reana-client 0.9.3

Description:

reanaclient 0.9.3

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

appimage: upgrade to Python 3.8.18 (#704) (783c17a)

Bug fixes

status: display correct duration of stopped workflows (#701) (b53def8), closes #699

Code refactoring

docs: move from reST to Markdown (#703) (c9c4d53)

Code style

black: format with black v24 (#702) (02dc830)

Test suite

snakemake: allow running Snakemake 7 tests on Python 3.11+ (#700) (8ad7ff1), closes #655

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 of all (#703) (fe0b00a)
release-please: initial configuration (#695) (5b278f1)
shellcheck: fix exit code propagation (#698) (fe696ea)

Documentation

authors: complete list of contributors (#705) (875997c)

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 contain inputs 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 and restart 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 and status 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 in REANA_WORKON correctly.
Fixes secrets-delete command error message when deleting non existing secrets.
Fixes start command to report failed workflows as errors.
Fixes start and run 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 the files 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 in reana.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 version 3.1.20210628163208.
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 the validate 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 and reana.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 and secrets-delete.
Enhances run and create 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 in reana.yaml specification file
allowing to declare computing resources needed for workflow runs, such as the
CVMFS repositories via cvmfs 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 to list 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 to ls 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, now validate 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.