0.6.0

CHANGES:

core library:

• added ifelse and trywith constructs
• moved bio-stuff in new package bistro-bio

engine:

• precious items
• repo clipping

ppx:

• include script mechanism

bio:

• added Bedtools.merge
• added Samtools.faidx
• added SE_or_PE
• new wrapper rnaspades
• new wrapper busco

bistro 0.5.0

v0.5.0 2019-08-20 Lyon

new design: 'a workflow evals to 'a

• workflows can now compute any (serializable) value besides paths

• list workflows can be spawned for parallel execution

• execution engine entirely rewritten, still allows exact incremental
  garbage collection

• templates for bash script can now contain int and string variable
  parts

• singularity support

• multinode execution engine

• HTML reports

• dynamic memory and processor requirements

• utils.Repo are best-effort rendered in case of errors

• many new modules in bioinfo

• ppx for templates with antiquotations

bistro 0.4.0

v0.4.0 2018-06-16 Lyon

• ppx syntax extension to write workflow steps as regular OCaml functions
• new workflow type, that maps a command on all files of a directory in //
• use class types for phantom typing
• started a documentation!
• dry-run execution mode
• new docker files

bistro 0.3.0

• Compilation via jbuilder
• more docker images and wrappers
• various bug fixes

Bistro 0.2.0

Major rewrite:

• new execution engine
  • generic notion of task graph (DAG)
  • compilation of workflow representation to a task DAG
  • logging facilities
  • transparent execution of commands through docker container
  • removal of intermediate targets during execution
  • notion of precious workflow (that should be kept no matter what)
• call of regular ocaml function as new type of workflow
• applicative term to express an action that should be performed after a
  set of workflows has been successfully executed
• text logging
• logging as HTML report
• added a collection of Dockerfile scripts
• new bioinfomatics wrappers (many contributed by Sylvere Bastien)

and many bug fixes.

Bistro 0.1.0

Many minor changes in API.

Installation scripts for tools are no longer considered part of
analysis workflow. Installing programs should be dealt with outside
bistro.

Features:

• heredoc for shell EDSL
• new np and mem tokens for scripts, as a way to use only the
  resources that were allocated to a run

Bug fixes:

• bistro execution hangs on utop (f4f932f)
• don't save workflow in database statistics, just its id (issue #4)

Bistro 0.0.0

First release on OPAM