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biocaml/biocaml 104

OCaml Bioinformatics Library

pveber/bistro 43

A library to build and execute typed scientific workflows

flass/pantagruel 29

a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome

biocaml/cfstream 13

Stream operations in the style of Core's API.

IFB-ElixirFr/ReproHackathon 12

Série de hackathons pour la reproductibilité - Une action MaDICS ReproVirtuFlow

biocaml/phylogenetics 11

Algorithms and datastructures for phylogenetics

biocaml/biopam 9

OPAM repository for bioinformatics tools.

CarineRey/caars 7

CAARS: Comparative Assembly and Annotation of RNA-Seq data

pveber/biotk 5

Toolkit for bioinformatics in OCaml

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Philippe Veber

commit sha b27c15a4285abdc3525df135e2293ebfaa1dec9d

Dataframe: small optimization

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Philippe Veber

commit sha 545d1d1839c79aae1a543d332ff6b63d2b186c9c

Dataframe: fix bug introduced in e28a75a

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Philippe Veber

commit sha f04a717efec0d631c4b362ec09eeb67926421c06

Dataframe.Parser: fix incorrect error reporting (+test)

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PR opened ocaml-community/awesome-ocaml

update info on bistro

bistro is the (not so) new name of guizmin (I'm the author)

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pveber

commit sha 3b0d0a1815f4036bcd72c6d1987b13c5f53ce56d

update info on bistro bistro is the (not so) new name of guizmin (I'm the author)

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fork pveber/awesome-ocaml

A curated collection of awesome OCaml tools, frameworks, libraries and articles.

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issue openedCraigFe/progress

Interaction with fork.

I have a program that forks repeatedly inside a Progress.with_reporter call, and it seems each time it happens, there's a return carriage that gets printed to the screen. Next time the bar is rendered, it is added below the former render, instead of replacing it, like in:

Processing alignments  0/10 [------------------------------------------------------------------------------------------------------------------] 00:02
Processing alignments  1/10 [###########-------------------------------------------------------------------------------------------------------] 00:33
Processing alignments  2/10 [######################--------------------------------------------------------------------------------------------] 00:34

I'm not absolutely sure this is due to forking, but I highly suspect it. I see no reason for this, however. Maybe there's something I could call in the child process to disable any further interaction with the terminal?

created time in 12 days

issue commentCraigFe/progress

Line.eta is not nice to slow processes.

Thanks for your answer! I'm not sure I get your point about precision: it seems a Flow_meter.t keeps an array of all last n values that were recorded, along with the corresponding timestamps. So computing the rate by summing and dividing by the total time interval as a float should be plenty accurate. It is true that rounding errors accumulate when you performs lots of operations that involve numbers several orders of magnitude apart, but it doesn't seem to me that we are in that kind of situation here. Also no worries if you don't have time to get back to this soon, thanks again for the early feedback!

pveber

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issue openedCraigFe/progress

Line.eta is not nice to slow processes.

First, thanks for this awesome library! I'm trying to use Line.eta but I always get a --:-- display. I figured out that in my case the event rate is less than 1. This is a problem because this rate seems to be represented by an integer (see the variable per_second).

More generally I don't really understand why Flow_meter.per_second doesn't return a float, since it basically computes a sample estimate of a rate.

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branch : dataframe-parser-combinator-alternative

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Philippe Veber

commit sha e28a75a484b51510b14f7b4a87a75aac0f768b40

Dataframe: refactoring + fixed line number in error message

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Philippe Veber

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Dataframe: added parser combinators

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pull request commentocaml/opam-repository

[new release] bistro and bistro-bio (0.6.0)

Indeed, seems that biocaml needs to have a lower bound on core_kernel, although I am not sure which yet

I'll investigate and submit a separate PR.

pveber

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pveber

commit sha c2d3a18fb413c24e9d4da00d0b51c6acfe1f6d07

Update packages/bistro/bistro.0.6.0/opam Co-authored-by: Marcello Seri <mseri@users.noreply.github.com>

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pveber

commit sha 4d9617df9a8ff66871480f7509e1462f5c41434e

Update packages/bistro/bistro.0.6.0/opam Co-authored-by: Marcello Seri <mseri@users.noreply.github.com>

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pveber

commit sha edab656083a0728247edc5326dd60680a61cf5fe

Update packages/bistro-bio/bistro-bio.0.6.0/opam Co-authored-by: Marcello Seri <mseri@users.noreply.github.com>

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pull request commentocaml/opam-repository

[new release] bistro and bistro-bio (0.6.0)

The remaining compilation failure is due to a missing constraint in future I believe.

pveber

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pveber

commit sha bff4afd0e596442338fe1b9a55ea3f23cbc51e46

bistro: fix lower bounds on tyxml and base64

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Philippe Veber

commit sha ebf87b3aef63babe9b41b9d44c303f61f7921205

updated README

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Philippe Veber

commit sha 7301758a2a0aaf2c32b26df876e9ec43265ad740

[new release] bistro and bistro-bio (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

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release pveber/bistro

v0.6.0

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created tagpveber/bistro

tagv0.6.0

A library to build and execute typed scientific workflows

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delete tag pveber/bistro

delete tag : v0.6.0

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PR opened ocaml/opam-repository

[new release] bistro and bistro-bio (0.6.0)

A library to build and run distributed scientific workflows

  • Project page: <a href="https://github.com/pveber/bistro/">https://github.com/pveber/bistro/</a>
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
+106 -0

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create barnchpveber/opam-repository

branch : release-bistro-v0.6.0

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release pveber/bistro

v0.6.0

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created tagpveber/bistro

tagv0.6.0

A library to build and execute typed scientific workflows

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issue commentocamllabs/dune-release

dune-release picks wrong DIST_NAME

Same problem here. I think this is related to the function Pkg.dune_project_name, see that snippet:

      Bos.OS.File.read_lines file >>| fun lines ->
      List.fold_left
        (fun acc line ->
          (* sorry *)
          match String.cut ~sep:"(name " (String.trim line) with
          | Some (_, s) ->
              Some
                (String.trim
                   ~drop:(function ')' | ' ' -> true | _ -> false)
                   s)
          | _ -> acc)
        None lines

which shows that the function keeps the last name it found (because fold_left processes from beginning to end of the list). Problem is usually the name of the project is at the beginning of the file, then come the package stanzas, which also have a (name ...) field. In my case, changing the order of the packages to set the one with the intended project name last fixes the problem.

Anyway, this parsing of the dune-project file seems a bit brittle to me. Maybe some code from dune could be called instead?

mattjbray

comment created time in 21 days

issue closedpveber/bistro

build failure with Ocaml 4.13

File "ppx/bistro_script.ml", line 205, characters 58-59:
File "ppx/bistro_script.ml", line 205, characters 58-59:
205 |           (new ast_translation loc'.loc_start)#expression e
205 |           (new ast_translation loc'.loc_start)#expression e
                                                                ^
                                                                ^
Error: This expression has type Parsetree.expression
Error: This expression has type Parsetree.expression
       but an expression was expected of type
       but an expression was expected of type
         Ppxlib.Ast.expression = Astlib.Ast_412.Parsetree.expression
         Ppxlib.Ast.expression = Astlib.Ast_412.Parsetree.expression

closed time in 21 days

bcdarwin

issue commentpveber/bistro

build failure with Ocaml 4.13

Thanks for reporting, I believe this error is caused by the fix you sent (#48). I checked that the current master (fb285b2) compiles against 4.13. Thanks again!

bcdarwin

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Philippe Veber

commit sha fb285b2c6d8adccda3c71e2293bceb01febd6624

bio: fixed warnings

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PR closed pveber/bistro

bistro_script.ml: fix build with ppxlib 0.23

Fixes #47.

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bcdarwin

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pull request commentpveber/bistro

bistro_script.ml: fix build with ppxlib 0.23

Thanks for the PR, unfortunately the fix doesn't compile. I pushed a somewhat similar modification (b82548b). Thanks again!

bcdarwin

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