[Question][devLake UI] Helm chart deployed successful but UI show "New Migration Scripts Detected"

Question
This is a fresh installation on GKE cluster. Helm chart deployed successful with newly created ENCRYPTION_SECRET.
helm install devlake devlake/devlake --version=1.0.1-beta9 --set lake.encryptionSecret.secret=$ENCRYPTION_SECRET --set commonEnvs.TZ="EST",grafana.env.TZ="EST" -n devlake
Port forward to my local:
kubectl -n devlake port-forward service/devlake-ui  30090:4000
Open browser to "http://localhost:30090/", then it redirect to migration page.
This is a new fresh installation(first time deploy to GKE and in a newly created namespace), why it redirect to migration page?
Screenshots

Additional context
Add any other context here.

I did created encryption secret, here is the exact command I run:
➜  tmp ENCRYPTION_SECRET=$(openssl rand -base64 2000 | tr -dc 'A-Z' | fold -w 128 | head -n 1)
➜  tmp helm install devlake devlake/devlake --version=1.0.1-beta9 --set lake.encryptionSecret.secret=$ENCRYPTION_SECRET -n devlake
➜  tmp kubectl -n devlake get secret
NAME                            TYPE                 DATA   AGE
devlake-encryption-secret       Opaque               1      7s
devlake-grafana                 Opaque               3      7s
devlake-mysql-auth              Opaque               6      7s
sh.helm.release.v1.devlake.v1   helm.sh/release.v1   1      7s
➜  tmp kubectl -n devlake get cm
NAME               DATA   AGE
devlake-grafana    1      16s
kube-root-ca.crt   1      3d23h
➜  tmp kubectl -n devlake get pod
NAME                               READY   STATUS    RESTARTS   AGE
devlake-grafana-84958c46df-9zls7   1/1     Running   0          2m21s
devlake-lake-5889879f98-gf5m2      1/1     Running   0          2m21s
devlake-mysql-0                    1/1     Running   0          2m20s
devlake-ui-6896bdcb9f-jq864        1/1     Running   0          2m21s
➜  tmp kubectl -n devlake get service
NAME              TYPE        CLUSTER-IP      EXTERNAL-IP   PORT(S)          AGE
devlake-grafana   ClusterIP   <IP_ADDRESS>           80/TCP           2m45s
devlake-lake      ClusterIP   <IP_ADDRESS>            8080/TCP         2m45s
devlake-mysql     ClusterIP   <IP_ADDRESS>            3306/TCP         2m45s
devlake-ui        NodePort    <IP_ADDRESS>            4000:32001/TCP   2m45s
With port-forwarding to my local, I still get the same error
➜  tmp kubectl port-forward service/devlake-ui  4000:4000 -n devlake
Forwarding from <IP_ADDRESS>:4000 -> 4000
Forwarding from [::1]:4000 -> 4000
Handling connection for 4000
Handling connection for 4000

Can you log into the mysql container and check if there is any record in the _devlake_migration_history table?

yes, there are 220 rows of records, but this is a new fresh installation, how come it has migration history?
mysql> select * from _devlake_migration_history;
+-------------------------+----------------+---------------------------------------------------------------------------------------------------------------+------------------+
| created_at              | script_version | script_name                                                                                | comment          |
+-------------------------+----------------+---------------------------------------------------------------------------------------------------------------+------------------+
| 2024-09-06 10:29:31.241 |       20240115 | Bitbucket Server init schema 20240115                                                                         | bitbucket_server |
| 2024-09-06 10:29:31.416 |<PHONE_NUMBER>33 | add commit line change table                                                                                | Framework        |
| 2024-09-06 10:29:31.444 |<PHONE_NUMBER>938 | add column `repo_id` and `commit_sha` at _tool_bitbucket_pipelines                                            | bitbucket        |
| 2024-09-06 10:29:31.683 |<PHONE_NUMBER>2344 | create init schemas                                                                                | Framework        |
| 2024-09-06 10:29:31.732 |<PHONE_NUMBER>1138 | Jira init schemas                                                                                | jira             |
| 2024-09-06 10:29:31.752 |<PHONE_NUMBER>2344 | Rename source to connection                                                                                | jira             |
| 2024-09-06 10:29:31.770 |<PHONE_NUMBER>2344 | Rename step to stage                                                                                | Framework        |
| 2024-09-06 10:29:31.801 |<PHONE_NUMBER>0005 | add column `subtasks` at _devlake_tasks                                                                       | Framework        |
| 2024-09-06 10:29:31.842 |<PHONE_NUMBER>0537 | add mode field to blueprint                                                                                | Framework        |
| 2024-09-06 10:29:31.925 |<PHONE_NUMBER>0537 | blueprint normal mode support                                                                                | Framework        |
| 2024-09-06 10:29:33.247 |<PHONE_NUMBER>2344 | create domain layer init schemas                                                                              | Framework        |
| 2024-09-06 10:29:33.292 |<PHONE_NUMBER>0001 | create subtask schema                                                                                | Framework        |
| 2024-09-06 10:29:33.806 |<PHONE_NUMBER>1133 | AE init schemas                                                                                | ae               |
| 2024-09-06 10:29:33.930 |<PHONE_NUMBER>1237 | Jenkins init schemas                                                                                | jenkins          |
| 2024-09-06 10:29:34.715 |<PHONE_NUMBER>1236 | Gitlab init schemas                                                                                | gitlab           |
| 2024-09-06 10:29:35.510 |<PHONE_NUMBER>1268 | Gitee init schemas                                                                                | gitee            |
| 2024-09-06 10:29:36.438 |<PHONE_NUMBER>0001 | Github init schemas 20220707                                                                                | github           |
| 2024-09-06 10:29:37.499 |<PHONE_NUMBER>1138 | Jira init schemas                                                                                | jira             |
| 2024-09-06 10:29:37.616 |<PHONE_NUMBER>5805 | add commit_file_components components table,update commit_files table                                         | Framework        |
| 2024-09-06 10:29:37.648 |<PHONE_NUMBER>2355 | add project_mapping table to domain layer                                                                     | Framework        |
| 2024-09-06 10:29:37.667 |<PHONE_NUMBER>5805 | remove notes from domain layer                                                                                | Framework        |
| 2024-09-06 10:29:37.704 |<PHONE_NUMBER>0001 | Github add github_runs table                                                                                | github           |
| 2024-09-06 10:29:37.744 |<PHONE_NUMBER>0001 | Github add github_jobs table                                                                                | github           |
| 2024-09-06 10:29:37.776 |<PHONE_NUMBER>5805 | rename pull_request_number to pull_request_key, issue_number to issue_key                                     | Framework        |
| 2024-09-06 10:29:37.860 |<PHONE_NUMBER>1236 | pipeline and job                                                                                | gitlab           |
| 2024-09-06 10:29:38.128 |<PHONE_NUMBER>1237 | Jenkins modify build and job                                                                                | jenkins          |
| 2024-09-06 10:29:38.370 |<PHONE_NUMBER>2735 | add NoPKModel to commit_parents                                                                               | Framework        |
| 2024-09-06 10:29:38.414 |<PHONE_NUMBER>0001 | Github add github_pipelines table                                                                             | github           |
| 2024-09-06 10:29:38.921 |<PHONE_NUMBER>0824 | Bitbucket init schema 20220803                                                                                | bitbucket        |
| 2024-09-06 10:29:38.990 |<PHONE_NUMBER>0912 | add pipeline id to job                                                                                | gitlab           |
| 2024-09-06 10:29:39.117 |<PHONE_NUMBER>2735 | add cicd models                                                                                | Framework        |
| 2024-09-06 10:29:39.267 |<PHONE_NUMBER>0824 | rename user_id to account_id in pull_request_comments and issue_comments                                      | Framework        |
| 2024-09-06 10:29:39.446 |<PHONE_NUMBER>2735 | modify tables for dora                                                                                | Framework        |
| 2024-09-06 10:29:39.471 |<PHONE_NUMBER>2321 | add column `type` at boards                                                                                | Framework        |
| 2024-09-06 10:29:39.595 |<PHONE_NUMBER>2321 | encrypt Blueprint                                                                                | Framework        |
| 2024-09-06 10:29:39.658 |<PHONE_NUMBER>2121 | encrypt Pipeline                                                                                | Framework        |
| 2024-09-06 10:29:39.877 |<PHONE_NUMBER>2735 | modify cicd pipeline                                                                                | Framework        |
| 2024-09-06 10:29:39.950 |<PHONE_NUMBER>0005 | UpdateSchemas for fixDurationToFloat8                                                                         | gitlab           |
| 2024-09-06 10:29:39.992 |<PHONE_NUMBER>0912 | gitlab add _tool_gitlab_pipeline_projects table                                                               | gitlab           |
| 2024-09-06 10:29:40.051 |<PHONE_NUMBER>0001 | Github delete github_pipelines table                                                                          | github           |
| 2024-09-06 10:29:40.030 |<PHONE_NUMBER>0001 | webhook init schemas                                                                                | webhook          |
| 2024-09-06 10:29:40.079 |<PHONE_NUMBER>2735 | modify cicd tasks                                                                                | Framework        |
| 2024-09-06 10:29:40.334 |<PHONE_NUMBER>5805 | add length of commit_file file_path                                                                           | Framework        |
| 2024-09-06 10:29:40.433 |<PHONE_NUMBER>2735 | modify board repos                                                                                | Framework        |
| 2024-09-06 10:29:40.528 |<PHONE_NUMBER>5535 | add origin change lead time for pr                                                                            | Framework        |
| 2024-09-06 10:29:40.566 |<PHONE_NUMBER>1223 | bitbucket add _tool_bitbucket_pipelines table                                                                 | bitbucket        |
| 2024-09-06 10:29:40.683 |<PHONE_NUMBER>0025 | UpdateSchemas for renamePipelineCommits                                                                       | Framework        |
| 2024-09-06 10:29:40.819 |<PHONE_NUMBER>1237 | Jenkins modify build primary key                                                                              | jenkins          |
| 2024-09-06 10:29:40.855 |<PHONE_NUMBER>3048 | add column `head_repo_id` at tool_github_pull_requests                                                        | github           |
| 2024-09-06 10:29:40.888 |<PHONE_NUMBER>0001 | add dora benchmark                                                                                | dora             |
| 2024-09-06 10:29:40.952 |<PHONE_NUMBER>5125 | modify lead_time_minutes                                                                                | Framework        |
| 2024-09-06 10:29:40.987 |<PHONE_NUMBER>2354 | bitbucket add _tool_bitbucket_pull_requests_commits table                                                     | bitbucket        |
| 2024-09-06 10:29:41.018 |<PHONE_NUMBER>1241 | add snapshot table                                                                                | Framework        |
| 2024-09-06 10:29:41.051 |<PHONE_NUMBER>2349 | bitbucket add _tool_bitbucket_deployments table                                                               | bitbucket        |
| 2024-09-06 10:29:41.091 |<PHONE_NUMBER>4623 | add column `repo_id` and `commit_sha` at _tool_bitbucket_pipelines                                            | bitbucket        |
| 2024-09-06 10:29:41.129 |<PHONE_NUMBER>3022 | create _tool_icla_committers                                                                                | icla             |
| 2024-09-06 10:29:41.156 |<PHONE_NUMBER>0001 | Create collector state table                                                                                | Framework        |
| 2024-09-06 10:29:41.172 |<PHONE_NUMBER>0001 | Remove cicd_pipeline_relation                                                                                | Framework        |
| 2024-09-06 10:29:41.224 |<PHONE_NUMBER>5744 | add skip_on_fail to _devlake_pipelines and _devlake_blueprint                                                 | Framework        |
| 2024-09-06 10:29:41.342 |<PHONE_NUMBER>1237 | add fields for jenkins jobs                                                                                | jenkins          |
| 2024-09-06 10:29:41.403 |<PHONE_NUMBER>1237 | add job path for builds                                                                                | jenkins          |
| 2024-09-06 10:29:41.489 |<PHONE_NUMBER>4734 | add project tables                                                                                | Framework        |
| 2024-09-06 10:29:43.418 |<PHONE_NUMBER>1138 | Tapd init schemas                                                                                | tapd             |
| 2024-09-06 10:29:43.516 |<PHONE_NUMBER>2735 | modify commits diffs                                                                                | Framework        |
| 2024-09-06 10:29:43.597 |<PHONE_NUMBER>1237 | add url to jenkinsJob                                                                                | jenkins          |
| 2024-09-06 10:29:43.864 |<PHONE_NUMBER>0001 | add project pr metric tables                                                                                | Framework        |
| 2024-09-06 10:29:43.887 |<PHONE_NUMBER>0008 | UpdateSchemas for addEnableGraphqlForConnection                                                               | github           |
| 2024-09-06 10:29:44.298 |<PHONE_NUMBER>0001 | Opsgenie init schemas                                                                                | opsgenie         |
| 2024-09-06 10:29:44.490 |<PHONE_NUMBER>0001 | PagerDuty init schemas                                                                                | pagerduty        |
| 2024-09-06 10:29:44.562 |<PHONE_NUMBER>0034 | add labels' schema for blueprint and pipeline                                                                 | Framework        |
| 2024-09-06 10:29:44.620 |<PHONE_NUMBER>2534 | add table _tool_jira_transformation_rules, add transformation_rule_id to _tool_jira_boards                    | jira             |
| 2024-09-06 10:29:44.646 |<PHONE_NUMBER>4342 | add project to blueprint                                                                                | Framework        |
| 2024-09-06 10:29:44.697 |<PHONE_NUMBER>0001 | add project issue metric tables                                                                               | Framework        |
| 2024-09-06 10:29:44.734 |<PHONE_NUMBER>0038 | save state for collector                                                                                | Framework        |
| 2024-09-06 10:29:44.805 |<PHONE_NUMBER>2502 | add table _tool_gitlab_transformation_rules, add transformation_rule_id and html_url to _tool_gitlab_projects | gitlab           |
| 2024-09-06 10:29:44.935 |<PHONE_NUMBER>0008 | add full name for builds                                                                                | jenkins          |
| 2024-09-06 10:29:44.954 |<PHONE_NUMBER>0001 | rename fields in project pr metric tables                                                                     | Framework        |
| 2024-09-06 10:29:44.979 |<PHONE_NUMBER>0341 | add enable to project metric                                                                                | Framework        |
| 2024-09-06 10:29:45.046 |<PHONE_NUMBER>3502 | add table _tool_jenkins_transformation_rules, add transformation_rule_id to _tool_jenkins_jobs                | jenkins          |
| 2024-09-06 10:29:45.134 |<PHONE_NUMBER>0001 | add cicd scope and add cicd_scope_id and drop builds&jobs                                                     | Framework        |
| 2024-09-06 10:29:45.416 |<PHONE_NUMBER>5902 | add table _tool_github_transformation_rules, add transformation_rule_id&clone_url to _tool_github_repos       | github           |
| 2024-09-06 10:29:45.550 |<PHONE_NUMBER>5900 | concat owner and name for old github_repos and drop owner for github_repos                                    | github           |
| 2024-09-06 10:29:45.584 |<PHONE_NUMBER>2316 | add project_name to _tool_jira_issues                                                                         | jira             |
| 2024-09-06 10:29:45.614 |<PHONE_NUMBER>2543 | add original_project to issues                                                                                | Framework        |
| 2024-09-06 10:29:45.668 |<PHONE_NUMBER>0548 | add error_name to _devlake_tasks and _devlake_pipelines                                                       | Framework        |
| 2024-09-06 10:29:45.733 |<PHONE_NUMBER>2121 | encrypt task.options                                                                                | Framework        |
| 2024-09-06 10:29:45.820 |<PHONE_NUMBER>5900 | add std type to github issue                                                                                | github           |
| 2024-09-06 10:29:45.767 |<PHONE_NUMBER>5900 | add std type to gitlab issue                                                                                | gitlab           |
| 2024-09-06 10:29:45.849 |<PHONE_NUMBER>2121 | add original type to issue                                                                                | Framework        |
| 2024-09-06 10:29:45.867 |<PHONE_NUMBER>1424 | rename project metrics                                                                                | Framework        |
| 2024-09-06 10:29:45.885 |<PHONE_NUMBER>1138 | Tapd encode connection token                                                                                | tapd             |
| 2024-09-06 10:29:45.942 |<PHONE_NUMBER>0000 | add connection config fields                                                                                | pagerduty        |
| 2024-09-06 10:29:45.985 |<PHONE_NUMBER>5901 | add multiauth to _tool_jira_connections                                                                       | jira             |
| 2024-09-06 10:29:46.015 |<PHONE_NUMBER>3311 | add _tool_customized_fields                                                                                | customize        |
| 2024-09-06 10:29:46.077 |<PHONE_NUMBER>1814 | add endpoint/proxy to opsgenie connection                                                                     | opsgenie         |
| 2024-09-06 10:29:46.025 |<PHONE_NUMBER>1814 | add endpoint/proxy to pagerduty connection                                                                    | pagerduty        |
| 2024-09-06 10:29:46.628 |<PHONE_NUMBER>0008 | add scope and table _tool_bitbucket_transformation_rules                                                      | bitbucket        |
| 2024-09-06 10:29:46.653 |<PHONE_NUMBER>0040 | add time_after to _devlake_collector_latest_state                                                             | Framework        |
| 2024-09-06 10:29:46.726 |<PHONE_NUMBER>5125 | modify issues story_point from int64 to float64                                                               | Framework        |
| 2024-09-06 10:29:46.751 |<PHONE_NUMBER>2735 | remove _tool_jira_issues column std_story_point                                                               | jira             |
| 2024-09-06 10:29:47.102 |<PHONE_NUMBER>0009 | add pipeline step                                                                                | bitbucket        |
| 2024-09-06 10:29:47.215 |<PHONE_NUMBER>5127 | add commit_sha index for commit_files                                                                         | Framework        |
| 2024-09-06 10:29:47.398 |<PHONE_NUMBER>3154 | add host, namespace, repo_name to issue_repo_commits                                                          | Framework        |
| 2024-09-06 10:29:47.424 |<PHONE_NUMBER>2532 | add remotelink_repo_pattern to _tool_jira_transformation_rules                                                | jira             |
| 2024-09-06 10:29:47.442 |<PHONE_NUMBER>0040 | remove created_date_after from _devlake_collector_latest_state                                                | Framework        |
| 2024-09-06 10:29:47.739 |<PHONE_NUMBER>0071 | sonarqube init schemas                                                                                | sonarqube        |
| 2024-09-06 10:29:47.823 |<PHONE_NUMBER>1031 | add IsDetailRequired to _tool_gitlab_merge_requests and _tool_gitlab_pipelines                                | gitlab           |
| 2024-09-06 10:29:47.990 |<PHONE_NUMBER>0082 | add code quality domain                                                                                | Framework        |
| 2024-09-06 10:29:48.048 |<PHONE_NUMBER>1814 | add transformation rules to opsgenie                                                                          | opsgenie         |
| 2024-09-06 10:29:48.104 |<PHONE_NUMBER>1814 | add transformation rules to pagerduty                                                                         | pagerduty        |
| 2024-09-06 10:29:48.517 |<PHONE_NUMBER>0014 | trello init schemas                                                                                | trello           |
| 2024-09-06 10:29:48.972 |<PHONE_NUMBER>0001 | teambition init schemas                                                                                | teambition       |
| 2024-09-06 10:29:49.479 |<PHONE_NUMBER>5035 | bamboo init schemas                                                                                | bamboo           |
| 2024-09-06 10:29:49.581 |<PHONE_NUMBER>0071 | sonarqube modify character set                                                                                | sonarqube        |
| 2024-09-06 10:29:49.737 |<PHONE_NUMBER>0003 | expend project_key                                                                                | sonarqube        |
| 2024-09-06 10:29:49.992 |<PHONE_NUMBER>0357 | add connection_id to _tool_bamboo_transformation_rules                                                        | bamboo           |
| 2024-09-06 10:29:50.022 |<PHONE_NUMBER>0357 | add connection_id to _tool_bitbucket_transformation_rules                                                     | bitbucket        |
| 2024-09-06 10:29:49.873 |<PHONE_NUMBER>0357 | add connection_id to _tool_github_transformation_rules                                                        | github           |
| 2024-09-06 10:29:50.051 |<PHONE_NUMBER>0357 | add connection_id to _tool_gitlab_transformation_rules                                                        | gitlab           |
| 2024-09-06 10:29:49.766 |<PHONE_NUMBER>0357 | add connection_id to _tool_jenkins_transformation_rules                                                       | jenkins          |
| 2024-09-06 10:29:49.963 |<PHONE_NUMBER>0357 | add connection_id to _tool_jira_transformation_rules                                                          | jira             |
| 2024-09-06 10:29:49.798 |<PHONE_NUMBER>0357 | add connection_id to _tool_trello_transformation_rules                                                        | trello           |
| 2024-09-06 10:29:49.933 |<PHONE_NUMBER>0357 | add type/env to github runs and run_jobs                                                                      | github           |
| 2024-09-06 10:29:49.845 |<PHONE_NUMBER>0357 | add type/env to gitlab pipelines                                                                              | gitlab           |
| 2024-09-06 10:29:50.370 |<PHONE_NUMBER>3324 | expand _tool_jira_remotelinks.url and _tool_jira_issue_commits.commit_url to LONGTEXT                         | jira             |
| 2024-09-06 10:29:50.606 |<PHONE_NUMBER>0003 | Tapd add transformation, update _raw_data_params                                                              | tapd             |
| 2024-09-06 10:29:50.622 |<PHONE_NUMBER>0004 | Tapd delete issue and remote link                                                                             | tapd             |
| 2024-09-06 10:29:50.876 |<PHONE_NUMBER>0003 | circleci init schemas                                                                                | circleci         |
| 2024-09-06 10:29:50.913 |<PHONE_NUMBER>0041 | add issue_assignees table                                                                                | Framework        |
| 2024-09-06 10:29:50.933 |<PHONE_NUMBER>0001 | Rename Collector state table for Singer Taps                                                                  | Framework        |
| 2024-09-06 10:29:50.955 |<PHONE_NUMBER>0701 | Rename cicd_piopeline_commits repo to repo_url                                                                | Framework        |
| 2024-09-06 10:29:51.062 |<PHONE_NUMBER>0357 | add type/env to bitbucket pipelines and pipeline_steps                                                        | bitbucket        |
| 2024-09-06 10:29:58.376 |<PHONE_NUMBER>0004 | modify tapd custom field name                                                                                | tapd             |
| 2024-09-06 10:29:58.482 |<PHONE_NUMBER>0011 | add issue desc and comments                                                                                | jira             |
| 2024-09-06 10:29:58.582 |<PHONE_NUMBER>0015 | modify tapd custom field name                                                                                | tapd             |
| 2024-09-06 10:29:58.617 |<PHONE_NUMBER>2316 | add changelog_total field to _tool_jira_issues                                                                | jira             |
| 2024-09-06 10:29:58.633 |<PHONE_NUMBER>0701 | Rename project_pr_metrics.deployment_id to deployment_commit_id                                               | Framework        |
| 2024-09-06 10:29:58.818 |<PHONE_NUMBER>0357 | add repo_id to pr as part of the primary key                                                                  | bitbucket        |
| 2024-09-06 10:29:58.872 |<PHONE_NUMBER>5129 | add commit author info to _tool_github_pull_request_commits table                                             | github           |
| 2024-09-06 10:29:59.015 |<PHONE_NUMBER>1352 | add type and environment to bamboo build tables                                                               | bamboo           |
| 2024-09-06 10:29:59.071 |<PHONE_NUMBER>5129 | add commit author info to pull_request_commits table                                                          | Framework        |
| 2024-09-06 10:29:59.181 |<PHONE_NUMBER>5129 | add commit author info to _tool_bitbucket_pull_request_commits table                                          | bitbucket        |
| 2024-09-06 10:29:59.126 |<PHONE_NUMBER>5129 | add commit author info to _tool_gitee_pull_request_commits table                                              | gitee            |
| 2024-09-06 10:29:59.233 |<PHONE_NUMBER>5129 | add commit author info to _tool_gitlab_mr_commits table                                                       | gitlab           |
| 2024-09-06 10:29:59.478 |<PHONE_NUMBER>0001 | Feishu init schemas                                                                                | feishu           |
| 2024-09-06 10:29:59.336 |<PHONE_NUMBER>0001 | Slack init schemas                                                                                | slack            |
| 2024-09-06 10:29:59.522 |<PHONE_NUMBER>0702 | add cicd_deployment_commits table                                                                             | Framework        |
| 2024-09-06 10:29:59.584 |<PHONE_NUMBER>0010 | UpdateSchemas for addGithubMultiAuth                                                                          | github           |
| 2024-09-06 10:29:59.828 |<PHONE_NUMBER>0001 | initialize schemas for Azure Devops                                                                           | azuredevops      |
| 2024-09-06 10:30:00.438 |<PHONE_NUMBER>0001 | zentao init schemas                                                                                | zentao           |
| 2024-09-06 10:30:00.468 |<PHONE_NUMBER>2121 | add original status to pull_requests                                                                          | Framework        |
| 2024-09-06 10:30:00.531 |<PHONE_NUMBER>0029 | expand _tool_jira_remotelinks.self to LONGTEXT                                                                | jira             |
| 2024-09-06 10:30:00.568 |<PHONE_NUMBER>0001 | add calendar months                                                                                | Framework        |
| 2024-09-06 10:30:00.594 |<PHONE_NUMBER>3738 | add repo_url to _tool_jira_issue_commits                                                                      | jira             |
| 2024-09-06 10:30:00.700 |<PHONE_NUMBER>0001 | change pull_request_comments.pr_id to varchar(255) type                                                       | Framework        |
| 2024-09-06 10:30:00.716 |<PHONE_NUMBER>0002 | Rename finished_commits_diffs to _tool_refdiff_finished_commits_diffs                                         | Framework        |
| 2024-09-06 10:30:00.746 |<PHONE_NUMBER>2121 | add updated_date to issue_comments                                                                            | Framework        |
| 2024-09-06 10:30:00.825 |<PHONE_NUMBER>0002 | UpdateSchemas for fixRunNameToText                                                                            | github           |
| 2024-09-06 10:30:00.881 |<PHONE_NUMBER>1352 | rename transformation rule to scope config                                                                    | bamboo           |
| 2024-09-06 10:30:01.067 |<PHONE_NUMBER>1430 | add_build_id_as_job_primary_key                                                                               | azuredevops      |
| 2024-09-06 10:30:01.128 |<PHONE_NUMBER>1352 | rename transformation rule to scope config                                                                    | bitbucket        |
| 2024-09-06 10:30:01.339 |<PHONE_NUMBER>1352 | rename transformation rule to scope config for github                                                         | github           |
| 2024-09-06 10:30:01.403 |<PHONE_NUMBER>3435 | rename transformation rule to scope config for gitlab                                                         | gitlab           |
| 2024-09-06 10:30:01.467 |<PHONE_NUMBER>4905 | rename transformation rule to scope config for jenkins                                                        | jenkins          |
| 2024-09-06 10:30:01.530 |<PHONE_NUMBER>0031 | rename transformation rule to scope config for jira                                                           | jira             |
| 2024-09-06 10:30:01.570 |<PHONE_NUMBER>1510 | add _tool_github_issue_assignees table                                                                        | github           |
| 2024-09-06 10:30:01.706 |<PHONE_NUMBER>0109 | rename transformation rule to scope config for opsgenie                                                       | opsgenie         |
| 2024-09-06 10:30:01.638 |<PHONE_NUMBER>0109 | rename transformation rule to scope config for pagerduty                                                      | pagerduty        |
| 2024-09-06 10:30:01.775 |<PHONE_NUMBER>5926 | rename transformation rule to scope config for tapd                                                           | tapd             |
| 2024-09-06 10:30:01.835 |<PHONE_NUMBER>0250 | rename transformation rule to scope config for trello                                                         | trello           |
| 2024-09-06 10:30:01.863 |<PHONE_NUMBER>3738 | add application_type to _tool_jira_scope_configs                                                              | jira             |
| 2024-09-06 10:30:02.372 |<PHONE_NUMBER>0001 | zentao add scope config tables                                                                                | zentao           |
| 2024-09-06 10:30:02.619 |<PHONE_NUMBER>0011 | zentao add issue repo commits tables                                                                          | zentao           |
| 2024-09-06 10:30:02.635 |<PHONE_NUMBER>0109 | remove _tool_opsgenie_scope_configs table                                                                     | opsgenie         |
| 2024-09-06 10:30:02.650 |<PHONE_NUMBER>0109 | remove _tool_pagerduty_scope_configs table                                                                    | pagerduty        |
| 2024-09-06 10:30:02.691 |<PHONE_NUMBER>0339 | add _tool_gitlab_issue_assignees table                                                                        | gitlab           |
| 2024-09-06 10:30:02.712 |<PHONE_NUMBER>5630 | rename_tx_rule_table_to_scope_config                                                                          | azuredevops      |
| 2024-09-06 10:30:02.735 |<PHONE_NUMBER>5630 | add entities column to gitrepositoryconfig table                                                              | azuredevops      |
| 2024-09-06 10:30:02.899 |<PHONE_NUMBER>0001 | zentao init changelog schemas                                                                                | zentao           |
| 2024-09-06 10:30:02.902 |<PHONE_NUMBER>3856 | clear the value of _tool_jira_scope_configs.remotelink_repo_pattern                                           | jira             |
| 2024-09-06 10:30:02.934 |<PHONE_NUMBER>4111 | add full_name to _tool_github_repos                                                                           | github           |
| 2024-09-06 10:30:02.990 |<PHONE_NUMBER>0339 | add squash and diff sha columns                                                                               | gitlab           |
| 2024-09-06 10:30:03.035 |<PHONE_NUMBER>0001 | zentao init changelog schemas                                                                                | zentao           |
| 2024-09-06 10:30:03.038 |<PHONE_NUMBER>0001 | populated _raw_data_table column for azuredevops git repos                                                    | azuredevops      |
| 2024-09-06 10:30:03.049 |<PHONE_NUMBER>0002 | populated _raw_data columns for jenkins jobs                                                                  | jenkins          |
| 2024-09-06 10:30:03.058 |<PHONE_NUMBER>0002 | populated _raw_data columns for opsgenie services                                                             | opsgenie         |
| 2024-09-06 10:30:03.061 |<PHONE_NUMBER>0002 | populated _raw_data columns for pagerduty services                                                            | pagerduty        |
| 2024-09-06 10:30:03.042 |<PHONE_NUMBER>0002 | populated _raw_data columns for tapd workspaces                                                               | tapd             |
| 2024-09-06 10:30:03.055 |<PHONE_NUMBER>0002 | populated _raw_data columns for trello boards                                                                 | trello           |
| 2024-09-06 10:30:03.052 |<PHONE_NUMBER>0002 | populated _raw_data columns for zentao projects                                                               | zentao           |
| 2024-09-06 10:30:03.336 |<PHONE_NUMBER>5809 | add table _tool_zentao_execution_stories, _tool_zentao_execution_summary and _tool_zentao_product_summary     | zentao           |
| 2024-09-06 10:30:03.361 |<PHONE_NUMBER>5900 | add archived to _tool_gitlab_projects                                                                         | gitlab           |
| 2024-09-06 10:30:03.364 |<PHONE_NUMBER>0001 | populated _raw_data columns for azuredevops                                                                   | azuredevops      |
| 2024-09-06 10:30:03.396 |<PHONE_NUMBER>3602 | add scope_config_id to _tool_bamboo_plans                                                                     | bamboo           |
| 2024-09-06 10:30:03.453 |<PHONE_NUMBER>2900 | add api key tables                                                                                | Framework        |
| 2024-09-06 10:30:03.491 |<PHONE_NUMBER>2534 | add table _tool_jira_issue_relationships table                                                                | jira             |
| 2024-09-06 10:30:03.558 |<PHONE_NUMBER>2121 | tasks uses json                                                                                | Framework        |
| 2024-09-06 10:30:03.579 |<PHONE_NUMBER>3814 | add env_name_pattern to _tool_bamboo_scope_configs                                                            | bamboo           |
| 2024-09-06 10:30:03.589 |<PHONE_NUMBER>0001 | rename startTime/finishTime to start_time/finish_time                                                         | azuredevops      |
| 2024-09-06 10:30:03.618 |<PHONE_NUMBER>5723 | drop the column total_real from the table _tool_zentao_projects                                               | zentao           |
| 2024-09-06 10:30:03.698 |<PHONE_NUMBER>5119 | add plan_result_key to _tool_bamboo_deploy_build and _tool_bamboo_plan_build_commits                          | bamboo           |
| 2024-09-06 10:30:03.722 |<PHONE_NUMBER>2534 | add table _tool_jira_issues.all_fields column                                                                 | jira             |
| 2024-09-06 10:30:03.763 |<PHONE_NUMBER>0001 | add issue_relationships table                                                                                | Framework        |
| 2024-09-06 10:30:03.821 |<PHONE_NUMBER>5125 | modify cicd_pipelines name from varchar to text                                                               | Framework        |
| 2024-09-06 10:30:03.844 |<PHONE_NUMBER>5125 | drop _devlake_collector_tap_state table                                                                       | Framework        |
| 2024-09-06 10:30:04.094 |<PHONE_NUMBER>0504 | Decrypt Azure DevOps connection fields                                                                        | azuredevops      |
| 2024-09-06 10:30:04.106 |<PHONE_NUMBER>0421 | add missing migrations from 0.17 to 0.18                                                                      | azuredevops      |
| 2024-09-06 10:30:04.268 |<PHONE_NUMBER>5125 | normalize bp settings to multiple tables                                                                      | Framework        |
| 2024-09-06 10:30:04.325 |<PHONE_NUMBER>2403 | add cicd deployments table                                                                                | Framework        |
| 2024-09-06 10:30:04.338 |<PHONE_NUMBER>0000 | add connection config fields                                                                                | opsgenie         |
| 2024-09-06 10:30:04.444 |<PHONE_NUMBER>0041 | add sync policy to _devlake_blueprints and _devlake_pipelines table                                           | Framework        |
| 2024-09-06 10:30:04.482 |<PHONE_NUMBER>0100 | add github deployment table                                                                                | github           |
| 2024-09-06 10:30:04.502 |<PHONE_NUMBER>0000 | rename _tool_bamboo_deploy_build to _tool_bamboo_deploy_builds                                                | bamboo           |
| 2024-09-06 10:30:04.529 |<PHONE_NUMBER>0001 | rename _tool_bamboo_deploy_environment to _tool_bamboo_deploy_environments                                    | bamboo           |
| 2024-09-06 10:30:04.554 |<PHONE_NUMBER>0001 | rename raw tables' name to their plural form                                                                  | bamboo           |
| 2024-09-06 10:30:04.586 |<PHONE_NUMBER>0004 | add priority to _tool_pagerduty_incidents table                                                               | pagerduty        |
| 2024-09-06 10:30:04.625 |<PHONE_NUMBER>0083 | add issue custom array field                                                                                | Framework        |
| 2024-09-06 10:30:04.687 |<PHONE_NUMBER>2829 | add scope_config_id to _tool_gitee_repos table                                                                | gitee            |
| 2024-09-06 10:30:04.654 |<PHONE_NUMBER>2829 | add scope_config_id to _tool_sonarqube_projects table                                                         | sonarqube        |
| 2024-09-06 10:30:04.740 |<PHONE_NUMBER>0000 | add deployment table in tool layer                                                                            | gitlab           |
+-------------------------+----------------+---------------------------------------------------------------------------------------------------------------+------------------+
220 rows in set (0.00 sec)

mysql>

I see these PV get created, and looks like not cleaned up when uninstall helm chart? I uninstalled and installed several times in the past few days.
➜  tmp kubectl -n devlake get pv -n devlake |grep mysql
pvc-6f10b9ba-f1bb-4477-870c-b6595c7da39b   50Gi       RWO            Delete           Bound      default/devlake-mysql-data-devlake-mysql-0   standard                22h
pvc-de9144d5-506c-428a-a8ae-bd49191db5cd   50Gi       RWO            Delete           Bound      devlake/devlake-mysql-data-devlake-mysql-0   standard                3d22h

Delete all devlake pvc and pv, and re-install helm chart, proceed migration process.
Wait a few mins and it successfully landed to the DevLake home page.
However, mysql command hanging on below:
mysql> use lake;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

This could help: https://dba.stackexchange.com/questions/99304/use-db-name-takes-too-long-to-change-when-login-remotely

Delete all devlake pvc and pv, and re-install helm chart, proceed migration process. Wait a few mins and it successfully landed to the DevLake home page.
However, mysql command hanging on below:
mysql> use lake;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

I would guess the container somehow got killed during the first boot-up, and you were actually seeing the second boot with some previously executed scripts.

Looks like that is what happened.
However, the pv reclaim policy is "delete", it should be cleaned up when uninstall helm chart, right? but it didn't and left over which was picked up later by a new helm chart installation.

@diwangcanada I am not familiar with helm-chart.
Can you check why it got killed on the first boot? I think we need to address the problem because there were already a couple of reports.

The pvc did not release after uninstall helm chart because of the protection. This is properly by design, but does it make more sense to set pv reclaim policy to "retain"?
➜  tmp kubectl -n devlake describe pvc devlake-mysql-data-devlake-mysql-0
Name:          devlake-mysql-data-devlake-mysql-0
Namespace:     devlake
StorageClass:  standard
Status:        Bound
Volume:        pvc-1ebb7410-0e43-460f-af0b-f7d4be573b2a
Labels:        app.kubernetes.io/instance=devlake
               app.kubernetes.io/name=devlake
Annotations:   pv.kubernetes.io/bind-completed: yes
               pv.kubernetes.io/bound-by-controller: yes
               volume.beta.kubernetes.io/storage-provisioner: pd.csi.storage.gke.io
               volume.kubernetes.io/storage-provisioner: pd.csi.storage.gke.io
**Finalizers:    [kubernetes.io/pvc-protection]**
Capacity:      50Gi
Access Modes:  RWO
VolumeMode:    Filesystem
Used By:       <none>
Events:        <none>

@diwangcanada I am not familiar with helm-chart.
Can you check why it got killed on the first boot? I think we need to address the problem because there were already a couple of reports.

Unfortunately, I re-installed a few times, but can't reproduce the same issue again.

@diwangcanada I am not familiar with helm-chart.
Can you check why it got killed on the first boot? I think we need to address the problem because there were already a couple of reports.

Unfortunately, I re-installed a few times, but can't reproduce the same issue again.

No worry.
Let me know if you run into the problem again.

install helm chart because of the protection. This is properly by design, but does it make more sense to set pv reclaim policy

I think it makes more sense to delete all related pvc when users explicitly uninstall the helm-chart intentionally.
However, I wonder what would happen when upgrading:

helm-chart operates in an uninstall/install manner and would delete all those PVCs
or would it keep those PVCs during upgrading or downgrading?


java.util.NoSuchElementException: Param binSampleCount does not exist on LightGBM

Describe the bug
binSampleCount does not exist
Instantiation of LightGBM
model = LightGBMClassifier(featuresCol="idfFeatures", labelCol="label")
pipeline_cv_lr = Pipeline().setStages(
    [nltk_cleaner, count_vectorizer, idf, model]
)

model_cv_lr = pipeline_cv_lr.fit(train_data)
predictions_cv_lr = model_cv_lr.transform(test_data)

Info (please complete the following information):

MMLSpark Version: mmlspark_2.11;1.0.0-rc3
Spark Version e.g. 2.4.5
Spark Platform: Local Jupyter

** Error**
Py4JJavaError: An error occurred while calling o80.getParam.
: java.util.NoSuchElementException: Param binSampleCount does not exist.
	at org.apache.spark.ml.param.Params$$anonfun$getParam$2.apply(params.scala:729)
	at org.apache.spark.ml.param.Params$$anonfun$getParam$2.apply(params.scala:729)
	at scala.Option.getOrElse(Option.scala:121)
	at org.apache.spark.ml.param.Params$class.getParam(params.scala:728)
	at org.apache.spark.ml.PipelineStage.getParam(Pipeline.scala:42)
	at sun.reflect.GeneratedMethodAccessor28.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
	at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
	at py4j.Gateway.invoke(Gateway.java:282)
	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
	at py4j.commands.CallCommand.execute(CallCommand.java:79)
	at py4j.GatewayConnection.run(GatewayConnection.java:238)
	at java.lang.Thread.run(Thread.java:748)

AB#1164920

@sarmientoj24 very strange, it should just work.  What kind of environment/cluster are you running on?  Maybe this way doesn't work there?  It is possible there are multiple mmlspark versions installed there somehow?

@imatiach-msft I met the same error as above, and I am thinking this is due to installation issues. I have spark 3.1.2 in my local jupyter notebook, and I followed the python installation method as in this official website:
(https://microsoft.github.io/SynapseML/)
I use this code for installation as I use 3.1.2 spark:
spark = SparkSession.builder.appName("MyApp") \             .config("spark.jars.packages", "com.microsoft.azure:synapseml_2.12:0.9.5-13-d1b51517-SNAPSHOT") \             .config("spark.jars.repositories", "https://mmlspark.azureedge.net/maven") \             .getOrCreate()
But if failed when I run "import synapse", it said no module found. I also tried in Kaggle notebook and GCP Dataproc, both had same error. Ultimately, I had to use pip install synapseml, and pip install synapse so that I can run the LightGBM model and import this module.
Could you please help me with this installation issue if possible? Thanks a lot!


updated target sdk 28. updated android gradle plugin. updated other libraries including support, build tools version and butter knife

This PR contains following changes:

updated target sdk is 28 now.
updated android gradle plugin.
updated other libraries including support libs, build tools version, etc
also, updated butterknife library to latest version, which is, v8.8.1

LGTM, thank you.


Fill out contribution guidelines

It should include instructions for pre-commit:
pip install pre-commit
pre-commit install


Terminal breaks copied text at window line wraps, even when the text has no new-line characters

I recall this was working in older versions of Terminal and in Windows' copy of the console window, but it seems to have broken more recently.
Environment
Windows build number: 18363.720 (Windows 10 ver. 1909 with update KB4551762)
Windows Terminal version: 0.10.781.0
Steps to reproduce

Open this file in an editor: C:\Windows\System32\WindowsCodecsRaw.txt
Notice that the last line of the file "THE SOFTWARE IS PROVIDED".... is over 500 characters long.
Open Terminal to the Command Prompt or PowerShell, then run:
type C:\Windows\System32\WindowsCodecsRaw.txt
Drag to select text from multiple in-window lines of the last line of the file, then right-click to copy.
Paste the clipping into a new file in Notepad.

Expected and actual behavior
Expected: the text is all on one line.
Actual: the text is split into multiple lines.

Here's my profiles.json file in case that matters, though I can't see anything that stands out:
{
  "$schema": "https://aka.ms/terminal-profiles-schema",
  "defaultProfile": "{0caa0dad-35be-5f56-a8ff-afceeeaa6101}",
  "initialCols": 120,
  "initialRows": 40,
  "profiles": {
    "defaults": {
      "fontFace": "Consolas",
      "fontSize": 11,
      "historySize": 9999
    },
    "list": [
      {
        "guid": "{0caa0dad-35be-5f56-a8ff-afceeeaa6101}",
        "name": "Command Prompt",
        "commandline": "%comspec%",
        "startingDirectory": "C:\\Windows\\System32",
        "hidden": false
      },
      {
        "guid": "{61c54bbd-c2c6-5271-96e7-009a87ff44bf}",
        "name": "Windows PowerShell",
        "commandline": "C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\powershell.exe",
        "startingDirectory": "C:\\Windows\\System32",
        "hidden": false
      },
      {
        "guid": "{c6eaf9f4-32a7-5fdc-b5cf-066e8a4b1e40}",
        "hidden": false,
        "name": "Ubuntu-18.04",
        "source": "Windows.Terminal.Wsl"
      },
      {
        "guid": "{b453ae62-4e3d-5e58-b989-0a998ec441b8}",
        "hidden": false,
        "name": "Azure Cloud Shell",
        "source": "Windows.Terminal.Azure"
      }
    ]
  },
  "schemes": [],
  "keybindings": []
}

same issue, need to support, please :))

I have the issue. Seems to have been introduced in v0.10.761.0

Okay so we’ve been seeing various reports of this in the most recent build, despite doing some work to specifically handle this better.
Turns out, it’ll only happen when it causes the viewport to scroll – like when you’re emitting text at the bottom of the window. This explains why it seems like sometimes it works fine and other times it doesn’t.
Now that we’ve got a consistent repro, it should make debugging much easier.

Turns out, it’ll only happen when it causes the viewport to scroll – like when you’re emitting text at the bottom of the window.

I'm not sure that's quite right? I just tried starting Terminal with the profiles.json above and typing out the file, which doesn't cause a scroll of the displayed area as far as I can see. After copying the first 3 displayed lines of the "THE SOFTWARE" line of text (up to "OR ANY DAMAGES W"), I get 2 lines in Notepad.

I mean, here's what I'm seeing when I do type C:\Windows\System32\WindowsCodecsRaw.txt with a fresh WT:

(note the line numbers in Sublime, behind WT)
Then, performing it a second time, which causes the scrolling:

@zadjii-msft I can constantly reproduce it even when the viewport does not scroll. I found it's related to this:
https://github.com/microsoft/terminal/blob/d47da2d617dbda3a46a1a052122536eca123b722/src/buffer/out/textBuffer.cpp#L1543
If I remove this mechanism, the copied text will not have extra new-lines.

For me as an Admin and DevOps this is a major issue - for example: ssh pubkeys are breaking when being copied and pasted.
For anyone who need to downgrade due to this, I can recommend to do this via choco like this:
choco list microsoft-windows-terminal --all
choco uninstall microsoft-windows-terminal
choco install microsoft-windows-terminal --version 0.10.761.0

Hope this helps.

For me as an Admin and DevOps this is a major issue - for example: ssh pubkeys are breaking when being copied and pasted.
For anyone who need to downgrade due to this, I can recommend to do this via choco like this:
choco list microsoft-windows-terminal --all
choco uninstall microsoft-windows-terminal
choco install microsoft-windows-terminal --version 0.10.761.0

The version 0.10.761.0 exhibits the same behavior

@paul-michalik you're in luck because I'm working on this pretty aggressively over in #5181

As a workaround for now, resize the terminal window (enlarge or shrink) and try to copy&paste it again. It works for me.

Does anyone know what's needed to get this into Cygwin?

This is still broken in "1.0.1811.0".

Still broken in Cygwin too fwiw.

@nvonwolf This was a pretty specific scenario that should have been fixed by #5181. If you're still seeing this behavior, could you file a new issue with exact repro steps, so we could track the new regression? Thanks!

I'm at 1.17.11461.0 and still have this issue. Not with scrolling, but always. :(
Anything I can do about it? Should I open a new issue or stick to this one?

@lindhe I'd recommend filing a new issue, with more details about your setup. Also, I'd recommend trying out Terminal Preview - I'm pretty sure there were some fixes in the 1.18/1.19 timeframe that might have helped with some scenarios around this topic.


some QoL improvement?

some things were bothering me, so i made a tampermonkey script to fix some. here: https://github.com/ForwardFeed/dekzeh-pokemon-calc-utilities
I wanted to shared it so maybe it could be integrated directly into the app.

Closed because of https://github.com/dekzeh/calc/pull/2


feat: Add exclude-ignores flag and --config-file attribute

This is intended for adding exclude-ignores flag and --config-file attribute.
In some cases, we want to enforce some rules and remove the ability to #tfsec:ignore

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.


group_concat not fully supported yet in 0.46

group_concat(
  DISTINCT a,b
  ORDER BY c, d
  SEPARATOR ';'
)

SEPARATOR  still cause error:
ParserError("Expected ), found: SEPARATOR at Line: *, Column *

#1225

i just found it was resolved and not in 0.46.


there is no 404 error handler page in flask app

Is your feature request related to a problem? Please describe.
if user hits the url which not exits that he will get 404 not found error .
Describe the solution you'd like
adding a 404 error handler page in flask app to handle this error.

i want to work on this if possible please can you assign me this issue.


Terminal process failed to launch: make more clear that the default shell was used.

Testing #101299

I got that message but the terminal did still launch. I would suggest to reword the message saying that the path doesn't exist and that the default shell was used.

Actually this is not the case.


NTRs: Protein extraction from membranes

Hi GO,
I would need a bunch of terms to describe membrane extraction of mislocalized transmembrane proteins
2 different proteins mediate this activity:

SPF1 in S. cerevisiae (P39986) and its human homolog ATP13A1 (Q9HD20): dislocase that specifically extracts mitochondrial transmembrane proteins from the endoplasmic reticulum membrane. Has an atypically large substrate-binding pocket that recognizes and binds moderately hydrophobic transmembranes with short hydrophilic lumenal domains. Uses ATP as an energy source to dislocate mislocalized transmembrane proteins from the endoplasmic reticulum membrane.

RX PubMed=32973005; DOI=10.1126/science.abc5809
RA McKenna M.J., Sim S.I., Ordureau A., Wei L., Harper J.W., Shao S., Park E.
RT The endoplasmic reticulum P5A-ATPase is a transmembrane helix dislocase.
RL journal article: Science 369:0-0 (2020)

MSP1 in S. cerevisiae (P28737) and its human homolog ATAD1 (Q8NBU5): dislocase that specifically extracts endoplasmic reticulum transmembrane proteins from the outer mitochondrion membrane.

RX PubMed=24821790; DOI=10.1073/pnas.1405755111
RA Okreglak V., Walter P.
RT The conserved AAA-ATPase Msp1 confers organelle specificity to tail-anchored proteins.
RL journal article: Proc. Natl. Acad. Sci. U.S.A. 111:8019-8024 (2014)
RX PubMed=28712723; DOI=10.1016/j.molcel.2017.06.019
RA Wohlever M.L., Mateja A., McGilvray P.T., Day K.J., Keenan R.J.
RT Msp1 Is a Membrane Protein Dislocase for Tail-Anchored Proteins.
RL journal article: Mol. Cell 67:194-202.e6-194-202.e6 (2017)
We already have a Function term for these proteins: GO:0008320 protein transmembrane transporter activity
But I would need some 3 Process terms to describe extraction of proteins from the membrane.
GO:XXXXXXX protein extraction from membrane
Category: Process
Definition: The process that results in the extraction of a protein from a biological membrane. Extraction in this context means having some part or covalently attached group that is removed from the hydrophobic region of one or both bilayers.
Child of GO:0090150 establishment of protein localization to membrane
PMID:24821790
PMID:28712723
PMID:32973005
GO:XXXXXXX tail-anchored membrane protein extraction from ER membrane
Category: Process
PMID:32973005
Definition: A process of protein extraction from the endoplasmic reticulum (ER) membrane in which a tail-anchored (TA) transmembrane protein is removed from an endoplasmic reticulum (ER) membrane. TA transmembrane protein, also named type III transmembrane proteins, contain a single C-terminal transmembrane region.
Child of GO:XXXXXXX protein extraction from membrane
Child of GO:0007029 endoplasmic reticulum organization
GO:XXXXXXX tail-anchored membrane protein extraction from outer mitochondrion membrane
Category: Process
Definition: A process of protein extraction from the outer mitochondrion membrane in which a tail-anchored (TA) transmembrane protein is removed from an outer mitochondrion membrane. TA transmembrane protein, also named type III transmembrane proteins, contain a single C-terminal transmembrane region.
Child of GO:XXXXXXX protein extraction from membrane
Child of GO:0007008 outer mitochondrial membrane organization
PMID:24821790
PMID:28712723
Thanks
Sylvain

Hi Karen (@krchristie)
I hope you and your family are doing well in these strange times
I discussed with Pascale and she mentioned the GO:0030970 retrograde protein transport, ER to cytosol, which has the synonym: protein dislocation from ER"
However, this cannot be used in my case because: 1) it is not a retrograde transport 2) despite its name, proteins are not dislocated, they are extracted, and, in the case of MSP1, they are targeted to their appropriate location once extracted (PMID:31445887)
She also mentioned correctly the the term GO:0008320 protein transmembrane transporter activity cannot be used since it does not represent a transmembrane transport. I submitted reactions to Rhea and will let you know their conclusions. We will probably have to create new reactions/GO terms to represent membrane extraction.
I will keep you in the loop
Thanks
Sylvain

Hi Sylvain (@sylvainpoux)
Thanks, we are all healthy though remote learning is hard for the kids. I hope you and your family are all doing well too.
I look forward to reading these very interesting papers. I have some other priorities for the next week, so I will look at them after that and see where I think they belong in GO. It will be great for you to keep me in the loop about any new Rhea reactions so that I can make sure the GO terms align with the Rhea.
Many thanks,
-Karen

Hi Karen,
Rhea created a reaction for transmembrane-proteins extraction from membranes. RHEA:66168 describes this activity (not sure it is already available, but this term is clearly wother creating a GO term
CC       Reaction=[protein]-with a C-terminal TM segment(out) + ATP + H2O =
CC         [protein]-with a C-terminal TM segment(in) + ADP + H(+) + phosphate;
CC         Xref=Rhea:RHEA:66168, Rhea:RHEA-COMP:16963, ChEBI:CHEBI:15377,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:90782, ChEBI:CHEBI:456216;
CC         Evidence={ECO:0000305|PubMed:24843043};
Cheers
Sylvain

Ah! If there is a RHEA, then this should be a MF, and not a BP, shouldn't it ?

Hi Pascale,
both actually, I requested a BP (still valid) and a MF could be created thanks to the Rhea
Sylvain

"GO:0008320 protein transmembrane transporter activity" describes transport across a membrane; extraction does not apply, as far as I understand what you describe

The 3 processes you request sound more like MF, in that they are single steps. The process would be some quality process that rectifies mislocalized transmembrane proteins; wouldn't it ?

Thanks, Pascale

Hi Pascale,
I think we should request:

one MF to represent transmembrane-proteins extraction from membranes. RHEA:66168 describes this activity

CC Reaction=[protein]-with a C-terminal TM segment(out) + ATP + H2O =
CC [protein]-with a C-terminal TM segment(in) + ADP + H(+) + phosphate;
CC Xref=Rhea:RHEA:66168,
I don't know which parent terms to assign. And yes, you are correct, it is not related to GO:0008320 protein transmembrane transporter activity"
I think 2 BP are needed to describe extraction from different membranes. The MF is the same for both proteins. And I suspect, other dislocases for other subcellular locations will be discoved in the future. But the MF will be the same

GO:XXXXXXX tail-anchored membrane protein extraction from ER membrane
Category: Process
PMID:32973005
Definition: A process of protein extraction from the endoplasmic reticulum (ER) membrane in which a tail-anchored (TA) transmembrane protein is removed from an endoplasmic reticulum (ER) membrane. TA transmembrane protein, also named type III transmembrane proteins, contain a single C-terminal transmembrane region.
Child of GO:XXXXXXX protein extraction from membrane
Child of GO:0007029 endoplasmic reticulum organization

GO:XXXXXXX tail-anchored membrane protein extraction from outer mitochondrion membrane
Category: Process
Definition: A process of protein extraction from the outer mitochondrion membrane in which a tail-anchored (TA) transmembrane protein is removed from an outer mitochondrion membrane. TA transmembrane protein, also named type III transmembrane proteins, contain a single C-terminal transmembrane region.
Child of GO:XXXXXXX protein extraction from membrane
Child of GO:0007008 outer mitochondrial membrane organization
PMID:24821790
PMID:28712723

Thanks
Sylvain

Hi @sylvainpoux
Here's what I propose, it's more specific than what you had proposed, but all papers you cite talk about extraction of mislocalized proteins. We can create other processes if the extraction takes places in other contexts. Let me know if you want any modifications.
+[Term]
+id: GO:0140567
+name: transmembrane protein dislocase activity
+namespace: molecular_function
+def: "The activity of removing a protein from a membrane, by binding to a transmembrane helical fragment of a tail-anchored protein and releasing it from the the hydrophobic region of one or both lipid bilayers." [PMID:24821790, PMID:28712723, PMID:32973005]
+synonym: "transmembrane helix dislocase" RELATED []
+is_a: GO:0140318 ! protein transporter activity
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/20237 xsd:anyURI
+created_by: pg
+creation_date: 2020-12-15T07:13:21Z
+
+[Term]
+id: GO:0140568
+name: extraction of mislocalized protein from membrane
+def: "The removal of a mislocalized protein from a cellular membrane." [PMID:24821790, PMID:28712723, PMID:32973005]
+is_a: GO:0090150 ! establishment of protein localization to membrane
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/20237 xsd:anyURI
+created_by: pg
+creation_date: 2020-12-15T07:35:10Z
+
+[Term]
+id: GO:0140569
+name: extraction of mislocalized protein from ER membrane
+def: "The removal of a mislocalized protein from the endoplasmic reticulum (ER) membrane." [PMID:32973005]
+is_a: GO:0140568 ! extraction of mislocalized protein from membrane
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/20237 xsd:anyURI
+created_by: pg
+creation_date: 2020-12-15T07:36:46Z
+
+[Term]
+id: GO:0140570
+name: extraction of mislocalized protein from the mitochondrial outer membrane
+def: "The removal of a mislocalized protein from the mitochondrial outer membrane." [PMID:32973005]
+synonym: "extraction of mislocalized protein from outer mitochondrion membrane" EXACT []
+is_a: GO:0140568 ! extraction of mislocalized protein from membrane
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/20237 xsd:anyURI
+created_by: pg
+creation_date: 2020-12-15T07:37:12Z
Thanks, Pascale

@ValWood I wonder if we should create some 'protein quality control' grouping parent ? That would also cover degradation of misfolded proteins (protein quality control for misfolded or incompletely synthesized proteins & children)

@krchristie I took this ticket because if I recall this is not a GO tickets week for you, and Sylvain wanted this before the holidays.

@sylvainpoux I closed this but please reopen if needed.

@ValWood I wonder if we should create some 'protein quality control' grouping parent ? That would also cover degradation of misfolded proteins (protein quality control for misfolded or incompletely synthesized proteins & children)

yes!
https://github.com/geneontology/go-ontology/issues/13717
and
https://github.com/geneontology/go-ontology/labels/protein quality control

@krchristie I took this ticket because if I recall this is not a GO tickets week for you, and Sylvain wanted this before the holidays.

Thanks @pgaudet - I'd planned to get to this ticket last week, but one of the other new term requests I worked on turned out to be complicated. I should have put it aside for a while and done a couple of the well defined ones first.

Could these terms specify "tail-anchored proteins" since that is what they apply to?
or at least in the def and maybe with an exact synonym.

Hi @ValWood,
I'm not sure we should specify this. These last years, a number of publications reported the extraction of proteins from membranes (a number of ATPases mediate this extraction) and I suppose that this process does not only concern tail-anchored proteins but also multi-pass membrane proteins.
Sylvain

OK,  I will add a narrow synonym. The paper I was curating yesterday the ATPase had multiple roles.


Add last resolved value to async props

like in observables
maybe merge the two interfaces? (I think they're already pretty similar anyway)

Done. To be released on v20.


Remove --enable-swift-testing et al. from swift build.

The enable/disable testing library options are no longer used by swift build and can be removed.

@swift-ci please test

@plemarquand Please confirm this won't break the VSCode plugin.

LGTM, VS Code does a swift build --build-tests prior to doing a debug run, but isn't picky about building both test executables.


Test Spring-boot-starter-client-springmvc

get

This task is complete. Please close it. @dengliming @yu199195

This task is complete. Please close it. @dengliming @yu199195


PaymentProtocol.verifyCertChain support for mixed chain signature types

PaymentProtocol.verifyCertChain assumed that all the certificates in the chain had the same sig type as the signing certificate. An example of a certificate of type RSA-SHA1 is added which is signed by certificates of type RSA-SHA256.

Test not browser compatible.

Was this solved by specifying sha256 in the payment request?
BTW, there are two implementations, once in index.js and another in browser.js (e.g. https://github.com/bitpay/bitcore-payment-protocol/blob/master/lib/browser.js#L69)  areas that are shared are in common.js. So if index.js is updated it's likely that browser.js may need to be as well.


buffer: draining any zero byte fragments (#9837) (#109)

Given that we allow creating zero byte fragments, it'd be good to proactively drain them. For example if someone is doing timing instrumentation and wants to know when Network::Connection data is written to the kernel, it could be useful to have a zero byte sentinel.
Risk Level: Low (I don't think anyone is adding zero byte fragments yet)
Testing: new unit test
Docs Changes: n/a
Release Notes: n/a
Signed-off-by: Alyssa Wilk<EMAIL_ADDRESS>

@lizan could you make the @googlebot happy?

/retest

/hold


Support for updating roles on iTunes Connect members

Checklist

[x] I've run bundle exec rspec from the root directory to see all new and existing tests pass
[x] I've followed the fastlane code style and run bundle exec rubocop -a to ensure the code style is valid
[x] I've read the Contribution Guidelines
[x] I've updated the documentation if necessary.

Motivation and Context
Spaceship has support for creating new members in iTunes Connect, but once they are created, you can change the roles. We want to use fastlane/spaceship to set the 'App Manager' role on some members on multiple accounts temporary and revoke it afterwards.
I've tested this with my local branch as a local gem in Gemfile. I've changed the roles on our members from 'Developer' and 'Finance' to 'App Manager' and 'Finance' and back.
Description
This change adds support for updating the roles of a member. The given member object isn't updated. A new request to get the member is required to get an updated list of roles.

I signed it!

That's awesome, thanks for the PR. Should we add some docs also to DeveloperPortal.md? Also it seems like the Google CLA bot isn't happy, because the git commit seems to not be associated with your username? Could you confirm that the code change is from you, and that you agree with the CLA? :)
Thanks

D'oh! I used the wrong mail address when I made the commit. I don't want to have this merged with this mail address. I will create a new pull request with the same commit but with my github mail address.
I will reference it here when the pull request is ready.

Alright, perfect, thanks 👍

I've created a new pull request with the right mail address: #10257


Possible mistake in config schema

Description: A clear and concise description of what the bug is.
Currently the config/model.json schema simultaneously allows UniformLevels and MaxIts to be contained in the Refinement object, but it's unclear as a user what behavior to expect; I'd imagine the former triggers uniform refinement whereas the latter triggers AMR.
@hughcars
To reproduce: Please provide minimal example that reproduces the error. For existing
examples, please provide a link.
Error message: Paste the complete error message or log, if applicable.
Environment: Any environment details, such as operating system, compiler, etc.

This is intended behavior, it's valid to consider the "starting point" for AMR as a mesh with a certain number of levels of uniform refinement. I'm not sure it is a good idea, but it is a valid one. Is there a problem you experienced?

No, no problems. Just confusion on my side as I thought these two refinement modes couldn't be performed in the same job. This could be made clearer in the docs. But ok, it totally makes sense that it should be possible to do uniform refinement prior to adaptive.

Closed by https://github.com/awslabs/palace/pull/146


Are the testing cases on project pages generated from texts?

Hey there! Thanks for your great work.
I'm curious about the testing cases displayed on the project pages. Are these generated from text prompts or randomly collected from the internet?
It would be incredibly helpful if you could share some information about it.
Thank you!

Yeah, they are generated using sdxl1.0, and selected by us with background removed, in order to compare with MVDream.

Thanks for your reply.
My understanding is that these cases have high matched image-text correspondence which make sure the generated results are high quality.
Have you test ImageDream on real images? Since real images do not have highly accurate text correspondence, I am curious about the performance on real cases or other images not generated from SD.

Sure, in this work we majorly focused on generated images, while the training is mostly on real image+ renderred images from objaverse. I think it should also work with real images, with the code you may easily test it on any images you like : )


Can the global and table-level columns filter be applied to both database navigator and ER diagrams?

Currently the ER diagram always show all columns of selected tables. I am looking for a way to hide some columns on the ER diagram by pattern matching.

Yep, this would be a good enhancement.

verified


create glossary doc

From https://github.com/iterative/dvc.org/issues/321#issuecomment-491665471

[ ] Create new Glossary doc with definitions to relevant DVC concepts and terms. Use appropriate links to other docs in these definitions.
[ ] Mention to "utilize the terminology listed in the glossary(linked) consistently" in the docs contribute guidelines guide.

I would like to work on this after completing #396

@kurianbenoy sure! but let's coordinate here first with @jorgeorpinel, what terms we should put into Glossary, their definitions, etc.

To start the list, here are a few suggestions:

Pipeline/computation graph
Cache and workspace
Metric
Dvcfile

@kurianbenoy let's work together on it. I am also working on a tutorial which is about to complete.

To start the list, here are a few suggestions:

Pipeline/computation graph
Cache and workspace
Metric
Dvcfile

Further,

repro
staging
remote
lock
workflow

Related #296 . I would say glossary should be very simple and it's main purpose probably to serve as an index and as a guide for contributors. While #296 should introduce DVC concepts like cache, workspace, etc in more details.

@shcheklein  Who is working on this? I can take this up if it is unassigned. :)

@kurianbenoy have you started working on this? @algomaster99 it would be great, please coordinate with @jorgeorpinel on this as well.

Thanks for all the interest guys. I came up with this suggestion mainly for some key concepts that aren't really explained in user guides and which probably don't need a full doc each. All of the terms you have listed above I think are already well explained though, so they may not need a glossary entry. Or maybe we can just list them in the glossary without a description, just linked to an appropriate user guide/get started chapter/command ref.
We need to explore the docs in full to find DVC-specific concepts that aren't explained anywhere yet. Maybe the DAG? Stage vs. stage file (aka DVC-file), stage file vs. DVC-file, DVC-file vs Dvcfile, orphan stage file, things like that. Things that need disambiguation I guess.

p.s. should we discuss the details on Discord so everyone in the team can comment and to keep this issue from growing too long in its comments?

Hi. Please see the updated description and notice that a good way to browse for terms that should probably be listed in the glossary and linked to in their original documents is searching for **bold** and _underline_ terms.
Should we also remove all these bold/underline and just link instead @shcheklein ? As well as search for the terms everywhere to find instances that are NOT currently bold/underline in order to link those too.
I think at least the first occurrence of glossary terms in each document should be linked and subsequent ones can remain with bold or underline. I also vote to switch to use only underline since bold is already widely used to emphasize some phrases in the docs. (BTW all this could perhaps be done automatically in the future.)

I agree with both - linking it once and removing bold, italic, etc. We definitely should be doing this automatically. I would prefer to have something like Github does when you specify Fixes ### - it provides a hover message + and a nicely done way to highlight the link.

Sounds like the glossary relates to several special features desired that would have to be built into the docs engine.  Perhaps the glossary should be based on a JSON file instead of an MD file, and from therer the engine can load all the terms in order to provide links, tooltips, and generate the glossary page?
cc @algomaster99

@jorgeorpinel Even I was thinking this! Yeah, will try doing that way.


[Feature] Sodium Settings Integration

Inject NTR settings into Sodium as an alternate GUI

Resolved in 1.0.1 https://github.com/rfresh2/NoTextureRotations/releases/tag/1.0.1


V11 react step 1 completed

Closes #
{{short description}}
Changelog
New

{{new thing}}

Changed

{{change thing}}

Removed

{{removed thing}}

close


fmriprep - brain_mask.nii.gz outputs are empty/impossible to open

Dear fmriprep experts,
I have just finished the preprocessing and everything seems alright since no errors were reported.
However, I have noticed that I cannot open the “sub-XX_desc-brain_mask.nii” file.
I use MRIcron to open these images and when I click on it it says “Invalid floating point operation. Press OK to ignore and risk data corruption.
Basically, I cannot even explore the mask since it contains NaN. Any idea why that is the case?
I have notices WARNINGS during the anatomical and functional processing in which data types were converted from float32 to uint8 for the brain masks. These are the only files I cannot open. I wonder whether the two things are related
I am looking forward to hearing from your opinions
best wishes
Loris

Would you be able to share the mask?

Hi,
These are two of the files in the "anat" folder that won't open. They are
attached below.
Please let me know if you have any idea about what went wrong.
Loris
On Thu, Aug 19, 2021 at 3:00 PM Chris Markiewicz @.***>
wrote:

Would you be able to share the mask?
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GitHub strips attachments. Please upload via the web interface.

Hi
Apologies for that. I will attach them through the web. I hope you can see them now.
sub-3000_desc-brain_mask.nii.gz
sub-3000_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-3000_space-MNI152NLin2009cAsym_dseg.nii.gz
Can you open them now?
Loris

I also see these fail to open with mricron, but they look reasonable in nibabel:
In [1]: import nibabel as nb

In [2]: import numpy as np

In [3]: mask1 = nb.load('sub-3000_desc-brain_mask.nii.gz')

In [4]: mask2 = nb.load('sub-3000_space-MNI152NLin2009cAsym_desc-brain_mask.nii.
   ...: gz')

In [5]: dseg = nb.load('sub-3000_space-MNI152NLin2009cAsym_dseg.nii.gz')

In [6]: np.unique(mask1.dataobj)
Out[6]: array([0, 1], dtype=uint8)

In [7]: np.unique(mask2.dataobj)
Out[7]: array([0, 1], dtype=uint8)

In [8]: np.unique(dseg.dataobj)
Out[8]: array([0, 1, 2, 3], dtype=int16)

And using mask1.orthoview(), etc...

So this seems to be a bug in mricron.

Hi,
Thank you very much for this. This is a relief somehow because it means the entire analysis was OK.
Can I ask you if nibabel has a gui similar to MRIcron to open these images? I mean I come from Matlab and R and I have just strated Python.  It would simplify my life a lot. Or alternative solutions?
Thank you very much
Loris

You can view an image using nibabel like so:
import nibabel as nb
from matplotlib import pyplot as plt

img = nb.load("/path/to/file")
img.orthoview()

plt.show()  # This is typically required, but sometimes img.orthoview() will pop up a window without making this call

Great. Thank you. Shall we close the thread?
Loris.

Sounds good. Would you mind posting to https://github.com/neurolabusc/MRIcron/issues as well?

MRIcron is showing these images accurately. The plots shown by @effigies do not take account for the scl_slope and scl_inter.
Any value multiplied by or added to a Not-A-Number is necessarily not a number. You can see the issue by examining the header:
fslhd sub-3000_desc-brain_mask.nii
...
scl_slope	nan
scl_inter	nan

The NIfTI file is explicitly stating that all voxels are not a number. I suspect this is a limitation of the images, and the intended scl_slope = 1.0 and scl_inter = 0. In this case, the images are incorrect. MRIcron is scaling the images as required by the standard.

SPM also detects these images are defective:
>> hdr = spm_vol( 'sub-3000_desc-brain_mask.nii')
Error using  ~
NaN's cannot be converted to logicals.

Error in nifti (line 63)
        if ~vol.hdr.scl_slope && ~vol.hdr.scl_inter

Error in spm_vol_nifti (line 19)
    N = nifti(P);

Error in spm_vol>spm_vol_hdr (line 128)
V = spm_vol_nifti(p,n);

Error in spm_vol (line 61)
        v = spm_vol_hdr(deblank(P(i,:)));

MRIcron is showing these images accurately. The plots shown by @effigies do not take account for the scl_slope and scl_inter.
Any value multiplied by or added to a Not-A-Number is necessarily not a number. You can see the issue by examining the header:
fslhd sub-3000_desc-brain_mask.nii
...
scl_slope	nan
scl_inter	nan

The NIfTI file is explicitly stating that all voxels are not a number. I suspect this is a limitation of the images, and the intended scl_slope = 1.0 and scl_inter = 0. In this case, the images are incorrect. MRIcron is scaling the images as required by the standard.

Thank you for this.
That is what I also tried with SPM. I knew the mask contained NaNs but I do not understand why. Is there a way to turn around this problem with MRIcron? I need these masks to go on  with skull stripping and the analysis but if I cannot open them with SPM...it is bad. Any advice?
Thank you
Loris

I had checked this, but I saw:
$ fslhd sub-3000_desc-brain_mask.nii.gz
filename       sub-3000_desc-brain_mask.nii.gz
[...]
scl_slope      0.000000
scl_inter      0.000000

From the standard:

   If the scl_slope field is nonzero, then each voxel value in the dataset
   should be scaled as
      y = scl_slope * x + scl_inter
   where x = voxel value stored
         y = "true" voxel value

Being a bit more careful:
In [1]: import nibabel as nb

In [2]: import gzip

In [3]: with gzip.open('sub-3000_desc-brain_mask.nii.gz', 'rb') as fobj:
   ...:     hdr = nb.Nifti1Header.from_fileobj(fobj)

In [4]: print(hdr)
<class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
[...]
scl_slope       : nan
scl_inter       : nan
[...]

So it seems we need to ensure that we set slope/inter to 1/0.
In the meantime, you can fix this with:
import nibabel as nb

img = nb.load(fname, mmap=False)
img.header.set_slope_inter(slope=1, inter=0)
nb.Nifti1Image(np.array(img.dataobj), None, img.header).to_filename(fname)

Thank you @effigies
Just to let you aware that the same error is also in the "func" folder for the brain mask, not only in thr "anat"
Also, does that line of code also resave the mask with slope = 1 and inter = 1, i.e. overwrite the previously wrong header?
Thank you for the support
Loris

@lorisnaspi Apologies, I didn't see that. The line of code would overwrite the previously wrong header.
This issue will be fixed in 20.2.4 and 21.0.0.

Has this bug been fixed in version 20.2.4 onwards?

Hi, yes. This has been fixed in 20.2.4 and up.


Calculation for human gene coverage appears to be incorrect

This was already fixed in the 1.5.4, RDMM was just a version behind.


ferry_generator is incompatible with build_runner >=1.12.0

environment:
sdk: ">=2.7.0 <3.0.0"
dependencies:
gql_link: ^0.3.1
gql_http_link: ^0.3.2
ferry: ^0.9.4
ferry_hive_store: ^0.3.2
ferry_flutter: ^0.4.0
hive: ^2.0.0
hive_flutter: ^1.0.0
get_it: ^6.0.0
flutter:
sdk: flutter
dev_dependencies:
build_runner: ^1.12.2
gql_build: ^0.1.4+2
gql_code_builder: ^0.1.4+1
ferry_generator: ^0.3.3
flutter_test:
sdk: flutter
Error message: Because every version of ferry_generator depends on build ^1.2.2 and build_runner >=1.12.0 depends on build >=2.0.0 <2.1.0, ferry_generator is incompatible with build_runner >=1.12.0.
So, because app depends on both build_runner ^1.12.2 and ferry_generator ^0.3.3, version solving failed.

Fixing build_runner to 1.10.1 should fix this for now.

closing, but let me know if this issue persists


[WIP] Use node IP instead of localhost for etcd nodePort

Coverage decreased (-0.1%) to 76.074% when pulling 30a9e0658d0ad28e408ab70fbe28acb8d487930b on lukasmacko:hostIP into 141cb4e172d8405b1fb35fcb07627dbd826b8acb on contiv:master.


Improve server initialising in generator

Related to https://github.com/nuxt/nuxt.js/pull/6525#issuecomment-539433370

Do you think we can close this @clarkdo?

I think it's fine, there are no many issue reports for this and the development focus has shifted to 3.0.


Use consistent env variable names to configure auth

We're currently using both CLIENTID, CLIENTSECRET, CLIENT_ID, CLIENT_SECRET, TOKEN_ENDPOINT and AUTHSERVER.
These variable names should be consistent across Abacus:

CLIENT_ID: OAuth client id
CLIENT_SECRET: OAuth client secret
TOKEN_ENDPOINT: used in the cfoauth module to configure the OAuth token endpoint
AUTH_SERVER: an authorization server which will return the token endpoint

Fixed in 5628951.


CASMMON-331 Add kafka-connect dashboard in cray-sysmgmt-health

Summary and Scope
Dashboard for kafka-connect after implementation of the jmx-exporter in CASMMON-330.
Issues and Related PRs

Resolves CASMMON-331
Merge after <https://github.hpe.com/hpe/hpc-car-sma-kafka-connect/pull/17>

Testing
Tested on:

<mug>
<hela>
Local development environment

Test description:
The changes tested and success verified.
https://grafana.cmn.mug.hpc.amslabs.hpecorp.net/d/connect/kafka-connect?orgId=1&refresh=10s
ncn-m001:/mnt/developer/sum # helm upgrade -n sma cp-kafka-connect cp-kafka-connect-1.4.0.tgz
Release "cp-kafka-connect" has been upgraded. Happy Helming!
NAME: cp-kafka-connect
LAST DEPLOYED: Thu Jul  6 05:32:58 2023
NAMESPACE: sma
STATUS: deployed
REVISION: 26
TEST SUITE: None
NOTES:
This chart installs a Confluent Kafka Connect

https://docs.confluent.io/current/connect/index.html

ncn-m001:/mnt/developer/sum # kubectl get all -n sma | grep connect
pod/cp-kafka-connect-c4dfdfb5c-26f8x                2/2     Running     0          2m49s
service/cp-kafka-connect                            ClusterIP      <IP_ADDRESS>    <none>         8083/TCP,5556/TCP              2m49s
deployment.apps/cp-kafka-connect               1/1     1            1           2m49s
replicaset.apps/cp-kafka-connect-c4dfdfb5c                1         1         1       2m49s

Pull Request Checklist

[x] Version number(s) incremented, if applicable
[x] License file intact
[x] Target branch correct

/backport stable/1.5


[Bug]: public_hoist_packages does not hoist dependencies in bazel-bin/node_modules

What happened?
I am migrating my vue project to bazel and rules_js.
I used<EMAIL_ADDRESS>which transitively uses plugins such as @vue/cli-plugin-babel, but without declaring it in dependencies. So I plan to use public_hoist_packages to make @vue/cli-service aware of @vue/cli-plugin-babel.
But the public_hoist_packages field did not hoist @vue/cli-plugin-babel in bazel-bin/node_modules.
Based on docs, public_hoist_packages will do the same thing as public-hoist-pattern in pnpm. I also tried bazelbuild/examples/frontend and didn't see changes in bazel-bin/node_modules either.
Version
Development (host) and target OS/architectures:
x86_64 GNU/Linux ubuntu focal
Output of bazel --version:
bazel 7.0.0
Version of the Aspect rules, or other relevant rules from your
WORKSPACE or MODULE.bazel file:
rules_js version is 1.34.1
How to reproduce
I built all targets in bazelbuild/examples/frontend and didn't see hoisting in bazel-bin/node_modules
tusen@desk-0181:~/examples/frontend$ bazel build ...
INFO: Analyzed 69 targets (1236 packages loaded, 10039 targets configured).
INFO: Found 69 targets...
INFO: Elapsed time: 9.104s, Critical Path: 0.09s
INFO: 1 process: 1 internal.
INFO: Build completed successfully, 1 total action
tusen@desk-0181:~/examples/frontend$ ls bazel-bin/node_modules/
jsdom  vitest

I tried pnpm i with public_hoist_pattern which did the hoisting in node_modules directory.
tusen@desk-0181:~/examples/frontend$ pnpm i
Scope: all 7 workspace projects
Lockfile is up to date, resolution step is skipped
Already up to date
Done in 1.6s
tusen@desk-0181:~/examples/frontend$ ls node_modules/
@next                        eslint-import-resolver-typescript  eslint-plugin-jsx-a11y         eslint-utils
eslint                       eslint-module-utils                eslint-plugin-react            eslint-visitor-keys
eslint-config-next           eslint-plugin-flowtype             eslint-plugin-react-hooks      jsdom
eslint-config-react-app      eslint-plugin-import               eslint-plugin-testing-library  vitest
eslint-import-resolver-node  eslint-plugin-jest                 eslint-scope
tusen@desk-0181:~/examples/frontend$ cat .npmrc
# Disabling pnpm [hoisting](https://pnpm.io/npmrc#hoist) by setting `hoist=false` is recommended on
# projects using rules_js so that pnpm outside of Bazel lays out a node_modules tree similar to what
# rules_js lays out under Bazel (without a hidden node_modules/.pnpm/node_modules). See
# https://github.com/aspect-build/rules_js/blob/7377f2d0387cc2a9251137929b1c53ccdb3fbcf0/docs/npm_import.md#npm_translate_lock
# documentation for more information.
hoist=false

public-hoist-pattern[]=@next/eslint-plugin-next*
public-hoist-pattern[]=eslint*

Hi just got the same issue in https://github.com/aspect-build/rules_js/issues/1884 and I notice that you need to reference the hoisted dependency in root package instead of sub package. e.g. //:node_modules/@vue/cli-plugin-babel instead of //my-vue-project:node_modules/@vue/cli-plugin-babel


[FEEDBACK] About the contributing

Hello,
First of all, thank you for this great project 👍
In the development part you talk about NVM and Gitpod, but in the repo there is no config file for these two tools, which in my opinion is not practical.
Nvm allows contributors to have the same versions of Node and Yarn that you use. ( I couldn't find the exact versions 😢 )
Gitpod allows the contributor to have a development environment very quickly to help you with the configuration you want
Would it be possible to add these two configuration files to facilitate the contribution to your project?
Disclaimer: Sorry for my english 😭

Hey @Singebob,
Absolutely, I can add configuration files for those platforms, it's a good idea :)
In the meantime, you can find the GitPod, and CodeSpaces links in the readme,  and the node version in the package.json

https://github.com/Lissy93/dashy/blob/2e63da041ab8a8ddb18a8ef219b4830214654a07/package.json#L67-L69

Hiya @Singebob,
I've added a .gitpod.yml in #557 / V 2.0.6
Let me know how you get on with that :)


Failing to build sample example on Ubuntu and Windows (using Cygwin)

Failing with following error when trying to build using: make example_android
FAILURE: Build failed with an exception.

Where:
Build file '/home/prashant/Work/Djinni/example/android/app/build.gradle' line: 17

What went wrong:
A problem occurred evaluating project ':app'.

Ambiguous method overloading for method java.io.File#.
Cannot resolve which method to invoke for [null, class java.lang.String] due to overlapping prototypes between:
[class java.lang.String, class java.lang.String]
[class java.io.File, class java.lang.String]

Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

Please suggest

Make sure you have a local.properties file for your android project.  This is necessary to configure the android sdk and ndk location.  For a (perhaps) better supported example project check out mx3

Thanks


Update with latest lua-simdjson changes

This includes the following:

Windows support (https://github.com/FourierTransformer/lua-simdjson/pull/82)
arm64 support (https://github.com/FourierTransformer/lua-simdjson/pull/87)
use of the on demand parser, which should be faster (https://github.com/FourierTransformer/lua-simdjson/pull/83)

I've run the haxe test suite on linux with this updated version and everything seems to work well now.

Hmm, this is the kind of PR that I'd typically "Rebase and merge", but Github tells me "This branch cannot be rebased due to conflicts" if I try that.

It may be best to merge it with a normal merge, that way github will say that it is in sync with the upstream repo. If it is rebased then github will say it is still behind.


[MINOR] Fix build on master

Change Logs
As above.
Impact
master is broken.  This fixes the issue.
Risk level
none
Documentation Update
N/A
Contributor's checklist

[ ] Read through contributor's guide
[ ] Change Logs and Impact were stated clearly
[ ] Adequate tests were added if applicable
[ ] CI passed

Build passes.  Merging this PR to unblock master.


[GSSoC '21] Bubble sort simulation with GUI

Aim

Show how bubble sort algorithm works.

Details

The script will provide a simulation of bubble sort algorithm to show the user how it works.

@amrzaki2000  updates?

@amrzaki2000  updates?

I'll make a pull request by tomorrow morning .
Almost finished


Remove mentions of "request reader" across the docs

Thanks a lot @BenFradet!

Current coverage is 74.56% (diff: 100%)

Merging #623 into master will not change coverage

Powered by Codecov. Last update 7b5de3f...8faf732


Revert "Merge pull request #1552 from ehazlett/b2d-next"

This reverts commit 736ebb14fbca35ba8bd554d3abcf8c5f35c5d854, reversing
changes made to c6660bf62c403f71c4ae6ad32a14edd619618528.
Previously we were planning to move to a new Debian-based boot2docker, but it was decided at a high level that we were trying to do so too fast to do it properly for the 0.4.0 release.  So, we are reverting this for now to revisit the issue for the next release, ideally with a proper migration path and strategy in place.
Signed-off-by: Nathan LeClaire<EMAIL_ADDRESS>

LGTM

:+1:

@ehazlett will the new b2d be used in the next release of machine ? is there a PR that brings this back ?

@runseb At some point, we will migrate over to a new OS for Machine (there have been some chronic issues with TCL), but due to the migration issues we are likely to encounter (custom b2d setups etc.) we're delaying it until we are very convinced it will be worth it to prioritize.

ok @nathanleclaire thanks, just curious as I have a b2d variant I would love to use with machine. need to test how to make it work with current vbox provider.

@runseb Cool in the meantime you can load custom ISOs with the --virtualbox-boot2docker-url flag (you might know that already), we are open as well to improving the VirtualBox driver as well to be more flexible, just haven't had time to work on it ourselves.

ok @nathanleclaire will try to have a look


Create determine_id and a overriding function in Image

Ticket: #1788
Issue
This re-organizes the Attachment::init method and separates out a determine_id method (same as Post) to handle the logic of "wait, what attachment is the user really trying to get?
This allows us to also isolate the remaining piece of Image code (which handles posts with thumbnail_ids) and move it into the Image class itself.
Considerations
The piece of isolated Image code for determining ID (which extrapolates that when a user sends a "regular" Post they probably intend to get the thumbnail_id associated with said post) is overly-opinionated and could cause unexpected behavior. I move that we deprecate this functionality.
Testing
TestTimberImage::testTimberImageFromPost currently passes, but once we remove the deprecated functionality, it fails.
	function testTimberImageFromPost() {
		$post = $this->get_post_with_image();
		$image = $post->thumbnail();
		$post = get_post($post->ID);

		$str = '{{ Image(post).src }}';
		$result = Timber::compile_string( $str, array('post' => $post) );

		$this->assertEquals($image->src(), $result);
	}

this shows the functionality it preserves though. As you can see, I don't see it to be particularly helpful or useful

Okay, now it’s clearer what that function does. But I think it’s really an edge case and hardly anyone would expect Timber to do that. It’s probably more intuitive to write:
{% if post.thumbnail %}
    <img src="{{ Image(post.thumbnail).src }}">
{% endif %}

So I’d be up for deprecating that functionality 👍

Thanks @gchtr and @pascalknecht — I've incorporated all those notes into the PR. Of course, I managed to screw something up in trying to resolve a merge conflict so I started in clean in #1794. Once those tests pass I'll merge into #1788 and we can wrap things up from there