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168 changes: 105 additions & 63 deletions CHANGELOG.md
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## lifebit-ai/cloudos-cli: changelog

## v2.92.0 (2026-06-23)

### Feat

- Add support for procurement images set/reset for azure provider
- Consolidate the image type to regular sessions

## v2.91.0 (2026-05-28)

### Feat:
### Feat

- Implements linking of files in interactive session creation
- Implements linking of files in `cloudos link`
- Removes support for linking while resuming a paused interactive session
- Enforces a maximum of 100 linked items per interactive session
- Adds clearer, actionable error messages when mounts fail (e.g. translates "prefix does not exist" / "access denied" into workspace-permission guidance)

### Breaking:
### Breaking

- `cloudos link` and `cloudos datasets link`: File Explorer paths must now be RELATIVE to `--project-name` (do NOT prepend the project name). Previously the leading `<project>/` segment was advertised but produced confusing errors; it is now rejected up front with a clear message pointing to the correct form. `cloudos interactive-session create --link` still uses `<project>/<folder-path>` format — see each command's `--help` for the explicit cross-reference.


## v2.90.2 (2026-05-07)

### Patch
Expand Down Expand Up @@ -210,14 +216,12 @@

- adds tablular standard output for job list


## v2.74.0 (2025-12-05)

### Feat

- Adds bulk deletion script with documentation


## v2.73.0 (2025-12-02)

### Feat
Expand Down Expand Up @@ -263,30 +267,26 @@
- Adds (deletion) status check for job workdir
- Adds error message for when trying to get workdirs or results that have been deleted


## v2.68.0 (2025-11-07)

### Feat

- Adds checks for linking job completion
- Fix workdir command to return correct path for resumed jobs.


## v2.67.0 (2025-11-06)

### Feat

- Implement viewing related job analyses


## v2.66.2 (2025-11-5)

### Patch

- Fix job help message for resume and clone
- Implements datasets ls for single files


## v2.66.1 (2025-10-29)

### Patch
Expand Down Expand Up @@ -438,10 +438,10 @@

- Adds support for querying the working directory of a job.


## v2.55.0 (2025-08-27)

### Feat

- changes column name in datasets ls --details command from "File Name" to "Virtual Name".
- Improved error message when attempting to move an item to an S3 folder
- Changed terminology in messages in datasets rm
Expand All @@ -461,19 +461,17 @@
- Enables cloning existing jobs with parameter overrides including queue-name, cost-limit, master-instance, job-name, nextflow-version, branch, nextflow-profile, save-logs, use-fusion, workflow-name, and parameter
- Provides comprehensive parameter validation and error handling for job cloning operations


## v2.52.0 (2025-08-25)

### Feat

- Implements filtering options for `cloudos job list` (`filter_status`, `filter_job_name`, `filter_project`, `filter_workflow`, `filter_job_id`, `filter_only_mine` , `filter_owner`, `filter_queue` )
- Implements filtering options for `cloudos job list` (`filter_status`, `filter_job_name`, `filter_project`, `filter_workflow`, `filter_job_id`, `filter_only_mine` , `filter_owner`, `filter_queue` )

## v2.51.0 (2025-08-21)

### Fix

- set image name

- set image name

## v2.50.0 (2025-08-14)

Expand Down Expand Up @@ -603,7 +601,7 @@

### Feat

- Adds command to create new folders
- Adds command to create new folders

## v2.34.0 (2025-06-25)

Expand Down Expand Up @@ -695,7 +693,7 @@

- Updates jobs POST endpoint from v1 to v2
- Removes `cloudos job run-curated-examples` functionality, as it was deprecated from the platform
- Removes the following deprecated `cloudos job run` flags: `spot`, `ignite`, `batch`
- Removes the following deprecated `cloudos job run` flags: `spot`, `ignite`, `batch`
- Adds `--git-branch` to `cloudos job run` command, to be able to specify the git branch to run

## v2.22.0 (2025-05-15)
Expand Down Expand Up @@ -865,138 +863,180 @@
- 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.
`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`
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.
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.
`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.
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`.
`--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.
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.
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.
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.
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.
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.
`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.
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 $.
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`
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').
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
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.
collect all the workflows data from a given workspace.
- Adds JSON output for `cloudos job list` and `cloudos workflow list`
commands.
commands.

### 0.0.9 - 2022-06-28

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

- 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.
- 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
- 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
Expand All @@ -1006,6 +1046,8 @@ functionality. This way, now the tool can be used with:
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.
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