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CHANGELOG.md

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lifebit-ai/cloudos-cli: changelog

v2.16.0 (2025-01-21)

Feature

  • Adds the new parameter --use_private_docker_repository to launch jobs using private docker images from a linked docker.io account.

v2.15.0 (2025-01-16)

Feature

  • Updates GET workflows endpoint to v3.

v2.14.0 (2024-12-18)

  • Adds the new --accelerate-file-staging parameter to job submission to add support for AWS S3 mountpoint for quicker file staging.

v2.13.0 (2024-12-03)

Feature

  • Adds new --archived flag to cloudos job list to allow getting archived jobs list.

Patch

  • Updates GET job list to use API v2 endpoint.

v2.12.0 (2024-11-27)

Feature

  • Adds the new parameter --nextflow-version to select the Nextflow version for job submissions.
  • Now --cloudos-url can also take URLs with a trailing /

v2.11.2 (2024-11-6)

Fix

  • Updates API requests to only use API key via HTTP header. Done in preparation for the upcoming deprecation of API key via parameters in CloudOS API.

v2.11.1 (2024-10-22)

Fix

  • Updates queue support to disallow queue selection on fixed-queue workflows.

v2.11.0 (2024-04-16)

  • Now, the default cloudos job run command will save job process logs. To prevent saving process logs, you can use the new flag --do-not-save-logs.
  • Removes unsupported --spot option from cloudos job run.

v2.10.0 (2024-04-11)

  • Adds the new parameter --workflow-docs-link to add a documentation link to the imported workflow.

v2.9.0 (2024-04-09)

  • Adds workflow import command, allowing user to import Nextflow workflows to CloudOS.

v2.8.0 (2024-04-05)

  • Adds support for using CloudOS HPC executor.

v2.7.0 (2024-03-21)

Feature

  • Changes the default Nextflow executor to be AWSbatch. Now, the --batch flag is no longer necessary (although it's maintained for backwards compatibility) and a new --ignite flag is created to support ignite if available.
  • Selects the CloudOS workspace default queue, when no valid --job-queue is provided.

v2.6.3 (2024-03-19)

Fix

  • Discards archived worflows from the executable ones, as they will always produce an error.

v2.6.2 (2024-01-12)

Fix

  • Adds an error strategy to retry GET/POST requests on time-out errors.

v2.6.1 (2023-10-11)

Fix

  • Improve parsing of parameters added with -p. Now they can include internal = symbols.

v2.6.0 (2023-06-22)

Feature

  • adds Azure support

v2.5.0 (2023-05-02)

Feature

  • adds job queue support to batch runs

v2.4.0 (2023-04-28)

Feature

  • add queue list command

v2.3.0 (2023-04-26)

Feature

  • add run-curated-examples command

v2.2.0 (2023-04-19)

Documentation

  • add commitizen support

Feature

  • add project list
  • add workflows list --curated option

2.1.0 - 2023-03-30

  • Feature: cloudos job list has the new parameter --last-n-jobs n, if used, the last n jobs from the user will be collected. Default is last 30, which was the previous behaviour.

2.0.1 - 2023-03-07

  • Removes some default fields returned from cloudos job list command in preparation for its deprecation from the CloudOS API. In particular, the following fields were removed:
    • resumeWorkDir
    • project.user
    • project.team

2.0.0 - 2023-02-20

  • Remove all cohort browser functionality that will be maintained in a separated repository.

1.3.2 - 2023-02-08

  • Patch: fixes problems with CloudOS environments using the new API specification for projects endpoint while maintaining backwards compatibility.

1.3.1 - 2022-12-01

  • Patch: fixes BarRequestException and TimeOutException messages when the response from the API server is empty.

1.3.0 - 2022-11-07

  • All Cromwell functionality works now with personal API key. The --cromwell-token argument is maintained for backwards compatibility, but can be completely substituted by --apikey.
  • Changes --wdl-importsfile parameter to be optional even when running a WDL pipeline as importsFiles are not always present in WDL pipelines.
  • Fixes some incomplete error messages.

1.2.1 - 2022-11-03

  • Modifies default --cost-limit from infinite (-1) to 30.0. This will prevent wasting resources without a purpose of running a pipeline.

1.2.0 - 2022-10-28

  • Adds --disable-ssl-verification new flag to be able to disable SSL certificate verification when required. It also disables urllib3 associated warning messages.
  • Adds --ssl-cert new option to specify the path to the corresponding SSL certificate file.

1.1.0 - 2022-09-29

  • Adds --request-interval new parameter to allow the custom time specification for job status request. This will be useful for big jobs, to specify a bigger interval since a smaller one is causing the API to consider it as spam or simply to crash.
  • Changes REQUEST_INTERVAL for REQUEST_INTERVAL_CROMWELL. This is only used in the cromwell workflows.

1.0.0 - 2022-07-28

  • Adds --parameter / -p new argument to allow to specify the job parameters using the command-line. This version introduces a backwards incompatible change The -p flag is now used for parameters and not for the nextflow profile. Commands that utilised -p for denoting a profile will break with this release.

0.1.4 - 2022-07-27

  • Unittests added for method load and create from class Cloudos

0.1.3 - 2022-07-26

  • Adds --cost-limit <float> to cloudos job run command. It is used to indicate the job cost limit, in $.

0.1.2b - 2022-07-26

  • Adds worked example of CohortBrowser to README

0.1.2 - 2022-07-14

  • Adds WDL pipeline support, iteration 2: WDL workflows can be run using the regular cloudos job run using the new arguments:
    • --wdl-mainfile
    • --wdl-importsfile
    • --cromwell-token
  • Adds the new argument --repository-platform to specify the repository platform (Default: 'github').

0.1.1 - 2022-07-12

  • Adds WDL pipeline support, iteration 1: cromwell server managing. Now, a new command cloudos cromwell is available, with the following subcommands:
    • status
    • start
    • stop

0.1.0 - 2022-07-07

  • Adds cloudos workflow list command. This command allows to collect all the workflows data from a given workspace.
  • Adds JSON output for cloudos job list and cloudos workflow list commands.

0.0.9 - 2022-06-28

  • Adds support for lustre storage with the new --storage-mode and --lustre-size parameters.

0.0.8 - 2022-06-16

  • Adds --nextflow-profile parameter to accept nextflow profiles. It also makes --job-config parameter optional, as a run with only profiles is possible.

0.0.7a - 2022-04-07

  • Hotfix: extends the wait time from 1s to 60s when checking for job status (--wait-completion true). This helps preventing API call errors from CloudOS API server.

0.0.7 - 2021-03-10

  • Adds support for aborted jobs
  • Adds --batch option to job subtool to be able to use batch executor instead of the default ignite in CloudOS.

0.0.6 - 2021-12-09

  • Unittests added for method process_job_list from class Cloudos
  • Unittests added for method convert_nextflow_to_json from class Jobs

0.0.5b - 2021-11-24

  • Adds Cohort class

0.0.5 - 2021-11-16

  • Adds git-commit and --git-tag optional arguments to cloudos job run to be able to set the github commit or tag to run.

0.0.4 - 2021-10-15

  • Changes --job-params to --job-config
  • Removes the collection of the project.description column from the returned json when listing all jobs, as this column is not available in all the CloudOS workspaces.

0.0.3 - 2021-09-08

  • Adds cloudos job list command.
  • Minor changes in stdout of the other commands to improve readability.
  • Adds a small docstring to each command.

0.0.2 - 2021-09-07

  • Refactors runjob and jobstatus commands. Now, the main cloudos tool have the job subtool which in turn has its run and status commands performing the previous functionality. This way, now the tool can be used with: cloudos job run [OPTIONS] and cloudos job status [OPTIONS].
  • Adding --wait-completion option to cloudos job run command, to be able to wait until job completion or failure.

0.0.1 - 2021-08-18

Initial implementation of the cloudos python package:

  • Implements runjob and jobstatus commands to send jobs and get their status, respectively.