colors (colours) not working on windows 10

I followed the instructions on setting up. Seemed to install fine, also running (clippyColorsEnabled) in sbt came back as true. I tried using these terminals cmd, gitmsys and powershell. The colors seems the same as before.

note it might be partially working. when compile error occurs on long line, then function name is coloured yellow, and towards the end of the line it changes to purple. if I reduce the one long line to 2 lines, then this time the function name is not coloured yellow, the purple towards the end of the line is still purple.

Thanks for reporting @arobson73
@adamw I did some initial investigation.  For some reason the Ammonite highlighter doesn't properly use the fansi.Attr.Reset param passed here:  https://github.com/softwaremill/scala-clippy/blob/master/plugin/src/main/scala-2.11/com/softwaremill/clippy/DelegatingPosition.scala#L19
Changing to fansi.color.Reset ot fansi.Color.makeAttr(Console.RESET, 0) doesn't do the trick either.
One possible but risky workaround would be to use the "light gray" color here instead of "Reset". However, this may affect output if someone uses custom terminal colors instead of light gray.
I built a snapshot release with this workaround applied.
@arobson73 could you try clippy version 0.5.1-SNAPSHOT? First, please make sure you have snapshot resolver added, for example in your .sbt/clippy.sbt file (the same place where you have defined clippyColorsEnabled := true):
resolvers +=
  "Sonatype OSS Snapshots" at "https://oss.sonatype.org/content/repositories/snapshots"

import com.softwaremill.clippy.ClippySbtPlugin._
resolvers += "Sonatype OSS Snapshots" at "https://oss.sonatype.org/content/repositories/snapshots"
clippyColorsEnabled := true
the above is now in my ~.sbt\0.13\build.sbt
is this correct ?
still seems to grab the 0.5.0 version
[debug] Calling Scala compiler with arguments  (CompilerInterface):
[debug]         -P:clippy:colors=true
[debug]         -Xplugin:C:\Users\andy.ivy2\cache\com.softwaremill.clippy\plugin_2.12\jars\plugin_2.12-0.5.0-bundle.jar
[debug]         -bootclasspath

@arobson73 you also need to change version to 0.5.1-SNAPSHOT in .sbt/0.13/plugins/build.sbt

yes tried that. here is my .sbt/0.13/plugins/build.sbt
addSbtPlugin("com.softwaremill.clippy" % "plugin-sbt" % "0.5.1-SNAPSHOT")
here is my .sbt/0.13/build.sbt
resolvers += "Sonatype OSS Snapshots" at "https://oss.sonatype.org/content/repositories/snapshots"
import com.softwaremill.clippy.ClippySbtPlugin._
clippyColorsEnabled := true
here is the error I keep getting
[info] Loading global plugins from C:\Users\andy.sbt\0.13\plugins
[info] Updating {file:/C:/Users/andy/.sbt/0.13/plugins/}global-plugins...
[info] Resolving com.softwaremill.clippy#plugin-sbt;0.5.1-SNAPSHOT ...
[warn]  module not found: com.softwaremill.clippy#plugin-sbt;0.5.1-SNAPSHOT
[warn] ==== typesafe-ivy-releases: tried
[warn]   https://repo.typesafe.com/typesafe/ivy-releases/com.softwaremill.clippy/plugin-sbt/scala_2.10/sbt_0.13/0.5.1-SNAPSHOT/ivys/ivy.xml
[warn] ==== sbt-plugin-releases: tried
[warn]   https://repo.scala-sbt.org/scalasbt/sbt-plugin-releases/com.softwaremill.clippy/plugin-sbt/scala_2.10/sbt_0.13/0.5.1-SNAPSHOT/ivys/ivy.xml
[warn] ==== local: tried
[warn]   C:\Users\andy.ivy2\local\com.softwaremill.clippy\plugin-sbt\scala_2.10\sbt_0.13\0.5.1-SNAPSHOT\ivys\ivy.xml
[warn] ==== public: tried
[warn]   https://repo1.maven.org/maven2/com/softwaremill/clippy/plugin-sbt_2.10_0.13/0.5.1-SNAPSHOT/plugin-sbt-0.5.1-SNAPSHOT.pom
[info] Resolving org.fusesource.jansi#jansi;1.4 ...
[warn]  ::::::::::::::::::::::::::::::::::::::::::::::
[warn]  ::          UNRESOLVED DEPENDENCIES         ::
[warn]  ::::::::::::::::::::::::::::::::::::::::::::::
[warn]  :: com.softwaremill.clippy#plugin-sbt;0.5.1-SNAPSHOT: not found
[warn]  ::::::::::::::::::::::::::::::::::::::::::::::
[warn]
[warn]  Note: Some unresolved dependencies have extra attributes.  Check that these dependencies exist with the requested attributes.
[warn]          com.softwaremill.clippy:plugin-sbt:0.5.1-SNAPSHOT (scalaVersion=2.10, sbtVersion=0.13)
[warn]
[warn]  Note: Unresolved dependencies path:
[warn]          com.softwaremill.clippy:plugin-sbt:0.5.1-SNAPSHOT (scalaVersion=2.10, sbtVersion=0.13) (C:\Users\andy.sbt\0.13\plugins\build.sbt#L1-2)
[warn]            +- org.scala-sbt:global-plugins:0.0 (scalaVersion=2.10, sbtVersion=0.13)
[trace] Stack trace suppressed: run last :update for the full output.
[error] (:update) sbt.ResolveException: unresolved dependency: com.softwaremill.clippy#plugin-sbt;0.5.1-SNAPSHOT: not found
Project loading failed: (r)etry, (q)uit, (l)ast, or (i)gnore?

@arobson73 looks like snapshots repo is not being used. Could you also add the resolver line:
resolvers +=
 "Sonatype OSS Snapshots" at "https://oss.sonatype.org/content/repositories/snapshots"

to .sbt/0.13/plugins/build.sbt ?

looks better now. thanks


Added basic tests for ActionServer.

Let me know if you prefer to have the source for tests to run through babel as well.

Doesn't look like Circle-CI is enabled on pull requests, I would do that before merging this one.

could you open another PR? i've enabled CI builds on PR.


datable compost: Replace straight quotes with apostrophe

https://www.carbondesignsystem.com/components/data-table/code
@alisonjoseph
see below: "Maureen’s VM Groups..."

This is pulling in from the core carbon library, transferring the issue over to that repo


Switch checkpointing to time based system

This could avoid a lot of headaches - due to the priority queue it should already be a simple addition

Done!


Mismatching Field Width: Line 1036 of schema_fgdb_v2.py

Hey Tom and Jason,
My spam continues...
Regarding line 1036 in the schema_fgdb_v2.py file:
https://github.com/NENA911/NG911GISDataModel/blob/986686da9ae68cdcadf9766cd5943f93969fbbf9/esri_geodatabase/NENA_NG911_Scripts/schema/schema_fgdb_v2.py#L1036-L1037
In the GIS Data Model, the field width for St_PreDir field is capped at 9 characters, but the schema template on line 1036 reflects 10 characters:

-- David L.

This is an error in NENA-STA-006.2-2022, the French directionals include lengths that are 10-characters long. It will be addressed in NENA-STA-006.2.0.a-2022.

This is an error in NENA-STA-006.2-2022, the French directionals include lengths that are 10-characters long. It will be addressed in NENA-STA-006.2.0.a-2022.


Two players duping at the same time has some problems?

Haven't seen this one, but can test.

Can't reproduce


Database security

If my page cant be found then my database is secured? what do i have to do to disable it?

Yes if they cannot access your database file then they won't be able to access it.

how do i disable my security?

You mean how to make it so that everyone can access the file? If you're using Apache then you can disable it by editing the .htaccess file and removing the whole  block (line 2 to 4).

I cant open .htaccess file.

Open the .htaccess file with a text editor and change it. If it's on a remote webserver then you can first download the .htaccess file, then edit it and then upload it again.

i did it, nothing changed

Then it might be an IIS server, in that case you can just delete the web.config file.

deleted it, still nothing

Then you didn't modify the .htaccess folder correctly, those two are the only files that limit access to the database file. Unless your webhost itself somehow blocks all .db files from being accessed.

There could also be a .htaccess file inside the db folder as well if you didn't edit/remove that, I'm not currently at my computer so I can't check if there is.

why cant i load folders into public html?

can i just copy files without folders?

It depends on how you upload things, some built-in webhost file managers aren't very good. I would recommend using either FTP or seeing if you can extract .zip files in your file manager.
But to disable the .db protection first edit the .htaccess in the main folder and remove the lines (line 2 to 4), then remove the web.config file and then finally remove the .htaccess file inside the db folder if there is a .htaccess there. That should be enough.

Yes all files need to be in their respective folders, but you can usually create folders inside the webhost file manager and copy files into that which was what I meant. Easiest way to upload is usually via FTP or .zip extraction if supported.

yeah i extracted them in their respective folders, but it was only working when i put db into publilc_html

Yes everything needs to look like this https://github.com/UnamSanctam/UnamWebPanel/tree/master/UnamWebPanel (folders and files) for it to work.

yes everything looks fine, but not working

What isn't working, the webpanel or trying to disable the database security?

You mean mysite.com/db/unamwebpanel.db? Is it still forbidden?

oh, yeah i forgot that i put it back into the folder. Its working now its just a white screen

cant see the login screen when i go to my site just a white screen. What should i do? PHP version is 8

Well your file sizes don't look correct in your latest screenshot, open up the files in the file manager there and see what they contain.

i have an error and i cant find logs in the unam lib folder. chrome says my site is deceptive

Which error? And Chrome "malicious/deceptive" site detection is based on URLs usually, so your URL has been scanned/reported and placed into a blacklist. Though that won't affect the miner in any way.

application error

Then it sounds like not all files have been uploaded correctly.

Everything seems to be on the place

Then it should be working, for 000webhost (which it looks like you might be using) then all you need to do for it to work is to

Change PHP version to 7.4 or above
Upload all the files
Then everything will work.

yes, ty. When i copied all these files the original .htaccess file was missing


XML/JSON parsers should fail for the elements that can't be recognised.

We make use of HAPI parsers for the validation purpose. Right now parsers accept content that contains unsupported elements (it ignores such elements). For example content below passes validation:
<Patient>
    <someUnsupportedElement/>
</Patient>

Is it possible to configure parsers so it fails in mentioned scenario.

It's the same problem with single element added twice for example:

FYI- My plan for addressing this issue is to add a 'strict' mode to the parser, probably next week some time.
Per a discussion with Bill De Beaubien, we should also error out if a resource contains an empty tag (i.e. no term)

Is it still on your roadmap? Will this be a part of 1.0 or 1.1 release?

Hi All,
This is still very much on the roadmap. Unfortunately it did not make it in
for the 1.0 release, which I wanted to get out quickly because there are a
few minor breaking API changes needed for the harmonization work we're
doing with the HL7.org Java RI. This should land in the development builds
fairly soon.
Cheers,
James
On Thu, May 14, 2015 at 8:19 AM, izi<EMAIL_ADDRESS>wrote:

Is it still on your roadmap? Will this be a part of 1.0 or 1.1 release?
—
Reply to this email directly or view it on GitHub
https://github.com/jamesagnew/hapi-fhir/issues/152#issuecomment-102018977
.


target pitch issue after training (not appearing if using the pretrained checkpoint)

Hi, I'm running trainings with and w/o using the pretained checkpoint (VCTK) as initial state. However, in both cases the target pitch is affected by the input pitch (e.g. from female to male conversion, the target pitch will be higher, like somewhere between the source and target speakers range). This was not happening with the pre-trained model itself. Would you mind to share some comments on things that were considered to trained the pre-trrained model that may be missing in the paper or here in this repository?, did you experience this in your experimentation?, thanks in advance.

I think your speakers should be recorded with many different pitches, not just 1 pitch, I think this can be fixed


Added Resource (YouTube Video) for Spring Boot Master Class.( changes made )

What does this PR do?
Add resource(s)
For resources
Description
It is a YouTube Video for Spring Boot Tutorail
Why is this valuable (or not)?
It is a free, comprehensive resource for people wishing to learn Spring Boot.
How do we know it's really free?
It is available on YouTube, a public platform.
For book lists, is it a book? For course lists, is it a course? etc.
It is a course.
Checklist:

[x] Read our contributing guidelines.
[x] Search for duplicates.
[x] Include author(s) and platform where appropriate.
[x] Put lists in alphabetical order, correct spacing.
[x] Add needed indications (PDF, access notes, under construction).
[x] Used an informative name for this pull request.

Follow-up

Check the status of GitHub Actions and resolve any reported warnings!

when you've made changes, please add (changes made) to the title of your PR

Hi @eshellman , changes have been made to the PR as per the review comments. Thanks!


The End of the game screen contains a button Go to Overview. Upon clicking the button the user is directed to the Overview Screen.

commit: 2ef404b


Getting Error AlreadyAllocated calling waveInOpen ..

Getting this error every time when i start recording.
AlreadyAllocated calling waveInOpen   at NAudio.Wave.WaveIn.OpenWaveInDevice()

I think this error can occur when another program is also trying to record from the same device. I think some device drivers don't support multiple applications recording at once.


v2.0.0-alpha3 Most icons missing from the release

icon directory contains svg only instead of items, skills, spells, svg

Intentionally removed, a migration will be performed.


Add chef-server logs to buildkite

Description
This PR adds the ability to capture content to buildkite from integration test instances on failure
Signed-off-by: Christopher A. Snapp<EMAIL_ADDRESS>Issues Resolved
#1959
Check List

[ ] New functionality includes tests
[ ] All buildkite tests pass
[ ] Full omnibus build and tests in buildkite pass
[ ] All commits have been signed-off for the Developer Certificate of Origin. See https://github.com/chef/chef/blob/master/CONTRIBUTING.md#developer-certification-of-origin-dco
[ ] PR title is a worthy inclusion in the CHANGELOG

An example of this in action can be found on this failed scenario:
https://buildkite.com/chef/chef-chef-server-master-integration-test/builds/90#cf75115c-ec50-4845-8cae-2a7771fd696a


Shell command exited with exit status 2 instead of 0.

integrating fastlane with sonarqube using https://docs.fastlane.tools/actions/sonar/
this log:
42s
Run fastlane deploy_to_sonarqube
fastlane deploy_to_sonarqube
shell: /bin/bash -e {0}
env:
JAVA_HOME_11.0.12_x64: /Users/runner/hostedtoolcache/jdk/11.0.12/x64
JAVA_HOME: /Users/runner/hostedtoolcache/jdk/11.0.12/x64
JAVA_HOME_11_0_12_X64: /Users/runner/hostedtoolcache/jdk/11.0.12/x64
[08:58:27]: fastlane detected a Gemfile in the current directory
[08:58:27]: However, it seems like you didn't use bundle exec
[08:58:27]: To launch fastlane faster, please use
[08:58:27]:
[08:58:27]: $ bundle exec fastlane deploy_to_sonarqube
[08:58:27]:
[08:58:27]: Get started using a Gemfile for fastlane https://docs.fastlane.tools/getting-started/ios/setup/#use-a-gemfile
[08:58:29]: ------------------------------
[08:58:29]: --- Step: default_platform ---
[08:58:29]: ------------------------------
[08:58:29]: Driving the lane 'android deploy_to_sonarqube' 🚀
[08:58:29]: -------------------
[08:58:29]: --- Step: sonar ---
[08:58:29]: -------------------
[08:58:32]: ▸ INFO: Scanner configuration file: /usr/local/Cellar/sonar-scanner/<IP_ADDRESS>2_1/libexec/conf/sonar-scanner.properties
[08:58:32]: ▸ INFO: Project root configuration file: NONE
[08:58:32]: ▸ INFO: SonarScanner <IP_ADDRESS>2
[08:58:32]: ▸ INFO: Java 11.0.12 Homebrew (64-bit)
[08:58:32]: ▸ INFO: Mac OS X 10.15.7 x86_64
[08:58:33]: ▸ INFO: User cache: /Users/runner/.sonar/cache
[08:58:36]: ▸ INFO: Scanner configuration file: /usr/local/Cellar/sonar-scanner/<IP_ADDRESS>2_1/libexec/conf/sonar-scanner.properties
[08:58:36]: ▸ INFO: Project root configuration file: NONE
[08:58:36]: ▸ INFO: Analyzing on SonarCloud
[08:58:36]: ▸ INFO: Default locale: "en_US", source code encoding: "UTF-8" (analysis is platform dependent)
[08:58:36]: ▸ INFO: Load global settings
[08:58:37]: ▸ INFO: Load global settings (done) | time=556ms
[08:58:37]: ▸ INFO: Server id: 1BD809FA-AWHW8ct9-T_TB3XqouNu
[08:58:37]: ▸ INFO: User cache: /Users/runner/.sonar/cache
[08:58:37]: ▸ INFO: Load/download plugins
[08:58:37]: ▸ INFO: Load plugins index
[08:58:37]: ▸ INFO: Load plugins index (done) | time=135ms
[08:59:04]: ▸ INFO: Load/download plugins (done) | time=27804ms
[08:59:05]: ▸ INFO: Loaded core extensions: developer-scanner
[08:59:05]: ▸ INFO: Found an active CI vendor: 'Github Actions'
[08:59:05]: ▸ INFO: Load project settings for component key: 'com.exa.nanashopper'
[08:59:05]: ▸ INFO: Process project properties
[08:59:05]: ▸ ERROR: Invalid value of sonar.sources for com.exa.nanashopper
[08:59:05]: ▸ INFO: ------------------------------------------------------------------------
[08:59:05]: ▸ INFO: EXECUTION FAILURE
[08:59:05]: ▸ INFO: ------------------------------------------------------------------------
[08:59:05]: ▸ INFO: Total time: 33.249s
[08:59:05]: ▸ INFO: Final Memory: 6M/24M
[08:59:05]: ▸ INFO: ------------------------------------------------------------------------
[08:59:05]: ▸ ERROR: Error during SonarScanner execution
[08:59:05]: ▸ ERROR: The folder '/Users/runner/work/android-shopperapp/android-shopperapp/NanaApp' does not exist for 'com.exa.nanashopper' (base directory = /Users/runner/work/android-shopperapp/android-shopperapp)
[08:59:05]: ▸ ERROR:
[08:59:05]: ▸ ERROR: Re-run SonarScanner using the -X switch to enable full debug logging.
+------------------+-----------------------------+
|                  Lane Context                  |
+------------------+-----------------------------+
| DEFAULT_PLATFORM | android                     |
| PLATFORM_NAME    | android                     |
| LANE_NAME        | android deploy_to_sonarqube |
+------------------+-----------------------------+
[08:59:05]: Shell command exited with exit status 2 instead of 0.
INFO: Scanner configuration file: /usr/local/Cellar/sonar-scanner/<IP_ADDRESS>2_1/libexec/conf/sonar-scanner.properties
INFO: Project root configuration file: NONE
INFO: SonarScanner <IP_ADDRESS>2
INFO: Java 11.0.12 Homebrew (64-bit)
INFO: Mac OS X 10.15.7 x86_64
INFO: User cache: /Users/runner/.sonar/cache
INFO: Scanner configuration file: /usr/local/Cellar/sonar-scanner/<IP_ADDRESS>2_1/libexec/conf/sonar-scanner.properties
INFO: Project root configuration file: NONE
INFO: Analyzing on SonarCloud
INFO: Default locale: "en_US", source code encoding: "UTF-8" (analysis is platform dependent)
INFO: Load global settings
INFO: Load global settings (done) | time=556ms
INFO: Server id: 1BD809FA-AWHW8ct9-T_TB3XqouNu
INFO: User cache: /Users/runner/.sonar/cache
INFO: Load/download plugins
INFO: Load plugins index
INFO: Load plugins index (done) | time=135ms
INFO: Load/download plugins (done) | time=27804ms
INFO: Loaded core extensions: developer-scanner
INFO: Found an active CI vendor: 'Github Actions'
INFO: Load project settings for component key: 'com.exa.nanashopper'
INFO: Process project properties
ERROR: Invalid value of sonar.sources for com.exa.nanashopper
INFO: ------------------------------------------------------------------------
INFO: EXECUTION FAILURE
INFO: ------------------------------------------------------------------------
INFO: Total time: 33.249s
INFO: Final Memory: 6M/24M
INFO: ------------------------------------------------------------------------
ERROR: Error during SonarScanner execution
ERROR: The folder '/Users/runner/work/android-shopperapp/android-shopperapp/NanaApp' does not exist for 'com.exa.nanashopper' (base directory = /Users/runner/work/android-shopperapp/android-shopperapp)
ERROR:
ERROR: Re-run SonarScanner using the -X switch to enable full debug logging.
+------+------------------+-------------+
|           fastlane summary            |
+------+------------------+-------------+
| Step | Action           | Time (in s) |
+------+------------------+-------------+
| 1    | default_platform | 0           |
| 💥   | sonar            | 36          |
+------+------------------+-------------+
[08:59:05]: fastlane finished with errors
Looking for related GitHub issues on fastlane/fastlane...
#######################################################################
fastlane 2.193.1 is available.
You should use the latest version.
Please update using gem install fastlane.
#######################################################################
2.193.1 Improvements

[gradle] add output context with "tasks" options (#19312) via David Kuo
[match] ignore force_for_new_devices for developer_id provisioning type (#19314) via Vitalii Budnik
[match] don't force update macos development certs if macos device count unchanged (#19315) via Vitalii Budnik
[pilot][upload_to_testflight] add missing method (#19319) via David Brunow

Please update using gem install fastlane
/usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane_core/lib/fastlane_core/ui/interface.rb:153:in shell_error!': \e[31m[!] Shell command exited with exit status 2 instead of 0. (FastlaneCore::Interface::FastlaneShellError) INFO: Scanner configuration file: /usr/local/Cellar/sonar-scanner/<IP_ADDRESS>2_1/libexec/conf/sonar-scanner.properties INFO: Project root configuration file: NONE INFO: SonarScanner <IP_ADDRESS>2 INFO: Java 11.0.12 Homebrew (64-bit) INFO: Mac OS X 10.15.7 x86_64 INFO: User cache: /Users/runner/.sonar/cache INFO: Scanner configuration file: /usr/local/Cellar/sonar-scanner/<IP_ADDRESS>2_1/libexec/conf/sonar-scanner.properties INFO: Project root configuration file: NONE INFO: Analyzing on SonarCloud INFO: Default locale: "en_US", source code encoding: "UTF-8" (analysis is platform dependent) INFO: Load global settings INFO: Load global settings (done) | time=556ms INFO: Server id: 1BD809FA-AWHW8ct9-T_TB3XqouNu INFO: User cache: /Users/runner/.sonar/cache INFO: Load/download plugins INFO: Load plugins index INFO: Load plugins index (done) | time=135ms INFO: Load/download plugins (done) | time=27804ms INFO: Loaded core extensions: developer-scanner INFO: Found an active CI vendor: 'Github Actions' INFO: Load project settings for component key: 'com.exa.nanashopper' INFO: Process project properties ERROR: Invalid value of sonar.sources for com.exa.nanashopper INFO: ------------------------------------------------------------------------ INFO: EXECUTION FAILURE INFO: ------------------------------------------------------------------------ INFO: Total time: 33.249s INFO: Final Memory: 6M/24M INFO: ------------------------------------------------------------------------ ERROR: Error during SonarScanner execution ERROR: The folder '/Users/runner/work/android-shopperapp/android-shopperapp/NanaApp' does not exist for 'com.exa.nanashopper' (base directory = /Users/runner/work/android-shopperapp/android-shopperapp) ERROR:  ERROR: Re-run SonarScanner using the -X switch to enable full debug logging. \e[0m 	from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane_core/lib/fastlane_core/ui/ui.rb:17:in method_missing'
from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/helper/sh_helper.rb:80:in sh_control_output' 	from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/actions/sonar.rb:38:in run'
from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/runner.rb:263:in block (2 levels) in execute_action' 	from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/actions/actions_helper.rb:69:in execute_action'
from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/runner.rb:255:in block in execute_action' 	from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/runner.rb:229:in chdir'
from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/runner.rb:229:in execute_action' 	from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/runner.rb:157:in trigger_action_by_name'
from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/fast_file.rb:159:in method_missing' 	from Fastfile:68:in block (2 levels) in parsing_binding'
from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/lane.rb:33:in call' 	from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/runner.rb:49:in block in execute'
from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/runner.rb:45:in chdir' 	from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/runner.rb:45:in execute'
from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/lane_manager.rb:47:in cruise_lane' 	from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/command_line_handler.rb:36:in handle'
from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/commands_generator.rb:109:in block (2 levels) in run' 	from /usr/local/lib/ruby/gems/2.7.0/gems/commander-4.6.0/lib/commander/command.rb:187:in call'
from /usr/local/lib/ruby/gems/2.7.0/gems/commander-4.6.0/lib/commander/command.rb:157:in run' 	from /usr/local/lib/ruby/gems/2.7.0/gems/commander-4.6.0/lib/commander/runner.rb:444:in run_active_command'
from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane_core/lib/fastlane_core/ui/fastlane_runner.rb:117:in run!' 	from /usr/local/lib/ruby/gems/2.7.0/gems/commander-4.6.0/lib/commander/delegates.rb:18:in run!'
from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/commands_generator.rb:353:in run' 	from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/commands_generator.rb:42:in start'
from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/fastlane/lib/fastlane/cli_tools_distributor.rb:122:in take_off' 	from /usr/local/lib/ruby/gems/2.7.0/gems/fastlane-2.193.0/bin/fastlane:23:in <top (required)>'
from /usr/local/lib/ruby/gems/2.7.0/bin/fastlane:25:in load' 	from /usr/local/lib/ruby/gems/2.7.0/bin/fastlane:25:in '
Error: Process completed with exit code 1.

Traceback (most recent call last):
        36: from /usr/local/bin/fastlane:23:in `<main>'
        35: from /usr/local/bin/fastlane:23:in `load'
        34: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/bin/fastlane:23:in `<top (required)>'
        33: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/cli_tools_distributor.rb:122:in `take_off'
        32: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/commands_generator.rb:42:in `start'
        31: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/commands_generator.rb:353:in `run'
        30: from /Library/Ruby/Gems/2.6.0/gems/commander-4.6.0/lib/commander/delegates.rb:18:in `run!'
        29: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane_core/lib/fastlane_core/ui/fastlane_runner.rb:117:in `run!'
        28: from /Library/Ruby/Gems/2.6.0/gems/commander-4.6.0/lib/commander/runner.rb:444:in `run_active_command'
        27: from /Library/Ruby/Gems/2.6.0/gems/commander-4.6.0/lib/commander/command.rb:157:in `run'
        26: from /Library/Ruby/Gems/2.6.0/gems/commander-4.6.0/lib/commander/command.rb:187:in `call'
        25: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/commands_generator.rb:109:in `block (2 levels) in run'
        24: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/command_line_handler.rb:36:in `handle'
        23: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/lane_manager.rb:47:in `cruise_lane'
        22: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/runner.rb:45:in `execute'
        21: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/runner.rb:45:in `chdir'
        20: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/runner.rb:49:in `block in execute'
        19: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/lane.rb:33:in `call'
        18: from Fastfile:38:in `block (2 levels) in parsing_binding'
        17: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/fast_file.rb:159:in `method_missing'
        16: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/runner.rb:146:in `trigger_action_by_name'
        15: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/runner.rb:204:in `try_switch_to_lane'
        14: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/lane.rb:33:in `call'
        13: from Fastfile_Generic:22:in `block (2 levels) in parsing_binding'
        12: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/fast_file.rb:159:in `method_missing'
        11: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/runner.rb:157:in `trigger_action_by_name'
        10: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/runner.rb:229:in `execute_action'
         9: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/runner.rb:229:in `chdir'
         8: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/runner.rb:255:in `block in execute_action'
         7: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/actions/actions_helper.rb:69:in `execute_action'
         6: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/runner.rb:263:in `block (2 levels) in execute_action'
         5: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/actions/gradle.rb:60:in `run'
         4: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/helper/gradle_helper.rb:32:in `trigger'
         3: from /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/forwardable.rb:230:in `sh'
         2: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane/lib/fastlane/helper/sh_helper.rb:80:in `sh_control_output'
         1: from /Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane_core/lib/fastlane_core/ui/ui.rb:17:in `method_missing'
/Library/Ruby/Gems/2.6.0/gems/fastlane-2.194.0/fastlane_core/lib/fastlane_core/ui/interface.rb:153:in `shell_error!': [!] Shell command exited with exit status 1 instead of 0. (FastlaneCore::Interface::FastlaneShellError)

<details><summary>🚫 fastlane environment 🚫</summary>

### Stack

| Key                         | Value                                                          |
| --------------------------- | -------------------------------------------------------------- |
| OS                          | 11.5.2                                                         |
| Ruby                        | 2.6.3                                                          |
| Bundler?                    | false                                                          |
| Git                         | git version 2.23.0                                             |
| Installation Source         | /usr/local/bin/fastlane                                        |
| Host                        | macOS 11.5.2 (20G95)                                           |
| Ruby Lib Dir                | /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib |
| OpenSSL Version             | LibreSSL 2.8.3                                                 |
| Is contained                | false                                                          |
| Is homebrew                 | false                                                          |
| Is installed via Fabric.app | false                                                          |
| Xcode Path                  | /Library/Developer/CommandLineTools/                           |
| Xcode Version               |                                                                |
| Swift Version               | 5.3.2                                                          |

### System Locale

| Error                       |
| --------------------------- |
| No Locale with UTF8 found 🚫 |

### fastlane files:

<details><summary>`./fastlane/Fastfile`</summary>

```ruby
# This file contains the fastlane.tools configuration
# You can find the documentation at https://docs.fastlane.tools
#
# For a list of all available actions, check out
#
#     https://docs.fastlane.tools/actions
#
# For a list of all available plugins, check out
#
#     https://docs.fastlane.tools/plugins/available-plugins
#
import("./Fastfile_Before")
import("./Fastfile_Generic")

default_platform(:android)

platform :android do

  desc "Run Unit Tests"
    lane :unit_tests do
      assemble(
        build_task: "test",
        build_flavor: "dev",
        build_type: "Debug"
      )
  end

  desc "Run Instrumented tests"
    lane :instrumented_tests do
      gradle(task: "connectedProdDebugAndroidTest")
  end

  desc "Distribute a new version on Firebase"
  lane :distribute_firebase do |options|
    build_type = options[:type] || "APK"
    build_task = (build_type == "AAB" ? "bundle" : "assemble")

    assemble(
      build_task: build_task,
      build_flavor: "Dev",
      build_type: "Release"
    )

    upload_to_firebase(
        release_notes: options[:release_notes],
        build_type: build_type
    )

    message = getBuildVersion() + " is ready to test on AppTester (Firebase) !"
    post_success_on_slack(message: message)
  end

  desc "Deploy a new version to the Google Play"
  lane :deploy_play_store do |options|
    unit_tests

    assemble(
      build_task: "clean assemble",
      build_flavor: "prod",
      build_type: "Release",
      build_properties: true
    )

   build_track = options[:build_track] || "internal"
   build_rollout = options[:build_track] || 1
   deploy_to_play_store(
    build_track: build_track,
    build_rollout: build_rollout
   )
  end

  desc "Update Strings from POEditor for all projects and subprojects"
  lane :update_strings do

    # Strings for app-pro
    update_loop_strings(
      project_id: ENV["POE_EDITOR_APP_PRO_PROJECT_ID"],
      output_path: ENV["POE_EDITOR_APP_PRO_OUTPUT_PATH"]
    )

    # Strings for adjust_actuators
    update_loop_strings(
      project_id: ENV["POE_EDITOR_ADJUST_ACTUATORS_PROJECT_ID"],
      output_path: ENV["POE_EDITOR_ADJUST_ACTUATORS_OUTPUT_PATH"]
    )

    # Langs not in commun between two projects. Need to be removed in future.
    update_loop_strings(
      langs: ["sk"],
      project_id: ENV["POE_EDITOR_APP_PRO_PROJECT_ID"],
      output_path: ENV["POE_EDITOR_APP_PRO_OUTPUT_PATH"]
    )
  end

  desc "Update XML for adjust_actuators module from Github"
  lane :update_xml do
    sh "./script/class/adjust_actuators/update_xml.sh"
  end
end

`./fastlane/Appfile`
json_key_file("./app/google-services.json") # Path to the json secret file - Follow https://docs.fastlane.tools/actions/supply/#setup to get one
package_name("com.somfy.pro") # e.g. com.krausefx.app

fastlane gems

Gem
Version
Update-Status

fastlane
2.194.0
✅ Up-To-Date

Loaded fastlane plugins:

Plugin
Version
Update-Status

fastlane-plugin-firebase_app_distribution
0.3.1
✅ Up-To-Date

fastlane-plugin-versioning_android
0.1.0
✅ Up-To-Date

fastlane-plugin-poeditor_export
0.3.0
✅ Up-To-Date

Loaded gems

Gem
Version

did_you_mean
1.3.0

atomos
0.1.3

claide
1.0.3

colored2
3.1.2

nanaimo
0.3.0

rexml
3.2.5

xcodeproj
1.21.0

rouge
2.0.7

xcpretty
0.3.0

terminal-notifier
2.0.0

unicode-display_width
1.7.0

terminal-table
1.8.0

plist
3.6.0

public_suffix
4.0.6

addressable
2.8.0

multipart-post
2.0.0

word_wrap
1.0.0

optparse
0.1.1

tty-screen
0.8.1

tty-cursor
0.7.1

tty-spinner
0.9.3

artifactory
3.0.15

babosa
1.0.4

colored
1.2

highline
2.0.3

commander
4.6.0

excon
0.85.0

faraday-em_http
1.0.0

faraday-em_synchrony
1.0.0

faraday-excon
1.1.0

faraday-httpclient
1.0.1

faraday-net_http
1.0.1

faraday-net_http_persistent
1.2.0

faraday-patron
1.0.0

faraday-rack
1.0.0

ruby2_keywords
0.0.5

faraday
1.7.0

unf_ext
<IP_ADDRESS>

unf
0.1.4

domain_name
0.5.20190701

http-cookie
1.0.4

faraday-cookie_jar
0.0.7

faraday_middleware
1.1.0

fastimage
2.2.5

gh_inspector
1.1.3

mini_magick
4.11.0

naturally
2.2.1

rubyzip
2.3.2

security
0.1.3

xcpretty-travis-formatter
1.0.1

dotenv
2.7.6

bundler
2.2.22

simctl
1.6.8

jwt
2.2.3

uber
0.1.0

declarative
0.0.20

trailblazer-option
0.1.1

representable
3.1.1

retriable
3.1.2

mini_mime
1.1.1

memoist
0.16.2

multi_json
1.15.0

os
1.1.1

signet
0.15.0

googleauth
0.17.0

httpclient
2.8.3

google-apis-core
0.4.1

google-apis-playcustomapp_v1
0.5.0

google-apis-androidpublisher_v3
0.10.0

google-cloud-env
1.5.0

google-cloud-errors
1.1.0

google-cloud-core
1.6.0

google-apis-iamcredentials_v1
0.7.0

google-apis-storage_v1
0.6.0

digest-crc
0.6.4

google-cloud-storage
1.34.1

emoji_regex
3.2.2

jmespath
1.4.0

aws-partitions
1.491.0

aws-eventstream
1.1.1

aws-sigv4
1.2.4

aws-sdk-core
3.119.1

aws-sdk-kms
1.46.0

aws-sdk-s3
1.99.0

CFPropertyList
3.0.3

json
2.5.1

webrick
1.7.0

rake
13.0.6

forwardable
1.2.0

logger
1.3.0

date
2.0.0

stringio
0.0.2

ipaddr
1.2.2

openssl
2.1.2

zlib
1.0.0

mutex_m
0.1.0

ostruct
0.1.0

strscan
1.0.0

io-console
0.4.7

fileutils
1.1.0

etc
1.0.1

libxml-ruby
3.1.0

psych
3.1.0

fastlane-plugin-firebase_app_distribution
0.3.1

fastlane-plugin-versioning_android
0.1.0

fastlane-plugin-poeditor_export
0.3.0

generated on: 2021-09-17

```

Hi, I think that you should take a look at deploy_to_sonarqube in your Fastfile. Maybe adjusting sources_path would help?

Comma-separated paths to directories containing source files. Must either be specified here or inside the sonar project configuration file

as written in docs https://docs.fastlane.tools/actions/sonar/
It looks like sonar tries to access directory that doesn't exist:

ERROR: Invalid value of sonar.sources for com.exa.nanashopper
...
ERROR: Error during SonarScanner execution
ERROR: The folder '/Users/runner/work/android-shopperapp/android-shopperapp/NanaApp' does not exist for 'com.exa.nanashopper' (base directory = /Users/runner/work/android-shopperapp/android-shopperapp)

Very informative post. I really do hope and pray this stuff works.


pydantic.mypy reports Unexpected keyword argument

Initial Checks

[X] I confirm that I'm using Pydantic V2

Description
When enabling the pydantic plugin for mypy, a new error appears,
test/c.py:11: error: Unexpected keyword argument "field3" for "F"; did you mean "field1"?  [call-arg]

Two conditions are required to make this occur.

The base class must forbid allow extra values.
There must be a type alias.

Example Code
-- a.py
import pydantic

class F(pydantic.BaseModel):
    model_config = {"extra": "forbid"}

    field1: bool

-- b.py
from . import a

F = a.F

-- c.py
from . import b

class F(b.F):
    field3: bool

f = F(field1=True, field3=False)

Python, Pydantic & OS Version
pydantic version: 2.1.1
        pydantic-core version: 2.4.0
          pydantic-core build: profile=release pgo=false mimalloc=true
                 install path: /Users/michaelfraenkel/workspace/test/.venv/lib/python3.11/site-packages/pydantic
               python version: 3.11.4 (main, Jun 20 2023, 16:59:59) [Clang 14.0.3 (clang-14<IP_ADDRESS>.1)]
                     platform: macOS-13.5-x86_64-i386-64bit
     optional deps. installed: ['typing-extensions']

Selected Assignee: @hramezani

Works fine if you change c.py to
from . import a

class F(a.F):
    field3: bool

f = F(field1=True, field3=False)

On the other hand, if you change these examples to use dataclass, it works fine even with the intermediate model.
@dmontagu any idea if there's some more powerful way to resolve the parent class?

I have no idea. But I would guess the answer is "probably". 😄
But this seems very suspicious, it's very weird to me that it thinks field1 exists and field3 doesn't; I would expect the other way around.
I suspect this will require some painful debugging of the mypy plugin and looking at exactly what's happening. I tried to base most of the metadata storage/retrieval on the dataclasses plugin, but I guess something's out of sync.
Happy to look at this more the next time I work on the mypy plugin, or to review a PR if someone is able to get to the bottom of it sooner.


Socratic Seminar 14 Reading List (March 2023)

Drop links here!

[bitcoin-dev] Ephemeral Anchors: Fixing V3 Package RBF againstpackage limit pinning
https://lists.linuxfoundation.org/pipermail/bitcoin-dev/2023-January/021373.html

https://rollkit.dev/blog/sovereign-rollups-on-bitcoin

Muun submarine swaps quickly expanding UTXO set
https://twitter.com/mononautical/status/1621663167582437376
v3 Transaction Policy + Transaction Pinning
https://github.com/bitcoin/bitcoin/pull/25038
https://bitcoinops.org/en/topics/transaction-pinning/
BOLT 12
https://github.com/lightning/bolts/pull/798

rust-bitcoin v0.30.0 is out https://rust-bitcoin.org/blog/release-0.30.0/
TypeScript library for miniscript descriptors released: The TypeScript-based Bitcoin Descriptors Library has support for PSBTs, descriptors, and miniscript. This includes support for signing directly or when using certain hardware signing devices. (discussion point: Can we do this with rust-bitcoin + wasm?)
BTCPay Server coinjoin plugin released: The Wasabi Wallet announcement notes that any BTCPay Server merchant can activate the optional plugin which supports the WabiSabi protocol for coinjoins.
BDK 1.0.0-alpha #793 is a major restructuring of the library based on the work of the bdk_core sub-project. According to the PR description, it “maintains the existing wallet API as much as possible and adds very little.” Three API endpoints with seemingly minor changes are listed in the PR description. (it has been a long time coming)
Lightning on Blockstream Green presumably using Greenlight, like the new Breez SDK announced in a recent blog post,
mempool.space explorer enhances CPFP support: The mempool.space explorer announced additional support for CPFP-related transactions. showing the CPFP visualization could be a great way to supplement earlier discussions that garnered large interest around fee bumping (rbf). Also, mempools around the world are full!
Bank failure, reactions (https://www.federalreserve.gov/newsevents/pressreleases/monetary20230319a.htm), and FED rate hikes. Printing + rate hikes = 😵💫?
Balaji's PR stunt https://twitter.com/balajis/status/1636822077775941633


SSL test version?

Question, I was at the bsideslv powercat talk.  You were talking about a SSL enabled version that was just having issues with the server side stuff.  I'd love to see about helping out with that, is there any chance you could put what you've worked on in a branch or something?

Ugh, upon doing further research, there doesn't seem to be a good way to add support for TLS 1.1 or 1.2.  Almost everything I'm reading says "Use .net 4.5" which wouldn't work for this.  In other news, I did get a SSL client mode working, and I'm working on a SSL listener mode.  Main issue on listener mode is that you need a x509 cert.  They aren't terribly hard to make, but in the interest of usability, I'm working on some code to auto generate a self signed cert for the listener portion.


127 error code on using backup within Lute

Notes from discord chat:

root@63dce09ff1c7:/# mysqldump --version
mysqldump  Ver 10.19 Distrib 10.7.8-MariaDB, for debian-linux-gnu (aarch64)

Lute v1.1.7
Dump in terminal works:
# mysqldump -u root --password=root lute > /lute/backup.sql
root@63dce09ff1c7:/# cd lute
root@63dce09ff1c7:/lute# ls
backup.sql

Possible solution in https://stackoverflow.com/questions/43772985/php-system-return-127-error-code
If this solution works, need to add some notes to the wiki.
Regardless, should add more error message details to the screen, just showing the code might not be enough.

Closing, with v2 we're moving away from Mysql.


Fix naming of sans family

Fix #21

Thank you for your work!
But some of the test fails due to the existing build error, so I'm going to investigate it ahead of review.
I'm going to create another PR fixing the problem, merge it toward main branch and re-run CI on this PR.

Build error in CI on main branch must be solved on #24 , but the same error occurs... 🤔
The error was solved by refreshing the build cache on GitHub Actions and currently failing job on this PR uses the same cached artifacts.
So I have thought everything should go well, but...

As a workaround, stopped using cache temporarily.


fix: mainnet projection issues

Context
When running projection services on mainnet, we ran into several issues:

Projector stops due to local state queries being unavailable in Byron era
Fails to insert some pool registrations, where cost or pledge exceeds postgres bigint (signed 64bit integer)

Proposed Solution
See commits

Please provide a progress update on the local mainnet sync @mkazlauskas


Fixes in open tracing usage

Signed-off-by: Andrey Sobolev<EMAIL_ADDRESS>
Description
Opentracing should be used properly to ensure context is passing a correct span ids.
Motivation and Context
To see a full trace from client to endpoint. This is first part of improving traces.
How Has This Been Tested?

[x] Covered by existing integration testing
[x] Added integration testing to cover
[x] Tested locally
[ ] Have not tested

Types of changes

[x] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)

Checklist:

[ ] My change requires a change to the documentation.
[ ] I have updated the documentation accordingly.

Please consider moving to util function the code like:
if opentracing.IsGlobalTracerRegistered() {
	span, ctx = opentracing.StartSpanFromContext(ctx, "...")
	defer span.Finish()
}
logger := common.LogFromSpan(span)

But overall looks good

This is not possible, since it need defer, and it still be about 2 lines :-(

@edwarnicke please consider merging this PR, since tests failures are not related to changes.


fix: Track mismatches in compare_dict

Reason for Change

Some times test fails on this check and there is no information to help debug. This track the mismatches between two dicts and prints them out if the any are found. This also use unittest syntax to keep error reporting consistent.

Changes

make compare_dicts errors visible to unittest
rename compare_dicts to assert_dicts_equal

Closing because of issues getting unit tests to pass with this change.


Don't require typing_extensions to be installed

Only needed for testing. Also, not mentioned in pyproject.toml ;-)

Pull Request Test Coverage Report for Build<PHONE_NUMBER>2
Details

0 of 0   changed or added relevant lines in 0 files are covered.
310 unchanged lines in 18 files lost coverage.
Overall coverage decreased (-0.5%) to 82.342%

Files with Coverage Reduction
New Missed Lines
%

opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/mqttproto/sync_client.py
4
89.66%

opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/mqttproto/sync_client.py
4
89.66%

opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/mqttproto/sync_client.py
4
89.66%

opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/mqttproto/sync_client.py
5
89.66%

opt/hostedtoolcache/Python/3.13.0/x64/lib/python3.13/site-packages/mqttproto/sync_client.py
5
89.66%

opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/mqttproto/sync_client.py
5
89.66%

opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/mqttproto/async_client.py
23
84.87%

opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/mqttproto/_types.py
23
96.32%

opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/mqttproto/_types.py
23
96.32%

opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/mqttproto/async_client.py
23
84.87%

Totals

Change from base Build<PHONE_NUMBER>3:
-0.5%

Covered Lines:
8002

Relevant Lines:
9718

💛  - Coveralls

Good catch, but it really should go into the install dependencies. Not having it there may cause a problem when someone else tries to type check their own project where mqttproto is a dependency.

Good enough, though I still think you shouldn't actually import it when type checking isn't active.

I recall there was a linting rule in Ruff that moved all the annotation-only imports under if TYPE_CHECKING. Do I misremember? Perhaps it was in another linter?

Ah, these ones: https://docs.astral.sh/ruff/rules/#flake8-type-checking-tch


Improve performance of shape 1024x1024x1024 out of box

Close https://github.com/intel/intel-xpu-backend-for-triton/issues/2822
After:
90% -> 103%

Any explanation? Does XeTLA use prefetch distance 4?

XeTLA use prefetch distance 3 for all cases, but 3 is not optimum for this Triton case from tuning.


few questions

Hello,
I have few questions regarding clickhouse:
1.What is doing distributed_directory_monitor_batch_inserts ? In case you have it enable and write via a distributed table you don't have to batch the inserts on the client side ?

In case of a replicated table where partition is Date type and also the primary key is a timestamp of DateTime, when you have to search in a certain interval it's better to put in the where clause both ? I mean filter partiton and the timestamp field ? helps somehow ? or it's enough to filter by the timestamp field

Silviu

No, you still need to batch the inserts on the client side.
By default, when you insert data into distributed table, it firstly stores inserted batch as a part on local file system (or set of parts). Then, distributed table sends each part to remote node.
When distributed_directory_monitor_batch_inserts is enabled, distributed table groups parts for the same node into batch and uses single connection, which is usually more effective.
However, without batching the inserts on the client side, you will have a lot of small files on local file system.
If you have timestamp DateTime which is in primary key and partition key like toDate(timestamp), that it's not necessary to use condition with date. If timestamp has no connection with partition key, then use both condition.

Hello @KochetovNicolai ,
Thanks a lot for your answers. In my case partition is toDate(timestamp) so becomes pointless
I initially thought it helps on selecting the partitions that needs to scan but seems only primary key is used. Also in case the primary key is composed from multiple fields when I filter it matters the order I specify them ? Like in SQl database ? I mean if yo have an index (a,b) you need to filter a =? & b = ? not b= ? & a = ?
Silviu

Thanks a lot !


Try to publish unscoped packages too

🌮 Current Behavior

package name (in package.json) is package-a

Wix internal registry will publish:

package-a
@wix/package-a

Public npm registry will publish:

@wix/package-a

package name (in package.json) is @wix/package-a

Wix internal registry will publish:

@wix/package-a

Public npm registry will publish:

@wix/package-a

🤝 New, expected behavior:

package name (in package.json) is package-a

stays the same as before

package name (in package.json) is @wix/package-a

Wix internal registry will publish:

package-a
@wix/package-a

Public npm registry will publish:

@wix/package-a

a package that doesn't have wix internal registry as the publish config registry (like @wix/draft-js, yoshi):

Wix internal registry will publish:

@wix/draft-js

Public npm registry will publish:

@wix/draft-js

cc @yairhaimo @mastertheblaster

Great job, but maybe you would like some safety trigger to quickly disable this feature? For example using some ENV variable.

Thanks for this awesome review, @mastertheblaster 😸
I still have an open question: why should I update lockfiles when I publish the unscoped packages?


Consolidate jobs in one workflow

every job now has dedicated shell script under ./tools/ci/
there is one main workflow "Build and Test"

Pre-Review Checklist for the PR Author

[x] Code follows the coding style of CONTRIBUTING.md
[x] Tests follow the best practice for testing
[x] Changelog updated in the unreleased section including API breaking changes
[x] Branch follows the naming format (iox-#123-this-is-a-branch)
[x] Commits messages are according to this guideline

[x] Commit messages have the issue ID (iox-#123 commit text)
[x] Commit messages are signed (git commit -s)
[x] Commit author matches Eclipse Contributor Agreement (and ECA is signed)

[x] Update the PR title

Follow the same conventions as for commit messages
Link to the relevant issue

[x] Relevant issues are linked
[x] Add sensible notes for the reviewer
[x] All checks have passed (except task-list-completed)
[x] Assign PR to reviewer

Notes for Reviewer

Checklist for the PR Reviewer

[ ] Commits are properly organized and messages are according to the guideline
[ ] Code according to our coding style and naming conventions
[ ] Unit tests have been written for new behavior
[ ] Public API changes are documented via doxygen
[ ] Copyright owner are updated in the changed files
[ ] PR title describes the changes

Post-review Checklist for the PR Author

[ ] All open points are addressed and tracked via issues

References

Closes #891

@r7vme I've a question regarding failed builds. Up until now when a job failed, not everything needed to be rebuild, just a subset from the same github action file. With this changes, would everything need to be rebuild if one job fails?

@r7vme I've a question regarding failed builds. Up until now when a job failed, not everything needed to be rebuild, just a subset from the same github action file. With this changes, would everything need to be rebuild if one job fails?

you're right, github actions seems force to rerun whole workflow, which is meh...

At least this is an incentive to fix flaky tests :smile:

@dkroenke @elBoberido ready for review

@dkroenke @elBoberido ready for review
EDIT: In settings for the repo, if this PR will be merged, we need to change required jobs, because jobs were renamed

Yes, will take care of that.

@r7vme I've a question regarding failed builds. Up until now when a job failed, not everything needed to be rebuild, just a subset from the same github action file. With this changes, would everything need to be rebuild if one job fails?

you're right, github actions seems force to rerun whole workflow, which is meh...
EDIT: one workaround to add if: steps.last_run_status.outputs.last_run_status != 'success' to every step, which is also meh...

I would propose the following:
Let's run the newly created workflow multiple times to see if there are tests failing or hanging. If that's not the case then we are good to go here.

@r7vme I've a question regarding failed builds. Up until now when a job failed, not everything needed to be rebuild, just a subset from the same github action file. With this changes, would everything need to be rebuild if one job fails?

you're right, github actions seems force to rerun whole workflow, which is meh...
EDIT: one workaround to add if: steps.last_run_status.outputs.last_run_status != 'success' to every step, which is also meh...

@r7vme
I think you can add these state checks at job level too: https://github.blog/changelog/2019-10-01-github-actions-new-workflow-syntax-features/#if-at-the-job-level
We can add this in the next iteration.


test migrating some cloud grafana plugins

test migrating some cloud grafana plugins (without committing the result upstream) to validate migrate is doing the correct work.
Such as:

https://github.com/grafana/x-ray-datasource
https://github.com/grafana/azure-data-explorer-datasource
https://github.com/grafana/athena-datasource
https://github.com/grafana/redshift-datasource
https://github.com/grafana/timestream-datasource

I tested the migration of all the mentioned plugins and only found problems related to the migration itself and not create-plugin:

A common error in tests:

    Invalid hook call. Hooks can only be called inside of the body of a function component. This could happen for one of the following reasons

That can be solved by installing react and react-router in the same version as defined by @grafana/ui

A regular problem was create-plugin updating the @grafana/* dependencies and the project not compiling. This is being addressed here https://github.com/grafana/plugin-tools/issues/49. Manually changing the dependencies back to their originally defined version solved the problem.

In one of the projects the tsconfig had custom configurations such as implicitAny: true  that is not part of the create-plugin configuration. Because create-plugin overwrites the tsconfig file it means that migrated projects will have to re-check and re-configure custom settings. This also happened in one of the projects with estlint and the hooks dependencies rule.


Ability to delete/remove user/agent response from chat

Describe the feature
Sometimes you have a good thread going with chatGPT but send a bad user response that throws the whole thing off.
Add the ability to delete a chat (from either user or agent) so that you can try to continue the conversation with different context.

I don't think this is available via official APIs nor ChatGPT web. Let me know if you know of a way to achieve that. You may do some prompt engineering to ask ChatGPT to ignore some of the previous messages I guess. That would be outside of this extension's capability though.
I have the edit your previous message feature available. You can try that as well.


reduce file size for e2e

Signed-off-by: Ke Xu<EMAIL_ADDRESS>
Description

Checklist

[ ] I have added screenshots above for all UI changes.
[ ] I have added e2e tests for all UI changes.
[ ] Documentation was updated if it was needed.

Codecov Report

Merging #1723 (a2310df) into main (8f1161c) will decrease coverage by 5.27%.
The diff coverage is n/a.

:exclamation: Current head a2310df differs from pull request most recent head 5cfd943. Consider uploading reports for the commit 5cfd943 to get more accurate results

@@            Coverage Diff             @@
##             main    #1723      +/-   ##
==========================================
- Coverage   89.00%   83.73%   -5.28%
==========================================
  Files         105       22      -83
  Lines        5577      418    -5159
==========================================
- Hits         4964      350    -4614
+ Misses        613       68     -545

Flag
Coverage Δ

unittests
83.73% <ø> (-5.28%)
:arrow_down:

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

Impacted Files
Coverage Δ

...ibleai/_tools/shared/state_directory_management.py

raiwidgets/raiwidgets/__init__.py

...eai/responsibleai/managers/data_balance_manager.py

erroranalysis/erroranalysis/version.py

...ai/responsibleai/_tools/causal/causal_constants.py

raiwidgets/raiwidgets/model_analysis_dashboard.py

...s/erroranalysis/_internal/error_report/__init__.py

...i/responsibleai/managers/error_analysis_manager.py

responsibleai/responsibleai/__version__.py

erroranalysis/erroranalysis/__init__.py

... and 73 more

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.


[Feature][dolphinscheduler-master] Add loop task

Search before asking

[X] I had searched in the issues and found no similar feature requirement.

Description
Add a loop task, such as executing the subsequent process multiple times in a loop. By using the loop task node, can conveniently call it multiple times. Currently, in order to implement this function, a new task script has to be added, which is implemented by calling the interface multiple times. This is very cumbersome.
Use case
Create a loop task, increase the number of loops, this number can be obtained from the previous task, and execute the subsequent process multiple times according to the number of loops.
Related issues
No response
Are you willing to submit a PR?

[ ] Yes I am willing to submit a PR!

Code of Conduct

[X] I agree to follow this project's Code of Conduct

We have the same requirement, any progress ?

is this same or like dynamic task? https://dolphinscheduler.apache.org/en-us/docs/3.2.0/guide/task/dynamic

这是相同还是相似的动态任务？https://dolphinscheduler.apache.org/en-us/docs/3.2.0/guide/task/dynamic

希望可以前置任务生成参数列表，然后进入循环任务节点，选择
需要循环的工作流。中间设置生成子工作流实例并行个数

这是相同还是相似的动态任务？https://dolphinscheduler.apache.org/en-us/docs/3.2.0/guide/task/dynamic

希望可以前置任务生成参数列表，然后进入循环任务节点，选择
需要循环的工作流。中间设置生成子工作流实例并行个数

is this same or like dynamic task? https://dolphinscheduler.apache.org/en-us/docs/3.2.0/guide/task/dynamic

I hope to generate a parameter list in a preprocessing task, then enter a loop task node to select the workflow that needs to be looped. During this process, choose to generate sub-workflow instances, either in serial or parallel, and determine the number of instances.


row click notification

would be nice to be able to know what item was clicked with a bindable event as well as row highlighting.

This has been added to v0.1.5, which is now available.
Row Click Notification


Add CMake build for opencv-ndarray-conversion

The CMakeList.txt has been tested under ubuntu.
For Mac OSX, CMake will produce a  examples.dylib fie instead of examples.so.
Any idea to improve so that it will work on both platform?

Thanks for this. I tried out the build on my Fedora box and the OpenCV finder script seems to have some issues with my OpenCV installation directory. It might even be just my system with many versions of OpenCV here and there. Let me just be sure what it is before I merge.
Thanks :)

Ok, thank you.
By the way, I have figured out why I can not compile using the same cmake file on mac osx. The main problem is that cmake does not work well with brew installed python. I have found the solution here:
https://github.com/Homebrew/homebrew/issues/25118
In case you also want to use it under mac osx and meet with the same problem.


Implement a push notification service in the application

Strong suggestion here: Onesignal
This needs to be coordinated with Backend team, so discuss with someone on the team to let them discuss the choice also.

Free version is not GDPR compliant from the chart the have.

Free version is not GDPR compliant from the chart the have.

This requires investigation then before picking a platform, whoever picks this issue, please perform a decision log on it

I would suggest https://www.twilio.com/notify since we'll have a meeting to get free credits

I would suggest https://www.twilio.com/notify since we'll have a meeting to get free credits

@webmonger do you have info on this one to see if it's GDPR compliant?

I think we need some requirements or a functional specification from backend on this feature. I feel like we may be over complicating things a tiny bit here. Is in-house development of this completely out of the question?
This was recently implemented into an app at work. We used firebase. The documentation is very good, and you can actually find a pretty good guide on it written on medium:
<EMAIL_ADDRESS>Here is the official latest integration guide for backend: https://invertase.io/oss/react-native-firebase/v6/messaging/quick-start#messaging-quick-start

Had a productive conversation with David regarding GDPR compliance. Pasting it here for transparency.
`David Alecrim:flag-pt:  18 minutes ago
We can, I just think that the hard part here is not the implementation (I also implemented this kind of features before), the problem here is the compliance regarding GDPR, which is why I'm blocked here
David Alecrim:flag-pt:  17 minutes ago
Either way, it's in the backend board now also
AlexV  4 minutes ago
Alright, so that's a loaded question which goes much further than the reach of this app... While many of the GDPR controls are going to be specific with how the apps control and process EU citizen data, there also needs to be considerations on the organization level as well.
With firebase we are considered the data controller. If we sign the necessary paperwork(which I think is only available on the paid plan), Google is our data processor. If we don’t sign anything with google, we are considered the processor AND controller.
So even with google as our processor, we still can't pass on any GDPR obligations on to Google. They only perform a technical service for us, no organizational and legal services. Their privacy policy is not a dependency or part of our privacy policy. Because we are the controller and they the processor, they may only process the data as we instruct them to, and we are responsible whatever happens.
AlexV  2 minutes ago
GDPR is not so much about ticking boxes like storing data “securely”, but about planning any processing of personal data in accordance with certain principles (like data minimisation, using a proper legal basis, ect (all explained in gdpr text). Following these principles are not something that can be outsourced.
David Alecrim:flag-pt:  1 minute ago
I  get your point here, then let's add @Wilson Rodrigues and the backend team to the conversation, to see how we will deal with this data flow that is necessary to have
AlexV  < 1 minute ago
Maintaining records of processing is only necessary under certain circumstances. The choice of our tech stack does not affect this. Even if you are not required to keep these records, they are a good exercise to make sure you are demonstrably GDPR-compliant.
Also, processing data that is subject to the GDPR in third countries like the US is fine as long as you take suitable precautions. The data processing agreement Google offers to you will likely already list the necessary aspects. Technically, you either need an EU adequacy decision or other suitable safeguards in the data processing agreement contract to transfer data internationally. The US privacy shield is currently recognized as adequate.
AlexV  < 1 minute ago
perfect
AlexV  < 1 minute ago
I'll actually copy and paste this all into the github ticket.`

I think we need some requirements or a functional specification from backend on this feature. I feel like we may be over complicating things a tiny bit here. Is in-house development of this completely out of the question?
This was recently implemented into an app at work. We used firebase. The documentation is very good, and you can actually find a pretty good guide on it written on medium:
<EMAIL_ADDRESS>Here is the official latest integration guide for backend: https://invertase.io/oss/react-native-firebase/v6/messaging/quick-start#messaging-quick-start

so have we decided to proceed with firebase cloud messaging?
I have experience integrating FCM into web apps using their web SDK and also with react native apps as mentioned above.
This is the document that outlines firebase's data security and privacy details: https://firebase.google.com/support/privacy
if we decide on using this, I can integrate FCM into the web-client app


run muver on FASTA instead of FASTQ

Hi,
Was wondering if it is possible to run muver starting from FASTA files instead of FASTQ file.
I see that the run_pipeline requires the FASTQ_list with mate 1 and 2 columns, information that I do not have.
Please let me know. Thank you in advance!
Marius

Hi Marius,
Muver was designed to work with Illumina sequencing data, which is typically delivered in FASTQ format. If you have next generation sequencing reads in FASTA format, the pipeline can be run manually, however, the process is lengthy, and requires some commands be run with specific parameters to maintain compatibility with downstream steps. If you are able to install the package from github rather than utilizing the docker container, a minor modification of this file, https://github.com/NIEHS/muver/raw/master/muver/wrappers/bowtie2.py, can add support for FASTA input. Simply change the parameter on line 34 from '-q' to '-f', which indicates that the aligner, bowtie2, should expect FASTA rather than FASTQ input. When you generate the “FASTQ_list” file, you can include just the “Mate 1 FASTQ” column, just as you would with single-end FASTQ input, but list the names of your FASTA files instead.
You may be able to replace the original with an updated copy within the docker container by specifying ‘-u 0’ in the run command to enter the shell as root. The file to be replaced is:
/usr/local/lib/python2.7/dist-packages/muver-0.1.0-py2.7.egg/muver/wrappers/bowtie2.py
…and you can place the modified copy in your mounted data directory.
I was able perform the modification successfully on two different Linux-based docker environments, however, depending on how your system is configured, this approach may not work for you.
Thanks,
Adam
From: Marius Gheorghe<EMAIL_ADDRESS>Sent: Tuesday, March 31, 2020 8:43 AM
To: NIEHS/muver<EMAIL_ADDRESS>Cc: Subscribed<EMAIL_ADDRESS>Subject: [NIEHS/muver] run muver on FASTA instead of FASTQ (#6)
Hi,
Was wondering if it is possible to run muver starting from FASTA files instead of FASTQ file.
I see that the run_pipeline requires the FASTQ_list with mate 1 and 2 columns, information that I do not have.
Please let me know. Thank you in advance!
Marius
—
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Reply to this email directly, view it on GitHubhttps://github.com/NIEHS/muver/issues/6, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADCMIB2FBF3RUCOD2ZDJZP3RKHQL3ANCNFSM4LXQQ2TA.

Hi Adam,
Thank you for you quick and detailed reply.
I knew that there is an option in bowtie for it but after trying to fiddle with the docker image and get access to the source code from within it and having it failed several times (including the standalone installation due to errors in the dependencies installation #7  I gave up.
For now, I have converted FASTA to FASTQ with some fake scores, but will follow your instructions and modify the code hopefully and launch the pipeline.
I read more carefully the doc and I eventually figured out that FASTQ mate 2 is not actually mandatory.
Thanks again for the support!
Marius

Hi again,
When trying to install it from the GIT repo, under python 2.7 I get an error. Complete log below:
marius@onco:~/projects/genomes/muver$ sudo python2.7 setup.py install
running install
running bdist_egg
running egg_info
writing requirements to muver.egg-info/requires.txt
writing muver.egg-info/PKG-INFO
writing top-level names to muver.egg-info/top_level.txt
writing dependency_links to muver.egg-info/dependency_links.txt
writing entry points to muver.egg-info/entry_points.txt
reading manifest file 'muver.egg-info/SOURCES.txt'
writing manifest file 'muver.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/reference.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/__init__.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/fitting.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/read_processing.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/allelic_fraction.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/utils.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/pipeline.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/repeats.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/cli.py -> build/bdist.linux-x86_64/egg/muver
creating build/bdist.linux-x86_64/egg/muver/wrappers
copying build/lib.linux-x86_64-2.7/muver/wrappers/__init__.py -> build/bdist.linux-x86_64/egg/muver/wrappers
copying build/lib.linux-x86_64-2.7/muver/wrappers/bowtie2.py -> build/bdist.linux-x86_64/egg/muver/wrappers
copying build/lib.linux-x86_64-2.7/muver/wrappers/samtools.py -> build/bdist.linux-x86_64/egg/muver/wrappers
copying build/lib.linux-x86_64-2.7/muver/wrappers/picard.py -> build/bdist.linux-x86_64/egg/muver/wrappers
copying build/lib.linux-x86_64-2.7/muver/wrappers/gatk.py -> build/bdist.linux-x86_64/egg/muver/wrappers
copying build/lib.linux-x86_64-2.7/muver/variant_list.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/depth_ratios.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/repeat_indels.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/depth_distribution.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/bias_distribution.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/variant.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/sample.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/depth_correction.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/call_mutations.py -> build/bdist.linux-x86_64/egg/muver
byte-compiling build/bdist.linux-x86_64/egg/muver/reference.py to reference.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/fitting.py to fitting.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/read_processing.py to read_processing.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/allelic_fraction.py to allelic_fraction.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/utils.py to utils.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/pipeline.py to pipeline.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/repeats.py to repeats.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/cli.py to cli.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/wrappers/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/wrappers/bowtie2.py to bowtie2.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/wrappers/samtools.py to samtools.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/wrappers/picard.py to picard.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/wrappers/gatk.py to gatk.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/variant_list.py to variant_list.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/depth_ratios.py to depth_ratios.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/repeat_indels.py to repeat_indels.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/depth_distribution.py to depth_distribution.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/bias_distribution.py to bias_distribution.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/variant.py to variant.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/sample.py to sample.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/depth_correction.py to depth_correction.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/call_mutations.py to call_mutations.pyc
installing package data to build/bdist.linux-x86_64/egg
running install_data
creating build/bdist.linux-x86_64/egg/config
copying paths.cfg -> build/bdist.linux-x86_64/egg/config
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/muver-0.1.0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing muver-0.1.0-py2.7.egg
removing '/usr/local/lib/python2.7/dist-packages/muver-0.1.0-py2.7.egg' (and everything under it)
creating /usr/local/lib/python2.7/dist-packages/muver-0.1.0-py2.7.egg
Extracting muver-0.1.0-py2.7.egg to /usr/local/lib/python2.7/dist-packages
muver 0.1.0 is already the active version in easy-install.pth
Installing muver script to /usr/local/bin

Installed /usr/local/lib/python2.7/dist-packages/muver-0.1.0-py2.7.egg
Processing dependencies for muver==0.1.0
Searching for scipy>=0.18.1
Reading https://pypi.org/simple/scipy/
Downloading https://files.pythonhosted.org/packages/04/ab/e2eb3e3f90b9363040a3d885ccc5c79fe20c5b8a3caa8fe3bf47ff653260/scipy-1.4.1.tar.gz#sha256=dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59
Best match: scipy 1.4.1
Processing scipy-1.4.1.tar.gz
Writing /tmp/easy_install-5z5aLu/scipy-1.4.1/setup.cfg
Running scipy-1.4.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-5z5aLu/scipy-1.4.1/egg-dist-tmp-FPpPMM
Traceback (most recent call last):
  File "setup.py", line 65, in <module>
    data_files=[('config', ['paths.cfg'])],
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/__init__.py", line 145, in setup
    return distutils.core.setup(**attrs)
  File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/install.py", line 67, in run
    self.do_egg_install()
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/install.py", line 117, in do_egg_install
    cmd.run()
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 418, in run
    self.easy_install(spec, not self.no_deps)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 660, in easy_install
    return self.install_item(None, spec, tmpdir, deps, True)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 707, in install_item
    self.process_distribution(spec, dist, deps)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 752, in process_distribution
    [requirement], self.local_index, self.easy_install
  File "/home/marius/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 782, in resolve
    replace_conflicting=replace_conflicting
  File "/home/marius/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1065, in best_match
    return self.obtain(req, installer)
  File "/home/marius/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1077, in obtain
    return installer(requirement)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 679, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 705, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1158, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1144, in run_setup
    run_setup(setup_script, args)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
    raise
  File "/usr/lib/python2.7/contextlib.py", line 35, in __exit__
    self.gen.throw(type, value, traceback)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/usr/lib/python2.7/contextlib.py", line 35, in __exit__
    self.gen.throw(type, value, traceback)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
    saved_exc.resume()
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
    six.reraise(type, exc, self._tb)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
    yield saved
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
    _execfile(setup_script, ns)
  File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 45, in _execfile
    exec(code, globals, locals)
  File "/tmp/easy_install-5z5aLu/scipy-1.4.1/setup.py", line 31, in <module>
    name='muver',
RuntimeError: Python version >= 3.5 required.

I can install it successfully under python 3.6, but when trying to run the index_reference I get the error:
marius@onco:~/projects/covid19/test_muver_fasta$ muver index_reference wuhan_hu1.fa
Traceback (most recent call last):
  File "/usr/local/bin/muver", line 11, in <module>
    load_entry_point('muver==0.1.0', 'console_scripts', 'muver')()
  File "/home/marius/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 490, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/home/marius/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2853, in load_entry_point
    return ep.load()
  File "/home/marius/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2444, in load
    return self.resolve()
  File "/home/marius/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2450, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/usr/local/lib/python3.6/dist-packages/muver-0.1.0-py3.6.egg/muver/cli.py", line 8, in <module>
    from allelic_fraction import get_allelic_fractions
ModuleNotFoundError: No module named 'allelic_fraction'

Will then try to replace the bowtie2 wrapper inside the Docker image and try running it from there.
Becomes messy for such simple tasks
Marius

OK. I ran the docker image with the -u 0 parameter setting, as you mentioned, to be root and replaced the bowtie2 wrapper with the "custom" version for FASTA.
Now it seems to work (i.e., no crash yet) :]
Hopefully it will complete successfully
Thank you for your support. Will bug you if I run in other problems :grin:
I consider the issue closed
Marius

It seems your problem is related to python 2.7 compatibility issues among some of the dependencies, particularly scipy. I’ve modified the install script to limit versions of dependencies to those released prior to the January 1st, 2020 deprecation deadline for python 2.7 and created a new release of muver, 1.2.1. I will investigate the python 3 compatibility issue in the near future.
Thanks,
Adam
From: Marius Gheorghe<EMAIL_ADDRESS>Sent: Wednesday, April 1, 2020 8:03 AM
To: NIEHS/muver<EMAIL_ADDRESS>Cc: Burkholder, Adam (NIH/NIEHS) [E]<EMAIL_ADDRESS>Comment<EMAIL_ADDRESS>Subject: Re: [NIEHS/muver] run muver on FASTA instead of FASTQ (#6)
Hi again,
When trying to install it from the GIT repo, under python 2.7 I get an error. Complete log below:
marius@onco:~/projects/genomes/muver$ sudo python2.7 setup.py install
running install
running bdist_egg
running egg_info
writing requirements to muver.egg-info/requires.txt
writing muver.egg-info/PKG-INFO
writing top-level names to muver.egg-info/top_level.txt
writing dependency_links to muver.egg-info/dependency_links.txt
writing entry points to muver.egg-info/entry_points.txt
reading manifest file 'muver.egg-info/SOURCES.txt'
writing manifest file 'muver.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/reference.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/init.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/fitting.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/read_processing.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/allelic_fraction.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/utils.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/pipeline.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/repeats.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/cli.py -> build/bdist.linux-x86_64/egg/muver
creating build/bdist.linux-x86_64/egg/muver/wrappers
copying build/lib.linux-x86_64-2.7/muver/wrappers/init.py -> build/bdist.linux-x86_64/egg/muver/wrappers
copying build/lib.linux-x86_64-2.7/muver/wrappers/bowtie2.py -> build/bdist.linux-x86_64/egg/muver/wrappers
copying build/lib.linux-x86_64-2.7/muver/wrappers/samtools.py -> build/bdist.linux-x86_64/egg/muver/wrappers
copying build/lib.linux-x86_64-2.7/muver/wrappers/picard.py -> build/bdist.linux-x86_64/egg/muver/wrappers
copying build/lib.linux-x86_64-2.7/muver/wrappers/gatk.py -> build/bdist.linux-x86_64/egg/muver/wrappers
copying build/lib.linux-x86_64-2.7/muver/variant_list.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/depth_ratios.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/repeat_indels.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/depth_distribution.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/bias_distribution.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/variant.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/sample.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/depth_correction.py -> build/bdist.linux-x86_64/egg/muver
copying build/lib.linux-x86_64-2.7/muver/call_mutations.py -> build/bdist.linux-x86_64/egg/muver
byte-compiling build/bdist.linux-x86_64/egg/muver/reference.py to reference.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/init.py to init.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/fitting.py to fitting.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/read_processing.py to read_processing.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/allelic_fraction.py to allelic_fraction.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/utils.py to utils.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/pipeline.py to pipeline.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/repeats.py to repeats.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/cli.py to cli.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/wrappers/init.py to init.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/wrappers/bowtie2.py to bowtie2.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/wrappers/samtools.py to samtools.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/wrappers/picard.py to picard.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/wrappers/gatk.py to gatk.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/variant_list.py to variant_list.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/depth_ratios.py to depth_ratios.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/repeat_indels.py to repeat_indels.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/depth_distribution.py to depth_distribution.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/bias_distribution.py to bias_distribution.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/variant.py to variant.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/sample.py to sample.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/depth_correction.py to depth_correction.pyc
byte-compiling build/bdist.linux-x86_64/egg/muver/call_mutations.py to call_mutations.pyc
installing package data to build/bdist.linux-x86_64/egg
running install_data
creating build/bdist.linux-x86_64/egg/config
copying paths.cfg -> build/bdist.linux-x86_64/egg/config
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying muver.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/muver-0.1.0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing muver-0.1.0-py2.7.egg
removing '/usr/local/lib/python2.7/dist-packages/muver-0.1.0-py2.7.egg' (and everything under it)
creating /usr/local/lib/python2.7/dist-packages/muver-0.1.0-py2.7.egg
Extracting muver-0.1.0-py2.7.egg to /usr/local/lib/python2.7/dist-packages
muver 0.1.0 is already the active version in easy-install.pth
Installing muver script to /usr/local/bin
Installed /usr/local/lib/python2.7/dist-packages/muver-0.1.0-py2.7.egg
Processing dependencies for muver==0.1.0
Searching for scipy>=0.18.1
Reading https://pypi.org/simple/scipy/
Downloading https://files.pythonhosted.org/packages/04/ab/e2eb3e3f90b9363040a3d885ccc5c79fe20c5b8a3caa8fe3bf47ff653260/scipy-1.4.1.tar.gz#sha256=dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59
Best match: scipy 1.4.1
Processing scipy-1.4.1.tar.gz
Writing /tmp/easy_install-5z5aLu/scipy-1.4.1/setup.cfg
Running scipy-1.4.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-5z5aLu/scipy-1.4.1/egg-dist-tmp-FPpPMM
Traceback (most recent call last):
File "setup.py", line 65, in
data_files=[('config', ['paths.cfg'])],

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/init.py", line 145, in setup
return distutils.core.setup(**attrs)

File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()

File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)

File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/install.py", line 67, in run
self.do_egg_install()

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/install.py", line 117, in do_egg_install
cmd.run()

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 418, in run
self.easy_install(spec, not self.no_deps)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 660, in easy_install
return self.install_item(None, spec, tmpdir, deps, True)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 707, in install_item
self.process_distribution(spec, dist, deps)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 752, in process_distribution
[requirement], self.local_index, self.easy_install

File "/home/marius/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 782, in resolve
replace_conflicting=replace_conflicting

File "/home/marius/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 1065, in best_match
return self.obtain(req, installer)

File "/home/marius/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 1077, in obtain
return installer(requirement)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 679, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 705, in install_item
dists = self.install_eggs(spec, download, tmpdir)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs
return self.build_and_install(setup_script, setup_base)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1158, in build_and_install
self.run_setup(setup_script, setup_base, args)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1144, in run_setup
run_setup(setup_script, args)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
raise

File "/usr/lib/python2.7/contextlib.py", line 35, in exit
self.gen.throw(type, value, traceback)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield

File "/usr/lib/python2.7/contextlib.py", line 35, in exit
self.gen.throw(type, value, traceback)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
saved_exc.resume()

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
six.reraise(type, exc, self._tb)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
yield saved

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
_execfile(setup_script, ns)

File "/home/marius/.local/lib/python2.7/site-packages/setuptools/sandbox.py", line 45, in _execfile
exec(code, globals, locals)

File "/tmp/easy_install-5z5aLu/scipy-1.4.1/setup.py", line 31, in
name='muver',

RuntimeError: Python version >= 3.5 required.
I can install it successfully under python 3.6, but when trying to run the index_reference I get the error:
marius@onco:~/projects/covid19/test_muver_fasta$ muver index_reference wuhan_hu1.fa
Traceback (most recent call last):
File "/usr/local/bin/muver", line 11, in
load_entry_point('muver==0.1.0', 'console_scripts', 'muver')()

File "/home/marius/.local/lib/python3.6/site-packages/pkg_resources/init.py", line 490, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)

File "/home/marius/.local/lib/python3.6/site-packages/pkg_resources/init.py", line 2853, in load_entry_point
return ep.load()

File "/home/marius/.local/lib/python3.6/site-packages/pkg_resources/init.py", line 2444, in load
return self.resolve()

File "/home/marius/.local/lib/python3.6/site-packages/pkg_resources/init.py", line 2450, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)

File "/usr/local/lib/python3.6/dist-packages/muver-0.1.0-py3.6.egg/muver/cli.py", line 8, in
from allelic_fraction import get_allelic_fractions

ModuleNotFoundError: No module named 'allelic_fraction'
Will then try to replace the bowtie2 wrapper inside the Docker image and try running it from there.
Becomes messy for such simple tasks
Marius
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Hi Adam,
Yeah, saw it was complaining about scipy, but just wanted to post the installation log here to help you and others running into the same problem.
Thanks for taking your time for the fix!
The pipeline I launched a couple of hours ago is still running (I hope.. at least the processors are sweating) but dunno where the workflow is wrt to completion, as there is no textual output to provide feedback. Is that normal? Let's hope it finishes :crossed_fingers:
Marius

There will generally be no text output to the console, however, the indel realignment and identification of potential mutations performed by GATK will write output to the “logs” folder under your results directory.
From: Marius Gheorghe<EMAIL_ADDRESS>Sent: Wednesday, April 1, 2020 10:27 AM
To: NIEHS/muver<EMAIL_ADDRESS>Cc: Burkholder, Adam (NIH/NIEHS) [E]<EMAIL_ADDRESS>Comment<EMAIL_ADDRESS>Subject: Re: [NIEHS/muver] run muver on FASTA instead of FASTQ (#6)
Hi Adam,
Yeah, saw it was complaining about scipy, but just wanted to post the installation log here to help you and others running into the same problem.
Thanks for taking your time for the fix!
The pipeline I launched a couple of hours ago is still running (I hope.. at least the processors are sweating) but dunno where the workflow is wrt to completion, as there is no textual output to provide feedback. Is that normal? Let's hope it finishes 🤞
Marius
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PR: Remove extra remove window action from window menu and use file menu instead

Description

Fixes https://github.com/napari/napari/issues/2445#issuecomment-803779101
@jni could you check it solves the issue?
Type of change

[x] Bug-fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update

References

Remove the extra close window on the Window menu. On OSX the close window seems to be on the File menu for differents programs I checked.

Is this different for other operating systems @napari/core-devs ?
How has this been tested?

[ ] example: the test suite for my feature covers cases x, y, and z
[ ] example: all tests pass with my change

Final checklist:

[ ] My PR is the minimum possible work for the desired functionality
[ ] I have commented my code, particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation
[ ] I have added tests that prove my fix is effective or that my feature works

Works for me on Mac.

Removing from close window makes sense to me. This looks good to me, but maybe @jni can check behaviour on linux is fixed before merge. If it is feel free to approve and merge