames.
This performance decrease only happens when running the Rendering library.
Example: Before using BoxESP example code: 120 FPS, after: 13 FPS.
Device name	...
Processor	Intel(R) Core(TM) i5-9300H CPU @ 2.40GHz   2.40 GHz
Installed RAM	8.00 GB (7.82 GB usable)
Device ID ...
Product ID	...
System type	64-bit operating system, x64-based processor

Sorry but what do you exactly mean with rendering library?

He means raylib, the overlay. I brought this issue up in the discord a while ago. The overlay is very heavy on the GPU, even at low frame rates. 60fps for example uses around 20% gpu usage for me on a RTX2060. Took a look through the source and not really sure what could be causing it.

h8rr, pointed it out.

I see. I'm having around ~15% GPU usage with the overlay test on a 3080. Did you guys noticed if this is a general thing with raylib? Like @h8rr said, I don't see a reason why especially pyMeow's code should cause that gpu usage.

So I made a quick test with the python bindings for raylib which uses the same GPU usage for me:
from pyray import *
set_target_fps(144)
set_config_flags(ConfigFlags.FLAG_WINDOW_UNDECORATED)
set_config_flags(ConfigFlags.FLAG_WINDOW_MOUSE_PASSTHROUGH)
set_config_flags(ConfigFlags.FLAG_WINDOW_TRANSPARENT)
set_config_flags(ConfigFlags.FLAG_WINDOW_TOPMOST)
set_config_flags(ConfigFlags.FLAG_MSAA_4X_HINT)
init_window(800, 450, "Hello")
while not window_should_close():
    begin_drawing()
    draw_text("Hello world", 190, 200, 20, VIOLET)
    end_drawing()
    clear_background(BLANK)
close_window()

pyMeow:
import pyMeow as pm
pm.overlay_init(fps=144)
while pm.overlay_loop():
    pm.begin_drawing()
    pm.draw_text("Hello World", 400, 800, 12, pm.get_color("white"))
    pm.end_drawing()

Both solutions use around 15%. But however in @ImInTheICU case it seems like his game performance is decreasing a lot after running the overlay. Are your gpu drivers up to date?

I have a 3060 TI, but I don't use it often for game cheating, I usually use a separate computer as I also cheat in Rust and other games.


Chapter3 MNIST  error about show X[0] of datasets

when I try to run the code below
%matplotlib inline
import matplotlib as mpl
import matplotlib.pyplot as plt

some_digit = X[0]
some_digit_image = some_digit.reshape(28, 28)
plt.imshow(some_digit_image, cmap = mpl.cm.binary, interpolation="nearest")
plt.axis("off")

save_fig("some_digit_plot")
plt.show()

I got the error below
**KeyError                                  Traceback (most recent call last)
~/ML/fi_env/lib/python3.7/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
2897             try:
-> 2898                 return self._engine.get_loc(casted_key)
2899             except KeyError as err:
pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()
pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()
KeyError: 0
The above exception was the direct cause of the following exception:
KeyError                                  Traceback (most recent call last)
 in
3 import matplotlib.pyplot as plt
4
----> 5 some_digit = X[0]
6 some_digit_image = some_digit.reshape(28, 28)
7 plt.imshow(some_digit_image, cmap = mpl.cm.binary, interpolation="nearest")
~/ML/fi_env/lib/python3.7/site-packages/pandas/core/frame.py in getitem(self, key)
2904             if self.columns.nlevels > 1:
2905                 return self._getitem_multilevel(key)
-> 2906             indexer = self.columns.get_loc(key)
2907             if is_integer(indexer):
2908                 indexer = [indexer]
~/ML/fi_env/lib/python3.7/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
2898                 return self._engine.get_loc(casted_key)
2899             except KeyError as err:
-> 2900                 raise KeyError(key) from err
2901
2902         if tolerance is not None:
KeyError: 0
**
Please help me!!!!  Dear friend
Thanks!!!!!!!!!!!!!

I remember this error was because some_index and not some_digit
Le dim. 14 mars 2021 à 3:50 PM, Onlymman @.***> a
écrit :

when I try to run the code below
%matplotlib inlineimport matplotlib as mplimport matplotlib.pyplot as plt
some_digit = X[0]some_digit_image = some_digit.reshape(28, 28)plt.imshow(some_digit_image, cmap = mpl.cm.binary, interpolation="nearest")plt.axis("off")
save_fig("some_digit_plot")plt.show()
I got the error below
**KeyError Traceback (most recent call last)
~/ML/fi_env/lib/python3.7/site-packages/pandas/core/indexes/base.py in
get_loc(self, key, method, tolerance)
2897 try:
-> 2898 return self._engine.get_loc(casted_key)
2899 except KeyError as err:
pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()
pandas/_libs/hashtable_class_helper.pxi in
pandas._libs.hashtable.PyObjectHashTable.get_item()
pandas/_libs/hashtable_class_helper.pxi in
pandas._libs.hashtable.PyObjectHashTable.get_item()
KeyError: 0
The above exception was the direct cause of the following exception:
KeyError Traceback (most recent call last)
in
3 import matplotlib.pyplot as plt
4
----> 5 some_digit = X[0]
6 some_digit_image = some_digit.reshape(28, 28)
7 plt.imshow(some_digit_image, cmap = mpl.cm.binary,
interpolation="nearest")
~/ML/fi_env/lib/python3.7/site-packages/pandas/core/frame.py in getitem(self,
key)
2904 if self.columns.nlevels > 1:
2905 return self._getitem_multilevel(key)
-> 2906 indexer = self.columns.get_loc(key)
2907 if is_integer(indexer):
2908 indexer = [indexer]
~/ML/fi_env/lib/python3.7/site-packages/pandas/core/indexes/base.py in
get_loc(self, key, method, tolerance)
2898 return self._engine.get_loc(casted_key)
2899 except KeyError as err:
-> 2900 raise KeyError(key) from err
2901
2902 if tolerance is not None:
KeyError: 0
**
Please help me!!!! Dear friend
Thanks!!!!!!!!!!!!!
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.

--
Mohamed A. Al Moghalis

Is this because I didn't download the dataset of MNIST successfully?

Could you tell me more about it? Thanks.

Hi there,
Thanks for your feedback. It looks like your dataset is a Pandas DataFrame, when it should be a NumPy array. This is probably due to a change in the function fetch_openml() which occurred in Scikit-Learn 0.24: it now returns a DataFrame by default. To prevent this from happening (and hopefully fix the issue), you should pass as_frame=False when calling the fetch_openml() function. I fixed a few weeks ago in the notebooks, so you can just git pull the latest code.
Hope this helps.

Try accessing it with iloc and converting it to a np array.
some_digit=np.array(X.iloc[0])
comment out some_digit=X[0]

Please see my answer instead. Using iloc will work, but it will require changing a lot of code, and you'll run into errors if you forget just one. It's much simpler to just call fetch_openml(..., as_frame=False) if you want the code in the book to run without other changes.

Thank you so much.

Hi there, Thanks for your feedback. It looks like your dataset is a Pandas DataFrame, when it should be a NumPy array. This is probably due to a change in the function fetch_openml() which occurred in Scikit-Learn 0.24: it now returns a DataFrame by default. To prevent this from happening (and hopefully fix the issue), you should pass as_frame=False when calling the fetch_openml() function. I fixed a few weeks ago in the notebooks, so you can just git pull the latest code.
Hope this helps.

Thank you, it really helped me :)

Please see my answer instead. Using iloc will work, but it will require changing a lot of code, and you'll run into errors if you forget just one. It's much simpler to just call fetch_openml(..., as_frame=False) if you want the code in the book to run without other changes.

very thanks


Added pagerduty

Adds the following events or companies:

Pagerduty

Checklist

[x] I have updated the event or company counts
[x] I have put the most recent relevant date in the "Last Update" column
[x] I have linked to the article about the change, not the company's website

Resolved the merge conflicts, those came too fast

Hi there! We recently re-worked the site to use yaml data files. We'd be happy to accept your PR once it's been reworked to use the right format.
Thanks!

Closing this as a duplicate of #416, which you also submitted. Thanks!


Congenital heart disease, multiple types-GATA4

Preferred gene-related syndrome label
Congenital heart disease, multiple types-GATA4
on behalf of the ClinGen Congenital Heart Disease GCEP
Synonyms
Parent term (use OLS, or your favorite ontology browser)
Definition
Please write the definition in the format: Any [parent class] in which the cause of the disease is a mutation in the [gene name] gene. For example: Any congenital myopathy in which the cause of the disease is a mutation in the TPM3 gene.
**Definition source (Please give PubMed ID, if applicable, in format PMID:#######)
Children terms (if applicable) Should any existing terms be re-classified as children underneath this new proposed term?
Your nano-attribution (ORCID) or URL for a working group
If you don't have an ORCID, you can sign up for one here

@eedoh01 is this your GCEP:
https://clinicalgenome.org/affiliation/40104/
?

@eedoh01 could you please provide more details in this request? Could you please write a definition for this term and provide a source (like a reference to a paper in PubMed (the PubMed ID)?
thank you!

parent class should be 'congenital heart disease'
these should be children of the new class

Hi Nicole,
My apologies for the delay. I believe the previous emails may have gone
into my spam folder. I will get back to you this week with more details for
the definition and confirm your follow up question.
Respectfully,
Enyo
On Wed, Feb 1, 2023 at 3:24 PM Nicole Vasilevsky @.***>
wrote:

parent class should be 'congenital heart disease'
these should be children of the new class
[image: image]
https://user-images.githubusercontent.com/6722114/216155218-27f76d82-9fb1-43a1-89b4-65b4275e096b.png
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Thanks @eedoh01!

Hi Nicole,
Our GCEP is https://clinicalgenome.org/affiliation/40130/. The parent class
should have congenital heart disease with the children of the new class
including Atrial septal defect 2, tetralogy of fallot, ventricular septal
defect, patent foramen ovale..
Term: Structural congenital heart disease, multiple types - GATA4
Definition: A heart disease that is present at birth. Representative
examples include atrial septal defect, ventricular septal defect, tetralogy
of Fallot, and patent foramen ovale.
PMID: 15810002, 28991257, 18672102, 22101736
Please let me know if you need any additional information.
Respectfully,
Enyo
On Wed, Feb 1, 2023 at 5:47 PM Enyonam Edoh @.***>
wrote:

Hi Nicole,
My apologies for the delay. I believe the previous emails may have gone
into my spam folder. I will get back to you this week with more details for
the definition and confirm your follow up question.
Respectfully,
Enyo
On Wed, Feb 1, 2023 at 3:24 PM Nicole Vasilevsky @.***>
wrote:

parent class should be 'congenital heart disease'
these should be children of the new class
[image: image]
https://user-images.githubusercontent.com/6722114/216155218-27f76d82-9fb1-43a1-89b4-65b4275e096b.png
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Thank you very much!
On Wed, Feb 8, 2023 at 4:20 PM Nicole Vasilevsky @.***>
wrote:

Closed #5796 https://github.com/monarch-initiative/mondo/issues/5796 as
completed via #5889
https://github.com/monarch-initiative/mondo/pull/5889.
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Hi Nicole,
I was wondering if the term has been added to MONDO? I did notice that the
completed is "congenital heart disease, multiple types - GATA4" but it
should be "Structural congenital heart disease, multiple types - GATA"
Respectfully,
Enyo
On Wed, Feb 8, 2023 at 5:11 PM Enyonam Edoh @.***>
wrote:

Thank you very much!
On Wed, Feb 8, 2023 at 4:20 PM Nicole Vasilevsky @.***>
wrote:

Closed #5796 https://github.com/monarch-initiative/mondo/issues/5796
as completed via #5889
https://github.com/monarch-initiative/mondo/pull/5889.
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Hi @eedoh01 thanks for letting us know, our curator @sabrinatoro fixed this for you and she'll be doing a release tomorrow.

Hi Monarch-Initiative/Mondo,
I wanted to check in to see how this is going. We still aren't able to see
the released term on our end.
Respectfully,
Enyo
On Tue, Feb 28, 2023 at 7:23 PM Nicole Vasilevsky @.***>
wrote:

Hi @eedoh01 https://github.com/eedoh01 thanks for letting us know, our
curator @sabrinatoro https://github.com/sabrinatoro fixed this for you
and she'll be doing a release tomorrow.
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This term is now available, see
https://www.ebi.ac.uk/ols4/ontologies/mondo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0100009
The ID is: MONDO:0100009

Hi @eedoh01 - if you are having issues with the ClinGen curation app, unfortunately, we at Mondo are unable to help with that.
Is there an issue with Mondo that we can help with?
Best,
Nicole

I think this can be closed. @eedoh01 please reopen if any action is needed from our team, thanks!


cms:helper:asset_url no longer works

I am upgrading from ruby 2.4, rails 5.1.4, and cms branch rails5.1 to ruby 2.5.1, rails 5.2.0, cms 2.0.17. I am getting errors when i try to render some of my snippets. it seems like the line comes from:
Color Copy (8.5"x11") Templates
I have a lot of assets in the asset pipeline (that are cached on an amazon cloudfront CDN) that are images, zip files ,etc. I used the cms::helper::asset_url to get the URLs of them. However, with the upgrade, it seems like this method no longer exists. I see that there is an asset helper but in the documentation it says it only works for css and js files?
Any idea what i should do to get this working?
thanks.

That tag doesn't look like that in 2.0. Take a look at the upgrading wiki entry: https://github.com/comfy/comfortable-mexican-sofa/wiki/HowTo:-Upgrade-CMS-From-1.12-to-2.0
And the new tag structure is documented here: https://github.com/comfy/comfortable-mexican-sofa/wiki/Docs:-Content-Tags#helper

Thanks! i didnt realize there was a section in the wiki for upgrading.


Add 'take_buf' method to BufReader.

Hello!
I'm using the latest 0.9.x release on a project I'm working on, and I'm quite in need of this method. As I'd like to release my project on crates.io soon, I was hoping you would merge this in and then release a new version of hyper 0.9.x on crates.io. I understand that 0.9.x has effectively been abandoned in favor of 0.10, so I hope it won't be too much trouble.
Thanks!
Sergio

Note that the Travis-CI failure is unrelated to my PR.

@seanmonstar ping.

This actually worries me a little. What happens if you take the buf and then try to keep on reading on the Request? It's internal counter of whether it can keep-alive will be all ruined, won't it?

@seanmonstar Everything works as expected: the buffer will be refilled, and reading will continue. I explicitly tested that keep-alive continues working as expected.

Reading through the code, it looks like HttpReader wraps BufReaders, so the SizedReader (and Chunked) will not have counted how many bytes have been read off the socket, only how many have been read from the buffer.
What depends on this?

That's right, but the original Reader shouldn't be used after calling take_buf. Even then, in the worst case, the SizedReader will simply say that there was an eof.
In a soon-to-be released project, I keep the TCP stream around for later reading. The current API forces me to keep around two lifetimes if I want to keep the TCP stream around, neither of which are necessary. With this API, I don't need to keep any lifetimes around, and I can rewrap the stream in more friendly APIs.

Hi @seanmonstar, still waiting on this. With very high probability, I'll be publishing my crate next week, and I'd really like to not have a fork of Hyper in crates.io. Let me know. If it helps with getting this out, I'd be happy to add a #[doc(hidden)] tag so that others don't use this unnecessarily.

@seanmonstar Can we get a new release with this change?

I published 0.9.14 a few days ago that included this.
On Thu, Dec 15, 2016, 4:35 PM Sergio Benitez<EMAIL_ADDRESS>wrote:

@seanmonstar https://github.com/seanmonstar Can we get a new release
with this change?
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An error occurred on the oracle-server node and node-red stopped.

The cause of the error is the loss of the oracle connection.It happened shortly after upgrading to<EMAIL_ADDRESS>and oracle instant client 19.10.
14 Apr 04:56:26 - [info] [oracledb:XXXXDB] Oracle query start execution
14 Apr 04:56:26 - [info] [oracledb:XXXXDB] Oracle query execution started
14 Apr 04:56:26 - [error] [oracledb:XXXXDB] Oracle query error: ORA-03113: end-of-file on communication channel
プロセスID: 15532942
セッションID: 3421、シリアル番号: 531
14 Apr 04:56:26 - [info] [oracle-server:3bd2bc9d.276314] Oracle server connection lost, retry in 60000 ms
14 Apr 04:57:26 - [red] Uncaught Exception:
14 Apr 04:57:26 - TypeError: requestingNode.log is not a function
at Timeout.OracleServer.node.query [as _onTimeout] (C:\node-red\xxx\my_node-red\node_modules\node-red-contrib-oracledb-mod\lib\oracledb.js:200:28)
at listOnTimeout (internal/timers.js:556:17)
at processTimers (internal/timers.js:497:7)
14 Apr 04:57:27 - [info]
OS : Windows Server 2012 R2
<EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS>oracle instant client 19.10
Worked around the issue by downgrading to<EMAIL_ADDRESS>Is there any good way to solve it?

Hi I am facing the same issue, please let me know how did you solve your issue, my node version is 0.6.3.

Hi akhiljakka.
Sorry, I have not been able to resolve this issue. I have downgraded to<EMAIL_ADDRESS>


FR typo fix

changing quote to curly quote

@pantkowiak We have split Release 1.2 into the release branch. Can you re-submit this PR for that branch (i.e. not master) ?

re-submitted this PR for branch release https://github.com/adobe/brackets/pull/10625


Pasting base64 images broken

Describe the bug
In HTML it is possible to specify an image inline with a base64 encoded source, like:
<img src="data:image/jpeg;base64,/9j/4AAQSkZJRgABAQEAkACQAAD/2wBDAAMCAgICAgM...">
Images created in Jupyter notebooks, like graphs generated with the matplotlib Python package, are for example of that form. In the latest version(s) of BookStack it is not possible to copy/paste those images, at least not in the WYSIWYG editor. Neither by copying or by dragging them. One has to save the image and upload them separately.
Steps To Reproduce
Steps to reproduce the behavior:

Create a new page with the WYSIWYG editor
Go to https://nbviewer.jupyter.org/github/empet/Math/blob/master/DomainColoring.ipynb
Right-click on one of the color wheel images and click 'Copy image'
Go back to the editor and try to paste (ctrl+v, right clicking does not give the option to paste)
Nothing happens
Open for instance the Gimp, press ctrl+v and the image is pasted correctly there

Alternatively:

Create a new page with the WYSIWYG editor
Go to https://nbviewer.jupyter.org/github/empet/Math/blob/master/DomainColoring.ipynb
Drag and drop one of the color wheel images into the bookstack editor; the image appears
Save the page; the image is not there
Click 'Edit' again, the image is there again, but saving again still doesn't show it
Delete the image, and try to drag and drop again; this doesn't work anymore and no image is shown

This second set of steps only works in Firefox, dragging from Chrome has the same result as trying to copy/paste, i.e. the image doesn't show up in the editor at all.
Expected behavior
Base64 encoded images can be copied or dragged into the editor, and are there after the page is saved.
Your Configuration (please complete the following information):

Exact BookStack Version (Found in settings): v0.27.4
PHP Version: 7.1
Hosting Method (Nginx/Apache/Docker): Docker (FROM php:7.1-apache-stretch)
Browsers: Firefox 69.0.1, Chrome 77.0.3865.90
OS: Ubuntu 18.04

Additional context
This could be related to #1651, but seemed different enough to report separately.

Hi @sgvandijk,
Thanks for the detail and clear steps.
I'm pretty sure this is the same issue as #1651, AFAIK, it shouldn't matter how the original image data was defined on the source page, copying as image should produce the same result.
I've marked #1651 to be looked at for the next patch release. I've marked this for the same release, so this is at least checked after the fix is applied.

Thanks, let me know if any more info is useful! I should have mentioned that I am not experiencing #1651 and copying other images does work for me. For instance copy-pasting or drag-and-dropping the first image in https://nbviewer.jupyter.org/github/empet/Math/blob/master/DomainColoring.ipynb, the RGB cube, works fine for me.

I have just commited a83a7f34f4d4c85bfb208eb1abfdd77743856680 which should fix this. I've tested on both FireFox and Chrome on Ubuntu, and the defined test case works where it did not before. This fix is in master and will be part of the next release ,v0.28, which is due for the end of the year.
I'll therefore close this. If you continue to have problems after v0.28, Please open a new issue referencing this one.
Thanks again @sgvandijk for reporting and making the issue clear!


Label / endpoint caching for better performance

Looks good. You only have a single thread using these caches right?
Also, there are a number of unused imports - policy_agent.py / policy_parser.py / network_policy.py /pod.py

Yep. That part is all single threaded.
I'll fix up the imports.


Segmentation Fault with ph4

Hi,
I was using Amuse-ph4 last November and everything was working fine.
In the intervening time I updated my OS to ubuntu 20.04
Now, trying to picking up Amuse again, I get some kind of segmentation fault when trying to use ph4. I have made a quick script to reproduce the following error
$ python run_evol.py  [andrew-XPS-13-9360:72878] *** Process received signal *** [andrew-XPS-13-9360:72878] Signal: Segmentation fault (11) [andrew-XPS-13-9360:72878] Signal code: Address not mapped (1) [andrew-XPS-13-9360:72878] Failing at address: (nil) [andrew-XPS-13-9360:72878] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x46210)[0x7fa148935210] [andrew-XPS-13-9360:72878] [ 1] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_ess_singleton.so(+0x319b)[0x7fa11fbc119b] [andrew-XPS-13-9360:72878] [ 2] /usr/lib/x86_64-linux-gnu/libopen-rte.so.20(orte_init+0x22e)[0x7fa12133d1de] [andrew-XPS-13-9360:72878] [ 3] /usr/lib/x86_64-linux-gnu/libmpi.so.20(ompi_mpi_init+0x30e)[0x7fa1215f827e] [andrew-XPS-13-9360:72878] [ 4] /usr/lib/x86_64-linux-gnu/libmpi.so.20(PMPI_Init_thread+0x79)[0x7fa121619439] [andrew-XPS-13-9360:72878] [ 5] /home/andrew/Documents/Physics/Tools/Amuse-env4/lib/python3.8/site-packages/mpi4py/MPI.cpython-38-x86_64-linux-gnu.so(+0x3046d)[0x7fa1218d346d] [andrew-XPS-13-9360:72878] [ 6] python(PyModule_ExecDef+0x4c)[0x6a592c] [andrew-XPS-13-9360:72878] [ 7] python[0x684437] [andrew-XPS-13-9360:72878] [ 8] python[0x5c4b10] [andrew-XPS-13-9360:72878] [ 9] python(PyVectorcall_Call+0x58)[0x5f3798] [andrew-XPS-13-9360:72878] [10] python(_PyEval_EvalFrameDefault+0x6435)[0x570f85] [andrew-XPS-13-9360:72878] [11] python(_PyEval_EvalCodeWithName+0x26a)[0x56955a] [andrew-XPS-13-9360:72878] [12] python(_PyFunction_Vectorcall+0x393)[0x5f7323] [andrew-XPS-13-9360:72878] [13] python(_PyEval_EvalFrameDefault+0x5736)[0x570286] [andrew-XPS-13-9360:72878] [14] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [15] python(_PyEval_EvalFrameDefault+0x849)[0x56b399] [andrew-XPS-13-9360:72878] [16] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [17] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] [18] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [19] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] [20] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [21] python[0x5f4ca1] [andrew-XPS-13-9360:72878] [22] python(_PyObject_CallMethodIdObjArgs+0x198)[0x5f5108] [andrew-XPS-13-9360:72878] [23] python(PyImport_ImportModuleLevelObject+0x823)[0x552f53] [andrew-XPS-13-9360:72878] [24] python[0x4f5bd8] [andrew-XPS-13-9360:72878] [25] python(PyCFunction_Call+0x59)[0x5f4249] [andrew-XPS-13-9360:72878] [26] python(_PyEval_EvalFrameDefault+0x6435)[0x570f85] [andrew-XPS-13-9360:72878] [27] python(_PyEval_EvalCodeWithName+0x26a)[0x56955a] [andrew-XPS-13-9360:72878] [28] python(_PyFunction_Vectorcall+0x393)[0x5f7323] [andrew-XPS-13-9360:72878] [29] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] *** End of error message *** Segmentation fault (core dumped)
I've attached the script and an additional document.
I have performed a clean environment install and still I get the same error.
If anyone has any suggestions, I would appreciate it a lot.
Cheers
ph4issue.zip

Dear Andrew,
runs fine with me (see below):
Mayn you can try to make clean and make again, and then retry?
(base) spz@Flater:~/AMUSE/tmp/ph4$ python run_evol.py
You have used the following codes, which contain literature references:
"AMUSE"
Portegies Zwart, S. & McMillan, S.L.W., 2018, "Astrophysical Recipes: the art of AMUSE", AAS IOP Astronomy publishing (411 pages) [2018araa.book.....P]
** Portegies Zwart, S. et al., 2013, Multi-physics Simulations Using a Hierarchical Interchangeable Software Interface, Computer Physics Communications 183, 456-468 [2013CoPhC.183..456P]
** Pelupessy, F. I. et al., 2013, The Astrophysical Multipurpose Software Environment, Astronomy and Astrophysics 557, 84 [2013A&A...557A..84P]
Portegies Zwart, S. et al., 2009, A multiphysics and multiscale software environment for modeling astrophysical systems, New Astronomy, Volume 14, Issue 4, 369-378 [2009NewA...14..369P]
Simon
On Jan 5 2021, at 4:01 pm, Andrew Cheek<EMAIL_ADDRESS>wrote:

Hi,
I was using Amuse-ph4 last November and everything was working fine.
In the intervening time I updated my OS to ubuntu 20.04
Now, trying to picking up Amuse again, I get some kind of segmentation fault when trying to use ph4. I have made a quick script to reproduce the following error
$ python run_evol.py [andrew-XPS-13-9360:72878] *** Process received signal *** [andrew-XPS-13-9360:72878] Signal: Segmentation fault (11) [andrew-XPS-13-9360:72878] Signal code: Address not mapped (1) [andrew-XPS-13-9360:72878] Failing at address: (nil) [andrew-XPS-13-9360:72878] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x46210)[0x7fa148935210] [andrew-XPS-13-9360:72878] [ 1] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_ess_singleton.so(+0x319b)[0x7fa11fbc119b] [andrew-XPS-13-9360:72878] [ 2] /usr/lib/x86_64-linux-gnu/libopen-rte.so.20(orte_init+0x22e)[0x7fa12133d1de] [andrew-XPS-13-9360:72878] [ 3] /usr/lib/x86_64-linux-gnu/libmpi.so.20(ompi_mpi_init+0x30e)[0x7fa1215f827e] [andrew-XPS-13-9360:72878] [ 4] /usr/lib/x86_64-linux-gnu/libmpi.so.20(PMPI_Init_thread+0x79)[0x7fa121619439] [andrew-XPS-13-9360:72878] [ 5] /home/andrew/Documents/Physics/Tools/Amuse-env4/lib/python3.8/site-packages/mpi4py/MPI.cpython-38-x86_64-linux-gnu.so(+0x3046d)[0x7fa1218d346d] [andrew-XPS-13-9360:72878] [ 6] python(PyModule_ExecDef+0x4c)[0x6a592c] [andrew-XPS-13-9360:72878] [ 7] python[0x684437] [andrew-XPS-13-9360:72878] [ 8] python[0x5c4b10] [andrew-XPS-13-9360:72878] [ 9] python(PyVectorcall_Call+0x58)[0x5f3798] [andrew-XPS-13-9360:72878] [10] python(_PyEval_EvalFrameDefault+0x6435)[0x570f85] [andrew-XPS-13-9360:72878] [11] python(_PyEval_EvalCodeWithName+0x26a)[0x56955a] [andrew-XPS-13-9360:72878] [12] python(_PyFunction_Vectorcall+0x393)[0x5f7323] [andrew-XPS-13-9360:72878] [13] python(_PyEval_EvalFrameDefault+0x5736)[0x570286] [andrew-XPS-13-9360:72878] [14] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [15] python(_PyEval_EvalFrameDefault+0x849)[0x56b399] [andrew-XPS-13-9360:72878] [16] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [17] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] [18] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [19] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] [20] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [21] python[0x5f4ca1] [andrew-XPS-13-9360:72878] [22] python(_PyObject_CallMethodIdObjArgs+0x198)[0x5f5108] [andrew-XPS-13-9360:72878] [23] python(PyImport_ImportModuleLevelObject+0x823)[0x552f53] [andrew-XPS-13-9360:72878] [24] python[0x4f5bd8] [andrew-XPS-13-9360:72878] [25] python(PyCFunction_Call+0x59)[0x5f4249] [andrew-XPS-13-9360:72878] [26] python(_PyEval_EvalFrameDefault+0x6435)[0x570f85] [andrew-XPS-13-9360:72878] [27] python(_PyEval_EvalCodeWithName+0x26a)[0x56955a] [andrew-XPS-13-9360:72878] [28] python(_PyFunction_Vectorcall+0x393)[0x5f7323] [andrew-XPS-13-9360:72878] [29] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] *** End of error message *** Segmentation fault (core dumped)
I've attached the script and an additional document.
I have performed a clean environment install and still I get the same error.
If anyone has any suggestions, I would appreciate it a lot.
Cheers
ph4issue.zip (https://github.com/amusecode/amuse/files/5770883/ph4issue.zip)
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Dear Andrew,
runs fine with me (see below):
Mayn you can try to make clean and make again, and then retry?
(base) spz@Flater:~/AMUSE/tmp/ph4$ python run_evol.py
You have used the following codes, which contain literature references:
"AMUSE"
Portegies Zwart, S. & McMillan, S.L.W., 2018, "Astrophysical Recipes: the art of AMUSE", AAS IOP Astronomy publishing (411 pages) [2018araa.book.....P]
** Portegies Zwart, S. et al., 2013, Multi-physics Simulations Using a Hierarchical Interchangeable Software Interface, Computer Physics Communications 183, 456-468 [2013CoPhC.183..456P]
** Pelupessy, F. I. et al., 2013, The Astrophysical Multipurpose Software Environment, Astronomy and Astrophysics 557, 84 [2013A&A...557A..84P]
Portegies Zwart, S. et al., 2009, A multiphysics and multiscale software environment for modeling astrophysical systems, New Astronomy, Volume 14, Issue 4, 369-378 [2009NewA...14..369P]
Simon
On Jan 5 2021, at 4:01 pm, Andrew Cheek<EMAIL_ADDRESS>wrote:

Hi,
I was using Amuse-ph4 last November and everything was working fine.
In the intervening time I updated my OS to ubuntu 20.04
Now, trying to picking up Amuse again, I get some kind of segmentation fault when trying to use ph4. I have made a quick script to reproduce the following error
$ python run_evol.py [andrew-XPS-13-9360:72878] *** Process received signal *** [andrew-XPS-13-9360:72878] Signal: Segmentation fault (11) [andrew-XPS-13-9360:72878] Signal code: Address not mapped (1) [andrew-XPS-13-9360:72878] Failing at address: (nil) [andrew-XPS-13-9360:72878] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x46210)[0x7fa148935210] [andrew-XPS-13-9360:72878] [ 1] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_ess_singleton.so(+0x319b)[0x7fa11fbc119b] [andrew-XPS-13-9360:72878] [ 2] /usr/lib/x86_64-linux-gnu/libopen-rte.so.20(orte_init+0x22e)[0x7fa12133d1de] [andrew-XPS-13-9360:72878] [ 3] /usr/lib/x86_64-linux-gnu/libmpi.so.20(ompi_mpi_init+0x30e)[0x7fa1215f827e] [andrew-XPS-13-9360:72878] [ 4] /usr/lib/x86_64-linux-gnu/libmpi.so.20(PMPI_Init_thread+0x79)[0x7fa121619439] [andrew-XPS-13-9360:72878] [ 5] /home/andrew/Documents/Physics/Tools/Amuse-env4/lib/python3.8/site-packages/mpi4py/MPI.cpython-38-x86_64-linux-gnu.so(+0x3046d)[0x7fa1218d346d] [andrew-XPS-13-9360:72878] [ 6] python(PyModule_ExecDef+0x4c)[0x6a592c] [andrew-XPS-13-9360:72878] [ 7] python[0x684437] [andrew-XPS-13-9360:72878] [ 8] python[0x5c4b10] [andrew-XPS-13-9360:72878] [ 9] python(PyVectorcall_Call+0x58)[0x5f3798] [andrew-XPS-13-9360:72878] [10] python(_PyEval_EvalFrameDefault+0x6435)[0x570f85] [andrew-XPS-13-9360:72878] [11] python(_PyEval_EvalCodeWithName+0x26a)[0x56955a] [andrew-XPS-13-9360:72878] [12] python(_PyFunction_Vectorcall+0x393)[0x5f7323] [andrew-XPS-13-9360:72878] [13] python(_PyEval_EvalFrameDefault+0x5736)[0x570286] [andrew-XPS-13-9360:72878] [14] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [15] python(_PyEval_EvalFrameDefault+0x849)[0x56b399] [andrew-XPS-13-9360:72878] [16] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [17] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] [18] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [19] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] [20] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [21] python[0x5f4ca1] [andrew-XPS-13-9360:72878] [22] python(_PyObject_CallMethodIdObjArgs+0x198)[0x5f5108] [andrew-XPS-13-9360:72878] [23] python(PyImport_ImportModuleLevelObject+0x823)[0x552f53] [andrew-XPS-13-9360:72878] [24] python[0x4f5bd8] [andrew-XPS-13-9360:72878] [25] python(PyCFunction_Call+0x59)[0x5f4249] [andrew-XPS-13-9360:72878] [26] python(_PyEval_EvalFrameDefault+0x6435)[0x570f85] [andrew-XPS-13-9360:72878] [27] python(_PyEval_EvalCodeWithName+0x26a)[0x56955a] [andrew-XPS-13-9360:72878] [28] python(_PyFunction_Vectorcall+0x393)[0x5f7323] [andrew-XPS-13-9360:72878] [29] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] *** End of error message *** Segmentation fault (core dumped)
I've attached the script and an additional document.
I have performed a clean environment install and still I get the same error.
If anyone has any suggestions, I would appreciate it a lot.
Cheers
ph4issue.zip (https://github.com/amusecode/amuse/files/5770883/ph4issue.zip)
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Indeed I performed a clean installation and it worked this time.
I'm not sure exactly what happened here.
Thanks,

Indeed I performed a clean installation and it worked this time.
I'm not sure exactly what happened here.
Thanks,


Learn basics of flask and how to define backend API functions

I think we can close this one ? We should pretty much know the basics of it all


Is there any installation doc for BJLS?

Is there any installation doc for BJLS?
How can I make BJLS working in Emacs with lsp-java enabled?

@PMitrafanau

Any update on this? I'll be happy with a "build from source" that gets me an executable BJLS.jar


Typescript support

Does it work with Typescript? i'm getting the declaration types error and can't find the correspondent @types.

Try install @iconify/iconify@2, it's rewritten in TypeScript

@types packages are needed only for libraries that do not have TypeScript definition files. Iconify packages are written in TypeScript and have definition files.
What NPM package are you experiencing issues with?


Can't build demo for mac without EGL

This worked
RUSTFLAGS='--cfg target_os="macos" --cfg feature="no-pkg-config"' cargo run --release


Not getting challenge from Enable Events tool

Description
Moving bot from socket mode to HTTP events for release. When inputting my URL, the app shows that it iss not sending any challenge data. Nor am I seeing any in the request logs.
What type of issue is this? (place an x in one of the [ ])

[ ] bug
[ ] enhancement (feature request)
[ x] question
[ ] documentation related
[ ] example code related
[ ] testing related
[ ] discussion

Requirements (place an x in each of the [ ])

[x ] I've read and understood the Contributing guidelines and have done my best effort to follow them.
[ x] I've read and agree to the Code of Conduct.
[ x] I've searched for any related issues and avoided creating a duplicate issue.

Bug Report
Filling out the following details about bugs will help us solve your issue sooner.
Reproducible in:
package version: ^3.4.0
node version: 15.x
OS version(s): OSX 11.5.1
Steps to reproduce:

Turn on server with logs
Fill out form with URL
Wait for response

Expected result:
POST response with data.
Actual result:
POST response with no data.
Attachments:

Hi @jp555soul! This definitely threw me at first: I've never seen a case where the token and challenge are both missing entirely.
I tried to reproduce your situation, beginning with a Socket Mode-enabled app and switching to HTTP. For the sake of ease, I used ngrok as a tunnel, though the result should be the same if I were deploying to Heroku and a successful connection was made.
After switching out the Socket Mode-specific properties (appToken, socketMode: true) in the App instantiation for non-Socket Mode ones (token, signingSecret), and restarting the server, all worked as expected and the verification succeeded.
Can you confirm on the Heroku end that the updated App code with the non-Socket Mode credentials is what's currently being served from that new Request URL?

@misscoded Thanks for your response. I've gone ahead and updated the code (posted below) as well as pointed it to a new route to confirm an update, but I'm still getting the same results. Code and screenshot attached below.
Code
require('dotenv').config();
const massive = require('massive')
const express = require('express')
const config = require('../config')
const { InstallProvider } = require('@slack/oauth');
const { App, ExpressReceiver, LogLevel } = require('@slack/bolt');
const uuid = require("uuid");
const packageJson = require('../package.json');

const app = express();
var http = require('http').Server(app);

//LOGGING
let agent = undefined;
const developerMode = true;
const logLevel = process.env.SLACK_LOG_LEVEL || LogLevel.DEBUG;

massive(config.database).then(async i => {
  // Start your app
  app.set('db', i);
  console.log('Connected to DB');
  http.listen(config.app.port, config.app.host, async () => {
    console.log(`Server running on ${config.app.host}:${config.app.port}`)
  });
}).catch(err => {
  console.log("Unable to instantiate database, ", err);
});

const installer = new InstallProvider({
  clientId: process.env.SLACK_CLIENT_ID,
  clientSecret: process.env.SLACK_CLIENT_SECRET,
  stateSecret: process.env.STATE_SECRET,
  authVersion: 'v2',
  //logLevel,
  installationStore: {
    storeInstallation: async (installation) => {
      console.log('storeInstallation -- installer')
      const db = app.get('db');
      // change the line below so it saves to your database
      if (installation.isEnterpriseInstall && installation.enterprise !== undefined) {
        // support for org wide app installation
        let entAccount = await db.table.findOne({ enterprise: installation.enterprise.id });
        if (entAccount) {
          const criteria = {
            enterprise: installation.enterprise.id
          }

          let changes;

          changes = {
            'token': installation['bot']['token'],
            'tokenraw': JSON.stringify(installation)
          }

          return await db.table.update(criteria, changes)
          .then(success => {
            console.log("The app was installed successfully. ENT");
          }).catch(err => { console.log(err) });
        } else {
          return await db.table.insert({
            enterprise: installation.enterprise.id,
            token: installation['bot']['token'],
            tokenraw: JSON.stringify(installation)
          })
          .then(success => {
            console.log("The app was installed successfully. ENT");
          }).catch(err => { console.log(err) });
        }
      }
      if (installation.team !== undefined) {
        // single team app installation
        let teamAccount = await db.table.findOne({ team: installation.team.id });
        if (teamAccount) {
          const criteria = {
            team: installation.team.id
          }

          let changes;

          changes = {
            'token': installation['bot']['token'],
            'tokenraw': JSON.stringify(installation)
          }

          return await db.table.update(criteria, changes)
          .then(success => {
            console.log("The app was installed successfully. TEAM");
          }).catch(err => { console.log(err) });
        } else {
          return await db.table.insert({
            team: installation.team.id,
            token: installation['bot']['token'],
            tokenraw: JSON.stringify(installation)
          })
          .then(success => {
            console.log("The app was installed successfully. TEAM");
          }).catch(err => { console.log(err) });
        }
      }
      throw new Error('Failed saving installation data to installationStore');
    },
  },
  installerOptions: {
    installPath: 'slack/install',
    redirectUriPath: 'slack/oauth_redirect',
  }
});

const bolt = new App({
  signingSecret: process.env.SLACK_SIGNING_SECRET,
  clientId: process.env.SLACK_CLIENT_ID,
  clientSecret: process.env.SLACK_CLIENT_SECRET,
  stateSecret: process.env.STATE_SECRET,
  //token: process.env.SLACK_APP_TOKEN,
  //socketMode: true,
  //agent,
  //logLevel,
  //developerMode,
  stateVerification: false,
  installationStore: {
    storeInstallation: async (installation) => {
      console.log('storeInstallation -- bolt')
      //console.log(installation)
      const db = app.get('db');
      // change the line below so it saves to your database
      if (installation.isEnterpriseInstall && installation.enterprise !== undefined) {
        // support for org wide app installation
        let entAccount = await db.table.findOne({ enterprise: installation.enterprise.id });
        if (entAccount) {
          const criteria = {
            enterprise: installation.enterprise.id
          }

          let changes;

          changes = {
            'token': installation['bot']['token'],
            'tokenraw': JSON.stringify(installation)
          }

          return await db.table.update(criteria, changes)
        } else {
          return await db.table.insert({
            enterprise: installation.enterprise.id,
            token: installation['bot']['token'],
            tokenraw: JSON.stringify(installation)
          });
        }
      }
      if (installation.team !== undefined) {
        // single team app installation
        let teamAccount = await db.table.findOne({ team: installation.team.id });
        if (teamAccount) {
          const criteria = {
            team: installation.team.id
          }

          let changes;

          changes = {
            'token': installation['bot']['token'],
            'tokenraw': JSON.stringify(installation)
          }

          return await db.table.update(criteria, changes)
        } else {
          return await db.table.insert({
            team: installation.team.id,
            token: installation['bot']['token'],
            tokenraw: JSON.stringify(installation)
          })
          .then(success => {
            console.log("The app was installed successfully.");
          }).catch(err => { console.log(err) });
        }
      }
      throw new Error('Failed saving installation data to installationStore');
    },
    fetchInstallation: async (installQuery) => {
      console.log('fetchInstallation - BOLT')
      const db = app.get('db');
      // change the line below so it fetches from your database
      if (installQuery.isEnterpriseInstall && installQuery.enterpriseId !== undefined) {
        // org wide app installation lookup
        return await db.table.findOne({
          enterprise: installQuery.enterpriseId
        });
      }
      if (installQuery.teamId !== undefined) {
        // single team app installation lookup
        let data = await db.table.findOne({ team: installQuery.teamId });
        let token = JSON.parse(data.tokenraw);
        return token;
      }
      throw new Error('Failed fetching installation');
    },
    deleteInstallation: async (installQuery) => {
      console.log('deleteInstallation - BOLT')
      const db = app.get('db');
      // change the line below so it deletes from your database
      if (installQuery.isEnterpriseInstall && installQuery.enterpriseId !== undefined) {
        // org wide app installation deletion
        return await db.table.destroy({
          enterprise: installQuery.enterpriseId
        });
      }
      if (installQuery.teamId !== undefined) {
        // single team app installation deletion
        return await db.table.destroy({
          team: installQuery.teamId
        });
      }
      throw new Error('Failed to delete installation');
    },
  },
  installerOptions: {
    installPath: '/slack/install',
    redirectUriPath: '/slack/oauth_redirect',
  }
});

bolt.event('app_home_opened', async ({ event, client }) => {
  try {
    // Call views.publish with the built-in client
    const result = await client.views.publish({
      // Use the user ID associated with the event
      user_id: event.user,
      view: {
        // Home tabs must be enabled in your app configuration page under "App Home"
        "type": "home",
        "blocks": [{
            "type": "section",
            "text": {
              "type": "mrkdwn",
              "text": "*Welcome <@" + event.user + "> :hand: :rocket:*"
            }
          },
          {
            "type": "section",
            "text": {
              "type": "mrkdwn",
              "text": "New features coming soon."
            }
          }
        ]
      }
    });
  } catch (error) {
    console.error(error);
  }
});

bolt.event("app_mention", async ({ logger, event, say }) => {
  //logger.debug("app_mention event payload:\n\n" + JSON.stringify(event, null, 2) + "\n");
  const result = await say({
    text: `:wave<EMAIL_ADDRESS>Hi there!`,
  });
  //logger.debug("say result:\n\n" + JSON.stringify(result, null, 2) + "\n");
});

app.get('/', async (req, res) => {
  res.redirect('slack/install');
});

app.get('/slack/install', async (req, res, next) => {
  try {
    // feel free to modify the scopes
    const genUrl = await installer.generateInstallUrl({
      scopes: [
        'channels:read',
        'app_mentions:read',
        'channels:history',
        'channels:join',
        'chat:write',
        'commands',
        'emoji:read',
        'groups:history',
        'im:history',
        'incoming-webhook',
        'mpim:history',
        'reactions:write',
        'conversations.connect:manage',
        'chat:write.public',
        'conversations.connect:read',
        'conversations.connect:write',
        'im:read',
        'im:write',
        'mpim:read',
        'mpim:write',
      ],
    })

    res.send(`<img alt=""Add to Slack"" height="40" width="139" src="https://platform.slack-edge.com/img/add_to_slack.png" srcset="https://platform.slack-edge.com/img/add_to_slack.png 1x<EMAIL_ADDRESS>2x" />`);
  } catch (error) {
    console.log(error)
  }
});

app.get('/slack/oauth_redirect', (req, res) => {
  installer.handleCallback(req, res);
});

app.post('/slack/events', (req, res) => {
  console.log('SLACK EVENTS')
  console.log(req.params)
  console.log(req.body)
  // if (req.body.type === 'url_verification') {
  //   res.send(req.body.challenge);
  // }
  res.send(bolt.receiver.endpoints[0]);
});

app.use('/slack/enable_events', (req, res) => {
  console.log('SLACK ENABLE EVENTS')
  console.log(req.params)
  console.log(req.body)
  // if (req.body.type === 'url_verification') {
  //   res.send(req.body.challenge);
  // }
  res.send(bolt.receiver.endpoints[0]);
});

(async () => {
  await bolt.start(config.app.bolt);
  console.log('⚡ Bolt app is running!');
})();

Screenshot

Thanks for providing this code sample -- super helpful to be able to work from!
I ran your implementation locally (though commented out the DB-related items for testing purposes). The only thing I needed to change to get a successful verification was the port value being used for bolt.start(config.app.bolt). Since I have no visibility into what your value is, I replaced it to align with my own local implementation, which happened to be 3000.
Our Heroku deployment guide links out to this documentation regarding selecting the correct port, which might be worth a glance if you haven't already seen it.
Can you verify that the port value assigned to config.app.bolt matches what is expected on the Heroku side?

@misscoded Thanks for the assist. It ended up being a port issue with Heroku and I ended up moving to have the app completely in Bolt with it working.


Eye.json

Your function works when N and M are different values but if N and M are same, then it throws an error.
For instance, if N = M = 3, then I am supposed to get a 3x3 matrix with 1s across the diagnoals.
If you could test your functions thoroughly before you send them, that'd be great!
Also, your design can improve to avoid crossing operations.