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snakemake: 5.17.0 -> 5.19.3 #92127

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merged 1 commit into from Jul 3, 2020
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@veprbl veprbl commented Jul 3, 2020

Motivation for this change
Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.

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veprbl commented Jul 3, 2020

[5.19.3] - 2020-06-16

Changed

  • Performance improvements for DAG generation (up to 7x in the google cloud, anything from a little to massive in a cluster, depending on the overall filesystem performance).
  • Made harcoded bucket in google cloud executor configurable.
  • Improved speed of --unlock command.

[5.19.2] - 2020-06-04

Changed

  • Fixed a bug in script and wrapper directives. Tried to decode a str.

[5.19.1] - 2020-06-03

Changed

  • Fixed an issue with the parameter linting code, that could cause an index out of bounds exception.

[5.19.0] - 2020-06-02

Added

  • The multiext function now allows arbitrary file extensions (no longer required to start with a "." (thanks to @jafors)
  • The include directive can now also take a Pathlib Path object (thanks to @mbhall88).

Changed

  • Jupyter notebook integration no longer automatically starts a browser.
  • Empty directories are cleaned up after workflow execution.
  • Fixed directory handling: no longer fail if the same job writes both a dir and a contained file.
  • Linter now recommends using spaces only for indentation.
  • Persistence dir "aux" has been renamed to "auxilliary" in order to make windows happy.
  • Linter now distinguishes awk syntax from regular variable usage.
  • Various bug fixes for Windows (thanks to @melund).

[5.18.0] - 2020-05-21

Added

  • Native Google Cloud support via the (despite the name generic) lifesciences API.
  • Ability to optionally exchange the conda frontend to mamba (faster and sometimes more correct) instead of conda.

Changed

  • Improved notebook integration experience, with various removed bugs and pitfalls.
  • Auto-retry google storage API calls on transient or checksum errors.

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I have tested. Looks fine to me.

  • Built on an ArchLinux system
  • Tested using nixpkgs-review pr 92127
  • Tested execution of all binary files (usually in ./result/bin/)

@veprbl veprbl merged commit b234812 into NixOS:master Jul 3, 2020
@veprbl veprbl deleted the pr/snakemake_5_19_3 branch July 3, 2020 18:03
@veprbl veprbl restored the pr/snakemake_5_19_3 branch December 1, 2020 16:46
@veprbl veprbl deleted the pr/snakemake_5_19_3 branch December 1, 2020 16:59
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2 participants