WIP: Cleans up project warnings

Eigen's gotten into a very poor state, with compiler warnings and static analyzer warnings everywhere. With all this noise, valid warnings get lost and we lose advantages of using a compiler.
This PR addresses the warnings to get us here:

It does this in a few ways:

Isolate deprecated UIKit APIs into Objective-C files and silence the warnings.
Address all Swift/UIKit/Foundation deprecation warnings.
Clean up static analyzer warnings.
Updates to latest Xcode recommended settings.

This is a WIP because it requires extensive testing and I don't want to merge before the eigen release is out.

          2 Errors

:no_entry_sign:
No CHANGELOG changes made

:no_entry_sign:
Developer Specific file shouldn’t be changed

          1 Warning

:warning:
Needs testing on a Phone if change is non-trivial

  Generated by :no_entry_sign: Danger

@erikdstock please do ask about everything! These should all be well-documented. If they're not, let me know.

I wonder if this would be a good time to enable the "treat warnings as errors" option 🤔 Maybe not locally but on CI alone somehow?

Ah yeah, great stuff, @ashfurrow 🙌
LGTM 👍

It would be pretty easy to pass -Werror only during make test so that we could treat warnings as errors on CI, but locally wouldn't impact development. I think it's worth trying for a while, any opinions?

I think that's reasonable - it's not like they're hidden from you on day to day and then just appear 30 minutes later on CI.

Still getting deprecation warnings from a pod we're importing. Going to look into later.

Okay, I've got this wrapped up. Expecting Danger to be 🔴 but otherwise CI should pass.

Okay, this is passing on CI and is ready for final review /cc @orta.

interesting - @ashfurrow this should fail on my new build

:O - the flag didn't work?

The warning pictured is from a pod, but it is odd. I'll make sure it fails with the make command before merging 👍

Just a typo, it's OTHER_CFLAGS with an underscore. I'll push a fix.

Okay, getting similar warnings when I enable the flag as on CI:
❌  /Users/distiller/eigen/Artsy/View_Controllers/Fair/Guides/ARFairGuideViewController.m:3:9: 'ARSwitchView.h' file not found

#import "ARSwitchView.h"
        ^

▸ Compiling ARAuctionArtworkTableViewCell.m
** BUILD FAILED **

Going to investigate.

I've tested this locally that it fails when I have an unused variable, so I think this is set to go after the CI passes 👍

Rock

Awesome! Thanks so much 💯


Uploaded, but not visible

I receive ok response with url to uploaded image:
http://scontent-ams3-1.cdninstagram.com/hphotos-xfa1/t51.2885-15/s640x640/e15/11909384_737295289715655_379475796_n.jpg
but I can't see this photo on my profile photos.

ok, it works for 1280x1280px images


Fix 20363

Brief Information
This pull request is in the type of:

[x] bug fixing
[ ] new feature
[ ] others

What does this PR do?

Fixed issues
#20363
Details
Before: What was the problem?
The maximum value symbol in polar coordinate system scatter chart of radiusAxis is not displayed
After: How does it behave after the fixing?
Display the symbol
Document Info
One of the following should be checked.

[x] This PR doesn't relate to document changes
[ ] The document should be updated later
[ ] The document changes have been made in apache/echarts-doc#xxx

Misc
ZRender Changes

[ ] This PR depends on ZRender changes (ecomfe/zrender#xxx).

Related test cases or examples to use the new APIs
N.A.
Others
Merging options

[x] Please squash the commits into a single one when merging.

Other information

We sincerely appreciate your valuable contributions! We are currently running a special promotion for users who submit a Pull Request between September 25, 2024, and December 31, 2024. Eligible participants will receive a two-year enterprise membership to Baidu Comate, valued at 2000 RMB (approximately 285 USD).
To learn more about this product, please visit https://comate.baidu.com/. If you are interested in this offer, kindly send an email with the link to your Pull Request along with your Comate username and email address to<EMAIL_ADDRESS>to claim your membership.
Thank you once again for your support!


Add Yield

Hi, @MiTeePingWin thanks for your contribution. May I ask you to replace the address with the EIP-55 version?

Hi, @MiTeePingWin thanks for your contribution. May I ask you to replace the address with the EIP-55 version?

Apologies for the oversight, I've updated the address.

Apologies for the oversight, I've updated the address.

Afternoon! Any update here?
Thanks much!

Afternoon! Any update here?
Thanks much!


Error when converting sequential model to HF

I am trying to convert a locally trained gpt-neox model to huggingface and I encounter the following error:
Detected MLP naming convention: new   0%|                                                                                | 0/16 [00:00<?, ?it/s] Traceback (most recent call last):   File "gpt-neox/tools/ckpts/convert_neox_to_hf.py", line 906, in <module>     main()   File "gpt-neox/tools/ckpts/convert_neox_to_hf.py", line 856, in main     hf_model = convert(   File "gpt-neox/tools/ckpts/convert_neox_to_hf.py", line 609, in convert     get_state(   File "gpt-neox/tools/ckpts/convert_neox_to_hf.py", line 198, in get_state     return [state_dict["module"][key] for state_dict in state_dicts]   File "gpt-neox/tools/ckpts/convert_neox_to_hf.py", line 198, in <listcomp>     return [state_dict["module"][key] for state_dict in state_dicts] KeyError: 'sequential.2.input_layernorm.weight'
The relevant config params are as follows:
{
"tokenizer_type": "SPMTokenizer",
"vocab_file": "./model.model",
"num_layers": 16,
"hidden_size": 1024,
"intermediate_size": 4096,
"num_attention_heads": 16,
"seq_length": 256,
"init_method": "small_init",
"output_layer_init_method": "wang_init",
"no_weight_tying": true,
"activation": "gelu",
"attention_config": [[["global"], 16]],
"pos_emb": "rotary",
"max_position_embeddings": 256,
"train_micro_batch_size_per_gpu": 64,
"gradient_accumulation_steps": 1,
"num_nodes": 1,
"train_iters": 100000,
"lr_decay_style": "cosine",
"lr_decay_iters": 38000,
"warmup": 0.05,
"optimizer": {
"type": "Adam",
"params": {
"lr": 0.0001,
"betas": [0.9, 0.95],
"eps": 1.0e-8,
}
},
"deepspeed": true,
"weight_decay": 0.1,
"norm": "rms",
"rms_norm_epsilon": 0.01,
#"finetune": true,
"bf16": {
"enabled": false,
"loss_scale": 0,
"loss_scale_window": 1000,
"hysteresis": 2,
"min_loss_scale": 1
},
"precision": "bfloat16",
"fp32_allreduce": true,
"distributed_backend": "nccl",
"pipe_parallel_size": 0,
"model_parallel_size": 1,
"log_dir": "logs",
"log_interval": 1,
"tensorboard_dir": "test_neo",
}
Any help would be appreciated!

Disclosure: I'm not a maintainer.
I think the problem might be that the models on the huggingface side are very limited in what they can do. if you're trying to convert to GPTNeoXForCausalLM, I think the problem is that it doesn't support RMSNorm, and expects you to use layernorm instead.


Format python code using black

so we can have a consistent Python code format.
$ black modules/

https://github.com/psf/black

Hi @nishantsharmax any comment on this PR? This is not urgent though.
I was going through the code, and I thought it would be better if we have conventions on how we write the code. As code is written once and read many times.

Hi @za, the change in term of lines affected is quite big and will take time/effort to review. And, as it is just for formatting, it is not worth reviewing. Hence, closing this one without merging.

Hi @nishantsharmax thanks for the response.
Definitely this PR is not urgent. We can take our time if we need to carefully review it. I am hoping by having standardized format, more people comfortable reading the code and bringing more contributors.
Cheers.


Unable to get hmr running with the latest version

I'm submitting a ...
[X] bug report

Do you want to request a feature or report a bug?
Bug

What is the current behavior?
Downloaded the app, followed the instructions. I successfully ran the application using npm start , but it won't run using npm run server:dev:hmr. It errors in the console with "Uncaught ReferenceError: Zone is not defined"

What is the expected behavior?
The application should start with hot module replacement.

Please tell us about your environment:
Windows 10
Chrome Version 62.0.3202.94 (Official Build) (64-bit)
Angular version: 5.0.1 (as per demo)
npm -v 3.10.10
node -v 6.11.0

Script from following the instructions:
Installing node-pre-gyp:
E:\>cd angular-starter-master

E:\angular-starter-master>npm install -g node-pre-gyp
C:\Users\tonyz\AppData\Roaming\npm\node-pre-gyp -> C:\Users\tonyz\AppData\Roaming\npm\node_modules\node-pre-gyp\bin\node-pre-gyp
C:\Users\tonyz\AppData\Roaming\npm
`--<EMAIL_ADDRESS>  +--<EMAIL_ADDRESS>  +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | `--<EMAIL_ADDRESS>  +--<EMAIL_ADDRESS>  | `--<EMAIL_ADDRESS>  +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | `--<EMAIL_ADDRESS>  |   +--<EMAIL_ADDRESS>  |   `--<EMAIL_ADDRESS>  +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | | `--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | | +--<EMAIL_ADDRESS>  | | +--<EMAIL_ADDRESS>  | | +--<EMAIL_ADDRESS>  | | +--<EMAIL_ADDRESS>  | | +--<EMAIL_ADDRESS>  | | | +--<EMAIL_ADDRESS>  | | | `--<EMAIL_ADDRESS>  | | |   `--<EMAIL_ADDRESS>  | | +--<EMAIL_ADDRESS>  | | | `--<EMAIL_ADDRESS>  | | `--<EMAIL_ADDRESS>  | `--<EMAIL_ADDRESS>  +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | `--<EMAIL_ADDRESS>  +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | | `--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | | `--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | | +--<EMAIL_ADDRESS>  | | | +--<EMAIL_ADDRESS>  | | | `--<EMAIL_ADDRESS>  | | |   `--<EMAIL_ADDRESS>  | | `--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | | +--<EMAIL_ADDRESS>  | | +--<EMAIL_ADDRESS>  | | | +--<EMAIL_ADDRESS>  | | | +--<EMAIL_ADDRESS>  | | | +--<EMAIL_ADDRESS>  | | | `--<EMAIL_ADDRESS>  | | |   `--<EMAIL_ADDRESS>  | | `--<EMAIL_ADDRESS>  | |   +--<EMAIL_ADDRESS>  | |   +--<EMAIL_ADDRESS>  | |   +--<EMAIL_ADDRESS>  | |   +--<EMAIL_ADDRESS>  | |   | `--<EMAIL_ADDRESS>  | |   +--<EMAIL_ADDRESS>  | |   +--<EMAIL_ADDRESS>  | |   | `--<EMAIL_ADDRESS>  | |   +--<EMAIL_ADDRESS>  | |   `--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | | `--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | | `--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | `--<EMAIL_ADDRESS>  +--<EMAIL_ADDRESS>  | `--<EMAIL_ADDRESS>  |   +--<EMAIL_ADDRESS>  |   +--<EMAIL_ADDRESS>  |   +--<EMAIL_ADDRESS>  |   | `--<EMAIL_ADDRESS>  |   |   +--<EMAIL_ADDRESS>  |   |   `--<EMAIL_ADDRESS>  |   `--<EMAIL_ADDRESS>  +--<EMAIL_ADDRESS>  +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | +--<EMAIL_ADDRESS>  | | `--<EMAIL_ADDRESS>  | `--<EMAIL_ADDRESS>  `--<EMAIL_ADDRESS>    +--<EMAIL_ADDRESS>    | `--<EMAIL_ADDRESS>    +--<EMAIL_ADDRESS>    +--<EMAIL_ADDRESS>    | `--<EMAIL_ADDRESS>    +--<EMAIL_ADDRESS>    | +--<EMAIL_ADDRESS>    | +--<EMAIL_ADDRESS>    | +--<EMAIL_ADDRESS>    | +--<EMAIL_ADDRESS>    | `--<EMAIL_ADDRESS>    `--<EMAIL_ADDRESS>

npm install:
E:\angular-starter-master>npm install
npm WARN deprecated<EMAIL_ADDRESS>Use uuid module instead
npm WARN deprecated<EMAIL_ADDRESS>CoffeeScript on NPM has moved to "coffeescript" (no hyphen)
npm WARN prefer global<EMAIL_ADDRESS>should be installed with -g
npm WARN prefer global<EMAIL_ADDRESS>should be installed with -g
npm WARN prefer global<EMAIL_ADDRESS>should be installed with -g
npm WARN prefer global<EMAIL_ADDRESS>should be installed with -g

><EMAIL_ADDRESS>install E:\angular-starter-master\node_modules\node-sass
> node scripts/install.js

Downloading binary from https://github.com/sass/node-sass/releases/download/v4.7.2/win32-x64-48_binding.node
Download complete..] - :
Binary saved to E:\angular-starter-master\node_modules\node-sass\vendor\win32-x64-48\binding.node
Caching binary to C:\Users\tonyz\AppData\Roaming\npm-cache\node-sass\4.7.2\win32-x64-48_binding.node

><EMAIL_ADDRESS>postinstall E:\angular-starter-master\node_modules\webpack\node_modules\uglifyjs-webpack-plugin
> node lib/post_install.js

><EMAIL_ADDRESS>postinstall E:\angular-starter-master\node_modules\node-sass
> node scripts/build.js

Binary found at E:\angular-starter-master\node_modules\node-sass\vendor\win32-x64-48\binding.node
Testing binary
Binary is fine

><EMAIL_ADDRESS>postinstall E:\angular-starter-master
> npm run webdriver:update

><EMAIL_ADDRESS>webdriver:update E:\angular-starter-master
> node ./node_modules/protractor/bin/webdriver-manager update

[20:06:18] I/file_manager - creating folder E:\angular-starter-master\node_modules\protractor\node_modules\webdriver-manager\selenium
[20:06:25] I/update - chromedriver: unzipping chromedriver_2.33.zip
[20:06:48] I/update - geckodriver: unzipping geckodriver-v0.19.1.zip
<EMAIL_ADDRESS>E:\angular-starter-master
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`--<EMAIL_ADDRESS>| | |   `--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   `--<EMAIL_ADDRESS>| |     `--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   `--<EMAIL_ADDRESS>|     +--<EMAIL_ADDRESS>|     `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   `--<EMAIL_ADDRESS>| |     `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>|   `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>|   `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| |   `--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | | `--<EMAIL_ADDRESS>|   | |   +--<EMAIL_ADDRESS>|   | |   `--<EMAIL_ADDRESS>|   | |     `--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | | +--<EMAIL_ADDRESS>|   | | `--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | | +--<EMAIL_ADDRESS>|   | | `--<EMAIL_ADDRESS>|   | |   `--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | `--<EMAIL_ADDRESS>|   |   `--<EMAIL_ADDRESS>|   |     +--<EMAIL_ADDRESS>|   |     `--<EMAIL_ADDRESS>|   |       `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | | `--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | | `--<EMAIL_ADDRESS>|   | `--<EMAIL_ADDRESS>|   |   `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | `--<EMAIL_ADDRESS>|   |   `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   | `--<EMAIL_ADDRESS>|   |   +--<EMAIL_ADDRESS>|   |   | +--<EMAIL_ADDRESS>|   |   | | `--<EMAIL_ADDRESS>|   |   | +--<EMAIL_ADDRESS>|   |   | +--<EMAIL_ADDRESS>|   |   | +--<EMAIL_ADDRESS>|   |   | +--<EMAIL_ADDRESS>|   |   | +--<EMAIL_ADDRESS>|   |   | +--<EMAIL_ADDRESS>|   |   | `--<EMAIL_ADDRESS>|   |   +--<EMAIL_ADDRESS>|   |   | `--<EMAIL_ADDRESS>|   |   |   `--<EMAIL_ADDRESS>|   |   `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>+-- UNMET PEER DEPENDENCY<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | | `--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | | `--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | | `--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| |   `--<EMAIL_ADDRESS>| |     `--<EMAIL_ADDRESS>| |       +--<EMAIL_ADDRESS>| |       | `--<EMAIL_ADDRESS>| |       `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   | `--<EMAIL_ADDRESS>|   `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | | +--<EMAIL_ADDRESS>| | | | | `--<EMAIL_ADDRESS>| | | | +--<EMAIL_ADDRESS>| | | | | `--<EMAIL_ADDRESS>| | | | `--<EMAIL_ADDRESS>| | | |   `--<EMAIL_ADDRESS>| | | |     `--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | | +--<EMAIL_ADDRESS>| | | | +--<EMAIL_ADDRESS>| | | | +--<EMAIL_ADDRESS>| | | | | +--<EMAIL_ADDRESS>| | | | | +--<EMAIL_ADDRESS>| | | | | +--<EMAIL_ADDRESS>| | | | | `--<EMAIL_ADDRESS>| | | | `--<EMAIL_ADDRESS>| | | |   `--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | | +--<EMAIL_ADDRESS>| | | | +--<EMAIL_ADDRESS>| | | | | `--<EMAIL_ADDRESS>| | | | `--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | | `--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | | +--<EMAIL_ADDRESS>|   | | +--<EMAIL_ADDRESS>|   | | +--<EMAIL_ADDRESS>|   | | | `--<EMAIL_ADDRESS>|   | | +--<EMAIL_ADDRESS>|   | | `--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | | `--<EMAIL_ADDRESS>|   | `--<EMAIL_ADDRESS>|   |   `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | `--<EMAIL_ADDRESS>|   |   +--<EMAIL_ADDRESS>|   |   | `--<EMAIL_ADDRESS>|   |   `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | `--<EMAIL_ADDRESS>|   |   `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   | +--<EMAIL_ADDRESS>| |   | | `--<EMAIL_ADDRESS>| |   | |   +--<EMAIL_ADDRESS>| |   | |   +--<EMAIL_ADDRESS>| |   | |   `--<EMAIL_ADDRESS>| |   | |     +--<EMAIL_ADDRESS>| |   | |     | `--<EMAIL_ADDRESS>| |   | |     `--<EMAIL_ADDRESS>| |   | `--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   | `--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   | `--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   | +--<EMAIL_ADDRESS>| |   | `--<EMAIL_ADDRESS>| |   `--<EMAIL_ADDRESS>| |     `--<EMAIL_ADDRESS>| |       `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| |   `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| |   `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | |   `--<EMAIL_ADDRESS>| | |     `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| |   `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | | `--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   | `--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   +--<EMAIL_ADDRESS>| |   `--<EMAIL_ADDRESS>| |     `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| +--<EMAIL_ADDRESS>| | `--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   | +--<EMAIL_ADDRESS>|   | `--<EMAIL_ADDRESS>|   |   `--<EMAIL_ADDRESS>|   +--<EMAIL_ADDRESS>|   `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>| `--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>`--<EMAIL_ADDRESS>
npm WARN optional SKIPPING OPTIONAL DEPENDENCY<EMAIL_ADDRESS>(node_modules\chokidar\node_modules\fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for<EMAIL_ADDRESS>wanted {"os":"darwin","arch":"any"} (current: {"os":"win32","arch":"x64"})
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS><2.5 but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>|| >=4.0.0-beta <5.0.0 but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>|| >=4.0.0-beta <5.0.0 but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.

npm start (this is successful, the application runs on http://localhost:3000/. For completeness, here is the output from npm:
E:\angular-starter-master>npm start

><EMAIL_ADDRESS>start E:\angular-starter-master
> npm run server:dev

><EMAIL_ADDRESS>server:dev E:\angular-starter-master
> npm run webpack-dev-server -- --config config/webpack.dev.js --open --progress --profile --watch --content-base src/

><EMAIL_ADDRESS>webpack-dev-server E:\angular-starter-master
> node --max_old_space_size=4096 node_modules/webpack-dev-server/bin/webpack-dev-server.js "--config" "config/webpack.dev.js" "--open" "--progress" "--profile" "--watch" "--content-base" "src/"

 10% building modules 2/2 modules 0 active
Project is running at http://localhost:3000/
webpack output is served from /
Content not from webpack is served from E:\angular-starter-master\src
404s will fallback to /index.html                                              11% building modules 9/9 modules 0 activewebpack: wait until bundle finished: /                                        5899ms building modules
14ms sealing
1ms optimizing
1ms basic module optimization
11ms module optimization
5ms advanced module optimization
5ms basic chunk optimization
1ms chunk optimization
0ms advanced chunk optimization
1ms module and chunk tree optimization
0ms chunk modules optimization
0ms advanced chunk modules optimization
5ms module reviving
4ms module order optimization
7ms module id optimization
2ms chunk reviving
0ms chunk order optimization
18ms chunk id optimization
38ms hashing
1ms module assets processing
3106ms chunk assets processing
1ms additional chunk assets processing
1ms recording
0ms additional asset processing
1ms chunk asset optimization
132ms asset optimization
51ms emitting
Hash: e4852c97149fe02578dc
Version: webpack 3.10.0
Time: 9329ms
                                 Asset       Size  Chunks                    Chunk Names
      assets/icon/apple-icon-60x60.png    3.56 kB          [emitted]
                            0.chunk.js    9.46 kB       0  [emitted]
                            2.chunk.js    9.46 kB       2  [emitted]
                            3.chunk.js    9.45 kB       3  [emitted]
                            4.chunk.js  876 bytes       4  [emitted]
                        main.bundle.js      10 MB       5  [emitted]  [big]  main
                   polyfills.bundle.js    1.47 MB       6  [emitted]  [big]  polyfills
                      inline.bundle.js     5.8 kB       7  [emitted]         inline
                   assets/css/.gitkeep   14 bytes          [emitted]
  assets/icon/android-icon-144x144.png    8.43 kB          [emitted]
                      assets/data.json   30 bytes          [emitted]
    assets/icon/android-icon-36x36.png     2.3 kB          [emitted]
                     assets/humans.txt  251 bytes          [emitted]
    assets/icon/android-icon-48x48.png    2.92 kB          [emitted]
  assets/icon/android-icon-192x192.png    9.71 kB          [emitted]
    assets/icon/android-icon-96x96.png     5.6 kB          [emitted]
    assets/icon/android-icon-72x72.png    4.23 kB          [emitted]
    assets/icon/apple-icon-114x114.png    6.55 kB          [emitted]
    assets/icon/apple-icon-120x120.png    6.92 kB          [emitted]
    assets/icon/apple-icon-144x144.png    8.43 kB          [emitted]
    assets/icon/apple-icon-152x152.png    8.99 kB          [emitted]
    assets/icon/apple-icon-180x180.png      11 kB          [emitted]
      assets/icon/apple-icon-57x57.png     3.4 kB          [emitted]
                            1.chunk.js    9.45 kB       1  [emitted]
      assets/icon/apple-icon-72x72.png    4.23 kB          [emitted]
      assets/icon/apple-icon-76x76.png    4.46 kB          [emitted]
            assets/icon/apple-icon.png    10.3 kB          [emitted]
assets/icon/apple-icon-precomposed.png    10.3 kB          [emitted]
         assets/icon/browserconfig.xml  281 bytes          [emitted]
         assets/icon/favicon-16x16.png    1.52 kB          [emitted]
         assets/icon/favicon-32x32.png    2.07 kB          [emitted]
         assets/icon/favicon-96x96.png     5.6 kB          [emitted]
               assets/icon/favicon.ico    1.15 kB          [emitted]
       assets/icon/ms-icon-144x144.png    8.43 kB          [emitted]
       assets/icon/ms-icon-150x150.png    8.88 kB          [emitted]
         assets/icon/ms-icon-70x70.png    4.12 kB          [emitted]
       assets/icon/ms-icon-310x310.png    24.1 kB          [emitted]
                assets/img/angular.png      19 kB          [emitted]
                  assets/manifest.json  654 bytes          [emitted]
                   assets/img/tipe.png    45.9 kB          [emitted]
                     assets/robots.txt   31 bytes          [emitted]
       assets/mock-data/mock-data.json   22 bytes          [emitted]
              assets/service-worker.js   44 bytes          [emitted]
                            humans.txt  251 bytes          [emitted]
                            robots.txt   31 bytes          [emitted]
                            index.html    2.79 kB          [emitted]
<EMAIL_ADDRESS><EMAIL_ADDRESS>24.8 kB {5} [built]
       [] -> factory:686ms building:102ms dependencies:5ms = 793ms
[./node_modules/core-js/es6/reflect.js] ./node_modules/core-js/es6/reflect.js 718 bytes {6} [built]
       [] -> factory:678ms building:20ms = 698ms
[./node_modules/core-js/es7/reflect.js] ./node_modules/core-js/es7/reflect.js 510 bytes {6} [built]
       [] -> factory:678ms building:29ms dependencies:438ms = 1145ms
[./node_modules/url/url.js] ./node_modules/url/url.js 23.3 kB {5} {6} [built]
       [] -> factory:34ms building:275ms = 309ms
[./node_modules/webpack-dev-server/client/index.js?http://localhost:3000] (webpack)-dev-server/client?http://localhost:3000 5.83 kB {5} {6} [built]
       [] -> factory:2253ms building:50ms = 2303ms
[./node_modules/webpack-dev-server/client/overlay.js] (webpack)-dev-server/client/overlay.js 3.6 kB {5} {6} [built]
       [] -> factory:34ms building:280ms = 314ms
[./node_modules/webpack-dev-server/client/socket.js] (webpack)-dev-server/client/socket.js 856 bytes {5} {6} [built]
       [] -> factory:33ms building:265ms = 298ms
[./node_modules/webpack/hot ^\.\/log$] (webpack)/hot nonrecursive ^\.\/log$ 170 bytes {5} {6} [built]
       [] -> factory:41ms building:276ms = 317ms
[./node_modules/zone.js/dist/zone.js] ./node_modules/zone.js/dist/zone.js 126 kB {6} [built]
       [] -> factory:679ms building:81ms dependencies:1ms = 761ms
[./src/app/index.ts] ./src/app/index.ts 49 bytes {5} [built]
       [] -> factory:582ms building:1ms = 583ms
[./src/environments/environment.ts] ./src/environments/environment.ts 854 bytes {5} [built]
       [] -> factory:295ms building:3ms = 298ms
[./src/main.browser.ts] ./src/main.browser.ts 1 kB {5} [built]
       [] -> factory:2317ms building:16ms = 2333ms
[./src/polyfills.browser.ts] ./src/polyfills.browser.ts 2.72 kB {6} [built]
       [] -> factory:2317ms building:8ms = 2325ms
   [0] multi (webpack)-dev-server/client?http://localhost:3000 ./src/polyfills.browser.ts 40 bytes {6} [built]
        factory:1ms building:1ms = 2ms
   [1] multi (webpack)-dev-server/client?http://localhost:3000 ./src/main.browser.ts 40 bytes {5} [built]
        factory:0ms building:0ms dependencies:2253ms = 2253ms
    + 311 hidden modules
Child html-webpack-plugin for "index.html":
     1 asset
    [./node_modules/html-webpack-plugin/lib/loader.js!./src/index.html] ./node_modules/html-webpack-plugin/lib/loader.js!./src/index.html 2.1 kB {0} [built]
            factory:2241ms building:46ms = 2287ms
    [./node_modules/lodash/lodash.js] ./node_modules/lodash/lodash.js 540 kB {0} [built]
           [] -> factory:40ms building:283ms = 323ms
    [./node_modules/webpack/buildin/global.js] (webpack)/buildin/global.js 509 bytes {0} [built]
           [] -> factory:38ms building:14ms = 52ms
    [./node_modules/webpack/buildin/module.js] (webpack)/buildin/module.js 517 bytes {0} [built]
           [] -> factory:38ms building:14ms = 52ms
webpack: Compiled successfully.

Ok, so I stopped that , and instead decided to run hot module replacement.
npm run server:dev:hmr
This FAILS in the browser (Chrome) with the following error message in the console:
only-dev-server.js:70 Uncaught Error: [HMR] Hot Module Replacement is disabled.
    at eval (only-dev-server.js:70)
    at Object../node_modules/webpack/hot/only-dev-server.js (polyfills.bundle.js:1383)
    at __webpack_require__ (inline.bundle.js:55)
    at Object.0 (polyfills.bundle.js:1406)
    at __webpack_require__ (inline.bundle.js:55)
    at webpackJsonpCallback (inline.bundle.js:26)
    at polyfills.bundle.js:2
(anonymous) @ only-dev-server.js:70
./node_modules/webpack/hot/only-dev-server.js @ polyfills.bundle.js:1383
__webpack_require__ @ inline.bundle.js:55
0 @ polyfills.bundle.js:1406
__webpack_require__ @ inline.bundle.js:55
webpackJsonpCallback @ inline.bundle.js:26
(anonymous) @ polyfills.bundle.js:2
long-stack-trace-zone.js:85 Uncaught ReferenceError: Zone is not defined
    at eval (long-stack-trace-zone.js:85)
    at NEWLINE (long-stack-trace-zone.js:9)
    at eval (long-stack-trace-zone.js:12)
    at Object../node_modules/zone.js/dist/long-stack-trace-zone.js (main.bundle.js:1423)
    at __webpack_require__ (inline.bundle.js:55)
    at eval (environment.ts:8)
    at Object../src/environments/environment.ts (main.bundle.js:1612)
    at __webpack_require__ (inline.bundle.js:55)
    at eval (main.browser.ts:4)
    at Object../src/main.browser.ts (main.bundle.js:1620)
    at __webpack_require__ (inline.bundle.js:55)
    at Object.1 (main.bundle.js:1643)
    at __webpack_require__ (inline.bundle.js:55)
    at webpackJsonpCallback (inline.bundle.js:26)
    at main.bundle.js:2
(anonymous) @ long-stack-trace-zone.js:85
NEWLINE @ long-stack-trace-zone.js:9
(anonymous) @ long-stack-trace-zone.js:12
./node_modules/zone.js/dist/long-stack-trace-zone.js @ main.bundle.js:1423
__webpack_require__ @ inline.bundle.js:55
(anonymous) @ environment.ts:8
./src/environments/environment.ts @ main.bundle.js:1612
__webpack_require__ @ inline.bundle.js:55
(anonymous) @ main.browser.ts:4
./src/main.browser.ts @ main.bundle.js:1620
__webpack_require__ @ inline.bundle.js:55
1 @ main.bundle.js:1643
__webpack_require__ @ inline.bundle.js:55
webpackJsonpCallback @ inline.bundle.js:26
(anonymous) @ main.bundle.js:2
client*:64 [WDS] Hot Module Replacement enabled.

The output from npm is as follows:
E:\angular-starter-master>npm run server:dev:hmr

><EMAIL_ADDRESS>server:dev:hmr E:\angular-starter-master
> npm run server:dev -- --hotOnly

><EMAIL_ADDRESS>server:dev E:\angular-starter-master
> npm run webpack-dev-server -- --config config/webpack.dev.js --open --progress --profile --watch --content-base src/ "--hotOnly"

><EMAIL_ADDRESS>webpack-dev-server E:\angular-starter-master
> node --max_old_space_size=4096 node_modules/webpack-dev-server/bin/webpack-dev-server.js "--config" "config/webpack.dev.js" "--open" "--progress" "--profile" "--watch" "--content-base" "src/" "--hotOnly"

 10% building modules 2/2 modules 0 active
Project is running at http://localhost:3000/
webpack output is served from /
Content not from webpack is served from E:\angular-starter-master\src
404s will fallback to /index.html                                              11% building modules 10/11 modules 1 active ...odules\webpack\hot\only-dev-s5689ms building modules
12ms sealing
1ms optimizing
1ms basic module optimization
10ms module optimization
6ms advanced module optimization
4ms basic chunk optimization
0ms chunk optimization
1ms advanced chunk optimization
0ms module and chunk tree optimization
0ms chunk modules optimization
1ms advanced chunk modules optimization
9ms module reviving
4ms module order optimization
5ms module id optimization
3ms chunk reviving
1ms chunk order optimization
9ms chunk id optimization
40ms hashing
1ms module assets processing
3046ms chunk assets processing
2ms additional chunk assets processing
1ms recording
1ms additional asset processing
0ms chunk asset optimization
133ms asset optimization
56ms emitting
Hash: a6c2fe9136a6483be345
Version: webpack 3.10.0
Time: 9059ms
                                 Asset       Size  Chunks                    Chunk Names
      assets/icon/apple-icon-60x60.png    3.56 kB          [emitted]
                            0.chunk.js    9.46 kB       0  [emitted]
                            2.chunk.js    9.46 kB       2  [emitted]
                            3.chunk.js    9.45 kB       3  [emitted]
                            4.chunk.js  876 bytes       4  [emitted]
                        main.bundle.js    10.1 MB       5  [emitted]  [big]  main
                   polyfills.bundle.js    1.48 MB       6  [emitted]  [big]  polyfills
                      inline.bundle.js     5.8 kB       7  [emitted]         inline
                   assets/css/.gitkeep   14 bytes          [emitted]
  assets/icon/android-icon-144x144.png    8.43 kB          [emitted]
                     assets/humans.txt  251 bytes          [emitted]
    assets/icon/android-icon-36x36.png     2.3 kB          [emitted]
                      assets/data.json   30 bytes          [emitted]
    assets/icon/android-icon-48x48.png    2.92 kB          [emitted]
    assets/icon/android-icon-72x72.png    4.23 kB          [emitted]
  assets/icon/android-icon-192x192.png    9.71 kB          [emitted]
    assets/icon/android-icon-96x96.png     5.6 kB          [emitted]
    assets/icon/apple-icon-114x114.png    6.55 kB          [emitted]
    assets/icon/apple-icon-120x120.png    6.92 kB          [emitted]
    assets/icon/apple-icon-152x152.png    8.99 kB          [emitted]
    assets/icon/apple-icon-144x144.png    8.43 kB          [emitted]
    assets/icon/apple-icon-180x180.png      11 kB          [emitted]
      assets/icon/apple-icon-57x57.png     3.4 kB          [emitted]
                            1.chunk.js    9.45 kB       1  [emitted]
      assets/icon/apple-icon-72x72.png    4.23 kB          [emitted]
      assets/icon/apple-icon-76x76.png    4.46 kB          [emitted]
assets/icon/apple-icon-precomposed.png    10.3 kB          [emitted]
            assets/icon/apple-icon.png    10.3 kB          [emitted]
         assets/icon/browserconfig.xml  281 bytes          [emitted]
         assets/icon/favicon-16x16.png    1.52 kB          [emitted]
         assets/icon/favicon-32x32.png    2.07 kB          [emitted]
         assets/icon/favicon-96x96.png     5.6 kB          [emitted]
               assets/icon/favicon.ico    1.15 kB          [emitted]
       assets/icon/ms-icon-144x144.png    8.43 kB          [emitted]
       assets/icon/ms-icon-150x150.png    8.88 kB          [emitted]
       assets/icon/ms-icon-310x310.png    24.1 kB          [emitted]
         assets/icon/ms-icon-70x70.png    4.12 kB          [emitted]
                assets/img/angular.png      19 kB          [emitted]
                  assets/manifest.json  654 bytes          [emitted]
                   assets/img/tipe.png    45.9 kB          [emitted]
       assets/mock-data/mock-data.json   22 bytes          [emitted]
                     assets/robots.txt   31 bytes          [emitted]
              assets/service-worker.js   44 bytes          [emitted]
                            robots.txt   31 bytes          [emitted]
                            humans.txt  251 bytes          [emitted]
                            index.html    2.71 kB          [emitted]
<EMAIL_ADDRESS><EMAIL_ADDRESS>24.8 kB {5} [built]
       [] -> factory:691ms building:87ms dependencies:5ms = 783ms
[./node_modules/core-js/es7/reflect.js] ./node_modules/core-js/es7/reflect.js 510 bytes {6} [built]
       [] -> factory:680ms building:34ms dependencies:415ms = 1129ms
[./node_modules/loglevel/lib/loglevel.js] ./node_modules/loglevel/lib/loglevel.js 7.86 kB {5} {6} [built]
       [] -> factory:720ms building:35ms = 755ms
[./node_modules/webpack-dev-server/client/index.js?http://localhost:3000] (webpack)-dev-server/client?http://localhost:3000 5.83 kB {5} {6} [built]
       [] -> factory:2248ms building:30ms = 2278ms
[./node_modules/webpack-dev-server/client/overlay.js] (webpack)-dev-server/client/overlay.js 3.6 kB {5} {6} [built]
       [] -> factory:54ms building:67ms = 121ms
[./node_modules/webpack-dev-server/client/socket.js] (webpack)-dev-server/client/socket.js 856 bytes {5} {6} [built]
       [] -> factory:53ms building:29ms = 82ms
[./node_modules/webpack/hot ^\.\/log$] (webpack)/hot nonrecursive ^\.\/log$ 170 bytes {5} {6} [built]
       [] -> factory:57ms building:5ms = 62ms
[./node_modules/webpack/hot/emitter.js] (webpack)/hot/emitter.js 77 bytes {5} {6} [built]
       [] -> factory:366ms building:9ms = 375ms
[./node_modules/webpack/hot/only-dev-server.js] (webpack)/hot/only-dev-server.js 2.37 kB {5} {6} [built]
       [] -> factory:2625ms building:21ms = 2646ms
[./node_modules/zone.js/dist/zone.js] ./node_modules/zone.js/dist/zone.js 126 kB {6} [built]
       [] -> factory:680ms building:71ms dependencies:1ms = 752ms
[./src/app/index.ts] ./src/app/index.ts 49 bytes {5} [built]
       [] -> factory:596ms building:1ms = 597ms
[./src/main.browser.ts] ./src/main.browser.ts 1 kB {5} [built]
       [] -> factory:2310ms building:14ms = 2324ms
[./src/polyfills.browser.ts] ./src/polyfills.browser.ts 2.72 kB {6} [built]
       [] -> factory:2310ms building:8ms = 2318ms
   [0] multi (webpack)-dev-server/client?http://localhost:3000 webpack/hot/only-dev-server ./src/polyfills.browser.ts 52 bytes {6} [built]
        factory:0ms building:2ms = 2ms
   [1] multi (webpack)-dev-server/client?http://localhost:3000 webpack/hot/only-dev-server ./src/main.browser.ts 52 bytes {5} [built]
        factory:0ms building:1ms dependencies:2625ms = 2626ms
    + 312 hidden modules
Child html-webpack-plugin for "index.html":
     1 asset
    [./node_modules/html-webpack-plugin/lib/loader.js!./src/index.html] ./node_modules/html-webpack-plugin/lib/loader.js!./src/index.html 2.1 kB {0} [built]
            factory:2251ms building:59ms = 2310ms
    [./node_modules/lodash/lodash.js] ./node_modules/lodash/lodash.js 540 kB {0} [built]
           [] -> factory:35ms building:290ms = 325ms
    [./node_modules/webpack/buildin/global.js] (webpack)/buildin/global.js 509 bytes {0} [built]
           [] -> factory:20ms building:11ms = 31ms
    [./node_modules/webpack/buildin/module.js] (webpack)/buildin/module.js 517 bytes {0} [built]
           [] -> factory:20ms building:11ms = 31ms
webpack: Compiled successfully.

 Does not work.


Fetching elements of 2-D array using for-each

Please provide a suitable description.

done kindly check


[INFINITY-2223] determine upgradesFrom and downgradesTo automatically

This PR backports the ability to determine upgradesFrom and downgradesTo for packages at build time. This should greatly simplify the release process in future.
I followed the following steps:

Sync master:/tools with 0.30.X:/tools. This means that #1616 is superseded.
Copy builds.sh from master.
Copy sdk/bootstrap/build.sh from master
For each framework:

Copy frameworks/<framework>/build.sh from master and remove the beta-references
Add upgradesTo and downgradesFrom templates to package.json
Replace dcos-<framework> with dcos-service-cli in resource.json

I built each framework locally to generate the upgradesFrom and downgradesTo for the universe PRs.
I could have hunted through the master history to find the individual commits to cherry-pick, but thought that this would be simpler. I am open to suggestions though.
@nickbp @paegun given the recent changes to the go-vendoring, are the any reasons that the changes described here could cause issues?
@benclarkwood do we rely on any special properties of the 0.30.X branch to get the CI builds to work?

Not sure what the deal is with template but LGTM otherwise

@elezar No, we do not rely on anything special about the branch (other than its name)
I'm not sure what is up with template. That is very odd.

template somehow still had an old version of build.sh. Should be fixed now.

Thanks @nickbp. Yes, I forgot to update template.


Issue with uniting two mols to a new mol

Description:
there are two mols

‘Rb’ is a placeholder. I want to unit them to a new mol

I try to use
<<Chem.ReplaceSubstructs(), but it can't
Please help me, thanks!

Let's walk through this.
You have two molecules
>>> s1 = "[Rb]c1ccccc1"
>>> Chem.MolFromSmiles(s1)
>>> s2= "[Rb]OC[Cs]"
>>> m2 = Chem.MolFromSmiles(s2)

And you want to combine that at the atoms next to [Rb].  I expect you were attempting something like this:
>>> mols = Chem.ReplaceSubstructs(m1, Chem.MolFromSmarts("[Rb"]), m2)
>>> print(mols[0])
'[Cs]CO[Rb]c1ccccc1'

And were annoyed that [Rb] was still left over.  The issue here is that ReplaceSubstruct doesn't change any atoms in the replacement.  There are two options:

Drop Rb from the second molecule and always make it so the first atom  is the one you want to bond.  (this is the default)

>>> s2= "OC[Cs]"
>>> m2 = Chem.MolFromSmiles(s2)
>>> Chem.ReplaceSubstructs(m1, Chem.MolFromSmarts("[Rb]"), m2, replacementConnectionPoint=0)
>>> print(mols[0])
'[Cs]COc1ccccc1'

Make a reaction.  The following takes two molecules and bonds anything connected to rubidium in mol1 to anything bonded to a rubidium in molecule 2 but doesn't copy the rubidium over to the final product(s).

>>> from rdkit.Chem import AllChem
>>> rxn = AllChem.ReactionFromSmarts("[Rb][*:1].[Rb][*:2]>>[*:1][*:2]")
>>> s1 = "[Rb]c1ccccc1"
>>> Chem.MolFromSmiles(s1)
>>> s2= "[Rb]OC[Cs]"
>>> m2 = Chem.MolFromSmiles(s2)
>>> results = rxn.RunReactants( [m1, m2] )
>>> for products in results:
...    for mol in products:
...        print(Chem.MolToSmiles(mol))
'[Cs]COc1ccccc1'

Hope this helps.


"auto pause after combat" option can hang the game if a cut scene would auto play.

The "auto pause after combat" option can hang the game if a cut scene would auto play.
Attached is a save from the end of the CoTM campaign, just before this happens.
NB. This save was from <IP_ADDRESS> dev branch with some local changes (extra crafting recpies for rapiers).
I get a mod stability warning when loading the save using <IP_ADDRESS> and a game hangs.
I've included my local changes in the zip from today's dev so you can make a build that will load the save (still get the stability warning, but save loads OK).
Feel free to merge the extra rapier recipes into the CE if you want
Files.zip
.

Rapier recipes added. Thanks

Still researching how to fix the auto pause.

This is a hard one to fix so will add a disclaimer on mod UI


fix: scheduler typo

Signed-off-by: Gaius<EMAIL_ADDRESS>
Description

Fix scheduler typo.

Related Issue

Motivation and Context

Screenshots (if appropriate)
Types of changes

[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to change)
[ ] Documentation Update (if none of the other choices apply)

Checklist

[ ] My change requires a change to the documentation.
[ ] I have updated the documentation accordingly.
[x] I have read the CONTRIBUTING document.
[ ] I have added tests to cover my changes.

Codecov Report

Merging #1297 (99d7fc5) into main (655d450) will decrease coverage by 0.12%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main    #1297      +/-   ##
==========================================
- Coverage   46.33%   46.21%   -0.13%
==========================================
  Files         137      137
  Lines       11625    11625
==========================================
- Hits         5387     5373      -14
- Misses       5649     5659      +10
- Partials      589      593       +4

Flag
Coverage Δ

Object-compatibility-e2etests
?

e2etests
?

unittests
46.21% <ø> (-0.13%)
:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files
Coverage Δ

scheduler/config/config.go
47.41% <ø> (ø)

scheduler/config/dynconfig.go
37.71% <ø> (ø)

scheduler/resource/cdn.go
62.29% <ø> (ø)

scheduler/resource/host.go
87.75% <ø> (ø)

scheduler/resource/host_manager.go
100.00% <ø> (ø)

scheduler/resource/peer.go
77.55% <ø> (ø)

scheduler/resource/peer_manager.go
95.91% <ø> (ø)

scheduler/resource/resource.go
82.60% <ø> (ø)

scheduler/resource/task.go
81.65% <ø> (ø)

scheduler/resource/task_manager.go
100.00% <ø> (ø)

... and 9 more


net: openthread: echo server do not work in userspace

Describe the bug
In echo server demo sample there is a openthread overlay. I have sucessfully tested that with nrf52840dk and border router setup on RPi. Based on that I have made my own app for tests.
I have tried to run it in userspace with no positive result. No matter if it is original sample or my own.
Is there something I am missing? Or current OT implementation in Zephyr do not support userspace?
All tests were performed on Zephyr 3.2 and Nordic NRF52840DK
To Reproduce
Steps to reproduce the behavior:
Build sample with OT overlay and additional configs:
CONFIG_USERSPACE=y
CONFIG_NET_IF_UNICAST_IPV6_ADDR_COUNT=10
CONFIG_NET_IF_MCAST_IPV6_ADDR_COUNT=10
Try to run the sample
Expected behavior
The application should run in userspace.

@pawelosyp-hid I've identified some issues with userspace support in the sample (must've decayed over time as I'm pretty convinced it used to work). I've submitted fixes related to the sample itself in https://github.com/zephyrproject-rtos/zephyr/pull/55329.
Please note however, that I've identified one other issue that prevents the sample from running in userspace, related to logging (https://github.com/zephyrproject-rtos/zephyr/issues/55323). As a temporary workaround, you can simply disable CONFIG_LOG_RUNTIME_FILTERING=n in the project file to prevent a logger crash. I've successfully ran the sample with userspace enabled, after combining this workaround with the changes from my PR.
A second note - if you plan to use echo_client as well, it has a similar issue with k_work API usage as echo_server - fixing this however will require some more serious sample refactoring, hence will be submitted separately later.

@rlubos Thank you for the responce. I have checked the solution and can confirm that it works both on Zephyrs and mine sample.


ISPN-10267 Rethrow remote exceptions

https://issues.jboss.org/browse/ISPN-10267
Fixes 2 CI failures

Fixed checkstyle

Integrated, thanks Galder!

run performance tests please
library dist reads


one weird wrap-ansi-cjs fix

Current dependencies on/for this PR:

main

PR #279   👈

This comment was auto-generated by Graphite.


Cleanup repo

We have been cleaning up our repositories in light of changes, and to take care of technical debt.
Please have a look at these items, and apply as needed to this repo.
Please create a Pull Request for these changes.
README (Sign-up name in checklist below)
Replace "Bluemix" with "IBM Cloud"
Change "Journey" to "Code Pattern"
Ensure there are steps after "Flow"
Cleanup old READMEs to align with new template
Double check links section syncs up with IBMCode site
Add blog ? No
Add video?  Yup
Remove "With Watson" blocks
Add "Learn More" sections: https://gist.github.com/dolph/8d5f1c34eb6f46f275563dbe9abdef14
Template for Code Pattern Readme:
https://github.ibm.com/developer-journeys/journey-docs/blob/master/_content/resources/templates/readme_template.md
Example commit:
https://github.com/IBM/watson-conversation-slots-intro/commit/f406290db07d2b180b52408344129cecb64faa84

Hi,
No that is not required. Please ensure that the names of the text files in the object storage matches.
If not, you can go to global variables section and change the names of the files.
Also, ensure that the credentials variable name is credentials_1.
Thanks,
Balaji

Hi rishank1312,
I have updated the earlier comment with more information.
Request you to create a new issue if the above suggestions do not resolve the issue as this issue deals with cleaning up the repository.
Thanks,
Balaji


Template merge

Template merge
PR checklist

[x] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!

[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.

[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR> -stub).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

@jemten Markdown and yaml tests are removed from the ci workflows so I think it should be fine to merge this PR as it is. But perhaps we should change the branch protection rules to not expect these tests to run in the upcoming PRs?


Revisit scoping of the checklist

code state: d447c22d3bf175dea68f0cf917c53f743d9efe1b

FWIW, here's some more phrases we had:
Tom: I’ve been thinking a gap in this approach is filtering out types of software that are not in scope. For instance, deployed or live services. Software not used for research (maybe).
“This tool is intended for …” focus on the middle type (prototypes)
Maybe some wording about how it is available excluding commercial software
Code you’ve written, not the code you’ve used
“About you: you’re an creator of software…”
After we make changes, it's probably a good idea to revisit the questions and check that they make sense given the scope definition.

I think I'm happy with the scoping for the moment.

In the unexpanded preamble of the software checklist, we have "research software authors" and a definition of "the software".
In the expanded/on-demand text, there is more detail available about what metadata should be included (only "bundled") and what should not be included (anything from APIs). It also differentiates between human readable metadata (READMEs and such) v machine readable metadata (CITATION.cff, pyproject.toml, .zenodo.json, etc).
While the text is not explicit, it is clear that the checklist is not meant for assessing a service (but it could be used to assess the software of such a service).

If you agree @tom-h, I would like to close this issue.

In the interests of getting this out there, I basically agree. I like the benefits and "calls to action" you've included. I think that is a great way to frame it.
I had imagined making the scope narrower, but it's implied. For instance, we assume openly available software... but then where else would they put their badge? So I think we can leave it as is.


MIME type error when inputting Japanese causes focus loss in iframe

Describe the bug
I am using the chainlit library to develop a conversational frontend. When I input "こんにちは" (hello in Japanese), the following error message appears in the console:

Skipped "/" because it is not a valid MIME type. Check https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_types/Common_types for a list of valid MIME types.

This error does not impact the application when used standalone. However, when the chat interface is embedded within an iframe, the cursor loses focus from the input field while typing.
To Reproduce

Set up a conversational frontend using chainlit.
Input "こんにちは" in the chat window.
Observe the error message in the console.
Embed the chat window within an iframe.
Again, input "こんにちは" and observe that the cursor loses focus from the input field.

Expected behavior
The input field should retain focus while typing, even when the chat interface is embedded within an iframe. The error message regarding the MIME type should not appear in the console.
Screenshots

Desktop (please complete the following information):

OS: [Windows 11]
Browser [chrome]
Version [131.0.6778.86（Official Build） （64 bit）]

Additional context
This issue seems specific to inputting text in Japanese and does not occur with other languages like English. Attempts to resolve the focus issue have been unsuccessful so far.

I'm pretty sure that this error shows up even for non-Kanjii. In which case this is a different issue.
Could you please check that?


svm.cpp - Incorrect error about k_fold parameter?

Using train_auto() function, today I came across the following error message (svm.cpp, lines 1436-1439):
    //check that while cross-validation there were the samples from all the classes
    if( class_ranges[class_count] <= 0 )
        CV_Error( CV_StsBadArg, "While cross-validation one or more of the classes have "
        "been fell out of the sample. Try to enlarge <Params::k_fold>" );

I understand that the problem is that one the k_fold subsets does not contain samples from one of the classes. However, the recommendation is to enlarge k_fold. Shouldn't it be the way around, i.e. reduce the parameter?
Example: let's say we have 10 negative samples and 3 positive ones in the training dataset. Using k_fold = 4, one of the subsets won't have a positive sample, and thus the error will appear. If we enlarge k_fold to 6, then 3 of the subsets won't have a positive sample - we don't fix the error but make it worse.
If I'm right, I'll be glad to provide the corresponding PR.

Can I work on this issue?

@IshankGulati you can. When you are done just open a Pullrequest referencing this issue.

Fixed by PR #6860


Implement Concatenating OperandRegistry YAMLs

Introduced a new function ConcatenateRegistries essentially combines the Operators from two OperandRegistry objects and returns the concatenated YAML representation of the modified OperandRegistry.
for issue: https://github.ibm.com/ibmprivatecloud/roadmap/issues/58224
The function performs the following steps:

It creates two OperandRegistry objects: baseRegistry and insertedRegistry by unmarshaling the YAML templates using the applyTemplate function.
It appends the Operators from insertedRegistry to the existing Operators in baseRegistry.
It marshals the modified base object back to YAML format using json.Marshal.
It returns the resulting YAML string and any error that occurred during the process.

Verify
test image: quay.io/yuchen_shen/cs_operator:split_opreg
delete origin OprandRegistry and it will create a new one with the entries of CP2 and followed by the entries of CP3.

Hold the PR, it would be merged together with ODLM's enhancement.

Latest update:

on-prem

in CSV2OpReg: ibm-mongodb-operator (no-op), ibm-commonui-operator (no-op), ibm-iam-operator (no-op), and ibm-zen-operator (no-op)
in CSV3OpReg: ibm-mongodb-operator-v4.0, ibm-idp-config-ui-operator-v4.0, ibm-im-operator-v4.0, ibm-im-operator, ibm-platformui-operator-v4.0 and ibm-platformui-operator
CSV3OperandRegistry = CSV2OpReg + CSV3OpReg

Saas

in CSV2SaasOpReg: ibm-mongodb-operator (no-op), ibm-iam-operator (no-op), and ibm-zen-operator (no-op)
in CSV3SaasOpReg: ibm-mongodb-operator-v4.0， ibm-im-operator-v4.0, ibm-im-operator, ibm-platformui-operator-v4.0 and ibm-platformui-operator
CSV3SaasOperandRegistry = CSV2SaasOpReg + CSV3SaasOpReg

@YCShen1010
Could we update the OperandConfig for ibm-im-operator and ibm-im-operator-v4.0?
It's OperandRequest should include CP3 MongoDB and CommonUI.
I believe we could try to play some tricks on this
- name: ibm-im-operator
  spec:
    operandRequest:
      requests:
        - operands:
            - name: ibm-mongodb-operator-{{ .Channel }}
            - name: ibm-idp-config-ui-operator-{{ .Channel }}
- name: ibm-im-operator-v4.0
  spec:
    operandRequest:
      requests:
        - operands:
            - name: ibm-mongodb-operator-v4.0
            - name: ibm-idp-config-ui-operator-v4.0

Test and verified that Bedrock and Zen could be installed successfully.


Missing images

Maybe this is an edge case too odd to look, but here's the link: https://amy-juan-li.medium.com/use-obsidian-for-content-creators-build-notion-like-database-views-ab8b48304659.
The problem is that there are places in the article when the author has two images side by side (when she refers to the "left" and "right" images in the description).  They don't get downloaded or even have links in the markdown.  I was able to copy and paste the images in, so that's a workaround.
Again, maybe not worth your time.
Would like to see a release with issue 191 fixed.  Any idea when a new release may be coming?

same with this one https://github.com/deathau/markdownload/issues/129

workaround: use "local image plus"

Workaround: Use "Local image plus".

It's ok when markdownload works. But with some websites clipping doesn't work for links/images. https://learn.microsoft.com/en-us/windows/package-manager/winget/ for example.


RF: Lofreq

With reference to discussions here (https://github.com/chapmanb/bcbio-nextgen/issues/112) , any new thoughts on including lofreq among the callers in bcbio?

We'd like to look at LoFreq and I've had some success using it for low frequency calling in HIV variants. In terms of priorities, the plans are to first upgrade FreeBayes to the latest version (#1634) and then integration/validate Octopus (#1591) so we won't have resources to work on this in the short term. As always, we'd be happy to help with anyone who wants to work on contributing this (http://bcbio-nextgen.readthedocs.io/en/latest/contents/code.html#variant-caller). Thanks much.

Thanks. If I manage to find some time I'll take a look at it.
Both Octopus and the new version of Freebayes look good!
//Pär

Closing this out as it is pretty old; we've done some other work with low frequency variant calling that hopefully should suffice.


add deprecation to the docs, haven't added warning messages to code yet

I want to add the deprecation note to the docs and rebuild the documentation / re-push to pypi because we fixed some broken tests recently.

added warning messages to code