Shayan Doust pushed to branch master 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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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