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Update odgi to 0.9.0 #51405

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Oct 16, 2024
Merged

Update odgi to 0.9.0 #51405

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ad4aace
Update odgi to 0.9.0
BiocondaBot Oct 15, 2024
fcef977
clean up recipe
mencian Oct 15, 2024
f357705
do not build on aarch64/arm64
mencian Oct 15, 2024
dc5529c
add python back to host
mencian Oct 15, 2024
3c618ba
revert to skipping osx
mencian Oct 16, 2024
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39 changes: 22 additions & 17 deletions recipes/odgi/build.sh
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Original file line number Diff line number Diff line change
@@ -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' \
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⚠️ Potential issue

Reconsider the use of architecture-specific and aggressive optimization flags

The flag -march=sandybridge targets a specific CPU architecture, which might not be compatible with all users' systems. This could result in binaries that fail to run on older or different CPUs. For broader compatibility, consider using a more generic architecture flag like -march=core2 or omitting the -march flag altogether.

Additionally, the -Ofast optimization level enables aggressive optimizations that may disregard strict compliance with standards, potentially leading to unexpected behavior or instability. It might be safer to use -O2 or -O3 for optimization to balance performance and reliability.

Apply the following changes to address the concerns:

-    -DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DEXTRA_FLAGS='-march=sandybridge -Ofast' \
+    -DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DEXTRA_FLAGS='-O3' \
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DEXTRA_FLAGS='-march=sandybridge -Ofast' \
-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DEXTRA_FLAGS='-O3' \

"${CONFIG_ARGS}"
cmake --build build --target install -j "${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"
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⚠️ Potential issue

Avoid hardcoding Python implementation-specific patterns

The use of *cpython* in the copy command assumes that the Python implementation is CPython. This may not be compatible with other Python implementations like PyPy.

Consider using a more general pattern or querying Python for the correct paths. For example:

-PYVER=`python -c 'import sys; print(str(sys.version_info[0])+"."+str(sys.version_info[1]))'`
+PYTHON_SITE_PACKAGES=`python -c 'import site; print(site.getsitepackages()[0])'`

Then adjust the copy command accordingly:

-mkdir -p "${PREFIX}/lib/python${PYVER}/site-packages"
-cp -rf lib/*cpython* "${PREFIX}/lib/python${PYVER}/site-packages"
+mkdir -p "${PYTHON_SITE_PACKAGES}"
+cp -rf lib/* "${PYTHON_SITE_PACKAGES}"

This approach ensures that the modules are placed in the correct directory regardless of the Python implementation.

Committable suggestion was skipped due to low confidence.

cp -rf lib/* "${PREFIX}/lib"
Comment on lines +24 to +25
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🛠️ Refactor suggestion

Use standard installation methods for Python packages

Copying files directly with cp -rf to the site-packages directory can overlook important installation steps and may lead to issues with package discovery or dependencies. It's recommended to use standard Python installation mechanisms to ensure proper setup.

Consider modifying the build process to install the Python modules using a setup script or ensure that CMake handles the installation correctly. For example:

  • Modify CMakeLists.txt to include proper installation commands for Python modules.
  • Use setup.py or pyproject.toml if applicable.

31 changes: 19 additions & 12 deletions recipes/odgi/meta.yaml
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Original file line number Diff line number Diff line change
@@ -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
12 changes: 0 additions & 12 deletions recipes/odgi/patch
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