Update revbayes to v1.2.4 (#52069)

* Update revbayes to v1.2.4

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update build.sh

* Update build.sh

* skip building on linux-aarch64; builds successfully but goes over time limit ;_;

recipes/revbayes/build.sh

@@ -1,53 +1,47 @@
-#!/usr/bin/env bash
+#!/bin/bash
 
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
+mkdir -p $PREFIX/bin
 cd projects/cmake
 
-if [ ! -d build ]; then
-	mkdir build
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
 fi
 
-./generate_version_number.sh
-mv GitVersion.cpp ../../src/revlanguage/utils/
-
 # MPI version
 ./regenerate.sh -mpi true
 
-cd build
+./build.sh -mpi true -help2yml true \
+	-DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_PREFIX_PATH="${PREFIX}" \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	-boost_root "${PREFIX}" \
+	-j "${CPU_COUNT}" \
+	"${CONFIG_ARGS}"
 
-# If cmake finds a boost version compiled with cmake, it always links to it unless both
-# Boost_NO_SYSTEM_PATHS=ON and Boost_NO_BOOST_CMAKE=ON (probably a bug in cmake)
-cmake -DCMAKE_PREFIX_PATH=$PREFIX \
-	-DBOOST_ROOT=$PREFIX \
-	-DBoost_NO_SYSTEM_PATHS=ON \
-	-DBoost_NO_BOOST_CMAKE=ON \
-	.
-
-make
-
-cd ..
-mkdir -p $PREFIX/bin
-mv rb $PREFIX/bin/rb-mpi
+chmod 0755 rb-mpi rb-mpi-help2yml
+mv rb-mpi rb-mpi-help2yml $PREFIX/bin/
 
 
 # Non-mpi version
-rm -rf build
-mkdir build
+rm -rf build-mpi
 
 ./regenerate.sh
 
-cd build
-
-# If cmake finds a boost version compiled with cmake, it always links to it unless both
-# Boost_NO_SYSTEM_PATHS=ON and Boost_NO_BOOST_CMAKE=ON (probably a bug in cmake)
-cmake -DCMAKE_PREFIX_PATH=$PREFIX \
-	-DBOOST_ROOT=$PREFIX \
-	-DBoost_NO_SYSTEM_PATHS=ON \
-	-DBoost_NO_BOOST_CMAKE=ON \
-	.
+./build.sh -mpi false -help2yml true \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_PREFIX_PATH="${PREFIX}" \
+        -DCMAKE_CXX_COMPILER="${CXX}" \
+        -boost_root "${PREFIX}" \
+        -j "${CPU_COUNT}" \
+        "${CONFIG_ARGS}"
 
-make
-
-cd ..
-mkdir -p $PREFIX/bin
-mv rb $PREFIX/bin
+chmod 0755 rb rb-help2yml
+mv rb rb-help2yml $PREFIX/bin/
 
+rm -rf build

recipes/revbayes/meta.yaml

@@ -1,43 +1,57 @@
-{% set version = "1.0.13" %}
+{% set name = "revbayes" %}
+{% set version = "1.2.4" %}
 
 package:
-  name: revbayes
+  name: {{ name }}
   version: {{ version }}
 
-build:
-  number: 7
-
 source:
-  url: https://github.com/revbayes/revbayes.archive/archive/v{{ version }}.tar.gz
-  sha256: e85e2e1fe182fe9f504900150d936a06d252a362c591b9d3d8272dd085aa85d9
+  url: https://github.com/revbayes/revbayes/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 020aa32b32db5896b081e14613c754fbb5523f01fa64262f502a6b693db9058a
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('revbayes', max_pin="x") }}
 
 requirements:
   build:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - cmake >=2.6
+    - cmake
   host:
-    - boost-cpp >=1.60
+    - boost-cpp >=1.71
     - openmpi
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
   run:
-    - boost-cpp >=1.60
+    - boost-cpp >=1.71
     - openmpi
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
 
 test:
   commands:
-    - rb -v
     - rb -h
-    - rb-mpi -v
     - rb-mpi -h
 
 about:
-  home: https://revbayes.github.io/
-  license: GPLv3
+  home: "https://revbayes.github.io"
+  license: "GPL-3.0-or-later"
+  license_family: GPL3
   license_file: LICENSE
-  summary: Bayesian phylogenetic inference using probabilistic graphical models and an interactive language.
+  summary: "Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language."
+  dev_url: "https://github.com/revbayes/revbayes"
+  doc_url: "https://revbayes.github.io/tutorials"
 
 extra:
   container:
     # openmpi needs ssh/rsh
-    extended-base: true
+    extended-base: True
+  identifiers:
+    - biotools:revbayes
+    - doi:10.1093/sysbio/syw021
+    - doi:10.1093/sysbio/syu039
+  additional-platforms:
+    - osx-arm64