Use case 11 issues

Use case 11: Related Proteins/Metabolites across DCCs

Few steps did not work for this workflow, e.g., - Mano

[ ]

Reformat and graph plot of StringDB PPI didn’t display or took long time. - Mano

[ ]

The references in the sentences related to MetGENE metanodes seem to be unformatted. - Mano

[ ]

MetGENE metabolites didn’t seem to work (not a valid JSON).  - Mano

[ ]

MetGENE studies table displayed by 1st column was showing as <a href … instead of as a clickable URL. - Mano

@mano-at-sdsc

@u8sand @susrinivasan MetGENE metabolites is working now (issue was due to wrong path in a file on the server-side).

@susrinivasan
Re studies table, kegg compound ID column, either remove html tags in REST output, or just use
          `${val.KEGG_COMPOUND_ID}`	 in metgene_study_table/index.tsx instead of


Translations update from Hosted Weblate

Translations update from Hosted Weblate for Nickvision Tagger/App.
It also includes following components:

Nickvision Tagger/Docs

Current translation status:

@fsobolev DocsUpdateYelp and DocsUpdateHtml is needed before merge...I'm currently not home so if you can run that then we can merge


Use standard logging API for quieter codegen verification

Printing this to stdout means it gets printed every time and is quite noisy. This changes it to log the start and happy path to info, and warn on errors

I think this PR will address this issue https://github.com/apollographql/apollo-android/pull/1451

Yep. I am going to update it real quick. Also these messages are not going to be this frequent anyways. They will only be logged when actual codegen runs.

I believe we can close this as it was addressed as part of https://github.com/apollographql/apollo-android/pull/1451


DO NOT MERGE YET Enable support of extensions for v17

except for Rust extensions and
ones that do not have new release yet.
Add comments for each extension.
Do not merge this PR, until we run backward compatibility tests and ensured that extension updates do not break exising installations.
See https://github.com/neondatabase/cloud/issues/18138
TODO:

[x] fix rdkit build
[x] fix plv8 build dependencies
[x] fix  postgis-build /usr/bin/install: cannot stat 'pgsql2shp': No such file or directory

Tested image on my project on staging. Unexpected findings after upgrade:

[x]  ip4r, pg_ivm  plpgsql_check, unit, not available. Fixed

[x] could not load library "/usr/local/lib/postgis_sfcgal-3.so": /usr/local/lib/postgis_sfcgal-3.so: undefined symbol: sfcgal_geometry_visibility_point.  Fixed by using sfcgal 1.4

[x] extract PR with unchanged extensions and ones that are version specific and thus don't require update for older versions

[ ] plcoffee and plls don't have default version. Checked in v16, they are ok.

[x] test simple extensions that are most likely version independent, extract PR with them

[ ] add vector support

[ ] add timescale support

Are there some easier parts of this that could be merged first?

Closed in favor of
https://github.com/neondatabase/neon/pull/9322 and https://github.com/neondatabase/neon/pull/9389


Python version of BYR-Navi

I use BYR-Navi as my personal navigation website and I really like its design concept. But I am not familiar with Jekyll. Thus, I modified it with Python and Plotly DASH. I have already put your BYR-Navi info under the bottom of the website for copyright purpose.
Hope you won't mind it.
Demo
Link: ChaQi.net
Github: github

@fundviz Hi! Many thanks for your affection and affirmation of BYR-Navi and the efforts within. Unfortunately, your demo seems to be failed, which might be result of some internal errors on your server. I am looking forward to seeing a actively live version of your website soon. Good luck!

@fundviz By the way, I read your code and found out you are trying to use Flask. If you are deploy a Flask app on Ubuntu or other Linux/UNIX-like operating systems, I would recommend you to use Flask (with Jinjia) + uWSGI + NGINX as a deployment stack on a production server, according to my experiences.

you are right, I feel like FLASK+JINJA2 will be more suitable than DASH framework for the lightweight web. I realized DASH will load too much unnecessary JS files to serve its framework, which is not a elegant way to display a website. Thanks for your advice. I appreciate it.

@fundviz For my point of view, if you understand Jinja templating philosophy, it won't be any obstacles to adopt the Liquid templating engine, which is used by Jekyll. Their syntaxes are almost the same. Once you understand how light-weight to build a static website using Jekyll, you can simply upload the generated site files under _site directory to your server web root and host it using NGINX, since NGINX is best known for its outstanding static file performance.

wow, I didnt even know they have so much in common.  I like the way Jekyll delivers the static HTML but sometimes feel like I need a website more than just static HTML. I mainly use DASH framework for my data visualization and never use FLASK before. But I feel like DASH and FLASK are pretty much the same somehow.  Actually, I have made some changes such as instant internal search, tooltips on your Jekyll-based  BYR-Navi before for my another navigation website. Here is the link, www.smzdcha.com.

@fundviz Precisely, a static website is not an equivalent to a website of pure HTML pages. In my opinion, the major differences between a static website and a non-static website are the way of the content delivery and how the contents are stored and rendered.
According to Wikipedia:

A static web page (sometimes called a flat page/stationary page) is a web page that is delivered to the user exactly as stored, in contrast to dynamic web pages which are generated by a web application.
Consequently, a static web page displays the same information for all users, from all contexts, subject to modern capabilities of a web server to negotiate content-type or language of the document where such versions are available and the server is configured to do so.

and

A server-side dynamic web page is a web page whose construction is controlled by an application server processing server-side scripts. In server-side scripting, parameters determine how the assembly of every new web page proceeds, including the setting up of more client-side processing.
A client-side dynamic web page processes the web page using HTML scripting running in the browser as it loads. JavaScript and other scripting languages determine the way the HTML in the received page is parsed into the Document Object Model, or DOM, that represents the loaded web page. The same client-side techniques can then dynamically update or change the DOM in the same way.

Hence, you can still do some dynamic tricks with JS to the so-called static website.

Thanks for the clarification. I have learned FLASK for the whole day yesterday and realized there are so much in common between FLASK and JEKYLL. I also feel like Flask is more efficient and handy to build up a website like BYR-Navi as you said.  I am so glad to have such a discussion with you !


Update Posts “a-scheduled-post”

Automatically generated by Netlify CMS

👷 Deploy Preview for thunderous-brigadeiros-23902d processing.

Name
Link

🔨 Latest commit
ce73ce037673e15a5eb2cfa5d3fac2128933e24d

🔍 Latest deploy log
https://app.netlify.com/sites/thunderous-brigadeiros-23902d/deploys/6331b8700f23d7000762daa5


Continue Server is not getting started.

Describe the bug
I have installed the continue extension. But when I open the extension window I see the loading continue server forever
To Reproduce
Steps to reproduce the behavior:

Just installed Continue extension and was not able to start Continue server.
VS code version details below,

Version: 1.81.1
Commit: 6c3e3dba23e8fadc360aed75ce363ba185c49794
Date: 2023-08-09T22:20:33.924Z
Electron: 22.3.18
ElectronBuildId: 22689846
Chromium: 108.0.5359.215
Node.js: 16.17.1
V8: <IP_ADDRESS>-electron.0
OS: Darwin x64 19.6.0

Expected behavior
Should start continue server and work normally.
Screenshots

Environment

Operating System: [MACOS - Catalina - 10.15.7]
Python Version: [3.10 and 3.11] installed via brew
Continue Version: [v0.0.316]

Console logs

Additional context
I am trying to use Continue for the first time.

@vigneshrams I tried a fresh re-install on my own computer (also a Mac) by deleting the .continue folder and found that there were a couple of errors, so I fixed those, and a new version is out with those changes, but it doesn't look (from the logs you've sent) like that is the problem.
It's possible that we built a binary that doesn't work on Mac Intel chips, which I will take a deeper look at tomorrow. If you try to run the binary at ~/.vscode/extensions/continue.continue-0.0.316/server/exe/run, this would directly show whether the server is able to start, and would be helpful for further debugging.

@sestinj From running the cmd to start the server manually, Below is the error I got. Hope it has to do with MacOS Version.
[16002] Error loading Python lib '/var/folders/5m/fcsn_rpx17zf0gm7fzzmk_k80000gn/T/_MEIxGPKJ2/libpython3.10.dylib': dlopen: dlopen(/var/folders/5m/fcsn_rpx17zf0gm7fzzmk_k80000gn/T/_MEIxGPKJ2/libpython3.10.dylib, 10): Symbol not found: _preadv
  Referenced from: /var/folders/5m/fcsn_rpx17zf0gm7fzzmk_k80000gn/T/_MEIxGPKJ2/libpython3.10.dylib (which was built for Mac OS X 11.7)
  Expected in: /usr/lib/libSystem.B.dylib
 in /var/folders/5m/fcsn_rpx17zf0gm7fzzmk_k80000gn/T/_MEIxGPKJ2/libpython3.10.dylib

Thanks for sharing. MacOS architecture likely the issue. We're working on getting around GitHub's lack of Apple Silicon support, will update once solved

Thanks for the update. If you want anything from my end please let me know.
I'm really excited to try continue.
On Tue, Aug 22, 2023, 11:00 PM Nate Sesti @.***> wrote:

Thanks for sharing. MacOS architecture likely the issue. We're working on
getting around GitHub's lack of Apple Silicon support, will update once
solved
—
Reply to this email directly, view it on GitHub
https://github.com/continuedev/continue/issues/387#issuecomment-1688627252,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AAEBEHFAUMJD5NZ2KQDKFPDXWTUE3ANCNFSM6AAAAAA3WKXPNU
.
You are receiving this because you were mentioned.Message ID:
@.***>

Also happening to me. I was using Continue just fine as of last week, a coworker mentioned being unable to use the extension today, just checked and I'm also unable to load the server anymore.

@vigneshrams @matiasdominguez I've just shipped a version (v0.0.323) that will use a mac m1 binary, and I expect this was the cause of these problems. Please let me know if this solves the problems—if not, I'll dig back in.

@vigneshrams @matiasdominguez I've just shipped a version (v0.0.323) that will use a mac m1 binary, and I expect this was the cause of these problems. Please let me know if this solves it—if not, I'll dig back in.

thanks! just did a fresh install and it worked.
steps to fix it:

update continue
rm -rf ~/.continue

@sestinj v0.0.323 did not fix it for me. I am using an Intel MacBook. Hope that could be the reason.

@matiasdominguez glad you were able to figure this out so fast and it's working! I did notice that we seem to be not correctly updating the server upon extension update, this is probably what was happening.
@vigneshrams Good to know—means these were probably two separate issues. I'm doing a lot of debugging tonight and will let you know what progress I make. Are you still seeing the same error as before (Error loading python lib?)

fresh first time install of continue extension and I am running into this issue. It is a MacBook 2019 Intel with Ventura 13.5.1
If you need help testing something, let me know.

I also had a similar issue. (I'm on a M1 mac). But instead of continue.log, the console mentioned server_version.txt was missing. After I copied the file from ~/.vscode/extensions/continue.continue-0.0.326/server_version.txt to ~/.continue/server/server_version.txt and restarted VS Code, it loaded properly

@tomasmcm That is the correct solution, and I've already updated the extension in v0.0.328 to solve the issue, so it should now work out-of-the-box.
@gkrawiec @joshpc is everything now working okay for you in v0.0.328?

yes, it is working now. Thank you.

Super glad to hear it! If more questions arise you're always free to message in our Discord: https://discord.gg/NWtdYexhMs

@sestinj yep -- deleted everything under ~/.continue and reinstalled, works great out of the box. thanks!

Environment

Operating System: [MACOS - Catalina - 10.15.7]
Python Version: [3.10 and 3.11] installed via brew
Continue Version: [v0.0.380]

bisect

the oldest version that runs without any issues is [v0.0.236] (2023-08-01T22:23:56.24Z)
at [v0.0.237] (2023-08-02T06:04:22.12Z) the user encounters the issue described by @vigneshrams

in [v0.0.236] the run binary was created locally, judging from the log messages in the Console

in [v0.0.237] the binary is downloaded from somewhere

git history between the dates for [v0.0.236] [v0.0.237]

git log --since='2023-08-01T22:23:56.24Z' --until='2023-08-02T06:04:22.12Z' --pretty=format:"%cd  %h  %s" --date=human

# Wed Aug 2 06:00  85a4f317  Update package.json version [skip ci]
# Tue Aug 1 22:54  0f55a01f  correct package.json version
# Tue Aug 1 22:47  582d8d06  npx vsce
# Tue Aug 1 22:37  f5f9d771  full vsce publish workflow
# Tue Aug 1 20:56  0a7cd1d0  purge unecessary functions in envSetup (finally)
# Tue Aug 1 20:32  e17388ee  fix icon sizes
# Tue Aug 1 18:53  10e5b827  fix exe paths
# Tue Aug 1 18:39  29096f50  reorder, don't push for now
# Tue Aug 1 18:35  a0157175  Merge branch 'package-python' of https://github.com/continuedev/continue into package-python
# Tue Aug 1 18:35  e5a97251  uncomment pyinstaller
# Wed Aug 2 01:35  bf72167f  Update package.json version [skip ci]
# Tue Aug 1 18:33  5e2cf036  correctly place permissions at job-level
# Tue Aug 1 18:31  29fd79a2  write permissions to push package.json update
# Tue Aug 1 18:19  100c15ec  purge styled-icons
# Tue Aug 1 18:15  6a396783  use hero-icons, instead of styled-icons/heroicons
# Tue Aug 1 17:59  9d1be885  --legacy-peer-deps for react-app
# Tue Aug 1 17:50  17de821b  npm install @styled-icons/styled-icon
# Tue Aug 1 17:38  9e94d4f1  remove --legacy-peer-deps flag
# Tue Aug 1 17:34  57bcd162  add back typegen script
# Tue Aug 1 17:30  4eb1a505  install @nestjs/common
# Tue Aug 1 17:22  aa196c22  remove poetry build from package.json
# Tue Aug 1 17:19  d3152e3d  use nodejs version 19.0.0
# Tue Aug 1 17:13  414d102c  again update package.json
# Tue Aug 1 17:07  2ad87111  remove unnecessary npm packages
# Tue Aug 1 17:03  9cabb68b  node-16 buster, not 14
# Tue Aug 1 17:02  22576f48  install android arm
# Tue Aug 1 16:57  2374d1be  delete poetry install from main.yaml
# Tue Aug 1 16:53  de976046  testing buster
# Tue Aug 1 16:43  5fd25cb9  use correct poetry path
# Tue Aug 1 16:36  398c4830  run publish on macos, not ubuntu
# Tue Aug 1 16:29  2a9d057c  fixes to main.yaml, build nodejs
# Tue Aug 1 16:06  f9148fd2  tweaking main.yml
# Tue Aug 1 16:01  39845167  newer version of setup-python workflow setp
# Tue Aug 1 15:54  74472c52  main.yaml package only dist/run
# Tue Aug 1 15:49  2d5d4985  main.yaml only setup python once
# Tue Aug 1 15:40  9513bcd1  use python 3.11 for pyinstaller

workaround
idea 1

just use [v0.0.236] 😅

idea 2

build the run binary yourself locally on macOS 10.15 and run it every time you launch VSCode

[!IMPORTANT]
On macOS, system components from one version of the OS are usually compatible with later versions, but they may not work with earlier versions. While PyInstaller does not collect system components of the OS, the collected 3rd party binaries (e.g., python extension modules) are built against specific version of the OS libraries, and may or may not support older OS versions. [...]
For example, to ensure compatibility with “Mojave” (10.14) and later versions, you should set up a full environment (i.e., install python, PyInstaller, your application’s code, and all its dependencies) in a copy of macOS 10.14, using a virtual machine if necessary. Then use PyInstaller to freeze your application in that environment; the generated frozen application should be compatible with that and later versions of macOS.
Source: pyinstaller - making-macos-apps-forward-compatible

git clone git@github.com:continuedev/continue.git
chmod +x ./build.sh
./build.sh
# ...
# 51745 INFO: Appending PKG archive to EXE
# 51929 INFO: Fixing EXE headers for code signing
# 51967 INFO: Rewriting the executable's macOS SDK version (12.1.0) to match the SDK version of the Python library (10.15.6) in order to avoid inconsistent behavior and potential UI issues in the frozen application.
# 51969 INFO: Re-signing the EXE
# 52372 INFO: Building EXE from EXE-00.toc completed successfully.
./dist/run
# start vscode and it should work 🍀

image running successfully [v0.0.380] on macOS 10.15

tl;dr

the run binary that gets downloaded from the server was created in a later macOS environment and won't run on macOS 10.15

@LangLangBart thanks for being so detailed here! It looks like the furthest that GitHub Actions supports is MacOS 11 (https://github.com/actions/runner-images#available-images), which might not be enough given the pyinstaller snippet you shared. It might be possible to setup a self-hosted runner to perform this job though, which I'll look into first.
Another supporting solution might be to include instructions for manually running the server upon failure. Or even just attempting this automatically as a fallback. Theoretically this is as easy as pip install continuedev && python -m continuedev. I'll give this a shot and see if it is a consistent enough fix.

the binary runs successfully when using a python version above 3.10.0 and below 3.10.9 or using any python version above 3.11.0  (currently 3.11.5 is the latest)

individually tested  ⏳

a comment from 12/Aug/22 on a similar issue also suggested the python version to be set above 3.10.0

https://github.com/pyinstaller/pyinstaller/issues/7022#issuecomment-1213056801

for version in {0..13}; do
        echo -n "Python 3.10.$version: "
        curl -s https://www.python.org/downloads/release/python-310$version/ |
        grep "Release Date:" | sed 's/^[ \t]*//;s/<[^>]*>//g'
done
# Python 3.10.0: Release Date: Oct. 4, 2021
# Python 3.10.1: Release Date: Dec. 6, 2021
# Python 3.10.2: Release Date: Jan. 14, 2022
# Python 3.10.3: Release Date: March 16, 2022
# Python 3.10.4: Release Date: March 24, 2022
# Python 3.10.5: Release Date: June 6, 2022
# Python 3.10.6: Release Date: Aug. 2, 2022
# Python 3.10.7: Release Date: Sept. 6, 2022
# Python 3.10.8: Release Date: Oct. 11, 2022
# Python 3.10.9: Release Date: Dec. 6, 2022
# Python 3.10.10: Release Date: Feb. 8, 2023
# Python 3.10.11: Release Date: April 5, 2023
# Python 3.10.12: Release Date: June 6, 2023
# Python 3.10.13: Release Date: Aug. 24, 2023

diff
--- a/.github/workflows/main.yaml
+++ b/.github/workflows/main.yaml
@@ -17,7 +17,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.10.8"

       - name: Install dependencies
         run: |
@@ -64,7 +64,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.10.8"

       - name: Install Pyinstaller
         run: |

@sestinj worth a try ?

@LangLangBart Yeah! I'll make this change in the next update, nice find

Alright, update is released along with new binaries. Lmk if it works?

🟢  [v0.0.390]  works for me on macOS 10.15

@vigneshrams can you confirm ?

@LangLangBart @sestinj Its works fine now. I am using the latest version. Thanks a lot for the support.


Check colorhandle against DL and VRT

Check colorhandle

[ ] matches DL
[ ] check VRT passes
[ ] check and update migration guides example

Positioning is off.

Yeah the loupe has scooted over a little...


[flutter-web] How to save cookie to browser?

I tried some packages:
import 'package:flutter_inappwebview/flutter_inappwebview.dart';

//...

CookieManager().setCookie(
        url: 'http://localhost:11812/#/',
        name: 'test',
        value: 'ooo',
        domain: 'localhost:11812');

but didn't work.

Is there a way to do this?

Hi @TheCGDF
flutter_inappwebview is a 3rd party app
you may want to open an issue in the dedicated github
Closing, as this isn't an issue with Flutter itself,
if you disagree please write in the comments and I will reopen it
Thank you

Hi @TheCGDF
flutter_inappwebview is a 3rd party app
you may want to open an issue in the dedicated github
Closing, as this isn't an issue with Flutter itself,
if you disagree please write in the comments and I will reopen it
Thank you

I just mean I tried some 3rd apps.
I opened this issue here because I'm not sure whether flutter offical provided a way to do this.

Hi @TheCGDF
Please see https://flutter.dev/community for resources and asking questions like this,
you may also get some help if you post it on Stack Overflow.
You may want to check this sub-reddit
Thank you


Rough Draft Sheet for homebrew system Seven Deadly Sins

Would like this in the repository so that my DM can use it =)

Alright. Should I put the link to the rules in instructions? Or some other place in the json?

Greetings @Kumatei
You could link in the sheet.json if you wanted to but its not necessary. I just need a link in these comments so I can review the rule set & ensure the rules are available to the public in some sort of published format.
Thanks,
Cassie

Alright, here's the rulebook. http://arsgothicus.com/rulebook.pdf

Greetings @Kumatei
FYI, your sheet.json was not named sheet.json. It is named sds.json which will cause the sheet to fail to load. I fixed this so the sheet could be merged and it is now live. You'll want to update your local copy.
Thanks,
Cassie


Link to Factsheets on Webplatform

@aljacob, @tiacop,
In the ADO project fact sheets were produced for the indices that we are showing. I think it would be a pitty not to show them on the webplatform, because they contain valuable information and are designed nicely as well.
@aljacob, can you confirm that the final version of the fact sheets is here: ADO Sharepoint / Documents / T1 / Factsheets / Final
@tiacop, could you let me know where in the repo to store the fact sheets? They are PDFs that should be linked in the "About the data" section. I suggest with a new sub-header under drought indices: "Factsheets"

@tiacop, could you give me the rights to edit the repo? then I'd do the work - according to your idea where to create the folder and how to call it.

hey @przell, you should have all the rights to edit the repo ... you have the role "maintain" for ado-data, next role would be "admin" ... .
I would suggest to create a folder "factsheets" on toplevel, put pdf there and link them on the about page.
An addition could be to show the factsheet link also in the timeseries and the info text. We have done this for DOI by adding the doi to the metadata json. A lonely  example for spi-1 already exists. See shots

We could do the same for the factsheets and add the url to a new field "factsheet" in the metadata json files. What do you think?

hey @przell,
I fixed the urls (deleted the "/blob" from the factsheet urls https://github.com/Eurac-Research/ado-data/commit/a10483d33340c78cb49bdb79784bdb8e194e12cd) and merged with the main branch. Also the website code on main branch is pushed ... the features are live.
Regarding missing doi field, no problem. If there is a doi or a factsheet or both we simply show it ;) See the SMA example with just the factsheet. Looks good to me. https://ado.eurac.edu/sma

@tiacop, added the missing doi and factsheet links to all collections where available in: ado-data/json/nuts/metadata
Once pushed to live and checked, we can consider this closed 📕

closed by #13


FritzDectThermostat 301 - wrong current  temperature

Wrong current temperature

I have the same issue, that setting the temperature via Homekit is highly unreliable. Even when it works one day, the other day it might already be buggy. I'm not fully clear though, what the root cause is, if it is the plugin, or Homekit, or the FritzBox.
For example, I have added a new scene "Living Room 20 Degrees", where all three thermostats should go to 20° C. Now since two days, all of a sudden one of them goes to 17°, a value that I use in a totally different scene "Saving Mode", where all thermostats are set to 17° while I'm away for a longer period of time.
Even when I manually trigger the scene, the thermostats take the right values (20°/20°/20°) and then immediately change to the faulty one again (20°/20°/17°).
Please let me know how I could support further the resolution here, to make the setting of temperature fully reliable.
Thanks


Mail Bouncing Trick/Attention

System that listens for e.g. http input and then sends an email when it's received. Could potentially be trivial once #6 is finished.

Made a custom attention file in https://github.com/FrostTusk/pay-attention


Install some playwright dependencies on Ubuntu.2204.Amd64* helix agents

Could  the libgbm1, and libxkbcommon0 packages be installed for the Ubuntu.2204.Amd64, and Ubuntu.2204.Amd64.Open helix queues? These are needed for running Playwright on the linux helix agents. And it would allow us to remove
https://github.com/dotnet/aspire/blob/faf26a8700c79ec435c2348d566caf4c1a4ebc13/tests/helix/send-to-helix-inner.proj#L77-L78
cc @joperezr

Release Note Category

[x] Feature changes/additions
[ ] Bug fixes
[ ] Internal Infrastructure Improvements

Release Note Description
Add libgbm1, and libxkbcommon0 packages to ubuntu.2204.amd64[.open] queues. This eases Playwright setup on those agents and avoids some system-wide changes during workitem execution.

confirmed this rolled out, was reverted, but is now present in the two requested queues. see entries in https://helix.dot.net and let us know if the installed packages disappear

confirmed this rolled out, was reverted, but is now present in the two requested queues. see entries in helix.dot.net and let us know if the installed packages disappear

Thank you!!

confirmed this rolled out, was reverted, but is now present in the two requested queues. see entries in helix.dot.net and let us know if the installed packages disappear

The packages do show up on that page. When should I expect the new VMs for these updated images to show up? I tried to enable the tests but they still fail - https://dev.azure.com/dnceng-public/public/_build/results?buildId=754402&view=ms.vss-test-web.build-test-results-tab&runId=19118936&resultId=100001&paneView=debug .

Reopening to see what's going on. Might be a $PATH issue for example…


fix: multi-line command desc not captured properly

Problem:
If the builtin command description spans multiple lines, only the first line is captured and showed and the remaining lines won't be matched. I believe the issue lies in mistakenly writing + as %+ in the regex.
Solution:
Correct the regex in string.match() and properly prepend a whitespace when concatenating multiple lines.

Ty @rockyzhang24!


fix row_neon.cc 591 612

Hey, @intraceting! This repository is just an unofficial mirror - please submit your contribution upstream:
https://chromium.googlesource.com/libyuv/libyuv/


A special size measurements test for global frames with text content is failing with different results in different places.

@seanparsons If this is still a problem, please can you add the test name

This is the failing test: https://github.com/concrete-utopia/utopia/blob/3b67f43733ee88651b704e442c0292ce8dc158c2/editor/src/core/model/element-metadata.spec.browser2.tsx#L1434


Remove support for Python 2

... and reformat using black

Coverage decreased (-0.06%) to 98.0% when pulling dbc421670978302c9bd9e6b118a2ab51947b7a69 on py3-only into 6a8b95357c8f6e222ecad1717a5855ef60ca5a24 on master.


model weights download

Hi!
Got error while trying to run demo:
python demo.py --imagedir=data/abandonedfactory --calib=calib/tartan.txt --stride=2
error:
  File "/root/miniconda3/envs/droidenv/lib/python3.9/site-packages/torch/serialization.py", line 211, in __init__
    super(_open_file, self).__init__(open(name, mode))
FileNotFoundError: [Errno 2] No such file or directory: 'demo.pth'

There is no information in the readme how/where to download the model weights file. Can you provide an URL please?
Thank you!

a

Thanks for your attention! Could you provide me with your email? Please update the lowMem_defSample.cu in offersample_LGU.

<EMAIL_ADDRESS>


Massive internalBinding errors (esm_loader.js) upon running 'hugo server -DF --disableFastRender'

Thank you and your contributors for this well-documented theme. I'm excited to dig into it.
Following your installation instructions, I got this terminal output at hugo server DF --disableFastRender
`PS C:\Users\Public\HugoSites\northeast> hugo server -DF --disableFastRender
Start building sites …
hugo v0.92.0-B3549403+extended windows/amd64 BuildDate=2022-01-12T08:23:18Z VendorInfo=gohugoio
ERROR 2022/04/20 06:59:08 POSTCSS: failed to transform "css/light.css" (text/css): internal/process/esm_loader.js:74
internalBinding('errors').triggerUncaughtException(
^
Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by the default ESM loader
at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
at Loader.resolve (internal/modules/esm/loader.js:85:40)
at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
at link (internal/modules/esm/module_job.js:50:36) {
code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
}
ERROR 2022/04/20 06:59:08 POSTCSS: failed to transform "css/dark.css" (text/css): internal/process/esm_loader.js:74
internalBinding('errors').triggerUncaughtException(
^
Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by the default ESM loader
at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
at Loader.resolve (internal/modules/esm/loader.js:85:40)
at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
at link (internal/modules/esm/module_job.js:50:36) {
code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
}
Error: Error building site: POSTCSS: failed to transform "css/northeast-tailwind.css" (text/css): internal/process/esm_loader.js:74
internalBinding('errors').triggerUncaughtException(
^
Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by the default ESM loader
at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
at Loader.resolve (internal/modules/esm/loader.js:85:40)
at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
at link (internal/modules/esm/module_job.js:50:36) {
code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
}
Built in 4741 ms
PS C:\Users\Public\HugoSites\northeast> hugo server -DF --disableFastRender
Start building sites …
hugo v0.92.0-B3549403+extended windows/amd64 BuildDate=2022-01-12T08:23:18Z VendorInfo=gohugoio
ERROR 2022/04/20 07:01:42 POSTCSS: failed to transform "css/light.css" (text/css): internal/process/esm_loader.js:74
internalBinding('errors').triggerUncaughtException(
^
Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by the default ESM loader
at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
at Loader.resolve (internal/modules/esm/loader.js:85:40)
at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
}
ERROR 2022/04/20 07:01:42 POSTCSS: failed to transform "css/dark.css" (text/css): internal/process/esm_loader.js:74
internalBinding('errors').triggerUncaughtException(
^
Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by the default ESM loader
at Loader.resolve (internal/modules/esm/loader.js:85:40)
at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
at link (internal/modules/esm/module_job.js:50:36) {
code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
}
Error: Error building site: POSTCSS: failed to transform "css/northeast-tailwind.css" (text/css): internal/process/esm_loader.js:74
^
Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by the default ESM loader
at Loader.resolve (internal/modules/esm/loader.js:85:40)
at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
at link (internal/modules/esm/module_job.js:50:36) {
code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
}
Built in 2501 ms
PS C:\Users\Public\HugoSites\northeast> cd themes/northeastPS C:\Users\Public\HugoSites\northeast> hugo server -DF --disableFastRender
At line:1 char:1

cd themes/northeastPS C:\Users\Public\HugoSites\northeast> hugo serve ...

  + CategoryInfo          : InvalidArgument: (:) [Set-Location], ParameterBindingException
  + FullyQualifiedErrorId : PositionalParameterNotFound,Microsoft.PowerShell.Commands.SetLocationCommand

PS C:\Users\Public\HugoSites\northeast> Start building sites .
At line:1 char:1

  + CategoryInfo          : InvalidArgument: (:) [Start-Process], ParameterBindingException
  + FullyQualifiedErrorId : PositionalParameterNotFound,Microsoft.PowerShell.Commands.StartProcessCommand

PS C:\Users\Public\HugoSites\northeast> hugo v0.92.0-B3549403+extended windows/amd64 BuildDate=2022-01-12T08:23:18Z VendorInfo=gohugoio
Error: unknown command "v0.92.0-B3549403+extended" for "hugo"
Run 'hugo --help' for usage.
PS C:\Users\Public\HugoSites\northeast> ERROR 2022/04/20 06:59:08 POSTCSS: failed to transform "css/light.css" (text/css)text/css : The term 'text/css' is not recognized as the name of a cmdlet, function, script file, or operable program.
Check the spelling of the name, or if a path was included, verify that the path is correct and try again.
At line:1 char:73

... :59:08 POSTCSS: failed to transform "css/light.css" (text/css): inter ...

                                                     ~~~~~~~~

CategoryInfo          : ObjectNotFound: (text/css:String) [], CommandNotFoundException
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     internalBinding('errors').triggerUncaughtException(

                          ^

internalBinding('errors').triggerUncaughtException(

                                                   ~

Missing ')' in method call.
+ CategoryInfo          : ParserError: (:) [], ParentContainsErrorRecordException
+ FullyQualifiedErrorId : MissingEndParenthesisInMethodCall
PS C:\Users\Public\HugoSites\northeast>
PS C:\Users\Public\HugoSites\northeast> Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by
the default ESM loader
Error : The term 'Error' is not recognized as the name of a cmdlet, function, script file, or operable program. Check
At line:1 char:1

Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are s ...

  + CategoryInfo          : ObjectNotFound: (Error:String) [], CommandNotFoundException
  + FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
internal/modules/esm/resolve.js:781:11 : The term 'internal/modules/esm/resolve.js:781:11' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
At line:1 char:45

... defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)

                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/resolve.js:781:11:String) [], CommandNotFoundExcept
ion
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.resolve (internal/modules/esm/loader.js:85:40)
internal/modules/esm/loader.js:85:40 : The term 'internal/modules/esm/loader.js:85:40' is not recognized as the name of
a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included, verify
that the path is correct and try again.
At line:1 char:24

                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/loader.js:85:40:String) [], CommandNotFoundExceptio
n
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
internal/modules/esm/loader.js:229:28 : The term 'internal/modules/esm/loader.js:229:28' is not recognized as the name
of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included,
verify that the path is correct and try again.
At line:1 char:29

at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)

CategoryInfo          : ObjectNotFound: (internal/modules/esm/loader.js:229:28:String) [], CommandNotFoundExcepti
on
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
internal/modules/esm/module_job.js:51:40 : The term 'internal/modules/esm/module_job.js:51:40' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
included, verify that the path is correct and try again.
At line:1 char:32

                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/module_job.js:51:40:String) [], CommandNotFoundExce
ption
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at link (internal/modules/esm/module_job.js:50:36) {

code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
internal/modules/esm/module_job.js:50:36 : The term 'internal/modules/esm/module_job.js:50:36' is not recognized as the
included, verify that the path is correct and try again.
At line:1 char:14

at link (internal/modules/esm/module_job.js:50:36) {

         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/module_job.js:50:36:String) [], CommandNotFoundExce
ption
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast> ERROR 2022/04/20 06:59:08 POSTCSS: failed to transform "css/dark.css" (text/css):text/css : The term 'text/css' is not recognized as the name of a cmdlet, function, script file, or operable program.
Check the spelling of the name, or if a path was included, verify that the path is correct and try again.
At line:1 char:72

... 6:59:08 POSTCSS: failed to transform "css/dark.css" (text/css): inter ...

                                                     ~~~~~~~~

CategoryInfo          : ObjectNotFound: (text/css:String) [], CommandNotFoundException
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     internalBinding('errors').triggerUncaughtException(

                          ^

internalBinding('errors').triggerUncaughtException(

                                                   ~

Missing ')' in method call.
+ CategoryInfo          : ParserError: (:) [], ParentContainsErrorRecordException
+ FullyQualifiedErrorId : MissingEndParenthesisInMethodCall
PS C:\Users\Public\HugoSites\northeast>
PS C:\Users\Public\HugoSites\northeast> Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by
the default ESM loader
Error : The term 'Error' is not recognized as the name of a cmdlet, function, script file, or operable program. Check
At line:1 char:1

Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are s ...

  + CategoryInfo          : ObjectNotFound: (Error:String) [], CommandNotFoundException
  + FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
internal/modules/esm/resolve.js:781:11 : The term 'internal/modules/esm/resolve.js:781:11' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
At line:1 char:45

... defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)

                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/resolve.js:781:11:String) [], CommandNotFoundExcept
ion
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.resolve (internal/modules/esm/loader.js:85:40)
internal/modules/esm/loader.js:85:40 : The term 'internal/modules/esm/loader.js:85:40' is not recognized as the name of
a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included, verify
that the path is correct and try again.
At line:1 char:24

                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/loader.js:85:40:String) [], CommandNotFoundExceptio
n
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
internal/modules/esm/loader.js:229:28 : The term 'internal/modules/esm/loader.js:229:28' is not recognized as the name
of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included,
verify that the path is correct and try again.
At line:1 char:29

at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)

CategoryInfo          : ObjectNotFound: (internal/modules/esm/loader.js:229:28:String) [], CommandNotFoundExcepti
on
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
internal/modules/esm/module_job.js:51:40 : The term 'internal/modules/esm/module_job.js:51:40' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
included, verify that the path is correct and try again.
At line:1 char:32

                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/module_job.js:51:40:String) [], CommandNotFoundExce
ption
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at link (internal/modules/esm/module_job.js:50:36) {

code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
internal/modules/esm/module_job.js:50:36 : The term 'internal/modules/esm/module_job.js:50:36' is not recognized as the
included, verify that the path is correct and try again.
At line:1 char:14

at link (internal/modules/esm/module_job.js:50:36) {

         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/module_job.js:50:36:String) [], CommandNotFoundExce
ption
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast> Error: Error building site: POSTCSS: failed to transform "css/northeast-tailwind.text/css : The term 'text/css' is not recognized as the name of a cmdlet, function, script file, or operable program.
Check the spelling of the name, or if a path was included, verify that the path is correct and try again.
At line:1 char:88

... S: failed to transform "css/northeast-tailwind.css" (text/css): inter ...

                                                     ~~~~~~~~

CategoryInfo          : ObjectNotFound: (text/css:String) [], CommandNotFoundException
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     internalBinding('errors').triggerUncaughtException(

                          ^

internalBinding('errors').triggerUncaughtException(

                                                   ~

Missing ')' in method call.
+ CategoryInfo          : ParserError: (:) [], ParentContainsErrorRecordException
+ FullyQualifiedErrorId : MissingEndParenthesisInMethodCall
PS C:\Users\Public\HugoSites\northeast>
PS C:\Users\Public\HugoSites\northeast> Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by
the default ESM loader
Error : The term 'Error' is not recognized as the name of a cmdlet, function, script file, or operable program. Check
At line:1 char:1

Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are s ...

  + CategoryInfo          : ObjectNotFound: (Error:String) [], CommandNotFoundException
  + FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
internal/modules/esm/resolve.js:781:11 : The term 'internal/modules/esm/resolve.js:781:11' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
At line:1 char:45

... defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)

                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/resolve.js:781:11:String) [], CommandNotFoundExcept
ion
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.resolve (internal/modules/esm/loader.js:85:40)
internal/modules/esm/loader.js:85:40 : The term 'internal/modules/esm/loader.js:85:40' is not recognized as the name of
a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included, verify
that the path is correct and try again.
At line:1 char:24

                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/loader.js:85:40:String) [], CommandNotFoundExceptio
n
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
internal/modules/esm/loader.js:229:28 : The term 'internal/modules/esm/loader.js:229:28' is not recognized as the name
of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included,
verify that the path is correct and try again.
At line:1 char:29

                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/loader.js:229:28:String) [], CommandNotFoundExcepti
on
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
internal/modules/esm/module_job.js:51:40 : The term 'internal/modules/esm/module_job.js:51:40' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
At line:1 char:32

...  at ModuleWrap. (internal/modules/esm/module_job.js:51:40)

                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/module_job.js:51:40:String) [], CommandNotFoundExce
ption
FullyQualifiedErrorId : CommandNotFoundException

code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
}
internal/modules/esm/module_job.js:50:36 : The term 'internal/modules/esm/module_job.js:50:36' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
included, verify that the path is correct and try again.
At line:1 char:14

at link (internal/modules/esm/module_job.js:50:36) {

         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

ption

FullyQualifiedErrorId : CommandNotFoundException

Built : The term 'Built' is not recognized as the name of a cmdlet, function, script file, or operable program. Check
the spelling of the name, or if a path was included, verify that the path is correct and try again.
At line:1 char:1

Built in 4741 ms

  + CategoryInfo          : ObjectNotFound: (Built:String) [], CommandNotFoundException
  + FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast> PS C:\Users\Public\HugoSites\northeast> hugo server -DF --disableFastRender
At line:1 char:1

PS C:\Users\Public\HugoSites\northeast> hugo server -DF --disableFast ...

  + CategoryInfo          : InvalidArgument: (:) [Get-Process], ParameterBindingException
  + FullyQualifiedErrorId : PositionalParameterNotFound,Microsoft.PowerShell.Commands.GetProcessCommand

PS C:\Users\Public\HugoSites\northeast> Start building sites .
At line:1 char:1

  + CategoryInfo          : InvalidArgument: (:) [Start-Process], ParameterBindingException
  + FullyQualifiedErrorId : PositionalParameterNotFound,Microsoft.PowerShell.Commands.StartProcessCommand

PS C:\Users\Public\HugoSites\northeast> hugo v0.92.0-B3549403+extended windows/amd64 BuildDate=2022-01-12T08:23:18Z VendorInfo=gohugoio
Error: unknown command "v0.92.0-B3549403+extended" for "hugo"
Run 'hugo --help' for usage.
PS C:\Users\Public\HugoSites\northeast> ERROR 2022/04/20 07:01:42 POSTCSS: failed to transform "css/light.css" (text/css)text/css : The term 'text/css' is not recognized as the name of a cmdlet, function, script file, or operable program.
Check the spelling of the name, or if a path was included, verify that the path is correct and try again.
At line:1 char:73

... :01:42 POSTCSS: failed to transform "css/light.css" (text/css): inter ...

                                                     ~~~~~~~~

CategoryInfo          : ObjectNotFound: (text/css:String) [], CommandNotFoundException
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     internalBinding('errors').triggerUncaughtException(

                          ^

internalBinding('errors').triggerUncaughtException(

                                                   ~

Missing ')' in method call.
+ CategoryInfo          : ParserError: (:) [], ParentContainsErrorRecordException
+ FullyQualifiedErrorId : MissingEndParenthesisInMethodCall
PS C:\Users\Public\HugoSites\northeast>
PS C:\Users\Public\HugoSites\northeast> Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by
the default ESM loader
Error : The term 'Error' is not recognized as the name of a cmdlet, function, script file, or operable program. Check
At line:1 char:1

Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are s ...

  + CategoryInfo          : ObjectNotFound: (Error:String) [], CommandNotFoundException
  + FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
internal/modules/esm/resolve.js:781:11 : The term 'internal/modules/esm/resolve.js:781:11' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
At line:1 char:45

... defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)

                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/resolve.js:781:11:String) [], CommandNotFoundExcept
ion
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.resolve (internal/modules/esm/loader.js:85:40)
internal/modules/esm/loader.js:85:40 : The term 'internal/modules/esm/loader.js:85:40' is not recognized as the name of
a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included, verify
that the path is correct and try again.
At line:1 char:24

                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/loader.js:85:40:String) [], CommandNotFoundExceptio
n
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
internal/modules/esm/loader.js:229:28 : The term 'internal/modules/esm/loader.js:229:28' is not recognized as the name
of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included,
verify that the path is correct and try again.
At line:1 char:29

at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)

CategoryInfo          : ObjectNotFound: (internal/modules/esm/loader.js:229:28:String) [], CommandNotFoundExcepti
on
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
internal/modules/esm/module_job.js:51:40 : The term 'internal/modules/esm/module_job.js:51:40' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
included, verify that the path is correct and try again.
At line:1 char:32

                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/module_job.js:51:40:String) [], CommandNotFoundExce
ption
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at link (internal/modules/esm/module_job.js:50:36) {

code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
internal/modules/esm/module_job.js:50:36 : The term 'internal/modules/esm/module_job.js:50:36' is not recognized as the
included, verify that the path is correct and try again.
At line:1 char:14

at link (internal/modules/esm/module_job.js:50:36) {

         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/module_job.js:50:36:String) [], CommandNotFoundExce
ption
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast> ERROR 2022/04/20 07:01:42 POSTCSS: failed to transform "css/dark.css" (text/css):text/css : The term 'text/css' is not recognized as the name of a cmdlet, function, script file, or operable program.
Check the spelling of the name, or if a path was included, verify that the path is correct and try again.
At line:1 char:72

... 7:01:42 POSTCSS: failed to transform "css/dark.css" (text/css): inter ...

                                                     ~~~~~~~~

CategoryInfo          : ObjectNotFound: (text/css:String) [], CommandNotFoundException
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     internalBinding('errors').triggerUncaughtException(

                          ^

internalBinding('errors').triggerUncaughtException(

                                                   ~

Missing ')' in method call.
+ CategoryInfo          : ParserError: (:) [], ParentContainsErrorRecordException
+ FullyQualifiedErrorId : MissingEndParenthesisInMethodCall
PS C:\Users\Public\HugoSites\northeast>
PS C:\Users\Public\HugoSites\northeast> Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by
the default ESM loader
Error : The term 'Error' is not recognized as the name of a cmdlet, function, script file, or operable program. Check
At line:1 char:1

Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are s ...

  + CategoryInfo          : ObjectNotFound: (Error:String) [], CommandNotFoundException
  + FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
internal/modules/esm/resolve.js:781:11 : The term 'internal/modules/esm/resolve.js:781:11' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
At line:1 char:45

... defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)

                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/resolve.js:781:11:String) [], CommandNotFoundExcept
ion
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.resolve (internal/modules/esm/loader.js:85:40)
internal/modules/esm/loader.js:85:40 : The term 'internal/modules/esm/loader.js:85:40' is not recognized as the name of
a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included, verify
that the path is correct and try again.
At line:1 char:24

                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/loader.js:85:40:String) [], CommandNotFoundExceptio
n
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
internal/modules/esm/loader.js:229:28 : The term 'internal/modules/esm/loader.js:229:28' is not recognized as the name
of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included,
verify that the path is correct and try again.
At line:1 char:29

at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)

CategoryInfo          : ObjectNotFound: (internal/modules/esm/loader.js:229:28:String) [], CommandNotFoundExcepti
on
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
internal/modules/esm/module_job.js:51:40 : The term 'internal/modules/esm/module_job.js:51:40' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
included, verify that the path is correct and try again.
At line:1 char:32

                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/module_job.js:51:40:String) [], CommandNotFoundExce
ption
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at link (internal/modules/esm/module_job.js:50:36) {

code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
internal/modules/esm/module_job.js:50:36 : The term 'internal/modules/esm/module_job.js:50:36' is not recognized as the
included, verify that the path is correct and try again.
At line:1 char:14

at link (internal/modules/esm/module_job.js:50:36) {

         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/module_job.js:50:36:String) [], CommandNotFoundExce
ption
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast> Error: Error building site: POSTCSS: failed to transform "css/northeast-tailwind.text/css : The term 'text/css' is not recognized as the name of a cmdlet, function, script file, or operable program.
Check the spelling of the name, or if a path was included, verify that the path is correct and try again.
At line:1 char:88

... S: failed to transform "css/northeast-tailwind.css" (text/css): inter ...

                                                     ~~~~~~~~

CategoryInfo          : ObjectNotFound: (text/css:String) [], CommandNotFoundException
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     internalBinding('errors').triggerUncaughtException(

                          ^

internalBinding('errors').triggerUncaughtException(

                                                   ~

Missing ')' in method call.
+ CategoryInfo          : ParserError: (:) [], ParentContainsErrorRecordException
+ FullyQualifiedErrorId : MissingEndParenthesisInMethodCall
PS C:\Users\Public\HugoSites\northeast>
PS C:\Users\Public\HugoSites\northeast> Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by
the default ESM loader
Error : The term 'Error' is not recognized as the name of a cmdlet, function, script file, or operable program. Check
At line:1 char:1

Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are s ...

  + CategoryInfo          : ObjectNotFound: (Error:String) [], CommandNotFoundException
  + FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
internal/modules/esm/resolve.js:781:11 : The term 'internal/modules/esm/resolve.js:781:11' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
At line:1 char:45

... defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)

                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/resolve.js:781:11:String) [], CommandNotFoundExcept
ion
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.resolve (internal/modules/esm/loader.js:85:40)
internal/modules/esm/loader.js:85:40 : The term 'internal/modules/esm/loader.js:85:40' is not recognized as the name of
a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included, verify
that the path is correct and try again.
At line:1 char:24

                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/loader.js:85:40:String) [], CommandNotFoundExceptio
n
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
internal/modules/esm/loader.js:229:28 : The term 'internal/modules/esm/loader.js:229:28' is not recognized as the name
of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included,
verify that the path is correct and try again.
At line:1 char:29

at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)

                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/loader.js:229:28:String) [], CommandNotFoundExcepti
on
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
internal/modules/esm/module_job.js:51:40 : The term 'internal/modules/esm/module_job.js:51:40' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
included, verify that the path is correct and try again.
At line:1 char:32

...  at ModuleWrap. (internal/modules/esm/module_job.js:51:40)

                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/module_job.js:51:40:String) [], CommandNotFoundExce
ption
FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\Public\HugoSites\northeast>     at link (internal/modules/esm/module_job.js:50:36) {

code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
}
internal/modules/esm/module_job.js:50:36 : The term 'internal/modules/esm/module_job.js:50:36' is not recognized as the
name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was
included, verify that the path is correct and try again.
At line:1 char:14

at link (internal/modules/esm/module_job.js:50:36) {

         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CategoryInfo          : ObjectNotFound: (internal/modules/esm/module_job.js:50:36:String) [], CommandNotFoundExce
ption
FullyQualifiedErrorId : CommandNotFoundException`

Does this look familiar to anyone?
I also don't find the expected postCSS and tailwindcss config files. Thank you in advance.

I realized that the installation instructions forgot to mention copying everything in the exampleSite folder into the main site folder. So I did that and tried hugo server -DF --disableFastRender again, but got these same errors:
`PS C:\Users\Public\HugoSites\northeast> hugo server -DF --disableFastRender
Start building sites …
hugo v0.92.0-B3549403+extended windows/amd64 BuildDate=2022-01-12T08:23:18Z VendorInfo=gohugoio
ERROR 2022/04/20 07:18:10 Failed to read Git log: fatal: your current branch 'master' does not have any commits yet
ERROR 2022/04/20 07:18:12 instagram shortcode: Missing config value for services.instagram.accessToken. This can be set in config.toml, but it is recommended to configure this via the HUGO_SERVICES_INSTAGRAM_ACCESSTOKEN OS environment variable. If you are using a Client Access Token, remember that you must combine it with your App ID using a pipe symbol (|) otherwise the request will fail.
If you feel that this should not be logged as an ERROR, you can ignore it by adding this to your site config:
ignoreErrors = ["error-missing-instagram-accesstoken"]
WARN 2022/04/20 07:18:12 The "tweet" shortcode will soon require two named parameters: user and id. See "C:\Users\Public\HugoSites\northeast\content\posts\hugo-shortcodes\index.md:47:1"
ERROR 2022/04/20 07:18:14 POSTCSS: failed to transform "css/light.css" (text/css): internal/process/esm_loader.js:74
internalBinding('errors').triggerUncaughtException(
^
Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by the default ESM loader
at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
at Loader.resolve (internal/modules/esm/loader.js:85:40)
at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
at link (internal/modules/esm/module_job.js:50:36) {
code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
}
ERROR 2022/04/20 07:18:14 POSTCSS: failed to transform "css/dark.css" (text/css): internal/process/esm_loader.js:74
internalBinding('errors').triggerUncaughtException(
^
Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by the default ESM loader
at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
at Loader.resolve (internal/modules/esm/loader.js:85:40)
at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
at link (internal/modules/esm/module_job.js:50:36) {
code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
}
Error: Error building site: POSTCSS: failed to transform "css/northeast-tailwind.css" (text/css): internal/process/esm_loader.js:74
internalBinding('errors').triggerUncaughtException(
^
Error [ERR_UNSUPPORTED_ESM_URL_SCHEME]: Only file and data URLs are supported by the default ESM loader
at Loader.defaultResolve [as _resolve] (internal/modules/esm/resolve.js:781:11)
at Loader.resolve (internal/modules/esm/loader.js:85:40)
at Loader.getModuleJob (internal/modules/esm/loader.js:229:28)
at ModuleWrap. (internal/modules/esm/module_job.js:51:40)
at link (internal/modules/esm/module_job.js:50:36) {
code: 'ERR_UNSUPPORTED_ESM_URL_SCHEME'
}
Built in 4257 ms`
Thank you.

Googling the error, I believe I just need to upgrade my node.js
Currently: v14.8.0
EDIT: updated and ran hugo server again.
Got a "failed to read git log" fatal error. Set
enableGitInfo = false  in config.toml
Ran hugo server again... got this:
 ERROR 2022/04/20 07:35:43 instagram shortcode: Missing config value for services.instagram.accessToken. This can be set in config.toml, but it is recommended to configure this via the HUGO_SERVICES_INSTAGRAM_ACCESSTOKEN OS environment variable. If you are using a Client Access Token, remember that you must combine it with your App ID using a pipe symbol (<APPID>|<CLIENTTOKEN>) otherwise the request will fail. If you feel that this should not be logged as an ERROR, you can ignore it by adding this to your site config: ignoreErrors = ["error-missing-instagram-accesstoken"] WARN 2022/04/20 07:35:43 The "tweet" shortcode will soon require two named parameters: user and id. See "C:\Users\Public\HugoSites\northeast\content\posts\hugo-shortcodes\index.md:47:1" Error: Error building site: "C:\Users\Public\HugoSites\northeast\content\posts\first-post\index.md:83:1": failed to render shortcode "figure": failed to process shortcode: "C:\Users\Public\HugoSites\northeast\themes\hugo-northeast\layouts\shortcodes\figure.html:4:23": execute of template failed: template: shortcodes/figure.html:4:23: executing "shortcodes/figure.html" at <$asset.RelPermalink>: nil pointer evaluating resource.Resource.RelPermalink Built in 35913 ms
(We're getting closer!) ;)

Hi @darrenaddy, thanks for sharing the debugging process. Seems like I was assuming $asset is always present. Will push a fix shortly.


HTMD tutorial

@simonbray @tsenapathi @bgruening
The layout of the tutorial created from the MD run and analysis workflow.  Still much more to do.

Just made a few minor changes to the analysis section. Looks good already :+1:

ping @simonbray, at last, it is out for review

@chrisbarnettster, looks great. I don't have any other things to change.
Just one idea: is it worth keeping the mmgbsa section in the online version of the tutorial (maybe in an optional section, or in a 'hidden' box)? I think we should definitely do mmgbsa in the GCC training, even if we need to provide users with longer pre-generated trajectories for it.

Okay, finally merged! Maybe we can discuss updating with the MMGBSA tool later.


[Suggestion] : Replace json with simplejson for Decimal serializing

When serializing a Decimal object obtained from a mysql query, the following exception is thrown
TypeError: Object of type Decimal is not JSON serializable

Replacing json with simplejson in flask_restful/representations/json.py:4 fixes the issue. I haven't found anyone else with the same issue so may not be very important. And also requires another dependancy

I don't get it. I see the issue was marked as completed, but looking at the code, the change isn't there. The default json is still used and so DECIMAL can't be serialised.


Fix missing quotes in refresh check

Summary
Fixes missing quotes around a potentially empty env var. Without the quotes and with the var unset, we get the following error message:
cat: .terraform/refreshed_at: No such file or directory
It has been awhile since the last refresh. It is time.
/bin/bash: line 0: [: !=: unary operator expected
remote backend does not support the refresh command, skipping
/Users/foo/work/shared-infra/.fogg/tfenv/versions/0.12.24/terraform plan  -refresh=false -input=false

The missing env leaves nothing for bash to interpret, and the != comparator fails since it doesn't have a string on the left side. This fixes that, and updates the golden files.
Test Plan
Tested locally; error message disappeared. Passes unit tests.

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@92ee41f). Click here to learn what that means.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master     #448   +/-   ##
=========================================
  Coverage          ?   61.33%
=========================================
  Files             ?       19
  Lines             ?     1906
  Branches          ?        0
=========================================
  Hits              ?     1169
  Misses            ?      586
  Partials          ?      151

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 92ee41f...7dcdf95. Read the comment docs.


Perform base decoding when a small charset's present

(aka how to cheat at restricted source)
It would be cool if, when a program consists of 4 or less (subject to change) distinct characters each occuring at least thrice each, the program is decoded as unary/binary/ternary/etc using those chars. Maybe the first n characters could define the encoding?
For example, xyxyxxxxyyyxyyyxxx could be decoded as binary, with the xy representing that x represents 0 and y represents 1. This would become 17336, which would become CḂ when interpreted as code.
Thoughts?

This sounds cool, but we might want to add a flag to disable it, just in case.

Is this still a good idea?

It feels a bit cheaty. Isn't there the option of range coding now, anyway?


Fixed Graphnode port separation.

This fixes the spacing of the Graphnode ports when using custom separation.
"fixes #32474"

You mean this issue? #32474

Yes, that's correct.

Why close this?

I thought it was done?  Sorry this is my first attempt at doing a pull request, don't understand the procedure.

The issue is still not fixed. Normally you don't manually close the PRs, they are automatically closed when they are merged. Often you have to be patient though, some PRs wait long time to be reviewed due to reasons.

Ah ok, yeah it's been months and I thought it was dead so I was just going to remove it.

Could you rebase to squash the commits into one?
https://docs.godotengine.org/en/latest/community/contributing/pr_workflow.html#the-interactive-rebase

Could you rebase to squash the commits into one?
https://docs.godotengine.org/en/latest/community/contributing/pr_workflow.html#the-interactive-rebase

Did so myself.

Thanks!

Cherry-picked for 3.2.3.


Editor actions in widgets stop working randomly

Use vscode for awhile
Open find widget, press enter to go to next match, or esc to close it
Nothing happens when I press enter or esc
Same in other widgets like the f2 "rename" box
Reload window
It works again

I've seen this a couple times in the past week and I debugged a bit.
It seems to go wrong at this line to pick which editor to send the command to: https://github.com/Microsoft/vscode/blob/master/src/vs/editor/browser/editorExtensions.ts#L156
After this, editor is the debug console repl input which is not focused or open although I used it a lot in this session.
Stepping into here: https://github.com/microsoft/vscode/blob/a817a588c72fe3d41ad0d1d8f3599742dc12267a/src/vs/editor/browser/services/abstractCodeEditorService.ts#L73
the repl editor claims to have widget focus. So I guess it got stuck in a state where widget focus is set to true but never reset to false. Can't figure out how to get it in or out of that state. I see this change which could be related: https://github.com/Microsoft/vscode/commit/a98ae682dca9588eacc633aaebf030ac528595c9

Thanks for tracking this down! :heart:
I've logically reverted the change in a98ae68 and also removed an old workaround that we had for IE which was the root cause of #71553


Upgrade to Express 4.x

i am working on the implementation of a newer express version in pump.io.
i miss a few functions and this will solve my problems (hope so).
is there a reason against this?

FWIW this work is going on in the express-3.x branch. The plan is to do a release with Express 3.x so we get some feedback on regressions, etc., then move to Express 4.x. (The latter change will probably be much easier.)

Removing webui label as this powers the API as well as the web UI.

This just landed in #1208; pump.io 4.0 will be powered by Express 4.x.


clone-env says dev environment doesn't exist

You can see below first the results of terminus site environments, and then you see an attempt to clone live to dev, with Terminus saying that dev doesn't exist.  We did this for a different site just before this one, and that worked fine.  When I logged in to the Dashboard, we could see the dev site and successfully cloned live to dev.
  12. test-cms
  13. other-site
  14. qasac-americas
  15. wdcpc-new-method

Choose site: 14
+-------------+------------+----------------------------------------+---------------+---------+
| Name        | Created    | Domain                                 | OnServer Dev? | Locked? |
+-------------+------------+----------------------------------------+---------------+---------+
| test        |<PHONE_NUMBER> | test-qasac-americas.pantheon.io        | false         | true    |
| dev         |<PHONE_NUMBER> | dev-qasac-americas.pantheon.io         | false         | false   |
| live        |<PHONE_NUMBER> | live-qasac-americas.pantheon.io        | false         | false   |
| hotfix-sync |<PHONE_NUMBER> | hotfix-sync-qasac-americas.pantheon.io | false         | false   |
+-------------+------------+----------------------------------------+---------------+---------+
$ terminus site clone-env --db --files

------
  12. test-cms
  13. other-site
  14. qasac-americas
  15. wdcpc-new-method

Choose site: 14

  1. dev
  2. test
  3. live

Choose environment you want to clone from: 3

  1. dev
  2. test
  3. live

Choose environment you want to clone to: 1
Are you sure?
	Clone from LIVE to DEV
	Include: DATABASE and FILES
 [y/n] y
Error: The dev environment has not been created yet. run `terminus site create-env [--site=<env>]`

I can confirm this issue. It's only related to cloning to the dev environment and has to do with how the code detects the environment. I'm working on a fix and should have it in today.

Excellent. Thank you!
On March 6, 2015 1:05:25 PM CST, Michael Van Winkle<EMAIL_ADDRESS>wrote:

I can confirm this issue. It's only related to cloning to the dev
environment and has to do with how the code detects the environment.
I'm working on a fix and should have it in today.

Reply to this email directly or view it on GitHub:
https://github.com/pantheon-systems/cli/issues/173#issuecomment-77616096

--
Sent from my Android device with K-9 Mail. Please excuse my brevity.

This is fixed in version 0.5.5
https://github.com/pantheon-systems/cli/releases/tag/0.5.5


little error

Part 2 - S3 Static Hosting
The S3 powershell tools did not get installed by default.  Had to install with command:
Install-Module -Name AWS.Tools.S3

+1 as above


2142 topic markets

Coverage decreased (-0.03%) to 67.513% when pulling 947f86f0167a77d76fd8759c9dc566cf7bac3cd2 on 2142-topic-markets into fb934c819ee5391e7d9a752677a87179419d3773 on master.

Coverage decreased (-0.03%) to 67.513% when pulling 947f86f0167a77d76fd8759c9dc566cf7bac3cd2 on 2142-topic-markets into fb934c819ee5391e7d9a752677a87179419d3773 on master.

Coverage increased (+0.8%) to 68.355% when pulling ed2635054c4e74dfd9d03b2abcc1d278241471c9 on 2142-topic-markets into fb934c819ee5391e7d9a752677a87179419d3773 on master.


RPC docking APi gateway

Excuse me. We have a requirement that requires RPC to also connect to the APi gateway. Is there a corresponding document?

@aqa510415008 Is this RPC over HTTP? If so Ocelot supports http so it should work like any other url structure in a ReRoute.


Upgrade Azure AKS too 1.23.12 + configure autoscaler settings

Summary
This PR upgrades our AKS deployment to Kubernetes 1.23.12. It also disables the ingress controller, external dns and OPA that was being deployed and managed by Azure. Furthermore, it also updates our terraform module to be able to configure settings for the cluster autoscaler managed by Azure.
Test Plan
Local linking
Checklist

[ ]  No images hosted from dockerhub
[ ]  Are dashboards present to understand the health of the application.  There must be at least 1 of these

[ ]  all databases should have dashboards
[ ]  ideally also have at least cpu/mem utilization dashboards for webserver tier of the app
[ ]  you can use plural from-grafana to convert a grafana dashboard found via google to our CRD

[ ]  Are scaling runbooks present

[ ]  all databases must have scaling runbooks
[ ]  you can use the charts in pluralsh/module-library to accelerate this

[ ]  do you need to add config overlays?

[ ]  inputing secrets
[ ]  configuring autoscaling

[ ]  If there’s a web-facing component to the app, we need to support OIDC authentication and setting up private networks if no authentication option is viable
[ ]  All major clouds must be supported

[ ]  Azure
[ ]  AWS
[ ]  GCP

How much testing have we done for this so far?

It's what's deployed on our Azure cluster currently. The main thing that we need to be careful with is not destroying Azure clusters with invalid changes, which isn't the case here.


Material Sorting is not working with different numeric values

Can anyone explain how the material sorting is working? not able to understand the sorting logic.Attached the screenshot.

Angular Version:9.2.4
Material UI Version:9.2.4

This issue doesn't have enough information for the team to investigate. Please include:

A reproduction of the issue (preferably via StackBlitz)
Any relevant errors and stack traces
Any relevant details about your build environment
(this is a canned response)


fmriprep output report does not properly handle multiple resting state runs that differ only in contrast

fmriprep version 20.0.2
I ran an analysis to completion (no errors) that contained a T1w anatomic image and two resting state runs taken in the same session, one before Gd contrast was injected, and one several minutes after.  The subject folder was as follows:
sub-B13293
├── anat
│   ├── sub-B13293_T1w.json
│   └── sub-B13293_T1w.nii.gz
└── func
    ├── sub-B13293_task-rest_ce-Gd_bold.json
    ├── sub-B13293_task-rest_ce-Gd_bold.nii.gz
    ├── sub-B13293_task-rest_ce-none_bold.json
    └── sub-B13293_task-rest_ce-none_bold.nii.gz

As far as I can tell, both files were analyzed properly, and created all the appropriate outputs in the anat and func folders of derivatives/fmriprep /sub-B13293.  The  output files for ce-none and cd-Gd are different, and appear to reflect the actual input files.
sub-B13293
├── anat
│   ├── sub-B13293_desc-brain_mask.json
│   ├── sub-B13293_desc-brain_mask.nii.gz
│   ├── sub-B13293_desc-preproc_T1w.json
│   ├── sub-B13293_desc-preproc_T1w.nii.gz
│   ├── sub-B13293_dseg.nii.gz
│   ├── sub-B13293_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
│   ├── sub-B13293_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
│   ├── sub-B13293_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
│   ├── sub-B13293_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
│   ├── sub-B13293_label-CSF_probseg.nii.gz
│   ├── sub-B13293_label-GM_probseg.nii.gz
│   ├── sub-B13293_label-WM_probseg.nii.gz
│   ├── sub-B13293_space-MNI152NLin2009cAsym_desc-brain_mask.json
│   ├── sub-B13293_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
│   ├── sub-B13293_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
│   ├── sub-B13293_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
│   ├── sub-B13293_space-MNI152NLin2009cAsym_dseg.nii.gz
│   ├── sub-B13293_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
│   ├── sub-B13293_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
│   ├── sub-B13293_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
│   ├── sub-B13293_space-MNI152NLin6Asym_desc-brain_mask.json
│   ├── sub-B13293_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
│   ├── sub-B13293_space-MNI152NLin6Asym_desc-preproc_T1w.json
│   ├── sub-B13293_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz
│   ├── sub-B13293_space-MNI152NLin6Asym_dseg.nii.gz
│   ├── sub-B13293_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
│   ├── sub-B13293_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
│   └── sub-B13293_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
├── figures
│   ├── sub-B13293_desc-reconall_T1w.svg
│   ├── sub-B13293_dseg.svg
│   ├── sub-B13293_space-MNI152NLin2009cAsym_T1w.svg
│   ├── sub-B13293_space-MNI152NLin6Asym_T1w.svg
│   ├── sub-B13293_task-rest_desc-aroma_bold.svg
│   ├── sub-B13293_task-rest_desc-bbregister_bold.svg
│   ├── sub-B13293_task-rest_desc-carpetplot_bold.svg
│   ├── sub-B13293_task-rest_desc-compcorvar_bold.svg
│   ├── sub-B13293_task-rest_desc-confoundcorr_bold.svg
│   ├── sub-B13293_task-rest_desc-flirtbbr_bold.svg
│   ├── sub-B13293_task-rest_desc-rois_bold.svg
│   └── sub-B13293_task-rest_desc-sdc_bold.svg
├── func
│   ├── sub-B13293_task-rest_ce-Gd_AROMAnoiseICs.csv
│   ├── sub-B13293_task-rest_ce-Gd_boldref.nii.gz
│   ├── sub-B13293_task-rest_ce-Gd_desc-MELODIC_mixing.tsv
│   ├── sub-B13293_task-rest_ce-Gd_desc-brain_mask.json
│   ├── sub-B13293_task-rest_ce-Gd_desc-brain_mask.nii.gz
│   ├── sub-B13293_task-rest_ce-Gd_desc-confounds_regressors.json
│   ├── sub-B13293_task-rest_ce-Gd_desc-confounds_regressors.tsv
│   ├── sub-B13293_task-rest_ce-Gd_desc-preproc_bold.json
│   ├── sub-B13293_task-rest_ce-Gd_desc-preproc_bold.nii.gz
│   ├── sub-B13293_task-rest_ce-Gd_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
│   ├── sub-B13293_task-rest_ce-Gd_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│   ├── sub-B13293_task-rest_ce-Gd_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│   ├── sub-B13293_task-rest_ce-Gd_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│   ├── sub-B13293_task-rest_ce-Gd_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│   ├── sub-B13293_task-rest_ce-Gd_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
│   ├── sub-B13293_task-rest_ce-Gd_space-T1w_boldref.nii.gz
│   ├── sub-B13293_task-rest_ce-Gd_space-T1w_desc-brain_mask.json
│   ├── sub-B13293_task-rest_ce-Gd_space-T1w_desc-brain_mask.nii.gz
│   ├── sub-B13293_task-rest_ce-Gd_space-T1w_desc-preproc_bold.json
│   ├── sub-B13293_task-rest_ce-Gd_space-T1w_desc-preproc_bold.nii.gz
│   ├── sub-B13293_task-rest_ce-none_AROMAnoiseICs.csv
│   ├── sub-B13293_task-rest_ce-none_boldref.nii.gz
│   ├── sub-B13293_task-rest_ce-none_desc-MELODIC_mixing.tsv
│   ├── sub-B13293_task-rest_ce-none_desc-brain_mask.json
│   ├── sub-B13293_task-rest_ce-none_desc-brain_mask.nii.gz
│   ├── sub-B13293_task-rest_ce-none_desc-confounds_regressors.json
│   ├── sub-B13293_task-rest_ce-none_desc-confounds_regressors.tsv
│   ├── sub-B13293_task-rest_ce-none_desc-preproc_bold.json
│   ├── sub-B13293_task-rest_ce-none_desc-preproc_bold.nii.gz
│   ├── sub-B13293_task-rest_ce-none_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
│   ├── sub-B13293_task-rest_ce-none_space-MNI152NLin6Asym_res-2_boldref.nii.gz
│   ├── sub-B13293_task-rest_ce-none_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
│   ├── sub-B13293_task-rest_ce-none_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
│   ├── sub-B13293_task-rest_ce-none_space-MNI152NLin6Asym_res-2_desc-preproc_bold.json
│   ├── sub-B13293_task-rest_ce-none_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
│   ├── sub-B13293_task-rest_ce-none_space-T1w_boldref.nii.gz
│   ├── sub-B13293_task-rest_ce-none_space-T1w_desc-brain_mask.json
│   ├── sub-B13293_task-rest_ce-none_space-T1w_desc-brain_mask.nii.gz
│   ├── sub-B13293_task-rest_ce-none_space-T1w_desc-preproc_bold.json
│   └── sub-B13293_task-rest_ce-none_space-T1w_desc-preproc_bold.nii.gz
└── log

However as you can see in the figures folder, only one set of functional figures was produced -  sub-B13293_task-rest_desc*.  This matches the html output file - it says there are two input task-rest files, and shows two sets of images for the registration, confounds, and aroma analysis - but they are identical.  I've done this with datsets that have multiple _task-rest_run_X files, and those are handled properly - the report shows them as unique files.  But somewhere in the generation of the report and figures, it seems to throw away the "ce" BIDS entity and treat the files the same.

I'm wondering if this is actually a niworkflows bug.  Poking around in the fmriprep/interfaces/reports.py line 123 it looks like it gets the information from BIDS_NAME:
        counts = Counter(BIDS_NAME.search(series).groupdict()['task_id'][5:]
                         for series in bold_series)

So that will give the correct number of files, but in niworkflows.utils.bids:
BIDS_NAME = re.compile(
    r'^(.*\/)?'
    '(?P<subject_id>sub-[a-zA-Z0-9]+)'
    '(_(?P<session_id>ses-[a-zA-Z0-9]+))?'
    '(_(?P<task_id>task-[a-zA-Z0-9]+))?'
    '(_(?P<acq_id>acq-[a-zA-Z0-9]+))?'
    '(_(?P<rec_id>rec-[a-zA-Z0-9]+))?'
    '(_(?P<run_id>run-[a-zA-Z0-9]+))?')

BIDS_NAME seems to ignore the ce entity.  Would fixing this line fix the problem?

Certainly we should accept the ce entity, but I can't say for certain that it's the only place we're neglecting it, so this bug may originate elsewhere. Are you comfortable patching and testing?

I'm certainly up for giving it a go.  I'll go fork niworkflows and poke around.

@jdkent can surely help you with this.

I have a little more information on this now - testing this is slow, especially since every time I change the code, all the caches become invalid and it wants to run the entire analysis again (and report generation is the last step!)
As is often the case when debugging, I'm now in the "how did this ever work?" phase.  I've fixed BIDS_NAME to find ce_id, dir_id, and echo_id (the tags that were not being parsed), but I don't see anywhere that anything other than the task ID (no run_id or anything) gets passed on to the report generator.  It does infer the number of runs (by counting the number of series that match the task_id), but does not use the specific run_id tag anywhere.

@bbfrederick If you're using Docker, use fmriprep-docker -f $FMRIPREP_REPO/fmriprep -n $NIWORKFLOWS_REPO/niworkflows to patch these into an already-built container.
Also, one thing you'll probably need to do is update:
diff --git a/niworkflows/reports/figures.json b/niworkflows/reports/figures.json
index 7122243d0..4551f1786 100644
--- a/niworkflows/reports/figures.json
+++ b/niworkflows/reports/figures.json
@@ -113,6 +113,6 @@

     "default_path_patterns": [
         "sub-{subject}[/ses-{session}]/{datatype<anat|figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{contrast}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask>}.{extension<html|svg>}",
-        "sub-{subject}[/ses-{session}]/{datatype<func|figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_desc-{desc}]_{suffix<bold>}.{extension<html|svg>}"
+        "sub-{subject}[/ses-{session}]/{datatype<func|figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{contrast}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_desc-{desc}]_{suffix<bold>}.{extension<html|svg>}"
     ]
 }

This should allow CE agent to be added to the figure. It's possible that this is all that will be necessary for the report generator to figure it out.

Hi @bbfrederick, one more thing to help isolate this bug, inside the working directory there should be a directory named reportlets. Could you give the tree output for the participant sub-B13293 within the reportlets directory.
This will help differentiate: A) the situation where the ce- svg/html files are not being created, versus B) the svg files are created, but are incorrectly processed in some way for the report creation.
Thank you for debugging this!

Ah!  It's B.
[bbf-mbp16:MR_data/workdirs/prepostgad] frederic% tree reportlets
reportlets
└── fmriprep
    └── sub-B13293
        ├── anat
        │   ├── sub-B13293_desc-about_T1w.html
        │   ├── sub-B13293_desc-conform_T1w.html
        │   ├── sub-B13293_desc-summary_T1w.html
        │   ├── sub-B13293_dseg.svg
        │   ├── sub-B13293_space-MNI152NLin2009cAsym_T1w.svg
        │   └── sub-B13293_space-MNI152NLin6Asym_T1w.svg
        └── func
            ├── sub-B13293_task-rest_ce-Gd_desc-aroma_bold.svg
            ├── sub-B13293_task-rest_ce-Gd_desc-carpetplot_bold.svg
            ├── sub-B13293_task-rest_ce-Gd_desc-compcorvar_bold.svg
            ├── sub-B13293_task-rest_ce-Gd_desc-confoundcorr_bold.svg
            ├── sub-B13293_task-rest_ce-Gd_desc-flirtbbr_bold.svg
            ├── sub-B13293_task-rest_ce-Gd_desc-rois_bold.svg
            ├── sub-B13293_task-rest_ce-Gd_desc-sdc_bold.svg
            ├── sub-B13293_task-rest_ce-Gd_desc-summary_bold.html
            ├── sub-B13293_task-rest_ce-Gd_desc-validation_bold.html
            ├── sub-B13293_task-rest_ce-none_desc-aroma_bold.svg
            ├── sub-B13293_task-rest_ce-none_desc-carpetplot_bold.svg
            ├── sub-B13293_task-rest_ce-none_desc-compcorvar_bold.svg
            ├── sub-B13293_task-rest_ce-none_desc-confoundcorr_bold.svg
            ├── sub-B13293_task-rest_ce-none_desc-flirtbbr_bold.svg
            ├── sub-B13293_task-rest_ce-none_desc-rois_bold.svg
            ├── sub-B13293_task-rest_ce-none_desc-sdc_bold.svg
            ├── sub-B13293_task-rest_ce-none_desc-summary_bold.html
            └── sub-B13293_task-rest_ce-none_desc-validation_bold.html

4 directories, 24 files

ah, I think this needs to be changed in figures.json to be in line with pybids, that is at least one of the places.
diff --git a/niworkflows/reports/figures.json b/niworkflows/reports/figures.json
index 7122243..866d716 100644
--- a/niworkflows/reports/figures.json
+++ b/niworkflows/reports/figures.json
@@ -21,7 +21,7 @@
             "pattern": "[_/\\\\]acq-([a-zA-Z0-9]+)"
         },
         {
-            "name": "ce",
+            "name": "ceagent",
             "pattern": "[_/\\\\]ce-([a-zA-Z0-9]+)"
         },
         {

@bbfrederick, I think I have the fix for your situation, could you try running (yet again), with my branch/fork of niworkflows? (unless if your fix works, then I will need to re-evaluate).
And to help answer your question about how did this work in the first place, you should take a look in fmriprep.yml to see that fmriprep is looking at the different keys of a bids file.

I tried running your branch, and it complains:
Status: Downloaded newer image for poldracklab/fmriprep:20.0.4
RUNNING: docker run --rm -it -e DOCKER_VERSION_8395080871=19.03.8 -v /Users/frederic/code/niworkflows_jdkent/niworkflows:/usr/local/miniconda/lib/python3.7/site-packages/niworkflows:ro -v /Applications/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /Users/frederic/Dropbox_PHC/MR_data/ucb_data/prepostgad:/data:ro -v /Users/frederic/Dropbox_PHC/MR_data/ucb_data/prepostgad/derivatives:/out -v /Users/frederic/Documents/MR_data/workdirs/prepostgad:/scratch poldracklab/fmriprep:20.0.4 /data /out participant --participant_label=B13293 --mem_mb=24000 --nthreads=8 --omp-nthreads=8 --use-syn-sdc --use-aroma --fs-no-reconall -w /scratch --output-spaces MNI152NLin6Asym:res-2 anat func:res-native
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/fmriprep", line 10, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 296, in main
    opts = get_parser().parse_args()
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 42, in get_parser
    from niworkflows.utils.spaces import Reference, SpatialReferences, OutputReferencesAction
ModuleNotFoundError: No module named 'niworkflows.utils.spaces'
fMRIPrep: Please report errors to https://github.com/poldracklab/fmriprep/issues

It does run my version, however, which I updated with your fix (I have no idea why).  Unfortunately, that didn't seem to fix things either.  I've deleted everything (all work directories and derivative directories) and I'm trying again to see if maybe there was something cached that was causing the issue...

sorry about the error, it may be because the repo /Users/frederic/code/niworkflows_jdkent/ is from my master branch instead of the maint/1.1.x_fix_ceagent branch.
To check this you can type the following:
cd /Users/frederic/code/niworkflows_jdkent/
git branch

if you get something that looks like * master, then type this:
git fetch origin maint/1.1.x_fix_ceagent:maint/1.1.x_fix_ceagent
git checkout maint/1.1.x_fix_ceagent

then it should work more as expected :crossed_fingers:

Ran clean with my version, no joy.  Followed your instructions, switched to your version, deleted the figures directory and most of the associated work directories, again, the problem remains.  So now I'm deleting everything and running completely clean with your version.  I'll report back when done, but I'm not optimistic...  There still seems to be some critical piece missing.

just pushed some new commits, I'm reasonably confident those will address your issue. I locally replicated and repaired the issue on my end.
you can get the new commits with:
cd /Users/frederic/code/niworkflows_jdkent/
git pull origin maint/1.1.x_fix_ceagent

Thank you for your patience!

That did the trick!  Thank you!
In the end, what was the missing bit?
BTW, while you were in there, did you fix it for direction and echo as well?  It looked like those were not handled either.

@bbfrederick If you're still referring to the BIDS_NAME regex, I don't think it's really relevant. (The one place it's used, it's to parse the subject and session, and everything else is ignored anyway.) Please feel free to submit a PR with an updated regular expression, but I don't think it's necessary to hold up @jdkent's PR at this point.
Direction and echo are taken care of in the sections that James was working on that fixed your issue.

I agree.  I'll submit a separate PR after James' patch is applied just to satisfy my OCD.

PR merged on the niworkflows side. If you want this patch in the next fMRIPrep release, could you submit ASAP? Base your branch off of the maint/1.1.x branch.
If you don't care about it being in the next release, let me know and I'll start the release process.

I assume that was directed at @jdkent

@bbfrederick Nope that was directed at you. @jdkent's patch will be in this release.

@bbfrederick The missing bit was @effigies suggestion above, I didn't include it earlier since I didn't know where it was being used until recently.
The relevent bit is here.
The linked code above looks in the reportlets directory and if it finds an svg file, it generates a "bids" valid figure name based on figures.json, and copies the file over. The layout.build_path method is accepting of any key-value pair (i.e., will not raise an error), but it will ignore key-value pairs that are not a part of the default_build_patterns in figures.json, resulting in the bug you identified where the ce- key was being ignored which led to  build_path creating the same filename (e.g., instead of sub-01_task-rest_ce-Gd_bold.svg build_path returned sub-01_task-rest_bold.svg) repeatedly and copying the different files in the reportlets directory to the same filename in the figures directory, overwriting whatever file was there before. For example,
/work/reportlets/.../sub-01_task-rest_ce-Gd_bold.svg -> /fmriprep/.../figures/sub-01_task-rest_bold.svg
/work/reportlets/.../sub-01_task-rest_ce-none_bold.svg -> /fmriprep/.../figures/sub-01_task-rest_bold.svg # The file got overwritten!

Hope that makes sense!
@effigies I actually see some other items to clean in figures.json and I will open a pull request to deal with them.