fulcrumgenomics / dagr

A scala based DSL and framework for writing and executing bioinformatics pipelines as Directed Acyclic GRaphs
MIT License
69 stars 14 forks source link

Move cross-building to 2.12 and 2.13 #356

Closed tfenne closed 5 years ago

tfenne commented 5 years ago

I've gotten rid of most of the deprecations except for one huge class. For some reason Buffer.append(xs: A*) got deprecated, and we use that literally everywhere in dagr. To eliminate the deprecations we'd have to change e.g.:

args.append("-i", in) to args.appendAll(Seq("-i", in)) which just feels so much clunkier. So I'm leaving it for now and am wondering if we should have our own arg-builder class that we use instead in some future release.

codecov-io commented 5 years ago

Codecov Report

Merging #356 into master will increase coverage by 0.27%. The diff coverage is 88.37%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #356      +/-   ##
==========================================
+ Coverage   91.56%   91.84%   +0.27%     
==========================================
  Files          31       31              
  Lines        1150     1140      -10     
  Branches      107       71      -36     
==========================================
- Hits         1053     1047       -6     
+ Misses         97       93       -4
Impacted Files Coverage Δ
.../main/scala/dagr/core/execsystem/TaskManager.scala 91.54% <ø> (ø) :arrow_up:
...n/scala/dagr/core/execsystem/TaskManagerLike.scala 0% <ø> (ø) :arrow_up:
...in/scala/dagr/core/cmdline/DagrScriptManager.scala 76.36% <ø> (ø) :arrow_up:
...rc/main/scala/dagr/core/execsystem/Scheduler.scala 100% <ø> (ø) :arrow_up:
...in/scala/dagr/core/execsystem/NaiveScheduler.scala 96.55% <ø> (-0.12%) :arrow_down:
...src/main/scala/dagr/core/tasksystem/Pipeline.scala 89.47% <100%> (ø) :arrow_up:
.../main/scala/dagr/core/execsystem/ResourceSet.scala 100% <100%> (ø) :arrow_up:
...rc/main/scala/dagr/core/cmdline/DagrCoreMain.scala 82.6% <100%> (+1.75%) :arrow_up:
.../main/scala/dagr/core/execsystem/TaskTracker.scala 95.06% <100%> (ø) :arrow_up:
...a/dagr/core/execsystem/TopLikeStatusReporter.scala 96.15% <100%> (-0.04%) :arrow_down:
... and 14 more

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