snakemake: 6.7.0 -> 6.10.0

[veprbl]

Motivation for this change

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
• Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
• Tested compilation of all packages 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/)
• 21.11 Release Notes (or backporting 21.05 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md.

[veprbl]

Changelog

6.10.0 (2021-10-21)

Features

• Add more informative errors when evaluation of --default-resources fails (#1192) (b3c4e68)

Bug Fixes

• add quotes to each item of the wait_for_files list (#1160) (72856ed)
• caching process (#1225) (0825a29)
• enable usage of job grouping in GLS (#1054) (d243c22)
• Only --bind Snakemake when we're working with a Python script (#1206) (1d79f62)
• run dependencies with non-existent ancient files before the consuming job (#1202) (84d1f64), closes #946
• status cmd repeats until killed by 11 different signals (#1207) (8b28b57)
• typo in sourcecache use (#1229) (8b54bc5)
• wms monitor arg parsing now accepts any kind of value (#1181) (313de93)

Documentation

• Clarification of --cluster-stats docs & elaborating on the situation where job ids are not passed to the status script (#1221) (ed0e4a2)
• Combine CHANGELOG.rst with CHANGELOG.md (#1228) (19f5a43)
• Mention required openssl dep for rust-script (#1216) (fc8c5f6)
• Unpin docutils version (#1230) (15a82bf)

6.9.1 (2021-09-30)

Bug Fixes

• fix function call when creating report and hashes for between workflow caching (#1198) (a4f6836)

6.9.0 (2021-09-29)

Features

• autoconvert Path objects to str when passing to R or Julia scripts (80ec513)

Bug Fixes

• fix source retrieval during between workflow caching and report generation (2394ca4)

6.8.2 (2021-09-29)

Bug Fixes

• fix path returned by get_source() (ee05315)

6.8.1 (2021-09-24)

Bug Fixes

• async_run to allow nested event loops. (#1170) (5dc6bbd)
• merging of pipe groups when multiple rules are chained together via pipes (#1173) (de91d2c)
• potential memory corruption caused by Google storage objects accessed from different threads (#1174) (41a5071)

Performance Improvements

• more extensive caching of source files, including wrappers. (#1182) (bdb75f8)

Documentation

• move note (75a544b)
• polish (47a7b62)
• tutorial formatting (594f5fb)

6.8.0 (2021-09-06)

Features

• Add shadow: "copy-minimal" directive (#1155) (1803f0b)
• support XRootD as a default remote provider (#1017) (fe03157)

Bug Fixes

• AmbiguousRuleException bug caused by weak ordering of rules (#1124) (7f54c39)
• Bugfix tes add files (#1133) (8892bf2)
• Disable Persistence cache for snakemake jobs (#1159) (7110f9d)
• efficient job status checking when using DRMAA API (this should yield much better parallelization and performance when using --drmaa) (#1156) (ac004cb)
• improved error handling for cluster status scripts and smarter job selector choice in case of cluster submission (use greedy for single jobs). (#1142) (48d2dd9)
• Initialize assignments dictionary when setting rule-based resources (#1154) (68c13fd)
• key error when handling FileNotFoundError in input functions. (#1138) (d25f04d)
• linting of remote snakefiles (#1131) (2104e10)

Performance Improvements

• improve job selection performance in case of potential ambiguity that is resolved by comprehensive ruleorder statements. (#1147) (921f4f7)

[nrdxp]

Result of nixpkgs-review pr 142795 run on x86_64-linux 1

1 package built:

• snakemake

[cole-h]

@ofborg eval