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snakemake: 5.13.0 -> 5.15.0 #85913

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merged 2 commits into from Apr 25, 2020
Merged

snakemake: 5.13.0 -> 5.15.0 #85913

merged 2 commits into from Apr 25, 2020

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renatoGarcia
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Motivation for this change

Updating to a new release and updating homepage (code moved from bitbucket to github).

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.

@ofborg ofborg bot requested review from veprbl and Helkafen April 24, 2020 05:31
@veprbl
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veprbl commented Apr 24, 2020

https://github.com/snakemake/snakemake/blob/master/CHANGELOG.rst

[5.15.0] - 2020-04-21

Changed

  • The resource directive can now take strings, e.g. for defining a GPU model (see docs). This will e.g. be used for upcoming updates to cloud executors.
  • More extensive conda cleanup with --conda-cleanup-packages, meant for CI usage.
  • Further polish for reports.

[5.14.0] - 2020-04-08

Changed

  • Redesigned HTML reports, with improved interface and performance.
  • For big data, HTML reports can now be stored as ZIP, where files are not anymore embedded but rather are stored in an auxilliary folder, such that they don't have to be in memory during report rendering.
  • Added subcategories to report (see docs).
  • Fixed a bug linter, leading to only one rule or snakefile to be linted.
  • Breaking change in CLI: added flags --conda-cleanup-envs and --conda-cleanup-pkgs, removed flag --cleanup-conda.
  • Fixed scheduling of pipe jobs, they are now always scheduled, fixing a hangup.
  • Corrected quoting of shell command for cluster submission.

@ofborg ofborg bot requested a review from veprbl April 25, 2020 04:07
@veprbl veprbl merged commit 22133c6 into NixOS:master Apr 25, 2020
@renatoGarcia renatoGarcia deleted the snakemake branch April 25, 2020 17:22
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@Helkafen Helkafen Awaiting requested review from Helkafen

@veprbl veprbl Awaiting requested review from veprbl

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