[med-svn] [Git][med-team/pplacer][master] 2 commits: Adapt to new version of ocaml-batteries

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / pplacer


Commits:
cdaf120d by Andreas Tille at 2020-08-16T16:59:11+02:00
Adapt to new version of ocaml-batteries

- - - - -
45daec7e by Andreas Tille at 2020-08-16T17:02:12+02:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/ocaml-batteries.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,9 +1,10 @@
-pplacer (1.1~alpha19-3) UNRELEASED; urgency=medium
+pplacer (1.1~alpha19-3) unstable; urgency=medium
 
   * Include /usr/share/ocaml/ocamlvars.mk
     Closes: #968474
+  * Adapt to new version of ocaml-batteries
 
- -- Andreas Tille <tille at debian.org>  Sun, 16 Aug 2020 10:20:31 +0200
+ -- Andreas Tille <tille at debian.org>  Sun, 16 Aug 2020 16:59:18 +0200
 
 pplacer (1.1~alpha19-2) unstable; urgency=medium
 


=====================================
debian/patches/ocaml-batteries.patch
=====================================
@@ -0,0 +1,59 @@
+Date: Sun, 16 Aug 2020 14:42:59 +0200
+From: Stéphane Glondu <glondu at debian.org>
+Origin: https://bugs.debian.org/968474#19
+Description: Adapt to new version of ocaml-batteries
+
+--- a/pplacer_src/gcat_model.ml
++++ b/pplacer_src/gcat_model.ml
+@@ -436,7 +436,7 @@ struct
+      * invalid and `check` will raise an error. *)
+     if Array.length model.site_categories = Array.length mask then begin
+       model.site_categories <-
+-        (Enum.combine (Array.enum model.site_categories, Array.enum mask)
++        (Enum.combine (Array.enum model.site_categories) (Array.enum mask)
+          |> Enum.filter_map (function x, true -> Some x | _, false -> None)
+          |> Array.of_enum);
+       setup_occupied_rates model
+--- a/pplacer_src/guppy_cmdobjs.ml
++++ b/pplacer_src/guppy_cmdobjs.ml
+@@ -612,7 +612,7 @@ object (self)
+ 
+   method private filter_fal orig_length fal edges =
+     List.map (Array.filteri (fun i _ -> IntSet.mem i edges)) fal,
+-    Enum.combine (Enum.range 0, IntSet.enum edges) |> IntMap.of_enum,
++    Enum.combine (Enum.range 0) (IntSet.enum edges) |> IntMap.of_enum,
+     orig_length
+ 
+   method private filter_rep_edges prl fal =
+--- a/pplacer_src/guppy_mcl.ml
++++ b/pplacer_src/guppy_mcl.ml
+@@ -6,7 +6,7 @@ let of_pql ?inflation criterion pql =
+   let pqa = Array.of_list pql in
+   let name_map =
+     Enum.combine
+-      (Array.enum pqa |> Enum.map Pquery.name, Enum.range 0)
++      (Array.enum pqa |> Enum.map Pquery.name) (Enum.range 0)
+     |> StringMap.of_enum
+   in
+   let count = StringMap.cardinal name_map in
+--- a/pplacer_src/guppy_rarefact.ml
++++ b/pplacer_src/guppy_rarefact.ml
+@@ -66,7 +66,6 @@ object (self)
+               @ (if is_uniform_mass then [fmt qm] else [""]))
+         |> begin
+           if fv variance then
+-            curry
+               Enum.combine
+               (Rarefaction.variance_of_placerun criterion ?k_max pr)
+             |- Enum.map (fun ((_, uv, rv), sl) -> sl @ [fmt uv; fmt rv])
+--- a/pplacer_src/pplacer_run.ml
++++ b/pplacer_src/pplacer_run.ml
+@@ -85,7 +85,7 @@ let premask ?(discard_nonoverlapped = fa
+    * informative column of the reference sequence. *)
+   let overlaps_mask s = String.enum s
+     |> Enum.map Alignment.informative
+-    |> curry Enum.combine (Array.enum ref_mask)
++    |> Enum.combine (Array.enum ref_mask)
+     |> Enum.exists (uncurry (&&))
+   in
+   let query_list = List.filter


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ fix_makefile.patch
 ocaml_stdlib
 ocaml_bytes
 spelling.patch
+ocaml-batteries.patch



View it on GitLab: https://salsa.debian.org/med-team/pplacer/-/compare/be72aa6900febc487974f097a3e4df1c93cc4757...45daec7ebd867a33efe9d76c0d21bd79c3c99d6f

-- 
View it on GitLab: https://salsa.debian.org/med-team/pplacer/-/compare/be72aa6900febc487974f097a3e4df1c93cc4757...45daec7ebd867a33efe9d76c0d21bd79c3c99d6f
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