stable

python-smart_open-7.0.3-1.fc40, python-snakemake-executor-plugin-cluster-generic-1.0.9-1.fc40, & 8 more

FEDORA-2024-71d83d5898 created by music 3 months ago for Fedora 40

snakemake

snakemake 8.9.0 (2024-03-18)

Features

  • add function 'exists' for checking the prior existence of files or dirs before workflow execution while considering any remote storage settings. In addition: some bug fixes for error handling and the update/before_update functionality.

snakemake 8.8.0 (2024-03-15)

Features

  • Allow smart_open 7.x

Bug Fixes

  • various error handling improvements, fixed logging/error behavior (stdout from dryrun, stderr otherwise)

snakemake 8.7.0 (2024-03-13)

Features

  • add flag for marking output as being updated instead of rewritten (update("test.txt"))
  • allow default storage provider to be explicitly set to none

snakemake 8.6.0 (2024-03-11)

Features

  • add setting for defining separate local storage prefix for remote jobs; improved ergonomics for semantic helper functions
  • allow passing of lists of functions or single functions to expand

Bug Fixes

  • fix error message for invalid storage provider queries
  • fix premature deletion of temp files in combination with checkpoints

snakemake 8.5.5 (2024-03-07)

Bug Fixes

  • less frightening message when telling about missing output files as reason for running a job

snakemake 8.5.4 (2024-03-06)

Bug Fixes

  • fix bugs in --summary and --list-input-changes. Removed outdated statement in tutorial.

Documentation

  • fix explanation on how to use all cores in tutorial
  • fix syntax highlighting in tutorial

python-snakemake-executor-plugin-cluster-generic 1.0.9 (2024-03-11)

Bug Fixes

  • depend on latest executor interface

python-snakemake-executor-plugin-cluster-sync 0.1.4 (2024-03-12)

Bug Fixes

  • update interface dependency

python-snakemake-executor-plugin-kubernetes

Initial package.

python-snakemake-executor-plugin-slurm

Initial package.

python-snakemake-executor-plugin-slurm-jobstep 0.1.11 (2024-03-11)

Bug Fixes

  • avoid redundant steps related to shared fs usage

python-snakemake-executor-plugin-tes 0.1.3 (2024-03-12)

Bug Fixes

  • update interface

python-snakemake-interface-executor-plugins 9.0.0 (2024-03-11)

⚠ BREAKING CHANGES

  • pass common settings to SpawnedJobArgsFactory; shell command arg quoting fixes

python-snakemake-storage-plugin-ftp

Initial package.


python-smart_open

python-smart_open 7.0.3, 2024-03-21

  • add support for zst writing (PR #812
  • roll back PR #788, restore compatibility with built-in open function

python-smart_open 7.0.2, 2024-03-21

  • Add __next__ method to FileLikeProxy
  • Fix python_requires minimum python version in setup.py
  • Add activity check to cached sftp connections

python-smart_open 7.0.1, 2024-02-26

  • Do not touch botocore unless it is installed

python-smart_open 7.0.0, 2024-02-26

  • Upgrade dev status classifier to stable
  • Add zstandard compression support
  • Support moto 4 & 5
  • Add logic for handling large files in MultipartWriter uploads to S3
  • Add support for SSH connection via aliases from ~/.ssh/config
  • Secure the connection using SSL when connecting to the FTPS server
  • Make GCS I/O 1000x faster by avoiding unnecessary API call
  • Retry finalizing multipart S3 upload
  • Handle exceptions during writes to Azure
  • Fix formatting of python code in MIGRATING_FROM_OLDER_VERSIONS.rst
  • Fix str method in SinglepartWriter
  • Fix KeyError: 'ContentRange' when received full content from S3
  • Propagate __exit__ call to the underlying filestream

1.0.8 (2024-03-04)

Bug Fixes

  • Fix attribute errors in relation to status cmd and cancel cmd

How to install

Updates may require up to 24 hours to propagate to mirrors. If the following command doesn't work, please retry later:

sudo dnf upgrade --refresh --advisory=FEDORA-2024-71d83d5898

This update's test gating status has been changed to 'waiting'.

3 months ago

This update has obsoleted snakemake-8.5.5-1.fc40, and has inherited its bugs and notes.

3 months ago

This update's test gating status has been changed to 'ignored'.

3 months ago

music edited this update.

3 months ago

This update has been submitted for testing by bodhi.

3 months ago

This update has been pushed to testing.

3 months ago

music edited this update.

3 months ago

music edited this update.

3 months ago

music edited this update.

3 months ago

music edited this update.

3 months ago

music edited this update.

3 months ago

music edited this update.

New build(s):

  • python-snakemake-executor-plugin-slurm-jobstep-0.1.11-1.fc40
  • python-snakemake-executor-plugin-tes-0.1.3-1.fc40
  • python-snakemake-executor-plugin-cluster-sync-0.1.4-1.fc40
  • snakemake-8.6.0-2.fc40
  • python-snakemake-executor-plugin-cluster-generic-1.0.9-1.fc40
  • python-snakemake-interface-executor-plugins-9.0.0-1.fc40

Removed build(s):

  • snakemake-8.5.5-2.fc40

Karma has been reset.

3 months ago

This update has been submitted for testing by music.

3 months ago

This update has been pushed to testing.

3 months ago

music edited this update.

New build(s):

  • python-snakemake-executor-plugin-kubernetes-0.1.5-1.fc40

Karma has been reset.

3 months ago

This update has been submitted for testing by music.

3 months ago

music edited this update.

3 months ago

music edited this update.

New build(s):

  • snakemake-8.7.0-1.fc40

Removed build(s):

  • snakemake-8.6.0-2.fc40

Karma has been reset.

3 months ago

music edited this update.

3 months ago

music edited this update.

3 months ago

music edited this update.

3 months ago

music edited this update.

New build(s):

  • snakemake-8.8.0-1.fc40

Removed build(s):

  • snakemake-8.7.0-1.fc40

Karma has been reset.

3 months ago

music edited this update.

New build(s):

  • python-snakemake-storage-plugin-ftp-0.1.2-1.fc40
  • python-snakemake-executor-plugin-slurm-0.4.2-1.fc40

Karma has been reset.

3 months ago

This update has been pushed to testing.

3 months ago

This update has been submitted for stable by bodhi.

There is an ongoing freeze; this will be pushed to stable after the freeze is over.

3 months ago

This update has obsoleted python-snakemake-executor-plugin-cluster-generic-1.0.8-1.fc40, and has inherited its bugs and notes.

3 months ago

music edited this update.

New build(s):

  • snakemake-8.9.0-1.fc40

Removed build(s):

  • snakemake-8.8.0-1.fc40

Karma has been reset.

3 months ago

This update has been submitted for testing by music.

3 months ago

music edited this update.

3 months ago

This update has been pushed to testing.

3 months ago

music edited this update.

3 months ago

music edited this update.

New build(s):

  • python-smart_open-7.0.3-1.fc40

Removed build(s):

  • python-smart_open-7.0.1-1.fc40

Karma has been reset.

3 months ago

This update has been submitted for testing by music.

3 months ago

This update has been pushed to testing.

3 months ago

This update has been submitted for stable by bodhi.

3 months ago

This update has been pushed to stable.

3 months ago

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BZ#2260891 Review Request: python-snakemake-storage-plugin-ftp - A Snakemake plugin for handling input and output via FTP
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BZ#2261110 Review Request: python-snakemake-executor-plugin-slurm - A Snakemake executor plugin for submitting jobs to a SLURM cluster
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BZ#2262422 Review Request: python-snakemake-executor-plugin-kubernetes - A snakemake executor plugin for submission of jobs to Kubernetes
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BZ#2266009 python-smart_open-7.0.1 is available
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BZ#2267743 python-snakemake-executor-plugin-cluster-generic-1.0.8 is available
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BZ#2268374 snakemake-8.5.4 is available
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BZ#2268576 snakemake-8.5.5 is available
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BZ#2269080 python-snakemake-executor-plugin-cluster-generic-1.0.9 is available
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0
BZ#2269081 snakemake-8.6.0 is available
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0
BZ#2269082 python-snakemake-executor-plugin-slurm-jobstep-0.1.11 is available
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BZ#2269498 snakemake-8.7.0 is available
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BZ#2270394 snakemake-8.9.0 is available
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BZ#2270595 python-smart_open-7.0.3 is available
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Automated Test Results