[med-svn] [Git][med-team/pplacer][ralf] update patch for using ocaml bytes
Ralf Treinen
gitlab at salsa.debian.org
Sat Jun 13 20:12:10 BST 2020
Ralf Treinen pushed to branch ralf at Debian Med / pplacer
Commits:
d71eaaeb by Ralf Treinen at 2020-06-13T21:08:51+02:00
update patch for using ocaml bytes
- - - - -
1 changed file:
- debian/patches/ocaml_bytes
Changes:
=====================================
debian/patches/ocaml_bytes
=====================================
@@ -2,10 +2,10 @@ Author: Ralf Treinen <treinen at debian.org>
Description: ocaml strings are immutable in recent ocaml versions,
replace them by Bytes.t where necessary
-Index: pplacer/common_src/ppatteries.ml
+Index: pplacer-1.1~alpha19/common_src/ppatteries.ml
===================================================================
---- pplacer.orig/common_src/ppatteries.ml 2020-06-13 18:46:39.674407130 +0200
-+++ pplacer/common_src/ppatteries.ml 2020-06-13 18:46:39.670407109 +0200
+--- pplacer-1.1~alpha19.orig/common_src/ppatteries.ml 2020-06-13 18:52:38.000000000 +0200
++++ pplacer-1.1~alpha19/common_src/ppatteries.ml 2020-06-13 18:52:51.000000000 +0200
@@ -60,7 +60,7 @@
let maybe_cons o l = maybe_map_cons identity o l
@@ -37,10 +37,10 @@ Index: pplacer/common_src/ppatteries.ml
new_s
end
-Index: pplacer/json_src/json.ml
+Index: pplacer-1.1~alpha19/json_src/json.ml
===================================================================
---- pplacer.orig/json_src/json.ml 2020-06-13 18:46:39.674407130 +0200
-+++ pplacer/json_src/json.ml 2020-06-13 18:46:39.670407109 +0200
+--- pplacer-1.1~alpha19.orig/json_src/json.ml 2020-06-13 18:52:38.000000000 +0200
++++ pplacer-1.1~alpha19/json_src/json.ml 2020-06-13 18:52:51.000000000 +0200
@@ -72,7 +72,7 @@
let to_file name o =
let file = MaybeZipped.open_out name in
@@ -50,10 +50,10 @@ Index: pplacer/json_src/json.ml
(fun () -> IO.flush file)
in
to_formatter formatter o;
-Index: pplacer/common_src/alignment.ml
+Index: pplacer-1.1~alpha19/common_src/alignment.ml
===================================================================
---- pplacer.orig/common_src/alignment.ml 2020-06-13 18:46:39.674407130 +0200
-+++ pplacer/common_src/alignment.ml 2020-06-13 18:46:39.670407109 +0200
+--- pplacer-1.1~alpha19.orig/common_src/alignment.ml 2020-06-13 18:52:38.000000000 +0200
++++ pplacer-1.1~alpha19/common_src/alignment.ml 2020-06-13 18:52:51.000000000 +0200
@@ -102,7 +102,7 @@
Printf.fprintf ch "%d %d\n" (n_seqs align) (length align);
Array.iter (
@@ -63,10 +63,10 @@ Index: pplacer/common_src/alignment.ml
) align;
close_out ch
-Index: pplacer/pplacer_src/string_matrix.ml
+Index: pplacer-1.1~alpha19/pplacer_src/string_matrix.ml
===================================================================
---- pplacer.orig/pplacer_src/string_matrix.ml 2020-06-13 18:46:39.674407130 +0200
-+++ pplacer/pplacer_src/string_matrix.ml 2020-06-13 18:46:39.670407109 +0200
+--- pplacer-1.1~alpha19.orig/pplacer_src/string_matrix.ml 2020-06-13 18:52:38.000000000 +0200
++++ pplacer-1.1~alpha19/pplacer_src/string_matrix.ml 2020-06-13 18:52:51.000000000 +0200
@@ -50,7 +50,7 @@
let m = add_names [|"a";"b"|] [|[|"0";"1"|];[|"2";"3"|]|]
@@ -76,10 +76,10 @@ Index: pplacer/pplacer_src/string_matrix.ml
let write_row ch row =
Printf.fprintf ch "%s\n" (row_to_str " " row)
-Index: pplacer/pplacer_src/pplacer_run.ml
+Index: pplacer-1.1~alpha19/pplacer_src/pplacer_run.ml
===================================================================
---- pplacer.orig/pplacer_src/pplacer_run.ml 2020-06-13 18:46:39.674407130 +0200
-+++ pplacer/pplacer_src/pplacer_run.ml 2020-06-13 18:46:39.670407109 +0200
+--- pplacer-1.1~alpha19.orig/pplacer_src/pplacer_run.ml 2020-06-13 18:52:38.000000000 +0200
++++ pplacer-1.1~alpha19/pplacer_src/pplacer_run.ml 2020-06-13 18:52:51.000000000 +0200
@@ -118,7 +118,7 @@
(seq'.[!pos] <- seq.[e];
incr pos))
@@ -98,10 +98,10 @@ Index: pplacer/pplacer_src/pplacer_run.ml
end;
-Index: pplacer/json_src/jsonparse.mly
+Index: pplacer-1.1~alpha19/json_src/jsonparse.mly
===================================================================
---- pplacer.orig/json_src/jsonparse.mly 2020-06-13 18:46:39.674407130 +0200
-+++ pplacer/json_src/jsonparse.mly 2020-06-13 18:46:39.670407109 +0200
+--- pplacer-1.1~alpha19.orig/json_src/jsonparse.mly 2020-06-13 18:52:38.000000000 +0200
++++ pplacer-1.1~alpha19/json_src/jsonparse.mly 2020-06-13 18:52:51.000000000 +0200
@@ -42,7 +42,7 @@
| "t" -> "\t"
| _ ->
@@ -111,10 +111,10 @@ Index: pplacer/json_src/jsonparse.mly
) s
let add_to_hash h (s, v) = Hashtbl.add h s v; h
-Index: pplacer/pplacer_src/multiprocessing.ml
+Index: pplacer-1.1~alpha19/pplacer_src/multiprocessing.ml
===================================================================
---- pplacer.orig/pplacer_src/multiprocessing.ml 2020-06-13 18:46:39.674407130 +0200
-+++ pplacer/pplacer_src/multiprocessing.ml 2020-06-13 18:48:07.406882567 +0200
+--- pplacer-1.1~alpha19.orig/pplacer_src/multiprocessing.ml 2020-06-13 18:52:38.000000000 +0200
++++ pplacer-1.1~alpha19/pplacer_src/multiprocessing.ml 2020-06-13 18:52:51.000000000 +0200
@@ -71,11 +71,11 @@
in aux pipe_map
@@ -147,3 +147,49 @@ Index: pplacer/pplacer_src/multiprocessing.ml
| Done body, Needs_data (header, _) ->
let obj = Marshal.from_string (header ^ body) 0 in
self#obj_received obj;
+Index: pplacer-1.1~alpha19/pplacer_src/guppy_squash.ml
+===================================================================
+--- pplacer-1.1~alpha19.orig/pplacer_src/guppy_squash.ml 2020-06-13 18:52:51.000000000 +0200
++++ pplacer-1.1~alpha19/pplacer_src/guppy_squash.ml 2020-06-13 21:02:42.674037660 +0200
+@@ -174,7 +174,7 @@
+ Newick_gtree.to_file cluster_t (path cluster_tree_name);
+ let outdir = path mass_trees_dirname in mkdir outdir;
+ let pad_width = find_zero_pad_width (IntMap.cardinal blobim) in
+- let prefix_of_int i = Filename.concat outdir (zero_pad_int pad_width i) in
++ let prefix_of_int i = Filename.concat outdir (Bytes.to_string (zero_pad_int pad_width i)) in
+ (* make a tax tree here then run mimic on it *)
+ let wpt infix t i =
+ self#write_pre_tree (prefix_of_int i) infix t
+@@ -217,8 +217,8 @@
+ let (_, cluster_t, _) = our_make_cluster refpkgo mode_str boot_prl in
+ Newick_gtree.to_file
+ cluster_t
+- (path ("cluster."^(zero_pad_int pad_width i)^".tre"));
+- dprintf "Finished bootstrap %s/%d\n" (zero_pad_int pad_width i) (List.length boots);
++ (path ("cluster."^(Bytes.to_string (zero_pad_int pad_width i))^".tre"));
++ dprintf "Finished bootstrap %s/%d\n" (Bytes.to_string (zero_pad_int pad_width i)) (List.length boots);
+ in
+ match children with
+ | 1 -> List.iter run_boot boots
+Index: pplacer-1.1~alpha19/pam_src/pam_solver.ml
+===================================================================
+--- pplacer-1.1~alpha19.orig/pam_src/pam_solver.ml 2020-06-13 18:52:38.000000000 +0200
++++ pplacer-1.1~alpha19/pam_src/pam_solver.ml 2020-06-13 21:05:17.174881638 +0200
+@@ -20,7 +20,7 @@
+ let old_leaf_idx old = Array.findi ((=) (IntMap.find old transm)) leaf_arr
+ and rtrans i = IntMap.find i rtransm
+ and total_mass = I.total_mass mass in
+- let keep_string = String.make (Array.length leaf_arr) '\000' in
++ let keep_string = Bytes.make (Array.length leaf_arr) '\000' in
+ Option.may
+ (IntSet.iter (fun leaf -> keep_string.[old_leaf_idx leaf] <- '\001'))
+ keep;
+@@ -39,7 +39,7 @@
+ |> Matrix.of_arrays
+ (* rows are masses; columns are leaves. thus, we need to transpose *)
+ |> Matrix.rect_transpose
+- |> c_pam leaves keep_string
++ |> c_pam leaves (Bytes.to_string keep_string)
+ in
+ BA1.enum leaf_vec
+ |> Enum.map (Array.get leaf_arr %> rtrans)
View it on GitLab: https://salsa.debian.org/med-team/pplacer/-/commit/d71eaaeb12f9ce57c7b8a1f935b46dd9f92eb4fa
--
View it on GitLab: https://salsa.debian.org/med-team/pplacer/-/commit/d71eaaeb12f9ce57c7b8a1f935b46dd9f92eb4fa
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