Update odgi to 0.9.0 (#51405)

* Update odgi to 0.9.0

* clean up recipe

* do not build on aarch64/arm64

* add python back to host

* revert to skipping osx

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>

recipes/odgi/build.sh

@@ -1,20 +1,25 @@
 #!/bin/bash
-export LIBRARY_PATH=${PREFIX}/lib
-export LD_LIBRARY_PATH=${PREFIX}/lib
-export CPATH=${PREFIX}/include
-export C_INCLUDE_PATH=${PREFIX}/include
-export CPLUS_INCLUDE_PATH=${PREFIX}/include
-export CPP_INCLUDE_PATH=${PREFIX}/include
-export CXX_INCLUDE_PATH=${PREFIX}/include
-#cmake -H. -Bbuild -DPYTHON_EXECUTABLE:FILEPATH=$PYTHON -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast -Og'
-cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast'
-cmake --build build
+
 mkdir -p $PREFIX/bin
-mv bin/* $PREFIX/bin
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Generic \
+	-DCMAKE_INSTALL_PREFIX="${PREFIX}" -DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DEXTRA_FLAGS='-march=sandybridge -Ofast' \
+	"${CONFIG_ARGS}"
+cmake --build build --target install -j "${CPU_COUNT}" -v
+
 PYVER=`python -c 'import sys; print(str(sys.version_info[0])+"."+str(sys.version_info[1]))'`
-mkdir -p $PREFIX/lib/python$PYVER/site-packages
-cp lib/*cpython* $PREFIX/lib/python$PYVER/site-packages
-cp lib/* $PREFIX/lib
-#set -x
-#python -c "import sys; sys.path.append('./lib'); import odgi_ffi"
-#python -c "import sys; sys.path.append('./lib'); import odgi"
+mkdir -p "${PREFIX}/lib/python${PYVER}/site-packages"
+cp -rf lib/*cpython* "${PREFIX}/lib/python${PYVER}/site-packages"
+cp -rf lib/* "${PREFIX}/lib"

recipes/odgi/meta.yaml

@@ -1,50 +1,57 @@
 {% set name = "odgi" %}
-{% set version = "0.8.6" %}
+{% set version = "0.9.0" %}
 
 package:
   name: "{{ name }}"
   version: "{{ version }}"
 
 source:
   url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: a6db190b782608082b14b42c660389aa18010791de1e2d07e29f7f61d8787754
-  patches:
-    - patch
+  sha256: 73b181c371e619b5e3e5ee87649cb8de82b054e492dcd128d93cec42be062f2f
 
 build:
-  skip: True  # [osx or py27]
-  number: 2
+  skip: True  # [osx]
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
 requirements:
   build:
-    - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - llvm-openmp  # [osx]
-    - libgomp      # [linux]
     - cmake
     - make
   host:
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
     - zlib
-    - python
     - jemalloc
+    - python
     - pybind11
   run:
     - llvm-openmp  # [osx]
+    - libgomp      # [linux]
     - python
+    - jemalloc
     - pybind11
 
 test:
   commands:
     - odgi test
 
 about:
-  home: https://github.com/pangenome/odgi
+  home: "https://github.com/pangenome/odgi"
   license: MIT
+  license_family: MIT
   license_file: LICENSE
-  summary: An optimized dynamic genome/graph implementation
+  summary: "An optimized dynamic genome/graph implementation."
+  dev_url: "https://github.com/pangenome/odgi"
+  doc_url: "https://github.com/pangenome/odgi/blob/v{{ version }}/README.md"
 
 extra:
   recipe-maintainers:
     - AndreaGuarracino
+  identifiers:
+    - doi:10.1093/bioinformatics/btac308
+    - biotools:odgi
+    - usegalaxy-eu:odgi_viz
+    - usegalaxy-eu:odgi_build