From 5eb1b619edc6c8f0100b6afe8bd282bf2ef94bc9 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 2 Jan 2025 07:35:24 -0500
Subject: [PATCH] Update sdm to 3.08 (#52994)

* Update sdm to 3.07

* Test without the old patch

* Update sdm to 3.08

* Update Makefile patch

---------

Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
---
 recipes/sdm/meta.yaml                         |  6 ++---
 .../sdm/{sdm_1.83.patch => sdm_3.08.patch}    | 25 ++++++++-----------
 2 files changed, 14 insertions(+), 17 deletions(-)
 rename recipes/sdm/{sdm_1.83.patch => sdm_3.08.patch} (55%)

diff --git a/recipes/sdm/meta.yaml b/recipes/sdm/meta.yaml
index 53a9f3e6b6a51..aa1b42116cce8 100644
--- a/recipes/sdm/meta.yaml
+++ b/recipes/sdm/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "sdm" %}
-{% set version = "2.18" %}
+{% set version = "3.08" %}
 
 package:
   name: {{ name }}
@@ -7,9 +7,9 @@ package:
 
 source:
   url: https://github.com/hildebra/{{ name }}/archive/v{{ version }}.tar.gz
-  sha256: 4ae8d1b2be6c3571e9c2db964421e5065255dff209f8e060d43b843be0f04e82
+  sha256: 122fe90a715c0f8b7cc28e930fe8edd165a0e7d25763d8753a3ae57b8ee58736
   patches:
-    - sdm_1.83.patch
+    - sdm_3.08.patch
 
 build:
   number: 0
diff --git a/recipes/sdm/sdm_1.83.patch b/recipes/sdm/sdm_3.08.patch
similarity index 55%
rename from recipes/sdm/sdm_1.83.patch
rename to recipes/sdm/sdm_3.08.patch
index 9beda97e2e44c..7fbb4dec45bf8 100644
--- a/recipes/sdm/sdm_1.83.patch
+++ b/recipes/sdm/sdm_3.08.patch
@@ -1,30 +1,27 @@
 diff --git a/Makefile b/Makefile
-index df16bce..5967e96 100644
+index a22c3ed..53e2310 100644
 --- a/Makefile
 +++ b/Makefile
-@@ -15,13 +15,22 @@ program_INCLUDE_DIRS := ./
- program_LIBRARY_DIRS := ${CPATH}
- program_LIBRARIES :=
+@@ -15,13 +15,19 @@ isa_FLAGS2 :=
+ #isa_FLAGS := -D_isa1gzip
+ #isa_FLAGS2 := -lisal 
  
--
--CPPFLAGS += -O3 -std=c++17 -lrt
+-CPPFLAGS += -O3 -std=c++17 -lrt $(isa_FLAGS)
 +UNAME := $(shell uname)
-+CPPFLAGS += -O3 -std=c++17 -pthread
++CPPFLAGS += -O3 -std=c++17 -pthread $(isa_FLAGS)
+ #-D_isa1gzip
  CPPFLAGS += $(foreach includedir,$(program_INCLUDE_DIRS),-I$(includedir))
-+ifeq ($(UNAME), Darwin)
-+# 'shared_mutex' is available from macOS 10.12
-+CPPFLAGS += -mmacosx-version-min=10.12
-+endif
  CXXFLAGS=-D__STDC_CONSTANT_MACROS
 -LDFLAGS +=   $(foreach librarydir,$(program_LIBRARY_DIRS),-L$(librarydir)) -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
+-LDFLAGS += $(foreach library,$(program_LIBRARIES),-l$(library))  
 +LDFLAGS += $(foreach librarydir,$(program_LIBRARY_DIRS),-L$(librarydir))
- LDFLAGS += $(foreach library,$(program_LIBRARIES),-l$(library))
- LDLIBS += -lz
++LDLIBS += $(foreach library,$(program_LIBRARIES),-l$(library))
+ LDLIBS += -lz $(isa_FLAGS2)
 +ifeq ($(UNAME), Linux)
 +LDLIBS += -lrt -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
 +else
 +LDLIBS += -lpthread
 +endif
+ #-lisal 
  
- .PHONY: all clean distclean