update wrt core v0.15.0

pveber · May 7, 2022 · d363bd2 · d363bd2
1 parent fb285b2
commit d363bd2
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Showing 61 changed files with 97 additions and 69 deletions.
diff --git a/bistro.opam b/bistro.opam
@@ -27,7 +27,8 @@ depends: [
   "base64"
   "bos"
   "dune" {> "1.6"}
-  "core" {>= "0.12.0"}
+  "core" {>= "0.15.0"}
+  "core_unix" {>= "0.15.0"}
   "lwt" {>= "3.2.0"}
   "lwt_react"
   "ocamlgraph" {>= "1.8.7"}

diff --git a/dune-project b/dune-project
@@ -33,7 +33,8 @@ Features:
     base64
     bos
     (dune (> 1.6))
-    (core (>= 0.12.0))
+    (core (>= 0.15.0))
+    (core_unix (>= 0.15.0))
     (lwt (>= 3.2.0))
     lwt_react
     (ocamlgraph (>= 1.8.7))

diff --git a/lib/bio/ChIPQC.ml b/lib/bio/ChIPQC.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 open Formats

diff --git a/lib/bio/DESeq2.ml b/lib/bio/DESeq2.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/alignment_stats.ml b/lib/bio/alignment_stats.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Formats
 

diff --git a/lib/bio/bed.ml b/lib/bio/bed.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/bedtools.ml b/lib/bio/bedtools.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/bowtie.ml b/lib/bio/bowtie.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/bowtie2.ml b/lib/bio/bowtie2.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/busco.ml b/lib/bio/busco.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/cisa.ml b/lib/bio/cisa.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/cisbp.ml b/lib/bio/cisbp.ml
@@ -1,6 +1,8 @@
-open Core_kernel
+open Core
 open Bistro
 
+module Sys = Sys_unix
+
 let fetch_pwm_archive : [`cisbp] directory =
   Bistro_unix.wget Biotk.Cisbp.pwm_archive_url
   |> Bistro_unix.unzip
@@ -55,7 +57,7 @@ let annotated_motifs =
         let threshold = Biotk.Pwm_stats.TFM_pvalue.score_of_pvalue pwm (Biotk.Pwm.flat_background ()) 1e-4 in
         let rc_pwm = Biotk.Pwm.reverse_complement pwm in
         ignore (
-          Sys.command (sprintf "echo %s %s %d/%d >> delme" Time.(now () |> to_string) tf_name i n)
+          Sys.command (sprintf "echo %s %s %d/%d >> delme" Time_unix.(now () |> to_string) tf_name i n)
           : int
         ) ;
         { id ; tf_name ; pwm ; rc_pwm ; threshold ; infos }

diff --git a/lib/bio/comparative_genomics.ml b/lib/bio/comparative_genomics.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 
 let select_refseq_genomes ~pattern = [%workflow

diff --git a/lib/bio/deeptools.ml b/lib/bio/deeptools.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/dnaseq_with_reference_genome.ml b/lib/bio/dnaseq_with_reference_genome.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Biotk
 open Formats

diff --git a/lib/bio/dune b/lib/bio/dune
@@ -1,5 +1,5 @@
 (library
   (name bistro_bio)
   (public_name bistro-bio)
-  (libraries biocaml.ez biotk bistro.unix tyxml)
+  (libraries biocaml.ez biotk bistro.unix core_unix.time_unix core_unix.sys_unix tyxml)
   (preprocess (pps ppx_bistro ppx_sexp_conv)))
diff --git a/lib/bio/ensembl.ml b/lib/bio/ensembl.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/examples/chen2008.ml b/lib/bio/examples/chen2008.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro_bio
 open Biotk

diff --git a/lib/bio/fastq.ml b/lib/bio/fastq.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/fastq_sample.ml b/lib/bio/fastq_sample.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Biotk
 open Formats

diff --git a/lib/bio/fastq_screen.ml b/lib/bio/fastq_screen.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/hisat2.ml b/lib/bio/hisat2.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/idba.ml b/lib/bio/idba.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/iqtree.ml b/lib/bio/iqtree.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/jaspar.ml b/lib/bio/jaspar.ml
@@ -1,6 +1,8 @@
-open Core_kernel
+open Core
 open Bistro
 
+module Sys = Sys_unix
+
 let core_vertebrates_non_redundant =
   Bistro_unix.wget
     ~user_agent:{|"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.22 (KHTML, like Gecko) Ubuntu Chromium/25.0.1364.160 Chrome/25.0.1364.160 Safari/537.22"|}

diff --git a/lib/bio/kallisto.ml b/lib/bio/kallisto.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/macs.ml b/lib/bio/macs.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 open Formats

diff --git a/lib/bio/macs2.ml b/lib/bio/macs2.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 open Formats

diff --git a/lib/bio/meme_suite.ml b/lib/bio/meme_suite.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/ncbi_genome.ml b/lib/bio/ncbi_genome.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 
 let assembly_summary =
   Bistro_unix.wget Biotk.Ncbi_genome.refseq_assembly_summary_url

diff --git a/lib/bio/picardtools.ml b/lib/bio/picardtools.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/prokka.ml b/lib/bio/prokka.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/raxml.ml b/lib/bio/raxml.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/samtools.ml b/lib/bio/samtools.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/spades.ml b/lib/bio/spades.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/sra_toolkit.ml b/lib/bio/sra_toolkit.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/srst2.ml b/lib/bio/srst2.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/star.ml b/lib/bio/star.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/subread.ml b/lib/bio/subread.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/tophat.ml b/lib/bio/tophat.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 

diff --git a/lib/bio/trinity.ml b/lib/bio/trinity.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 
@@ -43,9 +43,9 @@ let trinity ?(mem = 128) ?(threads = 4) ?no_normalize_reads ?run_as_paired
       option (flag string "--run_as_paired") run_as_paired ;
       option (opt "--min_kmer_cov" int) min_kmer_cov ;
       option ss_lib_type_option ss_lib_type ;
-      opt "--CPU" ident np ;
-      opt "--max_memory" ident (seq [ string "$((" ; Bistro.Shell_dsl.mem ; string " / 1024))G" ]) ;
-      opt "--output" ident tmp_dest ;
+      opt "--CPU" Fun.id np ;
+      opt "--max_memory" Fun.id (seq [ string "$((" ; Bistro.Shell_dsl.mem ; string " / 1024))G" ]) ;
+      opt "--output" Fun.id tmp_dest ;
     ] ;
     cmd "mv" [
       tmp_dest // "Trinity.fasta" ;
@@ -93,12 +93,12 @@ let insilico_read_normalization ?(mem = 128) ?pairs_together ?parallel_stats ~ma
     cmd "$TRINITY_HOME/util/insilico_read_normalization.pl" [
       string "--seqType fq" ;
       fq_option_template se_or_pe_fq ;
-      opt "--CPU" ident np ;
-      opt "--JM" ident (seq [ string "$((" ; Bistro.Shell_dsl.mem ; string " / 1024))G" ]) ;
+      opt "--CPU" Fun.id np ;
+      opt "--JM" Fun.id (seq [ string "$((" ; Bistro.Shell_dsl.mem ; string " / 1024))G" ]) ;
       opt "--max_cov" int max_cov ;
       option (flag string "--pairs_together") pairs_together ;
       option (flag string "--PARALLEL_STATS") parallel_stats ;
-      opt "--output" ident tmp ;
+      opt "--output" Fun.id tmp ;
     ]
   in
   let workflow post =

diff --git a/lib/bio/ucsc_gb.ml b/lib/bio/ucsc_gb.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro
 open Bistro.Shell_dsl
 open Formats
@@ -143,7 +143,7 @@ let faToTwoBit fa =
   ]
 
 (* (\* let fetch_sequences (File seq2b) locations = *\) *)
-(* (\*   let open Core_kernel in *\) *)
+(* (\*   let open Core in *\) *)
 (* (\*   Core_extended.Sys_utils.with_tmp ~pre:"gzm" ~suf:".seqList" (fun seqList -> *\) *)
 (* (\*     Core_extended.Sys_utils.with_tmp ~pre:"gzm" ~suf:".fa" (fun fa -> *\) *)
 (* (\*       (\\* Write locations to a file *\\) *\) *)

diff --git a/lib/engine/db.ml b/lib/engine/db.ml
@@ -3,6 +3,9 @@
 open Core
 open Rresult
 
+module Sys = Sys_unix
+module Unix = Core_unix
+
 type id = string
 
 let ok_exn = function

diff --git a/lib/engine/dune b/lib/engine/dune
@@ -1,4 +1,4 @@
 (library
   (name bistro_engine)
   (public_name bistro.engine)
-  (libraries bistro bos core lwt.unix re rresult))
+  (libraries bistro bos core core_unix core_unix.sys_unix lwt.unix re rresult))
diff --git a/lib/engine/eval_thread.ml b/lib/engine/eval_thread.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 
 type 'a t = ('a, Execution_trace.Set.t) Lwt_result.t
 

diff --git a/lib/engine/execution_env.ml b/lib/engine/execution_env.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 open Bistro_internals
 
 module Unix = Caml_unix

diff --git a/lib/engine/execution_trace.ml b/lib/engine/execution_trace.ml
@@ -1,4 +1,4 @@
-open Core_kernel
+open Core
 
 module Outcome = struct
   type t = [

diff --git a/lib/engine/local_backend.ml b/lib/engine/local_backend.ml
@@ -2,6 +2,8 @@ open Core
 open Lwt.Infix
 open Bistro_internals
 
+module Unix = Core_unix
+
 type t = {
   logger : Logger.t ;
   db : Db.t ;
@@ -57,7 +59,7 @@ let eval _ () f x =
       (fun () ->
          let ic = Lwt_io.of_unix_fd ~mode:Lwt_io.input read_from_child in
          Lwt_io.read_value ic >>= fun (res : (unit, string) result) ->
-         Caml.Unix.kill (Pid.to_int pid) Caml.Sys.sigkill;
+         Caml_unix.kill (Pid.to_int pid) Caml.Sys.sigkill;
          Misc.waitpid (Pid.to_int pid) >>= fun _ ->
          Unix.close read_from_child ;
          Unix.close write_to_child ;

diff --git a/lib/engine/lwt_queue.ml b/lib/engine/lwt_queue.ml
@@ -1,5 +1,5 @@
 open Lwt.Infix
-open Core_kernel
+open Core
 
 type 'a t = {
   queue : 'a Queue.t ;

diff --git a/lib/engine/misc.ml b/lib/engine/misc.ml
@@ -1,5 +1,8 @@
 open Core
 
+module Sys = Sys_unix
+module Unix = Core_unix
+
 let digest x =
   Md5.to_hex (Md5.digest_string (Marshal.to_string x []))
 

diff --git a/lib/engine/path.ml b/lib/engine/path.ml
@@ -1,4 +1,6 @@
-open Core_kernel
+open Core
+
+module Sys = Sys_unix
 
 type t = string list
 [@@deriving sexp]