Add feedback option "Sample did not work"

Sometimes, we do not reach a result for a sample, as the concentration is too low or faulty handling by us. Instead of uploading a .zip file it would be great if we could trigger a feedback email via the admin panel/ the API saying.
Dear<EMAIL_ADDRESS>
Your sample 22_50_A1_pCW57_1 has been processed. However, no correct de-novo assembly has been determined. Please consider handing in this sample next week again.

Best wishes,

CircuitSEQ Team.

We could add two more parameters to the /admin/result endpoint:

primary_key (string)
success (boolean)
file (same as before)

To upload a results file you would set the primary_key, success=True, and the file as before
To send a message that there are no results you would set the primary_key and success=False
Would that work?
It could also do a consistency check between the zip filename and the primary_key (see also #84) before accepting the result.

@LArnoldt this is now implemented, see https://github.com/ssciwr/circuit_seq/blob/main/notebooks/api_examples.ipynb for examples of uploading analysis success and analysis failure. You can also do this manually from the admin page on the website.
Here is an example email for success="false":
Dear<EMAIL_ADDRESS>
Your sample 23_16_A1_asdsds has been processed, however no correct de-novo assembly has been determined.

Please consider handing in this sample next week again.

Best wishes,

CircuitSEQ Team.
https://circuitseq.iwr.uni-heidelberg.de

And here an example email for success="true" with fasta/gbk files attached (unchanged by this PR):
Dear<EMAIL_ADDRESS>
Your sample 23_16_A1_asdsds has been processed and the results are attached to this email.

You can also download the full analysis data by logging in to your account at https://circuitseq.iwr.uni-heidelberg.de

Best wishes,

CircuitSEQ Team.
https://circuitseq.iwr.uni-heidelberg.de


[iOS] Enable built from prebuilt

This PR enables build iOS app from prebuilt
model and library distro same as CLI

To use prebuilt , follow https://mlc.ai/mlc-llm/#windows-linux-mac to clone the

dist/prebuilt/lib
dist/prebuilt/RedPajama-INCITE-Chat-3B-v1-q4f16_0

Run prep_libs.sh and prep_params.sh


[INLONG-10287][Agent] Update the Redis Source

Fixes https://github.com/apache/inlong/issues/10287
Motivation
Update the Redis source for agent
Modifications
Modify TaskProfileDto and RedisTask to accept and parse the configuration.
Add RedisTask, RedisInstance, and RedisSource classes
Provide Unit Test
Verifying this change

@emptyOVO please click resolve if you fix the comment, and you do not need to open/close the PR again and again.

@emptyOVO please click resolve if you fix the comment, and you do not need to open/close the PR again and again.

got it


[1324] Actually fix authentication initializer

Resolves #1324 (and #1282 for real)

Ok, while testing this manually I ran into a second issue. When I merged in #1106 and created the cas_login field, I neglected to copy the username column into that one, so when the initializer runs (with CAS_AUTH set) it throws an error because there is no cas login set. Based on previous discussions / reading, I added a block to the migration that calls an SQL statement copying the username column into the cas_login column if the CAS_AUTH env variable is set (as opposed to using the User model).
This issue should be manually tested under the following cases:
Non-CAS:

check out v4.0.1-beta
rake db:reset minimal=true (enter CAS username since there was no other option)
check out this branch
rake db:migrate (you might run into issues in the first migration depending on what random reservations were seeded in step 2; in that case repeat steps 1-3)
rails c - verify that the first user has their username equal to their e-mail

CAS:

Follow steps 1-3 above
CAS_AUTH=1 rake db:migrate (same caveat as step 4 above)
CAS_AUTH=1 rails c - verify that the first user has both their username and cas_login equal to the CAS login you set during the database reset.

This was reviewed by @esoterik, merging!


Enable one or more dates???

Hi Guys,
I can set a enable date?
Eg:
I disable all days: 0->6
But i want to enable date: 26/10/2015 => Monday (day of date: 1).
How to  setup that?
....
daysOfWeekDisabled: [0,1,2,3,4,5,6],
...
Please help me.
Thanks so much.

I advise you to use beforeShowDay.
With something like this:
$('#sandbox-container input').datepicker({
  beforeShowDay: function (date){
    if (date.getTime() === (new Date(2015, 9, 26)).getTime()) {
      return false;
    }
  }
});

@Azaret  Thank man.


Remove OSAL last-gen compatibility complexity

Next gen OSAL is the only option with this release, remove conditionally compiled code related to supporting last gen.

Imported from trac issue 311.  Created by jhageman on 2019-07-12T13:06:06, last modified: 2019-08-14T11:36:26

Trac comment by jhageman on 2019-07-24 17:28:22:
As a part of this branch/tag last version that works with last gen (techdev-lastgenosal?)

Trac comment by jhageman on 2019-07-16 10:23:04:
Related to [cfs_osal:200], only do code in OSAL_OPAQUE_OBJECT_IDS and OSAL_ABSTRACT_FILESYS_TYPES ifdefs, remove other option (last gen).

Trac comment by jhageman on 2019-08-14 11:36:26:
Closing as duplicate of #345


Optimizer fixes and limit guesses

This adds:

Let minuit use bounds for rate multipliers by default. Scipy already did this; tensorflow-probability's optimizers do not support bounds and should not be used for WIMP limit setting currently (unless you like your WIMPs negative...)
Fix the default optimizer tolerances so that for all optimizers we support, to the best of my knowledge, llr_tolerance controls the absolute distance in -2 log likelihood between the solution and the true minimum. This is quite tricky and it's likely there are still some quite different behaviour, considering that each optimizer has a different algorithm and a different way of estimating the true distance to the minimum.
Change one_parameter_interval to no longer require a guess: we can make a reasonably good guess from the Hessian (or for boundary solutions, the gradient). Of course you can still provide a guess, though now you specify it via a float (or tuple of floats for central intervals) instead of a dictionary.

Minor bonus changes:

Fix a crash related to kwarg handling in _get_rate_mult. I had problems passing the rate_multipliers argument to simulate. Is this argument just a relic that can be removed? We can pass rate multipliers via the normal kwargs.
Let one_parameter_interval take kwargs
Remove the check that all sources must produce the same columns. With this check, I cannot simulate any combined ER + WIMP dataset (unless the WIMP rate multiplier is zero, of course).

We should probably refactor a bit, e.g. create a separate method for the limit guess.

Bonus change: ColumnSource now inherits from Source, and Sourcebase has been removed. This simplifies the code and avoids some missing method errors.
This does mean that ColumnSource will do batching and padding, which strictly speaking it doesn't need to. But this takes no extra logic and hardly any computation time. ColumnSource's random_truth (and therefore its simulator) always returns an empty dataframe (see #47), unless the user overrides this with a custom simulator.


Run tests in CI

Currently we don't run any tests in CI:
https://github.com/maplibre/maplibre-gl-geocoder/blob/cf3de577a3f0acc34da9e421e1b0e00afe330a58/.github/workflows/publish.yml#L23-L31
In the current situation, we might end up publishing something broken. I would recommend to run the tests right before npm publish and create a separate github actions workflow which runs the tests against all pull requests.

Running the tests in CI will also help managing dependabot pull requests. In GL JS we have the policy that we merge patch bumps if CI passes...

Tests are running as part of the CI, if there's anything else, feel free to open a different issue.


Feat/users

Hello @EdinsonRequena! Thanks for opening this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file users/views.py:

Line 96:80: E501 line too long (91 > 79 characters)
Line 116:80: E501 line too long (127 > 79 characters)
Line 120:80: E501 line too long (91 > 79 characters)
Line 137:80: E501 line too long (114 > 79 characters)
Line 139:80: E501 line too long (91 > 79 characters)


ci: fix working directoy

:tada: This PR is included in version 2.3.1 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


Add workaround for CockroachDB issue

Description
Refs cockroachdb/cockroach#101715.
Readiness checklist

[ ] I added/updated unit tests.
[ ] I added/updated integration/compatibility tests.
[x] I added/updated comments and checked rendering.
[ ] I made spot refactorings.
[ ] I updated user documentation.
[x] I ran task all, and it passed.
[x] I ensured that PR title is good enough for the changelog.
[x] (for maintainers only) I set Reviewers (@FerretDB/core), Labels, Project and project's Sprint fields.
[x] I marked all done items in this checklist.

oops!


Support PHP Namespaces (Ignore Backlashes)

At PHP, the folder representation is a backlash, so a PHP Class:
Illuminate\Database\Eloquent\Model will be at folder Illuminate/Database/Eloquent/Model.php.
I think we should ignore backlashes or replace \with /, as i never saw any file using \ on it.
If i search for Illuminate/Database/Eloquent/Model or IlluminateDatabaseEloquentModel works just fine, so either way works, ignoring or replacing.

I just saw https://github.com/atom/fuzzy-finder/pull/51, which is basically the same thing, but rails uses :: instead of \.

I have exact same problem.  Model.php should really be near the top of the list by just searching for Model, but fuzzy finder doesn't even show this file in the result set unless more info is given.
Example Screencast
Maybe related to scoring as well?  See... https://github.com/atom/fuzzy-finder/issues/57


Problem with Health Indicator.

I've build a simple config server to test the Health Indicator .
Here goes my configuration:
server:
  port: 8080
spring:
  application:
    name: microservice-config-server
  cloud:
    config:
      server:
        git:
          uri: https://github.com/eacdy/spring-cloud-test-for-issue/
          username: null
          password: null
          search-paths:
            - config-repo
        health:
          repositories:
            a-foo:
              label: master
              name: microservice-foo
              profiles: dev

When I come to the /health endpoint, I can get this:
{
    "status": "UP",
    "configServer": {
        "status": "UP",
        "repositories": [
            {
                "sources": [
                    "https://github.com/eacdy/spring-cloud-test-for-issue/config-repo/microservice-foo-dev.properties",
                    "https://github.com/eacdy/spring-cloud-test-for-issue/config-repo/microservice-foo.properties"
                ],
                "name": "microservice-foo",
                "profiles": [
                    "dev"
                ],
                "label": "master"
            }
        ]
    },
    "diskSpace": {
        "status": "UP",
        "total":<PHONE_NUMBER>56,
        "free":<PHONE_NUMBER>8,
        "threshold": 10485760
    },
    "refreshScope": {
        "status": "UP"
    }
}

I found that https://github.com/eacdy/spring-cloud-test-for-issue/config-repo/microservice-foo-dev.properties returns 404. The right url is https://github.com/eacdy/spring-cloud-test-for-issue/blob/master/config-repo/microservice-foo-dev.properties
Code in org.springframework.cloud.config.server.environment.EnvironmentCleaner :
	public Environment clean(Environment value, String workingDir, String uri) {
		Environment result = new Environment(value);
		for (PropertySource source : value.getPropertySources()) {
			String name = source.getName().replace(workingDir, "");
			name = name.replace("applicationConfig: [", "");
			name = uri + "/" + name.replace("]", "");
			result.add(new PropertySource(name, source.getSource()));
		}
		return result;
	}

I think it should be
	public Environment clean(Environment value, String workingDir, String uri) {
		Environment result = new Environment(value);
		for (PropertySource source : value.getPropertySources()) {
			String name = source.getName().replace(workingDir, "");
			name = name.replace("applicationConfig: [", "");
			name = uri + "/blob/master/" + name.replace("]", "");
			result.add(new PropertySource(name, source.getSource()));
		}
		return result;
	}

Is it just a bug? Thanks a lot.

@dsyer Could you help me?

It's not really a bug. Those URLs are not really supposed to represent real resources. They are just unique (but helpful) identifiers.

@dsyer Thank you very much.

I think it's not a bug

I am reading your book  Chapter 9，Take a bubble~


Add support for docker image names with tags.

Fix for #6856 add support for updating tagged images by using BuiltDockerImages to map from the original name to the digest based name.

Is it possible to add some logging output to this task? I have a lot of trouble in my releases to tell if this is working or not.

@mgreen you can request that as a separate issue, or add it in a PR if you like.

@NCarlsonMSFT Are we good to merge this?