REANA client
Project description
REANA-Client
About
REANA-Client is a component of the REANA reusable and reproducible research data analysis platform. It provides a command-line tool that allows researchers to submit, run, and manage their computational workflows.
- seed workspace with input code and data
- run computational workflows on remote compute clouds
- list submitted workflows and enquire about their statuses
- download results of finished workflows
Installation
$ # create new virtual environment
$ virtualenv ~/.virtualenvs/reana
$ source ~/.virtualenvs/reana/bin/activate
$ # install reana-client
$ pip install reana-client
Usage
The detailed information on how to install and use REANA can be found in docs.reana.io.
Useful links
- REANA project home page
- REANA user documentation
- REANA user support forum
- REANA-Client releases
- REANA-Client developer documentation
- REANA-Client known issues
- REANA-Client source code
Changelog
0.9.3 (2024-03-13)
Build
Bug fixes
Code refactoring
Code style
Test suite
Continuous integration
- commitlint: addition of commit message linter (#695) (2de7d61)
- commitlint: allow release commit style (#708) (f552752)
- commitlint: check for the presence of concrete PR number (#698) (fa5b7c7)
- pytest: install
tests
package variant instead ofall
(#703) (fe0b00a) - release-please: initial configuration (#695) (5b278f1)
- shellcheck: fix exit code propagation (#698) (fe696ea)
Documentation
0.9.2 (2023-12-19)
- Changes
validate
command to show detailed errors when the specification file is not a valid YAML file. - Changes the validation of specification files to show improved validation warnings, which also indicate where unexpected properties are located in the file.
- Fixes
create_workflow_from_json
API function to always load and send the workflow specification to the server. - Fixes
list
command to accept case-insensitive column names when sorting the returned workflow runs via the--sort
option. - Fixes
run
wrapper command for workflows that do not containinputs
clause in their specification.
0.9.1 (2023-09-27)
- Adds support for Python 3.12.
- Adds
prune
command to delete all intermediate files of a given workflow. Use with care. - Changes
open
command to inform user about the auto-closure of interactive sessions after a certain inactivity timeout. - Changes
validate
command to display non-critical validation warnings when checking the REANA specification file. - Fixes
list
command to correctly list workflows when sorting them by their run number or by the size of their workspace. - Fixes
du
command help message typo. - Fixes
validation --environments
command to correctly handle fully-qualified image names.
0.9.0 (2023-01-26)
- Adds support for Python 3.11.
- Adds support for
.gitignore
and.reanaignore
to specify files that should not be uploaded to REANA. - Adds
retention-rules-list
command to list the retention rules of a workflow. - Changes REANA specification loading and validation functionalities by porting some of the logic to
reana-commons
. - Changes
create
andrestart
commands to always upload the REANA specification file. - Changes
delete
command to always delete the workflow's workspace. - Changes
delete_workflow
Python API function to always delete the workflow's workspace. - Changes
download
command to add the possibility to write files to the standard output via-o -
option. - Changes
list
command to hide deleted workflows by default. - Changes
list
command to allow displaying deleted workflows via--all
and--show-deleted-runs
options. - Changes
list
andstatus
commands to allow displaying the duration of workflows with the--include-duration
option. - Changes
mv
command to allow moving files while a workflow is running. - Changes
upload
command to prevent uploading symlinks. - Changes
validation --environment
command to use Docker registry v2 APIs to check that a Docker image exists in DockerHub. - Fixes
list
command to highlight the workflow specified inREANA_WORKON
correctly. - Fixes
secrets-delete
command error message when deleting non existing secrets. - Fixes
start
command to report failed workflows as errors. - Fixes
start
andrun
commands to correctly follow the execution of the workflow until termination. - Fixes
status
command to respect output format provided by the--format
option. - Fixes
upload
command to report when input directories are listed under thefiles
section in the REANA specification file and vice versa. - Fixes
validate --environment
command to detect illegal whitespace characters in Docker image names.
0.8.1 (2022-02-15)
- Adds support for creating reana-client standalone AppImage executables.
- Adds support for Python 3.10.
- Adds workflow name validation for
create_workflow_from_json()
Python API function. - Fixes formatting of error messages and sets appropriate exit status codes.
0.8.0 (2021-11-24)
- Adds support for running and validating Snakemake workflows.
- Adds support for
outputs.directories
inreana.yaml
allowing to easily download output directories. - Adds new command
quota-show
to retrieve information about total CPU and Disk usage and quota limits. - Adds new command
info
that retrieves general information about the cluster, such as available workspace path settings. - Changes
validate
command to add the possibility to check the workflow against server capabilities such as desired workspace path via--server-capabilities
option. - Changes
list
command to add the possibility to filter by workflow status and search by workflow name via--filter
option. - Changes
list
command to add the possibility to filter and display all the runs of a given workflow via-w
option. - Changes
list
command to stop including workflow progress and workspace size by default. Please use new options--include-progress
and--include-workspace-size
to show this information. - Changes
list --sessions
command to display the status of interactive sessions. - Changes
logs
command to display also the start and finish times of individual jobs. - Changes
ls
command to add the possibility to filter by file name, size and last-modified values via--filter
option. - Changes
du
command to add the possibility filter by file name and size via--filter
option. - Changes
delete
command to prevent hard-deletion of workflows. - Changes Yadage workflow specification loading to be done in
reana-commons
. - Changes CWL workflow engine to
cwltool
version3.1.20210628163208
. - Removes support for Python 2.7. Please use Python 3.6 or higher from now on.
0.7.5 (2021-07-05)
- Changes workflow validation to display more granular output.
- Changes workflow parameters validation to warn about misused parameters for each step.
- Changes dependencies to unpin six so that client may be installed in more contexts.
- Fixes environment image validation not to test repetitively the same image.
- Fixes
upload_to_server()
Python API function to silently skip uploading in case of none-like inputs.
0.7.4 (2021-04-28)
- Adds support of wildcard patterns to
ls
command. - Adds support of directory download and wildcard patterns to
download
command. - Changes
list
command to include deleted workflows by default. - Fixes environment image validation info message where UIDs were switched.
0.7.3 (2021-03-24)
- Adds validation of workflow input parameters to the
validate
command. - Adds optional validation of workflow environment images (
--environments
) to thevalidate
command.
0.7.2 (2021-01-15)
- Adds support for Python 3.9.
- Fixes exception handling when uploading files.
- Fixes minor code warnings.
- Fixes traling slash issue from user exported REANA_SERVER_URL.
0.7.1 (2020-11-10)
- Changes
ping
command output to include REANA client and server version information. - Fixes
upload
command to properly display errors.
0.7.0 (2020-10-20)
- Adds option to
logs
command to filter job logs according to compute backend, docker image, status and step name. - Adds new
restart
command to restart previously run or failed workflows. - Adds possibility to specify operational options in the
reana.yaml
of the workflow. - Fixes user experience by preventing dots as part of the workflow name to avoid confusion with restart runs.
- Changes
du
command output format. - Changes file loading to optimise CLI performance.
- Changes
logs
command to enhance formatting using marks and colours. - Changes from Bravado to requests to improve download performance.
- Changes
ping
command to perform user access token validation. - Changes defaults to accept both
reana.yaml
andreana.yml
filenames. - Changes
diff
command to improve output formatting. - Changes code formatting to respect
black
coding style. - Changes documentation to single-page layout.
0.6.1 (2020-06-09)
- Fixes installation troubles for REANA 0.6.x release series by pinning several dependencies.
0.6.0 (2019-12-27)
- Introduces user secrets management commands
secrets-add
,secrets-list
andsecrets-delete
. - Enhances
run
andcreate
commands to allow specifying workfow via the--workflow
flag. - Introduces new command
version
to report client version. - Fixes
upload
command behaviour for uploading very large files. - Simplifies
run
command by removing free upload parameters. - Upgrades
cwltool
to 1.0.20191022103248. - Disables SSL verification warnings when talking to self-signed server certificates.
0.5.0 (2019-04-24)
- Introduces new
resources
field inreana.yaml
specification file allowing to declare computing resources needed for workflow runs, such as the CVMFS repositories viacvmfs
subfield. - Improves
reana-client
embedded command-line documentation (-help
) by grouping commands and providing concrete usage examples for all commands. - Enhances workflow
start
command allowing to override input parameters (--parameter
) and to specify additional operational options (--option
). - Introduces new workflow
run
wrapper command that creates workflow, uploads its input data and code and starts its execution. - Introduces new workflow
stop
command for stopping a running workflow. - Enhances workflow
logs
command output capabilities via new--json
option. - Introduces new workflow
diff
command for comparing two workflow runs. - Introduces new workflow
delete
command for deleting one or more workflow runs. - Introduces new session
open
command allowing to run interactive sessions such as Jupyter notebook upon workflow workspace. - Introduces new session
close
command for closing interactive sessions. - Renames past
workflows
command tolist
allowing to list both workflow runs and interactive sessions. - Introduces new workspace
du
command for checking workspace disk usage. - Introduces new workspace
mv
command for moving files within workspace. - Introduces new workspace
rm
command for removing files within workspace. - Renames past workspace
list
command tols
allowing to list workspace files. Enhances its output capabilities via new--format
option. - Introduces new API function
create_workflow_from_json()
which allows developers and third-party systems to create workflows directly from JSON specification.
0.4.0 (2018-11-07)
- Enhances test suite and increases code coverage.
- Changes license to MIT.
0.3.1 (2018-09-25)
- Amends upload and download commands that will now upload/download all the
files specified in
reana.yaml
in case no arguments are provided. - Fixes
status
command's JSON output mode. - Upgrades CWL reference implementation to version
1.0.20180912090223
. - Renames Serial workflow operational parameter from
CACHING``to ``CACHE
. - Adds support for Python 3.7.
0.3.0 (2018-08-10)
-
Adds support for Serial workflows.
-
CLI refactored to a flat design:
inputs
/outputs
/code
removed, everything is a file managed : with upload/download/list commands.- Removes
workflow
command, workflows are managed with :create
/start
/status
.
-
Removes
analyes
command, nowvalidate
is first level command. -
status
now shows the selected workflow progress and current command on verbose mode. -
Requires the usage of an access token to talk to REANA Server.
-
Fixes bug when uploading binary files.
-
Supports addition of workflow engine parameters when using
start
for serial workflows. -
Improves error messages.
0.2.0 (2018-04-20)
- Adds support for Common Workflow Language workflows.
- Adds support for persistent user-selected workflow names.
- Enables file and directory input uploading using absolute paths.
- Adds new
status
command to display the current status of the client. - Reduces verbosity level for commands and improves error messages.
0.1.0 (2018-01-30)
- Initial public release.
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